From: Norman Geist (norman.geist_at_uni-greifswald.de)
Date: Thu Nov 14 2013 - 06:43:49 CST
If you need mpirun or charmrun depends on if you compiled namd against mpi
or charm++. If you just downloaded a precompiled build, it's likely without
mpi and charmrun needs to be used. If you need to add one of them in general
depends on if you use more than one physical node. For multiple nodes you
will of course need mpirun/charmrun. But, in case of charmrun the
machinefile (nodelist) has a different format:
group main
host node1
host node1
[.]
For mpirun simply:
node1
node2
[.]
For local parallel jobs you need at least a multicore build of namd which
has shared memory parallelism.
Norman Geist.
Von: owner-namd-l_at_ks.uiuc.edu [mailto:owner-namd-l_at_ks.uiuc.edu] Im Auftrag
von Nicolas Floquet
Gesendet: Donnerstag, 14. November 2013 12:18
An: namd-l_at_ks.uiuc.edu
Betreff: namd-l: NAMD 2.9 install on CLuster mpirun/charmrun with ibverb
version ?
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
This archive was generated by hypermail 2.1.6 : Tue Dec 31 2013 - 23:23:59 CST