[gmx-users] FYI: How to install Gromacs 4.6.5 on Windows 7: keep cygwin packages 1.7.1-2 for OpenMPI: version 1.7.4-2 for OpenMPI is compatibel

Mirco Wahab mirco.wahab at chemie.tu-freiberg.de
Thu Mar 13 14:47:33 CET 2014

On 13.03.2014 13:25, Szilárd Páll wrote:
>> 7) -DCMAKE_INSTALL_PREFIX="/cygdrive/c/Gromacs465" is the installation directory -DGMX_MPI=OFF With the second installation 10) to 13) you will replace the non-mpi mdrun.exe with one that can run on multiple cores. If you omit this step, the generated mdrun.exe will not work as it is not compatible with the current cygwin setup.
> It's not clear to me what is not compatible with cygwin? Is it
> thread-MPI you are referring to?
> Have you tried OpenMP parallelization?

Im not sure but the poster might refer to an older post in this forum
with a receipe:
"[gmx-users] mdrun - I/O or system error: No such file or directory".

The default compilation (tMPI) of recent gromacs on recent cygwin
(over some versions) will not lead to a useable mdrun executeable
with multiple cores - for unknown reasons. After some experimentation,
it turned out that the out-of-the-box OpenMPI in cygwin allows for
mdrun_mpi executables that work fine.
Any other gromacs tools will work (as far as I tested).

The other problems stated by the poster (which I did never experience)
maybe linked to particular/nonstandard cygwin installation conditions
(especially the cygwin $PATH overtaken from the Windows %PATH may
led to numerous problems depending on the stuff installed on the host).
I do, out of curiosity, cygwin installations on every new released
gromacs version. There were, aside from small, easily correcteable
problems, working fine.


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