[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,
> Adam


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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