From bugzilla-daemon at mcs.anl.gov  Mon Dec  3 15:59:35 2007
From: bugzilla-daemon at mcs.anl.gov (bugzilla-daemon at mcs.anl.gov)
Date: Mon,  3 Dec 2007 15:59:35 -0600 (CST)
Subject: [Swift-devel] [Bug 114] need to specify run directory name on
	remote site
In-Reply-To: <bug-114-21@http.bugzilla.mcs.anl.gov/swift/>
Message-ID: <20071203215935.2AAA4164EC@foxtrot.mcs.anl.gov>

http://bugzilla.mcs.anl.gov/swift/show_bug.cgi?id=114


benc at hawaga.org.uk changed:

           What    |Removed                     |Added
----------------------------------------------------------------------------
             Status|NEW                         |RESOLVED
         Resolution|                            |FIXED




------- Comment #1 from benc at hawaga.org.uk  2007-12-03 15:59 -------
r1504 introduces a command-line parameter -runid that allows this to be set.
Caution should be exercised when using this parameter to ensure an appropriate
degree of uniqueness.

>From the commit log:
Added -runid parameter that specifies the run identifier on the command line,
rather than having it automatically generated. This must be unique for every
invocation of a workflow and is used in several places to keep files from
different executions cleanly separated. By default, a datestamp and random
number are used to generate a run identifier. When using this parameter, care
should be taken to ensure that the run ID remains unique with respect to all
other run IDs that might be used, irrespective of (at least) expected run
location, workflow or user.


-- 
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From raffaele.montella at uniparthenope.it  Wed Dec  5 11:40:26 2007
From: raffaele.montella at uniparthenope.it (Dr. Raffaele Montella)
Date: Wed, 5 Dec 2007 11:40:26 -0600
Subject: [Swift-devel] (no subject)
Message-ID: <000301c83765$ebce75a0$c36b60e0$@montella@uniparthenope.it>

Hi!

I'm learning how to configure swift, developing swift workflows and I hope
contribute to the development as soon.

I installed Swift on a machine at CI where I have certificates in order to
execute on two machine at my home University in Naples.

On this two machine is installed GT4.0.5 with the gatekeeper up and running.

I can run jobs from floater-245.ci.uchicago.edu to data.uniparthenope.it
using globus-job-run and perform gridftp operations as here:

 

infonav at floater-245:~/swift$ globus-url-copy
file:////home/infonav/swift/hostname.swift
gsiftp://data.uniparthenope.it//tmp/hostname.swift

infonav at floater-245:~/swift$ globus-url-copy
gsiftp://data.uniparthenope.it//tmp/hostname.swift
file:////tmp/hostname.swift

infonav at floater-245:~/swift$ ls /tmp

VMW  hostname.swift  hsperfdata_globus  hsperfdata_infonav  mc-infonav
swift.log  x509up_u1001

infonav at floater-245:~/swift$ globus-job-run data.uniparthenope.it
/bin/hostname

data.uniparthenope.it

 

I configured my sites.xml in that way:

 

<config>

 

<!-- sites.xml specifies details of the sites that Swift can run on.

 

The first entry entry, for localhost, should work on most linux-like systems

without any change.

 

It may be necessary to change the two occurences of /var/tmp to a different

working directory.

 

-->

 

 

  <pool handle="localhost" sysinfo="INTEL32::LINUX">

    <gridftp  url="local://localhost" storage="/var/tmp" major="1" minor="0"
patch="0" />

    <execution provider="local" url="none" />

    <workdirectory >/var/tmp</workdirectory>

  </pool>

 

  <pool handle="data" sysinfo="INTEL32::LINUX">

    <gridftp  url="gsiftp://data.uniparthenope.it" storage="/tmp" major="2"
minor="2" patch="4">

    </gridftp>

    <jobmanager universe="vanilla"
url="data.uniparthenope.it/jobmanager-fork" major="2" minor="2" patch="4" />

    <workdirectory >/tmp</workdirectory>

  </pool>

 

 

  <pool handle="dgbeobi" sysinfo="INTEL32::LINUX">

    <gridftp  url="gsiftp://dgbeobi.uniparthenope.it" storage="/tmp"
major="2" minor="2" patch="4">

    </gridftp>

    <jobmanager universe="vanilla"
url="dgbeobi.uniparthenope.it/jobmanager-fork" major="2" minor="2" patch="4"
/>

    <workdirectory >/tmp</workdirectory>

  </pool>

</config>

 

And my tc.data as the following:

 

#This is the transformation catalog.

#

#It comes pre-configured with a number of simple transformations with

#paths that are likely to work on a linux box. However, on some systems,

#the paths to these executables will be different (for example, sometimes

#some of these programs are found in /usr/bin rather than in /bin)

#

#NOTE WELL: fields in this file must be separated by tabs, not spaces; and

#there must be no trailing whitespace at the end of each line.

#

# sitename  transformation  path   INSTALLED  platform  profiles

localhost       echo            /bin/echo       INSTALLED
INTEL32::LINUX  null

localhost       cat             /bin/cat        INSTALLED
INTEL32::LINUX  null

localhost       ls              /bin/ls         INSTALLED
INTEL32::LINUX  null

localhost       wc              /bin/wc         INSTALLED
INTEL32::LINUX  null

localhost       grep            /bin/grep       INSTALLED
INTEL32::LINUX  null

localhost       sort            /bin/sort       INSTALLED
INTEL32::LINUX  null

localhost       paste           /bin/paste      INSTALLED
INTEL32::LINUX  null

localhost       terrain /home/infonav/Germana/swift/do_terrain  INSTALLED
INTEL32::LINUX  null

data            hostname        /bin/hostname   INSTALLED
INTEL32::LINUX  null

dgbeobi         date            /bin/date       INSTALLED
INTEL32::LINUX  null

 

Using both the hostname.swift.

 

type file;

 

(file ofile)hostname() {

  app { hostname; }

}

 

file ofile <"hostname.txt">;

 

ofile = hostname();

 

.and date.swift code.

 

type file;

 

(file ofile)date() {

  app { date; }

}

 

file ofile <"date.txt">;

 

ofile = date();

 

I receive the following error in job cleanup:

 

Swift v0.3 r1319 (modified locally)

 

RunID: 20071204-2116-xvhkcj88

hostname started

Failed to clean up job

java.lang.IllegalStateException: No registered callback handler for
org.globus.gsi.gssapi.GlobusGSSCredentialImpl at 11b92ef

        at
org.globus.cog.abstraction.impl.execution.gt2.CallbackHandlerManager.decreas
eUsageCount(CallbackHandlerManager.java:33)

        at
org.globus.cog.abstraction.impl.execution.gt2.JobSubmissionTaskHandler.clean
up(JobSubmissionTaskHandler.java:482)

        at
org.globus.cog.abstraction.impl.execution.gt2.JobSubmissionTaskHandler.statu
sChanged(JobSubmissionTaskHandler.java:475)

        at org.globus.gram.GramJob.setStatus(GramJob.java:184)

        at org.globus.gram.GramCallbackHandler.run(CallbackHandler.java:176)

        at java.lang.Thread.run(Thread.java:619)

Failed to clean up job

java.lang.IllegalStateException: No registered callback handler for
org.globus.gsi.gssapi.GlobusGSSCredentialImpl at 11b92ef

        at
org.globus.cog.abstraction.impl.execution.gt2.CallbackHandlerManager.decreas
eUsageCount(CallbackHandlerManager.java:33)

        at
org.globus.cog.abstraction.impl.execution.gt2.JobSubmissionTaskHandler.clean
up(JobSubmissionTaskHandler.java:482)

        at
org.globus.cog.abstraction.impl.execution.gt2.JobSubmissionTaskHandler.statu
sChanged(JobSubmissionTaskHandler.java:475)

        at org.globus.gram.GramJob.setStatus(GramJob.java:184)

        at org.globus.gram.GramCallbackHandler.run(CallbackHandler.java:176)

        at java.lang.Thread.run(Thread.java:619)

Failed to clean up job

java.lang.IllegalStateException: No registered callback handler for
org.globus.gsi.gssapi.GlobusGSSCredentialImpl at 11b92ef

        at
org.globus.cog.abstraction.impl.execution.gt2.CallbackHandlerManager.decreas
eUsageCount(CallbackHandlerManager.java:33)

        at
org.globus.cog.abstraction.impl.execution.gt2.JobSubmissionTaskHandler.clean
up(JobSubmissionTaskHandler.java:482)

        at
org.globus.cog.abstraction.impl.execution.gt2.JobSubmissionTaskHandler.statu
sChanged(JobSubmissionTaskHandler.java:475)

        at org.globus.gram.GramJob.setStatus(GramJob.java:184)

        at org.globus.gram.GramCallbackHandler.run(CallbackHandler.java:176)

        at java.lang.Thread.run(Thread.java:619)

hostname failed

Execution failed:

        Exception in hostname:

Arguments: []

Host: data

Directory: hostname-20071204-2116-xvhkcj88/hostname-vg2dq1li

stderr.txt:

stdout.txt: data.uniparthenope.it

 

----

 

Caused by:

        The following output files were not created by the application:
hostname.txt

 

What do you think about it?

Do you have some suggestions?

I attached to this mail both files on floater-245 and data.

 

Thank you in advance.

  Raffaele

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From benc at hawaga.org.uk  Wed Dec  5 11:57:49 2007
From: benc at hawaga.org.uk (Ben Clifford)
Date: Wed, 5 Dec 2007 17:57:49 +0000 (GMT)
Subject: [Swift-devel] (no subject)
In-Reply-To: <000301c83765$ebce75a0$c36b60e0$@montella@uniparthenope.it>
References: <000301c83765$ebce75a0$c36b60e0$@montella@uniparthenope.it>
Message-ID: <Pine.LNX.4.64.0712051754230.28498@dildano.hawaga.org.uk>


Two problems - the IllegalStateException exception you see is something 
that I've seen one other person get but have been unable to recreate 
myself. I think Mihael probably also hasn't been able to recreate it.

What machine is floater-245? Is it your own personal machine?

> Failed to clean up job
> 
> java.lang.IllegalStateException: No registered callback handler for
> org.globus.gsi.gssapi.GlobusGSSCredentialImpl at 11b92ef


Also, you have a bug in your SwiftScript program:

> (file ofile)hostname() {
> 
>   app { hostname; }
> 
> }

You need to specify that the output from hostname goes into ofile. For 
example, say:

  (file ofile)hostname() {
    app { hostname stdout=@filename(ofile); }
  }







> 
>         at
> org.globus.cog.abstraction.impl.execution.gt2.CallbackHandlerManager.decreas
> eUsageCount(CallbackHandlerManager.java:33)
> 
>         at
> org.globus.cog.abstraction.impl.execution.gt2.JobSubmissionTaskHandler.clean
> up(JobSubmissionTaskHandler.java:482)
> 
>         at
> org.globus.cog.abstraction.impl.execution.gt2.JobSubmissionTaskHandler.statu
> sChanged(JobSubmissionTaskHandler.java:475)
> 
>         at org.globus.gram.GramJob.setStatus(GramJob.java:184)
> 
>         at org.globus.gram.GramCallbackHandler.run(CallbackHandler.java:176)
> 
>         at java.lang.Thread.run(Thread.java:619)
> 
> Failed to clean up job
> 
> java.lang.IllegalStateException: No registered callback handler for
> org.globus.gsi.gssapi.GlobusGSSCredentialImpl at 11b92ef
> 
>         at
> org.globus.cog.abstraction.impl.execution.gt2.CallbackHandlerManager.decreas
> eUsageCount(CallbackHandlerManager.java:33)
> 
>         at
> org.globus.cog.abstraction.impl.execution.gt2.JobSubmissionTaskHandler.clean
> up(JobSubmissionTaskHandler.java:482)
> 
>         at
> org.globus.cog.abstraction.impl.execution.gt2.JobSubmissionTaskHandler.statu
> sChanged(JobSubmissionTaskHandler.java:475)
> 
>         at org.globus.gram.GramJob.setStatus(GramJob.java:184)
> 
>         at org.globus.gram.GramCallbackHandler.run(CallbackHandler.java:176)
> 
>         at java.lang.Thread.run(Thread.java:619)
> 
> Failed to clean up job
> 
> java.lang.IllegalStateException: No registered callback handler for
> org.globus.gsi.gssapi.GlobusGSSCredentialImpl at 11b92ef
> 
>         at
> org.globus.cog.abstraction.impl.execution.gt2.CallbackHandlerManager.decreas
> eUsageCount(CallbackHandlerManager.java:33)
> 
>         at
> org.globus.cog.abstraction.impl.execution.gt2.JobSubmissionTaskHandler.clean
> up(JobSubmissionTaskHandler.java:482)
> 
>         at
> org.globus.cog.abstraction.impl.execution.gt2.JobSubmissionTaskHandler.statu
> sChanged(JobSubmissionTaskHandler.java:475)
> 
>         at org.globus.gram.GramJob.setStatus(GramJob.java:184)
> 
>         at org.globus.gram.GramCallbackHandler.run(CallbackHandler.java:176)
> 
>         at java.lang.Thread.run(Thread.java:619)
> 
> hostname failed
> 
> Execution failed:
> 
>         Exception in hostname:
> 
> Arguments: []
> 
> Host: data
> 
> Directory: hostname-20071204-2116-xvhkcj88/hostname-vg2dq1li
> 
> stderr.txt:
> 
> stdout.txt: data.uniparthenope.it
> 
>  
> 
> ----
> 
>  
> 
> Caused by:
> 
>         The following output files were not created by the application:
> hostname.txt
> 
>  
> 
> What do you think about it?
> 
> Do you have some suggestions?
> 
> I attached to this mail both files on floater-245 and data.
> 
>  
> 
> Thank you in advance.
> 
>   Raffaele
> 
> 


From foster at mcs.anl.gov  Wed Dec  5 12:03:17 2007
From: foster at mcs.anl.gov (Ian Foster)
Date: Wed, 05 Dec 2007 12:03:17 -0600
Subject: [Swift-devel] (no subject)
In-Reply-To: <Pine.LNX.4.64.0712051754230.28498@dildano.hawaga.org.uk>
References: <000301c83765$ebce75a0$c36b60e0$@montella@uniparthenope.it>
	<Pine.LNX.4.64.0712051754230.28498@dildano.hawaga.org.uk>
Message-ID: <4756E7E5.8080100@mcs.anl.gov>


should/could we generate warnings for such things?
>
> Also, you have a bug in your SwiftScript program:
>
>   
>> (file ofile)hostname() {
>>
>>   app { hostname; }
>>
>> }
>>     
>
> You need to specify that the output from hostname goes into ofile. For 
> example, say:
>
>   (file ofile)hostname() {
>     app { hostname stdout=@filename(ofile); }
>   }
>
>
>
>
>
>
>
>   
>>         at
>> org.globus.cog.abstraction.impl.execution.gt2.CallbackHandlerManager.decreas
>> eUsageCount(CallbackHandlerManager.java:33)
>>
>>         at
>> org.globus.cog.abstraction.impl.execution.gt2.JobSubmissionTaskHandler.clean
>> up(JobSubmissionTaskHandler.java:482)
>>
>>         at
>> org.globus.cog.abstraction.impl.execution.gt2.JobSubmissionTaskHandler.statu
>> sChanged(JobSubmissionTaskHandler.java:475)
>>
>>         at org.globus.gram.GramJob.setStatus(GramJob.java:184)
>>
>>         at org.globus.gram.GramCallbackHandler.run(CallbackHandler.java:176)
>>
>>         at java.lang.Thread.run(Thread.java:619)
>>
>> Failed to clean up job
>>
>> java.lang.IllegalStateException: No registered callback handler for
>> org.globus.gsi.gssapi.GlobusGSSCredentialImpl at 11b92ef
>>
>>         at
>> org.globus.cog.abstraction.impl.execution.gt2.CallbackHandlerManager.decreas
>> eUsageCount(CallbackHandlerManager.java:33)
>>
>>         at
>> org.globus.cog.abstraction.impl.execution.gt2.JobSubmissionTaskHandler.clean
>> up(JobSubmissionTaskHandler.java:482)
>>
>>         at
>> org.globus.cog.abstraction.impl.execution.gt2.JobSubmissionTaskHandler.statu
>> sChanged(JobSubmissionTaskHandler.java:475)
>>
>>         at org.globus.gram.GramJob.setStatus(GramJob.java:184)
>>
>>         at org.globus.gram.GramCallbackHandler.run(CallbackHandler.java:176)
>>
>>         at java.lang.Thread.run(Thread.java:619)
>>
>> Failed to clean up job
>>
>> java.lang.IllegalStateException: No registered callback handler for
>> org.globus.gsi.gssapi.GlobusGSSCredentialImpl at 11b92ef
>>
>>         at
>> org.globus.cog.abstraction.impl.execution.gt2.CallbackHandlerManager.decreas
>> eUsageCount(CallbackHandlerManager.java:33)
>>
>>         at
>> org.globus.cog.abstraction.impl.execution.gt2.JobSubmissionTaskHandler.clean
>> up(JobSubmissionTaskHandler.java:482)
>>
>>         at
>> org.globus.cog.abstraction.impl.execution.gt2.JobSubmissionTaskHandler.statu
>> sChanged(JobSubmissionTaskHandler.java:475)
>>
>>         at org.globus.gram.GramJob.setStatus(GramJob.java:184)
>>
>>         at org.globus.gram.GramCallbackHandler.run(CallbackHandler.java:176)
>>
>>         at java.lang.Thread.run(Thread.java:619)
>>
>> hostname failed
>>
>> Execution failed:
>>
>>         Exception in hostname:
>>
>> Arguments: []
>>
>> Host: data
>>
>> Directory: hostname-20071204-2116-xvhkcj88/hostname-vg2dq1li
>>
>> stderr.txt:
>>
>> stdout.txt: data.uniparthenope.it
>>
>>  
>>
>> ----
>>
>>  
>>
>> Caused by:
>>
>>         The following output files were not created by the application:
>> hostname.txt
>>
>>  
>>
>> What do you think about it?
>>
>> Do you have some suggestions?
>>
>> I attached to this mail both files on floater-245 and data.
>>
>>  
>>
>> Thank you in advance.
>>
>>   Raffaele
>>
>>
>>     
> _______________________________________________
> Swift-devel mailing list
> Swift-devel at ci.uchicago.edu
> http://mail.ci.uchicago.edu/mailman/listinfo/swift-devel
>
>   
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From wilde at mcs.anl.gov  Wed Dec  5 12:25:40 2007
From: wilde at mcs.anl.gov (Michael Wilde)
Date: Wed, 05 Dec 2007 12:25:40 -0600
Subject: [Swift-devel] (no subject)
In-Reply-To: <000301c83765$ebce75a0$c36b60e0$@montella@uniparthenope.it>
References: <000301c83765$ebce75a0$c36b60e0$@montella@uniparthenope.it>
Message-ID: <4756ED24.7070709@mcs.anl.gov>

Im in Raphaele's office working this problem out with him.

The gssapi error is what we've seen before - 0.3 running on Java 1.5.
Raphaele is now building trunk which should work.  We should post 
something on this or put out an 0.4, perhaps?

The other error was the fact that he needed to designate stdout and map 
the filename in hist hostname() function. I showed him the example for this.

- Mike




On 12/5/07 11:40 AM, Dr. Raffaele Montella wrote:
> Hi!
> 
> I'm learning how to configure swift, developing swift workflows and I hope
> contribute to the development as soon.
> 
> I installed Swift on a machine at CI where I have certificates in order to
> execute on two machine at my home University in Naples.
> 
> On this two machine is installed GT4.0.5 with the gatekeeper up and running.
> 
> I can run jobs from floater-245.ci.uchicago.edu to data.uniparthenope.it
> using globus-job-run and perform gridftp operations as here:
> 
>  
> 
> infonav at floater-245:~/swift$ globus-url-copy
> file:////home/infonav/swift/hostname.swift
> gsiftp://data.uniparthenope.it//tmp/hostname.swift
> 
> infonav at floater-245:~/swift$ globus-url-copy
> gsiftp://data.uniparthenope.it//tmp/hostname.swift
> file:////tmp/hostname.swift
> 
> infonav at floater-245:~/swift$ ls /tmp
> 
> VMW  hostname.swift  hsperfdata_globus  hsperfdata_infonav  mc-infonav
> swift.log  x509up_u1001
> 
> infonav at floater-245:~/swift$ globus-job-run data.uniparthenope.it
> /bin/hostname
> 
> data.uniparthenope.it
> 
>  
> 
> I configured my sites.xml in that way:
> 
>  
> 
> <config>
> 
>  
> 
> <!-- sites.xml specifies details of the sites that Swift can run on.
> 
>  
> 
> The first entry entry, for localhost, should work on most linux-like systems
> 
> without any change.
> 
>  
> 
> It may be necessary to change the two occurences of /var/tmp to a different
> 
> working directory.
> 
>  
> 
> -->
> 
>  
> 
>  
> 
>   <pool handle="localhost" sysinfo="INTEL32::LINUX">
> 
>     <gridftp  url="local://localhost" storage="/var/tmp" major="1" minor="0"
> patch="0" />
> 
>     <execution provider="local" url="none" />
> 
>     <workdirectory >/var/tmp</workdirectory>
> 
>   </pool>
> 
>  
> 
>   <pool handle="data" sysinfo="INTEL32::LINUX">
> 
>     <gridftp  url="gsiftp://data.uniparthenope.it" storage="/tmp" major="2"
> minor="2" patch="4">
> 
>     </gridftp>
> 
>     <jobmanager universe="vanilla"
> url="data.uniparthenope.it/jobmanager-fork" major="2" minor="2" patch="4" />
> 
>     <workdirectory >/tmp</workdirectory>
> 
>   </pool>
> 
>  
> 
>  
> 
>   <pool handle="dgbeobi" sysinfo="INTEL32::LINUX">
> 
>     <gridftp  url="gsiftp://dgbeobi.uniparthenope.it" storage="/tmp"
> major="2" minor="2" patch="4">
> 
>     </gridftp>
> 
>     <jobmanager universe="vanilla"
> url="dgbeobi.uniparthenope.it/jobmanager-fork" major="2" minor="2" patch="4"
> />
> 
>     <workdirectory >/tmp</workdirectory>
> 
>   </pool>
> 
> </config>
> 
>  
> 
> And my tc.data as the following:
> 
>  
> 
> #This is the transformation catalog.
> 
> #
> 
> #It comes pre-configured with a number of simple transformations with
> 
> #paths that are likely to work on a linux box. However, on some systems,
> 
> #the paths to these executables will be different (for example, sometimes
> 
> #some of these programs are found in /usr/bin rather than in /bin)
> 
> #
> 
> #NOTE WELL: fields in this file must be separated by tabs, not spaces; and
> 
> #there must be no trailing whitespace at the end of each line.
> 
> #
> 
> # sitename  transformation  path   INSTALLED  platform  profiles
> 
> localhost       echo            /bin/echo       INSTALLED
> INTEL32::LINUX  null
> 
> localhost       cat             /bin/cat        INSTALLED
> INTEL32::LINUX  null
> 
> localhost       ls              /bin/ls         INSTALLED
> INTEL32::LINUX  null
> 
> localhost       wc              /bin/wc         INSTALLED
> INTEL32::LINUX  null
> 
> localhost       grep            /bin/grep       INSTALLED
> INTEL32::LINUX  null
> 
> localhost       sort            /bin/sort       INSTALLED
> INTEL32::LINUX  null
> 
> localhost       paste           /bin/paste      INSTALLED
> INTEL32::LINUX  null
> 
> localhost       terrain /home/infonav/Germana/swift/do_terrain  INSTALLED
> INTEL32::LINUX  null
> 
> data            hostname        /bin/hostname   INSTALLED
> INTEL32::LINUX  null
> 
> dgbeobi         date            /bin/date       INSTALLED
> INTEL32::LINUX  null
> 
>  
> 
> Using both the hostname.swift.
> 
>  
> 
> type file;
> 
>  
> 
> (file ofile)hostname() {
> 
>   app { hostname; }
> 
> }
> 
>  
> 
> file ofile <"hostname.txt">;
> 
>  
> 
> ofile = hostname();
> 
>  
> 
> .and date.swift code.
> 
>  
> 
> type file;
> 
>  
> 
> (file ofile)date() {
> 
>   app { date; }
> 
> }
> 
>  
> 
> file ofile <"date.txt">;
> 
>  
> 
> ofile = date();
> 
>  
> 
> I receive the following error in job cleanup:
> 
>  
> 
> Swift v0.3 r1319 (modified locally)
> 
>  
> 
> RunID: 20071204-2116-xvhkcj88
> 
> hostname started
> 
> Failed to clean up job
> 
> java.lang.IllegalStateException: No registered callback handler for
> org.globus.gsi.gssapi.GlobusGSSCredentialImpl at 11b92ef
> 
>         at
> org.globus.cog.abstraction.impl.execution.gt2.CallbackHandlerManager.decreas
> eUsageCount(CallbackHandlerManager.java:33)
> 
>         at
> org.globus.cog.abstraction.impl.execution.gt2.JobSubmissionTaskHandler.clean
> up(JobSubmissionTaskHandler.java:482)
> 
>         at
> org.globus.cog.abstraction.impl.execution.gt2.JobSubmissionTaskHandler.statu
> sChanged(JobSubmissionTaskHandler.java:475)
> 
>         at org.globus.gram.GramJob.setStatus(GramJob.java:184)
> 
>         at org.globus.gram.GramCallbackHandler.run(CallbackHandler.java:176)
> 
>         at java.lang.Thread.run(Thread.java:619)
> 
> Failed to clean up job
> 
> java.lang.IllegalStateException: No registered callback handler for
> org.globus.gsi.gssapi.GlobusGSSCredentialImpl at 11b92ef
> 
>         at
> org.globus.cog.abstraction.impl.execution.gt2.CallbackHandlerManager.decreas
> eUsageCount(CallbackHandlerManager.java:33)
> 
>         at
> org.globus.cog.abstraction.impl.execution.gt2.JobSubmissionTaskHandler.clean
> up(JobSubmissionTaskHandler.java:482)
> 
>         at
> org.globus.cog.abstraction.impl.execution.gt2.JobSubmissionTaskHandler.statu
> sChanged(JobSubmissionTaskHandler.java:475)
> 
>         at org.globus.gram.GramJob.setStatus(GramJob.java:184)
> 
>         at org.globus.gram.GramCallbackHandler.run(CallbackHandler.java:176)
> 
>         at java.lang.Thread.run(Thread.java:619)
> 
> Failed to clean up job
> 
> java.lang.IllegalStateException: No registered callback handler for
> org.globus.gsi.gssapi.GlobusGSSCredentialImpl at 11b92ef
> 
>         at
> org.globus.cog.abstraction.impl.execution.gt2.CallbackHandlerManager.decreas
> eUsageCount(CallbackHandlerManager.java:33)
> 
>         at
> org.globus.cog.abstraction.impl.execution.gt2.JobSubmissionTaskHandler.clean
> up(JobSubmissionTaskHandler.java:482)
> 
>         at
> org.globus.cog.abstraction.impl.execution.gt2.JobSubmissionTaskHandler.statu
> sChanged(JobSubmissionTaskHandler.java:475)
> 
>         at org.globus.gram.GramJob.setStatus(GramJob.java:184)
> 
>         at org.globus.gram.GramCallbackHandler.run(CallbackHandler.java:176)
> 
>         at java.lang.Thread.run(Thread.java:619)
> 
> hostname failed
> 
> Execution failed:
> 
>         Exception in hostname:
> 
> Arguments: []
> 
> Host: data
> 
> Directory: hostname-20071204-2116-xvhkcj88/hostname-vg2dq1li
> 
> stderr.txt:
> 
> stdout.txt: data.uniparthenope.it
> 
>  
> 
> ----
> 
>  
> 
> Caused by:
> 
>         The following output files were not created by the application:
> hostname.txt
> 
>  
> 
> What do you think about it?
> 
> Do you have some suggestions?
> 
> I attached to this mail both files on floater-245 and data.
> 
>  
> 
> Thank you in advance.
> 
>   Raffaele
> 
> 
> 
> 
> ------------------------------------------------------------------------
> 
> _______________________________________________
> Swift-devel mailing list
> Swift-devel at ci.uchicago.edu
> http://mail.ci.uchicago.edu/mailman/listinfo/swift-devel


From mikekubal at yahoo.com  Wed Dec  5 12:39:07 2007
From: mikekubal at yahoo.com (Mike Kubal)
Date: Wed, 5 Dec 2007 10:39:07 -0800 (PST)
Subject: [Swift-devel] parameter not supported error message
Message-ID: <58122.23201.qm@web52304.mail.re2.yahoo.com>

When Swift returns  the following, to what parameter
is it referring?

run_fred failed
The following errors have occurred:
1. Application "run_fred" failed (Parameter not
supported)
        Arguments: "-rec 1beh.oeb.gz -dbase
Marsha_lig_1.mol2 -prefix Marsha_lig_1"
        Host: Lear
        Directory:
run_fred-3l1v4yauk3pz0/run_fred-98r673li
        STDERR: 
        STDOUT:

Thanks,

Mike


      ____________________________________________________________________________________
Never miss a thing.  Make Yahoo your home page. 
http://www.yahoo.com/r/hs


From raffaele.montella at uniparthenope.it  Wed Dec  5 14:25:10 2007
From: raffaele.montella at uniparthenope.it (Dr. Raffaele Montella)
Date: Wed, 5 Dec 2007 14:25:10 -0600
Subject: [Swift-devel] Testing Swift using machine at UoNaplesParthenope
	(aka uniParthenope)
Message-ID: <002101c8377c$ef3242a0$cd96c7e0$@montella@uniparthenope.it>

Hi,

I thank you because the suggestions in solving some problems about using
Swift.

Attached to this email the CA certificate could be installed in order to
submit jobs to the grid at University of Naples Parthenope.

Actually because we moved from one building to another we have just 1 server
and 1 cluster, but when we come back in production we can share more than
100 cpus.

 

This is the pool setup tested with swift.

 

<pool handle="data">

    <gridftp  url="gsiftp://data.uniparthenope.it" />

    <execution provider="gt2" url="data.uniparthenope.it/jobmanager-fork" />

    <workdirectory >/tmp</workdirectory>

  </pool>

 

  <pool handle="dgbeobi">

    <gridftp  url="gsiftp://dgbeobi.uniparthenope.it" />

    <execution provider="gt2" url="dgbeobi.uniparthenope.it/jobmanager-fork"
/>

    <workdirectory >/tmp</workdirectory>

  </pool>

 

  <pool handle="dgbeobiGT4">

    <gridftp  url="gsiftp://dgbeobi.uniparthenope.it" />

    <execution provider="gt4" url="https://dgbeobi.uniparthenope.it:8443" />

    <workdirectory >/tmp</workdirectory>

  </pool>

 

Dgbeobi is the cluster, data is a server.

Both machines are installed with GT4.0.5 and gatekeeper for GT2
compatibility. I tested successfully Swift with the GT2 provider, but I
don't know how to setup the url (or any other parameters) in order to use
the execution service. May you suggest me how to?

 

Feel free to use machines at uniPathenope as you wish. I'm happy about it.

Raffaele

 

  PS: All machines in our grid use GT4 and Torque/PBS as local scheduler.
Actually on this machine PBS is not yet configured.

I'll update you on new machines availability.

 

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From mikekubal at yahoo.com  Wed Dec  5 14:56:52 2007
From: mikekubal at yahoo.com (Mike Kubal)
Date: Wed, 5 Dec 2007 12:56:52 -0800 (PST)
Subject: [Swift-devel] script that returns bad parameter error
Message-ID: <753687.67764.qm@web52301.mail.re2.yahoo.com>

Any thoughts on what might cause? 

type file {}

(file score, file docked) run_fred (string
ligand_prefix, file ligand_file, file receptor_file){
        app {
             run_fred "-rec" receptor_file "-dbase"
ligand_file "-prefix" ligand_prefix;
        }
}


string receptor_prefix = "1beh";

file receptor_file
<single_file_mapper;file=@strcat(receptor_prefix,".oeb.gz")>;

file
fls[]<filesys_mapper;pattern="Marsha_lig_*.mol2",location=".">;

foreach ligand_file in fls{

        string ligand_prefix =
@strcut(@ligand_file,"\.\/(.*)\.mol2");
        string score_file_name =
@strcat(ligand_prefix,"_chemgauss3_scores.txt");
        string docked_file_name =
@strcat(ligand_prefix,"_chemgauss3_docked.mol2");
        file score_file
<single_file_mapper;file=@strcat(ligand_prefix,"_chemgauss3_scores.txt")>;
        file docked_file
<single_file_mapper;file=@strcat(ligand_prefix,"_chemgauss3_docked.mol2")>;

        (score_file,docked_file) =
run_fred(ligand_prefix,ligand_file,receptor_file);

}


Thanks,

Mike Kubal


      ____________________________________________________________________________________
Never miss a thing.  Make Yahoo your home page. 
http://www.yahoo.com/r/hs


From hategan at mcs.anl.gov  Wed Dec  5 15:16:51 2007
From: hategan at mcs.anl.gov (Mihael Hategan)
Date: Wed, 05 Dec 2007 15:16:51 -0600
Subject: [Swift-devel] parameter not supported error message
In-Reply-To: <58122.23201.qm@web52304.mail.re2.yahoo.com>
References: <58122.23201.qm@web52304.mail.re2.yahoo.com>
Message-ID: <1196889411.3978.5.camel@blabla.mcs.anl.gov>

You probably have something in the sites file that upsets GRAM. Can you
post that?

On Wed, 2007-12-05 at 10:39 -0800, Mike Kubal wrote:
> When Swift returns  the following, to what parameter
> is it referring?
> 
> run_fred failed
> The following errors have occurred:
> 1. Application "run_fred" failed (Parameter not
> supported)
>         Arguments: "-rec 1beh.oeb.gz -dbase
> Marsha_lig_1.mol2 -prefix Marsha_lig_1"
>         Host: Lear
>         Directory:
> run_fred-3l1v4yauk3pz0/run_fred-98r673li
>         STDERR: 
>         STDOUT:
> 
> Thanks,
> 
> Mike
> 
> 
>       ____________________________________________________________________________________
> Never miss a thing.  Make Yahoo your home page. 
> http://www.yahoo.com/r/hs
> _______________________________________________
> 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  Wed Dec  5 15:59:21 2007
From: benc at hawaga.org.uk (Ben Clifford)
Date: Wed, 5 Dec 2007 21:59:21 +0000 (GMT)
Subject: [Swift-devel] script that returns bad parameter error
In-Reply-To: <753687.67764.qm@web52301.mail.re2.yahoo.com>
References: <753687.67764.qm@web52301.mail.re2.yahoo.com>
Message-ID: <Pine.LNX.4.64.0712052157470.28498@dildano.hawaga.org.uk>



On Wed, 5 Dec 2007, Mike Kubal wrote:

>              run_fred "-rec" receptor_file "-dbase"
> ligand_file "-prefix" ligand_prefix;

In here, take the filenames of each file by saying 
@filenmame(receptor_file), like this:

>             run_fred "-rec" @filename(receptor_file) "-dbase"
> @filename(ligand_file) "-prefix" ligand_prefix;

-- 


From benc at hawaga.org.uk  Wed Dec  5 16:04:15 2007
From: benc at hawaga.org.uk (Ben Clifford)
Date: Wed, 5 Dec 2007 22:04:15 +0000 (GMT)
Subject: [Swift-devel] (no subject)
In-Reply-To: <4756ED24.7070709@mcs.anl.gov>
References: <000301c83765$ebce75a0$c36b60e0$@montella@uniparthenope.it>
	<4756ED24.7070709@mcs.anl.gov>
Message-ID: <Pine.LNX.4.64.0712052201020.28498@dildano.hawaga.org.uk>



On Wed, 5 Dec 2007, Michael Wilde wrote:

> The gssapi error is what we've seen before - 0.3 running on Java 1.5.
> Raphaele is now building trunk which should work.  We should post something on
> this or put out an 0.4, perhaps?

If a new release will make it better, then it would not be too bad to have 
a 0.4 in the next week or so. I'd like to figure out whether that helps or 
not though (for example, if I build it on my system, will it still break 
for others?). For that, better testing of the release candidate (when it 
appears) should probably happen by people other than me.

-- 


From benc at hawaga.org.uk  Wed Dec  5 16:09:20 2007
From: benc at hawaga.org.uk (Ben Clifford)
Date: Wed, 5 Dec 2007 22:09:20 +0000 (GMT)
Subject: [Swift-devel] (no subject)
In-Reply-To: <4756E7E5.8080100@mcs.anl.gov>
References: <000301c83765$ebce75a0$c36b60e0$@montella@uniparthenope.it>
	<Pine.LNX.4.64.0712051754230.28498@dildano.hawaga.org.uk>
	<4756E7E5.8080100@mcs.anl.gov>
Message-ID: <Pine.LNX.4.64.0712052207330.23250@dildano.hawaga.org.uk>



On Wed, 5 Dec 2007, Ian Foster wrote:

> should/could we generate warnings for such things?

I've been working on better compile-time type checking. There is probably 
more stuff that could happen there in this situation.
 
-- 


From foster at mcs.anl.gov  Wed Dec  5 16:14:47 2007
From: foster at mcs.anl.gov (Ian Foster)
Date: Wed, 05 Dec 2007 16:14:47 -0600
Subject: [Swift-devel] (no subject)
In-Reply-To: <Pine.LNX.4.64.0712052207330.23250@dildano.hawaga.org.uk>
References: <000301c83765$ebce75a0$c36b60e0$@montella@uniparthenope.it>
	<Pine.LNX.4.64.0712051754230.28498@dildano.hawaga.org.uk>
	<4756E7E5.8080100@mcs.anl.gov>
	<Pine.LNX.4.64.0712052207330.23250@dildano.hawaga.org.uk>
Message-ID: <475722D7.103@mcs.anl.gov>

It seemed to me that this example is a case of "variable that is never 
assigned" -- that could perhaps be detected.

Ben Clifford wrote:
> 
> On Wed, 5 Dec 2007, Ian Foster wrote:
> 
>> should/could we generate warnings for such things?
> 
> I've been working on better compile-time type checking. There is probably 
> more stuff that could happen there in this situation.
>  


From benc at hawaga.org.uk  Wed Dec  5 16:27:49 2007
From: benc at hawaga.org.uk (Ben Clifford)
Date: Wed, 5 Dec 2007 22:27:49 +0000 (GMT)
Subject: [Swift-devel] (no subject)
In-Reply-To: <475722D7.103@mcs.anl.gov>
References: <000301c83765$ebce75a0$c36b60e0$@montella@uniparthenope.it>
	<Pine.LNX.4.64.0712051754230.28498@dildano.hawaga.org.uk>
	<4756E7E5.8080100@mcs.anl.gov>
	<Pine.LNX.4.64.0712052207330.23250@dildano.hawaga.org.uk>
	<475722D7.103@mcs.anl.gov>
Message-ID: <Pine.LNX.4.64.0712052220130.23250@dildano.hawaga.org.uk>



On Wed, 5 Dec 2007, Ian Foster wrote:

> It seemed to me that this example is a case of "variable that is never
> assigned" -- that could perhaps be detected.

There are some application invocations at the moment that don't explicitly 
indicate file outputs, though.

For example, some of the fmri apps output a .hdr file and a .img file with 
the same base name and take only a .hdr filename as command-line parameter 
- its 'good' behaviour that an output parameter isn't explicitly 
mentioned.

There's a bunch of stuff that could be done to the application description 
constructs in SwiftScript. However, as it is so far work-aroundable (as 
in, fix the bug in your swiftscript), its automatically deprioritised.

-- 


From mikekubal at yahoo.com  Wed Dec  5 16:33:41 2007
From: mikekubal at yahoo.com (Mike Kubal)
Date: Wed, 5 Dec 2007 14:33:41 -0800 (PST)
Subject: [Swift-devel] script that returns bad parameter error
In-Reply-To: <Pine.LNX.4.64.0712052157470.28498@dildano.hawaga.org.uk>
Message-ID: <488755.34200.qm@web52304.mail.re2.yahoo.com>

Unfortunately I still get the same error:

run_fred failed
The following errors have occurred:
1. Application "run_fred" failed (Parameter not
supported)
        Arguments: "-rec, 1beh.oeb.gz, -dbase,
Marsha_lig_1.mol2, -prefix, Marsha_lig_1"
        Host: Lear
        Directory:
run_fred-2k0629rvbffz0/run_fred-r81pg3li
        STDERR: 
        STDOUT:

Does 'Parameter not supported' usually refer to an
argument of the remote application? I wonder if it
does not like the .oeb.gz file?



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

> 
> 
> On Wed, 5 Dec 2007, Mike Kubal wrote:
> 
> >              run_fred "-rec" receptor_file
> "-dbase"
> > ligand_file "-prefix" ligand_prefix;
> 
> In here, take the filenames of each file by saying 
> @filenmame(receptor_file), like this:
> 
> >             run_fred "-rec"
> @filename(receptor_file) "-dbase"
> > @filename(ligand_file) "-prefix" ligand_prefix;
> 
> -- 
> _______________________________________________
> Swift-devel mailing list
> Swift-devel at ci.uchicago.edu
>
http://mail.ci.uchicago.edu/mailman/listinfo/swift-devel
> 
> 



      ____________________________________________________________________________________
Be a better friend, newshound, and 
know-it-all with Yahoo! Mobile.  Try it now.  http://mobile.yahoo.com/;_ylt=Ahu06i62sR8HDtDypao8Wcj9tAcJ 



From foster at mcs.anl.gov  Wed Dec  5 16:41:35 2007
From: foster at mcs.anl.gov (Ian Foster)
Date: Wed, 05 Dec 2007 16:41:35 -0600
Subject: [Swift-devel] (no subject)
In-Reply-To: <Pine.LNX.4.64.0712052220130.23250@dildano.hawaga.org.uk>
References: <000301c83765$ebce75a0$c36b60e0$@montella@uniparthenope.it>
	<Pine.LNX.4.64.0712051754230.28498@dildano.hawaga.org.uk>
	<4756E7E5.8080100@mcs.anl.gov>
	<Pine.LNX.4.64.0712052207330.23250@dildano.hawaga.org.uk>
	<475722D7.103@mcs.anl.gov>
	<Pine.LNX.4.64.0712052220130.23250@dildano.hawaga.org.uk>
Message-ID: <4757291F.4030307@mcs.anl.gov>

makes sense!

Ben Clifford wrote:
> 
> On Wed, 5 Dec 2007, Ian Foster wrote:
> 
>> It seemed to me that this example is a case of "variable that is never
>> assigned" -- that could perhaps be detected.
> 
> There are some application invocations at the moment that don't explicitly 
> indicate file outputs, though.
> 
> For example, some of the fmri apps output a .hdr file and a .img file with 
> the same base name and take only a .hdr filename as command-line parameter 
> - its 'good' behaviour that an output parameter isn't explicitly 
> mentioned.
> 
> There's a bunch of stuff that could be done to the application description 
> constructs in SwiftScript. However, as it is so far work-aroundable (as 
> in, fix the bug in your swiftscript), its automatically deprioritised.
> 


From hategan at mcs.anl.gov  Wed Dec  5 16:45:01 2007
From: hategan at mcs.anl.gov (Mihael Hategan)
Date: Wed, 05 Dec 2007 16:45:01 -0600
Subject: [Swift-devel] script that returns bad parameter error
In-Reply-To: <488755.34200.qm@web52304.mail.re2.yahoo.com>
References: <488755.34200.qm@web52304.mail.re2.yahoo.com>
Message-ID: <1196894701.6069.0.camel@blabla.mcs.anl.gov>

Post the sites file.

On Wed, 2007-12-05 at 14:33 -0800, Mike Kubal wrote:
> Unfortunately I still get the same error:
> 
> run_fred failed
> The following errors have occurred:
> 1. Application "run_fred" failed (Parameter not
> supported)
>         Arguments: "-rec, 1beh.oeb.gz, -dbase,
> Marsha_lig_1.mol2, -prefix, Marsha_lig_1"
>         Host: Lear
>         Directory:
> run_fred-2k0629rvbffz0/run_fred-r81pg3li
>         STDERR: 
>         STDOUT:
> 
> Does 'Parameter not supported' usually refer to an
> argument of the remote application? I wonder if it
> does not like the .oeb.gz file?
> 
> 
> 
> --- Ben Clifford <benc at hawaga.org.uk> wrote:
> 
> > 
> > 
> > On Wed, 5 Dec 2007, Mike Kubal wrote:
> > 
> > >              run_fred "-rec" receptor_file
> > "-dbase"
> > > ligand_file "-prefix" ligand_prefix;
> > 
> > In here, take the filenames of each file by saying 
> > @filenmame(receptor_file), like this:
> > 
> > >             run_fred "-rec"
> > @filename(receptor_file) "-dbase"
> > > @filename(ligand_file) "-prefix" ligand_prefix;
> > 
> > -- 
> > _______________________________________________
> > Swift-devel mailing list
> > Swift-devel at ci.uchicago.edu
> >
> http://mail.ci.uchicago.edu/mailman/listinfo/swift-devel
> > 
> > 
> 
> 
> 
>       ____________________________________________________________________________________
> Be a better friend, newshound, and 
> know-it-all with Yahoo! Mobile.  Try it now.  http://mobile.yahoo.com/;_ylt=Ahu06i62sR8HDtDypao8Wcj9tAcJ 
> 
> _______________________________________________
> 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 Dec  5 17:42:28 2007
From: wilde at mcs.anl.gov (Michael Wilde)
Date: Wed, 05 Dec 2007 17:42:28 -0600
Subject: [Swift-devel] script that returns bad parameter error
In-Reply-To: <1196894701.6069.0.camel@blabla.mcs.anl.gov>
References: <488755.34200.qm@web52304.mail.re2.yahoo.com>
	<1196894701.6069.0.camel@blabla.mcs.anl.gov>
Message-ID: <47573764.2010009@mcs.anl.gov>

Mike,

Mihael suspects that a bad globus parameter in your sites.xml file is 
causing this error message.  So please send that so we can take a look.

Thanks,

MikeW

On 12/5/07 4:45 PM, Mihael Hategan wrote:
> Post the sites file.
> 
> On Wed, 2007-12-05 at 14:33 -0800, Mike Kubal wrote:
>> Unfortunately I still get the same error:
>>
>> run_fred failed
>> The following errors have occurred:
>> 1. Application "run_fred" failed (Parameter not
>> supported)
>>         Arguments: "-rec, 1beh.oeb.gz, -dbase,
>> Marsha_lig_1.mol2, -prefix, Marsha_lig_1"
>>         Host: Lear
>>         Directory:
>> run_fred-2k0629rvbffz0/run_fred-r81pg3li
>>         STDERR: 
>>         STDOUT:
>>
>> Does 'Parameter not supported' usually refer to an
>> argument of the remote application? I wonder if it
>> does not like the .oeb.gz file?
>>
>>
>>
>> --- Ben Clifford <benc at hawaga.org.uk> wrote:
>>
>>>
>>> On Wed, 5 Dec 2007, Mike Kubal wrote:
>>>
>>>>              run_fred "-rec" receptor_file
>>> "-dbase"
>>>> ligand_file "-prefix" ligand_prefix;
>>> In here, take the filenames of each file by saying 
>>> @filenmame(receptor_file), like this:
>>>
>>>>             run_fred "-rec"
>>> @filename(receptor_file) "-dbase"
>>>> @filename(ligand_file) "-prefix" ligand_prefix;
>>> -- 
>>> _______________________________________________
>>> Swift-devel mailing list
>>> Swift-devel at ci.uchicago.edu
>>>
>> http://mail.ci.uchicago.edu/mailman/listinfo/swift-devel
>>>
>>
>>
>>       ____________________________________________________________________________________
>> Be a better friend, newshound, and 
>> know-it-all with Yahoo! Mobile.  Try it now.  http://mobile.yahoo.com/;_ylt=Ahu06i62sR8HDtDypao8Wcj9tAcJ 
>>
>> _______________________________________________
>> 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 hategan at mcs.anl.gov  Wed Dec  5 17:45:42 2007
From: hategan at mcs.anl.gov (Mihael Hategan)
Date: Wed, 05 Dec 2007 17:45:42 -0600
Subject: [Swift-devel] script that returns bad parameter error
In-Reply-To: <47573764.2010009@mcs.anl.gov>
References: <488755.34200.qm@web52304.mail.re2.yahoo.com>
	<1196894701.6069.0.camel@blabla.mcs.anl.gov>
	<47573764.2010009@mcs.anl.gov>
Message-ID: <1196898342.7620.0.camel@blabla.mcs.anl.gov>

Sorry. My email wasn't very friendly. I was trying to type less :)

On Wed, 2007-12-05 at 17:42 -0600, Michael Wilde wrote:
> Mike,
> 
> Mihael suspects that a bad globus parameter in your sites.xml file is 
> causing this error message.  So please send that so we can take a look.
> 
> Thanks,
> 
> MikeW
> 
> On 12/5/07 4:45 PM, Mihael Hategan wrote:
> > Post the sites file.
> > 
> > On Wed, 2007-12-05 at 14:33 -0800, Mike Kubal wrote:
> >> Unfortunately I still get the same error:
> >>
> >> run_fred failed
> >> The following errors have occurred:
> >> 1. Application "run_fred" failed (Parameter not
> >> supported)
> >>         Arguments: "-rec, 1beh.oeb.gz, -dbase,
> >> Marsha_lig_1.mol2, -prefix, Marsha_lig_1"
> >>         Host: Lear
> >>         Directory:
> >> run_fred-2k0629rvbffz0/run_fred-r81pg3li
> >>         STDERR: 
> >>         STDOUT:
> >>
> >> Does 'Parameter not supported' usually refer to an
> >> argument of the remote application? I wonder if it
> >> does not like the .oeb.gz file?
> >>
> >>
> >>
> >> --- Ben Clifford <benc at hawaga.org.uk> wrote:
> >>
> >>>
> >>> On Wed, 5 Dec 2007, Mike Kubal wrote:
> >>>
> >>>>              run_fred "-rec" receptor_file
> >>> "-dbase"
> >>>> ligand_file "-prefix" ligand_prefix;
> >>> In here, take the filenames of each file by saying 
> >>> @filenmame(receptor_file), like this:
> >>>
> >>>>             run_fred "-rec"
> >>> @filename(receptor_file) "-dbase"
> >>>> @filename(ligand_file) "-prefix" ligand_prefix;
> >>> -- 
> >>> _______________________________________________
> >>> Swift-devel mailing list
> >>> Swift-devel at ci.uchicago.edu
> >>>
> >> http://mail.ci.uchicago.edu/mailman/listinfo/swift-devel
> >>>
> >>
> >>
> >>       ____________________________________________________________________________________
> >> Be a better friend, newshound, and 
> >> know-it-all with Yahoo! Mobile.  Try it now.  http://mobile.yahoo.com/;_ylt=Ahu06i62sR8HDtDypao8Wcj9tAcJ 
> >>
> >> _______________________________________________
> >> 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 wilde at mcs.anl.gov  Wed Dec  5 17:47:41 2007
From: wilde at mcs.anl.gov (Michael Wilde)
Date: Wed, 05 Dec 2007 17:47:41 -0600
Subject: [Swift-devel] script that returns bad parameter error
In-Reply-To: <753687.67764.qm@web52301.mail.re2.yahoo.com>
References: <753687.67764.qm@web52301.mail.re2.yahoo.com>
Message-ID: <4757389D.7030309@mcs.anl.gov>

I need to take a close look later when I get a chance, but i'm a bit 
suspicious of the use of the file type variables receptor_file and 
ligand_file without the @ or @filename inside your app{} construct in 
run_fred().

Will check later if thats what gives this message.

you want to say:

         app {
              run_fred "-rec" @receptor_file "-dbase"
  @ligand_file "-prefix" ligand_prefix;>         }

See the users guide at http://www.ci.uchicago.edu/swift/guides/userguide.php
sec 2.3.1

and the tutorial example, Mike.

- MikeW


On 12/5/07 2:56 PM, Mike Kubal wrote:
> Any thoughts on what might cause? 
> 
> type file {}
> 
> (file score, file docked) run_fred (string
> ligand_prefix, file ligand_file, file receptor_file){
>         app {
>              run_fred "-rec" receptor_file "-dbase"
> ligand_file "-prefix" ligand_prefix;
>         }
> }
> 
> 
> string receptor_prefix = "1beh";
> 
> file receptor_file
> <single_file_mapper;file=@strcat(receptor_prefix,".oeb.gz")>;
> 
> file
> fls[]<filesys_mapper;pattern="Marsha_lig_*.mol2",location=".">;
> 
> foreach ligand_file in fls{
> 
>         string ligand_prefix =
> @strcut(@ligand_file,"\.\/(.*)\.mol2");
>         string score_file_name =
> @strcat(ligand_prefix,"_chemgauss3_scores.txt");
>         string docked_file_name =
> @strcat(ligand_prefix,"_chemgauss3_docked.mol2");
>         file score_file
> <single_file_mapper;file=@strcat(ligand_prefix,"_chemgauss3_scores.txt")>;
>         file docked_file
> <single_file_mapper;file=@strcat(ligand_prefix,"_chemgauss3_docked.mol2")>;
> 
>         (score_file,docked_file) =
> run_fred(ligand_prefix,ligand_file,receptor_file);
> 
> }
> 
> 
> Thanks,
> 
> Mike Kubal
> 
> 
>       ____________________________________________________________________________________
> Never miss a thing.  Make Yahoo your home page. 
> http://www.yahoo.com/r/hs
> _______________________________________________
> Swift-devel mailing list
> Swift-devel at ci.uchicago.edu
> http://mail.ci.uchicago.edu/mailman/listinfo/swift-devel
> 
> 


From tiberius at ci.uchicago.edu  Wed Dec  5 17:54:03 2007
From: tiberius at ci.uchicago.edu (Tiberiu Stef-Praun)
Date: Wed, 5 Dec 2007 17:54:03 -0600
Subject: [Swift-devel] (no subject)
In-Reply-To: <Pine.LNX.4.64.0712052201020.28498@dildano.hawaga.org.uk>
References: <4756ED24.7070709@mcs.anl.gov>
	<Pine.LNX.4.64.0712052201020.28498@dildano.hawaga.org.uk>
Message-ID: <fec1351f0712051554n6ff4647fxc71831ee16b42f8c@mail.gmail.com>

Ben, I am getting the same error as Rafaelle, and I can reproduce it
Tell me what version of swift to test, to check whether the problem
has been resolved

Tibi

On Dec 5, 2007 4:04 PM, Ben Clifford <benc at hawaga.org.uk> wrote:
>
>
> On Wed, 5 Dec 2007, Michael Wilde wrote:
>
> > The gssapi error is what we've seen before - 0.3 running on Java 1.5.
> > Raphaele is now building trunk which should work.  We should post something on
> > this or put out an 0.4, perhaps?
>
> If a new release will make it better, then it would not be too bad to have
> a 0.4 in the next week or so. I'd like to figure out whether that helps or
> not though (for example, if I build it on my system, will it still break
> for others?). For that, better testing of the release candidate (when it
> appears) should probably happen by people other than me.
>
> --
> _______________________________________________
> Swift-devel mailing list
> Swift-devel at ci.uchicago.edu
> http://mail.ci.uchicago.edu/mailman/listinfo/swift-devel
>



-- 
Tiberiu (Tibi) Stef-Praun, PhD
Research Staff, Computation Institute
5640 S. Ellis Ave, #405
University of Chicago
http://www-unix.mcs.anl.gov/~tiberius/


From benc at hawaga.org.uk  Wed Dec  5 17:55:48 2007
From: benc at hawaga.org.uk (Ben Clifford)
Date: Wed, 5 Dec 2007 23:55:48 +0000 (GMT)
Subject: [Swift-devel] (no subject)
In-Reply-To: <fec1351f0712051554n6ff4647fxc71831ee16b42f8c@mail.gmail.com>
References: <4756ED24.7070709@mcs.anl.gov>
	<Pine.LNX.4.64.0712052201020.28498@dildano.hawaga.org.uk>
	<fec1351f0712051554n6ff4647fxc71831ee16b42f8c@mail.gmail.com>
Message-ID: <Pine.LNX.4.64.0712052355190.23250@dildano.hawaga.org.uk>



On Wed, 5 Dec 2007, Tiberiu Stef-Praun wrote:

> Ben, I am getting the same error as Rafaelle, and I can reproduce it
> Tell me what version of swift to test, to check whether the problem
> has been resolved

What host, swift version, machine?

-- 



From hategan at mcs.anl.gov  Wed Dec  5 17:59:18 2007
From: hategan at mcs.anl.gov (Mihael Hategan)
Date: Wed, 05 Dec 2007 17:59:18 -0600
Subject: [Swift-devel] (no subject)
In-Reply-To: <fec1351f0712051554n6ff4647fxc71831ee16b42f8c@mail.gmail.com>
References: <4756ED24.7070709@mcs.anl.gov>
	<Pine.LNX.4.64.0712052201020.28498@dildano.hawaga.org.uk>
	<fec1351f0712051554n6ff4647fxc71831ee16b42f8c@mail.gmail.com>
Message-ID: <1196899159.7896.0.camel@blabla.mcs.anl.gov>


On Wed, 2007-12-05 at 17:54 -0600, Tiberiu Stef-Praun wrote:
> Ben, I am getting the same error as Rafaelle, and I can reproduce it
> Tell me what version of swift to test, to check whether the problem
> has been resolved

Actually I'd like to know where your version is installed. When I
"fixed" it, I didn't really understand what was happening, so I want to
correct that.

> 
> Tibi
> 
> On Dec 5, 2007 4:04 PM, Ben Clifford <benc at hawaga.org.uk> wrote:
> >
> >
> > On Wed, 5 Dec 2007, Michael Wilde wrote:
> >
> > > The gssapi error is what we've seen before - 0.3 running on Java 1.5.
> > > Raphaele is now building trunk which should work.  We should post something on
> > > this or put out an 0.4, perhaps?
> >
> > If a new release will make it better, then it would not be too bad to have
> > a 0.4 in the next week or so. I'd like to figure out whether that helps or
> > not though (for example, if I build it on my system, will it still break
> > for others?). For that, better testing of the release candidate (when it
> > appears) should probably happen by people other than me.
> >
> > --
> > _______________________________________________
> > Swift-devel mailing list
> > Swift-devel at ci.uchicago.edu
> > http://mail.ci.uchicago.edu/mailman/listinfo/swift-devel
> >
> 
> 
> 



From tiberius at ci.uchicago.edu  Wed Dec  5 18:05:54 2007
From: tiberius at ci.uchicago.edu (Tiberiu Stef-Praun)
Date: Wed, 5 Dec 2007 18:05:54 -0600
Subject: [Swift-devel] (no subject)
In-Reply-To: <1196899159.7896.0.camel@blabla.mcs.anl.gov>
References: <4756ED24.7070709@mcs.anl.gov>
	<Pine.LNX.4.64.0712052201020.28498@dildano.hawaga.org.uk>
	<fec1351f0712051554n6ff4647fxc71831ee16b42f8c@mail.gmail.com>
	<1196899159.7896.0.camel@blabla.mcs.anl.gov>
Message-ID: <fec1351f0712051605i3d9eee02j9bc58f008966f7d0@mail.gmail.com>

I use swift 0.3 with java 1.5 on one of the virtual machines that I
use for the Econ project
Luckily Mike's comment brought some light on why I could not run my
workflows any more.

Tibi

On Dec 5, 2007 5:59 PM, Mihael Hategan <hategan at mcs.anl.gov> wrote:
>
> On Wed, 2007-12-05 at 17:54 -0600, Tiberiu Stef-Praun wrote:
> > Ben, I am getting the same error as Rafaelle, and I can reproduce it
> > Tell me what version of swift to test, to check whether the problem
> > has been resolved
>
> Actually I'd like to know where your version is installed. When I
> "fixed" it, I didn't really understand what was happening, so I want to
> correct that.
>
>
> >
> > Tibi
> >
> > On Dec 5, 2007 4:04 PM, Ben Clifford <benc at hawaga.org.uk> wrote:
> > >
> > >
> > > On Wed, 5 Dec 2007, Michael Wilde wrote:
> > >
> > > > The gssapi error is what we've seen before - 0.3 running on Java 1.5.
> > > > Raphaele is now building trunk which should work.  We should post something on
> > > > this or put out an 0.4, perhaps?
> > >
> > > If a new release will make it better, then it would not be too bad to have
> > > a 0.4 in the next week or so. I'd like to figure out whether that helps or
> > > not though (for example, if I build it on my system, will it still break
> > > for others?). For that, better testing of the release candidate (when it
> > > appears) should probably happen by people other than me.
> > >
> > > --
> > > _______________________________________________
> > > Swift-devel mailing list
> > > Swift-devel at ci.uchicago.edu
> > > http://mail.ci.uchicago.edu/mailman/listinfo/swift-devel
> > >
> >
> >
> >
>
>



-- 
Tiberiu (Tibi) Stef-Praun, PhD
Research Staff, Computation Institute
5640 S. Ellis Ave, #405
University of Chicago
http://www-unix.mcs.anl.gov/~tiberius/


From hategan at mcs.anl.gov  Wed Dec  5 18:09:46 2007
From: hategan at mcs.anl.gov (Mihael Hategan)
Date: Wed, 05 Dec 2007 18:09:46 -0600
Subject: [Swift-devel] (no subject)
In-Reply-To: <fec1351f0712051605i3d9eee02j9bc58f008966f7d0@mail.gmail.com>
References: <4756ED24.7070709@mcs.anl.gov>
	<Pine.LNX.4.64.0712052201020.28498@dildano.hawaga.org.uk>
	<fec1351f0712051554n6ff4647fxc71831ee16b42f8c@mail.gmail.com>
	<1196899159.7896.0.camel@blabla.mcs.anl.gov>
	<fec1351f0712051605i3d9eee02j9bc58f008966f7d0@mail.gmail.com>
Message-ID: <1196899787.8155.0.camel@blabla.mcs.anl.gov>


On Wed, 2007-12-05 at 18:05 -0600, Tiberiu Stef-Praun wrote:
> I use swift 0.3 with java 1.5 on one of the virtual machines that I
> use for the Econ project

Hmm. I have a hunch. Thanks.

> Luckily Mike's comment brought some light on why I could not run my
> workflows any more.
> 
> Tibi
> 
> On Dec 5, 2007 5:59 PM, Mihael Hategan <hategan at mcs.anl.gov> wrote:
> >
> > On Wed, 2007-12-05 at 17:54 -0600, Tiberiu Stef-Praun wrote:
> > > Ben, I am getting the same error as Rafaelle, and I can reproduce it
> > > Tell me what version of swift to test, to check whether the problem
> > > has been resolved
> >
> > Actually I'd like to know where your version is installed. When I
> > "fixed" it, I didn't really understand what was happening, so I want to
> > correct that.
> >
> >
> > >
> > > Tibi
> > >
> > > On Dec 5, 2007 4:04 PM, Ben Clifford <benc at hawaga.org.uk> wrote:
> > > >
> > > >
> > > > On Wed, 5 Dec 2007, Michael Wilde wrote:
> > > >
> > > > > The gssapi error is what we've seen before - 0.3 running on Java 1.5.
> > > > > Raphaele is now building trunk which should work.  We should post something on
> > > > > this or put out an 0.4, perhaps?
> > > >
> > > > If a new release will make it better, then it would not be too bad to have
> > > > a 0.4 in the next week or so. I'd like to figure out whether that helps or
> > > > not though (for example, if I build it on my system, will it still break
> > > > for others?). For that, better testing of the release candidate (when it
> > > > appears) should probably happen by people other than me.
> > > >
> > > > --
> > > > _______________________________________________
> > > > Swift-devel mailing list
> > > > Swift-devel at ci.uchicago.edu
> > > > http://mail.ci.uchicago.edu/mailman/listinfo/swift-devel
> > > >
> > >
> > >
> > >
> >
> >
> 
> 
> 



From bugzilla-daemon at mcs.anl.gov  Thu Dec  6 10:03:15 2007
From: bugzilla-daemon at mcs.anl.gov (bugzilla-daemon at mcs.anl.gov)
Date: Thu,  6 Dec 2007 10:03:15 -0600 (CST)
Subject: [Swift-devel] [Bug 115] New: Swift users encounter long delays
	waiting for random name generation
Message-ID: <bug-115-21@http.bugzilla.mcs.anl.gov/swift/>

http://bugzilla.mcs.anl.gov/swift/show_bug.cgi?id=115

           Summary: Swift users encounter long delays waiting for random
                    name generation
           Product: Swift
           Version: unspecified
          Platform: All
        OS/Version: All
            Status: NEW
          Severity: major
          Priority: P1
         Component: SwiftScript language
        AssignedTo: benc at hawaga.org.uk
        ReportedBy: wilde at mcs.anl.gov


When using swift on headless hosts (ie ones with a low level of entropy) swift
users encounter length delays - 10s of seconds to many minutes) waiting for the
generation of random names for files, workflows etc.


-- 
Configure bugmail: http://bugzilla.mcs.anl.gov/swift/userprefs.cgi?tab=email
------- You are receiving this mail because: -------
You reported the bug, or are watching the reporter.


From wilde at mcs.anl.gov  Thu Dec  6 10:06:32 2007
From: wilde at mcs.anl.gov (Michael Wilde)
Date: Thu, 06 Dec 2007 10:06:32 -0600
Subject: [Swift-devel] Is problem of slow random name generation fixed?
Message-ID: <47581E08.5050302@mcs.anl.gov>

I didnt see any email or bugzilla traffic on this (may have missed it) 
so I filed bug 115 to track it.

I think its a high prio to fix, as it had a very serious impact on our 
last training session, and Ive been plagued by it often myself.


From bugzilla-daemon at mcs.anl.gov  Thu Dec  6 10:09:32 2007
From: bugzilla-daemon at mcs.anl.gov (bugzilla-daemon at mcs.anl.gov)
Date: Thu,  6 Dec 2007 10:09:32 -0600 (CST)
Subject: [Swift-devel] [Bug 115] Swift users encounter long delays waiting
	for random name generation
In-Reply-To: <bug-115-21@http.bugzilla.mcs.anl.gov/swift/>
Message-ID: <20071206160932.B138F164EC@foxtrot.mcs.anl.gov>

http://bugzilla.mcs.anl.gov/swift/show_bug.cgi?id=115





------- Comment #1 from benc at hawaga.org.uk  2007-12-06 10:09 -------
this should have been fixed (again) in r1496 some days ago. do you see delay
with >=1496?


-- 
Configure bugmail: http://bugzilla.mcs.anl.gov/swift/userprefs.cgi?tab=email
------- You are receiving this mail because: -------
You reported the bug, or are watching the reporter.


From benc at hawaga.org.uk  Thu Dec  6 10:10:49 2007
From: benc at hawaga.org.uk (Ben Clifford)
Date: Thu, 6 Dec 2007 16:10:49 +0000 (GMT)
Subject: [Swift-devel] Is problem of slow random name generation fixed?
In-Reply-To: <47581E08.5050302@mcs.anl.gov>
References: <47581E08.5050302@mcs.anl.gov>
Message-ID: <Pine.LNX.4.64.0712061610220.28498@dildano.hawaga.org.uk>


On Thu, 6 Dec 2007, Michael Wilde wrote:

> I didnt see any email or bugzilla traffic on this (may have missed it) 
> so I filed bug 115 to track it.

You should have seen the commit go by in the commit history though... 
r1496.

-- 


From mikekubal at yahoo.com  Thu Dec  6 10:15:11 2007
From: mikekubal at yahoo.com (Mike Kubal)
Date: Thu, 6 Dec 2007 08:15:11 -0800 (PST)
Subject: [Swift-devel] script that returns bad parameter error
In-Reply-To: <1196898342.7620.0.camel@blabla.mcs.anl.gov>
Message-ID: <25134.71170.qm@web52312.mail.re2.yahoo.com>

Hi Mihael,

No need to apologize, I appreciate your feedback.

Here is the sites file.

<?xml version="1.0" encoding="UTF-8"?>
<config
xmlns="http://www.griphyn.org/chimera/GVDS-PoolConfig"
xsi:schemaLocation="http://www.griphyn.org/chimera/GVDS
 http://www.griphyn.org/chimera/gvds-poolcfg-1.5.xsd"
xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
version="1.5">

<pool handle="Lear" sysinfo="INTEL64::LINUX">
    <gridftp 
url="gsiftp://gridftp.purdue.teragrid.org"
storage="/autohome/u102/mkubal/SWIFT_working_dir"
major="2" minor="2" patch="4">
    </gridftp>
    <profile namespace="globus"
key="project">UC-MCA01S018</profile>
    <jobmanager universe="vanilla"
url="tg-gatekeeper.purdue.teragrid.org:2119/jobmanager-fork"
major="2" minor="0" patch="0"/>
   
<workdirectory>/autohome/u102/mkubal/SWIFT_working_dir</workdirectory>
  </pool>
</config>

I  have also tried the condor job manager at Purdue
that has the same url except that it ends in '-condor'
instead of '-fork' . I get the same error.

Cheers,

Mike





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

> Sorry. My email wasn't very friendly. I was trying
> to type less :)
> 
> On Wed, 2007-12-05 at 17:42 -0600, Michael Wilde
> wrote:
> > Mike,
> > 
> > Mihael suspects that a bad globus parameter in
> your sites.xml file is 
> > causing this error message.  So please send that
> so we can take a look.
> > 
> > Thanks,
> > 
> > MikeW
> > 
> > On 12/5/07 4:45 PM, Mihael Hategan wrote:
> > > Post the sites file.
> > > 
> > > On Wed, 2007-12-05 at 14:33 -0800, Mike Kubal
> wrote:
> > >> Unfortunately I still get the same error:
> > >>
> > >> run_fred failed
> > >> The following errors have occurred:
> > >> 1. Application "run_fred" failed (Parameter not
> > >> supported)
> > >>         Arguments: "-rec, 1beh.oeb.gz, -dbase,
> > >> Marsha_lig_1.mol2, -prefix, Marsha_lig_1"
> > >>         Host: Lear
> > >>         Directory:
> > >> run_fred-2k0629rvbffz0/run_fred-r81pg3li
> > >>         STDERR: 
> > >>         STDOUT:
> > >>
> > >> Does 'Parameter not supported' usually refer to
> an
> > >> argument of the remote application? I wonder if
> it
> > >> does not like the .oeb.gz file?
> > >>
> > >>
> > >>
> > >> --- Ben Clifford <benc at hawaga.org.uk> wrote:
> > >>
> > >>>
> > >>> On Wed, 5 Dec 2007, Mike Kubal wrote:
> > >>>
> > >>>>              run_fred "-rec" receptor_file
> > >>> "-dbase"
> > >>>> ligand_file "-prefix" ligand_prefix;
> > >>> In here, take the filenames of each file by
> saying 
> > >>> @filenmame(receptor_file), like this:
> > >>>
> > >>>>             run_fred "-rec"
> > >>> @filename(receptor_file) "-dbase"
> > >>>> @filename(ligand_file) "-prefix"
> ligand_prefix;
> > >>> -- 
> > >>>
> _______________________________________________
> > >>> Swift-devel mailing list
> > >>> Swift-devel at ci.uchicago.edu
> > >>>
> > >>
>
http://mail.ci.uchicago.edu/mailman/listinfo/swift-devel
> > >>>
> > >>
> > >>
> > >>      
>
____________________________________________________________________________________
> > >> Be a better friend, newshound, and 
> > >> know-it-all with Yahoo! Mobile.  Try it now. 
>
http://mobile.yahoo.com/;_ylt=Ahu06i62sR8HDtDypao8Wcj9tAcJ
> 
> > >>
> > >> _______________________________________________
> > >> 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
> > > 
> > > 
> > 
> 
> _______________________________________________
> Swift-devel mailing list
> Swift-devel at ci.uchicago.edu
>
http://mail.ci.uchicago.edu/mailman/listinfo/swift-devel
> 
> 



      ____________________________________________________________________________________
Looking for last minute shopping deals?  
Find them fast with Yahoo! Search.  http://tools.search.yahoo.com/newsearch/category.php?category=shopping


From hategan at mcs.anl.gov  Thu Dec  6 10:30:05 2007
From: hategan at mcs.anl.gov (Mihael Hategan)
Date: Thu, 06 Dec 2007 10:30:05 -0600
Subject: [Swift-devel] script that returns bad parameter error
In-Reply-To: <25134.71170.qm@web52312.mail.re2.yahoo.com>
References: <25134.71170.qm@web52312.mail.re2.yahoo.com>
Message-ID: <1196958605.14888.3.camel@blabla.mcs.anl.gov>

I think I've seen fork complaining about "project" before. Can you try
to comment that profile tag out and run with fork again?

It may also be useful to post the logs since they may contain stack
traces that point more accurately towards the problem.

Mihael

On Thu, 2007-12-06 at 08:15 -0800, Mike Kubal wrote:
> Hi Mihael,
> 
> No need to apologize, I appreciate your feedback.
> 
> Here is the sites file.
> 
> <?xml version="1.0" encoding="UTF-8"?>
> <config
> xmlns="http://www.griphyn.org/chimera/GVDS-PoolConfig"
> xsi:schemaLocation="http://www.griphyn.org/chimera/GVDS
>  http://www.griphyn.org/chimera/gvds-poolcfg-1.5.xsd"
> xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
> version="1.5">
> 
> <pool handle="Lear" sysinfo="INTEL64::LINUX">
>     <gridftp 
> url="gsiftp://gridftp.purdue.teragrid.org"
> storage="/autohome/u102/mkubal/SWIFT_working_dir"
> major="2" minor="2" patch="4">
>     </gridftp>
>     <profile namespace="globus"
> key="project">UC-MCA01S018</profile>
>     <jobmanager universe="vanilla"
> url="tg-gatekeeper.purdue.teragrid.org:2119/jobmanager-fork"
> major="2" minor="0" patch="0"/>
>    
> <workdirectory>/autohome/u102/mkubal/SWIFT_working_dir</workdirectory>
>   </pool>
> </config>
> 
> I  have also tried the condor job manager at Purdue
> that has the same url except that it ends in '-condor'
> instead of '-fork' . I get the same error.
> 
> Cheers,
> 
> Mike
> 
> 
> 
> 
> 
> --- Mihael Hategan <hategan at mcs.anl.gov> wrote:
> 
> > Sorry. My email wasn't very friendly. I was trying
> > to type less :)
> > 
> > On Wed, 2007-12-05 at 17:42 -0600, Michael Wilde
> > wrote:
> > > Mike,
> > > 
> > > Mihael suspects that a bad globus parameter in
> > your sites.xml file is 
> > > causing this error message.  So please send that
> > so we can take a look.
> > > 
> > > Thanks,
> > > 
> > > MikeW
> > > 
> > > On 12/5/07 4:45 PM, Mihael Hategan wrote:
> > > > Post the sites file.
> > > > 
> > > > On Wed, 2007-12-05 at 14:33 -0800, Mike Kubal
> > wrote:
> > > >> Unfortunately I still get the same error:
> > > >>
> > > >> run_fred failed
> > > >> The following errors have occurred:
> > > >> 1. Application "run_fred" failed (Parameter not
> > > >> supported)
> > > >>         Arguments: "-rec, 1beh.oeb.gz, -dbase,
> > > >> Marsha_lig_1.mol2, -prefix, Marsha_lig_1"
> > > >>         Host: Lear
> > > >>         Directory:
> > > >> run_fred-2k0629rvbffz0/run_fred-r81pg3li
> > > >>         STDERR: 
> > > >>         STDOUT:
> > > >>
> > > >> Does 'Parameter not supported' usually refer to
> > an
> > > >> argument of the remote application? I wonder if
> > it
> > > >> does not like the .oeb.gz file?
> > > >>
> > > >>
> > > >>
> > > >> --- Ben Clifford <benc at hawaga.org.uk> wrote:
> > > >>
> > > >>>
> > > >>> On Wed, 5 Dec 2007, Mike Kubal wrote:
> > > >>>
> > > >>>>              run_fred "-rec" receptor_file
> > > >>> "-dbase"
> > > >>>> ligand_file "-prefix" ligand_prefix;
> > > >>> In here, take the filenames of each file by
> > saying 
> > > >>> @filenmame(receptor_file), like this:
> > > >>>
> > > >>>>             run_fred "-rec"
> > > >>> @filename(receptor_file) "-dbase"
> > > >>>> @filename(ligand_file) "-prefix"
> > ligand_prefix;
> > > >>> -- 
> > > >>>
> > _______________________________________________
> > > >>> Swift-devel mailing list
> > > >>> Swift-devel at ci.uchicago.edu
> > > >>>
> > > >>
> >
> http://mail.ci.uchicago.edu/mailman/listinfo/swift-devel
> > > >>>
> > > >>
> > > >>
> > > >>      
> >
> ____________________________________________________________________________________
> > > >> Be a better friend, newshound, and 
> > > >> know-it-all with Yahoo! Mobile.  Try it now. 
> >
> http://mobile.yahoo.com/;_ylt=Ahu06i62sR8HDtDypao8Wcj9tAcJ
> > 
> > > >>
> > > >> _______________________________________________
> > > >> 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
> > > > 
> > > > 
> > > 
> > 
> > _______________________________________________
> > Swift-devel mailing list
> > Swift-devel at ci.uchicago.edu
> >
> http://mail.ci.uchicago.edu/mailman/listinfo/swift-devel
> > 
> > 
> 
> 
> 
>       ____________________________________________________________________________________
> Looking for last minute shopping deals?  
> Find them fast with Yahoo! Search.  http://tools.search.yahoo.com/newsearch/category.php?category=shopping
> 



From mikekubal at yahoo.com  Thu Dec  6 11:15:45 2007
From: mikekubal at yahoo.com (Mike Kubal)
Date: Thu, 6 Dec 2007 09:15:45 -0800 (PST)
Subject: [Swift-devel] script that returns bad parameter error
In-Reply-To: <1196958605.14888.3.camel@blabla.mcs.anl.gov>
Message-ID: <782829.23701.qm@web52304.mail.re2.yahoo.com>

I took out the project tag and same results. Here's
the section run_fred****.log where the failure occurs:

2007-12-06 10:44:14,968 DEBUG Loader Recompilation
suppressed.
2007-12-06 10:44:19,096 INFO  unknown Using sites
file: sites-purdue-64-gram.xml
2007-12-06 10:44:19,097 INFO  unknown Using tc.data:
tc-purdue.data
2007-12-06 10:44:22,303 DEBUG GetFieldValue
GetFieldValue(true)
2007-12-06 10:44:22,311 DEBUG GetFieldValue
GetFieldValue(true)
2007-12-06 10:44:28,408 DEBUG TaskImpl Task(type=4,
identity=urn:0-0-1-0-1196959457323) setting status to
Active
2007-12-06 10:44:28,502 DEBUG TaskImpl Task(type=4,
identity=urn:0-0-1-0-1196959457323) setting status to
Completed
2007-12-06 10:44:28,553 DEBUG TaskImpl Task(type=2,
identity=urn:0-0-1-0-1196959457326) setting status to
Submitted
2007-12-06 10:44:28,554 DEBUG TaskImpl Task(type=2,
identity=urn:0-0-1-0-1196959457326) setting status to
Active
2007-12-06 10:44:29,022 DEBUG TaskImpl Task(type=2,
identity=urn:0-0-1-0-1196959457326) setting status to
Completed
2007-12-06 10:44:29,026 DEBUG TaskImpl Task(type=2,
identity=urn:0-0-1-0-1196959457330) setting status to
Submitted
2007-12-06 10:44:29,026 DEBUG TaskImpl Task(type=2,
identity=urn:0-0-1-0-1196959457330) setting status to
Active
2007-12-06 10:44:29,464 DEBUG TaskImpl Task(type=2,
identity=urn:0-0-1-0-1196959457330) setting status to
Completed
2007-12-06 10:44:29,470 DEBUG vdl:execute2 Job
run_fred-fqolp4li running in thread 0-0-1-0 run
zh499u762hal2
2007-12-06 10:44:29,482 INFO  vdl:execute2 Creating
temporary directory
run_fred-zh499u762hal2/run_fred-fqolp4li on Lear
2007-12-06 10:44:29,500 INFO  vdl:createdirs Creating
directory structure  in run_fred-zh499u762hal2/shared
(run_fred-zh499u762hal2/shared/)
2007-12-06 10:44:29,502 DEBUG TaskImpl Task(type=4,
identity=urn:0-0-1-0-1196959457333) setting status to
Active
2007-12-06 10:44:29,525 DEBUG TaskImpl Task(type=4,
identity=urn:0-0-1-0-1196959457333) setting status to
Completed
2007-12-06 10:44:29,538 DEBUG TaskImpl Task(type=4,
identity=urn:0-0-1-0-2-1196959457335) setting status
to Active
2007-12-06 10:44:29,540 DEBUG TaskImpl Task(type=4,
identity=urn:0-0-1-0-1-1196959457338) setting status
to Active
2007-12-06 10:44:29,542 DEBUG TaskImpl Task(type=4,
identity=urn:0-0-1-0-2-1196959457335) setting status
to Completed
2007-12-06 10:44:29,551 DEBUG TaskImpl Task(type=4,
identity=urn:0-0-1-0-1-1196959457338) setting status
to Completed
2007-12-06 10:44:29,566 INFO  vdl:dostagein Staging in
Marsha_lig_1.mol2 ( - Marsha_lig_1.mol2 to
run_fred-zh499u762hal2/shared/ on Lear
2007-12-06 10:44:29,567 INFO  vdl:dostagein Staging in
1beh.oeb.gz ( - 1beh.oeb.gz to
run_fred-zh499u762hal2/shared/ on Lear
2007-12-06 10:44:29,570 DEBUG TaskImpl Task(type=2,
identity=urn:0-0-1-0-1-1196959457342) setting status
to Submitted
2007-12-06 10:44:29,571 DEBUG TaskImpl Task(type=2,
identity=urn:0-0-1-0-1-1196959457342) setting status
to Active
2007-12-06 10:44:29,571 DEBUG TaskImpl Task(type=2,
identity=urn:0-0-1-0-2-1196959457345) setting status
to Submitted
2007-12-06 10:44:29,572 DEBUG TaskImpl Task(type=2,
identity=urn:0-0-1-0-2-1196959457345) setting status
to Active
2007-12-06 10:44:30,005 DEBUG TaskImpl Task(type=2,
identity=urn:0-0-1-0-1-1196959457342) setting status
to Completed
2007-12-06 10:44:30,007 INFO  vdl:dostagein Staged in
Marsha_lig_1.mol2 to run_fred-zh499u762hal2/shared/ on
Lear
2007-12-06 10:44:31,703 DEBUG TaskImpl Task(type=2,
identity=urn:0-0-1-0-2-1196959457345) setting status
to Completed
2007-12-06 10:44:31,705 INFO  vdl:dostagein Staged in
1beh.oeb.gz to run_fred-zh499u762hal2/shared/ on Lear
2007-12-06 10:44:31,707 INFO  vdl:execute2 Running job
run_fred-fqolp4li run_fred with arguments [-rec,
1beh.oeb.gz, -dbase, Marsha_lig_1.mol2, -prefix,
Marsha_li\
g_1] in run_fred-zh499u762hal2/run_fred-fqolp4li on
Lear
2007-12-06 10:44:32,925 DEBUG TaskImpl Task(type=1,
identity=urn:0-0-1-0-1196959457349) setting status to
Failed Parameter not supported
2007-12-06 10:44:32,938 DEBUG vdl:execute2 Application
exception: Parameter not supported
        task:execute @ vdl-int.k, line: 328
        sys:sequential @ vdl-int.k, line: 316
        sys:try @ vdl-int.k, line: 315
        task:allocatehost @ vdl-int.k, line: 298
        vdl:execute2 @ execute-default.k, line: 22
        sys:restartonerror @ execute-default.k, line:
20
        sys:sequential @ execute-default.k, line: 19
        sys:try @ execute-default.k, line: 18
        sys:if @ execute-default.k, line: 17
        sys:then @ execute-default.k, line: 16
        sys:if @ execute-default.k, line: 15
        vdl:execute @ run_fred.kml, line: 20
        run_fred @ run_fred.kml, line: 151
        sys:parallel @ run_fred.kml, line: 150
        sys:parallelfor @ run_fred.kml, line: 80
        sys:parallel @ run_fred.kml, line: 79
        vdl:mainp @ run_fred.kml, line: 78
        mainp @ vdl.k, line: 141
        vdl:mains @ run_fred.kml, line: 77
        vdl:mains @ run_fred.kml, line: 77
        rlog:restartlog @ run_fred.kml, line: 75
        kernel:project @ run_fred.kml, line: 2
        run_fred-zh499u762hal2
Caused by: org.globus.gram.GramException: Parameter
not supported


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

> I think I've seen fork complaining about "project"
> before. Can you try
> to comment that profile tag out and run with fork
> again?
> 
> It may also be useful to post the logs since they
> may contain stack
> traces that point more accurately towards the
> problem.
> 
> Mihael
> 
> On Thu, 2007-12-06 at 08:15 -0800, Mike Kubal wrote:
> > Hi Mihael,
> > 
> > No need to apologize, I appreciate your feedback.
> > 
> > Here is the sites file.
> > 
> > <?xml version="1.0" encoding="UTF-8"?>
> > <config
> >
>
xmlns="http://www.griphyn.org/chimera/GVDS-PoolConfig"
> >
>
xsi:schemaLocation="http://www.griphyn.org/chimera/GVDS
> > 
> http://www.griphyn.org/chimera/gvds-poolcfg-1.5.xsd"
> >
>
xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
> > version="1.5">
> > 
> > <pool handle="Lear" sysinfo="INTEL64::LINUX">
> >     <gridftp 
> > url="gsiftp://gridftp.purdue.teragrid.org"
> > storage="/autohome/u102/mkubal/SWIFT_working_dir"
> > major="2" minor="2" patch="4">
> >     </gridftp>
> >     <profile namespace="globus"
> > key="project">UC-MCA01S018</profile>
> >     <jobmanager universe="vanilla"
> >
>
url="tg-gatekeeper.purdue.teragrid.org:2119/jobmanager-fork"
> > major="2" minor="0" patch="0"/>
> >    
> >
>
<workdirectory>/autohome/u102/mkubal/SWIFT_working_dir</workdirectory>
> >   </pool>
> > </config>
> > 
> > I  have also tried the condor job manager at
> Purdue
> > that has the same url except that it ends in
> '-condor'
> > instead of '-fork' . I get the same error.
> > 
> > Cheers,
> > 
> > Mike
> > 
> > 
> > 
> > 
> > 
> > --- Mihael Hategan <hategan at mcs.anl.gov> wrote:
> > 
> > > Sorry. My email wasn't very friendly. I was
> trying
> > > to type less :)
> > > 
> > > On Wed, 2007-12-05 at 17:42 -0600, Michael Wilde
> > > wrote:
> > > > Mike,
> > > > 
> > > > Mihael suspects that a bad globus parameter in
> > > your sites.xml file is 
> > > > causing this error message.  So please send
> that
> > > so we can take a look.
> > > > 
> > > > Thanks,
> > > > 
> > > > MikeW
> > > > 
> > > > On 12/5/07 4:45 PM, Mihael Hategan wrote:
> > > > > Post the sites file.
> > > > > 
> > > > > On Wed, 2007-12-05 at 14:33 -0800, Mike
> Kubal
> > > wrote:
> > > > >> Unfortunately I still get the same error:
> > > > >>
> > > > >> run_fred failed
> > > > >> The following errors have occurred:
> > > > >> 1. Application "run_fred" failed (Parameter
> not
> > > > >> supported)
> > > > >>         Arguments: "-rec, 1beh.oeb.gz,
> -dbase,
> > > > >> Marsha_lig_1.mol2, -prefix, Marsha_lig_1"
> > > > >>         Host: Lear
> > > > >>         Directory:
> > > > >> run_fred-2k0629rvbffz0/run_fred-r81pg3li
> > > > >>         STDERR: 
> > > > >>         STDOUT:
> > > > >>
> > > > >> Does 'Parameter not supported' usually
> refer to
> > > an
> > > > >> argument of the remote application? I
> wonder if
> > > it
> > > > >> does not like the .oeb.gz file?
> > > > >>
> > > > >>
> > > > >>
> > > > >> --- Ben Clifford <benc at hawaga.org.uk>
> wrote:
> > > > >>
> > > > >>>
> > > > >>> On Wed, 5 Dec 2007, Mike Kubal wrote:
> > > > >>>
> > > > >>>>              run_fred "-rec"
> receptor_file
> > > > >>> "-dbase"
> > > > >>>> ligand_file "-prefix" ligand_prefix;
> > > > >>> In here, take the filenames of each file
> by
> > > saying 
> > > > >>> @filenmame(receptor_file), like this:
> > > > >>>
> > > > >>>>             run_fred "-rec"
> > > > >>> @filename(receptor_file) "-dbase"
> > > > >>>> @filename(ligand_file) "-prefix"
> > > ligand_prefix;
> > > > >>> -- 
> > > > >>>
> > > _______________________________________________
> > > > >>> Swift-devel mailing list
> > > > >>> Swift-devel at ci.uchicago.edu
> > > > >>>
> > > > >>
> > >
> >
>
http://mail.ci.uchicago.edu/mailman/listinfo/swift-devel
> > > > >>>
> > > > >>
> > > > >>
> > > > >>      
> > >
> >
>
____________________________________________________________________________________
> > > > >> Be a better friend, newshound, and 
> > > > >> know-it-all with Yahoo! Mobile.  Try it
> now. 
> > >
> >
>
http://mobile.yahoo.com/;_ylt=Ahu06i62sR8HDtDypao8Wcj9tAcJ
> > > 
> > > > >>
> > > > >>
> _______________________________________________
> > > > >> 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
> > > > > 
> > > > > 
> > > > 
> > > 
> > > _______________________________________________
> > > Swift-devel mailing list
> > > Swift-devel at ci.uchicago.edu
> > >
> >
>
http://mail.ci.uchicago.edu/mailman/listinfo/swift-devel
> > > 
> > > 
> > 
> > 
> > 
> >      
>
____________________________________________________________________________________
> > Looking for last minute shopping deals?  
> > Find them fast with Yahoo! Search. 
>
http://tools.search.yahoo.com/newsearch/category.php?category=shopping
> > 
> 
> _______________________________________________
> Swift-devel mailing list
> 
=== message truncated ===



      ____________________________________________________________________________________
Looking for last minute shopping deals?  
Find them fast with Yahoo! Search.  http://tools.search.yahoo.com/newsearch/category.php?category=shopping


From hategan at mcs.anl.gov  Thu Dec  6 11:21:11 2007
From: hategan at mcs.anl.gov (Mihael Hategan)
Date: Thu, 06 Dec 2007 11:21:11 -0600
Subject: [Swift-devel] script that returns bad parameter error
In-Reply-To: <782829.23701.qm@web52304.mail.re2.yahoo.com>
References: <782829.23701.qm@web52304.mail.re2.yahoo.com>
Message-ID: <1196961671.15996.0.camel@blabla.mcs.anl.gov>

What does tc.data say?

Mihael

On Thu, 2007-12-06 at 09:15 -0800, Mike Kubal wrote:
> I took out the project tag and same results. Here's
> the section run_fred****.log where the failure occurs:
> 
> 2007-12-06 10:44:14,968 DEBUG Loader Recompilation
> suppressed.
> 2007-12-06 10:44:19,096 INFO  unknown Using sites
> file: sites-purdue-64-gram.xml
> 2007-12-06 10:44:19,097 INFO  unknown Using tc.data:
> tc-purdue.data
> 2007-12-06 10:44:22,303 DEBUG GetFieldValue
> GetFieldValue(true)
> 2007-12-06 10:44:22,311 DEBUG GetFieldValue
> GetFieldValue(true)
> 2007-12-06 10:44:28,408 DEBUG TaskImpl Task(type=4,
> identity=urn:0-0-1-0-1196959457323) setting status to
> Active
> 2007-12-06 10:44:28,502 DEBUG TaskImpl Task(type=4,
> identity=urn:0-0-1-0-1196959457323) setting status to
> Completed
> 2007-12-06 10:44:28,553 DEBUG TaskImpl Task(type=2,
> identity=urn:0-0-1-0-1196959457326) setting status to
> Submitted
> 2007-12-06 10:44:28,554 DEBUG TaskImpl Task(type=2,
> identity=urn:0-0-1-0-1196959457326) setting status to
> Active
> 2007-12-06 10:44:29,022 DEBUG TaskImpl Task(type=2,
> identity=urn:0-0-1-0-1196959457326) setting status to
> Completed
> 2007-12-06 10:44:29,026 DEBUG TaskImpl Task(type=2,
> identity=urn:0-0-1-0-1196959457330) setting status to
> Submitted
> 2007-12-06 10:44:29,026 DEBUG TaskImpl Task(type=2,
> identity=urn:0-0-1-0-1196959457330) setting status to
> Active
> 2007-12-06 10:44:29,464 DEBUG TaskImpl Task(type=2,
> identity=urn:0-0-1-0-1196959457330) setting status to
> Completed
> 2007-12-06 10:44:29,470 DEBUG vdl:execute2 Job
> run_fred-fqolp4li running in thread 0-0-1-0 run
> zh499u762hal2
> 2007-12-06 10:44:29,482 INFO  vdl:execute2 Creating
> temporary directory
> run_fred-zh499u762hal2/run_fred-fqolp4li on Lear
> 2007-12-06 10:44:29,500 INFO  vdl:createdirs Creating
> directory structure  in run_fred-zh499u762hal2/shared
> (run_fred-zh499u762hal2/shared/)
> 2007-12-06 10:44:29,502 DEBUG TaskImpl Task(type=4,
> identity=urn:0-0-1-0-1196959457333) setting status to
> Active
> 2007-12-06 10:44:29,525 DEBUG TaskImpl Task(type=4,
> identity=urn:0-0-1-0-1196959457333) setting status to
> Completed
> 2007-12-06 10:44:29,538 DEBUG TaskImpl Task(type=4,
> identity=urn:0-0-1-0-2-1196959457335) setting status
> to Active
> 2007-12-06 10:44:29,540 DEBUG TaskImpl Task(type=4,
> identity=urn:0-0-1-0-1-1196959457338) setting status
> to Active
> 2007-12-06 10:44:29,542 DEBUG TaskImpl Task(type=4,
> identity=urn:0-0-1-0-2-1196959457335) setting status
> to Completed
> 2007-12-06 10:44:29,551 DEBUG TaskImpl Task(type=4,
> identity=urn:0-0-1-0-1-1196959457338) setting status
> to Completed
> 2007-12-06 10:44:29,566 INFO  vdl:dostagein Staging in
> Marsha_lig_1.mol2 ( - Marsha_lig_1.mol2 to
> run_fred-zh499u762hal2/shared/ on Lear
> 2007-12-06 10:44:29,567 INFO  vdl:dostagein Staging in
> 1beh.oeb.gz ( - 1beh.oeb.gz to
> run_fred-zh499u762hal2/shared/ on Lear
> 2007-12-06 10:44:29,570 DEBUG TaskImpl Task(type=2,
> identity=urn:0-0-1-0-1-1196959457342) setting status
> to Submitted
> 2007-12-06 10:44:29,571 DEBUG TaskImpl Task(type=2,
> identity=urn:0-0-1-0-1-1196959457342) setting status
> to Active
> 2007-12-06 10:44:29,571 DEBUG TaskImpl Task(type=2,
> identity=urn:0-0-1-0-2-1196959457345) setting status
> to Submitted
> 2007-12-06 10:44:29,572 DEBUG TaskImpl Task(type=2,
> identity=urn:0-0-1-0-2-1196959457345) setting status
> to Active
> 2007-12-06 10:44:30,005 DEBUG TaskImpl Task(type=2,
> identity=urn:0-0-1-0-1-1196959457342) setting status
> to Completed
> 2007-12-06 10:44:30,007 INFO  vdl:dostagein Staged in
> Marsha_lig_1.mol2 to run_fred-zh499u762hal2/shared/ on
> Lear
> 2007-12-06 10:44:31,703 DEBUG TaskImpl Task(type=2,
> identity=urn:0-0-1-0-2-1196959457345) setting status
> to Completed
> 2007-12-06 10:44:31,705 INFO  vdl:dostagein Staged in
> 1beh.oeb.gz to run_fred-zh499u762hal2/shared/ on Lear
> 2007-12-06 10:44:31,707 INFO  vdl:execute2 Running job
> run_fred-fqolp4li run_fred with arguments [-rec,
> 1beh.oeb.gz, -dbase, Marsha_lig_1.mol2, -prefix,
> Marsha_li\
> g_1] in run_fred-zh499u762hal2/run_fred-fqolp4li on
> Lear
> 2007-12-06 10:44:32,925 DEBUG TaskImpl Task(type=1,
> identity=urn:0-0-1-0-1196959457349) setting status to
> Failed Parameter not supported
> 2007-12-06 10:44:32,938 DEBUG vdl:execute2 Application
> exception: Parameter not supported
>         task:execute @ vdl-int.k, line: 328
>         sys:sequential @ vdl-int.k, line: 316
>         sys:try @ vdl-int.k, line: 315
>         task:allocatehost @ vdl-int.k, line: 298
>         vdl:execute2 @ execute-default.k, line: 22
>         sys:restartonerror @ execute-default.k, line:
> 20
>         sys:sequential @ execute-default.k, line: 19
>         sys:try @ execute-default.k, line: 18
>         sys:if @ execute-default.k, line: 17
>         sys:then @ execute-default.k, line: 16
>         sys:if @ execute-default.k, line: 15
>         vdl:execute @ run_fred.kml, line: 20
>         run_fred @ run_fred.kml, line: 151
>         sys:parallel @ run_fred.kml, line: 150
>         sys:parallelfor @ run_fred.kml, line: 80
>         sys:parallel @ run_fred.kml, line: 79
>         vdl:mainp @ run_fred.kml, line: 78
>         mainp @ vdl.k, line: 141
>         vdl:mains @ run_fred.kml, line: 77
>         vdl:mains @ run_fred.kml, line: 77
>         rlog:restartlog @ run_fred.kml, line: 75
>         kernel:project @ run_fred.kml, line: 2
>         run_fred-zh499u762hal2
> Caused by: org.globus.gram.GramException: Parameter
> not supported
> 
> 
> --- Mihael Hategan <hategan at mcs.anl.gov> wrote:
> 
> > I think I've seen fork complaining about "project"
> > before. Can you try
> > to comment that profile tag out and run with fork
> > again?
> > 
> > It may also be useful to post the logs since they
> > may contain stack
> > traces that point more accurately towards the
> > problem.
> > 
> > Mihael
> > 
> > On Thu, 2007-12-06 at 08:15 -0800, Mike Kubal wrote:
> > > Hi Mihael,
> > > 
> > > No need to apologize, I appreciate your feedback.
> > > 
> > > Here is the sites file.
> > > 
> > > <?xml version="1.0" encoding="UTF-8"?>
> > > <config
> > >
> >
> xmlns="http://www.griphyn.org/chimera/GVDS-PoolConfig"
> > >
> >
> xsi:schemaLocation="http://www.griphyn.org/chimera/GVDS
> > > 
> > http://www.griphyn.org/chimera/gvds-poolcfg-1.5.xsd"
> > >
> >
> xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
> > > version="1.5">
> > > 
> > > <pool handle="Lear" sysinfo="INTEL64::LINUX">
> > >     <gridftp 
> > > url="gsiftp://gridftp.purdue.teragrid.org"
> > > storage="/autohome/u102/mkubal/SWIFT_working_dir"
> > > major="2" minor="2" patch="4">
> > >     </gridftp>
> > >     <profile namespace="globus"
> > > key="project">UC-MCA01S018</profile>
> > >     <jobmanager universe="vanilla"
> > >
> >
> url="tg-gatekeeper.purdue.teragrid.org:2119/jobmanager-fork"
> > > major="2" minor="0" patch="0"/>
> > >    
> > >
> >
> <workdirectory>/autohome/u102/mkubal/SWIFT_working_dir</workdirectory>
> > >   </pool>
> > > </config>
> > > 
> > > I  have also tried the condor job manager at
> > Purdue
> > > that has the same url except that it ends in
> > '-condor'
> > > instead of '-fork' . I get the same error.
> > > 
> > > Cheers,
> > > 
> > > Mike
> > > 
> > > 
> > > 
> > > 
> > > 
> > > --- Mihael Hategan <hategan at mcs.anl.gov> wrote:
> > > 
> > > > Sorry. My email wasn't very friendly. I was
> > trying
> > > > to type less :)
> > > > 
> > > > On Wed, 2007-12-05 at 17:42 -0600, Michael Wilde
> > > > wrote:
> > > > > Mike,
> > > > > 
> > > > > Mihael suspects that a bad globus parameter in
> > > > your sites.xml file is 
> > > > > causing this error message.  So please send
> > that
> > > > so we can take a look.
> > > > > 
> > > > > Thanks,
> > > > > 
> > > > > MikeW
> > > > > 
> > > > > On 12/5/07 4:45 PM, Mihael Hategan wrote:
> > > > > > Post the sites file.
> > > > > > 
> > > > > > On Wed, 2007-12-05 at 14:33 -0800, Mike
> > Kubal
> > > > wrote:
> > > > > >> Unfortunately I still get the same error:
> > > > > >>
> > > > > >> run_fred failed
> > > > > >> The following errors have occurred:
> > > > > >> 1. Application "run_fred" failed (Parameter
> > not
> > > > > >> supported)
> > > > > >>         Arguments: "-rec, 1beh.oeb.gz,
> > -dbase,
> > > > > >> Marsha_lig_1.mol2, -prefix, Marsha_lig_1"
> > > > > >>         Host: Lear
> > > > > >>         Directory:
> > > > > >> run_fred-2k0629rvbffz0/run_fred-r81pg3li
> > > > > >>         STDERR: 
> > > > > >>         STDOUT:
> > > > > >>
> > > > > >> Does 'Parameter not supported' usually
> > refer to
> > > > an
> > > > > >> argument of the remote application? I
> > wonder if
> > > > it
> > > > > >> does not like the .oeb.gz file?
> > > > > >>
> > > > > >>
> > > > > >>
> > > > > >> --- Ben Clifford <benc at hawaga.org.uk>
> > wrote:
> > > > > >>
> > > > > >>>
> > > > > >>> On Wed, 5 Dec 2007, Mike Kubal wrote:
> > > > > >>>
> > > > > >>>>              run_fred "-rec"
> > receptor_file
> > > > > >>> "-dbase"
> > > > > >>>> ligand_file "-prefix" ligand_prefix;
> > > > > >>> In here, take the filenames of each file
> > by
> > > > saying 
> > > > > >>> @filenmame(receptor_file), like this:
> > > > > >>>
> > > > > >>>>             run_fred "-rec"
> > > > > >>> @filename(receptor_file) "-dbase"
> > > > > >>>> @filename(ligand_file) "-prefix"
> > > > ligand_prefix;
> > > > > >>> -- 
> > > > > >>>
> > > > _______________________________________________
> > > > > >>> Swift-devel mailing list
> > > > > >>> Swift-devel at ci.uchicago.edu
> > > > > >>>
> > > > > >>
> > > >
> > >
> >
> http://mail.ci.uchicago.edu/mailman/listinfo/swift-devel
> > > > > >>>
> > > > > >>
> > > > > >>
> > > > > >>      
> > > >
> > >
> >
> ____________________________________________________________________________________
> > > > > >> Be a better friend, newshound, and 
> > > > > >> know-it-all with Yahoo! Mobile.  Try it
> > now. 
> > > >
> > >
> >
> http://mobile.yahoo.com/;_ylt=Ahu06i62sR8HDtDypao8Wcj9tAcJ
> > > > 
> > > > > >>
> > > > > >>
> > _______________________________________________
> > > > > >> 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
> > > > > > 
> > > > > > 
> > > > > 
> > > > 
> > > > _______________________________________________
> > > > Swift-devel mailing list
> > > > Swift-devel at ci.uchicago.edu
> > > >
> > >
> >
> http://mail.ci.uchicago.edu/mailman/listinfo/swift-devel
> > > > 
> > > > 
> > > 
> > > 
> > > 
> > >      
> >
> ____________________________________________________________________________________
> > > Looking for last minute shopping deals?  
> > > Find them fast with Yahoo! Search. 
> >
> http://tools.search.yahoo.com/newsearch/category.php?category=shopping
> > > 
> > 
> > _______________________________________________
> > Swift-devel mailing list
> > 
> === message truncated ===
> 
> 
> 
>       ____________________________________________________________________________________
> Looking for last minute shopping deals?  
> Find them fast with Yahoo! Search.  http://tools.search.yahoo.com/newsearch/category.php?category=shopping
> 



From wilde at mcs.anl.gov  Thu Dec  6 12:42:04 2007
From: wilde at mcs.anl.gov (Michael Wilde)
Date: Thu, 06 Dec 2007 12:42:04 -0600
Subject: [Swift-devel] script that returns bad parameter error
In-Reply-To: <4757389D.7030309@mcs.anl.gov>
References: <753687.67764.qm@web52301.mail.re2.yahoo.com>
	<4757389D.7030309@mcs.anl.gov>
Message-ID: <4758427C.4040608@mcs.anl.gov>

MikeK, did you see this message and adjust your code accordingly?

I suspect this is the problem.

- MikeW

On 12/5/07 5:47 PM, Michael Wilde wrote:
> I need to take a close look later when I get a chance, but i'm a bit 
> suspicious of the use of the file type variables receptor_file and 
> ligand_file without the @ or @filename inside your app{} construct in 
> run_fred().
> 
> Will check later if thats what gives this message.
> 
> you want to say:
> 
>         app {
>              run_fred "-rec" @receptor_file "-dbase"
>  @ligand_file "-prefix" ligand_prefix;>         }
> 
> See the users guide at 
> http://www.ci.uchicago.edu/swift/guides/userguide.php
> sec 2.3.1
> 
> and the tutorial example, Mike.
> 
> - MikeW
> 
> 
> On 12/5/07 2:56 PM, Mike Kubal wrote:
>> Any thoughts on what might cause?
>> type file {}
>>
>> (file score, file docked) run_fred (string
>> ligand_prefix, file ligand_file, file receptor_file){
>>         app {
>>              run_fred "-rec" receptor_file "-dbase"
>> ligand_file "-prefix" ligand_prefix;
>>         }
>> }
>>
>>
>> string receptor_prefix = "1beh";
>>
>> file receptor_file
>> <single_file_mapper;file=@strcat(receptor_prefix,".oeb.gz")>;
>>
>> file
>> fls[]<filesys_mapper;pattern="Marsha_lig_*.mol2",location=".">;
>>
>> foreach ligand_file in fls{
>>
>>         string ligand_prefix =
>> @strcut(@ligand_file,"\.\/(.*)\.mol2");
>>         string score_file_name =
>> @strcat(ligand_prefix,"_chemgauss3_scores.txt");
>>         string docked_file_name =
>> @strcat(ligand_prefix,"_chemgauss3_docked.mol2");
>>         file score_file
>> <single_file_mapper;file=@strcat(ligand_prefix,"_chemgauss3_scores.txt")>; 
>>
>>         file docked_file
>> <single_file_mapper;file=@strcat(ligand_prefix,"_chemgauss3_docked.mol2")>; 
>>
>>
>>         (score_file,docked_file) =
>> run_fred(ligand_prefix,ligand_file,receptor_file);
>>
>> }
>>
>>
>> Thanks,
>>
>> Mike Kubal
>>
>>
>>       
>> ____________________________________________________________________________________ 
>>
>> Never miss a thing.  Make Yahoo your home page. http://www.yahoo.com/r/hs
>> _______________________________________________
>> 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 wilde at mcs.anl.gov  Thu Dec  6 12:43:56 2007
From: wilde at mcs.anl.gov (Michael Wilde)
Date: Thu, 06 Dec 2007 12:43:56 -0600
Subject: [Swift-devel] script that returns bad parameter error
In-Reply-To: <488755.34200.qm@web52304.mail.re2.yahoo.com>
References: <488755.34200.qm@web52304.mail.re2.yahoo.com>
Message-ID: <475842EC.4090000@mcs.anl.gov>

OK, sorry - I see. I missed this message.

- Mike

On 12/5/07 4:33 PM, Mike Kubal wrote:
> Unfortunately I still get the same error:
> 
> run_fred failed
> The following errors have occurred:
> 1. Application "run_fred" failed (Parameter not
> supported)
>         Arguments: "-rec, 1beh.oeb.gz, -dbase,
> Marsha_lig_1.mol2, -prefix, Marsha_lig_1"
>         Host: Lear
>         Directory:
> run_fred-2k0629rvbffz0/run_fred-r81pg3li
>         STDERR: 
>         STDOUT:
> 
> Does 'Parameter not supported' usually refer to an
> argument of the remote application? I wonder if it
> does not like the .oeb.gz file?
> 
> 
> 
> --- Ben Clifford <benc at hawaga.org.uk> wrote:
> 
>>
>> On Wed, 5 Dec 2007, Mike Kubal wrote:
>>
>>>              run_fred "-rec" receptor_file
>> "-dbase"
>>> ligand_file "-prefix" ligand_prefix;
>> In here, take the filenames of each file by saying 
>> @filenmame(receptor_file), like this:
>>
>>>             run_fred "-rec"
>> @filename(receptor_file) "-dbase"
>>> @filename(ligand_file) "-prefix" ligand_prefix;
>> -- 
>> _______________________________________________
>> Swift-devel mailing list
>> Swift-devel at ci.uchicago.edu
>>
> http://mail.ci.uchicago.edu/mailman/listinfo/swift-devel
>>
> 
> 
> 
>       ____________________________________________________________________________________
> Be a better friend, newshound, and 
> know-it-all with Yahoo! Mobile.  Try it now.  http://mobile.yahoo.com/;_ylt=Ahu06i62sR8HDtDypao8Wcj9tAcJ 
> 
> _______________________________________________
> 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 Dec  6 16:22:35 2007
From: benc at hawaga.org.uk (Ben Clifford)
Date: Thu, 6 Dec 2007 22:22:35 +0000 (GMT)
Subject: [Swift-devel] dataset marking
Message-ID: <Pine.LNX.4.64.0712062159530.28498@dildano.hawaga.org.uk>


The present SwiftScript->karajan compiler contains a bunch of code to do 
'dataset marking'.

Its a bit tangled, as the other code has evolved around it, and my 
understanding of it is correspondingly tangled. So please speak out if 
there is a problem with the following.

The purpose of the dataset marking is to identify which dataset 
declarations in a SwiftScript program are inputs (to the whole workflow) 
and mark them as such in the compiled code. A dataset is an input if it is 
never assigned to; if it is assigned to then it is not an input.

I worked on some code that changes the way that arrays are closed, by 
identifying which statements write to a dataset, at compile time.

This information is also what is needed, I think, to do the above 
mentioned dataset marking - the same code which finds out that some 
statements are writing to a dataset will also find out that some datasets 
have no statements at all writing to them.

-- 


From hategan at mcs.anl.gov  Fri Dec  7 10:50:02 2007
From: hategan at mcs.anl.gov (Mihael Hategan)
Date: Fri, 07 Dec 2007 10:50:02 -0600
Subject: [Swift-devel] dataset marking
In-Reply-To: <Pine.LNX.4.64.0712062159530.28498@dildano.hawaga.org.uk>
References: <Pine.LNX.4.64.0712062159530.28498@dildano.hawaga.org.uk>
Message-ID: <1197046202.7260.1.camel@blabla.mcs.anl.gov>

That's my understanding of it, too.

There are some special cases. Static mappers. They know how many
elements there are in an array, so for those the array can be closed as
soon as they are mapped. But this applies to the other problem.

On Thu, 2007-12-06 at 22:22 +0000, Ben Clifford wrote:
> The present SwiftScript->karajan compiler contains a bunch of code to do 
> 'dataset marking'.
> 
> Its a bit tangled, as the other code has evolved around it, and my 
> understanding of it is correspondingly tangled. So please speak out if 
> there is a problem with the following.
> 
> The purpose of the dataset marking is to identify which dataset 
> declarations in a SwiftScript program are inputs (to the whole workflow) 
> and mark them as such in the compiled code. A dataset is an input if it is 
> never assigned to; if it is assigned to then it is not an input.
> 
> I worked on some code that changes the way that arrays are closed, by 
> identifying which statements write to a dataset, at compile time.
> 
> This information is also what is needed, I think, to do the above 
> mentioned dataset marking - the same code which finds out that some 
> statements are writing to a dataset will also find out that some datasets 
> have no statements at all writing to them.
> 



From benc at hawaga.org.uk  Fri Dec  7 10:54:12 2007
From: benc at hawaga.org.uk (Ben Clifford)
Date: Fri, 7 Dec 2007 16:54:12 +0000 (GMT)
Subject: [Swift-devel] dataset marking
In-Reply-To: <1197046202.7260.1.camel@blabla.mcs.anl.gov>
References: <Pine.LNX.4.64.0712062159530.28498@dildano.hawaga.org.uk>
	<1197046202.7260.1.camel@blabla.mcs.anl.gov>
Message-ID: <Pine.LNX.4.64.0712071652040.23250@dildano.hawaga.org.uk>


On Fri, 7 Dec 2007, Mihael Hategan wrote:

> There are some special cases. Static mappers. They know how many 
> elements there are in an array, so for those the array can be closed as 
> soon as they are mapped. But this applies to the other problem.

OK. That should be ok here still. All existing closings still happen 
except for the one that happened at the end of every compound procedure on 
the procedure outputs (which is what is replaced by the stuff I have been 
playing with).

-- 



From hategan at mcs.anl.gov  Fri Dec  7 12:28:41 2007
From: hategan at mcs.anl.gov (Mihael Hategan)
Date: Fri, 07 Dec 2007 12:28:41 -0600
Subject: [Swift-devel] dataset marking
In-Reply-To: <Pine.LNX.4.64.0712071652040.23250@dildano.hawaga.org.uk>
References: <Pine.LNX.4.64.0712062159530.28498@dildano.hawaga.org.uk>
	<1197046202.7260.1.camel@blabla.mcs.anl.gov>
	<Pine.LNX.4.64.0712071652040.23250@dildano.hawaga.org.uk>
Message-ID: <1197052121.7631.0.camel@blabla.mcs.anl.gov>

Sounds right then.

On Fri, 2007-12-07 at 16:54 +0000, Ben Clifford wrote:
> On Fri, 7 Dec 2007, Mihael Hategan wrote:
> 
> > There are some special cases. Static mappers. They know how many 
> > elements there are in an array, so for those the array can be closed as 
> > soon as they are mapped. But this applies to the other problem.
> 
> OK. That should be ok here still. All existing closings still happen 
> except for the one that happened at the end of every compound procedure on 
> the procedure outputs (which is what is replaced by the stuff I have been 
> playing with).
> 



From raffaele.montella at uniparthenope.it  Fri Dec  7 14:16:00 2007
From: raffaele.montella at uniparthenope.it (Dr. Raffaele Montella)
Date: Fri, 7 Dec 2007 14:16:00 -0600
Subject: [Swift-devel] On demand weather forecast using Swift
Message-ID: <002701c8390d$fc8e9560$f5abc020$@montella@uniparthenope.it>

Hi,

just to practicing in swift I'm porting my grid application for on demand
weather forecast  from a xml based workflow engine to Swift a workflow.

The Swift expression capability is great.

With this email here you are my (not full working) Swift code.

I have few questions:

1)      The most part of functions retrieves and array of files I
implemented using the filesys_mapper. I hope I used the right syntax, but
Swift simply does nothing. I mean, the job is not submitted to the remote
machine. I have to stop it with CTRL+C. On the logfile I have this message:

 

2007-12-07 20:07:49,210+0000 DEBUG Loader Recompilation suppressed.

2007-12-07 20:07:52,507+0000 INFO  unknown Using sites file: sites.xml

2007-12-07 20:07:52,508+0000 INFO  unknown Using tc.data: tc.data

2007-12-07 20:07:54,287+0000 WARN  JavaUtils Unable to find required classes
(javax.activation.DataHandler and javax.mail.internet.MimeMultipart).
Attachment support is disabled.

2007-12-07 20:07:56,560+0000 INFO  unknown Swift v0.3-dev r1507

 

2007-12-07 20:07:56,563+0000 INFO  unknown RunID: 20071207-2007-95unaxd2

2007-12-07 20:07:56,898+0000 INFO  AbstractDataNode Adding handle listener
"Open, 0 elements, no listeners" to "terrainDomains.$[]/0"

2007-12-07 20:07:56,927+0000 INFO  AbstractDataNode Adding handle listener
"F/terrainDomains.$[]/0" to "terrainDomains.$[]/0"

 

2)      All modules belonging my applications want in the ./input input
files and produce in ./output their results. I never reached this point
because the point 1 fails, how work the file mapper in this case? I mean, if
the regrid produces the regridDomains array of files mapped somewhere but
./output/REGRID_DOMAINx.gz when it is staged-in as input for the interpf
where it is copied? ./output/. ? Eventually, how can I change this behavior
in order to stage in in ./input what previously whas staged out from
./output?

 

Thank you in advance,

  A Swift enthusiastic - Raffaele

-----------------------

The Swift Workflow:

 

// Data type definition

type terrainDomainType;

 

type initialDataType;

type dataFileType;

type sstFileType;

type snowFileType;

 

type regridDomainType;

 

type mmInputDomainType;

type bdyOutDomainType;

type lowBdyDomainType;

 

type mmOutputDomainType;

 

// Terrain function

(terrainDomainType terrainDomains[])terrain(string lon, string lat, int
nests) {

  app { terrain lon lat nests @terrainDomains; }

}

 

// Pregrid function

(dataFileType dataFiles[], sstFileType sstFiles[], snowFileType snowFiles[]
)pregrid(string iDate, int hours, initialDataType initalData) {

  app { pregrid iDate hours @filename(initaialData) @dataFiles @sstFiles
@snowFiles; }

}

 

// Regrid function

(regridDomainType regridDomains[]) regrdi( terrainDomainType terrainDomain,
dataFileType dataFiles, sstFileType sstFiles, snowFileType snowFiles) {

  app { regrid @terrainDomain @dataFiles @sstFIles @snowFiles
@regridDomains; }

}

 

// Interpf function

(mmInputDomainType mmInputDomains[], bdyOutDomainType dbyOutDomains[],
lowBdyDomainType lowBdyDomains[]) interpf (regridDomainType regridDomain) {

  app { interpf @regridDomain @mmInputDomains @dbyOutDOmains @lowBdyDomains;
}

}

 

// Mpp (parallel MM5) function

(mmOutputDomainType mmOutputDomains[])mmp( terrainDomainType
terrainDomains[], mmInputDomainType mmInputDomains[], bdyOutDomainType
dbyOutDomains[], lowBdyDomainType lowBdyDomains[]) {

  app { mmp @terrainDomains @mmInputDomains @bdyOutDomains @lowBdyDomains
@mmOutputDomains; }

}

 

// Terrain output

terrainDomainType terrainDomains[] <filesys_mapper;location="./output/",
prefix="TERRAIN_DOMAIN", suffix=".gz">;

 

// Pregrid input data

initialDataType initialData[] <filesys_mapper;
location="gsiftp://data.uniparthenope.it//home/infonav/data/ncep/20071207/20
071207Z00", prefix="gfs">;

 

// Pregrid outputs

dataFileType dataFiles[] <filesys_mapper;location="./output/",
prefix="FILE", suffix=".gz">;

sstFileType sstFiles[] <filesys_mapper;location="./output/", prefix="SST",
suffix=".gz">;

snowFileType snowFiles[] <filesys_mapper;location="./output/",
prefix="SNOW", suffix=".gz">;

 

// Regrid outputs

regridDomainType regridDomains[] <filesys_mapper; location="./output/",
prefix="REGRID_DOMAIN", suffix=".gz">;

 

// Interpf outputs

mmInputDomainType mmInputDomains[] <filesys_mapper; location="./output/",
prefix="MMINPUT_DOMAIN", suffix=".gz">;

bdyOutDomainType bdyOutDomains[] <filesys_mapper; location="./output/",
prefix="BDYOUT_DOMAIN", suffix=".gz">;

lowBdyDomainType lowBdyDomains[] <filesys_mapper; location="./output/",
prefix="LOWBDY_DOMAIN", suffix=".gz">;

 

// MM5 output arrays

mmOutputDomainType mmOutputDomains[] <filesys_mapper; location="./output/",
prefix="MMOUTPUT_DOMAIN", suffix=".gz">;

 

//
----------------------------------------------------------------------------
--------

// THE WORKFLOW: on demand weather forecast

//
----------------------------------------------------------------------------
--------

 

// Create the terrain centered on Chicago Pier (two nest levels, max ground
resolution 27km)

terrainDomains = terrain("-87.5992", "41.8919", 2);

 

// Retrieve initial and boundary conditions and prepare data files for next
modules

//(dataFiles, sstFiles, snowFiles) = pregrid( "20071207Z00", 24,
initialData);

 

// Prepare data for each nested domain...

foreach terrainDomain,i in terrainDomains

{

  // Interpolate initial and boundary conditions over the terrain model

  //regridFiles[i] = regrid( terrainDomain, dataFiles, sstFiles, snowFiles);

 

  // Perform more forward interpolation and produce input data form MM5

  //(mmInputDomains[i],bdyOutDomains[i],lowBdyDomains[i]) =
interpf(regridFiles[i]);

}

 

// Run the model

//mmOutputDomains = mpp(terrainDomains, mmInputDomains, bdyOutDomains,
lowBdyDomains);

                                                                       

 

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From benc at hawaga.org.uk  Fri Dec  7 16:21:37 2007
From: benc at hawaga.org.uk (Ben Clifford)
Date: Fri, 7 Dec 2007 22:21:37 +0000 (GMT)
Subject: [Swift-devel] On demand weather forecast using Swift
In-Reply-To: <002701c8390d$fc8e9560$f5abc020$@montella@uniparthenope.it>
References: <002701c8390d$fc8e9560$f5abc020$@montella@uniparthenope.it>
Message-ID: <Pine.LNX.4.64.0712072219300.28498@dildano.hawaga.org.uk>


I think the below fragment of your SwiftScript is the piece that should 
execute before everything else.

Its not clear what the command line for 'terrain' should look like - can 
you post an example of how to manually invoke the terrain application, 
including a real command line?

On Fri, 7 Dec 2007, Dr. Raffaele Montella wrote:

> type terrainDomainType;

> // Terrain function
> 
> (terrainDomainType terrainDomains[])terrain(string lon, string lat, int
> nests) {
> 
>   app { terrain lon lat nests @terrainDomains; }
> 
> }

> terrainDomainType terrainDomains[] <filesys_mapper;location="./output/",
> prefix="TERRAIN_DOMAIN", suffix=".gz">;

> terrainDomains = terrain("-87.5992", "41.8919", 2);



-- 



From raffaele.montella at uniparthenope.it  Fri Dec  7 17:50:06 2007
From: raffaele.montella at uniparthenope.it (Dr. Raffaele Montella)
Date: Fri, 7 Dec 2007 17:50:06 -0600
Subject: [Swift-devel] terrain example
Message-ID: <000001c8392b$e55a3390$b00e9ab0$@montella@uniparthenope.it>

Hi!

 

This is the GRIDMM5_ROOT structure:

 

GRIDMM5_ROOT

!

!--bin

!--data

!     !--terrain

!           !--data

!           !--data30s

!--sbin

!--tars

 

The terrain script is invoked with the following command line syntax:

$GRIDMM5_ROOT/bin/terrain lon lat nests

Where:

(lon,lat): the earth point center of the weather forecast domain

Nests: number of nested domains. For example in nests is equal to 1 is
generated a digital elevation model plus landuse and water/land mask data
centered in (lon,lat) and wide 91 (with a 27km edge) cells west/east ward
and 91 cells north/southward (basically lon,lat is in the middle of a square
domain).

If nests is equal to 2 do domains are generated both centered in (lon, lat).
The first as in the case of nest=1 and the second again wide 91*91 cells,
but each cell is now 27/3 km wide.

The terrain script invokes internally the $GRIDMM5_ROOT/sbin/do_terrain
script (a most general version) filling automatically some parameters
dynamically related (the current scratch directoy) and installation related
(the directory where dem dan high resolution dem data are stored).

The terrain script produces a TERRAIN_DOMAINx.gz file (with x=1..nests) in
the ./output directory.

 

The pregrid script is invoked with the following command line syntax:

$GRIDMM5/bin/pregrid idate hours

Where:

Idate: is the date in the ncep format: YYYYMMDDZHH for example 20071207Z00
(Z00 means data initialized at 00 zuli)

Hours: the number of hours have to be simulated, for example 24.

In order to work, pregrid needs in the directory ./input the content of the
directory:

Gsiftp://data.uniparthenope.it//home/infonav/data/ncep/YYYYMMDD/YYYYMMDDZHH

As output the script produces three gzipped files in ./output directory:
FILE.gz, SST.gz and SNOW.gz that will be used in next steps.

 

Bye and thank you,

  Raffaele

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From benc at hawaga.org.uk  Sun Dec  9 09:38:46 2007
From: benc at hawaga.org.uk (Ben Clifford)
Date: Sun, 9 Dec 2007 15:38:46 +0000 (GMT)
Subject: [Swift-devel] terrain example
In-Reply-To: <000001c8392b$e55a3390$b00e9ab0$@montella@uniparthenope.it>
References: <000001c8392b$e55a3390$b00e9ab0$@montella@uniparthenope.it>
Message-ID: <Pine.LNX.4.64.0712091435000.28498@dildano.hawaga.org.uk>



On Fri, 7 Dec 2007, Dr. Raffaele Montella wrote:

> The terrain script produces a TERRAIN_DOMAINx.gz file (with x=1..nests) in
> the ./output directory.

At the moment, Swift cannot deal with variable numbers of output files 
from a program.

In your code, you map this:

  terrainDomainType terrainDomains[] <filesys_mapper;
     location="./output/", 
     prefix="TERRAIN_DOMAIN",
     suffix=".gz">;

and then try to use this as a return value, like this:

  (terrainDomainType terrainDomains[])terrain(string lon, string lat, int 
   nests) {

At the moment, Swift doesn't know how to deal with that - it does not know 
how to deal with output files where the names are not known before 
invocation.

You might be able to hack around in certain cases by explicitly listing 
the files - declare terrainDomains like this:

terrainDomainType terrainDomains[] <fixed_array_mapper;
  files="output/TERRAIN_DOMAIN1.gz output/TERRAIN_DOMAIN2.gz">;

However, this needs to a different declaration for every different value 
of nests, so is not a very good solution.

Better handling of this kind of situation is on the to-do list, but it 
won't happen soon.

-- 


From raffaele.montella at uniparthenope.it  Sun Dec  9 12:45:10 2007
From: raffaele.montella at uniparthenope.it (Dr. Raffaele Montella)
Date: Sun, 9 Dec 2007 12:45:10 -0600
Subject: R: [Swift-devel] terrain example
In-Reply-To: <Pine.LNX.4.64.0712091435000.28498@dildano.hawaga.org.uk>
References: <000001c8392b$e55a3390$b00e9ab0$@montella@uniparthenope.it>
	<Pine.LNX.4.64.0712091435000.28498@dildano.hawaga.org.uk>
Message-ID: <000a01c83a93$a0803760$e180a620$@montella@uniparthenope.it>

Hi Ben!
Thank you! I will hack around using a fixed number of nests as a better
solution will be available!
I'll post my code as soon as it will be working.
Bye,
  Raffaele

-----Messaggio originale-----
Da: Ben Clifford [mailto:benc at hawaga.org.uk] 
Inviato: domenica 9 dicembre 2007 9.39
A: Dr. Raffaele Montella
Cc: swift-devel at ci.uchicago.edu
Oggetto: Re: [Swift-devel] terrain example



On Fri, 7 Dec 2007, Dr. Raffaele Montella wrote:

> The terrain script produces a TERRAIN_DOMAINx.gz file (with x=1..nests) in
> the ./output directory.

At the moment, Swift cannot deal with variable numbers of output files 
from a program.

In your code, you map this:

  terrainDomainType terrainDomains[] <filesys_mapper;
     location="./output/", 
     prefix="TERRAIN_DOMAIN",
     suffix=".gz">;

and then try to use this as a return value, like this:

  (terrainDomainType terrainDomains[])terrain(string lon, string lat, int 
   nests) {

At the moment, Swift doesn't know how to deal with that - it does not know 
how to deal with output files where the names are not known before 
invocation.

You might be able to hack around in certain cases by explicitly listing 
the files - declare terrainDomains like this:

terrainDomainType terrainDomains[] <fixed_array_mapper;
  files="output/TERRAIN_DOMAIN1.gz output/TERRAIN_DOMAIN2.gz">;

However, this needs to a different declaration for every different value 
of nests, so is not a very good solution.

Better handling of this kind of situation is on the to-do list, but it 
won't happen soon.

-- 




From bugzilla-daemon at mcs.anl.gov  Mon Dec 10 08:23:20 2007
From: bugzilla-daemon at mcs.anl.gov (bugzilla-daemon at mcs.anl.gov)
Date: Mon, 10 Dec 2007 08:23:20 -0600 (CST)
Subject: [Swift-devel] [Bug 116] New: simple_mapper handling of numbered
	files in arrays broken
Message-ID: <bug-116-21@http.bugzilla.mcs.anl.gov/swift/>

http://bugzilla.mcs.anl.gov/swift/show_bug.cgi?id=116

           Summary: simple_mapper handling of numbered files in arrays
                    broken
           Product: Swift
           Version: unspecified
          Platform: Macintosh
        OS/Version: All
            Status: NEW
          Severity: normal
          Priority: P2
         Component: General
        AssignedTo: benc at hawaga.org.uk
        ReportedBy: benc at hawaga.org.uk
                CC: swift-devel at ci.uchicago.edu


simple mapper is formatting numbers used to index arrays that it maps in a way
that is incompatible with the filename on disk.

With:

$ ls *.in
1.in 2.in

the declaration:
file inputs[] <simple_mapper;suffix=".in">;
correctly creates an array with two elements, having detected 1.in and 2.in on
disk; however when mapping filenames for inputs[1] and inputs[2], the filenames
are padded to 0001.in and 0002.in which are not the correct filenames. This
causes runtime error.

This is with version r1515


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From mikekubal at yahoo.com  Mon Dec 10 17:47:00 2007
From: mikekubal at yahoo.com (Mike Kubal)
Date: Mon, 10 Dec 2007 15:47:00 -0800 (PST)
Subject: [Swift-devel] script that returns bad parameter error
In-Reply-To: <475842EC.4090000@mcs.anl.gov>
Message-ID: <176887.83362.qm@web52304.mail.re2.yahoo.com>

My bad parameter error was fixed by removing the
Globus node type variable from my tc.file. Thanks for
everyone's help.

Cheers,

Mike
--- Michael Wilde <wilde at mcs.anl.gov> wrote:

> OK, sorry - I see. I missed this message.
> 
> - Mike
> 
> On 12/5/07 4:33 PM, Mike Kubal wrote:
> > Unfortunately I still get the same error:
> > 
> > run_fred failed
> > The following errors have occurred:
> > 1. Application "run_fred" failed (Parameter not
> > supported)
> >         Arguments: "-rec, 1beh.oeb.gz, -dbase,
> > Marsha_lig_1.mol2, -prefix, Marsha_lig_1"
> >         Host: Lear
> >         Directory:
> > run_fred-2k0629rvbffz0/run_fred-r81pg3li
> >         STDERR: 
> >         STDOUT:
> > 
> > Does 'Parameter not supported' usually refer to an
> > argument of the remote application? I wonder if it
> > does not like the .oeb.gz file?
> > 
> > 
> > 
> > --- Ben Clifford <benc at hawaga.org.uk> wrote:
> > 
> >>
> >> On Wed, 5 Dec 2007, Mike Kubal wrote:
> >>
> >>>              run_fred "-rec" receptor_file
> >> "-dbase"
> >>> ligand_file "-prefix" ligand_prefix;
> >> In here, take the filenames of each file by
> saying 
> >> @filenmame(receptor_file), like this:
> >>
> >>>             run_fred "-rec"
> >> @filename(receptor_file) "-dbase"
> >>> @filename(ligand_file) "-prefix" ligand_prefix;
> >> -- 
> >> _______________________________________________
> >> Swift-devel mailing list
> >> Swift-devel at ci.uchicago.edu
> >>
> >
>
http://mail.ci.uchicago.edu/mailman/listinfo/swift-devel
> >>
> > 
> > 
> > 
> >      
>
____________________________________________________________________________________
> > Be a better friend, newshound, and 
> > know-it-all with Yahoo! Mobile.  Try it now. 
>
http://mobile.yahoo.com/;_ylt=Ahu06i62sR8HDtDypao8Wcj9tAcJ
> 
> > 
> > _______________________________________________
> > Swift-devel mailing list
> > Swift-devel at ci.uchicago.edu
> >
>
http://mail.ci.uchicago.edu/mailman/listinfo/swift-devel
> > 
> > 
> 



      ____________________________________________________________________________________
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know-it-all with Yahoo! Mobile.  Try it now.  http://mobile.yahoo.com/;_ylt=Ahu06i62sR8HDtDypao8Wcj9tAcJ 



From bugzilla-daemon at mcs.anl.gov  Tue Dec 11 16:41:52 2007
From: bugzilla-daemon at mcs.anl.gov (bugzilla-daemon at mcs.anl.gov)
Date: Tue, 11 Dec 2007 16:41:52 -0600 (CST)
Subject: [Swift-devel] [Bug 116] simple_mapper handling of numbered files in
	arrays broken
In-Reply-To: <bug-116-21@http.bugzilla.mcs.anl.gov/swift/>
Message-ID: <20071211224152.8983516487@foxtrot.mcs.anl.gov>

http://bugzilla.mcs.anl.gov/swift/show_bug.cgi?id=116





------- Comment #1 from tiberius at mcs.anl.gov  2007-12-11 16:41 -------
(In reply to comment #0)

Also, I am using simple mapper to generate file names use as outputs for
parameter sweeps, and I am running out of the name space (4 digits for
numbering is limiting)

Eg:

(file resultsOut[]) paramSweep (){

 foreach i{
   foreach j{
     resultsOut[i*iSize+j] = atomicProcedure(i,j); 
   }
  }
}


file results[]<simple_mapper; prefix="item_", suffix=".txt">;
results = paramSweep();


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From bugzilla-daemon at mcs.anl.gov  Thu Dec 13 07:37:17 2007
From: bugzilla-daemon at mcs.anl.gov (bugzilla-daemon at mcs.anl.gov)
Date: Thu, 13 Dec 2007 07:37:17 -0600 (CST)
Subject: [Swift-devel] [Bug 117] New: multidimensional array support
Message-ID: <bug-117-21@http.bugzilla.mcs.anl.gov/swift/>

http://bugzilla.mcs.anl.gov/swift/show_bug.cgi?id=117

           Summary: multidimensional array support
           Product: Swift
           Version: unspecified
          Platform: Macintosh
        OS/Version: Mac OS
            Status: NEW
          Severity: normal
          Priority: P2
         Component: SwiftScript language
        AssignedTo: benc at hawaga.org.uk
        ReportedBy: benc at hawaga.org.uk
                CC: swift-devel at ci.uchicago.edu


Add multidimensional array support (eg. be able to write  a[i][j])

The main thing that needs to happen here is type system reworking, which isn't
expressive enough at the moment. A small change (actually a simplification) in
the parser allows multiple array access operators ( these -> []) in a row and
lots of stuff related to mulidimensional arrays already works in that case
(though not everything).


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From bugzilla-daemon at mcs.anl.gov  Thu Dec 13 07:38:45 2007
From: bugzilla-daemon at mcs.anl.gov (bugzilla-daemon at mcs.anl.gov)
Date: Thu, 13 Dec 2007 07:38:45 -0600 (CST)
Subject: [Swift-devel] [Bug 115] Swift users encounter long delays waiting
	for random name generation
In-Reply-To: <bug-115-21@http.bugzilla.mcs.anl.gov/swift/>
Message-ID: <20071213133845.92E6B164BB@foxtrot.mcs.anl.gov>

http://bugzilla.mcs.anl.gov/swift/show_bug.cgi?id=115


benc at hawaga.org.uk changed:

           What    |Removed                     |Added
----------------------------------------------------------------------------
             Status|NEW                         |RESOLVED
         Resolution|                            |FIXED




------- Comment #2 from benc at hawaga.org.uk  2007-12-13 07:38 -------
no response to question from reporter. closing.


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From bugzilla-daemon at mcs.anl.gov  Fri Dec 14 07:21:26 2007
From: bugzilla-daemon at mcs.anl.gov (bugzilla-daemon at mcs.anl.gov)
Date: Fri, 14 Dec 2007 07:21:26 -0600 (CST)
Subject: [Swift-devel] [Bug 118] New: syntax error report when [] used
	incorrectly in an expression
Message-ID: <bug-118-21@http.bugzilla.mcs.anl.gov/swift/>

http://bugzilla.mcs.anl.gov/swift/show_bug.cgi?id=118

           Summary: syntax error report when [] used incorrectly in an
                    expression
           Product: Swift
           Version: unspecified
          Platform: Macintosh
        OS/Version: All
            Status: NEW
          Severity: normal
          Priority: P2
         Component: SwiftScript language
        AssignedTo: benc at hawaga.org.uk
        ReportedBy: benc at hawaga.org.uk
                CC: swift-devel at ci.uchicago.edu


volume brainatlas = average(aligned[]);

gives error:

Could not compile SwiftScript source: line 45:19: unexpected token: =

pointing to the = of assignment. It would be preferable if the error is
reported at the incorrect [] pair 
Perhaps indicate missing constant there, as that seems closest to what would be
syntactically correct; although in this case the [] shouldn't have been there
at all.


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From bugzilla-daemon at mcs.anl.gov  Fri Dec 14 09:05:35 2007
From: bugzilla-daemon at mcs.anl.gov (bugzilla-daemon at mcs.anl.gov)
Date: Fri, 14 Dec 2007 09:05:35 -0600 (CST)
Subject: [Swift-devel] [Bug 119] New: kickstart transfer errors mask
	underlying application errors
Message-ID: <bug-119-21@http.bugzilla.mcs.anl.gov/swift/>

http://bugzilla.mcs.anl.gov/swift/show_bug.cgi?id=119

           Summary: kickstart transfer errors mask underlying application
                    errors
           Product: Swift
           Version: unspecified
          Platform: Macintosh
        OS/Version: Mac OS
            Status: NEW
          Severity: normal
          Priority: P2
         Component: SwiftScript language
        AssignedTo: benc at hawaga.org.uk
        ReportedBy: benc at hawaga.org.uk
                CC: swift-devel at ci.uchicago.edu





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From bugzilla-daemon at mcs.anl.gov  Fri Dec 14 09:07:09 2007
From: bugzilla-daemon at mcs.anl.gov (bugzilla-daemon at mcs.anl.gov)
Date: Fri, 14 Dec 2007 09:07:09 -0600 (CST)
Subject: [Swift-devel] [Bug 120] New: kickstart transfer errors mask
	underlying application errors
Message-ID: <bug-120-21@http.bugzilla.mcs.anl.gov/swift/>

http://bugzilla.mcs.anl.gov/swift/show_bug.cgi?id=120

           Summary: kickstart transfer errors mask underlying application
                    errors
           Product: Swift
           Version: unspecified
          Platform: Macintosh
        OS/Version: Mac OS
            Status: NEW
          Severity: normal
          Priority: P2
         Component: SwiftScript language
        AssignedTo: benc at hawaga.org.uk
        ReportedBy: benc at hawaga.org.uk
                CC: swift-devel at ci.uchicago.edu


in r1515
with kickstart enabled
when an application error occurs so that no kickstart record is produced (for
example, missing input file)

then:
the reported error on the console is a kickstart record missing error, rather
than the probably more appropriate application exception. the application
exception continues to appear in the log file.

cat started
Failed to transfer kickstart records from
mfd-20071214-1503-6jtdb0e0/kickstart/z/localhostFile not found:
/var/tmp/mfd-20071214-1503-6jtdb0e0/kickstart/z/cat-zkk7rhli-kickstart.xml
        task:transfer @ vdl-int.k, line: 326
        sys:try @ vdl-int.k, line: 326
        vdl:transferkickstartrec @ vdl-int.k, line: 413
        sys:set @ vdl-int.k, line: 413


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From bugzilla-daemon at mcs.anl.gov  Fri Dec 14 09:07:38 2007
From: bugzilla-daemon at mcs.anl.gov (bugzilla-daemon at mcs.anl.gov)
Date: Fri, 14 Dec 2007 09:07:38 -0600 (CST)
Subject: [Swift-devel] [Bug 119] kickstart transfer errors mask underlying
	application errors
In-Reply-To: <bug-119-21@http.bugzilla.mcs.anl.gov/swift/>
Message-ID: <20071214150738.9774C16487@foxtrot.mcs.anl.gov>

http://bugzilla.mcs.anl.gov/swift/show_bug.cgi?id=119


benc at hawaga.org.uk changed:

           What    |Removed                     |Added
----------------------------------------------------------------------------
             Status|NEW                         |RESOLVED
         Resolution|                            |INVALID




------- Comment #1 from benc at hawaga.org.uk  2007-12-14 09:07 -------
submitted too early


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From bugzilla-daemon at mcs.anl.gov  Fri Dec 14 11:40:42 2007
From: bugzilla-daemon at mcs.anl.gov (bugzilla-daemon at mcs.anl.gov)
Date: Fri, 14 Dec 2007 11:40:42 -0600 (CST)
Subject: [Swift-devel] [Bug 118] syntax error report when [] used
	incorrectly in an expression
In-Reply-To: <bug-118-21@http.bugzilla.mcs.anl.gov/swift/>
Message-ID: <20071214174042.165E1164BB@foxtrot.mcs.anl.gov>

http://bugzilla.mcs.anl.gov/swift/show_bug.cgi?id=118


benc at hawaga.org.uk changed:

           What    |Removed                     |Added
----------------------------------------------------------------------------
             Status|NEW                         |RESOLVED
         Resolution|                            |FIXED




------- Comment #1 from benc at hawaga.org.uk  2007-12-14 11:40 -------
r1516 has a change in the parser for this case. the example line is now
reported as:

Could not compile SwiftScript source: line 1:36: expecting ')', found '['

with column 36 being a closer location.


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From bugzilla-daemon at mcs.anl.gov  Sat Dec 15 09:58:04 2007
From: bugzilla-daemon at mcs.anl.gov (bugzilla-daemon at mcs.anl.gov)
Date: Sat, 15 Dec 2007 09:58:04 -0600 (CST)
Subject: [Swift-devel] [Bug 121] New: declarations with procedure calls do
	not allow declarations of arrays.
Message-ID: <bug-121-21@http.bugzilla.mcs.anl.gov/swift/>

http://bugzilla.mcs.anl.gov/swift/show_bug.cgi?id=121

           Summary: declarations with procedure calls do not allow
                    declarations of arrays.
           Product: Swift
           Version: unspecified
          Platform: All
        OS/Version: All
            Status: NEW
          Severity: normal
          Priority: P2
         Component: SwiftScript language
        AssignedTo: benc at hawaga.org.uk
        ReportedBy: benc at hawaga.org.uk
                CC: swift-devel at ci.uchicago.edu


In r1516, this is not permitted

  file g[] = p(x);

but this is:

  file g[];  g=p(x);

They should both be permitted and should both mean the same thing.


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From benc at hawaga.org.uk  Sun Dec 16 07:38:34 2007
From: benc at hawaga.org.uk (Ben Clifford)
Date: Sun, 16 Dec 2007 13:38:34 +0000 (GMT)
Subject: [Swift-devel] app syntax ambiguity
Message-ID: <Pine.LNX.4.64.0712161331530.18006@dildano.hawaga.org.uk>


Expressions have been mostly self delimiting, which is useful in the app{} 
block syntax where there are no delimiters between the parameters of an 
application. For example, given the input: 21*33 14*96 that can be parsed 
as two expressions, the first one 21*33 and the second one 14*96.

The sequence of tokens for this coming out of the lexer is: 21 * 33 14 * 
96

There's some ambiguity when it comes to unary +/- eg 21 -33 could be 
either a single expression (21-33) or two expressions 21 and -33.

However, no one has commented on having trouble with this before.

Putting in multi-dimensional array support adds more ambiguity along the 
same lines, this time interacting with array literals.

i[1][2] might mean two parameters i[1] and an array literal [2] or it 
might mean one parameter accessing a multidimensional array i[1][2].

Changing the syntax used to specify array literals would resolve this, as 
would putting in specific delimiters in the app block. The former is 
probably the least intrusive in terms of already written user scripts.

-- 


From hategan at mcs.anl.gov  Sun Dec 16 11:57:20 2007
From: hategan at mcs.anl.gov (Mihael Hategan)
Date: Sun, 16 Dec 2007 11:57:20 -0600
Subject: [Swift-devel] app syntax ambiguity
In-Reply-To: <Pine.LNX.4.64.0712161331530.18006@dildano.hawaga.org.uk>
References: <Pine.LNX.4.64.0712161331530.18006@dildano.hawaga.org.uk>
Message-ID: <1197827840.3307.7.camel@blabla.mcs.anl.gov>


On Sun, 2007-12-16 at 13:38 +0000, Ben Clifford wrote:
> Expressions have been mostly self delimiting, which is useful in the app{} 
> block syntax where there are no delimiters between the parameters of an 
> application. For example, given the input: 21*33 14*96 that can be parsed 
> as two expressions, the first one 21*33 and the second one 14*96.
> 
> The sequence of tokens for this coming out of the lexer is: 21 * 33 14 * 
> 96
> 
> There's some ambiguity when it comes to unary +/- eg 21 -33 could be 
> either a single expression (21-33) or two expressions 21 and -33.

Would we be ok (from an aesthetic/usability) perspective with commas as
separators there? Or even with representing the args as an array?

If not, then I think the unary operators should have precedence and if
the user wants to have a single expression, parentheses can be used
(e.g. (21-33) (14+16))

> 
> However, no one has commented on having trouble with this before.
> 
> Putting in multi-dimensional array support adds more ambiguity along the 
> same lines, this time interacting with array literals.
> 
> i[1][2] might mean two parameters i[1] and an array literal [2] or it 
> might mean one parameter accessing a multidimensional array i[1][2].

Or both? As in multidimensional arrays are arrays of arrays. What we
want, I'm guessing, is the possibility to easily pass i[1] as an array
parameter instead of using something like i[i, *].

> 
> Changing the syntax used to specify array literals would resolve this, as 
> would putting in specific delimiters in the app block. The former is 
> probably the least intrusive in terms of already written user scripts.
> 



From benc at hawaga.org.uk  Sun Dec 16 12:15:23 2007
From: benc at hawaga.org.uk (Ben Clifford)
Date: Sun, 16 Dec 2007 18:15:23 +0000 (GMT)
Subject: [Swift-devel] app syntax ambiguity
In-Reply-To: <1197827840.3307.7.camel@blabla.mcs.anl.gov>
References: <Pine.LNX.4.64.0712161331530.18006@dildano.hawaga.org.uk>
	<1197827840.3307.7.camel@blabla.mcs.anl.gov>
Message-ID: <Pine.LNX.4.64.0712161810190.18006@dildano.hawaga.org.uk>



On Sun, 16 Dec 2007, Mihael Hategan wrote:

> Or both? As in multidimensional arrays are arrays of arrays. What we
> want, I'm guessing, is the possibility to easily pass i[1] as an array
> parameter instead of using something like i[i, *].

That's how it looks like it works out anyway. You can already say

  [ [ "foo", "bar" ], ["one", "two", "three" ]]

in the language at the moment - the type system isn't expressive enough to 
represent what the type of the above expression (an array of arrays of 
strings) but the appropriate DSHandle is constructed if you put the above 
in a program (because there's no type checking on array construction).

I think you get what I meant by the ambiguity, though, here:

>> i[1][2] might mean two parameters i[1] and an array literal [2] or it 
>> might mean one parameter accessing a multidimensional array i[1][2].

If i was the above, then i[1][2] might be "bar" (a string), or it might be 
two expressions:
the array with two strings
   ["foo", "bar"]
and then an array with one integer member
   [ 2 ]

In practice, I guess, the greedy-from-the-left way of parsing seems to 
work in all the cases that anyone has come across so far so I'll probably 
leave it.

-- 


From hategan at mcs.anl.gov  Sun Dec 16 14:43:25 2007
From: hategan at mcs.anl.gov (Mihael Hategan)
Date: Sun, 16 Dec 2007 14:43:25 -0600
Subject: [Swift-devel] app syntax ambiguity
In-Reply-To: <Pine.LNX.4.64.0712161810190.18006@dildano.hawaga.org.uk>
References: <Pine.LNX.4.64.0712161331530.18006@dildano.hawaga.org.uk>
	<1197827840.3307.7.camel@blabla.mcs.anl.gov>
	<Pine.LNX.4.64.0712161810190.18006@dildano.hawaga.org.uk>
Message-ID: <1197837805.5877.5.camel@blabla.mcs.anl.gov>


On Sun, 2007-12-16 at 18:15 +0000, Ben Clifford wrote:
> 
> On Sun, 16 Dec 2007, Mihael Hategan wrote:
> 
> > Or both? As in multidimensional arrays are arrays of arrays. What we
> > want, I'm guessing, is the possibility to easily pass i[1] as an array
> > parameter instead of using something like i[i, *].
> 
> That's how it looks like it works out anyway. You can already say
> 
>   [ [ "foo", "bar" ], ["one", "two", "three" ]]
> 
> in the language at the moment - the type system isn't expressive enough to 
> represent what the type of the above expression (an array of arrays of 
> strings) but the appropriate DSHandle is constructed if you put the above 
> in a program (because there's no type checking on array construction).
> 
> I think you get what I meant by the ambiguity, though, here:

I didn't. But I do now.

> 
> >> i[1][2] might mean two parameters i[1] and an array literal [2] or it 
> >> might mean one parameter accessing a multidimensional array i[1][2].
> 
> If i was the above, then i[1][2] might be "bar" (a string), or it might be 
> two expressions:
> the array with two strings
>    ["foo", "bar"]
> and then an array with one integer member
>    [ 2 ]
> 
> In practice, I guess, the greedy-from-the-left way of parsing seems to 
> work in all the cases that anyone has come across so far so I'll probably 
> leave it.

So let's be clear. This only applies to app{} blocks, right?

The syntax is somewhat ambiguous there. But the least surprise in the
context in which our multi-dimensional arrays are accessed as a[i][j]...
is for i[1][2] to mean i[1, 2]. I think the distinction can be made
based on whitespace between ']' and '['. I.e. i[1][2] vs. i[1] [2].

> 



From benc at hawaga.org.uk  Sun Dec 16 14:53:16 2007
From: benc at hawaga.org.uk (Ben Clifford)
Date: Sun, 16 Dec 2007 20:53:16 +0000 (GMT)
Subject: [Swift-devel] app syntax ambiguity
In-Reply-To: <1197837805.5877.5.camel@blabla.mcs.anl.gov>
References: <Pine.LNX.4.64.0712161331530.18006@dildano.hawaga.org.uk> 
	<1197827840.3307.7.camel@blabla.mcs.anl.gov> 
	<Pine.LNX.4.64.0712161810190.18006@dildano.hawaga.org.uk>
	<1197837805.5877.5.camel@blabla.mcs.anl.gov>
Message-ID: <Pine.LNX.4.64.0712162052220.18006@dildano.hawaga.org.uk>



On Sun, 16 Dec 2007, Mihael Hategan wrote:

> So let's be clear. This only applies to app{} blocks, right?

Yes. Every other place where expressions appear has unambiguous 
delimination of expressions (eg end of a statement or a comma between 
parameters)

-- 


From mikekubal at yahoo.com  Mon Dec 17 23:15:15 2007
From: mikekubal at yahoo.com (Mike Kubal)
Date: Mon, 17 Dec 2007 21:15:15 -0800 (PST)
Subject: [Swift-devel] how to increment int?
Message-ID: <459440.30098.qm@web52306.mail.re2.yahoo.com>

In the swift code loop below I need to increment the
start_job variable by 1, however I get the error that
start_job is already assigned, how should I do it? 

thanks Mike Kubal 


int start_job = 10000001;

while( start_job < 10000998){
        string job_number = start_job;
        file score_file
<single_file_mapper;file=@strcat 
(job_number,"_chemgauss3_scores.txt")>;
        file docked_file
<single_file_mapper;file=@strcat(job_number,"_chemgauss3_docked.mol2")>;
        (score_file,docked_file) =
run_fred(job_number);
        start_job = start_job + 1;
}



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From hategan at mcs.anl.gov  Tue Dec 18 00:22:48 2007
From: hategan at mcs.anl.gov (Mihael Hategan)
Date: Tue, 18 Dec 2007 00:22:48 -0600
Subject: [Swift-devel] how to increment int?
In-Reply-To: <459440.30098.qm@web52306.mail.re2.yahoo.com>
References: <459440.30098.qm@web52306.mail.re2.yahoo.com>
Message-ID: <1197958968.17591.16.camel@blabla.mcs.anl.gov>

You cannot increment things in Swift. It's a data-flow like language.
Variables are "virtual" nodes in a dependency graph. A variable
depending on itself (i.e. x = f(x)) has no well-defined meaning, at
least as far as the current model goes.

But you can probably construct an array and iterate over it:

int job_numbers[] = [10000001:10000998];

foreach job_number in job_numbers {
  ...
}

Mihael

On Mon, 2007-12-17 at 21:15 -0800, Mike Kubal wrote:
> In the swift code loop below I need to increment the
> start_job variable by 1, however I get the error that
> start_job is already assigned, how should I do it? 
> 
> thanks Mike Kubal 
> 
> 
> int start_job = 10000001;
> 
> while( start_job < 10000998){
>         string job_number = start_job;
>         file score_file
> <single_file_mapper;file=@strcat 
> (job_number,"_chemgauss3_scores.txt")>;
>         file docked_file
> <single_file_mapper;file=@strcat(job_number,"_chemgauss3_docked.mol2")>;
>         (score_file,docked_file) =
> run_fred(job_number);
>         start_job = start_job + 1;
> }
> 
> 
> 
>       ____________________________________________________________________________________
> Be a better friend, newshound, and 
> know-it-all with Yahoo! Mobile.  Try it now.  http://mobile.yahoo.com/;_ylt=Ahu06i62sR8HDtDypao8Wcj9tAcJ 
> 
> _______________________________________________
> 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  Tue Dec 18 06:16:27 2007
From: benc at hawaga.org.uk (Ben Clifford)
Date: Tue, 18 Dec 2007 12:16:27 +0000 (GMT)
Subject: [Swift-devel] how to increment int?
In-Reply-To: <459440.30098.qm@web52306.mail.re2.yahoo.com>
References: <459440.30098.qm@web52306.mail.re2.yahoo.com>
Message-ID: <Pine.LNX.4.64.0712181210190.26117@dildano.hawaga.org.uk>



> In the swift code loop below I need to increment the
> start_job variable by 1, however I get the error that
> start_job is already assigned, how should I do it? 

> while( start_job < 10000998){

Don't use while - it shouldn't even be in the language, in my opinion, 
given that I've never seen a successful use of it.

Here are two ways of saying what I think you want:

THere's an 'iterate' statement that will give you a counter for each loop.

Section 2.6.4 in here: 
http://www.ci.uchicago.edu/swift/guides/userguide.php#id2663424

something like

iterate i {
    int job_number = i + 10000000;
    [...]
} until(job_number >= 1000098)


You could also express it as this, which perhaps better expresses the 
parallelism (though I think both the iterate use above and the foreach use 
below will behave about the same).

foreach job_number in [1000000:10000098] {
   [....]
}


-- 




From benc at hawaga.org.uk  Tue Dec 18 06:36:04 2007
From: benc at hawaga.org.uk (Ben Clifford)
Date: Tue, 18 Dec 2007 12:36:04 +0000 (GMT)
Subject: [Swift-devel] remove while
Message-ID: <Pine.LNX.4.64.0712181234390.18006@dildano.hawaga.org.uk>

given that I've seen exactly 0 successful uses of while and no one has 
managed ever to come up with a non-contrived example about launching 
rockets or wierd stuff like that, I'm going to remove it from the language 
unless someone comes up with some decent justification (like a set of 
sensible coded examples written in SwiftScript).

--



From hategan at mcs.anl.gov  Tue Dec 18 07:35:19 2007
From: hategan at mcs.anl.gov (Mihael Hategan)
Date: Tue, 18 Dec 2007 07:35:19 -0600
Subject: [Swift-devel] remove while
In-Reply-To: <Pine.LNX.4.64.0712181234390.18006@dildano.hawaga.org.uk>
References: <Pine.LNX.4.64.0712181234390.18006@dildano.hawaga.org.uk>
Message-ID: <1197984919.18225.1.camel@blabla.mcs.anl.gov>


On Tue, 2007-12-18 at 12:36 +0000, Ben Clifford wrote:
> given that I've seen exactly 0 successful uses of while and no one has 
> managed ever to come up with a non-contrived example about launching 
> rockets or wierd stuff like that,

Hey, I did mention the rockets!

>  I'm going to remove it from the language 
> unless someone comes up with some decent justification (like a set of 
> sensible coded examples written in SwiftScript).
> 
> --
> 
> _______________________________________________
> Swift-devel mailing list
> Swift-devel at ci.uchicago.edu
> http://mail.ci.uchicago.edu/mailman/listinfo/swift-devel
> 



From mikekubal at yahoo.com  Tue Dec 18 08:03:30 2007
From: mikekubal at yahoo.com (Mike Kubal)
Date: Tue, 18 Dec 2007 06:03:30 -0800 (PST)
Subject: [Swift-devel] how to increment int?
In-Reply-To: <Pine.LNX.4.64.0712181210190.26117@dildano.hawaga.org.uk>
Message-ID: <928045.71133.qm@web52301.mail.re2.yahoo.com>

Thanks Ben,

I tried both approaches, but I get the following
errors:

Could not compile SwiftScript source: line 9:11:
unexpected token: {
with the line:  

iterate i {  

I get a similar error 

Could not compile SwiftScript source: line 12:23:
unexpected token: [

with the line 

foreach job_number in [1000000:10000098]

Thanks,

Mike


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

> 
> 
> > In the swift code loop below I need to increment
> the
> > start_job variable by 1, however I get the error
> that
> > start_job is already assigned, how should I do it?
> 
> 
> > while( start_job < 10000998){
> 
> Don't use while - it shouldn't even be in the
> language, in my opinion, 
> given that I've never seen a successful use of it.
> 
> Here are two ways of saying what I think you want:
> 
> THere's an 'iterate' statement that will give you a
> counter for each loop.
> 
> Section 2.6.4 in here: 
>
http://www.ci.uchicago.edu/swift/guides/userguide.php#id2663424
> 
> something like
> 
> iterate i {
>     int job_number = i + 10000000;
>     [...]
> } until(job_number >= 1000098)
> 
> 
> You could also express it as this, which perhaps
> better expresses the 
> parallelism (though I think both the iterate use
> above and the foreach use 
> below will behave about the same).
> 
> foreach job_number in [1000000:10000098] {
>    [....]
> }
> 
> 
> -- 
> 
> 
> _______________________________________________
> Swift-devel mailing list
> Swift-devel at ci.uchicago.edu
>
http://mail.ci.uchicago.edu/mailman/listinfo/swift-devel
> 
> 



      ____________________________________________________________________________________
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From benc at hawaga.org.uk  Tue Dec 18 08:08:23 2007
From: benc at hawaga.org.uk (Ben Clifford)
Date: Tue, 18 Dec 2007 14:08:23 +0000 (GMT)
Subject: [Swift-devel] how to increment int?
In-Reply-To: <928045.71133.qm@web52301.mail.re2.yahoo.com>
References: <928045.71133.qm@web52301.mail.re2.yahoo.com>
Message-ID: <Pine.LNX.4.64.0712181405520.18006@dildano.hawaga.org.uk>



On Tue, 18 Dec 2007, Mike Kubal wrote:

> I tried both approaches, but I get the following
> errors:

what version of swift are you using? Both of those errors look like the 
sort of thing I'd expect from a version earlier than v0.3.

-- 


From bugzilla-daemon at mcs.anl.gov  Tue Dec 18 14:31:05 2007
From: bugzilla-daemon at mcs.anl.gov (bugzilla-daemon at mcs.anl.gov)
Date: Tue, 18 Dec 2007 14:31:05 -0600 (CST)
Subject: [Swift-devel] [Bug 122] New: regexp_mapper transformation
	enhancements
Message-ID: <bug-122-21@http.bugzilla.mcs.anl.gov/swift/>

http://bugzilla.mcs.anl.gov/swift/show_bug.cgi?id=122

           Summary: regexp_mapper transformation enhancements
           Product: Swift
           Version: unspecified
          Platform: Macintosh
        OS/Version: Mac OS
            Status: NEW
          Severity: normal
          Priority: P2
         Component: SwiftScript language
        AssignedTo: benc at hawaga.org.uk
        ReportedBy: tiberius at mcs.anl.gov


I would like to have the ability to derive the output file name from the input
file name using simple arithmetic operations on the matched fields :

E.g. functionality:
step_0_theta_4.txt -> step_1_theta_4.txt


Also, it would be good to have the regexp_mapper work on string[] and produce
string[] as well


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From bugzilla-daemon at mcs.anl.gov  Tue Dec 18 14:37:25 2007
From: bugzilla-daemon at mcs.anl.gov (bugzilla-daemon at mcs.anl.gov)
Date: Tue, 18 Dec 2007 14:37:25 -0600 (CST)
Subject: [Swift-devel] [Bug 123] New: Array mappers should accept
	programmatically-built string[]s
Message-ID: <bug-123-21@http.bugzilla.mcs.anl.gov/swift/>

http://bugzilla.mcs.anl.gov/swift/show_bug.cgi?id=123

           Summary: Array mappers should accept programmatically-built
                    string[]s
           Product: Swift
           Version: unspecified
          Platform: Macintosh
        OS/Version: Mac OS
            Status: NEW
          Severity: normal
          Priority: P2
         Component: SwiftScript language
        AssignedTo: benc at hawaga.org.uk
        ReportedBy: tiberius at mcs.anl.gov


I expected this to work:

type file{};

int rangeMax=3;
int stepRange=[1:rangeMax];

string oldvalfilenames[];

foreach step in stepRange{
        oldvalfilenames[step] = @strcat("step_",step,"_theta.txt");
        trace(oldvalfilenames[step]);
}

file oldvalfile[] <array_mapper; files=oldvalfilenames>;

trace(@filenames(oldvalfile));

Please suggest a solution for completely customizable file names in array
mappers:

E.g.
step_3_theta_5.txt, step_4_theta6.txt


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From benc at hawaga.org.uk  Fri Dec 21 10:39:51 2007
From: benc at hawaga.org.uk (Ben Clifford)
Date: Fri, 21 Dec 2007 16:39:51 +0000 (GMT)
Subject: [Swift-devel] multidimensional arrays
Message-ID: <Pine.LNX.4.64.0712211637320.18006@dildano.hawaga.org.uk>


A couple of people have talked about wanting multidimensional arrays.

I've been playing with this a bit. The code is not ready to commit yet.

However for people who want to play right now, here's a tarball of my 
development tree with the changes.

http://www.ci.uchicago.edu/~benc/swift-0.3-benc-arrays.tar.gz (22mb)

-- 


From benc at hawaga.org.uk  Fri Dec 28 04:49:22 2007
From: benc at hawaga.org.uk (Ben Clifford)
Date: Fri, 28 Dec 2007 10:49:22 +0000 (GMT)
Subject: [Swift-devel] build dependencies
Message-ID: <Pine.LNX.4.64.0712281043080.18006@dildano.hawaga.org.uk>


I've been building provider-deef on my machine recently by having it 
listed as a dependency of swift in build.xml (a patch in my quilt stack 
adds that in as part of my local configuration). This seems to solve the 
'provider-deef overwriting the log config file' problem for me.

It might be interesting to make it possible to specify dependencies like 
this at build time on the commandline to ant.

(this is very similar to the unix world way of saying:

> ./configure --enable-ipv6 --disable-sasl
> make

in order to determine if you want to have dependencies or not on ipv6 and 
sasl (and hence corresponding features) in some software)

-- 


From hategan at mcs.anl.gov  Fri Dec 28 11:50:45 2007
From: hategan at mcs.anl.gov (Mihael Hategan)
Date: Fri, 28 Dec 2007 11:50:45 -0600
Subject: [Swift-devel] build dependencies
In-Reply-To: <Pine.LNX.4.64.0712281043080.18006@dildano.hawaga.org.uk>
References: <Pine.LNX.4.64.0712281043080.18006@dildano.hawaga.org.uk>
Message-ID: <1198864246.25031.1.camel@blabla.mcs.anl.gov>

On Fri, 2007-12-28 at 10:49 +0000, Ben Clifford wrote:
> I've been building provider-deef on my machine recently by having it 
> listed as a dependency of swift in build.xml (a patch in my quilt stack 
> adds that in as part of my local configuration). This seems to solve the 
> 'provider-deef overwriting the log config file' problem for me.
> 
> It might be interesting to make it possible to specify dependencies like 
> this at build time on the commandline to ant.
> 
> (this is very similar to the unix world way of saying:
> 
> > ./configure --enable-ipv6 --disable-sasl
> > make
> 
> in order to determine if you want to have dependencies or not on ipv6 and 
> sasl (and hence corresponding features) in some software)

A similar thing can be done by passing properties to ant and then using
them to drive certain parts of the build (or not). Though it looks more
like -Denable-ipv6=true.

> 



From iraicu at cs.uchicago.edu  Fri Dec 28 11:54:01 2007
From: iraicu at cs.uchicago.edu (Ioan Raicu)
Date: Fri, 28 Dec 2007 11:54:01 -0600
Subject: [Swift-devel] build dependencies
In-Reply-To: <1198864246.25031.1.camel@blabla.mcs.anl.gov>
References: <Pine.LNX.4.64.0712281043080.18006@dildano.hawaga.org.uk>
	<1198864246.25031.1.camel@blabla.mcs.anl.gov>
Message-ID: <47753839.6070901@cs.uchicago.edu>

So how can we use the patch?  Do we just update Swift and do ant dist?  
Or what other options should we use to build the provider-deef at the 
same time we build swift?
Thanks,
Ioan

Mihael Hategan wrote:
> On Fri, 2007-12-28 at 10:49 +0000, Ben Clifford wrote:
>   
>> I've been building provider-deef on my machine recently by having it 
>> listed as a dependency of swift in build.xml (a patch in my quilt stack 
>> adds that in as part of my local configuration). This seems to solve the 
>> 'provider-deef overwriting the log config file' problem for me.
>>
>> It might be interesting to make it possible to specify dependencies like 
>> this at build time on the commandline to ant.
>>
>> (this is very similar to the unix world way of saying:
>>
>>     
>>> ./configure --enable-ipv6 --disable-sasl
>>> make
>>>       
>> in order to determine if you want to have dependencies or not on ipv6 and 
>> sasl (and hence corresponding features) in some software)
>>     
>
> A similar thing can be done by passing properties to ant and then using
> them to drive certain parts of the build (or not). Though it looks more
> like -Denable-ipv6=true.
>
>   
>
> _______________________________________________
> Swift-devel mailing list
> Swift-devel at ci.uchicago.edu
> http://mail.ci.uchicago.edu/mailman/listinfo/swift-devel
>
>   

-- 
==================================================
Ioan Raicu
Ph.D. Candidate
==================================================
Distributed Systems Laboratory
Computer Science Department
University of Chicago
1100 E. 58th Street, Ryerson Hall
Chicago, IL 60637
==================================================
Email: iraicu at cs.uchicago.edu
Web:   http://www.cs.uchicago.edu/~iraicu
http://dev.globus.org/wiki/Incubator/Falkon
http://www.ci.uchicago.edu/wiki/bin/view/VDS/DslCS
==================================================
==================================================




From hategan at mcs.anl.gov  Fri Dec 28 12:08:41 2007
From: hategan at mcs.anl.gov (Mihael Hategan)
Date: Fri, 28 Dec 2007 12:08:41 -0600
Subject: [Swift-devel] build dependencies
In-Reply-To: <47753839.6070901@cs.uchicago.edu>
References: <Pine.LNX.4.64.0712281043080.18006@dildano.hawaga.org.uk>
	<1198864246.25031.1.camel@blabla.mcs.anl.gov>
	<47753839.6070901@cs.uchicago.edu>
Message-ID: <1198865321.25524.0.camel@blabla.mcs.anl.gov>

There is no patch yet.

On Fri, 2007-12-28 at 11:54 -0600, Ioan Raicu wrote:
> So how can we use the patch?  Do we just update Swift and do ant dist?  
> Or what other options should we use to build the provider-deef at the 
> same time we build swift?
> Thanks,
> Ioan
> 
> Mihael Hategan wrote:
> > On Fri, 2007-12-28 at 10:49 +0000, Ben Clifford wrote:
> >   
> >> I've been building provider-deef on my machine recently by having it 
> >> listed as a dependency of swift in build.xml (a patch in my quilt stack 
> >> adds that in as part of my local configuration). This seems to solve the 
> >> 'provider-deef overwriting the log config file' problem for me.
> >>
> >> It might be interesting to make it possible to specify dependencies like 
> >> this at build time on the commandline to ant.
> >>
> >> (this is very similar to the unix world way of saying:
> >>
> >>     
> >>> ./configure --enable-ipv6 --disable-sasl
> >>> make
> >>>       
> >> in order to determine if you want to have dependencies or not on ipv6 and 
> >> sasl (and hence corresponding features) in some software)
> >>     
> >
> > A similar thing can be done by passing properties to ant and then using
> > them to drive certain parts of the build (or not). Though it looks more
> > like -Denable-ipv6=true.
> >
> >   
> >
> > _______________________________________________
> > 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  Fri Dec 28 12:50:06 2007
From: hategan at mcs.anl.gov (Mihael Hategan)
Date: Fri, 28 Dec 2007 12:50:06 -0600
Subject: [Swift-devel] build dependencies
In-Reply-To: <1198865321.25524.0.camel@blabla.mcs.anl.gov>
References: <Pine.LNX.4.64.0712281043080.18006@dildano.hawaga.org.uk>
	<1198864246.25031.1.camel@blabla.mcs.anl.gov>
	<47753839.6070901@cs.uchicago.edu>
	<1198865321.25524.0.camel@blabla.mcs.anl.gov>
Message-ID: <1198867806.26481.1.camel@blabla.mcs.anl.gov>

As of r1525 there is one.

Use it like this:

ant -Dwith-provider-deef=true dist

provider-deef has to be in cog/modules.

On Fri, 2007-12-28 at 12:08 -0600, Mihael Hategan wrote:
> There is no patch yet.
> 
> On Fri, 2007-12-28 at 11:54 -0600, Ioan Raicu wrote:
> > So how can we use the patch?  Do we just update Swift and do ant dist?  
> > Or what other options should we use to build the provider-deef at the 
> > same time we build swift?
> > Thanks,
> > Ioan
> > 
> > Mihael Hategan wrote:
> > > On Fri, 2007-12-28 at 10:49 +0000, Ben Clifford wrote:
> > >   
> > >> I've been building provider-deef on my machine recently by having it 
> > >> listed as a dependency of swift in build.xml (a patch in my quilt stack 
> > >> adds that in as part of my local configuration). This seems to solve the 
> > >> 'provider-deef overwriting the log config file' problem for me.
> > >>
> > >> It might be interesting to make it possible to specify dependencies like 
> > >> this at build time on the commandline to ant.
> > >>
> > >> (this is very similar to the unix world way of saying:
> > >>
> > >>     
> > >>> ./configure --enable-ipv6 --disable-sasl
> > >>> make
> > >>>       
> > >> in order to determine if you want to have dependencies or not on ipv6 and 
> > >> sasl (and hence corresponding features) in some software)
> > >>     
> > >
> > > A similar thing can be done by passing properties to ant and then using
> > > them to drive certain parts of the build (or not). Though it looks more
> > > like -Denable-ipv6=true.
> > >
> > >   
> > >
> > > _______________________________________________
> > > 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 iraicu at cs.uchicago.edu  Fri Dec 28 12:53:03 2007
From: iraicu at cs.uchicago.edu (Ioan Raicu)
Date: Fri, 28 Dec 2007 12:53:03 -0600
Subject: [Swift-devel] build dependencies
In-Reply-To: <1198867806.26481.1.camel@blabla.mcs.anl.gov>
References: <Pine.LNX.4.64.0712281043080.18006@dildano.hawaga.org.uk>	
	<1198864246.25031.1.camel@blabla.mcs.anl.gov>	
	<47753839.6070901@cs.uchicago.edu>	
	<1198865321.25524.0.camel@blabla.mcs.anl.gov>
	<1198867806.26481.1.camel@blabla.mcs.anl.gov>
Message-ID: <4775460F.9040003@cs.uchicago.edu>

Great, thanks!  We'll give it a try!

Ioan

Mihael Hategan wrote:
> As of r1525 there is one.
>
> Use it like this:
>
> ant -Dwith-provider-deef=true dist
>
> provider-deef has to be in cog/modules.
>
> On Fri, 2007-12-28 at 12:08 -0600, Mihael Hategan wrote:
>   
>> There is no patch yet.
>>
>> On Fri, 2007-12-28 at 11:54 -0600, Ioan Raicu wrote:
>>     
>>> So how can we use the patch?  Do we just update Swift and do ant dist?  
>>> Or what other options should we use to build the provider-deef at the 
>>> same time we build swift?
>>> Thanks,
>>> Ioan
>>>
>>> Mihael Hategan wrote:
>>>       
>>>> On Fri, 2007-12-28 at 10:49 +0000, Ben Clifford wrote:
>>>>   
>>>>         
>>>>> I've been building provider-deef on my machine recently by having it 
>>>>> listed as a dependency of swift in build.xml (a patch in my quilt stack 
>>>>> adds that in as part of my local configuration). This seems to solve the 
>>>>> 'provider-deef overwriting the log config file' problem for me.
>>>>>
>>>>> It might be interesting to make it possible to specify dependencies like 
>>>>> this at build time on the commandline to ant.
>>>>>
>>>>> (this is very similar to the unix world way of saying:
>>>>>
>>>>>     
>>>>>           
>>>>>> ./configure --enable-ipv6 --disable-sasl
>>>>>> make
>>>>>>       
>>>>>>             
>>>>> in order to determine if you want to have dependencies or not on ipv6 and 
>>>>> sasl (and hence corresponding features) in some software)
>>>>>     
>>>>>           
>>>> A similar thing can be done by passing properties to ant and then using
>>>> them to drive certain parts of the build (or not). Though it looks more
>>>> like -Denable-ipv6=true.
>>>>
>>>>   
>>>>
>>>> _______________________________________________
>>>> 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
>>
>>     
>
>
>   

-- 
==================================================
Ioan Raicu
Ph.D. Candidate
==================================================
Distributed Systems Laboratory
Computer Science Department
University of Chicago
1100 E. 58th Street, Ryerson Hall
Chicago, IL 60637
==================================================
Email: iraicu at cs.uchicago.edu
Web:   http://www.cs.uchicago.edu/~iraicu
http://dev.globus.org/wiki/Incubator/Falkon
http://www.ci.uchicago.edu/wiki/bin/view/VDS/DslCS
==================================================
==================================================