Molpro 2006 Installation Instructions for Linux

	Recent news WebMO 10.1 is now available for free download! WebMO 10.1 Pro and Enterprise have a variety of additional features and is available for purchase. WebMO can now be installed on Windows, Mac, and Unix servers!
September 3, 2010

Molpro 2006 Installation Instructions for Linux

Obtain a Molpro username and password
Molpo is a commercial software product, and a license must be purchased from www.molpro.net. Registered licensees will receive a Molpro username and password, which grant access to the download area of the Molpro website.

Download Molpro source code and license token
At the Molpro website, note the current version of Molpro. Follow the For Licensees link, and supply your Molpro username and password. Download a copy of the license token. Follow the Download link, select the current version of Molpro, and download the "Base source code" (which includes the latest patches and documenation).

Compiling Molpro requires one of the following compilers:

ifort Intel fortran compiler
pgf Portland Group fortran compiler
path Pathscale fortran compiler

Optionally, obtain and install an optimized BLAS and LAPACK library:

Install license token
$ cd ~
$ mkdir ~/.molpro
$ chmod 700 ~/.molpro
$ cd ~/.molpro
$ cp -p /{download_dir}token .
$ chmod 600 token

Extract Molpro files
$ cd ~
$ mkdir -p source/molpro
$ cd source/molpro
$ cp -p /{download_dir}/molpro.2006.1.tar.gz .
$ tar xzf molpro.2006.1.tar.gz
$ cd molpro2006.1

If necessary, setup fortran compiler
For the 64-bit Intel fortran compiler:
$ source /opt/intel/fce/9.0/bin/ifortvars.sh

Configure Molpro
Use -i4 or -i8 to select 4-byte (32-bit compiler) or 8-byte (64-bit compiler) integer size
Use -ifort, -pgf, or -path to select the compiler
Use "-blas 0" for molpro's unoptimized blas and lapack routines, or use "-blas 3" if supplying optimized libraries
Accept all defaults except if you wish to change installation directory locations or need to specify BLAS and LAPACK library locations:

For the 64-bit Intel compiler using molpro's routines:
$ ./configure -i8 -ifort -blas 0

Building program for processor type=x86_64
Program may not run on other platforms
You can choose another processor type using the [p3|p4|athlon|x86_64|ia64] option

found /usr/bin/perl version 5.008006
Machine architecture is unix unix-i8 unix-linux unix-linux-x86_64

File size greater than 2GB allowed

Intel(R) Fortran Compiler for Intel(R) EM64T-based applications, Version 9.0 Build 20060222 Package ID: l_fc_c_9.0.033

Using Intel Fortran compiler (ifort for x86_64) version 9

Enter max number of atoms [ 200]: 
Enter max number of valence orbitals [ 300]: 
Enter max number of basis functions [2000]: 
Enter max number of states per symmetry [  20]: 
Enter max number of state symmetries [  16]: 
 
You are not using an optimised blas library

You are not using an optimised lapack library

Installed binaries directory [/usr/local/molpro/bin]

Installed auxiliary directory [/usr/local/molpro/lib/molpro-Linux-x86_64-i8-2006.1]

Installed HTML documentation directory [/home/polik/public_html/molpro/molpro2006.1]
/var/www/html/molpro2006.1            <---!!!!!
Installed CGI script directory [/home/polik/public_html/molpro/molpro2006.1]
/var/www/html/molpro2006.1            <---!!!!!
Found glob.h
Using getopt_long from system library
parse-x86_64-unknown-linux-gnu-i8.o.gz is your object.

CONFIG file created; proceed to compilation

Save the CONFIG file, inspect the contents, and edit if necessary:
$ cp -p CONFIG CONFIG.000
$ more CONFIG

For the 64-bit Intel compiler using acml's routines:
$ ./configure -i8 -ifort -blas 3

Building program for processor type=x86_64
Program may not run on other platforms
You can choose another processor type using the [p3|p4|athlon|x86_64|ia64] option

found /usr/bin/perl version 5.008006
Machine architecture is unix unix-i8 unix-linux unix-linux-x86_64

File size greater than 2GB allowed

Intel(R) Fortran Compiler for Intel(R) EM64T-based applications, Version 9.0 Build 20060222 Package ID: l_fc_c_9.0.033

Using Intel Fortran compiler (ifort for x86_64) version 9

searching for blas libraries...

blaslibold=
plese select blas library from above list
(default ):
-L/opt/acml3.6.0/ifort64/lib -lacml -lacml_mv            <---!!!!!
acml library contains full lapack implementation

Enter max number of atoms [ 200]: 
Enter max number of valence orbitals [ 300]: 
Enter max number of basis functions [2000]: 
Enter max number of states per symmetry [  20]: 
Enter max number of state symmetries [  16]: 
 
If you wish to use a system BLAS library, please give the maximum
level (0, 1, 2, 3, or 4) of BLAS to be supplied by the system
If the system blas only supports 32 bit integers, only 0 or 4 can be used
4 is recommended for IBM, SGI-IRIX, SUN, FUJITSU
(default 3): 

Installed binaries directory [/usr/local/molpro/bin]

Installed auxiliary directory [/usr/local/molpro/lib/molpro-Linux-x86_64-i8-2006.1]

Installed HTML documentation directory [/home/polik/public_html/molpro/molpro2006.1]
/var/www/html/molpro2006.1            <---!!!!!
Installed CGI script directory [/home/polik/public_html/molpro/molpro2006.1]
/var/www/html/molpro2006.1            <---!!!!!
Found glob.h
Using getopt_long from system library
parse-x86_64-unknown-linux-gnu-i8.o.gz is your object.

CONFIG file created; proceed to compilation

Save the CONFIG file, inspect the contents, and edit if necessary:
$ cp -p CONFIG CONFIG.000
$ more CONFIG

Compile Molpro source code
$ make

make[1]: Entering directory `/home/webmo/source/molpro/molpro2006.1/utilities'
echo.c: compiling ... done
linking echo
...
A skeleton molpro configuration file has been set up in /home/polik/source/molpro/molpro2006.1/bin/molpros_2006_1_i8_x86_64.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/molpro2006.1/lib/    # directory containing library files
-x/home/webmo/source/molpro/molpro2006.1/bin/molpros_2006_1_i8_x86_64.exe    # executable
-m8000000    # default memory in 8-byte words
-K131072    # mxma cache size in 8-byte words
-B64    # mxma blocking size
--environment MOLPRO_COMPILER=ifort9.0

Please check it, and add options according to the molpro command description
...
Basis library indexed successfully
make[1]: Leaving directory `/home/webmo/source/molpro/molpro2006.1/lib'

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

Optionally, check the speed of your BLAS implementation
$ bin/molpro <mpptune.com

...
        MXMA_MPP:           CPU= 0.80    (  4423.680 MFLOP)
...

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

Run a test suite
$ make quicktest
$ more testjobs/test.log

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

Optionally, customize the default environment
$ su
# cd /usr/local/molpro/bin
# cp -p molpros_2006_1_i8_x86_64 molpros_2006_1_i8_x86_64.000
# vi molpros_2006_1_i8_x86_64
Make desired changes to default environment
# mv molpro molpro.000
# ln -s molpros_2006_1_i8_x86_64 molpro
# 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 molpro2006.1 molpro
# exit
Molpro documentation can be accessed at http://server.edu/molpro

Run jobs as a normal user
Submit a file locally:
$ /usr/local/molpro/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 $PBS_O_WORKDIR
/usr/local/molpro/bin/molpro <<"@" >$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 library files cannot be found, add the path to them to /etc/ld.so.conf (or to a new /etc/ld.so.conf.d/*.conf file) and then refresh the dynamic library loader
# vi /etc/ld.so.conf
# ldconfig
Alternatively, if library files cannot be found, define the LD_LIBRARY_PATH environmental variable to define their location, for example
$ LD_LIBRARY_PATH=/usr/pgi/linux86-64/6.1/libso; export LD_LIBRARY_PATH
If the files in /usr/local/molpro are transferred or shared to a different computer on which library files do not exist, copy the files to the other computer ($ ldd {executable} is useful for seeing what library files are being loaded)
When installation documentation, rename the molpro2006.1 directory to molpro2006-1 to workaround dvi2ps error regarding $TMP file containing a period; after installation of documentation, change name back to original