[gmx-users] gromacs 2018 with OpenMPI + OpenMP

Deepak Porwal deepak.porwal at iiitb.net
Wed Dec 12 12:14:00 CET 2018

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


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.

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:


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.


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