VMD-L Mailing List

From: Adupa Vasista (adupavasista_at_gmail.com)
Date: Wed Jul 01 2020 - 04:06:33 CDT

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
> 

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