[EMBOSS] Jemboss with openPBS?
Jerome
jerome at ibt.unam.mx
Thu Feb 24 23:44:49 UTC 2005
Hi,
I'm trying to use jemboss with the scheduling server pbs. As it's
described in the documentation, i've put this piece of code in the
JembossAuthServer.java file:
// COMMENT THIS LINE TO USE QUEUEING SOFTWARE
/*
boolean lforkB = aj.forkBatch(userName,passwd,environ,
embossCommand,project);
*/
// UNCOMMENT ONE OF THESE LINE TO USE QUEUEING SOFTWARE
// runAsBatch(aj,userName,passwd,project,quoteMe(embossCommand));
// runAsGNQSBatch(aj,userName,passwd,project,quoteMe(embossCommand));
runAsPBSBatch(aj,userName,passwd,project,quoteMe(embossCommand));
and in the runAsPBSBatch method:
String batchCommand = "/usr/local/Torque/bin/qsub "+scriptFile;
now the fact is that it don't send anything to the server. The script
file is good writed, and i can read in the jemboss.log, this type of
entries:
mode=batch Thu Feb 24 17_34_02 CST 2005 cutseq -sequence cutseq0 -from
1 -to 10 -auto
Total Memory : 13893632 bytes, Free Memory : 5362592 bytes
That seem that i don't make the batchCommand, this line :
lfork = aj.forkEmboss(userName,passwd,environ,
batchCommand,project);
I don't know really where to find the source of this problem.. Does
someone achieve working with Pbs system ?
Thank's a lot for this program..
--
-- Jérôme
- Maraud, faquin, butor de pied plat ridicule !
- Ah ?.. Et moi, Cyrano Savinien-Hercule
De Bergerac.
(Edmond Rostand, Cyrano de Bergerac)
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