[Swift-devel] Re: catsn on beagle

Jonathan S Monette jonmon at utexas.edu
Sat Jun 4 13:12:11 CDT 2011 

Ok.  Thanks.  and the (none) also appeared when I was on
login1.beagle.ci.uchicago.edu.  Thanks Ketan.

On Sat, Jun 4, 2011 at 1:09 PM, ketan <ketancmaheshwari at gmail.com> wrote:

>  Yes, you should bring this to the attention of beagle sysadmins.
>
>
> On 6/4/11 1:01 PM, Jonathan S Monette wrote:
>
> Ok.  I have my job submitted and it is currently waiting in the queue.
>  besides manually resetting this variable everytime I am on beagle what else
> can be done?  Is this something that I should bring to the attention of the
> sys admins for beagle?
>
> On Sat, Jun 4, 2011 at 12:51 PM, Ketan Maheshwari <
> ketancmaheshwari at gmail.com> wrote:
>
>> Alright, so this is the issue. GLOBUS_HOSTNAME is picked up from HOSTNAME
>> and I do not know where does this none comes in your case.
>>
>> In my case I get hostname: login2.beagle.ci.uchicago.edu
>>
>> see if you can manually change this env variable and try to run again.
>>
>>
>> On Sat, Jun 4, 2011 at 12:49 PM, Jonathan S Monette <jonmon at utexas.edu>wrote:
>>
>>> login2.beagle.ci.uchicago.edu.(none)
>>>
>>>  when you ran your test was in on login1 or login2?
>>>
>>>
>>> On Sat, Jun 4, 2011 at 12:47 PM, Ketan Maheshwari <
>>> ketancmaheshwari at gmail.com> wrote:
>>>
>>>> What does
>>>>
>>>> echo $HOSTNAME give?
>>>>
>>>>
>>>> On Sat, Jun 4, 2011 at 12:44 PM, Jonathan S Monette <jonmon at utexas.edu>wrote:
>>>>
>>>>> I am not sure why that (none) appears.  Is this a variable that the
>>>>> system sets or do I need to set it?
>>>>>
>>>>>
>>>>> On Sat, Jun 4, 2011 at 12:39 PM, Ketan Maheshwari <
>>>>> ketancmaheshwari at gmail.com> wrote:
>>>>>
>>>>>> This suprises me because, I do not see that (none) in my commandline.
>>>>>>
>>>>>>
>>>>>>  On Sat, Jun 4, 2011 at 12:38 PM, Jonathan S Monette <
>>>>>> jonmon at utexas.edu> wrote:
>>>>>>
>>>>>>> I added
>>>>>>> echo ${OPTIONS}
>>>>>>>     echo ${COG_OPTS}
>>>>>>>     echo ${LOCALCLASSPATH}
>>>>>>>     echo ${EXEC}
>>>>>>>     echo ${CMDLINE}
>>>>>>>
>>>>>>>  to the script.  It seems in the $OPTIONS variable this appears.
>>>>>>>
>>>>>>>  -Xmx8192M
>>>>>>> -Djava.endorsed.dirs=/home/jonmon/Library/Swift/swift-0.92/bin/../lib/endorsed
>>>>>>> -DUID=1881 -DGLOBUS_HOSTNAME=login2.beagle.ci.uchicago.edu.(none)
>>>>>>> -DCOG_INSTALL_PATH=/home/jonmon/Library/Swift/swift-0.92/bin/..
>>>>>>> -Dswift.home=/home/jonmon/Library/Swift/swift-0.92/bin/..
>>>>>>> -Djava.security.egd=file:///dev/urandom
>>>>>>>
>>>>>>>  There is the line
>>>>>>> DGLOBUS_HOSTNAME=login2.beagle.ci.uchicago.edu.(none)  I believe that is the
>>>>>>> parenthesis that is causing this to fail.  Now How do I fix it.
>>>>>>>
>>>>>>> On Sat, Jun 4, 2011 at 12:36 PM, Jonathan S Monette <
>>>>>>> jonmon at utexas.edu> wrote:
>>>>>>>
>>>>>>>> I may have found the error.  I download 0.92 binaries and changed
>>>>>>>> the swift command script.  I added
>>>>>>>>
>>>>>>>>
>>>>>>>> On Sat, Jun 4, 2011 at 12:26 PM, Jonathan S Monette <
>>>>>>>> jonmon at utexas.edu> wrote:
>>>>>>>>
>>>>>>>>> Same result. Same error
>>>>>>>>>
>>>>>>>>>
>>>>>>>>> On Sat, Jun 4, 2011 at 12:24 PM, ketan <ketancmaheshwari at gmail.com
>>>>>>>>> > wrote:
>>>>>>>>>
>>>>>>>>>>  can you try running the commandline by copying from run.sh and
>>>>>>>>>> pasting it at the prompt.
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>> On 6/4/11 12:18 PM, Jonathan S Monette wrote:
>>>>>>>>>>
>>>>>>>>>> I do have that project.  I did projects --avail and got back
>>>>>>>>>>
>>>>>>>>>>  Project      PI                      Title
>>>>>>>>>>
>>>>>>>>>> ------------------------------------------------------------------------------
>>>>>>>>>> CI-CCR000013 Michael Wilde           The Swift Parallel Scripting
>>>>>>>>>> System
>>>>>>>>>>
>>>>>>>>>>  Here is my run.sh file.  I execute with ./run.sh after I did
>>>>>>>>>> chmod +x run.sh
>>>>>>>>>>
>>>>>>>>>>  #!/bin/bash
>>>>>>>>>> swift -config cf -tc.file tc -sites.file beagle-coaster.xml
>>>>>>>>>> catsn.swift -n=1
>>>>>>>>>>
>>>>>>>>>>  I do have sh and cat in my path.  I can execute them.  Here is
>>>>>>>>>> what which sh and which cat produced.
>>>>>>>>>>
>>>>>>>>>>  sh is /usr/bin/sh
>>>>>>>>>> cat is /bin/cat
>>>>>>>>>>
>>>>>>>>>> On Sat, Jun 4, 2011 at 12:10 PM, ketan <
>>>>>>>>>> ketancmaheshwari at gmail.com> wrote:
>>>>>>>>>>
>>>>>>>>>>>  Can you try "projects --avail" command on beagle to see if you
>>>>>>>>>>> are member of a project.
>>>>>>>>>>>
>>>>>>>>>>> Else you will need to request membership. You can do this from
>>>>>>>>>>> this page:
>>>>>>>>>>>
>>>>>>>>>>> http://pads.ci.uchicago.edu/access/
>>>>>>>>>>>
>>>>>>>>>>> In any case, your error does not seem to be because of the above.
>>>>>>>>>>> Looks like '(' has sneaked in because of some unexpected typo in commandline
>>>>>>>>>>> .. can you doublecheck it.
>>>>>>>>>>>
>>>>>>>>>>> Also can you make sure that you have all the files: tc,
>>>>>>>>>>> beagle-coasters.xml cf in PATH, ie. are you able to access them w/o ./
>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>> On 6/4/11 12:03 PM, Jonathan S Monette wrote:
>>>>>>>>>>>
>>>>>>>>>>>  I did change the work directory.  I however did not change the
>>>>>>>>>>> project name.  I do not know my project name so I kept the same project that
>>>>>>>>>>> was in there.  Here is my modified beagle-coasters.xml
>>>>>>>>>>>
>>>>>>>>>>>    <config>
>>>>>>>>>>>   <pool handle="pbs">
>>>>>>>>>>>     <execution provider="coaster" jobmanager="local:pbs"/>
>>>>>>>>>>>     <profile namespace="globus"
>>>>>>>>>>> key="project">CI-CCR000013</profile>
>>>>>>>>>>>
>>>>>>>>>>>      <profile namespace="globus"
>>>>>>>>>>> key="ppn">24:cray:pack</profile>
>>>>>>>>>>>
>>>>>>>>>>>      <profile namespace="globus"
>>>>>>>>>>> key="workersPerNode">24</profile>
>>>>>>>>>>>     <profile namespace="globus" key="maxTime">1000</profile>
>>>>>>>>>>>     <profile namespace="globus" key="slots">1</profile>
>>>>>>>>>>>     <profile namespace="globus" key="nodeGranularity">1</profile>
>>>>>>>>>>>     <profile namespace="globus" key="maxNodes">1</profile>
>>>>>>>>>>>
>>>>>>>>>>>      <profile namespace="karajan"
>>>>>>>>>>> key="jobThrottle">.63</profile>
>>>>>>>>>>>     <profile namespace="karajan"
>>>>>>>>>>> key="initialScore">10000</profile>
>>>>>>>>>>>
>>>>>>>>>>>      <filesystem provider="local"/>
>>>>>>>>>>>     <workdirectory
>>>>>>>>>>> >/lustre/beagle/jonmon/Swift/work</workdirectory>
>>>>>>>>>>>   </pool>
>>>>>>>>>>> </config>
>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>>   On Sat, Jun 4, 2011 at 12:00 PM, Ketan Maheshwari <
>>>>>>>>>>> ketancmaheshwari at gmail.com> wrote:
>>>>>>>>>>>
>>>>>>>>>>>>  Jon,
>>>>>>>>>>>>
>>>>>>>>>>>> Thanks for trying out catsn on Beagle.
>>>>>>>>>>>>
>>>>>>>>>>>> I just tried it myself but could not reproduce the error you are
>>>>>>>>>>>> getting. Have you made the changes that are mentioned in the README:
>>>>>>>>>>>> ==
>>>>>>>>>>>> Change workdir location in beagle-coaster.xml
>>>>>>>>>>>> Change the project entry in the beagle-coaster.xml to your
>>>>>>>>>>>> project name
>>>>>>>>>>>> ==
>>>>>>>>>>>>
>>>>>>>>>>>> Ketan
>>>>>>>>>>>>
>>>>>>>>>>>>
>>>>>>>>>>>>  On Sat, Jun 4, 2011 at 11:50 AM, Jonathan S Monette <
>>>>>>>>>>>> jonmon at utexas.edu> wrote:
>>>>>>>>>>>>
>>>>>>>>>>>>>  Hello,
>>>>>>>>>>>>>    I am trying to run the catsn test on beagle using the files
>>>>>>>>>>>>> in ~ketan/catsn.  I have copied over this directory over to my home
>>>>>>>>>>>>> directory and I believe I set it up correctly.  I did module load swift and
>>>>>>>>>>>>> the ran run.sh that was in this directory.  I get this error.
>>>>>>>>>>>>>
>>>>>>>>>>>>>    /soft/swift/0.92/bin/swift: eval: line 152: syntax error
>>>>>>>>>>>>> near unexpected token `('
>>>>>>>>>>>>>  /soft/swift/0.92/bin/swift: eval: line 152: `java -Xmx8192M
>>>>>>>>>>>>> -Djava.endorsed.dirs=/soft/swift/0.92/bin/../lib/endorsed -DUID=1881
>>>>>>>>>>>>> -DGLOBUS_HOSTNAME=login2.beagle.ci.uchicago.edu.(none)
>>>>>>>>>>>>> -DCOG_INSTALL_PATH=/soft/swift/0.92/bin/..
>>>>>>>>>>>>> -Dswift.home=/soft/swift/0.92/bin/.. -Djava.security.egd=
>>>>>>>>>>>>> file:///dev/urandom -classpath
>>>>>>>>>>>>> /soft/swift/0.92/bin/../etc:/soft/swift/0.92/bin/../libexec:/soft/swift/0.92/bin/../lib/addressing-1.0.jar:/soft/swift/0.92/bin/../lib/ant.jar:/soft/swift/0.92/bin/../lib/antlr-2.7.5.jar:/soft/swift/0.92/bin/../lib/axis.jar:/soft/swift/0.92/bin/../lib/axis-url.jar:/soft/swift/0.92/bin/../lib/backport-util-concurrent.jar:/soft/swift/0.92/bin/../lib/castor-0.9.6.jar:/soft/swift/0.92/bin/../lib/coaster-bootstrap.jar:/soft/swift/0.92/bin/../lib/cog-abstraction-common-2.4.jar:/soft/swift/0.92/bin/../lib/cog-axis.jar:/soft/swift/0.92/bin/../lib/cog-grapheditor-0.47.jar:/soft/swift/0.92/bin/../lib/cog-jglobus-1.7.0.jar:/soft/swift/0.92/bin/../lib/cog-karajan-0.36-dev.jar:/soft/swift/0.92/bin/../lib/cog-provider-clref-gt4_0_0.jar:/soft/swift/0.92/bin/../lib/cog-provider-coaster-0.3.jar:/soft/swift/0.92/bin/../lib/cog-provider-dcache-0.1.jar:/soft/swift/0.92/bin/../lib/cog-provider-gt2-2.4.jar:/soft/swift/0.92/bin/../lib/cog-provider-gt4_0_0-2.5.jar:/soft/swift/0.92/bin/../lib/cog-pro
>>>>>>>>>>>>> vider-local-2.2.jar:/soft/swift/0.92/bin/../lib/cog-provider-localscheduler-0.4.jar:/soft/swift/0.92/bin/../lib/cog-provider-ssh-2.4.jar:/soft/swift/0.92/bin/../lib/cog-provider-webdav-2.1.jar:/soft/swift/0.92/bin/../lib/cog-resources-1.0.jar:/soft/swift/0.92/bin/../lib/cog-swift-svn.jar:/soft/swift/0.92/bin/../lib/cog-trap-1.0.jar:/soft/swift/0.92/bin/../lib/cog-url.jar:/soft/swift/0.92/bin/../lib/cog-util-0.92.jar:/soft/swift/0.92/bin/../lib/commonj.jar:/soft/swift/0.92/bin/../lib/commons-beanutils.jar:/soft/swift/0.92/bin/../lib/commons-collections-3.0.jar:/soft/swift/0.92/bin/../lib/commons-digester.jar:/soft/swift/0.92/bin/../lib/commons-discovery.jar:/soft/swift/0.92/bin/../lib/commons-httpclient.jar:/soft/swift/0.92/bin/../lib/commons-logging-1.1.jar:/soft/swift/0.92/bin/../lib/concurrent.jar:/soft/swift/0.92/bin/../lib/cryptix32.jar:/soft/swift/0.92/bin/../lib/cryptix-asn1.jar:/soft/swift/0.92/bin/../lib/cryptix.jar:/soft/swift/0.92/bin/../lib/globus_delegation_servic
>>>>>>>>>>>>> e.jar:/soft/swift/0.92/bin/../lib/globus_delegation_stubs.jar:/soft/swift/0.92/bin/../lib/globus_wsrf_mds_aggregator_stubs.jar:/soft/swift/0.92/bin/../lib/globus_wsrf_rendezvous_service.jar:/soft/swift/0.92/bin/../lib/globus_wsrf_rendezvous_stubs.jar:/soft/swift/0.92/bin/../lib/globus_wsrf_rft_stubs.jar:/soft/swift/0.92/bin/../lib/gram-client.jar:/soft/swift/0.92/bin/../lib/gram-stubs.jar:/soft/swift/0.92/bin/../lib/gram-utils.jar:/soft/swift/0.92/bin/../lib/j2ssh-common-0.2.2.jar:/soft/swift/0.92/bin/../lib/j2ssh-core-0.2.2-patch-b.jar:/soft/swift/0.92/bin/../lib/jakarta-regexp-1.2.jar:/soft/swift/0.92/bin/../lib/jakarta-slide-webdavlib-2.0.jar:/soft/swift/0.92/bin/../lib/jaxrpc.jar:/soft/swift/0.92/bin/../lib/jce-jdk13-131.jar:/soft/swift/0.92/bin/../lib/jgss.jar:/soft/swift/0.92/bin/../lib/jline-0.9.94.jar:/soft/swift/0.92/bin/../lib/jsr173_1.0_api.jar:/soft/swift/0.92/bin/../lib/jug-lgpl-2.0.0.jar:/soft/swift/0.92/bin/../lib/junit.jar:/soft/swift/0.92/bin/../lib/log4j-1.2
>>>>>>>>>>>>> .8.jar:/soft/swift/0.92/bin/../lib/naming-common.jar:/soft/swift/0.92/bin/../lib/naming-factory.jar:/soft/swift/0.92/bin/../lib/naming-java.jar:/soft/swift/0.92/bin/../lib/naming-resources.jar:/soft/swift/0.92/bin/../lib/opensaml.jar:/soft/swift/0.92/bin/../lib/puretls.jar:/soft/swift/0.92/bin/../lib/resolver.jar:/soft/swift/0.92/bin/../lib/saaj.jar:/soft/swift/0.92/bin/../lib/stringtemplate.jar:/soft/swift/0.92/bin/../lib/vdldefinitions.jar:/soft/swift/0.92/bin/../lib/wsdl4j.jar:/soft/swift/0.92/bin/../lib/wsrf_core.jar:/soft/swift/0.92/bin/../lib/wsrf_core_stubs.jar:/soft/swift/0.92/bin/../lib/wsrf_mds_index_stubs.jar:/soft/swift/0.92/bin/../lib/wsrf_mds_usefulrp_schema_stubs.jar:/soft/swift/0.92/bin/../lib/wsrf_provider_jce.jar:/soft/swift/0.92/bin/../lib/wsrf_tools.jar:/soft/swift/0.92/bin/../lib/wss4j.jar:/soft/swift/0.92/bin/../lib/xalan.jar:/soft/swift/0.92/bin/../lib/xbean.jar:/soft/swift/0.92/bin/../lib/xbean_xpath.jar:/soft/swift/0.92/bin/../lib/xercesImpl.jar:/soft
>>>>>>>>>>>>> /swift/0.92/bin/../lib/xml-apis.jar:/soft/swift/0.92/bin/../lib/xmlsec.jar:/soft/swift/0.92/bin/../lib/xpp3-1.1.3.4d_b4_min.jar:/soft/swift/0.92/bin/../lib/xstream-1.1.1-patched.jar:
>>>>>>>>>>>>> org.griphyn.vdl.karajan.Loader '-config' 'cf' '-tc.file' 'tc' '-sites.file'
>>>>>>>>>>>>> 'beagle-coaster.xml' 'catsn.swift' '-n=1''
>>>>>>>>>>>>>
>>>>>>>>>>>>>  I there something else I need to load on beagle to make swift
>>>>>>>>>>>>> run accordingly?
>>>>>>>>>>>>>
>>>>>>>>>>>>> --
>>>>>>>>>>>>>
>>>>>>>>>>>>> Any intelligent fool can make things bigger and more complex...
>>>>>>>>>>>>> It takes a touch of genius - and a lot of courage to move in the opposite
>>>>>>>>>>>>> direction.
>>>>>>>>>>>>>
>>>>>>>>>>>>> - Albert Einstein
>>>>>>>>>>>>>
>>>>>>>>>>>>>
>>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>> --
>>>>>>>>>>>
>>>>>>>>>>> Any intelligent fool can make things bigger and more complex...
>>>>>>>>>>> It takes a touch of genius - and a lot of courage to move in the opposite
>>>>>>>>>>> direction.
>>>>>>>>>>>
>>>>>>>>>>> - Albert Einstein
>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>> --
>>>>>>>>>>
>>>>>>>>>> Any intelligent fool can make things bigger and more complex... It
>>>>>>>>>> takes a touch of genius - and a lot of courage to move in the opposite
>>>>>>>>>> direction.
>>>>>>>>>>
>>>>>>>>>> - Albert Einstein
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>
>>>>>>>>>
>>>>>>>>> --
>>>>>>>>>
>>>>>>>>> Any intelligent fool can make things bigger and more complex... It
>>>>>>>>> takes a touch of genius - and a lot of courage to move in the opposite
>>>>>>>>> direction.
>>>>>>>>>
>>>>>>>>> - Albert Einstein
>>>>>>>>>
>>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>> --
>>>>>>>>
>>>>>>>> Any intelligent fool can make things bigger and more complex... It
>>>>>>>> takes a touch of genius - and a lot of courage to move in the opposite
>>>>>>>> direction.
>>>>>>>>
>>>>>>>> - Albert Einstein
>>>>>>>>
>>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>> --
>>>>>>>
>>>>>>> Any intelligent fool can make things bigger and more complex... It
>>>>>>> takes a touch of genius - and a lot of courage to move in the opposite
>>>>>>> direction.
>>>>>>>
>>>>>>> - Albert Einstein
>>>>>>>
>>>>>>>
>>>>>>
>>>>>
>>>>>
>>>>> --
>>>>>
>>>>> Any intelligent fool can make things bigger and more complex... It
>>>>> takes a touch of genius - and a lot of courage to move in the opposite
>>>>> direction.
>>>>>
>>>>> - Albert Einstein
>>>>>
>>>>>
>>>>
>>>
>>>
>>> --
>>>
>>> Any intelligent fool can make things bigger and more complex... It takes
>>> a touch of genius - and a lot of courage to move in the opposite direction.
>>>
>>> - Albert Einstein
>>>
>>>
>>
>
>
> --
>
> Any intelligent fool can make things bigger and more complex... It takes a
> touch of genius - and a lot of courage to move in the opposite direction.
>
> - Albert Einstein
>
>


-- 

Any intelligent fool can make things bigger and more complex... It takes a
touch of genius - and a lot of courage to move in the opposite direction.

- Albert Einstein
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