From: John Stone (johns_at_ks.uiuc.edu)
Date: Wed Jul 01 2020 - 09:30:41 CDT

Hi,
  Axel's response was most informative.
Again:
  By default, VMD is not compiled with MPI support enabled.
It can be compiled with OpenMPI, MPICH, and MVAPICH, among others,
but this requires using the source distribution and is somewhat
involved since VMD has many dependencies. For the most computationally
intensive tasks, VMD generally makes use of multi-core CPUs or
GPU accelerators. The main benefit of using the MPI-enabled versions
of VMD to to exploit parallel I/O, and to parallelize user-written
analysis scripts on a large scale, but as Axel already pointed out,
there are other alternatives if you don't want to have to compile
VMD from source.

Best regards,
  John Stone
  vmd_at_ks.uiuc.edu

On Wed, Jul 01, 2020 at 10:37:23AM +0000, Jesper Lykkegaard Karlsen wrote:
> 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 <[1]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 <[2]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) [3]http://www.ks.uiuc.edu/Research/vmd/
>
> Info) Email questions and bug reports to [4]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) [5]http://www.ks.uiuc.edu/Research/vmd/
>
> Info) Email questions and bug reports to [6]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) [7]http://www.ks.uiuc.edu/Research/vmd/
>
> Info) Email questions and bug reports to [8]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
>
> --
>
> References
>
> Visible links
> 1. mailto:asharjm_at_gmail.com
> 2. mailto:adupavasista_at_gmail.com
> 3. http://www.ks.uiuc.edu/Research/vmd/
> 4. mailto:vmd_at_ks.uiuc.edu
> 5. http://www.ks.uiuc.edu/Research/vmd/
> 6. mailto:vmd_at_ks.uiuc.edu
> 7. http://www.ks.uiuc.edu/Research/vmd/
> 8. mailto:vmd_at_ks.uiuc.edu

-- 
NIH Center for Macromolecular Modeling and Bioinformatics
Beckman Institute for Advanced Science and Technology
University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
http://www.ks.uiuc.edu/~johns/           Phone: 217-244-3349
http://www.ks.uiuc.edu/Research/vmd/