[Swift-devel] Re: catsn on beagle
ketan
ketancmaheshwari at gmail.com
Sat Jun 4 13:09:35 CDT 2011
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 <mailto: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
> <http://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 <mailto: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
> <mailto: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 <mailto: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
> <mailto: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
> <mailto: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
> <mailto: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
> <mailto:jonmon at utexas.edu>> wrote:
>
> Same result. Same error
>
>
> On Sat, Jun 4, 2011 at 12:24 PM, ketan
> <ketancmaheshwari at gmail.com
> <mailto: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
>> <mailto: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
>>> <mailto: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
>>> <mailto: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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