Hi Reuti, Everything seems to be working fine now. My $SGE_ROOT is located on a SAN volume, connected to me cluster via NFS. Would network saturation issues might cause this type of behaviour?
Thanks in advance S On 2013-10-31, at 1:25 PM, Reuti wrote: > Hi, > > Am 31.10.2013 um 15:38 schrieb Sylvain Foisy Ph. D.: > >> I sent a whole bunch of next gen sequencing alignment jobs on our cluster >> that completed just fine on the slaves but my qmaster process dies along the >> way and I had to restart it. Following this, I tried to submit sleeper.sh >> test jobs to check if everytinng was fine but they get stuck in the queue in >> qw state, never being submitted for execution. When I look into the qmaster >> log file, I see this message a number of times (I guess that each time the >> master tries to submit): >> >> rule "default rule (spool dir)" in spooling context "flatfile spooling" >> failed writing an object >> >> Ok, I did my googling on this and found out that the problem is lack of >> space for spooling into the $SGE_ROOT folder. All good and fine but my df >> inspection shows me that my $SGE_ROOT is only at 90% free... > > The spool directory is at the location you specified during installation. So > all the flat files are in $SGE_ROOT/default/spool/qmaster? This location is > writable too? > > -- Reuti > > >> Before I go and restart the master server, is there anything that I should >> be looking for? >> >> Best regards and thanks in advance >> >> Sylvain >> >> ============================================================== >> Sylvain Foisy, Ph. D. >> Chargé de projet | Project Manager >> Bioinformatics >> Labo. de génétique et médecine génomique de l'inflammation >> Centre de recherche >> Institut de cardiologie de Montréal >> 5000 Bélanger Est >> Montréal, Qc H1T 1C8 >> CANADA >> ============================================================== >> >> _______________________________________________ >> users mailing list >> [email protected] >> https://gridengine.org/mailman/listinfo/users > > > Email secured by Check Point _______________________________________________ users mailing list [email protected] https://gridengine.org/mailman/listinfo/users
