How to Use the Molecular Modeling Facility Cluster

If you want to get an account on the cluster, please contact the Director at 4-4508 or e-mail to .

From a workstation X11 terminal, you can open a secure shell connection:
ssh -Y

General Admonitions

  1. Change your temporary password immediately.
  2. Do not share your account with anyone else.
  3. Do not run any calculations on the head node -- use the queuing system.
  4. Do not run any calculations that read and write big files in your home directory -- use your assigned scratch space (/work/username for single node jobs and /work/cluster/username for multinode jobs).

Login Nodes ( and gplogin2)

Non-compute-intensive programs can be run on the login nodes. These include result-visualization and molecule-building programs like:
  1. ECCE/ebuilder
  2. Molden
  3. GaussView
  4. VMD
  5. Maestro/MacroModel

Compute Nodes

The following packages are set up to run from the queue on the compute nodes:
  1. Turbomole 6.2
  2. Gaussian 03
  3. NAMD 2.7
  4. CP2K 2.1.394

Torque/Maui Queuing System

Full documentation can be found on the Adaptive Computing website. but here is a short list:
Command: Description:
qsub submission_script - submits a job
qdel job_number - kills a job
qstat -u $USER - shows your current jobs
qstat -n - gives detailed info on your jobs
qstat - shows everyone's jobs

You will also need to copy the example run script to your calculation setup directory:

cp /modfac/etc/run_pbsjob ~/path/to/your/calculation/input/directory/

Go to your calculation directory and edit the run script per its internal documentation (use gedit, gvim, emacs, etc.)

The job submission queues are listed below:

Name Time limit Notes
mf_short 3h can run in any free space
mf_medium 14h
mf_long 60h
mf_verylong 336h
mf_infinity none
mf_prefinity none can be put to sleep by high-priority jobs

Once your job is ready to go, type "qsub run_pbsjob" and patiently wait for your results to come back.