From wilde at mcs.anl.gov  Tue Mar  2 18:31:13 2010
From: wilde at mcs.anl.gov (wilde at mcs.anl.gov)
Date: Tue, 2 Mar 2010 18:31:13 -0600 (CST)
Subject: [Swift-devel] Problem with coaster workers shutting down early
In-Reply-To: <19709316.1058031267575705449.JavaMail.root@zimbra>
Message-ID: <1696956.1058231267576273817.JavaMail.root@zimbra>

Mihael, I dont yet have all the evidence for this issue collected nice and clean, but I want to send you what I have to start looking at this.

Ive been trying to recreate a problem that Zhao is encountering where he's trying to run >15,000 short (~ 1-second) jobs on PADS under coasters.

Basically, the worker jobs seem to be exiting for no reason that I can discern.

Ive re-created something that looks similar using this:

cd ~wilde/swift/lab
swift -tc.file tc -sites.file pbscoast.xml cats.swift

Log is /home/wilde/swift/lab/cats-20100302-1751-8qy7m21c.log

Coaster worker logs are in ~wilde/globus.coasters

Seems to work OK when I request 1 node blocks
With 2-node blocks, the workers seem to shutdown for no apparent reason, after about 2 seconds.

...more details later when I get a chance.

- Mike



From wilde at mcs.anl.gov  Wed Mar  3 09:43:55 2010
From: wilde at mcs.anl.gov (Michael Wilde)
Date: Wed, 3 Mar 2010 09:43:55 -0600 (CST)
Subject: [Swift-devel] Problem with coaster workers shutting down early
In-Reply-To: <1696956.1058231267576273817.JavaMail.root@zimbra>
Message-ID: <31008313.1070161267631035903.JavaMail.root@zimbra>

This is fixed in CoG rev 2725.

The problem was causing all multi-node coaster blocks to fail to start.

- Mike

----- wilde at mcs.anl.gov wrote:

> Mihael, I dont yet have all the evidence for this issue collected nice
> and clean, but I want to send you what I have to start looking at
> this.
> 
> Ive been trying to recreate a problem that Zhao is encountering where
> he's trying to run >15,000 short (~ 1-second) jobs on PADS under
> coasters.
> 
> Basically, the worker jobs seem to be exiting for no reason that I can
> discern.
> 
> Ive re-created something that looks similar using this:
> 
> cd ~wilde/swift/lab
> swift -tc.file tc -sites.file pbscoast.xml cats.swift
> 
> Log is /home/wilde/swift/lab/cats-20100302-1751-8qy7m21c.log
> 
> Coaster worker logs are in ~wilde/globus.coasters
> 
> Seems to work OK when I request 1 node blocks
> With 2-node blocks, the workers seem to shutdown for no apparent
> reason, after about 2 seconds.
> 
> ...more details later when I get a chance.
> 
> - Mike
> 
> _______________________________________________
> Swift-devel mailing list
> Swift-devel at ci.uchicago.edu
> http://mail.ci.uchicago.edu/mailman/listinfo/swift-devel


From wilde at mcs.anl.gov  Wed Mar  3 13:47:28 2010
From: wilde at mcs.anl.gov (wilde at mcs.anl.gov)
Date: Wed, 3 Mar 2010 13:47:28 -0600 (CST)
Subject: [Swift-devel] [gt-dev] Google Summer of Code 2010 - Please
	contribute project ideas (fwd)
In-Reply-To: <13221894.1084001267645360491.JavaMail.root@zimbra>
Message-ID: <12619091.1084741267645648607.JavaMail.root@zimbra>

Ben, sorry I missed this message; Borja just pointed it out to me.

Both ideas sound interesting, and the first would be uniquely in your interest camp. Im very interested in also enhancing the imperative control structures, and then comparing the functional vs. imperative approaches.

Regarding the second one: Ive made recent progress in calling Swift from within R, in an R-ish manner (ie you dont see any Swift); since R is rather functional and also of great interest to the analytics community, perhaps we can coordinate a joint SoC effort around that.

I hope to get other Swift SoC projects on the table soon.

- Mike





----- "Ben Clifford" <benc at hawaga.org.uk> wrote:

> This has been good before. I'm probably still interested in mentoring
> 
> (seeing as it pays out beer money and a tshirt to the mentor) 
> language-related projects:
>  * actually implementing map/fold like operators 
> would be one, if it was likely to be accepted as a contribution into
> the 
> production codebase (which I'm not sure what the feel is for that); 
> 
>  * a prototype haskell (or other functional language) implementation
> in 
> order to explore that space (with no intention that this would become
> 
> production code - intention would be to give more practical experience
> for 
> fuel in long-winded debates about whether SwiftScript would be better
> 
> implemented inside some other langauge)
> 
> -- 
> http://www.hawaga.org.uk/ben/
> 
> ---------- Forwarded message ----------
> Date: Fri, 19 Feb 2010 07:40:52 -0600
> From: Borja Sotomayor <borja at borjanet.com>
> To: gt-dev <gt-dev at lists.globus.org>
> Subject: [gt-dev] Google Summer of Code 2010 - Please contribute
> project ideas
> 
> Hi everyone,
> 
> Globus has participated in Google Summer of Code
> (http://code.google.com/soc/) for the last two years, giving us the
> opportunity to work with talented students, expand our community, and
> develop cool projects that would have otherwise languished on a
> wishlist
> somewhere (see http://tinyurl.com/globus-gsoc09 for details on last
> summer's projects, and http://tinyurl.com/globus-gsoc08 for the 2008
> projects).
> 
> We will be applying again this year to be a mentoring organization in
> Summer of Code, and a big part of the application is preparing a
> strong
> list of student projects. I am writing to encourage members of the
> Globus community to add cool and interesting project ideas to the
> following wiki page:
> 
> 	http://dev.globus.org/wiki/Google_Summer_of_Code_2010_Ideas
> 
> You will find more information on GSoC and detailed instructions on
> how
> to add a GSoC project idea in the above URL. Even though new project
> ideas are preferable, past GSoC mentors should feel free to re-offer
> any
> idea that was not developed last year (see last year's list:
> http://dev.globus.org/wiki/Google_Summer_of_Code_2009_Ideas)
> 
> The GSoC deadline for mentoring organizations is March 12th, but we
> would like all project ideas to be added by March 10th so we can have
> time to polish them up, ask committers for clarifications, etc.
> 
> If you have any questions, please don't hesitate to reply to this
> thread.
> 
> Cheers!
> -- 
> ::::::::::::::::::::::::::::::::::::::::::::::::::::
> Borja Sotomayor, University of Chicago
>  Ph.D. Candidate, Department of Computer Science
>  Ryerson 257-C, 1100 East 58th Street, Chicago, IL
>  http://people.cs.uchicago.edu/~borja/
> Haizea: http://haizea.cs.uchicago.edu/
> ????????????????????????????????????????????????????
>     "Dis maschine vill run und run!"
>           -- Kurt G?del (on the Turing Machine)
> ::::::::::::::::::::::::::::::::::::::::::::::::::::
> _______________________________________________
> Swift-devel mailing list
> Swift-devel at ci.uchicago.edu
> http://mail.ci.uchicago.edu/mailman/listinfo/swift-devel


From HodgessE at uhd.edu  Wed Mar  3 14:12:03 2010
From: HodgessE at uhd.edu (Hodgess, Erin)
Date: Wed, 3 Mar 2010 14:12:03 -0600
Subject: [Swift-devel] [gt-dev] Google Summer of Code 2010 -
	Pleasecontribute project ideas (fwd)
In-Reply-To: <12619091.1084741267645648607.JavaMail.root@zimbra>
References: <13221894.1084001267645360491.JavaMail.root@zimbra>
	<12619091.1084741267645648607.JavaMail.root@zimbra>
Message-ID: <101CBF5360343B45B9C9B0B05D71474C02E7FA35@BALI.uhd.campus>

Hi Mike!

If you do R and Swift for the SoC, could I be involved in that, too, please?

Thanks,
Erin


-----Original Message-----
From: swift-devel-bounces at ci.uchicago.edu [mailto:swift-devel-bounces at ci.uchicago.edu] On Behalf Of wilde at mcs.anl.gov
Sent: Wednesday, March 03, 2010 1:47 PM
To: Ben Clifford
Cc: Borja Sotomayor; swift-devel at ci.uchicago.edu
Subject: Re: [Swift-devel] [gt-dev] Google Summer of Code 2010 - Pleasecontribute project ideas (fwd)

Ben, sorry I missed this message; Borja just pointed it out to me.

Both ideas sound interesting, and the first would be uniquely in your interest camp. Im very interested in also enhancing the imperative control structures, and then comparing the functional vs. imperative approaches.

Regarding the second one: Ive made recent progress in calling Swift from within R, in an R-ish manner (ie you dont see any Swift); since R is rather functional and also of great interest to the analytics community, perhaps we can coordinate a joint SoC effort around that.

I hope to get other Swift SoC projects on the table soon.

- Mike





----- "Ben Clifford" <benc at hawaga.org.uk> wrote:

> This has been good before. I'm probably still interested in mentoring
> 
> (seeing as it pays out beer money and a tshirt to the mentor) 
> language-related projects:
>  * actually implementing map/fold like operators 
> would be one, if it was likely to be accepted as a contribution into
> the 
> production codebase (which I'm not sure what the feel is for that); 
> 
>  * a prototype haskell (or other functional language) implementation
> in 
> order to explore that space (with no intention that this would become
> 
> production code - intention would be to give more practical experience
> for 
> fuel in long-winded debates about whether SwiftScript would be better
> 
> implemented inside some other langauge)
> 
> -- 
> http://www.hawaga.org.uk/ben/
> 
> ---------- Forwarded message ----------
> Date: Fri, 19 Feb 2010 07:40:52 -0600
> From: Borja Sotomayor <borja at borjanet.com>
> To: gt-dev <gt-dev at lists.globus.org>
> Subject: [gt-dev] Google Summer of Code 2010 - Please contribute
> project ideas
> 
> Hi everyone,
> 
> Globus has participated in Google Summer of Code
> (http://code.google.com/soc/) for the last two years, giving us the
> opportunity to work with talented students, expand our community, and
> develop cool projects that would have otherwise languished on a
> wishlist
> somewhere (see http://tinyurl.com/globus-gsoc09 for details on last
> summer's projects, and http://tinyurl.com/globus-gsoc08 for the 2008
> projects).
> 
> We will be applying again this year to be a mentoring organization in
> Summer of Code, and a big part of the application is preparing a
> strong
> list of student projects. I am writing to encourage members of the
> Globus community to add cool and interesting project ideas to the
> following wiki page:
> 
> 	http://dev.globus.org/wiki/Google_Summer_of_Code_2010_Ideas
> 
> You will find more information on GSoC and detailed instructions on
> how
> to add a GSoC project idea in the above URL. Even though new project
> ideas are preferable, past GSoC mentors should feel free to re-offer
> any
> idea that was not developed last year (see last year's list:
> http://dev.globus.org/wiki/Google_Summer_of_Code_2009_Ideas)
> 
> The GSoC deadline for mentoring organizations is March 12th, but we
> would like all project ideas to be added by March 10th so we can have
> time to polish them up, ask committers for clarifications, etc.
> 
> If you have any questions, please don't hesitate to reply to this
> thread.
> 
> Cheers!
> -- 
> ::::::::::::::::::::::::::::::::::::::::::::::::::::
> Borja Sotomayor, University of Chicago
>  Ph.D. Candidate, Department of Computer Science
>  Ryerson 257-C, 1100 East 58th Street, Chicago, IL
>  http://people.cs.uchicago.edu/~borja/
> Haizea: http://haizea.cs.uchicago.edu/
> ????????????????????????????????????????????????????
>     "Dis maschine vill run und run!"
>           -- Kurt G?del (on the Turing Machine)
> ::::::::::::::::::::::::::::::::::::::::::::::::::::
> _______________________________________________
> Swift-devel mailing list
> Swift-devel at ci.uchicago.edu
> http://mail.ci.uchicago.edu/mailman/listinfo/swift-devel
_______________________________________________
Swift-devel mailing list
Swift-devel at ci.uchicago.edu
http://mail.ci.uchicago.edu/mailman/listinfo/swift-devel

From benc at hawaga.org.uk  Sat Mar  6 06:55:02 2010
From: benc at hawaga.org.uk (Ben Clifford)
Date: Sat, 6 Mar 2010 12:55:02 +0000 (GMT)
Subject: [Swift-devel] [gt-dev] Google Summer of Code 2010 - Please
	contribute project ideas (fwd)
In-Reply-To: <12619091.1084741267645648607.JavaMail.root@zimbra>
References: <12619091.1084741267645648607.JavaMail.root@zimbra>
Message-ID: <Pine.LNX.4.64.1003061239480.15193@dildano.hawaga.org.uk>


> Im very interested in also enhancing the imperative 
> control structures, and then comparing the functional vs. imperative 
> approaches.

I'm fairly firmly convinced that imperative structures fit in poorly, and 
(perhaps because of that) have a hard time envisioning specific 
improvements (as in, a concrete specification of what they should do that 
would survive a week on this mailing list ;)

> Regarding the second one: Ive made recent progress in calling Swift from 
> within R, in an R-ish manner (ie you dont see any Swift); since R is 
> rather functional and also of great interest to the analytics community, 
> perhaps we can coordinate a joint SoC effort around that.

That's different to what I intended by my suggestion.

I was suggesting that the question:

  "can (something like) SwiftScript be implemented by embedding in another 
language rather than having a separate implementation of parsers, type 
systems, numerical operators, ...?"

... rather than (which I think is what you are suggesting) a language 
binding from another language (R) to use the existing SwiftScript 
implementation, which is something different.

That latter is probably something interesting, though its not interesting 
enough to me to mentor.

> I hope to get other Swift SoC projects on the table soon.

The submission to google happens early next week, so its useful to have 
ideas (even in rough form) on the wiki by then.

-- 



From wilde at mcs.anl.gov  Wed Mar 10 15:51:13 2010
From: wilde at mcs.anl.gov (wilde at mcs.anl.gov)
Date: Wed, 10 Mar 2010 15:51:13 -0600 (CST)
Subject: [Swift-devel] Re: [GSoC] Reminder: contribute GSoC project ideas
	this week
In-Reply-To: <7708046.1285911268257199353.JavaMail.root@zimbra>
Message-ID: <30326670.1286901268257873941.JavaMail.root@zimbra>

Here are the projects I'd like to consider for SoC

--

Implementing efficient MapReduce models using the Swift parallel scripting language

The Swift parallel scripting language (www.ci.uchicago.edu/swift) enables you to run many (up to tens of thousands and more) application programs in parallel on clusters, grids, clouds, and supercomputers, as well on on multicore workstations. While Swift, as a functional-inspired programming language makes it easy to specify a map-and-reduce style of scripting, as a general programming language it does not intrinsically use the key-value data model of Google and Hadoop MapReduce, and lacks the ability to automatically sort, partition, and reduce results. This project will focus on creating a map-reduce library tailored for Swift execution.

--

Integrating Swift parallel scripting semantics into Python, R, Octave, and MATLAB


--

Integrating serviceaccess capabilities in the Swift parallel scripting language

--

Measuring and enhancing multi-site parallel scheduling in Swift

--

Enabling distributed, interactive debugging and status monitoring/reporting under Swift

--

Flexible cloud resource management for the Swift parallel scripting language

--

Reworking the Swift mapper model and toolset

--

Integrating typecasting into Swift

--



----- "Borja Sotomayor" <borja at cs.uchicago.edu> wrote:

> Hi mentors and prospective mentors.
> 
> Just a reminder that GSoC project ideas are due this Friday (at 6pm 
> Central) although, if possible, I would appreciate if you could get
> them 
> to me before the end of Wednesday. You can either add them to this
> wiki 
> page (if you have a dev.globus wiki account):
> 
> 	http://dev.globus.org/wiki/Google_Summer_of_Code_2010_Ideas
> 
> Or send them to me directly. Some mentors have already added ideas, 
> which can give you an idea of the level of specificity we're looking 
> for. You can also check the project ideas guidelines:
> 
> http://dev.globus.org/wiki/Google_Summer_of_Code_2010_Ideas#Project_idea_guidelines
> 
> Cheers!
> --Borja
> 
> 
> -------- Original Message --------
> Subject: Google Summer of Code 2010 - Please contribute project ideas
> Date: Fri, 19 Feb 2010 07:40:52 -0600
> From: Borja Sotomayor <borja at borjanet.com>
> To: gt-dev <gt-dev at lists.globus.org>
> 
> Hi everyone,
> 
> Globus has participated in Google Summer of Code
> (http://code.google.com/soc/) for the last two years, giving us the
> opportunity to work with talented students, expand our community, and
> develop cool projects that would have otherwise languished on a
> wishlist
> somewhere (see http://tinyurl.com/globus-gsoc09 for details on last
> summer's projects, and http://tinyurl.com/globus-gsoc08 for the 2008
> projects).
> 
> We will be applying again this year to be a mentoring organization in
> Summer of Code, and a big part of the application is preparing a
> strong
> list of student projects. I am writing to encourage members of the
> Globus community to add cool and interesting project ideas to the
> following wiki page:
> 
> 	http://dev.globus.org/wiki/Google_Summer_of_Code_2010_Ideas
> 
> You will find more information on GSoC and detailed instructions on
> how
> to add a GSoC project idea in the above URL. Even though new project
> ideas are preferable, past GSoC mentors should feel free to re-offer
> any
> idea that was not developed last year (see last year's list:
> http://dev.globus.org/wiki/Google_Summer_of_Code_2009_Ideas)
> 
> The GSoC deadline for mentoring organizations is March 12th, but we
> would like all project ideas to be added by March 10th so we can have
> time to polish them up, ask committers for clarifications, etc.
> 
> If you have any questions, please don't hesitate to reply to this
> thread.
> 
> Cheers!
> -- 
> ::::::::::::::::::::::::::::::::::::::::::::::::::::
> Borja Sotomayor, University of Chicago
>   Ph.D. Candidate, Department of Computer Science
>   Ryerson 257-C, 1100 East 58th Street, Chicago, IL
>   http://people.cs.uchicago.edu/~borja/
> Haizea: http://haizea.cs.uchicago.edu/
> ????????????????????????????????????????????????????
>      "Dis maschine vill run und run!"
>            -- Kurt G?del (on the Turing Machine)
> ::::::::::::::::::::::::::::::::::::::::::::::::::::
> 
> 
> 
> -- 
> ::::::::::::::::::::::::::::::::::::::::::::::::::
> Borja Sotomayor, University of Chicago
>   Ph.D. Candidate, Department of Computer Science
>   Ryerson 257-C, 1100 East 58th Street, Chicago, IL
>   http://people.cs.uchicago.edu/~borja/
> Haizea: http://haizea.cs.uchicago.edu/
> ??????????????????????????????????????????????????
>     "Dis maschine vill run und run!"
>           -- Kurt G?del (on the Turing Machine)
> ::::::::::::::::::::::::::::::::::::::::::::::::::
> 
> 
> -- 
> ::::::::::::::::::::::::::::::::::::::::::::::::::::
> Borja Sotomayor, University of Chicago
>   Ph.D. Candidate, Department of Computer Science
>   Ryerson 257-C, 1100 East 58th Street, Chicago, IL
>   http://people.cs.uchicago.edu/~borja/
> Haizea: http://haizea.cs.uchicago.edu/
> ????????????????????????????????????????????????????
>      "Dis maschine vill run und run!"
>            -- Kurt G?del (on the Turing Machine)
> ::::::::::::::::::::::::::::::::::::::::::::::::::::

-- 
Michael Wilde
Computation Institute, University of Chicago
Mathematics and Computer Science Division
Argonne National Laboratory



From wilde at mcs.anl.gov  Wed Mar 10 16:02:21 2010
From: wilde at mcs.anl.gov (Michael Wilde)
Date: Wed, 10 Mar 2010 16:02:21 -0600 (CST)
Subject: [Swift-devel] Re: [GSoC] Reminder: contribute GSoC project
	ideas this week
In-Reply-To: <30326670.1286901268257873941.JavaMail.root@zimbra>
Message-ID: <13284781.1287401268258541898.JavaMail.root@zimbra>

Sorry - sent by mistake; still editing this...

- Mike

----- wilde at mcs.anl.gov wrote:

> Here are the projects I'd like to consider for SoC
> 
> --
> 
> Implementing efficient MapReduce models using the Swift parallel
> scripting language
> 
> The Swift parallel scripting language (www.ci.uchicago.edu/swift)
> enables you to run many (up to tens of thousands and more) application
> programs in parallel on clusters, grids, clouds, and supercomputers,
> as well on on multicore workstations. While Swift, as a
> functional-inspired programming language makes it easy to specify a
> map-and-reduce style of scripting, as a general programming language
> it does not intrinsically use the key-value data model of Google and
> Hadoop MapReduce, and lacks the ability to automatically sort,
> partition, and reduce results. This project will focus on creating a
> map-reduce library tailored for Swift execution.
> 
> --
> 
> Integrating Swift parallel scripting semantics into Python, R, Octave,
> and MATLAB
> 
> 
> --
> 
> Integrating serviceaccess capabilities in the Swift parallel scripting
> language
> 
> --
> 
> Measuring and enhancing multi-site parallel scheduling in Swift
> 
> --
> 
> Enabling distributed, interactive debugging and status
> monitoring/reporting under Swift
> 
> --
> 
> Flexible cloud resource management for the Swift parallel scripting
> language
> 
> --
> 
> Reworking the Swift mapper model and toolset
> 
> --
> 
> Integrating typecasting into Swift
> 
> --
> 
> 
> 
> ----- "Borja Sotomayor" <borja at cs.uchicago.edu> wrote:
> 
> > Hi mentors and prospective mentors.
> > 
> > Just a reminder that GSoC project ideas are due this Friday (at 6pm
> 
> > Central) although, if possible, I would appreciate if you could get
> > them 
> > to me before the end of Wednesday. You can either add them to this
> > wiki 
> > page (if you have a dev.globus wiki account):
> > 
> > 	http://dev.globus.org/wiki/Google_Summer_of_Code_2010_Ideas
> > 
> > Or send them to me directly. Some mentors have already added ideas,
> 
> > which can give you an idea of the level of specificity we're looking
> 
> > for. You can also check the project ideas guidelines:
> > 
> >
> http://dev.globus.org/wiki/Google_Summer_of_Code_2010_Ideas#Project_idea_guidelines
> > 
> > Cheers!
> > --Borja
> > 
> > 
> > -------- Original Message --------
> > Subject: Google Summer of Code 2010 - Please contribute project
> ideas
> > Date: Fri, 19 Feb 2010 07:40:52 -0600
> > From: Borja Sotomayor <borja at borjanet.com>
> > To: gt-dev <gt-dev at lists.globus.org>
> > 
> > Hi everyone,
> > 
> > Globus has participated in Google Summer of Code
> > (http://code.google.com/soc/) for the last two years, giving us the
> > opportunity to work with talented students, expand our community,
> and
> > develop cool projects that would have otherwise languished on a
> > wishlist
> > somewhere (see http://tinyurl.com/globus-gsoc09 for details on last
> > summer's projects, and http://tinyurl.com/globus-gsoc08 for the
> 2008
> > projects).
> > 
> > We will be applying again this year to be a mentoring organization
> in
> > Summer of Code, and a big part of the application is preparing a
> > strong
> > list of student projects. I am writing to encourage members of the
> > Globus community to add cool and interesting project ideas to the
> > following wiki page:
> > 
> > 	http://dev.globus.org/wiki/Google_Summer_of_Code_2010_Ideas
> > 
> > You will find more information on GSoC and detailed instructions on
> > how
> > to add a GSoC project idea in the above URL. Even though new
> project
> > ideas are preferable, past GSoC mentors should feel free to
> re-offer
> > any
> > idea that was not developed last year (see last year's list:
> > http://dev.globus.org/wiki/Google_Summer_of_Code_2009_Ideas)
> > 
> > The GSoC deadline for mentoring organizations is March 12th, but we
> > would like all project ideas to be added by March 10th so we can
> have
> > time to polish them up, ask committers for clarifications, etc.
> > 
> > If you have any questions, please don't hesitate to reply to this
> > thread.
> > 
> > Cheers!
> > -- 
> > ::::::::::::::::::::::::::::::::::::::::::::::::::::
> > Borja Sotomayor, University of Chicago
> >   Ph.D. Candidate, Department of Computer Science
> >   Ryerson 257-C, 1100 East 58th Street, Chicago, IL
> >   http://people.cs.uchicago.edu/~borja/
> > Haizea: http://haizea.cs.uchicago.edu/
> > ????????????????????????????????????????????????????
> >      "Dis maschine vill run und run!"
> >            -- Kurt G?del (on the Turing Machine)
> > ::::::::::::::::::::::::::::::::::::::::::::::::::::
> > 
> > 
> > 
> > -- 
> > ::::::::::::::::::::::::::::::::::::::::::::::::::
> > Borja Sotomayor, University of Chicago
> >   Ph.D. Candidate, Department of Computer Science
> >   Ryerson 257-C, 1100 East 58th Street, Chicago, IL
> >   http://people.cs.uchicago.edu/~borja/
> > Haizea: http://haizea.cs.uchicago.edu/
> > ??????????????????????????????????????????????????
> >     "Dis maschine vill run und run!"
> >           -- Kurt G?del (on the Turing Machine)
> > ::::::::::::::::::::::::::::::::::::::::::::::::::
> > 
> > 
> > -- 
> > ::::::::::::::::::::::::::::::::::::::::::::::::::::
> > Borja Sotomayor, University of Chicago
> >   Ph.D. Candidate, Department of Computer Science
> >   Ryerson 257-C, 1100 East 58th Street, Chicago, IL
> >   http://people.cs.uchicago.edu/~borja/
> > Haizea: http://haizea.cs.uchicago.edu/
> > ????????????????????????????????????????????????????
> >      "Dis maschine vill run und run!"
> >            -- Kurt G?del (on the Turing Machine)
> > ::::::::::::::::::::::::::::::::::::::::::::::::::::
> 
> -- 
> Michael Wilde
> Computation Institute, University of Chicago
> Mathematics and Computer Science Division
> Argonne National Laboratory
> 
> _______________________________________________
> Swift-devel mailing list
> Swift-devel at ci.uchicago.edu
> http://mail.ci.uchicago.edu/mailman/listinfo/swift-devel

-- 
Michael Wilde
Computation Institute, University of Chicago
Mathematics and Computer Science Division
Argonne National Laboratory



From wwj at ci.uchicago.edu  Thu Mar 11 14:20:44 2010
From: wwj at ci.uchicago.edu (Wenjun Wu)
Date: Thu, 11 Mar 2010 14:20:44 -0600
Subject: [Swift-devel] Re: can't run ssh:pbs coaster again
In-Reply-To: <32353207.1312921268329562287.JavaMail.root@zimbra>
References: <32353207.1312921268329562287.JavaMail.root@zimbra>
Message-ID: <4B99509C.3060703@ci.uchicago.edu>

Hi Mike,
  I posted tc.data, sites.xml and coasters.log here.

Wenjun

coasterpads     LoopModel        
/autonfs/gpfs-pads/oops/scienceportal/oops-svn/protlib2/bin/LoopModel.sh       
null    null    GLOBUS::maxwalltime="02:00:00"
localhost       PrepLoop         
/autonfs/gpfs-pads/oops/scienceportal/oops-svn/protlib2/bin/preploop.sh        
null    null    null
localhost       PostProcessLoops 
/autonfs/gpfs-pads/oops/scienceportal/oops-svn/protlib2/bin/PostProcessLoops.sh        
null    null    null

<pool handle="coasterpads">
    <execution provider="coaster" url="login.pads.ci.uchicago.edu" 
jobmanager="ssh:pbs"/>

    <profile namespace="globus" key="workersPerNode">2</profile>
    <profile namespace="globus" key="slots">1</profile>
    <profile namespace="globus" key="nodeGranularity">1</profile>
    <profile namespace="globus" key="maxNodes">10</profile>
    <profile namespace="karajan" key="jobThrottle">0.5</profile>
    <profile namespace="karajan" key="initialScore">10000</profile>

    <filesystem provider="ssh" url="login.pads.ci.uchicago.edu"/>
    <workdirectory>/gpfs/pads/oops/workflows</workdirectory>
  </pool>

2010-03-11 11:02:50,617 1195158935 Processing file list
2010-03-11 11:02:50,646 1195158935 Updating jars
2010-03-11 11:02:50,869 1195158935 Forking service
2010-03-11 11:02:50,869 1195158935 Moved coaster jar to head of classpath
2010-03-11 11:02:50,870 1195158935 Args: [nice, -n, 2, 
/home/wwj/Desktop/jdk1.5.0_07/bin/java, -Xmx256M, 
-DGLOBUS_HOSTNAME=login.pads.ci.uchicago.edu, 
-Djava.security.egd=file:///dev/urandom, -cp, 
/home/wwj/.globus/coasters/cache/cog-provider-coaster-0.3-ad4cd4f04d7ce5e14eb3cb2fe39b9d60.jar:/home/wwj/.globus/coasters/cache/backport-util

> Wenjun, its possible that your sites.xml is specifying parameters that are not grantable by the cluster.  Eg, a queue that doesnt exist, more nodes than exist, more time than is valid for a queue, etc.
>
> Please post your sites.xml and tc files - thats the first place to look for these problems.
>
> The cause may be visible in logs from PBS under $HOME/.globus/{coasters,...}
>
> - Mike
>
> ----- "Wenjun Wu" <wwj at ci.uchicago.edu> wrote:
>
>   
>> Hi Mike,
>>  I encountered a problem with running coaster on pad again.
>>  From the attached log file, the error message says:
>>  "Caused by: Could not submit job
>> Caused by: 
>> org.globus.cog.abstraction.impl.common.task.TaskSubmissionException: 
>> Could not submit job
>> Caused by: 
>> org.globus.cog.abstraction.impl.common.task.TaskSubmissionException: 
>> Could not start coaster service
>> Caused by: 
>> org.globus.cog.abstraction.impl.common.task.TaskSubmissionException: 
>> Task ended before registration was received. "
>>
>> Is there any way to figure what might cause this?
>> Thanks,
>>
>> Wenjun
>>     
>>> Hi Mike,
>>>  Right now I can run the loop model using ssh:pbs through coaster.
>>>       
>> But 
>>     
>>> it can only run one job on one node at one moment.
>>>  Whenever I increase the values for workersPerNode, maxNodes and 
>>> jobThrottle so that the workflow can run on multiple nodes through 
>>> coaster,
>>>  it run into a problem. Please take a look at the error message.
>>>
>>> Thanks,
>>>
>>> Wenjun
>>>
>>> Begin PBS Epilogue Mon Mar  1 15:51:56 CST 2010
>>> Job ID:        5754.svc.pads.ci.uchicago.edu
>>> Username:    wwj
>>> Group:        ci-users
>>> Job Name:    null
>>> Session:    32252
>>> Limits:        nodes=5,walltime=04:00:00
>>> Resources:    cput=00:00:00,mem=708kb,vmem=8400kb,walltime=00:00:02
>>> Nodes:        
>>>
>>>       
>> c48.pads.ci.uchicago.edu,c46.pads.ci.uchicago.edu,c45.pads.ci.uchicago.edu,c06.pads.ci.uchicago.edu,c07.pads.ci.uchicago.edu
>>
>>     
>>> End PBS Epilogue Mon Mar  1 15:51:56 CST 2010
>>> ----------------------------------------
>>>
>>>
>>>
>>>    at 
>>>
>>>       
>> org.globus.cog.karajan.workflow.events.FailureNotificationEvent.<init>(FailureNotificationEvent.java:36)
>>
>>     
>>>    at 
>>>
>>>       
>> org.globus.cog.karajan.workflow.events.FailureNotificationEvent.<init>(FailureNotificationEvent.java:42)
>>
>>     
>>>    at 
>>>
>>>       
>> org.globus.cog.karajan.workflow.nodes.FlowNode.failImmediately(FlowNode.java:147)
>>
>>     
>>>    at 
>>>
>>>       
>> org.globus.cog.karajan.workflow.nodes.grid.GridExec.taskFailed(GridExec.java:320)
>>
>>     
>>>    at 
>>>
>>>       
>> org.globus.cog.karajan.workflow.nodes.grid.AbstractGridNode.statusChanged(AbstractGridNode.java:276)
>>
>>     
>>>    at
>>>       
>> org.griphyn.vdl.karajan.lib.Execute.statusChanged(Execute.java:104)
>>     
>>>    at 
>>>
>>>       
>> org.globus.cog.karajan.scheduler.AbstractScheduler.fireJobStatusChangeEvent(AbstractScheduler.java:168)
>>
>>     
>>>    at 
>>>
>>>       
>> org.globus.cog.karajan.scheduler.LateBindingScheduler.statusChanged(LateBindingScheduler.java:661)
>>
>>     
>>>    at 
>>>
>>>       
>> org.globus.cog.karajan.scheduler.WeightedHostScoreScheduler.statusChanged(WeightedHostScoreScheduler.java:424)
>>
>>     
>>>    at 
>>>
>>>       
>> org.griphyn.vdl.karajan.VDSAdaptiveScheduler.statusChanged(VDSAdaptiveScheduler.java:410)
>>
>>     
>>>    at 
>>>
>>>       
>> org.globus.cog.abstraction.impl.common.task.TaskImpl.notifyListeners(TaskImpl.java:236)
>>
>>     
>>>    at 
>>>
>>>       
>> org.globus.cog.abstraction.impl.common.task.TaskImpl.setStatus(TaskImpl.java:224)
>>
>>     
>>>    at 
>>>
>>>       
>> org.globus.cog.abstraction.impl.execution.coaster.NotificationManager.setStatus(NotificationManager.java:112)
>>
>>     
>>>    at 
>>>
>>>       
>> org.globus.cog.abstraction.impl.execution.coaster.NotificationManager.notificationReceived(NotificationManager.java:78)
>>
>>     
>>>    at 
>>>
>>>       
>> org.globus.cog.abstraction.coaster.service.local.JobStatusHandler.requestComplete(JobStatusHandler.java:45)
>>
>>     
>>>    at 
>>>
>>>       
>> org.globus.cog.karajan.workflow.service.handlers.RequestHandler.receiveCompleted(RequestHandler.java:84)
>>
>>     
>>>    at 
>>>
>>>       
>> org.globus.cog.karajan.workflow.service.channels.AbstractKarajanChannel.handleRequest(AbstractKarajanChannel.java:348)
>>
>>     
>>>    at 
>>>
>>>       
>> org.globus.cog.karajan.workflow.service.channels.AbstractStreamKarajanChannel.step(AbstractStreamKarajanChannel.java:156)
>>
>>     
>>>    at 
>>>
>>>       
>> org.globus.cog.karajan.workflow.service.channels.AbstractStreamKarajanChannel$Multiplexer.run(AbstractStreamKarajanChannel.java:365)
>>
>>     
>>> 2010-03-01 15:52:00,639-0600 INFO  ExecutionContext Detailed
>>>       
>> exception:
>>     
>>> Exception in LoopModel:
>>> Arguments: [output/data//T0510D1.pdb, output/run/T0510D1.14.pdb]
>>> Host: coasterpads
>>> Directory:
>>>       
>> psim.loops-20100301-1551-7qejrfd0/jobs/8/LoopModel-89hxehoj
>>     
>>> stderr.txt:
>>>
>>> stdout.txt:
>>>
>>> ----
>>>
>>> Caused by: Task failed: 0301-510351-000000 Block task ended
>>>       
>> prematurely
>>     
>>>> Wenjun, I'll be at Argonne in about an hour - lets try to debug
>>>>         
>> this 
>>     
>>>> together.
>>>>
>>>> Lets do it step by step: first lets test that we can submit ssh
>>>>         
>> jobs 
>>     
>>>> from communicado to pads; then do coasters on top of that 
>>>> (provider=ssh:pbs) unless you suggest differently, Mihael.
>>>>
>>>> (The other possibility is ssh from communicado to run *swift* on 
>>>> pads. Given that the share /home and /gpfs/pads, this might be a
>>>>         
>> good 
>>     
>>>> easy option?)
>>>>
>>>> - Mike
>>>>
>>>> ----- "Wenjun Wu" <wwj at ci.uchicago.edu> wrote:
>>>>
>>>>  
>>>>         
>>>>> Hi Mihael,
>>>>>   Please find the attached log file and sites.xml.
>>>>>   I run the swift script from sidgrid to pads. And ssh "which
>>>>>           
>> qsub" 
>>     
>>>>> returns the right path.
>>>>>   But the coaster didn't work for me.
>>>>>
>>>>>  Thanks!
>>>>>
>>>>> Wenjun
>>>>>    
>>>>>           
>>>>>> I think what's happening in Wenjun's case is that qsub is not in
>>>>>>       
>>>>>>             
>>>>> the
>>>>>    
>>>>>           
>>>>>> path. I suppose this could be tested by running a simple ssh job
>>>>>>       
>>>>>>             
>>>>> that
>>>>>    
>>>>>           
>>>>>> does "which qsub".
>>>>>>
>>>>>> On Thu, 2010-02-25 at 16:08 -0600, Michael Wilde wrote:
>>>>>>        
>>>>>>             
>>>>>>> Was: Re: [PADS Support #3457] globus services for accessing
>>>>>>>               
>> PADS
>>     
>>>>>>> -- 
>>>>>>>
>>>>>>> Hi Wenjun,
>>>>>>>
>>>>>>> Are you doing this from communicado? If so, you need to use ssh
>>>>>>>               
>> to
>>     
>>>>>>>         
>>>>>>>               
>>>>> get
>>>>>    
>>>>>           
>>>>>>> from communicado to PADS. And since when you get there you want
>>>>>>>               
>> to
>>     
>>>>>>>         
>>>>>>>               
>>>>> run
>>>>>    
>>>>>           
>>>>>>> coasters. you need I think to use the coaster provider and
>>>>>>>         
>>>>>>>               
>>>>> jobmanager
>>>>>    
>>>>>           
>>>>>>> = ssh:pbs.
>>>>>>>
>>>>>>> I'm cc'ing swift-user and Mihael to discuss the exact sites
>>>>>>>         
>>>>>>>               
>>>>> options
>>>>>    
>>>>>           
>>>>>>> needed.
>>>>>>>
>>>>>>> We'd want coasters to use ssh to launch one PBS job to launch
>>>>>>>               
>> all
>>     
>>>>>>>         
>>>>>>>               
>>>>> the
>>>>>    
>>>>>           
>>>>>>> workers.
>>>>>>> I think there are still some issues on PADS with interpreting
>>>>>>>         
>>>>>>>               
>>>>> #nodes
>>>>>    
>>>>>           
>>>>>>> and workerspernode correctly, so please bear with us while we
>>>>>>>         
>>>>>>>               
>>>>> figure
>>>>>    
>>>>>           
>>>>>>> this out.
>>>>>>>
>>>>>>> I'll try this myself later tonight, but if you discover
>>>>>>>               
>> anything
>>     
>>>>>>> (either working of failing) please post to the User list.
>>>>>>>
>>>>>>> Thanks,
>>>>>>>
>>>>>>> Mike
>>>>>>>
>>>>>>>
>>>>>>> ----- "Wenjun Wu" <wwj at ci.uchicago.edu> wrote:
>>>>>>>
>>>>>>>            
>>>>>>>               
>>>>>>>> Hi Mike,
>>>>>>>>   I tried to run loop model through ssh+pbs on PADS. The ssh
>>>>>>>>           
>>>>>>>>                 
>>>>> provider
>>>>>    
>>>>>           
>>>>>>>> seems working but pbs not.
>>>>>>>>   Please check the site file and error message in the below:
>>>>>>>>  
>>>>>>>> Wenjun
>>>>>>>>                
>>>>>>>>                 
>>>>>>>>> Wenjun,
>>>>>>>>>
>>>>>>>>> I think having GRAM (GRAM5 especially) on PADS would be
>>>>>>>>>                   
>> useful.
>>     
>>>>>>>>> But in the meantime, I think you can also use swift's ssh
>>>>>>>>>             
>>>>>>>>>                   
>>>>> provider
>>>>>    
>>>>>           
>>>>>>>>>                     
>>>>>>>>>                   
>>>>>>>> to get to PADS.
>>>>>>>>                
>>>>>>>>                 
>>>>>>>>> We'll need to try that.
>>>>>>>>>
>>>>>>>>> - Mike
>>>>>>>>>
>>>>>>>>>                       
>>>>>>>>>                   
>>>>>>>> <pool handle="pads">
>>>>>>>>     <!-- gridftp url="gsiftp://stor.ci.uchicago.edu"/ -->
>>>>>>>>     <filesystem url="login.pads.ci.uchicago.edu"
>>>>>>>>                 
>> provider="ssh"
>>     
>>>>>>>>           
>>>>>>>>                 
>>>>> />
>>>>>    
>>>>>           
>>>>>>>>     <execution provider="pbs" url="svc.pads.ci.uchicago.edu"
>>>>>>>>                 
>> />
>>     
>>>>>>>>     <workdirectory>/gpfs/pads/oops/workflows</workdirectory>
>>>>>>>>     <profile namespace="karajan"
>>>>>>>>                 
>> key="jobThrottle">0.03</profile>
>>     
>>>>>>>>     <profile namespace="karajan"
>>>>>>>>           
>>>>>>>>                 
>>>>> key="initialScore">10000</profile>
>>>>>    
>>>>>           
>>>>>>>>  </pool>
>>>>>>>>
>>>>>>>> Caused by: qstat failed (exit code 255)
>>>>>>>>
>>>>>>>>         at
>>>>>>>>           
>>>>>>>>                 
>> org.globus.cog.karajan.workflow.events.FailureNotificationEvent.<init>(FailureNotificationEvent.java:36)
>>
>>     
>>>>>    
>>>>>           
>>>>>>>>         at
>>>>>>>>           
>>>>>>>>                 
>> org.globus.cog.karajan.workflow.events.FailureNotificationEvent.<init>(FailureNotificationEvent.java:42)
>>
>>     
>>>>>    
>>>>>           
>>>>>>>>         at
>>>>>>>>           
>>>>>>>>                 
>> org.globus.cog.karajan.workflow.nodes.FlowNode.failImmediately(FlowNode.java:147)
>>
>>     
>>>>>    
>>>>>           
>>>>>>>>         at
>>>>>>>>           
>>>>>>>>                 
>> org.globus.cog.karajan.workflow.nodes.grid.GridExec.taskFailed(GridExec.java:320)
>>
>>     
>>>>>    
>>>>>           
>>>>>>>>         at
>>>>>>>>           
>>>>>>>>                 
>> org.globus.cog.karajan.workflow.nodes.grid.AbstractGridNode.statusChanged(AbstractGridNode.java:276)
>>
>>     
>>>>>    
>>>>>           
>>>>>>>>         at
>>>>>>>>           
>>>>>>>>                 
>> org.griphyn.vdl.karajan.lib.Execute.statusChanged(Execute.java:104)
>>     
>>>>>    
>>>>>           
>>>>>>>>         at
>>>>>>>>           
>>>>>>>>                 
>> org.globus.cog.karajan.scheduler.AbstractScheduler.fireJobStatusChangeEvent(AbstractScheduler.java:168)
>>
>>     
>>>>>    
>>>>>           
>>>>>>>>         at
>>>>>>>>           
>>>>>>>>                 
>> org.globus.cog.karajan.scheduler.LateBindingScheduler.statusChanged(LateBindingScheduler.java:661)
>>
>>     
>>>>>    
>>>>>           
>>>>>>>>         at
>>>>>>>>           
>>>>>>>>                 
>> org.globus.cog.karajan.scheduler.WeightedHostScoreScheduler.statusChanged(WeightedHostScoreScheduler.java:424)
>>
>>     
>>>>>    
>>>>>           
>>>>>>>>         at
>>>>>>>>           
>>>>>>>>                 
>> org.griphyn.vdl.karajan.VDSAdaptiveScheduler.statusChanged(VDSAdaptiveScheduler.java:410)
>>
>>     
>>>>>    
>>>>>           
>>>>>>>>         at
>>>>>>>>           
>>>>>>>>                 
>> org.globus.cog.abstraction.impl.common.task.TaskImpl.notifyListeners(TaskImpl.java:236)
>>
>>     
>>>>>    
>>>>>           
>>>>>>>>         at
>>>>>>>>           
>>>>>>>>                 
>> org.globus.cog.abstraction.impl.common.task.TaskImpl.setStatus(TaskImpl.java:224)
>>
>>     
>>>>>    
>>>>>           
>>>>>>>>         at
>>>>>>>>           
>>>>>>>>                 
>> org.globus.cog.abstraction.impl.common.AbstractDelegatedTaskHandler.failTask(AbstractDelegatedTaskHandler.java:54)
>>
>>     
>>>>>    
>>>>>           
>>>>>>>>         at
>>>>>>>>           
>>>>>>>>                 
>> org.globus.cog.abstraction.impl.scheduler.common.AbstractJobSubmissionTaskHandler.processFailed(AbstractJobSubmissionTaskHandler.java:101)
>>
>>     
>>>>>    
>>>>>           
>>>>>>>>         at
>>>>>>>>           
>>>>>>>>                 
>> org.globus.cog.abstraction.impl.scheduler.common.AbstractExecutor.processFailed(AbstractExecutor.java:246)
>>
>>     
>>>>>    
>>>>>           
>>>>>>>>         at
>>>>>>>>           
>>>>>>>>                 
>> org.globus.cog.abstraction.impl.scheduler.common.Job.fail(Job.java:198)
>>     
>>>>>    
>>>>>           
>>>>>>>>         at
>>>>>>>>           
>>>>>>>>                 
>> org.globus.cog.abstraction.impl.scheduler.common.AbstractQueuePoller.failAll(AbstractQueuePoller.java:141)
>>
>>     
>>>>>    
>>>>>           
>>>>>>>>         at
>>>>>>>>           
>>>>>>>>                 
>> org.globus.cog.abstraction.impl.scheduler.common.AbstractQueuePoller.pollQueue(AbstractQueuePoller.java:172)
>>
>>     
>>>>>    
>>>>>           
>>>>>>>>         at
>>>>>>>>           
>>>>>>>>                 
>> org.globus.cog.abstraction.impl.scheduler.common.AbstractQueuePoller.run(AbstractQueuePoller.java:80)
>>
>>     
>>>>>    
>>>>>           
>>>>>>>>         ... 1 more
>>>>>>>>
>>>>>>>>
>>>>>>>>                
>>>>>>>>                 
>>>>>>>>> ----- "Ti Leggett" <pads-support at ci.uchicago.edu> wrote:
>>>>>>>>>
>>>>>>>>>                      
>>>>>>>>>                   
>>>>>>>>>> There are currently no Globus job managers, but GridFTP is
>>>>>>>>>>                     
>> at
>>     
>>>>>>>>>> stor.ci.uchicago.edu.
>>>>>>>>>>
>>>>>>>>>> I'll work on getting GRAM up. Do you need WSRF or Pre-WS
>>>>>>>>>>                     
>> GRAM?
>>     
>>>>>>>>>> On Wed Feb 24 14:45:57 2010, wwj at ci.uchicago.edu wrote:
>>>>>>>>>>                            
>>>>>>>>>>                     
>>>>>>>>>>> Hello,
>>>>>>>>>>>    Could you please tell me whether there is any globus
>>>>>>>>>>>                 
>>>>>>>>>>>                       
>>>>> services
>>>>>    
>>>>>           
>>>>>>>>>>>                             
>>>>>>>>>>>                       
>>>>>>>> for
>>>>>>>>                
>>>>>>>>                 
>>>>>>>>>>>       PADS such as GridFTP and GRAM?
>>>>>>>>>>>    I'm trying to launch jobs to PADS remotely but can't
>>>>>>>>>>>                       
>> figure
>>     
>>>>>>>>>>>                             
>>>>>>>>>>>                       
>>>>>>>> out
>>>>>>>>                
>>>>>>>>                 
>>>>>>>>>>>                                   
>>>>>>>>>>>                       
>>>>>>>>>> what                            
>>>>>>>>>>                     
>>>>>>>>>>> are the right URLs for the GridFTP
>>>>>>>>>>>    service and GRAM.
>>>>>>>>>>>    Thanks!
>>>>>>>>>>>
>>>>>>>>>>> Wenjun
>>>>>>>>>>>                                   
>>>>>>>>>>>                       
>>>>>>>>>                     
>>>>>>>>>                   
>>>>>>         
>>>>>>             
>>>>> 2010-02-25 17:12:00,157-0600 DEBUG Loader Max heap: 266403840
>>>>> 2010-02-25 17:12:00,159-0600 DEBUG Loader kmlversion is
>>>>>    
>>>>>           
>>>>>> cd1f7f6b-6e05-4723-ac70-e8683b56ae98<
>>>>>>       
>>>>>>             
>>>>> 2010-02-25 17:12:00,159-0600 DEBUG Loader build version is
>>>>>    
>>>>>           
>>>>>> f3073b05-a317-4f56-a26f-f87b6abd1af3<
>>>>>>       
>>>>>>             
>>>>> 2010-02-25 17:12:00,159-0600 INFO  Loader psim.loops.swift:
>>>>>           
>> source
>>     
>>>>> file was compiled with a different version of Swift. Recompiling.
>>>>> 2010-02-25 17:12:01,274-0600 INFO  Karajan Validation of XML
>>>>> intermediate file was successful
>>>>> 2010-02-25 17:12:01,982-0600 INFO  VDL2ExecutionContext Stack
>>>>>           
>> dump:
>>     
>>>>> Level 1
>>>>> [iA = 0, iB = 0, bA = false, bB = false]
>>>>>     vdl:instanceconfig = Swift configuration []
>>>>>     vdl:operation = run
>>>>>     swift.home =
>>>>> /home/wwj/SIDGrid/swift/cog-branch/modules/swift/dist/swift-svn
>>>>>     PATH_SEPARATOR = /
>>>>>
>>>>>
>>>>> 2010-02-25 17:12:02,907-0600 INFO  unknown Using sites file:
>>>>> ./sites.xml
>>>>> 2010-02-25 17:12:02,908-0600 INFO  unknown Using tc.data:
>>>>>           
>> ./tc.data
>>     
>>>>> 2010-02-25 17:12:03,089-0600 INFO  AbstractScheduler Setting
>>>>>           
>> resources
>>     
>>>>> to: {pads=pads, localhost=localhost, pbs=pbs,
>>>>> pbs-coaster=pbs-coaster}
>>>>> 2010-02-25 17:12:03,711-0600 INFO  unknown Swift svn swift-r3246
>>>>> cog-r2721
>>>>>
>>>>> 2010-02-25 17:12:03,713-0600 INFO  unknown RUNID
>>>>> id=tag:benc at ci.uchicago.edu,2007:swift:run:20100225-1712-3zrtb5i5
>>>>> 2010-02-25 17:12:03,916-0600 INFO  AbstractDataNode closed
>>>>> org.griphyn.vdl.mapping.RootDataNode identifier
>>>>>
>>>>>           
>> tag:benc at ci.uchicago.edu,2008:swift:dataset:20100225-1712-kjif48ad:720000000001
>>
>>     
>>>>> type string value=input dataset=unnamed SwiftScript value
>>>>>           
>> (closed)
>>     
>>>>> 2010-02-25 17:12:03,925-0600 INFO  New NEW
>>>>>
>>>>>           
>> id=tag:benc at ci.uchicago.edu,2008:swift:dataset:20100225-1712-kjif48ad:720000000001
>>
>>     
>>>>> 2010-02-25 17:12:03,925-0600 INFO  AbstractDataNode closed
>>>>> org.griphyn.vdl.mapping.RootDataNode identifier
>>>>>
>>>>>           
>> tag:benc at ci.uchicago.edu,2008:swift:dataset:20100225-1712-kjif48ad:720000000002
>>
>>     
>>>>> type string value=LoopModelResults.map dataset=unnamed
>>>>>           
>> SwiftScript
>>     
>>>>> value (closed)
>>>>> 2010-02-25 17:12:03,925-0600 INFO  New NEW
>>>>>
>>>>>           
>> id=tag:benc at ci.uchicago.edu,2008:swift:dataset:20100225-1712-kjif48ad:720000000002
>>
>>     
>>>>> 2010-02-25 17:12:03,925-0600 INFO  AbstractDataNode closed
>>>>> org.griphyn.vdl.mapping.RootDataNode identifier
>>>>>
>>>>>           
>> tag:benc at ci.uchicago.edu,2008:swift:dataset:20100225-1712-kjif48ad:720000000003
>>
>>     
>>>>> type string value=indir dataset=unnamed SwiftScript value
>>>>>           
>> (closed)
>>     
>>>>> 2010-02-25 17:12:03,926-0600 INFO  New NEW
>>>>>
>>>>>           
>> id=tag:benc at ci.uchicago.edu,2008:swift:dataset:20100225-1712-kjif48ad:720000000003
>>
>>     
>>>>> 2010-02-25 17:12:03,926-0600 INFO  AbstractDataNode closed
>>>>> org.griphyn.vdl.mapping.RootDataNode identifier
>>>>>
>>>>>           
>> tag:benc at ci.uchicago.edu,2008:swift:dataset:20100225-1712-kjif48ad:720000000004
>>
>>     
>>>>> type string value=output dataset=unnamed SwiftScript value
>>>>>           
>> (closed)
>>     
>>>>> 2010-02-25 17:12:03,926-0600 INFO  New NEW
>>>>>
>>>>>           
>> id=tag:benc at ci.uchicago.edu,2008:swift:dataset:20100225-1712-kjif48ad:720000000004
>>
>>     
>>>>> 2010-02-25 17:12:03,926-0600 INFO  AbstractDataNode closed
>>>>> org.griphyn.vdl.mapping.RootDataNode identifier
>>>>>
>>>>>           
>> tag:benc at ci.uchicago.edu,2008:swift:dataset:20100225-1712-kjif48ad:720000000005
>>
>>     
>>>>> type string value=outdir dataset=unnamed SwiftScript value
>>>>>           
>> (closed)
>>     
>>>>> 2010-02-25 17:12:03,926-0600 INFO  New NEW
>>>>>
>>>>>           
>> id=tag:benc at ci.uchicago.edu,2008:swift:dataset:20100225-1712-kjif48ad:720000000005
>>
>>     
>>>>> 2010-02-25 17:12:03,926-0600 INFO  AbstractDataNode closed
>>>>> org.griphyn.vdl.mapping.RootDataNode identifier
>>>>>
>>>>>           
>> tag:benc at ci.uchicago.edu,2008:swift:dataset:20100225-1712-kjif48ad:720000000006
>>
>>     
>>>>> type string value=protein dataset=unnamed SwiftScript value
>>>>>           
>> (closed)
>>     
>>>>> 2010-02-25 17:12:03,927-0600 INFO  New NEW
>>>>>
>>>>>           
>> id=tag:benc at ci.uchicago.edu,2008:swift:dataset:20100225-1712-kjif48ad:720000000006
>>
>>     
>>>>> 2010-02-25 17:12:03,927-0600 INFO  AbstractDataNode closed
>>>>> org.griphyn.vdl.mapping.RootDataNode identifier
>>>>>
>>>>>           
>> tag:benc at ci.uchicago.edu,2008:swift:dataset:20100225-1712-kjif48ad:720000000007
>>
>>     
>>>>> type string value=LoopModelData.map dataset=unnamed SwiftScript
>>>>>           
>> value
>>     
>>>>> (closed)
>>>>> 2010-02-25 17:12:03,927-0600 INFO  New NEW
>>>>>
>>>>>           
>> id=tag:benc at ci.uchicago.edu,2008:swift:dataset:20100225-1712-kjif48ad:720000000007
>>
>>     
>>>>> 2010-02-25 17:12:03,927-0600 INFO  AbstractDataNode closed
>>>>> org.griphyn.vdl.mapping.RootDataNode identifier
>>>>>
>>>>>           
>> tag:benc at ci.uchicago.edu,2008:swift:dataset:20100225-1712-kjif48ad:720000000008
>>
>>     
>>>>> type string value=4 dataset=unnamed SwiftScript value (closed)
>>>>> 2010-02-25 17:12:03,927-0600 INFO  New NEW
>>>>>
>>>>>           
>> id=tag:benc at ci.uchicago.edu,2008:swift:dataset:20100225-1712-kjif48ad:720000000008
>>
>>     
>>>>> 2010-02-25 17:12:03,928-0600 INFO  AbstractDataNode closed
>>>>> org.griphyn.vdl.mapping.RootDataNode identifier
>>>>>
>>>>>           
>> tag:benc at ci.uchicago.edu,2008:swift:dataset:20100225-1712-kjif48ad:720000000009
>>
>>     
>>>>> type string value=LoopModelOutArray.map dataset=unnamed
>>>>>           
>> SwiftScript
>>     
>>>>> value (closed)
>>>>> 2010-02-25 17:12:03,928-0600 INFO  New NEW
>>>>>
>>>>>           
>> id=tag:benc at ci.uchicago.edu,2008:swift:dataset:20100225-1712-kjif48ad:720000000009
>>
>>     
>>>>> 2010-02-25 17:12:03,928-0600 INFO  AbstractDataNode closed
>>>>> org.griphyn.vdl.mapping.RootDataNode identifier
>>>>>
>>>>>           
>> tag:benc at ci.uchicago.edu,2008:swift:dataset:20100225-1712-kjif48ad:720000000010
>>
>>     
>>>>> type string value=LoopModelIn.map dataset=unnamed SwiftScript
>>>>>           
>> value
>>     
>>>>> (closed)
>>>>> 2010-02-25 17:12:03,928-0600 INFO  New NEW
>>>>>
>>>>>           
>> id=tag:benc at ci.uchicago.edu,2008:swift:dataset:20100225-1712-kjif48ad:720000000010
>>
>>     
>>>>> 2010-02-25 17:12:03,928-0600 INFO  AbstractDataNode closed
>>>>> org.griphyn.vdl.mapping.RootDataNode identifier
>>>>>
>>>>>           
>> tag:benc at ci.uchicago.edu,2008:swift:dataset:20100225-1712-kjif48ad:720000000011
>>
>>     
>>>>> type string value=nSim dataset=unnamed SwiftScript value (closed)
>>>>> 2010-02-25 17:12:03,928-0600 INFO  New NEW
>>>>>
>>>>>           
>> id=tag:benc at ci.uchicago.edu,2008:swift:dataset:20100225-1712-kjif48ad:720000000011
>>
>>     
>>>>> 2010-02-25 17:12:03,932-0600 INFO  AbstractDataNode closed
>>>>> org.griphyn.vdl.mapping.RootDataNode identifier
>>>>>
>>>>>           
>> tag:benc at ci.uchicago.edu,2008:swift:dataset:20100225-1712-kjif48ad:720000000012
>>
>>     
>>>>> type int value=1.0 dataset=unnamed SwiftScript value (closed)
>>>>> 2010-02-25 17:12:03,932-0600 INFO  New NEW
>>>>>
>>>>>           
>> id=tag:benc at ci.uchicago.edu,2008:swift:dataset:20100225-1712-kjif48ad:720000000012
>>
>>     
>>>>> 2010-02-25 17:12:03,933-0600 INFO  AbstractDataNode closed
>>>>> org.griphyn.vdl.mapping.RootDataNode identifier
>>>>>
>>>>>           
>> tag:benc at ci.uchicago.edu,2008:swift:dataset:20100225-1712-kjif48ad:720000000013
>>
>>     
>>>>> type int value=0.0 dataset=unnamed SwiftScript value (closed)
>>>>> 2010-02-25 17:12:03,933-0600 INFO  New NEW
>>>>>
>>>>>           
>> id=tag:benc at ci.uchicago.edu,2008:swift:dataset:20100225-1712-kjif48ad:720000000013
>>
>>     
>>>>> 2010-02-25 17:12:03,946-0600 INFO  modelloops STARTCOMPOUND
>>>>>           
>> thread=0-1
>>     
>>>>> name=ModelLoops
>>>>> 2010-02-25 17:12:03,973-0600 INFO  New NEW
>>>>>
>>>>>           
>> id=tag:benc at ci.uchicago.edu,2008:swift:dataset:20100225-1712-kjif48ad:720000000014
>>
>>     
>>>>> 2010-02-25 17:12:03,976-0600 INFO  New NEW
>>>>>
>>>>>           
>> id=tag:benc at ci.uchicago.edu,2008:swift:dataset:20100225-1712-kjif48ad:720000000015
>>
>>     
>>>>> 2010-02-25 17:12:03,978-0600 INFO  New NEW
>>>>>
>>>>>           
>> id=tag:benc at ci.uchicago.edu,2008:swift:dataset:20100225-1712-kjif48ad:720000000016
>>
>>     
>>>>> 2010-02-25 17:12:03,979-0600 INFO  New NEW
>>>>>
>>>>>           
>> id=tag:benc at ci.uchicago.edu,2008:swift:dataset:20100225-1712-kjif48ad:720000000017
>>
>>     
>>>>> 2010-02-25 17:12:03,985-0600 INFO  New NEW
>>>>>
>>>>>           
>> id=tag:benc at ci.uchicago.edu,2008:swift:dataset:20100225-1712-kjif48ad:720000000018
>>
>>     
>>>>> 2010-02-25 17:12:03,987-0600 INFO  AbstractDataNode Adding handle
>>>>> listener "org.griphyn.vdl.mapping.RootDataNode identifier
>>>>>
>>>>>           
>> tag:benc at ci.uchicago.edu,2008:swift:dataset:20100225-1712-kjif48ad:720000000019
>>
>>     
>>>>> type LoopModelIn with no value at dataset=modelIn (not closed)"
>>>>>           
>> to
>>     
>>>>> "org.griphyn.vdl.mapping.RootDataNode identifier
>>>>>
>>>>>           
>> tag:benc at ci.uchicago.edu,2008:swift:dataset:20100225-1712-kjif48ad:720000000018
>>
>>     
>>>>> type string with no value at dataset=swift#mapper#17007 (not
>>>>>           
>> closed)"
>>     
>>>>> 2010-02-25 17:12:03,987-0600 INFO  New NEW
>>>>>
>>>>>           
>> id=tag:benc at ci.uchicago.edu,2008:swift:dataset:20100225-1712-kjif48ad:720000000019
>>
>>     
>>>>> 2010-02-25 17:12:03,989-0600 INFO  New NEW
>>>>>
>>>>>           
>> id=tag:benc at ci.uchicago.edu,2008:swift:dataset:20100225-1712-kjif48ad:720000000020
>>
>>     
>>>>> 2010-02-25 17:12:03,991-0600 INFO  AbstractDataNode Adding handle
>>>>> listener "org.griphyn.vdl.mapping.RootDataNode identifier
>>>>>
>>>>>           
>> tag:benc at ci.uchicago.edu,2008:swift:dataset:20100225-1712-kjif48ad:720000000021
>>
>>     
>>>>> type LoopModelData with no value at dataset=modelData (not
>>>>>           
>> closed)" to
>>     
>>>>> "org.griphyn.vdl.mapping.RootDataNode identifier
>>>>>
>>>>>           
>> tag:benc at ci.uchicago.edu,2008:swift:dataset:20100225-1712-kjif48ad:720000000020
>>
>>     
>>>>> type string with no value at dataset=swift#mapper#17009 (not
>>>>>           
>> closed)"
>>     
>>>>> 2010-02-25 17:12:03,991-0600 INFO  New NEW
>>>>>
>>>>>           
>> id=tag:benc at ci.uchicago.edu,2008:swift:dataset:20100225-1712-kjif48ad:720000000021
>>
>>     
>>>>> 2010-02-25 17:12:03,993-0600 INFO  New NEW
>>>>>
>>>>>           
>> id=tag:benc at ci.uchicago.edu,2008:swift:dataset:20100225-1712-kjif48ad:720000000022
>>
>>     
>>>>> 2010-02-25 17:12:03,997-0600 INFO  AbstractDataNode Adding handle
>>>>> listener "modelOut.$[]/0" to
>>>>>           
>> "org.griphyn.vdl.mapping.RootDataNode
>>     
>>>>> identifier
>>>>>
>>>>>           
>> tag:benc at ci.uchicago.edu,2008:swift:dataset:20100225-1712-kjif48ad:720000000022
>>
>>     
>>>>> type string with no value at dataset=swift#mapper#17011 (not
>>>>>           
>> closed)"
>>     
>>>>> 2010-02-25 17:12:03,997-0600 INFO  New NEW
>>>>>
>>>>>           
>> id=tag:benc at ci.uchicago.edu,2008:swift:dataset:20100225-1712-kjif48ad:720000000023
>>
>>     
>>>>> 2010-02-25 17:12:03,999-0600 INFO  New NEW
>>>>>
>>>>>           
>> id=tag:benc at ci.uchicago.edu,2008:swift:dataset:20100225-1712-kjif48ad:720000000024
>>
>>     
>>>>> 2010-02-25 17:12:04,001-0600 INFO  AbstractDataNode Adding handle
>>>>> listener "org.griphyn.vdl.mapping.RootDataNode identifier
>>>>>
>>>>>           
>> tag:benc at ci.uchicago.edu,2008:swift:dataset:20100225-1712-kjif48ad:720000000025
>>
>>     
>>>>> type LoopModelResults with no value at dataset=modelResults (not
>>>>> closed)" to "org.griphyn.vdl.mapping.RootDataNode identifier
>>>>>
>>>>>           
>> tag:benc at ci.uchicago.edu,2008:swift:dataset:20100225-1712-kjif48ad:720000000024
>>
>>     
>>>>> type string with no value at dataset=swift#mapper#17013 (not
>>>>>           
>> closed)"
>>     
>>>>> 2010-02-25 17:12:04,001-0600 INFO  New NEW
>>>>>
>>>>>           
>> id=tag:benc at ci.uchicago.edu,2008:swift:dataset:20100225-1712-kjif48ad:720000000025
>>
>>     
>>>>> 2010-02-25 17:12:04,007-0600 INFO  SetFieldValue Setting
>>>>> org.griphyn.vdl.mapping.RootDataNode identifier
>>>>>
>>>>>           
>> tag:benc at ci.uchicago.edu,2008:swift:dataset:20100225-1712-kjif48ad:720000000018
>>
>>     
>>>>> type string with no value at dataset=swift#mapper#17007 (not
>>>>>           
>> closed)
>>     
>>>>> to LoopModelIn.map
>>>>> 2010-02-25 17:12:04,007-0600 INFO  AbstractDataNode closed
>>>>> org.griphyn.vdl.mapping.RootDataNode identifier
>>>>>
>>>>>           
>> tag:benc at ci.uchicago.edu,2008:swift:dataset:20100225-1712-kjif48ad:720000000026
>>
>>     
>>>>> type string value=4 dataset=unnamed SwiftScript value (closed)
>>>>> 2010-02-25 17:12:04,007-0600 INFO  VDLFunction FUNCTION id=451000
>>>>> name=arg
>>>>>
>>>>>           
>> result=tag:benc at ci.uchicago.edu,2008:swift:dataset:20100225-1712-kjif48ad:720000000026
>>
>>     
>>>>> 2010-02-25 17:12:04,007-0600 INFO  VDLFunction FUNCTIONPARAMETER
>>>>> id=451000
>>>>>
>>>>>           
>> input=tag:benc at ci.uchicago.edu,2008:swift:dataset:20100225-1712-kjif48ad:720000000011
>>
>>     
>>>>> name=name
>>>>> 2010-02-25 17:12:04,007-0600 INFO  VDLFunction FUNCTIONPARAMETER
>>>>> id=451000
>>>>>
>>>>>           
>> input=tag:benc at ci.uchicago.edu,2008:swift:dataset:20100225-1712-kjif48ad:720000000008
>>
>>     
>>>>> name=value
>>>>> 2010-02-25 17:12:04,008-0600 INFO  SetFieldValue Setting
>>>>> org.griphyn.vdl.mapping.RootDataNode identifier
>>>>>
>>>>>           
>> tag:benc at ci.uchicago.edu,2008:swift:dataset:20100225-1712-kjif48ad:720000000020
>>
>>     
>>>>> type string with no value at dataset=swift#mapper#17009 (not
>>>>>           
>> closed)
>>     
>>>>> to LoopModelData.map
>>>>> 2010-02-25 17:12:04,008-0600 INFO  AbstractDataNode Notifying
>>>>>           
>> listener
>>     
>>>>> "org.griphyn.vdl.mapping.RootDataNode identifier
>>>>>
>>>>>           
>> tag:benc at ci.uchicago.edu,2008:swift:dataset:20100225-1712-kjif48ad:720000000021
>>
>>     
>>>>> type LoopModelData with no value at dataset=modelData (not
>>>>>           
>> closed)"
>>     
>>>>> about "org.griphyn.vdl.mapping.RootDataNode identifier
>>>>>
>>>>>           
>> tag:benc at ci.uchicago.edu,2008:swift:dataset:20100225-1712-kjif48ad:720000000020
>>
>>     
>>>>> type string value=LoopModelData.map dataset=swift#mapper#17009
>>>>> (closed)"
>>>>> 2010-02-25 17:12:04,008-0600 INFO  AbstractDataNode Adding handle
>>>>> listener "org.griphyn.vdl.mapping.RootDataNode identifier
>>>>>
>>>>>           
>> tag:benc at ci.uchicago.edu,2008:swift:dataset:20100225-1712-kjif48ad:720000000021
>>
>>     
>>>>> type LoopModelData with no value at dataset=modelData (not
>>>>>           
>> closed)" to
>>     
>>>>> "org.griphyn.vdl.mapping.RootDataNode identifier
>>>>>
>>>>>           
>> tag:benc at ci.uchicago.edu,2008:swift:dataset:20100225-1712-kjif48ad:720000000017
>>
>>     
>>>>> type string with no value at dataset=outdir (not closed)"
>>>>> 2010-02-25 17:12:04,008-0600 INFO  AbstractDataNode closed
>>>>> org.griphyn.vdl.mapping.RootDataNode identifier
>>>>>
>>>>>           
>> tag:benc at ci.uchicago.edu,2008:swift:dataset:20100225-1712-kjif48ad:720000000020
>>
>>     
>>>>> type string value=LoopModelData.map dataset=swift#mapper#17009
>>>>> (closed)
>>>>> 2010-02-25 17:12:04,008-0600 INFO  SetFieldValue Setting
>>>>> org.griphyn.vdl.mapping.RootDataNode identifier
>>>>>
>>>>>           
>> tag:benc at ci.uchicago.edu,2008:swift:dataset:20100225-1712-kjif48ad:720000000022
>>
>>     
>>>>> type string with no value at dataset=swift#mapper#17011 (not
>>>>>           
>> closed)
>>     
>>>>> to LoopModelOutArray.map
>>>>> 2010-02-25 17:12:04,009-0600 INFO  AbstractDataNode Notifying
>>>>>           
>> listener
>>     
>>>>> "modelOut.$[]/0" about "org.griphyn.vdl.mapping.RootDataNode
>>>>> identifier
>>>>>
>>>>>           
>> tag:benc at ci.uchicago.edu,2008:swift:dataset:20100225-1712-kjif48ad:720000000022
>>
>>     
>>>>> type string value=LoopModelOutArray.map
>>>>>           
>> dataset=swift#mapper#17011
>>     
>>>>> (closed)"
>>>>> 2010-02-25 17:12:04,009-0600 INFO  AbstractDataNode Adding handle
>>>>> listener "modelOut.$[]/0" to
>>>>>           
>> "org.griphyn.vdl.mapping.RootDataNode
>>     
>>>>> identifier
>>>>>
>>>>>           
>> tag:benc at ci.uchicago.edu,2008:swift:dataset:20100225-1712-kjif48ad:720000000014
>>
>>     
>>>>> type int with no value at dataset=nSim (not closed)"
>>>>> 2010-02-25 17:12:04,009-0600 INFO  AbstractDataNode closed
>>>>> org.griphyn.vdl.mapping.RootDataNode identifier
>>>>>
>>>>>           
>> tag:benc at ci.uchicago.edu,2008:swift:dataset:20100225-1712-kjif48ad:720000000022
>>
>>     
>>>>> type string value=LoopModelOutArray.map
>>>>>           
>> dataset=swift#mapper#17011
>>     
>>>>> (closed)
>>>>> 2010-02-25 17:12:04,009-0600 INFO  SetFieldValue Setting
>>>>> org.griphyn.vdl.mapping.RootDataNode identifier
>>>>>
>>>>>           
>> tag:benc at ci.uchicago.edu,2008:swift:dataset:20100225-1712-kjif48ad:720000000024
>>
>>     
>>>>> type string with no value at dataset=swift#mapper#17013 (not
>>>>>           
>> closed)
>>     
>>>>> to LoopModelResults.map
>>>>> 2010-02-25 17:12:04,009-0600 INFO  AbstractDataNode Notifying
>>>>>           
>> listener
>>     
>>>>> "org.griphyn.vdl.mapping.RootDataNode identifier
>>>>>
>>>>>           
>> tag:benc at ci.uchicago.edu,2008:swift:dataset:20100225-1712-kjif48ad:720000000025
>>
>>     
>>>>> type LoopModelResults with no value at dataset=modelResults (not
>>>>> closed)" about "org.griphyn.vdl.mapping.RootDataNode identifier
>>>>>
>>>>>           
>> tag:benc at ci.uchicago.edu,2008:swift:dataset:20100225-1712-kjif48ad:720000000024
>>
>>     
>>>>> type string value=LoopModelResults.map dataset=swift#mapper#17013
>>>>> (closed)"
>>>>> 2010-02-25 17:12:04,009-0600 INFO  AbstractDataNode Adding handle
>>>>> listener "org.griphyn.vdl.mapping.RootDataNode identifier
>>>>>
>>>>>           
>> tag:benc at ci.uchicago.edu,2008:swift:dataset:20100225-1712-kjif48ad:720000000025
>>
>>     
>>>>> type LoopModelResults with no value at dataset=modelResults (not
>>>>> closed)" to "org.griphyn.vdl.mapping.RootDataNode identifier
>>>>>
>>>>>           
>> tag:benc at ci.uchicago.edu,2008:swift:dataset:20100225-1712-kjif48ad:720000000017
>>
>>     
>>>>> type string with no value at dataset=outdir (not closed)"
>>>>> 2010-02-25 17:12:04,009-0600 INFO  AbstractDataNode closed
>>>>> org.griphyn.vdl.mapping.RootDataNode identifier
>>>>>
>>>>>           
>> tag:benc at ci.uchicago.edu,2008:swift:dataset:20100225-1712-kjif48ad:720000000024
>>
>>     
>>>>> type string value=LoopModelResults.map dataset=swift#mapper#17013
>>>>> (closed)
>>>>> 2010-02-25 17:12:04,009-0600 INFO  AbstractDataNode closed
>>>>> org.griphyn.vdl.mapping.RootDataNode identifier
>>>>>
>>>>>           
>> tag:benc at ci.uchicago.edu,2008:swift:dataset:20100225-1712-kjif48ad:720000000027
>>
>>     
>>>>> type string value=T0510D1 dataset=unnamed SwiftScript value
>>>>>           
>> (closed)
>>     
>>>>> 2010-02-25 17:12:04,009-0600 INFO  VDLFunction FUNCTION id=451001
>>>>> name=arg
>>>>>
>>>>>           
>> result=tag:benc at ci.uchicago.edu,2008:swift:dataset:20100225-1712-kjif48ad:720000000027
>>
>>     
>>>>> 2010-02-25 17:12:04,010-0600 INFO  VDLFunction FUNCTIONPARAMETER
>>>>> id=451001
>>>>>
>>>>>           
>> input=tag:benc at ci.uchicago.edu,2008:swift:dataset:20100225-1712-kjif48ad:720000000006
>>
>>     
>>>>> name=name
>>>>> 2010-02-25 17:12:04,010-0600 INFO  SetFieldValue Setting
>>>>> org.griphyn.vdl.mapping.RootDataNode identifier
>>>>>
>>>>>           
>> tag:benc at ci.uchicago.edu,2008:swift:dataset:20100225-1712-kjif48ad:720000000015
>>
>>     
>>>>> type string with no value at dataset=proteinId (not closed) to
>>>>> T0510D1
>>>>> 2010-02-25 17:12:04,010-0600 INFO  AbstractDataNode closed
>>>>> org.griphyn.vdl.mapping.RootDataNode identifier
>>>>>
>>>>>           
>> tag:benc at ci.uchicago.edu,2008:swift:dataset:20100225-1712-kjif48ad:720000000015
>>
>>     
>>>>> type string value=T0510D1 dataset=proteinId (closed)
>>>>> 2010-02-25 17:12:04,010-0600 INFO  CloseDataset Partially closing
>>>>> T0510D1 for statement 88013
>>>>> 2010-02-25 17:12:04,011-0600 INFO  CloseDataset var is T0510D1
>>>>> 2010-02-25 17:12:04,011-0600 INFO  CloseDataset var hash is
>>>>>           
>> 28062585
>>     
>>>>> 2010-02-25 17:12:04,011-0600 INFO  CloseDataset variable already
>>>>> closed - skipping partial close processing
>>>>> 2010-02-25 17:12:04,011-0600 INFO  AbstractDataNode closed
>>>>> org.griphyn.vdl.mapping.RootDataNode identifier
>>>>>
>>>>>           
>> tag:benc at ci.uchicago.edu,2008:swift:dataset:20100225-1712-kjif48ad:720000000028
>>
>>     
>>>>> type string value=input dataset=unnamed SwiftScript value
>>>>>           
>> (closed)
>>     
>>>>> 2010-02-25 17:12:04,011-0600 INFO  VDLFunction FUNCTION id=451002
>>>>> name=arg
>>>>>
>>>>>           
>> result=tag:benc at ci.uchicago.edu,2008:swift:dataset:20100225-1712-kjif48ad:720000000028
>>
>>     
>>>>> 2010-02-25 17:12:04,011-0600 INFO  VDLFunction FUNCTIONPARAMETER
>>>>> id=451002
>>>>>
>>>>>           
>> input=tag:benc at ci.uchicago.edu,2008:swift:dataset:20100225-1712-kjif48ad:720000000003
>>
>>     
>>>>> name=name
>>>>> 2010-02-25 17:12:04,011-0600 INFO  VDLFunction FUNCTIONPARAMETER
>>>>> id=451002
>>>>>
>>>>>           
>> input=tag:benc at ci.uchicago.edu,2008:swift:dataset:20100225-1712-kjif48ad:720000000001
>>
>>     
>>>>> name=value
>>>>> 2010-02-25 17:12:04,011-0600 INFO  SetFieldValue Setting
>>>>> org.griphyn.vdl.mapping.RootDataNode identifier
>>>>>
>>>>>           
>> tag:benc at ci.uchicago.edu,2008:swift:dataset:20100225-1712-kjif48ad:720000000016
>>
>>     
>>>>> type string with no value at dataset=indir (not closed) to input
>>>>> 2010-02-25 17:12:04,012-0600 INFO  AbstractDataNode closed
>>>>> org.griphyn.vdl.mapping.RootDataNode identifier
>>>>>
>>>>>           
>> tag:benc at ci.uchicago.edu,2008:swift:dataset:20100225-1712-kjif48ad:720000000016
>>
>>     
>>>>> type string value=input dataset=indir (closed)
>>>>> 2010-02-25 17:12:04,012-0600 INFO  AbstractDataNode Notifying
>>>>>           
>> listener
>>     
>>>>> "org.griphyn.vdl.mapping.RootDataNode identifier
>>>>>
>>>>>           
>> tag:benc at ci.uchicago.edu,2008:swift:dataset:20100225-1712-kjif48ad:720000000019
>>
>>     
>>>>> type LoopModelIn with no value at dataset=modelIn (not closed)"
>>>>>           
>> about
>>     
>>>>> "org.griphyn.vdl.mapping.RootDataNode identifier
>>>>>
>>>>>           
>> tag:benc at ci.uchicago.edu,2008:swift:dataset:20100225-1712-kjif48ad:720000000018
>>
>>     
>>>>> type string value=LoopModelIn.map dataset=swift#mapper#17007
>>>>> (closed)"
>>>>> 2010-02-25 17:12:04,012-0600 INFO  AbstractDataNode closed
>>>>> org.griphyn.vdl.mapping.RootDataNode identifier
>>>>>
>>>>>           
>> tag:benc at ci.uchicago.edu,2008:swift:dataset:20100225-1712-kjif48ad:720000000029
>>
>>     
>>>>> type string value=output dataset=unnamed SwiftScript value
>>>>>           
>> (closed)
>>     
>>>>> 2010-02-25 17:12:04,012-0600 INFO  VDLFunction FUNCTION id=451003
>>>>> name=arg
>>>>>
>>>>>           
>> result=tag:benc at ci.uchicago.edu,2008:swift:dataset:20100225-1712-kjif48ad:720000000029
>>
>>     
>>>>> 2010-02-25 17:12:04,012-0600 INFO  VDLFunction FUNCTIONPARAMETER
>>>>> id=451003
>>>>>
>>>>>           
>> input=tag:benc at ci.uchicago.edu,2008:swift:dataset:20100225-1712-kjif48ad:720000000005
>>
>>     
>>>>> name=name
>>>>> 2010-02-25 17:12:04,012-0600 INFO  VDLFunction FUNCTIONPARAMETER
>>>>> id=451003
>>>>>
>>>>>           
>> input=tag:benc at ci.uchicago.edu,2008:swift:dataset:20100225-1712-kjif48ad:720000000004
>>
>>     
>>>>> name=value
>>>>> 2010-02-25 17:12:04,012-0600 INFO  SetFieldValue Setting
>>>>> org.griphyn.vdl.mapping.RootDataNode identifier
>>>>>
>>>>>           
>> tag:benc at ci.uchicago.edu,2008:swift:dataset:20100225-1712-kjif48ad:720000000017
>>
>>     
>>>>> type string with no value at dataset=outdir (not closed) to
>>>>>           
>> output
>>     
>>>>> 2010-02-25 17:12:04,012-0600 INFO  AbstractDataNode Notifying
>>>>>           
>> listener
>>     
>>>>> "org.griphyn.vdl.mapping.RootDataNode identifier
>>>>>
>>>>>           
>> tag:benc at ci.uchicago.edu,2008:swift:dataset:20100225-1712-kjif48ad:720000000021
>>
>>     
>>>>> type LoopModelData with no value at dataset=modelData (not
>>>>>           
>> closed)"
>>     
>>>>> about "org.griphyn.vdl.mapping.RootDataNode identifier
>>>>>
>>>>>           
>> tag:benc at ci.uchicago.edu,2008:swift:dataset:20100225-1712-kjif48ad:720000000017
>>
>>     
>>>>> type string value=output dataset=outdir (closed)"
>>>>> 2010-02-25 17:12:04,027-0600 INFO  AbstractDataNode closed
>>>>> org.griphyn.vdl.mapping.DataNode identifier
>>>>>
>>>>>           
>> tag:benc at ci.uchicago.edu,2008:swift:dataset:20100225-1712-kjif48ad:720000000030
>>
>>     
>>>>> type PDB with no value at dataset=modelIn path=.pdb (closed)
>>>>> 2010-02-25 17:12:04,030-0600 INFO  AbstractDataNode Found data
>>>>> org.griphyn.vdl.mapping.RootDataNode identifier
>>>>>
>>>>>           
>> tag:benc at ci.uchicago.edu,2008:swift:dataset:20100225-1712-kjif48ad:720000000019
>>
>>     
>>>>> type LoopModelIn with no value at dataset=modelIn (not
>>>>>           
>> closed)..pdb
>>     
>>>>> 2010-02-25 17:12:04,030-0600 INFO  AbstractDataNode closed
>>>>> org.griphyn.vdl.mapping.DataNode identifier
>>>>>
>>>>>           
>> tag:benc at ci.uchicago.edu,2008:swift:dataset:20100225-1712-kjif48ad:720000000031
>>
>>     
>>>>> type Text with no value at dataset=modelIn path=.params (closed)
>>>>> 2010-02-25 17:12:04,032-0600 INFO  AbstractDataNode Found data
>>>>> org.griphyn.vdl.mapping.RootDataNode identifier
>>>>>
>>>>>           
>> tag:benc at ci.uchicago.edu,2008:swift:dataset:20100225-1712-kjif48ad:720000000019
>>
>>     
>>>>> type LoopModelIn with no value at dataset=modelIn (not
>>>>> closed)..params
>>>>> 2010-02-25 17:12:04,032-0600 INFO  AbstractDataNode closed
>>>>> org.griphyn.vdl.mapping.DataNode identifier
>>>>>
>>>>>           
>> tag:benc at ci.uchicago.edu,2008:swift:dataset:20100225-1712-kjif48ad:720000000032
>>
>>     
>>>>> type LoopRange with no value at dataset=modelIn path=.range
>>>>>           
>> (closed)
>>     
>>>>> 2010-02-25 17:12:04,032-0600 INFO  AbstractDataNode Found data
>>>>> org.griphyn.vdl.mapping.RootDataNode identifier
>>>>>
>>>>>           
>> tag:benc at ci.uchicago.edu,2008:swift:dataset:20100225-1712-kjif48ad:720000000019
>>
>>     
>>>>> type LoopModelIn with no value at dataset=modelIn (not
>>>>>           
>> closed)..range
>>     
>>>>> 2010-02-25 17:12:04,033-0600 INFO  AbstractDataNode closed
>>>>> org.griphyn.vdl.mapping.RootDataNode identifier
>>>>>
>>>>>           
>> tag:benc at ci.uchicago.edu,2008:swift:dataset:20100225-1712-kjif48ad:720000000019
>>
>>     
>>>>> type LoopModelIn with no value at dataset=modelIn (closed)
>>>>> 2010-02-25 17:12:04,033-0600 INFO  AbstractDataNode closed
>>>>> org.griphyn.vdl.mapping.RootDataNode identifier
>>>>>
>>>>>           
>> tag:benc at ci.uchicago.edu,2008:swift:dataset:20100225-1712-kjif48ad:720000000018
>>
>>     
>>>>> type string value=LoopModelIn.map dataset=swift#mapper#17007
>>>>>           
>> (closed)
>>     
>>>>> 2010-02-25 17:12:04,034-0600 INFO  CloseDataset Partially closing
>>>>> input for statement 88014
>>>>> 2010-02-25 17:12:04,035-0600 INFO  CloseDataset var is input
>>>>> 2010-02-25 17:12:04,035-0600 INFO  CloseDataset var hash is
>>>>>           
>> 21684929
>>     
>>>>> 2010-02-25 17:12:04,035-0600 INFO  CloseDataset variable already
>>>>> closed - skipping partial close processing
>>>>> 2010-02-25 17:12:04,040-0600 INFO  loopprepare PROCEDURE line=112
>>>>> thread=0-1-8 name=loopPrepare
>>>>> 2010-02-25 17:12:04,041-0600 INFO  AbstractDataNode Found mapped
>>>>>           
>> data
>>     
>>>>> org.griphyn.vdl.mapping.RootDataNode identifier
>>>>>
>>>>>           
>> tag:benc at ci.uchicago.edu,2008:swift:dataset:20100225-1712-kjif48ad:720000000021
>>
>>     
>>>>> type LoopModelData with no value at dataset=modelData (not
>>>>> closed)..fasta
>>>>> 2010-02-25 17:12:04,041-0600 INFO  AbstractDataNode Found mapped
>>>>>           
>> data
>>     
>>>>> org.griphyn.vdl.mapping.RootDataNode identifier
>>>>>
>>>>>           
>> tag:benc at ci.uchicago.edu,2008:swift:dataset:20100225-1712-kjif48ad:720000000021
>>
>>     
>>>>> type LoopModelData with no value at dataset=modelData (not
>>>>> closed)..pdb
>>>>> 2010-02-25 17:12:04,041-0600 INFO  AbstractDataNode Found mapped
>>>>>           
>> data
>>     
>>>>> org.griphyn.vdl.mapping.RootDataNode identifier
>>>>>
>>>>>           
>> tag:benc at ci.uchicago.edu,2008:swift:dataset:20100225-1712-kjif48ad:720000000021
>>
>>     
>>>>> type LoopModelData with no value at dataset=modelData (not
>>>>> closed)..native
>>>>> 2010-02-25 17:12:04,041-0600 INFO  AbstractDataNode Found mapped
>>>>>           
>> data
>>     
>>>>> org.griphyn.vdl.mapping.RootDataNode identifier
>>>>>
>>>>>           
>> tag:benc at ci.uchicago.edu,2008:swift:dataset:20100225-1712-kjif48ad:720000000021
>>
>>     
>>>>> type LoopModelData with no value at dataset=modelData (not
>>>>> closed)..index
>>>>> 2010-02-25 17:12:04,041-0600 INFO  strtoi STARTCOMPOUND
>>>>>           
>> thread=0-1-0
>>     
>>>>> name=strtoi
>>>>> 2010-02-25 17:12:04,041-0600 INFO  AbstractDataNode Found mapped
>>>>>           
>> data
>>     
>>>>> org.griphyn.vdl.mapping.RootDataNode identifier
>>>>>
>>>>>           
>> tag:benc at ci.uchicago.edu,2008:swift:dataset:20100225-1712-kjif48ad:720000000021
>>
>>     
>>>>> type LoopModelData with no value at dataset=modelData (not
>>>>> closed)..params
>>>>> 2010-02-25 17:12:04,041-0600 INFO  AbstractDataNode Found mapped
>>>>>           
>> data
>>     
>>>>> org.griphyn.vdl.mapping.RootDataNode identifier
>>>>>
>>>>>           
>> tag:benc at ci.uchicago.edu,2008:swift:dataset:20100225-1712-kjif48ad:720000000021
>>
>>     
>>>>> type LoopModelData with no value at dataset=modelData (not
>>>>> closed)..range
>>>>> 2010-02-25 17:12:04,042-0600 INFO  AbstractDataNode Found mapped
>>>>>           
>> data
>>     
>>>>> org.griphyn.vdl.mapping.RootDataNode identifier
>>>>>
>>>>>           
>> tag:benc at ci.uchicago.edu,2008:swift:dataset:20100225-1712-kjif48ad:720000000021
>>
>>     
>>>>> type LoopModelData with no value at dataset=modelData (not
>>>>> closed)..rama
>>>>> 2010-02-25 17:12:04,042-0600 INFO  AbstractDataNode Found mapped
>>>>>           
>> data
>>     
>>>>> org.griphyn.vdl.mapping.RootDataNode identifier
>>>>>
>>>>>           
>> tag:benc at ci.uchicago.edu,2008:swift:dataset:20100225-1712-kjif48ad:720000000021
>>
>>     
>>>>> type LoopModelData with no value at dataset=modelData (not
>>>>> closed)..map
>>>>> 2010-02-25 17:12:04,042-0600 INFO  AbstractDataNode Found mapped
>>>>>           
>> data
>>     
>>>>> org.griphyn.vdl.mapping.RootDataNode identifier
>>>>>
>>>>>           
>> tag:benc at ci.uchicago.edu,2008:swift:dataset:20100225-1712-kjif48ad:720000000021
>>
>>     
>>>>> type LoopModelData with no value at dataset=modelData (not
>>>>> closed)..secseq
>>>>> 2010-02-25 17:12:04,047-0600 INFO  AbstractDataNode Notifying
>>>>>           
>> listener
>>     
>>>>> "org.griphyn.vdl.mapping.RootDataNode identifier
>>>>>
>>>>>           
>> tag:benc at ci.uchicago.edu,2008:swift:dataset:20100225-1712-kjif48ad:720000000025
>>
>>     
>>>>> type LoopModelResults with no value at dataset=modelResults (not
>>>>> closed)" about "org.griphyn.vdl.mapping.RootDataNode identifier
>>>>>
>>>>>           
>> tag:benc at ci.uchicago.edu,2008:swift:dataset:20100225-1712-kjif48ad:720000000017
>>
>>     
>>>>> type string value=output dataset=outdir (closed)"
>>>>> 2010-02-25 17:12:04,051-0600 INFO  loopmodelanalysis PROCEDURE
>>>>> line=122 thread=0-1-10 name=loopModelAnalysis
>>>>> 2010-02-25 17:12:04,053-0600 INFO  doloopround STARTCOMPOUND
>>>>> thread=0-1-9 name=doLoopRound
>>>>> 2010-02-25 17:12:04,058-0600 INFO  New NEW
>>>>>
>>>>>           
>> id=tag:benc at ci.uchicago.edu,2008:swift:dataset:20100225-1712-kjif48ad:720000000042
>>
>>     
>>>>> 2010-02-25 17:12:04,058-0600 INFO  AbstractDataNode Found mapped
>>>>>           
>> data
>>     
>>>>> org.griphyn.vdl.mapping.RootDataNode identifier
>>>>>
>>>>>           
>> tag:benc at ci.uchicago.edu,2008:swift:dataset:20100225-1712-kjif48ad:720000000025
>>
>>     
>>>>> type LoopModelResults with no value at dataset=modelResults (not
>>>>> closed)..pwPlot
>>>>> 2010-02-25 17:12:04,058-0600 INFO  AbstractDataNode Found mapped
>>>>>           
>> data
>>     
>>>>> org.griphyn.vdl.mapping.RootDataNode identifier
>>>>>
>>>>>           
>> tag:benc at ci.uchicago.edu,2008:swift:dataset:20100225-1712-kjif48ad:720000000025
>>
>>     
>>>>> type LoopModelResults with no value at dataset=modelResults (not
>>>>> closed)..best
>>>>> 2010-02-25 17:12:04,059-0600 INFO  AbstractDataNode Found mapped
>>>>>           
>> data
>>     
>>>>> org.griphyn.vdl.mapping.RootDataNode identifier
>>>>>
>>>>>           
>> tag:benc at ci.uchicago.edu,2008:swift:dataset:20100225-1712-kjif48ad:720000000025
>>
>>     
>>>>> type LoopModelResults with no value at dataset=modelResults (not
>>>>> closed)..ligationPlot
>>>>> 2010-02-25 17:12:04,059-0600 INFO  AbstractDataNode closed
>>>>> org.griphyn.vdl.mapping.RootDataNode identifier
>>>>>
>>>>>           
>> tag:benc at ci.uchicago.edu,2008:swift:dataset:20100225-1712-kjif48ad:720000000017
>>
>>     
>>>>> type string value=output dataset=outdir (closed)
>>>>> 2010-02-25 17:12:04,059-0600 INFO  CloseDataset Partially closing
>>>>> output for statement 88015
>>>>> 2010-02-25 17:12:04,059-0600 INFO  CloseDataset var is output
>>>>> 2010-02-25 17:12:04,060-0600 INFO  CloseDataset var hash is
>>>>>           
>> 23848591
>>     
>>>>> 2010-02-25 17:12:04,060-0600 INFO  CloseDataset variable already
>>>>> closed - skipping partial close processing
>>>>> 2010-02-25 17:12:04,062-0600 INFO  AbstractDataNode Adding handle
>>>>> listener "F/modelOut.$[]/0" to
>>>>> "org.griphyn.vdl.mapping.RootArrayDataNode identifier
>>>>>
>>>>>           
>> tag:benc at ci.uchicago.edu,2008:swift:dataset:20100225-1712-kjif48ad:720000000023
>>
>>     
>>>>> type LoopModelOut[] with no value at dataset=modelOut (not
>>>>>           
>> closed)"
>>     
>>>>> 2010-02-25 17:12:04,062-0600 INFO  AbstractDataNode Adding handle
>>>>> listener "F/org.griphyn.vdl.mapping.RootDataNode identifier
>>>>>
>>>>>           
>> tag:benc at ci.uchicago.edu,2008:swift:dataset:20100225-1712-kjif48ad:720000000014
>>
>>     
>>>>> type int with no value at dataset=nSim (not closed)" to
>>>>> "org.griphyn.vdl.mapping.RootDataNode identifier
>>>>>
>>>>>           
>> tag:benc at ci.uchicago.edu,2008:swift:dataset:20100225-1712-kjif48ad:720000000014
>>
>>     
>>>>> type int with no value at dataset=nSim (not closed)"
>>>>> 2010-02-25 17:12:04,065-0600 INFO  strtoi INTERNALPROC_START
>>>>> thread=0-1-0-1 name=readData
>>>>> 2010-02-25 17:12:04,068-0600 INFO  AbstractDataNode Adding handle
>>>>> listener "F/org.griphyn.vdl.mapping.RootDataNode identifier
>>>>>
>>>>>           
>> tag:benc at ci.uchicago.edu,2008:swift:dataset:20100225-1712-kjif48ad:720000000042
>>
>>     
>>>>> type file with no value at dataset=f (not closed)" to
>>>>> "org.griphyn.vdl.mapping.RootDataNode identifier
>>>>>
>>>>>           
>> tag:benc at ci.uchicago.edu,2008:swift:dataset:20100225-1712-kjif48ad:720000000042
>>
>>     
>>>>> type file with no value at dataset=f (not closed)"
>>>>> 2010-02-25 17:12:04,068-0600 INFO  echos PROCEDURE line=68
>>>>> thread=0-1-0-0 name=echos
>>>>> 2010-02-25 17:12:04,077-0600 INFO  AbstractDataNode closed
>>>>> org.griphyn.vdl.mapping.RootDataNode identifier
>>>>>
>>>>>           
>> tag:benc at ci.uchicago.edu,2008:swift:dataset:20100225-1712-kjif48ad:720000000046
>>
>>     
>>>>> type string
>>>>> value=_concurrent/f-7a608b5e-b445-46f4-8cb2-bff8a73b52ec-1-0
>>>>> dataset=unnamed SwiftScript value (closed)
>>>>> 2010-02-25 17:12:04,077-0600 INFO  VDLFunction FUNCTIONPARAMETER
>>>>> id=451004
>>>>>
>>>>>           
>> input=tag:benc at ci.uchicago.edu,2008:swift:dataset:20100225-1712-kjif48ad:720000000042
>>
>>     
>>>>> name=input
>>>>> 2010-02-25 17:12:04,077-0600 INFO  VDLFunction FUNCTION id=451004
>>>>> name=filename
>>>>>
>>>>>           
>> result=tag:benc at ci.uchicago.edu,2008:swift:dataset:20100225-1712-kjif48ad:720000000046
>>
>>     
>>>>> 2010-02-25 17:12:04,077-0600 INFO  AbstractDataNode closed
>>>>> org.griphyn.vdl.mapping.RootDataNode identifier
>>>>>
>>>>>           
>> tag:benc at ci.uchicago.edu,2008:swift:dataset:20100225-1712-kjif48ad:720000000047
>>
>>     
>>>>> type string value=input/T0510D1.pdb dataset=unnamed SwiftScript
>>>>>           
>> value
>>     
>>>>> (closed)
>>>>> 2010-02-25 17:12:04,078-0600 INFO  VDLFunction FUNCTIONPARAMETER
>>>>> id=451005
>>>>>
>>>>>           
>> input=tag:benc at ci.uchicago.edu,2008:swift:dataset:20100225-1712-kjif48ad:720000000030
>>
>>     
>>>>> name=input
>>>>> 2010-02-25 17:12:04,078-0600 INFO  VDLFunction FUNCTION id=451005
>>>>> name=filename
>>>>>
>>>>>           
>> result=tag:benc at ci.uchicago.edu,2008:swift:dataset:20100225-1712-kjif48ad:720000000047
>>
>>     
>>>>> 2010-02-25 17:12:04,078-0600 INFO  AbstractDataNode closed
>>>>> org.griphyn.vdl.mapping.RootDataNode identifier
>>>>>
>>>>>           
>> tag:benc at ci.uchicago.edu,2008:swift:dataset:20100225-1712-kjif48ad:720000000048
>>
>>     
>>>>> type string value=output/data//T0510D1.pdb dataset=unnamed
>>>>>           
>> SwiftScript
>>     
>>>>> value (closed)
>>>>> 2010-02-25 17:12:04,078-0600 INFO  VDLFunction FUNCTIONPARAMETER
>>>>> id=451006
>>>>>
>>>>>           
>> input=tag:benc at ci.uchicago.edu,2008:swift:dataset:20100225-1712-kjif48ad:720000000034
>>
>>     
>>>>> name=input
>>>>> 2010-02-25 17:12:04,078-0600 INFO  VDLFunction FUNCTION id=451006
>>>>> name=filename
>>>>>
>>>>>           
>> result=tag:benc at ci.uchicago.edu,2008:swift:dataset:20100225-1712-kjif48ad:720000000048
>>
>>     
>>>>> 2010-02-25 17:12:04,084-0600 INFO  vdl:execute START
>>>>>           
>> thread=0-1-0-0
>>     
>>>>> tr=echo
>>>>> 2010-02-25 17:12:04,085-0600 INFO  vdl:execute START thread=0-1-8
>>>>> tr=PrepLoop
>>>>> 2010-02-25 17:12:04,112-0600 INFO  WeightedHostScoreScheduler
>>>>>           
>> Sorted:
>>     
>>>>> [localhost:10,000.000(99.854):0/3 overload: 0]
>>>>> 2010-02-25 17:12:04,112-0600 INFO  WeightedHostScoreScheduler
>>>>> CONTACT_SELECTED host=localhost, score=99.854
>>>>> 2010-02-25 17:12:04,113-0600 INFO  WeightedHostScoreScheduler
>>>>>           
>> Sorted:
>>     
>>>>> [localhost:10,000.000(99.854):1/3 overload: 0]
>>>>> 2010-02-25 17:12:04,114-0600 INFO  WeightedHostScoreScheduler
>>>>> CONTACT_SELECTED host=localhost, score=99.854
>>>>> 2010-02-25 17:12:04,120-0600 INFO  GlobalSubmitQueue No global
>>>>>           
>> submit
>>     
>>>>> throttle set. Using default (100)
>>>>> 2010-02-25 17:12:04,136-0600 DEBUG TaskImpl
>>>>>           
>> Task(type=FILE_OPERATION,
>>     
>>>>> identity=urn:0-1-0-0-1-1267139524101) setting status to
>>>>>           
>> Submitting
>>     
>>>>> 2010-02-25 17:12:04,148-0600 DEBUG TaskImpl
>>>>>           
>> Task(type=FILE_OPERATION,
>>     
>>>>> identity=urn:0-1-0-0-1-1267139524101) setting status to Submitted
>>>>> 2010-02-25 17:12:04,148-0600 DEBUG TaskImpl
>>>>>           
>> Task(type=FILE_OPERATION,
>>     
>>>>> identity=urn:0-1-0-0-1-1267139524101) setting status to Active
>>>>> 2010-02-25 17:12:04,149-0600 DEBUG TaskImpl
>>>>>           
>> Task(type=FILE_OPERATION,
>>     
>>>>> identity=urn:0-1-0-0-1-1267139524101) setting status to Completed
>>>>> 2010-02-25 17:12:04,149-0600 INFO  LateBindingScheduler
>>>>> Task(type=FILE_OPERATION, identity=urn:0-1-0-0-1-1267139524101)
>>>>> Completed. Waiting: 0, Running: 0. Heap size: 14M, Heap free: 5M,
>>>>>           
>> Max
>>     
>>>>> heap: 254M
>>>>> 2010-02-25 17:12:04,155-0600 DEBUG TaskImpl
>>>>>           
>> Task(type=FILE_OPERATION,
>>     
>>>>> identity=urn:0-1-0-0-1-1267139524104) setting status to
>>>>>           
>> Submitting
>>     
>>>>> 2010-02-25 17:12:04,155-0600 DEBUG TaskImpl
>>>>>           
>> Task(type=FILE_OPERATION,
>>     
>>>>> identity=urn:0-1-0-0-1-1267139524104) setting status to Submitted
>>>>> 2010-02-25 17:12:04,155-0600 DEBUG TaskImpl
>>>>>           
>> Task(type=FILE_OPERATION,
>>     
>>>>> identity=urn:0-1-0-0-1-1267139524104) setting status to Active
>>>>> 2010-02-25 17:12:04,155-0600 DEBUG TaskImpl
>>>>>           
>> Task(type=FILE_OPERATION,
>>     
>>>>> identity=urn:0-1-0-0-1-1267139524104) setting status to Completed
>>>>> 2010-02-25 17:12:04,155-0600 INFO  LateBindingScheduler
>>>>> Task(type=FILE_OPERATION, identity=urn:0-1-0-0-1-1267139524104)
>>>>> Completed. Waiting: 0, Running: 0. Heap size: 14M, Heap free: 4M,
>>>>>           
>> Max
>>     
>>>>> heap: 254M
>>>>> 2010-02-25 17:12:04,158-0600 INFO  vdl:initshareddir START
>>>>> host=localhost - Initializing shared directory
>>>>> 2010-02-25 17:12:04,161-0600 DEBUG TaskImpl
>>>>>           
>> Task(type=FILE_OPERATION,
>>     
>>>>> identity=urn:0-1-8-1-1267139524106) setting status to Submitting
>>>>> 2010-02-25 17:12:04,162-0600 DEBUG TaskImpl
>>>>>           
>> Task(type=FILE_OPERATION,
>>     
>>>>> identity=urn:0-1-8-1-1267139524106) setting status to Submitted
>>>>> 2010-02-25 17:12:04,162-0600 DEBUG TaskImpl
>>>>>           
>> Task(type=FILE_OPERATION,
>>     
>>>>> identity=urn:0-1-8-1-1267139524106) setting status to Active
>>>>> 2010-02-25 17:12:04,163-0600 DEBUG TaskImpl
>>>>>           
>> Task(type=FILE_OPERATION,
>>     
>>>>> identity=urn:0-1-8-1-1267139524106) setting status to Completed
>>>>> 2010-02-25 17:12:04,163-0600 INFO  LateBindingScheduler
>>>>> Task(type=FILE_OPERATION, identity=urn:0-1-8-1-1267139524106)
>>>>> Completed. Waiting: 0, Running: 0. Heap size: 14M, Heap free: 4M,
>>>>>           
>> Max
>>     
>>>>> heap: 254M
>>>>> 2010-02-25 17:12:04,185-0600 DEBUG TaskImpl
>>>>>           
>> Task(type=FILE_TRANSFER,
>>     
>>>>> identity=urn:0-1-8-1-1267139524109) setting status to Submitting
>>>>> 2010-02-25 17:12:04,185-0600 DEBUG TaskImpl
>>>>>           
>> Task(type=FILE_TRANSFER,
>>     
>>>>> identity=urn:0-1-8-1-1267139524109) setting status to Submitted
>>>>> 2010-02-25 17:12:04,187-0600 DEBUG TaskImpl
>>>>>           
>> Task(type=FILE_TRANSFER,
>>     
>>>>> identity=urn:0-1-8-1-1267139524109) setting status to Active
>>>>> 2010-02-25 17:12:04,190-0600 DEBUG TaskImpl
>>>>>           
>> Task(type=FILE_TRANSFER,
>>     
>>>>> identity=urn:0-1-8-1-1267139524109) setting status to Completed
>>>>> 2010-02-25 17:12:04,190-0600 INFO  LateBindingScheduler
>>>>> Task(type=FILE_TRANSFER, identity=urn:0-1-8-1-1267139524109)
>>>>> Completed. Waiting: 0, Running: 0. Heap size: 14M, Heap free: 5M,
>>>>>           
>> Max
>>     
>>>>> heap: 254M
>>>>> 2010-02-25 17:12:04,191-0600 DEBUG TaskImpl
>>>>>           
>> Task(type=FILE_TRANSFER,
>>     
>>>>> identity=urn:0-1-8-1-1267139524112) setting status to Submitting
>>>>> 2010-02-25 17:12:04,191-0600 DEBUG TaskImpl
>>>>>           
>> Task(type=FILE_TRANSFER,
>>     
>>>>> identity=urn:0-1-8-1-1267139524112) setting status to Submitted
>>>>> 2010-02-25 17:12:04,191-0600 DEBUG TaskImpl
>>>>>           
>> Task(type=FILE_TRANSFER,
>>     
>>>>> identity=urn:0-1-8-1-1267139524112) setting status to Active
>>>>> 2010-02-25 17:12:04,236-0600 DEBUG TaskImpl
>>>>>           
>> Task(type=FILE_TRANSFER,
>>     
>>>>> identity=urn:0-1-8-1-1267139524112) setting status to Completed
>>>>> 2010-02-25 17:12:04,236-0600 INFO  LateBindingScheduler
>>>>> Task(type=FILE_TRANSFER, identity=urn:0-1-8-1-1267139524112)
>>>>> Completed. Waiting: 0, Running: 0. Heap size: 14M, Heap free: 5M,
>>>>>           
>> Max
>>     
>>>>> heap: 254M
>>>>> 2010-02-25 17:12:04,237-0600 DEBUG TaskImpl
>>>>>           
>> Task(type=FILE_OPERATION,
>>     
>>>>> identity=urn:0-1-8-1-1267139524115) setting status to Submitting
>>>>> 2010-02-25 17:12:04,237-0600 DEBUG TaskImpl
>>>>>           
>> Task(type=FILE_OPERATION,
>>     
>>>>> identity=urn:0-1-8-1-1267139524115) setting status to Submitted
>>>>> 2010-02-25 17:12:04,237-0600 DEBUG TaskImpl
>>>>>           
>> Task(type=FILE_OPERATION,
>>     
>>>>> identity=urn:0-1-8-1-1267139524115) setting status to Active
>>>>> 2010-02-25 17:12:04,238-0600 DEBUG TaskImpl
>>>>>           
>> Task(type=FILE_OPERATION,
>>     
>>>>> identity=urn:0-1-8-1-1267139524115) setting status to Completed
>>>>> 2010-02-25 17:12:04,238-0600 INFO  LateBindingScheduler
>>>>> Task(type=FILE_OPERATION, identity=urn:0-1-8-1-1267139524115)
>>>>> Completed. Waiting: 0, Running: 0. Heap size: 14M, Heap free: 5M,
>>>>>           
>> Max
>>     
>>>>> heap: 254M
>>>>> 2010-02-25 17:12:04,239-0600 DEBUG TaskImpl
>>>>>           
>> Task(type=FILE_OPERATION,
>>     
>>>>> identity=urn:0-1-8-1-1267139524117) setting status to Submitting
>>>>> 2010-02-25 17:12:04,239-0600 DEBUG TaskImpl
>>>>>           
>> Task(type=FILE_OPERATION,
>>     
>>>>> identity=urn:0-1-8-1-1267139524117) setting status to Submitted
>>>>> 2010-02-25 17:12:04,239-0600 DEBUG TaskImpl
>>>>>           
>> Task(type=FILE_OPERATION,
>>     
>>>>> identity=urn:0-1-8-1-1267139524117) setting status to Active
>>>>> 2010-02-25 17:12:04,240-0600 DEBUG TaskImpl
>>>>>           
>> Task(type=FILE_OPERATION,
>>     
>>>>> identity=urn:0-1-8-1-1267139524117) setting status to Completed
>>>>> 2010-02-25 17:12:04,240-0600 INFO  LateBindingScheduler
>>>>> Task(type=FILE_OPERATION, identity=urn:0-1-8-1-1267139524117)
>>>>> Completed. Waiting: 0, Running: 0. Heap size: 14M, Heap free: 5M,
>>>>>           
>> Max
>>     
>>>>> heap: 254M
>>>>> 2010-02-25 17:12:04,241-0600 DEBUG TaskImpl
>>>>>           
>> Task(type=FILE_OPERATION,
>>     
>>>>> identity=urn:0-1-8-1-1267139524119) setting status to Submitting
>>>>> 2010-02-25 17:12:04,244-0600 DEBUG TaskImpl
>>>>>           
>> Task(type=FILE_OPERATION,
>>     
>>>>> identity=urn:0-1-8-1-1267139524119) setting status to Submitted
>>>>> 2010-02-25 17:12:04,244-0600 DEBUG TaskImpl
>>>>>           
>> Task(type=FILE_OPERATION,
>>     
>>>>> identity=urn:0-1-8-1-1267139524119) setting status to Active
>>>>> 2010-02-25 17:12:04,244-0600 DEBUG TaskImpl
>>>>>           
>> Task(type=FILE_OPERATION,
>>     
>>>>> identity=urn:0-1-8-1-1267139524119) setting status to Completed
>>>>> 2010-02-25 17:12:04,244-0600 INFO  LateBindingScheduler
>>>>> Task(type=FILE_OPERATION, identity=urn:0-1-8-1-1267139524119)
>>>>> Completed. Waiting: 0, Running: 0. Heap size: 14M, Heap free: 5M,
>>>>>           
>> Max
>>     
>>>>> heap: 254M
>>>>> 2010-02-25 17:12:04,245-0600 INFO  vdl:initshareddir END
>>>>> host=localhost - Done initializing shared directory
>>>>> 2010-02-25 17:12:04,248-0600 DEBUG vdl:execute2
>>>>>           
>> THREAD_ASSOCIATION
>>     
>>>>> jobid=echo-xkjtxaoj thread=0-1-0-0-1 host=localhost
>>>>> replicationGroup=ukjtxaoj
>>>>> 2010-02-25 17:12:04,250-0600 DEBUG vdl:execute2
>>>>>           
>> THREAD_ASSOCIATION
>>     
>>>>> jobid=PrepLoop-ykjtxaoj thread=0-1-8-1 host=localhost
>>>>> replicationGroup=vkjtxaoj
>>>>> 2010-02-25 17:12:04,255-0600 INFO  vdl:createdirset START
>>>>> jobid=echo-xkjtxaoj host=localhost - Initializing directory
>>>>>           
>> structure
>>     
>>>>> 2010-02-25 17:12:04,257-0600 INFO  vdl:createdirs START
>>>>> path=_concurrent dir=psim.loops-20100225-1712-3zrtb5i5/shared -
>>>>> Creating directory structure
>>>>> 2010-02-25 17:12:04,257-0600 INFO  vdl:createdirset START
>>>>> jobid=PrepLoop-ykjtxaoj host=localhost - Initializing directory
>>>>> structure
>>>>> 2010-02-25 17:12:04,258-0600 INFO  vdl:createdirs START
>>>>>           
>> path=input
>>     
>>>>> dir=psim.loops-20100225-1712-3zrtb5i5/shared - Creating directory
>>>>> structure
>>>>> 2010-02-25 17:12:04,258-0600 DEBUG TaskImpl
>>>>>           
>> Task(type=FILE_OPERATION,
>>     
>>>>> identity=urn:0-1-0-0-1-1267139524121) setting status to
>>>>>           
>> Submitting
>>     
>>>>> 2010-02-25 17:12:04,258-0600 DEBUG TaskImpl
>>>>>           
>> Task(type=FILE_OPERATION,
>>     
>>>>> identity=urn:0-1-0-0-1-1267139524121) setting status to Submitted
>>>>> 2010-02-25 17:12:04,258-0600 DEBUG TaskImpl
>>>>>           
>> Task(type=FILE_OPERATION,
>>     
>>>>> identity=urn:0-1-0-0-1-1267139524121) setting status to Active
>>>>> 2010-02-25 17:12:04,259-0600 DEBUG TaskImpl
>>>>>           
>> Task(type=FILE_OPERATION,
>>     
>>>>> identity=urn:0-1-8-1-1267139524123) setting status to Submitting
>>>>> 2010-02-25 17:12:04,259-0600 DEBUG TaskImpl
>>>>>           
>> Task(type=FILE_OPERATION,
>>     
>>>>> identity=urn:0-1-8-1-1267139524123) setting status to Submitted
>>>>> 2010-02-25 17:12:04,259-0600 DEBUG TaskImpl
>>>>>           
>> Task(type=FILE_OPERATION,
>>     
>>>>> identity=urn:0-1-8-1-1267139524123) setting status to Active
>>>>> 2010-02-25 17:12:04,261-0600 DEBUG TaskImpl
>>>>>           
>> Task(type=FILE_OPERATION,
>>     
>>>>> identity=urn:0-1-0-0-1-1267139524121) setting status to Completed
>>>>> 2010-02-25 17:12:04,261-0600 DEBUG TaskImpl
>>>>>           
>> Task(type=FILE_OPERATION,
>>     
>>>>> identity=urn:0-1-8-1-1267139524123) setting status to Completed
>>>>> 2010-02-25 17:12:04,261-0600 INFO  LateBindingScheduler
>>>>> Task(type=FILE_OPERATION, identity=urn:0-1-0-0-1-1267139524121)
>>>>> Completed. Waiting: 0, Running: 1. Heap size: 14M, Heap free: 4M,
>>>>>           
>> Max
>>     
>>>>> heap: 254M
>>>>> 2010-02-25 17:12:04,262-0600 INFO  LateBindingScheduler
>>>>> Task(type=FILE_OPERATION, identity=urn:0-1-8-1-1267139524123)
>>>>> Completed. Waiting: 0, Running: 1. Heap size: 14M, Heap free: 4M,
>>>>>           
>> Max
>>     
>>>>> heap: 254M
>>>>> 2010-02-25 17:12:04,262-0600 INFO  vdl:createdirset END
>>>>> jobid=echo-xkjtxaoj - Done initializing directory structure
>>>>> 2010-02-25 17:12:04,263-0600 INFO  vdl:createdirs START
>>>>> path=output/data/ dir=psim.loops-20100225-1712-3zrtb5i5/shared -
>>>>> Creating directory structure
>>>>> 2010-02-25 17:12:04,263-0600 INFO  vdl:dostagein START
>>>>> jobid=echo-xkjtxaoj - Staging in files
>>>>> 2010-02-25 17:12:04,263-0600 DEBUG TaskImpl
>>>>>           
>> Task(type=FILE_OPERATION,
>>     
>>>>> identity=urn:0-1-8-1-1267139524126) setting status to Submitting
>>>>> 2010-02-25 17:12:04,263-0600 DEBUG TaskImpl
>>>>>           
>> Task(type=FILE_OPERATION,
>>     
>>>>> identity=urn:0-1-8-1-1267139524126) setting status to Submitted
>>>>> 2010-02-25 17:12:04,264-0600 INFO  vdl:dostagein END
>>>>> jobid=echo-xkjtxaoj - Staging in finished
>>>>> 2010-02-25 17:12:04,269-0600 DEBUG TaskImpl
>>>>>           
>> Task(type=FILE_OPERATION,
>>     
>>>>> identity=urn:0-1-8-1-1267139524126) setting status to Active
>>>>> 2010-02-25 17:12:04,274-0600 DEBUG TaskImpl
>>>>>           
>> Task(type=FILE_OPERATION,
>>     
>>>>> identity=urn:0-1-8-1-1267139524126) setting status to Completed
>>>>> 2010-02-25 17:12:04,274-0600 INFO  LateBindingScheduler
>>>>> Task(type=FILE_OPERATION, identity=urn:0-1-8-1-1267139524126)
>>>>> Completed. Waiting: 0, Running: 0. Heap size: 14M, Heap free: 5M,
>>>>>           
>> Max
>>     
>>>>> heap: 254M
>>>>> 2010-02-25 17:12:04,275-0600 DEBUG vdl:execute2 JOB_START
>>>>> jobid=echo-xkjtxaoj tr=echo arguments=[4]
>>>>> tmpdir=psim.loops-20100225-1712-3zrtb5i5/jobs/x/echo-xkjtxaoj
>>>>> host=localhost
>>>>> 2010-02-25 17:12:04,275-0600 INFO  vdl:createdirs START path=
>>>>> dir=psim.loops-20100225-1712-3zrtb5i5/shared - Creating directory
>>>>> structure
>>>>> 2010-02-25 17:12:04,276-0600 DEBUG TaskImpl
>>>>>           
>> Task(type=FILE_OPERATION,
>>     
>>>>> identity=urn:0-1-8-1-1267139524128) setting status to Submitting
>>>>> 2010-02-25 17:12:04,276-0600 DEBUG TaskImpl
>>>>>           
>> Task(type=FILE_OPERATION,
>>     
>>>>> identity=urn:0-1-8-1-1267139524128) setting status to Submitted
>>>>> 2010-02-25 17:12:04,276-0600 DEBUG TaskImpl
>>>>>           
>> Task(type=FILE_OPERATION,
>>     
>>>>> identity=urn:0-1-8-1-1267139524128) setting status to Active
>>>>> 2010-02-25 17:12:04,276-0600 DEBUG TaskImpl
>>>>>           
>> Task(type=FILE_OPERATION,
>>     
>>>>> identity=urn:0-1-8-1-1267139524128) setting status to Completed
>>>>> 2010-02-25 17:12:04,276-0600 INFO  LateBindingScheduler
>>>>> Task(type=FILE_OPERATION, identity=urn:0-1-8-1-1267139524128)
>>>>> Completed. Waiting: 0, Running: 0. Heap size: 14M, Heap free: 5M,
>>>>>           
>> Max
>>     
>>>>> heap: 254M
>>>>> 2010-02-25 17:12:04,277-0600 INFO  vdl:createdirset END
>>>>> jobid=PrepLoop-ykjtxaoj - Done initializing directory structure
>>>>> 2010-02-25 17:12:04,278-0600 INFO  vdl:dostagein START
>>>>> jobid=PrepLoop-ykjtxaoj - Staging in files
>>>>> 2010-02-25 17:12:04,283-0600 DEBUG TaskImpl
>>>>>           
>> Task(type=FILE_OPERATION,
>>     
>>>>> identity=urn:0-1-8-1-1-1267139524131) setting status to
>>>>>           
>> Submitting
>>     
>>>>> 2010-02-25 17:12:04,283-0600 DEBUG TaskImpl
>>>>>           
>> Task(type=FILE_OPERATION,
>>     
>>>>> identity=urn:0-1-8-1-1-1267139524131) setting status to Submitted
>>>>> 2010-02-25 17:12:04,283-0600 DEBUG TaskImpl
>>>>>           
>> Task(type=FILE_OPERATION,
>>     
>>>>> identity=urn:0-1-8-1-1-1267139524131) setting status to Active
>>>>> 2010-02-25 17:12:04,284-0600 DEBUG TaskImpl
>>>>>           
>> Task(type=FILE_OPERATION,
>>     
>>>>> identity=urn:0-1-8-1-3-1267139524132) setting status to
>>>>>           
>> Submitting
>>     
>>>>> 2010-02-25 17:12:04,285-0600 DEBUG TaskImpl
>>>>>           
>> Task(type=FILE_OPERATION,
>>     
>>>>> identity=urn:0-1-8-1-3-1267139524132) setting status to Submitted
>>>>> 2010-02-25 17:12:04,287-0600 DEBUG TaskImpl
>>>>>           
>> Task(type=FILE_OPERATION,
>>     
>>>>> identity=urn:0-1-8-1-3-1267139524132) setting status to Active
>>>>> 2010-02-25 17:12:04,288-0600 DEBUG TaskImpl
>>>>>           
>> Task(type=FILE_OPERATION,
>>     
>>>>> identity=urn:0-1-8-1-1-1267139524131) setting status to Completed
>>>>> 2010-02-25 17:12:04,288-0600 INFO  LateBindingScheduler
>>>>> Task(type=FILE_OPERATION, identity=urn:0-1-8-1-1-1267139524131)
>>>>> Completed. Waiting: 0, Running: 2. Heap size: 14M, Heap free: 5M,
>>>>>           
>> Max
>>     
>>>>> heap: 254M
>>>>> 2010-02-25 17:12:04,289-0600 DEBUG TaskImpl
>>>>>           
>> Task(type=FILE_OPERATION,
>>     
>>>>> identity=urn:0-1-8-1-3-1267139524132) setting status to Completed
>>>>> 2010-02-25 17:12:04,289-0600 INFO  LateBindingScheduler
>>>>> Task(type=FILE_OPERATION, identity=urn:0-1-8-1-3-1267139524132)
>>>>> Completed. Waiting: 0, Running: 1. Heap size: 14M, Heap free: 5M,
>>>>>           
>> Max
>>     
>>>>> heap: 254M
>>>>> 2010-02-25 17:12:04,290-0600 DEBUG TaskImpl
>>>>>           
>> Task(type=FILE_OPERATION,
>>     
>>>>> identity=urn:0-1-8-1-2-1267139524134) setting status to
>>>>>           
>> Submitting
>>     
>>>>> 2010-02-25 17:12:04,290-0600 DEBUG TaskImpl
>>>>>           
>> Task(type=FILE_OPERATION,
>>     
>>>>> identity=urn:0-1-8-1-2-1267139524134) setting status to Submitted
>>>>> 2010-02-25 17:12:04,290-0600 DEBUG TaskImpl
>>>>>           
>> Task(type=FILE_OPERATION,
>>     
>>>>> identity=urn:0-1-8-1-2-1267139524134) setting status to Active
>>>>> 2010-02-25 17:12:04,291-0600 DEBUG TaskImpl
>>>>>           
>> Task(type=FILE_OPERATION,
>>     
>>>>> identity=urn:0-1-8-1-2-1267139524134) setting status to Completed
>>>>> 2010-02-25 17:12:04,291-0600 INFO  LateBindingScheduler
>>>>> Task(type=FILE_OPERATION, identity=urn:0-1-8-1-2-1267139524134)
>>>>> Completed. Waiting: 0, Running: 0. Heap size: 14M, Heap free: 5M,
>>>>>           
>> Max
>>     
>>>>> heap: 254M
>>>>> 2010-02-25 17:12:04,295-0600 INFO  Execute jobid=echo-xkjtxaoj
>>>>> task=Task(type=JOB_SUBMISSION,
>>>>>           
>> identity=urn:0-1-0-0-1-1267139524137)
>>     
>>>>> 2010-02-25 17:12:04,303-0600 DEBUG vdl:dostagein
>>>>>           
>> FILE_STAGE_IN_START
>>     
>>>>> file=file://localhost/input/T0510D1.range srchost=localhost
>>>>> srcdir=input srcname=T0510D1.range desthost=localhost
>>>>> destdir=psim.loops-20100225-1712-3zrtb5i5/shared/input
>>>>>           
>> provider=file
>>     
>>>>> 2010-02-25 17:12:04,304-0600 DEBUG vdl:dostagein
>>>>>           
>> FILE_STAGE_IN_START
>>     
>>>>> file=file://localhost/input/T0510D1.params srchost=localhost
>>>>> srcdir=input srcname=T0510D1.params desthost=localhost
>>>>> destdir=psim.loops-20100225-1712-3zrtb5i5/shared/input
>>>>>           
>> provider=file
>>     
>>>>> 2010-02-25 17:12:04,305-0600 DEBUG vdl:dostagein
>>>>>           
>> FILE_STAGE_IN_START
>>     
>>>>> file=file://localhost/input/T0510D1.pdb srchost=localhost
>>>>>           
>> srcdir=input
>>     
>>>>> srcname=T0510D1.pdb desthost=localhost
>>>>> destdir=psim.loops-20100225-1712-3zrtb5i5/shared/input
>>>>>           
>> provider=file
>>     
>>>>> 2010-02-25 17:12:04,305-0600 DEBUG TaskImpl
>>>>>           
>> Task(type=JOB_SUBMISSION,
>>     
>>>>> identity=urn:0-1-0-0-1-1267139524137) setting status to
>>>>>           
>> Submitting
>>     
>>>>> 2010-02-25 17:12:04,305-0600 INFO  JobSubmissionTaskHandler
>>>>>           
>> Submitting
>>     
>>>>> task Task(type=JOB_SUBMISSION,
>>>>>           
>> identity=urn:0-1-0-0-1-1267139524137)
>>     
>>>>> 2010-02-25 17:12:04,305-0600 INFO  JobSubmissionTaskHandler
>>>>>           
>> Submitting
>>     
>>>>> single job
>>>>> 2010-02-25 17:12:04,306-0600 DEBUG TaskImpl
>>>>>           
>> Task(type=JOB_SUBMISSION,
>>     
>>>>> identity=urn:0-1-0-0-1-1267139524137) setting status to Submitted
>>>>> 2010-02-25 17:12:04,306-0600 DEBUG TaskImpl
>>>>>           
>> Task(type=FILE_TRANSFER,
>>     
>>>>> identity=urn:0-1-8-1-1-1267139524141) setting status to
>>>>>           
>> Submitting
>>     
>>>>> 2010-02-25 17:12:04,306-0600 DEBUG TaskImpl
>>>>>           
>> Task(type=FILE_TRANSFER,
>>     
>>>>> identity=urn:0-1-8-1-1-1267139524141) setting status to Submitted
>>>>> 2010-02-25 17:12:04,306-0600 DEBUG TaskImpl
>>>>>           
>> Task(type=FILE_TRANSFER,
>>     
>>>>> identity=urn:0-1-8-1-2-1267139524139) setting status to
>>>>>           
>> Submitting
>>     
>>>>> 2010-02-25 17:12:04,306-0600 DEBUG TaskImpl
>>>>>           
>> Task(type=FILE_TRANSFER,
>>     
>>>>> identity=urn:0-1-8-1-2-1267139524139) setting status to Submitted
>>>>> 2010-02-25 17:12:04,307-0600 DEBUG TaskImpl
>>>>>           
>> Task(type=FILE_TRANSFER,
>>     
>>>>> identity=urn:0-1-8-1-1-1267139524141) setting status to Active
>>>>> 2010-02-25 17:12:04,307-0600 DEBUG TaskImpl
>>>>>           
>> Task(type=FILE_TRANSFER,
>>     
>>>>> identity=urn:0-1-8-1-2-1267139524139) setting status to Active
>>>>> 2010-02-25 17:12:04,308-0600 DEBUG TaskImpl
>>>>>           
>> Task(type=FILE_TRANSFER,
>>     
>>>>> identity=urn:0-1-8-1-3-1267139524143) setting status to
>>>>>           
>> Submitting
>>     
>>>>> 2010-02-25 17:12:04,308-0600 DEBUG TaskImpl
>>>>>           
>> Task(type=FILE_TRANSFER,
>>     
>>>>> identity=urn:0-1-8-1-3-1267139524143) setting status to Submitted
>>>>> 2010-02-25 17:12:04,312-0600 DEBUG TaskImpl
>>>>>           
>> Task(type=FILE_TRANSFER,
>>     
>>>>> identity=urn:0-1-8-1-2-1267139524139) setting status to Completed
>>>>> 2010-02-25 17:12:04,312-0600 DEBUG TaskImpl
>>>>>           
>> Task(type=JOB_SUBMISSION,
>>     
>>>>> identity=urn:0-1-0-0-1-1267139524137) setting status to Active
>>>>> 2010-02-25 17:12:04,313-0600 INFO  LateBindingScheduler
>>>>> Task(type=FILE_TRANSFER, identity=urn:0-1-8-1-2-1267139524139)
>>>>> Completed. Waiting: 0, Running: 3. Heap size: 14M, Heap free: 4M,
>>>>>           
>> Max
>>     
>>>>> heap: 254M
>>>>> 2010-02-25 17:12:04,321-0600 DEBUG vdl:dostagein
>>>>>           
>> FILE_STAGE_IN_END
>>     
>>>>> file=file://localhost/input/T0510D1.range srchost=localhost
>>>>> srcdir=input srcname=T0510D1.range desthost=localhost
>>>>> destdir=psim.loops-20100225-1712-3zrtb5i5/shared/input
>>>>>           
>> provider=file
>>     
>>>>> 2010-02-25 17:12:04,323-0600 DEBUG TaskImpl
>>>>>           
>> Task(type=FILE_TRANSFER,
>>     
>>>>> identity=urn:0-1-8-1-1-1267139524141) setting status to Completed
>>>>> 2010-02-25 17:12:04,324-0600 INFO  LateBindingScheduler
>>>>> Task(type=FILE_TRANSFER, identity=urn:0-1-8-1-1-1267139524141)
>>>>> Completed. Waiting: 0, Running: 2. Heap size: 14M, Heap free: 5M,
>>>>>           
>> Max
>>     
>>>>> heap: 254M
>>>>> 2010-02-25 17:12:04,325-0600 DEBUG vdl:dostagein
>>>>>           
>> FILE_STAGE_IN_END
>>     
>>>>> file=file://localhost/input/T0510D1.params srchost=localhost
>>>>> srcdir=input srcname=T0510D1.params desthost=localhost
>>>>> destdir=psim.loops-20100225-1712-3zrtb5i5/shared/input
>>>>>           
>> provider=file
>>     
>>>>> 2010-02-25 17:12:04,325-0600 DEBUG TaskImpl
>>>>>           
>> Task(type=FILE_TRANSFER,
>>     
>>>>> identity=urn:0-1-8-1-3-1267139524143) setting status to Active
>>>>> 2010-02-25 17:12:04,327-0600 DEBUG TaskImpl
>>>>>           
>> Task(type=FILE_TRANSFER,
>>     
>>>>> identity=urn:0-1-8-1-3-1267139524143) setting status to Completed
>>>>> 2010-02-25 17:12:04,327-0600 INFO  LateBindingScheduler
>>>>> Task(type=FILE_TRANSFER, identity=urn:0-1-8-1-3-1267139524143)
>>>>> Completed. Waiting: 0, Running: 1. Heap size: 14M, Heap free: 5M,
>>>>>           
>> Max
>>     
>>>>> heap: 254M
>>>>> 2010-02-25 17:12:04,327-0600 DEBUG vdl:dostagein
>>>>>           
>> FILE_STAGE_IN_END
>>     
>>>>> file=file://localhost/input/T0510D1.pdb srchost=localhost
>>>>>           
>> srcdir=input
>>     
>>>>> srcname=T0510D1.pdb desthost=localhost
>>>>> destdir=psim.loops-20100225-1712-3zrtb5i5/shared/input
>>>>>           
>> provider=file
>>     
>>>>> 2010-02-25 17:12:04,327-0600 INFO  vdl:dostagein END
>>>>> jobid=PrepLoop-ykjtxaoj - Staging in finished
>>>>> 2010-02-25 17:12:04,328-0600 DEBUG vdl:execute2 JOB_START
>>>>> jobid=PrepLoop-ykjtxaoj tr=PrepLoop arguments=[input/T0510D1.pdb,
>>>>> output/data//T0510D1.pdb]
>>>>> tmpdir=psim.loops-20100225-1712-3zrtb5i5/jobs/y/PrepLoop-ykjtxaoj
>>>>> host=localhost
>>>>> 2010-02-25 17:12:04,339-0600 INFO  Execute
>>>>>           
>> jobid=PrepLoop-ykjtxaoj
>>     
>>>>> task=Task(type=JOB_SUBMISSION,
>>>>>           
>> identity=urn:0-1-8-1-1267139524148)
>>     
>>>>> 2010-02-25 17:12:04,340-0600 DEBUG TaskImpl
>>>>>           
>> Task(type=JOB_SUBMISSION,
>>     
>>>>> identity=urn:0-1-8-1-1267139524148) setting status to Submitting
>>>>> 2010-02-25 17:12:04,340-0600 INFO  JobSubmissionTaskHandler
>>>>>           
>> Submitting
>>     
>>>>> task Task(type=JOB_SUBMISSION,
>>>>>           
>> identity=urn:0-1-8-1-1267139524148)
>>     
>>>>> 2010-02-25 17:12:04,340-0600 INFO  JobSubmissionTaskHandler
>>>>>           
>> Submitting
>>     
>>>>> single job
>>>>> 2010-02-25 17:12:04,340-0600 DEBUG TaskImpl
>>>>>           
>> Task(type=JOB_SUBMISSION,
>>     
>>>>> identity=urn:0-1-8-1-1267139524148) setting status to Submitted
>>>>> 2010-02-25 17:12:04,343-0600 DEBUG TaskImpl
>>>>>           
>> Task(type=JOB_SUBMISSION,
>>     
>>>>> identity=urn:0-1-8-1-1267139524148) setting status to Active
>>>>> 2010-02-25 17:12:04,458-0600 DEBUG TaskImpl
>>>>>           
>> Task(type=JOB_SUBMISSION,
>>     
>>>>> identity=urn:0-1-0-0-1-1267139524137) setting status to Completed
>>>>> 2010-02-25 17:12:04,459-0600 INFO  LateBindingScheduler
>>>>> Task(type=JOB_SUBMISSION, identity=urn:0-1-0-0-1-1267139524137)
>>>>> Completed. Waiting: 0, Running: 1. Heap size: 14M, Heap free: 5M,
>>>>>           
>> Max
>>     
>>>>> heap: 254M
>>>>> 2010-02-25 17:12:04,460-0600 DEBUG vdl:checkjobstatus START
>>>>> jobid=echo-xkjtxaoj
>>>>> 2010-02-25 17:12:04,461-0600 DEBUG TaskImpl
>>>>>           
>> Task(type=FILE_OPERATION,
>>     
>>>>> identity=urn:0-1-0-0-1-1267139524150) setting status to
>>>>>           
>> Submitting
>>     
>>>>> 2010-02-25 17:12:04,462-0600 DEBUG TaskImpl
>>>>>           
>> Task(type=FILE_OPERATION,
>>     
>>>>> identity=urn:0-1-0-0-1-1267139524150) setting status to Submitted
>>>>> 2010-02-25 17:12:04,462-0600 DEBUG TaskImpl
>>>>>           
>> Task(type=FILE_OPERATION,
>>     
>>>>> identity=urn:0-1-0-0-1-1267139524150) setting status to Active
>>>>> 2010-02-25 17:12:04,462-0600 DEBUG TaskImpl
>>>>>           
>> Task(type=FILE_OPERATION,
>>     
>>>>> identity=urn:0-1-0-0-1-1267139524150) setting status to Completed
>>>>> 2010-02-25 17:12:04,462-0600 INFO  LateBindingScheduler
>>>>> Task(type=FILE_OPERATION, identity=urn:0-1-0-0-1-1267139524150)
>>>>> Completed. Waiting: 0, Running: 1. Heap size: 14M, Heap free: 5M,
>>>>>           
>> Max
>>     
>>>>> heap: 254M
>>>>> 2010-02-25 17:12:04,463-0600 INFO  vdl:checkjobstatus SUCCESS
>>>>> jobid=echo-xkjtxaoj - Success file found
>>>>> 2010-02-25 17:12:04,463-0600 DEBUG vdl:execute2 STAGING_OUT
>>>>> jobid=echo-xkjtxaoj
>>>>> 2010-02-25 17:12:04,464-0600 INFO  vdl:dostageout START
>>>>> jobid=echo-xkjtxaoj - Staging out files
>>>>> 2010-02-25 17:12:04,470-0600 DEBUG vdl:dostageout
>>>>>           
>> FILE_STAGE_OUT_START
>>     
>>>>> srcname=f-7a608b5e-b445-46f4-8cb2-bff8a73b52ec-1-0
>>>>> srcdir=psim.loops-20100225-1712-3zrtb5i5/shared/_concurrent
>>>>> srchost=localhost destdir=_concurrent desthost=localhost
>>>>> provider=file
>>>>> 2010-02-25 17:12:04,471-0600 DEBUG TaskImpl
>>>>>           
>> Task(type=FILE_OPERATION,
>>     
>>>>> identity=urn:0-1-0-0-1-1-1267139524152) setting status to
>>>>>           
>> Submitting
>>     
>>>>> 2010-02-25 17:12:04,471-0600 DEBUG TaskImpl
>>>>>           
>> Task(type=FILE_OPERATION,
>>     
>>>>> identity=urn:0-1-0-0-1-1-1267139524152) setting status to
>>>>>           
>> Submitted
>>     
>>>>> 2010-02-25 17:12:04,471-0600 DEBUG TaskImpl
>>>>>           
>> Task(type=FILE_OPERATION,
>>     
>>>>> identity=urn:0-1-0-0-1-1-1267139524152) setting status to Active
>>>>> 2010-02-25 17:12:04,471-0600 DEBUG TaskImpl
>>>>>           
>> Task(type=FILE_OPERATION,
>>     
>>>>> identity=urn:0-1-0-0-1-1-1267139524152) setting status to
>>>>>           
>> Completed
>>     
>>>>> 2010-02-25 17:12:04,471-0600 INFO  LateBindingScheduler
>>>>> Task(type=FILE_OPERATION, identity=urn:0-1-0-0-1-1-1267139524152)
>>>>> Completed. Waiting: 0, Running: 1. Heap size: 14M, Heap free: 5M,
>>>>>           
>> Max
>>     
>>>>> heap: 254M
>>>>> 2010-02-25 17:12:04,473-0600 DEBUG TaskImpl
>>>>>           
>> Task(type=FILE_TRANSFER,
>>     
>>>>> identity=urn:0-1-0-0-1-1-1267139524154) setting status to
>>>>>           
>> Submitting
>>     
>>>>> 2010-02-25 17:12:04,473-0600 DEBUG TaskImpl
>>>>>           
>> Task(type=FILE_TRANSFER,
>>     
>>>>> identity=urn:0-1-0-0-1-1-1267139524154) setting status to
>>>>>           
>> Submitted
>>     
>>>>> 2010-02-25 17:12:04,473-0600 DEBUG TaskImpl
>>>>>           
>> Task(type=FILE_TRANSFER,
>>     
>>>>> identity=urn:0-1-0-0-1-1-1267139524154) setting status to Active
>>>>> 2010-02-25 17:12:04,474-0600 DEBUG TaskImpl
>>>>>           
>> Task(type=FILE_TRANSFER,
>>     
>>>>> identity=urn:0-1-0-0-1-1-1267139524154) setting status to
>>>>>           
>> Completed
>>     
>>>>> 2010-02-25 17:12:04,474-0600 INFO  LateBindingScheduler
>>>>> Task(type=FILE_TRANSFER, identity=urn:0-1-0-0-1-1-1267139524154)
>>>>> Completed. Waiting: 0, Running: 1. Heap size: 14M, Heap free: 5M,
>>>>>           
>> Max
>>     
>>>>> heap: 254M
>>>>> 2010-02-25 17:12:04,474-0600 DEBUG vdl:dostageout
>>>>>           
>> FILE_STAGE_OUT_END
>>     
>>>>> srcname=f-7a608b5e-b445-46f4-8cb2-bff8a73b52ec-1-0
>>>>> srcdir=psim.loops-20100225-1712-3zrtb5i5/shared/_concurrent
>>>>> srchost=localhost destdir=_concurrent desthost=localhost
>>>>> provider=file
>>>>> 2010-02-25 17:12:04,475-0600 DEBUG TaskImpl
>>>>>           
>> Task(type=FILE_OPERATION,
>>     
>>>>> identity=urn:0-1-0-0-1-1-1267139524157) setting status to
>>>>>           
>> Submitting
>>     
>>>>> 2010-02-25 17:12:04,475-0600 DEBUG TaskImpl
>>>>>           
>> Task(type=FILE_OPERATION,
>>     
>>>>> identity=urn:0-1-0-0-1-1-1267139524157) setting status to
>>>>>           
>> Submitted
>>     
>>>>> 2010-02-25 17:12:04,475-0600 DEBUG TaskImpl
>>>>>           
>> Task(type=FILE_OPERATION,
>>     
>>>>> identity=urn:0-1-0-0-1-1-1267139524157) setting status to Active
>>>>> 2010-02-25 17:12:04,476-0600 DEBUG TaskImpl
>>>>>           
>> Task(type=FILE_OPERATION,
>>     
>>>>> identity=urn:0-1-0-0-1-1-1267139524157) setting status to
>>>>>           
>> Completed
>>     
>>>>> 2010-02-25 17:12:04,476-0600 INFO  LateBindingScheduler
>>>>> Task(type=FILE_OPERATION, identity=urn:0-1-0-0-1-1-1267139524157)
>>>>> Completed. Waiting: 0, Running: 1. Heap size: 14M, Heap free: 5M,
>>>>>           
>> Max
>>     
>>>>> heap: 254M
>>>>> 2010-02-25 17:12:04,479-0600 INFO  vdl:dostageout END
>>>>> jobid=echo-xkjtxaoj - Staging out finished
>>>>> 2010-02-25 17:12:04,482-0600 DEBUG vdl:execute2 JOB_END
>>>>> jobid=echo-xkjtxaoj
>>>>> 2010-02-25 17:12:04,484-0600 INFO  vdl:execute END_SUCCESS
>>>>> thread=0-1-0-0 tr=echo
>>>>> 2010-02-25 17:12:04,613-0600 INFO  CloseDataset Closing
>>>>> org.griphyn.vdl.mapping.RootDataNode identifier
>>>>>
>>>>>           
>> tag:benc at ci.uchicago.edu,2008:swift:dataset:20100225-1712-kjif48ad:720000000042
>>
>>     
>>>>> type file with no value at dataset=f (not closed)
>>>>> 2010-02-25 17:12:04,614-0600 INFO  AbstractDataNode Notifying
>>>>>           
>> listener
>>     
>>>>> "F/org.griphyn.vdl.mapping.RootDataNode identifier
>>>>>
>>>>>           
>> tag:benc at ci.uchicago.edu,2008:swift:dataset:20100225-1712-kjif48ad:720000000042
>>
>>     
>>>>> type file with no value at dataset=f (closed)" about
>>>>> "org.griphyn.vdl.mapping.RootDataNode identifier
>>>>>
>>>>>           
>> tag:benc at ci.uchicago.edu,2008:swift:dataset:20100225-1712-kjif48ad:720000000042
>>
>>     
>>>>> type file with no value at dataset=f (closed)"
>>>>> 2010-02-25 17:12:04,614-0600 INFO  AbstractDataNode closed
>>>>> org.griphyn.vdl.mapping.RootDataNode identifier
>>>>>
>>>>>           
>> tag:benc at ci.uchicago.edu,2008:swift:dataset:20100225-1712-kjif48ad:720000000042
>>
>>     
>>>>> type file with no value at dataset=f (closed)
>>>>> 2010-02-25 17:12:04,614-0600 INFO  AbstractDataNode Notifying
>>>>>           
>> listener
>>     
>>>>> "modelOut.$[]/0" about "org.griphyn.vdl.mapping.RootDataNode
>>>>> identifier
>>>>>
>>>>>           
>> tag:benc at ci.uchicago.edu,2008:swift:dataset:20100225-1712-kjif48ad:720000000014
>>
>>     
>>>>> type int value=4.0 dataset=nSim (closed)"
>>>>> 2010-02-25 17:12:04,615-0600 INFO  echos PROCEDURE_END line=68
>>>>> 2010-02-25 17:12:04,615-0600 INFO  CloseDataset Partially closing
>>>>> org.griphyn.vdl.mapping.RootDataNode identifier
>>>>>
>>>>>           
>> tag:benc at ci.uchicago.edu,2008:swift:dataset:20100225-1712-kjif48ad:720000000042
>>
>>     
>>>>> type file with no value at dataset=f (closed) for statement 88004
>>>>> 2010-02-25 17:12:04,615-0600 INFO  CloseDataset var is
>>>>> org.griphyn.vdl.mapping.RootDataNode identifier
>>>>>
>>>>>           
>> tag:benc at ci.uchicago.edu,2008:swift:dataset:20100225-1712-kjif48ad:720000000042
>>
>>     
>>>>> type file with no value at dataset=f (closed)
>>>>> 2010-02-25 17:12:04,615-0600 INFO  CloseDataset var hash is
>>>>>           
>> 21621663
>>     
>>>>> 2010-02-25 17:12:04,615-0600 INFO  CloseDataset variable already
>>>>> closed - skipping partial close processing
>>>>> 2010-02-25 17:12:04,682-0600 INFO  AbstractDataNode Found mapped
>>>>>           
>> data
>>     
>>>>> modelOut.$[]/1.[2].pdt
>>>>> 2010-02-25 17:12:04,682-0600 INFO  AbstractDataNode Found mapped
>>>>>           
>> data
>>     
>>>>> modelOut.$[]/2.[0].cfg
>>>>> 2010-02-25 17:12:04,682-0600 INFO  AbstractDataNode Found mapped
>>>>>           
>> data
>>     
>>>>> modelOut.$[]/3.[1].cfg
>>>>> 2010-02-25 17:12:04,682-0600 INFO  AbstractDataNode Found mapped
>>>>>           
>> data
>>     
>>>>> modelOut.$[]/4.[3].log
>>>>> 2010-02-25 17:12:04,682-0600 INFO  AbstractDataNode Found mapped
>>>>>           
>> data
>>     
>>>>> modelOut.$[]/4.[3].cfg
>>>>> 2010-02-25 17:12:04,682-0600 INFO  AbstractDataNode Found mapped
>>>>>           
>> data
>>     
>>>>> modelOut.$[]/4.[3].pdt
>>>>> 2010-02-25 17:12:04,682-0600 INFO  AbstractDataNode Found mapped
>>>>>           
>> data
>>     
>>>>> modelOut.$[]/4.[0].pdt
>>>>> 2010-02-25 17:12:04,682-0600 INFO  AbstractDataNode Found mapped
>>>>>           
>> data
>>     
>>>>> modelOut.$[]/4.[1].pdb
>>>>> 2010-02-25 17:12:04,682-0600 INFO  AbstractDataNode Found mapped
>>>>>           
>> data
>>     
>>>>> modelOut.$[]/4.[0].log
>>>>> 2010-02-25 17:12:04,683-0600 INFO  AbstractDataNode Found mapped
>>>>>           
>> data
>>     
>>>>> modelOut.$[]/4.[1].log
>>>>> 2010-02-25 17:12:04,683-0600 INFO  AbstractDataNode Found mapped
>>>>>           
>> data
>>     
>>>>> modelOut.$[]/4.[2].cfg
>>>>> 2010-02-25 17:12:04,683-0600 INFO  AbstractDataNode Found mapped
>>>>>           
>> data
>>     
>>>>> modelOut.$[]/4.[2].log
>>>>> 2010-02-25 17:12:04,683-0600 INFO  AbstractDataNode Found mapped
>>>>>           
>> data
>>     
>>>>> modelOut.$[]/4.[3].pdb
>>>>> 2010-02-25 17:12:04,683-0600 INFO  AbstractDataNode Found mapped
>>>>>           
>> data
>>     
>>>>> modelOut.$[]/4.[2].pdb
>>>>> 2010-02-25 17:12:04,683-0600 INFO  AbstractDataNode Found mapped
>>>>>           
>> data
>>     
>>>>> modelOut.$[]/4.[1].pdt
>>>>> 2010-02-25 17:12:04,683-0600 INFO  AbstractDataNode Found mapped
>>>>>           
>> data
>>     
>>>>> modelOut.$[]/4.[0].pdb
>>>>> 2010-02-25 17:12:04,683-0600 INFO  AbstractDataNode Notifying
>>>>>           
>> listener
>>     
>>>>> "F/modelOut.$[]/4" about
>>>>>           
>> "org.griphyn.vdl.mapping.RootArrayDataNode
>>     
>>>>> identifier
>>>>>
>>>>>           
>> tag:benc at ci.uchicago.edu,2008:swift:dataset:20100225-1712-kjif48ad:720000000023
>>
>>     
>>>>> type LoopModelOut[] with no value at dataset=modelOut (closed)"
>>>>> 2010-02-25 17:12:04,683-0600 INFO  AbstractDataNode closed
>>>>> org.griphyn.vdl.mapping.RootArrayDataNode identifier
>>>>>
>>>>>           
>> tag:benc at ci.uchicago.edu,2008:swift:dataset:20100225-1712-kjif48ad:720000000023
>>
>>     
>>>>> type LoopModelOut[] with no value at dataset=modelOut (closed)
>>>>> 2010-02-25 17:12:04,684-0600 INFO  AbstractDataNode Notifying
>>>>>           
>> listener
>>     
>>>>> "F/4" about "org.griphyn.vdl.mapping.RootDataNode identifier
>>>>>
>>>>>           
>> tag:benc at ci.uchicago.edu,2008:swift:dataset:20100225-1712-kjif48ad:720000000014
>>
>>     
>>>>> type int value=4.0 dataset=nSim (closed)"
>>>>> 2010-02-25 17:12:04,684-0600 INFO  AbstractDataNode closed
>>>>> org.griphyn.vdl.mapping.RootDataNode identifier
>>>>>
>>>>>           
>> tag:benc at ci.uchicago.edu,2008:swift:dataset:20100225-1712-kjif48ad:720000000014
>>
>>     
>>>>> type int value=4.0 dataset=nSim (closed)
>>>>> 2010-02-25 17:12:04,685-0600 INFO  AbstractDataNode closed
>>>>> org.griphyn.vdl.mapping.RootDataNode identifier
>>>>>
>>>>>           
>> tag:benc at ci.uchicago.edu,2008:swift:dataset:20100225-1712-kjif48ad:720000000069
>>
>>     
>>>>> type int value=3.0 dataset=unnamed SwiftScript value (closed)
>>>>> 2010-02-25 17:12:04,685-0600 INFO  strtoi INTERNALPROC_END
>>>>> thread=0-1-0-1
>>>>> 2010-02-25 17:12:04,685-0600 INFO  CloseDataset Closing 4
>>>>> 2010-02-25 17:12:04,686-0600 INFO  strtoi ENDCOMPOUND
>>>>>           
>> thread=0-1-0
>>     
>>>>> 2010-02-25 17:12:04,686-0600 INFO  CloseDataset Partially closing
>>>>>           
>> 4
>>     
>>>>> for statement 88012
>>>>> 2010-02-25 17:12:04,686-0600 INFO  CloseDataset var is 4
>>>>> 2010-02-25 17:12:04,686-0600 INFO  CloseDataset var hash is
>>>>>           
>> 2221396
>>     
>>>>> 2010-02-25 17:12:04,687-0600 INFO  CloseDataset variable already
>>>>> closed - skipping partial close processing
>>>>> 2010-02-25 17:12:04,687-0600 INFO  AbstractDataNode Adding handle
>>>>> listener "F/org.griphyn.vdl.mapping.DataNode identifier
>>>>>
>>>>>           
>> tag:benc at ci.uchicago.edu,2008:swift:dataset:20100225-1712-kjif48ad:720000000056
>>
>>     
>>>>> type ModelLog with no value at dataset=modelOut path=[3].log (not
>>>>> closed)" to "org.griphyn.vdl.mapping.DataNode identifier
>>>>>
>>>>>           
>> tag:benc at ci.uchicago.edu,2008:swift:dataset:20100225-1712-kjif48ad:720000000056
>>
>>     
>>>>> type ModelLog with no value at dataset=modelOut path=[3].log (not
>>>>> closed)"
>>>>> 2010-02-25 17:12:04,700-0600 INFO  AbstractDataNode closed
>>>>> org.griphyn.vdl.mapping.RootDataNode identifier
>>>>>
>>>>>           
>> tag:benc at ci.uchicago.edu,2008:swift:dataset:20100225-1712-kjif48ad:720000000071
>>
>>     
>>>>> type int value=0.0 dataset=unnamed SwiftScript value (closed)
>>>>> 2010-02-25 17:12:04,701-0600 INFO  AbstractDataNode closed
>>>>> org.griphyn.vdl.mapping.RootDataNode identifier
>>>>>
>>>>>           
>> tag:benc at ci.uchicago.edu,2008:swift:dataset:20100225-1712-kjif48ad:720000000072
>>
>>     
>>>>> type int value=1.0 dataset=unnamed SwiftScript value (closed)
>>>>> 2010-02-25 17:12:04,701-0600 INFO  AbstractDataNode closed
>>>>> org.griphyn.vdl.mapping.RootDataNode identifier
>>>>>
>>>>>           
>> tag:benc at ci.uchicago.edu,2008:swift:dataset:20100225-1712-kjif48ad:720000000073
>>
>>     
>>>>> type int value=2.0 dataset=unnamed SwiftScript value (closed)
>>>>> 2010-02-25 17:12:04,701-0600 INFO  AbstractDataNode closed
>>>>> org.griphyn.vdl.mapping.RootDataNode identifier
>>>>>
>>>>>           
>> tag:benc at ci.uchicago.edu,2008:swift:dataset:20100225-1712-kjif48ad:720000000074
>>
>>     
>>>>> type int value=3.0 dataset=unnamed SwiftScript value (closed)
>>>>> 2010-02-25 17:12:04,701-0600 INFO  AbstractDataNode closed
>>>>> org.griphyn.vdl.karajan.lib.Range$1 identifier
>>>>>
>>>>>           
>> tag:benc at ci.uchicago.edu,2008:swift:dataset:20100225-1712-kjif48ad:720000000070
>>
>>     
>>>>> type int[] with no value at dataset=unnamed SwiftScript value
>>>>> (closed)
>>>>> 2010-02-25 17:12:04,702-0600 INFO  doloopround FOREACH_IT_START
>>>>> line=130 thread=0-1-9-1-1
>>>>> 2010-02-25 17:12:04,703-0600 INFO  doloopround FOREACH_IT_START
>>>>> line=130 thread=0-1-9-1-2
>>>>> 2010-02-25 17:12:04,703-0600 INFO  doloopround FOREACH_IT_START
>>>>> line=130 thread=0-1-9-1-3
>>>>> 2010-02-25 17:12:04,703-0600 INFO  doloopround FOREACH_IT_START
>>>>> line=130 thread=0-1-9-1-4
>>>>> 2010-02-25 17:12:04,703-0600 INFO  doloopround SCOPE
>>>>>           
>> thread=0-1-9-1-2
>>     
>>>>> 2010-02-25 17:12:04,703-0600 INFO  doloopround SCOPE
>>>>>           
>> thread=0-1-9-1-3
>>     
>>>>> 2010-02-25 17:12:04,704-0600 INFO  doloopround SCOPE
>>>>>           
>> thread=0-1-9-1-4
>>     
>>>>> 2010-02-25 17:12:04,707-0600 INFO  loopmodel PROCEDURE line=117
>>>>> thread=0-1-9-1-2-1 name=loopModel
>>>>> 2010-02-25 17:12:04,707-0600 INFO  loopmodel PROCEDURE line=117
>>>>> thread=0-1-9-1-3-1 name=loopModel
>>>>> 2010-02-25 17:12:04,708-0600 INFO  loopmodel PROCEDURE line=117
>>>>> thread=0-1-9-1-4-1 name=loopModel
>>>>> 2010-02-25 17:12:04,710-0600 INFO  AbstractDataNode Adding handle
>>>>> listener "F/org.griphyn.vdl.mapping.DataNode identifier
>>>>>
>>>>>           
>> tag:benc at ci.uchicago.edu,2008:swift:dataset:20100225-1712-kjif48ad:720000000036
>>
>>     
>>>>> type RamaIndex with no value at dataset=modelData path=.index
>>>>>           
>> (not
>>     
>>>>> closed)" to "org.griphyn.vdl.mapping.DataNode identifier
>>>>>
>>>>>           
>> tag:benc at ci.uchicago.edu,2008:swift:dataset:20100225-1712-kjif48ad:720000000036
>>
>>     
>>>>> type RamaIndex with no value at dataset=modelData path=.index
>>>>>           
>> (not
>>     
>>>>> closed)"
>>>>> 2010-02-25 17:12:04,711-0600 INFO  doloopround SCOPE
>>>>>           
>> thread=0-1-9-1-1
>>     
>>>>> 2010-02-25 17:12:04,712-0600 INFO  loopmodel PROCEDURE line=117
>>>>> thread=0-1-9-1-1-1 name=loopModel
>>>>> 2010-02-25 17:12:16,434-0600 DEBUG TaskImpl
>>>>>           
>> Task(type=JOB_SUBMISSION,
>>     
>>>>> identity=urn:0-1-8-1-1267139524148) setting status to Completed
>>>>> 2010-02-25 17:12:16,434-0600 INFO  LateBindingScheduler
>>>>> Task(type=JOB_SUBMISSION, identity=urn:0-1-8-1-1267139524148)
>>>>> Completed. Waiting: 0, Running: 0. Heap size: 14M, Heap free: 4M,
>>>>>           
>> Max
>>     
>>>>> heap: 254M
>>>>> 2010-02-25 17:12:16,436-0600 DEBUG vdl:checkjobstatus START
>>>>> jobid=PrepLoop-ykjtxaoj
>>>>> 2010-02-25 17:12:16,444-0600 DEBUG TaskImpl
>>>>>           
>> Task(type=FILE_OPERATION,
>>     
>>>>> identity=urn:0-1-8-1-1267139524159) setting status to Submitting
>>>>> 2010-02-25 17:12:16,444-0600 DEBUG TaskImpl
>>>>>           
>> Task(type=FILE_OPERATION,
>>     
>>>>> identity=urn:0-1-8-1-1267139524159) setting status to Submitted
>>>>> 2010-02-25 17:12:16,444-0600 DEBUG TaskImpl
>>>>>           
>> Task(type=FILE_OPERATION,
>>     
>>>>> identity=urn:0-1-8-1-1267139524159) setting status to Active
>>>>> 2010-02-25 17:12:16,444-0600 DEBUG TaskImpl
>>>>>           
>> Task(type=FILE_OPERATION,
>>     
>>>>> identity=urn:0-1-8-1-1267139524159) setting status to Completed
>>>>> 2010-02-25 17:12:16,444-0600 INFO  LateBindingScheduler
>>>>> Task(type=FILE_OPERATION, identity=urn:0-1-8-1-1267139524159)
>>>>> Completed. Waiting: 0, Running: 0. Heap size: 14M, Heap free: 4M,
>>>>>           
>> Max
>>     
>>>>> heap: 254M
>>>>> 2010-02-25 17:12:16,445-0600 INFO  vdl:checkjobstatus SUCCESS
>>>>> jobid=PrepLoop-ykjtxaoj - Success file found
>>>>> 2010-02-25 17:12:16,447-0600 DEBUG vdl:execute2 STAGING_OUT
>>>>> jobid=PrepLoop-ykjtxaoj
>>>>> 2010-02-25 17:12:16,447-0600 INFO  vdl:dostageout START
>>>>> jobid=PrepLoop-ykjtxaoj - Staging out files
>>>>> 2010-02-25 17:12:16,454-0600 DEBUG vdl:dostageout
>>>>>           
>> FILE_STAGE_OUT_START
>>     
>>>>> srcname=T0510D1.rama_index
>>>>> srcdir=psim.loops-20100225-1712-3zrtb5i5/shared/output/data/
>>>>> srchost=localhost destdir=output/data/ desthost=localhost
>>>>> provider=file
>>>>> 2010-02-25 17:12:16,454-0600 DEBUG vdl:dostageout
>>>>>           
>> FILE_STAGE_OUT_START
>>     
>>>>> srcname=T0510D1.secseq
>>>>> srcdir=psim.loops-20100225-1712-3zrtb5i5/shared/output/data/
>>>>> srchost=localhost destdir=output/data/ desthost=localhost
>>>>> provider=file
>>>>> 2010-02-25 17:12:16,455-0600 DEBUG vdl:dostageout
>>>>>           
>> FILE_STAGE_OUT_START
>>     
>>>>> srcname=T0510D1.params
>>>>> srcdir=psim.loops-20100225-1712-3zrtb5i5/shared/output/data/
>>>>> srchost=localhost destdir=output/data/ desthost=localhost
>>>>> provider=file
>>>>> 2010-02-25 17:12:16,456-0600 DEBUG vdl:dostageout
>>>>>           
>> FILE_STAGE_OUT_START
>>     
>>>>> srcname=T0510D1.rama
>>>>> srcdir=psim.loops-20100225-1712-3zrtb5i5/shared/output/data/
>>>>> srchost=localhost destdir=output/data/ desthost=localhost
>>>>> provider=file
>>>>> 2010-02-25 17:12:16,456-0600 DEBUG vdl:dostageout
>>>>>           
>> FILE_STAGE_OUT_START
>>     
>>>>> srcname=T0510D1.rama_map
>>>>> srcdir=psim.loops-20100225-1712-3zrtb5i5/shared/output/data/
>>>>> srchost=localhost destdir=output/data/ desthost=localhost
>>>>> provider=file
>>>>> 2010-02-25 17:12:16,456-0600 DEBUG vdl:dostageout
>>>>>           
>> FILE_STAGE_OUT_START
>>     
>>>>> srcname=T0510D1.fasta
>>>>> srcdir=psim.loops-20100225-1712-3zrtb5i5/shared/output/data/
>>>>> srchost=localhost destdir=output/data/ desthost=localhost
>>>>> provider=file
>>>>> 2010-02-25 17:12:16,457-0600 DEBUG vdl:dostageout
>>>>>           
>> FILE_STAGE_OUT_START
>>     
>>>>> srcname=T0510D1.range
>>>>> srcdir=psim.loops-20100225-1712-3zrtb5i5/shared/output/data/
>>>>> srchost=localhost destdir=output/data/ desthost=localhost
>>>>> provider=file
>>>>> 2010-02-25 17:12:16,457-0600 DEBUG vdl:dostageout
>>>>>           
>> FILE_STAGE_OUT_START
>>     
>>>>> srcname=T0510D1.pdb
>>>>> srcdir=psim.loops-20100225-1712-3zrtb5i5/shared/output/data/
>>>>> srchost=localhost destdir=output/data/ desthost=localhost
>>>>> provider=file
>>>>> 2010-02-25 17:12:16,457-0600 DEBUG TaskImpl
>>>>>           
>> Task(type=FILE_OPERATION,
>>     
>>>>> identity=urn:0-1-8-1-1-1267139524162) setting status to
>>>>>           
>> Submitting
>>     
>>>>> 2010-02-25 17:12:16,458-0600 DEBUG TaskImpl
>>>>>           
>> Task(type=FILE_OPERATION,
>>     
>>>>> identity=urn:0-1-8-1-1-1267139524162) setting status to Submitted
>>>>> 2010-02-25 17:12:16,458-0600 DEBUG TaskImpl
>>>>>           
>> Task(type=FILE_OPERATION,
>>     
>>>>> identity=urn:0-1-8-1-1-1267139524162) setting status to Active
>>>>> 2010-02-25 17:12:16,458-0600 DEBUG TaskImpl
>>>>>           
>> Task(type=FILE_OPERATION,
>>     
>>>>> identity=urn:0-1-8-1-1-1267139524162) setting status to Completed
>>>>> 2010-02-25 17:12:16,458-0600 INFO  LateBindingScheduler
>>>>> Task(type=FILE_OPERATION, identity=urn:0-1-8-1-1-1267139524162)
>>>>> Completed. Waiting: 2, Running: 3. Heap size: 14M, Heap free: 4M,
>>>>>           
>> Max
>>     
>>>>> heap: 254M
>>>>> 2010-02-25 17:12:16,458-0600 DEBUG vdl:dostageout
>>>>>           
>> FILE_STAGE_OUT_START
>>     
>>>>> srcname=void srcdir=psim.loops-20100225-1712-3zrtb5i5/shared/
>>>>> srchost=localhost destdir= desthost=localhost provider=file
>>>>> 2010-02-25 17:12:16,458-0600 DEBUG TaskImpl
>>>>>           
>> Task(type=FILE_OPERATION,
>>     
>>>>> identity=urn:0-1-8-1-2-1267139524164) setting status to
>>>>>           
>> Submitting
>>     
>>>>> 2010-02-25 17:12:16,459-0600 DEBUG TaskImpl
>>>>>           
>> Task(type=FILE_OPERATION,
>>     
>>>>> identity=urn:0-1-8-1-2-1267139524164) setting status to Submitted
>>>>> 2010-02-25 17:12:16,459-0600 DEBUG TaskImpl
>>>>>           
>> Task(type=FILE_OPERATION,
>>     
>>>>> identity=urn:0-1-8-1-3-1267139524165) setting status to
>>>>>           
>> Submitting
>>     
>>>>> 2010-02-25 17:12:16,459-0600 DEBUG TaskImpl
>>>>>           
>> Task(type=FILE_OPERATION,
>>     
>>>>> identity=urn:0-1-8-1-3-1267139524165) setting status to Submitted
>>>>> 2010-02-25 17:12:16,459-0600 DEBUG TaskImpl
>>>>>           
>> Task(type=FILE_OPERATION,
>>     
>>>>> identity=urn:0-1-8-1-3-1267139524165) setting status to Active
>>>>> 2010-02-25 17:12:16,459-0600 DEBUG TaskImpl
>>>>>           
>> Task(type=FILE_OPERATION,
>>     
>>>>> identity=urn:0-1-8-1-3-1267139524165) setting status to Completed
>>>>> 2010-02-25 17:12:16,459-0600 INFO  LateBindingScheduler
>>>>> Task(type=FILE_OPERATION, identity=urn:0-1-8-1-3-1267139524165)
>>>>> Completed. Waiting: 0, Running: 8. Heap size: 14M, Heap free: 4M,
>>>>>           
>> Max
>>     
>>>>> heap: 254M
>>>>> 2010-02-25 17:12:16,459-0600 DEBUG TaskImpl
>>>>>           
>> Task(type=FILE_OPERATION,
>>     
>>>>> identity=urn:0-1-8-1-2-1267139524164) setting status to Active
>>>>> 2010-02-25 17:12:16,459-0600 DEBUG TaskImpl
>>>>>           
>> Task(type=FILE_OPERATION,
>>     
>>>>> identity=urn:0-1-8-1-2-1267139524164) setting status to Completed
>>>>> 2010-02-25 17:12:16,460-0600 INFO  LateBindingScheduler
>>>>> Task(type=FILE_OPERATION, identity=urn:0-1-8-1-2-1267139524164)
>>>>> Completed. Waiting: 0, Running: 7. Heap size: 14M, Heap free: 4M,
>>>>>           
>> Max
>>     
>>>>> heap: 254M
>>>>> 2010-02-25 17:12:16,460-0600 DEBUG TaskImpl
>>>>>           
>> Task(type=FILE_OPERATION,
>>     
>>>>> identity=urn:0-1-8-1-7-1267139524167) setting status to
>>>>>           
>> Submitting
>>     
>>>>> 2010-02-25 17:12:16,461-0600 DEBUG TaskImpl
>>>>>           
>> Task(type=FILE_OPERATION,
>>     
>>>>> identity=urn:0-1-8-1-7-1267139524167) setting status to Submitted
>>>>> 2010-02-25 17:12:16,461-0600 DEBUG TaskImpl
>>>>>           
>> Task(type=FILE_OPERATION,
>>     
>>>>> identity=urn:0-1-8-1-7-1267139524167) setting status to Active
>>>>> 2010-02-25 17:12:16,461-0600 DEBUG TaskImpl
>>>>>           
>> Task(type=FILE_OPERATION,
>>     
>>>>> identity=urn:0-1-8-1-7-1267139524167) setting status to Completed
>>>>> 2010-02-25 17:12:16,461-0600 INFO  LateBindingScheduler
>>>>> Task(type=FILE_OPERATION, identity=urn:0-1-8-1-7-1267139524167)
>>>>> Completed. Waiting: 0, Running: 8. Heap size: 14M, Heap free: 4M,
>>>>>           
>> Max
>>     
>>>>> heap: 254M
>>>>> 2010-02-25 17:12:16,462-0600 DEBUG TaskImpl
>>>>>           
>> Task(type=FILE_OPERATION,
>>     
>>>>> identity=urn:0-1-8-1-8-1267139524171) setting status to
>>>>>           
>> Submitting
>>     
>>>>> 2010-02-25 17:12:16,462-0600 DEBUG TaskImpl
>>>>>           
>> Task(type=FILE_OPERATION,
>>     
>>>>> identity=urn:0-1-8-1-8-1267139524171) setting status to Submitted
>>>>> 2010-02-25 17:12:16,462-0600 DEBUG TaskImpl
>>>>>           
>> Task(type=FILE_OPERATION,
>>     
>>>>> identity=urn:0-1-8-1-8-1267139524171) setting status to Active
>>>>> 2010-02-25 17:12:16,466-0600 DEBUG TaskImpl
>>>>>           
>> Task(type=FILE_OPERATION,
>>     
>>>>> identity=urn:0-1-8-1-6-1267139524173) setting status to
>>>>>           
>> Submitting
>>     
>>>>> 2010-02-25 17:12:16,466-0600 DEBUG TaskImpl
>>>>>           
>> Task(type=FILE_OPERATION,
>>     
>>>>> identity=urn:0-1-8-1-6-1267139524173) setting status to Submitted
>>>>> 2010-02-25 17:12:16,466-0600 DEBUG TaskImpl
>>>>>           
>> Task(type=FILE_OPERATION,
>>     
>>>>> identity=urn:0-1-8-1-6-1267139524173) setting status to Active
>>>>> 2010-02-25 17:12:16,466-0600 DEBUG TaskImpl
>>>>>           
>> Task(type=FILE_OPERATION,
>>     
>>>>> identity=urn:0-1-8-1-6-1267139524173) setting status to Completed
>>>>> 2010-02-25 17:12:16,466-0600 INFO  LateBindingScheduler
>>>>> Task(type=FILE_OPERATION, identity=urn:0-1-8-1-6-1267139524173)
>>>>> Completed. Waiting: 0, Running: 8. Heap size: 14M, Heap free: 5M,
>>>>>           
>> Max
>>     
>>>>> heap: 254M
>>>>> 2010-02-25 17:12:16,467-0600 DEBUG TaskImpl
>>>>>           
>> Task(type=FILE_OPERATION,
>>     
>>>>> identity=urn:0-1-8-1-8-1267139524171) setting status to Completed
>>>>> 2010-02-25 17:12:16,467-0600 INFO  LateBindingScheduler
>>>>> Task(type=FILE_OPERATION, identity=urn:0-1-8-1-8-1267139524171)
>>>>> Completed. Waiting: 0, Running: 7. Heap size: 14M, Heap free: 5M,
>>>>>           
>> Max
>>     
>>>>> heap: 254M
>>>>> 2010-02-25 17:12:16,467-0600 DEBUG TaskImpl
>>>>>           
>> Task(type=FILE_OPERATION,
>>     
>>>>> identity=urn:0-1-8-1-9-1267139524175) setting status to
>>>>>           
>> Submitting
>>     
>>>>> 2010-02-25 17:12:16,467-0600 DEBUG TaskImpl
>>>>>           
>> Task(type=FILE_OPERATION,
>>     
>>>>> identity=urn:0-1-8-1-9-1267139524175) setting status to Submitted
>>>>> 2010-02-25 17:12:16,467-0600 DEBUG TaskImpl
>>>>>           
>> Task(type=FILE_OPERATION,
>>     
>>>>> identity=urn:0-1-8-1-9-1267139524175) setting status to Active
>>>>> 2010-02-25 17:12:16,467-0600 DEBUG TaskImpl
>>>>>           
>> Task(type=FILE_OPERATION,
>>     
>>>>> identity=urn:0-1-8-1-9-1267139524175) setting status to Completed
>>>>> 2010-02-25 17:12:16,467-0600 INFO  LateBindingScheduler
>>>>> Task(type=FILE_OPERATION, identity=urn:0-1-8-1-9-1267139524175)
>>>>> Completed. Waiting: 1, Running: 6. Heap size: 14M, Heap free: 5M,
>>>>>           
>> Max
>>     
>>>>> heap: 254M
>>>>> 2010-02-25 17:12:16,468-0600 DEBUG TaskImpl
>>>>>           
>> Task(type=FILE_OPERATION,
>>     
>>>>> identity=urn:0-1-8-1-5-1267139524169) setting status to
>>>>>           
>> Submitting
>>     
>>>>> 2010-02-25 17:12:16,468-0600 DEBUG TaskImpl
>>>>>           
>> Task(type=FILE_OPERATION,
>>     
>>>>> identity=urn:0-1-8-1-5-1267139524169) setting status to Submitted
>>>>> 2010-02-25 17:12:16,468-0600 DEBUG TaskImpl
>>>>>           
>> Task(type=FILE_OPERATION,
>>     
>>>>> identity=urn:0-1-8-1-5-1267139524169) setting status to Active
>>>>> 2010-02-25 17:12:16,468-0600 DEBUG TaskImpl
>>>>>           
>> Task(type=FILE_OPERATION,
>>     
>>>>> identity=urn:0-1-8-1-5-1267139524169) setting status to Completed
>>>>> 2010-02-25 17:12:16,468-0600 INFO  LateBindingScheduler
>>>>> Task(type=FILE_OPERATION, identity=urn:0-1-8-1-5-1267139524169)
>>>>> Completed. Waiting: 3, Running: 5. Heap size: 14M, Heap free: 5M,
>>>>>           
>> Max
>>     
>>>>> heap: 254M
>>>>> 2010-02-25 17:12:16,469-0600 DEBUG TaskImpl
>>>>>           
>> Task(type=FILE_OPERATION,
>>     
>>>>> identity=urn:0-1-8-1-4-1267139524177) setting status to
>>>>>           
>> Submitting
>>     
>>>>> 2010-02-25 17:12:16,469-0600 DEBUG TaskImpl
>>>>>           
>> Task(type=FILE_OPERATION,
>>     
>>>>> identity=urn:0-1-8-1-4-1267139524177) setting status to Submitted
>>>>> 2010-02-25 17:12:16,469-0600 DEBUG TaskImpl
>>>>>           
>> Task(type=FILE_OPERATION,
>>     
>>>>> identity=urn:0-1-8-1-4-1267139524177) setting status to Active
>>>>> 2010-02-25 17:12:16,469-0600 DEBUG TaskImpl
>>>>>           
>> Task(type=FILE_OPERATION,
>>     
>>>>> identity=urn:0-1-8-1-4-1267139524177) setting status to Completed
>>>>> 2010-02-25 17:12:16,469-0600 INFO  LateBindingScheduler
>>>>> Task(type=FILE_OPERATION, identity=urn:0-1-8-1-4-1267139524177)
>>>>> Completed. Waiting: 4, Running: 4. Heap size: 14M, Heap free: 5M,
>>>>>           
>> Max
>>     
>>>>> heap: 254M
>>>>> 2010-02-25 17:12:16,469-0600 DEBUG TaskImpl
>>>>>           
>> Task(type=FILE_TRANSFER,
>>     
>>>>> identity=urn:0-1-8-1-3-1267139524181) setting status to
>>>>>           
>> Submitting
>>     
>>>>> 2010-02-25 17:12:16,470-0600 DEBUG TaskImpl
>>>>>           
>> Task(type=FILE_TRANSFER,
>>     
>>>>> identity=urn:0-1-8-1-3-1267139524181) setting status to Submitted
>>>>> 2010-02-25 17:12:16,470-0600 DEBUG TaskImpl
>>>>>           
>> Task(type=FILE_TRANSFER,
>>     
>>>>> identity=urn:0-1-8-1-1-1267139524179) setting status to
>>>>>           
>> Submitting
>>     
>>>>> 2010-02-25 17:12:16,470-0600 DEBUG TaskImpl
>>>>>           
>> Task(type=FILE_TRANSFER,
>>     
>>>>> identity=urn:0-1-8-1-1-1267139524179) setting status to Submitted
>>>>> 2010-02-25 17:12:16,470-0600 DEBUG TaskImpl
>>>>>           
>> Task(type=FILE_TRANSFER,
>>     
>>>>> identity=urn:0-1-8-1-2-1267139524183) setting status to
>>>>>           
>> Submitting
>>     
>>>>> 2010-02-25 17:12:16,470-0600 DEBUG TaskImpl
>>>>>           
>> Task(type=FILE_TRANSFER,
>>     
>>>>> identity=urn:0-1-8-1-2-1267139524183) setting status to Submitted
>>>>> 2010-02-25 17:12:16,470-0600 DEBUG TaskImpl
>>>>>           
>> Task(type=FILE_TRANSFER,
>>     
>>>>> identity=urn:0-1-8-1-2-1267139524183) setting status to Active
>>>>> 2010-02-25 17:12:16,471-0600 DEBUG TaskImpl
>>>>>           
>> Task(type=FILE_TRANSFER,
>>     
>>>>> identity=urn:0-1-8-1-2-1267139524183) setting status to Completed
>>>>> 2010-02-25 17:12:16,471-0600 INFO  LateBindingScheduler
>>>>> Task(type=FILE_TRANSFER, identity=urn:0-1-8-1-2-1267139524183)
>>>>> Completed. Waiting: 5, Running: 3. Heap size: 14M, Heap free: 5M,
>>>>>           
>> Max
>>     
>>>>> heap: 254M
>>>>> 2010-02-25 17:12:16,471-0600 DEBUG TaskImpl
>>>>>           
>> Task(type=FILE_TRANSFER,
>>     
>>>>> identity=urn:0-1-8-1-7-1267139524185) setting status to
>>>>>           
>> Submitting
>>     
>>>>> 2010-02-25 17:12:16,471-0600 DEBUG TaskImpl
>>>>>           
>> Task(type=FILE_TRANSFER,
>>     
>>>>> identity=urn:0-1-8-1-7-1267139524185) setting status to Submitted
>>>>> 2010-02-25 17:12:16,471-0600 DEBUG vdl:dostageout
>>>>>           
>> FILE_STAGE_OUT_END
>>     
>>>>> srcname=T0510D1.secseq
>>>>> srcdir=psim.loops-20100225-1712-3zrtb5i5/shared/output/data/
>>>>> srchost=localhost destdir=output/data/ desthost=localhost
>>>>> provider=file
>>>>> 2010-02-25 17:12:16,472-0600 DEBUG TaskImpl
>>>>>           
>> Task(type=FILE_TRANSFER,
>>     
>>>>> identity=urn:0-1-8-1-6-1267139524187) setting status to
>>>>>           
>> Submitting
>>     
>>>>> 2010-02-25 17:12:16,472-0600 DEBUG TaskImpl
>>>>>           
>> Task(type=FILE_TRANSFER,
>>     
>>>>> identity=urn:0-1-8-1-6-1267139524187) setting status to Submitted
>>>>> 2010-02-25 17:12:16,472-0600 DEBUG TaskImpl
>>>>>           
>> Task(type=FILE_OPERATION,
>>     
>>>>> identity=urn:0-1-8-1-2-1267139524198) setting status to
>>>>>           
>> Submitting
>>     
>>>>> 2010-02-25 17:12:16,472-0600 DEBUG TaskImpl
>>>>>           
>> Task(type=FILE_TRANSFER,
>>     
>>>>> identity=urn:0-1-8-1-6-1267139524187) setting status to Active
>>>>> 2010-02-25 17:12:16,472-0600 DEBUG TaskImpl
>>>>>           
>> Task(type=FILE_TRANSFER,
>>     
>>>>> identity=urn:0-1-8-1-1-1267139524179) setting status to Active
>>>>> 2010-02-25 17:12:16,473-0600 DEBUG TaskImpl
>>>>>           
>> Task(type=FILE_TRANSFER,
>>     
>>>>> identity=urn:0-1-8-1-6-1267139524187) setting status to Completed
>>>>> 2010-02-25 17:12:16,473-0600 INFO  LateBindingScheduler
>>>>> Task(type=FILE_TRANSFER, identity=urn:0-1-8-1-6-1267139524187)
>>>>> Completed. Waiting: 4, Running: 4. Heap size: 14M, Heap free: 5M,
>>>>>           
>> Max
>>     
>>>>> heap: 254M
>>>>> 2010-02-25 17:12:16,473-0600 DEBUG TaskImpl
>>>>>           
>> Task(type=FILE_TRANSFER,
>>     
>>>>> identity=urn:0-1-8-1-3-1267139524181) setting status to Active
>>>>> 2010-02-25 17:12:16,474-0600 DEBUG TaskImpl
>>>>>           
>> Task(type=FILE_TRANSFER,
>>     
>>>>> identity=urn:0-1-8-1-3-1267139524181) setting status to Completed
>>>>> 2010-02-25 17:12:16,474-0600 INFO  LateBindingScheduler
>>>>> Task(type=FILE_TRANSFER, identity=urn:0-1-8-1-3-1267139524181)
>>>>> Completed. Waiting: 4, Running: 3. Heap size: 14M, Heap free: 5M,
>>>>>           
>> Max
>>     
>>>>> heap: 254M
>>>>> 2010-02-25 17:12:16,475-0600 DEBUG vdl:dostageout
>>>>>           
>> FILE_STAGE_OUT_END
>>     
>>>>> srcname=T0510D1.range
>>>>> srcdir=psim.loops-20100225-1712-3zrtb5i5/shared/output/data/
>>>>> srchost=localhost destdir=output/data/ desthost=localhost
>>>>> provider=file
>>>>> 2010-02-25 17:12:16,475-0600 DEBUG vdl:dostageout
>>>>>           
>> FILE_STAGE_OUT_END
>>     
>>>>> srcname=T0510D1.params
>>>>> srcdir=psim.loops-20100225-1712-3zrtb5i5/shared/output/data/
>>>>> srchost=localhost destdir=output/data/ desthost=localhost
>>>>> provider=file
>>>>> 2010-02-25 17:12:16,476-0600 DEBUG TaskImpl
>>>>>           
>> Task(type=FILE_OPERATION,
>>     
>>>>> identity=urn:0-1-8-1-6-1267139524203) setting status to
>>>>>           
>> Submitting
>>     
>>>>> 2010-02-25 17:12:16,476-0600 DEBUG TaskImpl
>>>>>           
>> Task(type=FILE_OPERATION,
>>     
>>>>> identity=urn:0-1-8-1-6-1267139524203) setting status to Submitted
>>>>> 2010-02-25 17:12:16,476-0600 DEBUG TaskImpl
>>>>>           
>> Task(type=FILE_OPERATION,
>>     
>>>>> identity=urn:0-1-8-1-6-1267139524203) setting status to Active
>>>>> 2010-02-25 17:12:16,476-0600 DEBUG TaskImpl
>>>>>           
>> Task(type=FILE_OPERATION,
>>     
>>>>> identity=urn:0-1-8-1-6-1267139524203) setting status to Completed
>>>>> 2010-02-25 17:12:16,477-0600 INFO  LateBindingScheduler
>>>>> Task(type=FILE_OPERATION, identity=urn:0-1-8-1-6-1267139524203)
>>>>> Completed. Waiting: 2, Running: 6. Heap size: 14M, Heap free: 5M,
>>>>>           
>> Max
>>     
>>>>> heap: 254M
>>>>> 2010-02-25 17:12:16,477-0600 DEBUG TaskImpl
>>>>>           
>> Task(type=FILE_OPERATION,
>>     
>>>>> identity=urn:0-1-8-1-3-1267139524205) setting status to
>>>>>           
>> Submitting
>>     
>>>>> 2010-02-25 17:12:16,477-0600 DEBUG TaskImpl
>>>>>           
>> Task(type=FILE_OPERATION,
>>     
>>>>> identity=urn:0-1-8-1-3-1267139524205) setting status to Submitted
>>>>> 2010-02-25 17:12:16,477-0600 DEBUG TaskImpl
>>>>>           
>> Task(type=FILE_OPERATION,
>>     
>>>>> identity=urn:0-1-8-1-3-1267139524205) setting status to Active
>>>>> 2010-02-25 17:12:16,477-0600 DEBUG TaskImpl
>>>>>           
>> Task(type=FILE_OPERATION,
>>     
>>>>> identity=urn:0-1-8-1-3-1267139524205) setting status to Completed
>>>>> 2010-02-25 17:12:16,477-0600 INFO  LateBindingScheduler
>>>>> Task(type=FILE_OPERATION, identity=urn:0-1-8-1-3-1267139524205)
>>>>> Completed. Waiting: 2, Running: 5. Heap size: 14M, Heap free: 5M,
>>>>>           
>> Max
>>     
>>>>> heap: 254M
>>>>> 2010-02-25 17:12:16,478-0600 DEBUG TaskImpl
>>>>>           
>> Task(type=FILE_TRANSFER,
>>     
>>>>> identity=urn:0-1-8-1-8-1267139524191) setting status to
>>>>>           
>> Submitting
>>     
>>>>> 2010-02-25 17:12:16,478-0600 DEBUG TaskImpl
>>>>>           
>> Task(type=FILE_TRANSFER,
>>     
>>>>> identity=urn:0-1-8-1-8-1267139524191) setting status to Submitted
>>>>> 2010-02-25 17:12:16,478-0600 DEBUG TaskImpl
>>>>>           
>> Task(type=FILE_TRANSFER,
>>     
>>>>> identity=urn:0-1-8-1-9-1267139524189) setting status to
>>>>>           
>> Submitting
>>     
>>>>> 2010-02-25 17:12:16,478-0600 DEBUG TaskImpl
>>>>>           
>> Task(type=FILE_TRANSFER,
>>     
>>>>> identity=urn:0-1-8-1-9-1267139524189) setting status to Submitted
>>>>> 2010-02-25 17:12:16,478-0600 DEBUG TaskImpl
>>>>>           
>> Task(type=FILE_TRANSFER,
>>     
>>>>> identity=urn:0-1-8-1-8-1267139524191) setting status to Active
>>>>> 2010-02-25 17:12:16,479-0600 DEBUG TaskImpl
>>>>>           
>> Task(type=FILE_TRANSFER,
>>     
>>>>> identity=urn:0-1-8-1-8-1267139524191) setting status to Completed
>>>>> 2010-02-25 17:12:16,479-0600 INFO  LateBindingScheduler
>>>>> Task(type=FILE_TRANSFER, identity=urn:0-1-8-1-8-1267139524191)
>>>>> Completed. Waiting: 2, Running: 4. Heap size: 14M, Heap free: 5M,
>>>>>           
>> Max
>>     
>>>>> heap: 254M
>>>>> 2010-02-25 17:12:16,479-0600 DEBUG vdl:dostageout
>>>>>           
>> FILE_STAGE_OUT_END
>>     
>>>>> srcname=T0510D1.fasta
>>>>> srcdir=psim.loops-20100225-1712-3zrtb5i5/shared/output/data/
>>>>> srchost=localhost destdir=output/data/ desthost=localhost
>>>>> provider=file
>>>>> 2010-02-25 17:12:16,480-0600 DEBUG TaskImpl
>>>>>           
>> Task(type=FILE_OPERATION,
>>     
>>>>> identity=urn:0-1-8-1-8-1267139524208) setting status to
>>>>>           
>> Submitting
>>     
>>>>> 2010-02-25 17:12:16,480-0600 DEBUG TaskImpl
>>>>>           
>> Task(type=FILE_OPERATION,
>>     
>>>>> identity=urn:0-1-8-1-8-1267139524208) setting status to Submitted
>>>>> 2010-02-25 17:12:16,480-0600 DEBUG TaskImpl
>>>>>           
>> Task(type=FILE_OPERATION,
>>     
>>>>> identity=urn:0-1-8-1-8-1267139524208) setting status to Active
>>>>> 2010-02-25 17:12:16,481-0600 DEBUG TaskImpl
>>>>>           
>> Task(type=FILE_OPERATION,
>>     
>>>>> identity=urn:0-1-8-1-8-1267139524208) setting status to Completed
>>>>> 2010-02-25 17:12:16,481-0600 INFO  LateBindingScheduler
>>>>> Task(type=FILE_OPERATION, identity=urn:0-1-8-1-8-1267139524208)
>>>>> Completed. Waiting: 1, Running: 5. Heap size: 14M, Heap free: 4M,
>>>>>           
>> Max
>>     
>>>>> heap: 254M
>>>>> 2010-02-25 17:12:16,482-0600 DEBUG TaskImpl
>>>>>           
>> Task(type=FILE_TRANSFER,
>>     
>>>>> identity=urn:0-1-8-1-5-1267139524193) setting status to
>>>>>           
>> Submitting
>>     
>>>>> 2010-02-25 17:12:16,482-0600 DEBUG TaskImpl
>>>>>           
>> Task(type=FILE_TRANSFER,
>>     
>>>>> identity=urn:0-1-8-1-5-1267139524193) setting status to Submitted
>>>>> 2010-02-25 17:12:16,483-0600 DEBUG TaskImpl
>>>>>           
>> Task(type=FILE_TRANSFER,
>>     
>>>>> identity=urn:0-1-8-1-5-1267139524193) setting status to Active
>>>>> 2010-02-25 17:12:16,488-0600 DEBUG TaskImpl
>>>>>           
>> Task(type=FILE_TRANSFER,
>>     
>>>>> identity=urn:0-1-8-1-9-1267139524189) setting status to Active
>>>>> 2010-02-25 17:12:16,489-0600 DEBUG TaskImpl
>>>>>           
>> Task(type=FILE_TRANSFER,
>>     
>>>>> identity=urn:0-1-8-1-9-1267139524189) setting status to Completed
>>>>> 2010-02-25 17:12:16,489-0600 INFO  LateBindingScheduler
>>>>> Task(type=FILE_TRANSFER, identity=urn:0-1-8-1-9-1267139524189)
>>>>> Completed. Waiting: 1, Running: 4. Heap size: 14M, Heap free: 4M,
>>>>>           
>> Max
>>     
>>>>> heap: 254M
>>>>> 2010-02-25 17:12:16,490-0600 DEBUG TaskImpl
>>>>>           
>> Task(type=FILE_TRANSFER,
>>     
>>>>> identity=urn:0-1-8-1-4-1267139524195) setting st
>>>>>           
>> 2010-03-11 11:32:36,651-0600 DEBUG Loader Max heap: 266403840
>> 2010-03-11 11:32:36,652-0600 DEBUG Loader kmlversion is
>>     
>>> 783e9459-e981-4366-83ed-a7fe256e5175<
>>>       
>> 2010-03-11 11:32:36,652-0600 DEBUG Loader build version is
>>     
>>> 783e9459-e981-4366-83ed-a7fe256e5175<
>>>       
>> 2010-03-11 11:32:36,652-0600 DEBUG Loader Recompilation suppressed.
>> 2010-03-11 11:32:37,048-0600 INFO  VDL2ExecutionContext Stack dump:
>> Level 1
>> [iA = 0, iB = 0, bA = false, bB = false]
>> 	vdl:instanceconfig = Swift configuration []
>> 	vdl:operation = run
>> 	swift.home = /sandbox/wwj/oops/mike-swift/bin/..
>> 	PATH_SEPARATOR = /
>>
>>
>> 2010-03-11 11:32:37,993-0600 INFO  unknown Using sites file:
>> /sandbox/wwj/oops/mike-swift/bin/../etc/sites.xml
>> 2010-03-11 11:32:37,994-0600 INFO  unknown Using tc.data:
>> /sandbox/wwj/oops/mike-swift/bin/../etc/tc.data
>> 2010-03-11 11:32:38,183-0600 INFO  AbstractScheduler Setting resources
>> to: {coasterpads=coasterpads, localhost=localhost, Abe=Abe,
>> QueenBee=QueenBee}
>> 2010-03-11 11:32:38,857-0600 INFO  unknown Swift svn swift-r3255
>> (swift modified locally) cog-r2723
>>
>> 2010-03-11 11:32:38,858-0600 INFO  unknown RUNID
>> id=tag:benc at ci.uchicago.edu,2007:swift:run:20100311-1132-4huo5g08
>> 2010-03-11 11:32:38,977-0600 INFO  AbstractDataNode closed
>> org.griphyn.vdl.mapping.RootDataNode identifier
>> tag:benc at ci.uchicago.edu,2008:swift:dataset:20100311-1132-b8hclef8:720000000001
>> type string value=LoopModelResults.map dataset=unnamed SwiftScript
>> value (closed)
>> 2010-03-11 11:32:38,985-0600 INFO  New NEW
>> id=tag:benc at ci.uchicago.edu,2008:swift:dataset:20100311-1132-b8hclef8:720000000001
>> 2010-03-11 11:32:38,986-0600 INFO  AbstractDataNode closed
>> org.griphyn.vdl.mapping.RootDataNode identifier
>> tag:benc at ci.uchicago.edu,2008:swift:dataset:20100311-1132-b8hclef8:720000000002
>> type string value=input dataset=unnamed SwiftScript value (closed)
>> 2010-03-11 11:32:38,986-0600 INFO  New NEW
>> id=tag:benc at ci.uchicago.edu,2008:swift:dataset:20100311-1132-b8hclef8:720000000002
>> 2010-03-11 11:32:38,986-0600 INFO  AbstractDataNode closed
>> org.griphyn.vdl.mapping.RootDataNode identifier
>> tag:benc at ci.uchicago.edu,2008:swift:dataset:20100311-1132-b8hclef8:720000000003
>> type string value=indir dataset=unnamed SwiftScript value (closed)
>> 2010-03-11 11:32:38,986-0600 INFO  New NEW
>> id=tag:benc at ci.uchicago.edu,2008:swift:dataset:20100311-1132-b8hclef8:720000000003
>> 2010-03-11 11:32:38,987-0600 INFO  AbstractDataNode closed
>> org.griphyn.vdl.mapping.RootDataNode identifier
>> tag:benc at ci.uchicago.edu,2008:swift:dataset:20100311-1132-b8hclef8:720000000004
>> type string value=LoopModelData.map dataset=unnamed SwiftScript value
>> (closed)
>> 2010-03-11 11:32:38,987-0600 INFO  New NEW
>> id=tag:benc at ci.uchicago.edu,2008:swift:dataset:20100311-1132-b8hclef8:720000000004
>> 2010-03-11 11:32:38,987-0600 INFO  AbstractDataNode closed
>> org.griphyn.vdl.mapping.RootDataNode identifier
>> tag:benc at ci.uchicago.edu,2008:swift:dataset:20100311-1132-b8hclef8:720000000005
>> type string value=LoopModelIn.map dataset=unnamed SwiftScript value
>> (closed)
>> 2010-03-11 11:32:38,987-0600 INFO  New NEW
>> id=tag:benc at ci.uchicago.edu,2008:swift:dataset:20100311-1132-b8hclef8:720000000005
>> 2010-03-11 11:32:38,987-0600 INFO  AbstractDataNode closed
>> org.griphyn.vdl.mapping.RootDataNode identifier
>> tag:benc at ci.uchicago.edu,2008:swift:dataset:20100311-1132-b8hclef8:720000000006
>> type string value=protein dataset=unnamed SwiftScript value (closed)
>> 2010-03-11 11:32:38,987-0600 INFO  New NEW
>> id=tag:benc at ci.uchicago.edu,2008:swift:dataset:20100311-1132-b8hclef8:720000000006
>> 2010-03-11 11:32:38,988-0600 INFO  AbstractDataNode closed
>> org.griphyn.vdl.mapping.RootDataNode identifier
>> tag:benc at ci.uchicago.edu,2008:swift:dataset:20100311-1132-b8hclef8:720000000007
>> type string value=4 dataset=unnamed SwiftScript value (closed)
>> 2010-03-11 11:32:38,988-0600 INFO  New NEW
>> id=tag:benc at ci.uchicago.edu,2008:swift:dataset:20100311-1132-b8hclef8:720000000007
>> 2010-03-11 11:32:38,988-0600 INFO  AbstractDataNode closed
>> org.griphyn.vdl.mapping.RootDataNode identifier
>> tag:benc at ci.uchicago.edu,2008:swift:dataset:20100311-1132-b8hclef8:720000000008
>> type string value=nSim dataset=unnamed SwiftScript value (closed)
>> 2010-03-11 11:32:38,988-0600 INFO  New NEW
>> id=tag:benc at ci.uchicago.edu,2008:swift:dataset:20100311-1132-b8hclef8:720000000008
>> 2010-03-11 11:32:38,988-0600 INFO  AbstractDataNode closed
>> org.griphyn.vdl.mapping.RootDataNode identifier
>> tag:benc at ci.uchicago.edu,2008:swift:dataset:20100311-1132-b8hclef8:720000000009
>> type string value=output dataset=unnamed SwiftScript value (closed)
>> 2010-03-11 11:32:38,988-0600 INFO  New NEW
>> id=tag:benc at ci.uchicago.edu,2008:swift:dataset:20100311-1132-b8hclef8:720000000009
>> 2010-03-11 11:32:38,989-0600 INFO  AbstractDataNode closed
>> org.griphyn.vdl.mapping.RootDataNode identifier
>> tag:benc at ci.uchicago.edu,2008:swift:dataset:20100311-1132-b8hclef8:720000000010
>> type string value=outdir dataset=unnamed SwiftScript value (closed)
>> 2010-03-11 11:32:38,989-0600 INFO  New NEW
>> id=tag:benc at ci.uchicago.edu,2008:swift:dataset:20100311-1132-b8hclef8:720000000010
>> 2010-03-11 11:32:38,989-0600 INFO  AbstractDataNode closed
>> org.griphyn.vdl.mapping.RootDataNode identifier
>> tag:benc at ci.uchicago.edu,2008:swift:dataset:20100311-1132-b8hclef8:720000000011
>> type string value=LoopModelOutArray.map dataset=unnamed SwiftScript
>> value (closed)
>> 2010-03-11 11:32:38,989-0600 INFO  New NEW
>> id=tag:benc at ci.uchicago.edu,2008:swift:dataset:20100311-1132-b8hclef8:720000000011
>> 2010-03-11 11:32:38,989-0600 INFO  AbstractDataNode closed
>> org.griphyn.vdl.mapping.RootDataNode identifier
>> tag:benc at ci.uchicago.edu,2008:swift:dataset:20100311-1132-b8hclef8:720000000012
>> type int value=0.0 dataset=unnamed SwiftScript value (closed)
>> 2010-03-11 11:32:38,990-0600 INFO  New NEW
>> id=tag:benc at ci.uchicago.edu,2008:swift:dataset:20100311-1132-b8hclef8:720000000012
>> 2010-03-11 11:32:38,990-0600 INFO  AbstractDataNode closed
>> org.griphyn.vdl.mapping.RootDataNode identifier
>> tag:benc at ci.uchicago.edu,2008:swift:dataset:20100311-1132-b8hclef8:720000000013
>> type int value=1.0 dataset=unnamed SwiftScript value (closed)
>> 2010-03-11 11:32:38,990-0600 INFO  New NEW
>> id=tag:benc at ci.uchicago.edu,2008:swift:dataset:20100311-1132-b8hclef8:720000000013
>> 2010-03-11 11:32:39,007-0600 INFO  modelloops STARTCOMPOUND thread=0-1
>> name=ModelLoops
>> 2010-03-11 11:32:39,030-0600 INFO  New NEW
>> id=tag:benc at ci.uchicago.edu,2008:swift:dataset:20100311-1132-b8hclef8:720000000014
>> 2010-03-11 11:32:39,032-0600 INFO  New NEW
>> id=tag:benc at ci.uchicago.edu,2008:swift:dataset:20100311-1132-b8hclef8:720000000015
>> 2010-03-11 11:32:39,034-0600 INFO  New NEW
>> id=tag:benc at ci.uchicago.edu,2008:swift:dataset:20100311-1132-b8hclef8:720000000016
>> 2010-03-11 11:32:39,039-0600 INFO  New NEW
>> id=tag:benc at ci.uchicago.edu,2008:swift:dataset:20100311-1132-b8hclef8:720000000017
>> 2010-03-11 11:32:39,040-0600 INFO  New NEW
>> id=tag:benc at ci.uchicago.edu,2008:swift:dataset:20100311-1132-b8hclef8:720000000018
>> 2010-03-11 11:32:39,042-0600 INFO  AbstractDataNode Adding handle
>> listener "org.griphyn.vdl.mapping.RootDataNode identifier
>> tag:benc at ci.uchicago.edu,2008:swift:dataset:20100311-1132-b8hclef8:720000000019
>> type LoopModelIn with no value at dataset=modelIn (not closed)" to
>> "org.griphyn.vdl.mapping.RootDataNode identifier
>> tag:benc at ci.uchicago.edu,2008:swift:dataset:20100311-1132-b8hclef8:720000000018
>> type string with no value at dataset=swift#mapper#17007 (not closed)"
>> 2010-03-11 11:32:39,042-0600 INFO  New NEW
>> id=tag:benc at ci.uchicago.edu,2008:swift:dataset:20100311-1132-b8hclef8:720000000019
>> 2010-03-11 11:32:39,045-0600 INFO  New NEW
>> id=tag:benc at ci.uchicago.edu,2008:swift:dataset:20100311-1132-b8hclef8:720000000020
>> 2010-03-11 11:32:39,047-0600 INFO  AbstractDataNode Adding handle
>> listener "org.griphyn.vdl.mapping.RootDataNode identifier
>> tag:benc at ci.uchicago.edu,2008:swift:dataset:20100311-1132-b8hclef8:720000000021
>> type LoopModelData with no value at dataset=modelData (not closed)" to
>> "org.griphyn.vdl.mapping.RootDataNode identifier
>> tag:benc at ci.uchicago.edu,2008:swift:dataset:20100311-1132-b8hclef8:720000000020
>> type string with no value at dataset=swift#mapper#17009 (not closed)"
>> 2010-03-11 11:32:39,047-0600 INFO  New NEW
>> id=tag:benc at ci.uchicago.edu,2008:swift:dataset:20100311-1132-b8hclef8:720000000021
>> 2010-03-11 11:32:39,048-0600 INFO  New NEW
>> id=tag:benc at ci.uchicago.edu,2008:swift:dataset:20100311-1132-b8hclef8:720000000022
>> 2010-03-11 11:32:39,052-0600 INFO  AbstractDataNode Adding handle
>> listener "modelOut.$[]/0" to "org.griphyn.vdl.mapping.RootDataNode
>> identifier
>> tag:benc at ci.uchicago.edu,2008:swift:dataset:20100311-1132-b8hclef8:720000000022
>> type string with no value at dataset=swift#mapper#17011 (not closed)"
>> 2010-03-11 11:32:39,052-0600 INFO  New NEW
>> id=tag:benc at ci.uchicago.edu,2008:swift:dataset:20100311-1132-b8hclef8:720000000023
>> 2010-03-11 11:32:39,054-0600 INFO  New NEW
>> id=tag:benc at ci.uchicago.edu,2008:swift:dataset:20100311-1132-b8hclef8:720000000024
>> 2010-03-11 11:32:39,056-0600 INFO  AbstractDataNode Adding handle
>> listener "org.griphyn.vdl.mapping.RootDataNode identifier
>> tag:benc at ci.uchicago.edu,2008:swift:dataset:20100311-1132-b8hclef8:720000000025
>> type LoopModelResults with no value at dataset=modelResults (not
>> closed)" to "org.griphyn.vdl.mapping.RootDataNode identifier
>> tag:benc at ci.uchicago.edu,2008:swift:dataset:20100311-1132-b8hclef8:720000000024
>> type string with no value at dataset=swift#mapper#17013 (not closed)"
>> 2010-03-11 11:32:39,056-0600 INFO  New NEW
>> id=tag:benc at ci.uchicago.edu,2008:swift:dataset:20100311-1132-b8hclef8:720000000025
>> 2010-03-11 11:32:39,061-0600 INFO  SetFieldValue Setting
>> org.griphyn.vdl.mapping.RootDataNode identifier
>> tag:benc at ci.uchicago.edu,2008:swift:dataset:20100311-1132-b8hclef8:720000000018
>> type string with no value at dataset=swift#mapper#17007 (not closed)
>> to LoopModelIn.map
>> 2010-03-11 11:32:39,061-0600 INFO  AbstractDataNode closed
>> org.griphyn.vdl.mapping.RootDataNode identifier
>> tag:benc at ci.uchicago.edu,2008:swift:dataset:20100311-1132-b8hclef8:720000000026
>> type string value=1 dataset=unnamed SwiftScript value (closed)
>> 2010-03-11 11:32:39,061-0600 INFO  VDLFunction FUNCTION id=451000
>> name=arg
>> result=tag:benc at ci.uchicago.edu,2008:swift:dataset:20100311-1132-b8hclef8:720000000026
>> 2010-03-11 11:32:39,061-0600 INFO  VDLFunction FUNCTIONPARAMETER
>> id=451000
>> input=tag:benc at ci.uchicago.edu,2008:swift:dataset:20100311-1132-b8hclef8:720000000008
>> name=name
>> 2010-03-11 11:32:39,062-0600 INFO  VDLFunction FUNCTIONPARAMETER
>> id=451000
>> input=tag:benc at ci.uchicago.edu,2008:swift:dataset:20100311-1132-b8hclef8:720000000007
>> name=value
>> 2010-03-11 11:32:39,062-0600 INFO  SetFieldValue Setting
>> org.griphyn.vdl.mapping.RootDataNode identifier
>> tag:benc at ci.uchicago.edu,2008:swift:dataset:20100311-1132-b8hclef8:720000000020
>> type string with no value at dataset=swift#mapper#17009 (not closed)
>> to LoopModelData.map
>> 2010-03-11 11:32:39,062-0600 INFO  AbstractDataNode Notifying listener
>> "org.griphyn.vdl.mapping.RootDataNode identifier
>> tag:benc at ci.uchicago.edu,2008:swift:dataset:20100311-1132-b8hclef8:720000000021
>> type LoopModelData with no value at dataset=modelData (not closed)"
>> about "org.griphyn.vdl.mapping.RootDataNode identifier
>> tag:benc at ci.uchicago.edu,2008:swift:dataset:20100311-1132-b8hclef8:720000000020
>> type string value=LoopModelData.map dataset=swift#mapper#17009
>> (closed)"
>> 2010-03-11 11:32:39,062-0600 INFO  AbstractDataNode Adding handle
>> listener "org.griphyn.vdl.mapping.RootDataNode identifier
>> tag:benc at ci.uchicago.edu,2008:swift:dataset:20100311-1132-b8hclef8:720000000021
>> type LoopModelData with no value at dataset=modelData (not closed)" to
>> "org.griphyn.vdl.mapping.RootDataNode identifier
>> tag:benc at ci.uchicago.edu,2008:swift:dataset:20100311-1132-b8hclef8:720000000017
>> type string with no value at dataset=outdir (not closed)"
>> 2010-03-11 11:32:39,062-0600 INFO  AbstractDataNode closed
>> org.griphyn.vdl.mapping.RootDataNode identifier
>> tag:benc at ci.uchicago.edu,2008:swift:dataset:20100311-1132-b8hclef8:720000000020
>> type string value=LoopModelData.map dataset=swift#mapper#17009
>> (closed)
>> 2010-03-11 11:32:39,062-0600 INFO  SetFieldValue Setting
>> org.griphyn.vdl.mapping.RootDataNode identifier
>> tag:benc at ci.uchicago.edu,2008:swift:dataset:20100311-1132-b8hclef8:720000000022
>> type string with no value at dataset=swift#mapper#17011 (not closed)
>> to LoopModelOutArray.map
>> 2010-03-11 11:32:39,062-0600 INFO  AbstractDataNode Notifying listener
>> "modelOut.$[]/0" about "org.griphyn.vdl.mapping.RootDataNode
>> identifier
>> tag:benc at ci.uchicago.edu,2008:swift:dataset:20100311-1132-b8hclef8:720000000022
>> type string value=LoopModelOutArray.map dataset=swift#mapper#17011
>> (closed)"
>> 2010-03-11 11:32:39,063-0600 INFO  AbstractDataNode Adding handle
>> listener "modelOut.$[]/0" to "org.griphyn.vdl.mapping.RootDataNode
>> identifier
>> tag:benc at ci.uchicago.edu,2008:swift:dataset:20100311-1132-b8hclef8:720000000014
>> type int with no value at dataset=nSim (not closed)"
>> 2010-03-11 11:32:39,063-0600 INFO  AbstractDataNode closed
>> org.griphyn.vdl.mapping.RootDataNode identifier
>> tag:benc at ci.uchicago.edu,2008:swift:dataset:20100311-1132-b8hclef8:720000000022
>> type string value=LoopModelOutArray.map dataset=swift#mapper#17011
>> (closed)
>> 2010-03-11 11:32:39,063-0600 INFO  AbstractDataNode closed
>> org.griphyn.vdl.mapping.RootDataNode identifier
>> tag:benc at ci.uchicago.edu,2008:swift:dataset:20100311-1132-b8hclef8:720000000027
>> type string value=T0510D1 dataset=unnamed SwiftScript value (closed)
>> 2010-03-11 11:32:39,063-0600 INFO  VDLFunction FUNCTION id=451001
>> name=arg
>> result=tag:benc at ci.uchicago.edu,2008:swift:dataset:20100311-1132-b8hclef8:720000000027
>> 2010-03-11 11:32:39,063-0600 INFO  VDLFunction FUNCTIONPARAMETER
>> id=451001
>> input=tag:benc at ci.uchicago.edu,2008:swift:dataset:20100311-1132-b8hclef8:720000000006
>> name=name
>> 2010-03-11 11:32:39,063-0600 INFO  SetFieldValue Setting
>> org.griphyn.vdl.mapping.RootDataNode identifier
>> tag:benc at ci.uchicago.edu,2008:swift:dataset:20100311-1132-b8hclef8:720000000015
>> type string with no value at dataset=proteinId (not closed) to T0510D1
>> 2010-03-11 11:32:39,063-0600 INFO  AbstractDataNode closed
>> org.griphyn.vdl.mapping.RootDataNode identifier
>> tag:benc at ci.uchicago.edu,2008:swift:dataset:20100311-1132-b8hclef8:720000000015
>> type string value=T0510D1 dataset=proteinId (closed)
>> 2010-03-11 11:32:39,063-0600 INFO  AbstractDataNode Notifying listener
>> "org.griphyn.vdl.mapping.RootDataNode identifier
>> tag:benc at ci.uchicago.edu,2008:swift:dataset:20100311-1132-b8hclef8:720000000019
>> type LoopModelIn with no value at dataset=modelIn (not closed)" about
>> "org.griphyn.vdl.mapping.RootDataNode identifier
>> tag:benc at ci.uchicago.edu,2008:swift:dataset:20100311-1132-b8hclef8:720000000018
>> type string value=LoopModelIn.map dataset=swift#mapper#17007 (closed)"
>> 2010-03-11 11:32:39,063-0600 INFO  SetFieldValue Setting
>> org.griphyn.vdl.mapping.RootDataNode identifier
>> tag:benc at ci.uchicago.edu,2008:swift:dataset:20100311-1132-b8hclef8:720000000024
>> type string with no value at dataset=swift#mapper#17013 (not closed)
>> to LoopModelResults.map
>> 2010-03-11 11:32:39,064-0600 INFO  AbstractDataNode Adding handle
>> listener "org.griphyn.vdl.mapping.RootDataNode identifier
>> tag:benc at ci.uchicago.edu,2008:swift:dataset:20100311-1132-b8hclef8:720000000019
>> type LoopModelIn with no value at dataset=modelIn (not closed)" to
>> "org.griphyn.vdl.mapping.RootDataNode identifier
>> tag:benc at ci.uchicago.edu,2008:swift:dataset:20100311-1132-b8hclef8:720000000016
>> type string with no value at dataset=indir (not closed)"
>> 2010-03-11 11:32:39,064-0600 INFO  AbstractDataNode Notifying listener
>> "org.griphyn.vdl.mapping.RootDataNode identifier
>> tag:benc at ci.uchicago.edu,2008:swift:dataset:20100311-1132-b8hclef8:720000000025
>> type LoopModelResults with no value at dataset=modelResults (not
>> closed)" about "org.griphyn.vdl.mapping.RootDataNode identifier
>> tag:benc at ci.uchicago.edu,2008:swift:dataset:20100311-1132-b8hclef8:720000000024
>> type string value=LoopModelResults.map dataset=swift#mapper#17013
>> (closed)"
>> 2010-03-11 11:32:39,064-0600 INFO  AbstractDataNode closed
>> org.griphyn.vdl.mapping.RootDataNode identifier
>> tag:benc at ci.uchicago.edu,2008:swift:dataset:20100311-1132-b8hclef8:720000000018
>> type string value=LoopModelIn.map dataset=swift#mapper#17007 (closed)
>> 2010-03-11 11:32:39,064-0600 INFO  AbstractDataNode Adding handle
>> listener "org.griphyn.vdl.mapping.RootDataNode identifier
>> tag:benc at ci.uchicago.edu,2008:swift:dataset:20100311-1132-b8hclef8:720000000025
>> type LoopModelResults with no value at dataset=modelResults (not
>> closed)" to "org.griphyn.vdl.mapping.RootDataNode identifier
>> tag:benc at ci.uchicago.edu,2008:swift:dataset:20100311-1132-b8hclef8:720000000017
>> type string with no value at dataset=outdir (not closed)"
>> 2010-03-11 11:32:39,064-0600 INFO  AbstractDataNode closed
>> org.griphyn.vdl.mapping.RootDataNode identifier
>> tag:benc at ci.uchicago.edu,2008:swift:dataset:20100311-1132-b8hclef8:720000000024
>> type string value=LoopModelResults.map dataset=swift#mapper#17013
>> (closed)
>> 2010-03-11 11:32:39,064-0600 INFO  AbstractDataNode closed
>> org.griphyn.vdl.mapping.RootDataNode identifier
>> tag:benc at ci.uchicago.edu,2008:swift:dataset:20100311-1132-b8hclef8:720000000028
>> type string value=input dataset=unnamed SwiftScript value (closed)
>> 2010-03-11 11:32:39,065-0600 INFO  CloseDataset Partially closing
>> T0510D1 for statement 88013
>> 2010-03-11 11:32:39,065-0600 INFO  VDLFunction FUNCTION id=451002
>> name=arg
>> result=tag:benc at ci.uchicago.edu,2008:swift:dataset:20100311-1132-b8hclef8:720000000028
>> 2010-03-11 11:32:39,065-0600 INFO  CloseDataset var is T0510D1
>> 2010-03-11 11:32:39,065-0600 INFO  VDLFunction FUNCTIONPARAMETER
>> id=451002
>> input=tag:benc at ci.uchicago.edu,2008:swift:dataset:20100311-1132-b8hclef8:720000000003
>> name=name
>> 2010-03-11 11:32:39,065-0600 INFO  CloseDataset var hash is 23110255
>> 2010-03-11 11:32:39,065-0600 INFO  VDLFunction FUNCTIONPARAMETER
>> id=451002
>> input=tag:benc at ci.uchicago.edu,2008:swift:dataset:20100311-1132-b8hclef8:720000000002
>> name=value
>> 2010-03-11 11:32:39,065-0600 INFO  CloseDataset variable already
>> closed - skipping partial close processing
>> 2010-03-11 11:32:39,065-0600 INFO  SetFieldValue Setting
>> org.griphyn.vdl.mapping.RootDataNode identifier
>> tag:benc at ci.uchicago.edu,2008:swift:dataset:20100311-1132-b8hclef8:720000000016
>> type string with no value at dataset=indir (not closed) to input
>> 2010-03-11 11:32:39,065-0600 INFO  AbstractDataNode Notifying listener
>> "org.griphyn.vdl.mapping.RootDataNode identifier
>> tag:benc at ci.uchicago.edu,2008:swift:dataset:20100311-1132-b8hclef8:720000000019
>> type LoopModelIn with no value at dataset=modelIn (not closed)" about
>> "org.griphyn.vdl.mapping.RootDataNode identifier
>> tag:benc at ci.uchicago.edu,2008:swift:dataset:20100311-1132-b8hclef8:720000000016
>> type string value=input dataset=indir (closed)"
>> 2010-03-11 11:32:39,066-0600 INFO  AbstractDataNode closed
>> org.griphyn.vdl.mapping.RootDataNode identifier
>> tag:benc at ci.uchicago.edu,2008:swift:dataset:20100311-1132-b8hclef8:720000000029
>> type string value=output dataset=unnamed SwiftScript value (closed)
>> 2010-03-11 11:32:39,066-0600 INFO  VDLFunction FUNCTION id=451003
>> name=arg
>> result=tag:benc at ci.uchicago.edu,2008:swift:dataset:20100311-1132-b8hclef8:720000000029
>> 2010-03-11 11:32:39,069-0600 INFO  VDLFunction FUNCTIONPARAMETER
>> id=451003
>> input=tag:benc at ci.uchicago.edu,2008:swift:dataset:20100311-1132-b8hclef8:720000000010
>> name=name
>> 2010-03-11 11:32:39,069-0600 INFO  VDLFunction FUNCTIONPARAMETER
>> id=451003
>> input=tag:benc at ci.uchicago.edu,2008:swift:dataset:20100311-1132-b8hclef8:720000000009
>> name=value
>> 2010-03-11 11:32:39,069-0600 INFO  SetFieldValue Setting
>> org.griphyn.vdl.mapping.RootDataNode identifier
>> tag:benc at ci.uchicago.edu,2008:swift:dataset:20100311-1132-b8hclef8:720000000017
>> type string with no value at dataset=outdir (not closed) to output
>> 2010-03-11 11:32:39,069-0600 INFO  AbstractDataNode Notifying listener
>> "org.griphyn.vdl.mapping.RootDataNode identifier
>> tag:benc at ci.uchicago.edu,2008:swift:dataset:20100311-1132-b8hclef8:720000000021
>> type LoopModelData with no value at dataset=modelData (not closed)"
>> about "org.griphyn.vdl.mapping.RootDataNode identifier
>> tag:benc at ci.uchicago.edu,2008:swift:dataset:20100311-1132-b8hclef8:720000000017
>> type string value=output dataset=outdir (closed)"
>> 2010-03-11 11:32:39,135-0600 INFO  AbstractDataNode closed
>> org.griphyn.vdl.mapping.DataNode identifier
>> tag:benc at ci.uchicago.edu,2008:swift:dataset:20100311-1132-b8hclef8:720000000030
>> type PDB with no value at dataset=modelIn path=.pdb (closed)
>> 2010-03-11 11:32:39,137-0600 INFO  AbstractDataNode Found data
>> org.griphyn.vdl.mapping.RootDataNode identifier
>> tag:benc at ci.uchicago.edu,2008:swift:dataset:20100311-1132-b8hclef8:720000000019
>> type LoopModelIn with no value at dataset=modelIn (not closed)..pdb
>> 2010-03-11 11:32:39,137-0600 INFO  AbstractDataNode closed
>> org.griphyn.vdl.mapping.DataNode identifier
>> tag:benc at ci.uchicago.edu,2008:swift:dataset:20100311-1132-b8hclef8:720000000031
>> type Text with no value at dataset=modelIn path=.params (closed)
>> 2010-03-11 11:32:39,137-0600 INFO  AbstractDataNode Found data
>> org.griphyn.vdl.mapping.RootDataNode identifier
>> tag:benc at ci.uchicago.edu,2008:swift:dataset:20100311-1132-b8hclef8:720000000019
>> type LoopModelIn with no value at dataset=modelIn (not closed)..params
>> 2010-03-11 11:32:39,138-0600 INFO  AbstractDataNode closed
>> org.griphyn.vdl.mapping.DataNode identifier
>> tag:benc at ci.uchicago.edu,2008:swift:dataset:20100311-1132-b8hclef8:720000000032
>> type LoopRange with no value at dataset=modelIn path=.range (closed)
>> 2010-03-11 11:32:39,139-0600 INFO  AbstractDataNode Found data
>> org.griphyn.vdl.mapping.RootDataNode identifier
>> tag:benc at ci.uchicago.edu,2008:swift:dataset:20100311-1132-b8hclef8:720000000019
>> type LoopModelIn with no value at dataset=modelIn (not closed)..range
>> 2010-03-11 11:32:39,139-0600 INFO  AbstractDataNode closed
>> org.griphyn.vdl.mapping.RootDataNode identifier
>> tag:benc at ci.uchicago.edu,2008:swift:dataset:20100311-1132-b8hclef8:720000000019
>> type LoopModelIn with no value at dataset=modelIn (closed)
>> 2010-03-11 11:32:39,140-0600 INFO  AbstractDataNode closed
>> org.griphyn.vdl.mapping.RootDataNode identifier
>> tag:benc at ci.uchicago.edu,2008:swift:dataset:20100311-1132-b8hclef8:720000000016
>> type string value=input dataset=indir (closed)
>> 2010-03-11 11:32:39,141-0600 INFO  CloseDataset Partially closing
>> input for statement 88014
>> 2010-03-11 11:32:39,141-0600 INFO  CloseDataset var is input
>> 2010-03-11 11:32:39,141-0600 INFO  CloseDataset var hash is 22293109
>> 2010-03-11 11:32:39,141-0600 INFO  CloseDataset variable already
>> closed - skipping partial close processing
>> 2010-03-11 11:32:39,146-0600 INFO  loopprepare PROCEDURE line=112
>> thread=0-1-8 name=loopPrepare
>> 2010-03-11 11:32:39,146-0600 INFO  strtoi STARTCOMPOUND thread=0-1-0
>> name=strtoi
>> 2010-03-11 11:32:39,147-0600 INFO  AbstractDataNode Found mapped data
>> org.griphyn.vdl.mapping.RootDataNode identifier
>> tag:benc at ci.uchicago.edu,2008:swift:dataset:20100311-1132-b8hclef8:720000000021
>> type LoopModelData with no value at dataset=modelData (not
>> closed)..fasta
>> 2010-03-11 11:32:39,147-0600 INFO  AbstractDataNode Found mapped data
>> org.griphyn.vdl.mapping.RootDataNode identifier
>> tag:benc at ci.uchicago.edu,2008:swift:dataset:20100311-1132-b8hclef8:720000000021
>> type LoopModelData with no value at dataset=modelData (not
>> closed)..pdb
>> 2010-03-11 11:32:39,147-0600 INFO  AbstractDataNode Found mapped data
>> org.griphyn.vdl.mapping.RootDataNode identifier
>> tag:benc at ci.uchicago.edu,2008:swift:dataset:20100311-1132-b8hclef8:720000000021
>> type LoopModelData with no value at dataset=modelData (not
>> closed)..native
>> 2010-03-11 11:32:39,147-0600 INFO  AbstractDataNode Found mapped data
>> org.griphyn.vdl.mapping.RootDataNode identifier
>> tag:benc at ci.uchicago.edu,2008:swift:dataset:20100311-1132-b8hclef8:720000000021
>> type LoopModelData with no value at dataset=modelData (not
>> closed)..index
>> 2010-03-11 11:32:39,147-0600 INFO  AbstractDataNode Found mapped data
>> org.griphyn.vdl.mapping.RootDataNode identifier
>> tag:benc at ci.uchicago.edu,2008:swift:dataset:20100311-1132-b8hclef8:720000000021
>> type LoopModelData with no value at dataset=modelData (not
>> closed)..params
>> 2010-03-11 11:32:39,148-0600 INFO  AbstractDataNode Found mapped data
>> org.griphyn.vdl.mapping.RootDataNode identifier
>> tag:benc at ci.uchicago.edu,2008:swift:dataset:20100311-1132-b8hclef8:720000000021
>> type LoopModelData with no value at dataset=modelData (not
>> closed)..range
>> 2010-03-11 11:32:39,148-0600 INFO  AbstractDataNode Found mapped data
>> org.griphyn.vdl.mapping.RootDataNode identifier
>> tag:benc at ci.uchicago.edu,2008:swift:dataset:20100311-1132-b8hclef8:720000000021
>> type LoopModelData with no value at dataset=modelData (not
>> closed)..rama
>> 2010-03-11 11:32:39,148-0600 INFO  AbstractDataNode Found mapped data
>> org.griphyn.vdl.mapping.RootDataNode identifier
>> tag:benc at ci.uchicago.edu,2008:swift:dataset:20100311-1132-b8hclef8:720000000021
>> type LoopModelData with no value at dataset=modelData (not
>> closed)..map
>> 2010-03-11 11:32:39,148-0600 INFO  AbstractDataNode Found mapped data
>> org.griphyn.vdl.mapping.RootDataNode identifier
>> tag:benc at ci.uchicago.edu,2008:swift:dataset:20100311-1132-b8hclef8:720000000021
>> type LoopModelData with no value at dataset=modelData (not
>> closed)..secseq
>> 2010-03-11 11:32:39,148-0600 INFO  AbstractDataNode Notifying listener
>> "org.griphyn.vdl.mapping.RootDataNode identifier
>> tag:benc at ci.uchicago.edu,2008:swift:dataset:20100311-1132-b8hclef8:720000000025
>> type LoopModelResults with no value at dataset=modelResults (not
>> closed)" about "org.griphyn.vdl.mapping.RootDataNode identifier
>> tag:benc at ci.uchicago.edu,2008:swift:dataset:20100311-1132-b8hclef8:720000000017
>> type string value=output dataset=outdir (closed)"
>> 2010-03-11 11:32:39,148-0600 INFO  loopmodelanalysis PROCEDURE
>> line=122 thread=0-1-10 name=loopModelAnalysis
>> 2010-03-11 11:32:39,149-0600 INFO  doloopround STARTCOMPOUND
>> thread=0-1-9 name=doLoopRound
>> 2010-03-11 11:32:39,160-0600 INFO  New NEW
>> id=tag:benc at ci.uchicago.edu,2008:swift:dataset:20100311-1132-b8hclef8:720000000042
>> 2010-03-11 11:32:39,168-0600 INFO  AbstractDataNode Found mapped data
>> org.griphyn.vdl.mapping.RootDataNode identifier
>> tag:benc at ci.uchicago.edu,2008:swift:dataset:20100311-1132-b8hclef8:720000000025
>> type LoopModelResults with no value at dataset=modelResults (not
>> closed)..pwPlot
>> 2010-03-11 11:32:39,168-0600 INFO  AbstractDataNode Found mapped data
>> org.griphyn.vdl.mapping.RootDataNode identifier
>> tag:benc at ci.uchicago.edu,2008:swift:dataset:20100311-1132-b8hclef8:720000000025
>> type LoopModelResults with no value at dataset=modelResults (not
>> closed)..best
>> 2010-03-11 11:32:39,168-0600 INFO  AbstractDataNode Adding handle
>> listener "F/org.griphyn.vdl.mapping.RootDataNode identifier
>> tag:benc at ci.uchicago.edu,2008:swift:dataset:20100311-1132-b8hclef8:720000000014
>> type int with no value at dataset=nSim (not closed)" to
>> "org.griphyn.vdl.mapping.RootDataNode identifier
>> tag:benc at ci.uchicago.edu,2008:swift:dataset:20100311-1132-b8hclef8:720000000014
>> type int with no value at dataset=nSim (not closed)"
>> 2010-03-11 11:32:39,168-0600 INFO  AbstractDataNode Found mapped data
>> org.griphyn.vdl.mapping.RootDataNode identifier
>> tag:benc at ci.uchicago.edu,2008:swift:dataset:20100311-1132-b8hclef8:720000000025
>> type LoopModelResults with no value at dataset=modelResults (not
>> closed)..ligationPlot
>> 2010-03-11 11:32:39,168-0600 INFO  AbstractDataNode closed
>> org.griphyn.vdl.mapping.RootDataNode identifier
>> tag:benc at ci.uchicago.edu,2008:swift:dataset:20100311-1132-b8hclef8:720000000017
>> type string value=output dataset=outdir (closed)
>> 2010-03-11 11:32:39,169-0600 INFO  AbstractDataNode Adding handle
>> listener "F/modelOut.$[]/0" to
>> "org.griphyn.vdl.mapping.RootArrayDataNode identifier
>> tag:benc at ci.uchicago.edu,2008:swift:dataset:20100311-1132-b8hclef8:720000000023
>> type LoopModelOut[] with no value at dataset=modelOut (not closed)"
>> 2010-03-11 11:32:39,169-0600 INFO  CloseDataset Partially closing
>> output for statement 88015
>> 2010-03-11 11:32:39,169-0600 INFO  CloseDataset var is output
>> 2010-03-11 11:32:39,169-0600 INFO  CloseDataset var hash is 22608339
>> 2010-03-11 11:32:39,169-0600 INFO  CloseDataset variable already
>> closed - skipping partial close processing
>> 2010-03-11 11:32:39,170-0600 INFO  strtoi INTERNALPROC_START
>> thread=0-1-0-1 name=readData
>> 2010-03-11 11:32:39,172-0600 INFO  AbstractDataNode Adding handle
>> listener "F/org.griphyn.vdl.mapping.RootDataNode identifier
>> tag:benc at ci.uchicago.edu,2008:swift:dataset:20100311-1132-b8hclef8:720000000042
>> type file with no value at dataset=f (not closed)" to
>> "org.griphyn.vdl.mapping.RootDataNode identifier
>> tag:benc at ci.uchicago.edu,2008:swift:dataset:20100311-1132-b8hclef8:720000000042
>> type file with no value at dataset=f (not closed)"
>> 2010-03-11 11:32:39,173-0600 INFO  echos PROCEDURE line=68
>> thread=0-1-0-0 name=echos
>> 2010-03-11 11:32:39,181-0600 INFO  AbstractDataNode closed
>> org.griphyn.vdl.mapping.RootDataNode identifier
>> tag:benc at ci.uchicago.edu,2008:swift:dataset:20100311-1132-b8hclef8:720000000046
>> type string value=input/T0510D1.pdb dataset=unnamed SwiftScript value
>> (closed)
>> 2010-03-11 11:32:39,181-0600 INFO  VDLFunction FUNCTIONPARAMETER
>> id=451004
>> input=tag:benc at ci.uchicago.edu,2008:swift:dataset:20100311-1132-b8hclef8:720000000030
>> name=input
>> 2010-03-11 11:32:39,182-0600 INFO  VDLFunction FUNCTION id=451004
>> name=filename
>> result=tag:benc at ci.uchicago.edu,2008:swift:dataset:20100311-1132-b8hclef8:720000000046
>> 2010-03-11 11:32:39,182-0600 INFO  AbstractDataNode closed
>> org.griphyn.vdl.mapping.RootDataNode identifier
>> tag:benc at ci.uchicago.edu,2008:swift:dataset:20100311-1132-b8hclef8:720000000047
>> type string value=output/data//T0510D1.pdb dataset=unnamed SwiftScript
>> value (closed)
>> 2010-03-11 11:32:39,182-0600 INFO  VDLFunction FUNCTIONPARAMETER
>> id=451005
>> input=tag:benc at ci.uchicago.edu,2008:swift:dataset:20100311-1132-b8hclef8:720000000034
>> name=input
>> 2010-03-11 11:32:39,182-0600 INFO  VDLFunction FUNCTION id=451005
>> name=filename
>> result=tag:benc at ci.uchicago.edu,2008:swift:dataset:20100311-1132-b8hclef8:720000000047
>> 2010-03-11 11:32:39,183-0600 INFO  AbstractDataNode closed
>> org.griphyn.vdl.mapping.RootDataNode identifier
>> tag:benc at ci.uchicago.edu,2008:swift:dataset:20100311-1132-b8hclef8:720000000048
>> type string
>> value=_concurrent/f-19e32663-bd41-4000-a822-2d3f19dfccf1-1-0
>> dataset=unnamed SwiftScript value (closed)
>> 2010-03-11 11:32:39,183-0600 INFO  VDLFunction FUNCTIONPARAMETER
>> id=451006
>> input=tag:benc at ci.uchicago.edu,2008:swift:dataset:20100311-1132-b8hclef8:720000000042
>> name=input
>> 2010-03-11 11:32:39,183-0600 INFO  VDLFunction FUNCTION id=451006
>> name=filename
>> result=tag:benc at ci.uchicago.edu,2008:swift:dataset:20100311-1132-b8hclef8:720000000048
>> 2010-03-11 11:32:39,188-0600 INFO  vdl:execute START thread=0-1-0-0
>> tr=echo
>> 2010-03-11 11:32:39,188-0600 INFO  vdl:execute START thread=0-1-8
>> tr=PrepLoop
>> 2010-03-11 11:32:39,209-0600 INFO  WeightedHostScoreScheduler Sorted:
>> [localhost:10,000.000(99.854):0/3 overload: 0]
>> 2010-03-11 11:32:39,209-0600 INFO  WeightedHostScoreScheduler
>> CONTACT_SELECTED host=localhost, score=99.854
>> 2010-03-11 11:32:39,211-0600 INFO  WeightedHostScoreScheduler Sorted:
>> [localhost:10,000.000(99.854):1/3 overload: 0]
>> 2010-03-11 11:32:39,211-0600 INFO  WeightedHostScoreScheduler
>> CONTACT_SELECTED host=localhost, score=99.854
>> 2010-03-11 11:32:39,216-0600 INFO  GlobalSubmitQueue No global submit
>> throttle set. Using default (100)
>> 2010-03-11 11:32:39,232-0600 DEBUG TaskImpl Task(type=FILE_OPERATION,
>> identity=urn:0-1-0-0-1-1268328759207) setting status to Submitting
>> 2010-03-11 11:32:39,248-0600 DEBUG TaskImpl Task(type=FILE_OPERATION,
>> identity=urn:0-1-0-0-1-1268328759207) setting status to Submitted
>> 2010-03-11 11:32:39,248-0600 DEBUG TaskImpl Task(type=FILE_OPERATION,
>> identity=urn:0-1-0-0-1-1268328759207) setting status to Active
>> 2010-03-11 11:32:39,248-0600 DEBUG TaskImpl Task(type=FILE_OPERATION,
>> identity=urn:0-1-0-0-1-1268328759207) setting status to Completed
>> 2010-03-11 11:32:39,249-0600 INFO  LateBindingScheduler
>> Task(type=FILE_OPERATION, identity=urn:0-1-0-0-1-1268328759207)
>> Completed. Waiting: 0, Running: 0. Heap size: 9M, Heap free: 1M, Max
>> heap: 254M
>> 2010-03-11 11:32:39,251-0600 DEBUG TaskImpl Task(type=FILE_OPERATION,
>> identity=urn:0-1-0-0-1-1268328759210) setting status to Submitting
>> 2010-03-11 11:32:39,251-0600 DEBUG TaskImpl Task(type=FILE_OPERATION,
>> identity=urn:0-1-0-0-1-1268328759210) setting status to Submitted
>> 2010-03-11 11:32:39,251-0600 DEBUG TaskImpl Task(type=FILE_OPERATION,
>> identity=urn:0-1-0-0-1-1268328759210) setting status to Active
>> 2010-03-11 11:32:39,251-0600 DEBUG TaskImpl Task(type=FILE_OPERATION,
>> identity=urn:0-1-0-0-1-1268328759210) setting status to Completed
>> 2010-03-11 11:32:39,252-0600 INFO  LateBindingScheduler
>> Task(type=FILE_OPERATION, identity=urn:0-1-0-0-1-1268328759210)
>> Completed. Waiting: 0, Running: 0. Heap size: 9M, Heap free: 1M, Max
>> heap: 254M
>> 2010-03-11 11:32:39,254-0600 INFO  vdl:initshareddir START
>> host=localhost - Initializing shared directory
>> 2010-03-11 11:32:39,259-0600 DEBUG TaskImpl Task(type=FILE_OPERATION,
>> identity=urn:0-1-8-1-1268328759212) setting status to Submitting
>> 2010-03-11 11:32:39,259-0600 DEBUG TaskImpl Task(type=FILE_OPERATION,
>> identity=urn:0-1-8-1-1268328759212) setting status to Submitted
>> 2010-03-11 11:32:39,259-0600 DEBUG TaskImpl Task(type=FILE_OPERATION,
>> identity=urn:0-1-8-1-1268328759212) setting status to Active
>> 2010-03-11 11:32:39,260-0600 DEBUG TaskImpl Task(type=FILE_OPERATION,
>> identity=urn:0-1-8-1-1268328759212) setting status to Completed
>> 2010-03-11 11:32:39,260-0600 INFO  LateBindingScheduler
>> Task(type=FILE_OPERATION, identity=urn:0-1-8-1-1268328759212)
>> Completed. Waiting: 0, Running: 0. Heap size: 9M, Heap free: 0M, Max
>> heap: 254M
>> 2010-03-11 11:32:39,277-0600 DEBUG TaskImpl Task(type=FILE_TRANSFER,
>> identity=urn:0-1-8-1-1268328759215) setting status to Submitting
>> 2010-03-11 11:32:39,278-0600 DEBUG TaskImpl Task(type=FILE_TRANSFER,
>> identity=urn:0-1-8-1-1268328759215) setting status to Submitted
>> 2010-03-11 11:32:39,278-0600 DEBUG TaskImpl Task(type=FILE_TRANSFER,
>> identity=urn:0-1-8-1-1268328759215) setting status to Active
>> 2010-03-11 11:32:39,279-0600 DEBUG TaskImpl Task(type=FILE_TRANSFER,
>> identity=urn:0-1-8-1-1268328759215) setting status to Completed
>> 2010-03-11 11:32:39,279-0600 INFO  LateBindingScheduler
>> Task(type=FILE_TRANSFER, identity=urn:0-1-8-1-1268328759215)
>> Completed. Waiting: 0, Running: 0. Heap size: 9M, Heap free: 1M, Max
>> heap: 254M
>> 2010-03-11 11:32:39,281-0600 DEBUG TaskImpl Task(type=FILE_TRANSFER,
>> identity=urn:0-1-8-1-1268328759218) setting status to Submitting
>> 2010-03-11 11:32:39,281-0600 DEBUG TaskImpl Task(type=FILE_TRANSFER,
>> identity=urn:0-1-8-1-1268328759218) setting status to Submitted
>> 2010-03-11 11:32:39,281-0600 DEBUG TaskImpl Task(type=FILE_TRANSFER,
>> identity=urn:0-1-8-1-1268328759218) setting status to Active
>> 2010-03-11 11:32:39,282-0600 DEBUG TaskImpl Task(type=FILE_TRANSFER,
>> identity=urn:0-1-8-1-1268328759218) setting status to Completed
>> 2010-03-11 11:32:39,282-0600 INFO  LateBindingScheduler
>> Task(type=FILE_TRANSFER, identity=urn:0-1-8-1-1268328759218)
>> Completed. Waiting: 0, Running: 0. Heap size: 9M, Heap free: 1M, Max
>> heap: 254M
>> 2010-03-11 11:32:39,283-0600 DEBUG TaskImpl Task(type=FILE_OPERATION,
>> identity=urn:0-1-8-1-1268328759221) setting status to Submitting
>> 2010-03-11 11:32:39,283-0600 DEBUG TaskImpl Task(type=FILE_OPERATION,
>> identity=urn:0-1-8-1-1268328759221) setting status to Submitted
>> 2010-03-11 11:32:39,283-0600 DEBUG TaskImpl Task(type=FILE_OPERATION,
>> identity=urn:0-1-8-1-1268328759221) setting status to Active
>> 2010-03-11 11:32:39,283-0600 DEBUG TaskImpl Task(type=FILE_OPERATION,
>> identity=urn:0-1-8-1-1268328759221) setting status to Completed
>> 2010-03-11 11:32:39,283-0600 INFO  LateBindingScheduler
>> Task(type=FILE_OPERATION, identity=urn:0-1-8-1-1268328759221)
>> Completed. Waiting: 0, Running: 0. Heap size: 9M, Heap free: 1M, Max
>> heap: 254M
>> 2010-03-11 11:32:39,285-0600 DEBUG TaskImpl Task(type=FILE_OPERATION,
>> identity=urn:0-1-8-1-1268328759223) setting status to Submitting
>> 2010-03-11 11:32:39,285-0600 DEBUG TaskImpl Task(type=FILE_OPERATION,
>> identity=urn:0-1-8-1-1268328759223) setting status to Submitted
>> 2010-03-11 11:32:39,285-0600 DEBUG TaskImpl Task(type=FILE_OPERATION,
>> identity=urn:0-1-8-1-1268328759223) setting status to Active
>> 2010-03-11 11:32:39,285-0600 DEBUG TaskImpl Task(type=FILE_OPERATION,
>> identity=urn:0-1-8-1-1268328759223) setting status to Completed
>> 2010-03-11 11:32:39,286-0600 INFO  LateBindingScheduler
>> Task(type=FILE_OPERATION, identity=urn:0-1-8-1-1268328759223)
>> Completed. Waiting: 0, Running: 0. Heap size: 9M, Heap free: 1M, Max
>> heap: 254M
>> 2010-03-11 11:32:39,290-0600 DEBUG TaskImpl Task(type=FILE_OPERATION,
>> identity=urn:0-1-8-1-1268328759225) setting status to Submitting
>> 2010-03-11 11:32:39,290-0600 DEBUG TaskImpl Task(type=FILE_OPERATION,
>> identity=urn:0-1-8-1-1268328759225) setting status to Submitted
>> 2010-03-11 11:32:39,290-0600 DEBUG TaskImpl Task(type=FILE_OPERATION,
>> identity=urn:0-1-8-1-1268328759225) setting status to Active
>> 2010-03-11 11:32:39,290-0600 DEBUG TaskImpl Task(type=FILE_OPERATION,
>> identity=urn:0-1-8-1-1268328759225) setting status to Completed
>> 2010-03-11 11:32:39,291-0600 INFO  LateBindingScheduler
>> Task(type=FILE_OPERATION, identity=urn:0-1-8-1-1268328759225)
>> Completed. Waiting: 0, Running: 0. Heap size: 9M, Heap free: 1M, Max
>> heap: 254M
>> 2010-03-11 11:32:39,292-0600 INFO  vdl:initshareddir END
>> host=localhost - Done initializing shared directory
>> 2010-03-11 11:32:39,293-0600 DEBUG vdl:execute2 THREAD_ASSOCIATION
>> jobid=echo-mqsbkyoj thread=0-1-0-0-1 host=localhost
>> replicationGroup=kqsbkyoj
>> 2010-03-11 11:32:39,294-0600 DEBUG vdl:execute2 THREAD_ASSOCIATION
>> jobid=PrepLoop-nqsbkyoj thread=0-1-8-1 host=localhost
>> replicationGroup=lqsbkyoj
>> 2010-03-11 11:32:39,302-0600 INFO  vdl:createdirset START
>> jobid=echo-mqsbkyoj host=localhost - Initializing directory structure
>> 2010-03-11 11:32:39,303-0600 INFO  vdl:createdirset START
>> jobid=PrepLoop-nqsbkyoj host=localhost - Initializing directory
>> structure
>> 2010-03-11 11:32:39,304-0600 INFO  vdl:createdirs START
>> path=_concurrent dir=psim.loops-20100311-1132-4huo5g08/shared -
>> Creating directory structure
>> 2010-03-11 11:32:39,304-0600 INFO  vdl:createdirs START path=input
>> dir=psim.loops-20100311-1132-4huo5g08/shared - Creating directory
>> structure
>> 2010-03-11 11:32:39,305-0600 DEBUG TaskImpl Task(type=FILE_OPERATION,
>> identity=urn:0-1-0-0-1-1268328759227) setting status to Submitting
>> 2010-03-11 11:32:39,305-0600 DEBUG TaskImpl Task(type=FILE_OPERATION,
>> identity=urn:0-1-0-0-1-1268328759227) setting status to Submitted
>> 2010-03-11 11:32:39,305-0600 DEBUG TaskImpl Task(type=FILE_OPERATION,
>> identity=urn:0-1-0-0-1-1268328759227) setting status to Active
>> 2010-03-11 11:32:39,305-0600 DEBUG TaskImpl Task(type=FILE_OPERATION,
>> identity=urn:0-1-0-0-1-1268328759227) setting status to Completed
>> 2010-03-11 11:32:39,305-0600 DEBUG TaskImpl Task(type=FILE_OPERATION,
>> identity=urn:0-1-8-1-1268328759229) setting status to Submitting
>> 2010-03-11 11:32:39,305-0600 DEBUG TaskImpl Task(type=FILE_OPERATION,
>> identity=urn:0-1-8-1-1268328759229) setting status to Submitted
>> 2010-03-11 11:32:39,305-0600 DEBUG TaskImpl Task(type=FILE_OPERATION,
>> identity=urn:0-1-8-1-1268328759229) setting status to Active
>> 2010-03-11 11:32:39,306-0600 DEBUG TaskImpl Task(type=FILE_OPERATION,
>> identity=urn:0-1-8-1-1268328759229) setting status to Completed
>> 2010-03-11 11:32:39,306-0600 INFO  LateBindingScheduler
>> Task(type=FILE_OPERATION, identity=urn:0-1-8-1-1268328759229)
>> Completed. Waiting: 0, Running: 1. Heap size: 9M, Heap free: 0M, Max
>> heap: 254M
>> 2010-03-11 11:32:39,307-0600 INFO  LateBindingScheduler
>> Task(type=FILE_OPERATION, identity=urn:0-1-0-0-1-1268328759227)
>> Completed. Waiting: 0, Running: 0. Heap size: 9M, Heap free: 0M, Max
>> heap: 254M
>> 2010-03-11 11:32:39,307-0600 INFO  vdl:createdirset END
>> jobid=echo-mqsbkyoj - Done initializing directory structure
>> 2010-03-11 11:32:39,307-0600 INFO  vdl:createdirs START
>> path=output/data/ dir=psim.loops-20100311-1132-4huo5g08/shared -
>> Creating directory structure
>> 2010-03-11 11:32:39,311-0600 INFO  vdl:dostagein START
>> jobid=echo-mqsbkyoj - Staging in files
>> 2010-03-11 11:32:39,311-0600 INFO  vdl:dostagein END
>> jobid=echo-mqsbkyoj - Staging in finished
>> 2010-03-11 11:32:39,314-0600 DEBUG TaskImpl Task(type=FILE_OPERATION,
>> identity=urn:0-1-8-1-1268328759231) setting status to Submitting
>> 2010-03-11 11:32:39,314-0600 DEBUG vdl:execute2 JOB_START
>> jobid=echo-mqsbkyoj tr=echo arguments=[1]
>> tmpdir=psim.loops-20100311-1132-4huo5g08/jobs/m/echo-mqsbkyoj
>> host=localhost
>> 2010-03-11 11:32:39,314-0600 DEBUG TaskImpl Task(type=FILE_OPERATION,
>> identity=urn:0-1-8-1-1268328759231) setting status to Submitted
>> 2010-03-11 11:32:39,315-0600 DEBUG TaskImpl Task(type=FILE_OPERATION,
>> identity=urn:0-1-8-1-1268328759231) setting status to Active
>> 2010-03-11 11:32:39,316-0600 DEBUG TaskImpl Task(type=FILE_OPERATION,
>> identity=urn:0-1-8-1-1268328759231) setting status to Completed
>> 2010-03-11 11:32:39,317-0600 INFO  LateBindingScheduler
>> Task(type=FILE_OPERATION, identity=urn:0-1-8-1-1268328759231)
>> Completed. Waiting: 0, Running: 0. Heap size: 9M, Heap free: 1M, Max
>> heap: 254M
>> 2010-03-11 11:32:39,318-0600 INFO  vdl:createdirs START path=
>> dir=psim.loops-20100311-1132-4huo5g08/shared - Creating directory
>> structure
>> 2010-03-11 11:32:39,318-0600 DEBUG TaskImpl Task(type=FILE_OPERATION,
>> identity=urn:0-1-8-1-1268328759233) setting status to Submitting
>> 2010-03-11 11:32:39,318-0600 DEBUG TaskImpl Task(type=FILE_OPERATION,
>> identity=urn:0-1-8-1-1268328759233) setting status to Submitted
>> 2010-03-11 11:32:39,318-0600 DEBUG TaskImpl Task(type=FILE_OPERATION,
>> identity=urn:0-1-8-1-1268328759233) setting status to Active
>> 2010-03-11 11:32:39,319-0600 DEBUG TaskImpl Task(type=FILE_OPERATION,
>> identity=urn:0-1-8-1-1268328759233) setting status to Completed
>> 2010-03-11 11:32:39,319-0600 INFO  LateBindingScheduler
>> Task(type=FILE_OPERATION, identity=urn:0-1-8-1-1268328759233)
>> Completed. Waiting: 0, Running: 0. Heap size: 9M, Heap free: 0M, Max
>> heap: 254M
>> 2010-03-11 11:32:39,321-0600 INFO  vdl:createdirset END
>> jobid=PrepLoop-nqsbkyoj - Done initializing directory structure
>> 2010-03-11 11:32:39,322-0600 INFO  vdl:dostagein START
>> jobid=PrepLoop-nqsbkyoj - Staging in files
>> 2010-03-11 11:32:39,326-0600 DEBUG TaskImpl Task(type=FILE_OPERATION,
>> identity=urn:0-1-8-1-3-1268328759236) setting status to Submitting
>> 2010-03-11 11:32:39,326-0600 DEBUG TaskImpl Task(type=FILE_OPERATION,
>> identity=urn:0-1-8-1-3-1268328759236) setting status to Submitted
>> 2010-03-11 11:32:39,326-0600 DEBUG TaskImpl Task(type=FILE_OPERATION,
>> identity=urn:0-1-8-1-3-1268328759236) setting status to Active
>> 2010-03-11 11:32:39,328-0600 DEBUG TaskImpl Task(type=FILE_OPERATION,
>> identity=urn:0-1-8-1-1-1268328759237) setting status to Submitting
>> 2010-03-11 11:32:39,329-0600 DEBUG TaskImpl Task(type=FILE_OPERATION,
>> identity=urn:0-1-8-1-1-1268328759237) setting status to Submitted
>> 2010-03-11 11:32:39,329-0600 DEBUG TaskImpl Task(type=FILE_OPERATION,
>> identity=urn:0-1-8-1-1-1268328759237) setting status to Active
>> 2010-03-11 11:32:39,329-0600 DEBUG TaskImpl Task(type=FILE_OPERATION,
>> identity=urn:0-1-8-1-1-1268328759237) setting status to Completed
>> 2010-03-11 11:32:39,330-0600 INFO  LateBindingScheduler
>> Task(type=FILE_OPERATION, identity=urn:0-1-8-1-1-1268328759237)
>> Completed. Waiting: 0, Running: 2. Heap size: 9M, Heap free: 0M, Max
>> heap: 254M
>> 2010-03-11 11:32:39,331-0600 DEBUG TaskImpl Task(type=FILE_OPERATION,
>> identity=urn:0-1-8-1-3-1268328759236) setting status to Completed
>> 2010-03-11 11:32:39,331-0600 INFO  LateBindingScheduler
>> Task(type=FILE_OPERATION, identity=urn:0-1-8-1-3-1268328759236)
>> Completed. Waiting: 0, Running: 1. Heap size: 9M, Heap free: 0M, Max
>> heap: 254M
>> 2010-03-11 11:32:39,332-0600 DEBUG TaskImpl Task(type=FILE_OPERATION,
>> identity=urn:0-1-8-1-2-1268328759239) setting status to Submitting
>> 2010-03-11 11:32:39,332-0600 DEBUG TaskImpl Task(type=FILE_OPERATION,
>> identity=urn:0-1-8-1-2-1268328759239) setting status to Submitted
>> 2010-03-11 11:32:39,332-0600 DEBUG TaskImpl Task(type=FILE_OPERATION,
>> identity=urn:0-1-8-1-2-1268328759239) setting status to Active
>> 2010-03-11 11:32:39,333-0600 DEBUG TaskImpl Task(type=FILE_OPERATION,
>> identity=urn:0-1-8-1-2-1268328759239) setting status to Completed
>> 2010-03-11 11:32:39,335-0600 INFO  LateBindingScheduler
>> Task(type=FILE_OPERATION, identity=urn:0-1-8-1-2-1268328759239)
>> Completed. Waiting: 0, Running: 0. Heap size: 9M, Heap free: 0M, Max
>> heap: 254M
>> 2010-03-11 11:32:39,342-0600 INFO  Execute jobid=echo-mqsbkyoj
>> task=Task(type=JOB_SUBMISSION, identity=urn:0-1-0-0-1-1268328759242)
>> 2010-03-11 11:32:39,343-0600 DEBUG vdl:dostagein FILE_STAGE_IN_START
>> file=file://localhost/input/T0510D1.pdb srchost=localhost srcdir=input
>> srcname=T0510D1.pdb desthost=localhost
>> destdir=psim.loops-20100311-1132-4huo5g08/shared/input provider=file
>> 2010-03-11 11:32:39,344-0600 DEBUG vdl:dostagein FILE_STAGE_IN_START
>> file=file://localhost/input/T0510D1.range srchost=localhost
>> srcdir=input srcname=T0510D1.range desthost=localhost
>> destdir=psim.loops-20100311-1132-4huo5g08/shared/input provider=file
>> 2010-03-11 11:32:39,345-0600 DEBUG vdl:dostagein FILE_STAGE_IN_START
>> file=file://localhost/input/T0510D1.params srchost=localhost
>> srcdir=input srcname=T0510D1.params desthost=localhost
>> destdir=psim.loops-20100311-1132-4huo5g08/shared/input provider=file
>> 2010-03-11 11:32:39,346-0600 DEBUG TaskImpl Task(type=FILE_TRANSFER,
>> identity=urn:0-1-8-1-2-1268328759246) setting status to Submitting
>> 2010-03-11 11:32:39,346-0600 DEBUG TaskImpl Task(type=FILE_TRANSFER,
>> identity=urn:0-1-8-1-2-1268328759246) setting status to Submitted
>> 2010-03-11 11:32:39,346-0600 DEBUG TaskImpl Task(type=FILE_TRANSFER,
>> identity=urn:0-1-8-1-3-1268328759245) setting status to Submitting
>> 2010-03-11 11:32:39,346-0600 DEBUG TaskImpl Task(type=FILE_TRANSFER,
>> identity=urn:0-1-8-1-3-1268328759245) setting status to Submitted
>> 2010-03-11 11:32:39,346-0600 DEBUG TaskImpl Task(type=FILE_TRANSFER,
>> identity=urn:0-1-8-1-2-1268328759246) setting status to Active
>> 2010-03-11 11:32:39,346-0600 DEBUG TaskImpl Task(type=FILE_TRANSFER,
>> identity=urn:0-1-8-1-3-1268328759245) setting status to Active
>> 2010-03-11 11:32:39,347-0600 DEBUG TaskImpl Task(type=FILE_TRANSFER,
>> identity=urn:0-1-8-1-1-1268328759248) setting status to Submitting
>> 2010-03-11 11:32:39,347-0600 DEBUG TaskImpl Task(type=FILE_TRANSFER,
>> identity=urn:0-1-8-1-1-1268328759248) setting status to Submitted
>> 2010-03-11 11:32:39,348-0600 DEBUG TaskImpl Task(type=FILE_TRANSFER,
>> identity=urn:0-1-8-1-1-1268328759248) setting status to Active
>> 2010-03-11 11:32:39,349-0600 DEBUG TaskImpl Task(type=FILE_TRANSFER,
>> identity=urn:0-1-8-1-3-1268328759245) setting status to Completed
>> 2010-03-11 11:32:39,349-0600 INFO  LateBindingScheduler
>> Task(type=FILE_TRANSFER, identity=urn:0-1-8-1-3-1268328759245)
>> Completed. Waiting: 0, Running: 3. Heap size: 9M, Heap free: 0M, Max
>> heap: 254M
>> 2010-03-11 11:32:39,349-0600 DEBUG vdl:dostagein FILE_STAGE_IN_END
>> file=file://localhost/input/T0510D1.pdb srchost=localhost srcdir=input
>> srcname=T0510D1.pdb desthost=localhost
>> destdir=psim.loops-20100311-1132-4huo5g08/shared/input provider=file
>> 2010-03-11 11:32:39,350-0600 DEBUG TaskImpl Task(type=JOB_SUBMISSION,
>> identity=urn:0-1-0-0-1-1268328759242) setting status to Submitting
>> 2010-03-11 11:32:39,350-0600 DEBUG TaskImpl Task(type=FILE_TRANSFER,
>> identity=urn:0-1-8-1-1-1268328759248) setting status to Completed
>> 2010-03-11 11:32:39,351-0600 INFO  JobSubmissionTaskHandler Submitting
>> task Task(type=JOB_SUBMISSION, identity=urn:0-1-0-0-1-1268328759242)
>> 2010-03-11 11:32:39,351-0600 INFO  LateBindingScheduler
>> Task(type=FILE_TRANSFER, identity=urn:0-1-8-1-1-1268328759248)
>> Completed. Waiting: 0, Running: 2. Heap size: 9M, Heap free: 0M, Max
>> heap: 254M
>> 2010-03-11 11:32:39,351-0600 INFO  JobSubmissionTaskHandler Submitting
>> single job
>> 2010-03-11 11:32:39,351-0600 DEBUG TaskImpl Task(type=JOB_SUBMISSION,
>> identity=urn:0-1-0-0-1-1268328759242) setting status to Submitted
>> 2010-03-11 11:32:39,351-0600 DEBUG vdl:dostagein FILE_STAGE_IN_END
>> file=file://localhost/input/T0510D1.params srchost=localhost
>> srcdir=input srcname=T0510D1.params desthost=localhost
>> destdir=psim.loops-20100311-1132-4huo5g08/shared/input provider=file
>> 2010-03-11 11:32:39,356-0600 DEBUG TaskImpl Task(type=JOB_SUBMISSION,
>> identity=urn:0-1-0-0-1-1268328759242) setting status to Active
>> 2010-03-11 11:32:39,360-0600 DEBUG TaskImpl Task(type=FILE_TRANSFER,
>> identity=urn:0-1-8-1-2-1268328759246) setting status to Completed
>> 2010-03-11 11:32:39,361-0600 INFO  LateBindingScheduler
>> Task(type=FILE_TRANSFER, identity=urn:0-1-8-1-2-1268328759246)
>> Completed. Waiting: 0, Running: 1. Heap size: 9M, Heap free: 0M, Max
>> heap: 254M
>> 2010-03-11 11:32:39,361-0600 DEBUG vdl:dostagein FILE_STAGE_IN_END
>> file=file://localhost/input/T0510D1.range srchost=localhost
>> srcdir=input srcname=T0510D1.range desthost=localhost
>> destdir=psim.loops-20100311-1132-4huo5g08/shared/input provider=file
>> 2010-03-11 11:32:39,361-0600 INFO  vdl:dostagein END
>> jobid=PrepLoop-nqsbkyoj - Staging in finished
>> 2010-03-11 11:32:39,362-0600 DEBUG vdl:execute2 JOB_START
>> jobid=PrepLoop-nqsbkyoj tr=PrepLoop arguments=[input/T0510D1.pdb,
>> output/data//T0510D1.pdb]
>> tmpdir=psim.loops-20100311-1132-4huo5g08/jobs/n/PrepLoop-nqsbkyoj
>> host=localhost
>> 2010-03-11 11:32:39,376-0600 INFO  Execute jobid=PrepLoop-nqsbkyoj
>> task=Task(type=JOB_SUBMISSION, identity=urn:0-1-8-1-1268328759253)
>> 2010-03-11 11:32:39,377-0600 DEBUG TaskImpl Task(type=JOB_SUBMISSION,
>> identity=urn:0-1-8-1-1268328759253) setting status to Submitting
>> 2010-03-11 11:32:39,377-0600 INFO  JobSubmissionTaskHandler Submitting
>> task Task(type=JOB_SUBMISSION, identity=urn:0-1-8-1-1268328759253)
>> 2010-03-11 11:32:39,377-0600 INFO  JobSubmissionTaskHandler Submitting
>> single job
>> 2010-03-11 11:32:39,377-0600 DEBUG TaskImpl Task(type=JOB_SUBMISSION,
>> identity=urn:0-1-8-1-1268328759253) setting status to Submitted
>> 2010-03-11 11:32:39,381-0600 DEBUG TaskImpl Task(type=JOB_SUBMISSION,
>> identity=urn:0-1-8-1-1268328759253) setting status to Active
>> 2010-03-11 11:32:39,494-0600 DEBUG TaskImpl Task(type=JOB_SUBMISSION,
>> identity=urn:0-1-0-0-1-1268328759242) setting status to Completed
>> 2010-03-11 11:32:39,494-0600 INFO  LateBindingScheduler
>> Task(type=JOB_SUBMISSION, identity=urn:0-1-0-0-1-1268328759242)
>> Completed. Waiting: 0, Running: 1. Heap size: 9M, Heap free: 0M, Max
>> heap: 254M
>> 2010-03-11 11:32:39,497-0600 DEBUG vdl:checkjobstatus START
>> jobid=echo-mqsbkyoj
>> 2010-03-11 11:32:39,498-0600 DEBUG TaskImpl Task(type=FILE_OPERATION,
>> identity=urn:0-1-0-0-1-1268328759255) setting status to Submitting
>> 2010-03-11 11:32:39,498-0600 DEBUG TaskImpl Task(type=FILE_OPERATION,
>> identity=urn:0-1-0-0-1-1268328759255) setting status to Submitted
>> 2010-03-11 11:32:39,498-0600 DEBUG TaskImpl Task(type=FILE_OPERATION,
>> identity=urn:0-1-0-0-1-1268328759255) setting status to Active
>> 2010-03-11 11:32:39,498-0600 DEBUG TaskImpl Task(type=FILE_OPERATION,
>> identity=urn:0-1-0-0-1-1268328759255) setting status to Completed
>> 2010-03-11 11:32:39,498-0600 INFO  LateBindingScheduler
>> Task(type=FILE_OPERATION, identity=urn:0-1-0-0-1-1268328759255)
>> Completed. Waiting: 0, Running: 1. Heap size: 9M, Heap free: 0M, Max
>> heap: 254M
>> 2010-03-11 11:32:39,499-0600 INFO  vdl:checkjobstatus SUCCESS
>> jobid=echo-mqsbkyoj - Success file found
>> 2010-03-11 11:32:39,499-0600 DEBUG vdl:execute2 STAGING_OUT
>> jobid=echo-mqsbkyoj
>> 2010-03-11 11:32:39,500-0600 INFO  vdl:dostageout START
>> jobid=echo-mqsbkyoj - Staging out files
>> 2010-03-11 11:32:39,505-0600 DEBUG vdl:dostageout FILE_STAGE_OUT_START
>> srcname=f-19e32663-bd41-4000-a822-2d3f19dfccf1-1-0
>> srcdir=psim.loops-20100311-1132-4huo5g08/shared/_concurrent
>> srchost=localhost destdir=_concurrent desthost=localhost provider=file
>> 2010-03-11 11:32:39,506-0600 DEBUG TaskImpl Task(type=FILE_OPERATION,
>> identity=urn:0-1-0-0-1-1-1268328759257) setting status to Submitting
>> 2010-03-11 11:32:39,506-0600 DEBUG TaskImpl Task(type=FILE_OPERATION,
>> identity=urn:0-1-0-0-1-1-1268328759257) setting status to Submitted
>> 2010-03-11 11:32:39,506-0600 DEBUG TaskImpl Task(type=FILE_OPERATION,
>> identity=urn:0-1-0-0-1-1-1268328759257) setting status to Active
>> 2010-03-11 11:32:39,507-0600 DEBUG TaskImpl Task(type=FILE_OPERATION,
>> identity=urn:0-1-0-0-1-1-1268328759257) setting status to Completed
>> 2010-03-11 11:32:39,507-0600 INFO  LateBindingScheduler
>> Task(type=FILE_OPERATION, identity=urn:0-1-0-0-1-1-1268328759257)
>> Completed. Waiting: 0, Running: 1. Heap size: 9M, Heap free: 0M, Max
>> heap: 254M
>> 2010-03-11 11:32:39,508-0600 DEBUG TaskImpl Task(type=FILE_TRANSFER,
>> identity=urn:0-1-0-0-1-1-1268328759259) setting status to Submitting
>> 2010-03-11 11:32:39,508-0600 DEBUG TaskImpl Task(type=FILE_TRANSFER,
>> identity=urn:0-1-0-0-1-1-1268328759259) setting status to Submitted
>> 2010-03-11 11:32:39,508-0600 DEBUG TaskImpl Task(type=FILE_TRANSFER,
>> identity=urn:0-1-0-0-1-1-1268328759259) setting status to Active
>> 2010-03-11 11:32:39,509-0600 DEBUG TaskImpl Task(type=FILE_TRANSFER,
>> identity=urn:0-1-0-0-1-1-1268328759259) setting status to Completed
>> 2010-03-11 11:32:39,509-0600 INFO  LateBindingScheduler
>> Task(type=FILE_TRANSFER, identity=urn:0-1-0-0-1-1-1268328759259)
>> Completed. Waiting: 0, Running: 1. Heap size: 9M, Heap free: 0M, Max
>> heap: 254M
>> 2010-03-11 11:32:39,510-0600 DEBUG vdl:dostageout FILE_STAGE_OUT_END
>> srcname=f-19e32663-bd41-4000-a822-2d3f19dfccf1-1-0
>> srcdir=psim.loops-20100311-1132-4huo5g08/shared/_concurrent
>> srchost=localhost destdir=_concurrent desthost=localhost provider=file
>> 2010-03-11 11:32:39,510-0600 DEBUG TaskImpl Task(type=FILE_OPERATION,
>> identity=urn:0-1-0-0-1-1-1268328759262) setting status to Submitting
>> 2010-03-11 11:32:39,511-0600 DEBUG TaskImpl Task(type=FILE_OPERATION,
>> identity=urn:0-1-0-0-1-1-1268328759262) setting status to Submitted
>> 2010-03-11 11:32:39,511-0600 DEBUG TaskImpl Task(type=FILE_OPERATION,
>> identity=urn:0-1-0-0-1-1-1268328759262) setting status to Active
>> 2010-03-11 11:32:39,511-0600 DEBUG TaskImpl Task(type=FILE_OPERATION,
>> identity=urn:0-1-0-0-1-1-1268328759262) setting status to Completed
>> 2010-03-11 11:32:39,511-0600 INFO  LateBindingScheduler
>> Task(type=FILE_OPERATION, identity=urn:0-1-0-0-1-1-1268328759262)
>> Completed. Waiting: 0, Running: 1. Heap size: 9M, Heap free: 0M, Max
>> heap: 254M
>> 2010-03-11 11:32:39,514-0600 INFO  vdl:dostageout END
>> jobid=echo-mqsbkyoj - Staging out finished
>> 2010-03-11 11:32:39,518-0600 DEBUG TaskImpl Task(type=FILE_TRANSFER,
>> identity=urn:0-1-0-0-1-1268328759264) setting status to Submitting
>> 2010-03-11 11:32:39,518-0600 DEBUG TaskImpl Task(type=FILE_TRANSFER,
>> identity=urn:0-1-0-0-1-1268328759264) setting status to Submitted
>> 2010-03-11 11:32:39,518-0600 DEBUG TaskImpl Task(type=FILE_TRANSFER,
>> identity=urn:0-1-0-0-1-1268328759264) setting status to Active
>> 2010-03-11 11:32:39,519-0600 DEBUG TaskImpl Task(type=FILE_TRANSFER,
>> identity=urn:0-1-0-0-1-1268328759264) setting status to Completed
>> 2010-03-11 11:32:39,519-0600 INFO  LateBindingScheduler
>> Task(type=FILE_TRANSFER, identity=urn:0-1-0-0-1-1268328759264)
>> Completed. Waiting: 0, Running: 1. Heap size: 9M, Heap free: 0M, Max
>> heap: 254M
>> 2010-03-11 11:32:39,520-0600 DEBUG vdl:execute2 JOB_END
>> jobid=echo-mqsbkyoj
>> 2010-03-11 11:32:39,522-0600 INFO  vdl:execute END_SUCCESS
>> thread=0-1-0-0 tr=echo
>> 2010-03-11 11:32:39,676-0600 INFO  CloseDataset Closing
>> org.griphyn.vdl.mapping.RootDataNode identifier
>> tag:benc at ci.uchicago.edu,2008:swift:dataset:20100311-1132-b8hclef8:720000000042
>> type file with no value at dataset=f (not closed)
>> 2010-03-11 11:32:39,676-0600 INFO  AbstractDataNode Notifying listener
>> "F/org.griphyn.vdl.mapping.RootDataNode identifier
>> tag:benc at ci.uchicago.edu,2008:swift:dataset:20100311-1132-b8hclef8:720000000042
>> type file with no value at dataset=f (closed)" about
>> "org.griphyn.vdl.mapping.RootDataNode identifier
>> tag:benc at ci.uchicago.edu,2008:swift:dataset:20100311-1132-b8hclef8:720000000042
>> type file with no value at dataset=f (closed)"
>> 2010-03-11 11:32:39,677-0600 INFO  AbstractDataNode closed
>> org.griphyn.vdl.mapping.RootDataNode identifier
>> tag:benc at ci.uchicago.edu,2008:swift:dataset:20100311-1132-b8hclef8:720000000042
>> type file with no value at dataset=f (closed)
>> 2010-03-11 11:32:39,677-0600 INFO  echos PROCEDURE_END line=68
>> 2010-03-11 11:32:39,681-0600 INFO  AbstractDataNode Notifying listener
>> "modelOut.$[]/0" about "org.griphyn.vdl.mapping.RootDataNode
>> identifier
>> tag:benc at ci.uchicago.edu,2008:swift:dataset:20100311-1132-b8hclef8:720000000014
>> type int value=1.0 dataset=nSim (closed)"
>> 2010-03-11 11:32:39,681-0600 INFO  CloseDataset Partially closing
>> org.griphyn.vdl.mapping.RootDataNode identifier
>> tag:benc at ci.uchicago.edu,2008:swift:dataset:20100311-1132-b8hclef8:720000000042
>> type file with no value at dataset=f (closed) for statement 88004
>> 2010-03-11 11:32:39,681-0600 INFO  CloseDataset var is
>> org.griphyn.vdl.mapping.RootDataNode identifier
>> tag:benc at ci.uchicago.edu,2008:swift:dataset:20100311-1132-b8hclef8:720000000042
>> type file with no value at dataset=f (closed)
>> 2010-03-11 11:32:39,681-0600 INFO  CloseDataset var hash is 7971559
>> 2010-03-11 11:32:39,681-0600 INFO  CloseDataset variable already
>> closed - skipping partial close processing
>> 2010-03-11 11:32:39,739-0600 INFO  AbstractDataNode Found mapped data
>> modelOut.$[]/1.[0].cfg
>> 2010-03-11 11:32:39,739-0600 INFO  AbstractDataNode Found mapped data
>> modelOut.$[]/1.[0].pdt
>> 2010-03-11 11:32:39,739-0600 INFO  AbstractDataNode Found mapped data
>> modelOut.$[]/1.[0].log
>> 2010-03-11 11:32:39,739-0600 INFO  AbstractDataNode Found mapped data
>> modelOut.$[]/1.[0].pdb
>> 2010-03-11 11:32:39,739-0600 INFO  AbstractDataNode Notifying listener
>> "F/modelOut.$[]/1" about "org.griphyn.vdl.mapping.RootArrayDataNode
>> identifier
>> tag:benc at ci.uchicago.edu,2008:swift:dataset:20100311-1132-b8hclef8:720000000023
>> type LoopModelOut[] with no value at dataset=modelOut (closed)"
>> 2010-03-11 11:32:39,740-0600 INFO  AbstractDataNode closed
>> org.griphyn.vdl.mapping.RootArrayDataNode identifier
>> tag:benc at ci.uchicago.edu,2008:swift:dataset:20100311-1132-b8hclef8:720000000023
>> type LoopModelOut[] with no value at dataset=modelOut (closed)
>> 2010-03-11 11:32:39,740-0600 INFO  AbstractDataNode Notifying listener
>> "F/1" about "org.griphyn.vdl.mapping.RootDataNode identifier
>> tag:benc at ci.uchicago.edu,2008:swift:dataset:20100311-1132-b8hclef8:720000000014
>> type int value=1.0 dataset=nSim (closed)"
>> 2010-03-11 11:32:39,740-0600 INFO  AbstractDataNode closed
>> org.griphyn.vdl.mapping.RootDataNode identifier
>> tag:benc at ci.uchicago.edu,2008:swift:dataset:20100311-1132-b8hclef8:720000000014
>> type int value=1.0 dataset=nSim (closed)
>> 2010-03-11 11:32:39,741-0600 INFO  AbstractDataNode closed
>> org.griphyn.vdl.mapping.RootDataNode identifier
>> tag:benc at ci.uchicago.edu,2008:swift:dataset:20100311-1132-b8hclef8:720000000054
>> type int value=0.0 dataset=unnamed SwiftScript value (closed)
>> 2010-03-11 11:32:39,741-0600 INFO  strtoi INTERNALPROC_END
>> thread=0-1-0-1
>> 2010-03-11 11:32:39,741-0600 INFO  CloseDataset Closing 1
>> 2010-03-11 11:32:39,742-0600 INFO  strtoi ENDCOMPOUND thread=0-1-0
>> 2010-03-11 11:32:39,742-0600 INFO  AbstractDataNode Adding handle
>> listener "F/org.griphyn.vdl.mapping.DataNode identifier
>> tag:benc at ci.uchicago.edu,2008:swift:dataset:20100311-1132-b8hclef8:720000000052
>> type ModelLog with no value at dataset=modelOut path=[0].log (not
>> closed)" to "org.griphyn.vdl.mapping.DataNode identifier
>> tag:benc at ci.uchicago.edu,2008:swift:dataset:20100311-1132-b8hclef8:720000000052
>> type ModelLog with no value at dataset=modelOut path=[0].log (not
>> closed)"
>> 2010-03-11 11:32:39,749-0600 INFO  CloseDataset Partially closing 1
>> for statement 88012
>> 2010-03-11 11:32:39,749-0600 INFO  CloseDataset var is 1
>> 2010-03-11 11:32:39,749-0600 INFO  CloseDataset var hash is 29094346
>> 2010-03-11 11:32:39,749-0600 INFO  CloseDataset variable already
>> closed - skipping partial close processing
>> 2010-03-11 11:32:39,752-0600 INFO  AbstractDataNode closed
>> org.griphyn.vdl.mapping.RootDataNode identifier
>> tag:benc at ci.uchicago.edu,2008:swift:dataset:20100311-1132-b8hclef8:720000000056
>> type int value=0.0 dataset=unnamed SwiftScript value (closed)
>> 2010-03-11 11:32:39,752-0600 INFO  AbstractDataNode closed
>> org.griphyn.vdl.karajan.lib.Range$1 identifier
>> tag:benc at ci.uchicago.edu,2008:swift:dataset:20100311-1132-b8hclef8:720000000055
>> type int[] with no value at dataset=unnamed SwiftScript value (closed)
>> 2010-03-11 11:32:39,753-0600 INFO  doloopround FOREACH_IT_START
>> line=130 thread=0-1-9-1-1
>> 2010-03-11 11:32:39,754-0600 INFO  doloopround SCOPE thread=0-1-9-1-1
>> 2010-03-11 11:32:39,756-0600 INFO  loopmodel PROCEDURE line=117
>> thread=0-1-9-1-1-1 name=loopModel
>> 2010-03-11 11:32:39,757-0600 INFO  AbstractDataNode Adding handle
>> listener "F/org.griphyn.vdl.mapping.DataNode identifier
>> tag:benc at ci.uchicago.edu,2008:swift:dataset:20100311-1132-b8hclef8:720000000036
>> type RamaIndex with no value at dataset=modelData path=.index (not
>> closed)" to "org.griphyn.vdl.mapping.DataNode identifier
>> tag:benc at ci.uchicago.edu,2008:swift:dataset:20100311-1132-b8hclef8:720000000036
>> type RamaIndex with no value at dataset=modelData path=.index (not
>> closed)"
>> 2010-03-11 11:32:51,421-0600 DEBUG TaskImpl Task(type=JOB_SUBMISSION,
>> identity=urn:0-1-8-1-1268328759253) setting status to Completed
>> 2010-03-11 11:32:51,421-0600 INFO  LateBindingScheduler
>> Task(type=JOB_SUBMISSION, identity=urn:0-1-8-1-1268328759253)
>> Completed. Waiting: 0, Running: 0. Heap size: 9M, Heap free: 0M, Max
>> heap: 254M
>> 2010-03-11 11:32:51,422-0600 DEBUG vdl:checkjobstatus START
>> jobid=PrepLoop-nqsbkyoj
>> 2010-03-11 11:32:51,423-0600 DEBUG TaskImpl Task(type=FILE_OPERATION,
>> identity=urn:0-1-8-1-1268328759267) setting status to Submitting
>> 2010-03-11 11:32:51,424-0600 DEBUG TaskImpl Task(type=FILE_OPERATION,
>> identity=urn:0-1-8-1-1268328759267) setting status to Submitted
>> 2010-03-11 11:32:51,424-0600 DEBUG TaskImpl Task(type=FILE_OPERATION,
>> identity=urn:0-1-8-1-1268328759267) setting status to Active
>> 2010-03-11 11:32:51,425-0600 DEBUG TaskImpl Task(type=FILE_OPERATION,
>> identity=urn:0-1-8-1-1268328759267) setting status to Completed
>> 2010-03-11 11:32:51,425-0600 INFO  LateBindingScheduler
>> Task(type=FILE_OPERATION, identity=urn:0-1-8-1-1268328759267)
>> Completed. Waiting: 0, Running: 0. Heap size: 9M, Heap free: 0M, Max
>> heap: 254M
>> 2010-03-11 11:32:51,425-0600 INFO  vdl:checkjobstatus SUCCESS
>> jobid=PrepLoop-nqsbkyoj - Success file found
>> 2010-03-11 11:32:51,425-0600 DEBUG vdl:execute2 STAGING_OUT
>> jobid=PrepLoop-nqsbkyoj
>> 2010-03-11 11:32:51,426-0600 INFO  vdl:dostageout START
>> jobid=PrepLoop-nqsbkyoj - Staging out files
>> 2010-03-11 11:32:51,438-0600 DEBUG vdl:dostageout FILE_STAGE_OUT_START
>> srcname=T0510D1.secseq
>> srcdir=psim.loops-20100311-1132-4huo5g08/shared/output/data/
>> srchost=localhost destdir=output/data/ desthost=localhost
>> provider=file
>> 2010-03-11 11:32:51,438-0600 DEBUG vdl:dostageout FILE_STAGE_OUT_START
>> srcname=T0510D1.rama_map
>> srcdir=psim.loops-20100311-1132-4huo5g08/shared/output/data/
>> srchost=localhost destdir=output/data/ desthost=localhost
>> provider=file
>> 2010-03-11 11:32:51,438-0600 DEBUG vdl:dostageout FILE_STAGE_OUT_START
>> srcname=T0510D1.rama
>> srcdir=psim.loops-20100311-1132-4huo5g08/shared/output/data/
>> srchost=localhost destdir=output/data/ desthost=localhost
>> provider=file
>> 2010-03-11 11:32:51,438-0600 DEBUG vdl:dostageout FILE_STAGE_OUT_START
>> srcname=void srcdir=psim.loops-20100311-1132-4huo5g08/shared/
>> srchost=localhost destdir= desthost=localhost provider=file
>> 2010-03-11 11:32:51,438-0600 DEBUG vdl:dostageout FILE_STAGE_OUT_START
>> srcname=T0510D1.range
>> srcdir=psim.loops-20100311-1132-4huo5g08/shared/output/data/
>> srchost=localhost destdir=output/data/ desthost=localhost
>> provider=file
>> 2010-03-11 11:32:51,438-0600 DEBUG vdl:dostageout FILE_STAGE_OUT_START
>> srcname=T0510D1.pdb
>> srcdir=psim.loops-20100311-1132-4huo5g08/shared/output/data/
>> srchost=localhost destdir=output/data/ desthost=localhost
>> provider=file
>> 2010-03-11 11:32:51,438-0600 DEBUG vdl:dostageout FILE_STAGE_OUT_START
>> srcname=T0510D1.rama_index
>> srcdir=psim.loops-20100311-1132-4huo5g08/shared/output/data/
>> srchost=localhost destdir=output/data/ desthost=localhost
>> provider=file
>> 2010-03-11 11:32:51,439-0600 DEBUG vdl:dostageout FILE_STAGE_OUT_START
>> srcname=T0510D1.fasta
>> srcdir=psim.loops-20100311-1132-4huo5g08/shared/output/data/
>> srchost=localhost destdir=output/data/ desthost=localhost
>> provider=file
>> 2010-03-11 11:32:51,439-0600 DEBUG vdl:dostageout FILE_STAGE_OUT_START
>> srcname=T0510D1.params
>> srcdir=psim.loops-20100311-1132-4huo5g08/shared/output/data/
>> srchost=localhost destdir=output/data/ desthost=localhost
>> provider=file
>> 2010-03-11 11:32:51,440-0600 DEBUG TaskImpl Task(type=FILE_OPERATION,
>> identity=urn:0-1-8-1-2-1268328759269) setting status to Submitting
>> 2010-03-11 11:32:51,447-0600 DEBUG TaskImpl Task(type=FILE_OPERATION,
>> identity=urn:0-1-8-1-2-1268328759269) setting status to Submitted
>> 2010-03-11 11:32:51,447-0600 DEBUG TaskImpl Task(type=FILE_OPERATION,
>> identity=urn:0-1-8-1-2-1268328759269) setting status to Active
>> 2010-03-11 11:32:51,447-0600 DEBUG TaskImpl Task(type=FILE_OPERATION,
>> identity=urn:0-1-8-1-2-1268328759269) setting status to Completed
>> 2010-03-11 11:32:51,447-0600 INFO  LateBindingScheduler
>> Task(type=FILE_OPERATION, identity=urn:0-1-8-1-2-1268328759269)
>> Completed. Waiting: 1, Running: 7. Heap size: 9M, Heap free: 0M, Max
>> heap: 254M
>> 2010-03-11 11:32:51,440-0600 DEBUG TaskImpl Task(type=FILE_OPERATION,
>> identity=urn:0-1-8-1-5-1268328759272) setting status to Submitting
>> 2010-03-11 11:32:51,448-0600 DEBUG TaskImpl Task(type=FILE_OPERATION,
>> identity=urn:0-1-8-1-5-1268328759272) setting status to Submitted
>> 2010-03-11 11:32:51,448-0600 DEBUG TaskImpl Task(type=FILE_OPERATION,
>> identity=urn:0-1-8-1-5-1268328759272) setting status to Active
>> 2010-03-11 11:32:51,448-0600 DEBUG TaskImpl Task(type=FILE_OPERATION,
>> identity=urn:0-1-8-1-5-1268328759272) setting status to Completed
>> 2010-03-11 11:32:51,448-0600 INFO  LateBindingScheduler
>> Task(type=FILE_OPERATION, identity=urn:0-1-8-1-5-1268328759272)
>> Completed. Waiting: 2, Running: 6. Heap size: 9M, Heap free: 0M, Max
>> heap: 254M
>> 2010-03-11 11:32:51,448-0600 DEBUG TaskImpl Task(type=FILE_OPERATION,
>> identity=urn:0-1-8-1-7-1268328759273) setting status to Submitting
>> 2010-03-11 11:32:51,450-0600 DEBUG TaskImpl Task(type=FILE_OPERATION,
>> identity=urn:0-1-8-1-7-1268328759273) setting status to Submitted
>> 2010-03-11 11:32:51,450-0600 DEBUG TaskImpl Task(type=FILE_OPERATION,
>> identity=urn:0-1-8-1-7-1268328759273) setting status to Active
>> 2010-03-11 11:32:51,451-0600 DEBUG TaskImpl Task(type=FILE_OPERATION,
>> identity=urn:0-1-8-1-7-1268328759273) setting status to Completed
>> 2010-03-11 11:32:51,451-0600 INFO  LateBindingScheduler
>> Task(type=FILE_OPERATION, identity=urn:0-1-8-1-7-1268328759273)
>> Completed. Waiting: 0, Running: 8. Heap size: 9M, Heap free: 0M, Max
>> heap: 254M
>> 2010-03-11 11:32:51,449-0600 DEBUG TaskImpl Task(type=FILE_OPERATION,
>> identity=urn:0-1-8-1-4-1268328759276) setting status to Submitting
>> 2010-03-11 11:32:51,451-0600 DEBUG TaskImpl Task(type=FILE_OPERATION,
>> identity=urn:0-1-8-1-4-1268328759276) setting status to Submitted
>> 2010-03-11 11:32:51,451-0600 DEBUG TaskImpl Task(type=FILE_OPERATION,
>> identity=urn:0-1-8-1-4-1268328759276) setting status to Active
>> 2010-03-11 11:32:51,452-0600 DEBUG TaskImpl Task(type=FILE_OPERATION,
>> identity=urn:0-1-8-1-4-1268328759276) setting status to Completed
>> 2010-03-11 11:32:51,452-0600 INFO  LateBindingScheduler
>> Task(type=FILE_OPERATION, identity=urn:0-1-8-1-4-1268328759276)
>> Completed. Waiting: 0, Running: 8. Heap size: 9M, Heap free: 0M, Max
>> heap: 254M
>> 2010-03-11 11:32:51,451-0600 DEBUG TaskImpl Task(type=FILE_OPERATION,
>> identity=urn:0-1-8-1-6-1268328759277) setting status to Submitting
>> 2010-03-11 11:32:51,453-0600 DEBUG TaskImpl Task(type=FILE_OPERATION,
>> identity=urn:0-1-8-1-6-1268328759277) setting status to Submitted
>> 2010-03-11 11:32:51,453-0600 DEBUG TaskImpl Task(type=FILE_OPERATION,
>> identity=urn:0-1-8-1-6-1268328759277) setting status to Active
>> 2010-03-11 11:32:51,453-0600 DEBUG TaskImpl Task(type=FILE_OPERATION,
>> identity=urn:0-1-8-1-6-1268328759277) setting status to Completed
>> 2010-03-11 11:32:51,453-0600 INFO  LateBindingScheduler
>> Task(type=FILE_OPERATION, identity=urn:0-1-8-1-6-1268328759277)
>> Completed. Waiting: 1, Running: 7. Heap size: 9M, Heap free: 0M, Max
>> heap: 254M
>> 2010-03-11 11:32:51,453-0600 DEBUG TaskImpl Task(type=FILE_OPERATION,
>> identity=urn:0-1-8-1-9-1268328759279) setting status to Submitting
>> 2010-03-11 11:32:51,453-0600 DEBUG TaskImpl Task(type=FILE_OPERATION,
>> identity=urn:0-1-8-1-9-1268328759279) setting status to Submitted
>> 2010-03-11 11:32:51,453-0600 DEBUG TaskImpl Task(type=FILE_OPERATION,
>> identity=urn:0-1-8-1-9-1268328759279) setting status to Active
>> 2010-03-11 11:32:51,453-0600 DEBUG TaskImpl Task(type=FILE_OPERATION,
>> identity=urn:0-1-8-1-9-1268328759279) setting status to Completed
>> 2010-03-11 11:32:51,454-0600 INFO  LateBindingScheduler
>> Task(type=FILE_OPERATION, identity=urn:0-1-8-1-9-1268328759279)
>> Completed. Waiting: 1, Running: 7. Heap size: 9M, Heap free: 0M, Max
>> heap: 254M
>> 2010-03-11 11:32:51,454-0600 DEBUG TaskImpl Task(type=FILE_OPERATION,
>> identity=urn:0-1-8-1-1-1268328759281) setting status to Submitting
>> 2010-03-11 11:32:51,454-0600 DEBUG TaskImpl Task(type=FILE_OPERATION,
>> identity=urn:0-1-8-1-1-1268328759281) setting status to Submitted
>> 2010-03-11 11:32:51,454-0600 DEBUG TaskImpl Task(type=FILE_OPERATION,
>> identity=urn:0-1-8-1-1-1268328759281) setting status to Active
>> 2010-03-11 11:32:51,454-0600 DEBUG TaskImpl Task(type=FILE_OPERATION,
>> identity=urn:0-1-8-1-1-1268328759281) setting status to Completed
>> 2010-03-11 11:32:51,454-0600 INFO  LateBindingScheduler
>> Task(type=FILE_OPERATION, identity=urn:0-1-8-1-1-1268328759281)
>> Completed. Waiting: 2, Running: 6. Heap size: 9M, Heap free: 0M, Max
>> heap: 254M
>> 2010-03-11 11:32:51,455-0600 DEBUG TaskImpl Task(type=FILE_OPERATION,
>> identity=urn:0-1-8-1-8-1268328759283) setting status to Submitting
>> 2010-03-11 11:32:51,455-0600 DEBUG TaskImpl Task(type=FILE_OPERATION,
>> identity=urn:0-1-8-1-8-1268328759283) setting status to Submitted
>> 2010-03-11 11:32:51,455-0600 DEBUG TaskImpl Task(type=FILE_OPERATION,
>> identity=urn:0-1-8-1-8-1268328759283) setting status to Active
>> 2010-03-11 11:32:51,455-0600 DEBUG TaskImpl Task(type=FILE_OPERATION,
>> identity=urn:0-1-8-1-8-1268328759283) setting status to Completed
>> 2010-03-11 11:32:51,455-0600 INFO  LateBindingScheduler
>> Task(type=FILE_OPERATION, identity=urn:0-1-8-1-8-1268328759283)
>> Completed. Waiting: 3, Running: 5. Heap size: 9M, Heap free: 0M, Max
>> heap: 254M
>> 2010-03-11 11:32:51,455-0600 DEBUG TaskImpl Task(type=FILE_OPERATION,
>> identity=urn:0-1-8-1-3-1268328759285) setting status to Submitting
>> 2010-03-11 11:32:51,455-0600 DEBUG TaskImpl Task(type=FILE_OPERATION,
>> identity=urn:0-1-8-1-3-1268328759285) setting status to Submitted
>> 2010-03-11 11:32:51,455-0600 DEBUG TaskImpl Task(type=FILE_OPERATION,
>> identity=urn:0-1-8-1-3-1268328759285) setting status to Active
>> 2010-03-11 11:32:51,456-0600 DEBUG TaskImpl Task(type=FILE_TRANSFER,
>> identity=urn:0-1-8-1-2-1268328759287) setting status to Submitting
>> 2010-03-11 11:32:51,456-0600 DEBUG TaskImpl Task(type=FILE_OPERATION,
>> identity=urn:0-1-8-1-3-1268328759285) setting status to Completed
>> 2010-03-11 11:32:51,456-0600 DEBUG TaskImpl Task(type=FILE_TRANSFER,
>> identity=urn:0-1-8-1-2-1268328759287) setting status to Submitted
>> 2010-03-11 11:32:51,456-0600 INFO  LateBindingScheduler
>> Task(type=FILE_OPERATION, identity=urn:0-1-8-1-3-1268328759285)
>> Completed. Waiting: 4, Running: 4. Heap size: 9M, Heap free: 0M, Max
>> heap: 254M
>> 2010-03-11 11:32:51,457-0600 DEBUG TaskImpl Task(type=FILE_TRANSFER,
>> identity=urn:0-1-8-1-2-1268328759287) setting status to Active
>> 2010-03-11 11:32:51,457-0600 DEBUG TaskImpl Task(type=FILE_TRANSFER,
>> identity=urn:0-1-8-1-7-1268328759291) setting status to Submitting
>> 2010-03-11 11:32:51,457-0600 DEBUG TaskImpl Task(type=FILE_TRANSFER,
>> identity=urn:0-1-8-1-7-1268328759291) setting status to Submitted
>> 2010-03-11 11:32:51,457-0600 DEBUG TaskImpl Task(type=FILE_TRANSFER,
>> identity=urn:0-1-8-1-4-1268328759293) setting status to Submitting
>> 2010-03-11 11:32:51,457-0600 DEBUG TaskImpl Task(type=FILE_TRANSFER,
>> identity=urn:0-1-8-1-7-1268328759291) setting status to Active
>> 2010-03-11 11:32:51,458-0600 DEBUG TaskImpl Task(type=FILE_TRANSFER,
>> identity=urn:0-1-8-1-2-1268328759287) setting status to Completed
>> 2010-03-11 11:32:51,458-0600 INFO  LateBindingScheduler
>> Task(type=FILE_TRANSFER, identity=urn:0-1-8-1-2-1268328759287)
>> Completed. Waiting: 5, Running: 3. Heap size: 9M, Heap free: 0M, Max
>> heap: 254M
>> 2010-03-11 11:32:51,458-0600 DEBUG TaskImpl Task(type=FILE_TRANSFER,
>> identity=urn:0-1-8-1-5-1268328759289) setting status to Submitting
>> 2010-03-11 11:32:51,458-0600 DEBUG TaskImpl Task(type=FILE_TRANSFER,
>> identity=urn:0-1-8-1-5-1268328759289) setting status to Submitted
>> 2010-03-11 11:32:51,458-0600 DEBUG vdl:dostageout FILE_STAGE_OUT_END
>> srcname=T0510D1.secseq
>> srcdir=psim.loops-20100311-1132-4huo5g08/shared/output/data/
>> srchost=localhost destdir=output/data/ desthost=localhost
>> provider=file
>> 2010-03-11 11:32:51,459-0600 DEBUG TaskImpl Task(type=FILE_TRANSFER,
>> identity=urn:0-1-8-1-6-1268328759295) setting status to Submitting
>> 2010-03-11 11:32:51,459-0600 DEBUG TaskImpl Task(type=FILE_TRANSFER,
>> identity=urn:0-1-8-1-6-1268328759295) setting status to Submitted
>> 2010-03-11 11:32:51,459-0600 DEBUG TaskImpl Task(type=FILE_TRANSFER,
>> identity=urn:0-1-8-1-6-1268328759295) setting status to Active
>> 2010-03-11 11:32:51,460-0600 DEBUG TaskImpl Task(type=FILE_TRANSFER,
>> identity=urn:0-1-8-1-6-1268328759295) setting status to Completed
>> 2010-03-11 11:32:51,460-0600 INFO  LateBindingScheduler
>> Task(type=FILE_TRANSFER, identity=urn:0-1-8-1-6-1268328759295)
>> Completed. Waiting: 4, Running: 4. Heap size: 9M, Heap free: 0M, Max
>> heap: 254M
>> 2010-03-11 11:32:51,457-0600 DEBUG TaskImpl Task(type=FILE_TRANSFER,
>> identity=urn:0-1-8-1-4-1268328759293) setting status to Submitted
>> 2010-03-11 11:32:51,464-0600 DEBUG TaskImpl Task(type=FILE_TRANSFER,
>> identity=urn:0-1-8-1-9-1268328759297) setting status to Submitting
>> 2010-03-11 11:32:51,464-0600 DEBUG TaskImpl Task(type=FILE_TRANSFER,
>> identity=urn:0-1-8-1-9-1268328759297) setting status to Submitted
>> 2010-03-11 11:32:51,464-0600 DEBUG TaskImpl Task(type=FILE_TRANSFER,
>> identity=urn:0-1-8-1-9-1268328759297) setting status to Active
>> 2010-03-11 11:32:51,465-0600 DEBUG TaskImpl Task(type=FILE_TRANSFER,
>> identity=urn:0-1-8-1-5-1268328759289) setting status to Active
>> 2010-03-11 11:32:51,465-0600 DEBUG TaskImpl Task(type=FILE_OPERATION,
>> identity=urn:0-1-8-1-2-1268328759307) setting status to Submitting
>> 2010-03-11 11:32:51,465-0600 DEBUG TaskImpl Task(type=FILE_OPERATION,
>> identity=urn:0-1-8-1-2-1268328759307) setting status to Submitted
>> 2010-03-11 11:32:51,465-0600 DEBUG TaskImpl Task(type=FILE_OPERATION,
>> identity=urn:0-1-8-1-2-1268328759307) setting status to Active
>> 2010-03-11 11:32:51,466-0600 DEBUG TaskImpl Task(type=FILE_OPERATION,
>> identity=urn:0-1-8-1-2-1268328759307) setting status to Completed
>> 2010-03-11 11:32:51,466-0600 INFO  LateBindingScheduler
>> Task(type=FILE_OPERATION, identity=urn:0-1-8-1-2-1268328759307)
>> Completed. Waiting: 3, Running: 4. Heap size: 9M, Heap free: 0M, Max
>> heap: 254M
>> 2010-03-11 11:32:51,469-0600 DEBUG TaskImpl Task(type=FILE_TRANSFER,
>> identity=urn:0-1-8-1-7-1268328759291) setting status to Completed
>> 2010-03-11 11:32:51,470-0600 DEBUG TaskImpl Task(type=FILE_TRANSFER,
>> identity=urn:0-1-8-1-9-1268328759297) setting status to Completed
>> 2010-03-11 11:32:51,470-0600 INFO  LateBindingScheduler
>> Task(type=FILE_TRANSFER, identity=urn:0-1-8-1-7-1268328759291)
>> Completed. Waiting: 3, Running: 3. Heap size: 9M, Heap free: 0M, Max
>> heap: 254M
>> 2010-03-11 11:32:51,470-0600 DEBUG TaskImpl Task(type=FILE_TRANSFER,
>> identity=urn:0-1-8-1-1-1268328759299) setting status to Submitting
>> 2010-03-11 11:32:51,470-0600 DEBUG TaskImpl Task(type=FILE_TRANSFER,
>> identity=urn:0-1-8-1-1-1268328759299) setting status to Submitted
>> 2010-03-11 11:32:51,470-0600 DEBUG vdl:dostageout FILE_STAGE_OUT_END
>> srcname=T0510D1.rama
>> srcdir=psim.loops-20100311-1132-4huo5g08/shared/output/data/
>> srchost=localhost destdir=output/data/ desthost=localhost
>> provider=file
>> 2010-03-11 11:32:51,471-0600 DEBUG vdl:dostageout FILE_STAGE_OUT_END
>> srcname=T0510D1.range
>> srcdir=psim.loops-20100311-1132-4huo5g08/shared/output/data/
>> srchost=localhost destdir=output/data/ desthost=localhost
>> provider=file
>> 2010-03-11 11:32:51,471-0600 DEBUG TaskImpl Task(type=FILE_OPERATION,
>> identity=urn:0-1-8-1-7-1268328759312) setting status to Submitting
>> 2010-03-11 11:32:51,471-0600 DEBUG TaskImpl Task(type=FILE_OPERATION,
>> identity=urn:0-1-8-1-6-1268328759314) setting status to Submitting
>> 2010-03-11 11:32:51,471-0600 DEBUG TaskImpl Task(type=FILE_OPERATION,
>> identity=urn:0-1-8-1-6-1268328759314) setting status to Submitted
>> 2010-03-11 11:32:51,471-0600 DEBUG TaskImpl Task(type=FILE_OPERATION,
>> identity=urn:0-1-8-1-6-1268328759314) setting status to Active
>> 2010-03-11 11:32:51,472-0600 DEBUG TaskImpl Task(type=FILE_OPERATION,
>> identity=urn:0-1-8-1-6-1268328759314) setting status to Completed
>> 2010-03-11 11:32:51,472-0600 INFO  LateBindingScheduler
>> Task(type=FILE_OPERATION, identity=urn:0-1-8-1-6-1268328759314)
>> Completed. Waiting: 2, Running: 5. Heap size: 9M, Heap free: 0M, Max
>> heap: 254M
>> 2010-03-11 11:32:51,472-0600 DEBUG TaskImpl Task(type=FILE_TRANSFER,
>> identity=urn:0-1-8-1-4-1268328759293) setting status to Active
>> 2010-03-11 11:32:51,472-0600 INFO  LateBindingScheduler
>> Task(type=FILE_TRANSFER, identity=urn:0-1-8-1-9-1268328759297)
>> Completed. Waiting: 4, Running: 4. Heap size: 9M, Heap free: 0M, Max
>> heap: 254M
>> 2010-03-11 11:32:51,473-0600 DEBUG TaskImpl Task(type=FILE_TRANSFER,
>> identity=urn:0-1-8-1-8-1268328759301) setting status to Submitting
>> 2010-03-11 11:32:51,471-0600 DEBUG TaskImpl Task(type=FILE_OPERATION,
>> identity=urn:0-1-8-1-7-1268328759312) setting status to Submitted
>> 2010-03-11 11:32:51,473-0600 DEBUG TaskImpl Task(type=FILE_TRANSFER,
>> identity=urn:0-1-8-1-4-1268328759293) setting status to Completed
>> 2010-03-11 11:32:51,473-0600 DEBUG TaskImpl Task(type=FILE_TRANSFER,
>> identity=urn:0-1-8-1-1-1268328759299) setting status to Active
>> 2010-03-11 11:32:51,473-0600 DEBUG TaskImpl Task(type=FILE_TRANSFER,
>> identity=urn:0-1-8-1-8-1268328759301) setting status to Submitted
>> 2010-03-11 11:32:51,474-0600 DEBUG TaskImpl Task(type=FILE_TRANSFER,
>> identity=urn:0-1-8-1-8-1268328759301) setting status to Active
>> 2010-03-11 11:32:51,474-0600 DEBUG TaskImpl Task(type=FILE_TRANSFER,
>> identity=urn:0-1-8-1-8-1268328759301) setting status to Completed
>> 2010-03-11 11:32:51,475-0600 INFO  LateBindingScheduler
>> Task(type=FILE_TRANSFER, identity=urn:0-1-8-1-8-1268328759301)
>> Completed. Waiting: 1, Running: 4. Heap size: 9M, Heap free: 0M, Max
>> heap: 254M
>> 2010-03-11 11:32:51,475-0600 DEBUG TaskImpl Task(type=FILE_TRANSFER,
>> identity=urn:0-1-8-1-3-1268328759303) setting status to Submitting
>> 2010-03-11 11:32:51,475-0600 DEBUG TaskImpl Task(type=FILE_TRANSFER,
>> identity=urn:0-1-8-1-3-1268328759303) setting status to Submitted
>> 2010-03-11 11:32:51,475-0600 DEBUG vdl:dostageout FILE_STAGE_OUT_END
>> srcname=T0510D1.fasta
>> srcdir=psim.loops-20100311-1132-4huo5g08/shared/output/data/
>> srchost=localhost destdir=output/data/ desthost=localhost
>> provider=file
>> 2010-03-11 11:32:51,476-0600 DEBUG TaskImpl Task(type=FILE_TRANSFER,
>> identity=urn:0-1-8-1-3-1268328759303) setting status to Active
>> 2010-03-11 11:32:51,477-0600 DEBUG TaskImpl Task(type=FILE_TRANSFER,
>> identity=urn:0-1-8-1-3-1268328759303) setting status to Completed
>> 2010-03-11 11:32:51,477-0600 INFO  LateBindingScheduler
>> Task(type=FILE_TRANSFER, identity=urn:0-1-8-1-3-1268328759303)
>> Completed. Waiting: 0, Running: 5. Heap size: 9M, Heap free: 0M, Max
>> heap: 254M
>> 2010-03-11 11:32:51,477-0600 DEBUG vdl:dostageout FILE_STAGE_OUT_END
>> srcname=T0510D1.params
>> srcdir=psim.loops-20100311-1132-4huo5g08/shared/output/data/
>> srchost=localhost destdir=output/data/ desthost=localhost
>> provider=file
>> 2010-03-11 11:32:51,478-0600 DEBUG vdl:dostageout FILE_STAGE_OUT_END
>> srcname=T0510D1.pdb
>> srcdir=psim.loops-20100311-1132-4huo5g08/shared/output/data/
>> srchost=localhost destdir=output/data/ desthost=localhost
>> provider=file
>> 2010-03-11 11:32:51,480-0600 DEBUG TaskImpl Task(type=FILE_OPERATION,
>> identity=urn:0-1-8-1-8-1268328759319) setting status to Submitting
>> 2010-03-11 11:32:51,480-0600 DEBUG TaskImpl Task(type=FILE_OPERATION,
>> identity=urn:0-1-8-1-8-1268328759319) setting status to Submitted
>> 2010-03-11 11:32:51,481-0600 DEBUG TaskImpl Task(type=FILE_OPERATION,
>> identity=urn:0-1-8-1-8-1268328759319) setting status to Active
>> 2010-03-11 11:32:51,481-0600 DEBUG TaskImpl Task(type=FILE_OPERATION,
>> identity=urn:0-1-8-1-8-1268328759319) setting status to Completed
>> 2010-03-11 11:32:51,481-0600 INFO  LateBindingScheduler
>> Task(type=FILE_OPERATION, identity=urn:0-1-8-1-8-1268328759319)
>> Completed. Waiting: 0, Running: 6. Heap size: 9M, Heap free: 0M, Max
>> heap: 254M
>> 2010-03-11 11:32:51,495-0600 DEBUG TaskImpl Task(type=FILE_TRANSFER,
>> identity=urn:0-1-8-1-5-1268328759289) setting status to Completed
>> 2010-03-11 11:32:51,496-0600 INFO  LateBindingScheduler
>> Task(type=FILE_TRANSFER, identity=urn:0-1-8-1-5-1268328759289)
>> Completed. Waiting: 0, Running: 5. Heap size: 9M, Heap free: 0M, Max
>> heap: 254M
>> 2010-03-11 11:32:51,496-0600 DEBUG vdl:dostageout FILE_STAGE_OUT_END
>> srcname=T0510D1.rama_map
>> srcdir=psim.loops-20100311-1132-4huo5g08/shared/output/data/
>> srchost=localhost destdir=output/data/ desthost=localhost
>> provider=file
>> 2010-03-11 11:32:51,497-0600 DEBUG TaskImpl Task(type=FILE_TRANSFER,
>> identity=urn:0-1-8-1-1-1268328759299) setting status to Completed
>> 2010-03-11 11:32:51,497-0600 INFO  LateBindingScheduler
>> Task(type=FILE_TRANSFER, identity=urn:0-1-8-1-1-1268328759299)
>> Completed. Waiting: 0, Running: 5. Heap size: 9M, Heap free: 0M, Max
>> heap: 254M
>> 2010-03-11 11:32:51,497-0600 DEBUG TaskImpl Task(type=FILE_OPERATION,
>> identity=urn:0-1-8-1-3-1268328759322) setting status to Submitting
>> 2010-03-11 11:32:51,498-0600 DEBUG TaskImpl Task(type=FILE_OPERATION,
>> identity=urn:0-1-8-1-7-1268328759312) setting status to Active
>> 2010-03-11 11:32:51,498-0600 DEBUG TaskImpl Task(type=FILE_OPERATION,
>> identity=urn:0-1-8-1-3-1268328759322) setting status to Submitted
>> 2010-03-11 11:32:51,498-0600 DEBUG TaskImpl Task(type=FILE_OPERATION,
>> identity=urn:0-1-8-1-3-1268328759322) setting status to Active
>> 2010-03-11 11:32:51,498-0600 DEBUG TaskImpl Task(type=FILE_OPERATION,
>> identity=urn:0-1-8-1-7-1268328759312) setting status to Completed
>> 2010-03-11 11:32:51,498-0600 INFO  LateBindingScheduler
>> Task(type=FILE_OPERATION, identity=urn:0-1-8-1-7-1268328759312)
>> Completed. Waiting: 0, Running: 4. Heap size: 9M, Heap free: 0M, Max
>> heap: 254M
>> 2010-03-11 11:32:51,499-0600 DEBUG TaskImpl Task(type=FILE_OPERATION,
>> identity=urn:0-1-8-1-9-1268328759324) setting status to Submitting
>> 2010-03-11 11:32:51,499-0600 DEBUG TaskImpl Task(type=FILE_OPERATION,
>> identity=urn:0-1-8-1-9-1268328759324) setting status to Submitted
>> 2010-03-11 11:32:51,499-0600 DEBUG TaskImpl Task(type=FILE_OPERATION,
>> identity=urn:0-1-8-1-9-1268328759324) setting status to Active
>> 2010-03-11 11:32:51,500-0600 DEBUG TaskImpl Task(type=FILE_OPERATION,
>> identity=urn:0-1-8-1-9-1268328759324) setting status to Completed
>> 2010-03-11 11:32:51,500-0600 INFO  LateBindingScheduler
>> Task(type=FILE_OPERATION, identity=urn:0-1-8-1-9-1268328759324)
>> Completed. Waiting: 0, Running: 3. Heap size: 9M, Heap free: 0M, Max
>> heap: 254M
>> 2010-03-11 11:32:51,500-0600 DEBUG TaskImpl Task(type=FILE_OPERATION,
>> identity=urn:0-1-8-1-5-1268328759326) setting status to Submitting
>> 2010-03-11 11:32:51,500-0600 DEBUG TaskImpl Task(type=FILE_OPERATION,
>> identity=urn:0-1-8-1-5-1268328759326) setting status to Submitted
>> 2010-03-11 11:32:51,500-0600 DEBUG TaskImpl Task(type=FILE_OPERATION,
>> identity=urn:0-1-8-1-5-1268328759326) setting status to Active
>> 2010-03-11 11:32:51,500-0600 DEBUG TaskImpl Task(type=FILE_OPERATION,
>> identity=urn:0-1-8-1-5-1268328759326) setting status to Completed
>> 2010-03-11 11:32:51,500-0600 INFO  LateBindingScheduler
>> Task(type=FILE_OPERATION, identity=urn:0-1-8-1-5-1268328759326)
>> Completed. Waiting: 0, Running: 2. Heap size: 9M, Heap free: 0M, Max
>> heap: 254M
>> 2010-03-11 11:32:51,498-0600 INFO  LateBindingScheduler
>> Task(type=FILE_TRANSFER, identity=urn:0-1-8-1-4-1268328759293)
>> Completed. Waiting: 0, Running: 4. Heap size: 9M, Heap free: 0M, Max
>> heap: 254M
>> 2010-03-11 11:32:51,498-0600 DEBUG vdl:dostageout FILE_STAGE_OUT_END
>> srcname=T0510D1.rama_index
>> srcdir=psim.loops-20100311-1132-4huo5g08/shared/output/data/
>> srchost=localhost destdir=output/data/ desthost=localhost
>> provider=file
>> 2010-03-11 11:32:51,501-0600 DEBUG vdl:dostageout FILE_STAGE_OUT_END
>> srcname=void srcdir=psim.loops-20100311-1132-4huo5g08/shared/
>> srchost=localhost destdir= desthost=localhost provider=file
>> 2010-03-11 11:32:51,501-0600 DEBUG TaskImpl Task(type=FILE_OPERATION,
>> identity=urn:0-1-8-1-1-1268328759328) setting status to Submitting
>> 2010-03-11 11:32:51,498-0600 DEBUG TaskImpl Task(type=FILE_OPERATION,
>> identity=urn:0-1-8-1-3-1268328759322) setting status to Completed
>> 2010-03-11 11:32:51,502-0600 DEBUG TaskImpl Task(type=FILE_OPERATION,
>> identity=urn:0-1-8-1-1-1268328759328) setting status to Submitted
>> 2010-03-11 11:32:51,502-0600 INFO  LateBindingScheduler
>> Task(type=FILE_OPERATION, identity=urn:0-1-8-1-3-1268328759322)
>> Completed. Waiting: 0, Running: 2. Heap size: 9M, Heap free: 0M, Max
>> heap: 254M
>> 2010-03-11 11:32:51,502-0600 DEBUG TaskImpl Task(type=FILE_OPERATION,
>> identity=urn:0-1-8-1-1-1268328759328) setting status to Active
>> 2010-03-11 11:32:51,503-0600 DEBUG TaskImpl Task(type=FILE_OPERATION,
>> identity=urn:0-1-8-1-4-1268328759330) setting status to Submitting
>> 2010-03-11 11:32:51,503-0600 DEBUG TaskImpl Task(type=FILE_OPERATION,
>> identity=urn:0-1-8-1-1-1268328759328) setting status to Completed
>> 2010-03-11 11:32:51,503-0600 DEBUG TaskImpl Task(type=FILE_OPERATION,
>> identity=urn:0-1-8-1-4-1268328759330) setting status to Submitted
>> 2010-03-11 11:32:51,503-0600 INFO  LateBindingScheduler
>> Task(type=FILE_OPERATION, identity=urn:0-1-8-1-1-1268328759328)
>> Completed. Waiting: 0, Running: 1. Heap size: 9M, Heap free: 0M, Max
>> heap: 254M
>> 2010-03-11 11:32:51,503-0600 DEBUG TaskImpl Task(type=FILE_OPERATION,
>> identity=urn:0-1-8-1-4-1268328759330) setting status to Active
>> 2010-03-11 11:32:51,503-0600 DEBUG TaskImpl Task(type=FILE_OPERATION,
>> identity=urn:0-1-8-1-4-1268328759330) setting status to Completed
>> 2010-03-11 11:32:51,504-0600 INFO  LateBindingScheduler
>> Task(type=FILE_OPERATION, identity=urn:0-1-8-1-4-1268328759330)
>> Completed. Waiting: 0, Running: 0. Heap size: 9M, Heap free: 0M, Max
>> heap: 254M
>> 2010-03-11 11:32:51,506-0600 INFO  vdl:dostageout END
>> jobid=PrepLoop-nqsbkyoj - Staging out finished
>> 2010-03-11 11:32:51,512-0600 DEBUG TaskImpl Task(type=FILE_TRANSFER,
>> identity=urn:0-1-8-1-1268328759332) setting status to Submitting
>> 2010-03-11 11:32:51,512-0600 DEBUG TaskImpl Task(type=FILE_TRANSFER,
>> identity=urn:0-1-8-1-1268328759332) setting status to Submitted
>> 2010-03-11 11:32:51,512-0600 DEBUG TaskImpl Task(type=FILE_TRANSFER,
>> identity=urn:0-1-8-1-1268328759332) setting status to Active
>> 2010-03-11 11:32:51,513-0600 DEBUG TaskImpl Task(type=FILE_TRANSFER,
>> identity=urn:0-1-8-1-1268328759332) setting status to Completed
>> 2010-03-11 11:32:51,513-0600 INFO  LateBindingScheduler
>> Task(type=FILE_TRANSFER, identity=urn:0-1-8-1-1268328759332)
>> Completed. Waiting: 0, Running: 0. Heap size: 9M, Heap free: 0M, Max
>> heap: 254M
>> 2010-03-11 11:32:51,516-0600 DEBUG vdl:execute2 JOB_END
>> jobid=PrepLoop-nqsbkyoj
>> 2010-03-11 11:32:51,517-0600 INFO  vdl:execute END_SUCCESS
>> thread=0-1-8 tr=PrepLoop
>> 2010-03-11 11:32:52,179-0600 INFO  CloseDataset Closing
>> org.griphyn.vdl.mapping.RootDataNode identifier
>> tag:benc at ci.uchicago.edu,2008:swift:dataset:20100311-1132-b8hclef8:720000000021
>> type LoopModelData with no value at dataset=modelData (not closed)
>> 2010-03-11 11:32:52,179-0600 INFO  AbstractDataNode closed
>> org.griphyn.vdl.mapping.RootDataNode identifier
>> tag:benc at ci.uchicago.edu,2008:swift:dataset:20100311-1132-b8hclef8:720000000021
>> type LoopModelData with no value at dataset=modelData (closed)
>> 2010-03-11 11:32:52,179-0600 INFO  AbstractDataNode closed
>> org.griphyn.vdl.mapping.DataNode identifier
>> tag:benc at ci.uchicago.edu,2008:swift:dataset:20100311-1132-b8hclef8:720000000041
>> type SecSeq with no value at dataset=modelData path=.secseq (closed)
>> 2010-03-11 11:32:52,179-0600 INFO  AbstractDataNode Notifying listener
>> "F/org.griphyn.vdl.mapping.DataNode identifier
>> tag:benc at ci.uchicago.edu,2008:swift:dataset:20100311-1132-b8hclef8:720000000036
>> type RamaIndex with no value at dataset=modelData path=.index
>> (closed)" about "org.griphyn.vdl.mapping.DataNode identifier
>> tag:benc at ci.uchicago.edu,2008:swift:dataset:20100311-1132-b8hclef8:720000000036
>> type RamaIndex with no value at dataset=modelData path=.index
>> (closed)"
>> 2010-03-11 11:32:52,179-0600 INFO  AbstractDataNode closed
>> org.griphyn.vdl.mapping.DataNode identifier
>> tag:benc at ci.uchicago.edu,2008:swift:dataset:20100311-1132-b8hclef8:720000000036
>> type RamaIndex with no value at dataset=modelData path=.index (closed)
>> 2010-03-11 11:32:52,180-0600 INFO  AbstractDataNode closed
>> org.griphyn.vdl.mapping.DataNode identifier
>> tag:benc at ci.uchicago.edu,2008:swift:dataset:20100311-1132-b8hclef8:720000000037
>> type ProtlibParams with no value at dataset=modelData path=.params
>> (closed)
>> 2010-03-11 11:32:52,180-0600 INFO  AbstractDataNode closed
>> org.griphyn.vdl.mapping.DataNode identifier
>> tag:benc at ci.uchicago.edu,2008:swift:dataset:20100311-1132-b8hclef8:720000000035
>> type PDB with no value at dataset=modelData path=.native (closed)
>> 2010-03-11 11:32:52,180-0600 INFO  AbstractDataNode closed
>> org.griphyn.vdl.mapping.DataNode identifier
>> tag:benc at ci.uchicago.edu,2008:swift:dataset:20100311-1132-b8hclef8:720000000040
>> type RamaMap with no value at dataset=modelData path=.map (closed)
>> 2010-03-11 11:32:52,180-0600 INFO  AbstractDataNode closed
>> org.griphyn.vdl.mapping.DataNode identifier
>> tag:benc at ci.uchicago.edu,2008:swift:dataset:20100311-1132-b8hclef8:720000000038
>> type LoopRange with no value at dataset=modelData path=.range (closed)
>> 2010-03-11 11:32:52,180-0600 INFO  AbstractDataNode closed
>> org.griphyn.vdl.mapping.DataNode identifier
>> tag:benc at ci.uchicago.edu,2008:swift:dataset:20100311-1132-b8hclef8:720000000039
>> type Rama with no value at dataset=modelData path=.rama (closed)
>> 2010-03-11 11:32:52,180-0600 INFO  AbstractDataNode closed
>> org.griphyn.vdl.mapping.DataNode identifier
>> tag:benc at ci.uchicago.edu,2008:swift:dataset:20100311-1132-b8hclef8:720000000034
>> type PDB with no value at dataset=modelData path=.pdb (closed)
>> 2010-03-11 11:32:52,180-0600 INFO  AbstractDataNode closed
>> org.griphyn.vdl.mapping.DataNode identifier
>> tag:benc at ci.uchicago.edu,2008:swift:dataset:20100311-1132-b8hclef8:720000000033
>> type Fasta with no value at dataset=modelData path=.fasta (closed)
>> 2010-03-11 11:32:52,180-0600 INFO  loopprepare PROCEDURE_END line=112
>> 2010-03-11 11:32:52,180-0600 INFO  CloseDataset Partially closing
>> org.griphyn.vdl.mapping.RootDataNode identifier
>> tag:benc at ci.uchicago.edu,2008:swift:dataset:20100311-1132-b8hclef8:720000000021
>> type LoopModelData with no value at dataset=modelData (closed) for
>> statement 88016
>> 2010-03-11 11:32:52,180-0600 INFO  CloseDataset var is
>> org.griphyn.vdl.mapping.RootDataNode identifier
>> tag:benc at ci.uchicago.edu,2008:swift:dataset:20100311-1132-b8hclef8:720000000021
>> type LoopModelData with no value at dataset=modelData (closed)
>> 2010-03-11 11:32:52,181-0600 INFO  CloseDataset var hash is 18923308
>> 2010-03-11 11:32:52,181-0600 INFO  CloseDataset variable already
>> closed - skipping partial close processing
>> 2010-03-11 11:32:52,186-0600 INFO  AbstractDataNode closed
>> org.griphyn.vdl.mapping.RootDataNode identifier
>> tag:benc at ci.uchicago.edu,2008:swift:dataset:20100311-1132-b8hclef8:720000000057
>> type string value=output/data//T0510D1.pdb dataset=unnamed SwiftScript
>> value (closed)
>> 2010-03-11 11:32:52,186-0600 INFO  VDLFunction FUNCTIONPARAMETER
>> id=451007
>> input=tag:benc at ci.uchicago.edu,2008:swift:dataset:20100311-1132-b8hclef8:720000000034
>> name=input
>> 2010-03-11 11:32:52,186-0600 INFO  VDLFunction FUNCTION id=451007
>> name=filename
>> result=tag:benc at ci.uchicago.edu,2008:swift:dataset:20100311-1132-b8hclef8:720000000057
>> 2010-03-11 11:32:52,187-0600 INFO  AbstractDataNode closed
>> org.griphyn.vdl.mapping.RootDataNode identifier
>> tag:benc at ci.uchicago.edu,2008:swift:dataset:20100311-1132-b8hclef8:720000000058
>> type string value=output/run/T0510D1.0.pdb dataset=unnamed SwiftScript
>> value (closed)
>> 2010-03-11 11:32:52,187-0600 INFO  VDLFunction FUNCTIONPARAMETER
>> id=451008
>> input=tag:benc at ci.uchicago.edu,2008:swift:dataset:20100311-1132-b8hclef8:720000000053
>> name=input
>> 2010-03-11 11:32:52,187-0600 INFO  VDLFunction FUNCTION id=451008
>> name=filename
>> result=tag:benc at ci.uchicago.edu,2008:swift:dataset:20100311-1132-b8hclef8:720000000058
>> 2010-03-11 11:32:52,191-0600 INFO  vdl:execute START
>> thread=0-1-9-1-1-1 tr=LoopModel
>> 2010-03-11 11:32:52,193-0600 INFO  WeightedHostScoreScheduler Sorted:
>> [coasterpads:10,000.000(99.854):0/50 overload: 0]
>> 2010-03-11 11:32:52,194-0600 INFO  WeightedHostScoreScheduler
>> CONTACT_SELECTED host=coasterpads, score=99.854
>> 2010-03-11 11:32:52,195-0600 INFO  vdl:initshareddir START
>> host=coasterpads - Initializing shared directory
>> 2010-03-11 11:32:52,198-0600 DEBUG TaskImpl Task(type=FILE_OPERATION,
>> identity=urn:0-1-9-1-1-1-1-1268328759336) setting status to Submitting
>> 2010-03-11 11:32:52,261-0600 INFO  ConfigurationLoader JAVA version is
>> 1.5.0_07
>> 2010-03-11 11:32:52,282-0600 INFO  SshCipherFactory Loading supported
>> cipher algorithms
>> 2010-03-11 11:32:52,287-0600 INFO  SshKeyExchangeFactory Loading key
>> exchange methods
>> 2010-03-11 11:32:52,295-0600 INFO  SshKeyPairFactory Loading public
>> key algorithms
>> 2010-03-11 11:32:52,303-0600 INFO  SshCompressionFactory Loading
>> compression methods
>> 2010-03-11 11:32:52,305-0600 INFO  SshHmacFactory Loading message
>> authentication methods
>> 2010-03-11 11:32:52,316-0600 INFO  HostKeyVerification Determining
>> default host file
>> 2010-03-11 11:32:52,316-0600 INFO  HostKeyVerification Defaulting host
>> file to /home/wwj/.globus/conf/hosts.xml
>> 2010-03-11 11:32:52,487-0600 INFO  TransportProtocolCommon Starting
>> transport protocol
>> 2010-03-11 11:32:52,489-0600 INFO  TransportProtocolCommon Registering
>> transport protocol messages with inputstream
>> 2010-03-11 11:32:52,799-0600 INFO  TransportProtocolCommon Negotiating
>> protocol version
>> 2010-03-11 11:32:52,800-0600 INFO  TransportProtocolCommon Protocol
>> negotiation complete
>> 2010-03-11 11:32:52,800-0600 INFO  TransportProtocolCommon Sending
>> SSH_MSG_KEX_INIT
>> 2010-03-11 11:32:52,806-0600 INFO  TransportProtocolCommon Received
>> SSH_MSG_KEX_INIT
>> 2010-03-11 11:32:52,806-0600 INFO  TransportProtocolCommon Starting
>> key exchange
>> 2010-03-11 11:32:52,806-0600 INFO  DhGroup1Sha1 Starting client side
>> key exchange.
>> 2010-03-11 11:32:52,904-0600 INFO  TransportProtocolCommon Sending
>> SSH_MSG_KEXDH_INIT
>> 2010-03-11 11:32:52,947-0600 INFO  HostKeyVerification Verifying
>> login.pads.ci.uchicago.edu,192.5.86.6 host key
>> 2010-03-11 11:32:52,964-0600 INFO  TransportProtocolCommon The host
>> key signature is  valid
>> 2010-03-11 11:32:52,964-0600 INFO  TransportProtocolCommon Sending
>> SSH_MSG_NEWKEYS
>> 2010-03-11 11:32:52,965-0600 INFO  TransportProtocolCommon Completing
>> key exchange
>> 2010-03-11 11:32:52,965-0600 INFO  SshCipherFactory Creating new
>> 3des-cbc cipher instance
>> 2010-03-11 11:32:53,036-0600 INFO  SshCipherFactory Creating new
>> 3des-cbc cipher instance
>> 2010-03-11 11:32:53,048-0600 INFO  TransportProtocolCommon Sending
>> SSH_MSG_SERVICE_REQUEST
>> 2010-03-11 11:32:53,053-0600 INFO  TransportProtocolCommon Received
>> SSH_MSG_SERVICE_ACCEPT
>> 2010-03-11 11:32:53,075-0600 INFO  SshPrivateKeyFile Parsing private
>> key file
>> 2010-03-11 11:32:53,084-0600 INFO  SshPrivateKeyFile Private key is
>> not in the default format, attempting parse with other supported
>> formats
>> 2010-03-11 11:32:53,105-0600 INFO  PublicKeyAuthenticationClient
>> Generating data to sign
>> 2010-03-11 11:32:53,106-0600 INFO  PublicKeyAuthenticationClient
>> Preparing public key authentication request
>> 2010-03-11 11:32:53,139-0600 INFO  TransportProtocolCommon Sending
>> SSH_MSG_USERAUTH_REQUEST
>> 2010-03-11 11:32:53,181-0600 INFO  TransportProtocolCommon Received
>> SSH_MSG_USERAUTH_SUCCESS
>> 2010-03-11 11:32:53,181-0600 INFO  ConnectionProtocol Registering
>> connection protocol messages
>> 2010-03-11 11:32:53,184-0600 INFO  Service ssh-connection has been
>> requested
>> 2010-03-11 11:32:53,184-0600 INFO  Service Starting ssh-connection
>> service thread
>> 2010-03-11 11:32:53,190-0600 INFO  TransportProtocolCommon Sending
>> SSH_MSG_CHANNEL_OPEN
>> 2010-03-11 11:32:53,193-0600 INFO  TransportProtocolCommon Received
>> SSH_MSG_CHANNEL_OPEN_CONFIRMATION
>> 2010-03-11 11:32:53,194-0600 INFO  ConnectionProtocol Channel 0 is
>> open [Unnamed Channel]
>> 2010-03-11 11:32:53,216-0600 INFO  SessionChannelClient Starting sftp
>> subsystem
>> 2010-03-11 11:32:53,216-0600 INFO  TransportProtocolCommon Sending
>> SSH_MSG_CHANNEL_REQUEST
>> 2010-03-11 11:32:53,220-0600 INFO  TransportProtocolCommon Received
>> SSH_MSG_CHANNEL_WINDOW_ADJUST
>> 2010-03-11 11:32:53,220-0600 INFO  Service Routing
>> SSH_MSG_CHANNEL_WINDOW_ADJUST
>> 2010-03-11 11:32:53,221-0600 INFO  TransportProtocolCommon Received
>> SSH_MSG_CHANNEL_SUCCESS
>> 2010-03-11 11:32:53,221-0600 INFO  SftpSubsystemClient Initializing
>> SFTP protocol version 3
>> 2010-03-11 11:32:53,221-0600 INFO  SubsystemClient Sending
>> SSH_FXP_INIT subsystem message
>> 2010-03-11 11:32:53,222-0600 INFO  TransportProtocolCommon Sending
>> SSH_MSG_CHANNEL_DATA
>> 2010-03-11 11:32:53,222-0600 INFO  TransportProtocolCommon Sending
>> SSH_MSG_CHANNEL_DATA
>> 2010-03-11 11:32:55,520-0600 INFO  TransportProtocolCommon Received
>> SSH_MSG_CHANNEL_DATA
>> 2010-03-11 11:32:55,520-0600 INFO  Service Routing
>> SSH_MSG_CHANNEL_DATA
>> 2010-03-11 11:32:55,521-0600 INFO  SubsystemMessageStore Received
>> SSH_FXP_INIT subsystem message
>> 2010-03-11 11:32:55,521-0600 INFO  SftpSubsystemClient Server
>> responded with version 3
>> 2010-03-11 11:32:55,521-0600 INFO  SubsystemClient Sending
>> SSH_FXP_READPATH subsystem message
>> 2010-03-11 11:32:55,521-0600 INFO  TransportProtocolCommon Sending
>> SSH_MSG_CHANNEL_DATA
>> 2010-03-11 11:32:55,521-0600 INFO  TransportProtocolCommon Sending
>> SSH_MSG_CHANNEL_DATA
>> 2010-03-11 11:32:55,522-0600 INFO  SftpMessageStore Message store has
>> 0 messages
>> 2010-03-11 11:32:55,522-0600 INFO  SftpMessageStore Message store has
>> 0 messages
>> 2010-03-11 11:32:55,525-0600 INFO  TransportProtocolCommon Received
>> SSH_MSG_CHANNEL_DATA
>> 2010-03-11 11:32:55,525-0600 INFO  Service Routing
>> SSH_MSG_CHANNEL_DATA
>> 2010-03-11 11:32:55,529-0600 INFO  SubsystemMessageStore Received
>> SSH_FXP_NAME subsystem message
>> 2010-03-11 11:32:55,529-0600 DEBUG TaskImpl Task(type=FILE_OPERATION,
>> identity=urn:0-1-9-1-1-1-1-1268328759336) setting status to Submitted
>> 2010-03-11 11:32:55,529-0600 DEBUG TaskImpl Task(type=FILE_OPERATION,
>> identity=urn:0-1-9-1-1-1-1-1268328759336) setting status to Active
>> 2010-03-11 11:32:55,530-0600 INFO  SubsystemClient Sending
>> SSH_FXP_STAT subsystem message
>> 2010-03-11 11:32:55,530-0600 INFO  TransportProtocolCommon Sending
>> SSH_MSG_CHANNEL_DATA
>> 2010-03-11 11:32:55,530-0600 INFO  TransportProtocolCommon Sending
>> SSH_MSG_CHANNEL_DATA
>> 2010-03-11 11:32:55,530-0600 INFO  SftpMessageStore Message store has
>> 0 messages
>> 2010-03-11 11:32:55,530-0600 INFO  SftpMessageStore Message store has
>> 0 messages
>> 2010-03-11 11:32:56,167-0600 INFO  TransportProtocolCommon Received
>> SSH_MSG_CHANNEL_DATA
>> 2010-03-11 11:32:56,167-0600 INFO  Service Routing
>> SSH_MSG_CHANNEL_DATA
>> 2010-03-11 11:32:56,168-0600 INFO  SubsystemMessageStore Received
>> SSH_FXP_STATUS subsystem message
>> 2010-03-11 11:32:56,168-0600 INFO  SubsystemClient Sending
>> SSH_FXP_STAT subsystem message
>> 2010-03-11 11:32:56,168-0600 INFO  TransportProtocolCommon Sending
>> SSH_MSG_CHANNEL_DATA
>> 2010-03-11 11:32:56,168-0600 INFO  TransportProtocolCommon Sending
>> SSH_MSG_CHANNEL_DATA
>> 2010-03-11 11:32:56,169-0600 INFO  SftpMessageStore Message store has
>> 0 messages
>> 2010-03-11 11:32:56,169-0600 INFO  SftpMessageStore Message store has
>> 0 messages
>> 2010-03-11 11:32:56,172-0600 INFO  TransportProtocolCommon Received
>> SSH_MSG_CHANNEL_DATA
>> 2010-03-11 11:32:56,172-0600 INFO  Service Routing
>> SSH_MSG_CHANNEL_DATA
>> 2010-03-11 11:32:56,172-0600 INFO  SubsystemMessageStore Received
>> SSH_FXP_STATUS subsystem message
>> 2010-03-11 11:32:56,172-0600 INFO  SubsystemClient Sending
>> SSH_FXP_STAT subsystem message
>> 2010-03-11 11:32:56,172-0600 INFO  TransportProtocolC
>>     
>
>   



From wilde at mcs.anl.gov  Fri Mar 12 19:35:01 2010
From: wilde at mcs.anl.gov (Michael Wilde)
Date: Fri, 12 Mar 2010 19:35:01 -0600 (CST)
Subject: [Swift-devel] Re: can't run ssh:pbs coaster again
In-Reply-To: <4B99509C.3060703@ci.uchicago.edu>
Message-ID: <12253341.1361291268444101746.JavaMail.root@zimbra>

Wenjun, I just started looking into this problem.

Can you tell me:
- what directory was swift run from, and where is the swift .log file for this run?

- what swift was run?

- what machine was it run from?

- did this configuration, with ssh:pbs work for you in the past?

- did you create a valid proxy before running? Did your proxy perhaps expire? (If so there should be a message to that effect in the log).

- did you save all of Swift's stdout/stderr messages form this run, and if so where?

Thanks,

Mike


----- "Wenjun Wu" <wwj at ci.uchicago.edu> wrote:

> Hi Mike,
>   I posted tc.data, sites.xml and coasters.log here.
> 
> Wenjun
> 
> coasterpads     LoopModel        
> /autonfs/gpfs-pads/oops/scienceportal/oops-svn/protlib2/bin/LoopModel.sh
>       
> null    null    GLOBUS::maxwalltime="02:00:00"
> localhost       PrepLoop         
> /autonfs/gpfs-pads/oops/scienceportal/oops-svn/protlib2/bin/preploop.sh
>        
> null    null    null
> localhost       PostProcessLoops 
> /autonfs/gpfs-pads/oops/scienceportal/oops-svn/protlib2/bin/PostProcessLoops.sh
>        
> null    null    null
> 
> <pool handle="coasterpads">
>     <execution provider="coaster" url="login.pads.ci.uchicago.edu" 
> jobmanager="ssh:pbs"/>
> 
>     <profile namespace="globus" key="workersPerNode">2</profile>
>     <profile namespace="globus" key="slots">1</profile>
>     <profile namespace="globus" key="nodeGranularity">1</profile>
>     <profile namespace="globus" key="maxNodes">10</profile>
>     <profile namespace="karajan" key="jobThrottle">0.5</profile>
>     <profile namespace="karajan" key="initialScore">10000</profile>
> 
>     <filesystem provider="ssh" url="login.pads.ci.uchicago.edu"/>
>     <workdirectory>/gpfs/pads/oops/workflows</workdirectory>
>   </pool>
> 
> 2010-03-11 11:02:50,617 1195158935 Processing file list
> 2010-03-11 11:02:50,646 1195158935 Updating jars
> 2010-03-11 11:02:50,869 1195158935 Forking service
> 2010-03-11 11:02:50,869 1195158935 Moved coaster jar to head of
> classpath
> 2010-03-11 11:02:50,870 1195158935 Args: [nice, -n, 2, 
> /home/wwj/Desktop/jdk1.5.0_07/bin/java, -Xmx256M, 
> -DGLOBUS_HOSTNAME=login.pads.ci.uchicago.edu, 
> -Djava.security.egd=file:///dev/urandom, -cp, 
> /home/wwj/.globus/coasters/cache/cog-provider-coaster-0.3-ad4cd4f04d7ce5e14eb3cb2fe39b9d60.jar:/home/wwj/.globus/coasters/cache/backport-util
> 
> > Wenjun, its possible that your sites.xml is specifying parameters
> that are not grantable by the cluster.  Eg, a queue that doesnt exist,
> more nodes than exist, more time than is valid for a queue, etc.
> >
> > Please post your sites.xml and tc files - thats the first place to
> look for these problems.
> >
> > The cause may be visible in logs from PBS under
> $HOME/.globus/{coasters,...}
> >
> > - Mike
> >
> > ----- "Wenjun Wu" <wwj at ci.uchicago.edu> wrote:
> >
> >   
> >> Hi Mike,
> >>  I encountered a problem with running coaster on pad again.
> >>  From the attached log file, the error message says:
> >>  "Caused by: Could not submit job
> >> Caused by: 
> >>
> org.globus.cog.abstraction.impl.common.task.TaskSubmissionException: 
> >> Could not submit job
> >> Caused by: 
> >>
> org.globus.cog.abstraction.impl.common.task.TaskSubmissionException: 
> >> Could not start coaster service
> >> Caused by: 
> >>
> org.globus.cog.abstraction.impl.common.task.TaskSubmissionException: 
> >> Task ended before registration was received. "
> >>
> >> Is there any way to figure what might cause this?
> >> Thanks,
> >>
> >> Wenjun
> >>     
> >>> Hi Mike,
> >>>  Right now I can run the loop model using ssh:pbs through
> coaster.
> >>>       
> >> But 
> >>     
> >>> it can only run one job on one node at one moment.
> >>>  Whenever I increase the values for workersPerNode, maxNodes and 
> >>> jobThrottle so that the workflow can run on multiple nodes through
> 
> >>> coaster,
> >>>  it run into a problem. Please take a look at the error message.
> >>>
> >>> Thanks,
> >>>
> >>> Wenjun
> >>>
> >>> Begin PBS Epilogue Mon Mar  1 15:51:56 CST 2010
> >>> Job ID:        5754.svc.pads.ci.uchicago.edu
> >>> Username:    wwj
> >>> Group:        ci-users
> >>> Job Name:    null
> >>> Session:    32252
> >>> Limits:        nodes=5,walltime=04:00:00
> >>> Resources:   
> cput=00:00:00,mem=708kb,vmem=8400kb,walltime=00:00:02
> >>> Nodes:        
> >>>
> >>>       
> >>
> c48.pads.ci.uchicago.edu,c46.pads.ci.uchicago.edu,c45.pads.ci.uchicago.edu,c06.pads.ci.uchicago.edu,c07.pads.ci.uchicago.edu
> >>
> >>     
> >>> End PBS Epilogue Mon Mar  1 15:51:56 CST 2010
> >>> ----------------------------------------
> >>>
> >>>
> >>>
> >>>    at 
> >>>
> >>>       
> >>
> org.globus.cog.karajan.workflow.events.FailureNotificationEvent.<init>(FailureNotificationEvent.java:36)
> >>
> >>     
> >>>    at 
> >>>
> >>>       
> >>
> org.globus.cog.karajan.workflow.events.FailureNotificationEvent.<init>(FailureNotificationEvent.java:42)
> >>
> >>     
> >>>    at 
> >>>
> >>>       
> >>
> org.globus.cog.karajan.workflow.nodes.FlowNode.failImmediately(FlowNode.java:147)
> >>
> >>     
> >>>    at 
> >>>
> >>>       
> >>
> org.globus.cog.karajan.workflow.nodes.grid.GridExec.taskFailed(GridExec.java:320)
> >>
> >>     
> >>>    at 
> >>>
> >>>       
> >>
> org.globus.cog.karajan.workflow.nodes.grid.AbstractGridNode.statusChanged(AbstractGridNode.java:276)
> >>
> >>     
> >>>    at
> >>>       
> >>
> org.griphyn.vdl.karajan.lib.Execute.statusChanged(Execute.java:104)
> >>     
> >>>    at 
> >>>
> >>>       
> >>
> org.globus.cog.karajan.scheduler.AbstractScheduler.fireJobStatusChangeEvent(AbstractScheduler.java:168)
> >>
> >>     
> >>>    at 
> >>>
> >>>       
> >>
> org.globus.cog.karajan.scheduler.LateBindingScheduler.statusChanged(LateBindingScheduler.java:661)
> >>
> >>     
> >>>    at 
> >>>
> >>>       
> >>
> org.globus.cog.karajan.scheduler.WeightedHostScoreScheduler.statusChanged(WeightedHostScoreScheduler.java:424)
> >>
> >>     
> >>>    at 
> >>>
> >>>       
> >>
> org.griphyn.vdl.karajan.VDSAdaptiveScheduler.statusChanged(VDSAdaptiveScheduler.java:410)
> >>
> >>     
> >>>    at 
> >>>
> >>>       
> >>
> org.globus.cog.abstraction.impl.common.task.TaskImpl.notifyListeners(TaskImpl.java:236)
> >>
> >>     
> >>>    at 
> >>>
> >>>       
> >>
> org.globus.cog.abstraction.impl.common.task.TaskImpl.setStatus(TaskImpl.java:224)
> >>
> >>     
> >>>    at 
> >>>
> >>>       
> >>
> org.globus.cog.abstraction.impl.execution.coaster.NotificationManager.setStatus(NotificationManager.java:112)
> >>
> >>     
> >>>    at 
> >>>
> >>>       
> >>
> org.globus.cog.abstraction.impl.execution.coaster.NotificationManager.notificationReceived(NotificationManager.java:78)
> >>
> >>     
> >>>    at 
> >>>
> >>>       
> >>
> org.globus.cog.abstraction.coaster.service.local.JobStatusHandler.requestComplete(JobStatusHandler.java:45)
> >>
> >>     
> >>>    at 
> >>>
> >>>       
> >>
> org.globus.cog.karajan.workflow.service.handlers.RequestHandler.receiveCompleted(RequestHandler.java:84)
> >>
> >>     
> >>>    at 
> >>>
> >>>       
> >>
> org.globus.cog.karajan.workflow.service.channels.AbstractKarajanChannel.handleRequest(AbstractKarajanChannel.java:348)
> >>
> >>     
> >>>    at 
> >>>
> >>>       
> >>
> org.globus.cog.karajan.workflow.service.channels.AbstractStreamKarajanChannel.step(AbstractStreamKarajanChannel.java:156)
> >>
> >>     
> >>>    at 
> >>>
> >>>       
> >>
> org.globus.cog.karajan.workflow.service.channels.AbstractStreamKarajanChannel$Multiplexer.run(AbstractStreamKarajanChannel.java:365)
> >>
> >>     
> >>> 2010-03-01 15:52:00,639-0600 INFO  ExecutionContext Detailed
> >>>       
> >> exception:
> >>     
> >>> Exception in LoopModel:
> >>> Arguments: [output/data//T0510D1.pdb, output/run/T0510D1.14.pdb]
> >>> Host: coasterpads
> >>> Directory:
> >>>       
> >> psim.loops-20100301-1551-7qejrfd0/jobs/8/LoopModel-89hxehoj
> >>     
> >>> stderr.txt:
> >>>
> >>> stdout.txt:
> >>>
> >>> ----
> >>>
> >>> Caused by: Task failed: 0301-510351-000000 Block task ended
> >>>       
> >> prematurely
> >>     
> >>>> Wenjun, I'll be at Argonne in about an hour - lets try to debug
> >>>>         
> >> this 
> >>     
> >>>> together.
> >>>>
> >>>> Lets do it step by step: first lets test that we can submit ssh
> >>>>         
> >> jobs 
> >>     
> >>>> from communicado to pads; then do coasters on top of that 
> >>>> (provider=ssh:pbs) unless you suggest differently, Mihael.
> >>>>
> >>>> (The other possibility is ssh from communicado to run *swift* on
> 
> >>>> pads. Given that the share /home and /gpfs/pads, this might be a
> >>>>         
> >> good 
> >>     
> >>>> easy option?)
> >>>>
> >>>> - Mike
> >>>>
> >>>> ----- "Wenjun Wu" <wwj at ci.uchicago.edu> wrote:
> >>>>
> >>>>  
> >>>>         
> >>>>> Hi Mihael,
> >>>>>   Please find the attached log file and sites.xml.
> >>>>>   I run the swift script from sidgrid to pads. And ssh "which
> >>>>>           
> >> qsub" 
> >>     
> >>>>> returns the right path.
> >>>>>   But the coaster didn't work for me.
> >>>>>
> >>>>>  Thanks!
> >>>>>
> >>>>> Wenjun
> >>>>>    
> >>>>>           
> >>>>>> I think what's happening in Wenjun's case is that qsub is not
> in
> >>>>>>       
> >>>>>>             
> >>>>> the
> >>>>>    
> >>>>>           
> >>>>>> path. I suppose this could be tested by running a simple ssh
> job
> >>>>>>       
> >>>>>>             
> >>>>> that
> >>>>>    
> >>>>>           
> >>>>>> does "which qsub".
> >>>>>>
> >>>>>> On Thu, 2010-02-25 at 16:08 -0600, Michael Wilde wrote:
> >>>>>>        
> >>>>>>             
> >>>>>>> Was: Re: [PADS Support #3457] globus services for accessing
> >>>>>>>               
> >> PADS
> >>     
> >>>>>>> -- 
> >>>>>>>
> >>>>>>> Hi Wenjun,
> >>>>>>>
> >>>>>>> Are you doing this from communicado? If so, you need to use
> ssh
> >>>>>>>               
> >> to
> >>     
> >>>>>>>         
> >>>>>>>               
> >>>>> get
> >>>>>    
> >>>>>           
> >>>>>>> from communicado to PADS. And since when you get there you
> want
> >>>>>>>               
> >> to
> >>     
> >>>>>>>         
> >>>>>>>               
> >>>>> run
> >>>>>    
> >>>>>           
> >>>>>>> coasters. you need I think to use the coaster provider and
> >>>>>>>         
> >>>>>>>               
> >>>>> jobmanager
> >>>>>    
> >>>>>           
> >>>>>>> = ssh:pbs.
> >>>>>>>
> >>>>>>> I'm cc'ing swift-user and Mihael to discuss the exact sites
> >>>>>>>         
> >>>>>>>               
> >>>>> options
> >>>>>    
> >>>>>           
> >>>>>>> needed.
> >>>>>>>
> >>>>>>> We'd want coasters to use ssh to launch one PBS job to launch
> >>>>>>>               
> >> all
> >>     
> >>>>>>>         
> >>>>>>>               
> >>>>> the
> >>>>>    
> >>>>>           
> >>>>>>> workers.
> >>>>>>> I think there are still some issues on PADS with interpreting
> >>>>>>>         
> >>>>>>>               
> >>>>> #nodes
> >>>>>    
> >>>>>           
> >>>>>>> and workerspernode correctly, so please bear with us while we
> >>>>>>>         
> >>>>>>>               
> >>>>> figure
> >>>>>    
> >>>>>           
> >>>>>>> this out.
> >>>>>>>
> >>>>>>> I'll try this myself later tonight, but if you discover
> >>>>>>>               
> >> anything
> >>     
> >>>>>>> (either working of failing) please post to the User list.
> >>>>>>>
> >>>>>>> Thanks,
> >>>>>>>
> >>>>>>> Mike
> >>>>>>>
> >>>>>>>
> >>>>>>> ----- "Wenjun Wu" <wwj at ci.uchicago.edu> wrote:
> >>>>>>>
> >>>>>>>            
> >>>>>>>               
> >>>>>>>> Hi Mike,
> >>>>>>>>   I tried to run loop model through ssh+pbs on PADS. The ssh
> >>>>>>>>           
> >>>>>>>>                 
> >>>>> provider
> >>>>>    
> >>>>>           
> >>>>>>>> seems working but pbs not.
> >>>>>>>>   Please check the site file and error message in the below:
> >>>>>>>>  
> >>>>>>>> Wenjun
> >>>>>>>>                
> >>>>>>>>                 
> >>>>>>>>> Wenjun,
> >>>>>>>>>
> >>>>>>>>> I think having GRAM (GRAM5 especially) on PADS would be
> >>>>>>>>>                   
> >> useful.
> >>     
> >>>>>>>>> But in the meantime, I think you can also use swift's ssh
> >>>>>>>>>             
> >>>>>>>>>                   
> >>>>> provider
> >>>>>    
> >>>>>           
> >>>>>>>>>                     
> >>>>>>>>>                   
> >>>>>>>> to get to PADS.
> >>>>>>>>                
> >>>>>>>>                 
> >>>>>>>>> We'll need to try that.
> >>>>>>>>>
> >>>>>>>>> - Mike
> >>>>>>>>>
> >>>>>>>>>                       
> >>>>>>>>>                   
> >>>>>>>> <pool handle="pads">
> >>>>>>>>     <!-- gridftp url="gsiftp://stor.ci.uchicago.edu"/ -->
> >>>>>>>>     <filesystem url="login.pads.ci.uchicago.edu"
> >>>>>>>>                 
> >> provider="ssh"
> >>     
> >>>>>>>>           
> >>>>>>>>                 
> >>>>> />
> >>>>>    
> >>>>>           
> >>>>>>>>     <execution provider="pbs" url="svc.pads.ci.uchicago.edu"
> >>>>>>>>                 
> >> />
> >>     
> >>>>>>>>     <workdirectory>/gpfs/pads/oops/workflows</workdirectory>
> >>>>>>>>     <profile namespace="karajan"
> >>>>>>>>                 
> >> key="jobThrottle">0.03</profile>
> >>     
> >>>>>>>>     <profile namespace="karajan"
> >>>>>>>>           
> >>>>>>>>                 
> >>>>> key="initialScore">10000</profile>
> >>>>>    
> >>>>>           
> >>>>>>>>  </pool>
> >>>>>>>>
> >>>>>>>> Caused by: qstat failed (exit code 255)
> >>>>>>>>
> >>>>>>>>         at
> >>>>>>>>           
> >>>>>>>>                 
> >>
> org.globus.cog.karajan.workflow.events.FailureNotificationEvent.<init>(FailureNotificationEvent.java:36)
> >>
> >>     
> >>>>>    
> >>>>>           
> >>>>>>>>         at
> >>>>>>>>           
> >>>>>>>>                 
> >>
> org.globus.cog.karajan.workflow.events.FailureNotificationEvent.<init>(FailureNotificationEvent.java:42)
> >>
> >>     
> >>>>>    
> >>>>>           
> >>>>>>>>         at
> >>>>>>>>           
> >>>>>>>>                 
> >>
> org.globus.cog.karajan.workflow.nodes.FlowNode.failImmediately(FlowNode.java:147)
> >>
> >>     
> >>>>>    
> >>>>>           
> >>>>>>>>         at
> >>>>>>>>           
> >>>>>>>>                 
> >>
> org.globus.cog.karajan.workflow.nodes.grid.GridExec.taskFailed(GridExec.java:320)
> >>
> >>     
> >>>>>    
> >>>>>           
> >>>>>>>>         at
> >>>>>>>>           
> >>>>>>>>                 
> >>
> org.globus.cog.karajan.workflow.nodes.grid.AbstractGridNode.statusChanged(AbstractGridNode.java:276)
> >>
> >>     
> >>>>>    
> >>>>>           
> >>>>>>>>         at
> >>>>>>>>           
> >>>>>>>>                 
> >>
> org.griphyn.vdl.karajan.lib.Execute.statusChanged(Execute.java:104)
> >>     
> >>>>>    
> >>>>>           
> >>>>>>>>         at
> >>>>>>>>           
> >>>>>>>>                 
> >>
> org.globus.cog.karajan.scheduler.AbstractScheduler.fireJobStatusChangeEvent(AbstractScheduler.java:168)
> >>
> >>     
> >>>>>    
> >>>>>           
> >>>>>>>>         at
> >>>>>>>>           
> >>>>>>>>                 
> >>
> org.globus.cog.karajan.scheduler.LateBindingScheduler.statusChanged(LateBindingScheduler.java:661)
> >>
> >>     
> >>>>>    
> >>>>>           
> >>>>>>>>         at
> >>>>>>>>           
> >>>>>>>>                 
> >>
> org.globus.cog.karajan.scheduler.WeightedHostScoreScheduler.statusChanged(WeightedHostScoreScheduler.java:424)
> >>
> >>     
> >>>>>    
> >>>>>           
> >>>>>>>>         at
> >>>>>>>>           
> >>>>>>>>                 
> >>
> org.griphyn.vdl.karajan.VDSAdaptiveScheduler.statusChanged(VDSAdaptiveScheduler.java:410)
> >>
> >>     
> >>>>>    
> >>>>>           
> >>>>>>>>         at
> >>>>>>>>           
> >>>>>>>>                 
> >>
> org.globus.cog.abstraction.impl.common.task.TaskImpl.notifyListeners(TaskImpl.java:236)
> >>
> >>     
> >>>>>    
> >>>>>           
> >>>>>>>>         at
> >>>>>>>>           
> >>>>>>>>                 
> >>
> org.globus.cog.abstraction.impl.common.task.TaskImpl.setStatus(TaskImpl.java:224)
> >>
> >>     
> >>>>>    
> >>>>>           
> >>>>>>>>         at
> >>>>>>>>           
> >>>>>>>>                 
> >>
> org.globus.cog.abstraction.impl.common.AbstractDelegatedTaskHandler.failTask(AbstractDelegatedTaskHandler.java:54)
> >>
> >>     
> >>>>>    
> >>>>>           
> >>>>>>>>         at
> >>>>>>>>           
> >>>>>>>>                 
> >>
> org.globus.cog.abstraction.impl.scheduler.common.AbstractJobSubmissionTaskHandler.processFailed(AbstractJobSubmissionTaskHandler.java:101)
> >>
> >>     
> >>>>>    
> >>>>>           
> >>>>>>>>         at
> >>>>>>>>           
> >>>>>>>>                 
> >>
> org.globus.cog.abstraction.impl.scheduler.common.AbstractExecutor.processFailed(AbstractExecutor.java:246)
> >>
> >>     
> >>>>>    
> >>>>>           
> >>>>>>>>         at
> >>>>>>>>           
> >>>>>>>>                 
> >>
> org.globus.cog.abstraction.impl.scheduler.common.Job.fail(Job.java:198)
> >>     
> >>>>>    
> >>>>>           
> >>>>>>>>         at
> >>>>>>>>           
> >>>>>>>>                 
> >>
> org.globus.cog.abstraction.impl.scheduler.common.AbstractQueuePoller.failAll(AbstractQueuePoller.java:141)
> >>
> >>     
> >>>>>    
> >>>>>           
> >>>>>>>>         at
> >>>>>>>>           
> >>>>>>>>                 
> >>
> org.globus.cog.abstraction.impl.scheduler.common.AbstractQueuePoller.pollQueue(AbstractQueuePoller.java:172)
> >>
> >>     
> >>>>>    
> >>>>>           
> >>>>>>>>         at
> >>>>>>>>           
> >>>>>>>>                 
> >>
> org.globus.cog.abstraction.impl.scheduler.common.AbstractQueuePoller.run(AbstractQueuePoller.java:80)
> >>
> >>     
> >>>>>    
> >>>>>           
> >>>>>>>>         ... 1 more
> >>>>>>>>
> >>>>>>>>
> >>>>>>>>                
> >>>>>>>>                 
> >>>>>>>>> ----- "Ti Leggett" <pads-support at ci.uchicago.edu> wrote:
> >>>>>>>>>
> >>>>>>>>>                      
> >>>>>>>>>                   
> >>>>>>>>>> There are currently no Globus job managers, but GridFTP is
> >>>>>>>>>>                     
> >> at
> >>     
> >>>>>>>>>> stor.ci.uchicago.edu.
> >>>>>>>>>>
> >>>>>>>>>> I'll work on getting GRAM up. Do you need WSRF or Pre-WS
> >>>>>>>>>>                     
> >> GRAM?
> >>     
> >>>>>>>>>> On Wed Feb 24 14:45:57 2010, wwj at ci.uchicago.edu wrote:
> >>>>>>>>>>                            
> >>>>>>>>>>                     
> >>>>>>>>>>> Hello,
> >>>>>>>>>>>    Could you please tell me whether there is any globus
> >>>>>>>>>>>                 
> >>>>>>>>>>>                       
> >>>>> services
> >>>>>    
> >>>>>           
> >>>>>>>>>>>                             
> >>>>>>>>>>>                       
> >>>>>>>> for
> >>>>>>>>                
> >>>>>>>>                 
> >>>>>>>>>>>       PADS such as GridFTP and GRAM?
> >>>>>>>>>>>    I'm trying to launch jobs to PADS remotely but can't
> >>>>>>>>>>>                       
> >> figure
> >>     
> >>>>>>>>>>>                             
> >>>>>>>>>>>                       
> >>>>>>>> out
> >>>>>>>>                
> >>>>>>>>                 
> >>>>>>>>>>>                                   
> >>>>>>>>>>>                       
> >>>>>>>>>> what                            
> >>>>>>>>>>                     
> >>>>>>>>>>> are the right URLs for the GridFTP
> >>>>>>>>>>>    service and GRAM.
> >>>>>>>>>>>    Thanks!
> >>>>>>>>>>>
> >>>>>>>>>>> Wenjun
> >>>>>>>>>>>                                   
> >>>>>>>>>>>                       
> >>>>>>>>>                     
> >>>>>>>>>                   
> >>>>>>         
> >>>>>>             
> >>>>> 2010-02-25 17:12:00,157-0600 DEBUG Loader Max heap: 266403840
> >>>>> 2010-02-25 17:12:00,159-0600 DEBUG Loader kmlversion is
> >>>>>    
> >>>>>           
> >>>>>> cd1f7f6b-6e05-4723-ac70-e8683b56ae98<
> >>>>>>       
> >>>>>>             
> >>>>> 2010-02-25 17:12:00,159-0600 DEBUG Loader build version is
> >>>>>    
> >>>>>           
> >>>>>> f3073b05-a317-4f56-a26f-f87b6abd1af3<
> >>>>>>       
> >>>>>>             
> >>>>> 2010-02-25 17:12:00,159-0600 INFO  Loader psim.loops.swift:
> >>>>>           
> >> source
> >>     
> >>>>> file was compiled with a different version of Swift.
> Recompiling.
> >>>>> 2010-02-25 17:12:01,274-0600 INFO  Karajan Validation of XML
> >>>>> intermediate file was successful
> >>>>> 2010-02-25 17:12:01,982-0600 INFO  VDL2ExecutionContext Stack
> >>>>>           
> >> dump:
> >>     
> >>>>> Level 1
> >>>>> [iA = 0, iB = 0, bA = false, bB = false]
> >>>>>     vdl:instanceconfig = Swift configuration []
> >>>>>     vdl:operation = run
> >>>>>     swift.home =
> >>>>> /home/wwj/SIDGrid/swift/cog-branch/modules/swift/dist/swift-svn
> >>>>>     PATH_SEPARATOR = /
> >>>>>
> >>>>>
> >>>>> 2010-02-25 17:12:02,907-0600 INFO  unknown Using sites file:
> >>>>> ./sites.xml
> >>>>> 2010-02-25 17:12:02,908-0600 INFO  unknown Using tc.data:
> >>>>>           
> >> ./tc.data
> >>     
> >>>>> 2010-02-25 17:12:03,089-0600 INFO  AbstractScheduler Setting
> >>>>>           
> >> resources
> >>     
> >>>>> to: {pads=pads, localhost=localhost, pbs=pbs,
> >>>>> pbs-coaster=pbs-coaster}
> >>>>> 2010-02-25 17:12:03,711-0600 INFO  unknown Swift svn
> swift-r3246
> >>>>> cog-r2721
> >>>>>
> >>>>> 2010-02-25 17:12:03,713-0600 INFO  unknown RUNID
> >>>>>
> id=tag:benc at ci.uchicago.edu,2007:swift:run:20100225-1712-3zrtb5i5
> >>>>> 2010-02-25 17:12:03,916-0600 INFO  AbstractDataNode closed
> >>>>> org.griphyn.vdl.mapping.RootDataNode identifier
> >>>>>
> >>>>>           
> >>
> tag:benc at ci.uchicago.edu,2008:swift:dataset:20100225-1712-kjif48ad:720000000001
> >>
> >>     
> >>>>> type string value=input dataset=unnamed SwiftScript value
> >>>>>           
> >> (closed)
> >>     
> >>>>> 2010-02-25 17:12:03,925-0600 INFO  New NEW
> >>>>>
> >>>>>           
> >>
> id=tag:benc at ci.uchicago.edu,2008:swift:dataset:20100225-1712-kjif48ad:720000000001
> >>
> >>     
> >>>>> 2010-02-25 17:12:03,925-0600 INFO  AbstractDataNode closed
> >>>>> org.griphyn.vdl.mapping.RootDataNode identifier
> >>>>>
> >>>>>           
> >>
> tag:benc at ci.uchicago.edu,2008:swift:dataset:20100225-1712-kjif48ad:720000000002
> >>
> >>     
> >>>>> type string value=LoopModelResults.map dataset=unnamed
> >>>>>           
> >> SwiftScript
> >>     
> >>>>> value (closed)
> >>>>> 2010-02-25 17:12:03,925-0600 INFO  New NEW
> >>>>>
> >>>>>           
> >>
> id=tag:benc at ci.uchicago.edu,2008:swift:dataset:20100225-1712-kjif48ad:720000000002
> >>
> >>     
> >>>>> 2010-02-25 17:12:03,925-0600 INFO  AbstractDataNode closed
> >>>>> org.griphyn.vdl.mapping.RootDataNode identifier
> >>>>>
> >>>>>           
> >>
> tag:benc at ci.uchicago.edu,2008:swift:dataset:20100225-1712-kjif48ad:720000000003
> >>
> >>     
> >>>>> type string value=indir dataset=unnamed SwiftScript value
> >>>>>           
> >> (closed)
> >>     
> >>>>> 2010-02-25 17:12:03,926-0600 INFO  New NEW
> >>>>>
> >>>>>           
> >>
> id=tag:benc at ci.uchicago.edu,2008:swift:dataset:20100225-1712-kjif48ad:720000000003
> >>
> >>     
> >>>>> 2010-02-25 17:12:03,926-0600 INFO  AbstractDataNode closed
> >>>>> org.griphyn.vdl.mapping.RootDataNode identifier
> >>>>>
> >>>>>           
> >>
> tag:benc at ci.uchicago.edu,2008:swift:dataset:20100225-1712-kjif48ad:720000000004
> >>
> >>     
> >>>>> type string value=output dataset=unnamed SwiftScript value
> >>>>>           
> >> (closed)
> >>     
> >>>>> 2010-02-25 17:12:03,926-0600 INFO  New NEW
> >>>>>
> >>>>>           
> >>
> id=tag:benc at ci.uchicago.edu,2008:swift:dataset:20100225-1712-kjif48ad:720000000004
> >>
> >>     
> >>>>> 2010-02-25 17:12:03,926-0600 INFO  AbstractDataNode closed
> >>>>> org.griphyn.vdl.mapping.RootDataNode identifier
> >>>>>
> >>>>>           
> >>
> tag:benc at ci.uchicago.edu,2008:swift:dataset:20100225-1712-kjif48ad:720000000005
> >>
> >>     
> >>>>> type string value=outdir dataset=unnamed SwiftScript value
> >>>>>           
> >> (closed)
> >>     
> >>>>> 2010-02-25 17:12:03,926-0600 INFO  New NEW
> >>>>>
> >>>>>           
> >>
> id=tag:benc at ci.uchicago.edu,2008:swift:dataset:20100225-1712-kjif48ad:720000000005
> >>
> >>     
> >>>>> 2010-02-25 17:12:03,926-0600 INFO  AbstractDataNode closed
> >>>>> org.griphyn.vdl.mapping.RootDataNode identifier
> >>>>>
> >>>>>           
> >>
> tag:benc at ci.uchicago.edu,2008:swift:dataset:20100225-1712-kjif48ad:720000000006
> >>
> >>     
> >>>>> type string value=protein dataset=unnamed SwiftScript value
> >>>>>           
> >> (closed)
> >>     
> >>>>> 2010-02-25 17:12:03,927-0600 INFO  New NEW
> >>>>>
> >>>>>           
> >>
> id=tag:benc at ci.uchicago.edu,2008:swift:dataset:20100225-1712-kjif48ad:720000000006
> >>
> >>     
> >>>>> 2010-02-25 17:12:03,927-0600 INFO  AbstractDataNode closed
> >>>>> org.griphyn.vdl.mapping.RootDataNode identifier
> >>>>>
> >>>>>           
> >>
> tag:benc at ci.uchicago.edu,2008:swift:dataset:20100225-1712-kjif48ad:720000000007
> >>
> >>     
> >>>>> type string value=LoopModelData.map dataset=unnamed SwiftScript
> >>>>>           
> >> value
> >>     
> >>>>> (closed)
> >>>>> 2010-02-25 17:12:03,927-0600 INFO  New NEW
> >>>>>
> >>>>>           
> >>
> id=tag:benc at ci.uchicago.edu,2008:swift:dataset:20100225-1712-kjif48ad:720000000007
> >>
> >>     
> >>>>> 2010-02-25 17:12:03,927-0600 INFO  AbstractDataNode closed
> >>>>> org.griphyn.vdl.mapping.RootDataNode identifier
> >>>>>
> >>>>>           
> >>
> tag:benc at ci.uchicago.edu,2008:swift:dataset:20100225-1712-kjif48ad:720000000008
> >>
> >>     
> >>>>> type string value=4 dataset=unnamed SwiftScript value (closed)
> >>>>> 2010-02-25 17:12:03,927-0600 INFO  New NEW
> >>>>>
> >>>>>           
> >>
> id=tag:benc at ci.uchicago.edu,2008:swift:dataset:20100225-1712-kjif48ad:720000000008
> >>
> >>     
> >>>>> 2010-02-25 17:12:03,928-0600 INFO  AbstractDataNode closed
> >>>>> org.griphyn.vdl.mapping.RootDataNode identifier
> >>>>>
> >>>>>           
> >>
> tag:benc at ci.uchicago.edu,2008:swift:dataset:20100225-1712-kjif48ad:720000000009
> >>
> >>     
> >>>>> type string value=LoopModelOutArray.map dataset=unnamed
> >>>>>           
> >> SwiftScript
> >>     
> >>>>> value (closed)
> >>>>> 2010-02-25 17:12:03,928-0600 INFO  New NEW
> >>>>>
> >>>>>           
> >>
> id=tag:benc at ci.uchicago.edu,2008:swift:dataset:20100225-1712-kjif48ad:720000000009
> >>
> >>     
> >>>>> 2010-02-25 17:12:03,928-0600 INFO  AbstractDataNode closed
> >>>>> org.griphyn.vdl.mapping.RootDataNode identifier
> >>>>>
> >>>>>           
> >>
> tag:benc at ci.uchicago.edu,2008:swift:dataset:20100225-1712-kjif48ad:720000000010
> >>
> >>     
> >>>>> type string value=LoopModelIn.map dataset=unnamed SwiftScript
> >>>>>           
> >> value
> >>     
> >>>>> (closed)
> >>>>> 2010-02-25 17:12:03,928-0600 INFO  New NEW
> >>>>>
> >>>>>           
> >>
> id=tag:benc at ci.uchicago.edu,2008:swift:dataset:20100225-1712-kjif48ad:720000000010
> >>
> >>     
> >>>>> 2010-02-25 17:12:03,928-0600 INFO  AbstractDataNode closed
> >>>>> org.griphyn.vdl.mapping.RootDataNode identifier
> >>>>>
> >>>>>           
> >>
> tag:benc at ci.uchicago.edu,2008:swift:dataset:20100225-1712-kjif48ad:720000000011
> >>
> >>     
> >>>>> type string value=nSim dataset=unnamed SwiftScript value
> (closed)
> >>>>> 2010-02-25 17:12:03,928-0600 INFO  New NEW
> >>>>>
> >>>>>           
> >>
> id=tag:benc at ci.uchicago.edu,2008:swift:dataset:20100225-1712-kjif48ad:720000000011
> >>
> >>     
> >>>>> 2010-02-25 17:12:03,932-0600 INFO  AbstractDataNode closed
> >>>>> org.griphyn.vdl.mapping.RootDataNode identifier
> >>>>>
> >>>>>           
> >>
> tag:benc at ci.uchicago.edu,2008:swift:dataset:20100225-1712-kjif48ad:720000000012
> >>
> >>     
> >>>>> type int value=1.0 dataset=unnamed SwiftScript value (closed)
> >>>>> 2010-02-25 17:12:03,932-0600 INFO  New NEW
> >>>>>
> >>>>>           
> >>
> id=tag:benc at ci.uchicago.edu,2008:swift:dataset:20100225-1712-kjif48ad:720000000012
> >>
> >>     
> >>>>> 2010-02-25 17:12:03,933-0600 INFO  AbstractDataNode closed
> >>>>> org.griphyn.vdl.mapping.RootDataNode identifier
> >>>>>
> >>>>>           
> >>
> tag:benc at ci.uchicago.edu,2008:swift:dataset:20100225-1712-kjif48ad:720000000013
> >>
> >>     
> >>>>> type int value=0.0 dataset=unnamed SwiftScript value (closed)
> >>>>> 2010-02-25 17:12:03,933-0600 INFO  New NEW
> >>>>>
> >>>>>           
> >>
> id=tag:benc at ci.uchicago.edu,2008:swift:dataset:20100225-1712-kjif48ad:720000000013
> >>
> >>     
> >>>>> 2010-02-25 17:12:03,946-0600 INFO  modelloops STARTCOMPOUND
> >>>>>           
> >> thread=0-1
> >>     
> >>>>> name=ModelLoops
> >>>>> 2010-02-25 17:12:03,973-0600 INFO  New NEW
> >>>>>
> >>>>>           
> >>
> id=tag:benc at ci.uchicago.edu,2008:swift:dataset:20100225-1712-kjif48ad:720000000014
> >>
> >>     
> >>>>> 2010-02-25 17:12:03,976-0600 INFO  New NEW
> >>>>>
> >>>>>           
> >>
> id=tag:benc at ci.uchicago.edu,2008:swift:dataset:20100225-1712-kjif48ad:720000000015
> >>
> >>     
> >>>>> 2010-02-25 17:12:03,978-0600 INFO  New NEW
> >>>>>
> >>>>>           
> >>
> id=tag:benc at ci.uchicago.edu,2008:swift:dataset:20100225-1712-kjif48ad:720000000016
> >>
> >>     
> >>>>> 2010-02-25 17:12:03,979-0600 INFO  New NEW
> >>>>>
> >>>>>           
> >>
> id=tag:benc at ci.uchicago.edu,2008:swift:dataset:20100225-1712-kjif48ad:720000000017
> >>
> >>     
> >>>>> 2010-02-25 17:12:03,985-0600 INFO  New NEW
> >>>>>
> >>>>>           
> >>
> id=tag:benc at ci.uchicago.edu,2008:swift:dataset:20100225-1712-kjif48ad:720000000018
> >>
> >>     
> >>>>> 2010-02-25 17:12:03,987-0600 INFO  AbstractDataNode Adding
> handle
> >>>>> listener "org.griphyn.vdl.mapping.RootDataNode identifier
> >>>>>
> >>>>>           
> >>
> tag:benc at ci.uchicago.edu,2008:swift:dataset:20100225-1712-kjif48ad:720000000019
> >>
> >>     
> >>>>> type LoopModelIn with no value at dataset=modelIn (not closed)"
> >>>>>           
> >> to
> >>     
> >>>>> "org.griphyn.vdl.mapping.RootDataNode identifier
> >>>>>
> >>>>>           
> >>
> tag:benc at ci.uchicago.edu,2008:swift:dataset:20100225-1712-kjif48ad:720000000018
> >>
> >>     
> >>>>> type string with no value at dataset=swift#mapper#17007 (not
> >>>>>           
> >> closed)"
> >>     
> >>>>> 2010-02-25 17:12:03,987-0600 INFO  New NEW
> >>>>>
> >>>>>           
> >>
> id=tag:benc at ci.uchicago.edu,2008:swift:dataset:20100225-1712-kjif48ad:720000000019
> >>
> >>     
> >>>>> 2010-02-25 17:12:03,989-0600 INFO  New NEW
> >>>>>
> >>>>>           
> >>
> id=tag:benc at ci.uchicago.edu,2008:swift:dataset:20100225-1712-kjif48ad:720000000020
> >>
> >>     
> >>>>> 2010-02-25 17:12:03,991-0600 INFO  AbstractDataNode Adding
> handle
> >>>>> listener "org.griphyn.vdl.mapping.RootDataNode identifier
> >>>>>
> >>>>>           
> >>
> tag:benc at ci.uchicago.edu,2008:swift:dataset:20100225-1712-kjif48ad:720000000021
> >>
> >>     
> >>>>> type LoopModelData with no value at dataset=modelData (not
> >>>>>           
> >> closed)" to
> >>     
> >>>>> "org.griphyn.vdl.mapping.RootDataNode identifier
> >>>>>
> >>>>>           
> >>
> tag:benc at ci.uchicago.edu,2008:swift:dataset:20100225-1712-kjif48ad:720000000020
> >>
> >>     
> >>>>> type string with no value at dataset=swift#mapper#17009 (not
> >>>>>           
> >> closed)"
> >>     
> >>>>> 2010-02-25 17:12:03,991-0600 INFO  New NEW
> >>>>>
> >>>>>           
> >>
> id=tag:benc at ci.uchicago.edu,2008:swift:dataset:20100225-1712-kjif48ad:720000000021
> >>
> >>     
> >>>>> 2010-02-25 17:12:03,993-0600 INFO  New NEW
> >>>>>
> >>>>>           
> >>
> id=tag:benc at ci.uchicago.edu,2008:swift:dataset:20100225-1712-kjif48ad:720000000022
> >>
> >>     
> >>>>> 2010-02-25 17:12:03,997-0600 INFO  AbstractDataNode Adding
> handle
> >>>>> listener "modelOut.$[]/0" to
> >>>>>           
> >> "org.griphyn.vdl.mapping.RootDataNode
> >>     
> >>>>> identifier
> >>>>>
> >>>>>           
> >>
> tag:benc at ci.uchicago.edu,2008:swift:dataset:20100225-1712-kjif48ad:720000000022
> >>
> >>     
> >>>>> type string with no value at dataset=swift#mapper#17011 (not
> >>>>>           
> >> closed)"
> >>     
> >>>>> 2010-02-25 17:12:03,997-0600 INFO  New NEW
> >>>>>
> >>>>>           
> >>
> id=tag:benc at ci.uchicago.edu,2008:swift:dataset:20100225-1712-kjif48ad:720000000023
> >>
> >>     
> >>>>> 2010-02-25 17:12:03,999-0600 INFO  New NEW
> >>>>>
> >>>>>           
> >>
> id=tag:benc at ci.uchicago.edu,2008:swift:dataset:20100225-1712-kjif48ad:720000000024
> >>
> >>     
> >>>>> 2010-02-25 17:12:04,001-0600 INFO  AbstractDataNode Adding
> handle
> >>>>> listener "org.griphyn.vdl.mapping.RootDataNode identifier
> >>>>>
> >>>>>           
> >>
> tag:benc at ci.uchicago.edu,2008:swift:dataset:20100225-1712-kjif48ad:720000000025
> >>
> >>     
> >>>>> type LoopModelResults with no value at dataset=modelResults
> (not
> >>>>> closed)" to "org.griphyn.vdl.mapping.RootDataNode identifier
> >>>>>
> >>>>>           
> >>
> tag:benc at ci.uchicago.edu,2008:swift:dataset:20100225-1712-kjif48ad:720000000024
> >>
> >>     
> >>>>> type string with no value at dataset=swift#mapper#17013 (not
> >>>>>           
> >> closed)"
> >>     
> >>>>> 2010-02-25 17:12:04,001-0600 INFO  New NEW
> >>>>>
> >>>>>           
> >>
> id=tag:benc at ci.uchicago.edu,2008:swift:dataset:20100225-1712-kjif48ad:720000000025
> >>
> >>     
> >>>>> 2010-02-25 17:12:04,007-0600 INFO  SetFieldValue Setting
> >>>>> org.griphyn.vdl.mapping.RootDataNode identifier
> >>>>>
> >>>>>           
> >>
> tag:benc at ci.uchicago.edu,2008:swift:dataset:20100225-1712-kjif48ad:720000000018
> >>
> >>     
> >>>>> type string with no value at dataset=swift#mapper#17007 (not
> >>>>>           
> >> closed)
> >>     
> >>>>> to LoopModelIn.map
> >>>>> 2010-02-25 17:12:04,007-0600 INFO  AbstractDataNode closed
> >>>>> org.griphyn.vdl.mapping.RootDataNode identifier
> >>>>>
> >>>>>           
> >>
> tag:benc at ci.uchicago.edu,2008:swift:dataset:20100225-1712-kjif48ad:720000000026
> >>
> >>     
> >>>>> type string value=4 dataset=unnamed SwiftScript value (closed)
> >>>>> 2010-02-25 17:12:04,007-0600 INFO  VDLFunction FUNCTION
> id=451000
> >>>>> name=arg
> >>>>>
> >>>>>           
> >>
> result=tag:benc at ci.uchicago.edu,2008:swift:dataset:20100225-1712-kjif48ad:720000000026
> >>
> >>     
> >>>>> 2010-02-25 17:12:04,007-0600 INFO  VDLFunction
> FUNCTIONPARAMETER
> >>>>> id=451000
> >>>>>
> >>>>>           
> >>
> input=tag:benc at ci.uchicago.edu,2008:swift:dataset:20100225-1712-kjif48ad:720000000011
> >>
> >>     
> >>>>> name=name
> >>>>> 2010-02-25 17:12:04,007-0600 INFO  VDLFunction
> FUNCTIONPARAMETER
> >>>>> id=451000
> >>>>>
> >>>>>           
> >>
> input=tag:benc at ci.uchicago.edu,2008:swift:dataset:20100225-1712-kjif48ad:720000000008
> >>
> >>     
> >>>>> name=value
> >>>>> 2010-02-25 17:12:04,008-0600 INFO  SetFieldValue Setting
> >>>>> org.griphyn.vdl.mapping.RootDataNode identifier
> >>>>>
> >>>>>           
> >>
> tag:benc at ci.uchicago.edu,2008:swift:dataset:20100225-1712-kjif48ad:720000000020
> >>
> >>     
> >>>>> type string with no value at dataset=swift#mapper#17009 (not
> >>>>>           
> >> closed)
> >>     
> >>>>> to LoopModelData.map
> >>>>> 2010-02-25 17:12:04,008-0600 INFO  AbstractDataNode Notifying
> >>>>>           
> >> listener
> >>     
> >>>>> "org.griphyn.vdl.mapping.RootDataNode identifier
> >>>>>
> >>>>>           
> >>
> tag:benc at ci.uchicago.edu,2008:swift:dataset:20100225-1712-kjif48ad:720000000021
> >>
> >>     
> >>>>> type LoopModelData with no value at dataset=modelData (not
> >>>>>           
> >> closed)"
> >>     
> >>>>> about "org.griphyn.vdl.mapping.RootDataNode identifier
> >>>>>
> >>>>>           
> >>
> tag:benc at ci.uchicago.edu,2008:swift:dataset:20100225-1712-kjif48ad:720000000020
> >>
> >>     
> >>>>> type string value=LoopModelData.map dataset=swift#mapper#17009
> >>>>> (closed)"
> >>>>> 2010-02-25 17:12:04,008-0600 INFO  AbstractDataNode Adding
> handle
> >>>>> listener "org.griphyn.vdl.mapping.RootDataNode identifier
> >>>>>
> >>>>>           
> >>
> tag:benc at ci.uchicago.edu,2008:swift:dataset:20100225-1712-kjif48ad:720000000021
> >>
> >>     
> >>>>> type LoopModelData with no value at dataset=modelData (not
> >>>>>           
> >> closed)" to
> >>     
> >>>>> "org.griphyn.vdl.mapping.RootDataNode identifier
> >>>>>
> >>>>>           
> >>
> tag:benc at ci.uchicago.edu,2008:swift:dataset:20100225-1712-kjif48ad:720000000017
> >>
> >>     
> >>>>> type string with no value at dataset=outdir (not closed)"
> >>>>> 2010-02-25 17:12:04,008-0600 INFO  AbstractDataNode closed
> >>>>> org.griphyn.vdl.mapping.RootDataNode identifier
> >>>>>
> >>>>>           
> >>
> tag:benc at ci.uchicago.edu,2008:swift:dataset:20100225-1712-kjif48ad:720000000020
> >>
> >>     
> >>>>> type string value=LoopModelData.map dataset=swift#mapper#17009
> >>>>> (closed)
> >>>>> 2010-02-25 17:12:04,008-0600 INFO  SetFieldValue Setting
> >>>>> org.griphyn.vdl.mapping.RootDataNode identifier
> >>>>>
> >>>>>           
> >>
> tag:benc at ci.uchicago.edu,2008:swift:dataset:20100225-1712-kjif48ad:720000000022
> >>
> >>     
> >>>>> type string with no value at dataset=swift#mapper#17011 (not
> >>>>>           
> >> closed)
> >>     
> >>>>> to LoopModelOutArray.map
> >>>>> 2010-02-25 17:12:04,009-0600 INFO  AbstractDataNode Notifying
> >>>>>           
> >> listener
> >>     
> >>>>> "modelOut.$[]/0" about "org.griphyn.vdl.mapping.RootDataNode
> >>>>> identifier
> >>>>>
> >>>>>           
> >>
> tag:benc at ci.uchicago.edu,2008:swift:dataset:20100225-1712-kjif48ad:720000000022
> >>
> >>     
> >>>>> type string value=LoopModelOutArray.map
> >>>>>           
> >> dataset=swift#mapper#17011
> >>     
> >>>>> (closed)"
> >>>>> 2010-02-25 17:12:04,009-0600 INFO  AbstractDataNode Adding
> handle
> >>>>> listener "modelOut.$[]/0" to
> >>>>>           
> >> "org.griphyn.vdl.mapping.RootDataNode
> >>     
> >>>>> identifier
> >>>>>
> >>>>>           
> >>
> tag:benc at ci.uchicago.edu,2008:swift:dataset:20100225-1712-kjif48ad:720000000014
> >>
> >>     
> >>>>> type int with no value at dataset=nSim (not closed)"
> >>>>> 2010-02-25 17:12:04,009-0600 INFO  AbstractDataNode closed
> >>>>> org.griphyn.vdl.mapping.RootDataNode identifier
> >>>>>
> >>>>>           
> >>
> tag:benc at ci.uchicago.edu,2008:swift:dataset:20100225-1712-kjif48ad:720000000022
> >>
> >>     
> >>>>> type string value=LoopModelOutArray.map
> >>>>>           
> >> dataset=swift#mapper#17011
> >>     
> >>>>> (closed)
> >>>>> 2010-02-25 17:12:04,009-0600 INFO  SetFieldValue Setting
> >>>>> org.griphyn.vdl.mapping.RootDataNode identifier
> >>>>>
> >>>>>           
> >>
> tag:benc at ci.uchicago.edu,2008:swift:dataset:20100225-1712-kjif48ad:720000000024
> >>
> >>     
> >>>>> type string with no value at dataset=swift#mapper#17013 (not
> >>>>>           
> >> closed)
> >>     
> >>>>> to LoopModelResults.map
> >>>>> 2010-02-25 17:12:04,009-0600 INFO  AbstractDataNode Notifying
> >>>>>           
> >> listener
> >>     
> >>>>> "org.griphyn.vdl.mapping.RootDataNode identifier
> >>>>>
> >>>>>           
> >>
> tag:benc at ci.uchicago.edu,2008:swift:dataset:20100225-1712-kjif48ad:720000000025
> >>
> >>     
> >>>>> type LoopModelResults with no value at dataset=modelResults
> (not
> >>>>> closed)" about "org.griphyn.vdl.mapping.RootDataNode identifier
> >>>>>
> >>>>>           
> >>
> tag:benc at ci.uchicago.edu,2008:swift:dataset:20100225-1712-kjif48ad:720000000024
> >>
> >>     
> >>>>> type string value=LoopModelResults.map
> dataset=swift#mapper#17013
> >>>>> (closed)"
> >>>>> 2010-02-25 17:12:04,009-0600 INFO  AbstractDataNode Adding
> handle
> >>>>> listener "org.griphyn.vdl.mapping.RootDataNode identifier
> >>>>>
> >>>>>           
> >>
> tag:benc at ci.uchicago.edu,2008:swift:dataset:20100225-1712-kjif48ad:720000000025
> >>
> >>     
> >>>>> type LoopModelResults with no value at dataset=modelResults
> (not
> >>>>> closed)" to "org.griphyn.vdl.mapping.RootDataNode identifier
> >>>>>
> >>>>>           
> >>
> tag:benc at ci.uchicago.edu,2008:swift:dataset:20100225-1712-kjif48ad:720000000017
> >>
> >>     
> >>>>> type string with no value at dataset=outdir (not closed)"
> >>>>> 2010-02-25 17:12:04,009-0600 INFO  AbstractDataNode closed
> >>>>> org.griphyn.vdl.mapping.RootDataNode identifier
> >>>>>
> >>>>>           
> >>
> tag:benc at ci.uchicago.edu,2008:swift:dataset:20100225-1712-kjif48ad:720000000024
> >>
> >>     
> >>>>> type string value=LoopModelResults.map
> dataset=swift#mapper#17013
> >>>>> (closed)
> >>>>> 2010-02-25 17:12:04,009-0600 INFO  AbstractDataNode closed
> >>>>> org.griphyn.vdl.mapping.RootDataNode identifier
> >>>>>
> >>>>>           
> >>
> tag:benc at ci.uchicago.edu,2008:swift:dataset:20100225-1712-kjif48ad:720000000027
> >>
> >>     
> >>>>> type string value=T0510D1 dataset=unnamed SwiftScript value
> >>>>>           
> >> (closed)
> >>     
> >>>>> 2010-02-25 17:12:04,009-0600 INFO  VDLFunction FUNCTION
> id=451001
> >>>>> name=arg
> >>>>>
> >>>>>           
> >>
> result=tag:benc at ci.uchicago.edu,2008:swift:dataset:20100225-1712-kjif48ad:720000000027
> >>
> >>     
> >>>>> 2010-02-25 17:12:04,010-0600 INFO  VDLFunction
> FUNCTIONPARAMETER
> >>>>> id=451001
> >>>>>
> >>>>>           
> >>
> input=tag:benc at ci.uchicago.edu,2008:swift:dataset:20100225-1712-kjif48ad:720000000006
> >>
> >>     
> >>>>> name=name
> >>>>> 2010-02-25 17:12:04,010-0600 INFO  SetFieldValue Setting
> >>>>> org.griphyn.vdl.mapping.RootDataNode identifier
> >>>>>
> >>>>>           
> >>
> tag:benc at ci.uchicago.edu,2008:swift:dataset:20100225-1712-kjif48ad:720000000015
> >>
> >>     
> >>>>> type string with no value at dataset=proteinId (not closed) to
> >>>>> T0510D1
> >>>>> 2010-02-25 17:12:04,010-0600 INFO  AbstractDataNode closed
> >>>>> org.griphyn.vdl.mapping.RootDataNode identifier
> >>>>>
> >>>>>           
> >>
> tag:benc at ci.uchicago.edu,2008:swift:dataset:20100225-1712-kjif48ad:720000000015
> >>
> >>     
> >>>>> type string value=T0510D1 dataset=proteinId (closed)
> >>>>> 2010-02-25 17:12:04,010-0600 INFO  CloseDataset Partially
> closing
> >>>>> T0510D1 for statement 88013
> >>>>> 2010-02-25 17:12:04,011-0600 INFO  CloseDataset var is T0510D1
> >>>>> 2010-02-25 17:12:04,011-0600 INFO  CloseDataset var hash is
> >>>>>           
> >> 28062585
> >>     
> >>>>> 2010-02-25 17:12:04,011-0600 INFO  CloseDataset variable
> already
> >>>>> closed - skipping partial close processing
> >>>>> 2010-02-25 17:12:04,011-0600 INFO  AbstractDataNode closed
> >>>>> org.griphyn.vdl.mapping.RootDataNode identifier
> >>>>>
> >>>>>           
> >>
> tag:benc at ci.uchicago.edu,2008:swift:dataset:20100225-1712-kjif48ad:720000000028
> >>
> >>     
> >>>>> type string value=input dataset=unnamed SwiftScript value
> >>>>>           
> >> (closed)
> >>     
> >>>>> 2010-02-25 17:12:04,011-0600 INFO  VDLFunction FUNCTION
> id=451002
> >>>>> name=arg
> >>>>>
> >>>>>           
> >>
> result=tag:benc at ci.uchicago.edu,2008:swift:dataset:20100225-1712-kjif48ad:720000000028
> >>
> >>     
> >>>>> 2010-02-25 17:12:04,011-0600 INFO  VDLFunction
> FUNCTIONPARAMETER
> >>>>> id=451002
> >>>>>
> >>>>>           
> >>
> input=tag:benc at ci.uchicago.edu,2008:swift:dataset:20100225-1712-kjif48ad:720000000003
> >>
> >>     
> >>>>> name=name
> >>>>> 2010-02-25 17:12:04,011-0600 INFO  VDLFunction
> FUNCTIONPARAMETER
> >>>>> id=451002
> >>>>>
> >>>>>           
> >>
> input=tag:benc at ci.uchicago.edu,2008:swift:dataset:20100225-1712-kjif48ad:720000000001
> >>
> >>     
> >>>>> name=value
> >>>>> 2010-02-25 17:12:04,011-0600 INFO  SetFieldValue Setting
> >>>>> org.griphyn.vdl.mapping.RootDataNode identifier
> >>>>>
> >>>>>           
> >>
> tag:benc at ci.uchicago.edu,2008:swift:dataset:20100225-1712-kjif48ad:720000000016
> >>
> >>     
> >>>>> type string with no value at dataset=indir (not closed) to
> input
> >>>>> 2010-02-25 17:12:04,012-0600 INFO  AbstractDataNode closed
> >>>>> org.griphyn.vdl.mapping.RootDataNode identifier
> >>>>>
> >>>>>           
> >>
> tag:benc at ci.uchicago.edu,2008:swift:dataset:20100225-1712-kjif48ad:720000000016
> >>
> >>     
> >>>>> type string value=input dataset=indir (closed)
> >>>>> 2010-02-25 17:12:04,012-0600 INFO  AbstractDataNode Notifying
> >>>>>           
> >> listener
> >>     
> >>>>> "org.griphyn.vdl.mapping.RootDataNode identifier
> >>>>>
> >>>>>           
> >>
> tag:benc at ci.uchicago.edu,2008:swift:dataset:20100225-1712-kjif48ad:720000000019
> >>
> >>     
> >>>>> type LoopModelIn with no value at dataset=modelIn (not closed)"
> >>>>>           
> >> about
> >>     
> >>>>> "org.griphyn.vdl.mapping.RootDataNode identifier
> >>>>>
> >>>>>           
> >>
> tag:benc at ci.uchicago.edu,2008:swift:dataset:20100225-1712-kjif48ad:720000000018
> >>
> >>     
> >>>>> type string value=LoopModelIn.map dataset=swift#mapper#17007
> >>>>> (closed)"
> >>>>> 2010-02-25 17:12:04,012-0600 INFO  AbstractDataNode closed
> >>>>> org.griphyn.vdl.mapping.RootDataNode identifier
> >>>>>
> >>>>>           
> >>
> tag:benc at ci.uchicago.edu,2008:swift:dataset:20100225-1712-kjif48ad:720000000029
> >>
> >>     
> >>>>> type string value=output dataset=unnamed SwiftScript value
> >>>>>           
> >> (closed)
> >>     
> >>>>> 2010-02-25 17:12:04,012-0600 INFO  VDLFunction FUNCTION
> id=451003
> >>>>> name=arg
> >>>>>
> >>>>>           
> >>
> result=tag:benc at ci.uchicago.edu,2008:swift:dataset:20100225-1712-kjif48ad:720000000029
> >>
> >>     
> >>>>> 2010-02-25 17:12:04,012-0600 INFO  VDLFunction
> FUNCTIONPARAMETER
> >>>>> id=451003
> >>>>>
> >>>>>           
> >>
> input=tag:benc at ci.uchicago.edu,2008:swift:dataset:20100225-1712-kjif48ad:720000000005
> >>
> >>     
> >>>>> name=name
> >>>>> 2010-02-25 17:12:04,012-0600 INFO  VDLFunction
> FUNCTIONPARAMETER
> >>>>> id=451003
> >>>>>
> >>>>>           
> >>
> input=tag:benc at ci.uchicago.edu,2008:swift:dataset:20100225-1712-kjif48ad:720000000004
> >>
> >>     
> >>>>> name=value
> >>>>> 2010-02-25 17:12:04,012-0600 INFO  SetFieldValue Setting
> >>>>> org.griphyn.vdl.mapping.RootDataNode identifier
> >>>>>
> >>>>>           
> >>
> tag:benc at ci.uchicago.edu,2008:swift:dataset:20100225-1712-kjif48ad:720000000017
> >>
> >>     
> >>>>> type string with no value at dataset=outdir (not closed) to
> >>>>>           
> >> output
> >>     
> >>>>> 2010-02-25 17:12:04,012-0600 INFO  AbstractDataNode Notifying
> >>>>>           
> >> listener
> >>     
> >>>>> "org.griphyn.vdl.mapping.RootDataNode identifier
> >>>>>
> >>>>>           
> >>
> tag:benc at ci.uchicago.edu,2008:swift:dataset:20100225-1712-kjif48ad:720000000021
> >>
> >>     
> >>>>> type LoopModelData with no value at dataset=modelData (not
> >>>>>           
> >> closed)"
> >>     
> >>>>> about "org.griphyn.vdl.mapping.RootDataNode identifier
> >>>>>
> >>>>>           
> >>
> tag:benc at ci.uchicago.edu,2008:swift:dataset:20100225-1712-kjif48ad:720000000017
> >>
> >>     
> >>>>> type string value=output dataset=outdir (closed)"
> >>>>> 2010-02-25 17:12:04,027-0600 INFO  AbstractDataNode closed
> >>>>> org.griphyn.vdl.mapping.DataNode identifier
> >>>>>
> >>>>>           
> >>
> tag:benc at ci.uchicago.edu,2008:swift:dataset:20100225-1712-kjif48ad:720000000030
> >>
> >>     
> >>>>> type PDB with no value at dataset=modelIn path=.pdb (closed)
> >>>>> 2010-02-25 17:12:04,030-0600 INFO  AbstractDataNode Found data
> >>>>> org.griphyn.vdl.mapping.RootDataNode identifier
> >>>>>
> >>>>>           
> >>
> tag:benc at ci.uchicago.edu,2008:swift:dataset:20100225-1712-kjif48ad:720000000019
> >>
> >>     
> >>>>> type LoopModelIn with no value at dataset=modelIn (not
> >>>>>           
> >> closed)..pdb
> >>     
> >>>>> 2010-02-25 17:12:04,030-0600 INFO  AbstractDataNode closed
> >>>>> org.griphyn.vdl.mapping.DataNode identifier
> >>>>>
> >>>>>           
> >>
> tag:benc at ci.uchicago.edu,2008:swift:dataset:20100225-1712-kjif48ad:720000000031
> >>
> >>     
> >>>>> type Text with no value at dataset=modelIn path=.params
> (closed)
> >>>>> 2010-02-25 17:12:04,032-0600 INFO  AbstractDataNode Found data
> >>>>> org.griphyn.vdl.mapping.RootDataNode identifier
> >>>>>
> >>>>>           
> >>
> tag:benc at ci.uchicago.edu,2008:swift:dataset:20100225-1712-kjif48ad:720000000019
> >>
> >>     
> >>>>> type LoopModelIn with no value at dataset=modelIn (not
> >>>>> closed)..params
> >>>>> 2010-02-25 17:12:04,032-0600 INFO  AbstractDataNode closed
> >>>>> org.griphyn.vdl.mapping.DataNode identifier
> >>>>>
> >>>>>           
> >>
> tag:benc at ci.uchicago.edu,2008:swift:dataset:20100225-1712-kjif48ad:720000000032
> >>
> >>     
> >>>>> type LoopRange with no value at dataset=modelIn path=.range
> >>>>>           
> >> (closed)
> >>     
> >>>>> 2010-02-25 17:12:04,032-0600 INFO  AbstractDataNode Found data
> >>>>> org.griphyn.vdl.mapping.RootDataNode identifier
> >>>>>
> >>>>>           
> >>
> tag:benc at ci.uchicago.edu,2008:swift:dataset:20100225-1712-kjif48ad:720000000019
> >>
> >>     
> >>>>> type LoopModelIn with no value at dataset=modelIn (not
> >>>>>           
> >> closed)..range
> >>     
> >>>>> 2010-02-25 17:12:04,033-0600 INFO  AbstractDataNode closed
> >>>>> org.griphyn.vdl.mapping.RootDataNode identifier
> >>>>>
> >>>>>           
> >>
> tag:benc at ci.uchicago.edu,2008:swift:dataset:20100225-1712-kjif48ad:720000000019
> >>
> >>     
> >>>>> type LoopModelIn with no value at dataset=modelIn (closed)
> >>>>> 2010-02-25 17:12:04,033-0600 INFO  AbstractDataNode closed
> >>>>> org.griphyn.vdl.mapping.RootDataNode identifier
> >>>>>
> >>>>>           
> >>
> tag:benc at ci.uchicago.edu,2008:swift:dataset:20100225-1712-kjif48ad:720000000018
> >>
> >>     
> >>>>> type string value=LoopModelIn.map dataset=swift#mapper#17007
> >>>>>           
> >> (closed)
> >>     
> >>>>> 2010-02-25 17:12:04,034-0600 INFO  CloseDataset Partially
> closing
> >>>>> input for statement 88014
> >>>>> 2010-02-25 17:12:04,035-0600 INFO  CloseDataset var is input
> >>>>> 2010-02-25 17:12:04,035-0600 INFO  CloseDataset var hash is
> >>>>>           
> >> 21684929
> >>     
> >>>>> 2010-02-25 17:12:04,035-0600 INFO  CloseDataset variable
> already
> >>>>> closed - skipping partial close processing
> >>>>> 2010-02-25 17:12:04,040-0600 INFO  loopprepare PROCEDURE
> line=112
> >>>>> thread=0-1-8 name=loopPrepare
> >>>>> 2010-02-25 17:12:04,041-0600 INFO  AbstractDataNode Found
> mapped
> >>>>>           
> >> data
> >>     
> >>>>> org.griphyn.vdl.mapping.RootDataNode identifier
> >>>>>
> >>>>>           
> >>
> tag:benc at ci.uchicago.edu,2008:swift:dataset:20100225-1712-kjif48ad:720000000021
> >>
> >>     
> >>>>> type LoopModelData with no value at dataset=modelData (not
> >>>>> closed)..fasta
> >>>>> 2010-02-25 17:12:04,041-0600 INFO  AbstractDataNode Found
> mapped
> >>>>>           
> >> data
> >>     
> >>>>> org.griphyn.vdl.mapping.RootDataNode identifier
> >>>>>
> >>>>>           
> >>
> tag:benc at ci.uchicago.edu,2008:swift:dataset:20100225-1712-kjif48ad:720000000021
> >>
> >>     
> >>>>> type LoopModelData with no value at dataset=modelData (not
> >>>>> closed)..pdb
> >>>>> 2010-02-25 17:12:04,041-0600 INFO  AbstractDataNode Found
> mapped
> >>>>>           
> >> data
> >>     
> >>>>> org.griphyn.vdl.mapping.RootDataNode identifier
> >>>>>
> >>>>>           
> >>
> tag:benc at ci.uchicago.edu,2008:swift:dataset:20100225-1712-kjif48ad:720000000021
> >>
> >>     
> >>>>> type LoopModelData with no value at dataset=modelData (not
> >>>>> closed)..native
> >>>>> 2010-02-25 17:12:04,041-0600 INFO  AbstractDataNode Found
> mapped
> >>>>>           
> >> data
> >>     
> >>>>> org.griphyn.vdl.mapping.RootDataNode identifier
> >>>>>
> >>>>>           
> >>
> tag:benc at ci.uchicago.edu,2008:swift:dataset:20100225-1712-kjif48ad:720000000021
> >>
> >>     
> >>>>> type LoopModelData with no value at dataset=modelData (not
> >>>>> closed)..index
> >>>>> 2010-02-25 17:12:04,041-0600 INFO  strtoi STARTCOMPOUND
> >>>>>           
> >> thread=0-1-0
> >>     
> >>>>> name=strtoi
> >>>>> 2010-02-25 17:12:04,041-0600 INFO  AbstractDataNode Found
> mapped
> >>>>>           
> >> data
> >>     
> >>>>> org.griphyn.vdl.mapping.RootDataNode identifier
> >>>>>
> >>>>>           
> >>
> tag:benc at ci.uchicago.edu,2008:swift:dataset:20100225-1712-kjif48ad:720000000021
> >>
> >>     
> >>>>> type LoopModelData with no value at dataset=modelData (not
> >>>>> closed)..params
> >>>>> 2010-02-25 17:12:04,041-0600 INFO  AbstractDataNode Found
> mapped
> >>>>>           
> >> data
> >>     
> >>>>> org.griphyn.vdl.mapping.RootDataNode identifier
> >>>>>
> >>>>>           
> >>
> tag:benc at ci.uchicago.edu,2008:swift:dataset:20100225-1712-kjif48ad:720000000021
> >>
> >>     
> >>>>> type LoopModelData with no value at dataset=modelData (not
> >>>>> closed)..range
> >>>>> 2010-02-25 17:12:04,042-0600 INFO  AbstractDataNode Found
> mapped
> >>>>>           
> >> data
> >>     
> >>>>> org.griphyn.vdl.mapping.RootDataNode identifier
> >>>>>
> >>>>>           
> >>
> tag:benc at ci.uchicago.edu,2008:swift:dataset:20100225-1712-kjif48ad:720000000021
> >>
> >>     
> >>>>> type LoopModelData with no value at dataset=modelData (not
> >>>>> closed)..rama
> >>>>> 2010-02-25 17:12:04,042-0600 INFO  AbstractDataNode Found
> mapped
> >>>>>           
> >> data
> >>     
> >>>>> org.griphyn.vdl.mapping.RootDataNode identifier
> >>>>>
> >>>>>           
> >>
> tag:benc at ci.uchicago.edu,2008:swift:dataset:20100225-1712-kjif48ad:720000000021
> >>
> >>     
> >>>>> type LoopModelData with no value at dataset=modelData (not
> >>>>> closed)..map
> >>>>> 2010-02-25 17:12:04,042-0600 INFO  AbstractDataNode Found
> mapped
> >>>>>           
> >> data
> >>     
> >>>>> org.griphyn.vdl.mapping.RootDataNode identifier
> >>>>>
> >>>>>           
> >>
> tag:benc at ci.uchicago.edu,2008:swift:dataset:20100225-1712-kjif48ad:720000000021
> >>
> >>     
> >>>>> type LoopModelData with no value at dataset=modelData (not
> >>>>> closed)..secseq
> >>>>> 2010-02-25 17:12:04,047-0600 INFO  AbstractDataNode Notifying
> >>>>>           
> >> listener
> >>     
> >>>>> "org.griphyn.vdl.mapping.RootDataNode identifier
> >>>>>
> >>>>>           
> >>
> tag:benc at ci.uchicago.edu,2008:swift:dataset:20100225-1712-kjif48ad:720000000025
> >>
> >>     
> >>>>> type LoopModelResults with no value at dataset=modelResults
> (not
> >>>>> closed)" about "org.griphyn.vdl.mapping.RootDataNode identifier
> >>>>>
> >>>>>           
> >>
> tag:benc at ci.uchicago.edu,2008:swift:dataset:20100225-1712-kjif48ad:720000000017
> >>
> >>     
> >>>>> type string value=output dataset=outdir (closed)"
> >>>>> 2010-02-25 17:12:04,051-0600 INFO  loopmodelanalysis PROCEDURE
> >>>>> line=122 thread=0-1-10 name=loopModelAnalysis
> >>>>> 2010-02-25 17:12:04,053-0600 INFO  doloopround STARTCOMPOUND
> >>>>> thread=0-1-9 name=doLoopRound
> >>>>> 2010-02-25 17:12:04,058-0600 INFO  New NEW
> >>>>>
> >>>>>           
> >>
> id=tag:benc at ci.uchicago.edu,2008:swift:dataset:20100225-1712-kjif48ad:720000000042
> >>
> >>     
> >>>>> 2010-02-25 17:12:04,058-0600 INFO  AbstractDataNode Found
> mapped
> >>>>>           
> >> data
> >>     
> >>>>> org.griphyn.vdl.mapping.RootDataNode identifier
> >>>>>
> >>>>>           
> >>
> tag:benc at ci.uchicago.edu,2008:swift:dataset:20100225-1712-kjif48ad:720000000025
> >>
> >>     
> >>>>> type LoopModelResults with no value at dataset=modelResults
> (not
> >>>>> closed)..pwPlot
> >>>>> 2010-02-25 17:12:04,058-0600 INFO  AbstractDataNode Found
> mapped
> >>>>>           
> >> data
> >>     
> >>>>> org.griphyn.vdl.mapping.RootDataNode identifier
> >>>>>
> >>>>>           
> >>
> tag:benc at ci.uchicago.edu,2008:swift:dataset:20100225-1712-kjif48ad:720000000025
> >>
> >>     
> >>>>> type LoopModelResults with no value at dataset=modelResults
> (not
> >>>>> closed)..best
> >>>>> 2010-02-25 17:12:04,059-0600 INFO  AbstractDataNode Found
> mapped
> >>>>>           
> >> data
> >>     
> >>>>> org.griphyn.vdl.mapping.RootDataNode identifier
> >>>>>
> >>>>>           
> >>
> tag:benc at ci.uchicago.edu,2008:swift:dataset:20100225-1712-kjif48ad:720000000025
> >>
> >>     
> >>>>> type LoopModelResults with no value at dataset=modelResults
> (not
> >>>>> closed)..ligationPlot
> >>>>> 2010-02-25 17:12:04,059-0600 INFO  AbstractDataNode closed
> >>>>> org.griphyn.vdl.mapping.RootDataNode identifier
> >>>>>
> >>>>>           
> >>
> tag:benc at ci.uchicago.edu,2008:swift:dataset:20100225-1712-kjif48ad:720000000017
> >>
> >>     
> >>>>> type string value=output dataset=outdir (closed)
> >>>>> 2010-02-25 17:12:04,059-0600 INFO  CloseDataset Partially
> closing
> >>>>> output for statement 88015
> >>>>> 2010-02-25 17:12:04,059-0600 INFO  CloseDataset var is output
> >>>>> 2010-02-25 17:12:04,060-0600 INFO  CloseDataset var hash is
> >>>>>           
> >> 23848591
> >>     
> >>>>> 2010-02-25 17:12:04,060-0600 INFO  CloseDataset variable
> already
> >>>>> closed - skipping partial close processing
> >>>>> 2010-02-25 17:12:04,062-0600 INFO  AbstractDataNode Adding
> handle
> >>>>> listener "F/modelOut.$[]/0" to
> >>>>> "org.griphyn.vdl.mapping.RootArrayDataNode identifier
> >>>>>
> >>>>>           
> >>
> tag:benc at ci.uchicago.edu,2008:swift:dataset:20100225-1712-kjif48ad:720000000023
> >>
> >>     
> >>>>> type LoopModelOut[] with no value at dataset=modelOut (not
> >>>>>           
> >> closed)"
> >>     
> >>>>> 2010-02-25 17:12:04,062-0600 INFO  AbstractDataNode Adding
> handle
> >>>>> listener "F/org.griphyn.vdl.mapping.RootDataNode identifier
> >>>>>
> >>>>>           
> >>
> tag:benc at ci.uchicago.edu,2008:swift:dataset:20100225-1712-kjif48ad:720000000014
> >>
> >>     
> >>>>> type int with no value at dataset=nSim (not closed)" to
> >>>>> "org.griphyn.vdl.mapping.RootDataNode identifier
> >>>>>
> >>>>>           
> >>
> tag:benc at ci.uchicago.edu,2008:swift:dataset:20100225-1712-kjif48ad:720000000014
> >>
> >>     
> >>>>> type int with no value at dataset=nSim (not closed)"
> >>>>> 2010-02-25 17:12:04,065-0600 INFO  strtoi INTERNALPROC_START
> >>>>> thread=0-1-0-1 name=readData
> >>>>> 2010-02-25 17:12:04,068-0600 INFO  AbstractDataNode Adding
> handle
> >>>>> listener "F/org.griphyn.vdl.mapping.RootDataNode identifier
> >>>>>
> >>>>>           
> >>
> tag:benc at ci.uchicago.edu,2008:swift:dataset:20100225-1712-kjif48ad:720000000042
> >>
> >>     
> >>>>> type file with no value at dataset=f (not closed)" to
> >>>>> "org.griphyn.vdl.mapping.RootDataNode identifier
> >>>>>
> >>>>>           
> >>
> tag:benc at ci.uchicago.edu,2008:swift:dataset:20100225-1712-kjif48ad:720000000042
> >>
> >>     
> >>>>> type file with no value at dataset=f (not closed)"
> >>>>> 2010-02-25 17:12:04,068-0600 INFO  echos PROCEDURE line=68
> >>>>> thread=0-1-0-0 name=echos
> >>>>> 2010-02-25 17:12:04,077-0600 INFO  AbstractDataNode closed
> >>>>> org.griphyn.vdl.mapping.RootDataNode identifier
> >>>>>
> >>>>>           
> >>
> tag:benc at ci.uchicago.edu,2008:swift:dataset:20100225-1712-kjif48ad:720000000046
> >>
> >>     
> >>>>> type string
> >>>>> value=_concurrent/f-7a608b5e-b445-46f4-8cb2-bff8a73b52ec-1-0
> >>>>> dataset=unnamed SwiftScript value (closed)
> >>>>> 2010-02-25 17:12:04,077-0600 INFO  VDLFunction
> FUNCTIONPARAMETER
> >>>>> id=451004
> >>>>>
> >>>>>           
> >>
> input=tag:benc at ci.uchicago.edu,2008:swift:dataset:20100225-1712-kjif48ad:720000000042
> >>
> >>     
> >>>>> name=input
> >>>>> 2010-02-25 17:12:04,077-0600 INFO  VDLFunction FUNCTION
> id=451004
> >>>>> name=filename
> >>>>>
> >>>>>           
> >>
> result=tag:benc at ci.uchicago.edu,2008:swift:dataset:20100225-1712-kjif48ad:720000000046
> >>
> >>     
> >>>>> 2010-02-25 17:12:04,077-0600 INFO  AbstractDataNode closed
> >>>>> org.griphyn.vdl.mapping.RootDataNode identifier
> >>>>>
> >>>>>           
> >>
> tag:benc at ci.uchicago.edu,2008:swift:dataset:20100225-1712-kjif48ad:720000000047
> >>
> >>     
> >>>>> type string value=input/T0510D1.pdb dataset=unnamed SwiftScript
> >>>>>           
> >> value
> >>     
> >>>>> (closed)
> >>>>> 2010-02-25 17:12:04,078-0600 INFO  VDLFunction
> FUNCTIONPARAMETER
> >>>>> id=451005
> >>>>>
> >>>>>           
> >>
> input=tag:benc at ci.uchicago.edu,2008:swift:dataset:20100225-1712-kjif48ad:720000000030
> >>
> >>     
> >>>>> name=input
> >>>>> 2010-02-25 17:12:04,078-0600 INFO  VDLFunction FUNCTION
> id=451005
> >>>>> name=filename
> >>>>>
> >>>>>           
> >>
> result=tag:benc at ci.uchicago.edu,2008:swift:dataset:20100225-1712-kjif48ad:720000000047
> >>
> >>     
> >>>>> 2010-02-25 17:12:04,078-0600 INFO  AbstractDataNode closed
> >>>>> org.griphyn.vdl.mapping.RootDataNode identifier
> >>>>>
> >>>>>           
> >>
> tag:benc at ci.uchicago.edu,2008:swift:dataset:20100225-1712-kjif48ad:720000000048
> >>
> >>     
> >>>>> type string value=output/data//T0510D1.pdb dataset=unnamed
> >>>>>           
> >> SwiftScript
> >>     
> >>>>> value (closed)
> >>>>> 2010-02-25 17:12:04,078-0600 INFO  VDLFunction
> FUNCTIONPARAMETER
> >>>>> id=451006
> >>>>>
> >>>>>           
> >>
> input=tag:benc at ci.uchicago.edu,2008:swift:dataset:20100225-1712-kjif48ad:720000000034
> >>
> >>     
> >>>>> name=input
> >>>>> 2010-02-25 17:12:04,078-0600 INFO  VDLFunction FUNCTION
> id=451006
> >>>>> name=filename
> >>>>>
> >>>>>           
> >>
> result=tag:benc at ci.uchicago.edu,2008:swift:dataset:20100225-1712-kjif48ad:720000000048
> >>
> >>     
> >>>>> 2010-02-25 17:12:04,084-0600 INFO  vdl:execute START
> >>>>>           
> >> thread=0-1-0-0
> >>     
> >>>>> tr=echo
> >>>>> 2010-02-25 17:12:04,085-0600 INFO  vdl:execute START
> thread=0-1-8
> >>>>> tr=PrepLoop
> >>>>> 2010-02-25 17:12:04,112-0600 INFO  WeightedHostScoreScheduler
> >>>>>           
> >> Sorted:
> >>     
> >>>>> [localhost:10,000.000(99.854):0/3 overload: 0]
> >>>>> 2010-02-25 17:12:04,112-0600 INFO  WeightedHostScoreScheduler
> >>>>> CONTACT_SELECTED host=localhost, score=99.854
> >>>>> 2010-02-25 17:12:04,113-0600 INFO  WeightedHostScoreScheduler
> >>>>>           
> >> Sorted:
> >>     
> >>>>> [localhost:10,000.000(99.854):1/3 overload: 0]
> >>>>> 2010-02-25 17:12:04,114-0600 INFO  WeightedHostScoreScheduler
> >>>>> CONTACT_SELECTED host=localhost, score=99.854
> >>>>> 2010-02-25 17:12:04,120-0600 INFO  GlobalSubmitQueue No global
> >>>>>           
> >> submit
> >>     
> >>>>> throttle set. Using default (100)
> >>>>> 2010-02-25 17:12:04,136-0600 DEBUG TaskImpl
> >>>>>           
> >> Task(type=FILE_OPERATION,
> >>     
> >>>>> identity=urn:0-1-0-0-1-1267139524101) setting status to
> >>>>>           
> >> Submitting
> >>     
> >>>>> 2010-02-25 17:12:04,148-0600 DEBUG TaskImpl
> >>>>>           
> >> Task(type=FILE_OPERATION,
> >>     
> >>>>> identity=urn:0-1-0-0-1-1267139524101) setting status to
> Submitted
> >>>>> 2010-02-25 17:12:04,148-0600 DEBUG TaskImpl
> >>>>>           
> >> Task(type=FILE_OPERATION,
> >>     
> >>>>> identity=urn:0-1-0-0-1-1267139524101) setting status to Active
> >>>>> 2010-02-25 17:12:04,149-0600 DEBUG TaskImpl
> >>>>>           
> >> Task(type=FILE_OPERATION,
> >>     
> >>>>> identity=urn:0-1-0-0-1-1267139524101) setting status to
> Completed
> >>>>> 2010-02-25 17:12:04,149-0600 INFO  LateBindingScheduler
> >>>>> Task(type=FILE_OPERATION, identity=urn:0-1-0-0-1-1267139524101)
> >>>>> Completed. Waiting: 0, Running: 0. Heap size: 14M, Heap free:
> 5M,
> >>>>>           
> >> Max
> >>     
> >>>>> heap: 254M
> >>>>> 2010-02-25 17:12:04,155-0600 DEBUG TaskImpl
> >>>>>           
> >> Task(type=FILE_OPERATION,
> >>     
> >>>>> identity=urn:0-1-0-0-1-1267139524104) setting status to
> >>>>>           
> >> Submitting
> >>     
> >>>>> 2010-02-25 17:12:04,155-0600 DEBUG TaskImpl
> >>>>>           
> >> Task(type=FILE_OPERATION,
> >>     
> >>>>> identity=urn:0-1-0-0-1-1267139524104) setting status to
> Submitted
> >>>>> 2010-02-25 17:12:04,155-0600 DEBUG TaskImpl
> >>>>>           
> >> Task(type=FILE_OPERATION,
> >>     
> >>>>> identity=urn:0-1-0-0-1-1267139524104) setting status to Active
> >>>>> 2010-02-25 17:12:04,155-0600 DEBUG TaskImpl
> >>>>>           
> >> Task(type=FILE_OPERATION,
> >>     
> >>>>> identity=urn:0-1-0-0-1-1267139524104) setting status to
> Completed
> >>>>> 2010-02-25 17:12:04,155-0600 INFO  LateBindingScheduler
> >>>>> Task(type=FILE_OPERATION, identity=urn:0-1-0-0-1-1267139524104)
> >>>>> Completed. Waiting: 0, Running: 0. Heap size: 14M, Heap free:
> 4M,
> >>>>>           
> >> Max
> >>     
> >>>>> heap: 254M
> >>>>> 2010-02-25 17:12:04,158-0600 INFO  vdl:initshareddir START
> >>>>> host=localhost - Initializing shared directory
> >>>>> 2010-02-25 17:12:04,161-0600 DEBUG TaskImpl
> >>>>>           
> >> Task(type=FILE_OPERATION,
> >>     
> >>>>> identity=urn:0-1-8-1-1267139524106) setting status to
> Submitting
> >>>>> 2010-02-25 17:12:04,162-0600 DEBUG TaskImpl
> >>>>>           
> >> Task(type=FILE_OPERATION,
> >>     
> >>>>> identity=urn:0-1-8-1-1267139524106) setting status to Submitted
> >>>>> 2010-02-25 17:12:04,162-0600 DEBUG TaskImpl
> >>>>>           
> >> Task(type=FILE_OPERATION,
> >>     
> >>>>> identity=urn:0-1-8-1-1267139524106) setting status to Active
> >>>>> 2010-02-25 17:12:04,163-0600 DEBUG TaskImpl
> >>>>>           
> >> Task(type=FILE_OPERATION,
> >>     
> >>>>> identity=urn:0-1-8-1-1267139524106) setting status to Completed
> >>>>> 2010-02-25 17:12:04,163-0600 INFO  LateBindingScheduler
> >>>>> Task(type=FILE_OPERATION, identity=urn:0-1-8-1-1267139524106)
> >>>>> Completed. Waiting: 0, Running: 0. Heap size: 14M, Heap free:
> 4M,
> >>>>>           
> >> Max
> >>     
> >>>>> heap: 254M
> >>>>> 2010-02-25 17:12:04,185-0600 DEBUG TaskImpl
> >>>>>           
> >> Task(type=FILE_TRANSFER,
> >>     
> >>>>> identity=urn:0-1-8-1-1267139524109) setting status to
> Submitting
> >>>>> 2010-02-25 17:12:04,185-0600 DEBUG TaskImpl
> >>>>>           
> >> Task(type=FILE_TRANSFER,
> >>     
> >>>>> identity=urn:0-1-8-1-1267139524109) setting status to Submitted
> >>>>> 2010-02-25 17:12:04,187-0600 DEBUG TaskImpl
> >>>>>           
> >> Task(type=FILE_TRANSFER,
> >>     
> >>>>> identity=urn:0-1-8-1-1267139524109) setting status to Active
> >>>>> 2010-02-25 17:12:04,190-0600 DEBUG TaskImpl
> >>>>>           
> >> Task(type=FILE_TRANSFER,
> >>     
> >>>>> identity=urn:0-1-8-1-1267139524109) setting status to Completed
> >>>>> 2010-02-25 17:12:04,190-0600 INFO  LateBindingScheduler
> >>>>> Task(type=FILE_TRANSFER, identity=urn:0-1-8-1-1267139524109)
> >>>>> Completed. Waiting: 0, Running: 0. Heap size: 14M, Heap free:
> 5M,
> >>>>>           
> >> Max
> >>     
> >>>>> heap: 254M
> >>>>> 2010-02-25 17:12:04,191-0600 DEBUG TaskImpl
> >>>>>           
> >> Task(type=FILE_TRANSFER,
> >>     
> >>>>> identity=urn:0-1-8-1-1267139524112) setting status to
> Submitting
> >>>>> 2010-02-25 17:12:04,191-0600 DEBUG TaskImpl
> >>>>>           
> >> Task(type=FILE_TRANSFER,
> >>     
> >>>>> identity=urn:0-1-8-1-1267139524112) setting status to Submitted
> >>>>> 2010-02-25 17:12:04,191-0600 DEBUG TaskImpl
> >>>>>           
> >> Task(type=FILE_TRANSFER,
> >>     
> >>>>> identity=urn:0-1-8-1-1267139524112) setting status to Active
> >>>>> 2010-02-25 17:12:04,236-0600 DEBUG TaskImpl
> >>>>>           
> >> Task(type=FILE_TRANSFER,
> >>     
> >>>>> identity=urn:0-1-8-1-1267139524112) setting status to Completed
> >>>>> 2010-02-25 17:12:04,236-0600 INFO  LateBindingScheduler
> >>>>> Task(type=FILE_TRANSFER, identity=urn:0-1-8-1-1267139524112)
> >>>>> Completed. Waiting: 0, Running: 0. Heap size: 14M, Heap free:
> 5M,
> >>>>>           
> >> Max
> >>     
> >>>>> heap: 254M
> >>>>> 2010-02-25 17:12:04,237-0600 DEBUG TaskImpl
> >>>>>           
> >> Task(type=FILE_OPERATION,
> >>     
> >>>>> identity=urn:0-1-8-1-1267139524115) setting status to
> Submitting
> >>>>> 2010-02-25 17:12:04,237-0600 DEBUG TaskImpl
> >>>>>           
> >> Task(type=FILE_OPERATION,
> >>     
> >>>>> identity=urn:0-1-8-1-1267139524115) setting status to Submitted
> >>>>> 2010-02-25 17:12:04,237-0600 DEBUG TaskImpl
> >>>>>           
> >> Task(type=FILE_OPERATION,
> >>     
> >>>>> identity=urn:0-1-8-1-1267139524115) setting status to Active
> >>>>> 2010-02-25 17:12:04,238-0600 DEBUG TaskImpl
> >>>>>           
> >> Task(type=FILE_OPERATION,
> >>     
> >>>>> identity=urn:0-1-8-1-1267139524115) setting status to Completed
> >>>>> 2010-02-25 17:12:04,238-0600 INFO  LateBindingScheduler
> >>>>> Task(type=FILE_OPERATION, identity=urn:0-1-8-1-1267139524115)
> >>>>> Completed. Waiting: 0, Running: 0. Heap size: 14M, Heap free:
> 5M,
> >>>>>           
> >> Max
> >>     
> >>>>> heap: 254M
> >>>>> 2010-02-25 17:12:04,239-0600 DEBUG TaskImpl
> >>>>>           
> >> Task(type=FILE_OPERATION,
> >>     
> >>>>> identity=urn:0-1-8-1-1267139524117) setting status to
> Submitting
> >>>>> 2010-02-25 17:12:04,239-0600 DEBUG TaskImpl
> >>>>>           
> >> Task(type=FILE_OPERATION,
> >>     
> >>>>> identity=urn:0-1-8-1-1267139524117) setting status to Submitted
> >>>>> 2010-02-25 17:12:04,239-0600 DEBUG TaskImpl
> >>>>>           
> >> Task(type=FILE_OPERATION,
> >>     
> >>>>> identity=urn:0-1-8-1-1267139524117) setting status to Active
> >>>>> 2010-02-25 17:12:04,240-0600 DEBUG TaskImpl
> >>>>>           
> >> Task(type=FILE_OPERATION,
> >>     
> >>>>> identity=urn:0-1-8-1-1267139524117) setting status to Completed
> >>>>> 2010-02-25 17:12:04,240-0600 INFO  LateBindingScheduler
> >>>>> Task(type=FILE_OPERATION, identity=urn:0-1-8-1-1267139524117)
> >>>>> Completed. Waiting: 0, Running: 0. Heap size: 14M, Heap free:
> 5M,
> >>>>>           
> >> Max
> >>     
> >>>>> heap: 254M
> >>>>> 2010-02-25 17:12:04,241-0600 DEBUG TaskImpl
> >>>>>           
> >> Task(type=FILE_OPERATION,
> >>     
> >>>>> identity=urn:0-1-8-1-1267139524119) setting status to
> Submitting
> >>>>> 2010-02-25 17:12:04,244-0600 DEBUG TaskImpl
> >>>>>           
> >> Task(type=FILE_OPERATION,
> >>     
> >>>>> identity=urn:0-1-8-1-1267139524119) setting status to Submitted
> >>>>> 2010-02-25 17:12:04,244-0600 DEBUG TaskImpl
> >>>>>           
> >> Task(type=FILE_OPERATION,
> >>     
> >>>>> identity=urn:0-1-8-1-1267139524119) setting status to Active
> >>>>> 2010-02-25 17:12:04,244-0600 DEBUG TaskImpl
> >>>>>           
> >> Task(type=FILE_OPERATION,
> >>     
> >>>>> identity=urn:0-1-8-1-1267139524119) setting status to Completed
> >>>>> 2010-02-25 17:12:04,244-0600 INFO  LateBindingScheduler
> >>>>> Task(type=FILE_OPERATION, identity=urn:0-1-8-1-1267139524119)
> >>>>> Completed. Waiting: 0, Running: 0. Heap size: 14M, Heap free:
> 5M,
> >>>>>           
> >> Max
> >>     
> >>>>> heap: 254M
> >>>>> 2010-02-25 17:12:04,245-0600 INFO  vdl:initshareddir END
> >>>>> host=localhost - Done initializing shared directory
> >>>>> 2010-02-25 17:12:04,248-0600 DEBUG vdl:execute2
> >>>>>           
> >> THREAD_ASSOCIATION
> >>     
> >>>>> jobid=echo-xkjtxaoj thread=0-1-0-0-1 host=localhost
> >>>>> replicationGroup=ukjtxaoj
> >>>>> 2010-02-25 17:12:04,250-0600 DEBUG vdl:execute2
> >>>>>           
> >> THREAD_ASSOCIATION
> >>     
> >>>>> jobid=PrepLoop-ykjtxaoj thread=0-1-8-1 host=localhost
> >>>>> replicationGroup=vkjtxaoj
> >>>>> 2010-02-25 17:12:04,255-0600 INFO  vdl:createdirset START
> >>>>> jobid=echo-xkjtxaoj host=localhost - Initializing directory
> >>>>>           
> >> structure
> >>     
> >>>>> 2010-02-25 17:12:04,257-0600 INFO  vdl:createdirs START
> >>>>> path=_concurrent dir=psim.loops-20100225-1712-3zrtb5i5/shared -
> >>>>> Creating directory structure
> >>>>> 2010-02-25 17:12:04,257-0600 INFO  vdl:createdirset START
> >>>>> jobid=PrepLoop-ykjtxaoj host=localhost - Initializing directory
> >>>>> structure
> >>>>> 2010-02-25 17:12:04,258-0600 INFO  vdl:createdirs START
> >>>>>           
> >> path=input
> >>     
> >>>>> dir=psim.loops-20100225-1712-3zrtb5i5/shared - Creating
> directory
> >>>>> structure
> >>>>> 2010-02-25 17:12:04,258-0600 DEBUG TaskImpl
> >>>>>           
> >> Task(type=FILE_OPERATION,
> >>     
> >>>>> identity=urn:0-1-0-0-1-1267139524121) setting status to
> >>>>>           
> >> Submitting
> >>     
> >>>>> 2010-02-25 17:12:04,258-0600 DEBUG TaskImpl
> >>>>>           
> >> Task(type=FILE_OPERATION,
> >>     
> >>>>> identity=urn:0-1-0-0-1-1267139524121) setting status to
> Submitted
> >>>>> 2010-02-25 17:12:04,258-0600 DEBUG TaskImpl
> >>>>>           
> >> Task(type=FILE_OPERATION,
> >>     
> >>>>> identity=urn:0-1-0-0-1-1267139524121) setting status to Active
> >>>>> 2010-02-25 17:12:04,259-0600 DEBUG TaskImpl
> >>>>>           
> >> Task(type=FILE_OPERATION,
> >>     
> >>>>> identity=urn:0-1-8-1-1267139524123) setting status to
> Submitting
> >>>>> 2010-02-25 17:12:04,259-0600 DEBUG TaskImpl
> >>>>>           
> >> Task(type=FILE_OPERATION,
> >>     
> >>>>> identity=urn:0-1-8-1-1267139524123) setting status to Submitted
> >>>>> 2010-02-25 17:12:04,259-0600 DEBUG TaskImpl
> >>>>>           
> >> Task(type=FILE_OPERATION,
> >>     
> >>>>> identity=urn:0-1-8-1-1267139524123) setting status to Active
> >>>>> 2010-02-25 17:12:04,261-0600 DEBUG TaskImpl
> >>>>>           
> >> Task(type=FILE_OPERATION,
> >>     
> >>>>> identity=urn:0-1-0-0-1-1267139524121) setting status to
> Completed
> >>>>> 2010-02-25 17:12:04,261-0600 DEBUG TaskImpl
> >>>>>           
> >> Task(type=FILE_OPERATION,
> >>     
> >>>>> identity=urn:0-1-8-1-1267139524123) setting status to Completed
> >>>>> 2010-02-25 17:12:04,261-0600 INFO  LateBindingScheduler
> >>>>> Task(type=FILE_OPERATION, identity=urn:0-1-0-0-1-1267139524121)
> >>>>> Completed. Waiting: 0, Running: 1. Heap size: 14M, Heap free:
> 4M,
> >>>>>           
> >> Max
> >>     
> >>>>> heap: 254M
> >>>>> 2010-02-25 17:12:04,262-0600 INFO  LateBindingScheduler
> >>>>> Task(type=FILE_OPERATION, identity=urn:0-1-8-1-1267139524123)
> >>>>> Completed. Waiting: 0, Running: 1. Heap size: 14M, Heap free:
> 4M,
> >>>>>           
> >> Max
> >>     
> >>>>> heap: 254M
> >>>>> 2010-02-25 17:12:04,262-0600 INFO  vdl:createdirset END
> >>>>> jobid=echo-xkjtxaoj - Done initializing directory structure
> >>>>> 2010-02-25 17:12:04,263-0600 INFO  vdl:createdirs START
> >>>>> path=output/data/ dir=psim.loops-20100225-1712-3zrtb5i5/shared
> -
> >>>>> Creating directory structure
> >>>>> 2010-02-25 17:12:04,263-0600 INFO  vdl:dostagein START
> >>>>> jobid=echo-xkjtxaoj - Staging in files
> >>>>> 2010-02-25 17:12:04,263-0600 DEBUG TaskImpl
> >>>>>           
> >> Task(type=FILE_OPERATION,
> >>     
> >>>>> identity=urn:0-1-8-1-1267139524126) setting status to
> Submitting
> >>>>> 2010-02-25 17:12:04,263-0600 DEBUG TaskImpl
> >>>>>           
> >> Task(type=FILE_OPERATION,
> >>     
> >>>>> identity=urn:0-1-8-1-1267139524126) setting status to Submitted
> >>>>> 2010-02-25 17:12:04,264-0600 INFO  vdl:dostagein END
> >>>>> jobid=echo-xkjtxaoj - Staging in finished
> >>>>> 2010-02-25 17:12:04,269-0600 DEBUG TaskImpl
> >>>>>           
> >> Task(type=FILE_OPERATION,
> >>     
> >>>>> identity=urn:0-1-8-1-1267139524126) setting status to Active
> >>>>> 2010-02-25 17:12:04,274-0600 DEBUG TaskImpl
> >>>>>           
> >> Task(type=FILE_OPERATION,
> >>     
> >>>>> identity=urn:0-1-8-1-1267139524126) setting status to Completed
> >>>>> 2010-02-25 17:12:04,274-0600 INFO  LateBindingScheduler
> >>>>> Task(type=FILE_OPERATION, identity=urn:0-1-8-1-1267139524126)
> >>>>> Completed. Waiting: 0, Running: 0. Heap size: 14M, Heap free:
> 5M,
> >>>>>           
> >> Max
> >>     
> >>>>> heap: 254M
> >>>>> 2010-02-25 17:12:04,275-0600 DEBUG vdl:execute2 JOB_START
> >>>>> jobid=echo-xkjtxaoj tr=echo arguments=[4]
> >>>>> tmpdir=psim.loops-20100225-1712-3zrtb5i5/jobs/x/echo-xkjtxaoj
> >>>>> host=localhost
> >>>>> 2010-02-25 17:12:04,275-0600 INFO  vdl:createdirs START path=
> >>>>> dir=psim.loops-20100225-1712-3zrtb5i5/shared - Creating
> directory
> >>>>> structure
> >>>>> 2010-02-25 17:12:04,276-0600 DEBUG TaskImpl
> >>>>>           
> >> Task(type=FILE_OPERATION,
> >>     
> >>>>> identity=urn:0-1-8-1-1267139524128) setting status to
> Submitting
> >>>>> 2010-02-25 17:12:04,276-0600 DEBUG TaskImpl
> >>>>>           
> >> Task(type=FILE_OPERATION,
> >>     
> >>>>> identity=urn:0-1-8-1-1267139524128) setting status to Submitted
> >>>>> 2010-02-25 17:12:04,276-0600 DEBUG TaskImpl
> >>>>>           
> >> Task(type=FILE_OPERATION,
> >>     
> >>>>> identity=urn:0-1-8-1-1267139524128) setting status to Active
> >>>>> 2010-02-25 17:12:04,276-0600 DEBUG TaskImpl
> >>>>>           
> >> Task(type=FILE_OPERATION,
> >>     
> >>>>> identity=urn:0-1-8-1-1267139524128) setting status to Completed
> >>>>> 2010-02-25 17:12:04,276-0600 INFO  LateBindingScheduler
> >>>>> Task(type=FILE_OPERATION, identity=urn:0-1-8-1-1267139524128)
> >>>>> Completed. Waiting: 0, Running: 0. Heap size: 14M, Heap free:
> 5M,
> >>>>>           
> >> Max
> >>     
> >>>>> heap: 254M
> >>>>> 2010-02-25 17:12:04,277-0600 INFO  vdl:createdirset END
> >>>>> jobid=PrepLoop-ykjtxaoj - Done initializing directory structure
> >>>>> 2010-02-25 17:12:04,278-0600 INFO  vdl:dostagein START
> >>>>> jobid=PrepLoop-ykjtxaoj - Staging in files
> >>>>> 2010-02-25 17:12:04,283-0600 DEBUG TaskImpl
> >>>>>           
> >> Task(type=FILE_OPERATION,
> >>     
> >>>>> identity=urn:0-1-8-1-1-1267139524131) setting status to
> >>>>>           
> >> Submitting
> >>     
> >>>>> 2010-02-25 17:12:04,283-0600 DEBUG TaskImpl
> >>>>>           
> >> Task(type=FILE_OPERATION,
> >>     
> >>>>> identity=urn:0-1-8-1-1-1267139524131) setting status to
> Submitted
> >>>>> 2010-02-25 17:12:04,283-0600 DEBUG TaskImpl
> >>>>>           
> >> Task(type=FILE_OPERATION,
> >>     
> >>>>> identity=urn:0-1-8-1-1-1267139524131) setting status to Active
> >>>>> 2010-02-25 17:12:04,284-0600 DEBUG TaskImpl
> >>>>>           
> >> Task(type=FILE_OPERATION,
> >>     
> >>>>> identity=urn:0-1-8-1-3-1267139524132) setting status to
> >>>>>           
> >> Submitting
> >>     
> >>>>> 2010-02-25 17:12:04,285-0600 DEBUG TaskImpl
> >>>>>           
> >> Task(type=FILE_OPERATION,
> >>     
> >>>>> identity=urn:0-1-8-1-3-1267139524132) setting status to
> Submitted
> >>>>> 2010-02-25 17:12:04,287-0600 DEBUG TaskImpl
> >>>>>           
> >> Task(type=FILE_OPERATION,
> >>     
> >>>>> identity=urn:0-1-8-1-3-1267139524132) setting status to Active
> >>>>> 2010-02-25 17:12:04,288-0600 DEBUG TaskImpl
> >>>>>           
> >> Task(type=FILE_OPERATION,
> >>     
> >>>>> identity=urn:0-1-8-1-1-1267139524131) setting status to
> Completed
> >>>>> 2010-02-25 17:12:04,288-0600 INFO  LateBindingScheduler
> >>>>> Task(type=FILE_OPERATION, identity=urn:0-1-8-1-1-1267139524131)
> >>>>> Completed. Waiting: 0, Running: 2. Heap size: 14M, Heap free:
> 5M,
> >>>>>           
> >> Max
> >>     
> >>>>> heap: 254M
> >>>>> 2010-02-25 17:12:04,289-0600 DEBUG TaskImpl
> >>>>>           
> >> Task(type=FILE_OPERATION,
> >>     
> >>>>> identity=urn:0-1-8-1-3-1267139524132) setting status to
> Completed
> >>>>> 2010-02-25 17:12:04,289-0600 INFO  LateBindingScheduler
> >>>>> Task(type=FILE_OPERATION, identity=urn:0-1-8-1-3-1267139524132)
> >>>>> Completed. Waiting: 0, Running: 1. Heap size: 14M, Heap free:
> 5M,
> >>>>>           
> >> Max
> >>     
> >>>>> heap: 254M
> >>>>> 2010-02-25 17:12:04,290-0600 DEBUG TaskImpl
> >>>>>           
> >> Task(type=FILE_OPERATION,
> >>     
> >>>>> identity=urn:0-1-8-1-2-1267139524134) setting status to
> >>>>>           
> >> Submitting
> >>     
> >>>>> 2010-02-25 17:12:04,290-0600 DEBUG TaskImpl
> >>>>>           
> >> Task(type=FILE_OPERATION,
> >>     
> >>>>> identity=urn:0-1-8-1-2-1267139524134) setting status to
> Submitted
> >>>>> 2010-02-25 17:12:04,290-0600 DEBUG TaskImpl
> >>>>>           
> >> Task(type=FILE_OPERATION,
> >>     
> >>>>> identity=urn:0-1-8-1-2-1267139524134) setting status to Active
> >>>>> 2010-02-25 17:12:04,291-0600 DEBUG TaskImpl
> >>>>>           
> >> Task(type=FILE_OPERATION,
> >>     
> >>>>> identity=urn:0-1-8-1-2-1267139524134) setting status to
> Completed
> >>>>> 2010-02-25 17:12:04,291-0600 INFO  LateBindingScheduler
> >>>>> Task(type=FILE_OPERATION, identity=urn:0-1-8-1-2-1267139524134)
> >>>>> Completed. Waiting: 0, Running: 0. Heap size: 14M, Heap free:
> 5M,
> >>>>>           
> >> Max
> >>     
> >>>>> heap: 254M
> >>>>> 2010-02-25 17:12:04,295-0600 INFO  Execute jobid=echo-xkjtxaoj
> >>>>> task=Task(type=JOB_SUBMISSION,
> >>>>>           
> >> identity=urn:0-1-0-0-1-1267139524137)
> >>     
> >>>>> 2010-02-25 17:12:04,303-0600 DEBUG vdl:dostagein
> >>>>>           
> >> FILE_STAGE_IN_START
> >>     
> >>>>> file=file://localhost/input/T0510D1.range srchost=localhost
> >>>>> srcdir=input srcname=T0510D1.range desthost=localhost
> >>>>> destdir=psim.loops-20100225-1712-3zrtb5i5/shared/input
> >>>>>           
> >> provider=file
> >>     
> >>>>> 2010-02-25 17:12:04,304-0600 DEBUG vdl:dostagein
> >>>>>           
> >> FILE_STAGE_IN_START
> >>     
> >>>>> file=file://localhost/input/T0510D1.params srchost=localhost
> >>>>> srcdir=input srcname=T0510D1.params desthost=localhost
> >>>>> destdir=psim.loops-20100225-1712-3zrtb5i5/shared/input
> >>>>>           
> >> provider=file
> >>     
> >>>>> 2010-02-25 17:12:04,305-0600 DEBUG vdl:dostagein
> >>>>>           
> >> FILE_STAGE_IN_START
> >>     
> >>>>> file=file://localhost/input/T0510D1.pdb srchost=localhost
> >>>>>           
> >> srcdir=input
> >>     
> >>>>> srcname=T0510D1.pdb desthost=localhost
> >>>>> destdir=psim.loops-20100225-1712-3zrtb5i5/shared/input
> >>>>>           
> >> provider=file
> >>     
> >>>>> 2010-02-25 17:12:04,305-0600 DEBUG TaskImpl
> >>>>>           
> >> Task(type=JOB_SUBMISSION,
> >>     
> >>>>> identity=urn:0-1-0-0-1-1267139524137) setting status to
> >>>>>           
> >> Submitting
> >>     
> >>>>> 2010-02-25 17:12:04,305-0600 INFO  JobSubmissionTaskHandler
> >>>>>           
> >> Submitting
> >>     
> >>>>> task Task(type=JOB_SUBMISSION,
> >>>>>           
> >> identity=urn:0-1-0-0-1-1267139524137)
> >>     
> >>>>> 2010-02-25 17:12:04,305-0600 INFO  JobSubmissionTaskHandler
> >>>>>           
> >> Submitting
> >>     
> >>>>> single job
> >>>>> 2010-02-25 17:12:04,306-0600 DEBUG TaskImpl
> >>>>>           
> >> Task(type=JOB_SUBMISSION,
> >>     
> >>>>> identity=urn:0-1-0-0-1-1267139524137) setting status to
> Submitted
> >>>>> 2010-02-25 17:12:04,306-0600 DEBUG TaskImpl
> >>>>>           
> >> Task(type=FILE_TRANSFER,
> >>     
> >>>>> identity=urn:0-1-8-1-1-1267139524141) setting status to
> >>>>>           
> >> Submitting
> >>     
> >>>>> 2010-02-25 17:12:04,306-0600 DEBUG TaskImpl
> >>>>>           
> >> Task(type=FILE_TRANSFER,
> >>     
> >>>>> identity=urn:0-1-8-1-1-1267139524141) setting status to
> Submitted
> >>>>> 2010-02-25 17:12:04,306-0600 DEBUG TaskImpl
> >>>>>           
> >> Task(type=FILE_TRANSFER,
> >>     
> >>>>> identity=urn:0-1-8-1-2-1267139524139) setting status to
> >>>>>           
> >> Submitting
> >>     
> >>>>> 2010-02-25 17:12:04,306-0600 DEBUG TaskImpl
> >>>>>           
> >> Task(type=FILE_TRANSFER,
> >>     
> >>>>> identity=urn:0-1-8-1-2-1267139524139) setting status to
> Submitted
> >>>>> 2010-02-25 17:12:04,307-0600 DEBUG TaskImpl
> >>>>>           
> >> Task(type=FILE_TRANSFER,
> >>     
> >>>>> identity=urn:0-1-8-1-1-1267139524141) setting status to Active
> >>>>> 2010-02-25 17:12:04,307-0600 DEBUG TaskImpl
> >>>>>           
> >> Task(type=FILE_TRANSFER,
> >>     
> >>>>> identity=urn:0-1-8-1-2-1267139524139) setting status to Active
> >>>>> 2010-02-25 17:12:04,308-0600 DEBUG TaskImpl
> >>>>>           
> >> Task(type=FILE_TRANSFER,
> >>     
> >>>>> identity=urn:0-1-8-1-3-1267139524143) setting status to
> >>>>>           
> >> Submitting
> >>     
> >>>>> 2010-02-25 17:12:04,308-0600 DEBUG TaskImpl
> >>>>>           
> >> Task(type=FILE_TRANSFER,
> >>     
> >>>>> identity=urn:0-1-8-1-3-1267139524143) setting status to
> Submitted
> >>>>> 2010-02-25 17:12:04,312-0600 DEBUG TaskImpl
> >>>>>           
> >> Task(type=FILE_TRANSFER,
> >>     
> >>>>> identity=urn:0-1-8-1-2-1267139524139) setting status to
> Completed
> >>>>> 2010-02-25 17:12:04,312-0600 DEBUG TaskImpl
> >>>>>           
> >> Task(type=JOB_SUBMISSION,
> >>     
> >>>>> identity=urn:0-1-0-0-1-1267139524137) setting status to Active
> >>>>> 2010-02-25 17:12:04,313-0600 INFO  LateBindingScheduler
> >>>>> Task(type=FILE_TRANSFER, identity=urn:0-1-8-1-2-1267139524139)
> >>>>> Completed. Waiting: 0, Running: 3. Heap size: 14M, Heap free:
> 4M,
> >>>>>           
> >> Max
> >>     
> >>>>> heap: 254M
> >>>>> 2010-02-25 17:12:04,321-0600 DEBUG vdl:dostagein
> >>>>>           
> >> FILE_STAGE_IN_END
> >>     
> >>>>> file=file://localhost/input/T0510D1.range srchost=localhost
> >>>>> srcdir=input srcname=T0510D1.range desthost=localhost
> >>>>> destdir=psim.loops-20100225-1712-3zrtb5i5/shared/input
> >>>>>           
> >> provider=file
> >>     
> >>>>> 2010-02-25 17:12:04,323-0600 DEBUG TaskImpl
> >>>>>           
> >> Task(type=FILE_TRANSFER,
> >>     
> >>>>> identity=urn:0-1-8-1-1-1267139524141) setting status to
> Completed
> >>>>> 2010-02-25 17:12:04,324-0600 INFO  LateBindingScheduler
> >>>>> Task(type=FILE_TRANSFER, identity=urn:0-1-8-1-1-1267139524141)
> >>>>> Completed. Waiting: 0, Running: 2. Heap size: 14M, Heap free:
> 5M,
> >>>>>           
> >> Max
> >>     
> >>>>> heap: 254M
> >>>>> 2010-02-25 17:12:04,325-0600 DEBUG vdl:dostagein
> >>>>>           
> >> FILE_STAGE_IN_END
> >>     
> >>>>> file=file://localhost/input/T0510D1.params srchost=localhost
> >>>>> srcdir=input srcname=T0510D1.params desthost=localhost
> >>>>> destdir=psim.loops-20100225-1712-3zrtb5i5/shared/input
> >>>>>           
> >> provider=file
> >>     
> >>>>> 2010-02-25 17:12:04,325-0600 DEBUG TaskImpl
> >>>>>           
> >> Task(type=FILE_TRANSFER,
> >>     
> >>>>> identity=urn:0-1-8-1-3-1267139524143) setting status to Active
> >>>>> 2010-02-25 17:12:04,327-0600 DEBUG TaskImpl
> >>>>>           
> >> Task(type=FILE_TRANSFER,
> >>     
> >>>>> identity=urn:0-1-8-1-3-1267139524143) setting status to
> Completed
> >>>>> 2010-02-25 17:12:04,327-0600 INFO  LateBindingScheduler
> >>>>> Task(type=FILE_TRANSFER, identity=urn:0-1-8-1-3-1267139524143)
> >>>>> Completed. Waiting: 0, Running: 1. Heap size: 14M, Heap free:
> 5M,
> >>>>>           
> >> Max
> >>     
> >>>>> heap: 254M
> >>>>> 2010-02-25 17:12:04,327-0600 DEBUG vdl:dostagein
> >>>>>           
> >> FILE_STAGE_IN_END
> >>     
> >>>>> file=file://localhost/input/T0510D1.pdb srchost=localhost
> >>>>>           
> >> srcdir=input
> >>     
> >>>>> srcname=T0510D1.pdb desthost=localhost
> >>>>> destdir=psim.loops-20100225-1712-3zrtb5i5/shared/input
> >>>>>           
> >> provider=file
> >>     
> >>>>> 2010-02-25 17:12:04,327-0600 INFO  vdl:dostagein END
> >>>>> jobid=PrepLoop-ykjtxaoj - Staging in finished
> >>>>> 2010-02-25 17:12:04,328-0600 DEBUG vdl:execute2 JOB_START
> >>>>> jobid=PrepLoop-ykjtxaoj tr=PrepLoop
> arguments=[input/T0510D1.pdb,
> >>>>> output/data//T0510D1.pdb]
> >>>>>
> tmpdir=psim.loops-20100225-1712-3zrtb5i5/jobs/y/PrepLoop-ykjtxaoj
> >>>>> host=localhost
> >>>>> 2010-02-25 17:12:04,339-0600 INFO  Execute
> >>>>>           
> >> jobid=PrepLoop-ykjtxaoj
> >>     
> >>>>> task=Task(type=JOB_SUBMISSION,
> >>>>>           
> >> identity=urn:0-1-8-1-1267139524148)
> >>     
> >>>>> 2010-02-25 17:12:04,340-0600 DEBUG TaskImpl
> >>>>>           
> >> Task(type=JOB_SUBMISSION,
> >>     
> >>>>> identity=urn:0-1-8-1-1267139524148) setting status to
> Submitting
> >>>>> 2010-02-25 17:12:04,340-0600 INFO  JobSubmissionTaskHandler
> >>>>>           
> >> Submitting
> >>     
> >>>>> task Task(type=JOB_SUBMISSION,
> >>>>>           
> >> identity=urn:0-1-8-1-1267139524148)
> >>     
> >>>>> 2010-02-25 17:12:04,340-0600 INFO  JobSubmissionTaskHandler
> >>>>>           
> >> Submitting
> >>     
> >>>>> single job
> >>>>> 2010-02-25 17:12:04,340-0600 DEBUG TaskImpl
> >>>>>           
> >> Task(type=JOB_SUBMISSION,
> >>     
> >>>>> identity=urn:0-1-8-1-1267139524148) setting status to Submitted
> >>>>> 2010-02-25 17:12:04,343-0600 DEBUG TaskImpl
> >>>>>           
> >> Task(type=JOB_SUBMISSION,
> >>     
> >>>>> identity=urn:0-1-8-1-1267139524148) setting status to Active
> >>>>> 2010-02-25 17:12:04,458-0600 DEBUG TaskImpl
> >>>>>           
> >> Task(type=JOB_SUBMISSION,
> >>     
> >>>>> identity=urn:0-1-0-0-1-1267139524137) setting status to
> Completed
> >>>>> 2010-02-25 17:12:04,459-0600 INFO  LateBindingScheduler
> >>>>> Task(type=JOB_SUBMISSION, identity=urn:0-1-0-0-1-1267139524137)
> >>>>> Completed. Waiting: 0, Running: 1. Heap size: 14M, Heap free:
> 5M,
> >>>>>           
> >> Max
> >>     
> >>>>> heap: 254M
> >>>>> 2010-02-25 17:12:04,460-0600 DEBUG vdl:checkjobstatus START
> >>>>> jobid=echo-xkjtxaoj
> >>>>> 2010-02-25 17:12:04,461-0600 DEBUG TaskImpl
> >>>>>           
> >> Task(type=FILE_OPERATION,
> >>     
> >>>>> identity=urn:0-1-0-0-1-1267139524150) setting status to
> >>>>>           
> >> Submitting
> >>     
> >>>>> 2010-02-25 17:12:04,462-0600 DEBUG TaskImpl
> >>>>>           
> >> Task(type=FILE_OPERATION,
> >>     
> >>>>> identity=urn:0-1-0-0-1-1267139524150) setting status to
> Submitted
> >>>>> 2010-02-25 17:12:04,462-0600 DEBUG TaskImpl
> >>>>>           
> >> Task(type=FILE_OPERATION,
> >>     
> >>>>> identity=urn:0-1-0-0-1-1267139524150) setting status to Active
> >>>>> 2010-02-25 17:12:04,462-0600 DEBUG TaskImpl
> >>>>>           
> >> Task(type=FILE_OPERATION,
> >>     
> >>>>> identity=urn:0-1-0-0-1-1267139524150) setting status to
> Completed
> >>>>> 2010-02-25 17:12:04,462-0600 INFO  LateBindingScheduler
> >>>>> Task(type=FILE_OPERATION, identity=urn:0-1-0-0-1-1267139524150)
> >>>>> Completed. Waiting: 0, Running: 1. Heap size: 14M, Heap free:
> 5M,
> >>>>>           
> >> Max
> >>     
> >>>>> heap: 254M
> >>>>> 2010-02-25 17:12:04,463-0600 INFO  vdl:checkjobstatus SUCCESS
> >>>>> jobid=echo-xkjtxaoj - Success file found
> >>>>> 2010-02-25 17:12:04,463-0600 DEBUG vdl:execute2 STAGING_OUT
> >>>>> jobid=echo-xkjtxaoj
> >>>>> 2010-02-25 17:12:04,464-0600 INFO  vdl:dostageout START
> >>>>> jobid=echo-xkjtxaoj - Staging out files
> >>>>> 2010-02-25 17:12:04,470-0600 DEBUG vdl:dostageout
> >>>>>           
> >> FILE_STAGE_OUT_START
> >>     
> >>>>> srcname=f-7a608b5e-b445-46f4-8cb2-bff8a73b52ec-1-0
> >>>>> srcdir=psim.loops-20100225-1712-3zrtb5i5/shared/_concurrent
> >>>>> srchost=localhost destdir=_concurrent desthost=localhost
> >>>>> provider=file
> >>>>> 2010-02-25 17:12:04,471-0600 DEBUG TaskImpl
> >>>>>           
> >> Task(type=FILE_OPERATION,
> >>     
> >>>>> identity=urn:0-1-0-0-1-1-1267139524152) setting status to
> >>>>>           
> >> Submitting
> >>     
> >>>>> 2010-02-25 17:12:04,471-0600 DEBUG TaskImpl
> >>>>>           
> >> Task(type=FILE_OPERATION,
> >>     
> >>>>> identity=urn:0-1-0-0-1-1-1267139524152) setting status to
> >>>>>           
> >> Submitted
> >>     
> >>>>> 2010-02-25 17:12:04,471-0600 DEBUG TaskImpl
> >>>>>           
> >> Task(type=FILE_OPERATION,
> >>     
> >>>>> identity=urn:0-1-0-0-1-1-1267139524152) setting status to
> Active
> >>>>> 2010-02-25 17:12:04,471-0600 DEBUG TaskImpl
> >>>>>           
> >> Task(type=FILE_OPERATION,
> >>     
> >>>>> identity=urn:0-1-0-0-1-1-1267139524152) setting status to
> >>>>>           
> >> Completed
> >>     
> >>>>> 2010-02-25 17:12:04,471-0600 INFO  LateBindingScheduler
> >>>>> Task(type=FILE_OPERATION,
> identity=urn:0-1-0-0-1-1-1267139524152)
> >>>>> Completed. Waiting: 0, Running: 1. Heap size: 14M, Heap free:
> 5M,
> >>>>>           
> >> Max
> >>     
> >>>>> heap: 254M
> >>>>> 2010-02-25 17:12:04,473-0600 DEBUG TaskImpl
> >>>>>           
> >> Task(type=FILE_TRANSFER,
> >>     
> >>>>> identity=urn:0-1-0-0-1-1-1267139524154) setting status to
> >>>>>           
> >> Submitting
> >>     
> >>>>> 2010-02-25 17:12:04,473-0600 DEBUG TaskImpl
> >>>>>           
> >> Task(type=FILE_TRANSFER,
> >>     
> >>>>> identity=urn:0-1-0-0-1-1-1267139524154) setting status to
> >>>>>           
> >> Submitted
> >>     
> >>>>> 2010-02-25 17:12:04,473-0600 DEBUG TaskImpl
> >>>>>           
> >> Task(type=FILE_TRANSFER,
> >>     
> >>>>> identity=urn:0-1-0-0-1-1-1267139524154) setting status to
> Active
> >>>>> 2010-02-25 17:12:04,474-0600 DEBUG TaskImpl
> >>>>>           
> >> Task(type=FILE_TRANSFER,
> >>     
> >>>>> identity=urn:0-1-0-0-1-1-1267139524154) setting status to
> >>>>>           
> >> Completed
> >>     
> >>>>> 2010-02-25 17:12:04,474-0600 INFO  LateBindingScheduler
> >>>>> Task(type=FILE_TRANSFER,
> identity=urn:0-1-0-0-1-1-1267139524154)
> >>>>> Completed. Waiting: 0, Running: 1. Heap size: 14M, Heap free:
> 5M,
> >>>>>           
> >> Max
> >>     
> >>>>> heap: 254M
> >>>>> 2010-02-25 17:12:04,474-0600 DEBUG vdl:dostageout
> >>>>>           
> >> FILE_STAGE_OUT_END
> >>     
> >>>>> srcname=f-7a608b5e-b445-46f4-8cb2-bff8a73b52ec-1-0
> >>>>> srcdir=psim.loops-20100225-1712-3zrtb5i5/shared/_concurrent
> >>>>> srchost=localhost destdir=_concurrent desthost=localhost
> >>>>> provider=file
> >>>>> 2010-02-25 17:12:04,475-0600 DEBUG TaskImpl
> >>>>>           
> >> Task(type=FILE_OPERATION,
> >>     
> >>>>> identity=urn:0-1-0-0-1-1-1267139524157) setting status to
> >>>>>           
> >> Submitting
> >>     
> >>>>> 2010-02-25 17:12:04,475-0600 DEBUG TaskImpl
> >>>>>           
> >> Task(type=FILE_OPERATION,
> >>     
> >>>>> identity=urn:0-1-0-0-1-1-1267139524157) setting status to
> >>>>>           
> >> Submitted
> >>     
> >>>>> 2010-02-25 17:12:04,475-0600 DEBUG TaskImpl
> >>>>>           
> >> Task(type=FILE_OPERATION,
> >>     
> >>>>> identity=urn:0-1-0-0-1-1-1267139524157) setting status to
> Active
> >>>>> 2010-02-25 17:12:04,476-0600 DEBUG TaskImpl
> >>>>>           
> >> Task(type=FILE_OPERATION,
> >>     
> >>>>> identity=urn:0-1-0-0-1-1-1267139524157) setting status to
> >>>>>           
> >> Completed
> >>     
> >>>>> 2010-02-25 17:12:04,476-0600 INFO  LateBindingScheduler
> >>>>> Task(type=FILE_OPERATION,
> identity=urn:0-1-0-0-1-1-1267139524157)
> >>>>> Completed. Waiting: 0, Running: 1. Heap size: 14M, Heap free:
> 5M,
> >>>>>           
> >> Max
> >>     
> >>>>> heap: 254M
> >>>>> 2010-02-25 17:12:04,479-0600 INFO  vdl:dostageout END
> >>>>> jobid=echo-xkjtxaoj - Staging out finished
> >>>>> 2010-02-25 17:12:04,482-0600 DEBUG vdl:execute2 JOB_END
> >>>>> jobid=echo-xkjtxaoj
> >>>>> 2010-02-25 17:12:04,484-0600 INFO  vdl:execute END_SUCCESS
> >>>>> thread=0-1-0-0 tr=echo
> >>>>> 2010-02-25 17:12:04,613-0600 INFO  CloseDataset Closing
> >>>>> org.griphyn.vdl.mapping.RootDataNode identifier
> >>>>>
> >>>>>           
> >>
> tag:benc at ci.uchicago.edu,2008:swift:dataset:20100225-1712-kjif48ad:720000000042
> >>
> >>     
> >>>>> type file with no value at dataset=f (not closed)
> >>>>> 2010-02-25 17:12:04,614-0600 INFO  AbstractDataNode Notifying
> >>>>>           
> >> listener
> >>     
> >>>>> "F/org.griphyn.vdl.mapping.RootDataNode identifier
> >>>>>
> >>>>>           
> >>
> tag:benc at ci.uchicago.edu,2008:swift:dataset:20100225-1712-kjif48ad:720000000042
> >>
> >>     
> >>>>> type file with no value at dataset=f (closed)" about
> >>>>> "org.griphyn.vdl.mapping.RootDataNode identifier
> >>>>>
> >>>>>           
> >>
> tag:benc at ci.uchicago.edu,2008:swift:dataset:20100225-1712-kjif48ad:720000000042
> >>
> >>     
> >>>>> type file with no value at dataset=f (closed)"
> >>>>> 2010-02-25 17:12:04,614-0600 INFO  AbstractDataNode closed
> >>>>> org.griphyn.vdl.mapping.RootDataNode identifier
> >>>>>
> >>>>>           
> >>
> tag:benc at ci.uchicago.edu,2008:swift:dataset:20100225-1712-kjif48ad:720000000042
> >>
> >>     
> >>>>> type file with no value at dataset=f (closed)
> >>>>> 2010-02-25 17:12:04,614-0600 INFO  AbstractDataNode Notifying
> >>>>>           
> >> listener
> >>     
> >>>>> "modelOut.$[]/0" about "org.griphyn.vdl.mapping.RootDataNode
> >>>>> identifier
> >>>>>
> >>>>>           
> >>
> tag:benc at ci.uchicago.edu,2008:swift:dataset:20100225-1712-kjif48ad:720000000014
> >>
> >>     
> >>>>> type int value=4.0 dataset=nSim (closed)"
> >>>>> 2010-02-25 17:12:04,615-0600 INFO  echos PROCEDURE_END line=68
> >>>>> 2010-02-25 17:12:04,615-0600 INFO  CloseDataset Partially
> closing
> >>>>> org.griphyn.vdl.mapping.RootDataNode identifier
> >>>>>
> >>>>>           
> >>
> tag:benc at ci.uchicago.edu,2008:swift:dataset:20100225-1712-kjif48ad:720000000042
> >>
> >>     
> >>>>> type file with no value at dataset=f (closed) for statement
> 88004
> >>>>> 2010-02-25 17:12:04,615-0600 INFO  CloseDataset var is
> >>>>> org.griphyn.vdl.mapping.RootDataNode identifier
> >>>>>
> >>>>>           
> >>
> tag:benc at ci.uchicago.edu,2008:swift:dataset:20100225-1712-kjif48ad:720000000042
> >>
> >>     
> >>>>> type file with no value at dataset=f (closed)
> >>>>> 2010-02-25 17:12:04,615-0600 INFO  CloseDataset var hash is
> >>>>>           
> >> 21621663
> >>     
> >>>>> 2010-02-25 17:12:04,615-0600 INFO  CloseDataset variable
> already
> >>>>> closed - skipping partial close processing
> >>>>> 2010-02-25 17:12:04,682-0600 INFO  AbstractDataNode Found
> mapped
> >>>>>           
> >> data
> >>     
> >>>>> modelOut.$[]/1.[2].pdt
> >>>>> 2010-02-25 17:12:04,682-0600 INFO  AbstractDataNode Found
> mapped
> >>>>>           
> >> data
> >>     
> >>>>> modelOut.$[]/2.[0].cfg
> >>>>> 2010-02-25 17:12:04,682-0600 INFO  AbstractDataNode Found
> mapped
> >>>>>           
> >> data
> >>     
> >>>>> modelOut.$[]/3.[1].cfg
> >>>>> 2010-02-25 17:12:04,682-0600 INFO  AbstractDataNode Found
> mapped
> >>>>>           
> >> data
> >>     
> >>>>> modelOut.$[]/4.[3].log
> >>>>> 2010-02-25 17:12:04,682-0600 INFO  AbstractDataNode Found
> mapped
> >>>>>           
> >> data
> >>     
> >>>>> modelOut.$[]/4.[3].cfg
> >>>>> 2010-02-25 17:12:04,682-0600 INFO  AbstractDataNode Found
> mapped
> >>>>>           
> >> data
> >>     
> >>>>> modelOut.$[]/4.[3].pdt
> >>>>> 2010-02-25 17:12:04,682-0600 INFO  AbstractDataNode Found
> mapped
> >>>>>           
> >> data
> >>     
> >>>>> modelOut.$[]/4.[0].pdt
> >>>>> 2010-02-25 17:12:04,682-0600 INFO  AbstractDataNode Found
> mapped
> >>>>>           
> >> data
> >>     
> >>>>> modelOut.$[]/4.[1].pdb
> >>>>> 2010-02-25 17:12:04,682-0600 INFO  AbstractDataNode Found
> mapped
> >>>>>           
> >> data
> >>     
> >>>>> modelOut.$[]/4.[0].log
> >>>>> 2010-02-25 17:12:04,683-0600 INFO  AbstractDataNode Found
> mapped
> >>>>>           
> >> data
> >>     
> >>>>> modelOut.$[]/4.[1].log
> >>>>> 2010-02-25 17:12:04,683-0600 INFO  AbstractDataNode Found
> mapped
> >>>>>           
> >> data
> >>     
> >>>>> modelOut.$[]/4.[2].cfg
> >>>>> 2010-02-25 17:12:04,683-0600 INFO  AbstractDataNode Found
> mapped
> >>>>>           
> >> data
> >>     
> >>>>> modelOut.$[]/4.[2].log
> >>>>> 2010-02-25 17:12:04,683-0600 INFO  AbstractDataNode Found
> mapped
> >>>>>           
> >> data
> >>     
> >>>>> modelOut.$[]/4.[3].pdb
> >>>>> 2010-02-25 17:12:04,683-0600 INFO  AbstractDataNode Found
> mapped
> >>>>>           
> >> data
> >>     
> >>>>> modelOut.$[]/4.[2].pdb
> >>>>> 2010-02-25 17:12:04,683-0600 INFO  AbstractDataNode Found
> mapped
> >>>>>           
> >> data
> >>     
> >>>>> modelOut.$[]/4.[1].pdt
> >>>>> 2010-02-25 17:12:04,683-0600 INFO  AbstractDataNode Found
> mapped
> >>>>>           
> >> data
> >>     
> >>>>> modelOut.$[]/4.[0].pdb
> >>>>> 2010-02-25 17:12:04,683-0600 INFO  AbstractDataNode Notifying
> >>>>>           
> >> listener
> >>     
> >>>>> "F/modelOut.$[]/4" about
> >>>>>           
> >> "org.griphyn.vdl.mapping.RootArrayDataNode
> >>     
> >>>>> identifier
> >>>>>
> >>>>>           
> >>
> tag:benc at ci.uchicago.edu,2008:swift:dataset:20100225-1712-kjif48ad:720000000023
> >>
> >>     
> >>>>> type LoopModelOut[] with no value at dataset=modelOut (closed)"
> >>>>> 2010-02-25 17:12:04,683-0600 INFO  AbstractDataNode closed
> >>>>> org.griphyn.vdl.mapping.RootArrayDataNode identifier
> >>>>>
> >>>>>           
> >>
> tag:benc at ci.uchicago.edu,2008:swift:dataset:20100225-1712-kjif48ad:720000000023
> >>
> >>     
> >>>>> type LoopModelOut[] with no value at dataset=modelOut (closed)
> >>>>> 2010-02-25 17:12:04,684-0600 INFO  AbstractDataNode Notifying
> >>>>>           
> >> listener
> >>     
> >>>>> "F/4" about "org.griphyn.vdl.mapping.RootDataNode identifier
> >>>>>
> >>>>>           
> >>
> tag:benc at ci.uchicago.edu,2008:swift:dataset:20100225-1712-kjif48ad:720000000014
> >>
> >>     
> >>>>> type int value=4.0 dataset=nSim (closed)"
> >>>>> 2010-02-25 17:12:04,684-0600 INFO  AbstractDataNode closed
> >>>>> org.griphyn.vdl.mapping.RootDataNode identifier
> >>>>>
> >>>>>           
> >>
> tag:benc at ci.uchicago.edu,2008:swift:dataset:20100225-1712-kjif48ad:720000000014
> >>
> >>     
> >>>>> type int value=4.0 dataset=nSim (closed)
> >>>>> 2010-02-25 17:12:04,685-0600 INFO  AbstractDataNode closed
> >>>>> org.griphyn.vdl.mapping.RootDataNode identifier
> >>>>>
> >>>>>           
> >>
> tag:benc at ci.uchicago.edu,2008:swift:dataset:20100225-1712-kjif48ad:720000000069
> >>
> >>     
> >>>>> type int value=3.0 dataset=unnamed SwiftScript value (closed)
> >>>>> 2010-02-25 17:12:04,685-0600 INFO  strtoi INTERNALPROC_END
> >>>>> thread=0-1-0-1
> >>>>> 2010-02-25 17:12:04,685-0600 INFO  CloseDataset Closing 4
> >>>>> 2010-02-25 17:12:04,686-0600 INFO  strtoi ENDCOMPOUND
> >>>>>           
> >> thread=0-1-0
> >>     
> >>>>> 2010-02-25 17:12:04,686-0600 INFO  CloseDataset Partially
> closing
> >>>>>           
> >> 4
> >>     
> >>>>> for statement 88012
> >>>>> 2010-02-25 17:12:04,686-0600 INFO  CloseDataset var is 4
> >>>>> 2010-02-25 17:12:04,686-0600 INFO  CloseDataset var hash is
> >>>>>           
> >> 2221396
> >>     
> >>>>> 2010-02-25 17:12:04,687-0600 INFO  CloseDataset variable
> already
> >>>>> closed - skipping partial close processing
> >>>>> 2010-02-25 17:12:04,687-0600 INFO  AbstractDataNode Adding
> handle
> >>>>> listener "F/org.griphyn.vdl.mapping.DataNode identifier
> >>>>>
> >>>>>           
> >>
> tag:benc at ci.uchicago.edu,2008:swift:dataset:20100225-1712-kjif48ad:720000000056
> >>
> >>     
> >>>>> type ModelLog with no value at dataset=modelOut path=[3].log
> (not
> >>>>> closed)" to "org.griphyn.vdl.mapping.DataNode identifier
> >>>>>
> >>>>>           
> >>
> tag:benc at ci.uchicago.edu,2008:swift:dataset:20100225-1712-kjif48ad:720000000056
> >>
> >>     
> >>>>> type ModelLog with no value at dataset=modelOut path=[3].log
> (not
> >>>>> closed)"
> >>>>> 2010-02-25 17:12:04,700-0600 INFO  AbstractDataNode closed
> >>>>> org.griphyn.vdl.mapping.RootDataNode identifier
> >>>>>
> >>>>>           
> >>
> tag:benc at ci.uchicago.edu,2008:swift:dataset:20100225-1712-kjif48ad:720000000071
> >>
> >>     
> >>>>> type int value=0.0 dataset=unnamed SwiftScript value (closed)
> >>>>> 2010-02-25 17:12:04,701-0600 INFO  AbstractDataNode closed
> >>>>> org.griphyn.vdl.mapping.RootDataNode identifier
> >>>>>
> >>>>>           
> >>
> tag:benc at ci.uchicago.edu,2008:swift:dataset:20100225-1712-kjif48ad:720000000072
> >>
> >>     
> >>>>> type int value=1.0 dataset=unnamed SwiftScript value (closed)
> >>>>> 2010-02-25 17:12:04,701-0600 INFO  AbstractDataNode closed
> >>>>> org.griphyn.vdl.mapping.RootDataNode identifier
> >>>>>
> >>>>>           
> >>
> tag:benc at ci.uchicago.edu,2008:swift:dataset:20100225-1712-kjif48ad:720000000073
> >>
> >>     
> >>>>> type int value=2.0 dataset=unnamed SwiftScript value (closed)
> >>>>> 2010-02-25 17:12:04,701-0600 INFO  AbstractDataNode closed
> >>>>> org.griphyn.vdl.mapping.RootDataNode identifier
> >>>>>
> >>>>>           
> >>
> tag:benc at ci.uchicago.edu,2008:swift:dataset:20100225-1712-kjif48ad:720000000074
> >>
> >>     
> >>>>> type int value=3.0 dataset=unnamed SwiftScript value (closed)
> >>>>> 2010-02-25 17:12:04,701-0600 INFO  AbstractDataNode closed
> >>>>> org.griphyn.vdl.karajan.lib.Range$1 identifier
> >>>>>
> >>>>>           
> >>
> tag:benc at ci.uchicago.edu,2008:swift:dataset:20100225-1712-kjif48ad:720000000070
> >>
> >>     
> >>>>> type int[] with no value at dataset=unnamed SwiftScript value
> >>>>> (closed)
> >>>>> 2010-02-25 17:12:04,702-0600 INFO  doloopround FOREACH_IT_START
> >>>>> line=130 thread=0-1-9-1-1
> >>>>> 2010-02-25 17:12:04,703-0600 INFO  doloopround FOREACH_IT_START
> >>>>> line=130 thread=0-1-9-1-2
> >>>>> 2010-02-25 17:12:04,703-0600 INFO  doloopround FOREACH_IT_START
> >>>>> line=130 thread=0-1-9-1-3
> >>>>> 2010-02-25 17:12:04,703-0600 INFO  doloopround FOREACH_IT_START
> >>>>> line=130 thread=0-1-9-1-4
> >>>>> 2010-02-25 17:12:04,703-0600 INFO  doloopround SCOPE
> >>>>>           
> >> thread=0-1-9-1-2
> >>     
> >>>>> 2010-02-25 17:12:04,703-0600 INFO  doloopround SCOPE
> >>>>>           
> >> thread=0-1-9-1-3
> >>     
> >>>>> 2010-02-25 17:12:04,704-0600 INFO  doloopround SCOPE
> >>>>>           
> >> thread=0-1-9-1-4
> >>     
> >>>>> 2010-02-25 17:12:04,707-0600 INFO  loopmodel PROCEDURE line=117
> >>>>> thread=0-1-9-1-2-1 name=loopModel
> >>>>> 2010-02-25 17:12:04,7
> 
> [Message truncated]

-- 
Michael Wilde
Computation Institute, University of Chicago
Mathematics and Computer Science Division
Argonne National Laboratory



From iraicu at cs.uchicago.edu  Mon Mar 15 12:49:18 2010
From: iraicu at cs.uchicago.edu (Ioan Raicu)
Date: Mon, 15 Mar 2010 12:49:18 -0500
Subject: [Swift-devel] CFP deadline 3/17/10: IEEE 2010 Fourth International
 Workshop on Scientific Workflows (SWF 2010)
Message-ID: <4B9E731E.4070206@cs.uchicago.edu>

CALL FOR PAPERS
IEEE 2010 Fourth International Workshop on Scientific Workflows (SWF 2010)
http://www.cs.wayne.edu/~shiyong/swf
Miama, Florida, U.S.A., one day between July 5-10, 2010

In conjunction with IEEE ICWS 2010, IEEE SCC 2010, IEEE CLOUD 2010, and 
IEEE SERVICES 2010

Description
Scientific workflows have become an increasingly popular paradigm for 
scientists to formalize and structure complex scientific processes to 
enable and accelerate many significant scientific discoveries. A 
scientific workflow is a formal specification of a scientific process, 
which represents, streamlines, and automates the analytical and 
computational steps that a scientist needs to go through from dataset 
selection and integration, computation and analysis, to final data 
product presentation and visualization. A scientific workflow management 
system (SWFMS) is a system that supports the specification, 
modification, execution, failure handling, and monitoring of a 
scientific workflow using the workflow logic to control the order of 
executing workflow tasks. The importance of scientific workflows has 
been recognized by NSF since 2006 and was reemphasized recently in an 
science article titled ?Beyond the Data Deluge? (Science, Vol. 323. no. 
5919, pp. 1297 ? 1298, 2009), which concluded, ?In the future, the 
rapidity with which any given discipline advances is likely to depend on 
how well the community acquires the necessary expertise in database, 
workflow management, visualization, and cloud computing technologies.?

The goal of SWF 2010 is to provide a forum for researchers and 
practitioners to present their recent research results and best 
practices of scientific workflows, and identify the emerging trends, 
opportunities, problems, and challenges in this area. Authors are 
invited to submit regular papers (8 pages) and short papers (4 pages) 
that show original unpublished research results in all areas of 
scientific workflows. Topics of interest are listed below; however, 
submissions on all aspects of scientific workflows are welcome.

List of topics
* Scientific workflow provenance management and analytics
* Scientific workflow data, metadata, service, and task management
* Scientific workflow architectures, models, languages, systems, and 
algorithms
* Scientific workflow monitoring, debugging, and failure handling
* Streaming data processing in scientific workflows
* Pipelined, data, workflow, and task parallelism in scientific workflows
* Cloud, Service, Grid, or hybrid scientific workflows
* Data, metadata, compute, user-interaction, or visualization-intensive 
scientific workflows
* Scientific workflow composition
* Security issues in scientific workflows
* Data integration and service integration in scientific workflows
* Scientific workflow mapping, optimization, and scheduling
* Scientific workflow modeling, simulation, analysis, and verification
* Scalability, reliability, extensibility, agility, and interoperability
* Scientific workflow applications

Important dates
* Paper Submission March 17, 2010
* Decision Notification (Electronic) April 17, 2010
* Camera-Ready Submission & Pre-registration April 30, 2010

Paper submission
All papers should be submitted via the SWF workshop submission system at 
http://www.confhub.com/conf.php?id=175. First time users need to 
register with the system first.

Workshop chairs
* Shiyong Lu, Wayne State University, Email: shiyong at wayne.edu
* Calton Pu, Georgia Tech
* Liqiang Wang, University of Wyoming

Publication chairs
* Ilkay Altintas, San Diego Supercomputer Center
* Yogesh Simmhan, Microsoft Research
* Ioan Raicu, Northwestern University

Publicity chair
* Jamal Alhiyafi, Wayne State University, Email: alhiyafi at wayne.edu

Program committee
* Ilkay Altintas, San Diego Supercomputer Center, USA
* Roger Barga, Microsoft Research, USA
* Adam Barker, University of Oxford, UK
* Shawn Bowers, UC Davis Genome Center, USA
* Artem Chebotko, University of Texas at Pan American, USA
* Ian Gorton, PNNL
* Paul Groth, VU University Amsterdam
* Marta L. Queir?s Mattoso, Federal University of Rio de Janeiro, Brazil
* Luc Moreau, University of South Hampton
* Ioan Raicu, University of Chicago, USA
* Yogesh Simmhan, Microsoft Corporation, USA
* Chung-Wei Hang, North Carolina State University, USA
* Hasan Jamil, Wayne State University
* Ian Taylor, Cardiff University, UK
* Jianwu Wang, San Diego Supercomputer Center
* Wei Tan, ANL
* Ping Yang, Binghamton University, USA
* Ustun Yildiz, UC Davis
* Yong Zhao, Microsoft Corporation, USA
* Zhiming Zhao, University of Amsterdam, the Netherlands

-- 
=================================================================
Ioan Raicu, Ph.D.
NSF/CRA Computing Innovation Fellow
=================================================================
Center for Ultra-scale Computing and Information Security (CUCIS)
Department of Electrical Engineering and Computer Science
Northwestern University
2145 Sheridan Rd, Tech M384 
Evanston, IL 60208-3118
=================================================================
Cel:   1-847-722-0876
Tel:   1-847-491-8163
Email: iraicu at eecs.northwestern.edu
Web:   http://www.eecs.northwestern.edu/~iraicu/
       https://wiki.cucis.eecs.northwestern.edu/
=================================================================
=================================================================



-- 
=================================================================
Ioan Raicu, Ph.D.
NSF/CRA Computing Innovation Fellow
=================================================================
Center for Ultra-scale Computing and Information Security (CUCIS)
Department of Electrical Engineering and Computer Science
Northwestern University
2145 Sheridan Rd, Tech M384 
Evanston, IL 60208-3118
=================================================================
Cel:   1-847-722-0876
Tel:   1-847-491-8163
Email: iraicu at eecs.northwestern.edu
Web:   http://www.eecs.northwestern.edu/~iraicu/
       https://wiki.cucis.eecs.northwestern.edu/
=================================================================
=================================================================




From bugzilla-daemon at mcs.anl.gov  Tue Mar 16 20:20:07 2010
From: bugzilla-daemon at mcs.anl.gov (bugzilla-daemon at mcs.anl.gov)
Date: Tue, 16 Mar 2010 20:20:07 -0500 (CDT)
Subject: [Swift-devel] [Bug 223] New: wildcard fails in the pattern
 parameter for simple_mapper
Message-ID: <bug-223-21@http.bugzilla.mcs.anl.gov/swift/>

https://bugzilla.mcs.anl.gov/swift/show_bug.cgi?id=223

           Summary: wildcard fails in the pattern parameter for
                    simple_mapper
           Product: Swift
           Version: unspecified
          Platform: PC
        OS/Version: Windows
            Status: NEW
          Severity: normal
          Priority: P2
         Component: SwiftScript language
        AssignedTo: benc at hawaga.org.uk
        ReportedBy: skenny at uchicago.edu


the simple_mapper is meant to take a 'pattern' parameter which can contain
wildcards, however...

the following code:

file physdata<simple_mapper;location="rawphys/",pattern="*017*",suffix=".txt">;
trace(@filename(physdata));

produces this error:

Execution failed:
        java.lang.IllegalStateException: mapper.existing() returned a path
.r33subj017 that it cannot subsequently map


though, as i understand it, it should map a single file from this dir:

$ ls rawphys/
r33subj003.txt  r33subj017.txt


(workaround is to use filesys_mapper, so perhaps if this cannot be fixed it
could be altered in the documentation)

-- 
Configure bugmail: https://bugzilla.mcs.anl.gov/swift/userprefs.cgi?tab=email
------- You are receiving this mail because: -------
You are watching the assignee of the bug.


From aespinosa at cs.uchicago.edu  Fri Mar 19 12:51:36 2010
From: aespinosa at cs.uchicago.edu (Allan Espinosa)
Date: Fri, 19 Mar 2010 12:51:36 -0500
Subject: [Swift-devel] Re: simple_mapper auto-padding of "."
In-Reply-To: <50b07b4b1003191045p52bb6f23v4365dc6f1972b22@mail.gmail.com>
References: <50b07b4b1003191045p52bb6f23v4365dc6f1972b22@mail.gmail.com>
Message-ID: <50b07b4b1003191051g38ddc835x6974d9c7d3314fc4@mail.gmail.com>

Never mind.

I found the code that does the padding.  I'll just comment it out in
my Swift build

AbstractFileMapper.java:
    82                          if (!suffix.startsWith(".")) {
    83                                  PARAM_SUFFIX.setValue(this,
"." + suffix);
    84                          }

-Allan

2010/3/19 Allan Espinosa <aespinosa at cs.uchicago.edu>:
> Hi,
>
> Do we have a swift parameter to remove padding of "." in the suffix in
> the test tests/language-behavior/073-simplemapper.swift so that
> instead of having an expected output of
>
> 073-simplemapper.out
>
> I'll have
>
> 073-simplemapperout
>
> instead?
>
> Thanks,
> -Allan
>



-- 
Allan M. Espinosa <http://amespinosa.wordpress.com>
PhD student, Computer Science
University of Chicago <http://people.cs.uchicago.edu/~aespinosa>


From hategan at mcs.anl.gov  Fri Mar 19 13:00:52 2010
From: hategan at mcs.anl.gov (Mihael Hategan)
Date: Fri, 19 Mar 2010 13:00:52 -0500
Subject: [Swift-devel] Re: simple_mapper auto-padding of "."
In-Reply-To: <50b07b4b1003191051g38ddc835x6974d9c7d3314fc4@mail.gmail.com>
References: <50b07b4b1003191045p52bb6f23v4365dc6f1972b22@mail.gmail.com>
	<50b07b4b1003191051g38ddc835x6974d9c7d3314fc4@mail.gmail.com>
Message-ID: <1269021652.855.0.camel@localhost>

On Fri, 2010-03-19 at 12:51 -0500, Allan Espinosa wrote:
> Never mind.
> 
> I found the code that does the padding.  I'll just comment it out in
> my Swift build

Or you could add a parameter to do so in exchange for karma or imaginary
cookies :)




From aespinosa at cs.uchicago.edu  Fri Mar 19 12:45:53 2010
From: aespinosa at cs.uchicago.edu (Allan Espinosa)
Date: Fri, 19 Mar 2010 12:45:53 -0500
Subject: [Swift-devel] simple_mapper auto-padding of "."
Message-ID: <50b07b4b1003191045p52bb6f23v4365dc6f1972b22@mail.gmail.com>

Hi,

Do we have a swift parameter to remove padding of "." in the suffix in
the test tests/language-behavior/073-simplemapper.swift so that
instead of having an expected output of

073-simplemapper.out

I'll have

073-simplemapperout

instead?

Thanks,
-Allan


From iraicu at cs.uchicago.edu  Fri Mar 19 14:08:36 2010
From: iraicu at cs.uchicago.edu (Ioan Raicu)
Date: Fri, 19 Mar 2010 14:08:36 -0500
Subject: [Swift-devel] CFP deadline extension to 3/24/10: IEEE 2010 Fourth
 International Workshop on Scientific Workflows (SWF 2010)
Message-ID: <4BA3CBB4.2080807@cs.uchicago.edu>

CALL FOR PAPERS
IEEE 2010 Fourth International Workshop on Scientific Workflows (SWF 2010)
http://www.cs.wayne.edu/~shiyong/swf
Miama, Florida, U.S.A., one day between July 5-10, 2010

In conjunction with IEEE ICWS 2010, IEEE SCC 2010, IEEE CLOUD 2010, and 
IEEE SERVICES 2010

Description
Scientific workflows have become an increasingly popular paradigm for 
scientists to formalize and structure complex scientific processes to 
enable and accelerate many significant scientific discoveries. A 
scientific workflow is a formal specification of a scientific process, 
which represents, streamlines, and automates the analytical and 
computational steps that a scientist needs to go through from dataset 
selection and integration, computation and analysis, to final data 
product presentation and visualization. A scientific workflow management 
system (SWFMS) is a system that supports the specification, 
modification, execution, failure handling, and monitoring of a 
scientific workflow using the workflow logic to control the order of 
executing workflow tasks. The importance of scientific workflows has 
been recognized by NSF since 2006 and was reemphasized recently in an 
science article titled "Beyond the Data Deluge" (Science, Vol. 323. no. 
5919, pp. 1297 -- 1298, 2009), which concluded, "In the future, the 
rapidity with which any given discipline advances is likely to depend on 
how well the community acquires the necessary expertise in database, 
workflow management, visualization, and cloud computing technologies."

The goal of SWF 2010 is to provide a forum for researchers and 
practitioners to present their recent research results and best 
practices of scientific workflows, and identify the emerging trends, 
opportunities, problems, and challenges in this area. Authors are 
invited to submit regular papers (8 pages) and short papers (4 pages) 
that show original unpublished research results in all areas of 
scientific workflows. Topics of interest are listed below; however, 
submissions on all aspects of scientific workflows are welcome.

List of topics
* Scientific workflow provenance management and analytics
* Scientific workflow data, metadata, service, and task management
* Scientific workflow architectures, models, languages, systems, and 
algorithms
* Scientific workflow monitoring, debugging, and failure handling
* Streaming data processing in scientific workflows
* Pipelined, data, workflow, and task parallelism in scientific workflows
* Cloud, Service, Grid, or hybrid scientific workflows
* Data, metadata, compute, user-interaction, or visualization-intensive 
scientific workflows
* Scientific workflow composition
* Security issues in scientific workflows
* Data integration and service integration in scientific workflows
* Scientific workflow mapping, optimization, and scheduling
* Scientific workflow modeling, simulation, analysis, and verification
* Scalability, reliability, extensibility, agility, and interoperability
* Scientific workflow applications

Important dates
* Paper Submission Extended to March 24, 2010
* Decision Notification (Electronic) April 17, 2010
* Camera-Ready Submission & Pre-registration April 30, 2010

Paper submission
All papers should be submitted via the SWF workshop submission system at 
http://www.confhub.com/conf.php?id=175. First time users need to 
register with the system first.

Workshop chairs
* Shiyong Lu, Wayne State University, Email: shiyong at wayne.edu
* Calton Pu, Georgia Tech
* Liqiang Wang, University of Wyoming

Publication chairs
* Ilkay Altintas, San Diego Supercomputer Center
* Yogesh Simmhan, Microsoft Research
* Ioan Raicu, Northwestern University

Publicity chair
* Jamal Alhiyafi, Wayne State University, Email: alhiyafi at wayne.edu

Program committee
* Ilkay Altintas, San Diego Supercomputer Center, USA
* Roger Barga, Microsoft Research, USA
* Adam Barker, University of Oxford, UK
* Shawn Bowers, UC Davis Genome Center, USA
* Artem Chebotko, University of Texas at Pan American, USA
* Ian Gorton, PNNL
* Paul Groth, VU University Amsterdam
* Marta L. Queir?s Mattoso, Federal University of Rio de Janeiro, Brazil
* Luc Moreau, University of South Hampton
* Ioan Raicu, University of Chicago, USA
* Yogesh Simmhan, Microsoft Corporation, USA
* Chung-Wei Hang, North Carolina State University, USA
* Hasan Jamil, Wayne State University
* Ian Taylor, Cardiff University, UK
* Jianwu Wang, San Diego Supercomputer Center
* Wei Tan, ANL
* Ping Yang, Binghamton University, USA
* Ustun Yildiz, UC Davis
* Yong Zhao, Microsoft Corporation, USA
* Zhiming Zhao, University of Amsterdam, the Netherlands

-- 
=================================================================
Ioan Raicu, Ph.D.
NSF/CRA Computing Innovation Fellow
=================================================================
Center for Ultra-scale Computing and Information Security (CUCIS)
Department of Electrical Engineering and Computer Science
Northwestern University
2145 Sheridan Rd, Tech M384 Evanston, IL 60208-3118
=================================================================
Cel:   1-847-722-0876
Tel:   1-847-491-8163
Email: iraicu at eecs.northwestern.edu
Web:   http://www.eecs.northwestern.edu/~iraicu/
      https://wiki.cucis.eecs.northwestern.edu/
=================================================================
=================================================================




-- 
=================================================================
Ioan Raicu, Ph.D.
NSF/CRA Computing Innovation Fellow
=================================================================
Center for Ultra-scale Computing and Information Security (CUCIS)
Department of Electrical Engineering and Computer Science
Northwestern University
2145 Sheridan Rd, Tech M384 
Evanston, IL 60208-3118
=================================================================
Cel:   1-847-722-0876
Tel:   1-847-491-8163
Email: iraicu at eecs.northwestern.edu
Web:   http://www.eecs.northwestern.edu/~iraicu/
       https://wiki.cucis.eecs.northwestern.edu/
=================================================================
=================================================================


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From vipulkrsingh at gmail.com  Fri Mar 19 15:27:05 2010
From: vipulkrsingh at gmail.com (Vipul Kumar Singh)
Date: Sat, 20 Mar 2010 01:57:05 +0530
Subject: [Swift-devel] scheduling
Message-ID: <65fb392f1003191327o666e6697mc0a8a60d0c164268@mail.gmail.com>

Sir,

I am interested in working on the data-aware features in swift on two major
points

1) For jobs dependent on same data, scheduler tries to schedule them to same
resources.

               (i) The scheduler maintains a hash containing information
about (a) data files, (b)  jobs dependent on that data and (c) resources
that are executing (or scheduled to execute) those jobs.
               (ii) The information will be updated every time a job is
finished (on success/failure).
               (iii) When scheduling new jobs, the scheduler looks through
the hash and schedules new job to the resource that has data on which new
job is dependent (If the resource is not already overloaded).

2) Combining the tasks together that are dependent on same data files,
before scheduling. And i believe this can be added quickly using coasters (
or is the feature already there... ).

Currently i have setup some machines with globus and swift but am not able
to get swift submit jobs through gram4.....

Vipul Kumar Singh
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From hategan at mcs.anl.gov  Fri Mar 19 15:39:31 2010
From: hategan at mcs.anl.gov (Mihael Hategan)
Date: Fri, 19 Mar 2010 15:39:31 -0500
Subject: [Swift-devel] scheduling
In-Reply-To: <65fb392f1003191327o666e6697mc0a8a60d0c164268@mail.gmail.com>
References: <65fb392f1003191327o666e6697mc0a8a60d0c164268@mail.gmail.com>
Message-ID: <1269031171.4051.0.camel@localhost>

On Sat, 2010-03-20 at 01:57 +0530, Vipul Kumar Singh wrote:
>                (iii) When scheduling new jobs, the scheduler looks
> through the hash and schedules new job to the resource that has data
> on which new job is dependent (If the resource is not already
> overloaded).

Is that always the best choice?

Mihael



From iraicu at cs.uchicago.edu  Fri Mar 19 15:46:27 2010
From: iraicu at cs.uchicago.edu (Ioan Raicu)
Date: Fri, 19 Mar 2010 15:46:27 -0500
Subject: [Swift-devel] scheduling
In-Reply-To: <1269031171.4051.0.camel@localhost>
References: <65fb392f1003191327o666e6697mc0a8a60d0c164268@mail.gmail.com>
	<1269031171.4051.0.camel@localhost>
Message-ID: <4BA3E2A3.90802@cs.uchicago.edu>

For data intensive workloads, it usually is. The question is how do you 
determine "overloaded", and "data-intensive"?

Ioan

Mihael Hategan wrote:
> On Sat, 2010-03-20 at 01:57 +0530, Vipul Kumar Singh wrote:
>   
>>                (iii) When scheduling new jobs, the scheduler looks
>> through the hash and schedules new job to the resource that has data
>> on which new job is dependent (If the resource is not already
>> overloaded).
>>     
>
> Is that always the best choice?
>
> Mihael
>
> _______________________________________________
> Swift-devel mailing list
> Swift-devel at ci.uchicago.edu
> http://mail.ci.uchicago.edu/mailman/listinfo/swift-devel
>
>   

-- 
=================================================================
Ioan Raicu, Ph.D.
NSF/CRA Computing Innovation Fellow
=================================================================
Center for Ultra-scale Computing and Information Security (CUCIS)
Department of Electrical Engineering and Computer Science
Northwestern University
2145 Sheridan Rd, Tech M384 
Evanston, IL 60208-3118
=================================================================
Cel:   1-847-722-0876
Tel:   1-847-491-8163
Email: iraicu at eecs.northwestern.edu
Web:   http://www.eecs.northwestern.edu/~iraicu/
       https://wiki.cucis.eecs.northwestern.edu/
=================================================================
=================================================================


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From vipulkrsingh at gmail.com  Fri Mar 19 16:03:49 2010
From: vipulkrsingh at gmail.com (Vipul Kumar Singh)
Date: Sat, 20 Mar 2010 02:33:49 +0530
Subject: [Swift-devel] scheduling
In-Reply-To: <65fb392f1003191350u79a6822aw10707962af9ccf8c@mail.gmail.com>
References: <65fb392f1003191327o666e6697mc0a8a60d0c164268@mail.gmail.com> 
	<1269031171.4051.0.camel@localhost>
	<65fb392f1003191350u79a6822aw10707962af9ccf8c@mail.gmail.com>
Message-ID: <65fb392f1003191403i682f7036sd5d9d6dda51cc03e@mail.gmail.com>

no not always the best choice..only when data on which the job is dependent
are of large size ...

The situation is bad when the jobs require long processing time.. in such
cases it has to be decided what takes less overall time .. scheduling to new
resources (and data is fetched there)... on scheduling on the resource with
data..


On Sat, Mar 20, 2010 at 2:09 AM, Mihael Hategan <hategan at mcs.anl.gov> wrote:

> On Sat, 2010-03-20 at 01:57 +0530, Vipul Kumar Singh wrote:
> >                (iii) When scheduling new jobs, the scheduler looks
> > through the hash and schedules new job to the resource that has data
> > on which new job is dependent (If the resource is not already
> > overloaded).
>
> Is that always the best choice?
>
> Mihael
>
>
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From vipulkrsingh at gmail.com  Fri Mar 19 16:15:09 2010
From: vipulkrsingh at gmail.com (Vipul Kumar Singh)
Date: Sat, 20 Mar 2010 02:45:09 +0530
Subject: [Swift-devel] scheduling
In-Reply-To: <4BA3E2A3.90802@cs.uchicago.edu>
References: <65fb392f1003191327o666e6697mc0a8a60d0c164268@mail.gmail.com> 
	<1269031171.4051.0.camel@localhost> <4BA3E2A3.90802@cs.uchicago.edu>
Message-ID: <65fb392f1003191415w3aa87ba3p9099c10a25ee365d@mail.gmail.com>

We can use Size of data on which job is dependent to determine if it is data
incentive, and instead of having a fixed Size to determine we can make it
adapt based on the situations like.. in case rate of jobs being submitted is
increasing but so is the idle resource pool then the Size limit has to be
raised so that jobs are assigned to new resources and if in case rate of job
submission is going down but idle resource pool is decreasing or remains
constant the Size can be increased... or we can monitor the data transfers
if they are above some threshold Size can be decreased and vice-versa ...

On Sat, Mar 20, 2010 at 2:16 AM, Ioan Raicu <iraicu at cs.uchicago.edu> wrote:

>  For data intensive workloads, it usually is. The question is how do you
> determine "overloaded", and "data-intensive"?
>
> Ioan
>
> Mihael Hategan wrote:
>
> On Sat, 2010-03-20 at 01:57 +0530, Vipul Kumar Singh wrote:
>
>
>                 (iii) When scheduling new jobs, the scheduler looks
> through the hash and schedules new job to the resource that has data
> on which new job is dependent (If the resource is not already
> overloaded).
>
>
>  Is that always the best choice?
>
> Mihael
>
> _______________________________________________
> Swift-devel mailing listSwift-devel at ci.uchicago.eduhttp://mail.ci.uchicago.edu/mailman/listinfo/swift-devel
>
>
> --
> =================================================================
> Ioan Raicu, Ph.D.
> NSF/CRA Computing Innovation Fellow
> =================================================================
> Center for Ultra-scale Computing and Information Security (CUCIS)
> Department of Electrical Engineering and Computer Science
> Northwestern University
> 2145 Sheridan Rd, Tech M384
> Evanston, IL 60208-3118
> =================================================================
> Cel:   1-847-722-0876
> Tel:   1-847-491-8163
> Email: iraicu at eecs.northwestern.edu
> Web:   http://www.eecs.northwestern.edu/~iraicu/ <http://www.eecs.northwestern.edu/%7Eiraicu/>
>        https://wiki.cucis.eecs.northwestern.edu/
> =================================================================
> =================================================================
>
>
>
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From hategan at mcs.anl.gov  Fri Mar 19 16:27:33 2010
From: hategan at mcs.anl.gov (Mihael Hategan)
Date: Fri, 19 Mar 2010 16:27:33 -0500
Subject: [Swift-devel] scheduling
In-Reply-To: <65fb392f1003191403i682f7036sd5d9d6dda51cc03e@mail.gmail.com>
References: <65fb392f1003191327o666e6697mc0a8a60d0c164268@mail.gmail.com>
	<1269031171.4051.0.camel@localhost>
	<65fb392f1003191350u79a6822aw10707962af9ccf8c@mail.gmail.com>
	<65fb392f1003191403i682f7036sd5d9d6dda51cc03e@mail.gmail.com>
Message-ID: <1269034053.4456.2.camel@localhost>

On Sat, 2010-03-20 at 02:33 +0530, Vipul Kumar Singh wrote:
> 
> no not always the best choice..only when data on which the job is
> dependent are of large size ...
> 
> The situation is bad when the jobs require long processing time.. in
> such cases it has to be decided what takes less overall time ..
> scheduling to new resources (and data is fetched there)... on
> scheduling on the resource with data..
> 

Also, the resources speeds are not always the same.

Anyway, how would you go about deciding what takes less overall time?





From skenny at uchicago.edu  Fri Mar 19 16:40:36 2010
From: skenny at uchicago.edu (Sarah Kenny)
Date: Fri, 19 Mar 2010 16:40:36 -0500
Subject: [Swift-devel] array_mapper hangs
Message-ID: <843ba1aa1003191440r768b01a0w843a1335b53ce898@mail.gmail.com>

i'm trying to run the following code:

app (file physD[]) maptest(){
        touch @filename(physD[0]) @filename(physD[1]);
}

string conditions[] = ["rest1","emblem"];

string outfilenames[];
foreach cond,c in conditions{
        outfilenames[c] = @strcat(cond,"_physio.dat");
        trace(outfilenames[c]);
}

file f[] <array_mapper;files=outfilenames>;
f = maptest();

but when i try to run it it hangs indefinitely...in my experience this
*usually* means 'bad mapping' somewhere...not sure if i just have some
syntactical error here or if something's up with the array_mapper (?)
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From wilde at mcs.anl.gov  Fri Mar 19 21:01:43 2010
From: wilde at mcs.anl.gov (Michael Wilde)
Date: Fri, 19 Mar 2010 21:01:43 -0500 (CDT)
Subject: [Swift-devel] array_mapper hangs
In-Reply-To: <843ba1aa1003191440r768b01a0w843a1335b53ce898@mail.gmail.com>
Message-ID: <27015074.184361269050503837.JavaMail.root@zimbra>

Sarah,

The script is hanging because its trying to access the values of the array object f[], which is never set. Ie, at the point at which it wants a value for physD[0] and physD[1], physD itself - even though it has been *mapped* - has never been given a *value.

I think that (or some closely similar reason) is why this script hangs.

The *mapper*, however, os working fine. I re-wrote the script to use the same mapper in a context in which physD *is* set, and it then works, as below.

- Mike

$ cat am2.swift
type file;

app (file o) echo (string s)
{
  echo s stdout=@o;
}

(file physD[]) maptest() {
  foreach s, i in ["x","y"] {
    physD[i] = echo(s);
  }
}

string outfilenames[];
string conditions[] = ["rest1","emblem"];

foreach cond,c in conditions{
  outfilenames[c] = @strcat(cond,"_physio.dat");
}

string sdata[] = ["f1data","f2data"];
file f[] <array_mapper;files=outfilenames>;

f = maptest();
$ 
$ swift am2.swift
Swift svn swift-r3264 (swift modified locally) cog-r2730 (cog modified locally)

RunID: 20100319-2055-xhecsen3
Progress:
Final status:  Finished successfully:2
$ ls *.dat
emblem_physio.dat  rest1_physio.dat
$ more *.dat
::::::::::::::
emblem_physio.dat
::::::::::::::
y
::::::::::::::
rest1_physio.dat
::::::::::::::
x
$ 

----- "Sarah Kenny" <skenny at uchicago.edu> wrote:

> i'm trying to run the following code:
> 
> app (file physD[]) maptest(){
> touch @filename(physD[0]) @filename(physD[1]);
> }
> 
> string conditions[] = ["rest1","emblem"];
> 
> string outfilenames[];
> foreach cond,c in conditions{
> outfilenames[c] = @strcat(cond,"_physio.dat");
> trace(outfilenames[c]);
> }
> 
> file f[] <array_mapper;files=outfilenames>;
> f = maptest();
> 
> but when i try to run it it hangs indefinitely...in my experience this
> *usually* means 'bad mapping' somewhere...not sure if i just have some
> syntactical error here or if something's up with the array_mapper (?)
> 
> 
> _______________________________________________
> Swift-devel mailing list
> Swift-devel at ci.uchicago.edu
> http://mail.ci.uchicago.edu/mailman/listinfo/swift-devel

-- 
Michael Wilde
Computation Institute, University of Chicago
Mathematics and Computer Science Division
Argonne National Laboratory



From wilde at mcs.anl.gov  Fri Mar 19 21:43:36 2010
From: wilde at mcs.anl.gov (wilde at mcs.anl.gov)
Date: Fri, 19 Mar 2010 21:43:36 -0500 (CDT)
Subject: [Swift-devel] Re: scheduling
In-Reply-To: <7363198.184681269052526459.JavaMail.root@zimbra>
Message-ID: <19767280.184761269053016043.JavaMail.root@zimbra>

Hi Vipul,

The topic you propose here is both interesting and likely to be valuable for Swift users, and I'd like to help you develop the ideas further.  I'll try to respond to later comments on the discuss that started on your proposal, but first I'd like to offer a few thoughts on your initial message below.

----- "Vipul Kumar Singh" <vipulkrsingh at gmail.com> wrote:

> Sir,
> 
> I am interested in working on the data-aware features in swift on two
> major points
> 
> 1) For jobs dependent on same data, scheduler tries to schedule them
> to same resources.

The ability to *consider* the location of a data object when assigning a job to a site would be great.

> 
> (i) The scheduler maintains a hash containing information about (a)
> data files, (b) jobs dependent on that data and (c) resources that are
> executing (or scheduled to execute) those jobs.
> (ii) The information will be updated every time a job is finished (on
> success/failure).
> (iii) When scheduling new jobs, the scheduler looks through the hash
> and schedules new job to the resource that has data on which new job
> is dependent (If the resource is not already overloaded).

I think these heuristics are a very good first approximation; you'll need to refine the criteria as you get deeper into the code and also based on experiments and measurements.

It would be good to base a solution on a grid-wide file location catalog like the Globus RLS or similar. Ive long thought that file location could also be selected and/or influenced by mappers (like ext mapper scripts) but thats just a starting point to feed info to the site selection algorithm.

> 
> 2) Combining the tasks together that are dependent on same data files,
> before scheduling. And i believe this can be added quickly using
> coasters ( or is the feature already there... ).

I think a bit of work has been done towards this goal by a student a few summers back that could be used as a starting point.  In general, we've been interested in having Swift join tasks together in a shell-like pipeline when that would be optimal.

> 
> Currently i have setup some machines with globus and swift but am not
> able to get swift submit jobs through gram4.....

I think you'll get better results (and support) with GRAM 5, or even GRAM 2.4. And you could do initial experiments with just ssh and coasters. Let us know what problems youre havig (on swift-user at ci.uchicago.edu, and include your sites.xml, tc.data, swift.properties, and swift .log file when reporting problems, so we can diagnose them with less back-and-forth, OK?

I'm eager to see what kind of progress you can make on this problem, and very willing to help you think through it.

Regards,

Mike



> 
> Vipul Kumar Singh

-- 
Michael Wilde
Computation Institute, University of Chicago
Mathematics and Computer Science Division
Argonne National Laboratory



From aespinosa at cs.uchicago.edu  Sat Mar 20 03:31:58 2010
From: aespinosa at cs.uchicago.edu (Allan Espinosa)
Date: Sat, 20 Mar 2010 03:31:58 -0500
Subject: [Swift-devel] Re: simple_mapper auto-padding of "."
In-Reply-To: <1269021652.855.0.camel@localhost>
References: <50b07b4b1003191045p52bb6f23v4365dc6f1972b22@mail.gmail.com>
	<50b07b4b1003191051g38ddc835x6974d9c7d3314fc4@mail.gmail.com>
	<1269021652.855.0.camel@localhost>
Message-ID: <50b07b4b1003200131s1cfe9689u335180d3f99e8194@mail.gmail.com>

I'll be getting my cookies now :)

Patch available in
http://www.ci.uchicago.edu/~aespinosa/swift_mapper-noauto.patch

Test cases/ examples in
tests/language-behaviour/T078-simplemapper-nosuffix.swift and
tests/language-behaviour/T078-simplemapper-nosuffix.swift (Did i get
the exception handling practice correctly?)

diff --git a/src/org/griphyn/vdl/mapping/file/AbstractFileMapper.java
b/src/org/griphyn/vdl/mapping/file/AbstractF
index 362cb01..5b7b455 100644
--- a/src/org/griphyn/vdl/mapping/file/AbstractFileMapper.java
+++ b/src/org/griphyn/vdl/mapping/file/AbstractFileMapper.java
@@ -12,6 +12,7 @@ import org.apache.log4j.Logger;

 import org.griphyn.vdl.mapping.AbsFile;
 import org.griphyn.vdl.mapping.AbstractMapper;
+import org.griphyn.vdl.mapping.InvalidMappingParameterException;
 import org.griphyn.vdl.mapping.MappingParam;
 import org.griphyn.vdl.mapping.Path;
 import org.griphyn.vdl.mapping.PhysicalFormat;
@@ -36,6 +37,8 @@ import org.griphyn.vdl.mapping.PhysicalFormat;
   *                  this string. If suffix does not begin with a '.'
   *                  character, then a '.' will be added automatically to
   *                  separate the rest of the filename from the suffix</li>
+  *   <li>noauto - if specified as "true", then the suffix auto
addition of a'.'
+  *                  will be disabled.  Default value is "false".</li>
   *   <li>pattern - if specified, then filenames will be selected from
   *                 the location directory when they match the unix glob
   *                 pattern supplied in this parameter.</li>
@@ -47,6 +50,7 @@ public abstract class AbstractFileMapper extends
AbstractMapper {
        public static final MappingParam PARAM_SUFFIX = new
MappingParam("suffix", null);
        public static final MappingParam PARAM_PATTERN = new
MappingParam("pattern", null);
        public static final MappingParam PARAM_LOCATION = new
MappingParam("location", null);
+       public static final MappingParam PARAM_NOAUTO = new
MappingParam("noauto", "false");

        public static final Logger logger =
Logger.getLogger(AbstractFileMapper.class);

@@ -79,7 +83,12 @@ public abstract class AbstractFileMapper extends
AbstractMapper {
                super.setParams(params);
                if (PARAM_SUFFIX.isPresent(this)) {
                        String suffix = PARAM_SUFFIX.getStringValue(this);
-                       if (!suffix.startsWith(".")) {
+                       String noauto = PARAM_NOAUTO.getStringValue(this);
+                       if (!noauto.equals("true") && !noauto.equals("false")) {
+                               throw new
InvalidMappingParameterException("noauto parameter was set to 'true'
or
+                                               ". Value set was '" +
noauto + "'");
+                       }
+                       if (!suffix.startsWith(".") && noauto.equals("false")) {
                                PARAM_SUFFIX.setValue(this, "." + suffix);
...skipping...
+(messagefile t) write() {
+    app {
+        echo @filename(t) stdout=@filename(t);
+    }
+}
+
+messagefile outfile <simple_mapper;
+                     prefix="T078-simplemapper-nosuffix", noauto="true",
+                     suffix="_nodot.out">;
+
+outfile = write();
+
diff --git a/tests/language-behaviour/T078-simplemapper-nosuffix_nodot.out.expected
b/tests/language-behaviour/T07
new file mode 100644
index 0000000..4d96d92
--- /dev/null
+++ b/tests/language-behaviour/T078-simplemapper-nosuffix_nodot.out.expected
@@ -0,0 +1 @@
+T078-simplemapper-nosuffix_nodot.out
diff --git a/tests/language-behaviour/T079-simplemapper-nosuffix_exception.swift
b/tests/language-behaviour/T079-s
new file mode 100644
index 0000000..d7223ef
--- /dev/null
+++ b/tests/language-behaviour/T079-simplemapper-nosuffix_exception.swift
@@ -0,0 +1,16 @@
+// this one is like test T078-simplemapper-nosuffix, but demonstrates the
+// mapping exception on invalid values
+type messagefile;
+
+(messagefile t) write() {
+    app {
+        echo @filename(t) stdout=@filename(t);
+    }
+}
+
+messagefile outfile <simple_mapper;
+                     prefix="T078-simplemapper-nosuffix", noauto="exception",
+                     suffix="_nodot.out">;
+
+outfile = write();
+
[aespinosa at login2 swift]$ git diff master > ~/public_html/
.__acl                           index.html                       swift/
adopters_espinosa.pdf            jgi_blastp.tar.gz
swiftplot_svg-r2874.patch
bigdata/                         jobdirpath.tar.gz
swift_r2846_bgp.patch
blastp/                          log
test-20090124-0019-je79k4q4.log
dag.svg                          MosaStore-v0.8.09.tar.gz
to_jr_and_syrah.ogg
.DS_Store                        mpi-collective/                  top_vanilla.gz
espinosa_swift.tar.gz            mtdm/                            visual/
falkon/                          provider-coaster-cpu_fix.patch   workflow.svg
flow.png                         run4-trace.tgz
[aespinosa at login2 swift]$ git diff master > ~/public_html/mapper_noauto.patch
[aespinosa at login2 swift]$ cat ~/public_html/mapper_noauto.patch
diff --git a/src/org/griphyn/vdl/mapping/file/AbstractFileMapper.java
b/src/org/griphyn/vdl/mapping/file/AbstractFileMapper.java
index 362cb01..5b7b455 100644
--- a/src/org/griphyn/vdl/mapping/file/AbstractFileMapper.java
+++ b/src/org/griphyn/vdl/mapping/file/AbstractFileMapper.java
@@ -12,6 +12,7 @@ import org.apache.log4j.Logger;

 import org.griphyn.vdl.mapping.AbsFile;
 import org.griphyn.vdl.mapping.AbstractMapper;
+import org.griphyn.vdl.mapping.InvalidMappingParameterException;
 import org.griphyn.vdl.mapping.MappingParam;
 import org.griphyn.vdl.mapping.Path;
 import org.griphyn.vdl.mapping.PhysicalFormat;
@@ -36,6 +37,8 @@ import org.griphyn.vdl.mapping.PhysicalFormat;
   *                  this string. If suffix does not begin with a '.'
   *                  character, then a '.' will be added automatically to
   *                  separate the rest of the filename from the suffix</li>
+  *   <li>noauto - if specified as "true", then the suffix auto
addition of a'.'
+  *                  will be disabled.  Default value is "false".</li>
   *   <li>pattern - if specified, then filenames will be selected from
   *                 the location directory when they match the unix glob
   *                 pattern supplied in this parameter.</li>
@@ -47,6 +50,7 @@ public abstract class AbstractFileMapper extends
AbstractMapper {
 	public static final MappingParam PARAM_SUFFIX = new
MappingParam("suffix", null);
 	public static final MappingParam PARAM_PATTERN = new
MappingParam("pattern", null);
 	public static final MappingParam PARAM_LOCATION = new
MappingParam("location", null);
+	public static final MappingParam PARAM_NOAUTO = new
MappingParam("noauto", "false");

 	public static final Logger logger =
Logger.getLogger(AbstractFileMapper.class);

@@ -79,7 +83,12 @@ public abstract class AbstractFileMapper extends
AbstractMapper {
 		super.setParams(params);
 		if (PARAM_SUFFIX.isPresent(this)) {
 			String suffix = PARAM_SUFFIX.getStringValue(this);
-			if (!suffix.startsWith(".")) {
+			String noauto = PARAM_NOAUTO.getStringValue(this);
+			if (!noauto.equals("true") && !noauto.equals("false")) {
+				throw new InvalidMappingParameterException("noauto parameter was
set to 'true' or 'false'" +
+						". Value set was '" + noauto + "'");
+			}
+			if (!suffix.startsWith(".") && noauto.equals("false")) {
 				PARAM_SUFFIX.setValue(this, "." + suffix);
 			}
 		}
diff --git a/tests/language-behaviour/T078-simplemapper-nosuffix.swift
b/tests/language-behaviour/T078-simplemapper-nosuffix.swift
new file mode 100644
index 0000000..55c80de
--- /dev/null
+++ b/tests/language-behaviour/T078-simplemapper-nosuffix.swift
@@ -0,0 +1,17 @@
+// this one is like test 073-simplemapper, but doesn't
+// add the missing dot in front of the suffix
+
+type messagefile;
+
+(messagefile t) write() {
+    app {
+        echo @filename(t) stdout=@filename(t);
+    }
+}
+
+messagefile outfile <simple_mapper;
+                     prefix="T078-simplemapper-nosuffix", noauto="true",
+                     suffix="_nodot.out">;
+
+outfile = write();
+
diff --git a/tests/language-behaviour/T078-simplemapper-nosuffix_nodot.out.expected
b/tests/language-behaviour/T078-simplemapper-nosuffix_nodot.out.expected
new file mode 100644
index 0000000..4d96d92
--- /dev/null
+++ b/tests/language-behaviour/T078-simplemapper-nosuffix_nodot.out.expected
@@ -0,0 +1 @@
+T078-simplemapper-nosuffix_nodot.out
diff --git a/tests/language-behaviour/T079-simplemapper-nosuffix_exception.swift
b/tests/language-behaviour/T079-simplemapper-nosuffix_exception.swift
new file mode 100644
index 0000000..d7223ef
--- /dev/null
+++ b/tests/language-behaviour/T079-simplemapper-nosuffix_exception.swift
@@ -0,0 +1,16 @@
+// this one is like test T078-simplemapper-nosuffix, but demonstrates the
+// mapping exception on invalid values
+type messagefile;
+
+(messagefile t) write() {
+    app {
+        echo @filename(t) stdout=@filename(t);
+    }
+}
+
+messagefile outfile <simple_mapper;
+                     prefix="T078-simplemapper-nosuffix", noauto="exception",
+                     suffix="_nodot.out">;
+
+outfile = write();
+


Enjoy!
-Allan


2010/3/19 Mihael Hategan <hategan at mcs.anl.gov>:
> On Fri, 2010-03-19 at 12:51 -0500, Allan Espinosa wrote:
>> Never mind.
>>
>> I found the code that does the padding. ?I'll just comment it out in
>> my Swift build
>
> Or you could add a parameter to do so in exchange for karma or imaginary
> cookies :)
>
>
>
>



-- 
Allan M. Espinosa <http://amespinosa.wordpress.com>
PhD student, Computer Science
University of Chicago <http://people.cs.uchicago.edu/~aespinosa>


From aespinosa at cs.uchicago.edu  Sat Mar 20 03:33:13 2010
From: aespinosa at cs.uchicago.edu (Allan Espinosa)
Date: Sat, 20 Mar 2010 03:33:13 -0500
Subject: [Swift-devel] Re: simple_mapper auto-padding of "."
In-Reply-To: <50b07b4b1003200131s1cfe9689u335180d3f99e8194@mail.gmail.com>
References: <50b07b4b1003191045p52bb6f23v4365dc6f1972b22@mail.gmail.com>
	<50b07b4b1003191051g38ddc835x6974d9c7d3314fc4@mail.gmail.com>
	<1269021652.855.0.camel@localhost>
	<50b07b4b1003200131s1cfe9689u335180d3f99e8194@mail.gmail.com>
Message-ID: <50b07b4b1003200133i7e95cd98w6748076ebba10565@mail.gmail.com>

Oops.

the exception handling demonstration is in
tests/language-behaviour/T079-simplemapper-nosuffix_exception.swift
b/tests/language-behaviour/T079-simplemapper-nosuffix_exception.swift

-Allan

2010/3/20 Allan Espinosa <aespinosa at cs.uchicago.edu>:
> I'll be getting my cookies now :)
>
> Patch available in
> http://www.ci.uchicago.edu/~aespinosa/swift_mapper-noauto.patch
>
> Test cases/ examples in
> tests/language-behaviour/T078-simplemapper-nosuffix.swift and
> tests/language-behaviour/T078-simplemapper-nosuffix.swift (Did i get
> the exception handling practice correctly?)
>


From benc at hawaga.org.uk  Sat Mar 20 03:34:55 2010
From: benc at hawaga.org.uk (Ben Clifford)
Date: Sat, 20 Mar 2010 08:34:55 +0000 (GMT)
Subject: [Swift-devel] array_mapper hangs
In-Reply-To: <27015074.184361269050503837.JavaMail.root@zimbra>
References: <27015074.184361269050503837.JavaMail.root@zimbra>
Message-ID: <Pine.LNX.4.64.1003200831130.22136@dildano.hawaga.org.uk>

> The script is hanging because its trying to access the values of the 
> array object f[], which is never set. Ie, at the point at which it wants 
> a value for physD[0] and physD[1], physD itself - even though it has 
> been *mapped* - has never been given a *value.

Sarah's script doesn't ask for the values of physD[i]. It asks for the 
@filename of them. That 'should' work for anything that has been mapped 
even if it doesn't have a value.

-- 


From aespinosa at cs.uchicago.edu  Sat Mar 20 03:41:12 2010
From: aespinosa at cs.uchicago.edu (Allan Espinosa)
Date: Sat, 20 Mar 2010 03:41:12 -0500
Subject: [Swift-devel] Re: simple_mapper auto-padding of "."
In-Reply-To: <50b07b4b1003200131s1cfe9689u335180d3f99e8194@mail.gmail.com>
References: <50b07b4b1003191045p52bb6f23v4365dc6f1972b22@mail.gmail.com>
	<50b07b4b1003191051g38ddc835x6974d9c7d3314fc4@mail.gmail.com>
	<1269021652.855.0.camel@localhost>
	<50b07b4b1003200131s1cfe9689u335180d3f99e8194@mail.gmail.com>
Message-ID: <50b07b4b1003200141u2380db46tfadb3abbad0168c1@mail.gmail.com>

Oops (again).  I should have proofread my error messages first.  The
patch in the link below should be updated by now.

-Allan

2010/3/20 Allan Espinosa <aespinosa at cs.uchicago.edu>:
> I'll be getting my cookies now :)
>
> Patch available in
> http://www.ci.uchicago.edu/~aespinosa/swift_mapper-noauto.patch


From wilde at mcs.anl.gov  Sat Mar 20 10:13:17 2010
From: wilde at mcs.anl.gov (wilde at mcs.anl.gov)
Date: Sat, 20 Mar 2010 10:13:17 -0500 (CDT)
Subject: [Swift-devel] array_mapper hangs
In-Reply-To: <17088298.188741269097343891.JavaMail.root@zimbra>
Message-ID: <23653054.188781269097997420.JavaMail.root@zimbra>

I think the script is hanging because its trying to return physD[] without ever setting the return array parameter physD (or any member of it):

app (file physD[]) maptest(){
> touch @filename(physD[0]) @filename(physD[1]);
> }

The following examples don't use @filename in maptest. am3.swift hangs, am4.swift works. The difference is that am4 puts a value in f[] and am3 does not.

::::::::::::::
am3.swift
::::::::::::::
type file;

app (file physD[]) maptest() {
   echo "hi";
}

file f[];

f = maptest();
::::::::::::::
am4.swift
::::::::::::::
type file;

app (file o) echo (string s) { echo s stdout=@o; }

(file physD[]) maptest() {
   physD[0] = echo("hi");
}

file f[];

f = maptest();
$ 


----- "Ben Clifford" <benc at hawaga.org.uk> wrote:

> > The script is hanging because its trying to access the values of the
> 
> > array object f[], which is never set. Ie, at the point at which it
> wants 
> > a value for physD[0] and physD[1], physD itself - even though it has
> 
> > been *mapped* - has never been given a *value.
> 
> Sarah's script doesn't ask for the values of physD[i]. It asks for the
> 
> @filename of them. That 'should' work for anything that has been
> mapped 
> even if it doesn't have a value.
> 
> --

-- 
Michael Wilde
Computation Institute, University of Chicago
Mathematics and Computer Science Division
Argonne National Laboratory



From wilde at mcs.anl.gov  Sat Mar 20 10:19:03 2010
From: wilde at mcs.anl.gov (wilde at mcs.anl.gov)
Date: Sat, 20 Mar 2010 10:19:03 -0500 (CDT)
Subject: [Swift-devel] array_mapper hangs
In-Reply-To: <11969015.188871269098157273.JavaMail.root@zimbra>
Message-ID: <16942666.188941269098343225.JavaMail.root@zimbra>

Also, to clarify: Ben is right in pointing out that this part of my earlier reply:

"Ie, at the point at which it wants a value for physD[0] and physD[1]..." is irrelevant. The problem, I think, is the fact that a return value was never set in maptest().

So I *think* that Swift is behaving correctly in your original script, Sarah, and in all the tests I've tried based on it.

- Mike

----- wilde at mcs.anl.gov wrote:

> I think the script is hanging because its trying to return physD[]
> without ever setting the return array parameter physD (or any member
> of it):
> 
> app (file physD[]) maptest(){
> > touch @filename(physD[0]) @filename(physD[1]);
> > }
> 
> The following examples don't use @filename in maptest. am3.swift
> hangs, am4.swift works. The difference is that am4 puts a value in f[]
> and am3 does not.
> 
> ::::::::::::::
> am3.swift
> ::::::::::::::
> type file;
> 
> app (file physD[]) maptest() {
>    echo "hi";
> }
> 
> file f[];
> 
> f = maptest();
> ::::::::::::::
> am4.swift
> ::::::::::::::
> type file;
> 
> app (file o) echo (string s) { echo s stdout=@o; }
> 
> (file physD[]) maptest() {
>    physD[0] = echo("hi");
> }
> 
> file f[];
> 
> f = maptest();
> $ 
> 
> 
> ----- "Ben Clifford" <benc at hawaga.org.uk> wrote:
> 
> > > The script is hanging because its trying to access the values of
> the
> > 
> > > array object f[], which is never set. Ie, at the point at which
> it
> > wants 
> > > a value for physD[0] and physD[1], physD itself - even though it
> has
> > 
> > > been *mapped* - has never been given a *value.
> > 
> > Sarah's script doesn't ask for the values of physD[i]. It asks for
> the
> > 
> > @filename of them. That 'should' work for anything that has been
> > mapped 
> > even if it doesn't have a value.
> > 
> > --
> 
> -- 
> Michael Wilde
> Computation Institute, University of Chicago
> Mathematics and Computer Science Division
> Argonne National Laboratory
> 
> _______________________________________________
> Swift-devel mailing list
> Swift-devel at ci.uchicago.edu
> http://mail.ci.uchicago.edu/mailman/listinfo/swift-devel

-- 
Michael Wilde
Computation Institute, University of Chicago
Mathematics and Computer Science Division
Argonne National Laboratory



From wilde at mcs.anl.gov  Sat Mar 20 10:49:51 2010
From: wilde at mcs.anl.gov (wilde at mcs.anl.gov)
Date: Sat, 20 Mar 2010 10:49:51 -0500 (CDT)
Subject: [Swift-devel] array_mapper hangs
In-Reply-To: <15800197.189431269100187257.JavaMail.root@zimbra>
Message-ID: <32111796.189451269100191668.JavaMail.root@zimbra>

Examining this more closely, there is indeed "surprising behavior" in @filenames() (plural) evaluation, but I don't think it was affecting Sarah's original program.

Assuming the intention of maptest() was to test if the array_mapper was working as expected, the following variation am5.swift of Sarah's script works correctly and traces the mappings.

But the second variation on it, am6.swift, which uses @filenames() to fetch the mappings, hangs.

Its possible that you can't do @filenames() (plural) on an unclosed array, and that this behavior is consistent with current Swift semantics. I am guessing that since Swift doesn't know how many elements the argument array to @filenames() has if its not set/closed, that it blocks until its argument array is closed.

am5.swift works and prints the mappings:

$ cat am5.swift
type file;

app (file o) echo (string s) { echo s stdout=@o; }

# original mappings

string outfilenames[];
string conditions[] = ["rest1","emblem"];

foreach cond,c in conditions{
  outfilenames[c] = @strcat(cond,"_physio.dat");
}

file f[] <array_mapper;files=outfilenames>;

# test the mappings

(string mappings[] ) maptest(file physD[]) {
  mappings[0] = @filename(physD[0]);
  mappings[1] = @filename(physD[1]);
}

string m[];
m = maptest(f);
foreach s,i in m {
  trace("i", i, "s", s);
}
$ swift am5.swift
Swift svn swift-r3264 (swift modified locally) cog-r2730 (cog modified locally)

RunID: 20100320-1044-2jj6h45a
Progress:
SwiftScript trace: i, 0, s, rest1_physio.dat
SwiftScript trace: i, 1, s, emblem_physio.dat
Final status:

am6.swift hangs:


$ cat am6.swift
type file;

app (file o) echo (string s) { echo s stdout=@o; }

# original mappings

string outfilenames[];
string conditions[] = ["rest1","emblem"];

foreach cond,c in conditions{
  outfilenames[c] = @strcat(cond,"_physio.dat");
}

file f[] <array_mapper;files=outfilenames>;

# test the mappings

(string mappings[] ) maptest(file physD[]) {
  foreach fname, i in @filenames(physD) {   # <--- hangs here?
    mappings[i] = fname;
  }
}

string m[];
m = maptest(f);
foreach s,i in m {
  trace("i", i, "s", s);
}
$ swift am6.swift
Swift svn swift-r3264 (swift modified locally) cog-r2730 (cog modified locally)

RunID: 20100320-1044-slm1fdt8
Progress:

^^^ Hangs.

- Mike


----- wilde at mcs.anl.gov wrote:

> Also, to clarify: Ben is right in pointing out that this part of my
> earlier reply:
> 
> "Ie, at the point at which it wants a value for physD[0] and
> physD[1]..." is irrelevant. The problem, I think, is the fact that a
> return value was never set in maptest().
> 
> So I *think* that Swift is behaving correctly in your original script,
> Sarah, and in all the tests I've tried based on it.
> 
> - Mike
> 
> ----- wilde at mcs.anl.gov wrote:
> 
> > I think the script is hanging because its trying to return physD[]
> > without ever setting the return array parameter physD (or any
> member
> > of it):
> > 
> > app (file physD[]) maptest(){
> > > touch @filename(physD[0]) @filename(physD[1]);
> > > }
> > 
> > The following examples don't use @filename in maptest. am3.swift
> > hangs, am4.swift works. The difference is that am4 puts a value in
> f[]
> > and am3 does not.
> > 
> > ::::::::::::::
> > am3.swift
> > ::::::::::::::
> > type file;
> > 
> > app (file physD[]) maptest() {
> >    echo "hi";
> > }
> > 
> > file f[];
> > 
> > f = maptest();
> > ::::::::::::::
> > am4.swift
> > ::::::::::::::
> > type file;
> > 
> > app (file o) echo (string s) { echo s stdout=@o; }
> > 
> > (file physD[]) maptest() {
> >    physD[0] = echo("hi");
> > }
> > 
> > file f[];
> > 
> > f = maptest();
> > $ 
> > 
> > 
> > ----- "Ben Clifford" <benc at hawaga.org.uk> wrote:
> > 
> > > > The script is hanging because its trying to access the values
> of
> > the
> > > 
> > > > array object f[], which is never set. Ie, at the point at which
> > it
> > > wants 
> > > > a value for physD[0] and physD[1], physD itself - even though
> it
> > has
> > > 
> > > > been *mapped* - has never been given a *value.
> > > 
> > > Sarah's script doesn't ask for the values of physD[i]. It asks
> for
> > the
> > > 
> > > @filename of them. That 'should' work for anything that has been
> > > mapped 
> > > even if it doesn't have a value.
> > > 
> > > --
> > 
> > -- 
> > Michael Wilde
> > Computation Institute, University of Chicago
> > Mathematics and Computer Science Division
> > Argonne National Laboratory
> > 
> > _______________________________________________
> > Swift-devel mailing list
> > Swift-devel at ci.uchicago.edu
> > http://mail.ci.uchicago.edu/mailman/listinfo/swift-devel
> 
> -- 
> Michael Wilde
> Computation Institute, University of Chicago
> Mathematics and Computer Science Division
> Argonne National Laboratory
> 
> _______________________________________________
> Swift-devel mailing list
> Swift-devel at ci.uchicago.edu
> http://mail.ci.uchicago.edu/mailman/listinfo/swift-devel

-- 
Michael Wilde
Computation Institute, University of Chicago
Mathematics and Computer Science Division
Argonne National Laboratory



From iraicu at cs.uchicago.edu  Sat Mar 20 17:12:00 2010
From: iraicu at cs.uchicago.edu (Ioan Raicu)
Date: Sat, 20 Mar 2010 17:12:00 -0500
Subject: [Swift-devel] 2 interesting papers
Message-ID: <4BA54830.5000404@cs.uchicago.edu>

Hi,
I just came across 2 interesting papers, one on a system called Nexus
(UCBerkeley), and another on Clustera (UWMadison).
http://www.usenix.org/events/hotcloud09/tech/full_papers/hindman.pdf
http://portal.acm.org/citation.cfm?id=1453856.1453865

They should both be included as related work in future Swift and Falkon
papers.

Ioan

-- 
=================================================================
Ioan Raicu, Ph.D.
NSF/CRA Computing Innovation Fellow
=================================================================
Center for Ultra-scale Computing and Information Security (CUCIS)
Department of Electrical Engineering and Computer Science
Northwestern University
2145 Sheridan Rd, Tech M384
Evanston, IL 60208-3118
=================================================================
Cel:   1-847-722-0876
Tel:   1-847-491-8163
Email: iraicu at eecs.northwestern.edu
Web:   http://www.eecs.northwestern.edu/~iraicu/
        https://wiki.cucis.eecs.northwestern.edu/
=================================================================
=================================================================



From wilde at mcs.anl.gov  Sat Mar 20 20:32:01 2010
From: wilde at mcs.anl.gov (Michael Wilde)
Date: Sat, 20 Mar 2010 20:32:01 -0500 (CDT)
Subject: [Swift-user] Re: [Swift-devel] Problem with iterate
In-Reply-To: <4B7EC377.1030105@eecs.northwestern.edu>
Message-ID: <7309358.193901269135121897.JavaMail.root@zimbra>

This old message slipped through by mistake when I cleaned up pending list admin requests.  Please ignore - its been discussed already.

- Mike

----- "Ioan Raicu" <iraicu at eecs.northwestern.edu> wrote:

> But lets bring this back to a more real example. A user wanting to
> express some computations that have some dependencies, would write out
> their computations in some order, expecting their order to be
> preserved because of the dependencies. If you only support single
> assignment on variables (e.g. the data), then an example like the one
> below could never deadlock because the single assignment would be
> violated on the 2nd statement. Perhaps things are more complicated if
> you support multiple assignments per variables, but that is not the
> case for Swift, right?
> 
> I am trying to understand if this deadlock is happening in Swift due
> to some particular implementation detail in Swift (or underlying
> pieces), or is it a fundamental flaw in the DAG based approach with
> single assignment variables? Or is it due to something completely
> different?
> 
> Thanks,
> Ioan
> --
> =================================================================
> Ioan Raicu, Ph.D.
> NSF/CRA Computing Innovation Fellow
> =================================================================
> Center for Ultra-scale Computing and Information Security (CUCIS)
> Department of Electrical Engineering and Computer Science
> Northwestern University
> 2145 Sheridan Rd, Tech M384
> Evanston, IL 60208-3118
> =================================================================
> Cel:   1-847-722-0876
> Tel:   1-847-491-8163
> Email: iraicu at eecs.northwestern.edu Web:
> http://www.eecs.northwestern.edu/~iraicu/
> https://wiki.cucis.eecs.northwestern.edu/
> =================================================================
> =================================================================
> 
> Ben Clifford wrote:
> 
> 
> 
> Mathematically, the two different sequences evaluate to different
> values:
> 
> x = y + 1
> y = x + 1
> 
> assuming y = 0, x = 1 I mean in simultaneous equations (linear
> algebra) - in other words, "find
> (through whatever means you care to use) a value of x and y such that
> the
> above two equations are both satisfied" - there is no value of x and y
> that satisfies that. 
> _______________________________________________
> Swift-user mailing list
> Swift-user at ci.uchicago.edu
> http://mail.ci.uchicago.edu/mailman/listinfo/swift-user

-- 
Michael Wilde
Computation Institute, University of Chicago
Mathematics and Computer Science Division
Argonne National Laboratory



From wilde at mcs.anl.gov  Mon Mar 22 07:52:23 2010
From: wilde at mcs.anl.gov (Michael Wilde)
Date: Mon, 22 Mar 2010 07:52:23 -0500 (CDT)
Subject: [Swift-devel] Problem with array fields in structures
Message-ID: <14946763.204581269262343560.JavaMail.root@zimbra>

I suspect there is a bug in returning a structure from an app() when the structure contains an array.

Swift throws an exception "Mapper consistency check failed for s..vector[]/1. A HandleOpenException was thrown during consistency checking for s..vector[]/1
Caused by: Handle open: file[] s..vector[]/1

The following script distills it down from what I was seeing in a production script.

- Mike

pads1$ cat struct.swift
type file;

type struct {
  file scalar;
  file vector[];
}

struct s<ext; exec="struct.map">;

app (struct sa) a () { appa; }

s = a();

pads1$ cat struct.map
#! /bin/sh
echo scalar "f1"
echo vector[0] "f2"
pads1$ ./struct.map
scalar f1
vector[0] f2
pads1$ 
pads1$ swift struct.swift
Swift svn swift-r3264 (swift modified locally) cog-r2730 (cog modified locally)

RunID: 20100322-0746-7dygk1xa
Progress:
Execution failed:
        java.lang.RuntimeException: Mapper consistency check failed for s..vector[]/1. A HandleOpenException was thrown during consistency checking for s..vector[]/1
Caused by:
        Handle open: file[] s..vector[]/1
pads1$ cat struct.xml
<program xmlns="http://ci.uchicago.edu/swift/2009/02/swiftscript"
         xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
         xmlns:xs="http://www.w3.org/2001/XMLSchema">
  
  <types>
        <type>
                <typename>file</typename>
                <typealias>string</typealias>
                <typestructure></typestructure>
        </type>
        <type>
                <typename>struct</typename>
                <typealias></typealias>
                <typestructure>
                            <member>
                                        <membername>scalar</membername>
                                        <membertype>file</membertype>
                                </member>
                            <member>
                                        <membername>vector</membername>
                                        <membertype>file[]</membertype>
                                </member>
                </typestructure>
        </type>   
  </types>  
  <procedure name="a" src="line 10">

      <output 
    name="sa" type="struct"

     xsi:nil="true" />
    <binding>
      <application src="line 10">
        <executable>appa</executable>
      </application>
    </binding>
  </procedure>
  <variable name="s" type="struct" isGlobal="false">
    <mapping descriptor="ext">
      <param name="exec"><stringConstant>struct.map</stringConstant></param>
    </mapping>
  </variable>
  <call proc="a" src="line 12">
    <output><variableReference>s</variableReference></output>
  </call>
</program>
pads1$ 






-- 
Michael Wilde
Computation Institute, University of Chicago
Mathematics and Computer Science Division
Argonne National Laboratory



From wilde at mcs.anl.gov  Mon Mar 22 12:30:02 2010
From: wilde at mcs.anl.gov (Michael Wilde)
Date: Mon, 22 Mar 2010 12:30:02 -0500 (CDT)
Subject: [Swift-devel] Job ended mysteriously amidst coaster shutdowns
Message-ID: <24594434.220291269279002408.JavaMail.root@zimbra>

Hi Mihael,

Can you look at the Swift run in this dir:
  /home/wilde/protests/run.boostthread.6573
(sites.xml, tc, swift.properties, and work directory are all under that dir)

It looks similar to the problem from last week, where coaster block shutdown is causing other running jobs to fail.

What may have happened here is that a block hit its time limit while an app was running (in this case the summary job, after 300 simulation jobs). Its also possible that the summary job itself failed but with a zero exit code, causing Swift to think it was done and to then start looking for its files. Im looking into that, and will try a swift restart on this run.

There were 32 one-core workers in this pool; about 24 were active for the core of the run.

I have this pool on PADS set to use <scratch> to avoid overheating GPFS, which makes debugging a bit harder.

But can you do a quick look and see if this looks to you like a coaster block shutdown problem?

AM I correct in assuming that when a coaster block hits its time limit in the middle of running an app(), it should restart the app?  And that it should not confuse this with an app() termination?

Thanks,

Mike


-- 
Michael Wilde
Computation Institute, University of Chicago
Mathematics and Computer Science Division
Argonne National Laboratory



From hategan at mcs.anl.gov  Mon Mar 22 12:54:21 2010
From: hategan at mcs.anl.gov (Mihael Hategan)
Date: Mon, 22 Mar 2010 12:54:21 -0500
Subject: [Swift-devel] Re: Job ended mysteriously amidst coaster shutdowns
In-Reply-To: <24594434.220291269279002408.JavaMail.root@zimbra>
References: <24594434.220291269279002408.JavaMail.root@zimbra>
Message-ID: <1269280461.18129.4.camel@localhost>

Which run?

[hategan at login1 run.boostthread.6573]$ ls -al *.log
-rw-r--r-- 1 wilde ci-users 8532855 Mar 22 11:24
BoostThreader-20100322-1044-yuu1ihp4.log
-rw-r--r-- 1 wilde ci-users   17889 Mar 22 12:47
BoostThreader-20100322-1247-brlv8d44.log
-rw-r--r-- 1 wilde ci-users 1197335 Mar 22 12:48
BoostThreader-20100322-1248-m01fv1k3.log
-rw-r--r-- 1 wilde ci-users     228 Mar 22 12:48 swift.log


If it's -1044, then no. It fails because it can't find a file at some
point:
 File not
found: /home/wilde/protests/run.boostthread.6573/BoostThreader-20100322-1044-yuu1ihp4/shared/Results.Models/T0411D1.07.pdb

If you have eager errors turned on, then a failure in the middle of the
run will cause swift and running jobs to abort.

On Mon, 2010-03-22 at 12:30 -0500, Michael Wilde wrote:
> Hi Mihael,
> 
> Can you look at the Swift run in this dir:
>   /home/wilde/protests/run.boostthread.6573
> (sites.xml, tc, swift.properties, and work directory are all under that dir)
> 
> It looks similar to the problem from last week, where coaster block shutdown is causing other running jobs to fail.
> 
> What may have happened here is that a block hit its time limit while an app was running (in this case the summary job, after 300 simulation jobs). Its also possible that the summary job itself failed but with a zero exit code, causing Swift to think it was done and to then start looking for its files. Im looking into that, and will try a swift restart on this run.
> 
> There were 32 one-core workers in this pool; about 24 were active for the core of the run.
> 
> I have this pool on PADS set to use <scratch> to avoid overheating GPFS, which makes debugging a bit harder.
> 
> But can you do a quick look and see if this looks to you like a coaster block shutdown problem?
> 
> AM I correct in assuming that when a coaster block hits its time limit in the middle of running an app(), it should restart the app?  And that it should not confuse this with an app() termination?
> 
> Thanks,
> 
> Mike
> 
> 



From wilde at mcs.anl.gov  Mon Mar 22 12:58:50 2010
From: wilde at mcs.anl.gov (Michael Wilde)
Date: Mon, 22 Mar 2010 12:58:50 -0500 (CDT)
Subject: [Swift-devel] Re: Job ended mysteriously amidst coaster shutdowns
In-Reply-To: <1269280461.18129.4.camel@localhost>
Message-ID: <29806916.221651269280730326.JavaMail.root@zimbra>


----- "Mihael Hategan" <hategan at mcs.anl.gov> wrote:

> Which run?

> -rw-r--r-- 1 wilde ci-users 8532855 Mar 22 11:24
> BoostThreader-20100322-1044-yuu1ihp4.log

But hold off on looking for a moment; Ive just added "-resume" to re-execute the summary job (thats what these more recent logs were) and I think I'm seeing the same failure on a fresh coaster, so its most likely a problem in my script that cropped up at this larger scale.

Sorry for the likely false alarm.

- Mike


> 
> [hategan at login1 run.boostthread.6573]$ ls -al *.log
> -rw-r--r-- 1 wilde ci-users 8532855 Mar 22 11:24
> BoostThreader-20100322-1044-yuu1ihp4.log
> -rw-r--r-- 1 wilde ci-users   17889 Mar 22 12:47
> BoostThreader-20100322-1247-brlv8d44.log
> -rw-r--r-- 1 wilde ci-users 1197335 Mar 22 12:48
> BoostThreader-20100322-1248-m01fv1k3.log
> -rw-r--r-- 1 wilde ci-users     228 Mar 22 12:48 swift.log
> 
> 
> If it's -1044, then no. It fails because it can't find a file at some
> point:
>  File not
> found:
> /home/wilde/protests/run.boostthread.6573/BoostThreader-20100322-1044-yuu1ihp4/shared/Results.Models/T0411D1.07.pdb
> 
> If you have eager errors turned on, then a failure in the middle of
> the
> run will cause swift and running jobs to abort.
> 
> On Mon, 2010-03-22 at 12:30 -0500, Michael Wilde wrote:
> > Hi Mihael,
> > 
> > Can you look at the Swift run in this dir:
> >   /home/wilde/protests/run.boostthread.6573
> > (sites.xml, tc, swift.properties, and work directory are all under
> that dir)
> > 
> > It looks similar to the problem from last week, where coaster block
> shutdown is causing other running jobs to fail.
> > 
> > What may have happened here is that a block hit its time limit while
> an app was running (in this case the summary job, after 300 simulation
> jobs). Its also possible that the summary job itself failed but with a
> zero exit code, causing Swift to think it was done and to then start
> looking for its files. Im looking into that, and will try a swift
> restart on this run.
> > 
> > There were 32 one-core workers in this pool; about 24 were active
> for the core of the run.
> > 
> > I have this pool on PADS set to use <scratch> to avoid overheating
> GPFS, which makes debugging a bit harder.
> > 
> > But can you do a quick look and see if this looks to you like a
> coaster block shutdown problem?
> > 
> > AM I correct in assuming that when a coaster block hits its time
> limit in the middle of running an app(), it should restart the app? 
> And that it should not confuse this with an app() termination?
> > 
> > Thanks,
> > 
> > Mike
> > 
> >

-- 
Michael Wilde
Computation Institute, University of Chicago
Mathematics and Computer Science Division
Argonne National Laboratory



From aespinosa at cs.uchicago.edu  Wed Mar 24 16:31:11 2010
From: aespinosa at cs.uchicago.edu (Allan Espinosa)
Date: Wed, 24 Mar 2010 16:31:11 -0500
Subject: [Swift-devel] error in reading in files over gridftp
Message-ID: <50b07b4b1003241431g7c907724jd675c0bb29ba25c6@mail.gmail.com>

The file gets created in the work directory (probably via touch) but
has 0 bytes for size.

type messagefile;

(messagefile o) write(messagefile i) {
    app {
        echo @filename(i) stdout=@filename(o);
    }
}

messagefile infile
<"gsiftp://ff-grid.unl.edu//panfs/panasas/CMS/data/engage/swift/071-singlefilemapper-input.in">;
messagefile outfile <"071-singlefilemapper-input.out">;

outfile = write(infile);

session (with vanilla sites.xml):
swift-r3264 cog-r2728

RunID: test
Progress:
Progress: Failed but can retry:1
Failed to transfer wrapper log from
071-singlefilemapper-input-test/info/e on localhost
Progress: Failed but can retry:1
Failed to transfer wrapper log from
071-singlefilemapper-input-test/info/g on localhost
Progress:  Stage in:1
Progress: Failed but can retry:1
Failed to transfer wrapper log from
071-singlefilemapper-input-test/info/i on localhost
Execution failed:
        Exception in echo:
Arguments: [panfs/panasas/CMS/data/engage/swift/071-singlefilemapper-input.in]
Host: localhost
Directory: 071-singlefilemapper-input-test/jobs/i/echo-ic8o7kpj
stderr.txt:

stdout.txt:

----

Caused by:
        Exception in getFile
Caused by:
        Server refused performing the request. Custom message:  (error
code 1) [Nested exception message:  Custom message: Unexpected reply:
500 Command failed]

What command does getFile issue?  I can download the file manually via
globus-url-copy or uberftp

the logfile is also attached in this email.

thanks!
-Allan

-- 
Allan M. Espinosa <http://amespinosa.wordpress.com>
PhD student, Computer Science
University of Chicago <http://people.cs.uchicago.edu/~aespinosa>
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From hategan at mcs.anl.gov  Wed Mar 24 17:01:08 2010
From: hategan at mcs.anl.gov (Mihael Hategan)
Date: Wed, 24 Mar 2010 17:01:08 -0500
Subject: [Swift-devel] Re: simple_mapper auto-padding of "."
In-Reply-To: <50b07b4b1003200141u2380db46tfadb3abbad0168c1@mail.gmail.com>
References: <50b07b4b1003191045p52bb6f23v4365dc6f1972b22@mail.gmail.com>
	<50b07b4b1003191051g38ddc835x6974d9c7d3314fc4@mail.gmail.com>
	<1269021652.855.0.camel@localhost>
	<50b07b4b1003200131s1cfe9689u335180d3f99e8194@mail.gmail.com>
	<50b07b4b1003200141u2380db46tfadb3abbad0168c1@mail.gmail.com>
Message-ID: <1269468068.2146.1.camel@localhost>

Committed in trunk.

And here 2 virtual chocolate chip cookies: O O

On Sat, 2010-03-20 at 03:41 -0500, Allan Espinosa wrote:
> Oops (again).  I should have proofread my error messages first.  The
> patch in the link below should be updated by now.
> 
> -Allan
> 
> 2010/3/20 Allan Espinosa <aespinosa at cs.uchicago.edu>:
> > I'll be getting my cookies now :)
> >
> > Patch available in
> > http://www.ci.uchicago.edu/~aespinosa/swift_mapper-noauto.patch
> _______________________________________________
> Swift-devel mailing list
> Swift-devel at ci.uchicago.edu
> http://mail.ci.uchicago.edu/mailman/listinfo/swift-devel



From hategan at mcs.anl.gov  Wed Mar 24 17:02:48 2010
From: hategan at mcs.anl.gov (Mihael Hategan)
Date: Wed, 24 Mar 2010 17:02:48 -0500
Subject: [Swift-devel] error in reading in files over gridftp
In-Reply-To: <50b07b4b1003241431g7c907724jd675c0bb29ba25c6@mail.gmail.com>
References: <50b07b4b1003241431g7c907724jd675c0bb29ba25c6@mail.gmail.com>
Message-ID: <1269468168.2146.2.camel@localhost>

What happens if you add another forward slash after ".edu"?

On Wed, 2010-03-24 at 16:31 -0500, Allan Espinosa wrote:
> The file gets created in the work directory (probably via touch) but
> has 0 bytes for size.
> 
> type messagefile;
> 
> (messagefile o) write(messagefile i) {
>     app {
>         echo @filename(i) stdout=@filename(o);
>     }
> }
> 
> messagefile infile
> <"gsiftp://ff-grid.unl.edu//panfs/panasas/CMS/data/engage/swift/071-singlefilemapper-input.in">;
> messagefile outfile <"071-singlefilemapper-input.out">;
> 
> outfile = write(infile);
> 
> session (with vanilla sites.xml):
> swift-r3264 cog-r2728
> 
> RunID: test
> Progress:
> Progress: Failed but can retry:1
> Failed to transfer wrapper log from
> 071-singlefilemapper-input-test/info/e on localhost
> Progress: Failed but can retry:1
> Failed to transfer wrapper log from
> 071-singlefilemapper-input-test/info/g on localhost
> Progress:  Stage in:1
> Progress: Failed but can retry:1
> Failed to transfer wrapper log from
> 071-singlefilemapper-input-test/info/i on localhost
> Execution failed:
>         Exception in echo:
> Arguments: [panfs/panasas/CMS/data/engage/swift/071-singlefilemapper-input.in]
> Host: localhost
> Directory: 071-singlefilemapper-input-test/jobs/i/echo-ic8o7kpj
> stderr.txt:
> 
> stdout.txt:
> 
> ----
> 
> Caused by:
>         Exception in getFile
> Caused by:
>         Server refused performing the request. Custom message:  (error
> code 1) [Nested exception message:  Custom message: Unexpected reply:
> 500 Command failed]
> 
> What command does getFile issue?  I can download the file manually via
> globus-url-copy or uberftp
> 
> the logfile is also attached in this email.
> 
> thanks!
> -Allan
> 
> _______________________________________________
> Swift-devel mailing list
> Swift-devel at ci.uchicago.edu
> http://mail.ci.uchicago.edu/mailman/listinfo/swift-devel



From aespinosa at cs.uchicago.edu  Wed Mar 24 17:27:07 2010
From: aespinosa at cs.uchicago.edu (Allan Espinosa)
Date: Wed, 24 Mar 2010 17:27:07 -0500
Subject: [Swift-devel] error in reading in files over gridftp
In-Reply-To: <1269468168.2146.2.camel@localhost>
References: <50b07b4b1003241431g7c907724jd675c0bb29ba25c6@mail.gmail.com>
	<1269468168.2146.2.camel@localhost>
Message-ID: <50b07b4b1003241527l7832be0k6b16a3d9edafd8d0@mail.gmail.com>

the argument passed to the app gets prefixed another slash (both in
the session output and logfile)
swift-r3264 cog-r2728

RunID: test
Progress:
Progress: Failed but can retry:1
Failed to transfer wrapper log from
071-singlefilemapper-input-test/info/n on localhost
Execution failed:
        Exception in echo:
Arguments: [/panfs/panasas/CMS/data/engage/swift/071-singlefilemapper-input.in]
Host: localhost
Directory: 071-singlefilemapper-input-test/jobs/n/echo-nvkbakpj
stderr.txt:

stdout.txt:

----

Caused by:
        Exception in getFile
Caused by:
        Server refused performing the request. Custom message:  (error
code 1) [Nested exception message:  Custom message: Unexpected reply:
500 Command failed]


2010/3/24 Mihael Hategan <hategan at mcs.anl.gov>:
> What happens if you add another forward slash after ".edu"?
>
> On Wed, 2010-03-24 at 16:31 -0500, Allan Espinosa wrote:
>> The file gets created in the work directory (probably via touch) but
>> has 0 bytes for size.
>>
>> type messagefile;
>>
>> (messagefile o) write(messagefile i) {
>> ? ? app {
>> ? ? ? ? echo @filename(i) stdout=@filename(o);
>> ? ? }
>> }
>>
>> messagefile infile
>> <"gsiftp://ff-grid.unl.edu//panfs/panasas/CMS/data/engage/swift/071-singlefilemapper-input.in">;
>> messagefile outfile <"071-singlefilemapper-input.out">;
>>
>> outfile = write(infile);
>>
>> session (with vanilla sites.xml):
>> swift-r3264 cog-r2728
>>
>> RunID: test
>> Progress:
>> Progress: Failed but can retry:1
>> Failed to transfer wrapper log from
>> 071-singlefilemapper-input-test/info/e on localhost
>> Progress: Failed but can retry:1
>> Failed to transfer wrapper log from
>> 071-singlefilemapper-input-test/info/g on localhost
>> Progress: ?Stage in:1
>> Progress: Failed but can retry:1
>> Failed to transfer wrapper log from
>> 071-singlefilemapper-input-test/info/i on localhost
>> Execution failed:
>> ? ? ? ? Exception in echo:
>> Arguments: [panfs/panasas/CMS/data/engage/swift/071-singlefilemapper-input.in]
>> Host: localhost
>> Directory: 071-singlefilemapper-input-test/jobs/i/echo-ic8o7kpj
>> stderr.txt:
>>
>> stdout.txt:
>>
>> ----
>>
>> Caused by:
>> ? ? ? ? Exception in getFile
>> Caused by:
>> ? ? ? ? Server refused performing the request. Custom message: ?(error
>> code 1) [Nested exception message: ?Custom message: Unexpected reply:
>> 500 Command failed]
>>
>> What command does getFile issue? ?I can download the file manually via
>> globus-url-copy or uberftp
>>
>> the logfile is also attached in this email.
>>
>> thanks!
>> -Allan
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From hategan at mcs.anl.gov  Wed Mar 24 17:32:20 2010
From: hategan at mcs.anl.gov (Mihael Hategan)
Date: Wed, 24 Mar 2010 17:32:20 -0500
Subject: [Swift-devel] error in reading in files over gridftp
In-Reply-To: <50b07b4b1003241527l7832be0k6b16a3d9edafd8d0@mail.gmail.com>
References: <50b07b4b1003241431g7c907724jd675c0bb29ba25c6@mail.gmail.com>
	<1269468168.2146.2.camel@localhost>
	<50b07b4b1003241527l7832be0k6b16a3d9edafd8d0@mail.gmail.com>
Message-ID: <1269469940.3177.1.camel@localhost>

No good.

So, maybe there's one more thing to try, for completeness.

If you put the file in
~/panfs/panasas/CMS/data/engage/swift/071-singlefilemapper-input.in and
revert to the first form (i.e. 2 slashes), does that work?

On Wed, 2010-03-24 at 17:27 -0500, Allan Espinosa wrote:
> the argument passed to the app gets prefixed another slash (both in
> the session output and logfile)
> swift-r3264 cog-r2728
> 
> RunID: test
> Progress:
> Progress: Failed but can retry:1
> Failed to transfer wrapper log from
> 071-singlefilemapper-input-test/info/n on localhost
> Execution failed:
>         Exception in echo:
> Arguments: [/panfs/panasas/CMS/data/engage/swift/071-singlefilemapper-input.in]
> Host: localhost
> Directory: 071-singlefilemapper-input-test/jobs/n/echo-nvkbakpj
> stderr.txt:
> 
> stdout.txt:
> 
> ----
> 
> Caused by:
>         Exception in getFile
> Caused by:
>         Server refused performing the request. Custom message:  (error
> code 1) [Nested exception message:  Custom message: Unexpected reply:
> 500 Command failed]
> 
> 
> 2010/3/24 Mihael Hategan <hategan at mcs.anl.gov>:
> > What happens if you add another forward slash after ".edu"?
> >
> > On Wed, 2010-03-24 at 16:31 -0500, Allan Espinosa wrote:
> >> The file gets created in the work directory (probably via touch) but
> >> has 0 bytes for size.
> >>
> >> type messagefile;
> >>
> >> (messagefile o) write(messagefile i) {
> >>     app {
> >>         echo @filename(i) stdout=@filename(o);
> >>     }
> >> }
> >>
> >> messagefile infile
> >> <"gsiftp://ff-grid.unl.edu//panfs/panasas/CMS/data/engage/swift/071-singlefilemapper-input.in">;
> >> messagefile outfile <"071-singlefilemapper-input.out">;
> >>
> >> outfile = write(infile);
> >>
> >> session (with vanilla sites.xml):
> >> swift-r3264 cog-r2728
> >>
> >> RunID: test
> >> Progress:
> >> Progress: Failed but can retry:1
> >> Failed to transfer wrapper log from
> >> 071-singlefilemapper-input-test/info/e on localhost
> >> Progress: Failed but can retry:1
> >> Failed to transfer wrapper log from
> >> 071-singlefilemapper-input-test/info/g on localhost
> >> Progress:  Stage in:1
> >> Progress: Failed but can retry:1
> >> Failed to transfer wrapper log from
> >> 071-singlefilemapper-input-test/info/i on localhost
> >> Execution failed:
> >>         Exception in echo:
> >> Arguments: [panfs/panasas/CMS/data/engage/swift/071-singlefilemapper-input.in]
> >> Host: localhost
> >> Directory: 071-singlefilemapper-input-test/jobs/i/echo-ic8o7kpj
> >> stderr.txt:
> >>
> >> stdout.txt:
> >>
> >> ----
> >>
> >> Caused by:
> >>         Exception in getFile
> >> Caused by:
> >>         Server refused performing the request. Custom message:  (error
> >> code 1) [Nested exception message:  Custom message: Unexpected reply:
> >> 500 Command failed]
> >>
> >> What command does getFile issue?  I can download the file manually via
> >> globus-url-copy or uberftp
> >>
> >> the logfile is also attached in this email.
> >>
> >> thanks!
> >> -Allan
> _______________________________________________
> Swift-devel mailing list
> Swift-devel at ci.uchicago.edu
> http://mail.ci.uchicago.edu/mailman/listinfo/swift-devel



From aespinosa at cs.uchicago.edu  Wed Mar 24 17:48:41 2010
From: aespinosa at cs.uchicago.edu (Allan Espinosa)
Date: Wed, 24 Mar 2010 17:48:41 -0500
Subject: [Swift-devel] error in reading in files over gridftp
In-Reply-To: <1269469940.3177.1.camel@localhost>
References: <50b07b4b1003241431g7c907724jd675c0bb29ba25c6@mail.gmail.com>
	<1269468168.2146.2.camel@localhost>
	<50b07b4b1003241527l7832be0k6b16a3d9edafd8d0@mail.gmail.com>
	<1269469940.3177.1.camel@localhost>
Message-ID: <50b07b4b1003241548u56c6d6f5v9203ab325a08f7cf@mail.gmail.com>

Just created the said file in the home directory.  I tried using both
single slash and two slashes.   Both gave the same errors

still no good :(

swift-r3264 cog-r2728

RunID: test
Progress:
Progress: Failed but can retry:1
Failed to transfer wrapper log from
071-singlefilemapper-input-test/info/4 on localhost
Execution failed:
        Exception in echo:
Arguments: [panfs/panasas/CMS/data/engage/swift/071-singlefilemapper-input.in]
Host: localhost
Directory: 071-singlefilemapper-input-test/jobs/4/echo-44t4bkpj
stderr.txt:

stdout.txt:

----

Caused by:
        Exception in getFile
Caused by:
        Server refused performing the request. Custom message:  (error
code 1) [Nested exception message:  Custom message: Unexpected reply:
500 Command failed]



2010/3/24 Mihael Hategan <hategan at mcs.anl.gov>:
> No good.
>
> So, maybe there's one more thing to try, for completeness.
>
> If you put the file in
> ~/panfs/panasas/CMS/data/engage/swift/071-singlefilemapper-input.in and
> revert to the first form (i.e. 2 slashes), does that work?
>
> On Wed, 2010-03-24 at 17:27 -0500, Allan Espinosa wrote:
>> the argument passed to the app gets prefixed another slash (both in
>> the session output and logfile)
>> swift-r3264 cog-r2728
>>
>> RunID: test
>> Progress:
>> Progress: Failed but can retry:1
>> Failed to transfer wrapper log from
>> 071-singlefilemapper-input-test/info/n on localhost
>> Execution failed:
>> ? ? ? ? Exception in echo:
>> Arguments: [/panfs/panasas/CMS/data/engage/swift/071-singlefilemapper-input.in]
>> Host: localhost
>> Directory: 071-singlefilemapper-input-test/jobs/n/echo-nvkbakpj
>> stderr.txt:
>>
>> stdout.txt:
>>
>> ----
>>
>> Caused by:
>> ? ? ? ? Exception in getFile
>> Caused by:
>> ? ? ? ? Server refused performing the request. Custom message: ?(error
>> code 1) [Nested exception message: ?Custom message: Unexpected reply:
>> 500 Command failed]
>>
>>
>> 2010/3/24 Mihael Hategan <hategan at mcs.anl.gov>:
>> > What happens if you add another forward slash after ".edu"?
>> >
>> > On Wed, 2010-03-24 at 16:31 -0500, Allan Espinosa wrote:
>> >> The file gets created in the work directory (probably via touch) but
>> >> has 0 bytes for size.
>> >>
>> >> type messagefile;
>> >>
>> >> (messagefile o) write(messagefile i) {
>> >> ? ? app {
>> >> ? ? ? ? echo @filename(i) stdout=@filename(o);
>> >> ? ? }
>> >> }
>> >>
>> >> messagefile infile
>> >> <"gsiftp://ff-grid.unl.edu//panfs/panasas/CMS/data/engage/swift/071-singlefilemapper-input.in">;
>> >> messagefile outfile <"071-singlefilemapper-input.out">;
>> >>
>> >> outfile = write(infile);
>> >>
>> >> session (with vanilla sites.xml):
>> >> swift-r3264 cog-r2728
>> >>
>> >> RunID: test
>> >> Progress:
>> >> Progress: Failed but can retry:1
>> >> Failed to transfer wrapper log from
>> >> 071-singlefilemapper-input-test/info/e on localhost
>> >> Progress: Failed but can retry:1
>> >> Failed to transfer wrapper log from
>> >> 071-singlefilemapper-input-test/info/g on localhost
>> >> Progress: ?Stage in:1
>> >> Progress: Failed but can retry:1
>> >> Failed to transfer wrapper log from
>> >> 071-singlefilemapper-input-test/info/i on localhost
>> >> Execution failed:
>> >> ? ? ? ? Exception in echo:
>> >> Arguments: [panfs/panasas/CMS/data/engage/swift/071-singlefilemapper-input.in]
>> >> Host: localhost
>> >> Directory: 071-singlefilemapper-input-test/jobs/i/echo-ic8o7kpj
>> >> stderr.txt:
>> >>
>> >> stdout.txt:
>> >>
>> >> ----
>> >>
>> >> Caused by:
>> >> ? ? ? ? Exception in getFile
>> >> Caused by:
>> >> ? ? ? ? Server refused performing the request. Custom message: ?(error
>> >> code 1) [Nested exception message: ?Custom message: Unexpected reply:
>> >> 500 Command failed]
>> >>
>> >> What command does getFile issue? ?I can download the file manually via
>> >> globus-url-copy or uberftp
>> >>
>> >> the logfile is also attached in this email.
>> >>
>> >> thanks!
>> >> -Allan


From hategan at mcs.anl.gov  Wed Mar 24 17:54:58 2010
From: hategan at mcs.anl.gov (Mihael Hategan)
Date: Wed, 24 Mar 2010 17:54:58 -0500
Subject: [Swift-devel] error in reading in files over gridftp
In-Reply-To: <50b07b4b1003241548u56c6d6f5v9203ab325a08f7cf@mail.gmail.com>
References: <50b07b4b1003241431g7c907724jd675c0bb29ba25c6@mail.gmail.com>
	<1269468168.2146.2.camel@localhost>
	<50b07b4b1003241527l7832be0k6b16a3d9edafd8d0@mail.gmail.com>
	<1269469940.3177.1.camel@localhost>
	<50b07b4b1003241548u56c6d6f5v9203ab325a08f7cf@mail.gmail.com>
Message-ID: <1269471298.3730.1.camel@localhost>

May be the gridftp client-server interaction then. Can you test on a
gridftp server where I can reproduce it (e.g. pads, tp, tguc - if it
still exists -, surveyor)?

On Wed, 2010-03-24 at 17:48 -0500, Allan Espinosa wrote:
> Just created the said file in the home directory.  I tried using both
> single slash and two slashes.   Both gave the same errors
> 
> still no good :(
> 
> swift-r3264 cog-r2728
> 
> RunID: test
> Progress:
> Progress: Failed but can retry:1
> Failed to transfer wrapper log from
> 071-singlefilemapper-input-test/info/4 on localhost
> Execution failed:
>         Exception in echo:
> Arguments: [panfs/panasas/CMS/data/engage/swift/071-singlefilemapper-input.in]
> Host: localhost
> Directory: 071-singlefilemapper-input-test/jobs/4/echo-44t4bkpj
> stderr.txt:
> 
> stdout.txt:
> 
> ----
> 
> Caused by:
>         Exception in getFile
> Caused by:
>         Server refused performing the request. Custom message:  (error
> code 1) [Nested exception message:  Custom message: Unexpected reply:
> 500 Command failed]
> 
> 
> 
> 2010/3/24 Mihael Hategan <hategan at mcs.anl.gov>:
> > No good.
> >
> > So, maybe there's one more thing to try, for completeness.
> >
> > If you put the file in
> > ~/panfs/panasas/CMS/data/engage/swift/071-singlefilemapper-input.in and
> > revert to the first form (i.e. 2 slashes), does that work?
> >
> > On Wed, 2010-03-24 at 17:27 -0500, Allan Espinosa wrote:
> >> the argument passed to the app gets prefixed another slash (both in
> >> the session output and logfile)
> >> swift-r3264 cog-r2728
> >>
> >> RunID: test
> >> Progress:
> >> Progress: Failed but can retry:1
> >> Failed to transfer wrapper log from
> >> 071-singlefilemapper-input-test/info/n on localhost
> >> Execution failed:
> >>         Exception in echo:
> >> Arguments: [/panfs/panasas/CMS/data/engage/swift/071-singlefilemapper-input.in]
> >> Host: localhost
> >> Directory: 071-singlefilemapper-input-test/jobs/n/echo-nvkbakpj
> >> stderr.txt:
> >>
> >> stdout.txt:
> >>
> >> ----
> >>
> >> Caused by:
> >>         Exception in getFile
> >> Caused by:
> >>         Server refused performing the request. Custom message:  (error
> >> code 1) [Nested exception message:  Custom message: Unexpected reply:
> >> 500 Command failed]
> >>
> >>
> >> 2010/3/24 Mihael Hategan <hategan at mcs.anl.gov>:
> >> > What happens if you add another forward slash after ".edu"?
> >> >
> >> > On Wed, 2010-03-24 at 16:31 -0500, Allan Espinosa wrote:
> >> >> The file gets created in the work directory (probably via touch) but
> >> >> has 0 bytes for size.
> >> >>
> >> >> type messagefile;
> >> >>
> >> >> (messagefile o) write(messagefile i) {
> >> >>     app {
> >> >>         echo @filename(i) stdout=@filename(o);
> >> >>     }
> >> >> }
> >> >>
> >> >> messagefile infile
> >> >> <"gsiftp://ff-grid.unl.edu//panfs/panasas/CMS/data/engage/swift/071-singlefilemapper-input.in">;
> >> >> messagefile outfile <"071-singlefilemapper-input.out">;
> >> >>
> >> >> outfile = write(infile);
> >> >>
> >> >> session (with vanilla sites.xml):
> >> >> swift-r3264 cog-r2728
> >> >>
> >> >> RunID: test
> >> >> Progress:
> >> >> Progress: Failed but can retry:1
> >> >> Failed to transfer wrapper log from
> >> >> 071-singlefilemapper-input-test/info/e on localhost
> >> >> Progress: Failed but can retry:1
> >> >> Failed to transfer wrapper log from
> >> >> 071-singlefilemapper-input-test/info/g on localhost
> >> >> Progress:  Stage in:1
> >> >> Progress: Failed but can retry:1
> >> >> Failed to transfer wrapper log from
> >> >> 071-singlefilemapper-input-test/info/i on localhost
> >> >> Execution failed:
> >> >>         Exception in echo:
> >> >> Arguments: [panfs/panasas/CMS/data/engage/swift/071-singlefilemapper-input.in]
> >> >> Host: localhost
> >> >> Directory: 071-singlefilemapper-input-test/jobs/i/echo-ic8o7kpj
> >> >> stderr.txt:
> >> >>
> >> >> stdout.txt:
> >> >>
> >> >> ----
> >> >>
> >> >> Caused by:
> >> >>         Exception in getFile
> >> >> Caused by:
> >> >>         Server refused performing the request. Custom message:  (error
> >> >> code 1) [Nested exception message:  Custom message: Unexpected reply:
> >> >> 500 Command failed]
> >> >>
> >> >> What command does getFile issue?  I can download the file manually via
> >> >> globus-url-copy or uberftp
> >> >>
> >> >> the logfile is also attached in this email.
> >> >>
> >> >> thanks!
> >> >> -Allan
> _______________________________________________
> Swift-devel mailing list
> Swift-devel at ci.uchicago.edu
> http://mail.ci.uchicago.edu/mailman/listinfo/swift-devel



From aespinosa at cs.uchicago.edu  Wed Mar 24 18:20:11 2010
From: aespinosa at cs.uchicago.edu (Allan Espinosa)
Date: Wed, 24 Mar 2010 18:20:11 -0500
Subject: [Swift-devel] error in reading in files over gridftp
In-Reply-To: <1269471298.3730.1.camel@localhost>
References: <50b07b4b1003241431g7c907724jd675c0bb29ba25c6@mail.gmail.com>
	<1269468168.2146.2.camel@localhost>
	<50b07b4b1003241527l7832be0k6b16a3d9edafd8d0@mail.gmail.com>
	<1269469940.3177.1.camel@localhost>
	<50b07b4b1003241548u56c6d6f5v9203ab325a08f7cf@mail.gmail.com>
	<1269471298.3730.1.camel@localhost>
Message-ID: <50b07b4b1003241620l2e2c6775l56d7ccaf2db1987@mail.gmail.com>

weird.  i guess two gridftp servers has its own personality :(

it worked when having the file from ci!

type messagefile;

(messagefile o) write(messagefile i) {
    app {
        echo @filename(i) stdout=@filename(o);
    }
}

messagefile infile
    <"gsiftp://tp-grid.ci.uchicago.edu//home/aespinosa/workflows/testing/071-singlefilemapper-input.in">;

outfile = write(infile);

wow it worked!
swift-r3264 cog-r2728

RunID: test
Progress:
Final status:  Finished successfully:1


time to email the site administrators. thanks for you time Mihael!

-Allan


2010/3/24 Mihael Hategan <hategan at mcs.anl.gov>:
> May be the gridftp client-server interaction then. Can you test on a
> gridftp server where I can reproduce it (e.g. pads, tp, tguc - if it
> still exists -, surveyor)?
>
> On Wed, 2010-03-24 at 17:48 -0500, Allan Espinosa wrote:
>> Just created the said file in the home directory. ?I tried using both
>> single slash and two slashes. ? Both gave the same errors
>>
>> still no good :(
>>
>> swift-r3264 cog-r2728
>>
>> RunID: test
>> Progress:
>> Progress: Failed but can retry:1
>> Failed to transfer wrapper log from
>> 071-singlefilemapper-input-test/info/4 on localhost
>> Execution failed:
>> ? ? ? ? Exception in echo:
>> Arguments: [panfs/panasas/CMS/data/engage/swift/071-singlefilemapper-input.in]
>> Host: localhost
>> Directory: 071-singlefilemapper-input-test/jobs/4/echo-44t4bkpj
>> stderr.txt:
>>
>> stdout.txt:
>>
>> ----
>>
>> Caused by:
>> ? ? ? ? Exception in getFile
>> Caused by:
>> ? ? ? ? Server refused performing the request. Custom message: ?(error
>> code 1) [Nested exception message: ?Custom message: Unexpected reply:
>> 500 Command failed]
>>
>>
>>
>> 2010/3/24 Mihael Hategan <hategan at mcs.anl.gov>:
>> > No good.
>> >
>> > So, maybe there's one more thing to try, for completeness.
>> >
>> > If you put the file in
>> > ~/panfs/panasas/CMS/data/engage/swift/071-singlefilemapper-input.in and
>> > revert to the first form (i.e. 2 slashes), does that work?
>> >
>> > On Wed, 2010-03-24 at 17:27 -0500, Allan Espinosa wrote:
>> >> the argument passed to the app gets prefixed another slash (both in
>> >> the session output and logfile)
>> >> swift-r3264 cog-r2728
>> >>
>> >> RunID: test
>> >> Progress:
>> >> Progress: Failed but can retry:1
>> >> Failed to transfer wrapper log from
>> >> 071-singlefilemapper-input-test/info/n on localhost
>> >> Execution failed:
>> >> ? ? ? ? Exception in echo:
>> >> Arguments: [/panfs/panasas/CMS/data/engage/swift/071-singlefilemapper-input.in]
>> >> Host: localhost
>> >> Directory: 071-singlefilemapper-input-test/jobs/n/echo-nvkbakpj
>> >> stderr.txt:
>> >>
>> >> stdout.txt:
>> >>
>> >> ----
>> >>
>> >> Caused by:
>> >> ? ? ? ? Exception in getFile
>> >> Caused by:
>> >> ? ? ? ? Server refused performing the request. Custom message: ?(error
>> >> code 1) [Nested exception message: ?Custom message: Unexpected reply:
>> >> 500 Command failed]
>> >>
>> >>
>> >> 2010/3/24 Mihael Hategan <hategan at mcs.anl.gov>:
>> >> > What happens if you add another forward slash after ".edu"?
>> >> >
>> >> > On Wed, 2010-03-24 at 16:31 -0500, Allan Espinosa wrote:
>> >> >> The file gets created in the work directory (probably via touch) but
>> >> >> has 0 bytes for size.
>> >> >>
>> >> >> type messagefile;
>> >> >>
>> >> >> (messagefile o) write(messagefile i) {
>> >> >> ? ? app {
>> >> >> ? ? ? ? echo @filename(i) stdout=@filename(o);
>> >> >> ? ? }
>> >> >> }
>> >> >>
>> >> >> messagefile infile
>> >> >> <"gsiftp://ff-grid.unl.edu//panfs/panasas/CMS/data/engage/swift/071-singlefilemapper-input.in">;
>> >> >> messagefile outfile <"071-singlefilemapper-input.out">;
>> >> >>
>> >> >> outfile = write(infile);
>> >> >>
>> >> >> session (with vanilla sites.xml):
>> >> >> swift-r3264 cog-r2728
>> >> >>
>> >> >> RunID: test
>> >> >> Progress:
>> >> >> Progress: Failed but can retry:1
>> >> >> Failed to transfer wrapper log from
>> >> >> 071-singlefilemapper-input-test/info/e on localhost
>> >> >> Progress: Failed but can retry:1
>> >> >> Failed to transfer wrapper log from
>> >> >> 071-singlefilemapper-input-test/info/g on localhost
>> >> >> Progress: ?Stage in:1
>> >> >> Progress: Failed but can retry:1
>> >> >> Failed to transfer wrapper log from
>> >> >> 071-singlefilemapper-input-test/info/i on localhost
>> >> >> Execution failed:
>> >> >> ? ? ? ? Exception in echo:
>> >> >> Arguments: [panfs/panasas/CMS/data/engage/swift/071-singlefilemapper-input.in]
>> >> >> Host: localhost
>> >> >> Directory: 071-singlefilemapper-input-test/jobs/i/echo-ic8o7kpj
>> >> >> stderr.txt:
>> >> >>
>> >> >> stdout.txt:
>> >> >>
>> >> >> ----
>> >> >>
>> >> >> Caused by:
>> >> >> ? ? ? ? Exception in getFile
>> >> >> Caused by:
>> >> >> ? ? ? ? Server refused performing the request. Custom message: ?(error
>> >> >> code 1) [Nested exception message: ?Custom message: Unexpected reply:
>> >> >> 500 Command failed]
>> >> >>
>> >> >> What command does getFile issue? ?I can download the file manually via
>> >> >> globus-url-copy or uberftp
>> >> >>
>> >> >> the logfile is also attached in this email.
>> >> >>
>> >> >> thanks!
>> >> >> -Allan


From hategan at mcs.anl.gov  Wed Mar 24 18:50:08 2010
From: hategan at mcs.anl.gov (Mihael Hategan)
Date: Wed, 24 Mar 2010 18:50:08 -0500
Subject: [Swift-devel] error in reading in files over gridftp
In-Reply-To: <50b07b4b1003241620l2e2c6775l56d7ccaf2db1987@mail.gmail.com>
References: <50b07b4b1003241431g7c907724jd675c0bb29ba25c6@mail.gmail.com>
	<1269468168.2146.2.camel@localhost>
	<50b07b4b1003241527l7832be0k6b16a3d9edafd8d0@mail.gmail.com>
	<1269469940.3177.1.camel@localhost>
	<50b07b4b1003241548u56c6d6f5v9203ab325a08f7cf@mail.gmail.com>
	<1269471298.3730.1.camel@localhost>
	<50b07b4b1003241620l2e2c6775l56d7ccaf2db1987@mail.gmail.com>
Message-ID: <1269474608.4765.0.camel@localhost>

On Wed, 2010-03-24 at 18:20 -0500, Allan Espinosa wrote:
> Final status:  Finished successfully:1
> 
> 
> time to email the site administrators. thanks for you time Mihael!

We're not necessarily done yet. It may be the client who does weird
stuff.



From aespinosa at cs.uchicago.edu  Wed Mar 24 20:02:09 2010
From: aespinosa at cs.uchicago.edu (Allan Espinosa)
Date: Wed, 24 Mar 2010 20:02:09 -0500
Subject: filesys_mapper workaround (was Re: [Swift-devel] [Bug 223] New: 
	wildcard fails in the pattern parameter for simple_mapper)
Message-ID: <50b07b4b1003241802y34ec6af9t90f6831a3771d0b6@mail.gmail.com>

The filesys_wrapper workaround starts to break when the type is a
struct.  filesys_mapper is not supposed to work with structs so that's
reasonable.  Hence, we should fix this bug :)


typical workaround:
type messagefile;

(messagefile o) write(messagefile i) {
    app {
        echo @filename(i) stdout=@filename(o);
    }
}

messagefile infile[] <filesys_mapper;
prefix="071-singlefilemapper-input", suffix=".in",
     location="gsiftp://ff-grid.unl.edu//panfs/panasas/CMS/data/engage/swift">;


messagefile outfile <"071-singlefilemapper-input.out">;

trace(@infile[0]);
outfile = write(infile[0]);


used in structs:
type SgtDim;
type Variation;
type Seismogram;
type PeakValue;

type Station {
  string name;
  float lat;
  float lon;
  int erf;
  int variation_scenario;
}

type Sgt {
  SgtDim x;
  SgtDim y;
}

type Rupture {
  int source;
  int index;
  int size;
}

/* some constants used by the apps*/
global int num_time_steps = 3000;
global string spectra_period1 = "all";
global float filter_highhz = 5.0;
global float simulation_timeskip = 0.1;

app (Sgt _ext) extract(Sgt _sgt, Station _stat, Variation _var) {
  jbsim3d @strcat("stat=", _stat.name) "extract_sgt=1"
      @strcat("slon=", _stat.lon) @strcat("slat=", _stat.lat)

      @strcat("rupmodfile=", @filename(_var))
      @strcat("sgt_xfile=", @filename(_sgt.x))
      @strcat("sgt_yfile=", @filename(_sgt.y))
      @strcat("extract_sgt_xfile=", @filename(_ext.x))
      @strcat("extract_sgt_yfile=", @filename(_ext.y));
}

app (Seismogram _seis) seismogram(Sgt _sgt, Variation _var, Station _stat) {
  jbsim3d @strcat("stat=", _stat.name) "extract_sgt=0"
      @strcat("slon=", _stat.lon) @strcat("slat=", _stat.lat)
      "outputBinary=1" "mergeOutput=1" @strcat("ntout=", num_time_steps)

      @strcat("rupmodfile=", @filename(_var))
      @strcat("sgt_xfile=", @filename(_sgt.x))
      @strcat("sgt_yfile=", @filename(_sgt.y))
      @strcat("seis_file=", @filename(_seis));
}

app (PeakValue _peak) peak_calc(Seismogram _seis, Variation _var) {
//  touch @_peak;
  surfeis_rspectra "simulation_out_pointsX=2" "simulation_out_pointsY=1"
      "surfseis_rspectra_seismogram_units=cmpersec"
      "surfseis_rspectra_output_units=cmpersec2"
      "surfseis_rspectra_output_type=aa"
      "surfseis_rspectra_apply_byteswap=no"

      @strcat("simulation_out_timesamples=", num_time_steps)
      @strcat("simulation_out_timeskip=", simulation_timeskip)
      @strcat("surfseis_rspectra_period=", spectra_period1)
      @strcat(" surfseis_rspectra_apply_filter_highHZ=", filter_highhz)
      @strcat("in=", @filename(_seis))
      @strcat("out=", @filename(_peak));
}

// Auxillary functions for the mappers
type StationFile;
app (StationFile _stat) getsite_file(int _run_id) {
  getsite _run_id stdout=@filename(_stat);
}
(Station _stat) get_site(int _run_id) {
  StationFile file<"site_tmp">;
  file = getsite_file(_run_id);
  _stat = readData(file);
}

type RuptureFile;
app (RuptureFile _rup) getrupture_file(int _run_id) {
  getrupture _run_id stdout=@filename(_rup);
}
(Rupture _rup[]) get_ruptures(int _run_id) {
  RuptureFile file<"rup_tmp">;
  file = getrupture_file(_run_id);
  _rup = readData(file);
}

/* TODO: data management zip jobs */

int run_id = 644;
Station site = get_site(run_id);

Sgt sgt_var[] <filesys_mapper; noauto="true",
    location="gsiftp://ff-grid.unl.edu//panfs/panasas/CMS/data/engage/scec/data/SgtFiles/TEST/",
    prefix=@strcat(site.name, "_f"), suffix=@strcat("_", run_id,".sgt")>;

Rupture rups[] = get_ruptures(run_id);

foreach rup in rups {
  /* TODO: insert location parameters */
  string datadir =
      "gsiftp://ff-grid.unl.edu//panfs/panasas/CMS/data/engage/swift";
  string loc_sub = @strcat(rup.index, "/", rup.source);
  Sgt sub[] <filesys_mapper; location=loc_sub, suffix=".sgt",
      prefix=@strcat(site.name, "_", rup.source, "_", rup.index, "_subf")>;
  Variation vars[] <ext; exec="variation_mapper.rb", e=site.erf,
      v=site.variation_scenario, s=rup.source, r=rup.index>;

  sub[0] = extract(sgt_var[0],  site, vars[rup.size-1]);

  foreach var,i in vars {
    Seismogram seis[] <filesys_mapper; location=loc_sub,
prefix=@strcat("Seismogram_", site.name,
        "_", rup.source, "_", rup.index, "_", i), suffix=".grm">;
    PeakValue peak[] <filesys_mapper; location=loc_sub,
prefix=@strcat("PeakVals_", site.name,
        "_", rup.source, "_", rup.index, "_", i), suffix=".bsa">;

    seis[0] = seismogram(sub[0], var, site);
    peak[0] = peak_calc(seis[0], var);
  }
}


error message:
swift-r3264 cog-r2728

RunID: testing
Progress:
Progress:  Active:1  Checking status:1
Ex098
java.lang.RuntimeException: Inconsistency between type declaration and
handle for field 'y'
	at org.griphyn.vdl.mapping.AbstractDataNode.getFringePaths(AbstractDataNode.java:372)
	at org.griphyn.vdl.mapping.AbstractDataNode.getFringePaths(AbstractDataNode.java:353)
	at org.griphyn.vdl.karajan.lib.FringePaths.function(FringePaths.java:29)
	at org.griphyn.vdl.karajan.lib.VDLFunction.post(VDLFunction.java:67)
	at org.globus.cog.karajan.workflow.nodes.AbstractSequentialWithArguments.childCompleted(AbstractSequentialWithArguments.java:192)
	at org.globus.cog.karajan.workflow.nodes.Sequential.notificationEvent(Sequential.java:33)
	at org.globus.cog.karajan.workflow.nodes.FlowNode.event(FlowNode.java:334)
	at org.globus.cog.karajan.workflow.events.EventBus.send(EventBus.java:134)
	at org.globus.cog.karajan.workflow.events.EventBus.sendHooked(EventBus.java:108)
	at org.globus.cog.karajan.workflow.nodes.FlowNode.fireNotificationEvent(FlowNode.java:176)
	at org.globus.cog.karajan.workflow.nodes.FlowNode.complete(FlowNode.java:298)
	at org.globus.cog.karajan.workflow.nodes.FlowContainer.post(FlowContainer.java:58)
	at org.globus.cog.karajan.workflow.nodes.functions.AbstractFunction.post(AbstractFunction.java:28)
	at org.globus.cog.karajan.workflow.nodes.Sequential.startNext(Sequential.java:51)
	at org.globus.cog.karajan.workflow.nodes.Sequential.executeChildren(Sequential.java:27)
	at org.globus.cog.karajan.workflow.nodes.FlowContainer.execute(FlowContainer.java:63)
	at org.globus.cog.karajan.workflow.nodes.FlowNode.restart(FlowNode.java:233)
	at org.globus.cog.karajan.workflow.nodes.FlowNode.start(FlowNode.java:280)
	at org.globus.cog.karajan.workflow.nodes.FlowNode.controlEvent(FlowNode.java:393)
	at org.globus.cog.karajan.workflow.nodes.FlowNode.event(FlowNode.java:331)
	at org.globus.cog.karajan.workflow.FlowElementWrapper.event(FlowElementWrapper.java:229)
	at org.globus.cog.karajan.workflow.events.EventBus.send(EventBus.java:134)
	at org.globus.cog.karajan.workflow.events.EventBus.sendHooked(EventBus.java:108)
	at org.globus.cog.karajan.workflow.events.EventTargetPair.run(EventTargetPair.java:43)
	at edu.emory.mathcs.backport.java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:431)
	at edu.emory.mathcs.backport.java.util.concurrent.FutureTask.run(FutureTask.java:166)
	at edu.emory.mathcs.backport.java.util.concurrent.ThreadPoolExecutor$Worker.runTask(ThreadPoolExecutor.java:643)
	at edu.emory.mathcs.backport.java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:668)
	at java.lang.Thread.run(Thread.java:595)
Execution failed:
	java.lang.RuntimeException: Data set initialization failed for
org.griphyn.vdl.mapping.DataNode identifier
tag:benc at ci.uchicago.edu,2008:swift:dataset:20100324-1959-n2vdgijf:720000000115
type Sgt with no value at dataset=sgt_var path=[0] (closed). Missing
required field: y

I also attached the logfile.

-Allan

2010/3/16  <bugzilla-daemon at mcs.anl.gov>:
> https://bugzilla.mcs.anl.gov/swift/show_bug.cgi?id=223
>
> ? ? ? ? ? Summary: wildcard fails in the pattern parameter for
> ? ? ? ? ? ? ? ? ? ?simple_mapper
> ? ? ? ? ? Product: Swift
> ? ? ? ? ? Version: unspecified
> ? ? ? ? ?Platform: PC
> ? ? ? ?OS/Version: Windows
> ? ? ? ? ? ?Status: NEW
> ? ? ? ? ?Severity: normal
> ? ? ? ? ?Priority: P2
> ? ? ? ? Component: SwiftScript language
> ? ? ? ?AssignedTo: benc at hawaga.org.uk
> ? ? ? ?ReportedBy: skenny at uchicago.edu
>
>
> the simple_mapper is meant to take a 'pattern' parameter which can contain
> wildcards, however...
>
> the following code:
>
> file physdata<simple_mapper;location="rawphys/",pattern="*017*",suffix=".txt">;
> trace(@filename(physdata));
>
> produces this error:
>
> Execution failed:
> ? ? ? ?java.lang.IllegalStateException: mapper.existing() returned a path
> .r33subj017 that it cannot subsequently map
>
>
> though, as i understand it, it should map a single file from this dir:
>
> $ ls rawphys/
> r33subj003.txt ?r33subj017.txt
>
>
> (workaround is to use filesys_mapper, so perhaps if this cannot be fixed it
> could be altered in the documentation)
>
> --
> Configure bugmail: https://bugzilla.mcs.anl.gov/swift/userprefs.cgi?tab=email
> ------- You are receiving this mail because: -------
> You are watching the assignee of the bug.
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From hategan at mcs.anl.gov  Wed Mar 24 21:02:10 2010
From: hategan at mcs.anl.gov (Mihael Hategan)
Date: Wed, 24 Mar 2010 21:02:10 -0500
Subject: filesys_mapper workaround (was Re: [Swift-devel] [Bug 223]
	New: wildcard fails in the pattern parameter for simple_mapper)
In-Reply-To: <50b07b4b1003241802y34ec6af9t90f6831a3771d0b6@mail.gmail.com>
References: <50b07b4b1003241802y34ec6af9t90f6831a3771d0b6@mail.gmail.com>
Message-ID: <1269482530.7257.14.camel@localhost>

Would you like more virtual cookies?

On Wed, 2010-03-24 at 20:02 -0500, Allan Espinosa wrote:
> The filesys_wrapper workaround starts to break when the type is a
> struct.  filesys_mapper is not supposed to work with structs so that's
> reasonable.  Hence, we should fix this bug :)
> 
> 
> typical workaround:
> type messagefile;
> 
> (messagefile o) write(messagefile i) {
>     app {
>         echo @filename(i) stdout=@filename(o);
>     }
> }
> 
> messagefile infile[] <filesys_mapper;
> prefix="071-singlefilemapper-input", suffix=".in",
>      location="gsiftp://ff-grid.unl.edu//panfs/panasas/CMS/data/engage/swift">;
> 
> 
> messagefile outfile <"071-singlefilemapper-input.out">;
> 
> trace(@infile[0]);
> outfile = write(infile[0]);
> 
> 
> used in structs:
> type SgtDim;
> type Variation;
> type Seismogram;
> type PeakValue;
> 
> type Station {
>   string name;
>   float lat;
>   float lon;
>   int erf;
>   int variation_scenario;
> }
> 
> type Sgt {
>   SgtDim x;
>   SgtDim y;
> }
> 
> type Rupture {
>   int source;
>   int index;
>   int size;
> }
> 
> /* some constants used by the apps*/
> global int num_time_steps = 3000;
> global string spectra_period1 = "all";
> global float filter_highhz = 5.0;
> global float simulation_timeskip = 0.1;
> 
> app (Sgt _ext) extract(Sgt _sgt, Station _stat, Variation _var) {
>   jbsim3d @strcat("stat=", _stat.name) "extract_sgt=1"
>       @strcat("slon=", _stat.lon) @strcat("slat=", _stat.lat)
> 
>       @strcat("rupmodfile=", @filename(_var))
>       @strcat("sgt_xfile=", @filename(_sgt.x))
>       @strcat("sgt_yfile=", @filename(_sgt.y))
>       @strcat("extract_sgt_xfile=", @filename(_ext.x))
>       @strcat("extract_sgt_yfile=", @filename(_ext.y));
> }
> 
> app (Seismogram _seis) seismogram(Sgt _sgt, Variation _var, Station _stat) {
>   jbsim3d @strcat("stat=", _stat.name) "extract_sgt=0"
>       @strcat("slon=", _stat.lon) @strcat("slat=", _stat.lat)
>       "outputBinary=1" "mergeOutput=1" @strcat("ntout=", num_time_steps)
> 
>       @strcat("rupmodfile=", @filename(_var))
>       @strcat("sgt_xfile=", @filename(_sgt.x))
>       @strcat("sgt_yfile=", @filename(_sgt.y))
>       @strcat("seis_file=", @filename(_seis));
> }
> 
> app (PeakValue _peak) peak_calc(Seismogram _seis, Variation _var) {
> //  touch @_peak;
>   surfeis_rspectra "simulation_out_pointsX=2" "simulation_out_pointsY=1"
>       "surfseis_rspectra_seismogram_units=cmpersec"
>       "surfseis_rspectra_output_units=cmpersec2"
>       "surfseis_rspectra_output_type=aa"
>       "surfseis_rspectra_apply_byteswap=no"
> 
>       @strcat("simulation_out_timesamples=", num_time_steps)
>       @strcat("simulation_out_timeskip=", simulation_timeskip)
>       @strcat("surfseis_rspectra_period=", spectra_period1)
>       @strcat(" surfseis_rspectra_apply_filter_highHZ=", filter_highhz)
>       @strcat("in=", @filename(_seis))
>       @strcat("out=", @filename(_peak));
> }
> 
> // Auxillary functions for the mappers
> type StationFile;
> app (StationFile _stat) getsite_file(int _run_id) {
>   getsite _run_id stdout=@filename(_stat);
> }
> (Station _stat) get_site(int _run_id) {
>   StationFile file<"site_tmp">;
>   file = getsite_file(_run_id);
>   _stat = readData(file);
> }
> 
> type RuptureFile;
> app (RuptureFile _rup) getrupture_file(int _run_id) {
>   getrupture _run_id stdout=@filename(_rup);
> }
> (Rupture _rup[]) get_ruptures(int _run_id) {
>   RuptureFile file<"rup_tmp">;
>   file = getrupture_file(_run_id);
>   _rup = readData(file);
> }
> 
> /* TODO: data management zip jobs */
> 
> int run_id = 644;
> Station site = get_site(run_id);
> 
> Sgt sgt_var[] <filesys_mapper; noauto="true",
>     location="gsiftp://ff-grid.unl.edu//panfs/panasas/CMS/data/engage/scec/data/SgtFiles/TEST/",
>     prefix=@strcat(site.name, "_f"), suffix=@strcat("_", run_id,".sgt")>;
> 
> Rupture rups[] = get_ruptures(run_id);
> 
> foreach rup in rups {
>   /* TODO: insert location parameters */
>   string datadir =
>       "gsiftp://ff-grid.unl.edu//panfs/panasas/CMS/data/engage/swift";
>   string loc_sub = @strcat(rup.index, "/", rup.source);
>   Sgt sub[] <filesys_mapper; location=loc_sub, suffix=".sgt",
>       prefix=@strcat(site.name, "_", rup.source, "_", rup.index, "_subf")>;
>   Variation vars[] <ext; exec="variation_mapper.rb", e=site.erf,
>       v=site.variation_scenario, s=rup.source, r=rup.index>;
> 
>   sub[0] = extract(sgt_var[0],  site, vars[rup.size-1]);
> 
>   foreach var,i in vars {
>     Seismogram seis[] <filesys_mapper; location=loc_sub,
> prefix=@strcat("Seismogram_", site.name,
>         "_", rup.source, "_", rup.index, "_", i), suffix=".grm">;
>     PeakValue peak[] <filesys_mapper; location=loc_sub,
> prefix=@strcat("PeakVals_", site.name,
>         "_", rup.source, "_", rup.index, "_", i), suffix=".bsa">;
> 
>     seis[0] = seismogram(sub[0], var, site);
>     peak[0] = peak_calc(seis[0], var);
>   }
> }
> 
> 
> error message:
> swift-r3264 cog-r2728
> 
> RunID: testing
> Progress:
> Progress:  Active:1  Checking status:1
> Ex098
> java.lang.RuntimeException: Inconsistency between type declaration and
> handle for field 'y'
> 	at org.griphyn.vdl.mapping.AbstractDataNode.getFringePaths(AbstractDataNode.java:372)
> 	at org.griphyn.vdl.mapping.AbstractDataNode.getFringePaths(AbstractDataNode.java:353)
> 	at org.griphyn.vdl.karajan.lib.FringePaths.function(FringePaths.java:29)
> 	at org.griphyn.vdl.karajan.lib.VDLFunction.post(VDLFunction.java:67)
> 	at org.globus.cog.karajan.workflow.nodes.AbstractSequentialWithArguments.childCompleted(AbstractSequentialWithArguments.java:192)
> 	at org.globus.cog.karajan.workflow.nodes.Sequential.notificationEvent(Sequential.java:33)
> 	at org.globus.cog.karajan.workflow.nodes.FlowNode.event(FlowNode.java:334)
> 	at org.globus.cog.karajan.workflow.events.EventBus.send(EventBus.java:134)
> 	at org.globus.cog.karajan.workflow.events.EventBus.sendHooked(EventBus.java:108)
> 	at org.globus.cog.karajan.workflow.nodes.FlowNode.fireNotificationEvent(FlowNode.java:176)
> 	at org.globus.cog.karajan.workflow.nodes.FlowNode.complete(FlowNode.java:298)
> 	at org.globus.cog.karajan.workflow.nodes.FlowContainer.post(FlowContainer.java:58)
> 	at org.globus.cog.karajan.workflow.nodes.functions.AbstractFunction.post(AbstractFunction.java:28)
> 	at org.globus.cog.karajan.workflow.nodes.Sequential.startNext(Sequential.java:51)
> 	at org.globus.cog.karajan.workflow.nodes.Sequential.executeChildren(Sequential.java:27)
> 	at org.globus.cog.karajan.workflow.nodes.FlowContainer.execute(FlowContainer.java:63)
> 	at org.globus.cog.karajan.workflow.nodes.FlowNode.restart(FlowNode.java:233)
> 	at org.globus.cog.karajan.workflow.nodes.FlowNode.start(FlowNode.java:280)
> 	at org.globus.cog.karajan.workflow.nodes.FlowNode.controlEvent(FlowNode.java:393)
> 	at org.globus.cog.karajan.workflow.nodes.FlowNode.event(FlowNode.java:331)
> 	at org.globus.cog.karajan.workflow.FlowElementWrapper.event(FlowElementWrapper.java:229)
> 	at org.globus.cog.karajan.workflow.events.EventBus.send(EventBus.java:134)
> 	at org.globus.cog.karajan.workflow.events.EventBus.sendHooked(EventBus.java:108)
> 	at org.globus.cog.karajan.workflow.events.EventTargetPair.run(EventTargetPair.java:43)
> 	at edu.emory.mathcs.backport.java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:431)
> 	at edu.emory.mathcs.backport.java.util.concurrent.FutureTask.run(FutureTask.java:166)
> 	at edu.emory.mathcs.backport.java.util.concurrent.ThreadPoolExecutor$Worker.runTask(ThreadPoolExecutor.java:643)
> 	at edu.emory.mathcs.backport.java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:668)
> 	at java.lang.Thread.run(Thread.java:595)
> Execution failed:
> 	java.lang.RuntimeException: Data set initialization failed for
> org.griphyn.vdl.mapping.DataNode identifier
> tag:benc at ci.uchicago.edu,2008:swift:dataset:20100324-1959-n2vdgijf:720000000115
> type Sgt with no value at dataset=sgt_var path=[0] (closed). Missing
> required field: y
> 
> I also attached the logfile.
> 
> -Allan
> 
> 2010/3/16  <bugzilla-daemon at mcs.anl.gov>:
> > https://bugzilla.mcs.anl.gov/swift/show_bug.cgi?id=223
> >
> >           Summary: wildcard fails in the pattern parameter for
> >                    simple_mapper
> >           Product: Swift
> >           Version: unspecified
> >          Platform: PC
> >        OS/Version: Windows
> >            Status: NEW
> >          Severity: normal
> >          Priority: P2
> >         Component: SwiftScript language
> >        AssignedTo: benc at hawaga.org.uk
> >        ReportedBy: skenny at uchicago.edu
> >
> >
> > the simple_mapper is meant to take a 'pattern' parameter which can contain
> > wildcards, however...
> >
> > the following code:
> >
> > file physdata<simple_mapper;location="rawphys/",pattern="*017*",suffix=".txt">;
> > trace(@filename(physdata));
> >
> > produces this error:
> >
> > Execution failed:
> >        java.lang.IllegalStateException: mapper.existing() returned a path
> > .r33subj017 that it cannot subsequently map
> >
> >
> > though, as i understand it, it should map a single file from this dir:
> >
> > $ ls rawphys/
> > r33subj003.txt  r33subj017.txt
> >
> >
> > (workaround is to use filesys_mapper, so perhaps if this cannot be fixed it
> > could be altered in the documentation)
> >
> > --
> > Configure bugmail: https://bugzilla.mcs.anl.gov/swift/userprefs.cgi?tab=email
> > ------- You are receiving this mail because: -------
> > You are watching the assignee of the bug.
> _______________________________________________
> Swift-devel mailing list
> Swift-devel at ci.uchicago.edu
> http://mail.ci.uchicago.edu/mailman/listinfo/swift-devel



From benc at hawaga.org.uk  Thu Mar 25 10:59:30 2010
From: benc at hawaga.org.uk (Ben Clifford)
Date: Thu, 25 Mar 2010 15:59:30 +0000 (GMT)
Subject: [Swift-devel] Re: Swift Provenance
In-Reply-To: <4BAB7A8C.3070105@lncc.br>
References: <Pine.LNX.4.64.0910200827330.1500@dildano.hawaga.org.uk>
	<4BAA8A0A.6000705@lncc.br>
	<Pine.LNX.4.64.1003250920010.7818@dildano.hawaga.org.uk>
	<4BAB7A8C.3070105@lncc.br>
Message-ID: <Pine.LNX.4.64.1003251547290.7818@dildano.hawaga.org.uk>


(cc swift devel in case others are interested)

> We're going to work on making provenance more friendly to scientists, this
> will involve writing stored procedures (or something equivalent) on top of the
> provenance database to answer common questions that would be hard for a
> scientist to express in SQL.

ok.

VDS1 had a provenance query language that had roughly the same goals (I 
think)

I have some some criticisms of that:

The language tried to support multiple database backend formats (XML and 
SQL) and in doing so failed to support either well (for example, sometimes 
it was desirable to make a join, but this was not supported meaning that 
you had to drop out to the SQL database directly for such queries). Pick 
one model and support it (I think SQL is my preferred one, but you may 
differ).

Data was made available in a mishmash of models - for example, the 
abstract provenance query language would sometimes return an entire XML 
blob of data, which could not be further queried inside the provenance 
query language. This meant that having used to provenance query language 
to partly answer a question, in the end tools such as ad-hoc bad XML 
parsers written in perl ended up being used too (see the Provenance 
Challenge 1 queries for VDS for example). Make sure that whatever you 
produce can actually completely address the queries you are trying to 
address - if I have to hack some bodge on to the end of what you produce 
to answer my question, then I might as well have hit raw SQL in the first 
place.

I'm not sure what the other people involved in OPM are up to now, but 
maybe they have interesting scientist-friendly approaches. OPM feels like 
a very good fit for Swift's provenance, and so there is some potential 
there if anyone else is actually working in the "easy query" space (not 
sure if anyone is).

-- 



From lgadelha at lncc.br  Thu Mar 25 14:21:09 2010
From: lgadelha at lncc.br (Luiz M. R. Gadelha Jr.)
Date: Thu, 25 Mar 2010 14:21:09 -0500
Subject: [Swift-devel] Re: Swift Provenance
In-Reply-To: <Pine.LNX.4.64.1003251547290.7818@dildano.hawaga.org.uk>
References: <Pine.LNX.4.64.0910200827330.1500@dildano.hawaga.org.uk>
	<4BAA8A0A.6000705@lncc.br>
	<Pine.LNX.4.64.1003250920010.7818@dildano.hawaga.org.uk>
	<4BAB7A8C.3070105@lncc.br>
	<Pine.LNX.4.64.1003251547290.7818@dildano.hawaga.org.uk>
Message-ID: <4BABB7A5.1010706@lncc.br>

I agree that it's hard to make it generic. Initially, we are focusing on 
two users that will benefit from a simpler interface to the provenance 
database.

On 3/25/10 10:59 AM, Ben Clifford wrote:
>
> (cc swift devel in case others are interested)
>
>> We're going to work on making provenance more friendly to scientists, this
>> will involve writing stored procedures (or something equivalent) on top of the
>> provenance database to answer common questions that would be hard for a
>> scientist to express in SQL.
>
> ok.
>
> VDS1 had a provenance query language that had roughly the same goals (I
> think)
>
> I have some some criticisms of that:
>
> The language tried to support multiple database backend formats (XML and
> SQL) and in doing so failed to support either well (for example, sometimes
> it was desirable to make a join, but this was not supported meaning that
> you had to drop out to the SQL database directly for such queries). Pick
> one model and support it (I think SQL is my preferred one, but you may
> differ).
>
> Data was made available in a mishmash of models - for example, the
> abstract provenance query language would sometimes return an entire XML
> blob of data, which could not be further queried inside the provenance
> query language. This meant that having used to provenance query language
> to partly answer a question, in the end tools such as ad-hoc bad XML
> parsers written in perl ended up being used too (see the Provenance
> Challenge 1 queries for VDS for example). Make sure that whatever you
> produce can actually completely address the queries you are trying to
> address - if I have to hack some bodge on to the end of what you produce
> to answer my question, then I might as well have hit raw SQL in the first
> place.
>
> I'm not sure what the other people involved in OPM are up to now, but
> maybe they have interesting scientist-friendly approaches. OPM feels like
> a very good fit for Swift's provenance, and so there is some potential
> there if anyone else is actually working in the "easy query" space (not
> sure if anyone is).
>


-- 
Luiz M. R. Gadelha Jr.
http://www.lncc.br/~lgadelha



From wozniak at mcs.anl.gov  Fri Mar 26 15:58:17 2010
From: wozniak at mcs.anl.gov (Justin M Wozniak)
Date: Fri, 26 Mar 2010 15:58:17 -0500 (CDT)
Subject: [Swift-devel] Swift/Coasters/PBS on Intrepid
Message-ID: <alpine.DEB.2.00.1003261551400.10780@roberts-desktop.mcs.anl.gov>


This worked last week: I'm trying to use the pbs provider on Intrepid. 
Currently does not work, I have it tracked down to the error message and 
produced PBS script (sites.xml also):

Does anyone have a quick fix for this?  I'm wondering if the recent policy 
change affects this.  I'll keep looking...

qsub /home/wozniak/.globus/scripts/PBS24215.submit
Not all required arguments provided: time,nodecount needed

#PBS -S /bin/sh
#PBS -N null
#PBS -m n
#PBS -A PTMAP
#PBS -l nodes=64
#PBS -l walltime=00:49:00
#PBS -q prod-devel
#PBS -o /home/wozniak/.globus/scripts/PBS24215.submit.stdout
#PBS -e /home/wozniak/.globus/scripts/PBS24215.submit.stderr
ZOID_ENABLE_NAT=true
/usr/bin/perl /home/wozniak/.globus/coasters/cscript24214.pl 
http://172.17.5.143:57863 0326-490318-000000 /home/wozniak/
.globus/coasters
/bin/echo $? >/home/wozniak/.globus/scripts/PBS24215.submit.exitcode

<config>

   <pool handle="localhost" sysinfo="INTEL32::LINUX">
     <gridftp url="local://localhost" />
     <execution provider="local" url="none" />
     <workdirectory>/gpfs/home/wozniak/work</workdirectory>
   </pool>

   <pool handle="coasters_alcfbgp">
     <filesystem provider="local" />
     <execution provider="coaster" jobmanager="local:pbs"/>
     <profile namespace="globus" 
key="internalHostname">172.17.5.143</profile>
     <profile namespace="globus"  key="project">PTMAP</profile>
     <profile namespace="globus"  key="queue">prod-devel</profile>
     <profile namespace="globus"  key="kernelprofile">zeptoos</profile>
     <profile namespace="globus"  key="alcfbgpnat">true</profile>
     <profile namespace="karajan" key="jobthrottle">2.55</profile>
     <profile namespace="karajan" key="initialScore">10000</profile>
     <profile namespace="globus"  key="workersPerNode">4</profile>
     <profile namespace="globus"  key="slots">8</profile>
     <profile namespace="globus"  key="maxTime">3000</profile>
     <profile namespace="globus"  key="nodeGranularity">64</profile>
     <profile namespace="globus"  key="maxNodes">64</profile>
     <scratch>/scratch</scratch>
     <workdirectory >/gpfs/home/wozniak/work</workdirectory>
   </pool>

</config>


-- 
Justin M Wozniak


From aespinosa at cs.uchicago.edu  Fri Mar 26 16:53:38 2010
From: aespinosa at cs.uchicago.edu (Allan Espinosa)
Date: Fri, 26 Mar 2010 15:53:38 -0600
Subject: [Swift-devel] can't plot logfiles without coasters
Message-ID: <50b07b4b1003261453w52e5950yd27dec5d8b91678c@mail.gmail.com>

Hi,

I think the swift-plot-log script should check for this.

normalising time Fri Mar 26 16:51:53 CDT 2010
numbering events Fri Mar 26 16:51:53 CDT 2010
preparing plot file Fri Mar 26 16:51:53 CDT 2010
plotting Fri Mar 26 16:51:53 CDT 2010
done Fri Mar 26 16:51:53 CDT 2010
events-in-progress < karatasks.JOB_SUBMISSION.Queue.event >
karatasks.JOB_SUBMISSION.Queue.eip
event-duration-stats karatasks.JOB_SUBMISSION.Queue.event >
karatasks.JOB_SUBMISSION.Queue.stats
cat karatasks.JOB_SUBMISSION.Queue.event | sort -n -k 2 >
karatasks.JOB_SUBMISSION.Queue.sorted-by-duration
plot-duration-histogram
karatasks.JOB_SUBMISSION.Queue.sorted-by-duration
karatasks.JOB_SUBMISSION.Queue-duration-histogram.png
weights.sh /home/aespinosa/science/cybershake/swift/small/postproc-TEST.log
tscore.sh /home/aespinosa/science/cybershake/swift/small/postproc-TEST.log
| normalise-event-start-time | sed 's/\([^ ]*\) [^ ]* [^ ]* [^ ]* \([^
]*\) \([^ ]*\).*/\1 \2 \3/' > tscores.data
gnuplot /home/aespinosa/swift/vanilla/bin/../libexec/log-processing//tscores.plot
extract-coaster-timeline
/home/aespinosa/science/cybershake/swift/small/postproc-TEST.log
gnuplot /home/aespinosa/swift/vanilla/bin/../libexec/log-processing//coaster-block-timeline.plot

gnuplot> plot "coaster-blocks.data" u 1:2 w steps title "Queued
Workers", "coaster-blocks.data" u 1:3 w steps title "Running Workers"
              ^
         can't read data file "coaster-blocks.data"
         "/home/aespinosa/swift/vanilla/bin/../libexec/log-processing//coaster-block-timeline.plot",
line 6: util.c: No such file or directory

make: *** [coaster-block-timeline.png] Error 1
rm karatasks.FILE_OPERATION.sorted-start.event
karatasks.JOB_SUBMISSION.Active.event
karatasks.JOB_SUBMISSION.Queue.sorted-start.event karatasks.last
karatasks.JOB_SUBMISSION.seenstates
karatasks.FILE_TRANSFER.sorted-start.event
karatasks.JOB_SUBMISSION.Queue.eip
karatasks.JOB_SUBMISSION.Active.sorted-start.event
karatasks.FILE_OPERATION.seenstates
karatasks.JOB_SUBMISSION.Queue.sorted-by-duration
karatasks.FILE_OPERATION.eip karatasks.JOB_SUBMISSION.event
karatasks.FILE_TRANSFER.seenstates karatasks.FILE_OPERATION.event
karatasks.FILE_TRANSFER.eip
karatasks.JOB_SUBMISSION.Active.sorted-by-duration
karatasks.JOB_SUBMISSION.Active.eip karatasks.FILE_TRANSFER.event
karatasks.JOB_SUBMISSION.sorted-start.even

-Allan

-- 
Allan M. Espinosa <http://amespinosa.wordpress.com>
PhD student, Computer Science
University of Chicago <http://people.cs.uchicago.edu/~aespinosa>


From aespinosa at cs.uchicago.edu  Fri Mar 26 17:13:36 2010
From: aespinosa at cs.uchicago.edu (Allan Espinosa)
Date: Fri, 26 Mar 2010 16:13:36 -0600
Subject: [Swift-devel] Re: [Swift-user] mapping variables on the fly
In-Reply-To: <50b07b4b1003251426j31a092c5i72bd0e7640c5061d@mail.gmail.com>
References: <50b07b4b1003251328y4971c12eq71621ea650c12148@mail.gmail.com>
	<alpine.WNT.2.00.1003251545390.3264@justinwozniak>
	<50b07b4b1003251426j31a092c5i72bd0e7640c5061d@mail.gmail.com>
Message-ID: <50b07b4b1003261513i3be4619br56fda5c8a1fb6936@mail.gmail.com>

When I have the number of elements in rup[] relatively small (10
elements), the workflow does go through execution.  But sometimes it
doesn't.  I just run it again and again until it goes through.

Is there a deadlock somewhere in the execution of the workflow?  When
I have really large parallel workflows the swift interpreter shows
high cpu utilization.  But in here,I see the interpreter in a sleep
state.  How do I go to confirm/debug this?

-Allan

2010/3/25 Allan Espinosa <aespinosa at cs.uchicago.edu>:
> Hi Justin,
>
> Yes it does.
>
> Weird, I added @trace statements and the workflow went through.
>
> doing "@trace(rup.index); @trace(rup.source) ; @trace(rup.size); "
> inside the foreach loop works fine.
>
>
> -Allan
>


From aespinosa at cs.uchicago.edu  Fri Mar 26 17:19:20 2010
From: aespinosa at cs.uchicago.edu (Allan Espinosa)
Date: Fri, 26 Mar 2010 16:19:20 -0600
Subject: [Swift-devel] Re: [Swift-user] mapping variables on the fly
In-Reply-To: <50b07b4b1003261513i3be4619br56fda5c8a1fb6936@mail.gmail.com>
References: <50b07b4b1003251328y4971c12eq71621ea650c12148@mail.gmail.com>
	<alpine.WNT.2.00.1003251545390.3264@justinwozniak>
	<50b07b4b1003251426j31a092c5i72bd0e7640c5061d@mail.gmail.com>
	<50b07b4b1003261513i3be4619br56fda5c8a1fb6936@mail.gmail.com>
Message-ID: <50b07b4b1003261519j30922fckc93aba83088fb26e@mail.gmail.com>

Hmmm... how about this:

2010-03-26 17:12:08,895-0500 INFO  AbstractDataNode Notifying listener
"Open, 0 elements, 1 listeners" about
"org.griphyn.vdl.mapping.RootArrayDataNode identifier
tag:benc at ci.uchicago.edu,2008:swift:dataset:20100326-1712-itfxmive:720000000225
type Variation[] with no value at dataset=vars (closed)"
2010-03-26 17:12:08,895-0500 INFO  AbstractDataNode closed
org.griphyn.vdl.mapping.RootArrayDataNode identifier
tag:benc at ci.uchicago.edu,2008:swift:dataset:20100326-1712-itfxmive:720000000225
type Variation[] with no value at dataset=vars (closed)


Does this mean that vars didn't get mapped properly by my ext mapper
at some point?

2010/3/26 Allan Espinosa <aespinosa at cs.uchicago.edu>:
> When I have the number of elements in rup[] relatively small (10
> elements), the workflow does go through execution. ?But sometimes it
> doesn't. ?I just run it again and again until it goes through.
>
> Is there a deadlock somewhere in the execution of the workflow? ?When
> I have really large parallel workflows the swift interpreter shows
> high cpu utilization. ?But in here,I see the interpreter in a sleep
> state. ?How do I go to confirm/debug this?
>
> -Allan
>
> 2010/3/25 Allan Espinosa <aespinosa at cs.uchicago.edu>:
>> Hi Justin,
>>
>> Yes it does.
>>
>> Weird, I added @trace statements and the workflow went through.
>>
>> doing "@trace(rup.index); @trace(rup.source) ; @trace(rup.size); "
>> inside the foreach loop works fine.
>>
>>
>> -Allan


From wilde at mcs.anl.gov  Sat Mar 27 07:17:53 2010
From: wilde at mcs.anl.gov (wilde at mcs.anl.gov)
Date: Sat, 27 Mar 2010 07:17:53 -0500 (CDT)
Subject: [Swift-devel] Re: [Swift-user] mapping variables on the fly
In-Reply-To: <17111701.377611269692049992.JavaMail.root@zimbra>
Message-ID: <21422670.377641269692273408.JavaMail.root@zimbra>

Allan, I get similar messages in a different script:

SwiftScript trace: BT models closed, org.griphyn.vdl.mapping.DataNode identifier tag:benc at ci.uchicago.edu,2008:swift:dataset:20100326
-1423-kjpjsox8:720000000075 type RaptorModel with no value at dataset=models path=[0] (closed)
SwiftScript trace: BT summary closed, org.griphyn.vdl.mapping.RootDataNode identifier tag:benc at ci.uchicago.edu,2008:swift:dataset:201
00326-1423-kjpjsox8:720000000067 type RaptorSummary with no value at dataset=summary (closed)
SwiftScript trace: summary closed, org.griphyn.vdl.mapping.RootDataNode identifier tag:benc at ci.uchicago.edu,2008:swift:dataset:201003
26-1423-kjpjsox8:720000000067 type RaptorSummary with no value at dataset=summary (closed)

Ive been ignoring these because *I think* I investigated it back in November and if its the same message, I concluded that it was simply leftover debugging traces. I think back then I turn these messages off in a test version but never committed that change. As I recall Ben inserted these messages as part of some fix or improvement to array closing; (Ben, please inform if it rings a bell, thanks).

- Mike

----- "Allan Espinosa" <aespinosa at cs.uchicago.edu> wrote:

> Hmmm... how about this:
> 
> 2010-03-26 17:12:08,895-0500 INFO  AbstractDataNode Notifying
> listener
> "Open, 0 elements, 1 listeners" about
> "org.griphyn.vdl.mapping.RootArrayDataNode identifier
> tag:benc at ci.uchicago.edu,2008:swift:dataset:20100326-1712-itfxmive:720000000225
> type Variation[] with no value at dataset=vars (closed)"
> 2010-03-26 17:12:08,895-0500 INFO  AbstractDataNode closed
> org.griphyn.vdl.mapping.RootArrayDataNode identifier
> tag:benc at ci.uchicago.edu,2008:swift:dataset:20100326-1712-itfxmive:720000000225
> type Variation[] with no value at dataset=vars (closed)
> 
> 
> Does this mean that vars didn't get mapped properly by my ext mapper
> at some point?
> 
> 2010/3/26 Allan Espinosa <aespinosa at cs.uchicago.edu>:
> > When I have the number of elements in rup[] relatively small (10
> > elements), the workflow does go through execution. ?But sometimes
> it
> > doesn't. ?I just run it again and again until it goes through.
> >
> > Is there a deadlock somewhere in the execution of the workflow?
> ?When
> > I have really large parallel workflows the swift interpreter shows
> > high cpu utilization. ?But in here,I see the interpreter in a sleep
> > state. ?How do I go to confirm/debug this?
> >
> > -Allan
> >
> > 2010/3/25 Allan Espinosa <aespinosa at cs.uchicago.edu>:
> >> Hi Justin,
> >>
> >> Yes it does.
> >>
> >> Weird, I added @trace statements and the workflow went through.
> >>
> >> doing "@trace(rup.index); @trace(rup.source) ; @trace(rup.size); "
> >> inside the foreach loop works fine.
> >>
> >>
> >> -Allan
> _______________________________________________
> Swift-devel mailing list
> Swift-devel at ci.uchicago.edu
> http://mail.ci.uchicago.edu/mailman/listinfo/swift-devel

-- 
Michael Wilde
Computation Institute, University of Chicago
Mathematics and Computer Science Division
Argonne National Laboratory



From benc at hawaga.org.uk  Sat Mar 27 08:46:28 2010
From: benc at hawaga.org.uk (Ben Clifford)
Date: Sat, 27 Mar 2010 13:46:28 +0000 (GMT)
Subject: [Swift-devel] Re: [Swift-user] mapping variables on the fly
In-Reply-To: <21422670.377641269692273408.JavaMail.root@zimbra>
References: <21422670.377641269692273408.JavaMail.root@zimbra>
Message-ID: <Pine.LNX.4.64.1003271343250.7388@dildano.hawaga.org.uk>

> SwiftScript trace: BT models closed, org.griphyn.vdl.mapping.DataNode 
> identifier tag:benc at ci.uchicago.edu,2008:swift:dataset:20100326 
> -1423-kjpjsox8:720000000075 type RaptorModel with no value at 
> dataset=models path=[0] (closed) SwiftScript trace: BT summary closed, 
> org.griphyn.vdl.mapping.RootDataNode identifier 
> tag:benc at ci.uchicago.edu,2008:swift:dataset:201 
> 00326-1423-kjpjsox8:720000000067 type RaptorSummary with no value at 
> dataset=summary (closed) SwiftScript trace: summary closed, 
> org.griphyn.vdl.mapping.RootDataNode identifier 
> tag:benc at ci.uchicago.edu,2008:swift:dataset:201003 
> 26-1423-kjpjsox8:720000000067 type RaptorSummary with no value at 
> dataset=summary (closed)

> Ive been ignoring these because *I think* I investigated it back in 
> November and if its the same message, I concluded that it was simply 
> leftover debugging traces. I think back then I turn these messages off 
> in a test version but never committed that change. As I recall Ben 
> inserted these messages as part of some fix or improvement to array 
> closing; (Ben, please inform if it rings a bell, thanks).

Those come (I think) from when you try to display a SwfitScript 'thing' 
(eg a variable) that has no in-memory value (eg. 7, or "foo") but has 
still been closed (i.e. its had something assigned to it, or its an input 
file) - for example, if the 'thing' is a file-mapped variable, so will not 
have an in-memory value.

If thats the circumstance in which you're seeing the above, then thats OK.

-- 



From hategan at mcs.anl.gov  Sun Mar 28 23:17:42 2010
From: hategan at mcs.anl.gov (Mihael Hategan)
Date: Sun, 28 Mar 2010 23:17:42 -0500
Subject: [Swift-devel] deep field bug
Message-ID: <1269836262.21332.9.camel@localhost>

Mike (and possibly others) have been experiencing a bit of a problem
with a certain type of script.

The basic idea is an app returning a complex structure. The example Mike
gave was (irrelevant stuff removed):

type filestruct {
  file filefield;
}

app (filestruct fs[]) touchem () { touchem; }

Where fs is mapped properly with a fixed array mapper.

The problem with that is that closedataset (which is called when touchem
is done) only closes fs and fs[*], but not fs[*].filefield. For some
reason the method used internally is closeChildren().

Now, it seems quite obvious that that's bogus and a deep close should
be done instead when returning from an app. Furthermore, I see no need
for closeChildren() to ever be called on its own (other than perhaps by
a deep close). So I'm sending this email to see if anybody (Ben that is)
is of a different opinion.

In the mean-time, for those who want to test a possible solution (and
please run the whole test suite in the process):
http://www.mcs.anl.gov/~hategan/deepfieldbug.diff

(you need to apply it in swift/src/org/griphyn/vdl).



From benc at hawaga.org.uk  Mon Mar 29 03:12:14 2010
From: benc at hawaga.org.uk (Ben Clifford)
Date: Mon, 29 Mar 2010 08:12:14 +0000 (GMT)
Subject: [Swift-devel] deep field bug
In-Reply-To: <1269836262.21332.9.camel@localhost>
References: <1269836262.21332.9.camel@localhost>
Message-ID: <Pine.LNX.4.64.1003290809360.7388@dildano.hawaga.org.uk>


> Furthermore, I see no need for closeChildren() to ever be called on its 
> own (other than perhaps by a deep close).

I think that is probably true.

-- 


From yizhu at cs.uchicago.edu  Mon Mar 29 17:31:48 2010
From: yizhu at cs.uchicago.edu (Yi Zhu)
Date: Mon, 29 Mar 2010 17:31:48 -0500
Subject: [Swift-devel] How to add resources constraint in sites.xml for qsub
Message-ID: <4BB12A54.3010104@cs.uchicago.edu>

Hi everyone,

we've already known that we can describe the queue type in sites.xml:

e.g:

qsub -q short myjobs.pbs

can be written in sites.xml by  the following statement:

<profile namespace="globus" key="queue">short</profile>


But what if I want to specify some other resources constraint by using 
"-l argument":

e.g:

qsub -l mem=3gb myjobs.pbs

How can I describe that in sites.xml files?



Many Thanks!

-Yi Zhu


From vipulkrsingh at gmail.com  Tue Mar 30 17:13:52 2010
From: vipulkrsingh at gmail.com (Vipul Kumar Singh)
Date: Wed, 31 Mar 2010 03:43:52 +0530
Subject: [Swift-devel] Re: scheduling
In-Reply-To: <19767280.184761269053016043.JavaMail.root@zimbra>
References: <7363198.184681269052526459.JavaMail.root@zimbra> 
	<19767280.184761269053016043.JavaMail.root@zimbra>
Message-ID: <p2r65fb392f1003301513zf1337dc5n95437465f7a226f6@mail.gmail.com>

Hi,

Going through the code i realized that we could add to the
checkConstraints() which returns the desired sites to the
getNextResource()... We can add data dependencies as task constraints, the
constraints checker then checks the availability of data on sites based on
catalog, as you suggested. So the logical step would be to have the support
for RLS catalog in swift so it can be used to make scheduling decisions.

But I am having trouble figuring out how to get the mappers and catalog
concept work complementary to each other i.e. what would be first steps
towards having a catalog of data in swift..

Thank you

Vipul Kumar Singh




On Sat, Mar 20, 2010 at 8:13 AM, <wilde at mcs.anl.gov> wrote:

> Hi Vipul,
>
> The topic you propose here is both interesting and likely to be valuable
> for Swift users, and I'd like to help you develop the ideas further.  I'll
> try to respond to later comments on the discuss that started on your
> proposal, but first I'd like to offer a few thoughts on your initial message
> below.
>
> ----- "Vipul Kumar Singh" <vipulkrsingh at gmail.com> wrote:
>
> > Sir,
> >
> > I am interested in working on the data-aware features in swift on two
> > major points
> >
> > 1) For jobs dependent on same data, scheduler tries to schedule them
> > to same resources.
>
> The ability to *consider* the location of a data object when assigning a
> job to a site would be great.
>
> >
> > (i) The scheduler maintains a hash containing information about (a)
> > data files, (b) jobs dependent on that data and (c) resources that are
> > executing (or scheduled to execute) those jobs.
> > (ii) The information will be updated every time a job is finished (on
> > success/failure).
> > (iii) When scheduling new jobs, the scheduler looks through the hash
> > and schedules new job to the resource that has data on which new job
> > is dependent (If the resource is not already overloaded).
>
> I think these heuristics are a very good first approximation; you'll need
> to refine the criteria as you get deeper into the code and also based on
> experiments and measurements.
>
> It would be good to base a solution on a grid-wide file location catalog
> like the Globus RLS or similar. Ive long thought that file location could
> also be selected and/or influenced by mappers (like ext mapper scripts) but
> thats just a starting point to feed info to the site selection algorithm.
>
> >
> > 2) Combining the tasks together that are dependent on same data files,
> > before scheduling. And i believe this can be added quickly using
> > coasters ( or is the feature already there... ).
>
> I think a bit of work has been done towards this goal by a student a few
> summers back that could be used as a starting point.  In general, we've been
> interested in having Swift join tasks together in a shell-like pipeline when
> that would be optimal.
>
> >
> > Currently i have setup some machines with globus and swift but am not
> > able to get swift submit jobs through gram4.....
>
> I think you'll get better results (and support) with GRAM 5, or even GRAM
> 2.4. And you could do initial experiments with just ssh and coasters. Let us
> know what problems youre havig (on swift-user at ci.uchicago.edu, and include
> your sites.xml, tc.data, swift.properties, and swift .log file when
> reporting problems, so we can diagnose them with less back-and-forth, OK?
>
> I'm eager to see what kind of progress you can make on this problem, and
> very willing to help you think through it.
>
> Regards,
>
> Mike
>
>
>
> >
> > Vipul Kumar Singh
>
> --
> Michael Wilde
> Computation Institute, University of Chicago
> Mathematics and Computer Science Division
> Argonne National Laboratory
>
>
-------------- next part --------------
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From hategan at mcs.anl.gov  Tue Mar 30 17:27:19 2010
From: hategan at mcs.anl.gov (Mihael Hategan)
Date: Tue, 30 Mar 2010 17:27:19 -0500
Subject: [Swift-devel] Re: scheduling
In-Reply-To: <p2r65fb392f1003301513zf1337dc5n95437465f7a226f6@mail.gmail.com>
References: <7363198.184681269052526459.JavaMail.root@zimbra>
	<19767280.184761269053016043.JavaMail.root@zimbra>
	<p2r65fb392f1003301513zf1337dc5n95437465f7a226f6@mail.gmail.com>
Message-ID: <1269988039.6547.9.camel@localhost>

On Wed, 2010-03-31 at 03:43 +0530, Vipul Kumar Singh wrote:
> Hi,
> 
> Going through the code i realized that we could add to the
> checkConstraints() which returns the desired sites to the
> getNextResource()...

You're close to what I think should be done.

My opinion is that availability of files should bias the site scores
instead of imposing hard constraints. There would be a parameter that
would control the strength of that bias.

>  We can add data dependencies as task constraints, the constraints
> checker then checks the availability of data on sites based on
> catalog, as you suggested. So the logical step would be to have the
> support for RLS catalog in swift so it can be used to make scheduling
> decisions.
> 
> But I am having trouble figuring out how to get the mappers and
> catalog concept work complementary to each other i.e. what would be
> first steps towards having a catalog of data in swift..

Right. Swift would need some form of data catalog. Perhaps a simple
in-memory catalog would be a good first start. And before that there
would be a need for an API specification to which various
implementations could be plugged (e.g. in-memory, database, RLS).

Also, I would say ignore mappers for now. That is unless Mike has a good
reason for doing otherwise that I'm not aware of.

Mihael



From wilde at mcs.anl.gov  Tue Mar 30 17:32:55 2010
From: wilde at mcs.anl.gov (Michael Wilde)
Date: Tue, 30 Mar 2010 17:32:55 -0500 (CDT)
Subject: [Swift-devel] Re: scheduling
In-Reply-To: <1269988039.6547.9.camel@localhost>
Message-ID: <11231154.466981269988375726.JavaMail.root@zimbra>

I was thinking that mappers might be the place to look up the location of a logical file and return a physical one, but I can see how that would be hard to integrate into the scheduling model.

I'd say keep it on the idea stack, proceeding as Mihael suggest sounds great, and lets see where that takes us.

- Mike

----- "Mihael Hategan" <hategan at mcs.anl.gov> wrote:

> On Wed, 2010-03-31 at 03:43 +0530, Vipul Kumar Singh wrote:
> > Hi,
> > 
> > Going through the code i realized that we could add to the
> > checkConstraints() which returns the desired sites to the
> > getNextResource()...
> 
> You're close to what I think should be done.
> 
> My opinion is that availability of files should bias the site scores
> instead of imposing hard constraints. There would be a parameter that
> would control the strength of that bias.
> 
> >  We can add data dependencies as task constraints, the constraints
> > checker then checks the availability of data on sites based on
> > catalog, as you suggested. So the logical step would be to have the
> > support for RLS catalog in swift so it can be used to make
> scheduling
> > decisions.
> > 
> > But I am having trouble figuring out how to get the mappers and
> > catalog concept work complementary to each other i.e. what would be
> > first steps towards having a catalog of data in swift..
> 
> Right. Swift would need some form of data catalog. Perhaps a simple
> in-memory catalog would be a good first start. And before that there
> would be a need for an API specification to which various
> implementations could be plugged (e.g. in-memory, database, RLS).
> 
> Also, I would say ignore mappers for now. That is unless Mike has a
> good
> reason for doing otherwise that I'm not aware of.
> 
> Mihael
> 
> _______________________________________________
> Swift-devel mailing list
> Swift-devel at ci.uchicago.edu
> http://mail.ci.uchicago.edu/mailman/listinfo/swift-devel

-- 
Michael Wilde
Computation Institute, University of Chicago
Mathematics and Computer Science Division
Argonne National Laboratory



From benc at hawaga.org.uk  Wed Mar 31 02:53:56 2010
From: benc at hawaga.org.uk (Ben Clifford)
Date: Wed, 31 Mar 2010 07:53:56 +0000 (GMT)
Subject: [Swift-devel] Re: scheduling
In-Reply-To: <1269988039.6547.9.camel@localhost>
References: <7363198.184681269052526459.JavaMail.root@zimbra>
	<19767280.184761269053016043.JavaMail.root@zimbra>
	<p2r65fb392f1003301513zf1337dc5n95437465f7a226f6@mail.gmail.com>
	<1269988039.6547.9.camel@localhost>
Message-ID: <Pine.LNX.4.64.1003310750180.7388@dildano.hawaga.org.uk>


there was (and I think still is) a bluriness about what swift's data 
replication handling should be.

for example, should it be for swift to keep track of where it has placed 
data on sites? (Here is "mydata.txt" locally- process it and put the 
result back locally and if you happen to do some persistent replication 
that you cna use later, fine)

should it be for arbitrary actors (perhaps swift, perhaps other people) 
placing replicas of data in arbitrary locations on the network, not 
necessarily attached to 'sites' (in the sites.xml sense): (my data is 
stored at http://a.com/repo/foo.txt and also at 
http://b.com/guests/monkey/tree - I don't mind which you pull to an 
execution site as I am asserting that they are equal).

Those cases are similar but different and somehow I get the feeling that 
there is not a clearly defined consensus.

-- 
http://www.hawaga.org.uk/ben/



From wilde at mcs.anl.gov  Wed Mar 31 07:28:27 2010
From: wilde at mcs.anl.gov (wilde at mcs.anl.gov)
Date: Wed, 31 Mar 2010 07:28:27 -0500 (CDT)
Subject: [Swift-devel] Re: scheduling
In-Reply-To: <3113501.473511270038500715.JavaMail.root@zimbra>
Message-ID: <4745903.473531270038507652.JavaMail.root@zimbra>

To think through this question it helps to define the actors that are involved:

- input mappers, which have the opportunity to do their mapping from a replica catalog

- the site selector in Swift's scheduler, which could factor into its criteria where the data needed by an application lives (and perhaps where the output must go, or where the user prefers that it go)

- the Swift execution wrapper _swiftwrap and/or the post-execution logic and cache management logic in Swift which can influence whether and how long a file stays in the site shared/ cache

0 there also may be back-end replicators which go around replicating data objects for speed or reliability, but since these are typically asynchronous they dont affect the discussion much.

One model of replication (out of many possible) is then:

- Mappers use a replica catalog to map Swift objects to logical names

- The scheduler considers  available replicas when making a site selection, and then translates logical file names to physical site-specific names

- the post-job-execution logic updates a replica catalog with the cached location of results. Some aspect of or alternative to the shared/ directory persists across script executions.

- backend (and/or in-execution) logic does some cache cleanup and/or additional replication or relocation based on criterial like space and usage and other "policy".

One thing thats puzzles me is whether the mappers could or should do some level of site selection, but its not clear they could get access to the info they need. That would reduce impact on the scheduler code, but is perhaps not the ideal place to make the decision.

I suspect there are many complicating factors that would effect this analysis, and Im not sure I got all the details of current behavior right, but this is the way Ive been thinking about the problem to date.

It seems like a reasonable GSoC experiment.

- Mike

----- "Ben Clifford" <benc at hawaga.org.uk> wrote:

> there was (and I think still is) a bluriness about what swift's data 
> replication handling should be.
> 
> for example, should it be for swift to keep track of where it has
> placed 
> data on sites? (Here is "mydata.txt" locally- process it and put the 
> result back locally and if you happen to do some persistent
> replication 
> that you cna use later, fine)
> 
> should it be for arbitrary actors (perhaps swift, perhaps other
> people) 
> placing replicas of data in arbitrary locations on the network, not 
> necessarily attached to 'sites' (in the sites.xml sense): (my data is
> 
> stored at http://a.com/repo/foo.txt and also at 
> http://b.com/guests/monkey/tree - I don't mind which you pull to an 
> execution site as I am asserting that they are equal).
> 
> Those cases are similar but different and somehow I get the feeling
> that 
> there is not a clearly defined consensus.
> 
> -- 
> http://www.hawaga.org.uk/ben/
> 
> _______________________________________________
> Swift-devel mailing list
> Swift-devel at ci.uchicago.edu
> http://mail.ci.uchicago.edu/mailman/listinfo/swift-devel

-- 
Michael Wilde
Computation Institute, University of Chicago
Mathematics and Computer Science Division
Argonne National Laboratory



From hategan at mcs.anl.gov  Wed Mar 31 11:16:04 2010
From: hategan at mcs.anl.gov (Mihael Hategan)
Date: Wed, 31 Mar 2010 11:16:04 -0500
Subject: [Swift-devel] Re: scheduling
In-Reply-To: <4745903.473531270038507652.JavaMail.root@zimbra>
References: <4745903.473531270038507652.JavaMail.root@zimbra>
Message-ID: <1270052164.16103.10.camel@localhost>

A few comments:

I think we need to simplify the model here, because it's already hard to
reason about. I think we also need to keep it cohesive. So whether
information provided by the mappers is used for scheduling, no
scheduling decisions (logic) should be in mappers.

On Wed, 2010-03-31 at 07:28 -0500, wilde at mcs.anl.gov wrote:
> To think through this question it helps to define the actors that are
> involved:
> 
> - input mappers, which have the opportunity to do their mapping from a
> replica catalog

Again, I do not believe that mappers should play a role in scheduling
because without other knowledge about sites they would do a poor job at
making decisions about where to run things. And if they made scheduling
decisions, then they would be logically part of the scheduler which
sounds fishy.

> 
> - the site selector in Swift's scheduler, which could factor into its
> criteria where the data needed by an application lives (and perhaps
> where the output must go, or where the user prefers that it go)
> 
> - the Swift execution wrapper _swiftwrap and/or the post-execution
> logic and cache management logic in Swift which can influence whether
> and how long a file stays in the site shared/ cache

Assuming that there is a shared cache. The trend we're seeing with EAGER
is that there is no shared directory any more, which was used solely as
a caching mechanism due to the fact that the client did the staging.




From wilde at mcs.anl.gov  Wed Mar 31 12:25:38 2010
From: wilde at mcs.anl.gov (Michael Wilde)
Date: Wed, 31 Mar 2010 12:25:38 -0500 (CDT)
Subject: [Swift-devel] Re: scheduling
In-Reply-To: <1270052164.16103.10.camel@localhost>
Message-ID: <29813791.487201270056338837.JavaMail.root@zimbra>

Yeah, I agree with you on keeping scheduling decisions out of mappers.

But mappers could/should, I think, still be involved, if only to the extent that the name space they would work on in a replica-based environment would be the logical namespace of some (abstract) replica catalog (which is itself another mapping).

----- "Mihael Hategan" <hategan at mcs.anl.gov> wrote:

> A few comments:
> 
> I think we need to simplify the model here, because it's already hard
> to
> reason about. I think we also need to keep it cohesive. So whether
> information provided by the mappers is used for scheduling, no
> scheduling decisions (logic) should be in mappers.
> 
> On Wed, 2010-03-31 at 07:28 -0500, wilde at mcs.anl.gov wrote:
> > To think through this question it helps to define the actors that
> are
> > involved:
> > 
> > - input mappers, which have the opportunity to do their mapping from
> a
> > replica catalog
> 
> Again, I do not believe that mappers should play a role in scheduling
> because without other knowledge about sites they would do a poor job
> at
> making decisions about where to run things. And if they made
> scheduling
> decisions, then they would be logically part of the scheduler which
> sounds fishy.

This would not be a scheduling decision. By this part I meant that rather than returning physical filenames as a mapping, the mapper would return a logical file name (using the terminology of say the RLS).
> 
> > 
> > - the site selector in Swift's scheduler, which could factor into
> its
> > criteria where the data needed by an application lives (and perhaps
> > where the output must go, or where the user prefers that it go)
> > 
> > - the Swift execution wrapper _swiftwrap and/or the post-execution
> > logic and cache management logic in Swift which can influence
> whether
> > and how long a file stays in the site shared/ cache
> 
> Assuming that there is a shared cache. The trend we're seeing with
> EAGER
> is that there is no shared directory any more, which was used solely
> as
> a caching mechanism due to the fact that the client did the staging.

That makes sense for input data products. Output data products, though, could reasonably be copied from some local work directory to some locally accessible file cache, as well as to any remote file cache. 

There's also cases where neither the input nor output file *fits* into such a local cache. So both CDM (what you called EAGER) and a future replication model may need to address local and/or distributed persistent storage caches.

- Mike

-- 
Michael Wilde
Computation Institute, University of Chicago
Mathematics and Computer Science Division
Argonne National Laboratory



From benc at hawaga.org.uk  Wed Mar 31 12:30:33 2010
From: benc at hawaga.org.uk (Ben Clifford)
Date: Wed, 31 Mar 2010 17:30:33 +0000 (GMT)
Subject: [Swift-devel] Re: scheduling
In-Reply-To: <1270052164.16103.10.camel@localhost>
References: <4745903.473531270038507652.JavaMail.root@zimbra>
	<1270052164.16103.10.camel@localhost>
Message-ID: <Pine.LNX.4.64.1003311639300.25367@dildano.hawaga.org.uk>


> > - the Swift execution wrapper _swiftwrap and/or the post-execution
> > logic and cache management logic in Swift which can influence whether
> > and how long a file stays in the site shared/ cache
> 
> Assuming that there is a shared cache. The trend we're seeing with EAGER
> is that there is no shared directory any more, which was used solely as
> a caching mechanism due to the fact that the client did the staging.

That is the situation in other places where people might want to use Swift 
too, although not ones that have funding to be developed - one is the 
european model of a grid-central resource broker that carries everything 
along in a job submission, and the other is a condor pool running on 
workstations with no shared filesystem. (both of those have been 
prototyped with Swift in the past).

-- 


From hategan at mcs.anl.gov  Wed Mar 31 12:50:00 2010
From: hategan at mcs.anl.gov (Mihael Hategan)
Date: Wed, 31 Mar 2010 12:50:00 -0500
Subject: [Swift-devel] Re: scheduling
In-Reply-To: <29813791.487201270056338837.JavaMail.root@zimbra>
References: <29813791.487201270056338837.JavaMail.root@zimbra>
Message-ID: <1270057800.19795.22.camel@localhost>

On Wed, 2010-03-31 at 12:25 -0500, Michael Wilde wrote:
> Yeah, I agree with you on keeping scheduling decisions out of mappers.
> 
> But mappers could/should, I think, still be involved, if only to the
> extent that the name space they would work on in a replica-based
> environment would be the logical namespace of some (abstract) replica
> catalog (which is itself another mapping).

We've been using something that greatly simplified reasoning about
swift: local consistency (i.e. data in swift is organized as it would be
on a single filesystem; i.e. having swift data on a single machine
always works).

That means that with a data catalog there would be three sets:
1. mapped atomic data (i.e. variables; e.g. a, f[1], etc.)
2. local/logical files (e.g. a.txt, f0001.txt, etc.)
3. grid layer (e.g. (gsiftp://site1/a.txt, gsiftp://site2/a.txt),
(gsiftp://site3/f0001.txt), etc.)

They are isomorphic. That is, for each element in one set there is
exactly one element in the other set:
a <-> a.txt <-> (gsiftp://site1/a.txt, gsiftp://site2/a.txt)

Where 3 has tuples of physical files.

The exact morphisms that go from one to the other are:
1 <-> 2: mappers (i.e. a mapper defines what each mapped swift data
corresponds to in terms of logical files as well as defining what each
file corresponds to in terms of swift data).
2 <-> 3: replica catalog (I'm using that term loosely).

Currently our replica catalog is a special form of the identity mapping
(a.txt <-> (a.txt)).

We need to:
1. extend 2 <-> 3 to be more general (i.e. allow non-singular tuples in
set 3)
2. pass elements from set 3 to the scheduler
3. make the scheduler decide sites based on elements from set 3.

It's slightly more complex in practice because set 2 also allows things
of the form "gsiftp://site/file". But let's ignore that for now.




From hategan at mcs.anl.gov  Wed Mar 31 12:53:23 2010
From: hategan at mcs.anl.gov (Mihael Hategan)
Date: Wed, 31 Mar 2010 12:53:23 -0500
Subject: [Swift-devel] Re: scheduling
In-Reply-To: <Pine.LNX.4.64.1003311639300.25367@dildano.hawaga.org.uk>
References: <4745903.473531270038507652.JavaMail.root@zimbra>
	<1270052164.16103.10.camel@localhost>
	<Pine.LNX.4.64.1003311639300.25367@dildano.hawaga.org.uk>
Message-ID: <1270058003.19795.25.camel@localhost>

On Wed, 2010-03-31 at 17:30 +0000, Ben Clifford wrote:
> > > - the Swift execution wrapper _swiftwrap and/or the post-execution
> > > logic and cache management logic in Swift which can influence whether
> > > and how long a file stays in the site shared/ cache
> > 
> > Assuming that there is a shared cache. The trend we're seeing with EAGER
> > is that there is no shared directory any more, which was used solely as
> > a caching mechanism due to the fact that the client did the staging.
> 
> That is the situation in other places where people might want to use Swift 
> too, although not ones that have funding to be developed - one is the 
> european model of a grid-central resource broker that carries everything 
> along in a job submission, and the other is a condor pool running on 
> workstations with no shared filesystem. (both of those have been 
> prototyped with Swift in the past).
> 

Right. This is also the traditional GRAM model (GRAM does staging). We
avoided that because of the issues with WS-GRAM. However, now that
WS-GRAM is going to be slowly retired and because coasters support
client-to-worker-node staging, it is probably time to move away from
that choice.

It does, however, introduce some additional complications when it comes
to managing resources. As opposed to client-directed staging, where we
could say "initiate no more than 4 concurrent transfers", it's hard to
get a bunch of distributed entities to agree on when to transfer or not.