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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.


  • yum installed httpd
  • Installed on bs0 with the following params:
Path to perl:         /usr/bin/perl
Webserver name:
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/
  • 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


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

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


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 script in /cluster/generic/bin. First cd to the directory with your input files, and then do:

perl /cluster/generic/bin/ 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:

#PBS -N gaussian_test061.com_nodes=2:ppn=2
#PBS -o /cluster/home/skylar/bazaar/gaussian_nodes2/
#PBS -e /cluster/home/skylar/bazaar/gaussian_nodes2/
#PBS -q batch
#PBS -m abe
#PBS -l nodes=2:ppn=2
/cluster/bazaar/software/g03/bsd/g03l < /cluster/bazaar/software/g03/tests/com_smp4/ > /cluster/home/skylar/bazaar/gaussian_nodes2/
exit $!