Installation of VENUS-NWCHEM

[sovan...@gmail.com]

We have been trying to install VENES-NWCHEM code in our HPC. We have opted for an older version of the code (from http://cpc.cs.qub.ac.uk/summaries/AERS_v1_0.html)as provided in the Comp.Phys.Comm website. However, we have been facing some problem. The installation script and related log file are attached herewith. 

Could you please help us solve this problem ? 

we are using 

MPI - openmpi-1.4.4 

OS -  centos7 

the error message is like :

----------------------------------------------------------

ld: cannot find -lmpi_f77
ld: cannot find -lmpi_f90
make: *** [all] Error 1
rm: cannot remove ‘ven_nw.e’: No such file or directory
make: *** [clean] Error 1
ld: cannot find -lmpi_f77
ld: cannot find -lmpi_f90
make: *** [ven_nw.e] Error 1

------------------------------------------------------------------------

the build file we are using : 

#!/bin/bash
echo " "
#source  /opt/intel/Compiler/11.1/064/bin/ifortvars.sh intel64
#source  /opt/intel/Compiler/11.1/064/bin/iccvars.sh intel64
source /apps/intel/setvars.sh
#export LD_LIBRARY_PATH=/usr/lib64:$LD_LIBRARY_PATH
#export LD_LIBRARY_PATH=/apps/intel/mpi/2021.5.1/lib:/usr/lib64:$LD_LIBRARY_PATH

#export mpidir=/cm/shared/apps/openmpi/intel/64/1.3.3
## by s
#export mpidir=/apps/intel/mpi/2021.5.1/bin/mpirun
#export mpidir=/apps/openmpi-3/bin/mpirun
export mpidir=/apps/openmpi-1.4.4/bin/mpirun
export LD_LIBRARY_PATH=/apps/openmpi-1.4.4/lib:$LD_LIBRARY_PATH
export PATH=/apps/openmpi-1.4.4/bin:$PATH

######
#export LD_LIBRARY_PATH=/apps/openmpi-3/lib:$LD_LIBRARY_PATH
#export PATH=/apps/openmpi-3/bin:$PATH
#export mpidir=/apps/openmpi-3/lib
#cd /home/carolp/work/CPC-D-12-00495-REV/NWC/nwchem-6.1.1-src
cd /apps/venus/NWC/nwchem-6.1.1-src

export NWCHEM_TOP=`pwd`
length=`pwd | wc -m`
if [ $length -gt 64 ]
then
  echo "The directory name chosen for NWCHEM_TOP is longer"
  echo "than the maximum allowed value of 65 characters"
  echo "Please shorten the path"
  echo "Exiting"
  exit 1
fi
cd src
export TCGRSH=/usr/bin/ssh
export NWCHEM_TARGET=LINUX64
export USE_MPI=y
export USE_MPIF=y
export USE_MPIF4=y
export CFLAGS="-pc80 -axSSE4.2 -axSSE4.2 -O3 -ip -g"
export FFLAGS="-pc80 -axSSE4.2 -axSSE4.2 -O3 -ip -g"
export F90FLAGS="-pc80 -axSSE4.2 -axSSE4.2 O3 ip -g"
export MPI_LOC=$mpidir
export MPI_LIB=$MPI_LOC/lib64
export LIBMPI="-L$MPI_LIB -L/usr/lib64 -lmpi -lmpi_f77 -lmpi_f90"
export MPI_INCLUDE=$MPI_LOC/include
export ARMCI_DEFAULT_SHMMAX=256
export MA_USE_ARMCI_MEM=1
export LARGE_FILES="true"
export NWCHEM_MODULES="all"
export F77=ifort
export F90=ifort
export FC=ifort
export FL=ifort
export CC=icc
export CXX=icpc
make realclean
find . -name include_stamp -exec rm {} \; -print
make clean
make nwchem_config FC=ifort CC=icc > make.log
make CC=icc FC=ifort CXX=icpc >> make.log
echo "Done Making Nwchem"
export NWCHEM_MODULES="qm geninterface"
make nwchem_config NWCHEM_MODULES=venus
make nwchem_config
make CC=icc FC=ifort >> make.log
make stubs.o >> make.log
cd ../../
cd venus-nwchem
make clean > make-venus.log
make FC=ifort CC=icc CXX=icpc >> make-venus.log

[Edoardo Aprà]

What is the output of the command

/apps/openmpi-1.4.4/bin/mpif90 -show

[sovan...@gmail.com]

gfortran -I/apps/openmpi-1.4.4/include -pthread -I/apps/openmpi-1.4.4/lib -L/apps/openmpi-1.4.4/lib -lmpi_f90 -lmpi_f77 -lmpi -lopen-rte -lopen-pal -ldl -Wl,--export-dynamic -lnsl -lutil -lm -ldl

[Edoardo Aprà]

Please use the following MPI settings

MPI_LIB=/apps/openmpi-1.4.4/lib

MPI_INCLUDE="/apps/openmpi-1.4.4/include -pthread -I/apps/openmpi-1.4.4/lib"

LIBMPI="-lmpi_f90 -lmpi_f77 -lmpi -lopen-rte -lopen-pal -ldl -Wl,--export-dynamic -lnsl -lutil -lm"

[sovan...@gmail.com]

ld: cannot find -lmpi_f90
ld: cannot find -lmpi_f77
ld: cannot find -lopen-rte
ld: cannot find -lopen-pal

make: *** [ven_nw.e] Error 1

[Edoardo Aprà]

What about providing more details about your problem such as the full link command?

[Sovan Maiti]

Dear sir, 

now I am trying to install VENUS-NWCHEM

nwchem-6.5.tar.gz

OS : centos7 

ifort : ifort (IFORT) 2021.5.0 20211109

/apps/openmpi-1.4.4/bin/mpif90 -show : gfortran -I/apps/openmpi-1.4.4/include -pthread -I/apps/openmpi-1.4.4/lib -L/apps/openmpi-1.4.4/lib -lmpi_f90 -lmpi_f77 -lmpi -lopen-rte -lopen-pal -ldl -Wl,--export-dynamic -lnsl -lutil -lm -ldl

"""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""

error message : ifort: error #10236: File not found:  '/apps/VENUS-NWCHEM/III.VENUS-NWCHEM/Nwchem-6.5.revision26243-src.2014-09-10/src/stubs.o'

make: *** [ven_nw.e] Error 1

I am attaching build file, and log files.

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Regards.

Sovan Maiti

C/o. Apeejay Business Centre, Apeejay House,

Block-B, 8th Floor, 15 Park Street

Kolkata-700016
Mobile: 08335915343, Web: www.mpcl.in
Customer Support Engineer

[Sovan Maiti]

  Dear sir, 

now I am trying to install VENUS-NWCHEM

nwchem-6.5.tar.gz

OS : centos7 

ifort : ifort (IFORT) 2021.5.0 20211109

/apps/openmpi-1.4.4/bin/mpif90 -show : gfortran -I/apps/openmpi-1.4.4/include -pthread -I/apps/openmpi-1.4.4/lib -L/apps/openmpi-1.4.4/lib -lmpi_f90 -lmpi_f77 -lmpi -lopen-rte -lopen-pal -ldl -Wl,--export-dynamic -lnsl -lutil -lm -ldl

"""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""

error message : ifort: error #10236: File not found:  '/apps/VENUS-NWCHEM/III.VENUS-NWCHEM/Nwchem-6.5.revision26243-src.2014-09-10/src/stubs.o'

make: *** [ven_nw.e] Error 1

I am attaching the build file and the  log files.

On Fri, Sep 16, 2022 at 10:19 PM Edoardo Aprà <edoard...@gmail.com> wrote:

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Regards.

Sovan Maiti

[Edoardo Aprà]

I have generated a script that uses the current NWChem source code and the Computer Physics Communication Venus AERS zip code.

Please do not se any environment variable prior to execute the script.

The only requirements are a working MPI and gfortran installations plus 2GB of disk available

Here are the instructions for executing the script

wget http://github.com/edoapra/venus-nwchem/tarball/main -O venus-nwchem.tar.gz

tar xzf venus-nwchem.tar.gz

cd *-venus-nwchem-*

./download_and_build.sh

Once the code is installed, test input files are present in the test directory.
To execute, type the following command

mpirun -np 2 ../NWC/venus-nwchem/ven_nw.e < Input.dt

Repository URL

https://github.com/edoapra/venus-nwchem