From: Nicolas Floquet (nicolas.floquet_at_univ-montp1.fr)
Date: Thu Nov 14 2013 - 05:17:48 CST
Dear all ,
I try to install NAMD on a cluster with infiniband and tested different
versions of NAMD
My submission script is as follows (in which I tested different solutions):
#!/bin/sh
# @ job_name = TMD1
# @ output = $(job_name).out
# @ error = $(job_name).err
# @ environment = COPY_ALL
# @ class = specialIntel
# @ account_no = RCPGs2
# @ job_type = mpich
# @ notify_user = nicolas.floquet_at_univ-montp1.fr
# @ node = 10
# @ total_tasks = 120
# @ environment = COPY_ALL
# @ wall_clock_limit = 36:00:10,36:00:01
# @ queue
source
/opt/cluster/softs/gcc-4.6.x-soft/system/module/3.2.10/Modules/3.2.10/init/s
h
module load hpclr-wrapper gcc-4.6.4 openmpi-1.6.5-gcc
export CPPFLAGS=-I/opt/cluster/gcc-soft/fftw/3.3.3-shared-float/include
export LDFLAGS=-L/opt/cluster/gcc-soft/fftw/3.3.3-shared-float/lib
/opt/cluster/softs/gcc-4.6.x-soft/system/openmpi/1.6.5/bin/mpirun -x
LD_LIBRARY_PATH -np $LOADL_TOTAL_TASKS -machinefile $LOADL_HOSTFILE
/opt/cluster/gcc-soft/namd/2.9/NAMD_2.9_Linux-x86_64-ibverbs/namd2
/scratch/floquetn/NEURO/TMD2/POINT3/tmd1.namd
#/opt/cluster/softs/gcc-4.6.x-soft/system/openmpi/1.6.5/bin/mpirun -x
LD_LIBRARY_PATH -np $LOADL_TOTAL_TASKS -machinefile $LOADL_HOSTFILE
/opt/cluster/gcc-soft/namd/2.9/NAMD_2.9_Linux-x86_64/namd2
/scratch/floquetn/NEURO/TMD2/POINT3/tmd1.namd
#/opt/cluster/gcc-soft/namd/2.9/NAMD_2.9_Linux-x86_64/charmrun +p
$LOADL_TOTAL_TASKS ++nodelist $LOADL_HOSTFILE /opt/cluster/gcc-soft/namd/
2.9/NAMD_2.9_Linux-x86_64/namd2
/scratch/floquetn/NEURO/TMD2/POINT3/tmd1.namd
Which solution is the best one ?
The one selected seems to launch but not in parallel ? do I need to use
charmrun with the namd2 executable for iverbs ? do I need to include mpirun
as I did?
Thank you in advance for your help.
Nicolas Floquet
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