Dependencies

Perl

In order to use columbus you need your own version of perl and CPAN installed.

$ curl -L http://install.perlbrew.pl | bash
$ echo "source ~/perl5/perlbrew/etc/bashrc" >> $HOME/.profile
$ perlbrew install perl-5.19.5
$ perlbrew use perl-5.19.5

Alternatively, you can use install.hovr2pi

$ curl -l http://install.hovr2pi.org/perlbrew | bash

We will also need a way to install and manage perl packages. This can be done by CPAN but [cpanminus] does an excellent job when combined with [cpan-outdated] Install cpanium

$ curl -L http://cpanmin.us | perl - App::cpanminus

And then install cpan-outdated along with all perl modules using cpanm:

$ cpanm App::cpanoutdated

Now that that is bootstrapped, we can upgrade out perl modules automagically:

$ cpan-outdated -p | cpanm

And now we shall use cpanm to install Shell and Curses

$ cpanm Shell

$ cpanm Curses

Copy all of the perlscripts provided by Columbus into the perlbrew directory so we do not have to worry about maintining multiple locations of perl modules.

$ cp $COLUMBUS/perlscripts/* $HOME/perlbrew/perl-5.19.5/lib
$ cp $COLUMBUS/CPAN/* $HOME/perlbrew/perl-5.19.5/lib

Still, some packages are not in cpanm so we have to use CPAN.

$ cpan
$ install Devel::PPPort

$ printf 'CURSES_LDFLAGS=-lncursesw' >> $HOME/.bashrc

Installation of Columbus

$ wget http://www.univie.ac.at/columbus/C70_beta_pre-release/Columbus.7.0/Col7.0_2013-07-01_linux64.ifc.byterecl_src.tar.gz

$ tar xf Col7.0_2013-07-01_linux64.ifc.byterecl_src.tar.gz

$ export COLUMBUS=`pwd`/Columbus 
$ printf 'COLUMBUS'=`pwd`'/Columbus' >> $HOME/.bashrc

$ cd $COLUMBUS/../
$ ./install.automatic cpan

$ module load gsl ga && echo "module load gsl ga" >> $HOME/.bashrc

Now we will need molden. Note, you will need to use the molden from [install.hovr2pi.org/contrib/molden.tar.gz] due to the use of a deprecated makedepend script provided on their website.

To make things easier, do it in your top level directory of COLUMBUS

$ cd $COLUMBUS/.. &&  curl -l http://install.hovr2pi.org/molden | bash

Now we need to edit the config files for COLUMBUS

$ cd $COLUMBUS/machine.cfg

And update the file linux64.ifc.byterecl for stampede or download mine at (http://install.hovr2pi.org/configs/columbus/linux64.ifc.byterecl.stampede)

$ wget http://install.hovr2pi.org/configs/columbus/linux64.ifc.byterecl.stampede

Next is updating the install.config in $COLUMBUS/.. with the one I created

$ cd $COLUMBUS/..
$ curl -l http://install.hovr2pi.org/configs/columbus/install.config.stampede > install.config
$ mv install.config.stampede install.config

We will also need to change $COLUMBUS/makefile to point to the TACC installed GlobalArrays

$ cd $COLUMBUS
$ curl -l http://install.hovr2pi.org/configs/columbus/makefile > makefile

Finally, we need a new version of install.automatic. The released version had a few typos.

$ cd $COLUMBUS/../
$ curl -l http://install.hovr2pi.org/configs/columbus/install.automatic > install.automatic

Now we are ready to start actually instaling COLUMBUS

$ ./install.automatic -p linux64.ifc.byterecl standard grad cc parallel runtests

And the only other thing we need to do is replace the distributed Curses.so with the one we setup earlier

$ mv $COLUMBUS/CPAN/auto/curses/Curses.so $COLUMBUS/CPAN/auto/curses/Curses.so.orig
$ cp /home1/00416/csim/perl5/perlbrew/perls/perl-5.19.5/lib/site_perl/5.19.5/x86_64-linux/auto/Curses $COLUMBUS/CPAN/auto/curses/Curses.so

The columbus-stampede suite of scripts

columbus-stampede is a collection of scripts to drive columbus on stampede for the generation of potential energy surfaces that will be used to then calculation state to state reaction rates via QCT.

Installation

$ echo "module load git" >> ~/.bashrc
$ module load git 
$ cd $WORK
$ git clone https://github.com/hovr2pi/columbus-stampede.git