[gmx-users] openmpi execution using sbatch & mpirun every commandexecuted several times

[P C Kroon]

Although “don’t” does cover the best advice, there’s a workaround.

Srun -n 1 -c 1 gmx_mpi grompp ...

So run on 1 node (-n 1) with 1 CPU (-c 1). You’ll need to read the mpirun documentation to figure out the exact options for that.

Peter

From: Mark Abraham
Sent: 12 December 2017 21:45
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] openmpi execution using sbatch & mpirun every commandexecuted several times

Hi,

On Wed, Dec 13, 2017, 7:34 AM Vedat Durmaz <durmaz at zib.de> wrote:

>
> hi everybody,
>
> i'm working on an ubuntu 16.04 system with gromacs-openmpi (5.1.2)
> installed from the ubuntu repos. everything works fine when i submit
> job.slurm using sbatch where job.slurm roughly looks like this
>
> -------------------------
> #!/bin/bash -l
>
> #SBATCH -N 1
> #SBATCH -n 24
> #SBATCH -t 02:00:00
>
> cd $4
>
> cp file1 file2
> grompp ...
> mpirun -np 24 mdrun_mpi ...   ### WORKS FINE
> -------------------------
>
> and the mdrun_mpi output contains the following statements:
>
> -------------------------
> Using 24 MPI processes
> Using 1 OpenMP thread per MPI process
>
>   mdrun_mpi -v -deffnm em
>
> Number of logical cores detected (24) does not match the number reported
> by OpenMP (12).
> Consider setting the launch configuration manually!
>
> Running on 1 node with total 24 cores, 24 logical cores
> -------------------------
>
>
> now, i want to put the last 3 commands of job.slurm into an extra script
> (run_gmx.sh)
>

Don't. It doesn't work with any MPI application

Mark

-------------------------
> #!/bin/bash
>
> cp file1 file2
> grompp ...
> mdrun_mpi ...
> -------------------------
>
> that i start with mpirun
>
> -------------------------
> #!/bin/bash -l
>
> #SBATCH -N 1
> #SBATCH -n 24
> #SBATCH -t 02:00:00
>
> cd $4
> mpirun -np 24 run_gmx.sh
> -------------------------
>
> but now i get strange errors because every non-mpi programm (cp, grompp)
> is executed 24 times which gives a desaster in the file system.
>
>
> if i change job.slurm to
>
> -------------------------
> #!/bin/bash -l
>
> #SBATCH -N 1
> #SBATCH --ntasks-per-node=1
> #SBATCH -t 02:00:00
>
> cd $4
> mpirun run_gmx.sh
> -------------------------
>
> i get the following error in the output:
>
> Number of logical cores detected (24) does not match the number reported
> by OpenMP (1).
> Consider setting the launch configuration manually!
>
> Running on 1 node with total 24 cores, 24 logical cores
> Using 1 MPI process
> Using 24 OpenMP threads
>
> Fatal error:
> Your choice of 1 MPI rank and the use of 24 total threads leads to the use
> of 24 OpenMP threads, whereas we expect the optimum to be with more MPI
> ranks with 1 to 6 OpenMP threads. If you want to run with this many OpenMP
> threads, specify the -ntomp option. But we suggest to increase the number
> of MPI ranks.
>
>
> and if i use -ntomp
> -------------------------
> #!/bin/bash
>
> cp file1 file2
> grompp ...
> mdrun_mpi -ntomp 24 ...
> -------------------------
>
> things seem to work fine but mdrun_mpi is extremely slow as if it was
> running on one core only. and that's the output:
>
>   mdrun_mpi -ntomp 24 -v -deffnm em
>
> Number of logical cores detected (24) does not match the number reported
> by OpenMP (1).
> Consider setting the launch configuration manually!
>
> Running on 1 node with total 24 cores, 24 logical cores
>
> The number of OpenMP threads was set by environment variable
> OMP_NUM_THREADS to 24 (and the command-line setting agreed with that)
> Using 1 MPI process
> Using 24 OpenMP threads
>
> NOTE: You requested 24 OpenMP threads, whereas we expect the optimum to be
> with more MPI ranks with 1 to 6 OpenMP threads.
>
> Non-default thread affinity set probably by the OpenMP library,
> disabling internal thread affinity
>
>
>
> what am i doing wrong? what a the proper setting for my goal? i need to
> use an extra script executed with mpirun and i somehow need to reduce 24
> executions of serial commands to just one!
>
> any useful hint is appreciated.
>
> take care,
> vedat
>
>
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