[gmx-users] gromacs 2018 with OpenMPI + OpenMP

[Deepak Porwal]

> Are you sure that's better than mdrun's internal thread binding?
yes even with warnings I see better performance, so surely if we can remove
warnings and bind properly we will see much better performance than thread
MPI.


On Thu, Dec 13, 2018 at 3:41 AM Szilárd Páll <pall.szilard at gmail.com> wrote:

> On Wed, Dec 12, 2018 at 12:14 PM Deepak Porwal <deepak.porwal at iiitb.net>
> wrote:
> >
> > Hi
> > I build gromacs with OpenMPI + OpenMP.
> > When I am trying to run adh/adh_dodec workload with binding the MPI
> threads
> > to core/l3cache, I am seeing some warnings.
> > Command I used to run:  mpirun --map-by ppr:1:l3cache:pe=2  -x
> > OMP_NUM_THREADS=4 -x OMP_PROC_BIND=TRUE -x OMP_PLACES=cores gmx_mpi mdrun
>
> Are you sure that's better than mdrun's internal thread binding?
>
> >
> > ------------------------------------------------------------
> >
> > Program:     gmx grompp, version 2018.2
> >
> > Source file: src/gromacs/utility/futil.cpp (line 406)
> >
> >
> >
> > Fatal error:
> >
> > Won't make more than 99 backups of topol.tpr for you.
> >
> > The env.var. GMX_MAXBACKUP controls this maximum, -1 disables backups.
>
> There's the error: at startup mdrun will by default back up every file
> that already exists in the same location where a file would be
> written. List your output directory and it should be pretty obvious
> what the issue is.
>
> --
> Szilárd
>
> >
> >
> > For more information and tips for troubleshooting, please check the
> GROMACS
> >
> > website at http://www.gromacs.org/Documentation/Errors
> >
> > -------------------------------------------------------
> >
> >
> --------------------------------------------------------------------------
> >
> > MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD
> >
> > with errorcode 1.
> >
> >
> >
> > NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes.
> >
> > You may or may not see output from other processes, depending on
> >
> > exactly when Open MPI kills them.
> >
> >
> --------------------------------------------------------------------------
> >
> >
> --------------------------------------------------------------------------
> >
> > WARNING: a request was made to bind a process. While the system
> >
> > supports binding the process itself, at least one node does NOT
> >
> > support binding memory to the process location.
> >
> >
> >
> >   Node:  llvm-sp38
> >
> >
> >
> > Open MPI uses the "hwloc" library to perform process and memory
> >
> > binding. This error message means that hwloc has indicated that
> >
> > processor binding support is not available on this machine.
> >
> >
> >
> > On OS X, processor and memory binding is not available at all (i.e.,
> >
> > the OS does not expose this functionality).
> >
> >
> >
> > On Linux, lack of the functionality can mean that you are on a
> >
> > platform where processor and memory affinity is not supported in Linux
> >
> > itself, or that hwloc was built without NUMA and/or processor affinity
> >
> > support. When building hwloc (which, depending on your Open MPI
> >
> > installation, may be embedded in Open MPI itself), it is important to
> >
> > have the libnuma header and library files available. Different linux
> >
> > distributions package these files under different names; look for
> >
> > packages with the word "numa" in them. You may also need a developer
> >
> > version of the package (e.g., with "dev" or "devel" in the name) to
> >
> > obtain the relevant header files.
> >
> >
> >
> > If you are getting this message on a non-OS X, non-Linux platform,
> >
> > then hwloc does not support processor / memory affinity on this
> >
> > platform. If the OS/platform does actually support processor / memory
> >
> > affinity, then you should contact the hwloc maintainers:
> >
> > https://github.com/open-mpi/hwloc.
> >
> >
> > This is a warning only; your job will continue, though performance may
> >
> > be degraded.
> > -----------------------------------------------------------------------
> > Though the benchmark runs and give some score can we have some solution
> to
> > avoid this warning and do proper binding. I also tried with threadMPI and
> > didn't see this warnings.
> >
> > --
> > Thanks,
> > Deepak
> > --
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-- 
Thanks,
Deepak