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From: Jesper Lykkegaard Karlsen (jelka_at_mbg.au.dk)
Date: Wed Jul 01 2020 - 05:37:23 CDT
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Hi Adupa,
I do not think vmd is supporting OpenMPI.
And in that case your command asks for the job to be spread over 5 nodes (-N 5).
For vmd runs it is better to lock slurm run to one node only and then ask for more cpus-per-task (-c)
e.g.
srun -N 1 -n 1 -c 20 vmd -dispdev text -e poly.tcl
Cheers,
Jesper
--------------------------
Jesper Lykkegaard Karlsen
Scientific Computing
Centre for Structural Biology
Department of Molecular Biology and Genetics
Aarhus University
Gustav Wieds Vej 10
8000 Aarhus C
E-mail: jelka_at_mbg.au.dk
Tlf: +45 50906203
________________________________
Fra: owner-vmd-l_at_ks.uiuc.edu <owner-vmd-l_at_ks.uiuc.edu> på vegne af Adupa Vasista <adupavasista_at_gmail.com>
Sendt: 1. juli 2020 11:06
Til: Ashar Malik <asharjm_at_gmail.com>
Cc: vmd-l_at_ks.uiuc.edu <vmd-l_at_ks.uiuc.edu>
Emne: Re: vmd-l: VMD on HPC
I don't think that is the case, because the same command I am using to run namd, I never stumbled on this issue before.
Moreover, this morning I saw a similar mail in lammps mailing list, where the problem is said to be caused by VMD compiling without MPI support or using a mpirun command from a *different* MPI library. I messaged the system administrator about this, and will update as soon as he replies.
Thank you.
On Wed, Jul 1, 2020 at 1:49 PM Ashar Malik <asharjm_at_gmail.com<mailto:asharjm_at_gmail.com>> wrote:
It prints N times because you start "vmd" N times.
If you want to use "multiple cores" -- you should start VMD only once ... you can see that VMD in its (every) screen dump is listing that it's identifying 24 CPUs.
Following this, if the contents of poly.tcl are capable of scaling to many CPUs they will.
Additionally it will also depend on how this particular HPC node on which your job is going to end up running is set up, and if it allows a program to scale up.
On Wed, Jul 1, 2020 at 1:33 PM Adupa Vasista <adupavasista_at_gmail.com<mailto:adupavasista_at_gmail.com>> wrote:
Dear VMD users,
I am running VMD on HPC using the command
srun -N 5 vmd -dispdev text -e poly.tcl
But when I execute it, the vmd message is printed N number of times, like the below.
Info) VMD for LINUXAMD64, version 1.9.3 (November 30, 2016)
Info) http://www.ks.uiuc.edu/Research/vmd/
Info) Email questions and bug reports to vmd_at_ks.uiuc.edu<mailto:vmd_at_ks.uiuc.edu>
Info) Please include this reference in published work using VMD:
Info) Humphrey, W., Dalke, A. and Schulten, K., `VMD - Visual
Info) Molecular Dynamics', J. Molec. Graphics 1996, 14.1, 33-38.
Info) -------------------------------------------------------------
Info) Multithreading available, 24 CPUs detected.
Info) CPU features: SSE2 AVX AVX2 FMA
Info) VMD for LINUXAMD64, version 1.9.3 (November 30, 2016)
Info) http://www.ks.uiuc.edu/Research/vmd/
Info) Email questions and bug reports to vmd_at_ks.uiuc.edu<mailto:vmd_at_ks.uiuc.edu>
Info) Please include this reference in published work using VMD:
Info) Humphrey, W., Dalke, A. and Schulten, K., `VMD - Visual
Info) Molecular Dynamics', J. Molec. Graphics 1996, 14.1, 33-38.
Info) -------------------------------------------------------------
Info) Multithreading available, 24 CPUs detected.
Info) CPU features: SSE2 AVX AVX2 FMA
Info) Free system memory: 123GB (97%)
Info) Free system memory: 123GB (97%)
Info) No CUDA accelerator devices available.
Info) No CUDA accelerator devices available.
Info) VMD for LINUXAMD64, version 1.9.3 (November 30, 2016)
Info) http://www.ks.uiuc.edu/Research/vmd/
Info) Email questions and bug reports to vmd_at_ks.uiuc.edu<mailto:vmd_at_ks.uiuc.edu>
Info) Please include this reference in published work using VMD:
Info) Humphrey, W., Dalke, A. and Schulten, K., `VMD - Visual
Info) Molecular Dynamics', J. Molec. Graphics 1996, 14.1, 33-38.
Any insights on why this happens.
Thank you.
-- Best, /A --
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