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.
-Justin
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
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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