Try using the mpi submissions flags with just a test submission, you might have to look at the stats after 15 minutes though, as I do not know what would happen if it was not compiled with mpi (if they work or not), but they would make a noticable difference.
just a suggestion, there might be an easier way.
Stephan Watkins
Gesendet: Sonntag, 24. November 2013 um 23:13 Uhr
Von: "Andrew DeYoung" <[email protected]>
An: [email protected]
Betreff: [gmx-users] How can I tell whether or not Gromacs was compiled with MPI?
Von: "Andrew DeYoung" <[email protected]>
An: [email protected]
Betreff: [gmx-users] How can I tell whether or not Gromacs was compiled with MPI?
Hi,
I am running Gromacs version 4.5.5. However, I did not compile it myself;
the system administrator did many months ago. I have been running
"standard" MD simulations (i.e., no replica exchange) over the 24 cores that
are available on the node. To run "standard" MD, I just call mdrun directly
-- without referencing MPI or mpirun (at least not explicitly) -- using a
command like this:
mdrun -v -s topol.tpr -nt 24
>From looking at the old release notes, it looks like this "thread-based
parallelization" was introduced sometime in version 4.5 (maybe from the
beginning of version 4.5?). As the page
http://www.gromacs.org/About_Gromacs/Release_Notes/Versions_4.5.x says,
"Running on a multi-core node now uses thread-based parallelization to
automatically spawn the optimum number of threads in the default build. MPI
is now only required for parallelization over the network."
Now, however, I want to run replica exchange simulations. I have no
experience with such simulations, but the page
http://www.gromacs.org/Documentation/How-tos/REMD says:
"REMD with any version of GROMACS requires mdrun compiled with MPI (i.e. not
threading), and that the number of processors be a multiple of the number of
replicas."
But, my question is, how can I tell whether Gromacs was compiled with MPI?
Probably it was not compiled with MPI, since I am using threading, but how
can I be sure?
Thanks so much for your time!
Andrew DeYoung
Carnegie Mellon University
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I am running Gromacs version 4.5.5. However, I did not compile it myself;
the system administrator did many months ago. I have been running
"standard" MD simulations (i.e., no replica exchange) over the 24 cores that
are available on the node. To run "standard" MD, I just call mdrun directly
-- without referencing MPI or mpirun (at least not explicitly) -- using a
command like this:
mdrun -v -s topol.tpr -nt 24
>From looking at the old release notes, it looks like this "thread-based
parallelization" was introduced sometime in version 4.5 (maybe from the
beginning of version 4.5?). As the page
http://www.gromacs.org/About_Gromacs/Release_Notes/Versions_4.5.x says,
"Running on a multi-core node now uses thread-based parallelization to
automatically spawn the optimum number of threads in the default build. MPI
is now only required for parallelization over the network."
Now, however, I want to run replica exchange simulations. I have no
experience with such simulations, but the page
http://www.gromacs.org/Documentation/How-tos/REMD says:
"REMD with any version of GROMACS requires mdrun compiled with MPI (i.e. not
threading), and that the number of processors be a multiple of the number of
replicas."
But, my question is, how can I tell whether Gromacs was compiled with MPI?
Probably it was not compiled with MPI, since I am using threading, but how
can I be sure?
Thanks so much for your time!
Andrew DeYoung
Carnegie Mellon University
--
Gromacs Users mailing list
* Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!
* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to [email protected].
-- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!
* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to [email protected].
