error: Segmentation fault.
Clicked A Few Times
2:34:11 PM PDT - Thu, Apr 10th 2014
Good afternoon everyone.

This is my first post, so, i hope anyone can help me!!!

I have been trying to install Nwchem in my desktop PC (AMD FX 8150, 16GB RAM DDR3) with intel compiler and MKL's math libraries, once established the environmental variables i compiled the code and it ended successfully, but when execute the binary, the following error shows up.

The parallel code is compiled with openmpi 1.8, also compiled with intel compiler.

forrtl: severe (174): SIGSEGV, segmentation fault occurred
Image PC Routine Line Source
nwchem 00000000034C42C9 Unknown Unknown Unknown
nwchem 00000000034C2B9E Unknown Unknown Unknown
nwchem 000000000345BBC2 Unknown Unknown Unknown
nwchem 0000000003403C83 Unknown Unknown Unknown
nwchem 0000000003409F6B Unknown Unknown Unknown
libpthread.so.0 00002AF9F13B7BD0 Unknown Unknown Unknown
libmkl_def.so 00002AFA0430987F Unknown Unknown Unknown
forrtl: severe (174): SIGSEGV, segmentation fault occurred
Image PC Routine Line Source
nwchem 00000000034C42C9 Unknown Unknown Unknown
nwchem 00000000034C2B9E Unknown Unknown Unknown
nwchem 000000000345BBC2 Unknown Unknown Unknown
nwchem 0000000003403C83 Unknown Unknown Unknown
nwchem 0000000003409F6B Unknown Unknown Unknown
libpthread.so.0 00002B6A47CDFBD0 Unknown Unknown Unknown
libmkl_def.so 00002B6A5AC0987F Unknown Unknown Unknown

The next is the environmental variables that i used for the compilation:

setenv NWCHEM_TARGET LINUX64
setenv LARGE_FILES TRUE
setenv LIB_DEFINES -DDFLT_TOT_MEM=16777216
setenv TCGRSH /usr/bin/ssh
setenv NWCHEM_TOP /home/frank/bin/nwchem-6.3
setenv NWCHEM_TARGET LINUX64
setenv NWCHEM_MODULES all
setenv BLASOPT "-L/opt/intel/composer_xe_2013_sp1.2.144/mkl/lib/intel64 -lmkl_core -lmkl_sequential -lmkl_intel_ilp64"
setenv USE_MPI y
setenv USE_MPIF y
setenv USE_MPIF4 y
setenv MPI_LOC /home/frank/bin/openmpi
setenv MPI_INCLUDE /home/frank/bin/openmpi/include
setenv MPI_LIB /home/frank/bin/openmpi/lib
setenv LIBMPI "-lmpi_usempif08 -lmpi_usempi_ignore_tkr -lmpi_mpifh -lmpi"
cd $NWCHEM_TOP/src

setenv FOPTIMIZE "-O3 -xSSE2,SSE3,SSSE3,SSE4.1,SSE4.2 -no-prec-div -funroll-loops -unroll-aggressive"
setenv COPTIMIZE "-O3 -xSSE2,SSE3,SSSE3,SSE4.1,SSE4.2 -no-prec-div -funroll-loops"

make nwchem_config

make -j4 FC=ifort

cd $NWCHEM_TOP/contrib
setenv FC=gfortran

./getmem.nwchem

Hope i made myself clear, and hope anyone can help me.

Forum Vet
3:55:13 PM PDT - Thu, Apr 10th 2014
Frank
1) Could you please post the output of the following command

grep -i blas $NWCHEM_TOP/src/tools/build/config.log

2) Please do NOT redefine FOPTIMIZE and COPTIMIZE since we have validated the code with the default values assigned
by the NWChem makefile structure. My suggestion to you is to recompile the code after un-setting those two variables.

Cheers, Edo

Clicked A Few Times
7:46:53 PM PDT - Thu, Apr 10th 2014
Hello Edo.

Thank you so much for your quick response.

Next is the output of the command that you posted.

 $ ../ga-5-3/configure --prefix=/home/frank/bin/nwchem-6.3/src/tools/install --with-tcgmsg --with-mpi=-I/home/frank/bin/openmpi/include -L/home/frank/bin/openmpi/lib -lmpi_usempif08 -lmpi_usempi_ignore_tkr -lmpi_mpifh -lmpi /home/frank/bin/openmpi --enable-peigs --enable-underscoring --disable-mpi-tests --without-scalapack --without-lapack --with-blas8=-L/opt/intel/composer_xe_2013_sp1.2.144/mkl/lib/intel64 -lmkl_core -lmkl_sequential -lmkl_intel_ilp64 --with-mpi-ts CC=cc F77=ifort
configure:22357: Checks for BLAS,LAPACK,ScaLAPACK
configure:22605: Attempting to locate BLAS library
configure:22611: checking for BLAS with user-supplied flags
| #define HAVE_BLAS 1
| #define BLAS_SIZE 8
| #define HAVE_BLAS 1
| #define BLAS_SIZE 8
configure:43137: running /bin/bash ../../ga-5-3/armci/configure --disable-option-checking '--prefix=/home/frank/bin/nwchem-6.3/src/tools/install' '--with-tcgmsg' '--with-mpi=-I/home/frank/bin/openmpi/include -L/home/frank/bin/openmpi/lib -lmpi_usempif08 -lmpi_usempi_ignore_tkr -lmpi_mpifh -lmpi /home/frank/bin/openmpi' '--enable-peigs' '--enable-underscoring' '--disable-mpi-tests' '--without-scalapack' '--without-lapack' '--with-blas8=-L/opt/intel/composer_xe_2013_sp1.2.144/mkl/lib/intel64 -lmkl_core -lmkl_sequential -lmkl_intel_ilp64' '--with-mpi-ts' 'CC=cc' 'F77=ifort' --cache-file=/dev/null --srcdir=../../ga-5-3/armci
configure:43137: running /bin/bash ../../ga-5-3/comex/configure --disable-option-checking '--prefix=/home/frank/bin/nwchem-6.3/src/tools/install' '--with-tcgmsg' '--with-mpi=-I/home/frank/bin/openmpi/include -L/home/frank/bin/openmpi/lib -lmpi_usempif08 -lmpi_usempi_ignore_tkr -lmpi_mpifh -lmpi /home/frank/bin/openmpi' '--enable-peigs' '--enable-underscoring' '--disable-mpi-tests' '--without-scalapack' '--without-lapack' '--with-blas8=-L/opt/intel/composer_xe_2013_sp1.2.144/mkl/lib/intel64 -lmkl_core -lmkl_sequential -lmkl_intel_ilp64' '--with-mpi-ts' 'CC=cc' 'F77=ifort' --cache-file=/dev/null --srcdir=../../ga-5-3/comex
configure:43239: BLAS_LDFLAGS= -L/opt/intel/composer_xe_2013_sp1.2.144/mkl/lib/intel64
configure:43241: BLAS_LIBS= -lmkl_core -lmkl_sequential -lmkl_intel_ilp64
configure:43243: BLAS_CPPFLAGS= BLAS_CPPFLAGS=
 BLAS_LDFLAGS=' -L/opt/intel/composer_xe_2013_sp1.2.144/mkl/lib/intel64'
BLAS_LIBS=' -lmkl_core -lmkl_sequential -lmkl_intel_ilp64'
HAVE_BLAS_FALSE='#'
HAVE_BLAS_TRUE=
  1. define HAVE_BLAS 1
  2. define BLAS_SIZE 8

Thanks again.

Clicked A Few Times
8:34:11 PM PDT - Thu, Apr 10th 2014
Hello again Edo, i tried to re-install the nwchem code with your recommendation (un-setting COPTIMZIE and FOPTIMIZE before the compilation) but unfortunately the problem persists. I will be waiting for another suggestion.

By the way, the code that i am trying to compile is the one built in January.

Thank you so much for all of your help.

Cheers.

Forum Vet
10:43:53 AM PDT - Fri, Apr 11th 2014
OpenMPI version
Frank
What version of OpenMPI are you using? I believe you are using a pretty recent one -- that we might have not tested yet.
I was not aware of the use mpi_f08 option, too, that shows up in your MPI library settings.
Edo

Clicked A Few Times
3:22:30 PM PDT - Fri, Apr 11th 2014
Hello Edo.

I tried to install the code, but i change the compiler (GNU) and the math libraries (ACML), also i compiled the openmpi-1.6.5 code with GNU fortran, it did not work.

Here is the variables for the compilation of the code.

setenv NWCHEM_TARGET LINUX64
setenv LARGE_FILES TRUE
setenv LIB_DEFINES -DDFLT_TOT_MEM=16777216
setenv TCGRSH /usr/bin/ssh
setenv NWCHEM_TOP /home/frank/bin/nwchem-6.3
setenv NWCHEM_TARGET LINUX64
setenv NWCHEM_MODULES all
setenv BLASOPT "-L/opt/acml5.3.1/gfortran64_int64/lib/libacml -lacml"
setenv USE_MPI y
setenv USE_MPIF y
setenv USE_MPIF4 y
setenv MPI_LOC /home/frank/bin/openmpi
setenv MPI_INCLUDE /home/frank/bin/openmpi/include
setenv MPI_LIB /home/frank/bin/openmpi/lib
setenv LIBMPI "-lmpi_f90 -lmpi_f77 -lmpi -ldl -Wl,--export-dynamic -lnsl -lutil"
cd $NWCHEM_TOP/src

make nwchem_config

make -j4 FC=gfortran

cd $NWCHEM_TOP/contrib
setenv FC=gfortran

./getmem.nwchem

Kind regards.

Forum Vet
3:39:21 PM PDT - Fri, Apr 11th 2014
Could you try to unset BLASOPT and report the error you are getting out of this kind of installation? Could you please send us the output of the getmem script, too?

Clicked A Few Times
6:35:09 PM PDT - Fri, Apr 11th 2014
SOLVED!
Hello Edo.

I have been able to solve the problem, i do not know where i was doing things wrong but finally i have overcome this problem.

What i made, compile the code with openmpi-1.8 (latest version) with acml, gnu-fortran (one compilation), ifort and mkl (other compilation) both work just fine. Both codes were compiled with the suggested mpi's libraries (ompi-fort.pc file in $MPIROOT/lib/pkgconfig). I guess, what i did new, was a "realclean make" instead of a simple clean before "make nwchem_config".


Cheers, Edo.


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