[AMBER] constant pH caluculations with pmemd.cuda.MPI

From: Hofer, Florian <Florian.Hofer.uibk.ac.at>
Date: Wed, 15 Feb 2017 12:50:44 +0000

Dear AMBER Developers,
we are using the constant pH calculation algorithm in AMBER, espacially the newly implemented version for pmemd.CUDA in AMBER 16. Calculations of the same system using a single GPU and the pmemd.cuda executable work fine, however when we were trying to do the calcualtion with 2 GPUs and using the pmemd.cuda.MPI executable we noticed that the calculations get halted at about 15000 steps.
The caluclations produce regular outputfiles until they stop and the jobs drop from the GPU, without any error messages. However the jobs remain active on the CPU with 100% each.

The caluclations are done on a GPU cluster with the following specs:

MPI program: mpich-3.2
AMBER version: AMBER 16 updated on 10 Feb 2017
Queue system: SGE-6.2u5p3

Peer to Peer: Enabled
GeForce GTX 780 2x or GeForce GTX TITAN X 2x
Intel(R) Xeon(R) CPU E5-2609 v2 2x

Has anyone else noted similar behavior or can help us figure out the problem?

Really appreciating your help and best wishes,
Florian Hofer
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Received on Wed Feb 15 2017 - 05:00:02 PST
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