From: jnsong (jnsong_at_itcs.ecnu.edu.cn)
Date: Sun Nov 14 2010 - 06:25:21 CST
Dear all,
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
Thanks in advance!
Jianing
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