From justinbbt at gmail.com  Mon Sep  1 16:20:57 2014
From: justinbbt at gmail.com (Justin bbt)
Date: Mon, 1 Sep 2014 17:20:57 -0400
Subject: [Swift-user] running jobs on cluster or cloud
In-Reply-To: <CABubRoDk4J0JcHzzeJw9mMay6JHUaLyZrfv=uRUq_-T714FxNw@mail.gmail.com>
References: <CABubRoB=Sp-PeByMy37rx2BeP3TvFxzG-sYw9DxyisNZADQCJg@mail.gmail.com>
	<CANa904kApbFQTX4Q-d=bP6PYGQazPn7Rjrp-uqXggdNpOf6ZAg@mail.gmail.com>
	<CABubRoDk4J0JcHzzeJw9mMay6JHUaLyZrfv=uRUq_-T714FxNw@mail.gmail.com>
Message-ID: <CABubRoBhUf2JXk68z3yj5q5pC+mh-Xaxju8Mg5Au7NbY6rW3AA@mail.gmail.com>

I solved the permission problem with ssh-add command to add the key to list
of keys.  (This modification is required if the local system is linux- i am
using ubuntu)

(more here
https://help.github.com/articles/error-agent-admitted-failure-to-sign)

Now, start-coaster-service connect to the cluster without password, but it
does not terminate. The is the the output

Service address: localhost
Starting coaster-service
Service port: 35925
Local port: 40681
Generating sites.xml
Starting worker on W.X.Y.Z
WORKER_LOGGING_LEVEL=DEBUG: Command not found.



If I just use my sites.xml

<pool handle="persistent-coasters">
    <execution provider="coaster-persistent"
               url="http:// <http://localhost:37584/>urladdress"
               jobmanager="local:local"/>
    <profile namespace="globus" key="workerManager">passive</profile>
    <profile namespace="globus" key="jobsPerNode">1</profile>
    <profile key="jobThrottle" namespace="karajan">10</profile>
    <profile namespace="karajan" key="initialScore">10000</profile>
    <filesystem provider="local" url="none" />
    <workdirectory>.</workdirectory>
  </pool>


  it fails with the following error


Execution failed:
Exception in simulate:
    Arguments: []
    Host: persistent-coasters
    Directory: p1-20140901-1648-r8mdqbse/jobs/z/simulate-zcyxesvl

Caused by:
Could not submit job
Caused by:
Failed to create socket
Caused by:
Connection refused
simulation, p1.swift, line 9






On Sat, Aug 30, 2014 at 1:28 AM, Justin bbt <justinbbt at gmail.com> wrote:

> For cluster:
>
> When I run the start-caoster-service, I receive the following, in which it
> asks for password and then says Permission is denied
>
> Start-coaster-service...
> Configuration: /home/lenovo/swift-cloud-tutorial/scs/coaster-service.conf
> Service address: localhost
> Starting coaster-service
> Service port: 52809
> Local port: 58460
> Generating sites.xml
> username at ipadress's password:
> username at ipadress's password:
> Starting worker on username@
> lenovo at lenovo-laptop:~/swift-cloud-tutorial/scs$username at ipadress's
> password:
> Permission denied, please try again.
> username at ipadress's password:
> Permission denied, please try again.
> username at ipadress's password:
> Permission denied (publickey,gssapi-keyex,gssapi-with-mic,password).
>
> This happens though I have created my keys with ssh-keygen. (only changed
> that I made was to create rsa keys rather than dsa keys - my cluster did
> not accept dsa). I can connect with rsa keygen and my passphrase for
> regular ssh
>
> The output of my sites.xml  from this partial running of
> start-coaster-service is
>
>  <pool handle="persistent-coasters">
>     <execution provider="coaster-persistent"
>                url="http://localhost:37584"
>                jobmanager="local:local"/>
>     <profile namespace="globus" key="workerManager">passive</profile>
>     <profile namespace="globus" key="jobsPerNode">1</profile>
>     <profile key="jobThrottle" namespace="karajan">10</profile>
>     <profile namespace="karajan" key="initialScore">10000</profile>
>     <filesystem provider="local" url="none" />
>     <workdirectory>.</workdirectory>
>   </pool>
>
> Using this XML , I just get a sequence of job submission every 30 seconds,
> no finished jobs.
>
>
> BTW, I have a public ip for my cluster and then each compute node has a
> local/private ip.
> In
>  export WORKER_HOSTS="<IP of machine 1> <IP of machine 2>"
> currently I just set the public IP address which still I am not successful
> with this one node even. I was wondering how should I set the other IPs?
> Does it mean that I have to install swift on the cluster?
>
>
> I will look at the new  release of swift for AWS.
>
>
> Thanks,
> J.
>
>
>
>
>
> On Fri, Aug 29, 2014 at 11:43 AM, Yadu Nand <yadudoc1729 at gmail.com> wrote:
>
>> Hi Justin,
>>
>> ??Did you do the following steps:
>> export WORKER_LOCATION="/home/ubuntu"
>> export WORKER_HOSTS="<IP of machine 1> <IP of machine 2>"
>> export WORKER_USERNAME=ubuntu
>>
>> and then run "source setup.sh" ?
>> When you source the setup.sh scripts you must've gotten a sites.xml and a
>> start-coaster-service.log in your scs folder, could you send us those ?
>> The setup script should start a persistent coaster service and connect to
>> the nodes on amazon, start workers, and generate a sites.xml file
>> that would let your swift scripts run across the amazon nodes. You
>> shouldn't have to make changes to the sites.xml.
>>
>>  Alternatively, you could try using the beta release of swift, Swift 0.95
>> RC6 with the new cloud mechanism:
>> https://github.com/swift-lang/swift-on-cloud/tree/master/aws
>>
>> That will set you up with a headnode on AWS with a few worker nodes that
>> you define, with everything setup to run swift.
>>
>>
>> Thanks,
>> Yadu
>> ?
>>
>>
>>  On Thu, Aug 28, 2014 at 6:57 PM, Justin bbt <justinbbt at gmail.com> wrote:
>>
>>>
>>>
>>>
>>> Hi all,
>>>>
>>>>  I could successfully run swift on my local system.
>>>> Next, I want to use the swift to run some jobs on a cluster.
>>>>
>>>> I followed this tutorial.  (I am using just a simple cluster- I even
>>>> could not run the job on one remote node of the cluster)
>>>> http://swift-lang.org/tutorials/cloud/tutorial.html
>>>>
>>>> But, I get this when I run swift p1.swift or other swift
>>>>
>>>> Swift 0.94.1 swift-r7114 cog-r3803
>>>>
>>>> RunID: 20140828-1758-ea4phzag
>>>> Progress:  time: Thu, 28 Aug 2014 17:58:15 -0400
>>>> Progress:  time: Thu, 28 Aug 2014 17:58:24 -0400  Submitted:1
>>>> Execution failed:
>>>> Exception in simulate:
>>>>     Arguments: []
>>>>     Host: remotehost2
>>>>     Directory: p1-20140828-1758-ea4phzag/jobs/7/simulate-7k2fxlvl
>>>>
>>>> Caused by:
>>>> Job failed with an exit code of 127
>>>> simulation, p1.swift, line 9
>>>>
>>>>
>>>> --- this is my site.xml file setting
>>>>
>>>>    <pool handle="remotehost2">
>>>>       <execution provider="ssh" jobmanager="ssh:local"
>>>> url="myclusteturl"/>
>>>>       <filesystem provider="ssh" url="myclusteturl"/>
>>>>       <profile namespace="karajan" key="jobThrottle">0</profile>
>>>>       <profile namespace="karajan" key="initialScore">10000</profile>
>>>>       <workdirectory>/path/to/remote/workdirectory</workdirectory>
>>>>    </pool>
>>>>
>>>> --- if I use this one
>>>> <pool handle="persistent-coasters">
>>>>     <execution provider="coaster-persistent"
>>>>                url="myclusterurl"
>>>>                jobmanager="local:local"/>
>>>>     <profile namespace="globus" key="workerManager">passive</profile>
>>>>     <profile namespace="globus" key="jobsPerNode">1</profile>
>>>>     <profile key="jobThrottle" namespace="karajan">10</profile>
>>>>     <profile namespace="karajan" key="initialScore">10000</profile>
>>>>     <filesystem provider="local" url="none" />
>>>>     <workdirectory>.l</workdirectory>
>>>>   </pool>
>>>> --- then it loops to my localhost and just repeat submitting the jobs
>>>>
>>>> 1. Is this a correct setting?
>>>> 2. Should I use coaster? I could not understand the description in user
>>>> guides and documentation about the concepts of coaster and the required
>>>> setting. Is there any better tutorial which would describe the coaster ?
>>>> 3. I plan to use the swift later on the cloud (Microsoft Azure). What
>>>> are the setting required for that? for site.xml and if any other file
>>>>
>>>>
>>>> Thanks in Advance.
>>>>
>>>>
>>>
>>>
>>> _______________________________________________
>>> Swift-user mailing list
>>> Swift-user at ci.uchicago.edu
>>> https://lists.ci.uchicago.edu/cgi-bin/mailman/listinfo/swift-user
>>>
>>
>>
>>
>> --
>> Yadu Nand B
>>
>>
>
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From Matthew.Shaxted at som.com  Tue Sep  2 10:45:40 2014
From: Matthew.Shaxted at som.com (Matthew Shaxted)
Date: Tue, 2 Sep 2014 11:45:40 -0400
Subject: [Swift-user] Swift Coaster Service & Docker Containers
In-Reply-To: <41C141B3-570C-43A7-A30C-D6740B38E829@som.com>
References: <E606D0858F0AB941B6A9EB52730031F69685222D9C@CCRD007.mail.lan>
	<54012A0C.4070703@anl.gov>
	<CANa904n+Mj-zO+f0_dN2Ed3yHPj6XeL9HbodDC=kDtNJdSeHJA@mail.gmail.com>
	<41C141B3-570C-43A7-A30C-D6740B38E829@som.com>
Message-ID: <E606D0858F0AB941B6A9EB52730031F69685222EBF@CCRD007.mail.lan>

Hi Mike/Yadu,

Thanks for these suggestions. I am successfully starting the coaster-service, making the connection and running jobs on the docker containers with the below commands:

On the coaster-service host:

                                coaster-service -p 50200 -localport 50100 -nosec -passive &> /var/log/coaster-service.logs

On each container I start this command:

./worker.pl http://172.20.24.20:50100 172.20.24.101 ~/swiftwork



MATTHEW SHAXTED
SKIDMORE, OWINGS & MERRILL LLP
224 SOUTH MICHIGAN AVENUE
CHICAGO, IL 60604
T  (312) 360-4368
MATTHEW.SHAXTED at SOM.COM<mailto:MATTHEW.SHAXTED at SOM.COM>

[cid:image004.png at 01CFC69B.09BB3CD0]<http://www.som.com/>
The information contained in this communication may be confidential, is intended only for the use of the recipient(s) named above, and may be legally privileged. If the reader of this message is not the intended recipient, you are hereby notified that any dissemination, distribution, or copying of this communication, or any of its contents, is strictly prohibited and may be unlawful. If you have received this communication in error, please return it to the sen???der immediately and delete the original message and any copy of it from your computer system. If you have any questions concerning this message, please contact the sender.

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From: Matthew Shaxted
Sent: Saturday, August 30, 2014 8:40 AM
To: Yadu Nand
Cc: Michael Wilde; Swift User
Subject: Re: [Swift-user] Swift Coaster Service & Docker Containers

Thanks Mike and Yadu,

Yes it would be great if there is a published config for this use case, and I am willing to help in whatever capacity I can.

The docker containers can reach out to external IP addresses, so as you both mention the best way may be to run the worker.pl in each container and have it connect back to the coaster service. I start the coaster service on a known ip/port host using the command you specify.

I think I conceptually understand how this could work and will try to test something.

I have an ubuntu docker container configured to start ssh services at the command below. It sounds like, however, if I can run the worker.pl on each container and connect to the coaster service, ssh is not even required.

docker run -i -p 22 -t mattshax/precise_ep_node sh -c '/usr/sbin/sshd -D'




On Aug 29, 2014, at 9:33 PM, "Yadu Nand" <yadudoc1729 at gmail.com<mailto:yadudoc1729 at gmail.com>> wrote:
Hi Matthew,

You can use the coaster-service directly with the following arguments :
coaster-service -p $SERVICEPORT -localport $WORKERPORT -nosec -passive &> /var/log/coaster-service.logs

The workers running under docker should be connecting to the WORKERPORT and the swift client would use the SERVICEPORT.
Another thing to remember is to make sure that you use the the coaster-service and worker.pl<http://worker.pl> from the same swift release.

The start-coaster-service command is a wrapper over coaster-service which in addition to starting the coaster service, also
tries to ssh the worker.pl<http://worker.pl> to the WORKER_HOSTS. In the situation that you describe, I think it makes sense to have the workers
just connect back to the coaster-service which is listening on a known IP / port.

Thanks,
Yadu



On Fri, Aug 29, 2014 at 8:34 PM, Michael Wilde <wilde at anl.gov<mailto:wilde at anl.gov>> wrote:
Matthew,

I would treat this case similar to the configuration you'd use for a set of virtual machines.

Start one coaster service for each pool of identical docker containers that you want to run.

For each pool of containers, run a Swift worker (worker.pl<http://worker.pl>) in the container and have it connect back to the coaster service you designate to manage that pool.

I'm assuming that from a docker contained you can connect out to any reachable IP address.

Another approach is to treat the containers like a set of ad-hoc compute nodes, and ssh into them with automatic coasters using the ssh:local jobmanager setting.

We'll try to test and publish a config for such cases. We'd welcome your help with that.

- Mike


On 8/29/14, 7:48 PM, Matthew Shaxted wrote:
Hi All,

I?m trying to find a way to run Swift workflows on multi-host docker containers, and wondering if anybody has had success with this.

When I start a docker container and define specific ports to open on the container, they mapped to random ports on the host machine. So for example, I can start a container with an ssh port open from a host ?10.1.1.1?, and can then access this container across hosts with ?ssh compute at 10.1.1.1<mailto:compute at 10.1.1.1> ?p 49160?.

Now I?m hoping to link these docker containers to Swift?s start-coaster-service. I think it would be possible and relatively easy if I can say, start the coasters on a series of IP addresses AND ports. So a host?s file perhaps would look something like below, and coasters would be started on the correct docker container:

10.1.1.1<http://10.1.1.1>: 49160
10.1.1.2<http://10.1.1.2>: 34155
10.1.1.2<http://10.1.1.2>: 34156   ?

Does this make sense? Is it possible to start coasters by specifying an IP address and port number?

Any thoughts are greatly appreciated.

Thanks,
Matthew


MATTHEW SHAXTED
SKIDMORE, OWINGS & MERRILL LLP
224 SOUTH MICHIGAN AVENUE
CHICAGO, IL 60604
T  (312) 360-4368<tel:%28312%29%20360-4368>
MATTHEW.SHAXTED at SOM.COM<mailto:MATTHEW.SHAXTED at SOM.COM>

<ATT00002.png><http://www.som.com/>
The information contained in this communication may be confidential, is intended only for the use of the recipient(s) named above, and may be legally privileged. If the reader of this message is not the intended recipient, you are hereby notified that any dissemination, distribution, or copying of this communication, or any of its contents, is strictly prohibited and may be unlawful. If you have received this communication in error, please return it to the sen???der immediately and delete the original message and any copy of it from your computer system. If you have any questions concerning this message, please contact the sender.

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_______________________________________________

Swift-user mailing list

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--

Michael Wilde

Mathematics and Computer Science          Computation Institute

Argonne National Laboratory               The University of Chicago

_______________________________________________
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--
Yadu Nand B

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From yadudoc1729 at gmail.com  Tue Sep  2 12:13:45 2014
From: yadudoc1729 at gmail.com (Yadu Nand)
Date: Tue, 2 Sep 2014 12:13:45 -0500
Subject: [Swift-user] running jobs on cluster or cloud
In-Reply-To: <CABubRoBhUf2JXk68z3yj5q5pC+mh-Xaxju8Mg5Au7NbY6rW3AA@mail.gmail.com>
References: <CABubRoB=Sp-PeByMy37rx2BeP3TvFxzG-sYw9DxyisNZADQCJg@mail.gmail.com>
	<CANa904kApbFQTX4Q-d=bP6PYGQazPn7Rjrp-uqXggdNpOf6ZAg@mail.gmail.com>
	<CABubRoDk4J0JcHzzeJw9mMay6JHUaLyZrfv=uRUq_-T714FxNw@mail.gmail.com>
	<CABubRoBhUf2JXk68z3yj5q5pC+mh-Xaxju8Mg5Au7NbY6rW3AA@mail.gmail.com>
Message-ID: <CANa904mC7L-d8x0tEJuuhk7CPYfs3gSeAYHr_McBPFOeo25saQ@mail.gmail.com>

Hi Justin,

The sites.xml generated by start-coaster-service has to be used by swift,
so that swift can connect to the coaster service.
I do not understand if you are using the generated sites.xml, or some other
sites.xml file that you wrote. In the case where
coaster-service output says "Service port: 35925", the url in the sites.xml
should be http://localhost:35925.

Could you give me a paste of the sites.xml file that was generated by
start-coaster-service, the start-coaster-service.log,
and the logs from swift when you attempted to run a swift script.

Thanks,
Yadu






On Mon, Sep 1, 2014 at 4:20 PM, Justin bbt <justinbbt at gmail.com> wrote:

> I solved the permission problem with ssh-add command to add the key to
> list of keys.  (This modification is required if the local system is linux-
> i am using ubuntu)
>
> (more here
> https://help.github.com/articles/error-agent-admitted-failure-to-sign)
>
> Now, start-coaster-service connect to the cluster without password, but it
> does not terminate. The is the the output
>
> Service address: localhost
> Starting coaster-service
> Service port: 35925
> Local port: 40681
> Generating sites.xml
> Starting worker on W.X.Y.Z
> WORKER_LOGGING_LEVEL=DEBUG: Command not found.
>
>
>
> If I just use my sites.xml
>
> <pool handle="persistent-coasters">
>      <execution provider="coaster-persistent"
>                url="http:// <http://localhost:37584/>urladdress"
>                 jobmanager="local:local"/>
>     <profile namespace="globus" key="workerManager">passive</profile>
>     <profile namespace="globus" key="jobsPerNode">1</profile>
>     <profile key="jobThrottle" namespace="karajan">10</profile>
>     <profile namespace="karajan" key="initialScore">10000</profile>
>     <filesystem provider="local" url="none" />
>     <workdirectory>.</workdirectory>
>   </pool>
>
>
>   it fails with the following error
>
>
> Execution failed:
> Exception in simulate:
>     Arguments: []
>     Host: persistent-coasters
>     Directory: p1-20140901-1648-r8mdqbse/jobs/z/simulate-zcyxesvl
>
> Caused by:
> Could not submit job
> Caused by:
> Failed to create socket
> Caused by:
> Connection refused
> simulation, p1.swift, line 9
>
>
>
>
>
>
> On Sat, Aug 30, 2014 at 1:28 AM, Justin bbt <justinbbt at gmail.com> wrote:
>
>> For cluster:
>>
>> When I run the start-caoster-service, I receive the following, in which
>> it asks for password and then says Permission is denied
>>
>> Start-coaster-service...
>> Configuration: /home/lenovo/swift-cloud-tutorial/scs/coaster-service.conf
>> Service address: localhost
>> Starting coaster-service
>> Service port: 52809
>> Local port: 58460
>> Generating sites.xml
>> username at ipadress's password:
>> username at ipadress's password:
>> Starting worker on username@
>> lenovo at lenovo-laptop:~/swift-cloud-tutorial/scs$username at ipadress's
>> password:
>> Permission denied, please try again.
>> username at ipadress's password:
>> Permission denied, please try again.
>> username at ipadress's password:
>> Permission denied (publickey,gssapi-keyex,gssapi-with-mic,password).
>>
>> This happens though I have created my keys with ssh-keygen. (only changed
>> that I made was to create rsa keys rather than dsa keys - my cluster did
>> not accept dsa). I can connect with rsa keygen and my passphrase for
>> regular ssh
>>
>> The output of my sites.xml  from this partial running of
>> start-coaster-service is
>>
>>  <pool handle="persistent-coasters">
>>     <execution provider="coaster-persistent"
>>                url="http://localhost:37584"
>>                jobmanager="local:local"/>
>>     <profile namespace="globus" key="workerManager">passive</profile>
>>     <profile namespace="globus" key="jobsPerNode">1</profile>
>>     <profile key="jobThrottle" namespace="karajan">10</profile>
>>     <profile namespace="karajan" key="initialScore">10000</profile>
>>     <filesystem provider="local" url="none" />
>>     <workdirectory>.</workdirectory>
>>   </pool>
>>
>> Using this XML , I just get a sequence of job submission every 30
>> seconds, no finished jobs.
>>
>>
>> BTW, I have a public ip for my cluster and then each compute node has a
>> local/private ip.
>> In
>>  export WORKER_HOSTS="<IP of machine 1> <IP of machine 2>"
>> currently I just set the public IP address which still I am not
>> successful with this one node even. I was wondering how should I set the
>> other IPs? Does it mean that I have to install swift on the cluster?
>>
>>
>> I will look at the new  release of swift for AWS.
>>
>>
>> Thanks,
>> J.
>>
>>
>>
>>
>>
>> On Fri, Aug 29, 2014 at 11:43 AM, Yadu Nand <yadudoc1729 at gmail.com>
>> wrote:
>>
>>> Hi Justin,
>>>
>>> ??Did you do the following steps:
>>> export WORKER_LOCATION="/home/ubuntu"
>>> export WORKER_HOSTS="<IP of machine 1> <IP of machine 2>"
>>> export WORKER_USERNAME=ubuntu
>>>
>>> and then run "source setup.sh" ?
>>> When you source the setup.sh scripts you must've gotten a sites.xml and
>>> a start-coaster-service.log in your scs folder, could you send us those ?
>>> The setup script should start a persistent coaster service and connect
>>> to the nodes on amazon, start workers, and generate a sites.xml file
>>> that would let your swift scripts run across the amazon nodes. You
>>> shouldn't have to make changes to the sites.xml.
>>>
>>>  Alternatively, you could try using the beta release of swift, Swift
>>> 0.95 RC6 with the new cloud mechanism:
>>> https://github.com/swift-lang/swift-on-cloud/tree/master/aws
>>>
>>> That will set you up with a headnode on AWS with a few worker nodes that
>>> you define, with everything setup to run swift.
>>>
>>>
>>> Thanks,
>>> Yadu
>>> ?
>>>
>>>
>>>  On Thu, Aug 28, 2014 at 6:57 PM, Justin bbt <justinbbt at gmail.com>
>>> wrote:
>>>
>>>>
>>>>
>>>>
>>>> Hi all,
>>>>>
>>>>>  I could successfully run swift on my local system.
>>>>> Next, I want to use the swift to run some jobs on a cluster.
>>>>>
>>>>> I followed this tutorial.  (I am using just a simple cluster- I even
>>>>> could not run the job on one remote node of the cluster)
>>>>> http://swift-lang.org/tutorials/cloud/tutorial.html
>>>>>
>>>>> But, I get this when I run swift p1.swift or other swift
>>>>>
>>>>> Swift 0.94.1 swift-r7114 cog-r3803
>>>>>
>>>>> RunID: 20140828-1758-ea4phzag
>>>>> Progress:  time: Thu, 28 Aug 2014 17:58:15 -0400
>>>>> Progress:  time: Thu, 28 Aug 2014 17:58:24 -0400  Submitted:1
>>>>> Execution failed:
>>>>> Exception in simulate:
>>>>>     Arguments: []
>>>>>     Host: remotehost2
>>>>>     Directory: p1-20140828-1758-ea4phzag/jobs/7/simulate-7k2fxlvl
>>>>>
>>>>> Caused by:
>>>>> Job failed with an exit code of 127
>>>>> simulation, p1.swift, line 9
>>>>>
>>>>>
>>>>> --- this is my site.xml file setting
>>>>>
>>>>>    <pool handle="remotehost2">
>>>>>       <execution provider="ssh" jobmanager="ssh:local"
>>>>> url="myclusteturl"/>
>>>>>       <filesystem provider="ssh" url="myclusteturl"/>
>>>>>       <profile namespace="karajan" key="jobThrottle">0</profile>
>>>>>       <profile namespace="karajan" key="initialScore">10000</profile>
>>>>>       <workdirectory>/path/to/remote/workdirectory</workdirectory>
>>>>>    </pool>
>>>>>
>>>>> --- if I use this one
>>>>> <pool handle="persistent-coasters">
>>>>>     <execution provider="coaster-persistent"
>>>>>                url="myclusterurl"
>>>>>                jobmanager="local:local"/>
>>>>>     <profile namespace="globus" key="workerManager">passive</profile>
>>>>>     <profile namespace="globus" key="jobsPerNode">1</profile>
>>>>>     <profile key="jobThrottle" namespace="karajan">10</profile>
>>>>>     <profile namespace="karajan" key="initialScore">10000</profile>
>>>>>     <filesystem provider="local" url="none" />
>>>>>     <workdirectory>.l</workdirectory>
>>>>>   </pool>
>>>>> --- then it loops to my localhost and just repeat submitting the jobs
>>>>>
>>>>> 1. Is this a correct setting?
>>>>> 2. Should I use coaster? I could not understand the description in
>>>>> user guides and documentation about the concepts of coaster and the
>>>>> required setting. Is there any better tutorial which would describe the
>>>>> coaster ?
>>>>> 3. I plan to use the swift later on the cloud (Microsoft Azure). What
>>>>> are the setting required for that? for site.xml and if any other file
>>>>>
>>>>>
>>>>> Thanks in Advance.
>>>>>
>>>>>
>>>>
>>>>
>>>> _______________________________________________
>>>> Swift-user mailing list
>>>> Swift-user at ci.uchicago.edu
>>>> https://lists.ci.uchicago.edu/cgi-bin/mailman/listinfo/swift-user
>>>>
>>>
>>>
>>>
>>> --
>>> Yadu Nand B
>>>
>>>
>>
>


-- 
Yadu Nand B
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From ketan at mcs.anl.gov  Tue Sep  2 16:00:28 2014
From: ketan at mcs.anl.gov (Ketan Maheshwari)
Date: Tue, 2 Sep 2014 16:00:28 -0500
Subject: [Swift-user] new config for Cobalt provider option ignored
Message-ID: <CAMUuvirzthf+w2b+EYgdGHDUxL8Yyimj6f_2NKYF_rv0wP=eYg@mail.gmail.com>

Hi,

So, trying the new config from trunk for the cobalt provider, the config
translator is ignoring the script mode. Is there an alternative way to tell
Cobalt provider to be invoked in script mode? The old-style sites file is:

<?xml version="1.0" encoding="UTF-8"?>
<config xmlns="http://www.ci.uchicago.edu/swift/SwiftSites">

<pool handle="cluster">
<execution provider="coaster" jobmanager="local:cobalt" />

<profile namespace="globus" key="slots">1</profile>
<profile namespace="globus" key="mode">script</profile>

<profile namespace="karajan" key="jobThrottle">2.99</profile>
<profile namespace="karajan" key="initialScore">10000</profile>
<profile namespace="globus" key="jobsPerNode">4</profile>
<profile namespace="globus" key="maxwalltime">00:15:00</profile>
<profile namespace="globus" key="walltime">1500</profile>

<profile namespace="globus" key="maxnodes">128</profile>
<profile namespace="globus" key="nodegranularity">128</profile>

<workdirectory>/home/ketan/swiftwork</workdirectory>
<filesystem provider="local"/>

</pool>
</config>

The generated config is:

<snip>
options {
maxNodesPerJob: 128
maxJobs: 1
tasksPerNode: 4
# Option ignored: globus:mode = script
nodeGranularity: 128
# Option ignored: globus:walltime = 1500
}
...

Thanks,
Ketan
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From justinbbt at gmail.com  Tue Sep  2 13:26:28 2014
From: justinbbt at gmail.com (Justin bbt)
Date: Tue, 2 Sep 2014 14:26:28 -0400
Subject: [Swift-user] running jobs on cluster or cloud
In-Reply-To: <CABubRoBhUf2JXk68z3yj5q5pC+mh-Xaxju8Mg5Au7NbY6rW3AA@mail.gmail.com>
References: <CABubRoB=Sp-PeByMy37rx2BeP3TvFxzG-sYw9DxyisNZADQCJg@mail.gmail.com>
	<CANa904kApbFQTX4Q-d=bP6PYGQazPn7Rjrp-uqXggdNpOf6ZAg@mail.gmail.com>
	<CABubRoDk4J0JcHzzeJw9mMay6JHUaLyZrfv=uRUq_-T714FxNw@mail.gmail.com>
	<CABubRoBhUf2JXk68z3yj5q5pC+mh-Xaxju8Mg5Au7NbY6rW3AA@mail.gmail.com>
Message-ID: <CABubRoB7+kU4pvzQ5YUtMB9r_AX4KJ-9HYcjeUSS=uJiXWpHHw@mail.gmail.com>

I re-run my coaster to make sure I am sending you an updated log. Log is
attached. The sites.xml is this now

<config>
  <pool handle="persistent-coasters">
    <execution provider="coaster-persistent"
               url="http://localhost:53346"
               jobmanager="local:local"/>
    <profile namespace="globus" key="workerManager">passive</profile>
    <profile namespace="globus" key="jobsPerNode">1</profile>
    <profile key="jobThrottle" namespace="karajan">10</profile>
    <profile namespace="karajan" key="initialScore">10000</profile>
    <filesystem provider="local" url="none" />
    <workdirectory>/scratchspace</workdirectory>
  </pool>
</config>


The first question is why the start-coaster-service does not terminate?

Anyhow, if I use this sites.xml, then swift output is

lenovo at lenovo-laptop:~/swift-cloud-tutorial/part01$ swift p1.swift
Swift 0.94.1 swift-r7114 cog-r3803

RunID: 20140902-1406-he5yo1s3
Progress:  time: Tue, 02 Sep 2014 14:06:50 -0400
Progress:  time: Tue, 02 Sep 2014 14:07:20 -0400  Submitted:1
Progress:  time: Tue, 02 Sep 2014 14:07:50 -0400  Submitted:1
Progress:  time: Tue, 02 Sep 2014 14:08:20 -0400  Submitted:1
Progress:  time: Tue, 02 Sep 2014 14:08:50 -0400  Submitted:1
Progress:  time: Tue, 02 Sep 2014 14:09:20 -0400  Submitted:1
Progress:  time: Tue, 02 Sep 2014 14:09:50 -0400  Submitted:1
Progress:  time: Tue, 02 Sep 2014 14:10:20 -0400  Submitted:1
Progress:  time: Tue, 02 Sep 2014 14:10:50 -0400  Submitted:1
Progress:  time: Tue, 02 Sep 2014 14:11:20 -0400  Submitted:1
Progress:  time: Tue, 02 Sep 2014 14:11:50 -0400  Submitted:1
Progress:  time: Tue, 02 Sep 2014 14:12:20 -0400  Submitted:1
Progress:  time: Tue, 02 Sep 2014 14:12:50 -0400  Submitted:1
Progress:  time: Tue, 02 Sep 2014 14:13:20 -0400  Submitted:1
Progress:  time: Tue, 02 Sep 2014 14:13:50 -0400  Submitted:1
Progress:  time: Tue, 02 Sep 2014 14:14:20 -0400  Submitted:1
Progress:  time: Tue, 02 Sep 2014 14:14:50 -0400  Submitted:1
Progress:  time: Tue, 02 Sep 2014 14:15:20 -0400  Submitted:1
Progress:  time: Tue, 02 Sep 2014 14:15:50 -0400  Submitted:1


I am also attaching the log file for that.




On Mon, Sep 1, 2014 at 5:20 PM, Justin bbt <justinbbt at gmail.com> wrote:

> I solved the permission problem with ssh-add command to add the key to
> list of keys.  (This modification is required if the local system is linux-
> i am using ubuntu)
>
> (more here
> https://help.github.com/articles/error-agent-admitted-failure-to-sign)
>
> Now, start-coaster-service connect to the cluster without password, but it
> does not terminate. The is the the output
>
> Service address: localhost
> Starting coaster-service
> Service port: 35925
> Local port: 40681
> Generating sites.xml
> Starting worker on W.X.Y.Z
> WORKER_LOGGING_LEVEL=DEBUG: Command not found.
>
>
>
> If I just use my sites.xml
>
> <pool handle="persistent-coasters">
>     <execution provider="coaster-persistent"
>                url="http:// <http://localhost:37584/>urladdress"
>                jobmanager="local:local"/>
>     <profile namespace="globus" key="workerManager">passive</profile>
>     <profile namespace="globus" key="jobsPerNode">1</profile>
>     <profile key="jobThrottle" namespace="karajan">10</profile>
>     <profile namespace="karajan" key="initialScore">10000</profile>
>     <filesystem provider="local" url="none" />
>     <workdirectory>.</workdirectory>
>   </pool>
>
>
>   it fails with the following error
>
>
> Execution failed:
> Exception in simulate:
>     Arguments: []
>     Host: persistent-coasters
>     Directory: p1-20140901-1648-r8mdqbse/jobs/z/simulate-zcyxesvl
>
> Caused by:
> Could not submit job
> Caused by:
> Failed to create socket
> Caused by:
> Connection refused
> simulation, p1.swift, line 9
>
>
>
>
>
>
> On Sat, Aug 30, 2014 at 1:28 AM, Justin bbt <justinbbt at gmail.com> wrote:
>
>> For cluster:
>>
>> When I run the start-caoster-service, I receive the following, in which
>> it asks for password and then says Permission is denied
>>
>> Start-coaster-service...
>> Configuration: /home/lenovo/swift-cloud-tutorial/scs/coaster-service.conf
>> Service address: localhost
>> Starting coaster-service
>> Service port: 52809
>> Local port: 58460
>> Generating sites.xml
>> username at ipadress's password:
>> username at ipadress's password:
>> Starting worker on username@
>> lenovo at lenovo-laptop:~/swift-cloud-tutorial/scs$username at ipadress's
>> password:
>> Permission denied, please try again.
>> username at ipadress's password:
>> Permission denied, please try again.
>> username at ipadress's password:
>> Permission denied (publickey,gssapi-keyex,gssapi-with-mic,password).
>>
>> This happens though I have created my keys with ssh-keygen. (only changed
>> that I made was to create rsa keys rather than dsa keys - my cluster did
>> not accept dsa). I can connect with rsa keygen and my passphrase for
>> regular ssh
>>
>> The output of my sites.xml  from this partial running of
>> start-coaster-service is
>>
>>  <pool handle="persistent-coasters">
>>     <execution provider="coaster-persistent"
>>                url="http://localhost:37584"
>>                jobmanager="local:local"/>
>>     <profile namespace="globus" key="workerManager">passive</profile>
>>     <profile namespace="globus" key="jobsPerNode">1</profile>
>>     <profile key="jobThrottle" namespace="karajan">10</profile>
>>     <profile namespace="karajan" key="initialScore">10000</profile>
>>     <filesystem provider="local" url="none" />
>>     <workdirectory>.</workdirectory>
>>   </pool>
>>
>> Using this XML , I just get a sequence of job submission every 30
>> seconds, no finished jobs.
>>
>>
>> BTW, I have a public ip for my cluster and then each compute node has a
>> local/private ip.
>> In
>>  export WORKER_HOSTS="<IP of machine 1> <IP of machine 2>"
>> currently I just set the public IP address which still I am not
>> successful with this one node even. I was wondering how should I set the
>> other IPs? Does it mean that I have to install swift on the cluster?
>>
>>
>> I will look at the new  release of swift for AWS.
>>
>>
>> Thanks,
>> J.
>>
>>
>>
>>
>>
>> On Fri, Aug 29, 2014 at 11:43 AM, Yadu Nand <yadudoc1729 at gmail.com>
>> wrote:
>>
>>> Hi Justin,
>>>
>>> ??Did you do the following steps:
>>> export WORKER_LOCATION="/home/ubuntu"
>>> export WORKER_HOSTS="<IP of machine 1> <IP of machine 2>"
>>> export WORKER_USERNAME=ubuntu
>>>
>>> and then run "source setup.sh" ?
>>> When you source the setup.sh scripts you must've gotten a sites.xml and
>>> a start-coaster-service.log in your scs folder, could you send us those ?
>>> The setup script should start a persistent coaster service and connect
>>> to the nodes on amazon, start workers, and generate a sites.xml file
>>> that would let your swift scripts run across the amazon nodes. You
>>> shouldn't have to make changes to the sites.xml.
>>>
>>>  Alternatively, you could try using the beta release of swift, Swift
>>> 0.95 RC6 with the new cloud mechanism:
>>> https://github.com/swift-lang/swift-on-cloud/tree/master/aws
>>>
>>> That will set you up with a headnode on AWS with a few worker nodes that
>>> you define, with everything setup to run swift.
>>>
>>>
>>> Thanks,
>>> Yadu
>>> ?
>>>
>>>
>>>  On Thu, Aug 28, 2014 at 6:57 PM, Justin bbt <justinbbt at gmail.com>
>>> wrote:
>>>
>>>>
>>>>
>>>>
>>>> Hi all,
>>>>>
>>>>>  I could successfully run swift on my local system.
>>>>> Next, I want to use the swift to run some jobs on a cluster.
>>>>>
>>>>> I followed this tutorial.  (I am using just a simple cluster- I even
>>>>> could not run the job on one remote node of the cluster)
>>>>> http://swift-lang.org/tutorials/cloud/tutorial.html
>>>>>
>>>>> But, I get this when I run swift p1.swift or other swift
>>>>>
>>>>> Swift 0.94.1 swift-r7114 cog-r3803
>>>>>
>>>>> RunID: 20140828-1758-ea4phzag
>>>>> Progress:  time: Thu, 28 Aug 2014 17:58:15 -0400
>>>>> Progress:  time: Thu, 28 Aug 2014 17:58:24 -0400  Submitted:1
>>>>> Execution failed:
>>>>> Exception in simulate:
>>>>>     Arguments: []
>>>>>     Host: remotehost2
>>>>>     Directory: p1-20140828-1758-ea4phzag/jobs/7/simulate-7k2fxlvl
>>>>>
>>>>> Caused by:
>>>>> Job failed with an exit code of 127
>>>>> simulation, p1.swift, line 9
>>>>>
>>>>>
>>>>> --- this is my site.xml file setting
>>>>>
>>>>>    <pool handle="remotehost2">
>>>>>       <execution provider="ssh" jobmanager="ssh:local"
>>>>> url="myclusteturl"/>
>>>>>       <filesystem provider="ssh" url="myclusteturl"/>
>>>>>       <profile namespace="karajan" key="jobThrottle">0</profile>
>>>>>       <profile namespace="karajan" key="initialScore">10000</profile>
>>>>>       <workdirectory>/path/to/remote/workdirectory</workdirectory>
>>>>>    </pool>
>>>>>
>>>>> --- if I use this one
>>>>> <pool handle="persistent-coasters">
>>>>>     <execution provider="coaster-persistent"
>>>>>                url="myclusterurl"
>>>>>                jobmanager="local:local"/>
>>>>>     <profile namespace="globus" key="workerManager">passive</profile>
>>>>>     <profile namespace="globus" key="jobsPerNode">1</profile>
>>>>>     <profile key="jobThrottle" namespace="karajan">10</profile>
>>>>>     <profile namespace="karajan" key="initialScore">10000</profile>
>>>>>     <filesystem provider="local" url="none" />
>>>>>     <workdirectory>.l</workdirectory>
>>>>>   </pool>
>>>>> --- then it loops to my localhost and just repeat submitting the jobs
>>>>>
>>>>> 1. Is this a correct setting?
>>>>> 2. Should I use coaster? I could not understand the description in
>>>>> user guides and documentation about the concepts of coaster and the
>>>>> required setting. Is there any better tutorial which would describe the
>>>>> coaster ?
>>>>> 3. I plan to use the swift later on the cloud (Microsoft Azure). What
>>>>> are the setting required for that? for site.xml and if any other file
>>>>>
>>>>>
>>>>> Thanks in Advance.
>>>>>
>>>>>
>>>>
>>>>
>>>> _______________________________________________
>>>> Swift-user mailing list
>>>> Swift-user at ci.uchicago.edu
>>>> https://lists.ci.uchicago.edu/cgi-bin/mailman/listinfo/swift-user
>>>>
>>>
>>>
>>>
>>> --
>>> Yadu Nand B
>>>
>>>
>>
>
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From hategan at mcs.anl.gov  Tue Sep  2 17:09:11 2014
From: hategan at mcs.anl.gov (Mihael Hategan)
Date: Tue, 2 Sep 2014 15:09:11 -0700
Subject: [Swift-user] new config for Cobalt provider option ignored
In-Reply-To: <CAMUuvirzthf+w2b+EYgdGHDUxL8Yyimj6f_2NKYF_rv0wP=eYg@mail.gmail.com>
References: <CAMUuvirzthf+w2b+EYgdGHDUxL8Yyimj6f_2NKYF_rv0wP=eYg@mail.gmail.com>
Message-ID: <1409695751.16233.12.camel@echo>

Hi Ketan,

The config translator does not generally translate new features that
were added just now by you, and it even tells you when it doesn't
recognize an option:

# Option ignored: globus:mode = script

You can say instead:

options {
	mode: "script"
}

Mihael


On Tue, 2014-09-02 at 16:00 -0500, Ketan Maheshwari wrote:
> Hi,
> 
> So, trying the new config from trunk for the cobalt provider, the config
> translator is ignoring the script mode. Is there an alternative way to tell
> Cobalt provider to be invoked in script mode? The old-style sites file is:
> 
> <?xml version="1.0" encoding="UTF-8"?>
> <config xmlns="http://www.ci.uchicago.edu/swift/SwiftSites">
> 
> <pool handle="cluster">
> <execution provider="coaster" jobmanager="local:cobalt" />
> 
> <profile namespace="globus" key="slots">1</profile>
> <profile namespace="globus" key="mode">script</profile>
> 
> <profile namespace="karajan" key="jobThrottle">2.99</profile>
> <profile namespace="karajan" key="initialScore">10000</profile>
> <profile namespace="globus" key="jobsPerNode">4</profile>
> <profile namespace="globus" key="maxwalltime">00:15:00</profile>
> <profile namespace="globus" key="walltime">1500</profile>
> 
> <profile namespace="globus" key="maxnodes">128</profile>
> <profile namespace="globus" key="nodegranularity">128</profile>
> 
> <workdirectory>/home/ketan/swiftwork</workdirectory>
> <filesystem provider="local"/>
> 
> </pool>
> </config>
> 
> The generated config is:
> 
> <snip>
> options {
> maxNodesPerJob: 128
> maxJobs: 1
> tasksPerNode: 4
> # Option ignored: globus:mode = script
> nodeGranularity: 128
> # Option ignored: globus:walltime = 1500
> }
> ...
> 
> Thanks,
> Ketan
> _______________________________________________
> Swift-user mailing list
> Swift-user at ci.uchicago.edu
> https://lists.ci.uchicago.edu/cgi-bin/mailman/listinfo/swift-user




From jozik at uchicago.edu  Thu Sep  4 10:44:56 2014
From: jozik at uchicago.edu (Jonathan Ozik)
Date: Thu, 4 Sep 2014 10:44:56 -0500
Subject: [Swift-user] Bus Error
Message-ID: <E5F0A2F0-C1D2-4457-ACD8-CEEEBFD89119@uchicago.edu>

Hi all,

I?m trying to launch a large number of runs, 16807 to be precise, and am running into a couple of issues.
The first issue was a Java heap out of memory exception. I looked around to see where the best place to increase the max heap would be, and I settled on line 13 (?HEAPMAX=4096M?) of the swift executable. I should mention that all of this is using swift-0.95-RC6.
That did get rid of the out of memory exception, but this time I got a Bus error:

/home/ozik/swift_dist/swift-0.95-RC6/bin/swift: line 188: 108521 Bus error               (core dumped) java -Xmx4096M -XX:+HeapDumpOnOutOfMemoryError -Djava.endorsed.dirs=/home/ozik/swift_dist/swift-0.95-RC6/lib/endorsed -DUID=5702 -DGLOBUS_HOSTNAME=blogin3 -DCOG_INSTALL_PATH=/home/ozik/swift_dist/swift-0.95-RC6 -Dswift.home=/home/ozik/swift_dist/swift-0.95-RC6 -Djava.security.egd=file:///dev/urandom -Dscript.dir=/lcrc/project/gcmat/runs/heatmap7_7x7/complete_model/run003/scripts -Drestart.log.name=/lcrc/project/gcmat/runs/heatmap7_7x7/complete_model/run003/restart.log -Ddebug.dir.prefix=run003/ -classpath /home/ozik/swift_dist/swift-0.95-RC6/etc:/home/ozik/swift_dist/swift-0.95-RC6/libexec:/home/ozik/swift_dist/swift-0.95-RC6/lib/ant.jar:/home/ozik/swift_dist/swift-0.95-RC6/lib/antlr-2.7.5.jar:/home/ozik/swift_dist/swift-0.95-RC6/lib/castor-0.9.6.jar:/home/ozik/swift_dist/swift-0.95-RC6/lib/coaster-bootstrap.jar:/home/ozik/swift_dist/swift-0.95-RC6/lib/cog-abstraction-common-2.4.jar:/home/ozik/swift_dist/swift-0.95-RC6/lib/cog-grapheditor-0.47.jar:/home/ozik/swift_dist/swift-0.95-RC6/lib/cog-jglobus-1.7.0.jar:/home/ozik/swift_dist/swift-0.95-RC6/lib/cog-karajan-0.36-dev.jar:/home/ozik/swift_dist/swift-0.95-RC6/lib/cog-provider-coaster-0.3.jar:/home/ozik/swift_dist/swift-0.95-RC6/lib/cog-provider-dcache-0.1.jar:/home/ozik/swift_dist/swift-0.95-RC6/lib/cog-provider-gt2-2.4.jar:/home/ozik/swift_dist/swift-0.95-RC6/lib/cog-provider-local-2.2.jar:/home/ozik/swift_dist/swift-0.95-RC6/lib/cog-provider-localscheduler-0.4.jar:/home/ozik/swift_dist/swift-0.95-RC6/lib/cog-provider-ssh-2.4.jar:/home/ozik/swift_dist/swift-0.95-RC6/lib/cog-provider-webdav-2.1.jar:/home/ozik/swift_dist/swift-0.95-RC6/lib/cog-resources-1.0.jar:/home/ozik/swift_dist/swift-0.95-RC6/lib/cog-swift-svn.jar:/home/ozik/swift_dist/swift-0.95-RC6/lib/cog-util-0.92.jar:/home/ozik/swift_dist/swift-0.95-RC6/lib/commons-httpclient.jar:/home/ozik/swift_dist/swift-0.95-RC6/lib/commons-logging-1.1.jar:/home/ozik/swift_dist/swift-0.95-RC6/lib/cryptix32.jar:/home/ozik/swift_dist/swift-0.95-RC6/lib/cryptix-asn1.jar:/home/ozik/swift_dist/swift-0.95-RC6/lib/cryptix.jar:/home/ozik/swift_dist/swift-0.95-RC6/lib/j2ssh-common-0.2.2.jar:/home/ozik/swift_dist/swift-0.95-RC6/lib/j2ssh-core-0.2.2-patch-b.jar:/home/ozik/swift_dist/swift-0.95-RC6/lib/jakarta-regexp-1.2.jar:/home/ozik/swift_dist/swift-0.95-RC6/lib/jakarta-slide-webdavlib-2.0.jar:/home/ozik/swift_dist/swift-0.95-RC6/lib/jaxrpc.jar:/home/ozik/swift_dist/swift-0.95-RC6/lib/jce-jdk13-131.jar:/home/ozik/swift_dist/swift-0.95-RC6/lib/jcommon-1.0.18.jar:/home/ozik/swift_dist/swift-0.95-RC6/lib/jfreechart-1.0.15.jar:/home/ozik/swift_dist/swift-0.95-RC6/lib/jgss.jar:/home/ozik/swift_dist/swift-0.95-RC6/lib/jline-0.9.94.jar:/home/ozik/swift_dist/swift-0.95-RC6/lib/jsr173_1.0_api.jar:/home/ozik/swift_dist/swift-0.95-RC6/lib/jug-lgpl-2.0.0.jar:/home/ozik/swift_dist/swift-0.95-RC6/lib/junit.jar:/home/ozik/swift_dist/swift-0.95-RC6/lib/log4j-1.2.16.jar:/home/ozik/swift_dist/swift-0.95-RC6/lib/puretls.jar:/home/ozik/swift_dist/swift-0.95-RC6/lib/resolver.jar:/home/ozik/swift_dist/swift-0.95-RC6/lib/stringtemplate.jar:/home/ozik/swift_dist/swift-0.95-RC6/lib/vdldefinitions.jar:/home/ozik/swift_dist/swift-0.95-RC6/lib/xbean.jar:/home/ozik/swift_dist/swift-0.95-RC6/lib/xbean_xpath.jar: org.griphyn.vdl.karajan.Loader -runid run003 -logfile /lcrc/project/gcmat/runs/heatmap7_7x7/complete_model/run003/run003.log -sites.file /lcrc/project/gcmat/runs/heatmap7_7x7/complete_model/run003/sites.xml -tc.file /lcrc/project/gcmat/runs/heatmap7_7x7/complete_model/run003/apps -config /lcrc/project/gcmat/runs/heatmap7_7x7/complete_model/run003/cf repast.swift -lines=823543 -inst=16807 -upf=unrolledParamFile.txt

Any ideas on this?

Jonathan

From hategan at mcs.anl.gov  Thu Sep  4 14:28:50 2014
From: hategan at mcs.anl.gov (Mihael Hategan)
Date: Thu, 4 Sep 2014 12:28:50 -0700
Subject: [Swift-user] Bus Error
In-Reply-To: <E5F0A2F0-C1D2-4457-ACD8-CEEEBFD89119@uchicago.edu>
References: <E5F0A2F0-C1D2-4457-ACD8-CEEEBFD89119@uchicago.edu>
Message-ID: <1409858930.32145.3.camel@echo>

Hi Jonathan,

It's a bus error, which is just slightly worse than a segfault. both of
which would reflect bugs in the JVM.

Was there a hs_err_pid???.log produced? It might help.

Also, it might help to know the exact version of java as well as the
hardware details.

Mihael

On Thu, 2014-09-04 at 10:44 -0500, Jonathan Ozik wrote:
> Hi all,
> 
> I?m trying to launch a large number of runs, 16807 to be precise, and am running into a couple of issues.
> The first issue was a Java heap out of memory exception. I looked around to see where the best place to increase the max heap would be, and I settled on line 13 (?HEAPMAX=4096M?) of the swift executable. I should mention that all of this is using swift-0.95-RC6.
> That did get rid of the out of memory exception, but this time I got a Bus error:
> 
> /home/ozik/swift_dist/swift-0.95-RC6/bin/swift: line 188: 108521 Bus error               (core dumped) java -Xmx4096M -XX:+HeapDumpOnOutOfMemoryError -Djava.endorsed.dirs=/home/ozik/swift_dist/swift-0.95-RC6/lib/endorsed -DUID=5702 -DGLOBUS_HOSTNAME=blogin3 -DCOG_INSTALL_PATH=/home/ozik/swift_dist/swift-0.95-RC6 -Dswift.home=/home/ozik/swift_dist/swift-0.95-RC6 -Djava.security.egd=file:///dev/urandom -Dscript.dir=/lcrc/project/gcmat/runs/heatmap7_7x7/complete_model/run003/scripts -Drestart.log.name=/lcrc/project/gcmat/runs/heatmap7_7x7/complete_model/run003/restart.log -Ddebug.dir.prefix=run003/ -classpath /home/ozik/swift_dist/swift-0.95-RC6/etc:/home/ozik/swift_dist/swift-0.95-RC6/libexec:/home/ozik/swift_dist/swift-0.95-RC6/lib/ant.jar:/home/ozik/swift_dist/swift-0.95-RC6/lib/antlr-2.7.5.jar:/home/ozik/swift_dist/swift-0.95-RC6/lib/castor-0.9.6.jar:/home/ozik/swift_dist/swift-0.95-RC6/lib/coaster-bootstrap.jar:/home/ozik/swift_dist/swift-0.95-RC6/lib/cog-abstraction-common-2.4.jar:/home/ozik/swift_dist/swift-0.95-RC6/lib/cog-grapheditor-0.47.jar:/home/ozik/swift_dist/swift-0.95-RC6/lib/cog-jglobus-1.7.0.jar:/home/ozik/swift_dist/swift-0.95-RC6/lib/cog-karajan-0.36-dev.jar:/home/ozik/swift_dist/swift-0.95-RC6/lib/cog-provider-coaster-0.3.jar:/home/ozik/swift_dist/swift-0.95-RC6/lib/cog-provider-dcache-0.1.jar:/home/ozik/swift_dist/swift-0.95-RC6/lib/cog-provider-gt2-2.4.jar:/home/ozik/swift_dist/swift-0.95-RC6/lib/cog-provider-local-2.2.jar:/home/ozik/swift_dist/swift-0.95-RC6/lib/cog-provider-localscheduler-0.4.jar:/home/ozik/swift_dist/swift-0.95-RC6/lib/cog-provider-ssh-2.4.jar:/home/ozik/swift_dist/swift-0.95-RC6/lib/cog-provider-webdav-2.1.jar:/home/ozik/swift_dist/swift-0.95-RC6/lib/cog-resources-1.0.jar:/home/ozik/swift_dist/swift-0.95-RC6/lib/cog-swift-svn.jar:/home/ozik/swift_dist/swift-0.95-RC6/lib/cog-util-0.92.jar:/home/ozik/swift_dist/swift-0.95-RC6/lib/commons-httpclient.jar:/home/ozik/swift_dist/swift-0.95-RC6/lib/commons-logging-1.1.jar:/home/ozik/swift_dist/swift-0.95-RC6/lib/cryptix32.jar:/home/ozik/swift_dist/swift-0.95-RC6/lib/cryptix-asn1.jar:/home/ozik/swift_dist/swift-0.95-RC6/lib/cryptix.jar:/home/ozik/swift_dist/swift-0.95-RC6/lib/j2ssh-common-0.2.2.jar:/home/ozik/swift_dist/swift-0.95-RC6/lib/j2ssh-core-0.2.2-patch-b.jar:/home/ozik/swift_dist/swift-0.95-RC6/lib/jakarta-regexp-1.2.jar:/home/ozik/swift_dist/swift-0.95-RC6/lib/jakarta-slide-webdavlib-2.0.jar:/home/ozik/swift_dist/swift-0.95-RC6/lib/jaxrpc.jar:/home/ozik/swift_dist/swift-0.95-RC6/lib/jce-jdk13-131.jar:/home/ozik/swift_dist/swift-0.95-RC6/lib/jcommon-1.0.18.jar:/home/ozik/swift_dist/swift-0.95-RC6/lib/jfreechart-1.0.15.jar:/home/ozik/swift_dist/swift-0.95-RC6/lib/jgss.jar:/home/ozik/swift_dist/swift-0.95-RC6/lib/jline-0.9.94.jar:/home/ozik/swift_dist/swift-0.95-RC6/lib/jsr173_1.0_api.jar:/home/ozik/swift_dist/swift-0.95-RC6/lib/jug-lgpl-2.0.0.jar:/home/ozik/swift_dist/swift-0.95-RC6/lib/junit.jar:/home/ozik/swift_dist/swift-0.95-RC6/lib/log4j-1.2.16.jar:/home/ozik/swift_dist/swift-0.95-RC6/lib/puretls.jar:/home/ozik/swift_dist/swift-0.95-RC6/lib/resolver.jar:/home/ozik/swift_dist/swift-0.95-RC6/lib/stringtemplate.jar:/home/ozik/swift_dist/swift-0.95-RC6/lib/vdldefinitions.jar:/home/ozik/swift_dist/swift-0.95-RC6/lib/xbean.jar:/home/ozik/swift_dist/swift-0.95-RC6/lib/xbean_xpath.jar: org.griphyn.vdl.karajan.Loader -runid run003 -logfile /lcrc/project/gcmat/runs/heatmap7_7x7/complete_model/run003/run003.log -sites.file /lcrc/project/gcmat/runs/heatmap7_7x7/complete_model/run003/sites.xml -tc.file /lcrc/project/gcmat/runs/heatmap7_7x7/complete_model/run003/apps -config /lcrc/project/gcmat/runs/heatmap7_7x7/complete_model/run003/cf repast.swift -lines=823543 -inst=16807 -upf=unrolledParamFile.txt
> 
> Any ideas on this?
> 
> Jonathan
> _______________________________________________
> Swift-user mailing list
> Swift-user at ci.uchicago.edu
> https://lists.ci.uchicago.edu/cgi-bin/mailman/listinfo/swift-user




From jozik at uchicago.edu  Thu Sep  4 14:52:56 2014
From: jozik at uchicago.edu (Jonathan Ozik)
Date: Thu, 4 Sep 2014 14:52:56 -0500
Subject: [Swift-user] Bus Error
In-Reply-To: <1409858930.32145.3.camel@echo>
References: <E5F0A2F0-C1D2-4457-ACD8-CEEEBFD89119@uchicago.edu>
	<1409858930.32145.3.camel@echo>
Message-ID: <C570F8CA-4016-4510-9A50-00E6F0128FB9@uchicago.edu>

Hi Mihael,

This was on Blues, java version ?1.7.0_55?.

Theres a ~4GB core-java-7-5702-3026-108521-1409822206 core dump file that was generated. (Actually there were two, the other one is ~1.3GB.)
Following this (http://www.javacodegeeks.com/2013/02/analysing-a-java-core-dump.html), this is the error:
Program terminated with signal 7, Bus error.
#0  0x00002b873a0fe6e0 in signalHandler(int, siginfo*, void*) ()
   from /fusion/gpfs/software/linux-rhel5-x86_64/jdk/1.7.0_55/jre/lib/amd64/server/libjvm.so

And this is where it happened:
(gdb) where
#0  0x00002b873a0fe6e0 in signalHandler(int, siginfo*, void*) ()
   from /fusion/gpfs/software/linux-rhel5-x86_64/jdk/1.7.0_55/jre/lib/amd64/server/libjvm.so
#1  <signal handler called>
#2  0x00002b873a102428 in os::PlatformEvent::park(long) ()
   from /fusion/gpfs/software/linux-rhel5-x86_64/jdk/1.7.0_55/jre/lib/amd64/server/libjvm.so
#3  0x00002b873a0f12eb in ObjectMonitor::wait(long, bool, Thread*) ()
   from /fusion/gpfs/software/linux-rhel5-x86_64/jdk/1.7.0_55/jre/lib/amd64/server/libjvm.so
#4  0x00002b8739f63148 in JVM_MonitorWait ()
   from /fusion/gpfs/software/linux-rhel5-x86_64/jdk/1.7.0_55/jre/lib/amd64/server/libjvm.so
#5  0x00002b87402b1608 in ?? ()
#6  0x00000007c7208000 in ?? ()
#7  0x0000000000000000 in ?? ()

Does this help at all?

Jonathan

On Sep 4, 2014, at 2:28 PM, Mihael Hategan <hategan at mcs.anl.gov> wrote:

> Hi Jonathan,
> 
> It's a bus error, which is just slightly worse than a segfault. both of
> which would reflect bugs in the JVM.
> 
> Was there a hs_err_pid???.log produced? It might help.
> 
> Also, it might help to know the exact version of java as well as the
> hardware details.
> 
> Mihael
> 
> On Thu, 2014-09-04 at 10:44 -0500, Jonathan Ozik wrote:
>> Hi all,
>> 
>> I?m trying to launch a large number of runs, 16807 to be precise, and am running into a couple of issues.
>> The first issue was a Java heap out of memory exception. I looked around to see where the best place to increase the max heap would be, and I settled on line 13 (?HEAPMAX=4096M?) of the swift executable. I should mention that all of this is using swift-0.95-RC6.
>> That did get rid of the out of memory exception, but this time I got a Bus error:
>> 
>> /home/ozik/swift_dist/swift-0.95-RC6/bin/swift: line 188: 108521 Bus error               (core dumped) java -Xmx4096M -XX:+HeapDumpOnOutOfMemoryError -Djava.endorsed.dirs=/home/ozik/swift_dist/swift-0.95-RC6/lib/endorsed -DUID=5702 -DGLOBUS_HOSTNAME=blogin3 -DCOG_INSTALL_PATH=/home/ozik/swift_dist/swift-0.95-RC6 -Dswift.home=/home/ozik/swift_dist/swift-0.95-RC6 -Djava.security.egd=file:///dev/urandom -Dscript.dir=/lcrc/project/gcmat/runs/heatmap7_7x7/complete_model/run003/scripts -Drestart.log.name=/lcrc/project/gcmat/runs/heatmap7_7x7/complete_model/run003/restart.log -Ddebug.dir.prefix=run003/ -classpath /home/ozik/swift_dist/swift-0.95-RC6/etc:/home/ozik/swift_dist/swift-0.95-RC6/libexec:/home/ozik/swift_dist/swift-0.95-RC6/lib/ant.jar:/home/ozik/swift_dist/swift-0.95-RC6/lib/antlr-2.7.5.jar:/home/ozik/swift_dist/swift-0.95-RC6/lib/castor-0.9.6.jar:/home/ozik/swift_dist/swift-0.95-RC6/lib/coaster-bootstrap.jar:/home/ozik/swift_dist/swift-0.95-RC6/lib/cog-abstraction-common-2.4.jar:/home/ozik/swift_dist/swift-0.95-RC6/lib/cog-grapheditor-0.47.jar:/home/ozik/swift_dist/swift-0.95-RC6/lib/cog-jglobus-1.7.0.jar:/home/ozik/swift_dist/swift-0.95-RC6/lib/cog-karajan-0.36-dev.jar:/home/ozik/swift_dist/swift-0.95-RC6/lib/cog-provider-coaster-0.3.jar:/home/ozik/swift_dist/swift-0.95-RC6/lib/cog-provider-dcache-0.1.jar:/home/ozik/swift_dist/swift-0.95-RC6/lib/cog-provider-gt2-2.4.jar:/home/ozik/swift_dist/swift-0.95-RC6/lib/cog-provider-local-2.2.jar:/home/ozik/swift_dist/swift-0.95-RC6/lib/cog-provider-localscheduler-0.4.jar:/home/ozik/swift_dist/swift-0.95-RC6/lib/cog-provider-ssh-2.4.jar:/home/ozik/swift_dist/swift-0.95-RC6/lib/cog-provider-webdav-2.1.jar:/home/ozik/swift_dist/swift-0.95-RC6/lib/cog-resources-1.0.jar:/home/ozik/swift_dist/swift-0.95-RC6/lib/cog-swift-svn.jar:/home/ozik/swift_dist/swift-0.95-RC6/lib/cog-util-0.92.jar:/home/ozik/swift_dist/swift-0.95-RC6/lib/commons-httpclient.jar:/home/ozik/swift_dist/swift-0.95-RC6/lib/commons-logging-1.1.jar:/home/ozik/swift_dist/swift-0.95-RC6/lib/cryptix32.jar:/home/ozik/swift_dist/swift-0.95-RC6/lib/cryptix-asn1.jar:/home/ozik/swift_dist/swift-0.95-RC6/lib/cryptix.jar:/home/ozik/swift_dist/swift-0.95-RC6/lib/j2ssh-common-0.2.2.jar:/home/ozik/swift_dist/swift-0.95-RC6/lib/j2ssh-core-0.2.2-patch-b.jar:/home/ozik/swift_dist/swift-0.95-RC6/lib/jakarta-regexp-1.2.jar:/home/ozik/swift_dist/swift-0.95-RC6/lib/jakarta-slide-webdavlib-2.0.jar:/home/ozik/swift_dist/swift-0.95-RC6/lib/jaxrpc.jar:/home/ozik/swift_dist/swift-0.95-RC6/lib/jce-jdk13-131.jar:/home/ozik/swift_dist/swift-0.95-RC6/lib/jcommon-1.0.18.jar:/home/ozik/swift_dist/swift-0.95-RC6/lib/jfreechart-1.0.15.jar:/home/ozik/swift_dist/swift-0.95-RC6/lib/jgss.jar:/home/ozik/swift_dist/swift-0.95-RC6/lib/jline-0.9.94.jar:/home/ozik/swift_dist/swift-0.95-RC6/lib/jsr173_1.0_api.jar:/home/ozik/swift_dist/swift-0.95-RC6/lib/jug-lgpl-2.0.0.jar:/home/ozik/swift_dist/swift-0.95-RC6/lib/junit.jar:/home/ozik/swift_dist/swift-0.95-RC6/lib/log4j-1.2.16.jar:/home/ozik/swift_dist/swift-0.95-RC6/lib/puretls.jar:/home/ozik/swift_dist/swift-0.95-RC6/lib/resolver.jar:/home/ozik/swift_dist/swift-0.95-RC6/lib/stringtemplate.jar:/home/ozik/swift_dist/swift-0.95-RC6/lib/vdldefinitions.jar:/home/ozik/swift_dist/swift-0.95-RC6/lib/xbean.jar:/home/ozik/swift_dist/swift-0.95-RC6/lib/xbean_xpath.jar: org.griphyn.vdl.karajan.Loader -runid run003 -logfile /lcrc/project/gcmat/runs/heatmap7_7x7/complete_model/run003/run003.log -sites.file /lcrc/project/gcmat/runs/heatmap7_7x7/complete_model/run003/sites.xml -tc.file /lcrc/project/gcmat/runs/heatmap7_7x7/complete_model/run003/apps -config /lcrc/project/gcmat/runs/heatmap7_7x7/complete_model/run003/cf repast.swift -lines=823543 -inst=16807 -upf=unrolledParamFile.txt
>> 
>> Any ideas on this?
>> 
>> Jonathan
>> _______________________________________________
>> Swift-user mailing list
>> Swift-user at ci.uchicago.edu
>> https://lists.ci.uchicago.edu/cgi-bin/mailman/listinfo/swift-user
> 
> 



From ketan at mcs.anl.gov  Fri Sep  5 20:03:26 2014
From: ketan at mcs.anl.gov (Ketan Maheshwari)
Date: Fri, 5 Sep 2014 20:03:26 -0500
Subject: [Swift-user] Pointer to Swift tutorials for computational
 science education and research
In-Reply-To: <362b5dde41ab45f5a0f455a267c058da@GEORGE.anl.gov>
References: <539FC360.6090800@anl.gov>
	<59fc9be3f4d445ab8d502b2b1ce63af7@GEORGE.anl.gov>
	<CAMUuviqo8zhzvXVtJGEtV0TyoyW=D_EbVpNzL60BoNw60EEXEQ@mail.gmail.com>
	<CAN=xv+Zm+_VT5Ej4bDWiS8RotdgiuwYxRaF0CnZoV0si5hywQA@mail.gmail.com>
	<f41cf2675e66453d989165ca3231f73c@LUCKMAN.anl.gov>
	<CAMUuvirA+g6mQFBqw=u5p7kw+548VQ1q7g9wpyBxNz6792MOcw@mail.gmail.com>
	<13482362cf5c4f13a4d98c897b022f89@LUCKMAN.anl.gov>
	<CAMUuviq_v2oT2Gp-QVH94fevfzmx0R-5Y7bzZ-AYpNnb9zK5Nw@mail.gmail.com>
	<CAN=xv+b1z1CmwSM5b_gCi0D1vB15NBAKdtBs6nADgcQwgqRgDQ@mail.gmail.com>
	<362b5dde41ab45f5a0f455a267c058da@GEORGE.anl.gov>
Message-ID: <CAMUuviodRt37OwDVhhP==VKPusCXiV30sCRBS9_rOb9wOV3XWA@mail.gmail.com>

Hi Andrew,

Yes, I remember: thanks for getting back on this.

>From the error message and tc.data, indeed it looks like the executable is
provided as absolute path but somehow Swift is looking into system path and
not finding it. One possibility is that the node on which catnap.sh is
running does not have it installed on the path specified in the tc.data.
Can you also check if catnap.sh has the executable bit set. Less likely
that this is causing the issue though.

Also, from the tc.data line it looks like you are using persistent
coasters. Have started the coaster service beforehand and made sure the
service started correctly without any error messages. Could you indicate
more about your cluster. Depending on the type of cluster, it is possible
that we can run Swift in a non-persistent, implicit coasters mode.

Can you also send the Swift generated log for this run.

Thanks,
Ketan


On Fri, Sep 5, 2014 at 7:16 PM, Andrew Stocker <amstocker at dons.usfca.edu>
wrote:

>  Hi Ketan,
>
>  I'm not sure if you remember, but myself and my research advisor
> Xiaosheng spoke to you at LBL in Oakland at the beginning of the summer
> about starting to use Swift at our school.   We have been working hard on
> setting it up, and I am trying to get your demo to run but I'm having a
> problem.  For some reason I keep getting the following error when I try to
> run your catsnsleep demo:
>
>  Execution failed:
> Exception in catnap:
>     Arguments: [5, data.txt]
>     Host: persistent-coasters
>     Directory: catsnsleep-20140905-1702-mihcat06/jobs/u/catnap-utx080xl
>
>  Caused by:
> Cannot find executable catnap.sh on site system path
> catnap, catsnsleep.swift, line 13
>
>  However I'm not sure why.  In our tc.data file we have the line:
>
>  persistent-coasters catnap /usr/local/swift-0.94.1/oakland-demo/catnap.sh
>
>  which I think should work but obviously something is going wrong.  I
> have been browsing the documentation articles but I can't find anything
> about why this might be happening.  We would greatly appreciate your advice!
>
>  Regards,
>
>  Andrew Stocker
>
>
> On Fri, Jun 20, 2014 at 12:00 PM, Xiaosheng Huang <xhuang22 at usfca.edu>
> wrote:
>
>>
>> ---------- Forwarded message ----------
>> From: Ketan Maheshwari <ketan at mcs.anl.gov>
>> Date: Fri, Jun 20, 2014 at 11:45 AM
>> Subject: Re: Pointer to Swift tutorials for computational science
>> education and research
>> To: Xiaosheng Huang <xhuang22 at usfca.edu>
>> Cc: Wilde <wilde at mcs.anl.gov>
>>
>>
>> Hi Xiaosheng,
>>
>>  The tarball is: http://www.mcs.anl.gov/~ketan/oakland-demo.tgz
>>
>>  There is a small README in there which outlines the steps.
>>
>>  Best,
>> Ketan
>>
>>   ************************************************************
>> Xiaosheng Huang, Assistant Professor
>> Department of Physics and Astronomy
>> University of San Francisco
>> 2130 Fulton Street, San Francisco, CA 94117-1080
>>
>> Phone: (415) 422-6281
>> E-mail: xhuang22 at usfca.edu
>> ************************************************************
>>
>
>
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From jozik at uchicago.edu  Mon Sep  8 13:04:29 2014
From: jozik at uchicago.edu (Jonathan Ozik)
Date: Mon, 8 Sep 2014 13:04:29 -0500
Subject: [Swift-user] CPU failed leading to end of run
Message-ID: <E03138DA-46F3-4593-82CF-9E35C39D7BCC@uchicago.edu>

Hello all,

I?m getting failed runs on Blues which might be due to CPUs failing. I?ve put the run log at: /tmp/run004_ozik.log

Any help is greatly appreciated,

Jonathan



From yadunand at uchicago.edu  Mon Sep  8 13:18:57 2014
From: yadunand at uchicago.edu (Yadu Nand Babuji)
Date: Mon, 08 Sep 2014 13:18:57 -0500
Subject: [Swift-user] CPU failed leading to end of run
In-Reply-To: <E03138DA-46F3-4593-82CF-9E35C39D7BCC@uchicago.edu>
References: <E03138DA-46F3-4593-82CF-9E35C39D7BCC@uchicago.edu>
Message-ID: <540DF311.5080308@uchicago.edu>

Hi Jonathan,

Could you add read permissions to the log please ?

Thanks,
Yadu
On 09/08/2014 01:04 PM, Jonathan Ozik wrote:
> Hello all,
>
> I?m getting failed runs on Blues which might be due to CPUs failing. I?ve put the run log at: /tmp/run004_ozik.log
>
> Any help is greatly appreciated,
>
> Jonathan
>
> _______________________________________________
> Swift-user mailing list
> Swift-user at ci.uchicago.edu
> https://lists.ci.uchicago.edu/cgi-bin/mailman/listinfo/swift-user



From jozik at uchicago.edu  Mon Sep  8 13:45:25 2014
From: jozik at uchicago.edu (Jonathan Ozik)
Date: Mon, 8 Sep 2014 13:45:25 -0500
Subject: [Swift-user] CPU failed leading to end of run
In-Reply-To: <540DF311.5080308@uchicago.edu>
References: <E03138DA-46F3-4593-82CF-9E35C39D7BCC@uchicago.edu>
	<540DF311.5080308@uchicago.edu>
Message-ID: <23DDE6BD-5D60-41D4-BD84-22CEA340DEB2@uchicago.edu>

Yadu,

Here?s the location of the log and I did add read permissions: /lcrc/project/gcmat/runs/heatmap7_7x7/complete_model/run004/run004.log

Thank you,

Jonathan

On Sep 8, 2014, at 1:18 PM, Yadu Nand Babuji <yadunand at uchicago.edu> wrote:

> Hi Jonathan,
> 
> Could you add read permissions to the log please ?
> 
> Thanks,
> Yadu
> On 09/08/2014 01:04 PM, Jonathan Ozik wrote:
>> Hello all,
>> 
>> I?m getting failed runs on Blues which might be due to CPUs failing. I?ve put the run log at: /tmp/run004_ozik.log
>> 
>> Any help is greatly appreciated,
>> 
>> Jonathan
>> 
>> _______________________________________________
>> Swift-user mailing list
>> Swift-user at ci.uchicago.edu
>> https://lists.ci.uchicago.edu/cgi-bin/mailman/listinfo/swift-user
> 
> _______________________________________________
> Swift-user mailing list
> Swift-user at ci.uchicago.edu
> https://lists.ci.uchicago.edu/cgi-bin/mailman/listinfo/swift-user



From amstocker at dons.usfca.edu  Mon Sep  8 18:28:47 2014
From: amstocker at dons.usfca.edu (Andrew Stocker)
Date: Mon, 8 Sep 2014 16:28:47 -0700
Subject: [Swift-user] Pointer to Swift tutorials for computational
 science education and research
In-Reply-To: <CAMUuviodRt37OwDVhhP==VKPusCXiV30sCRBS9_rOb9wOV3XWA@mail.gmail.com>
References: <539FC360.6090800@anl.gov>
	<59fc9be3f4d445ab8d502b2b1ce63af7@GEORGE.anl.gov>
	<CAMUuviqo8zhzvXVtJGEtV0TyoyW=D_EbVpNzL60BoNw60EEXEQ@mail.gmail.com>
	<CAN=xv+Zm+_VT5Ej4bDWiS8RotdgiuwYxRaF0CnZoV0si5hywQA@mail.gmail.com>
	<f41cf2675e66453d989165ca3231f73c@LUCKMAN.anl.gov>
	<CAMUuvirA+g6mQFBqw=u5p7kw+548VQ1q7g9wpyBxNz6792MOcw@mail.gmail.com>
	<13482362cf5c4f13a4d98c897b022f89@LUCKMAN.anl.gov>
	<CAMUuviq_v2oT2Gp-QVH94fevfzmx0R-5Y7bzZ-AYpNnb9zK5Nw@mail.gmail.com>
	<CAN=xv+b1z1CmwSM5b_gCi0D1vB15NBAKdtBs6nADgcQwgqRgDQ@mail.gmail.com>
	<362b5dde41ab45f5a0f455a267c058da@GEORGE.anl.gov>
	<CAMUuviodRt37OwDVhhP==VKPusCXiV30sCRBS9_rOb9wOV3XWA@mail.gmail.com>
Message-ID: <CAOZiyaMk5gvktYBY7q3Mn1qme4R7JcpUP97rO8OMPbRt=eH1Fg@mail.gmail.com>

Thanks for your response!

Since we're just in the stages of experimentation, our preliminary cluster
is just four iMacs connected to a switch.  I set up password-less ssh
communication between the four and I'm able to start the coaster service
(in the folder with coaster-service.conf) without any errors.  I am running
Swift from the computer which has the catnap.sh installed at the correct
path, and I'm pretty sure it has the executable bit set ( #!/bin/sh is the
first line of the program).  None of the other three computers have Swift
installed, nor do they have catnap.sh at the location specified in tc.data,
is this a problem?

Attached is the log file from the run when I got the error I copy+pasted
above.  Interestingly, when I run the catnap swift script with only 3
concurrent instances, it seems to run fine since we allow 3 jobs per node
and so it is probably only running locally.

Regards,
Andrew

On Fri, Sep 5, 2014 at 6:03 PM, Ketan Maheshwari <ketan at mcs.anl.gov> wrote:

> Hi Andrew,
>
> Yes, I remember: thanks for getting back on this.
>
> From the error message and tc.data, indeed it looks like the executable is
> provided as absolute path but somehow Swift is looking into system path and
> not finding it. One possibility is that the node on which catnap.sh is
> running does not have it installed on the path specified in the tc.data.
> Can you also check if catnap.sh has the executable bit set. Less likely
> that this is causing the issue though.
>
> Also, from the tc.data line it looks like you are using persistent
> coasters. Have started the coaster service beforehand and made sure the
> service started correctly without any error messages. Could you indicate
> more about your cluster. Depending on the type of cluster, it is possible
> that we can run Swift in a non-persistent, implicit coasters mode.
>
> Can you also send the Swift generated log for this run.
>
> Thanks,
> Ketan
>
>
> On Fri, Sep 5, 2014 at 7:16 PM, Andrew Stocker <amstocker at dons.usfca.edu>
> wrote:
>
>>  Hi Ketan,
>>
>>  I'm not sure if you remember, but myself and my research advisor
>> Xiaosheng spoke to you at LBL in Oakland at the beginning of the summer
>> about starting to use Swift at our school.   We have been working hard on
>> setting it up, and I am trying to get your demo to run but I'm having a
>> problem.  For some reason I keep getting the following error when I try to
>> run your catsnsleep demo:
>>
>>  Execution failed:
>> Exception in catnap:
>>     Arguments: [5, data.txt]
>>     Host: persistent-coasters
>>     Directory: catsnsleep-20140905-1702-mihcat06/jobs/u/catnap-utx080xl
>>
>>  Caused by:
>> Cannot find executable catnap.sh on site system path
>> catnap, catsnsleep.swift, line 13
>>
>>  However I'm not sure why.  In our tc.data file we have the line:
>>
>>  persistent-coasters catnap
>> /usr/local/swift-0.94.1/oakland-demo/catnap.sh
>>
>>  which I think should work but obviously something is going wrong.  I
>> have been browsing the documentation articles but I can't find anything
>> about why this might be happening.  We would greatly appreciate your advice!
>>
>>  Regards,
>>
>>  Andrew Stocker
>>
>>
>> On Fri, Jun 20, 2014 at 12:00 PM, Xiaosheng Huang <xhuang22 at usfca.edu>
>> wrote:
>>
>>>
>>> ---------- Forwarded message ----------
>>> From: Ketan Maheshwari <ketan at mcs.anl.gov>
>>> Date: Fri, Jun 20, 2014 at 11:45 AM
>>> Subject: Re: Pointer to Swift tutorials for computational science
>>> education and research
>>> To: Xiaosheng Huang <xhuang22 at usfca.edu>
>>> Cc: Wilde <wilde at mcs.anl.gov>
>>>
>>>
>>> Hi Xiaosheng,
>>>
>>>  The tarball is: http://www.mcs.anl.gov/~ketan/oakland-demo.tgz
>>>
>>>  There is a small README in there which outlines the steps.
>>>
>>>  Best,
>>> Ketan
>>>
>>>   ************************************************************
>>> Xiaosheng Huang, Assistant Professor
>>> Department of Physics and Astronomy
>>> University of San Francisco
>>> 2130 Fulton Street, San Francisco, CA 94117-1080
>>>
>>> Phone: (415) 422-6281
>>> E-mail: xhuang22 at usfca.edu
>>> ************************************************************
>>>
>>
>>
>
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From ketan at mcs.anl.gov  Tue Sep  9 09:49:10 2014
From: ketan at mcs.anl.gov (Ketan Maheshwari)
Date: Tue, 9 Sep 2014 09:49:10 -0500
Subject: [Swift-user] Pointer to Swift tutorials for computational
 science education and research
In-Reply-To: <cceef1afa9e14a64b89c2acb2a9eb30d@GEORGE.anl.gov>
References: <539FC360.6090800@anl.gov>
	<59fc9be3f4d445ab8d502b2b1ce63af7@GEORGE.anl.gov>
	<CAMUuviqo8zhzvXVtJGEtV0TyoyW=D_EbVpNzL60BoNw60EEXEQ@mail.gmail.com>
	<CAN=xv+Zm+_VT5Ej4bDWiS8RotdgiuwYxRaF0CnZoV0si5hywQA@mail.gmail.com>
	<f41cf2675e66453d989165ca3231f73c@LUCKMAN.anl.gov>
	<CAMUuvirA+g6mQFBqw=u5p7kw+548VQ1q7g9wpyBxNz6792MOcw@mail.gmail.com>
	<13482362cf5c4f13a4d98c897b022f89@LUCKMAN.anl.gov>
	<CAMUuviq_v2oT2Gp-QVH94fevfzmx0R-5Y7bzZ-AYpNnb9zK5Nw@mail.gmail.com>
	<CAN=xv+b1z1CmwSM5b_gCi0D1vB15NBAKdtBs6nADgcQwgqRgDQ@mail.gmail.com>
	<362b5dde41ab45f5a0f455a267c058da@GEORGE.anl.gov>
	<CAMUuviodRt37OwDVhhP==VKPusCXiV30sCRBS9_rOb9wOV3XWA@mail.gmail.com>
	<cceef1afa9e14a64b89c2acb2a9eb30d@GEORGE.anl.gov>
Message-ID: <CAMUuvipogv8zDOLydj3OnYAA8s94xQCrCcwF7qyKEkuS-J12Tg@mail.gmail.com>

On Mon, Sep 8, 2014 at 6:28 PM, Andrew Stocker <amstocker at dons.usfca.edu>
wrote:

>  Thanks for your response!
>
>  Since we're just in the stages of experimentation, our preliminary
> cluster is just four iMacs connected to a switch.  I set up password-less
> ssh communication between the four and I'm able to start the coaster
> service (in the folder with coaster-service.conf) without any errors.  I am
> running Swift from the computer which has the catnap.sh installed at the
> correct path, and I'm pretty sure it has the executable bit set ( #!/bin/sh
> is the first line of the program).  None of the other three computers have
> Swift installed, nor do they have catnap.sh at the location specified in
> tc.data, is this a problem?
>

Yes, that seems to be the issue. The executable--catnap.sh in this case
must be available on all compute nodes in the location specified in the tc.

An alternative in this case is to use catnap.sh as data and move it along
with data to target compute nodes. However, we can do  that later. For now,
could you try to put catnap.sh in a common location on each of the compute
nodes and try again.

No, Swift is not needed to be installed on compute nodes. Swift just needs
to be on the submit node.


>
>  Attached is the log file from the run when I got the error I copy+pasted
> above.  Interestingly, when I run the catnap swift script with only 3
> concurrent instances, it seems to run fine since we allow 3 jobs per node
> and so it is probably only running locally.
>
>  Regards,
> Andrew
>
> On Fri, Sep 5, 2014 at 6:03 PM, Ketan Maheshwari <ketan at mcs.anl.gov>
> wrote:
>
>> Hi Andrew,
>>
>>  Yes, I remember: thanks for getting back on this.
>>
>>  From the error message and tc.data, indeed it looks like the executable
>> is provided as absolute path but somehow Swift is looking into system path
>> and not finding it. One possibility is that the node on which catnap.sh is
>> running does not have it installed on the path specified in the tc.data.
>> Can you also check if catnap.sh has the executable bit set. Less likely
>> that this is causing the issue though.
>>
>>  Also, from the tc.data line it looks like you are using persistent
>> coasters. Have started the coaster service beforehand and made sure the
>> service started correctly without any error messages. Could you indicate
>> more about your cluster. Depending on the type of cluster, it is possible
>> that we can run Swift in a non-persistent, implicit coasters mode.
>>
>>  Can you also send the Swift generated log for this run.
>>
>>  Thanks,
>> Ketan
>>
>>
>> On Fri, Sep 5, 2014 at 7:16 PM, Andrew Stocker <amstocker at dons.usfca.edu>
>> wrote:
>>
>>>  Hi Ketan,
>>>
>>>  I'm not sure if you remember, but myself and my research advisor
>>> Xiaosheng spoke to you at LBL in Oakland at the beginning of the summer
>>> about starting to use Swift at our school.   We have been working hard on
>>> setting it up, and I am trying to get your demo to run but I'm having a
>>> problem.  For some reason I keep getting the following error when I try to
>>> run your catsnsleep demo:
>>>
>>>  Execution failed:
>>> Exception in catnap:
>>>     Arguments: [5, data.txt]
>>>     Host: persistent-coasters
>>>     Directory: catsnsleep-20140905-1702-mihcat06/jobs/u/catnap-utx080xl
>>>
>>>  Caused by:
>>> Cannot find executable catnap.sh on site system path
>>> catnap, catsnsleep.swift, line 13
>>>
>>>  However I'm not sure why.  In our tc.data file we have the line:
>>>
>>>  persistent-coasters catnap
>>> /usr/local/swift-0.94.1/oakland-demo/catnap.sh
>>>
>>>  which I think should work but obviously something is going wrong.  I
>>> have been browsing the documentation articles but I can't find anything
>>> about why this might be happening.  We would greatly appreciate your advice!
>>>
>>>  Regards,
>>>
>>>  Andrew Stocker
>>>
>>>
>>> On Fri, Jun 20, 2014 at 12:00 PM, Xiaosheng Huang <xhuang22 at usfca.edu>
>>> wrote:
>>>
>>>>
>>>> ---------- Forwarded message ----------
>>>> From: Ketan Maheshwari <ketan at mcs.anl.gov>
>>>> Date: Fri, Jun 20, 2014 at 11:45 AM
>>>> Subject: Re: Pointer to Swift tutorials for computational science
>>>> education and research
>>>> To: Xiaosheng Huang <xhuang22 at usfca.edu>
>>>> Cc: Wilde <wilde at mcs.anl.gov>
>>>>
>>>>
>>>> Hi Xiaosheng,
>>>>
>>>>  The tarball is: http://www.mcs.anl.gov/~ketan/oakland-demo.tgz
>>>>
>>>>  There is a small README in there which outlines the steps.
>>>>
>>>>  Best,
>>>> Ketan
>>>>
>>>>   ************************************************************
>>>> Xiaosheng Huang, Assistant Professor
>>>> Department of Physics and Astronomy
>>>> University of San Francisco
>>>> 2130 Fulton Street, San Francisco, CA 94117-1080
>>>>
>>>> Phone: (415) 422-6281
>>>> E-mail: xhuang22 at usfca.edu
>>>> ************************************************************
>>>>
>>>
>>>
>>
>
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From ganesh at cs.utah.edu  Mon Sep  8 23:41:09 2014
From: ganesh at cs.utah.edu (Ganesh Gopalakrishnan)
Date: Mon, 8 Sep 2014 22:41:09 -0600
Subject: [Swift-user] Fwd: Fwd: Swift/K node creation
In-Reply-To: <53F78E7E.9010704@uchicago.edu>
References: <53F51FF7.7010107@cs.utah.edu> <53F6295F.5040402@anl.gov>
	<53F78E7E.9010704@uchicago.edu>
Message-ID: <CACRb4Zs1YRW1d7ODFHaWazGFksOWogVm0Zjh9pRwiQNt4FfXQg@mail.gmail.com>

Hi Yadu and Swift folks (and Martin B):

The new semester 'hit us' .  We are going to certainly follow up and let
you know . Thanks for your help!  (Just wanted to allay the impression that
we are ignoring you.)

Thanks again,

Ganesh



On Fri, Aug 22, 2014 at 12:39 PM, Yadu Nand Babuji <yadunand at uchicago.edu>
wrote:

>  Hi Ian,
>
> Reposting as I suspect that the original email bounced.
>
> Here's a tar ball of the swift tutorial with minor changes to the
> swift.properties config file to connect to a few
> remote machines :
> http://users.rcc.uchicago.edu/~yadunand/remote_pool.tar.gz
>
> Before you run the tests, please make sure to edit the
> remote_pool/swift.properties file to have the URLs of
> your remote machines.
>
> There's an online swift sandbox here -> http://swift-lang.org/tryswift/
>
> You can get documentation here for different releases of Swift ->
> http://swift-lang.org/docs/index.php
>
> I would recommend getting Swift 0.95-RC6 from (
> http://swift-lang.org/downloads/index.php).
>
> Thanks!
> Yadu
>
> On 08/21/2014 12:16 PM, Michael Wilde wrote:
>
>
>
>
> -------- Original Message --------  Subject: Fwd: Swift/K node creation  Date:
> Wed, 20 Aug 2014 16:23:51 -0600  From: Ganesh Gopalakrishnan
> <ganesh at cs.utah.edu> <ganesh at cs.utah.edu>  To: Michael Wilde
> <wilde at anl.gov> <wilde at anl.gov>  CC: Martin Burtscher
> <burtscher at txstate.edu> <burtscher at txstate.edu>, ian briggs
> <ianbriggs at comcast.net> <ianbriggs at comcast.net>, Mark Baranowski
> <u0485301 at utah.edu> <u0485301 at utah.edu>
>
> Hi Mike,
>
> After yesterday's call, Ian Briggs and Mark Baranowski have looked into
> Swift/K.  I encouraged them to post a question to the Swift group.    Hence
> this email is strictly redundant - but I thought I'd drop in an intro to
> give you some context for this question.  Thanks!
>
> Best,
>
> Ganesh
>
>
> -------- Original Message --------  Subject: Swift/K node creation  Date: Wed,
> 20 Aug 2014 16:19:57 -0600  From: Ian Briggs <ianbriggs at comcast.net>
> <ianbriggs at comcast.net>  To: swift-user at ci.uchicago.edu  CC: Ganesh
> Gopalakrishnan <ganesh at cs.utah.edu> <ganesh at cs.utah.edu>
>
>
> Thank you for reading this.
>
> I was able to install and run swift/k on my local computer.
> From here I would like to install it on a remote machine
> and use that machine as a remote site. How should I go
> about doing this? If there is a guide I missed I apologize.
>
> Thanks,
> Ian Briggs
>
>
>
>
>
>
>
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From burtscher at txstate.edu  Wed Sep 10 08:53:53 2014
From: burtscher at txstate.edu (Martin Burtscher)
Date: Wed, 10 Sep 2014 08:53:53 -0500
Subject: [Swift-user] Fwd: Fwd: Swift/K node creation
In-Reply-To: <CACRb4Zs1YRW1d7ODFHaWazGFksOWogVm0Zjh9pRwiQNt4FfXQg@mail.gmail.com>
References: <53F51FF7.7010107@cs.utah.edu>	<53F6295F.5040402@anl.gov>	<53F78E7E.9010704@uchicago.edu>
	<CACRb4Zs1YRW1d7ODFHaWazGFksOWogVm0Zjh9pRwiQNt4FfXQg@mail.gmail.com>
Message-ID: <541057F1.2090203@txstate.edu>

Hello all!

I'm also very busy with the start of the semester, but I have hired a 
student who has started to learn Swift.  He installed it successfully on 
one of our machines and is going through the tutorials now.  I hope to 
have some feedback from him to share with you soon.

Kind regards,
Martin


On 9/8/2014 11:41 PM, Ganesh Gopalakrishnan wrote:
> Hi Yadu and Swift folks (and Martin B):
>
> The new semester 'hit us' .  We are going to certainly follow up and let
> you know . Thanks for your help!  (Just wanted to allay the impression
> that we are ignoring you.)
>
> Thanks again,
>
> Ganesh
>
>
>
> On Fri, Aug 22, 2014 at 12:39 PM, Yadu Nand Babuji
> <yadunand at uchicago.edu <mailto:yadunand at uchicago.edu>> wrote:
>
>     Hi Ian,
>
>     Reposting as I suspect that the original email bounced.
>
>     Here's a tar ball of the swift tutorial with minor changes to the
>     swift.properties config file to connect to a few
>     remote machines :
>     http://users.rcc.uchicago.edu/~yadunand/remote_pool.tar.gz
>
>     Before you run the tests, please make sure to edit the
>     remote_pool/swift.properties file to have the URLs of
>     your remote machines.
>
>     There's an online swift sandbox here -> http://swift-lang.org/tryswift/
>
>     You can get documentation here for different releases of Swift ->
>     http://swift-lang.org/docs/index.php
>
>     I would recommend getting Swift 0.95-RC6 from
>     (http://swift-lang.org/downloads/index.php).
>
>     Thanks!
>     Yadu
>
>     On 08/21/2014 12:16 PM, Michael Wilde wrote:
>>
>>
>>
>>     -------- Original Message --------
>>     Subject: 	Fwd: Swift/K node creation
>>     Date: 	Wed, 20 Aug 2014 16:23:51 -0600
>>     From: 	Ganesh Gopalakrishnan <ganesh at cs.utah.edu>
>>     <mailto:ganesh at cs.utah.edu>
>>     To: 	Michael Wilde <wilde at anl.gov> <mailto:wilde at anl.gov>
>>     CC: 	Martin Burtscher <burtscher at txstate.edu>
>>     <mailto:burtscher at txstate.edu>, ian briggs <ianbriggs at comcast.net>
>>     <mailto:ianbriggs at comcast.net>, Mark Baranowski
>>     <u0485301 at utah.edu> <mailto:u0485301 at utah.edu>
>>
>>
>>
>>     Hi Mike,
>>
>>     After yesterday's call, Ian Briggs and Mark Baranowski have looked
>>     into Swift/K.  I encouraged them to post a question to the Swift
>>     group.    Hence this email is strictly redundant - but I thought
>>     I'd drop in an intro to give you some context for this question.
>>     Thanks!
>>
>>     Best,
>>
>>     Ganesh
>>
>>
>>     -------- Original Message --------
>>     Subject: 	Swift/K node creation
>>     Date: 	Wed, 20 Aug 2014 16:19:57 -0600
>>     From: 	Ian Briggs <ianbriggs at comcast.net>
>>     <mailto:ianbriggs at comcast.net>
>>     To: 	swift-user at ci.uchicago.edu <mailto:swift-user at ci.uchicago.edu>
>>     CC: 	Ganesh Gopalakrishnan <ganesh at cs.utah.edu>
>>     <mailto:ganesh at cs.utah.edu>
>>
>>
>>
>>     Thank you for reading this.
>>
>>     I was able to install and run swift/k on my local computer.
>>     >From here I would like to install it on a remote machine
>>     and use that machine as a remote site. How should I go
>>     about doing this? If there is a guide I missed I apologize.
>>
>>     Thanks,
>>     Ian Briggs
>>
>>
>>
>>
>
>

-- 
Martin Burtscher, Ph.D.            http://www.cs.txstate.edu/~burtscher/
Associate Professor                        E-mail: burtscher at txstate.edu
Department of Computer Science                     Phone: (512) 245-3443
Texas State University                                Office: Comal 309C


From amstocker at dons.usfca.edu  Wed Sep 10 20:45:50 2014
From: amstocker at dons.usfca.edu (Andrew Stocker)
Date: Wed, 10 Sep 2014 18:45:50 -0700
Subject: [Swift-user] Pointer to Swift tutorials for computational
 science education and research
In-Reply-To: <CAMUuvipogv8zDOLydj3OnYAA8s94xQCrCcwF7qyKEkuS-J12Tg@mail.gmail.com>
References: <539FC360.6090800@anl.gov>
	<59fc9be3f4d445ab8d502b2b1ce63af7@GEORGE.anl.gov>
	<CAMUuviqo8zhzvXVtJGEtV0TyoyW=D_EbVpNzL60BoNw60EEXEQ@mail.gmail.com>
	<CAN=xv+Zm+_VT5Ej4bDWiS8RotdgiuwYxRaF0CnZoV0si5hywQA@mail.gmail.com>
	<f41cf2675e66453d989165ca3231f73c@LUCKMAN.anl.gov>
	<CAMUuvirA+g6mQFBqw=u5p7kw+548VQ1q7g9wpyBxNz6792MOcw@mail.gmail.com>
	<13482362cf5c4f13a4d98c897b022f89@LUCKMAN.anl.gov>
	<CAMUuviq_v2oT2Gp-QVH94fevfzmx0R-5Y7bzZ-AYpNnb9zK5Nw@mail.gmail.com>
	<CAN=xv+b1z1CmwSM5b_gCi0D1vB15NBAKdtBs6nADgcQwgqRgDQ@mail.gmail.com>
	<362b5dde41ab45f5a0f455a267c058da@GEORGE.anl.gov>
	<CAMUuviodRt37OwDVhhP==VKPusCXiV30sCRBS9_rOb9wOV3XWA@mail.gmail.com>
	<cceef1afa9e14a64b89c2acb2a9eb30d@GEORGE.anl.gov>
	<CAMUuvipogv8zDOLydj3OnYAA8s94xQCrCcwF7qyKEkuS-J12Tg@mail.gmail.com>
Message-ID: <CAOZiyaNc2U_a6AQyhDszWVB10So2b7uxkdu5TcLmV9WmdXpVAQ@mail.gmail.com>

Ketan,

I copied the catnap executable to the same directory on each of the
computers and now the swift script is working perfectly without error.
 Thanks for your help!  What are the next steps we can take to set up our
cluster to not require the script to be on all the computers?  Since we are
fairly new to parallel computing with a cluster, could you point us towards
any resources regarding the technical configuration for Swift?  I've looked
at the documentation for tc.data but I am still a bit confused by it.

Thanks,

Andrew

On Tue, Sep 9, 2014 at 7:49 AM, Ketan Maheshwari <ketan at mcs.anl.gov> wrote:

>
> On Mon, Sep 8, 2014 at 6:28 PM, Andrew Stocker <amstocker at dons.usfca.edu>
> wrote:
>
>>  Thanks for your response!
>>
>>  Since we're just in the stages of experimentation, our preliminary
>> cluster is just four iMacs connected to a switch.  I set up password-less
>> ssh communication between the four and I'm able to start the coaster
>> service (in the folder with coaster-service.conf) without any errors.  I am
>> running Swift from the computer which has the catnap.sh installed at the
>> correct path, and I'm pretty sure it has the executable bit set ( #!/bin/sh
>> is the first line of the program).  None of the other three computers
>> have Swift installed, nor do they have catnap.sh at the location
>> specified in tc.data, is this a problem?
>>
>
> Yes, that seems to be the issue. The executable--catnap.sh in this case
> must be available on all compute nodes in the location specified in the tc.
>
> An alternative in this case is to use catnap.sh as data and move it along
> with data to target compute nodes. However, we can do  that later. For now,
> could you try to put catnap.sh in a common location on each of the compute
> nodes and try again.
>
> No, Swift is not needed to be installed on compute nodes. Swift just needs
> to be on the submit node.
>
>
>>
>>  Attached is the log file from the run when I got the error I
>> copy+pasted above.  Interestingly, when I run the catnap swift script with
>> only 3 concurrent instances, it seems to run fine since we allow 3 jobs per
>> node and so it is probably only running locally.
>>
>>  Regards,
>> Andrew
>>
>> On Fri, Sep 5, 2014 at 6:03 PM, Ketan Maheshwari <ketan at mcs.anl.gov>
>> wrote:
>>
>>> Hi Andrew,
>>>
>>>  Yes, I remember: thanks for getting back on this.
>>>
>>>  From the error message and tc.data, indeed it looks like the
>>> executable is provided as absolute path but somehow Swift is looking into
>>> system path and not finding it. One possibility is that the node on which
>>> catnap.sh is running does not have it installed on the path specified in
>>> the tc.data. Can you also check if catnap.sh has the executable bit set.
>>> Less likely that this is causing the issue though.
>>>
>>>  Also, from the tc.data line it looks like you are using persistent
>>> coasters. Have started the coaster service beforehand and made sure the
>>> service started correctly without any error messages. Could you indicate
>>> more about your cluster. Depending on the type of cluster, it is possible
>>> that we can run Swift in a non-persistent, implicit coasters mode.
>>>
>>>  Can you also send the Swift generated log for this run.
>>>
>>>  Thanks,
>>> Ketan
>>>
>>>
>>> On Fri, Sep 5, 2014 at 7:16 PM, Andrew Stocker <amstocker at dons.usfca.edu
>>> > wrote:
>>>
>>>>  Hi Ketan,
>>>>
>>>>  I'm not sure if you remember, but myself and my research advisor
>>>> Xiaosheng spoke to you at LBL in Oakland at the beginning of the summer
>>>> about starting to use Swift at our school.   We have been working hard on
>>>> setting it up, and I am trying to get your demo to run but I'm having a
>>>> problem.  For some reason I keep getting the following error when I try to
>>>> run your catsnsleep demo:
>>>>
>>>>  Execution failed:
>>>> Exception in catnap:
>>>>     Arguments: [5, data.txt]
>>>>     Host: persistent-coasters
>>>>     Directory: catsnsleep-20140905-1702-mihcat06/jobs/u/catnap-utx080xl
>>>>
>>>>  Caused by:
>>>> Cannot find executable catnap.sh on site system path
>>>> catnap, catsnsleep.swift, line 13
>>>>
>>>>  However I'm not sure why.  In our tc.data file we have the line:
>>>>
>>>>  persistent-coasters catnap
>>>> /usr/local/swift-0.94.1/oakland-demo/catnap.sh
>>>>
>>>>  which I think should work but obviously something is going wrong.  I
>>>> have been browsing the documentation articles but I can't find anything
>>>> about why this might be happening.  We would greatly appreciate your advice!
>>>>
>>>>  Regards,
>>>>
>>>>  Andrew Stocker
>>>>
>>>>
>>>> On Fri, Jun 20, 2014 at 12:00 PM, Xiaosheng Huang <xhuang22 at usfca.edu>
>>>> wrote:
>>>>
>>>>>
>>>>> ---------- Forwarded message ----------
>>>>> From: Ketan Maheshwari <ketan at mcs.anl.gov>
>>>>> Date: Fri, Jun 20, 2014 at 11:45 AM
>>>>> Subject: Re: Pointer to Swift tutorials for computational science
>>>>> education and research
>>>>> To: Xiaosheng Huang <xhuang22 at usfca.edu>
>>>>> Cc: Wilde <wilde at mcs.anl.gov>
>>>>>
>>>>>
>>>>> Hi Xiaosheng,
>>>>>
>>>>>  The tarball is: http://www.mcs.anl.gov/~ketan/oakland-demo.tgz
>>>>>
>>>>>  There is a small README in there which outlines the steps.
>>>>>
>>>>>  Best,
>>>>> Ketan
>>>>>
>>>>>   ************************************************************
>>>>> Xiaosheng Huang, Assistant Professor
>>>>> Department of Physics and Astronomy
>>>>> University of San Francisco
>>>>> 2130 Fulton Street, San Francisco, CA 94117-1080
>>>>>
>>>>> Phone: (415) 422-6281
>>>>> E-mail: xhuang22 at usfca.edu
>>>>> ************************************************************
>>>>>
>>>>
>>>>
>>>
>>
>
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From yadudoc1729 at gmail.com  Wed Sep 10 23:03:21 2014
From: yadudoc1729 at gmail.com (Yadu Nand)
Date: Wed, 10 Sep 2014 23:03:21 -0500
Subject: [Swift-user] Pointer to Swift tutorials for computational
 science education and research
In-Reply-To: <CAOZiyaNc2U_a6AQyhDszWVB10So2b7uxkdu5TcLmV9WmdXpVAQ@mail.gmail.com>
References: <539FC360.6090800@anl.gov>
	<59fc9be3f4d445ab8d502b2b1ce63af7@GEORGE.anl.gov>
	<CAMUuviqo8zhzvXVtJGEtV0TyoyW=D_EbVpNzL60BoNw60EEXEQ@mail.gmail.com>
	<CAN=xv+Zm+_VT5Ej4bDWiS8RotdgiuwYxRaF0CnZoV0si5hywQA@mail.gmail.com>
	<f41cf2675e66453d989165ca3231f73c@LUCKMAN.anl.gov>
	<CAMUuvirA+g6mQFBqw=u5p7kw+548VQ1q7g9wpyBxNz6792MOcw@mail.gmail.com>
	<13482362cf5c4f13a4d98c897b022f89@LUCKMAN.anl.gov>
	<CAMUuviq_v2oT2Gp-QVH94fevfzmx0R-5Y7bzZ-AYpNnb9zK5Nw@mail.gmail.com>
	<CAN=xv+b1z1CmwSM5b_gCi0D1vB15NBAKdtBs6nADgcQwgqRgDQ@mail.gmail.com>
	<362b5dde41ab45f5a0f455a267c058da@GEORGE.anl.gov>
	<CAMUuviodRt37OwDVhhP==VKPusCXiV30sCRBS9_rOb9wOV3XWA@mail.gmail.com>
	<cceef1afa9e14a64b89c2acb2a9eb30d@GEORGE.anl.gov>
	<CAMUuvipogv8zDOLydj3OnYAA8s94xQCrCcwF7qyKEkuS-J12Tg@mail.gmail.com>
	<CAOZiyaNc2U_a6AQyhDszWVB10So2b7uxkdu5TcLmV9WmdXpVAQ@mail.gmail.com>
Message-ID: <CANa904=nRjw7dAQt-7JgfSnJ6zhWzyWX5cY4XrKio3mmaDeukg@mail.gmail.com>

Hi Andrew,

If you would like to have swift move the executable for you, you could try
the method used in the following example :

type file;

/* App definition calls bash which in-turn executes the bash script defined
as an argument here
   Every file in the input parameter list is staged by swift to the worker
nodes
   Every file in the return list is staged back to the client node by swift
*/
app (file out, file err) foo (file script, file input)
{
    bash @script @input stdout=@out stderr=@err;
}

// Script to be executed
file wrapper <"wrapper.sh">;
file hello  <"hello.txt">;

file out    <"foo.out">;
file err    <"foo.err">;

(out, err) = foo (wrapper, hello);

Thanks,
Yadu



On Wed, Sep 10, 2014 at 8:45 PM, Andrew Stocker <amstocker at dons.usfca.edu>
wrote:

> Ketan,
>
> I copied the catnap executable to the same directory on each of the
> computers and now the swift script is working perfectly without error.
>  Thanks for your help!  What are the next steps we can take to set up our
> cluster to not require the script to be on all the computers?  Since we are
> fairly new to parallel computing with a cluster, could you point us towards
> any resources regarding the technical configuration for Swift?  I've looked
> at the documentation for tc.data but I am still a bit confused by it.
>
> Thanks,
>
> Andrew
>
> On Tue, Sep 9, 2014 at 7:49 AM, Ketan Maheshwari <ketan at mcs.anl.gov>
> wrote:
>
>>
>> On Mon, Sep 8, 2014 at 6:28 PM, Andrew Stocker <amstocker at dons.usfca.edu>
>> wrote:
>>
>>>  Thanks for your response!
>>>
>>>  Since we're just in the stages of experimentation, our preliminary
>>> cluster is just four iMacs connected to a switch.  I set up password-less
>>> ssh communication between the four and I'm able to start the coaster
>>> service (in the folder with coaster-service.conf) without any errors.  I am
>>> running Swift from the computer which has the catnap.sh installed at
>>> the correct path, and I'm pretty sure it has the executable bit set ( #!/bin/sh
>>> is the first line of the program).  None of the other three computers
>>> have Swift installed, nor do they have catnap.sh at the location
>>> specified in tc.data, is this a problem?
>>>
>>
>> Yes, that seems to be the issue. The executable--catnap.sh in this case
>> must be available on all compute nodes in the location specified in the tc.
>>
>> An alternative in this case is to use catnap.sh as data and move it along
>> with data to target compute nodes. However, we can do  that later. For now,
>> could you try to put catnap.sh in a common location on each of the compute
>> nodes and try again.
>>
>> No, Swift is not needed to be installed on compute nodes. Swift just
>> needs to be on the submit node.
>>
>>
>>>
>>>  Attached is the log file from the run when I got the error I
>>> copy+pasted above.  Interestingly, when I run the catnap swift script with
>>> only 3 concurrent instances, it seems to run fine since we allow 3 jobs per
>>> node and so it is probably only running locally.
>>>
>>>  Regards,
>>> Andrew
>>>
>>> On Fri, Sep 5, 2014 at 6:03 PM, Ketan Maheshwari <ketan at mcs.anl.gov>
>>> wrote:
>>>
>>>> Hi Andrew,
>>>>
>>>>  Yes, I remember: thanks for getting back on this.
>>>>
>>>>  From the error message and tc.data, indeed it looks like the
>>>> executable is provided as absolute path but somehow Swift is looking into
>>>> system path and not finding it. One possibility is that the node on which
>>>> catnap.sh is running does not have it installed on the path specified in
>>>> the tc.data. Can you also check if catnap.sh has the executable bit set.
>>>> Less likely that this is causing the issue though.
>>>>
>>>>  Also, from the tc.data line it looks like you are using persistent
>>>> coasters. Have started the coaster service beforehand and made sure the
>>>> service started correctly without any error messages. Could you indicate
>>>> more about your cluster. Depending on the type of cluster, it is possible
>>>> that we can run Swift in a non-persistent, implicit coasters mode.
>>>>
>>>>  Can you also send the Swift generated log for this run.
>>>>
>>>>  Thanks,
>>>> Ketan
>>>>
>>>>
>>>> On Fri, Sep 5, 2014 at 7:16 PM, Andrew Stocker <
>>>> amstocker at dons.usfca.edu> wrote:
>>>>
>>>>>  Hi Ketan,
>>>>>
>>>>>  I'm not sure if you remember, but myself and my research advisor
>>>>> Xiaosheng spoke to you at LBL in Oakland at the beginning of the summer
>>>>> about starting to use Swift at our school.   We have been working hard on
>>>>> setting it up, and I am trying to get your demo to run but I'm having a
>>>>> problem.  For some reason I keep getting the following error when I try to
>>>>> run your catsnsleep demo:
>>>>>
>>>>>  Execution failed:
>>>>> Exception in catnap:
>>>>>     Arguments: [5, data.txt]
>>>>>     Host: persistent-coasters
>>>>>     Directory: catsnsleep-20140905-1702-mihcat06/jobs/u/catnap-utx080xl
>>>>>
>>>>>  Caused by:
>>>>> Cannot find executable catnap.sh on site system path
>>>>> catnap, catsnsleep.swift, line 13
>>>>>
>>>>>  However I'm not sure why.  In our tc.data file we have the line:
>>>>>
>>>>>  persistent-coasters catnap
>>>>> /usr/local/swift-0.94.1/oakland-demo/catnap.sh
>>>>>
>>>>>  which I think should work but obviously something is going wrong.  I
>>>>> have been browsing the documentation articles but I can't find anything
>>>>> about why this might be happening.  We would greatly appreciate your advice!
>>>>>
>>>>>  Regards,
>>>>>
>>>>>  Andrew Stocker
>>>>>
>>>>>
>>>>> On Fri, Jun 20, 2014 at 12:00 PM, Xiaosheng Huang <xhuang22 at usfca.edu>
>>>>> wrote:
>>>>>
>>>>>>
>>>>>> ---------- Forwarded message ----------
>>>>>> From: Ketan Maheshwari <ketan at mcs.anl.gov>
>>>>>> Date: Fri, Jun 20, 2014 at 11:45 AM
>>>>>> Subject: Re: Pointer to Swift tutorials for computational science
>>>>>> education and research
>>>>>> To: Xiaosheng Huang <xhuang22 at usfca.edu>
>>>>>> Cc: Wilde <wilde at mcs.anl.gov>
>>>>>>
>>>>>>
>>>>>> Hi Xiaosheng,
>>>>>>
>>>>>>  The tarball is: http://www.mcs.anl.gov/~ketan/oakland-demo.tgz
>>>>>>
>>>>>>  There is a small README in there which outlines the steps.
>>>>>>
>>>>>>  Best,
>>>>>> Ketan
>>>>>>
>>>>>>   ************************************************************
>>>>>> Xiaosheng Huang, Assistant Professor
>>>>>> Department of Physics and Astronomy
>>>>>> University of San Francisco
>>>>>> 2130 Fulton Street, San Francisco, CA 94117-1080
>>>>>>
>>>>>> Phone: (415) 422-6281
>>>>>> E-mail: xhuang22 at usfca.edu
>>>>>> ************************************************************
>>>>>>
>>>>>
>>>>>
>>>>
>>>
>>
>
> _______________________________________________
> Swift-user mailing list
> Swift-user at ci.uchicago.edu
> https://lists.ci.uchicago.edu/cgi-bin/mailman/listinfo/swift-user
>



-- 
Yadu Nand B
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From ketan at mcs.anl.gov  Thu Sep 11 08:52:18 2014
From: ketan at mcs.anl.gov (Ketan Maheshwari)
Date: Thu, 11 Sep 2014 08:52:18 -0500
Subject: [Swift-user] Pointer to Swift tutorials for computational
 science education and research
In-Reply-To: <CANa904=nRjw7dAQt-7JgfSnJ6zhWzyWX5cY4XrKio3mmaDeukg@mail.gmail.com>
References: <539FC360.6090800@anl.gov>
	<59fc9be3f4d445ab8d502b2b1ce63af7@GEORGE.anl.gov>
	<CAMUuviqo8zhzvXVtJGEtV0TyoyW=D_EbVpNzL60BoNw60EEXEQ@mail.gmail.com>
	<CAN=xv+Zm+_VT5Ej4bDWiS8RotdgiuwYxRaF0CnZoV0si5hywQA@mail.gmail.com>
	<f41cf2675e66453d989165ca3231f73c@LUCKMAN.anl.gov>
	<CAMUuvirA+g6mQFBqw=u5p7kw+548VQ1q7g9wpyBxNz6792MOcw@mail.gmail.com>
	<13482362cf5c4f13a4d98c897b022f89@LUCKMAN.anl.gov>
	<CAMUuviq_v2oT2Gp-QVH94fevfzmx0R-5Y7bzZ-AYpNnb9zK5Nw@mail.gmail.com>
	<CAN=xv+b1z1CmwSM5b_gCi0D1vB15NBAKdtBs6nADgcQwgqRgDQ@mail.gmail.com>
	<362b5dde41ab45f5a0f455a267c058da@GEORGE.anl.gov>
	<CAMUuviodRt37OwDVhhP==VKPusCXiV30sCRBS9_rOb9wOV3XWA@mail.gmail.com>
	<cceef1afa9e14a64b89c2acb2a9eb30d@GEORGE.anl.gov>
	<CAMUuvipogv8zDOLydj3OnYAA8s94xQCrCcwF7qyKEkuS-J12Tg@mail.gmail.com>
	<CAOZiyaNc2U_a6AQyhDszWVB10So2b7uxkdu5TcLmV9WmdXpVAQ@mail.gmail.com>
	<CANa904=nRjw7dAQt-7JgfSnJ6zhWzyWX5cY4XrKio3mmaDeukg@mail.gmail.com>
Message-ID: <CAMUuviqy2T5WpCGP+1UmTgPzo_9j_7k7cNCoEzEaOxxM447B5Q@mail.gmail.com>

Andrew,

Just to be clear, in the new script that Yadu posted, you will need to add
one entry in your tc.data as follows:

persistent-coasters bash /bin/bash

Thanks,
Ketan



On Wed, Sep 10, 2014 at 11:03 PM, Yadu Nand <yadudoc1729 at gmail.com> wrote:

> Hi Andrew,
>
> If you would like to have swift move the executable for you, you could try
> the method used in the following example :
>
> type file;
>
> /* App definition calls bash which in-turn executes the bash script
> defined as an argument here
>    Every file in the input parameter list is staged by swift to the worker
> nodes
>    Every file in the return list is staged back to the client node by swift
> */
> app (file out, file err) foo (file script, file input)
> {
>     bash @script @input stdout=@out stderr=@err;
> }
>
> // Script to be executed
> file wrapper <"wrapper.sh">;
> file hello  <"hello.txt">;
>
> file out    <"foo.out">;
> file err    <"foo.err">;
>
> (out, err) = foo (wrapper, hello);
>
> Thanks,
> Yadu
>
>
>
> On Wed, Sep 10, 2014 at 8:45 PM, Andrew Stocker <amstocker at dons.usfca.edu>
> wrote:
>
>> Ketan,
>>
>> I copied the catnap executable to the same directory on each of the
>> computers and now the swift script is working perfectly without error.
>>  Thanks for your help!  What are the next steps we can take to set up our
>> cluster to not require the script to be on all the computers?  Since we are
>> fairly new to parallel computing with a cluster, could you point us towards
>> any resources regarding the technical configuration for Swift?  I've looked
>> at the documentation for tc.data but I am still a bit confused by it.
>>
>> Thanks,
>>
>> Andrew
>>
>> On Tue, Sep 9, 2014 at 7:49 AM, Ketan Maheshwari <ketan at mcs.anl.gov>
>> wrote:
>>
>>>
>>> On Mon, Sep 8, 2014 at 6:28 PM, Andrew Stocker <amstocker at dons.usfca.edu
>>> > wrote:
>>>
>>>>  Thanks for your response!
>>>>
>>>>  Since we're just in the stages of experimentation, our preliminary
>>>> cluster is just four iMacs connected to a switch.  I set up password-less
>>>> ssh communication between the four and I'm able to start the coaster
>>>> service (in the folder with coaster-service.conf) without any errors.  I am
>>>> running Swift from the computer which has the catnap.sh installed at
>>>> the correct path, and I'm pretty sure it has the executable bit set ( #!/bin/sh
>>>> is the first line of the program).  None of the other three computers
>>>> have Swift installed, nor do they have catnap.sh at the location
>>>> specified in tc.data, is this a problem?
>>>>
>>>
>>> Yes, that seems to be the issue. The executable--catnap.sh in this case
>>> must be available on all compute nodes in the location specified in the tc.
>>>
>>> An alternative in this case is to use catnap.sh as data and move it
>>> along with data to target compute nodes. However, we can do  that later.
>>> For now, could you try to put catnap.sh in a common location on each of the
>>> compute nodes and try again.
>>>
>>> No, Swift is not needed to be installed on compute nodes. Swift just
>>> needs to be on the submit node.
>>>
>>>
>>>>
>>>>  Attached is the log file from the run when I got the error I
>>>> copy+pasted above.  Interestingly, when I run the catnap swift script with
>>>> only 3 concurrent instances, it seems to run fine since we allow 3 jobs per
>>>> node and so it is probably only running locally.
>>>>
>>>>  Regards,
>>>> Andrew
>>>>
>>>> On Fri, Sep 5, 2014 at 6:03 PM, Ketan Maheshwari <ketan at mcs.anl.gov>
>>>> wrote:
>>>>
>>>>> Hi Andrew,
>>>>>
>>>>>  Yes, I remember: thanks for getting back on this.
>>>>>
>>>>>  From the error message and tc.data, indeed it looks like the
>>>>> executable is provided as absolute path but somehow Swift is looking into
>>>>> system path and not finding it. One possibility is that the node on which
>>>>> catnap.sh is running does not have it installed on the path specified in
>>>>> the tc.data. Can you also check if catnap.sh has the executable bit set.
>>>>> Less likely that this is causing the issue though.
>>>>>
>>>>>  Also, from the tc.data line it looks like you are using persistent
>>>>> coasters. Have started the coaster service beforehand and made sure the
>>>>> service started correctly without any error messages. Could you indicate
>>>>> more about your cluster. Depending on the type of cluster, it is possible
>>>>> that we can run Swift in a non-persistent, implicit coasters mode.
>>>>>
>>>>>  Can you also send the Swift generated log for this run.
>>>>>
>>>>>  Thanks,
>>>>> Ketan
>>>>>
>>>>>
>>>>> On Fri, Sep 5, 2014 at 7:16 PM, Andrew Stocker <
>>>>> amstocker at dons.usfca.edu> wrote:
>>>>>
>>>>>>  Hi Ketan,
>>>>>>
>>>>>>  I'm not sure if you remember, but myself and my research advisor
>>>>>> Xiaosheng spoke to you at LBL in Oakland at the beginning of the summer
>>>>>> about starting to use Swift at our school.   We have been working hard on
>>>>>> setting it up, and I am trying to get your demo to run but I'm having a
>>>>>> problem.  For some reason I keep getting the following error when I try to
>>>>>> run your catsnsleep demo:
>>>>>>
>>>>>>  Execution failed:
>>>>>> Exception in catnap:
>>>>>>     Arguments: [5, data.txt]
>>>>>>     Host: persistent-coasters
>>>>>>     Directory:
>>>>>> catsnsleep-20140905-1702-mihcat06/jobs/u/catnap-utx080xl
>>>>>>
>>>>>>  Caused by:
>>>>>> Cannot find executable catnap.sh on site system path
>>>>>> catnap, catsnsleep.swift, line 13
>>>>>>
>>>>>>  However I'm not sure why.  In our tc.data file we have the line:
>>>>>>
>>>>>>  persistent-coasters catnap
>>>>>> /usr/local/swift-0.94.1/oakland-demo/catnap.sh
>>>>>>
>>>>>>  which I think should work but obviously something is going wrong.
>>>>>>  I have been browsing the documentation articles but I can't find anything
>>>>>> about why this might be happening.  We would greatly appreciate your advice!
>>>>>>
>>>>>>  Regards,
>>>>>>
>>>>>>  Andrew Stocker
>>>>>>
>>>>>>
>>>>>> On Fri, Jun 20, 2014 at 12:00 PM, Xiaosheng Huang <xhuang22 at usfca.edu
>>>>>> > wrote:
>>>>>>
>>>>>>>
>>>>>>> ---------- Forwarded message ----------
>>>>>>> From: Ketan Maheshwari <ketan at mcs.anl.gov>
>>>>>>> Date: Fri, Jun 20, 2014 at 11:45 AM
>>>>>>> Subject: Re: Pointer to Swift tutorials for computational science
>>>>>>> education and research
>>>>>>> To: Xiaosheng Huang <xhuang22 at usfca.edu>
>>>>>>> Cc: Wilde <wilde at mcs.anl.gov>
>>>>>>>
>>>>>>>
>>>>>>> Hi Xiaosheng,
>>>>>>>
>>>>>>>  The tarball is: http://www.mcs.anl.gov/~ketan/oakland-demo.tgz
>>>>>>>
>>>>>>>  There is a small README in there which outlines the steps.
>>>>>>>
>>>>>>>  Best,
>>>>>>> Ketan
>>>>>>>
>>>>>>>   ************************************************************
>>>>>>> Xiaosheng Huang, Assistant Professor
>>>>>>> Department of Physics and Astronomy
>>>>>>> University of San Francisco
>>>>>>> 2130 Fulton Street, San Francisco, CA 94117-1080
>>>>>>>
>>>>>>> Phone: (415) 422-6281
>>>>>>> E-mail: xhuang22 at usfca.edu
>>>>>>> ************************************************************
>>>>>>>
>>>>>>
>>>>>>
>>>>>
>>>>
>>>
>>
>> _______________________________________________
>> Swift-user mailing list
>> Swift-user at ci.uchicago.edu
>> https://lists.ci.uchicago.edu/cgi-bin/mailman/listinfo/swift-user
>>
>
>
>
> --
> Yadu Nand B
>
>
> _______________________________________________
> Swift-user mailing list
> Swift-user at ci.uchicago.edu
> https://lists.ci.uchicago.edu/cgi-bin/mailman/listinfo/swift-user
>
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From amstocker at dons.usfca.edu  Fri Sep 12 18:23:13 2014
From: amstocker at dons.usfca.edu (Andrew Stocker)
Date: Fri, 12 Sep 2014 16:23:13 -0700
Subject: [Swift-user] Pointer to Swift tutorials for computational
 science education and research
In-Reply-To: <CAMUuviqy2T5WpCGP+1UmTgPzo_9j_7k7cNCoEzEaOxxM447B5Q@mail.gmail.com>
References: <539FC360.6090800@anl.gov>
	<59fc9be3f4d445ab8d502b2b1ce63af7@GEORGE.anl.gov>
	<CAMUuviqo8zhzvXVtJGEtV0TyoyW=D_EbVpNzL60BoNw60EEXEQ@mail.gmail.com>
	<CAN=xv+Zm+_VT5Ej4bDWiS8RotdgiuwYxRaF0CnZoV0si5hywQA@mail.gmail.com>
	<f41cf2675e66453d989165ca3231f73c@LUCKMAN.anl.gov>
	<CAMUuvirA+g6mQFBqw=u5p7kw+548VQ1q7g9wpyBxNz6792MOcw@mail.gmail.com>
	<13482362cf5c4f13a4d98c897b022f89@LUCKMAN.anl.gov>
	<CAMUuviq_v2oT2Gp-QVH94fevfzmx0R-5Y7bzZ-AYpNnb9zK5Nw@mail.gmail.com>
	<CAN=xv+b1z1CmwSM5b_gCi0D1vB15NBAKdtBs6nADgcQwgqRgDQ@mail.gmail.com>
	<362b5dde41ab45f5a0f455a267c058da@GEORGE.anl.gov>
	<CAMUuviodRt37OwDVhhP==VKPusCXiV30sCRBS9_rOb9wOV3XWA@mail.gmail.com>
	<cceef1afa9e14a64b89c2acb2a9eb30d@GEORGE.anl.gov>
	<CAMUuvipogv8zDOLydj3OnYAA8s94xQCrCcwF7qyKEkuS-J12Tg@mail.gmail.com>
	<CAOZiyaNc2U_a6AQyhDszWVB10So2b7uxkdu5TcLmV9WmdXpVAQ@mail.gmail.com>
	<CANa904=nRjw7dAQt-7JgfSnJ6zhWzyWX5cY4XrKio3mmaDeukg@mail.gmail.com>
	<CAMUuviqy2T5WpCGP+1UmTgPzo_9j_7k7cNCoEzEaOxxM447B5Q@mail.gmail.com>
Message-ID: <CAOZiyaNFi70z-MaTThp=JdDo7rGM+RbWsQ4wmccKNQAt5uRFnw@mail.gmail.com>

Ketan and Yadu,

I made changes to our Swift script according to your example and now things
are working fine without each node having the script.  Thanks very much for
your suggestions!

Andrew

On Thu, Sep 11, 2014 at 6:52 AM, Ketan Maheshwari <ketan at mcs.anl.gov> wrote:

> Andrew,
>
> Just to be clear, in the new script that Yadu posted, you will need to add
> one entry in your tc.data as follows:
>
> persistent-coasters bash /bin/bash
>
> Thanks,
> Ketan
>
>
>
> On Wed, Sep 10, 2014 at 11:03 PM, Yadu Nand <yadudoc1729 at gmail.com> wrote:
>
>> Hi Andrew,
>>
>> If you would like to have swift move the executable for you, you could
>> try the method used in the following example :
>>
>> type file;
>>
>> /* App definition calls bash which in-turn executes the bash script
>> defined as an argument here
>>    Every file in the input parameter list is staged by swift to the
>> worker nodes
>>    Every file in the return list is staged back to the client node by
>> swift
>> */
>> app (file out, file err) foo (file script, file input)
>> {
>>     bash @script @input stdout=@out stderr=@err;
>> }
>>
>> // Script to be executed
>> file wrapper <"wrapper.sh">;
>> file hello  <"hello.txt">;
>>
>> file out    <"foo.out">;
>> file err    <"foo.err">;
>>
>> (out, err) = foo (wrapper, hello);
>>
>> Thanks,
>> Yadu
>>
>>
>>
>> On Wed, Sep 10, 2014 at 8:45 PM, Andrew Stocker <amstocker at dons.usfca.edu
>> > wrote:
>>
>>> Ketan,
>>>
>>> I copied the catnap executable to the same directory on each of the
>>> computers and now the swift script is working perfectly without error.
>>>  Thanks for your help!  What are the next steps we can take to set up our
>>> cluster to not require the script to be on all the computers?  Since we are
>>> fairly new to parallel computing with a cluster, could you point us towards
>>> any resources regarding the technical configuration for Swift?  I've looked
>>> at the documentation for tc.data but I am still a bit confused by it.
>>>
>>> Thanks,
>>>
>>> Andrew
>>>
>>> On Tue, Sep 9, 2014 at 7:49 AM, Ketan Maheshwari <ketan at mcs.anl.gov>
>>> wrote:
>>>
>>>>
>>>> On Mon, Sep 8, 2014 at 6:28 PM, Andrew Stocker <
>>>> amstocker at dons.usfca.edu> wrote:
>>>>
>>>>>  Thanks for your response!
>>>>>
>>>>>  Since we're just in the stages of experimentation, our preliminary
>>>>> cluster is just four iMacs connected to a switch.  I set up password-less
>>>>> ssh communication between the four and I'm able to start the coaster
>>>>> service (in the folder with coaster-service.conf) without any errors.  I am
>>>>> running Swift from the computer which has the catnap.sh installed at
>>>>> the correct path, and I'm pretty sure it has the executable bit set ( #!/bin/sh
>>>>> is the first line of the program).  None of the other three computers
>>>>> have Swift installed, nor do they have catnap.sh at the location
>>>>> specified in tc.data, is this a problem?
>>>>>
>>>>
>>>> Yes, that seems to be the issue. The executable--catnap.sh in this case
>>>> must be available on all compute nodes in the location specified in the tc.
>>>>
>>>> An alternative in this case is to use catnap.sh as data and move it
>>>> along with data to target compute nodes. However, we can do  that later.
>>>> For now, could you try to put catnap.sh in a common location on each of the
>>>> compute nodes and try again.
>>>>
>>>> No, Swift is not needed to be installed on compute nodes. Swift just
>>>> needs to be on the submit node.
>>>>
>>>>
>>>>>
>>>>>  Attached is the log file from the run when I got the error I
>>>>> copy+pasted above.  Interestingly, when I run the catnap swift script with
>>>>> only 3 concurrent instances, it seems to run fine since we allow 3 jobs per
>>>>> node and so it is probably only running locally.
>>>>>
>>>>>  Regards,
>>>>> Andrew
>>>>>
>>>>> On Fri, Sep 5, 2014 at 6:03 PM, Ketan Maheshwari <ketan at mcs.anl.gov>
>>>>> wrote:
>>>>>
>>>>>> Hi Andrew,
>>>>>>
>>>>>>  Yes, I remember: thanks for getting back on this.
>>>>>>
>>>>>>  From the error message and tc.data, indeed it looks like the
>>>>>> executable is provided as absolute path but somehow Swift is looking into
>>>>>> system path and not finding it. One possibility is that the node on which
>>>>>> catnap.sh is running does not have it installed on the path specified in
>>>>>> the tc.data. Can you also check if catnap.sh has the executable bit set.
>>>>>> Less likely that this is causing the issue though.
>>>>>>
>>>>>>  Also, from the tc.data line it looks like you are using persistent
>>>>>> coasters. Have started the coaster service beforehand and made sure the
>>>>>> service started correctly without any error messages. Could you indicate
>>>>>> more about your cluster. Depending on the type of cluster, it is possible
>>>>>> that we can run Swift in a non-persistent, implicit coasters mode.
>>>>>>
>>>>>>  Can you also send the Swift generated log for this run.
>>>>>>
>>>>>>  Thanks,
>>>>>> Ketan
>>>>>>
>>>>>>
>>>>>> On Fri, Sep 5, 2014 at 7:16 PM, Andrew Stocker <
>>>>>> amstocker at dons.usfca.edu> wrote:
>>>>>>
>>>>>>>  Hi Ketan,
>>>>>>>
>>>>>>>  I'm not sure if you remember, but myself and my research advisor
>>>>>>> Xiaosheng spoke to you at LBL in Oakland at the beginning of the summer
>>>>>>> about starting to use Swift at our school.   We have been working hard on
>>>>>>> setting it up, and I am trying to get your demo to run but I'm having a
>>>>>>> problem.  For some reason I keep getting the following error when I try to
>>>>>>> run your catsnsleep demo:
>>>>>>>
>>>>>>>  Execution failed:
>>>>>>> Exception in catnap:
>>>>>>>     Arguments: [5, data.txt]
>>>>>>>     Host: persistent-coasters
>>>>>>>     Directory:
>>>>>>> catsnsleep-20140905-1702-mihcat06/jobs/u/catnap-utx080xl
>>>>>>>
>>>>>>>  Caused by:
>>>>>>> Cannot find executable catnap.sh on site system path
>>>>>>> catnap, catsnsleep.swift, line 13
>>>>>>>
>>>>>>>  However I'm not sure why.  In our tc.data file we have the line:
>>>>>>>
>>>>>>>  persistent-coasters catnap
>>>>>>> /usr/local/swift-0.94.1/oakland-demo/catnap.sh
>>>>>>>
>>>>>>>  which I think should work but obviously something is going wrong.
>>>>>>>  I have been browsing the documentation articles but I can't find anything
>>>>>>> about why this might be happening.  We would greatly appreciate your advice!
>>>>>>>
>>>>>>>  Regards,
>>>>>>>
>>>>>>>  Andrew Stocker
>>>>>>>
>>>>>>>
>>>>>>> On Fri, Jun 20, 2014 at 12:00 PM, Xiaosheng Huang <
>>>>>>> xhuang22 at usfca.edu> wrote:
>>>>>>>
>>>>>>>>
>>>>>>>> ---------- Forwarded message ----------
>>>>>>>> From: Ketan Maheshwari <ketan at mcs.anl.gov>
>>>>>>>> Date: Fri, Jun 20, 2014 at 11:45 AM
>>>>>>>> Subject: Re: Pointer to Swift tutorials for computational science
>>>>>>>> education and research
>>>>>>>> To: Xiaosheng Huang <xhuang22 at usfca.edu>
>>>>>>>> Cc: Wilde <wilde at mcs.anl.gov>
>>>>>>>>
>>>>>>>>
>>>>>>>> Hi Xiaosheng,
>>>>>>>>
>>>>>>>>  The tarball is: http://www.mcs.anl.gov/~ketan/oakland-demo.tgz
>>>>>>>>
>>>>>>>>  There is a small README in there which outlines the steps.
>>>>>>>>
>>>>>>>>  Best,
>>>>>>>> Ketan
>>>>>>>>
>>>>>>>>   ************************************************************
>>>>>>>> Xiaosheng Huang, Assistant Professor
>>>>>>>> Department of Physics and Astronomy
>>>>>>>> University of San Francisco
>>>>>>>> 2130 Fulton Street, San Francisco, CA 94117-1080
>>>>>>>>
>>>>>>>> Phone: (415) 422-6281
>>>>>>>> E-mail: xhuang22 at usfca.edu
>>>>>>>> ************************************************************
>>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>
>>>>>
>>>>
>>>
>>> _______________________________________________
>>> Swift-user mailing list
>>> Swift-user at ci.uchicago.edu
>>> https://lists.ci.uchicago.edu/cgi-bin/mailman/listinfo/swift-user
>>>
>>
>>
>>
>> --
>> Yadu Nand B
>>
>>
>> _______________________________________________
>> Swift-user mailing list
>> Swift-user at ci.uchicago.edu
>> https://lists.ci.uchicago.edu/cgi-bin/mailman/listinfo/swift-user
>>
>
>
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From justinbbt at gmail.com  Fri Sep 19 20:49:16 2014
From: justinbbt at gmail.com (Justin bbt)
Date: Fri, 19 Sep 2014 21:49:16 -0400
Subject: [Swift-user] number of simultaneous jobs on a node
Message-ID: <CABubRoBaX3Rte9FSztugjyu9=pZgbtqSsWYMcFMNc-xNQP-FnQ@mail.gmail.com>

Hi,

How can we configure the number of simultaneous jobs on  a node?
The goal is to utilize all cores of a multi-core node if the with
simultaneous running several instances of a program if the program itself
need only one core.


Best,

Justin
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From justinbbt at gmail.com  Fri Sep 19 20:48:48 2014
From: justinbbt at gmail.com (Justin bbt)
Date: Fri, 19 Sep 2014 21:48:48 -0400
Subject: [Swift-user] problem with running coaster
Message-ID: <CABubRoB-fS7e3R7wd936m8_SPY4u1T6fx56L+iq0DDWpskfrGA@mail.gmail.com>

Hi all

I have a problem in running swift over the cloud of Microsoft Azure. I have
two nodes on the cloud. I installed swift on one of them and I can run
part01-03 locally successfully. I am trying to use the coaster to run
part04-part-6 on the other node. Here is the output I get for "swift
p4.swift"


Swift 0.95 RC6 swift-r7900 cog-r3908
RunID: run005
Warning: The @ syntax for function invocation is deprecated
Progress: Sat, 20 Sep 2014 01:36:02+0000
Exception in thread "Scheduler" java.lang.NullPointerException
at
org.globus.cog.abstraction.impl.common.task.TaskImpl.hashCode(TaskImpl.java:364)
at java.util.HashMap.hash(HashMap.java:338)
at java.util.HashMap.get(HashMap.java:556)
at
org.griphyn.vdl.karajan.VDSAdaptiveScheduler.failTask(VDSAdaptiveScheduler.java:400)
at
org.globus.cog.karajan.scheduler.LateBindingScheduler.run(LateBindingScheduler.java:266)
Progress: Sat, 20 Sep 2014 01:36:03+0000  Selecting site:10
No events in 1s.
Finding dependency loops...

Waiting threads:
Thread: R-6, waiting on sims (declared on line 21)
swift:execute, p4, line 96
analyze, p4, line 211

Thread: R-5-2-3, waiting on simout (declared on line 24)
assignment, p4, line 28

Thread: R-5-7-3, waiting on simout (declared on line 24)
assignment, p4, line 28

Thread: R-5-8-3, waiting on simout (declared on line 24)
assignment, p4, line 28

Thread: R-5-9-3, waiting on simout (declared on line 24)
assignment, p4, line 28

Thread: R-5-3x2, waiting on simout (declared on line 24)
assignment, p4, line 28

Thread: R-5-0-3, waiting on simout (declared on line 24)
assignment, p4, line 28

Thread: R-5-1-3, waiting on simout (declared on line 24)
assignment, p4, line 28

Thread: R-5-6-3, waiting on simout (declared on line 24)
assignment, p4, line 28

Thread: R-5-4-3, waiting on simout (declared on line 24)
assignment, p4, line 28

Thread: R-5x2-3, waiting on simout (declared on line 24)
assignment, p4, line 28

----
No dependency loops found.

The following threads are independently hung:
Thread: R-6, waiting on sims (declared on line 21)
swift:execute, p4, line 96
analyze, p4, line 211

----

Irrecoverable error found. Exiting.





This is the content of my coaster-service.conf

export WORKER_LOCATION=.
export WORKER_HOSTS="191.238.1.187"
export WORKER_MODE=ssh
export WORKER_USERNAME=azureuser
export IPADDR=191.238.1.33
export WORKER_LOG_DIR=.
export WORK=/home/ubuntu/work
export JOBSPERNODE=1
export JOBTHROTTLE=10
export SSH_TUNNELING=yes


And here is the content of start-coaster-service.log


Running /home/azureuser/swift-0.95-RC6/bin/coaster-service -nosec -portfile
/tmp/tmp.8WkG0mKKzo -localportfile /tmp/tmp.hZvsxQd5J1 -passive
Switching log to: cps-2014-09-20_01-21-41.log
2014-09-20 01:21:41,305+0000 WARN  CoasterPersistentService Switching log
to: cps-2014-09-20_01-21-41.log
Local contacts: [http://100.74.60.3:55071]
2014-09-20 01:21:41,338+0000 INFO  Settings Local contacts: [
http://100.74.60.3:55071]
Starting... id=0920-2101410
2014-09-20 01:21:41,350+0000 INFO  BlockQueueProcessor Starting...
id=0920-2101410
Started local service: http://100.74.60.3:55071
2014-09-20 01:21:41,350+0000 INFO  CoasterService Started local service:
http://100.74.60.3:55071
Started coaster service: http://100.74.60.3:42972
2014-09-20 01:21:41,351+0000 INFO  CoasterService Started coaster service:
http://100.74.60.3:42972
Started coaster service: http://100.74.60.3:42972
Worker connection URL: http://100.74.60.3:55071
Running ssh -N -T -R *:55071:localhost:55071 azureuser at 191.238.1.187
Running ssh azureuser at 191.238.1.187 mkdir -p . && mkdir -p .
Running scp /home/azureuser/swift-0.95-RC6/bin/worker.pl
azureuser at 191.238.1.187:.
Running ssh azureuser at 191.238.1.187 WORKER_LOGGING_LEVEL= nohup ./worker.pl
http://191.238.1.33:55071 191.238.1.187 . &> /dev/null &
HeapMax: 13134987264, CrtHeap: 886571008, UsedHeap: 41712768
2014-09-20 01:21:51,356+0000 INFO  CoasterService HeapMax: 13134987264,
CrtHeap: 886571008, UsedHeap: 41712768
HeapMax: 13134987264, CrtHeap: 886571008, UsedHeap: 41712768
2014-09-20 01:22:01,364+0000 INFO  CoasterService HeapMax: 13134987264,
CrtHeap: 886571008, UsedHeap: 41712768


I had this problem before with my laptop connecting to a remote server and Yadu
Nand Babuji  told me it is because I don't have  a public ip.
But, I have the problem again now with my nodes in the cloud having the
public ip.
Though as  can be seen in the log, during the connection coaster uses the
private ip
(100.74.60.3)

Is this really a problem with public IP?
Does anybody know how to solve this problem ?
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From justinbbt at gmail.com  Mon Sep 22 12:24:45 2014
From: justinbbt at gmail.com (Justin bbt)
Date: Mon, 22 Sep 2014 13:24:45 -0400
Subject: [Swift-user] Fwd: number of simultaneous jobs on a node
In-Reply-To: <CABubRoBaX3Rte9FSztugjyu9=pZgbtqSsWYMcFMNc-xNQP-FnQ@mail.gmail.com>
References: <CABubRoBaX3Rte9FSztugjyu9=pZgbtqSsWYMcFMNc-xNQP-FnQ@mail.gmail.com>
Message-ID: <CABubRoBwZDaNxjACHberQ_vsGFUA8cYOqgGXsrWGZpa9cT2CGw@mail.gmail.com>

---------- Forwarded message ----------
From: Justin bbt <justinbbt at gmail.com>
Date: Fri, Sep 19, 2014 at 9:49 PM
Subject: number of simultaneous jobs on a node
To: Swift User <swift-user at ci.uchicago.edu>


Hi,

How can we configure the number of simultaneous jobs on  a node?
The goal is to utilize all cores of a multi-core node if the with
simultaneous running several instances of a program if the program itself
need only one core.


Best,

Justin
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From justinbbt at gmail.com  Mon Sep 22 12:22:12 2014
From: justinbbt at gmail.com (Justin bbt)
Date: Mon, 22 Sep 2014 13:22:12 -0400
Subject: [Swift-user] Fwd: problem with running coaster
In-Reply-To: <CABubRoB-fS7e3R7wd936m8_SPY4u1T6fx56L+iq0DDWpskfrGA@mail.gmail.com>
References: <CABubRoB-fS7e3R7wd936m8_SPY4u1T6fx56L+iq0DDWpskfrGA@mail.gmail.com>
Message-ID: <CABubRoCX7gYV6NeFHFqx2STyAP9YVEybu=z0Y2LMF6bz+pP_ew@mail.gmail.com>

---------- Forwarded message ----------
From: Justin bbt <justinbbt at gmail.com>
Date: Fri, Sep 19, 2014 at 9:48 PM
Subject: problem with running coaster
To: Swift User <swift-user at ci.uchicago.edu>
Cc: Yadu Nand <yadudoc1729 at gmail.com>


Hi all

I have a problem in running swift over the cloud of Microsoft Azure. I have
two nodes on the cloud. I installed swift on one of them and I can run
part01-03 locally successfully. I am trying to use the coaster to run
part04-part-6 on the other node. Here is the output I get for "swift
p4.swift"


Swift 0.95 RC6 swift-r7900 cog-r3908
RunID: run005
Warning: The @ syntax for function invocation is deprecated
Progress: Sat, 20 Sep 2014 01:36:02+0000
Exception in thread "Scheduler" java.lang.NullPointerException
at
org.globus.cog.abstraction.impl.common.task.TaskImpl.hashCode(TaskImpl.java:364)
at java.util.HashMap.hash(HashMap.java:338)
at java.util.HashMap.get(HashMap.java:556)
at
org.griphyn.vdl.karajan.VDSAdaptiveScheduler.failTask(VDSAdaptiveScheduler.java:400)
at
org.globus.cog.karajan.scheduler.LateBindingScheduler.run(LateBindingScheduler.java:266)
Progress: Sat, 20 Sep 2014 01:36:03+0000  Selecting site:10
No events in 1s.
Finding dependency loops...

Waiting threads:
Thread: R-6, waiting on sims (declared on line 21)
swift:execute, p4, line 96
analyze, p4, line 211

Thread: R-5-2-3, waiting on simout (declared on line 24)
assignment, p4, line 28

Thread: R-5-7-3, waiting on simout (declared on line 24)
assignment, p4, line 28

Thread: R-5-8-3, waiting on simout (declared on line 24)
assignment, p4, line 28

Thread: R-5-9-3, waiting on simout (declared on line 24)
assignment, p4, line 28

Thread: R-5-3x2, waiting on simout (declared on line 24)
assignment, p4, line 28

Thread: R-5-0-3, waiting on simout (declared on line 24)
assignment, p4, line 28

Thread: R-5-1-3, waiting on simout (declared on line 24)
assignment, p4, line 28

Thread: R-5-6-3, waiting on simout (declared on line 24)
assignment, p4, line 28

Thread: R-5-4-3, waiting on simout (declared on line 24)
assignment, p4, line 28

Thread: R-5x2-3, waiting on simout (declared on line 24)
assignment, p4, line 28

----
No dependency loops found.

The following threads are independently hung:
Thread: R-6, waiting on sims (declared on line 21)
swift:execute, p4, line 96
analyze, p4, line 211

----

Irrecoverable error found. Exiting.





This is the content of my coaster-service.conf

export WORKER_LOCATION=.
export WORKER_HOSTS="191.238.1.187"
export WORKER_MODE=ssh
export WORKER_USERNAME=azureuser
export IPADDR=191.238.1.33
export WORKER_LOG_DIR=.
export WORK=/home/ubuntu/work
export JOBSPERNODE=1
export JOBTHROTTLE=10
export SSH_TUNNELING=yes


And here is the content of start-coaster-service.log


Running /home/azureuser/swift-0.95-RC6/bin/coaster-service -nosec -portfile
/tmp/tmp.8WkG0mKKzo -localportfile /tmp/tmp.hZvsxQd5J1 -passive
Switching log to: cps-2014-09-20_01-21-41.log
2014-09-20 01:21:41,305+0000 WARN  CoasterPersistentService Switching log
to: cps-2014-09-20_01-21-41.log
Local contacts: [http://100.74.60.3:55071]
2014-09-20 01:21:41,338+0000 INFO  Settings Local contacts: [
http://100.74.60.3:55071]
Starting... id=0920-2101410
2014-09-20 01:21:41,350+0000 INFO  BlockQueueProcessor Starting...
id=0920-2101410
Started local service: http://100.74.60.3:55071
2014-09-20 01:21:41,350+0000 INFO  CoasterService Started local service:
http://100.74.60.3:55071
Started coaster service: http://100.74.60.3:42972
2014-09-20 01:21:41,351+0000 INFO  CoasterService Started coaster service:
http://100.74.60.3:42972
Started coaster service: http://100.74.60.3:42972
Worker connection URL: http://100.74.60.3:55071
Running ssh -N -T -R *:55071:localhost:55071 azureuser at 191.238.1.187
Running ssh azureuser at 191.238.1.187 mkdir -p . && mkdir -p .
Running scp /home/azureuser/swift-0.95-RC6/bin/worker.pl
azureuser at 191.238.1.187:.
Running ssh azureuser at 191.238.1.187 WORKER_LOGGING_LEVEL= nohup ./worker.pl
http://191.238.1.33:55071 191.238.1.187 . &> /dev/null &
HeapMax: 13134987264, CrtHeap: 886571008, UsedHeap: 41712768
2014-09-20 01:21:51,356+0000 INFO  CoasterService HeapMax: 13134987264,
CrtHeap: 886571008, UsedHeap: 41712768
HeapMax: 13134987264, CrtHeap: 886571008, UsedHeap: 41712768
2014-09-20 01:22:01,364+0000 INFO  CoasterService HeapMax: 13134987264,
CrtHeap: 886571008, UsedHeap: 41712768


I had this problem before with my laptop connecting to a remote server and Yadu
Nand Babuji  told me it is because I don't have  a public ip.
But, I have the problem again now with my nodes in the cloud having the
public ip.
Though as  can be seen in the log, during the connection coaster uses the
private ip
(100.74.60.3)

Is this really a problem with public IP?
Does anybody know how to solve this problem ?
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From justinbbt at gmail.com  Mon Sep 22 20:32:49 2014
From: justinbbt at gmail.com (Justin bbt)
Date: Mon, 22 Sep 2014 21:32:49 -0400
Subject: [Swift-user] question about xsede
Message-ID: <CABubRoCXRJrYbbY1TaamFRj08NunyQhBu5vrXSt6YTta0vVNPQ@mail.gmail.com>

Hi

If I want to use resources on the xsede
https://www.xsede.org/overview
which site config should I use ?
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From ketan at mcs.anl.gov  Tue Sep 23 09:31:53 2014
From: ketan at mcs.anl.gov (Ketan Maheshwari)
Date: Tue, 23 Sep 2014 09:31:53 -0500
Subject: [Swift-user] question about xsede
In-Reply-To: <CABubRoCXRJrYbbY1TaamFRj08NunyQhBu5vrXSt6YTta0vVNPQ@mail.gmail.com>
References: <CABubRoCXRJrYbbY1TaamFRj08NunyQhBu5vrXSt6YTta0vVNPQ@mail.gmail.com>
Message-ID: <CAMUuviqoZaNiN3ADtX-h4PtTPfL8jZKkmVC=YPw=k=i9rt1fsQ@mail.gmail.com>

Hi Justin,

If you are using xsede Stampede regular nodes (non xeon phi), here is a
site configuration that has worked for me in the past, connecting over ssh
to slurm:

<?xml version="1.0" encoding="UTF-8"?>
<config xmlns="http://www.ci.uchicago.edu/swift/SwiftSites">
 <pool handle="stampede">
   <execution provider="coaster" jobmanager="ssh-cl:slurm" url="
stampede.tacc.utexas.edu"/>
   <filesystem provider="local" />
   <profile namespace="globus"  key="jobsPerNode">1</profile>
   <profile namespace="globus"  key="ppn">1</profile>
   <profile namespace="globus"  key="maxTime">7500</profile>
   <profile namespace="globus"  key="maxwalltime">00:10:00</profile>
   <profile namespace="globus"  key="lowOverallocation">100</profile>
   <profile namespace="globus"  key="highOverallocation">100</profile>
   <profile namespace="globus"  key="queue">normal</profile>
   <profile namespace="globus"  key="nodeGranularity">1</profile>
   <profile namespace="globus"  key="maxNodes">1</profile>
   <profile namespace="globus" key="slots">1</profile>
   <profile namespace="globus"  key="project">TG-EAR130015</profile>
   <profile namespace="karajan" key="jobThrottle">.3199</profile>
   <profile namespace="karajan" key="initialScore">10000</profile>
   <workdirectory>/tmp/{env.USER}/swift.work</workdirectory>
  </pool>
</config>

You will need to replace project id with yours.

Thanks,
Ketan

On Mon, Sep 22, 2014 at 8:32 PM, Justin bbt <justinbbt at gmail.com> wrote:

> Hi
>
> If I want to use resources on the xsede
> https://www.xsede.org/overview
> which site config should I use ?
>
>
> _______________________________________________
> Swift-user mailing list
> Swift-user at ci.uchicago.edu
> https://lists.ci.uchicago.edu/cgi-bin/mailman/listinfo/swift-user
>
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From justinbbt at gmail.com  Tue Sep 23 17:22:07 2014
From: justinbbt at gmail.com (Justin bbt)
Date: Tue, 23 Sep 2014 18:22:07 -0400
Subject: [Swift-user] question about xsede
In-Reply-To: <CAMUuviqoZaNiN3ADtX-h4PtTPfL8jZKkmVC=YPw=k=i9rt1fsQ@mail.gmail.com>
References: <CABubRoCXRJrYbbY1TaamFRj08NunyQhBu5vrXSt6YTta0vVNPQ@mail.gmail.com>
	<CAMUuviqoZaNiN3ADtX-h4PtTPfL8jZKkmVC=YPw=k=i9rt1fsQ@mail.gmail.com>
Message-ID: <CABubRoAh3+j5MHtO18-X=MmCEho=2yLwKXnrNKtwOunmFKORdw@mail.gmail.com>

Thank you very much.

I am actually using the Blacklight, which I guess is PBS based.
So, should I use the Crays tutorial and setting ?
http://swift-lang.org/tutorials/cray/tutorial.html

On Tue, Sep 23, 2014 at 10:31 AM, Ketan Maheshwari <ketan at mcs.anl.gov>
wrote:

> Hi Justin,
>
> If you are using xsede Stampede regular nodes (non xeon phi), here is a
> site configuration that has worked for me in the past, connecting over ssh
> to slurm:
>
> <?xml version="1.0" encoding="UTF-8"?>
> <config xmlns="http://www.ci.uchicago.edu/swift/SwiftSites">
>  <pool handle="stampede">
>    <execution provider="coaster" jobmanager="ssh-cl:slurm" url="
> stampede.tacc.utexas.edu"/>
>    <filesystem provider="local" />
>    <profile namespace="globus"  key="jobsPerNode">1</profile>
>    <profile namespace="globus"  key="ppn">1</profile>
>    <profile namespace="globus"  key="maxTime">7500</profile>
>    <profile namespace="globus"  key="maxwalltime">00:10:00</profile>
>    <profile namespace="globus"  key="lowOverallocation">100</profile>
>    <profile namespace="globus"  key="highOverallocation">100</profile>
>    <profile namespace="globus"  key="queue">normal</profile>
>    <profile namespace="globus"  key="nodeGranularity">1</profile>
>    <profile namespace="globus"  key="maxNodes">1</profile>
>    <profile namespace="globus" key="slots">1</profile>
>    <profile namespace="globus"  key="project">TG-EAR130015</profile>
>    <profile namespace="karajan" key="jobThrottle">.3199</profile>
>    <profile namespace="karajan" key="initialScore">10000</profile>
>    <workdirectory>/tmp/{env.USER}/swift.work</workdirectory>
>   </pool>
> </config>
>
> You will need to replace project id with yours.
>
> Thanks,
> Ketan
>
> On Mon, Sep 22, 2014 at 8:32 PM, Justin bbt <justinbbt at gmail.com> wrote:
>
>> Hi
>>
>> If I want to use resources on the xsede
>> https://www.xsede.org/overview
>> which site config should I use ?
>>
>>
>> _______________________________________________
>> Swift-user mailing list
>> Swift-user at ci.uchicago.edu
>> https://lists.ci.uchicago.edu/cgi-bin/mailman/listinfo/swift-user
>>
>
>
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From wilde at anl.gov  Tue Sep 23 17:30:48 2014
From: wilde at anl.gov (Michael Wilde)
Date: Tue, 23 Sep 2014 17:30:48 -0500
Subject: [Swift-user] question about xsede
In-Reply-To: <CABubRoAh3+j5MHtO18-X=MmCEho=2yLwKXnrNKtwOunmFKORdw@mail.gmail.com>
References: <CABubRoCXRJrYbbY1TaamFRj08NunyQhBu5vrXSt6YTta0vVNPQ@mail.gmail.com>	<CAMUuviqoZaNiN3ADtX-h4PtTPfL8jZKkmVC=YPw=k=i9rt1fsQ@mail.gmail.com>
	<CABubRoAh3+j5MHtO18-X=MmCEho=2yLwKXnrNKtwOunmFKORdw@mail.gmail.com>
Message-ID: <5421F498.7070909@anl.gov>

Justin,

Blacklight is an SGI machine, and thus a more standard PBS machine to 
which the Cray-specific sites file settings do not apply.

It does seem to have a few quirks, though, as describe at:
   https://portal.xsede.org/psc-blacklight#running

In particular, the page above suggests using "-l ncpus=N" where N is the 
number of CPUS desired and a multiple of 16.  But by default Swift will 
generate "-l nodes=n" where n is the number of nodes.

So we'll need to either do some testing (once we get on the machine) or 
send you our best guess of the right sites settings and work with you to 
test them for us.

We'll look into this further and report back.

- Mike

On 9/23/14, 5:22 PM, Justin bbt wrote:
> Thank you very much.
>
> I am actually using the Blacklight, which I guess is PBS based.
> So, should I use the Crays tutorial and setting ? 
> http://swift-lang.org/tutorials/cray/tutorial.html
>
> On Tue, Sep 23, 2014 at 10:31 AM, Ketan Maheshwari <ketan at mcs.anl.gov 
> <mailto:ketan at mcs.anl.gov>> wrote:
>
>     Hi Justin,
>
>     If you are using xsede Stampede regular nodes (non xeon phi), here
>     is a site configuration that has worked for me in the past,
>     connecting over ssh to slurm:
>
>     <?xml version="1.0" encoding="UTF-8"?>
>     <config xmlns="http://www.ci.uchicago.edu/swift/SwiftSites">
>      <pool handle="stampede">
>        <execution provider="coaster" jobmanager="ssh-cl:slurm"
>     url="stampede.tacc.utexas.edu <http://stampede.tacc.utexas.edu>"/>
>        <filesystem provider="local" />
>        <profile namespace="globus"  key="jobsPerNode">1</profile>
>        <profile namespace="globus"  key="ppn">1</profile>
>        <profile namespace="globus"  key="maxTime">7500</profile>
>        <profile namespace="globus"  key="maxwalltime">00:10:00</profile>
>        <profile namespace="globus"  key="lowOverallocation">100</profile>
>        <profile namespace="globus"  key="highOverallocation">100</profile>
>        <profile namespace="globus"  key="queue">normal</profile>
>        <profile namespace="globus"  key="nodeGranularity">1</profile>
>        <profile namespace="globus"  key="maxNodes">1</profile>
>        <profile namespace="globus" key="slots">1</profile>
>        <profile namespace="globus"  key="project">TG-EAR130015</profile>
>        <profile namespace="karajan" key="jobThrottle">.3199</profile>
>        <profile namespace="karajan" key="initialScore">10000</profile>
>      <workdirectory>/tmp/{env.USER}/swift.work</workdirectory>
>       </pool>
>     </config>
>
>     You will need to replace project id with yours.
>
>     Thanks,
>     Ketan
>
>     On Mon, Sep 22, 2014 at 8:32 PM, Justin bbt <justinbbt at gmail.com
>     <mailto:justinbbt at gmail.com>> wrote:
>
>         Hi
>
>         If I want to use resources on the xsede
>         https://www.xsede.org/overview
>         which site config should I use ?
>
>
>         _______________________________________________
>         Swift-user mailing list
>         Swift-user at ci.uchicago.edu <mailto:Swift-user at ci.uchicago.edu>
>         https://lists.ci.uchicago.edu/cgi-bin/mailman/listinfo/swift-user
>
>
>
>
>
> _______________________________________________
> Swift-user mailing list
> Swift-user at ci.uchicago.edu
> https://lists.ci.uchicago.edu/cgi-bin/mailman/listinfo/swift-user

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

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From yadudoc1729 at gmail.com  Thu Sep 25 17:25:01 2014
From: yadudoc1729 at gmail.com (Yadu Nand)
Date: Thu, 25 Sep 2014 17:25:01 -0500
Subject: [Swift-user] question about xsede
In-Reply-To: <5421F498.7070909@anl.gov>
References: <CABubRoCXRJrYbbY1TaamFRj08NunyQhBu5vrXSt6YTta0vVNPQ@mail.gmail.com>
	<CAMUuviqoZaNiN3ADtX-h4PtTPfL8jZKkmVC=YPw=k=i9rt1fsQ@mail.gmail.com>
	<CABubRoAh3+j5MHtO18-X=MmCEho=2yLwKXnrNKtwOunmFKORdw@mail.gmail.com>
	<5421F498.7070909@anl.gov>
Message-ID: <CANa904=kSmmXMM2tYPLHfWA632P+6umBQ52_X2W7LPYJDaaqvw@mail.gmail.com>

Hi Justin,

Here are some tested configs and a small README from running the sanity
test on Blacklight:
http://users.rcc.uchicago.edu/~yadunand/blacklight-sanity/

There's an example each of configs for Swift 0.94, Swift 0.95 and the
configs we would use going
forward (Swift 0.96 and current trunk) in that folder.

In the example, I've used ppn=16 (or any multiple of 16) which seems to
work as a substitute for ncpus.

Hope that helps!

-Yadu


On Tue, Sep 23, 2014 at 5:30 PM, Michael Wilde <wilde at anl.gov> wrote:

>  Justin,
>
> Blacklight is an SGI machine, and thus a more standard PBS machine to
> which the Cray-specific sites file settings do not apply.
>
> It does seem to have a few quirks, though, as describe at:
>   https://portal.xsede.org/psc-blacklight#running
>
> In particular, the page above suggests using "-l ncpus=N" where N is the
> number of CPUS desired and a multiple of 16.  But by default Swift will
> generate "-l nodes=n" where n is the number of nodes.
>
> So we'll need to either do some testing (once we get on the machine) or
> send you our best guess of the right sites settings and work with you to
> test them for us.
>
> We'll look into this further and report back.
>
> - Mike
>
>
> On 9/23/14, 5:22 PM, Justin bbt wrote:
>
> Thank you very much.
>
> I am actually using the Blacklight, which I guess is PBS based.
>  So, should I use the Crays tutorial and setting ?
> http://swift-lang.org/tutorials/cray/tutorial.html
>
> On Tue, Sep 23, 2014 at 10:31 AM, Ketan Maheshwari <ketan at mcs.anl.gov>
> wrote:
>
>> Hi Justin,
>>
>>  If you are using xsede Stampede regular nodes (non xeon phi), here is a
>> site configuration that has worked for me in the past, connecting over ssh
>> to slurm:
>>
>>  <?xml version="1.0" encoding="UTF-8"?>
>> <config xmlns="http://www.ci.uchicago.edu/swift/SwiftSites">
>>  <pool handle="stampede">
>>    <execution provider="coaster" jobmanager="ssh-cl:slurm" url="
>> stampede.tacc.utexas.edu"/>
>>    <filesystem provider="local" />
>>    <profile namespace="globus"  key="jobsPerNode">1</profile>
>>    <profile namespace="globus"  key="ppn">1</profile>
>>    <profile namespace="globus"  key="maxTime">7500</profile>
>>    <profile namespace="globus"  key="maxwalltime">00:10:00</profile>
>>    <profile namespace="globus"  key="lowOverallocation">100</profile>
>>    <profile namespace="globus"  key="highOverallocation">100</profile>
>>    <profile namespace="globus"  key="queue">normal</profile>
>>    <profile namespace="globus"  key="nodeGranularity">1</profile>
>>    <profile namespace="globus"  key="maxNodes">1</profile>
>>    <profile namespace="globus" key="slots">1</profile>
>>    <profile namespace="globus"  key="project">TG-EAR130015</profile>
>>    <profile namespace="karajan" key="jobThrottle">.3199</profile>
>>    <profile namespace="karajan" key="initialScore">10000</profile>
>>    <workdirectory>/tmp/{env.USER}/swift.work</workdirectory>
>>   </pool>
>> </config>
>>
>>  You will need to replace project id with yours.
>>
>>  Thanks,
>> Ketan
>>
>>  On Mon, Sep 22, 2014 at 8:32 PM, Justin bbt <justinbbt at gmail.com> wrote:
>>
>>>  Hi
>>>
>>>  If I want to use resources on the xsede
>>> https://www.xsede.org/overview
>>>  which site config should I use ?
>>>
>>>
>>>  _______________________________________________
>>> Swift-user mailing list
>>> Swift-user at ci.uchicago.edu
>>> https://lists.ci.uchicago.edu/cgi-bin/mailman/listinfo/swift-user
>>>
>>
>>
>
>
> _______________________________________________
> Swift-user mailing listSwift-user at ci.uchicago.eduhttps://lists.ci.uchicago.edu/cgi-bin/mailman/listinfo/swift-user
>
>
> --
> Michael Wilde
> Mathematics and Computer Science          Computation Institute
> Argonne National Laboratory               The University of Chicago
>
>
> _______________________________________________
> Swift-user mailing list
> Swift-user at ci.uchicago.edu
> https://lists.ci.uchicago.edu/cgi-bin/mailman/listinfo/swift-user
>



-- 
??
Yadu Nand B
??
??
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From pwj3 at txstate.edu  Fri Sep 26 13:18:22 2014
From: pwj3 at txstate.edu (Janovics, Peter W)
Date: Fri, 26 Sep 2014 18:18:22 +0000
Subject: [Swift-user] Swift parallel scripting language questions
Message-ID: <20FEAE5E-D09E-404C-A82F-51CC5F5C5DB5@txstate.edu>

Dear Swift development team,

My name is Peter Janovics, and I am a researcher in Dr. Burtscher?s lab at Texas State University. For the past month I have been learning the Swift programming language because it supports parallel execution and can execute other applications that are parallel. I have several questions and encountered some difficulties that you may want to be made aware of.

I noticed that the ?Try Swift online? application on your webpage does not work and now appears to be offline. Is there a timeframe for when it will be back online and working?

Is an updated version of the tutorial available that requires a slightly lower learning curve and/or includes more examples with explanations? I have been trying to piece together information but feel that there is a gap between the tutorial, which is based on an older version of Swift, and the documentation, which explains some of the new keywords but does not give enough complete examples with descriptions.

Are there any examples of executing simple Linux commands using Swift? The documentation mentions having applications appended to a file. Does this mean that any command that I would like to execute in Swift needs to be included in this file, including shell commands?

There is a section that explains how to use Swift with MPI, but the files shown do not seem complete. Moreover, I would like to execute MPI code on a supercomputer in a batch environment. Are there any instructions on how to use Swift in such an environment? Also, what is the required folder structure to ensure that Swift will find the files needed to execute MPI code?

Thank you for your time,
Peter Janovics

From justinbbt at gmail.com  Sat Sep 27 14:41:53 2014
From: justinbbt at gmail.com (Justin bbt)
Date: Sat, 27 Sep 2014 15:41:53 -0400
Subject: [Swift-user] question about xsede
In-Reply-To: <CABubRoAh3+j5MHtO18-X=MmCEho=2yLwKXnrNKtwOunmFKORdw@mail.gmail.com>
References: <CABubRoCXRJrYbbY1TaamFRj08NunyQhBu5vrXSt6YTta0vVNPQ@mail.gmail.com>
	<CAMUuviqoZaNiN3ADtX-h4PtTPfL8jZKkmVC=YPw=k=i9rt1fsQ@mail.gmail.com>
	<CABubRoAh3+j5MHtO18-X=MmCEho=2yLwKXnrNKtwOunmFKORdw@mail.gmail.com>
Message-ID: <CABubRoB20KHEdAkgGtct5697o-rt_6SiEnabC-TOqvqARqRV_w@mail.gmail.com>

So, I am using this config


<pool handle="black">
    <execution provider="coaster" jobmanager="local:pbs" URL="none"/>
    <profile namespace="env"    key="PATHPREFIX">{env.PWD}/../app</profile>
    <profile namespace="globus" key="jobsPerNode">1</profile>
    <profile namespace="globus" key="queue">normal</profile>
<profile namespace="globus"  key="ppn">16</profile>
  <profile namespace="globus" key="maxWallTime">00:01:00</profile>
    <profile namespace="globus" key="maxTime">3600</profile>
    <profile namespace="globus" key="lowOverAllocation">100</profile>
    <profile namespace="globus" key="highOverAllocation">100</profile>
    <profile namespace="globus" key="slots">2</profile>
    <profile namespace="globus" key="maxNodes">1</profile>
    <profile namespace="globus" key="nodeGranularity">1</profile>
    <profile namespace="karajan" key="jobThrottle">.320</profile>
    <profile namespace="karajan" key="initialScore">10000</profile>
  <profile namespace="globus" key="slots">1</profile>
   <profile namespace="globus"  key="project">TG-CCR134513</profile>
    <workdirectory>/brashear/usrname</workdirectory>
      <profile namespace="swift" key="stagingMethod">local</profile>
<filesystem provider="local" />
</pool>

but, it does not work and give this error :

Swift 0.95 RC6 swift-r7900 cog-r3908
RunID: run011
Warning: The @ syntax for function invocation is deprecated
[Error] sites.xml, line 2, col 10: cvc-elt.1: Cannot find the declaration
of element 'config'.
Progress: Sat, 27 Sep 2014 15:35:52-0400

Could not submit job (qsub reported an exit code of 170).
qsub: Unknown queue MSG=cannot locate queue

Execution failed:
Exception in simulate:
    Arguments: [--timesteps, 1, --range, 100, --nvalues, 5]
    Host: black
    Directory: p4-run011/jobs/s/simulate-sdm041yl
exception @ swift-int-staging.k, line: 181
Caused by:
exception @ swift-int-staging.k, line: 177
Caused by: Block task failed: Error submitting block task
org.globus.cog.abstraction.impl.common.task.TaskSubmissionException: Could
not submit job (qsub reported an exit code of 170).
qsub: Unknown queue MSG=cannot locate queue

at
org.globus.cog.abstraction.impl.scheduler.common.AbstractJobSubmissionTaskHandler.submit(AbstractJobSubmissionTaskHandler.java:63)
at
org.globus.cog.abstraction.impl.common.AbstractTaskHandler.submit(AbstractTaskHandler.java:45)
at
org.globus.cog.abstraction.impl.common.task.ExecutionTaskHandler.submit(ExecutionTaskHandler.java:61)
at
org.globus.cog.abstraction.coaster.service.job.manager.BlockTaskSubmitter.run(BlockTaskSubmitter.java:70)
Caused by:
org.globus.cog.abstraction.impl.scheduler.common.ProcessException: Could
not submit job (qsub reported an exit code of 170).
qsub: Unknown queue MSG=cannot locate queue

at
org.globus.cog.abstraction.impl.scheduler.common.AbstractExecutor.start(AbstractExecutor.java:113)
at
org.globus.cog.abstraction.impl.scheduler.common.AbstractJobSubmissionTaskHandler.submit(AbstractJobSubmissionTaskHandler.java:53)
... 3 more



also, in some configs I saw this. But I dont know what this is and what
values should I set to

    <profile namespace="globus"
key="providerAttributes">pbs.aprun;pbs.mpp;depth=32</profile>


On Tue, Sep 23, 2014 at 6:22 PM, Justin bbt <justinbbt at gmail.com> wrote:

> Thank you very much.
>
> I am actually using the Blacklight, which I guess is PBS based.
> So, should I use the Crays tutorial and setting ?
> http://swift-lang.org/tutorials/cray/tutorial.html
>
> On Tue, Sep 23, 2014 at 10:31 AM, Ketan Maheshwari <ketan at mcs.anl.gov>
> wrote:
>
>> Hi Justin,
>>
>> If you are using xsede Stampede regular nodes (non xeon phi), here is a
>> site configuration that has worked for me in the past, connecting over ssh
>> to slurm:
>>
>> <?xml version="1.0" encoding="UTF-8"?>
>> <config xmlns="http://www.ci.uchicago.edu/swift/SwiftSites">
>>  <pool handle="stampede">
>>    <execution provider="coaster" jobmanager="ssh-cl:slurm" url="
>> stampede.tacc.utexas.edu"/>
>>    <filesystem provider="local" />
>>    <profile namespace="globus"  key="jobsPerNode">1</profile>
>>    <profile namespace="globus"  key="ppn">1</profile>
>>    <profile namespace="globus"  key="maxTime">7500</profile>
>>    <profile namespace="globus"  key="maxwalltime">00:10:00</profile>
>>    <profile namespace="globus"  key="lowOverallocation">100</profile>
>>    <profile namespace="globus"  key="highOverallocation">100</profile>
>>    <profile namespace="globus"  key="queue">normal</profile>
>>    <profile namespace="globus"  key="nodeGranularity">1</profile>
>>    <profile namespace="globus"  key="maxNodes">1</profile>
>>    <profile namespace="globus" key="slots">1</profile>
>>    <profile namespace="globus"  key="project">TG-EAR130015</profile>
>>    <profile namespace="karajan" key="jobThrottle">.3199</profile>
>>    <profile namespace="karajan" key="initialScore">10000</profile>
>>    <workdirectory>/tmp/{env.USER}/swift.work</workdirectory>
>>   </pool>
>> </config>
>>
>> You will need to replace project id with yours.
>>
>> Thanks,
>> Ketan
>>
>> On Mon, Sep 22, 2014 at 8:32 PM, Justin bbt <justinbbt at gmail.com> wrote:
>>
>>> Hi
>>>
>>> If I want to use resources on the xsede
>>> https://www.xsede.org/overview
>>> which site config should I use ?
>>>
>>>
>>> _______________________________________________
>>> Swift-user mailing list
>>> Swift-user at ci.uchicago.edu
>>> https://lists.ci.uchicago.edu/cgi-bin/mailman/listinfo/swift-user
>>>
>>
>>
>
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From hategan at mcs.anl.gov  Sat Sep 27 16:17:10 2014
From: hategan at mcs.anl.gov (Mihael Hategan)
Date: Sat, 27 Sep 2014 14:17:10 -0700
Subject: [Swift-user] question about xsede
In-Reply-To: <CABubRoB20KHEdAkgGtct5697o-rt_6SiEnabC-TOqvqARqRV_w@mail.gmail.com>
References: <CABubRoCXRJrYbbY1TaamFRj08NunyQhBu5vrXSt6YTta0vVNPQ@mail.gmail.com>
	<CAMUuviqoZaNiN3ADtX-h4PtTPfL8jZKkmVC=YPw=k=i9rt1fsQ@mail.gmail.com>
	<CABubRoAh3+j5MHtO18-X=MmCEho=2yLwKXnrNKtwOunmFKORdw@mail.gmail.com>
	<CABubRoB20KHEdAkgGtct5697o-rt_6SiEnabC-TOqvqARqRV_w@mail.gmail.com>
Message-ID: <1411852630.2517.1.camel@echo>

Hi Justin,

Is there a queue named "normal" on that machine (qstat -q should tell
you)?

Mihael

On Sat, 2014-09-27 at 15:41 -0400, Justin bbt wrote:
> So, I am using this config
> 
> 
> <pool handle="black">
>     <execution provider="coaster" jobmanager="local:pbs" URL="none"/>
>     <profile namespace="env"    key="PATHPREFIX">{env.PWD}/../app</profile>
>     <profile namespace="globus" key="jobsPerNode">1</profile>
>     <profile namespace="globus" key="queue">normal</profile>
> <profile namespace="globus"  key="ppn">16</profile>
>   <profile namespace="globus" key="maxWallTime">00:01:00</profile>
>     <profile namespace="globus" key="maxTime">3600</profile>
>     <profile namespace="globus" key="lowOverAllocation">100</profile>
>     <profile namespace="globus" key="highOverAllocation">100</profile>
>     <profile namespace="globus" key="slots">2</profile>
>     <profile namespace="globus" key="maxNodes">1</profile>
>     <profile namespace="globus" key="nodeGranularity">1</profile>
>     <profile namespace="karajan" key="jobThrottle">.320</profile>
>     <profile namespace="karajan" key="initialScore">10000</profile>
>   <profile namespace="globus" key="slots">1</profile>
>    <profile namespace="globus"  key="project">TG-CCR134513</profile>
>     <workdirectory>/brashear/usrname</workdirectory>
>       <profile namespace="swift" key="stagingMethod">local</profile>
> <filesystem provider="local" />
> </pool>
> 
> but, it does not work and give this error :
> 
> Swift 0.95 RC6 swift-r7900 cog-r3908
> RunID: run011
> Warning: The @ syntax for function invocation is deprecated
> [Error] sites.xml, line 2, col 10: cvc-elt.1: Cannot find the declaration
> of element 'config'.
> Progress: Sat, 27 Sep 2014 15:35:52-0400
> 
> Could not submit job (qsub reported an exit code of 170).
> qsub: Unknown queue MSG=cannot locate queue
> 
> Execution failed:
> Exception in simulate:
>     Arguments: [--timesteps, 1, --range, 100, --nvalues, 5]
>     Host: black
>     Directory: p4-run011/jobs/s/simulate-sdm041yl
> exception @ swift-int-staging.k, line: 181
> Caused by:
> exception @ swift-int-staging.k, line: 177
> Caused by: Block task failed: Error submitting block task
> org.globus.cog.abstraction.impl.common.task.TaskSubmissionException: Could
> not submit job (qsub reported an exit code of 170).
> qsub: Unknown queue MSG=cannot locate queue
> 
> at
> org.globus.cog.abstraction.impl.scheduler.common.AbstractJobSubmissionTaskHandler.submit(AbstractJobSubmissionTaskHandler.java:63)
> at
> org.globus.cog.abstraction.impl.common.AbstractTaskHandler.submit(AbstractTaskHandler.java:45)
> at
> org.globus.cog.abstraction.impl.common.task.ExecutionTaskHandler.submit(ExecutionTaskHandler.java:61)
> at
> org.globus.cog.abstraction.coaster.service.job.manager.BlockTaskSubmitter.run(BlockTaskSubmitter.java:70)
> Caused by:
> org.globus.cog.abstraction.impl.scheduler.common.ProcessException: Could
> not submit job (qsub reported an exit code of 170).
> qsub: Unknown queue MSG=cannot locate queue
> 
> at
> org.globus.cog.abstraction.impl.scheduler.common.AbstractExecutor.start(AbstractExecutor.java:113)
> at
> org.globus.cog.abstraction.impl.scheduler.common.AbstractJobSubmissionTaskHandler.submit(AbstractJobSubmissionTaskHandler.java:53)
> ... 3 more
> 
> 
> 
> also, in some configs I saw this. But I dont know what this is and what
> values should I set to
> 
>     <profile namespace="globus"
> key="providerAttributes">pbs.aprun;pbs.mpp;depth=32</profile>
> 
> 
> On Tue, Sep 23, 2014 at 6:22 PM, Justin bbt <justinbbt at gmail.com> wrote:
> 
> > Thank you very much.
> >
> > I am actually using the Blacklight, which I guess is PBS based.
> > So, should I use the Crays tutorial and setting ?
> > http://swift-lang.org/tutorials/cray/tutorial.html
> >
> > On Tue, Sep 23, 2014 at 10:31 AM, Ketan Maheshwari <ketan at mcs.anl.gov>
> > wrote:
> >
> >> Hi Justin,
> >>
> >> If you are using xsede Stampede regular nodes (non xeon phi), here is a
> >> site configuration that has worked for me in the past, connecting over ssh
> >> to slurm:
> >>
> >> <?xml version="1.0" encoding="UTF-8"?>
> >> <config xmlns="http://www.ci.uchicago.edu/swift/SwiftSites">
> >>  <pool handle="stampede">
> >>    <execution provider="coaster" jobmanager="ssh-cl:slurm" url="
> >> stampede.tacc.utexas.edu"/>
> >>    <filesystem provider="local" />
> >>    <profile namespace="globus"  key="jobsPerNode">1</profile>
> >>    <profile namespace="globus"  key="ppn">1</profile>
> >>    <profile namespace="globus"  key="maxTime">7500</profile>
> >>    <profile namespace="globus"  key="maxwalltime">00:10:00</profile>
> >>    <profile namespace="globus"  key="lowOverallocation">100</profile>
> >>    <profile namespace="globus"  key="highOverallocation">100</profile>
> >>    <profile namespace="globus"  key="queue">normal</profile>
> >>    <profile namespace="globus"  key="nodeGranularity">1</profile>
> >>    <profile namespace="globus"  key="maxNodes">1</profile>
> >>    <profile namespace="globus" key="slots">1</profile>
> >>    <profile namespace="globus"  key="project">TG-EAR130015</profile>
> >>    <profile namespace="karajan" key="jobThrottle">.3199</profile>
> >>    <profile namespace="karajan" key="initialScore">10000</profile>
> >>    <workdirectory>/tmp/{env.USER}/swift.work</workdirectory>
> >>   </pool>
> >> </config>
> >>
> >> You will need to replace project id with yours.
> >>
> >> Thanks,
> >> Ketan
> >>
> >> On Mon, Sep 22, 2014 at 8:32 PM, Justin bbt <justinbbt at gmail.com> wrote:
> >>
> >>> Hi
> >>>
> >>> If I want to use resources on the xsede
> >>> https://www.xsede.org/overview
> >>> which site config should I use ?
> >>>
> >>>
> >>> _______________________________________________
> >>> Swift-user mailing list
> >>> Swift-user at ci.uchicago.edu
> >>> https://lists.ci.uchicago.edu/cgi-bin/mailman/listinfo/swift-user
> >>>
> >>
> >>
> >
> _______________________________________________
> Swift-user mailing list
> Swift-user at ci.uchicago.edu
> https://lists.ci.uchicago.edu/cgi-bin/mailman/listinfo/swift-user




From justinbbt at gmail.com  Sun Sep 28 18:03:19 2014
From: justinbbt at gmail.com (Justin bbt)
Date: Sun, 28 Sep 2014 19:03:19 -0400
Subject: [Swift-user] question about xsede
In-Reply-To: <1411852630.2517.1.camel@echo>
References: <CABubRoCXRJrYbbY1TaamFRj08NunyQhBu5vrXSt6YTta0vVNPQ@mail.gmail.com>
	<CAMUuviqoZaNiN3ADtX-h4PtTPfL8jZKkmVC=YPw=k=i9rt1fsQ@mail.gmail.com>
	<CABubRoAh3+j5MHtO18-X=MmCEho=2yLwKXnrNKtwOunmFKORdw@mail.gmail.com>
	<CABubRoB20KHEdAkgGtct5697o-rt_6SiEnabC-TOqvqARqRV_w@mail.gmail.com>
	<1411852630.2517.1.camel@echo>
Message-ID: <CABubRoAygNQTA2D92szo-UkD=ruhwSfafiAuDm4v4eXRK9Y5dA@mail.gmail.com>

changing the queue to "batch", I get this
Execution failed:
Exception in simulate:
    Arguments: [--timesteps, 1, --range, 100, --nvalues, 5]
    Host: black
    Directory: p4-run026/jobs/5/simulate-58d6x2yl
exception @ swift-int-staging.k, line: 181
Caused by:
exception @ swift-int-staging.k, line: 177
Caused by: null
Caused by: org.globus.cog.abstraction.impl.common.execution.JobException:
Job failed with an exit code of 1

????

On Sat, Sep 27, 2014 at 5:17 PM, Mihael Hategan <hategan at mcs.anl.gov> wrote:

> Hi Justin,
>
> Is there a queue named "normal" on that machine (qstat -q should tell
> you)?
>
> Mihael
>
> On Sat, 2014-09-27 at 15:41 -0400, Justin bbt wrote:
> > So, I am using this config
> >
> >
> > <pool handle="black">
> >     <execution provider="coaster" jobmanager="local:pbs" URL="none"/>
> >     <profile namespace="env"
> key="PATHPREFIX">{env.PWD}/../app</profile>
> >     <profile namespace="globus" key="jobsPerNode">1</profile>
> >     <profile namespace="globus" key="queue">normal</profile>
> > <profile namespace="globus"  key="ppn">16</profile>
> >   <profile namespace="globus" key="maxWallTime">00:01:00</profile>
> >     <profile namespace="globus" key="maxTime">3600</profile>
> >     <profile namespace="globus" key="lowOverAllocation">100</profile>
> >     <profile namespace="globus" key="highOverAllocation">100</profile>
> >     <profile namespace="globus" key="slots">2</profile>
> >     <profile namespace="globus" key="maxNodes">1</profile>
> >     <profile namespace="globus" key="nodeGranularity">1</profile>
> >     <profile namespace="karajan" key="jobThrottle">.320</profile>
> >     <profile namespace="karajan" key="initialScore">10000</profile>
> >   <profile namespace="globus" key="slots">1</profile>
> >    <profile namespace="globus"  key="project">TG-CCR134513</profile>
> >     <workdirectory>/brashear/usrname</workdirectory>
> >       <profile namespace="swift" key="stagingMethod">local</profile>
> > <filesystem provider="local" />
> > </pool>
> >
> > but, it does not work and give this error :
> >
> > Swift 0.95 RC6 swift-r7900 cog-r3908
> > RunID: run011
> > Warning: The @ syntax for function invocation is deprecated
> > [Error] sites.xml, line 2, col 10: cvc-elt.1: Cannot find the declaration
> > of element 'config'.
> > Progress: Sat, 27 Sep 2014 15:35:52-0400
> >
> > Could not submit job (qsub reported an exit code of 170).
> > qsub: Unknown queue MSG=cannot locate queue
> >
> > Execution failed:
> > Exception in simulate:
> >     Arguments: [--timesteps, 1, --range, 100, --nvalues, 5]
> >     Host: black
> >     Directory: p4-run011/jobs/s/simulate-sdm041yl
> > exception @ swift-int-staging.k, line: 181
> > Caused by:
> > exception @ swift-int-staging.k, line: 177
> > Caused by: Block task failed: Error submitting block task
> > org.globus.cog.abstraction.impl.common.task.TaskSubmissionException:
> Could
> > not submit job (qsub reported an exit code of 170).
> > qsub: Unknown queue MSG=cannot locate queue
> >
> > at
> >
> org.globus.cog.abstraction.impl.scheduler.common.AbstractJobSubmissionTaskHandler.submit(AbstractJobSubmissionTaskHandler.java:63)
> > at
> >
> org.globus.cog.abstraction.impl.common.AbstractTaskHandler.submit(AbstractTaskHandler.java:45)
> > at
> >
> org.globus.cog.abstraction.impl.common.task.ExecutionTaskHandler.submit(ExecutionTaskHandler.java:61)
> > at
> >
> org.globus.cog.abstraction.coaster.service.job.manager.BlockTaskSubmitter.run(BlockTaskSubmitter.java:70)
> > Caused by:
> > org.globus.cog.abstraction.impl.scheduler.common.ProcessException: Could
> > not submit job (qsub reported an exit code of 170).
> > qsub: Unknown queue MSG=cannot locate queue
> >
> > at
> >
> org.globus.cog.abstraction.impl.scheduler.common.AbstractExecutor.start(AbstractExecutor.java:113)
> > at
> >
> org.globus.cog.abstraction.impl.scheduler.common.AbstractJobSubmissionTaskHandler.submit(AbstractJobSubmissionTaskHandler.java:53)
> > ... 3 more
> >
> >
> >
> > also, in some configs I saw this. But I dont know what this is and what
> > values should I set to
> >
> >     <profile namespace="globus"
> > key="providerAttributes">pbs.aprun;pbs.mpp;depth=32</profile>
> >
> >
> > On Tue, Sep 23, 2014 at 6:22 PM, Justin bbt <justinbbt at gmail.com> wrote:
> >
> > > Thank you very much.
> > >
> > > I am actually using the Blacklight, which I guess is PBS based.
> > > So, should I use the Crays tutorial and setting ?
> > > http://swift-lang.org/tutorials/cray/tutorial.html
> > >
> > > On Tue, Sep 23, 2014 at 10:31 AM, Ketan Maheshwari <ketan at mcs.anl.gov>
> > > wrote:
> > >
> > >> Hi Justin,
> > >>
> > >> If you are using xsede Stampede regular nodes (non xeon phi), here is
> a
> > >> site configuration that has worked for me in the past, connecting
> over ssh
> > >> to slurm:
> > >>
> > >> <?xml version="1.0" encoding="UTF-8"?>
> > >> <config xmlns="http://www.ci.uchicago.edu/swift/SwiftSites">
> > >>  <pool handle="stampede">
> > >>    <execution provider="coaster" jobmanager="ssh-cl:slurm" url="
> > >> stampede.tacc.utexas.edu"/>
> > >>    <filesystem provider="local" />
> > >>    <profile namespace="globus"  key="jobsPerNode">1</profile>
> > >>    <profile namespace="globus"  key="ppn">1</profile>
> > >>    <profile namespace="globus"  key="maxTime">7500</profile>
> > >>    <profile namespace="globus"  key="maxwalltime">00:10:00</profile>
> > >>    <profile namespace="globus"  key="lowOverallocation">100</profile>
> > >>    <profile namespace="globus"  key="highOverallocation">100</profile>
> > >>    <profile namespace="globus"  key="queue">normal</profile>
> > >>    <profile namespace="globus"  key="nodeGranularity">1</profile>
> > >>    <profile namespace="globus"  key="maxNodes">1</profile>
> > >>    <profile namespace="globus" key="slots">1</profile>
> > >>    <profile namespace="globus"  key="project">TG-EAR130015</profile>
> > >>    <profile namespace="karajan" key="jobThrottle">.3199</profile>
> > >>    <profile namespace="karajan" key="initialScore">10000</profile>
> > >>    <workdirectory>/tmp/{env.USER}/swift.work</workdirectory>
> > >>   </pool>
> > >> </config>
> > >>
> > >> You will need to replace project id with yours.
> > >>
> > >> Thanks,
> > >> Ketan
> > >>
> > >> On Mon, Sep 22, 2014 at 8:32 PM, Justin bbt <justinbbt at gmail.com>
> wrote:
> > >>
> > >>> Hi
> > >>>
> > >>> If I want to use resources on the xsede
> > >>> https://www.xsede.org/overview
> > >>> which site config should I use ?
> > >>>
> > >>>
> > >>> _______________________________________________
> > >>> Swift-user mailing list
> > >>> Swift-user at ci.uchicago.edu
> > >>> https://lists.ci.uchicago.edu/cgi-bin/mailman/listinfo/swift-user
> > >>>
> > >>
> > >>
> > >
> > _______________________________________________
> > Swift-user mailing list
> > Swift-user at ci.uchicago.edu
> > https://lists.ci.uchicago.edu/cgi-bin/mailman/listinfo/swift-user
>
>
>
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From wilde at anl.gov  Mon Sep 29 09:24:23 2014
From: wilde at anl.gov (Michael Wilde)
Date: Mon, 29 Sep 2014 09:24:23 -0500
Subject: [Swift-user] question about xsede
In-Reply-To: <CABubRoAygNQTA2D92szo-UkD=ruhwSfafiAuDm4v4eXRK9Y5dA@mail.gmail.com>
References: <CABubRoCXRJrYbbY1TaamFRj08NunyQhBu5vrXSt6YTta0vVNPQ@mail.gmail.com>	<CAMUuviqoZaNiN3ADtX-h4PtTPfL8jZKkmVC=YPw=k=i9rt1fsQ@mail.gmail.com>	<CABubRoAh3+j5MHtO18-X=MmCEho=2yLwKXnrNKtwOunmFKORdw@mail.gmail.com>	<CABubRoB20KHEdAkgGtct5697o-rt_6SiEnabC-TOqvqARqRV_w@mail.gmail.com>	<1411852630.2517.1.camel@echo>
	<CABubRoAygNQTA2D92szo-UkD=ruhwSfafiAuDm4v4eXRK9Y5dA@mail.gmail.com>
Message-ID: <54296B97.6060506@anl.gov>

Justin, in your sites entry below, this line looks suspect:

<workdirectory>/brashear/usrname</workdirectory>

That needs to be the name of a writable directory.

- Mike


On 9/28/14, 6:03 PM, Justin bbt wrote:
> changing the queue to "batch", I get this
> Execution failed:
> Exception in simulate:
>     Arguments: [--timesteps, 1, --range, 100, --nvalues, 5]
>     Host: black
>   Directory: p4-run026/jobs/5/simulate-58d6x2yl
> exception @ swift-int-staging.k, line: 181
> Caused by:
> exception @ swift-int-staging.k, line: 177
> Caused by: null
> Caused by: 
> org.globus.cog.abstraction.impl.common.execution.JobException: Job 
> failed with an exit code of 1
>
> ????
>
> On Sat, Sep 27, 2014 at 5:17 PM, Mihael Hategan <hategan at mcs.anl.gov 
> <mailto:hategan at mcs.anl.gov>> wrote:
>
>     Hi Justin,
>
>     Is there a queue named "normal" on that machine (qstat -q should tell
>     you)?
>
>     Mihael
>
>     On Sat, 2014-09-27 at 15:41 -0400, Justin bbt wrote:
>     > So, I am using this config
>     >
>     >
>     > <pool handle="black">
>     >     <execution provider="coaster" jobmanager="local:pbs"
>     URL="none"/>
>     >     <profile namespace="env"
>     key="PATHPREFIX">{env.PWD}/../app</profile>
>     >     <profile namespace="globus" key="jobsPerNode">1</profile>
>     >     <profile namespace="globus" key="queue">normal</profile>
>     > <profile namespace="globus" key="ppn">16</profile>
>     >   <profile namespace="globus" key="maxWallTime">00:01:00</profile>
>     >     <profile namespace="globus" key="maxTime">3600</profile>
>     >     <profile namespace="globus"
>     key="lowOverAllocation">100</profile>
>     >     <profile namespace="globus"
>     key="highOverAllocation">100</profile>
>     >     <profile namespace="globus" key="slots">2</profile>
>     >     <profile namespace="globus" key="maxNodes">1</profile>
>     >     <profile namespace="globus" key="nodeGranularity">1</profile>
>     >     <profile namespace="karajan" key="jobThrottle">.320</profile>
>     >     <profile namespace="karajan" key="initialScore">10000</profile>
>     >   <profile namespace="globus" key="slots">1</profile>
>     >    <profile namespace="globus" key="project">TG-CCR134513</profile>
>     >  <workdirectory>/brashear/usrname</workdirectory>
>     >       <profile namespace="swift" key="stagingMethod">local</profile>
>     > <filesystem provider="local" />
>     > </pool>
>     >
>     > but, it does not work and give this error :
>     >
>     > Swift 0.95 RC6 swift-r7900 cog-r3908
>     > RunID: run011
>     > Warning: The @ syntax for function invocation is deprecated
>     > [Error] sites.xml, line 2, col 10: cvc-elt.1: Cannot find the
>     declaration
>     > of element 'config'.
>     > Progress: Sat, 27 Sep 2014 15:35:52-0400
>     >
>     > Could not submit job (qsub reported an exit code of 170).
>     > qsub: Unknown queue MSG=cannot locate queue
>     >
>     > Execution failed:
>     > Exception in simulate:
>     >     Arguments: [--timesteps, 1, --range, 100, --nvalues, 5]
>     >     Host: black
>     >     Directory: p4-run011/jobs/s/simulate-sdm041yl
>     > exception @ swift-int-staging.k, line: 181
>     > Caused by:
>     > exception @ swift-int-staging.k, line: 177
>     > Caused by: Block task failed: Error submitting block task
>     >
>     org.globus.cog.abstraction.impl.common.task.TaskSubmissionException:
>     Could
>     > not submit job (qsub reported an exit code of 170).
>     > qsub: Unknown queue MSG=cannot locate queue
>     >
>     > at
>     >
>     org.globus.cog.abstraction.impl.scheduler.common.AbstractJobSubmissionTaskHandler.submit(AbstractJobSubmissionTaskHandler.java:63)
>     > at
>     >
>     org.globus.cog.abstraction.impl.common.AbstractTaskHandler.submit(AbstractTaskHandler.java:45)
>     > at
>     >
>     org.globus.cog.abstraction.impl.common.task.ExecutionTaskHandler.submit(ExecutionTaskHandler.java:61)
>     > at
>     >
>     org.globus.cog.abstraction.coaster.service.job.manager.BlockTaskSubmitter.run(BlockTaskSubmitter.java:70)
>     > Caused by:
>     >
>     org.globus.cog.abstraction.impl.scheduler.common.ProcessException:
>     Could
>     > not submit job (qsub reported an exit code of 170).
>     > qsub: Unknown queue MSG=cannot locate queue
>     >
>     > at
>     >
>     org.globus.cog.abstraction.impl.scheduler.common.AbstractExecutor.start(AbstractExecutor.java:113)
>     > at
>     >
>     org.globus.cog.abstraction.impl.scheduler.common.AbstractJobSubmissionTaskHandler.submit(AbstractJobSubmissionTaskHandler.java:53)
>     > ... 3 more
>     >
>     >
>     >
>     > also, in some configs I saw this. But I dont know what this is
>     and what
>     > values should I set to
>     >
>     >     <profile namespace="globus"
>     > key="providerAttributes">pbs.aprun;pbs.mpp;depth=32</profile>
>     >
>     >
>     > On Tue, Sep 23, 2014 at 6:22 PM, Justin bbt <justinbbt at gmail.com
>     <mailto:justinbbt at gmail.com>> wrote:
>     >
>     > > Thank you very much.
>     > >
>     > > I am actually using the Blacklight, which I guess is PBS based.
>     > > So, should I use the Crays tutorial and setting ?
>     > > http://swift-lang.org/tutorials/cray/tutorial.html
>     > >
>     > > On Tue, Sep 23, 2014 at 10:31 AM, Ketan Maheshwari
>     <ketan at mcs.anl.gov <mailto:ketan at mcs.anl.gov>>
>     > > wrote:
>     > >
>     > >> Hi Justin,
>     > >>
>     > >> If you are using xsede Stampede regular nodes (non xeon phi),
>     here is a
>     > >> site configuration that has worked for me in the past,
>     connecting over ssh
>     > >> to slurm:
>     > >>
>     > >> <?xml version="1.0" encoding="UTF-8"?>
>     > >> <config xmlns="http://www.ci.uchicago.edu/swift/SwiftSites">
>     > >>  <pool handle="stampede">
>     > >>    <execution provider="coaster" jobmanager="ssh-cl:slurm" url="
>     > >> stampede.tacc.utexas.edu <http://stampede.tacc.utexas.edu>"/>
>     > >>    <filesystem provider="local" />
>     > >>    <profile namespace="globus" key="jobsPerNode">1</profile>
>     > >>    <profile namespace="globus" key="ppn">1</profile>
>     > >>    <profile namespace="globus" key="maxTime">7500</profile>
>     > >>    <profile namespace="globus"
>     key="maxwalltime">00:10:00</profile>
>     > >>    <profile namespace="globus"
>     key="lowOverallocation">100</profile>
>     > >>    <profile namespace="globus"
>     key="highOverallocation">100</profile>
>     > >>    <profile namespace="globus" key="queue">normal</profile>
>     > >>    <profile namespace="globus" key="nodeGranularity">1</profile>
>     > >>    <profile namespace="globus" key="maxNodes">1</profile>
>     > >>    <profile namespace="globus" key="slots">1</profile>
>     > >>    <profile namespace="globus"
>     key="project">TG-EAR130015</profile>
>     > >>    <profile namespace="karajan" key="jobThrottle">.3199</profile>
>     > >>    <profile namespace="karajan"
>     key="initialScore">10000</profile>
>     > >> <workdirectory>/tmp/{env.USER}/swift.work</workdirectory>
>     > >>   </pool>
>     > >> </config>
>     > >>
>     > >> You will need to replace project id with yours.
>     > >>
>     > >> Thanks,
>     > >> Ketan
>     > >>
>     > >> On Mon, Sep 22, 2014 at 8:32 PM, Justin bbt
>     <justinbbt at gmail.com <mailto:justinbbt at gmail.com>> wrote:
>     > >>
>     > >>> Hi
>     > >>>
>     > >>> If I want to use resources on the xsede
>     > >>> https://www.xsede.org/overview
>     > >>> which site config should I use ?
>     > >>>
>     > >>>
>     > >>> _______________________________________________
>     > >>> Swift-user mailing list
>     > >>> Swift-user at ci.uchicago.edu <mailto:Swift-user at ci.uchicago.edu>
>     > >>>
>     https://lists.ci.uchicago.edu/cgi-bin/mailman/listinfo/swift-user
>     > >>>
>     > >>
>     > >>
>     > >
>     > _______________________________________________
>     > Swift-user mailing list
>     > Swift-user at ci.uchicago.edu <mailto:Swift-user at ci.uchicago.edu>
>     > https://lists.ci.uchicago.edu/cgi-bin/mailman/listinfo/swift-user
>
>
>
>
>
> _______________________________________________
> Swift-user mailing list
> Swift-user at ci.uchicago.edu
> https://lists.ci.uchicago.edu/cgi-bin/mailman/listinfo/swift-user

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

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From wilde at anl.gov  Mon Sep 29 12:23:04 2014
From: wilde at anl.gov (Michael Wilde)
Date: Mon, 29 Sep 2014 12:23:04 -0500
Subject: [Swift-user] question about xsede
In-Reply-To: <54296B97.6060506@anl.gov>
References: <CABubRoCXRJrYbbY1TaamFRj08NunyQhBu5vrXSt6YTta0vVNPQ@mail.gmail.com>	<CAMUuviqoZaNiN3ADtX-h4PtTPfL8jZKkmVC=YPw=k=i9rt1fsQ@mail.gmail.com>	<CABubRoAh3+j5MHtO18-X=MmCEho=2yLwKXnrNKtwOunmFKORdw@mail.gmail.com>	<CABubRoB20KHEdAkgGtct5697o-rt_6SiEnabC-TOqvqARqRV_w@mail.gmail.com>	<1411852630.2517.1.camel@echo>
	<CABubRoAygNQTA2D92szo-UkD=ruhwSfafiAuDm4v4eXRK9Y5dA@mail.gmail.com>
	<54296B97.6060506@anl.gov>
Message-ID: <54299578.5000301@anl.gov>

Justin, I see that Yadu provided tested configurations for running with 
Swift 0.94.1, 0.95RC7, and trunk, in his email to this list on 9/25 
(pasted below).

He pointed you to this directory for a sites.xml example for 0.94 and 0.95:
http://users.rcc.uchicago.edu/~yadunand/blacklight-sanity/0.94configs/sites.xml

The config he provided for 0.94.1 should also work for 0.95RC6 (which I 
see you are using)

(Note that we will be posting an 0.95 final release, or an RC7, by the 
end of this week).

Based on this discussion so far, I think the following is a good base 
for a sites entry for running on Blacklight:

<configxmlns="http://www.ci.uchicago.edu/swift/SwiftSites">
<poolhandle="blacklight">
<executionprovider="coaster"jobmanager="local:pbs"/>
<profilenamespace="globus"key="queue">debug</profile>
<profile namespace="karajan" key="jobThrottle">.320</profile>
<profilenamespace="karajan"key="initialScore">10000</profile>
<profilenamespace="globus"key="jobsPerNode">16</profile>
<profilenamespace="globus"key="maxtime">900</profile>
<profilenamespace="globus"key="maxwalltime">00:10:00</profile>
<profilenamespace="globus"key="ppn">16</profile>
<workdirectory>/usr/users/8/yadunand/swiftwork</workdirectory>
<filesystemprovider="local"/>
</pool>
</config>

for the "queue" tag, use either debug or batch.

for the "workdirectory" tag, specify a fully qualified directory 
pathname that you can write/create in. Note that you might have a 
different $HOME "users/N" dir than Yadu's.

Please double check the latest code at the link Yadu provided, to make 
sure I did not get anything wrong, above.

Regards,

- Mike


-------- Original Message --------
Subject: 	Re: [Swift-user] question about xsede
Date: 	Thu, 25 Sep 2014 17:25:01 -0500
From: 	Yadu Nand <yadudoc1729 at gmail.com>
To: 	Michael Wilde <wilde at anl.gov>
CC: 	Swift User <swift-user at ci.uchicago.edu>



Hi Justin,

Here are some tested configs and a small README from running the sanity 
test on Blacklight:
http://users.rcc.uchicago.edu/~yadunand/blacklight-sanity/ 
<http://users.rcc.uchicago.edu/%7Eyadunand/blacklight-sanity/>

There's an example each of configs for Swift 0.94, Swift 0.95 and the 
configs we would use going
forward (Swift 0.96 and current trunk) in that folder.

In the example, I've used ppn=16 (or any multiple of 16) which seems to 
work as a substitute for ncpus.

Hope that helps!

-Yadu


On 9/29/14, 9:24 AM, Michael Wilde wrote:
> Justin, in your sites entry below, this line looks suspect:
>
> <workdirectory>/brashear/usrname</workdirectory>
>
> That needs to be the name of a writable directory.
>
> - Mike
>
>
> On 9/28/14, 6:03 PM, Justin bbt wrote:
>> changing the queue to "batch", I get this
>> Execution failed:
>> Exception in simulate:
>>     Arguments: [--timesteps, 1, --range, 100, --nvalues, 5]
>>     Host: black
>>   Directory: p4-run026/jobs/5/simulate-58d6x2yl
>> exception @ swift-int-staging.k, line: 181
>> Caused by:
>> exception @ swift-int-staging.k, line: 177
>> Caused by: null
>> Caused by: 
>> org.globus.cog.abstraction.impl.common.execution.JobException: Job 
>> failed with an exit code of 1
>>
>> ????
>>
>> On Sat, Sep 27, 2014 at 5:17 PM, Mihael Hategan <hategan at mcs.anl.gov 
>> <mailto:hategan at mcs.anl.gov>> wrote:
>>
>>     Hi Justin,
>>
>>     Is there a queue named "normal" on that machine (qstat -q should tell
>>     you)?
>>
>>     Mihael
>>
>>     On Sat, 2014-09-27 at 15:41 -0400, Justin bbt wrote:
>>     > So, I am using this config
>>     >
>>     >
>>     > <pool handle="black">
>>     >     <execution provider="coaster" jobmanager="local:pbs"
>>     URL="none"/>
>>     >     <profile namespace="env"
>>     key="PATHPREFIX">{env.PWD}/../app</profile>
>>     >     <profile namespace="globus" key="jobsPerNode">1</profile>
>>     >     <profile namespace="globus" key="queue">normal</profile>
>>     > <profile namespace="globus" key="ppn">16</profile>
>>     >   <profile namespace="globus" key="maxWallTime">00:01:00</profile>
>>     >     <profile namespace="globus" key="maxTime">3600</profile>
>>     >     <profile namespace="globus"
>>     key="lowOverAllocation">100</profile>
>>     >     <profile namespace="globus"
>>     key="highOverAllocation">100</profile>
>>     >     <profile namespace="globus" key="slots">2</profile>
>>     >     <profile namespace="globus" key="maxNodes">1</profile>
>>     >     <profile namespace="globus" key="nodeGranularity">1</profile>
>>     >     <profile namespace="karajan" key="jobThrottle">.320</profile>
>>     >     <profile namespace="karajan" key="initialScore">10000</profile>
>>     >   <profile namespace="globus" key="slots">1</profile>
>>     >    <profile namespace="globus" key="project">TG-CCR134513</profile>
>>     >  <workdirectory>/brashear/usrname</workdirectory>
>>     >       <profile namespace="swift"
>>     key="stagingMethod">local</profile>
>>     > <filesystem provider="local" />
>>     > </pool>
>>     >
>>     > but, it does not work and give this error :
>>     >
>>     > Swift 0.95 RC6 swift-r7900 cog-r3908
>>     > RunID: run011
>>     > Warning: The @ syntax for function invocation is deprecated
>>     > [Error] sites.xml, line 2, col 10: cvc-elt.1: Cannot find the
>>     declaration
>>     > of element 'config'.
>>     > Progress: Sat, 27 Sep 2014 15:35:52-0400
>>     >
>>     > Could not submit job (qsub reported an exit code of 170).
>>     > qsub: Unknown queue MSG=cannot locate queue
>>     >
>>     > Execution failed:
>>     > Exception in simulate:
>>     >     Arguments: [--timesteps, 1, --range, 100, --nvalues, 5]
>>     >     Host: black
>>     >     Directory: p4-run011/jobs/s/simulate-sdm041yl
>>     > exception @ swift-int-staging.k, line: 181
>>     > Caused by:
>>     > exception @ swift-int-staging.k, line: 177
>>     > Caused by: Block task failed: Error submitting block task
>>     >
>>     org.globus.cog.abstraction.impl.common.task.TaskSubmissionException:
>>     Could
>>     > not submit job (qsub reported an exit code of 170).
>>     > qsub: Unknown queue MSG=cannot locate queue
>>     >
>>     > at
>>     >
>>     org.globus.cog.abstraction.impl.scheduler.common.AbstractJobSubmissionTaskHandler.submit(AbstractJobSubmissionTaskHandler.java:63)
>>     > at
>>     >
>>     org.globus.cog.abstraction.impl.common.AbstractTaskHandler.submit(AbstractTaskHandler.java:45)
>>     > at
>>     >
>>     org.globus.cog.abstraction.impl.common.task.ExecutionTaskHandler.submit(ExecutionTaskHandler.java:61)
>>     > at
>>     >
>>     org.globus.cog.abstraction.coaster.service.job.manager.BlockTaskSubmitter.run(BlockTaskSubmitter.java:70)
>>     > Caused by:
>>     >
>>     org.globus.cog.abstraction.impl.scheduler.common.ProcessException: Could
>>     > not submit job (qsub reported an exit code of 170).
>>     > qsub: Unknown queue MSG=cannot locate queue
>>     >
>>     > at
>>     >
>>     org.globus.cog.abstraction.impl.scheduler.common.AbstractExecutor.start(AbstractExecutor.java:113)
>>     > at
>>     >
>>     org.globus.cog.abstraction.impl.scheduler.common.AbstractJobSubmissionTaskHandler.submit(AbstractJobSubmissionTaskHandler.java:53)
>>     > ... 3 more
>>     >
>>     >
>>     >
>>     > also, in some configs I saw this. But I dont know what this is
>>     and what
>>     > values should I set to
>>     >
>>     >     <profile namespace="globus"
>>     > key="providerAttributes">pbs.aprun;pbs.mpp;depth=32</profile>
>>     >
>>     >
>>     > On Tue, Sep 23, 2014 at 6:22 PM, Justin bbt
>>     <justinbbt at gmail.com <mailto:justinbbt at gmail.com>> wrote:
>>     >
>>     > > Thank you very much.
>>     > >
>>     > > I am actually using the Blacklight, which I guess is PBS based.
>>     > > So, should I use the Crays tutorial and setting ?
>>     > > http://swift-lang.org/tutorials/cray/tutorial.html
>>     > >
>>     > > On Tue, Sep 23, 2014 at 10:31 AM, Ketan Maheshwari
>>     <ketan at mcs.anl.gov <mailto:ketan at mcs.anl.gov>>
>>     > > wrote:
>>     > >
>>     > >> Hi Justin,
>>     > >>
>>     > >> If you are using xsede Stampede regular nodes (non xeon
>>     phi), here is a
>>     > >> site configuration that has worked for me in the past,
>>     connecting over ssh
>>     > >> to slurm:
>>     > >>
>>     > >> <?xml version="1.0" encoding="UTF-8"?>
>>     > >> <config xmlns="http://www.ci.uchicago.edu/swift/SwiftSites">
>>     > >>  <pool handle="stampede">
>>     > >>    <execution provider="coaster" jobmanager="ssh-cl:slurm" url="
>>     > >> stampede.tacc.utexas.edu <http://stampede.tacc.utexas.edu>"/>
>>     > >>    <filesystem provider="local" />
>>     > >>    <profile namespace="globus" key="jobsPerNode">1</profile>
>>     > >>    <profile namespace="globus" key="ppn">1</profile>
>>     > >>    <profile namespace="globus" key="maxTime">7500</profile>
>>     > >>    <profile namespace="globus"
>>     key="maxwalltime">00:10:00</profile>
>>     > >>    <profile namespace="globus"
>>     key="lowOverallocation">100</profile>
>>     > >>    <profile namespace="globus"
>>     key="highOverallocation">100</profile>
>>     > >>    <profile namespace="globus" key="queue">normal</profile>
>>     > >>    <profile namespace="globus" key="nodeGranularity">1</profile>
>>     > >>    <profile namespace="globus" key="maxNodes">1</profile>
>>     > >>    <profile namespace="globus" key="slots">1</profile>
>>     > >>    <profile namespace="globus"
>>     key="project">TG-EAR130015</profile>
>>     > >>    <profile namespace="karajan"
>>     key="jobThrottle">.3199</profile>
>>     > >>    <profile namespace="karajan"
>>     key="initialScore">10000</profile>
>>     > >> <workdirectory>/tmp/{env.USER}/swift.work</workdirectory>
>>     > >>   </pool>
>>     > >> </config>
>>     > >>
>>     > >> You will need to replace project id with yours.
>>     > >>
>>     > >> Thanks,
>>     > >> Ketan
>>     > >>
>>     > >> On Mon, Sep 22, 2014 at 8:32 PM, Justin bbt
>>     <justinbbt at gmail.com <mailto:justinbbt at gmail.com>> wrote:
>>     > >>
>>     > >>> Hi
>>     > >>>
>>     > >>> If I want to use resources on the xsede
>>     > >>> https://www.xsede.org/overview
>>     > >>> which site config should I use ?
>>     > >>>
>>     > >>>
>>     > >>> _______________________________________________
>>     > >>> Swift-user mailing list
>>     > >>> Swift-user at ci.uchicago.edu <mailto:Swift-user at ci.uchicago.edu>
>>     > >>>
>>     https://lists.ci.uchicago.edu/cgi-bin/mailman/listinfo/swift-user
>>     > >>>
>>     > >>
>>     > >>
>>     > >
>>     > _______________________________________________
>>     > Swift-user mailing list
>>     > Swift-user at ci.uchicago.edu <mailto:Swift-user at ci.uchicago.edu>
>>     > https://lists.ci.uchicago.edu/cgi-bin/mailman/listinfo/swift-user
>>
>>
>>
>>
>>
>> _______________________________________________
>> Swift-user mailing list
>> Swift-user at ci.uchicago.edu
>> https://lists.ci.uchicago.edu/cgi-bin/mailman/listinfo/swift-user
>
> -- 
> Michael Wilde
> Mathematics and Computer Science          Computation Institute
> Argonne National Laboratory               The University of Chicago

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

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