[gmx-users] How to correctly setup gmx_mpi mdrun

Mark Abraham mark.j.abraham at gmail.com
Tue Sep 26 00:44:28 CEST 2017


You need a correctly set up MPI environment. My experience of linux distro
packages has been excellent, so pick one and consult its documentation.


On Fri, 22 Sep 2017 23:46 Zheng Ruan <zruan1991 at gmail.com> wrote:

> 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!
> Ruan
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