[gmx-users] Running on two nodes

[Searle Duay]

Hi Mark,

Thank you for pointing this out. I've seen in the log file that it's
running on 1 node only. In our local computing cluster, I requested for two
nodes for this run. Do you think there's something wrong with the GROMACS
command that I'm giving, that's why only 1 node is being used? Or is it
more an issue on our cluster?

The command I'm running is:

mpirun -np 4 gmx_mpi mdrun -v -nsteps 15000 -resetstep 12000 -s
production.tpr -noconfout -nb gpu -pme gpu -npme 1 -nstlist 80 -g
nstlist_80_4rank -ntomp 10 -gputasks 0011

Thanks,
Searle

On Sun, Aug 11, 2019 at 11:08 AM Mark Abraham <mark.j.abraham at gmail.com>
wrote:

> Hi,
>
> There's lots of this kind of information reported in the log file,
> including the number of nodes that the MPI environment has made available
> to mdrun.
>
> Mark
>
> On Sat, 10 Aug 2019 at 14:15, Searle Duay <searle.duay at uconn.edu> wrote:
>
> > Hello!
> >
> > I am trying to run a simulation on two nodes. Each node has 2 GPUs and 20
> > cores. I am not having problems with running it, but I am not sure if I
> am
> > really using both nodes or just one node because I am getting the
> following
> > warning:
> >
> > WARNING: On rank 0: oversubscribing the available 20 logical CPU cores
> per
> > node with 40 threads.
> >
> > The command that I run was:
> >
> > mpirun -np 4 gmx_mpi mdrun -v -nsteps 15000 -resetstep 12000 -s
> > production.tpr -noconfout -nb gpu -pme gpu -npme 1 -nstlist 80 -g
> > nstlist_80_4rank -ntomp 10 -gputasks 0011
> >
> > Am I using both nodes in this case?
> >
> > Thank you,
> > Searle
> >
> > --
> > Searle Aichelle S. Duay
> > Ph.D. Student
> > Chemistry Department, University of Connecticut
> > searle.duay at uconn.edu
> > --
> > Gromacs Users mailing list
> >
> > * Please search the archive at
> >
> https://nam01.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.gromacs.org%2FSupport%2FMailing_Lists%2FGMX-Users_List&amp;data=02%7C01%7Csearle.duay%40uconn.edu%7C74291cda61f043d5177e08d71e6db144%7C17f1a87e2a254eaab9df9d439034b080%7C0%7C0%7C637011328804143196&amp;sdata=pf2q61wpNQnE0OEs8hahXm6TOwKhC3285hoCpW2lXsI%3D&amp;reserved=0
> before
> > posting!
> >
> > * Can't post? Read
> https://nam01.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.gromacs.org%2FSupport%2FMailing_Lists&amp;data=02%7C01%7Csearle.duay%40uconn.edu%7C74291cda61f043d5177e08d71e6db144%7C17f1a87e2a254eaab9df9d439034b080%7C0%7C0%7C637011328804143196&amp;sdata=KKbBYjw0a0qdJ7X%2FfALA6NlhQ432PumfDUIJkrif%2FkU%3D&amp;reserved=0
> >
> > * For (un)subscribe requests visit
> >
> https://nam01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fmaillist.sys.kth.se%2Fmailman%2Flistinfo%2Fgromacs.org_gmx-users&amp;data=02%7C01%7Csearle.duay%40uconn.edu%7C74291cda61f043d5177e08d71e6db144%7C17f1a87e2a254eaab9df9d439034b080%7C0%7C0%7C637011328804153189&amp;sdata=Q7CwXXsIUcQm94UYtLsioe680KRB5%2FsAyqm9G5%2By0wc%3D&amp;reserved=0
> or
> > send a mail to gmx-users-request at gromacs.org.
> >
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> https://nam01.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.gromacs.org%2FSupport%2FMailing_Lists%2FGMX-Users_List&amp;data=02%7C01%7Csearle.duay%40uconn.edu%7C74291cda61f043d5177e08d71e6db144%7C17f1a87e2a254eaab9df9d439034b080%7C0%7C0%7C637011328804153189&amp;sdata=4pJpY0PjD%2BaO0OveKeJ7DFCOc84h3jlFp6nkdSi31iE%3D&amp;reserved=0
> before posting!
>
> * Can't post? Read
> https://nam01.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.gromacs.org%2FSupport%2FMailing_Lists&amp;data=02%7C01%7Csearle.duay%40uconn.edu%7C74291cda61f043d5177e08d71e6db144%7C17f1a87e2a254eaab9df9d439034b080%7C0%7C0%7C637011328804153189&amp;sdata=LBasxwzwxLpXjcryAnGk4pL755YotHuyH2NSi6K52rU%3D&amp;reserved=0
>
> * For (un)subscribe requests visit
>
> https://nam01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fmaillist.sys.kth.se%2Fmailman%2Flistinfo%2Fgromacs.org_gmx-users&amp;data=02%7C01%7Csearle.duay%40uconn.edu%7C74291cda61f043d5177e08d71e6db144%7C17f1a87e2a254eaab9df9d439034b080%7C0%7C0%7C637011328804153189&amp;sdata=Q7CwXXsIUcQm94UYtLsioe680KRB5%2FsAyqm9G5%2By0wc%3D&amp;reserved=0
> or send a mail to gmx-users-request at gromacs.org.
>


-- 
Searle Aichelle S. Duay
Ph.D. Student
Chemistry Department, University of Connecticut
searle.duay at uconn.edu