SIGSEGV: Segmentation fault

[Carlos Nieto]

Hi,

I'm trying to compile nwchem with python with this environment (Ubuntu 20.04, AMD type processor).

alias nwchem='/apps/nwchem/nwchem-7.2.2/bin/LINUX64/nwchem'
export PATH=/apps/nwchem/nwchem-7.2.2/bin/LINUX64:$PATH
export PATH=/usr/bin/mpif90.openmpi:$PATH
export CC=gcc
export FC=gfortran
export BUILD_OPENBLAS=1
export BUILD_SCALAPACK=1
export USE_NOFSCHECK=TRUE
export USE_SCALAPACK=y
export SCALAPACK_SIZE=4
export USE_64TO32=y
export BLAS_SIZE=4
export NWCHEM_TOP=/apps/nwchem/nwchem-7.2.2
export NWCHEM_TARGET=LINUX64
export LARGE_FILES=TRUE
export USE_NOFSCHECK=TRUE
export TCGRSH="/usr/bin/ssh"
export USE_MPI=y
export USE_MPIF=y
export USE_MPIF4=y
export MPI_LOC=/usr/lib/x86_64-linux-gnu/openmpi
export LD_LIBRARY_PATH=/usr/lib/x86_64-linux-gnu:$LD_LIBRARY_PATH
export LD_LIBRARY_PATH=/apps/anaconda3/lib:$LD_LIBRARY_PATH
export NWCHEM_MODULES="all python"
export PYTHONVERSION=3.8

when trying to run a water test, if returns the following:

Program received signal SIGSEGV: Segmentation fault - invalid memory reference.

Backtrace for this error:
#0  0x7f1fdaed208f in ???

when attempting with mpirun, the next one appears:

mpirun -np 2 /apps/nwchem/nwchem-7.2.2/bin/LINUX64/nwchem h2o.nw

Program received signal SIGSEGV: Segmentation fault - invalid memory reference.

Backtrace for this error:
#0  0x7fbc2a52808f in ???
#1  0x7fbc2aea5900 in format_hash
        at /home/builder/ktietz/cos6/ci_cos6/ctng-compilers_1622658800915/work/.build/x86_64-conda-linux-gnu/src/gcc/libgfortran/io/format.c:128
#2  0x7fbc2aea5900 in find_parsed_format
        at /home/builder/ktietz/cos6/ci_cos6/ctng-compilers_1622658800915/work/.build/x86_64-conda-linux-gnu/src/gcc/libgfortran/io/format.c:163
#3  0x7fbc2aeb0ac2 in data_transfer_init
        at /home/builder/ktietz/cos6/ci_cos6/ctng-compilers_1622658800915/work/.build/x86_64-conda-linux-gnu/src/gcc/libgfortran/io/transfer.c:2793
#4  0x55694e045f70 in get_input_filename_
        at /apps/nwchem/nwchem-7.2.2/src/input/get_inp_file.F:45
#5  0x55694e03ffb6 in nwchem
        at /apps/nwchem/nwchem-7.2.2/src/nwchem.F:114
#6  0x55694e040bc1 in main
        at /apps/nwchem/nwchem-7.2.2/src/nwchem.F:415

===================================================================================
=   BAD TERMINATION OF ONE OF YOUR APPLICATION PROCESSES
=   PID 1156806 RUNNING AT user01
=   EXIT CODE: 139
=   CLEANING UP REMAINING PROCESSES
=   YOU CAN IGNORE THE BELOW CLEANUP MESSAGES
===================================================================================
YOUR APPLICATION TERMINATED WITH THE EXIT STRING: Segmentation fault (signal 11)
This typically refers to a problem with your application.

Any idea of what is going on?

Thanks a lot

[Edoardo Aprà]

Could you post $NWCHEM_TOP/src/tools/build/config.log

[Carlos Nieto]

There you have :-), much appreciated.

[Edoardo Aprà]

Carlos

I have noticed that you are using Anaconda ... what about installing NWChem 7.2.2 from the conda-forge channel?

Do you really need to compile NWChem from source?

https://nwchemgit.github.io/Download.html#nwchem-installation-on-conda