I cannot connect to Chemfarm
Access to Chemfarm is possible only from the Weizmann network. Therefore, you have to be either connected to LAN, or to secure wireless, or via VPN. You have to contact your department secretary to arrange your network access.
What is my disk space quota?
To find the amount of space and files you use in all the areas use the following commands:
mmlsquota --block-size auto -u $USER data01
to see your personal usage. Or:
mmlsquota --block-size auto -g `id -gn` data01
to display usage of your group.
How many CPU cores can I use?
Some users have personal limits on private queues, according to a policy in their groups. In order to see your personal limit, type:
qmgr -c 'p s' | grep u:$USER
The limits are "soft" and "hard". The user is not allowed to run more jobs than are allowed by the hard limit. Please note that jobs running above the soft limit can be suspended in any queue. For the group limits:
qmgr -c 'p s' | grep g:`id -gn`
PBS Professional Cheat-Sheet
PBS Professional Quick Reference Guide for users
Starting MATLAB parpool fails or allocates too few workers
The best solution to avoid limitations on Parallel toolbox in MATLAB is to set a new MATLAB preferences folder location for each job. To do this add the line below to your submission script.
export MATLAB_PREFDIR=${WORK}/my_project/${PBS_JOBID}
It is a good idea to have a Job ID in a folder name. One can check the folder location from the MATLAB script, by running "prefdir" command.
Acknowledgments
Since 80% of the Ben May Center's annual budget goes toward the upkeep of Chemfarm. It would be very beneficial (and appropriate) to add to the "Acknowledgments" of any published paper that relies substantially[*] on CHEMFARM computation, a sentence along the following lines:
Computational work was carried out on the Faculty of Chemistry's high-performance computing facility CHEMFARM, which is supported in part by the Ben May Center for Chemical Theory and Computation.
[*] We are not asking you to do this for an experimental paper for which you ran 1 or 2 simulations that took 15 minutes. We're talking about papers that couldn't have been completed without major computation on CHEMFARM or a comparable HPC facility.
Chemfarm Wiki
You can find small pieces and recipes on the Chemfarm Wiki
Software Licensing
We recommend applying the following license language in software distributed through github and similar platforms. This license permits only non-commercial use of the software.
Licensed under the Non-Profit Open Software License version 3.0.
The full license is available here.