Thank you for the kind reply.
I have less understanding on -machinefile and~/mpd.hosts
I don't use any parallel job scheduler. In this situation how or from where I can get the machinefile and mpd.hosts info? Do I need to creat one? Sorry I am not aware of these issues.
I appreciate if you can help me here. I tried surf the net to get some info on this matter but no avail.
Regards.
Vijay Manickam Achari
(Phd Student c/o Prof Rauzah Hashim)
Chemistry Department,
University of Malaya,
Malaysia
vjramana.gmail.com
________________________________
From: Robert Crovella <RCrovella.nvidia.com>
To: AMBER Mailing List <amber.ambermd.org>
Sent: Saturday, 21 April 2012, 20:50
Subject: Re: [AMBER] using two GPUs
For MPICH2 you will need to start the mpi daemon first:
mpd &
mpirun -machinefile ~/mpd.hosts -np 2 ./pmemd.cuda.MPI -O -o mdout -x mdcrd -r restrt -inf mdinfo
something like that should work
your machinefile (mpd.hosts) would just have your hostname listed twice, like this:
hostname
hostname
The above assumes that your MPI is installed properly and that you have built pmemd.cuda.MPI according to the AMBER build instructions.
-----Original Message-----
From: Vijay Manickam Achari [mailto:vjrajamany.yahoo.com]
Sent: Friday, April 20, 2012 10:15 PM
To: AMBER Mailing List
Subject: Re: [AMBER] using two GPUs
Thanks for the info.
By the way I am using mpich2-1.4 version.
Anyone could help on this?
Regards
Vijay Manickam Achari
(Phd Student c/o Prof Rauzah Hashim)
Chemistry Department,
University of Malaya,
Malaysia
vjramana.gmail.com
________________________________
From: Robert Crovella <RCrovella.nvidia.com>
To: Amber mailing List <amber.ambermd.org>
Sent: Saturday, 21 April 2012, 10:07
Subject: Re: [AMBER] using two GPUs
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 [mailto:vjrajamany.yahoo.com]
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?
Thanks
Vijay Manickam Achari
(Phd Student c/o Prof Rauzah Hashim)
Chemistry Department,
University of Malaya,
Malaysia
vjramana.gmail.com
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Received on Mon Apr 23 2012 - 22:30:03 PDT
