ABINIT on WestGrid Systems
Introduction
ABINIT is a software package for electronic structure calculations, based on Density Functional Theory, for the treatment of molecules and periodic solids. It also includes options for molecular dynamics.
ABINIT is available on several WestGrid systems, including Bugaboo, Matrix and Snowpatch. See the main software table for the version installed on each system. Example job scripts for running ABINIT on Bugaboo and Matrix are shown below. Running on Snowpatch should be similar to Bugaboo.
Users are expected to be generally familiar with ABINIT capabilities and input file format. Documentation is available in the Infos subdirectory and input files for a tutorial are in the Tutorial subdirectory of the installation directory referenced above. You may find it more convenient to access the user's guide and tutorial at the ABINIT web site (www.abinit.org).
Running ABINIT on Bugaboo
Like other jobs on WestGrid systems, ABINIT jobs are run by submitting an appropriate script for batch scheduling using the qsub command. See documentation on running batch jobs for more information.
The following command submits a 4-processor 72-hour job based on the script fcc_fe_bugaboo.pbs.
qsub -l procs=4,walltime=72:00:00 fcc_fe_bugaboo.pbs
where an example of fcc_fe_bugaboo.pbs is:
#!/bin/bash
#PBS -S /bin/bash
# ABINIT example - Calculation for FCC FE
# Bugaboo version
# DSP 2009-11-05
cd $PBS_O_WORKDIR
echo "Current working directory is `pwd`"
echo "Node file: $PBS_NODEFILE :"
echo "---------------------"
cat $PBS_NODEFILE
echo "---------------------"
NUM_PROCS=`/bin/awk 'END {print NR}' $PBS_NODEFILE`
echo "Running on $NUM_PROCS processors."
echo "Starting run at: `date`"
mpiexec abinip < fcc_fe.files > fcc_fe.out
echo "Job finished at: `date`"
#PBS -S /bin/bash
# ABINIT example - Calculation for FCC FE
# Bugaboo version
# DSP 2009-11-05
cd $PBS_O_WORKDIR
echo "Current working directory is `pwd`"
echo "Node file: $PBS_NODEFILE :"
echo "---------------------"
cat $PBS_NODEFILE
echo "---------------------"
NUM_PROCS=`/bin/awk 'END {print NR}' $PBS_NODEFILE`
echo "Running on $NUM_PROCS processors."
echo "Starting run at: `date`"
mpiexec abinip < fcc_fe.files > fcc_fe.out
echo "Job finished at: `date`"
Modify the mpiexec line in the script to specify your own input and output files. For details of the input files used in this example, see the section on Matrix below.
Running ABINIT on Matrix
Like other jobs on WestGrid systems, ABINIT jobs are run by submitting an appropriate script for batch scheduling using the qsub command. See documentation on running batch jobs or more information.
The following command submits a 72-hour job based on the script fcc_fe_matrix.pbs.
qsub -l walltime=72:00:00 fcc_fe_matrix.pbs
where an example of fcc_fe_matrix.pbs is:
#!/bin/bash
#PBS -S /bin/bash
# ABINIT example - Calculation for FCC FE
# Matrix version
# DSP 2006-11-03
cd $PBS_O_WORKDIR
echo "Current working directory is `pwd`"
echo "Node file: $PBS_NODEFILE :"
echo "---------------------"
cat $PBS_NODEFILE
echo "---------------------"
NUM_PROCS=`/bin/awk 'END {print NR}' $PBS_NODEFILE`
echo "Running on $NUM_PROCS processors."
echo "Starting run at: `date`"
BINDIR=/usr/apps/src/abinit/abinit-4.6.5
MY_PROG="${BINDIR}/abinip < fcc_fe.files > fcc_fe.out"
/usr/apps/bin/PBS_mpirun $MY_PROG
echo "Job finished at: `date`"
#PBS -S /bin/bash
# ABINIT example - Calculation for FCC FE
# Matrix version
# DSP 2006-11-03
cd $PBS_O_WORKDIR
echo "Current working directory is `pwd`"
echo "Node file: $PBS_NODEFILE :"
echo "---------------------"
cat $PBS_NODEFILE
echo "---------------------"
NUM_PROCS=`/bin/awk 'END {print NR}' $PBS_NODEFILE`
echo "Running on $NUM_PROCS processors."
echo "Starting run at: `date`"
BINDIR=/usr/apps/src/abinit/abinit-4.6.5
MY_PROG="${BINDIR}/abinip < fcc_fe.files > fcc_fe.out"
/usr/apps/bin/PBS_mpirun $MY_PROG
echo "Job finished at: `date`"
Modify the MY_PROG line in the script to specify your own input and output files.
The sample script and input files are available on Matrix in the directory /usr/apps/examples/abinit/fcc_fe. See the README file in that directory if you would like to try the example.
In the FCC Fe example, the input file fcc_fe.files contains:
fcc_fe.in
fcc_fe.out
fcc_fe.i
fcc_fe.o
fcc_fe
26fe.pspnc
fcc_fe.out
fcc_fe.i
fcc_fe.o
fcc_fe
26fe.pspnc
The bulk of the problem definition is in the input file, fcc_fe.in (not shown here).
The last line of the fcc_fe.files file references the pseudopotential file to be used, in this case 26fe.pspnc. This is one of a number of such files distributed with ABINIT for testing (in /usr/apps/src/abinit/abinit-4.6.5/Psps_for_tests). Visit the ABINIT web site to download other pseudopotential files.
Updated 2009-11-05.
