[gmx-users] GROMACS 4.5.1 mdrun re-compile for MPI
Mark.Abraham at anu.edu.au
Thu Mar 24 14:00:37 CET 2011
On 24/03/2011 11:51 PM, 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
Yes, threading, enabled by default, and mutually incompatible with MPI.
> 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
Subsequently you have configured with --enable-mpi, so threading is
disabled. Now everything is probably a mess.
> 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.
> How can I update the parallel-capable "mdrun" executable with my changes?
Run "make distclean" and then re-configure.
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