NWChem 6.6 -segmentation fault

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Just Got Here
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Posts 4
Dear all,

I compiled NWChem 6.6 on Ubuntu 17.04. I used the following steps.


export NWCHEM_TOP=/home/ravi/Desktop/nwchem-6.6
export NWCHEM_TARGET=LINUX64
export NWCHEM_MODULES=all python

export USE_MPI=y
export USE_MPIF=y
export USE_MPIF4=y

export LIBMPI="-lmpi_usempif08 -lmpi_usempi_ignore_tkr -lmpi_mpifh -lmpi"
export MPI_LIB=/usr/lib/x86_64-linux-gnu/openmpi/lib
export MPI_INCLUDE=/usr/lib/x86_64-linux-gnu/openmpi/include

export USE_NOFSCHECK=TRUE
export MRCC_METHODS=TRUE

export PYTHONHOME=/usr/lib/python3.5
export PYTHONVERSION=3.5
export USE_PYTHONCONFIG=Y
export USE_PYTHON64=Y
export PYTHONLIBTYPE=so
export PYTHONCONFIGDIR=config-3.5m-x86_64-linux-gnu

export USE_SCALAPACK=y
export SCALAPACK="-L/usr/lib/libscalapack-openmpi.so.1 -llibblacs-openmpi.so.1"

> cd $NWCHEM_TOP/src
> make clean
> make 64_to_32

export BLASOPT="-lopenblas -lpthread -lrt"
export BLAS_SIZE=4
export USE_64TO32=y
export USE_INTERNALBLAS=y

   Compilation

> make nwchem_config
> make 64_to_32
> make cc=icc F=gfortran


I have got nwchem binaries, however, whilst trying to run a test job, I got segmentation fault error.

Here is the input file:

echo
title "Nitrogen cc-pvdz SCF geometry optimization"
geometry

 n 0 0 0

 n 0 0 1.08

end

basis

 n library cc-pvdz

end

scf

direct

end

task scf optimize


>nwchem n2.nw > n2.out

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

Backtrace for this error:

   0 0x7f819ed74ed7 in ???
1 0x7f819ed7410d in ???
2 0x7f819e4947ef in ???
3 0x7f819f0e8244 in ???
4 0x559d69bf316a in ???
5 0x559d69bf321b in ???
6 0x559d69bf208e in ???
7 0x559d672ed2de in nwchem

      at /home/ravi/Desktop/nwchem-6.6/src/nwchem.F:84

   8 0x559d672ede84 in main

      at /home/ravi/Desktop/nwchem-6.6/src/nwchem.F:369

Segmentation fault (core dumped)


Could someone please help to resolve the error?

Thank you.
KRISH

Forum Vet
Threads 9
Posts 1398
  • Python 3 is not supported

  • Did you apply the following patch?

http://www.nwchem-sw.org/download.php?f=Ga_argv.patch.gz

http://www.nwchem-sw.org/index.php/Special:AWCforum/st/id1269

Just Got Here
Threads 2
Posts 4
Dear Dr. Edoapra,

I applied the patch which you have mentioned. In addition, I modified the Python library details as shown below and recombiled nwchem.

export PYTHONHOME=/usr/lib/python2.7
export PYTHONVERSION=2.7
export PYTHONCONFIGDIR=config-x86_64-linux-gnu

>make clean
> make nwchem_config
> make 64_to_32
> make cc=icc FC=gfortran

Although I have got the nwchem binary, when I ran the n2-test run (input file -see the first post), I again got the similar segmentation fault error.

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

Backtrace for this error:
  1. 0 0x7f5a53569ed7 in ???
  2. 1 0x7f5a5356910d in ???
  3. 2 0x7f5a52c897ef in ???
  4. 3 0x7f5a538dd244 in ???
  5. 4 0x55c995bf91ab in ???
  6. 5 0x55c995bf925c in ???
  7. 6 0x55c995bf80cf in ???
  8. 7 0x55c9932f32de in nwchem
at /home/ravi/Desktop/nwchem-6.6/src/nwchem.F:84
  1. 8 0x55c9932f3e84 in main
at /home/ravi/Desktop/nwchem-6.6/src/nwchem.F:369
Segmentation fault (core dumped)

How can I solve this problem?

Thank you.
KRISH

Forum Vet
Threads 9
Posts 1398
Krish
My suggestion is for you to wait until the next release (6.8) of NWChem comes out


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