[Swift-user] Does SWIFT_JOBDIR_PATH work for output?

[Michael Wilde]

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.
>>>
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