[gmx-users] mdrun_command_not working in cygwin

Mirco Wahab mirco.wahab at chemie.tu-freiberg.de
Mon Nov 24 15:37:06 CET 2014

On 24.11.2014 14:23, Shahid Nayeem wrote:
> I do need Gromacs 4.5.4 as I have some comments in my paper where all work
> is done on this version. Please help.
> Initially with both version of Gromacs I was able to run mdrun but now I
> face problem.
> For mdrun_4.6.3 which is mdrun_d in my installation the error in running is
> as follows
>   mdrun_d -v -s prot_b4em.tpr
> ...
> ...
> Back Off! I just backed up md.log to ./#md.log.2#
> Reading file prot_b4em.tpr, VERSION 4.6.3 (double precision)
> tMPI error: I/O or system error: No such file or directory
> Aborted (core dumped)

This means: mdrun doesn't work in tMPI mode (compiled by the
default settings). You have to install OpenMPI in cygwin and
build a mdrun_mpi executable. This executable should, iirc,
work (in contrast to your "standard" one, which uses thread-MPI).
Maybe you can run it through explicitly requiring only "one thread"
(by mdrun -nt 1 ...) -- but im not sure (long ago).

There were almost always some other minor problems to solve
when installing older Gromacs versions on Cygwin/64.

You could also install a regular Linux distribution in a
virtual machine (e.g. in VmWare Workstation) and install
Gromacs there. But this requires you to have a relatively
powerful PC with enough RAM to be productive (at least
an extra 1.5-2GB for the 64-bit Linux).



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