From NWChem
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Gets Around
Threads 13
Posts 99
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| 8:32:38 PM PDT - Tue, May 15th 2012 |
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Edo,
It's such a classical thing: suddenly it works....(with external blas libs -- not internal). Internal libs are still throwing a seg violation.
The errors I posted came from a post ([1]) that I wrote a long time ago -- binaries which I don't have at hand anymore, and which were compiled without external blas libs.
In order to get the data you asked for I recompiled nwchem-6.1 with and without external BLAS libs on three different machines. I've done it repeatedly and have never had success running the binaries...until now. Suddenly I managed to get it working with external blas libs, but without external blas it still segfaults. I find it a bit puzzling, but that's fine -- it now works with openblas which is free and accessible to everyone.
It'd still be nice to have it working without external libs and I've posted a lot more detail from the segfaulting build (scripts, ldd output, errors, strace, ltrace, ar t libncwutil.a etc.) here: http://verahill.blogspot.com.au/2012/05/nwchem-61-diagnostic-data.html
__Good__ (edit src/config/makefile.h, line 1914 and add -lz -lssl for python support)
export LARGE_FILES=TRUE
export TCGRSH=/usr/bin/ssh
export NWCHEM_TOP=`pwd`
export NWCHEM_TARGET=LINUX64
export NWCHEM_MODULES="all python"
export PYTHONVERSION=2.7
export PYTHONHOME=/usr
export BLASOPT="-L/opt/openblas/lib -lopenblas -lopenblas_barcelona-r0.1.1"
export USE_MPI=y
export USE_MPIF=y
export USE_MPIF4=y
export MPI_LOC=/usr/lib/openmpi/lib
export MPI_INCLUDE=/usr/lib/openmpi/include
export LIBRARY_PATH=$LIBRARY_PATH:/usr/lib/openmpi/lib
export LIBMPI="-lmpi -lopen-rte -lopen-pal -ldl -lmpi_f77 -lpthread"
cd $NWCHEM_TOP/src
make clean
make nwchem_config
make FC=gfortran
ldd nwchem
linux-vdso.so.1 => (0x00007fff925ff000)
libopenblas.so.0 => /opt/openblas/lib/libopenblas.so.0 (0x00002ab79d8a8000)
libmpi.so.0 => /usr/lib/libmpi.so.0 (0x00002ab79e6b5000)
libopen-rte.so.0 => /usr/lib/libopen-rte.so.0 (0x00002ab79e968000)
libopen-pal.so.0 => /usr/lib/libopen-pal.so.0 (0x00002ab79ebb7000)
libdl.so.2 => /lib/x86_64-linux-gnu/libdl.so.2 (0x00002ab79ee0f000)
libmpi_f77.so.0 => /usr/lib/libmpi_f77.so.0 (0x00002ab79f013000)
libpthread.so.0 => /lib/x86_64-linux-gnu/libpthread.so.0 (0x00002ab79f24b000)
libutil.so.1 => /lib/x86_64-linux-gnu/libutil.so.1 (0x00002ab79f468000)
libz.so.1 => /usr/lib/x86_64-linux-gnu/libz.so.1 (0x00002ab79f66b000)
libssl.so.1.0.0 => /usr/lib/x86_64-linux-gnu/libssl.so.1.0.0 (0x00002ab79f881000)
libgfortran.so.3 => /usr/lib/x86_64-linux-gnu/libgfortran.so.3 (0x00002ab79fae0000)
libm.so.6 => /lib/x86_64-linux-gnu/libm.so.6 (0x00002ab79fdf6000)
libgcc_s.so.1 => /lib/x86_64-linux-gnu/libgcc_s.so.1 (0x00002ab7a0078000)
libquadmath.so.0 => /usr/lib/x86_64-linux-gnu/libquadmath.so.0 (0x00002ab7a028f000)
libc.so.6 => /lib/x86_64-linux-gnu/libc.so.6 (0x00002ab7a04c4000)
libcrypto.so.1.0.0 => /usr/lib/x86_64-linux-gnu/libcrypto.so.1.0.0 (0x00002ab7a084b000)
libnsl.so.1 => /lib/x86_64-linux-gnu/libnsl.so.1 (0x00002ab7a0c30000)
/lib64/ld-linux-x86-64.so.2 (0x00002ab79d686000)
__Bad___ (edit src/config/makefile.h, line 1914 and add -lz -lssl for python support)
export LARGE_FILES=TRUE
export TCGRSH=/usr/bin/ssh
export NWCHEM_TOP=`pwd`
export NWCHEM_TARGET=LINUX64
export NWCHEM_MODULES="all python"
export PYTHONHOME=/usr
export PYTHONVERSION=2.7
export USE_MPI=y
export USE_MPIF=y
export USE_MPIF4=y
export MPI_LOC=/usr/lib/openmpi/lib
export MPI_INCLUDE=/usr/lib/openmpi/include
export LIBRARY_PATH=$LIBRARY_PATH:/usr/lib/openmpi/lib
export LIBMPI="-lmpi -lopen-rte -lopen-pal -ldl -lmpi_f77 -lpthread"
cd $NWCHEM_TOP/src
make clean
make nwchem_config
make FC=gfortran
ldd nwchem
linux-vdso.so.1 => (0x00007fffccbff000)
libmpi.so.0 => /usr/lib/libmpi.so.0 (0x00002b7624cd9000)
libopen-rte.so.0 => /usr/lib/libopen-rte.so.0 (0x00002b7624f8d000)
libopen-pal.so.0 => /usr/lib/libopen-pal.so.0 (0x00002b76251dc000)
libdl.so.2 => /lib/x86_64-linux-gnu/libdl.so.2 (0x00002b7625433000)
libmpi_f77.so.0 => /usr/lib/libmpi_f77.so.0 (0x00002b7625638000)
libpthread.so.0 => /lib/x86_64-linux-gnu/libpthread.so.0 (0x00002b7625870000)
libutil.so.1 => /lib/x86_64-linux-gnu/libutil.so.1 (0x00002b7625a8c000)
libz.so.1 => /usr/lib/x86_64-linux-gnu/libz.so.1 (0x00002b7625c90000)
libssl.so.1.0.0 => /usr/lib/x86_64-linux-gnu/libssl.so.1.0.0 (0x00002b7625ea6000)
libgfortran.so.3 => /usr/lib/x86_64-linux-gnu/libgfortran.so.3 (0x00002b7626104000)
libm.so.6 => /lib/x86_64-linux-gnu/libm.so.6 (0x00002b762641b000)
libgcc_s.so.1 => /lib/x86_64-linux-gnu/libgcc_s.so.1 (0x00002b762669d000)
libquadmath.so.0 => /usr/lib/x86_64-linux-gnu/libquadmath.so.0 (0x00002b76268b3000)
libc.so.6 => /lib/x86_64-linux-gnu/libc.so.6 (0x00002b7626ae9000)
libcrypto.so.1.0.0 => /usr/lib/x86_64-linux-gnu/libcrypto.so.1.0.0 (0x00002b7626e70000)
libnsl.so.1 => /lib/x86_64-linux-gnu/libnsl.so.1 (0x00002b7627254000)
/lib64/ld-linux-x86-64.so.2 (0x00002b7624ab7000)
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