I work at the EBI where our computing pipelines rely extensively on LSF.
Thus, I've adapted the runCA script and called it runCA_LSF to run it on our computing farm to do some transcriptome assembly and optimize the memory and thread usage.
From my recent test on a 454 assembly (> 2M reads), it works well until the terminator step where I had probably a buffer overflow issue.
So, after recompiling AS_MSG_pmesg.c with a bigger msgMax, I'll see if I can complete the pipeline using LSF.
It would be useful if you could distribute my script with the wgs-assembler. I've adapted also the spec file so it does not mix with SGE commands.
# See http://sourceforge.net/apps/mediawiki/wgs-assembler/index.php?title=RunCA_and_Sun_Grid_Engine
# By default, do NOT use LSF. The use must manually override these with command-line options.
useGrid = 1
scriptOnGrid = 1
# Once LSF is enabled, also do fragment and overlap correction under LSF control.
# By default, overlap and consensus jobs are under LSF control.
ovlOnGrid = 1
frgCorrOnGrid = 1
ovlCorrOnGrid = 1
lsf = -q production
lsfScript = -n 1 -M 8192 -R "rusage[mem=8192]"
lsfOverlap = -n 2 -M 16384 -R "rusage[mem=16384]"
lsfMerOverlapSeed = -n 2 -M 16384 -R "rusage[mem=16384]"
lsfMerOverlapExtend = -n 2 -M 16384 -R "rusage[mem=16384]"
lsfConsensus = -n 1 -M 8192 -R "rusage[mem=8192]"
lsfFragmentCorrection = -n 2 -M 32000 -R "rusage[mem=32000]"
lsfOverlapCorrection = -n 1 -M 32000 -R "rusage[mem=32000]"
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