Compiling NWCHEM on Ubuntu 12.04.2 LTS (not as administrator)


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Clicked A Few Times
4:45:27 AM PDT - Sat, Sep 7th 2019
Dear Colleagues,

I tried to compile NWCHEM on Ubuntu 12.04.2 LTS with the following setting

#!/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 Automatic-NWchem-Compilation-2.0.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=/home/john/nwchem-6.8.1-release
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 Ubuntu 14.04 (Trusty Tahr)
export USE_MPI=y  
export NWCHEM_TARGET=LINUX64  
export USE_PYTHONCONFIG=y  
export PYTHONVERSION=2.7  
export PYTHONHOME=/usr 
export BLASOPT="-lopenblas -lpthread -lrt"  
export BLAS_SIZE=4  
export USE_64TO32=y

make nwchem_config NWCHEM_MODULES="all python" >& compile-config_J.log
make 64_to_32 >& compile-64_to_32_J.log
#make

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


But I have the following error

make[1]: /home/john/nwchem-6.8.1-release/src/config/64_to_32: Command not found
make[1]: *** [64_to_32] Error 127
make[1]: Leaving directory `/home/john/nwchem-6.8.1-release/src/basis'
make: *** [64_to_32] Error 1

Thank you very much for your help in advance.

Best Regards,
john

Forum Vet
11:32:35 AM PDT - Sun, Sep 8th 2019
NWCHEM_TOP
I believe that you might have the wrong value for NWCHEM_TOP
Could post the value of the command pwd in the src directory? The value of NWCHEM_TOP will be the output of pwd stripped of the last /src part

Clicked A Few Times
6:16:56 PM PDT - Sun, Sep 8th 2019
Thank you very much for your help. I followed your advice and successfully addressed the first error. 

export NWCHEM_TOP=/home/john/nwchem-6.8.1-release/src


But still have the following error:

make[1]: Entering directory `/home/john/nwchem-6.8.1-release/src/tools'
../config/makefile.h:202: /home/john/nwchem-6.8.1-release/src/src/config/nwchem_config.h: No such file or directory
make[1]: *** No rule to make target `/home/john/nwchem-6.8.1-release/src/src/config/nwchem_config.h'. Stop.
make[1]: Leaving directory `/home/john/nwchem-6.8.1-release/src/tools'
make: *** [64_to_32] Error 1

Thank you again in advance for your help.

Best Regards,
john

Forum Vet
9:29:57 AM PDT - Mon, Sep 9th 2019
Could you post the output of the pwd command when in the src directory?

Clicked A Few Times
5:52:42 PM PDT - Mon, Sep 9th 2019
It is

/home/john/nwchem-6.8.1-release/src

Thank you,
john

Forum Vet
9:35:02 AM PDT - Tue, Sep 10th 2019
Quote:John1234 Sep 9th 4:52 pm
It is

/home/john/nwchem-6.8.1-release/src

Thank you,
john

This means that you must set


NWCHEM_TOP=/home/john/nwchem-6.8.1-release

Clicked A Few Times
6:16:19 PM PDT - Tue, Sep 10th 2019
Thank you for your help.

export NWCHEM_TOP=/home/john/nwchem-6.8.1-release


was my first setting that resulted the following error

make[1]: /home/john/nwchem-6.8.1-release/src/config/64_to_32: Command not found
make[1]: *** [64_to_32] Error 127
make[1]: Leaving directory `/home/john/nwchem-6.8.1-release/src/basis'
make: *** [64_to_32] Error 1

Then I changed the set into 

export NWCHEM_TOP=/home/john/nwchem-6.8.1-release/src


And got the following error:

make[1]: Entering directory `/home/john/nwchem-6.8.1-release/src/tools'
../config/makefile.h:202: /home/john/nwchem-6.8.1-release/src/src/config/nwchem_config.h: No such file or directory
make[1]: *** No rule to make target `/home/john/nwchem-6.8.1-release/src/src/config/nwchem_config.h'. Stop.
make[1]: Leaving directory `/home/john/nwchem-6.8.1-release/src/tools'
make: *** [64_to_32] Error 1

Forum Vet
9:46:24 AM PDT - Wed, Sep 11th 2019
Could you please rename nwchem-6.8.1-release to nwchem-6.8.1, then set NWCHEM_TOP accordingly?


mv /home/john/nwchem-6.8.1-release /home/john/nwchem-6.8.1

export NWCHEM_TOP=/home/john/nwchem-6.8.1

Clicked A Few Times
6:03:34 PM PDT - Wed, Sep 11th 2019
Thank you again for your help. I received the following feedback

make[1]: Leaving directory `/home/john/nwchem-6.8.1/src'
for dir in tools include basis geom inp input pstat rtdb task symmetry util peigs perfm bq cons blas lapack NWints atomscf ddscf gradients moints nwdft rimp2 stepper driver optim cphf ccsd vib mcscf prepar esp hessian selci dplot mp2_grad qhop property solvation nwpw fft python analyz nwmd cafe space drdy vscf qmmm qmd etrans tce bq mm cons perfm dntmc dangchang ccca dimqm 64to32blas; do \
make -C $dir 64_to_32 || exit 1 ; \
done
make[1]: Entering directory `/home/john/nwchem-6.8.1/src/tools'
No blas conversion done here
make[1]: Leaving directory `/home/john/nwchem-6.8.1/src/tools'
make[1]: Entering directory `/home/john/nwchem-6.8.1/src/include'
Nothing to be done
make[1]: Leaving directory `/home/john/nwchem-6.8.1/src/include'
make[1]: Entering directory `/home/john/nwchem-6.8.1/src/basis'
/home/john/nwchem-6.8.1/src/config/64_to_32 bas_blas.F bas_blasP.F basis.F
make[1]: /home/john/nwchem-6.8.1/src/config/64_to_32: Command not found
make[1]: *** [64_to_32] Error 127
make[1]: Leaving directory `/home/john/nwchem-6.8.1/src/basis'
make: *** [64_to_32] Error 1

Forum Vet
11:55:47 AM PDT - Thu, Sep 12th 2019
Please send the output of the following commands



ls /home/john/nwchem-6.8.1/

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

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

which csh

which perl

Clicked A Few Times
6:29:22 PM PDT - Thu, Sep 12th 2019
Thank you for your help.

As below is the output of each comment

ls /home/john/nwchem-6.8.1/


bin
contrib
doc
examples
INSTALL
INSTALL.binbuilds
lib
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 /home/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 /home/john/nwchem-6.8.1/src/config/64_to_32


/home/john/nwchem-6.8.1/src/config/64_to_32

which csh


no output

which perl


/usr/bin/perl

Forum Vet
9:30:42 AM PDT - Fri, Sep 13th 2019
The output of the head command seems strange.
Could you please try again

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

Clicked A Few Times
7:15:52 PM PDT - Fri, Sep 13th 2019
Thank you. Yes, seems that I made a mistake. The new output is as below.

head /home/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

Forum Vet
11:03:27 AM PDT - Mon, Sep 16th 2019
csh/tcsh missing
You need to install tcsh or csh on your computer

Clicked A Few Times
5:39:48 PM PDT - Tue, Sep 17th 2019
Thank you. I will try to have tcsh or csh on my computer

Clicked A Few Times
10:53:56 PM PDT - Wed, Sep 18th 2019
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


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