AW: mpi with NAMD

From: Norman Geist (norman.geist_at_uni-greifswald.de)
Date: Fri Mar 29 2019 - 09:42:17 CDT

If you download namd precompiled, it is not MPI based, you rather use charmrun.

 

Von: owner-namd-l_at_ks.uiuc.edu [mailto:owner-namd-l_at_ks.uiuc.edu] Im Auftrag von John Hamre
Gesendet: Freitag, 29. März 2019 15:39
An: Norman Geist <norman.geist_at_uni-greifswald.de>
Cc: NAMD List <namd-l_at_ks.uiuc.edu>
Betreff: Re: namd-l: mpi with NAMD

 

Thank you, Norman!

 

Yes, I am having a difficult time getting the REMD example to go. I will look into SLURM. I am using 3 GPU's and 12 cores. I can't even get the example to work on my home CPU without CUDA, there is always some mpi error. I copy the namd executable in the folder I'm using so I use mpirun ./charmrun -n 3 ./namd2 +replicas 12 ... Thanks again.

 

John

 

On Fri, Mar 29, 2019 at 10:29 AM Norman Geist <norman.geist_at_uni-greifswald.de <mailto:norman.geist_at_uni-greifswald.de> > wrote:

Hey there,

 

I’m only using MPI builts of NAMD. If you have a queuing system like SLURM with e.g. OpenMPI (and SLURM support), simply “mpirun namd2 in.conf” is enough.

Otherwise, you need of course to tell NAMD aka OpenMPI the ressources it may use.

 

I do it like that for any NAMD version with and without GPU since version 2.10 up to todays 2.13

 

Norman

 

Von: owner-namd-l_at_ks.uiuc.edu <mailto:owner-namd-l_at_ks.uiuc.edu> [mailto:owner-namd-l_at_ks.uiuc.edu <mailto:owner-namd-l_at_ks.uiuc.edu> ] Im Auftrag von John Hamre
Gesendet: Freitag, 29. März 2019 15:19
An: NAMD List <namd-l_at_ks.uiuc.edu <mailto:namd-l_at_ks.uiuc.edu> >
Betreff: namd-l: mpi with NAMD

 

Does anyone use the mpirun command for use with their NAMD sims?

 

If so, can you tell me what your command run line is (mpirun -n 3 ./namd2 XXX) and what versions of mpi and namd you run? Thank you.

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