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Deprecated: please see new documentation site.



"NWChem is a computational chemistry package that is designed to run on high-performance parallel supercomputers as well as conventional workstation clusters. It aims to be scalable both in its ability to treat large problems efficiently, and in its usage of available parallel computing resources."

Version and availability

The parallel version of NWChem 5.1 is currently available on all LONI Linux clusters. NWChem 6.1 is currently available on Eric.

Note: On Queen Bee NWChem cannot be run with more than one node. We're working to resolve this problem. See the notes below for a workaround.

Usage

Step 1

Add the following line to the very top of your ~/.soft file and run the "resoft" command:

 +mvapich-1.1-intel-11.1
 +nwchem-5.1.1-intel-11.1-mvapich-1.1

Note: On Eric use "+nwchem-6.1-intel-11.1-mvapich-1.1" to use NWChem 6.1.

Step 2

Below is a sample script which can be used to run NWChem jobs through PBS:

#!/bin/sh
#
#PBS -A <your allocation>
#PBS -q checkpt
#PBS -M <your email>
#PBS -l nodes=8:ppn=4
#PBS -l walltime=1:00:00
#PBS -V
#PBS -o nwchem_h2o.out
#PBS -e nwchem_h2o.err
#PBS -N nwchem_h2o 

export EXEC=nwchem
export EXEC_DIR=/usr/local/packages/nwchem/5.1.1/intel-11.1-mvapich-1.1/bin/LINUX64
export WORK_DIR=$PBS_O_WORKDIR
export NPROCS=`wc -l $PBS_NODEFILE |gawk '//{print $1}'` 

cd $WORK_DIR
mpirun -machinefile $PBS_NODEFILE -np $NPROCS $EXEC_DIR/$EXEC $WORK_DIR/h2o.nw

Special notes for Queen Bee

Because of the problem we currently have with the MVAPICH version of NWChem, the MPICH version is still available on Queen Bee. To use the MPICH version, users need to add the two keys below to the very top their .soft file and resoft:

+mpich-1.2.7p1-Intel-fc-9.1+gcc-3.4.6
+nwchem-5.1-mpich

A sample script:

#!/bin/sh
#
#PBS -A <your allocation>
#PBS -q checkpt
#PBS -M <your email>
#PBS -l nodes=8:ppn=4
#PBS -l walltime=1:00:00
#PBS -V
#PBS -o nwchem_h2o.out
#PBS -e nwchem_h2o.err
#PBS -N nwchem_h2o 

export EXEC=nwchem
export EXEC_DIR=/usr/local/packages/nwchem-5.1-mpich-1.27p1-intel10.1/bin
export WORK_DIR=$PBS_O_WORKDIR
export NPROCS=`wc -l $PBS_NODEFILE |gawk '//{print $1}'` 

cd $WORK_DIR
mpirun -machinefile $PBS_NODEFILE -np $NPROCS $EXEC_DIR/$EXEC $WORK_DIR/h2o.nw 

References

NWChem website: http://www.emsl.pnl.gov/docs/nwchem/nwchem.html

User's manual: http://www.emsl.pnl.gov/docs/nwchem/doc/user/index.html

Programmer's manual: http://www.emsl.pnl.gov/docs/nwchem/doc/prog/index.html


Users may direct questions to sys-help@loni.org.

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