On 6/27/16 9:37 AM, יוכבד wrote:
but still shouldn't I see some acceleration?
The other process is not using the GPUs at all only CPUs
And your GPU run is trying to use the CPUs to do PME; you'll note from the .log
file that a large amount of time is being spent doing PME, which then becomes a
limiting factor in the progress of the GPU simulation. As I said, you need to
properly allocate the resources.
-Justin
On Mon, Jun 27, 2016 at 4:25 PM, Justin Lemkul <[email protected]> wrote:
On 6/27/16 9:12 AM, יוכבד wrote:
here's a link to the log file
https://drive.google.com/file/d/0By0KVsEJPLGjOU1oaGxzcjNBS28/view?usp=sharing
The computer is 4GPUs and 32 CPUs but some GPUs were in use hence only
15-16 were used.
That's not what
gmx mdrun -v -deffnm nvt_New -nb gpu
will do. That command will attempt to use all resources available on the
machine, all 32 CPU and all 4 GPU. The .log file confirms this is the
case. If you're running multiple processes on the same machine, you need
to appropriately define what should be used for each run, using -pin,
-pinoffset, -gpu_id, -nt, -ntmpi, etc as needed, otherwise they're all
going to try to use everything, and end up fighting each other, slowing
everything down.
-Justin
Thanks
On Mon, Jun 27, 2016 at 3:52 PM, Justin Lemkul <[email protected]> wrote:
On 6/27/16 8:49 AM, יוכבד wrote:
Hi
I've recently installed GROMACS 5.1.2.
I ran the benchmarks files of rnase (rnase_dodec_vsites) on my machine
using 4GPUs and 32 CPU and I got the performances of ~330ns/day
Now I'm tring to run my system but I don't see any acceleration (a 500ps
nvt equilibration takes close to 2hr (6.7ns/day)- This was using 4 GPUs
and
15 CPUs.
What am I missing here?
attached is my mdp file and the command used was
The list does not accept attachments. The .log files are the most
informative as the end contains a full performance breakdown; if you wish
to share them, upload them to a file sharing service and provide a URL.
The actual performance depends largely on the content/size of the system.
Perhaps you have a bottleneck due to the size of the system such that you
cannot efficiently utilize all 4 GPU and 15 CPUs (an odd combination,
anyway) simultaneously.
-Justin
--
==================================================
Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow
Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201
[email protected] | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul
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==================================================
Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow
Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201
[email protected] | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul
==================================================
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send a mail to [email protected].
--
==================================================
Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow
Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201
[email protected] | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul
==================================================
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