Compiling NWChem 6.1 on Rocks Cluster 6.0
Just Got Here
8:28:58 AM PDT - Wed, Oct 24th 2012
Dear NWChem's users,

Does anyone has any experience compiling Nwchem 6.1 or 6.1.1 on rocks cluster 6.0 based on CentOS 6.2?

I have many difficulties compiling by using gfortran (in openmpi environment) with gcc version 4.4.6 20110731 (Red Hat 4.4.6-3).

I must admit that I'm a beginner in compiling source code and probably the issue is relatively stupid.

Here, please find my env. variables:

export LARGE_FILES=TRUE
export TCGRSH=/usr/bin/ssh
export NWCHEM_TOP=/export/home/florent/tmp/nwchem/6.1/nwchem-6.1
export NWCHEM_TARGET=LINUX64
export NWCHEM_MODULES=all
export USE_MPI=y
export USE_MPIF=y
export USE_MPIF4=y
export MPI_LOC=/opt/openmpi
export MPI_LIB=/opt/openmpi/lib
export MPI_INCLUDE=/opt/openmpi/include
export LIBRARY_PATH=$LIBRARY_PATH:/opt/openmpi/lib
export LIBMPI="-lmpi_f90 -lmpi_f77 -lmpi -lopen-rte -lopen-pal -ldl -Wl,--export-dynamic -lnsl -lutil -lm -ldl"


And here, the permanent error message that I get:

gfortran -c -fdefault-integer-8 -Wextra -Wuninitialized  -O3  -mfpmath=sse -ffast-math -fprefetch-loop-arrays  -march=opteron -mtune=opteron -I. -I../include -I/export/home/florent/tmp/nwchem/6.1/nwchem-6.1/src/include -I/export/home/florent/tmp/nwchem/6.1/nwchem-6.1/src/tools/install/include -DEXT_INT -DLINUX -DLINUX64 -DGFORTRAN -DCHKUNDFLW -DGCC4 -DPARALLEL_DIAG   xc_spbe96.F
gfortran -c -fdefault-integer-8 -Wextra -Wuninitialized  -O3  -mfpmath=sse -ffast-math -fprefetch-loop-arrays  -march=opteron -mtune=opteron -I. -I../include -I/export/home/florent/tmp/nwchem/6.1/nwchem-6.1/src/include -I/export/home/florent/tmp/nwchem/6.1/nwchem-6.1/src/tools/install/include -DEXT_INT -DLINUX -DLINUX64 -DGFORTRAN -DCHKUNDFLW -DGCC4 -DPARALLEL_DIAG   xc_kt1.F
gfortran -c -fdefault-integer-8 -Wextra -Wuninitialized  -O3  -mfpmath=sse -ffast-math -fprefetch-loop-arrays  -march=opteron -mtune=opteron -I. -I../include -I/export/home/florent/tmp/nwchem/6.1/nwchem-6.1/src/include -I/export/home/florent/tmp/nwchem/6.1/nwchem-6.1/src/tools/install/include -DEXT_INT -DLINUX -DLINUX64 -DGFORTRAN -DCHKUNDFLW -DGCC4 -DPARALLEL_DIAG   xc_ssbD_1.F
gfortran -c -fdefault-integer-8 -Wextra -Wuninitialized  -O3  -mfpmath=sse -ffast-math -fprefetch-loop-arrays  -march=opteron -mtune=opteron -I. -I../include -I/export/home/florent/tmp/nwchem/6.1/nwchem-6.1/src/include -I/export/home/florent/tmp/nwchem/6.1/nwchem-6.1/src/tools/install/include -DEXT_INT -DLINUX -DLINUX64 -DGFORTRAN -DCHKUNDFLW -DGCC4 -DPARALLEL_DIAG   xc_camb88.F
gfortran -c -fdefault-integer-8 -Wextra -Wuninitialized  -O3  -mfpmath=sse -ffast-math -fprefetch-loop-arrays  -march=opteron -mtune=opteron -I. -I../include -I/export/home/florent/tmp/nwchem/6.1/nwchem-6.1/src/include -I/export/home/florent/tmp/nwchem/6.1/nwchem-6.1/src/tools/install/include -DEXT_INT -DLINUX -DLINUX64 -DGFORTRAN -DCHKUNDFLW -DGCC4 -DPARALLEL_DIAG   xc_att_xc.F
gfortran -c -fdefault-integer-8 -Wextra -Wuninitialized  -O3  -mfpmath=sse -ffast-math -fprefetch-loop-arrays  -march=opteron -mtune=opteron -I. -I../include -I/export/home/florent/tmp/nwchem/6.1/nwchem-6.1/src/include -I/export/home/florent/tmp/nwchem/6.1/nwchem-6.1/src/tools/install/include -DEXT_INT -DLINUX -DLINUX64 -DGFORTRAN -DCHKUNDFLW -DGCC4 -DPARALLEL_DIAG   xc_camxpbe96.F
gfortran -c -fdefault-integer-8 -Wextra -Wuninitialized  -O3  -mfpmath=sse -ffast-math -fprefetch-loop-arrays  -march=opteron -mtune=opteron -I. -I../include -I/export/home/florent/tmp/nwchem/6.1/nwchem-6.1/src/include -I/export/home/florent/tmp/nwchem/6.1/nwchem-6.1/src/tools/install/include -DEXT_INT -DLINUX -DLINUX64 -DGFORTRAN -DCHKUNDFLW -DGCC4 -DPARALLEL_DIAG   xc_camxlsd.F
gfortran -c -fdefault-integer-8 -Wextra -Wuninitialized  -O3  -mfpmath=sse -ffast-math -fprefetch-loop-arrays  -march=opteron -mtune=opteron -I. -I../include -I/export/home/florent/tmp/nwchem/6.1/nwchem-6.1/src/include -I/export/home/florent/tmp/nwchem/6.1/nwchem-6.1/src/tools/install/include -DEXT_INT -DLINUX -DLINUX64 -DGFORTRAN -DCHKUNDFLW -DGCC4 -DPARALLEL_DIAG   xc_xwpbe.F
gfortran -c -fdefault-integer-8 -Wextra -Wuninitialized  -O3  -mfpmath=sse -ffast-math -fprefetch-loop-arrays  -march=opteron -mtune=opteron -I. -I../include -I/export/home/florent/tmp/nwchem/6.1/nwchem-6.1/src/include -I/export/home/florent/tmp/nwchem/6.1/nwchem-6.1/src/tools/install/include -DEXT_INT -DLINUX -DLINUX64 -DGFORTRAN -DCHKUNDFLW -DGCC4 -DPARALLEL_DIAG   hse08fx.F
gfortran -c -fdefault-integer-8 -Wextra -Wuninitialized  -O3  -mfpmath=sse -ffast-math -fprefetch-loop-arrays  -march=opteron -mtune=opteron -I. -I../include -I/export/home/florent/tmp/nwchem/6.1/nwchem-6.1/src/include -I/export/home/florent/tmp/nwchem/6.1/nwchem-6.1/src/tools/install/include -DEXT_INT -DLINUX -DLINUX64 -DGFORTRAN -DCHKUNDFLW -DGCC4 -DPARALLEL_DIAG   steric_energy.F
gfortran: Internal error: Killed (program f951)
Please submit a full bug report.
See <http://bugzilla.redhat.com/bugzilla> for instructions.
make[3]: *** [/export/home/florent/tmp/nwchem/6.1/nwchem-6.1/lib/LINUX64/libnwdft.a(xc_vdw.o)] Error 1
make[2]: *** [optimized] Error 2
make[1]: *** [subdirs] Error 1
make: *** [libraries] Error 1


I would be grateful if someone could help me or give some advices to solve this problem.

Thanks in advance,

Florent

Forum Vet
5:03:09 PM PDT - Thu, Oct 25th 2012
This seems to be a compiler problem. Which compiler version (gfortran -v) do you have? Switching to a new one or older stable one (depending on what you have right now and how old it is) might help you here.

Bert


Quote:Flo-lim Oct 24th 3:28 pm
Dear NWChem's users,

Does anyone has any experience compiling Nwchem 6.1 or 6.1.1 on rocks cluster 6.0 based on CentOS 6.2?

I have many difficulties compiling by using gfortran (in openmpi environment) with gcc version 4.4.6 20110731 (Red Hat 4.4.6-3).

I must admit that I'm a beginner in compiling source code and probably the issue is relatively stupid.

Here, please find my env. variables:

export LARGE_FILES=TRUE
export TCGRSH=/usr/bin/ssh
export NWCHEM_TOP=/export/home/florent/tmp/nwchem/6.1/nwchem-6.1
export NWCHEM_TARGET=LINUX64
export NWCHEM_MODULES=all
export USE_MPI=y
export USE_MPIF=y
export USE_MPIF4=y
export MPI_LOC=/opt/openmpi
export MPI_LIB=/opt/openmpi/lib
export MPI_INCLUDE=/opt/openmpi/include
export LIBRARY_PATH=$LIBRARY_PATH:/opt/openmpi/lib
export LIBMPI="-lmpi_f90 -lmpi_f77 -lmpi -lopen-rte -lopen-pal -ldl -Wl,--export-dynamic -lnsl -lutil -lm -ldl"


And here, the permanent error message that I get:

gfortran -c -fdefault-integer-8 -Wextra -Wuninitialized  -O3  -mfpmath=sse -ffast-math -fprefetch-loop-arrays  -march=opteron -mtune=opteron -I. -I../include -I/export/home/florent/tmp/nwchem/6.1/nwchem-6.1/src/include -I/export/home/florent/tmp/nwchem/6.1/nwchem-6.1/src/tools/install/include -DEXT_INT -DLINUX -DLINUX64 -DGFORTRAN -DCHKUNDFLW -DGCC4 -DPARALLEL_DIAG   xc_spbe96.F
gfortran -c -fdefault-integer-8 -Wextra -Wuninitialized  -O3  -mfpmath=sse -ffast-math -fprefetch-loop-arrays  -march=opteron -mtune=opteron -I. -I../include -I/export/home/florent/tmp/nwchem/6.1/nwchem-6.1/src/include -I/export/home/florent/tmp/nwchem/6.1/nwchem-6.1/src/tools/install/include -DEXT_INT -DLINUX -DLINUX64 -DGFORTRAN -DCHKUNDFLW -DGCC4 -DPARALLEL_DIAG   xc_kt1.F
gfortran -c -fdefault-integer-8 -Wextra -Wuninitialized  -O3  -mfpmath=sse -ffast-math -fprefetch-loop-arrays  -march=opteron -mtune=opteron -I. -I../include -I/export/home/florent/tmp/nwchem/6.1/nwchem-6.1/src/include -I/export/home/florent/tmp/nwchem/6.1/nwchem-6.1/src/tools/install/include -DEXT_INT -DLINUX -DLINUX64 -DGFORTRAN -DCHKUNDFLW -DGCC4 -DPARALLEL_DIAG   xc_ssbD_1.F
gfortran -c -fdefault-integer-8 -Wextra -Wuninitialized  -O3  -mfpmath=sse -ffast-math -fprefetch-loop-arrays  -march=opteron -mtune=opteron -I. -I../include -I/export/home/florent/tmp/nwchem/6.1/nwchem-6.1/src/include -I/export/home/florent/tmp/nwchem/6.1/nwchem-6.1/src/tools/install/include -DEXT_INT -DLINUX -DLINUX64 -DGFORTRAN -DCHKUNDFLW -DGCC4 -DPARALLEL_DIAG   xc_camb88.F
gfortran -c -fdefault-integer-8 -Wextra -Wuninitialized  -O3  -mfpmath=sse -ffast-math -fprefetch-loop-arrays  -march=opteron -mtune=opteron -I. -I../include -I/export/home/florent/tmp/nwchem/6.1/nwchem-6.1/src/include -I/export/home/florent/tmp/nwchem/6.1/nwchem-6.1/src/tools/install/include -DEXT_INT -DLINUX -DLINUX64 -DGFORTRAN -DCHKUNDFLW -DGCC4 -DPARALLEL_DIAG   xc_att_xc.F
gfortran -c -fdefault-integer-8 -Wextra -Wuninitialized  -O3  -mfpmath=sse -ffast-math -fprefetch-loop-arrays  -march=opteron -mtune=opteron -I. -I../include -I/export/home/florent/tmp/nwchem/6.1/nwchem-6.1/src/include -I/export/home/florent/tmp/nwchem/6.1/nwchem-6.1/src/tools/install/include -DEXT_INT -DLINUX -DLINUX64 -DGFORTRAN -DCHKUNDFLW -DGCC4 -DPARALLEL_DIAG   xc_camxpbe96.F
gfortran -c -fdefault-integer-8 -Wextra -Wuninitialized  -O3  -mfpmath=sse -ffast-math -fprefetch-loop-arrays  -march=opteron -mtune=opteron -I. -I../include -I/export/home/florent/tmp/nwchem/6.1/nwchem-6.1/src/include -I/export/home/florent/tmp/nwchem/6.1/nwchem-6.1/src/tools/install/include -DEXT_INT -DLINUX -DLINUX64 -DGFORTRAN -DCHKUNDFLW -DGCC4 -DPARALLEL_DIAG   xc_camxlsd.F
gfortran -c -fdefault-integer-8 -Wextra -Wuninitialized  -O3  -mfpmath=sse -ffast-math -fprefetch-loop-arrays  -march=opteron -mtune=opteron -I. -I../include -I/export/home/florent/tmp/nwchem/6.1/nwchem-6.1/src/include -I/export/home/florent/tmp/nwchem/6.1/nwchem-6.1/src/tools/install/include -DEXT_INT -DLINUX -DLINUX64 -DGFORTRAN -DCHKUNDFLW -DGCC4 -DPARALLEL_DIAG   xc_xwpbe.F
gfortran -c -fdefault-integer-8 -Wextra -Wuninitialized  -O3  -mfpmath=sse -ffast-math -fprefetch-loop-arrays  -march=opteron -mtune=opteron -I. -I../include -I/export/home/florent/tmp/nwchem/6.1/nwchem-6.1/src/include -I/export/home/florent/tmp/nwchem/6.1/nwchem-6.1/src/tools/install/include -DEXT_INT -DLINUX -DLINUX64 -DGFORTRAN -DCHKUNDFLW -DGCC4 -DPARALLEL_DIAG   hse08fx.F
gfortran -c -fdefault-integer-8 -Wextra -Wuninitialized  -O3  -mfpmath=sse -ffast-math -fprefetch-loop-arrays  -march=opteron -mtune=opteron -I. -I../include -I/export/home/florent/tmp/nwchem/6.1/nwchem-6.1/src/include -I/export/home/florent/tmp/nwchem/6.1/nwchem-6.1/src/tools/install/include -DEXT_INT -DLINUX -DLINUX64 -DGFORTRAN -DCHKUNDFLW -DGCC4 -DPARALLEL_DIAG   steric_energy.F
gfortran: Internal error: Killed (program f951)
Please submit a full bug report.
See <http://bugzilla.redhat.com/bugzilla> for instructions.
make[3]: *** [/export/home/florent/tmp/nwchem/6.1/nwchem-6.1/lib/LINUX64/libnwdft.a(xc_vdw.o)] Error 1
make[2]: *** [optimized] Error 2
make[1]: *** [subdirs] Error 1
make: *** [libraries] Error 1


I would be grateful if someone could help me or give some advices to solve this problem.

Thanks in advance,

Florent

Just Got Here
1:34:30 AM PDT - Fri, Oct 26th 2012
Thanks for your answer.

the gfortran -v command returns "gcc version 4.4.6 20110731 (Red Hat 4.4.6-3)"

For the moment, and for an mysterious and unknown reason (at least for me) the 6.1.1 has been well compiled.

Anyway, the use of inter compiler will be done in few time.

Thanks,

Florent

Forum Vet
3:06:41 PM PDT - Mon, Oct 29th 2012
Florent,
Please correct me if I am wrong: your compilation with 6.1.1 was successful,
while the 6.1 crashed with the gfortran internal error, right?

Thanks, Edo

Just Got Here
4:44:45 AM PST - Sun, Nov 4th 2012
I'm sorry, I was really messy in my explanations!

It's exactly that. The 6.1 crashed with an internal gfortran ( 4.4.6 20110731 (Red Hat 4.4.6-3)) while the 6.1.1 has been well compiled.

Thanks,

Florent

Forum Vet
10:56:50 AM PST - Mon, Nov 5th 2012
Thanks for the feedback. That's consistent with my findings.
The culprint was the routine src/nwdft/xc/xc_vdw.F
This routine was modified and is now compiled in a different way in 6.1.1.
Please stick to 6.1.1

Cheers, Edo

Just Got Here
10:59:53 AM PST - Mon, Nov 5th 2012
Ok,

Thanks for your answer.

Cheers,

Flo


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