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1102 Natural Sciences 2
University of California, Irvine,
California, 92697-2025 ::
phone (949) 824-4097 ::
fax (949) 824-8571
How to Use the Molecular Modeling Facility Cluster
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If you want to get an account on the cluster, please contact the Director at 4-4508 or e-mail to
nathan.crawford@uci.edu .
From a workstation X11 terminal, you can open a secure shell connection:
ssh -Y username@gplogin1.ps.uci.edu.
General Admonitions
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Change your temporary password immediately.
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Do not share your account with anyone else.
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Do not run any calculations on the head node -- use the queuing system.
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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 (gplogin1.ps.uci.edu and gplogin2)
Non-compute-intensive programs can be run on the login nodes. These include result-visualization and molecule-building programs like:
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ECCE/ebuilder
"ebuilder"
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Molden
"gmolden"
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GaussView
"gv"
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VMD
"vmd"
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Maestro/MacroModel
"maestro"
Compute Nodes
The following packages are set up to run from the queue on the compute nodes:
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Turbomole 6.2
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Gaussian 03
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NAMD 2.7
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CP2K 2.1.394
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GAMESS-US
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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 |
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| 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.
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