[gmx-users] mdrun - I/O or system error: No such file or directory

[Mirco Wahab]

On 20.01.2014 11:30, Carlos Familia wrote:
> I was wondering if anybody come to this error with gromacs compiled under
> cygwin 32bits in windows 7.
>...
> tMPI error: I/O or system error: No such file or directory
>
> procedure.txt: line 7:  5624 Aborted   (core dumped) mdrun -v

Gromacs' mdrun won't work in tMPI-mode under Cygwin for now.
You have to build a real MPI-mdrun in order to get more than
one core to work (use the Cygwin-provided OpenMPI). I'd
recommend to use the 64-bit Cygwin-version if possible
(http://cygwin.com/setup-x86_64.exe).

Below is how I'd usually build everything for Cygwin
(using Cygwin-provided gcc 4.8.x).
This requires an extra build directory, like:

~/gromacs/
          |
          +- build/
          |
          +- gromacs-4.6.5/

Build scripts are in ~/gromacs/, the sources
have been extracted there (into ./gromacs-4.6.5/)
and you are in ./build/. There, you do

sh ../build_gromacs.sh

etc. Don't forget to clear the build directory
between builds.


-----------------------------------------
cat build_gromacs.sh
-----------------------------------------

#!/bin/sh
export GMXACCEL=SSE2
# SSE2, SSE4.1, AVX_128_FMA, AVX_256, IBM_QPX
export GMXVERSION=gromacs-4.6.5
export GMXTARGET=/opt/gromacs465

cmake ../${GMXVERSION}                    \
       -DCMAKE_INSTALL_PREFIX=${GMXTARGET} \
       -DGMX_X11=OFF                       \
       -DGMX_GPU=OFF                       \
       -DGMX_PREFER_STATIC_LIBS=ON         \
       -DGMX_CPU_ACCELERATION=${GMXACCEL}

make -j 4 install


-----------------------------------------
cat build_mdrun.sh
-----------------------------------------

#!/bin/sh
# SSE2, SSE4.1, AVX_128_FMA, AVX_256, IBM_QPX
ACCEL=SSE2
export GMXVERSION=gromacs-4.6.5
export GMXTARGET=/opt/gromacs465

cmake ../${GMXVERSION}                     \
       -DCMAKE_INSTALL_PREFIX=${GMXTARGET}  \
       -DGMX_GPU=OFF                         \
       -DGMX_MPI=ON                         \
       -DGMX_PREFER_STATIC_LIBS=ON          \
       -DGMX_CPU_ACCELERATION=${ACCEL}

make -j 4
make install-mdrun



Regards

M.