NAMD 2.9 install on CLuster mpirun/charmrun with ibverb version ?

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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