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c37a2 charmm with parallelization
#33680 03/30/14 02:48 AM
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I have install the c37a2 charmm with parallelization,and it shows that success,the installation commands is:
./install.com gun xxlarge M

However,when I submit a job, I found the rate is so slow! Even slower than the non-parallelization charmm with just only one CPU!
Besides,I submit the job to the cluster with qsub.and I just use just one node and each node has 8 CPUs.

Re: c37a2 charmm with parallelization
Yong Mao #33681 03/30/14 08:20 AM
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c37a2 is not a released version.

Please provide more detail about your benchmark: number of atoms, the input file used to run it, the timing data at the end of the output for both the serial and parallel runs (and for the parallel run it is useful to have the output for all nodes)


Lennart Nilsson
Karolinska Institutet
Stockholm, Sweden
Re: c37a2 charmm with parallelization
Yong Mao #33682 03/30/14 06:16 PM
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The results would seem to argue against a successful compilation, but as noted, the lack of detail makes it difficult to judge or offer suggestions. The only case I can think of where this might happen for correctly compiled code is a test system with a fairly small number of atoms.


Rick Venable
computational chemist


Moderated by  lennart, rmv 

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