Re: [AMBER] Regarding the MPI error in parallel running of 3D-RISM

From: David A Case <>
Date: Mon, 23 Jul 2018 11:50:33 -0400

On Mon, Jul 23, 2018, PRITI ROY wrote:
> I tried my system( 5550 atoms and TIP3P) with 48 to 144 cores with many
> type of combinations and ended up with no output for long run time
> (~3days). I think this problem is not due to memory problem or this
> calculation may stuck in infinite loop (might be I am wrong).

Try *much* smaller numbers of MPI threads. Use the --progress flag to
follow what is happening. The key point of your hardware is the amount
of memory, which you don't list.

If you are able to share your PDB file, you might post it, and we can
see if we see problems in running this through rism3d.snglpnt. 5000
atoms should not require extraordinary amounts of time, such as days.

....hope this helps...dac

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Received on Mon Jul 23 2018 - 09:00:02 PDT
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