[Swift-user] Does SWIFT_JOBDIR_PATH work for output?

Mon Mar 16 08:49:03 CDT 2009

Printenv indicates that SWIFT_JOBDIR_PATH is not getting into the app's 
environment:

int$ cat pe.swift
type file;

app (file o) printenv () { printenv stdout=@o; }

file ofile <"pe.out">;

ofile = printenv();
int$

int$ cat pe.out
PLOTICUS_HOME=/home/falkon/users/wilde/0922/ploticus
FALKON_CLIENT_HOME=/home/falkon/users/wilde/0922/client
GLOBUS_OPTIONS_MISC=-Xms512M -Xmx512M -Xss128K
GLOBUS_LOCATION=/home/falkon/users/wilde/0922/container
FALKON_CONFIG=/home/falkon/users/wilde/0922/config
GLOBUS_PATH=/home/falkon/users/wilde/0922/container
OLDPWD=/fuse/intrepid-fs0/users/wilde/persistent/oops/swift/work/pe-20090316-0845-sqceiryc
ANT_HOME=/home/falkon/users/wilde/0922/apache-ant-1.7.0
LD_LIBRARY_PATH=.:/lib:/fuse/lib:/fuse/usr/lib:/home/falkon/users/wilde/0922/container/lib:/lib:/fuse/lib:/fuse/usr/lib
FALKON_LOGS=/home/falkon/users/wilde/0922/logs
FALKON_CLIENT_WORKLOADS_HOME=/home/falkon/users/wilde/0922/workloads
FALKON_HOME=/home/falkon/users/wilde/0922
PATH=/home/falkon/users/wilde/0922/bin:/home/falkon/users/wilde/0922/service:/home/falkon/users/wilde/0922/worker:/home/falkon/users/wilde/0922/client:/home/falkon/users/wilde/0922/monitor:/home/falkon/users/wilde/0922/webserver:/home/falkon/users/wilde/0922/ploticus/src:/home/falkon/users/wilde/0922/apache-ant-1.7.0:/home/falkon/users/wilde/0922/apache-ant-1.7.0/bin:/home/falkon/users/wilde/0922/ibm-java2-ppc-50/jre:/home/falkon/users/wilde/0922/ibm-java2-ppc-50/jre/bin:/home/falkon/users/wilde/0922/container:/home/falkon/users/wilde/0922/container/bin:/home/falkon/users/wilde/0922/cog/modules/vdsk/dist/vdsk-svn/bin:/usr/local/bin:/bin:/usr/bin:/usr/X11R6/bin:.:/bin:/usr/bin
PWD=/fuse/intrepid-fs0/users/wilde/persistent/oops/swift/work/pe-20090316-0845-sqceiryc/jobs/r/printenv-rx6v318j
JAVA_HOME=/home/falkon/users/wilde/0922/ibm-java2-ppc-50/jre
COBALT_JOBID=113638
SWIFT_HOME=/home/falkon/users/wilde/0922/cog/modules/vdsk/dist/vdsk-svn
SHLVL=2
GLOBUS_TCP_PORT_RANGE=50000,59999
FALKON_WWW_HOME=/home/falkon/users/wilde/0922/webserver
BG_SIZE=64
FALKON_MONITOR_HOME=/home/falkon/users/wilde/0922/monitor
FALKON_WORKER_HOME=/home/falkon/users/wilde/0922/worker
FALKON_SERVICE_HOME=/home/falkon/users/wilde/0922/service
CONTROL_INIT=4195440,8,64,62,48
FALKON_ROOT=/home/falkon/users/wilde
_=/usr/bin/printenv

int$ cat sites.xml
<config>
   <pool handle="localhost" sysinfo="INTEL32::LINUX">
     <gridftp url="local://localhost" />
     <execution provider="local" url="none" />
     <workdirectory>/home/wilde/swiftwork/</workdirectory>
   </pool>
<pool handle="bgp000">
    <execution provider="deef" 
url="http://172.16.8.122:50001/wsrf/services/GenericPortal/core/WS/GPFactoryService"/>
    <gridftp url="local://localhost"/>

<workdirectory>/intrepid-fs0/users/wilde/persistent/oops/swift/work</workdirectory>
    <profile namespace="karajan" key="jobThrottle">8</profile>
    <profile namespace="karajan" key="initialScore">1000</profile>
    <profile namespace="env" key="SWIFT_JOBDIR_PATH">/dev/shm</profile>
</pool>
</config>

On 3/16/09 8:40 AM, Michael Wilde wrote:
> Ah, I see: in wrapper.sh the "info" function which logs the env etc is 
> only invoked on failure, it seems.  Unless you see an error in my 
> sites.xml below, I'll add extra logging to wrapper.sh to see what my env 
> is.  Or test with printenv as the app.
> 
> On 3/16/09 8:35 AM, Michael Wilde wrote:
>> Im still unable to get this to work.
>>
>> For the test case of specifying in sites.xml I have:
>>
>> <config>
>>   <pool handle="localhost" sysinfo="INTEL32::LINUX">
>>     <gridftp url="local://localhost" />
>>     <execution provider="local" url="none" />
>>     <workdirectory>/home/wilde/swiftwork/</workdirectory>
>>   </pool>
>> <pool handle="bgp000">
>>    <execution provider="deef" 
>> url="http://172.16.8.122:50001/wsrf/services/GenericPortal/core/WS/GPFactoryService"/> 
>>
>>    <gridftp url="local://localhost"/>
>>
>> <workdirectory>/intrepid-fs0/users/wilde/persistent/oops/swift/work</workdirectory> 
>>
>>    <profile namespace="karajan" key="jobThrottle">8</profile>
>>    <profile namespace="karajan" key="initialScore">1000</profile>
>>    <profile namespace="env" key="SWIFT_JOBDIR_PATH">/dev/shm</profile>
>> </pool>
>> </config>
>>
>> and in the info file I see whats pasted below.
>>
>> I *thought* this info file is a full wrapper.sh log and includes a 
>> section listing all the environment vars, so I could verify if 
>> SWIFT_JOBDIR_PATH made it into the environment.  Can you remind me how 
>> to turn that on? Cant find it in swift.properties, will check the 
>> wrapper.sh code.
>>
>> - Mike
>>
>>
>> int$ cat ./info/1/runrama-1in2318j-info
>> Progress  2009-03-16 08:24:53.%N-0500  LOG_START
>>
>> _____________________________________________________________________________ 
>>
>>
>>         Wrapper
>> _____________________________________________________________________________ 
>>
>>
>> Job directory mode is: link on shared filesystem
>> DIR=jobs/1/runrama-1in2318j
>> EXEC=/intrepid-fs0/users/wilde/persistent/oops/oops-r055/bin/runrama.sh
>> STDIN=
>> STDOUT=output/T1af7/0000_0001.log
>> STDERR=stderr.txt
>> DIRS=input/secseq^input/native^input/fasta^secseq/T1af7^input/rama^output/T1af7 
>>
>> INF=input/secseq/T1af7.secseq^input/native/T1af7.pdb^input/fasta/T1af7.fasta^secseq/T1af7/T1af7.0000.secseq^input/rama/T1af7.rama_index^input/rama/T1af7.rama_map 
>>
>> OUTF=output/T1af7/0000_0001.log^output/T1af7/0000_0001.rmsd^output/T1af7/0000_0001.pdt 
>>
>> KICKSTART=
>> ARGS=input/fasta/T1af7.fasta secseq/T1af7/T1af7.0000.secseq 
>> input/native/T1af7.pdb input/rama/T1af7.rama_map 
>> output/T1af7/0000_0001.pdt output/T1af7/0000_0001.rmsd 1 KILL_TIME_=_1
>> ARGC=8
>> Progress  2009-03-16 08:24:54.%N-0500  CREATE_JOBDIR
>> Created job directory: jobs/1/runrama-1in2318j
>>
>> ---
>>
>>
>>
>> On 3/16/09 8:03 AM, Michael Wilde wrote:
>>> I discovered I misspelled the var name, and am retesting specifying 
>>> it from both tc.data and sites.xml.
>>>
>>> On 3/16/09 7:43 AM, Ben Clifford wrote:
>>>> On Mon, 16 Mar 2009, Michael Wilde wrote:
>>>>
>>>>> But for the tests Im doing now this is not a problem.
>>>>
>>>> Please indicate what you discover anyway.
>>>>
>>> _______________________________________________
>>> Swift-user mailing list
>>> Swift-user at ci.uchicago.edu
>>> http://mail.ci.uchicago.edu/mailman/listinfo/swift-user
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