To add to Jason's answer - you can of course use the remaining 19 CPUs
(make sure there are really 20 cores in your machine and not 10 cores + 10
hyperthreads) for something else while the GPU run is running.
cd GPU_run
nohup $AMBERHOME/bin/pmemd.cuda -O -i ... &
cd ../CPU_run
nohup mpirun -np 19 $AMBERHOME/bin/pmemd.MPI -O -i ... &
All the best
Ross
On 5/14/14, 8:17 AM, "Jason Swails" <jason.swails.gmail.com> wrote:
>On Wed, 2014-05-14 at 17:49 +0300, MURAT OZTURK wrote:
>> I will be running on a single node with 20 cpus and 1 gpu installed.
>>
>> Do I have to use pmemd.cuda.MPI for this, or is pmemd.cuda enough..?
>>
>> How do I specify the number of cpus used with pmemd.cuda? I can't seem
>>to
>> find this information in the manual.
>
>Just pmemd.cuda. The thing about pmemd.cuda is that it runs the
>_entire_ calculation on the GPU, so adding CPUs buys you nothing.
>
>The way it is designed, each CPU thread will launch a GPU thread as well
>(so you are stuck using 1 CPU for each GPU).
>
>HTH,
>Jason
>
>--
>Jason M. Swails
>BioMaPS,
>Rutgers University
>Postdoctoral Researcher
>
>
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Received on Wed May 14 2014 - 09:30:02 PDT
