glite-CREAM adaptor: questions about the job description.

Added by Frizziero Eric over 11 years ago

Hi,

I'm using the glite-CREAM adaptor included on the following version of JSAGA engine:
-----------------------------------------
jsaga-help.sh -v
JSAGA Engine
IN2P3 Computing Center

SAGA specification version: 1.0 RC.6
JSAGA implementation version: 0.9.15
-----------------------------------------

Starting from the following jdl script (amberCE.jdl):
-----------------------------------------
Executable = "run_amber11.sh";
StdOutput = "std.out";
StdError = "std.err";
InputSandbox = {"./amber11.tgz","./run_amber11.sh"};
OutputSandbox = {"std.out", "std.err"};
OutputSandboxBaseDestURI="gsiftp://localhost";
-----------------------------------------

I have submitted a job using the jsaga command line (jsaga-job-run script) as follow:
----------------------------------------------------

jsaga-job-run.sh -b -Executable run_amber11.sh -Output std.out -Error std.err -FileTransfer 'gsiftp://localhost/out.out\<out.out  gsiftp://localhost/err.err\<err.err ./amber11.tgz\>amber11.tgz ./run_amber11.sh\>run_amber11.sh' -r cream://prod-ce-01.pd.infn.it:8443/cream-lsf-grid

[2013-03-07 13:57:05,614] INFO fr.in2p3.jsaga.adaptor.cream.job.CreamJobAdaptorAbstract : Connecting to prod-ce-01.pd.infn.it (interface version=2.1,service version=1.14 - EMI version: 2.6.1-1)
[cream://prod-ce-01.pd.infn.it:8443/cream-lsf-grid]-[CREAM219894746]
----------------------------------------------------

The JSAGA job description of that job is:
----------------------------------------------------
jsaga-job-run.sh -d -Executable run_amber11.sh -Output std.out -Error std.err -FileTransfer 'gsiftp://localhost/out.out\<out.out gsiftp://localhost/err.err\<err.err ./amber11.tgz\>amber11.tgz ./run_amber11.sh\>run_amber11.sh' -r cream://prod-ce-01.pd.infn.it:8443/cream-lsf-grid
[2013-03-07 13:58:05,340] INFO fr.in2p3.jsaga.adaptor.cream.job.CreamJobAdaptorAbstract : Connecting to prod-ce-01.pd.infn.it (interface version=2.1,service version=1.14 - EMI version: 2.6.1-1)
[
Type = "Job";

Executable = "run_amber11.sh";

CERequirements = "true ";
StdOutput = "std.out";
StdError = "std.err";
OutputSandboxPostStaging = {
};
OutputSandbox = {
"out.out"};
OutputSandboxDestURI = {
"gsiftp://localhost/out.out"};

BatchSystem = "lsf";

QueueName = "grid";

]
----------------------------------------------------

Questions:
1) Why isn't the file "err.err" included in the "outputSandbox" attribute?

2) Why isn't the attribute "inputSandbox" defined for the input files (amber11.tgz,run_amber11.sh)?

3) How should I define the attribute "inputSandbox" for the input files (amber11.tgz,run_amber11.sh)?

If I ask the job status using the EMI-UI, the output is the following:
----------------------------------------------------
glite-ce-job-status https://prod-ce-01.pd.infn.it:8443/CREAM219894746
2013-03-07 13:59:34,316 WARN - No configuration file suitable for loading. Using built-in configuration

JobID=[https://prod-ce-01.pd.infn.it:8443/CREAM219894746]
Status = [DONE-FAILED]
ExitCode = [N/A]
FailureReason = [./run_amber11.sh not found or unreadable; reason=1; ./run_amber11.sh not found or unreadable]

4) Moreover, how can I describe my amberCE job in a file "amberCE.jsaga" in order to submit it using the option "f" of the jsaga command line?
That is:
jsaga-job-run.sh -f amberCE.jsaga -r cream://prod-ce-01.pd.infn.it:8443/cream-lsf-grid

Thanks,
E r i c.

Replies (1)

RE: glite-CREAM adaptor: questions about the job description. - Added by Reynaud Sylvain over 11 years ago

Hi Eric,

1,2 and 3) When using single quote instead of double quotes, the JVM see the value of your FileTransfer option as 4 separate arguments instead of 1. That's why only the first file transfer appears in the JDL. After having fixed this, you will see another problem: the file separator is comma instead of space.

4) Use the same SAGA attribute names and values, but with the Java properties format instead of command line arguments:

Executable=run_amber11.sh
Output=std.out
Error=std.err
FileTransfer=gsiftp://localhost/out.out<out.out, gsiftp://localhost/err.err<err.err, ./amber11.tgz>amber11.tgz, ./run_amber11.sh>run_amber11.sh

Regards,
Sylvain

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