[gmx-users] How can I tell whether or not Gromacs was compiled with MPI?

[Mark Abraham]

Hi,

Yes, thread-MPI was introduced with 4.5. REMD will report an error
immediately if mdrun is not compiled with MPI. Or you can use ldd on your
mdrun to see if it is linked with MPI.

Mark


On Sun, Nov 24, 2013 at 11:13 PM, Andrew DeYoung <adeyoung at andrew.cmu.edu>wrote:

> 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
>
> --
> 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 gmx-users-request at gromacs.org.
>