Molpro 2002 Installation Instructions for Linux

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September 3, 2010

Molpro 2002 Installation Instructions for Linux

Obtain a Molpro license
MolPro is a commercial software product, and a license must be purchased from www.molpro.net. The license information will include a Molpro username, password, and license token.

Download Molpro
At the Molpro website, note the current version of Molpro. Follow the Download link, and supply your Molpro username and password. For the current version of Molpro, download the base souce code, recommended patch set, and documentation.

Install pre-requisite software
As root, install the following:

ifc Intel Fortran compiler
sharutils rpm package
# rpm -Uvh sharutils-4.2.1-14.i386.rpm
ncompress rpm package
# rpm -Uvh ncompress-4.2.4-33.i386.rpm

Optionally, obtain and install optimized BLAS libraries from the Molpro website, the Intel/Sandia ASCI project, the ATLAS website, or Goto's library from the van de Geijn group.

Extract Molpro files
As a regular user, untar the molpro source code and documentation:
$ cd ~
$ mkdir -p source/molpro
$ cd source/molpro
$ cp /{download_dir}/molpro.2002.6.tar.gz .
$ cp /{download_dir}/molpro.doc.2002.6.tar.gz .
$ cp /{download_dir}/molpro.patches.2002.6.tar.gz .
$ tar xzvf molpro.2002.6.tar.gz
$ tar xzvf molpro.doc.2002.6.tar.gz
$ cd molpro2002.6

Setup Intel Fortran compiler
$ source /opt/intel/compiler70/ia32/bin/ifcvars.sh
Note that on Redhat Linux 9, the ctype workaround described in the ifc installation instructions must be implemented in order to link pre-compiled object file(s) distributed with Molpro.

Configure Molpro
$ ./configure
Accept all defaults except where indicated:

Do you want to use large files? (y/n, default y) 
Please enter your licence key (default ): 
{license token}     <-----!!!!!
Enter max number of atoms [ 200]: 
Enter max number of valence orbitals [ 300]: 
Enter max number of basis functions [2000]: 
If you wish to use a system BLAS library, please give the maximum
level (0, 1, 2, 3) of BLAS to be supplied by the system (default 3): 
{Accept default, or enter 0 if no BLAS libraries are available on system}     <-----!!!!!
Please give any loader options (-L, -l) needed to access the BLAS library
(default -L/usr/lib -lblas -Wl,-rpath,/usr/lib  ): 
Please give any loader options (-L, -l) needed to access the LAPACK library
(default -L/usr/lib -llapack -Wl,-rpath,/usr/lib  ): 
Installed binaries directory [/usr/local/bin]
Installed auxiliary directory [/usr/local/lib/molpro-Linux-i686-i4-2002.6]
Installed HTML documentation directory [/home/webmo/public_html/molpro/molpro2002.6]
/var/www/html/molpro2002.6     <-----!!!!!
Installed CGI script directory [/home/webmo/public_html/molpro/molpro2002.6]
/var/www/html/molpro2002.6     <-----!!!!!
CONFIG file created; please inspect and edit if necessary before proceeding

On Redhat Linux 9, edit the CONFIG file as follows:
$ cp -p CONFIG CONFIG.000
$ vi CONFIG

Compile Molpro source code
$ make

make -C utilities echo
...
A skeleton molpro configuration file has been set up in /home/webmo/source/molpro/molpro2002.6/bin/molpros_2002_6_p4.rc
It contains the following:

-d/tmp/$LOGNAME    # directory in which the program should be run
-I/tmp/$LOGNAME    # directory to store permanent copies of int files (1)
-W$HOME/wfu    # directory to store permanent copies of wf files (2,3)
-L/home/webmo/source/molpro/molpro2002.6/lib/    # directory containing library files
-x/home/webmo/source/molpro/molpro2002.6/bin/molpros_2002_6_p4.exe    # executable
-m8000000    # default memory in 8-byte words
-K65536    # mxma cache size in 8-byte words
-B32    # mxma blocking size
-k {license token} #Licence key 
--environment MOLPRO_BLASLIB=blas

Please check it, and add options according to the molpro command description
make -C utilities cnvrt.exe
...
make[1]: Leaving directory `/home/webmo/source/molpro/molpro2002.6/lib'

Verify program operation
Run a single test:
$ cd testjobs
$ make h2o_vdz.out
$ more test.log
$ cd ..
Run a test suite:
$ make quicktest
$ more testjobs/test.log

Optionally, install patches
$ ./patcher
supply username and password for molpro website; patches are automatically downloaded and applied to source code
$ make
if prompted by make, run './configure' again, and make any necessary manual edits to CONFIG, e.g., to LIBS line
Note: 'patcher -n' obtains but does not apply patches; 'patcher -v' outputs additional information about patching process
Note: Alternatively, patches may be installed from local files as follows:
$ cd ~/.molpro/cache/2002.6
$ tar xzf ~/source/molpro/molpro.patches.2002.6.tar.gz
$ cd ~/source/molpro/molpro2002.6
$ ./patcher --local
$ make

Install production version
$ whoami
$ su
# make install
# chown -R {whoami_output}:{whoami_output} *
# exit

Optionally, customize the default environment
$ su
# cd /usr/local/bin
# vi molpros_2002_6
make desired changes to default environment
# exit

Install documentation
$ su
# cd doc
# make install
# vi /etc/httpd/conf/httpd.conf
<Directory /var/www/html/molpro*>
AllowOverride All
</Directory>
# /sbin/service httpd reload
# cd /var/www/html
# ln -s molpro2002.6 molpro
# cd /var/www/html/molpro2002.6
# chown -R root:root *
# exit
Molpro documentation can be accessed at http://server.edu/molpro

Run jobs as a normal user
Submit a file locally:
$ /usr/local/bin/molpro h2co.inp
where h2co.inp is a molpro input file like

***,H2CO HF/6-31G OPT
geometry={angstrom      ! geometry
C
O 1 B1
H 1 B2 2 A1
H 1 B2 2 A1 3 180.0
}
A1=121.9
B1=1.2
B2=1.1
basis=6-31G             ! basis
hf                      ! method
optg                    ! optimize
show,A1,B1,B2           ! output
show[1,6F15.8],ENERGY
---

Submit a file via PBS:
$qsub h2co
where h2co is a qsub script file like

#!/bin/sh
#PBS -j oe
#PBS -o pbs.out
cd $PBS_O_WORKDIR
/usr/local/bin/molpro <<"@" >$PBS_JOBNAME.out 2>$PBS_JOBNAME.err
***,H2CO HF/6-31G OPT
geometry={angstrom      ! geometry
C
O 1 B1
H 1 B2 2 A1
H 1 B2 2 A1 3 180.0
}
A1=121.9
B1=1.2
B2=1.1
basis=6-31G             ! basis
hf                      ! method
optg                    ! optimize
show,A1,B1,B2           ! output
show[1,6F15.8],ENERGY
---
@

Workarounds

If ksh is needed but not installed on the system
# cd /bin
# ln -s bash ksh
If ifc library files cannot be found
$ source /usr/local/intel/compiler70/ia32/bin/ifcvars.sh
or
# vi /etc/ld.so.conf
add /usr/local/intel/compiler70/ia32/bin
# ldconfig
If the files in /usr/local/molpro are transferred or shared to a different computer on which ifc libraries do not exist, copy /usr/local/intel/compiler70/ia32/bin/* to the other computer