Re: [AMBER] using two GPUs

From: Robert Crovella <>
Date: Fri, 20 Apr 2012 19:07:32 -0700

To use multiple GPUs, you must use the MPI build of GPU AMBER, i.e. pmemd.cuda.MPI

For MVAPICH2 1.6 version of MPI, a 2 gpu invocation might look something like this:
mpirun_rsh -ssh -hostfile ~/.amber.hosts.2 -np 2 pmemd.cuda.MPI -O -i mdin -c inpcrd -l logmpi -o ~/results/amber-2-gpus

you'll need to setup your hostfile properly for MPI

-----Original Message-----
From: Vijay Manickam Achari []
Sent: Friday, April 20, 2012 7:40 PM
To: Amber mailing List
Subject: [AMBER] using two GPUs

I am trying to use more then one GPU to run my job. For instance I would like to use two GPUs with its ID 2 and 3.

I used environment setup as given in Amber12 manual (page 247) as below

setenv $AMBERHOME /usr/local/apps/amber12 #setenv CUDA_VISIBLE_DEVICES 2,3 export CUDA_VISIBLE_DEVICES=2,3

But when I use top command I can see only one pmemd.cuda command is running not two.
IS there any way to make both the GPUs run on same job?


Vijay Manickam Achari
(Phd Student c/o Prof Rauzah Hashim)
Chemistry Department,
University of Malaya,
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Received on Fri Apr 20 2012 - 19:30:03 PDT
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