[gmx-users] Multithread run issues

[Mahmood Naderan]

>mpirun -np 1 mdrun_mpi -v -ntomp 2

Agree with that.

>This is not a problem to solve by running applications differently. You
>will have users running jobs with single ranks/processes that use threading
>of various kinds to fill the cores. That's a feature, not a bug. Either
>configure PBS to cope with decades-old technology, or don't worry about it.

I found this document
​(
https://wiki.anl.gov/cnm/HPC/Submitting_and_Managing_Jobs/Advanced_node_selection#Multithreading_using_OpenMP
)
​That is what I want to be sure that number of threads and cores used for
gromacs fits to the PBS stats.

Instead of the variable, I wrote



#PBS -l nodes=1:ppn=2​
export OMP_NUM_THREADS=2
mpirun  mdrun -v

So that will use two cores with 4 threads totally and PBS should report 4
processors are occupied.
However, gromacs failed with the following error




Regards,
Mahmood



On Mon, Oct 10, 2016 at 1:41 PM, Mark Abraham <mark.j.abraham at gmail.com>
wrote:

> Hi,
>
> Yeah, but that run is very likely
>
> a) useless because you're just running two copies of the same simulation
> because you're not running MPI-enabled mdrun
> b) and even if not, less efficient than the thread-MPI version
>
> mdrun -v -nt 2
>
> c) and even if not, likely slightly less efficient than the real-MPI
> version
>
> mpirun -np 1 mdrun_mpi -v -ntomp 2
>
> top isn't necessarily reporting anything relevant. A CPU can be nominally
> idle while waiting for communication, but what does top think about that?
>
> Mark
>
> On Mon, Oct 10, 2016 at 11:47 AM Mahmood Naderan <mahmood.nt at gmail.com>
> wrote:
>
> > OK. I understood the  documents.
> > Thing that I want is to see two processes (for example) each consumes
> 100%
> > cpu. The command for that is
> >
> > mpirun -np 2 mdrun -v -nt 1
> >
> > ​Thanks Mark.​
> >
> > Regards,
> > Mahmood
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