VMD-L Mailing List

From: Ashar Malik (asharjm_at_gmail.com)
Date: Wed Jul 01 2020 - 04:52:54 CDT

OK, I think I misunderstood this. I confused -N with -n. -n is for number
of tasks - so you would expect 5 vmd outputs. Sorry about that.

As such, if you want to access 24 threads per node and you want a total of
5 nodes (-N 5 as per slurm documentation) and from what I gather from your
email, then this output should be hardware information of the participating
nodes as below:

When compiled with MPI support and launched with the platform-dependent
> mpirun or site-specific launch commands (e.g., aprun, jsrun, or similar),
> VMD will automatically initialize MPI internally, and each parallel VMD
> instance will be assigned a unique MPI rank. During startup, a parallel
> launch of VMD will print hardware information about each of the
> participating compute nodes from node 0. When a parallel VMD run exits, all
> nodes are expected to call exit at the same time so that they shutdown
> MPI together.

from here:
https://www.ks.uiuc.edu/Training/Tutorials/vmd/tutorial-html/node8.html

so yes, it's probably MPI related.

On Wed, Jul 1, 2020 at 5:06 PM Adupa Vasista <adupavasista_at_gmail.com> wrote:

> 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> 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>
>> 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
>>>> 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
>>>> 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
>>>> 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
>>
>
>
> --
>
> 

-- 
Best,
/A