[torqueusers] segfault with many depencies

Naveed Near-Ansari naveed at caltech.edu
Thu Jul 23 11:17:49 MDT 2009


I alternet a submission script for FSL which is now being used by some
of my users. FSL submissions generate alot of depencies.  When the
number of dependencies get high, qsub segfaults. Is this a known
problem?  is their a workaround?  decreasing the depencies allows it to
work.



$ qsub -l nodes=1 -l pmem=256mb -V -d /home/user/ -q
short.q -M user at host.caltech.edu -N bpx_postproc -m ae -o
/home/user/data/maq004/dish1.bedpostX/logs//home/user/data/maq004/dish1.bed=
postX/logs.out
-e
/home/user/data/maq004/dish1.bedpostX/logs//home/user/data/maq004/dish1.=
bedpostX/logs.err
-W
depend=3Dafterany:9080:9081:9082:9083:9084:9085:9086:9087:9088:9089:9090=
:9091:9092:9093:9094:9095:9096:9097:9098:9099:9100:9101:9102:9103:9104:9105=
:9106:9107:9108:9109:9110:9111:9112:9113:9114:9115:9116:9117:9118:9119:9120=
:9121:9122:9123:9124:9125:9126:9127:9128:9129:9130:9131:9132:9133:9134:9135=
:9136:9137:9138:9139:9140:9141:9142:9143:9144:9145:9146:9147:9148:9149:9150=
:9151:9152:9153:9154:9155:9156:9157:9158:9159:9160:9161:9162:9163:9164
/tmp/tmp.hZBQb27634
Segmentation fault



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