Compiling NWCHEM on Ubuntu 12.04.2 LTS (not as administrator)


Jump to page 1Prev 16
Clicked A Few Times
Change machine
I change to new machine with csh:

LSB Version: :core-4.1-amd64:core-4.1-noarch:cxx-4.1-amd64:cxx-4.1-noarch:desktop-4.1-amd64:desktop-4.1-noarch:languages-4.1-amd64:languages-4.1-noarch:printing-4.1-amd64:printing-4.1-noarch
Distributor ID: CentOS
Description: CentOS Linux release 7.6.1810 (Core)
Release: 7.6.1810
Codename: Core

#!/bin/bash

# Dowload source code
# https://github.com/nwchemgit/nwchem/releases/tag/6.8.1-release
# nwchem-6.8.1-release.tar.gz
# /home/john
# tar -xzvf nwchem-6.8.1-release.tar.gz
# /home/john/nwchem-6.8.1-release

# Compiling NWChem from source
# https://github.com/nwchemgit/nwchem/wiki/Compiling-NWChem
# Setting up the proper environment variables
export NWCHEM_TOP=hpc/puhome/john/nwchem-6.8.1
export NWCHEM_TARGET=LINUX64
export ARMCI_NETWORK=OPENIB
# MPI variables
export USE_MPI=y
export USE_MPIF=y
export USE_MPIF4=y
export LIBMPI="-lmpi_f90 -lmpi_f77 -lmpi"
export MPI_LIB=/lib
export MPI_INCLUDE=/usr/include/mpi
export NWCHEM_MODULES="all python"
# Adding optional environmental variables
export USE_NOFSCHECK=TRUE
export USE_NOIO=TRUE
export LIB_DEFINES=-DDFLT_TOT_MEM=16777216
export MRCC_METHODS=TRUE
# Setting Python environment variables
export PYTHONVERSION=2.7
export PYTHONHOME=/usr/
export USE_PYTHONCONFIG=y
export USE_PYTHON64= y
export PYTHONLIBTYPE=so
export PYTHONCONFIGDIR=config-x86_64-linux-gnu
# Optimized math libraries
export BLASOPT="-lopenblas -lpthread -lrt"
export USE_SCALAPACK=y
export BLAS_SIZE=4

# NWChem 6.6 on Centos 7.1
export USE_MPI=y
export NWCHEM_TARGET=LINUX64
export USE_PYTHONCONFIG=y
export PYTHONVERSION=2.7
export PYTHONHOME=/usr
export USE_64TO32=y
export BLAS_SIZE=4
export BLASOPT="-lopenblas -lpthread -lrt"
export SCALAPACK_SIZE=4
export SCALAPACK="-L/usr/lib64/openmpi/lib -lscalapack -lmpiblacs"
export ELPA="-I/usr/lib64/gfortran/modules/openmpi -L/usr/lib64/openmpi/lib -lelpa"
export LD_LIBRARY_PATH=/usr/lib64/openmpi/lib/:$LD_LIBRARY_PATH
export PATH=/usr/lib64/openmpi/bin/:$PATH

make nwchem_config NWCHEM_MODULES="all python" >& compile-config_J.log
make >& compile-make-nwchem.log

# runned from: /home/john/nwchem-6.8.1/src


make[1]: Leaving directory `/hpc/puhome/john/nwchem-6.8.1/src/config'
test \! -f 64_to_32 -o \! -f 32_to_64 || rm -f 64_to_32 32_to_64
test -d hpc/puhome/john/nwchem-6.8.1/lib/LINUX64 || mkdir -p hpc/puhome/john/nwchem-6.8.1/lib/LINUX64
test -d hpc/puhome/john/nwchem-6.8.1/bin/LINUX64 || mkdir -p hpc/puhome/john/nwchem-6.8.1/bin/LINUX64
./util/util_nwchem_version.bash
fatal: Not a git repository (or any parent up to mount point /hpc)
Stopping at filesystem boundary (GIT_DISCOVERY_ACROSS_FILESYSTEM not set).
Making libraries in tools
make[1]: Entering directory `/hpc/puhome/john/nwchem-6.8.1/src/tools'
../config/makefile.h:202: hpc/puhome/john/nwchem-6.8.1/src/config/nwchem_config.h: No such file or directory
make[1]: *** No rule to make target `hpc/puhome/john/nwchem-6.8.1/src/config/nwchem_config.h'. Stop.
make[1]: Leaving directory `/hpc/puhome/john/nwchem-6.8.1/src/tools'
make: *** [libraries] Error 1


pwd


/puhome/john/nwchem-6.8.1/src

ls /puhome/john/nwchem-6.8.1/


contrib
doc
examples
INSTALL
INSTALL.binbuilds
LICENSE.TXT
QA
README.md
release.notes.3.2.1
release.notes.3.3
release.notes.4.0
release.notes.4.1
release.notes.4.5
release.notes.4.6
release.notes.4.7
release.notes.5.0
release.notes.5.1
release.notes.5.1.1
release.notes.6.0
release.notes.6.1
release.notes.6.8
release.notes.6.8.1
src
travis
web

ls /puhome/john/nwchem-6.8.1/src/config


32_to_64
32_to_64.pl
64_to_32
64_to_32.pl
census.skeleton
da_rec_size.f
data.64_to_32
data.check.pl
data.dbl2sngl
dbl2sngl.pl
dbl_to_sngl
dbl_to_sngl.2.sed
dbl_to_sngl.sed
depend.c
find_useblas
GNUmakefile
has_blas
hasblas.pl
has_dblas
hasdblas.pl
has_sblas
hassblas.pl
HOW_TO_ADD_A_MODULE
HOW_TO_CONFIGURE
lockfile
makefile.h
makefile-legacy.h
makelib.h
make_nwchem_config
modulesdep.py
NTenv.bash
NTenv.bat
NTmakefile.h
NTmakelib.h
NWCHEM_CONFIG
nwchem_config.h
nwchem_config_win32.h
show_blas
showblas.pl
show_dblas
showdblas.pl
show_sblas
showsblas.pl
simpledepend
sngl2dbl.pl
sngl_to_dbl
sngl_to_dbl.2.sed
sngl_to_dbl.sed
stripdepend
stub.skeleton
util_module_avail_F.begin
util_module_avail_F.end
win32

head /puhome/john/nwchem-6.8.1/src/config/64_to_32


#!/bin/csh -f
#
# $Id$
#
#
# modified to use the perl version to change back to the sed scripts
# reset useperl = 0
#
@ useperl = 1

which csh


/usr/bin/csh

which perl


/usr/bin/perl

Forum Vet
NWCHEM_TOP
You forgot a forward-slash character "/" at the beginning of the env. variable definition

NWCHEM_TOP=hpc/puhome/john/nwchem-6.8.1
should be changed to
NWCHEM_TOP=/hpc/puhome/john/nwchem-6.8.1

Clicked A Few Times
Thank you.

After changing I have the following error:

checking for C compiler vendor... gnu
checking whether a simple C MPI program compiles... no
configure: error: in `/hpc/puhome/john/nwchem-6.8.1/src/tools/build':
configure: error: could not compile simple C MPI program
See `config.log' for more details
make[1]: *** [build/config.status] Error 1
make[1]: Leaving directory `/hpc/puhome/john/nwchem-6.8.1/src/tools'
make: *** [libraries] Error 1

Forum Vet
If you are using Centos 7, NWChem is available from the EPEL 7 RPMs.
To install

sudo yum install https://dl.fedoraproject.org/pub/epel/epel-release-latest-7.noarch.rpm
sudo yum update
sudo yum install nwchem nwchem-openmpi

Clicked A Few Times
Thank you for your help. I am working on it and update you later

Clicked A Few Times
It works! Thank you so much!

Quote:Edoapra Sep 23rd 9:43 am
If you are using Centos 7, NWChem is available from the EPEL 7 RPMs.
To install

sudo yum install https://dl.fedoraproject.org/pub/epel/epel-release-latest-7.noarch.rpm
sudo yum update
sudo yum install nwchem nwchem-openmpi


Forum >> NWChem's corner >> Compiling NWChem
Jump to page 1Prev 16