[gmx-users] compiling with the pathscale compiler hangs on gmx_rms.c.o

[Szilárd Páll]

Hi,

I tried a Pathscale 4.0.12 nightly and except a few warnings
compilation went fine. I don't have 4.0.11 around, though.

However, mdrun segfaults at the very end of the run while generating
the cycle and time counter table. I don't have time to look into this,
but I'll get back to the issue when I'll have a bit of time to spare.

Cheers,
--
Szilárd



On Wed, Nov 30, 2011 at 9:44 PM, Chris Neale <chris.neale at utoronto.ca> wrote:
> Dear users:
>
> My compilation with the pathscale compiler hangs for over an hour on the
> gmx_rms.c.o file (or perhaps the one that comes next).
>
> [ 83%] Building C object src/tools/CMakeFiles/gmxana.dir/gmx_principal.c.o
> [ 84%] Building C object src/tools/CMakeFiles/gmxana.dir/gmx_polystat.c.o
> [ 84%] Building C object src/tools/CMakeFiles/gmxana.dir/gmx_potential.c.o
> [ 84%] Building C object src/tools/CMakeFiles/gmxana.dir/gmx_rama.c.o
> [ 84%] Building C object src/tools/CMakeFiles/gmxana.dir/gmx_rdf.c.o
> [ 84%] Building C object src/tools/CMakeFiles/gmxana.dir/gmx_rms.c.o
> [hangs here]
>
> I compiled like this:
>
> module purge
> module load pathscale/4.0.11
> module load openmpi_pathscale64/1.4.3_ofed
> module load cmake/2.8.5
> export CCDIR=/opt/ekopath/4.0.11/bin
>
> ## set the location of the single precision FFTW isntallation
> export FFTW_LOCATION=/home/nealechr/exe/pathscale/fftw-3.1.2/exec
>
> ##### Nothing below this line usually needs to be changed
>
> export CXX=pathCC
> export CC=pathcc
>
> cmake ../source/ \
>      -DFFTW3F_INCLUDE_DIR=$FFTW_LOCATION/include \
>      -DFFTW3F_LIBRARIES=$FFTW_LOCATION/lib/libfftw3f.a \
>      -DCMAKE_INSTALL_PREFIX=$(pwd) \
>      -DGMX_X11=OFF \
>      -DCMAKE_CXX_COMPILER=${CCDIR}/pathCC \
>      -DCMAKE_C_COMPILER=${CCDIR}/pathcc \
>      -DGMX_PREFER_STATIC_LIBS=ON \
>      -DGMX_MPI=OFF
>
>
> make
>
> make install
>
> #####################
>
> If anybody has successfully compiled with the pathscale compiler, I would
> love to hear any suggestions that you can offer.
>
> I have tried 3 fresh installations, and I have also tried cntrl^C and then
> run make again without a clean. It's always the same.
>
> Thank you,
> Chris.
>
> --
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