I am using a new cluster of Xeons and, to get the most efficient
compilation, I have compiled gromacs-4.5.4 separately with the intel,
pathscale, and pgi compilers.
With the pgi compiler, I am most concerned about this floating point
overflow warning:
...
[ 19%] Building C object src/gmxlib/CMakeFiles/gmx.dir/trajana/trajana.c.o
[ 19%] Building C object
src/gmxlib/CMakeFiles/gmx.dir/trajana/centerofmass.c.o
[ 19%] Building C object src/gmxlib/CMakeFiles/gmx.dir/trajana/nbsearch.c.o
PGC-W-0129-Floating point overflow. Check constants and constant
expressions
(/home/nealechr/exe/pgi/gromacs-4.5.4/source/src/gmxlib/trajana/nbsearch.c:
166)
PGC/x86-64 Linux 11.8-0: compilation completed with warnings
[ 19%] Building C object
src/gmxlib/CMakeFiles/gmx.dir/trajana/displacement.c.o
[ 19%] Building C object src/gmxlib/CMakeFiles/gmx.dir/trajana/position.c.o
...
There are also a lot of warnings about a type cast, which seems less
like a real problem:
...
[ 85%] Building C object src/mdlib/CMakeFiles/md.dir/gmx_qhop_xml.c.o
[ 85%] Building C object src/mdlib/CMakeFiles/md.dir/nsgrid.c.o
[ 85%] Building C object src/mdlib/CMakeFiles/md.dir/stat.c.o
[ 86%] Building C object src/mdlib/CMakeFiles/md.dir/mdebin_bar.c.o
[ 86%] Building C object src/mdlib/CMakeFiles/md.dir/genborn_sse2_double.c.o
[ 86%] Building C object src/mdlib/CMakeFiles/md.dir/pull.c.o
PGC-W-0095-Type cast required for this conversion
(/home/nealechr/exe/pgi/gromacs-4.5.4/source/src/mdlib/pull.c: 1213)
PGC-W-0095-Type cast required for this conversion
(/home/nealechr/exe/pgi/gromacs-4.5.4/source/src/mdlib/pull.c: 1213)
PGC/x86-64 Linux 11.8-0: compilation completed with warnings
[ 86%] Building C object src/mdlib/CMakeFiles/md.dir/force.c.o
PGC-W-0095-Type cast required for this conversion
(/home/nealechr/exe/pgi/gromacs-4.5.4/source/src/mdlib/force.c: 519)
PGC/x86-64 Linux 11.8-0: compilation completed with warnings
[ 86%] Building C object src/mdlib/CMakeFiles/md.dir/fft5d.c.o
[ 86%] Building C object src/mdlib/CMakeFiles/md.dir/tables.c.o
[ 86%] Building C object src/mdlib/CMakeFiles/md.dir/gmx_parallel_3dfft.c.o
[ 86%] Building C object src/mdlib/CMakeFiles/md.dir/qmmm.c.o
[ 88%] Building C object src/mdlib/CMakeFiles/md.dir/vcm.c.o
PGC-W-0095-Type cast required for this conversion
(/home/nealechr/exe/pgi/gromacs-4.5.4/source/src/mdlib/vcm.c: 83)
PGC/x86-64 Linux 11.8-0: compilation completed with warnings
[ 88%] Building C object src/mdlib/CMakeFiles/md.dir/sim_util.c.o
...
###############
I compiled like this:
module purge
module load pgi64/11.8 openmpi_pgi64/1.4.3_ofed
module load cmake/2.8.5
export CCDIR=/opt/pgi/linux86-64/11.8/bin
## set the location of the single precision FFTW isntallation
export FFTW_LOCATION=/home/nealechr/exe/pgi/fftw-3.1.2/exec
##### Nothing below this line usually needs to be changed
export CXX=pgCC
export CC=pgcc
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}/pgCC \
-DCMAKE_C_COMPILER=${CCDIR}/pgcc \
-DGMX_PREFER_STATIC_LIBS=ON \
-DGMX_MPI=OFF
make
make install
##########
I don't get any similar errors with the intel or pathscale compilers
(although intel gives me "icc: command line warning #10159: invalid
argument for option '-m'" a lot) and the pathscale compilation appears
to be hung on "[ 84%] Building C object
src/tools/CMakeFiles/gmxana.dir/gmx_rms.c.o", but I'll post a separate
ticket for that if it remains hung for a long time.
If anybody has run into this warning, or knows enough to be sure that I
don't need to worry about it during mdrun (it seems to be in an analysis
file, but I'm not entirely sure), then I would be happy to hear about
it. A gmx-users search for PGI returned zero results. I saw something
here, but it was not very specific about the problem with pgi (
http://www.levlafayette.com/node/175 ).
Thank you,
Chris.
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