Cluster:Gaussian

Web interface: WebMO

Users for WebMo:

• Create an LDAP user.
• Log in using that user's credentials
• Give the group password. (This is a one-time requirement. Future logins will not ask for it.)
• Use Gaussian.

An old WebMO configuration example

Notes below taken from here.

WebMO

• yum installed httpd
• Installed on bs0 with the following params:

Path to perl:         /usr/bin/perl
Webserver name:       bs0-new.cluster.earlham.edu
HTML directory:       /var/www/webmo
HTML URL:             /webmo
CGI script directory: /var/www/cgi-bin
CGI script URL:       /cgi-bin
User files directory: /mounts/bobsced/WebMO

• Get this error when authing with LDAP: Can't locate Authen/Simple/LDAP.pm
• yum installed perl-LDAP.noarch, didn't work, so used CPAN to install Authen::Simple::LDAP
• edited /var/www/cgi-bin/interfaces/authen.conf for our LDAP settings
• Before externally authenticated users can use it, you have to go in as administrator and check the box to allow them in the Webmo group (or whatever other group)
• Gamess:
  • yum install compat-gcc-34-g77.x86_64 and gfortran
  • Followed directions from Webmo site
• Added the following line to httpd.conf:

SuexecUserGroup bob users

• Gaussian 09 not supported, though it's installed in /mounts/bobsced/usr/local/g09
• Installed g03, except get errors:

Erroneous write during file extend. write 160 instead of 4096
Probably out of disk space.
Write error in NtrExt1: No such file or directory

or

Write error in NtrExt1: Bad address

• • To fix this, do echo 0 > /proc/sys/kernel/randomize_va_space
  • This needs to be set to happen all the time on boot

Older notes, c. 2005

• Gaussian environment
• Running Gaussian in parallel
• Sample Gaussian PBS script

Gaussian environment

I use this in my .bashrc:

       export GAUSS_EXEDIR=/cluster/bazaar/software/g03
       export GAUSS_LFLAGS='-nodelist "b0 b1" -opt "Tsnet.Node.lindarsharg: ssh " -mp 2'
       export GAUSS_SCRDIR=/tmp
       export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:/cluster/bazaar/software/g03
       export g03root=/cluster/bazaar/software
       export PATH=$PATH:/cluster/bazaar/software/g03

Seems to work, although you might want to tweak the node list.

Running Gaussian in parallel

Understand the distinction between nprocs and nprocl. nprocs is for a shared-memory (single-image) machine, whereas nprocl is for a distributed-memory (cluster) system. You want to use nprocl on all our computing systems. For example, if you want to run on eight processes (four nodes), add a line like this

%nprocl=8

to your input file. You should then specify qsub -l nodes=4:ppn=2 script on the command line to submit your PBS script with a requirement of four dual-processor machines.

Once you have the number of CPUs specified in the input file, make sure that your nodelist in GAUSS_LFLAGS is set properly. See Gaussian environment for details.

If you have a bunch of input files you want to modify, use the add_nproc.pl script in /cluster/generic/bin. First cd to the directory with your input files, and then do:

perl /cluster/generic/bin/add_nproc.pl n

where n is the number proecssors you want to run on.

After that, fire it up with $g03root/bsd/g03l.

Sample Gaussian PBS script

This is a sample PBS script for Gaussian:

#!/bin/sh
#PBS -N gaussian_test061.com_nodes=2:ppn=2
#PBS -o /cluster/home/skylar/bazaar/gaussian_nodes2/test061.com.out
#PBS -e /cluster/home/skylar/bazaar/gaussian_nodes2/test061.com.err
#PBS -q batch
#PBS -m abe
#PBS -l nodes=2:ppn=2

cd $PBS_O_WORKDIR
/cluster/bazaar/software/g03/bsd/g03l < /cluster/bazaar/software/g03/tests/com_smp4/test061.com > /cluster/home/skylar/bazaar/gaussian_nodes2/test061.com.log

exit $!