[gmx-users] error on opening gmx_mpi
pbuscemi at q.com
Wed Dec 19 18:36:10 CET 2018
( thinking a bit about the initial command structure does help....)
Now using the command:
gmx_mpi mdrun -deffnm PVP20k.nvt -nb gpu -ntomp 16 -npme 4
:-) GROMACS - gmx mdrun, 2018.4 (-:
gets past the v5 issue but a new nastygram is sent...
"The -dd or -npme option request a parallel simulation, but gmx mdrun was not
started through mpirun/mpiexec or only one rank was requested through
Inclusion of mpirun was attempted but I've not hit the proper format.
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On Dec 19 2018, at 11:08 am, pbuscemi at q.com wrote:
> Thank you - both - very much again.
> The "mpir_run -npx gmx -mdrun....." command was lifted from a Feb 2018
> response from Szilard , to a multi gpu, user which he used as an example.
> I'll crank on your pointers right now.
> -----Original Message-----
> From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se
> <gromacs.org_gmx-users-bounces at maillist.sys.kth.se> On Behalf Of Justin
> Sent: Wednesday, December 19, 2018 10:47 AM
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> Subject: Re: [gmx-users] error on opening gmx_mpi
> On Wed, Dec 19, 2018 at 11:44 AM p buscemi <pbuscemi at q.com> wrote:
> > Shi,
> > reinstalling the mpi version using gmx 18.4 did not help........any
> ideas ?
> > hms at rgb2 ~/Desktop/PVP20k $ mpirun -np 8 mdrun_mpi -deffnm PVP20k1.em
> > :-) GROMACS - mdrun_mpi, VERSION 5.1.2 (-:
> You're just calling the same (incorrect) command again. You installed
> "gmx_mpi" version 2018.4 but then your command uses "mdrun_mpi" instead.
> Apparently you have version 5.1.2 (perhaps from a package manager, based
> on the fact that it's installed in /usr/bin instead of
> /usr/local/gromacs/bin) that is being found in your PATH.
> If you've got multiple versions installed, either source GMXRC properly or
> use full PATH information in your commands. Above all, use the right
> binary name to start :)
> Justin A. Lemkul, Ph.D.
> Assistant Professor
> Office: 301 Fralin Hall
> Lab: 303 Engel Hall
> Virginia Tech Department of Biochemistry
> 340 West Campus Dr.
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> jalemkul at vt.edu | (540) 231-3129
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