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Can USERE subroutine run in parallel?
#28496 10/20/11 03:58 PM
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Hi All,
I'm adding a user supplied energy and force in my simulation through the USERE subroutine. It works in a serial compilation of CHARMM. I was wondering if it should also work in a parallel version? Or is USERE not setup to run in parallel?

I'm using CHARMM v35b5.
Thanks,
Ed

Re: Can USERE subroutine run in parallel?
Edo #28499 10/20/11 06:07 PM
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Of course. This is entirely up to you, as with all parallel programming. You have to do the partitioning of the work across the nodes. Coordinates and forces are communicated outside the energy calculation, so you should not have to worry about that. Caveat: With the current (c35) parallel implementation you can also assume that each node has access to all coordinates, but this will change in the next release which will also support spatial decomposition. There may be other data that you have to communicate using MPI.

Last edited by lennart; 10/20/11 09:14 PM. Reason: caveat about spatial decomposition

Lennart Nilsson
Karolinska Institutet
Stockholm, Sweden
Re: Can USERE subroutine run in parallel?
lennart #28511 10/21/11 12:03 PM
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Thank you Prof Nilsson for the info. I'm just applying a constant force onto a single atom (the AFM module is not sufficient for some of the things I want to do, which is why I coded it in usere). So it sounds like I won't need to modify my USERE code for it to work in parallel.

Re: Can USERE subroutine run in parallel?
Edo #28512 10/21/11 12:12 PM
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The PULL command does apply a constant force (or periodic in time) to one or more atoms. See cons.doc


Lennart Nilsson
Karolinska Institutet
Stockholm, Sweden
Re: Can USERE subroutine run in parallel?
lennart #28549 10/24/11 03:30 PM
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This is big help, thank you.
Ed


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