MOLPRO at NERSC

Contents

• Introduction
• Input
• Running MOLPRO at NERSC
• Restart Capabilities

Introduction

MOLPRO is a complete system of ab initio programs for molecular electronic structure calculations, written and maintained by H.-J. Werner and P. J. Knowles, and containing contributions from a number of other authors. As distinct from other commonly used quantum chemistry packages, the emphasis is on highly accurate computations, with extensive treatment of the electron correlation problem through the multiconfiguration-reference CI, coupled cluster and associated methods. Using recently developed integral-direct local electron correlation methods, which significantly reduce the increase of the computational cost with molecular size, accurate ab initio calculations can be performed for much larger molecules than with most other programs.

The heart of the program consists of the multiconfiguration SCF, multireference CI, and coupled-cluster routines, and these are accompanied by a full set of supporting features. For a full description of the program's capabilities, see the MOLPRO quantum chemistry package web site.

MOLPRO Input

The MOLPRO User's manual contains a detailed description of MOLPRO input.

Running MOLPRO at NERSC

The version of MOLPRO installed at NERSC is 2006.1. To access,

% module load molpro

To see where the molpro executables reside (the bin directory) and what environment variables it defines, type

% module show molpro

jacin01 z/zz217> module show molpro
-------------------------------------------------------------------
/usr/common/usg/Modules/modulefiles/molpro/2006.1:

prepend-path     PATH /usr/common/usg/molpro/2006.1/bin 
-------------------------------------------------------------------

The available executables are,

jacin01 z/zz217> ls -l /usr/common/usg/molpro/2006.1/bin
total 104
-rwxr-xr-x  1 zz217 usg  5207 Apr 20 23:12 molpro
lrwxrwxrwx  1 zz217 usg    28 Apr 20 09:56 molprop -> molprop_2006_1_i8_x86_64_mpi
-rwxr-xr-x  1 zz217 usg  1001 Apr 20 23:14 molprop_2006_1_i8_x86_64_mpi
-rwxr-xr-x  1 zz217 usg  1021 Apr 20 23:37 molprop_2006_1_i8_x86_64_mpi_scalapack
lrwxrwxrwx  1 zz217 usg    38 Apr 20 23:30 molprop_scal -> molprop_2006_1_i8_x86_64_mpi_scalapack
lrwxrwxrwx  1 zz217 usg     6 Apr 20 23:12 molpror -> molpro
lrwxrwxrwx  1 zz217 usg    24 Apr 20 10:18 molpros -> molpros_2006_1_i8_x86_64
-rwxr-xr-x  1 zz217 usg   855 Apr 20 10:18 molpros_2006_1_i8_x86_64
-rwxrwxr-x  1 zz217 usg 13736 Apr 16 22:10 mpirun
-rwxr-xr-x  1 zz217 usg 16416 Apr 20 23:12 swapdisks

Where molpros is the executable of the serial version, and molprop_scal and molprop are the parallel executables with and without scalapack enabled. A user should choose an appropriate executable to for his/her specific job run. Note, the scalapack enabled version (molprop_scal) might not always have better performance than the one without scalapack (molprop).

To run a serial job,

% molpro input > output

where input is the name of the input file, and output is the output file. Note: the input file can be provided as a command line argument, or read from the standard input.

To run a parallel job, one needs to write a job script, and submit to the batch queue using llsubmit or qsub command.

Running on Bassi

Here is an example batch script for Bassi.

bash-3.00$ cat test_molpro.ll
#@job_name=test_molprop_scal 
#@output=$(job_name).o$(jobid) 
#@error=$(job_name).e$(jobid)  
#@notification=always                        
#@job_type=parallel 
#@network.LAPI=sn_all,not_shared,us                
#@tasks_per_node=8
#@node=2 
#@class=interactive  
#@wall_clock_limit=30:00 
#@environment     = COPY_ALL
#@queue 
module load molpro/2006.1 
molprop_scal pentane_dflccsd.test

There are many other parameters to the Bassi batch system. For more details see The Bassi Batch System.

Running on Jacquard

Here is an example batch script for the jacquard.

jacin01 molpro2006.1/testjobs> cat test1.pbs
#PBS -S /usr/bin/tcsh
#PBS -N test_mol
#PBS -l nodes=8:ppn=2
#PBS -q debug 
#PBS -l walltime=00:30:00
#PBS -j oe
#PBS -V

cd $PBS_O_WORKDIR
module load molpro/2006.1
module load acml_i8
molprop_scal -n 16 pentane_dflccsd.test

There are many other parameters to the PBS batch system. For more details see Running Jobs on Jacquard.

Restart Capabilities

By default, the job is run so that all MOLPRO files are generated in $TMPDIR. This is fine if the calculation finishes in one job, but does not provide for restarts. This section describes techniques which can be used to restart calculations.

MOLPRO has three main files which contain information which can be used for a restart: file 1 is the main file, holding basis set, geometry, and the one and two electron integrals; file 2 is the dump file and used to store the wavefunction information, i.e. orbitals, CI coefficients, and density matrices; file 3 is an auxiliary file which can be used in addition to file 2 for restart purposes. File 1 is usually too large to be saved in permanent storage

By putting the following lines in the input file, the wavefunction file (file number 2) can be saved as file "h2.wfu",and the auxiliary file (file number 3) saved as "h2.aux". By default, the files are saved to the subdirectory "wfu" of your home directory if the job runs out of time.

***,H2
file,2,h2.wfu,new
file,3,h2.aux,new
basis=vdz;
geometry={angstrom;h1;h2,h1,.74}
optscf;

The directory where the files are saved may be changed using the "-W" command line option.

These files enable some restarts to be performed, as they provide snapshots of the calculation as each module finishes. Unfortunately, restarting an incomplete SCF or CI calculation is not possible. To use the files in a restart, remove the "new" qualifier from the "file" command:

***,H2
file,2,h2.wfu
file,3,h2.aux
basis=vdz;
geometry={angstrom;h1;h2,h1,.74}
optscf;