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Re: pthreads+bproc (was Re: [BProc] Re: bpslave dies)
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From: Nicholas H. <he...@se...> - 2003-04-10 17:08:01
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Again -- head node: 12867 ? S 0:00 bpsh -n 57 subtaskInvoker /scratch/user/sfischer/slot_1/result /genomics/binf/scratch/dotsBuilds/nicTest/mus/similarity/fin 12869 ? SW 0:00 \_ [subtaskInvoker] 12870 ? SW 0:01 \_ [blastSimilarity] 498 ? SW 0:00 \_ [sh] 499 ? SW 0:00 \_ [blastx] 512 ? SW 0:00 \_ [blastx] 513 ? SW 0:00 \_ [blastx] Node57: 568 ? S 0:09 /usr/sbin/bpslave -m /scratch/bpslave_new.strace -r 192.168.0.223 2223 569 ? S 0:00 \_ /usr/sbin/bpslave -m /scratch/bpslave_new.strace -r 192.168.0.223 2223 623 ? S 0:00 \_ mond -d 15333 ? S 0:00 \_ /bin/sh /proc/self/fd/3 /scratch/user/sfischer/slot_1/result /genomics/binf/scratch/dotsBuilds/nicTest/mus/similarity/f 15334 ? S 0:01 \_ /usr/bin/perl /home/sfischer/gushome/bin/blastSimilarity --blastBinDir /genomics/share/pkg/bio/wu-blast/current --d 17625 ? S 0:00 \_ sh -c /genomics/share/pkg/bio/wu-blast/current/blastx /scratch/user/sfischer/prodom.fsa seqTmp -wordmask=seg+xn 17626 ? S 0:00 \_ /genomics/share/pkg/bio/wu-blast/current/blastx /scratch/user/sfischer/prodom.fsa seqTmp -wordmask seg+xnu 17639 ? S 0:00 \_ /genomics/share/pkg/bio/wu-blast/current/blastx /scratch/user/sfischer/prodom.fsa seqTmp -wordmask seg+ 17640 ? S 0:00 \_ /genomics/share/pkg/bio/wu-blast/current/blastx /scratch/user/sfischer/prodom.fsa seqTmp -wordmask After the kill -9 17626 17639 17640 : 568 ? S 0:09 /usr/sbin/bpslave -m /scratch/bpslave_new.strace -r 192.168.0.223 2223 569 ? S 0:00 \_ /usr/sbin/bpslave -m /scratch/bpslave_new.strace -r 192.168.0.223 2223 623 ? S 0:00 \_ mond -d 17640 ? S 0:00 \_ /genomics/share/pkg/bio/wu-blast/current/blastx /scratch/user/sfischer/prodom.fsa seqTmp -wordmask seg+xnu W 3 T 1000 B 15333 ? S 0:00 \_ /bin/sh /proc/self/fd/3 /scratch/user/sfischer/slot_1/result /genomics/binf/scratch/dotsBuilds/nicTest/mus/similarity/f 15334 ? S 0:01 \_ /usr/bin/perl /home/sfischer/gushome/bin/blastSimilarity --blastBinDir /genomics/share/pkg/bio/wu-blast/current --d 17625 ? Z 0:00 \_ [sh <defunct>] Now again kill -9 17640: 568 ? S 0:09 /usr/sbin/bpslave -m /scratch/bpslave_new.strace -r 192.168.0.223 2223 569 ? S 0:00 \_ /usr/sbin/bpslave -m /scratch/bpslave_new.strace -r 192.168.0.223 2223 623 ? S 0:00 \_ mond -d 15333 ? S 0:00 \_ /bin/sh /proc/self/fd/3 /scratch/user/sfischer/slot_1/result /genomics/binf/scratch/dotsBuilds/nicTest/mus/similarity/f 15334 ? S 0:01 \_ /usr/bin/perl /home/sfischer/gushome/bin/blastSimilarity --blastBinDir /genomics/share/pkg/bio/wu-blast/current --d 17792 ? S 0:00 \_ sh -c /genomics/share/pkg/bio/wu-blast/current/blastx /scratch/user/sfischer/prodom.fsa seqTmp -wordmask=seg+xn 17793 ? R 0:00 \_ /genomics/share/pkg/bio/wu-blast/current/blastx /scratch/user/sfischer/prodom.fsa seqTmp -wordmask seg+xnu 17806 ? S 0:00 \_ /genomics/share/pkg/bio/wu-blast/current/blastx /scratch/user/sfischer/prodom.fsa seqTmp -wordmask seg+ 17807 ? R 0:00 \_ /genomics/share/pkg/bio/wu-blast/current/blastx /scratch/user/sfischer/prodom.fsa seqTmp -wordmask --This shows that it died, and the user's program started a new blast on the node. Trace :http://www.liniac.upenn.edu/~henken/bproc/node57.trace Ok -- hope these help. If you need anything else -- please holler at me. Nic -- Nicholas Henke Penguin Herder & Linux Cluster System Programmer Liniac Project - Univ. of Pennsylvania |
