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How do I run NAMD2 production jobs ?

Please note: The FAQ pages at the HPCVL website are continuously being revised. Some pages might pertain to an older configuration of the system. Please let us know if you encounter problems or inaccuracies, and we will correct the entries.

Only short test jobs of application software can be run interactively on HPCVL machines. Production jobs must be submitted via the scheduling software Grid Engine. For usage of this software, please consult our Grid Engine FAQ.

In most cases, you will be running NAMD production jobs in parallel mode. This means that you need to specify a number of CPUs that should be reserved to run each independent NAMD thread. This is done in a Grid Engine submission script.

The items in the template that are enclosed in mustr be replaced by the appropriate values. Lines that start with "#$" containn information for Grid Engine. The "#$ -V" line tells GE to inherit the shell setup from the calling shell, for instance the $PATH variable. "#$ -cwd" tells the system to start from the current working directory. "#$ -M" lets the system know you email address, so it can notify you when the job starts and ends. The "#$ -o" and "#$ -e" lines are there to define files that capture output that would go to the screen in an interactive run, coming from the program and the system, repsectively. Finally, the "#$ -pe" line serves to define the number of CPUs to be reserved. The number you insert here will be reused through the environment variable $NSLOTS, so that you do not have to type it again in the namd command line.

Note that the name of the configuration file that replaces "configuration file" in the script template, should have file extension .namd, just as in the interactive run.

Once you have a proper script file (let's call it namd.sh) you can submit your production job by typing

qsub namd.sh

The Grid Engine will take care of the rest.

 

Only short test jobs of application software can be run interactively on HPCVL machines. Production jobs must be submitted via the scheduling software Grid Engine. For usage of this software, please consult our Grid Engine FAQ.

In most cases, you will be running NAMD production jobs in parallel mode. This means that you need to specify a number of CPUs that should be reserved to run each independent NAMD thread. This is done in a Grid Engine submission script. You can use this sample script as a template.

The items in the template that are enclosed in {} mustr be replaced by the appropriate values. Lines that start with "#$" containn information for Grid Engine. The "#$ -V" line tells GE to inherit the shell setup from the calling shell, for instance the $PATH variable. "#$ -cwd" tells the system to start from the current working directory. "#$ -M" lets the system know you email address, so it can notify you when the job starts and ends. The "#$ -o" and "#$ -e" lines are there to define files that capture output that would go to the screen in an interactive run, coming from the program and the system, repsectively. Finally, the "#$ -pe" line serves to define the number of CPUs to be reserved. The number you insert here will be reused through the environment variable $NSLOTS, so that you do not have to type it again in the namd command line.

Note that the name of the configuration file that replaces "{configuration file}" in the script template, should have file extension .namd, just as in the interactive run.

Once you have a proper script file (let's call it namd.sh) you can submit your production job by typing

qsub namd.sh

The Grid Engine will take care of the rest.