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
- 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)
- 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
- To fix this, do
Older notes, c. 2005
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 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