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.
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