[gmx-users] GROMACS 4.5.1 mdrun re-compile for MPI
Justin A. Lemkul
jalemkul at vt.edu
Thu Mar 24 13:56:38 CET 2011
Adam Herbst wrote:
> Dear GROMACS users,
> I successfully installed GROMACS 4.5.1 several months ago on a Mac Pro
> with 12 CPUs, and the "mdrun" command (not "mpirun mdrun_mpi") allows
> parallel simulations--it automatically uses multiple processors, while
> the number of processors can be manually specified as N with the flag
> "mdrun -nt N". I understand that this is a feature of GROMACS 4 and
> later. Now I am making minor changes to the mdrun source code, and I
> want to recompile such that the parallel version of mdrun is updated
> with my changes. But when I run:
> make mdrun (or just make)
> make install-mdrun (or just make install)
> from the top-level source directory, the only executables that are
> updated are the ones with the _mpi suffix, such as mdrun_mpi. The
> version of mdrun in src/kernel/ is updated, but this one has no -nt flag
> and cannot seem to run on multiple processors. And when I run
Please post your actual configuration command. Did you properly --enable-mpi
and --disable-threads? What MPI library are you using? Do other processes
executed via mpirun work as expected?
> mpirun -np N mdrun_mpi [options],
> the same simulation is started separately on each processor, leading to
> a crash. If I use
> mpirun -np 1 -cpus-per-proc N mdrun_mpi [options],
> I get an error message that this is not supported on my computer ("An
> attempt to set processor affinity has failed").
> I can't configure the input .tpr file for parallel because grompp
> doesn't have the -np flag in GROMACS 4.
There is no need to do this anymore. mdrun deals with all aspects of
parallelization. A .tpr file can then be run on as many processors as you like.
> How can I update the parallel-capable "mdrun" executable with my changes?
> Thanks in advance,
Justin A. Lemkul
ICTAS Doctoral Scholar
Department of Biochemistry
jalemkul[at]vt.edu | (540) 231-9080
More information about the gromacs.org_gmx-users