glite-CREAM adaptor: questions about the job description.

Added by Frizziero Eric about 6 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


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 about 6 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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