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【求助】the usage of ++nodelist and ++local
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各位大侠，请教一个问题，非常感谢回答： Is NAMD_2.7_Linux-x86_64 only used in the Individual Linux Workstations, other than the infiniband network, even if I add ++nodelist in the command line? This question initiates from Recently, I'm relating to using NAMD_2.7_Linux-x86_64 in the Linux cluster of infiniband Network. When I sub my job, in the log file, there are just two lines: Warning> Randomization of stack pointer is turned on in kernel, thread migration may not work! Run 'echo 0 > /proc/sys/kernel/randomize_va_space' as root to disable it, or try run with '+isomalloc_sync'. Charm++: scheduler running in netpoll mode. No more information write out in the log file. Then I change the last command line in job-sub-file to: $NAMD/charmrun ++local +p${n_proc} $NAMD/namd2 2rh1.md > 2rh1_64cpu.log It can run normally. So, I'm confused about the usage of ++nodelist and ++local. Because my Linux cluster is infiniband network, then it may be right to use ++nodelist, but the ++nodelist can not work. Furthermore, if I change to ++local, the speed of calculation is much slower than the NAMD_2.7_Linux-x86_64-ibverbs. Could anyone help me understand this? My job-submitting file is: >cat sub.sh #!/bin/bash -x #PBS -N 2rh1_nodelist_10 #PBS -l nodes=8:ppn=8 #PBS -j oe #PBS -q parallel # #define variables # n_proc=$(cat $PBS_NODEFILE | wc -l) echo $PBS_NODEFILE $n_proc # #running jobs # cd $PBS_O_WORKDIR echo $PBS_O_WORKDIR # # Setup the MPI topology # export CONV_RSH=ssh echo "group main" >node1 awk '{print "host ", $1}' $PBS_NODEFILE >>node1 export NAMD=/home/users/ymei/sjn/NAMD_2.7_Linux-x86_64 $NAMD/charmrun ++nodelist node1 +p${n_proc} $NAMD/namd2 2rh1.md > 2rh1_64cpu.log |
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2楼2014-04-21 20:37:45
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