[Swift-devel] Re: catsn on beagle

Jonathan S Monette jonmon at utexas.edu
Sat Jun 4 13:01:12 CDT 2011 

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
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