[gmx-users] How to correctly setup gmx_mpi mdrun

Zheng Ruan zruan1991 at gmail.com
Fri Sep 22 23:45:42 CEST 2017

Hi Gromacs Users,

I'm learning how to run a simple replica exchange MD simulation on my own
computer. My computer has 12 Xeon E5-2630 CPUs and 1 GeForce GTX 770 GPU.

I used to compile gromacs without the -DGMX_MPI option and it runs fine for
normal MD. I can control the number of CPUs to use by specifying the
-nt option.

However, for REMD I think an MPI version is required. So I compiled
the gromacs-5.1.4 using "cmake .. -DGMX_BUILD_OWN_FFTW=ON
showed up at this point. But when I try the "make check" command, the "Test
20: MdrunMpiTests" never finishes until a timeout message is shown.

I also tried to run a REMD job using the compiled binary file by using
"mpirun -np 2 gmx_mpi mdrun -s TOPO/topol -multi 2 -replex 100". But the
program will just hang and never print any message. As a test, I can print
out the help message by using "gmx_mpi mdrun -h" without using the mpirun.
Any suggestions on how to solve the problem? Is it possible to run REMD on
my personal computer?

Thank you!

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