Mark,
You're right, sorry. I actually mixed up -nt (total number of threads)
with -ntomp (per rank), lack of sleep will do that to me sometimes.
Yes. The -ntomp, -nt, and -ntmpi options have always been different from
each other, and still work as they always did. See
http://manual.gromacs.org/documentation/2018-latest/user-guide/mdrun-performance.html.
There are 8 ranks. You specified one to do PME work, and for all PP work
and all PME work to go on GPUs, and that 7 of the GPU tasks go on GPU 0 and
one on GPU 1. Please check out the docs for each option rather than guess
:-)
Yup, i will go through it again. -gputasks appears to provide much more
control over what specifically happens on the GPU side, so i'll try my
best to use it without guessing. Feel free to tell me to RTFM anytime. ;)
Thanks,
Alex
On 2/9/2018 8:25 AM, Szilárd Páll wrote:
Hi,
First of all,have you read the docs (admittedly somewhat brief):
http://manual.gromacs.org/documentation/2018/user-guide/mdrun-performance.html#types-of-gpu-tasks
The current PME GPU was optimized for single-GPU runs. Using multiple
GPUs
with PME offloaded works, but this mode hasn't been an optimization
target
and it will often not give very good performance. Using multiple GPUs
requires a separate PME rank (as you have realized), only one can be used
(as we don't support PME decomposition on GPUs) and it comes some
inherent
scaling drawbacks. For this reason, unless you _need_ your single run to
be
as fast as possible, you'll be better off running multiple simulations
side-by side.
A few tips for tuning the performance of a multi-GPU run with PME
offload:
* expect to get at best 1.5 scaling to 2 GPUs (rarely 3 if the tasks
allow)
* generally it's best to use about the same decomposition that you'd use
with nonbonded-only offload, e.g. in your case 6-8 ranks
* map the GPU task alone or at most together with 1 PP rank to a GPU,
i.e.
use the new -gputasks option
e.g. for your case I'd expect the following to work ~best:
gmx mdrun -v -deffnm md -pme gpu -nb gpu -ntmpi 8 -ntomp 6 -npme 1
-gputasks 00000001
or
gmx mdrun -v -deffnm md -pme gpu -nb gpu -ntmpi 8 -ntomp 6 -npme 1
-gputasks 00000011
Let me know if that gave some improvement.
Cheers,
--
Szilárd
On Fri, Feb 9, 2018 at 8:51 AM, Gmx QA <gmxquesti...@gmail.com> wrote:
Hi list,
I am trying out the new gromacs 2018 (really nice so far), but have a
few
questions about what command line options I should specify, specifically
with the new gnu pme implementation.
My computer has two CPUs (with 12 cores each, 24 with hyper threading)
and
two GPUs, and I currently (with 2018) start simulations like this:
$ gmx mdrun -v -deffnm md -pme gpu -nb gpu -ntmpi 2 -npme 1 -ntomp 24
-gpu_id 01
this works, but gromacs prints the message that 24 omp threads per mpi
rank
is likely inefficient. However, trying to reduce the number of omp
threads
I see a reduction in performance. Is this message no longer relevant
with
gpu pme or am I overlooking something?
Thanks
/PK
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