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CHARMM on a cluster
#172 10/20/03 09:21 AM
Joined: Oct 2003
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tjaart Offline OP
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We have managed to get CHARMM compiled and running on a Linux cluster. We intend to run protein minimization and dynamics and I have the following questions:
How can a process involving sequential calculations like minimization or dynamics, be run on a cluster?
Is a cluster (Linux or otherwise) really suitable for running protein minimizations and dynamics?

Any comments welcome.


Tjaart de Beer
Re: CHARMM on a cluster
tjaart #173 10/20/03 10:50 AM
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A cluster is very useful for minimizations and dynamics. If you want to run a series of jobs one after the other you can use a script that submits the next job after the first one is finished:
#!/bin/ksh
cd my_dir
charmm < my_input.inp > my_output.out
qsub -q parallel next_job

This basic script can of course be made more elegant, allowing a predefined number of resubmissions.

Note that if you use MPI you may have to run charmm using a slightly more complicated way due to the fact that with MPI stdin can not be rewound:

charmm < stdin.inp > my_output.out ZZZ=my_input.inp

where stdin.inp looks like this
* input prologue allowing stdin-rewinding under MPI
*
stream @ZZZ
stop

Note also that in this case the name of your input name cannot contain a mix of upper- and lowercase letters.


Lennart Nilsson
Karolinska Institutet
Stockholm, Sweden

Moderated by  lennart, rmv 

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