Hi,
Yes that's expected. If you want to run two simulations in parallel then
you need to follow the advice in the user guide. Two plain calls to gmx
mdrun cannot work usefully.
Mark
On Fri., 13 Dec. 2019, 11:22 Nikhil Maroli, wrote:
> Initially, I tried to run 2+ jobs in my workstation with
Hi,
Those commands are listed in the user guide, please look there :-)
Mark
On Fri., 13 Dec. 2019, 10:10 Pragati Sharma, wrote:
> Hi Paul,
>
> The option -pme gpu works when I give pme order = 4 in mdp file instead of
> 3. but it gives me an increase of 6-7 ns/day.
>
> @Dave M : I am also
Initially, I tried to run 2+ jobs in my workstation with multiple GPU, what
I found is running one simulation at a time is much faster than running in
parallel.
You are not going to get equal or exactly half the performance during
parallel inputs.
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Hi Paul,
The option -pme gpu works when I give pme order = 4 in mdp file instead of
3. but it gives me an increase of 6-7 ns/day.
@Dave M : I am also getting same observation. "If I run just one
simulation, I get almost double performance compared to when I run two
simulations in two GPUs as
Hi Paul,
I just jumped in this discussion. But I am wondering is
CUDA_VISIBLE_DEVICES equivalent to providing gpu_id in mdrun?
Also, my multiple simulations run slower in the same node with multiple
gpus. e.g. in a node with 4 GPU and 64 CPU
mpirun -np 1 mdrun -ntomp 24 -gpu_id 0 -pin on
mpirun
Hello,
the error you are getting in the end means that your simulation likely
does not use PME, or uses it in a way that is not implemented to run on
the GPU.
You can still run the nonbonded calculations on the GPU, just remove the
-pme gpu flag.
For running different simulations on your
Thanks Nikhil.
About the second question. It is actually implemented , as you can see the
link below, however I cannot run these commands without error.
https://mailman-1.sys.kth.se/pipermail/gromacs.org_gmx-users/2019-July/126012.html
On Fri, Dec 13, 2019 at 12:28 PM Nikhil Maroli wrote:
>
You can assign part of the core and 1 GPU to one job and another part with
separate command.
For ex.
1. gmx mdrun -ntmpi XX -ntomp YY -gpu_id K1
2. gmx mdrun -ntmpi XX2 -ntomp YY2 -gpu_id K2
the second part of the question is related to the implementation of such
calculations in GPU< which is
Hello all,
I am running a polymer melt with 10 atoms, 2 fs time step, PME, on a
workstation with specifications:
2X Intel Xeon 6128 3.4 2666 MHz 6-core CPU
2X16B DDR4 RAM
2XRTX 2080Ti 11 GB
I have installed *GPU and thread_mpi *enabled gromacs 2019.0 version using:
cmake ..
