Diff for "Cluster_software_-_RPMS" - Niflheim Linux supercomputer cluster

Differences between revisions 105 and 523 (spanning 418 versions)

This page below describes:

configuration of the fys yum repository,
the necessary steps to build RPM software packages on a custom RPM-based (currently el, fc) system and the login nodes fjorm or thul.

Warning: campos-dacapo-python provides a python interface to campos-dacapo Fortran code, through campos-ase2. On a 64-bit machine campos-ase2 works only with python <= 2.4, due to the unmaintained python-numeric package. Users on modern systems can use instead the campos-ase3 package and skip installation of any packages related to campos-ase2.

Warning: on 64-bit machines el5 installs often only 32-bit versions of packages. Please verify that 64-bit versions are installed, otherwise run the corresponding yum install package again.

Contents

Configure fys yum repository

We host a yum repository, which contains RPM packages of our software for the following systems: el (RedHat Enterprise Linux, or CentOS), fc (Fedora), openSUSE (openSUSE):

configure fys yum repository:
```
yum -y install yum-utils wget
cd /etc/yum.repos.d
wget --no-check-certificate https://svn.fysik.dtu.dk/projects/rpmbuild/trunk/SOURCES/fys_el.repo
```
Note on a RedHat system the value of $releasever in the fys_el.repo file need to be edited manually (changed for example into 5Client, 5Server, etc).

Note on RedHat 6 or clone systems (Scientific Linux, CentOS) the value of $releasever in the fys_el.repo file may need to be edited manually (set explicitly to 6).

Note on a Fedora system download fys_fc.repo instead, and use fys_fc identifier in the command below. Moreover on a fc system you do not need to include any external repositories.

Note on an openSUSE system download fys_openSUSE.repo instead and save it under /etc/zypp/repos.d, and use fys_openSUSE identifier in the command below. You need to include additional external openSUSE repositories: see configure external repositories
list all packages available in the fys yum repository, maybe you need some of them?:
```
yum list available --disablerepo=* --enablerepo=fys_el
```
Note: on el configure external repositories as installation of most packages requires enabling epel or atrpms repositories:
```
yum -y install --enablerepo=fys_el,epel,atrpms campos-dacapo
```
Note: most of the fys packages are relocatable with the default prefix of /usr. As an example one installs campos-dacapo into the /opt/campos-dacapo-2.7.16 prefix as follows:
```
mkdir fys && cd fys # fys directory stores downloaded RPMS
yumdownloader --resolve --enablerepo=fys_el,epel,atrpms campos-dacapo-2.7.16
mkdir tmp && mv campos-dacapo-2.7.16* tmp
yum -y localinstall *
rpm -ivh --relocate "/usr"="/opt/campos-dacapo-2.7.16" tmp/campos-dacapo-*
mv tmp/campos-dacapo-* . && rmdir tmp
```
Have a look at the /opt/campos-dacapo-2.7.16/share/campos-dacapo/*.*sh to see what environment variables need to be set in case of an installation into a non-default prefix. There is also a template modulefile /opt/campos-dacapo-2.7.16/share/campos-dacapo/campos-dacapo-2.7.16* that contains `prereq`ired modules (modulefiles surely are different on your system).

On systems where you don't have root access you can consider downloading RPMS individually and extracting the contents of the RPMS, for example:
```
mkdir ~/fys && cd ~/fys
rpm2cpio http://packages/pub/linux/fys/el/5/x86_64/campos-dacapo-pseudopotentials-1-2.el5.fys.noarch.rpm | cpio -idmv
```

Configure external repos

On openSUSE, as root:

enable the packman repository as described at http://opensuse-community.org/Repositories/Packman

add multimedia:/photo repository, e.g. for opensuse-11.2:

zypper addrepo --repo http://download.opensuse.org/repositories/multimedia:/photo/openSUSE_11.2/multimedia:photo.repo # python-sphinx is there!!!

On RedHat Enterprise Linux or CentOS, as root:

create yum repository definitions (do not enable them):

ATrpms:

official way: follow ATrpms installation instructions and edit /etc/yum.repos.d/atrpms.repo so it contains:
```
enabled=0
```

fast way:

echo '[atrpms]' > /etc/yum.repos.d/atrpms.repo
echo 'name=CentOS $releasever - $basearch - ATrpms' >> /etc/yum.repos.d/atrpms.repo
echo 'baseurl=http://dl.atrpms.net/el$releasever-$basearch/atrpms/stable' >> /etc/yum.repos.d/atrpms.repo
echo '#baseurl=http://mirrors.ircam.fr/pub/atrpms/el$releasever-$basearch/atrpms/stable' >> /etc/yum.repos.d/atrpms.repo
echo 'gpgkey=http://ATrpms.net/RPM-GPG-KEY.atrpms' >> /etc/yum.repos.d/atrpms.repo
echo 'gpgcheck=1' >> /etc/yum.repos.d/atrpms.repo
echo 'enabled=0' >> /etc/yum.repos.d/atrpms.repo

EPEL:

official way: follow EPEL/FAQ/howtouse and edit /etc/yum.repos.d/epel.repo so it contains:
```
enabled=0
```

fast way:

echo '[epel]' > /etc/yum.repos.d/epel.repo
echo 'name=CentOS $releasever - $basearch - EPEL' >> /etc/yum.repos.d/epel.repo
echo 'baseurl=http://download.fedora.redhat.com/pub/epel/$releasever/$basearch' >> /etc/yum.repos.d/epel.repo
echo 'gpgkey=http://download.fedora.redhat.com/pub/epel/RPM-GPG-KEY-EPEL' >> /etc/yum.repos.d/epel.repo
echo 'gpgcheck=1' >> /etc/yum.repos.d/epel.repo
echo 'enabled=0' >> /etc/yum.repos.d/epel.repo

install, as root:

yum install yum-utils wget
# /var directories must be created
yum search --enablerepo=atrpms arpack-devel
yum search --enablerepo=epel jmol

Configure rpmbuild

create and retrieve the rpmbuild project (as rpmbuild user):

cd
svn co https://svn.fysik.dtu.dk/projects/rpmbuild/trunk ~/rpmbuild

include the rpmbuild environment configuration script in ~/.bashrc:

copy the script:
cp ~/rpmbuild/SOURCES/.bashrc_rpmbuild ~/
Note: if installing on a system different than el5 edit the rpm_platform and egg_info variables.
and add the following to ~/.bashrc:
if [ -r "${HOME}/.bashrc_rpmbuild" ]; then
    . ${HOME}/.bashrc_rpmbuild
fi
Note on Niflheim the variables:
export FYS_PLATFORM=Intel-Nehalem-el5 # thul
export FYS_PLATFORM=AMD-Opteron-el5 # fjorm
will be set automatically by /home/camp/modulefiles.sh if the environment-modules package is installed.

create temporary directory:
```
mkdir -p /scratch/$USER
```
apply settings from ~/.bashrc by:
```
. ~/.bashrc
```
use the following ~rpmbuild/.rpmmacros:
```
cp ~/rpmbuild/SOURCES/.rpmmacros ~/
```

create directories:

mkdir -p ~/${FYS_PLATFORM}/{RPMS,SRPMS,BUILD}
mkdir -p ~/${FYS_PLATFORM}/{SPECS,SOURCES} # needed only by openmpi

Install external packages

download official packages, as rpmbuild:

cd ~/${FYS_PLATFORM}/RPMS
mkdir external; cd external
# packages from other distributions
yumdownloader --resolve texlive-latex emacs-auctex tex-preview # Fedora
yast -i Modules texlive-latex emacs-auctex # openSUSE
yast -i python-gtk python-xml python-lxml # openSUSE
yast -i python-matplotlib python-numpy # openSUSE
yast -i gcc-fortran gcc44-fortran libgfortran44 # openSUSE-11.2
yast -i openmpi-devel blas lapack # openSUSE
# el5 packages
yumdownloader --resolve emacs binutils-devel glib-devel libstdc++-devel
yumdownloader --resolve gcc-gfortran blas-devel lapack-devel python-devel python-sphinx
yumdownloader --resolve gnuplot libXi-devel xorg-x11-fonts-100dpi pexpect tetex-latex tkinter qt-devel
yumdownloader --resolve openmpi openmpi-devel openmpi-libs compat-dapl libibverbs librdmacm openib
yumdownloader --resolve pygtk2-devel gtk2-devel tk-devel agg ghostscript libtiff-devel xterm
yumdownloader --resolve libX11-devel libXext-devel openmotif openmotif-devel gd-devel libXpm-devel
yumdownloader --resolve compat-libstdc++-33 # for mathematica
yumdownloader --resolve MySQL-python # for CMR
yumdownloader --resolve perl-XML-SAX # for exciting
yumdownloader --resolve ImageMagick # for ASE3

yumdownloader --resolve gcc43-c++ gcc43-gfortran # only on EL5 == 5.2
yum localinstall * # as root

download atrpms packages, as rpmbuild (vtk-python is currently unavailable 16 Apr 2009):

cd ~/${FYS_PLATFORM}/RPMS/external
yumdownloader --resolve --enablerepo=atrpms vtk-python arpack-devel graphviz
wget http://ATrpms.net/RPM-GPG-KEY.atrpms
rpm --import RPM-GPG-KEY.atrpms # as root
yum localinstall * # as root

download the packages from epel, as rpmbuild:

~/${FYS_PLATFORM}/RPMS/external
yumdownloader --resolve --enablerepo=epel jmol gsl-devel python-lxml
yumdownloader --resolve --enablerepo=epel environment-modules suitesparse-devel
wget http://download.fedora.redhat.com/pub/epel/RPM-GPG-KEY-EPEL
rpm --import RPM-GPG-KEY-EPEL # as root
yum localinstall * # as root

on Niflheim only: remove default openmpi:
```
yum remove openmpi openmpi-libs
```

edit /etc/yum.conf so it contains:

exclude=netcdf-* netcdf3-* fftw-* fftw2-* fftw3-* python-numeric openmpi-* libgfortran4* gcc4* libstdc++4* libgomp-* ScientificPython-*

It's time to build custom RPMS

compilers and tools

open64

Install (on the login and computes nodes) Install Open64 Compiler Suite RPM (available under ~rpmbuild/${FYS_PLATFORM}/RPMS/external/prefix), and deploy module file under ` ~rpmbuild/modulefiles/${FYS_PLATFORM}/open64`. Install using --relocate option:

rpm -ivh --relocate "/opt/open64"="/opt/open64/4.2.1" open64-4.2.1-0.x86_64.rpm

The module file is available as svn checkout at https://svn.fysik.dtu.dk/projects/modulefiles/trunk. Note: the module file should contain at least:

prepend-path     PATH /opt/open64/4.2.1/lib/gcc-lib/x86_64-open64-linux/4.2.1
prepend-path     PATH /opt/open64/4.2.1/bin
prepend-path     LD_LIBRARY_PATH /opt/open64/4.2.1/lib/gcc-lib/x86_64-open64-linux/4.2.1

g95

Install (on the login and computes nodes) g95 RPM (available under ~rpmbuild/${FYS_PLATFORM}/RPMS/external/prefix), and deploy module file under ` ~rpmbuild/modulefiles/${FYS_PLATFORM}/g95`. Install using --relocate option:

rpm -ivh --relocate "/usr/local"="/opt/g95/0.91" g95-0.91-4.x86_64.rpm

The module file is available as svn checkout at https://svn.fysik.dtu.dk/projects/modulefiles/trunk. Note: the module file should contain at least (do not add the lib directory to LD_LIBRARY_PATH):

prepend-path     PATH /opt/g95/0.91/lib/gcc-lib/x86_64-unknown-linux-gnu/4.0.3
prepend-path     PATH /opt/g95/0.91/bin

intel

Note: to enable new intell products upgrading of licenses may be necessary, see http://software.intel.com/en-us/articles/workaround-non-upgraded-serial-numbers-disappear-from-the-intel-registration-center-irc-list/

Note: intel changes packaging quite often, here are the installation instructions for the 12.0 compilers:

install RPMS (only on the login node) found in l_ccompxe_2011.1.107 manually (using rpm -ivh):

intel-{compilerpro,idb,idbcdt,ipp,sourcechecker,tbb}*noarch* # exclude intel-compilerpro-common if installed already by mkl
intel-{compilerpro,idb,ipp,sourcechecker}*x86_64*

and from l_fcompxe_2011.1.107:

intel-compilerprof*{noarch,x86_64}*

create a link (only on thul):

mkdir -p /opt/intel/Compiler/2011.1
cd /opt/intel/Compiler/2011.1 && ln -s /opt/intel/composerxe-2011.1.107 107

build intel compatibility packages (only on thul):

cd ~/rpmbuild/SPECS
rpmbuild -bb ${modules_usage} --with major_version=2011 --with version1=1 --with version2=107 intel-redist.spec

Note: do not install the RPMS generated in the last step on the login node. They need to be installed only on compute nodes. On the login node only the module file needs to be deployed under ~rpmbuild/modulefiles, as rpmbuild. Note that this directory is available as svn checkout at https://svn.fysik.dtu.dk/projects/modulefiles/trunk. Here is what need to be done for a new version of the package:

mkdir ~rpmbuild/modulefiles/${FYS_PLATFORM}/ifort
cp /scratch/rpmbuild/intel-2011.1.107/2011.1.107-1.intel64${disttag} ~rpmbuild/modulefiles/${FYS_PLATFORM}/ifort
cd ~rpmbuild/modulefiles/${FYS_PLATFORM}/ifort
ln -s 2011.1.107-1.intel64${disttag} 12.0-1

Note: modify the file so it contains at least:

setenv INTEL_LICENSE_FILE /opt/intel/licenses

# generated by intel-redist.spec and installed on compute nodes
prepend-path    LD_LIBRARY_PATH      /opt/intel/Compiler/2011.1/107/lib/intel64
# original locations from intel
prepend-path    LD_LIBRARY_PATH      /opt/intel/composerxe-2011.1.107/compiler/lib/intel64
prepend-path    LD_LIBRARY_PATH      /opt/intel/composerxe-2011.1.107/debugger/lib/intel64
prepend-path    PATH                 /opt/intel/composerxe-2011.1.107/bin/intel64
prepend-path    MANPATH              :
prepend-path    MANPATH              /opt/intel/composerxe-2011.1.107/man
# ipp
prepend-path    PATH                 /opt/intel/composerxe-2011.1.107/ipp/bin/intel64
prepend-path    LD_LIBRARY_PATH      /opt/intel/composerxe-2011.1.107/ipp/lib/intel64
# sourcechecker
prepend-path    PATH                 /opt/intel/composerxe-2011.1.107/bin/sourcechecker/bin/intel64
prepend-path    LD_LIBRARY_PATH      /opt/intel/composerxe-2011.1.107/bin/sourcechecker/lib/intel64

Note: intel changes packaging quite often, here are the installation instructions for the 11.1 compilers:

install RPMS (only on the login node) found in l_cproc_p_11.1.046_intel64 manually (using rpm -ivh):

intel-cproc046-11.1-1.x86_64.rpm
intel-cproidb046-11.1-1.x86_64.rpm
intel-cprolib046-11.1-1.x86_64.rpm
intel-cprolibdev046-11.1-1.x86_64.rpm
intel-cprotbblib046-11.1-1.noarch.rpm
intel-cprotbblibdev046-11.1-1.noarch.rpm
intel-cprocsdk046-11.1-1.noarch.rpm
intel-cproidbsdk046-11.1-1.noarch.rpm

and from l_cprof_p_11.1.046_intel64:

intel-cprof046-11.1-1.x86_64.rpm
intel-cproflib046-11.1-1.x86_64.rpm
intel-cprofsdk046-11.1-1.noarch.rpm

enable them (only on thul):

. /opt/intel/Compiler/11.1/046/bin/intel64/ifortvars_intel64.sh
. /opt/intel/Compiler/11.1/046/bin/intel64/iccvars_intel64.sh

build intel compatibility packages as rpmbuild (only on thul):

cd ~/rpmbuild/SPECS
rpmbuild -bb ${modules_usage} intel-redist.spec

mkdir ~rpmbuild/modulefiles/${FYS_PLATFORM}/ifort
cp /scratch/rpmbuild/intel-11.1.046/11.1.046-1.intel64${disttag} ~rpmbuild/modulefiles/${FYS_PLATFORM}/ifort
cd ~rpmbuild/modulefiles/${FYS_PLATFORM}/ifort
ln -s 11.1.046-1.intel64${disttag} 11.1-1 # version < 12
ln -s 2011.1.107-1.intel64${disttag} 2011.1.107-1

Note: the above module file should contain at least:

prepend-path    LD_LIBRARY_PATH      /opt/intel/Compiler/11.1/046/lib/intel64
prepend-path    LD_LIBRARY_PATH      /opt/intel/Compiler/11.1/046/idb/lib/intel64
prepend-path    PATH                 /opt/intel/Compiler/11.1/046/bin/intel64
prepend-path    MANPATH              :
prepend-path    MANPATH              /opt/intel/Compiler/11.1/046/man

Note: intel changes packaging quite often, here are the installation instructions for the 10.1.015 compilers:

install RPMS (on the login and compute nodes) found in l_cc_p_10.1.015_intel64.tar.gz and l_fc_p_10.1.015_intel64.tar.gz manually (using rpm -ivh):

intel-icce101015-10.1.015-1.em64t.rpm
intel-iidbe101015-10.1.015-1.em64t.rpm
intel-isubhe101015-10.1.015-1.em64t.rpm
intel-iforte101015-10.1.015-1.em64t.rpm

replace the installation path in the scripts (action necessary only on the login node):

files=`grep "<INSTALLDIR>" -r /opt/intel/cce/ | cut -d":" -f 1 | uniq`
for file in $files;
do
    echo $file
    sed -i 's#<INSTALLDIR>#/opt/intel/cce/10.1.015#g' $file
done
files=`grep "<INSTALLDIR>" -r /opt/intel/fce/ | cut -d":" -f 1 | uniq`
for file in $files;
do
    echo $file
    sed -i 's#<INSTALLDIR>#/opt/intel/fce/10.1.015#g' $file
done
files=`grep "<INSTALLDIR>" -r /opt/intel/idbe/ | cut -d":" -f 1 | uniq`
for file in $files;
do
    echo $file
    sed -i 's#<INSTALLDIR>#/opt/intel/idbe/10.1.015#g' $file
done

provide the module file ~rpmbuild/modulefiles/${FYS_PLATFORM}/ifort/10.1.015-1.intel64${disttag}:

prepend-path    LD_LIBRARY_PATH      /opt/intel/cce/10.1.015/lib
prepend-path    LD_LIBRARY_PATH      /opt/intel/fce/10.1.015/lib

prepend-path    PATH                 /opt/intel/cce/10.1.015/bin
prepend-path    PATH                 /opt/intel/fce/10.1.015/bin
prepend-path    PATH                 /opt/intel/idbe/10.1.015/bin
prepend-path    MANPATH              :
prepend-path    MANPATH              /opt/intel/cce/10.1.015/man
prepend-path    MANPATH              /opt/intel/fce/10.1.015/man
prepend-path    MANPATH              /opt/intel/idbe/10.1.015/man

and the link:

cd ~rpmbuild/modulefiles/${FYS_PLATFORM}/ifort
ln -s 10.1.015-1.intel64${disttag} 10.1-1

Moreover: intel-*intel64* RPMS need to be installed with --nodeps, so move them into a special directory:

mkdir -p ~/${FYS_PLATFORM}/RPMS/nodeps
mv ~/${FYS_PLATFORM}/RPMS/intel-*intel64* ~/${FYS_PLATFORM}/RPMS/nodeps

intel mkl

Install mkl RPMS intel-mkl-*, intel-openmp-*, intel-compilerpro-* (intel-mkl, intel-mkllibdev, intel-mkllib for mkl version < 10.3), and build mkl compatibility package (only on thul):

# for mkl 10.3, as root
cd /opt/intel/mkl # packaging of mkl changes again so link is necessary
ln -s ../composerxe-2011.3.174/mkl/ 10.3.3.174
ln -s /opt/intel/composerxe-2011.3.174/man 10.3.3.174/man
# as rpmbuild
cd ~/rpmbuild/SOURCES
export mkl=10.3.3.174
mkdir ${mkl}
cp -rp /opt/intel/mkl/${mkl}/lib ${mkl}
cp -rpf /opt/intel/mkl/${mkl}/doc ${mkl} # for mkl < 10.3
cp -rpf /opt/intel/composerxe-2011.3.174/compiler/lib ${mkl} # for mkl >= 10.3
tar zcf intel-redist-mkl-${mkl}.tar.gz ${mkl}

cd ~/rpmbuild/SPECS # as rpmbuild
rpmbuild -bb --with version1=3 --with version2=3 --with version3=174 ${modules_usage} --with platform=intel64 intel-redist-mkl.spec
# **Warning**: mkl < 10.3 uses em64t
rpmbuild -bb --with version1=1 --with version2=3 --with version3=027 ${modules_usage} intel-redist-mkl.spec

Note: do not install the resulting RPM on the login node. It needs to be installed only on compute nodes. On the login node only the module file needs to be deployed under ~rpmbuild/modulefiles, as rpmbuild. Note that this directory is available as svn checkout at https://svn.fysik.dtu.dk/projects/modulefiles/trunk. Here is what need to be done for a new version of the package:

mkdir ~rpmbuild/modulefiles/${FYS_PLATFORM}/mkl
cp /tmp/intel-mkl-${mkl}/${mkl}-1${disttag}.em64t ~rpmbuild/modulefiles/${FYS_PLATFORM}/mkl
cd ~rpmbuild/modulefiles/${FYS_PLATFORM}/mkl
ln -s ${mkl}-1${disttag}.em64t 10.1p-027

Note: the above module file should contain at least:

prepend-path    LD_LIBRARY_PATH      /opt/intel/mkl/10.1.3.027/lib/em64t

Build mkl/fftw (as root):

export mkl=10.1.3.027
. /opt/intel/Compiler/11.0/083/bin/intel64/ifortvars_intel64.sh
cd /opt/intel/mkl/${mkl}/interfaces/fftw2xf
make libem64t
cd /opt/intel/mkl/${mkl}/lib/em64t
ln -s libfftw2xf_intel.a libfftw.a

Logout and login as rpmbuild.

Unfortunately, from 10.3 version mkl depends on intel libraries located in directories outside of mkl. This causes troubles for numpy which requires (is there a way to fix that?) all non-standard libraries to be located in one directory. Therefore one may need to create a link (currently not performed):

cd /opt/intel/mkl/10.3.4.191/lib/intel64
ln -s /opt/intel/composerxe-2011.4.191/compiler/lib/intel64/libiomp5.so .

openmpi

Build a custom openmpi, using torque support:

# openmpi-1.4.3
wget http://www.open-mpi.org/software/ompi/v1.4/downloads/openmpi-1.4.3.tar.bz2 \
     -O ~/rpmbuild/SOURCES/openmpi-1.4.3.tar.bz2
module load open64/4.2.4-0
sh ./buildrpm-1.4.3-1.open64.4.2.4.sh ../SOURCES/openmpi-1.4.3.tar.bz2 2>&1 | tee buildrpm-1.4.3-1.open64.4.2.4.sh.log.${FYS_PLATFORM}
module unload open64/4.2.4-0
module load ifort/12.0-4
sh ./buildrpm-1.4.3-1.ifort.12.0.4.sh ../SOURCES/openmpi-1.4.3.tar.bz2 2>&1 | tee buildrpm-1.4.3-1.ifort.12.0.4.sh.log.${FYS_PLATFORM} # thul only
module unload ifort/12.0-4

# openmpi-1.3.3
wget http://www.open-mpi.org/software/ompi/v1.3/downloads/openmpi-1.3.3.tar.bz2 \
     -O ~/rpmbuild/SOURCES/openmpi-1.3.3.tar.bz2
sh ./buildrpm-1.3.3-1.gfortran.sh ../SOURCES/openmpi-1.3.3.tar.bz2 2>&1 | tee buildrpm-1.3.3-1.gfortran.sh.log.${FYS_PLATFORM}
sh ./buildrpm-1.3.3-1.gfortran43.sh ../SOURCES/openmpi-1.3.3.tar.bz2 2>&1 | tee buildrpm-1.3.3-1.gfortran43.sh.log.${FYS_PLATFORM}
sh ./buildrpm-1.3.3-1.pathscale.sh ../SOURCES/openmpi-1.3.3.tar.bz2 2>&1 | tee buildrpm-1.3.3-1.pathscale.sh.log.${FYS_PLATFORM}
sh ./buildrpm-1.3.3-1.ifort.11.0.sh ../SOURCES/openmpi-1.3.3.tar.bz2 2>&1 | tee buildrpm-1.3.3-1.ifort.11.0.sh.log.${FYS_PLATFORM} # thul only
sh ./buildrpm-1.3.3-1.ifort.11.1.sh ../SOURCES/openmpi-1.3.3.tar.bz2 2>&1 | tee buildrpm-1.3.3-1.ifort.11.1.sh.log.${FYS_PLATFORM} # thul only
module load g95
sh ./buildrpm-1.3.3-1.g95.sh ../SOURCES/openmpi-1.3.3.tar.bz2 2>&1 | tee buildrpm-1.3.3-1.g95.sh.log.${FYS_PLATFORM} # fjorm only
module unload g95
module load open64/4.2.1-0 # 24 June 2009: build fails on Nehalem with *configure: error: TM support requested but not found.  Aborting*
sh ./buildrpm-1.3.3-1.open64.4.2.1.sh ../SOURCES/openmpi-1.3.3.tar.bz2 2>&1 | tee buildrpm-1.3.3-1.open64.4.2.1.sh.log.${FYS_PLATFORM}
module unload open64/4.2.1-0
module load open64/4.2.3-0 # 24 June 2009: build fails on Nehalem with *configure: error: TM support requested but not found.  Aborting*
sh ./buildrpm-1.3.3-1.open64.4.2.3.sh ../SOURCES/openmpi-1.3.3.tar.bz2 2>&1 | tee buildrpm-1.3.3-1.open64.4.2.3.sh.log.${FYS_PLATFORM}
module unload open64/4.2.3-0

Note: intel openmpi needs to be installed ignoring dependencies:

rpm -ivh --nodeps --oldpackage ~rpmbuild/${FYS_PLATFORM}/RPMS/openmpi-1.3.3-1${disttag}.ifort.11.1.x86_64.rpm

acml

Note this package is not relocatable!

AMD Core Math Library contains optimized BLAS and LAPACK libraries for AMD opteron processors (work also on intel), and is available for download after registration.

Build the following RPMS:

. fys.set.Niflheim.gfortran.4.1.2.sh
. fys.set.blas.acml.4.0.1.sh

. fys.build.acml.sh
#
. fys.set.Niflheim.pathscale.3.2.sh
. fys.set.blas.acml.4.0.1.sh

. fys.build.acml.sh
#
. fys.set.Niflheim.gfortran43.4.3.2.sh
. fys.set.blas.acml.4.3.0.sh

. fys.build.acml.sh
#
. fys.set.Niflheim.gfortran43.4.3.2.sh
. fys.set.blas.acml.4.3.0_mp.sh

. fys.build.acml.sh

#
. fys.set.Niflheim.gfortran43.4.3.2.sh
. fys.set.blas.acml.4.4.0.sh

. fys.build.acml.sh

#
. fys.set.Niflheim.ifort.11.0.sh
. fys.set.blas.acml.4.4.0.sh

. fys.build.acml.sh
#
. fys.set.Niflheim.open64.4.2.3.sh
. fys.set.blas.acml.4.4.0.sh

. fys.build.acml.sh

Note problems with dgemm acml 4.1.0 and 4.2.0 have been reported. Moreover campos-dacapo built with acml-4-1-0-pathscale-64bit.tgz fails with "ZINSC 2 returned info= 2" for the following job:

#!/usr/bin/env python
from Dacapo import Calculator
from ASE.IO.xyz import ReadXYZ
from ASE.Dynamics.Langevin import Langevin

prefix = 'D'
atoms = ReadXYZ('32H2O.xyz')
L = 9.8553729
atoms.SetUnitCell([L, L, L], fix=True)
atoms.SetBoundaryConditions(True)
r = 1
atoms = atoms.Repeat([r, r, r])
n = 48 * r
calc = Calculator(nbands=128 * r**3, planewavecutoff=350,
                  densitycutoff=500, xc='PBE')
atoms.SetCalculator(calc)

from time import time
atoms.GetPotentialEnergy()
pos=atoms[0].GetCartesianPosition()
atoms[0].SetCartesianPosition(pos+0.005)
t0=time()
atoms.GetPotentialEnergy()
print time()-t0

Download 32H2O.xyz

goto

GotoBLAS contains optimized BLAS libraries.

Download GotoBLAS-1.26.tar.gz (Warning outdated release of GotoBLAS is no longer available) and GotoBLAS2-1.13_bsd.tar.gz (supports Nehalem) to ~/rpmbuild/SOURCES. The default build process searches your $PATH for available compilers. Priority order is PathScale, PGI, Intel, gfortran, g95 and g77, therefore setting compilers explicitly is needed.

On a custom system build the following RPMS:
. fys.set.gfortran.default.sh

(rpm_prefix=/usr && . fys.build.goto2.sh)
On Niflheim build RPMS (on the target compute node!) using the following command:
. fys.set.Niflheim.gfortran.4.1.2.sh

. fys.build.goto2.sh

#
. fys.set.Niflheim.gfortran43.4.3.2.sh

. fys.build.goto2.sh

#
. fys.set.Niflheim.open64.4.2.3.sh

. fys.build.goto2.sh

#
. fys.set.Niflheim.open64.4.2.4.sh

. fys.build.goto2.sh

# older version of goto
#
blas_version=1.26
. fys.set.Niflheim.gfortran.4.1.2.sh

. fys.build.goto.sh

#
blas_version=1.26
. fys.set.Niflheim.gfortran43.4.3.2.sh

. fys.build.goto.sh

#
blas_version=1.26
. fys.set.Niflheim.pathscale.3.2.sh

. fys.build.goto.sh
#
blas_version=1.26
. fys.set.Niflheim.open64.4.2.1.sh

. fys.build.goto.sh
#
blas_version=1.26
. fys.set.Niflheim.open64.4.2.3.sh

. fys.build.goto.sh
Note - 1.26 version fails on Nehalem with:
../../../param.h:1195:21: error: division by zero in #if

atlas

Note this package is not relocatable!

On a custom system build the following RPMS:

blas_version=3.8.3
. fys.set.gfortran.default.sh
(rpm_prefix=/usr/local/atlas && default_version_usage="--with default_version" && . fys.build.atlas.sh)

On Niflheim build the following RPMS:

blas_version=3.8.3
. fys.set.Niflheim.gfortran.4.1.2.sh

. fys.build.atlas.sh

#
blas_version=3.8.3
. fys.set.Niflheim.gfortran43.4.3.2.sh

. fys.build.atlas.sh

Note: - 3.8.3 version fails on Opteron with open64 with:

/scratch/rpmbuild/ATLAS/RpmObjs/..//CONFIG/src/backend/comptestC.c:5: undefined reference to `__pathscale_malloc_alg'

rasmol

Required by campos-ase2.

Note that rasmol is built for 32bit architecture, so make sure that your system fulfills "BuildRequires" for both 64 and 32bit:
rpmbuild --nobuild RasMol.spec
On a custom system build the following RPMS:
(rpm_prefix=/usr && . fys.build.RasMol.2.7.3.sh)
On Niflheim build the following RPMS:
. fys.build.RasMol.2.7.3.sh

cblas

Required by campos-ase2.

On a custom system build the following RPMS:
. fys.set.gfortran.default.sh
. fys.set.blas.default.sh

(rpm_prefix=/usr && . fys.build.cblas.sh)
On Niflheim build the following RPMS:
. fys.set.Niflheim.gfortran.4.1.2.sh
. fys.set.blas.acml.4.0.1.sh

. fys.build.cblas.sh

python-setuptools

On a custom system build the following RPMS:
(rpm_prefix=/usr && . fys.build.setuptools.0.6c9.sh)
On Niflheim build the following RPMS:
. fys.build.setuptools.0.6c9.sh
If using modules:
module load python-setuptools
else, if not using the default "/usr" prefix:
. /etc/profile.d/python-setuptools.sh

python-nose

On a custom system build the following RPMS:
(rpm_prefix=/usr && . fys.build.nose.0.10.4.sh)
On Niflheim build the following RPMS:
. fys.build.nose.0.10.4.sh
If using modules:
module load python-nose
else, if not using the default "/usr" prefix:
. /etc/profile.d/python-nose.sh

numpy

On a custom system build the following RPMS:

. fys.set.gfortran.default.sh
. fys.set.blas.default.sh
. fys.set.lapack.default.sh
. fys.set.Niflheim.cblas.2.23.3.sh

 (rpm_prefix=/usr && . fys.build.numpy.1.3.0.sh)

On Niflheim build the following RPMS:

module load python-setuptools
module load python-nose

. fys.set.Niflheim.numpy.1.3.0.gfortran.4.1.2.acml.4.0.1.cblas.none.sh

. fys.build.numpy.1.3.0.sh

# only on thul
. fys.set.Niflheim.numpy.1.3.0.gfortran.4.1.2.mkl.10.1.3.027.cblas.mkl.10.1.3.027.sh

. fys.build.numpy.1.3.0.sh

# building using cblas/acml causes the test below to fail
. fys.set.Niflheim.numpy.1.3.0.gfortran.4.1.2.acml.4.0.1.cblas.2.23.3.sh

. fys.build.numpy.1.3.0.sh

After installing python-numeric make a very rough check:

is using modules:

module load ${blas}-${compiler}64/${blas_version}-1${disttag}
module load cblas-${blas}-${compiler}64/2.23.3-1${disttag}.${compiler}.${compiler_version}.${blas}.${blas_version}
module load numpy/1.3.0-1${disttag}.${compiler}.${compiler_version}.python${python_version}.${blas}.${blas_version}.${lapack}.${lapack_version}
python -c "import numpy; from numpy.core.multiarray import dot; b = numpy.ones(13, numpy.complex); dot(b, b)"
python -c "import numpy; numpy.test()"

else, if not using the default "/usr" prefix:
```
. /etc/profile.d/numpy.sh
```

gnuplot-py

Required by campos-ase2.

On a custom system build the following RPMS:
(rpm_prefix=/usr && . fys.build.gnuplot-py.1.8.sh)
On Niflheim build the following RPMS:
. fys.build.gnuplot-py.1.8.sh
If using modules:
module load gnuplot-py
else, if not using the default "/usr" prefix:
. /etc/profile.d/gnuplot-py.sh

python-numeric

Required by campos-ase2.

Warning: on a 64-bit machine works only with python <= 2.4.

We must install 24.2 version, and we keep the default version:

cd ~/${FYS_PLATFORM}/RPMS/external
rpm -e --nodeps python-numeric # as root
yumdownloader --resolve --disableexcludes=main python-numeric
cd ~/rpmbuild/SPECS

On a custom system build the following RPMS:

. fys.set.gfortran.default.sh
. fys.set.blas.default.sh
. fys.set.lapack.default.sh
. fys.set.Niflheim.cblas.2.23.3.sh

. fys.build.Numeric.24.2.sh

On Niflheim build the following RPMS:

. fys.set.Niflheim.Numeric.24.2.gfortran.4.1.2.acml.4.0.1.cblas.2.23.3.sh

. fys.build.Numeric.24.2.sh

Note: (16 Apr 2009) currently Numeric's test.py results in (we ignore this error):

glibc detected *** python: free(): invalid next size (normal): 0x09aee970 ***

After installing python-numeric make a very rough check:

is using modules:

module load ${blas}-${compiler}64/${blas_version}-1${disttag}
module load cblas-${blas}-${compiler}64/2.23.3-1${disttag}.${compiler}.${compiler_version}.${blas}.${blas_version}
module load python-numeric/24.2-4${disttag}.${compiler}.${compiler_version}.python${python_version}.${blas}.${blas_version}.${lapack}.${lapack_version}
python -c "import lapack_lite"
ldd `rpm -ql python-numeric-24.2-4${disttag}.${compiler}.${compiler_version}.python${python_version}.${blas}.${blas_version}.${lapack}.${lapack_version} | grep lapack_lite.so`
ldd `rpm -ql python-numeric-24.2-4${disttag}.${compiler}.${compiler_version}.python${python_version}.${blas}.${blas_version}.${lapack}.${lapack_version} | grep _dotblas.so`

else:

. /etc/profile.d/python-numeric.sh
python -c "import lapack_lite"
ldd `rpm -ql python-numeric | grep lapack_lite.so`
ldd `rpm -ql python-numeric | grep _dotblas.so`

and reinstall the default version:

rpm -ivh --oldpackage ~/${FYS_PLATFORM}/RPMS/external/python-numeric-23.*.rpm

hdf5

HDF5 is a data model, library, and file format for storing and managing data.

We prefer version 1.8.6.

On a custom system build the following RPMS:

. fys.set.gfortran.default.sh
. fys.set.openmpi.default.sh

(rpm_prefix=/usr && . fys.build.hdf5.sh)

On Niflheim build the following RPMS:

#
module load open64/4.2.4-0
. fys.set.Niflheim.open64.4.2.4.sh
. fys.set.Niflheim.openmpi.1.4.3.sh

. fys.build.hdf5.1.8.6.sh
module unload open64/4.2.4-0

# older builds
#
. fys.set.Niflheim.gfortran.4.1.2.sh
. fys.set.Niflheim.openmpi.1.3.3.sh

. fys.build.hdf5.1.8.6.sh

#
. fys.set.Niflheim.gfortran43.4.3.2.sh
. fys.set.Niflheim.openmpi.1.3.3.sh

. fys.build.hdf5.1.8.6.sh

#
module load open64/4.2.3-0
. fys.set.Niflheim.open64.4.2.3.sh
. fys.set.Niflheim.openmpi.1.3.3.sh

. fys.build.hdf5.1.8.6.sh
module unload open64/4.2.4-0

# only on thul
module load ifort/11.1-1
. fys.set.Niflheim.ifort.11.1.sh
. fys.set.Niflheim.openmpi.1.3.3.sh

. fys.build.hdf5.1.8.6.sh
module unload ifort/11.1-1

netcdf

NetCDF (network Common Data Form) is an interface for array-oriented data access and a library that provides an implementation of the interface. The NetCDF library also defines a machine-independent format for representing scientific data.

We prefer version 3.6.1 or higher (note that version 3.6.2 has fortran interface in libnetcdff.a).

On a custom system build the following RPMS:

. fys.set.gfortran.default.sh

(rpm_prefix=/usr && . fys.build.netcdf4.4.0.1.sh)

On Niflheim build the following RPMS:

 #
 . fys.set.Niflheim.open64.4.2.4.sh
 . fys.set.Niflheim.netcdf4.4.1.2.sh

 . fys.build.netcdf4.4.1.2.sh

# older builds
#
 . fys.set.Niflheim.gfortran.4.1.2.sh
 . fys.set.Niflheim.netcdf4.4.0.1.sh

 . fys.build.netcdf4.4.0.1.sh

 #
 . fys.set.Niflheim.gfortran43.4.3.2.sh
 . fys.set.Niflheim.netcdf4.4.0.1.sh

 . fys.build.netcdf4.4.0.1.sh

 # only on fjorm
 . fys.set.Niflheim.pathscale.3.2.sh
 . fys.set.Niflheim.netcdf4.4.0.1.sh

 . fys.build.netcdf4.4.0.1.sh

 # only on thul
 . fys.set.Niflheim.ifort.11.0.sh
 . fys.set.Niflheim.netcdf4.4.0.1.sh

 . fys.build.netcdf4.4.0.1.sh

 # only on fjorm
 . fys.set.Niflheim.open64.4.2.1.sh
 . fys.set.Niflheim.netcdf4.4.0.1.sh

 . fys.build.netcdf4.4.0.1.sh

 #
 . fys.set.Niflheim.open64.4.2.3.sh
 . fys.set.Niflheim.netcdf4.4.0.1.sh

 . fys.build.netcdf4.4.0.1.sh
 # only on thul
 . fys.set.Niflheim.ifort.11.1.sh
 . fys.set.Niflheim.netcdf4.4.0.1.sh

 . fys.build.netcdf4.4.0.1.sh

etsf_io

ETSF_IO: A library of F90 routines to read/write the ETSF file format has been written. It is called ETSF_IO and available under LGPL.

On a custom system build the following RPMS:

. fys.set.gfortran.default.sh
. fys.set.netcdf.default.sh
. fys.set.hdf5.default.sh

(. fys.build.etsf_io.sh)

On Niflheim build the following RPMS:

#
. fys.set.Niflheim.gfortran43.4.3.2.sh
. fys.set.Niflheim.netcdf4.4.0.1.sh
hdf=none

. fys.build.etsf_io.sh

# Oct 4 2010:  fatal error: gfc_todo: Not Implemented: complex character array constructors
. fys.set.Niflheim.gfortran.4.1.2.sh
. fys.set.Niflheim.netcdf4.4.0.1.sh
hdf=none

. fys.build.etsf_io.sh

# Oct 04 2010: tests/group_level failed
. fys.set.Niflheim.open64.4.2.3.sh
. fys.set.Niflheim.netcdf4.4.0.1.sh
hdf=none

. fys.build.etsf_io.sh

# Apr 18 2010: tests/group_level failed
. fys.set.Niflheim.open64.4.2.4.sh
. fys.set.Niflheim.netcdf4.4.1.2.sh
hdf=none

. fys.build.etsf_io.sh

ScientificPython 2.6.2

Warning: version 2.6.2 required by campos-ase2. Later versions are needed by campos-ase3. Note that versions 2.6.2 and >= 2.8 are mutually exclusive if installed in the default "/usr" prefix.

On a custom system build the following RPMS:
. fys.set.ScientificPython.2.6.2.default.sh

(rpm_prefix=/usr && . fys.build.ScientificPython.sh)
On Niflheim build the following RPMS:
. fys.set.Niflheim.ScientificPython.2.6.2.gfortran.4.1.2.openmpi.1.3.3.numeric.sh

. fys.build.ScientificPython.sh

ScientificPython 2.8 or later

Note that versions 2.6.2 and >= 2.8 are mutually exclusive if installed in the default "/usr" prefix.

Required by campos-ase3.

On a custom system build the following RPMS:
. fys.set.ScientificPython.2.8.default.sh

(rpm_prefix=/usr && . fys.build.ScientificPython.sh)
On Niflheim build the following RPMS:
. fys.set.Niflheim.ScientificPython.2.8.gfortran.4.1.2.serial_version.only.numpy.sh

. fys.build.ScientificPython.sh

python-docutils

On a custom system build the following RPMS:
(rpm_prefix=/usr && . fys.build.docutils.0.5.sh)
On Niflheim build the following RPMS:
. fys.build.docutils.0.5.sh
If using modules:
module load python-docutils
else, if not using the default "/usr" prefix:
. /etc/profile.d/python-docutils.sh

pytz

On a custom system build the following RPMS:
(rpm_prefix=/usr && . fys.build.pytz.2008g.sh)
On Niflheim build the following RPMS:
. fys.build.pytz.2008g.sh
If using modules:
module load pytz
else, if not using the default "/usr" prefix:
. /etc/profile.d/pytz.sh

python-dateutil

On a custom system build the following RPMS:
(rpm_prefix=/usr && . fys.build.python-dateutil.1.4.1.sh)
On Niflheim build the following RPMS:
. fys.build.python-dateutil.1.4.1.sh
If using modules:
module load python-dateutil
else, if not using the default "/usr" prefix:
. /etc/profile.d/python-dateutil.sh

python-matplotlib

On a custom system build the following RPMS:
(rpm_prefix=/usr && . fys.build.python-matplotlib.sh)
On Niflheim build the following RPMS:
module load NUMPY
module load python-docutils
module load pytz
module load python-dateutil

. fys.build.python-matplotlib.1.0.1.sh

campos-ase2

On a custom system build the following RPMS:
(rpm_prefix=/usr && . fys.build.ase2.2.3.13.sh)
On Niflheim build the following RPMS:
. fys.build.ase2.2.3.13.sh

fftw2

We use version 2.1.5.

On a custom system build the following RPMS:

. fys.set.fftw2.default.sh

(rpm_prefix=/usr && . fys.build.fftw2.2.1.5.sh)

On Niflheim build the following RPMS:

. fys.set.Niflheim.gfortran.4.1.2.sh

. fys.build.fftw2.2.1.5.sh

#
. fys.set.Niflheim.gfortran43.4.3.2.sh

. fys.build.fftw2.2.1.5.sh

#
. fys.set.Niflheim.pathscale.3.2.sh

. fys.build.fftw2.2.1.5.sh

# only on fjorm
. fys.set.Niflheim.open64.4.2.1.sh

. fys.build.fftw2.2.1.5.sh

#
. fys.set.Niflheim.open64.4.2.3.sh

. fys.build.fftw2.2.1.5.sh

#
. fys.set.Niflheim.open64.4.2.4.sh

. fys.build.fftw2.2.1.5.sh

# Note: 24 June 2009: ifort fails to build static fftw2
. fys.set.Niflheim.ifort.11.0.sh

. fys.build.fftw2.2.1.5.sh

campos-dacapo-pseudopotentials

Note this package is not relocatable! campos-dacapo-pseudopotentials

On a custom system build the following RPMS:
(default_version_usage="--with default_version" && modules_usage="--without modules" && . fys.build.dacapo-pseudopotentials.1.sh)
On Niflheim build the following RPMS:
. fys.build.dacapo-pseudopotentials.1.sh

campos-dacapo-python

Requires campos-ase2.

On a custom system build the following RPMS:
(rpm_prefix=/usr && . fys.build.dacapo-python.0.9.4.sh)
On Niflheim build the following RPMS:
. fys.build.dacapo-python.0.9.4.sh

campos-dacapo

Note: fftw version 3 is incompatible with dacapo.

If you build only a serial version add "--without parallel" to the rpmbuild options. Another useful option is "--without default_version" that does not put /etc/profile.d scripts, nor modules under /opt/modulefiles that allows the package to be relocatable.

Warning: currently (9 Oct 2008) packaging of openmpi on FC8/FC9 requires the following link to be made:

ln -s /usr/include/openmpi/1.2.4-gcc/32/mpif-config.h /usr/include/openmpi/1.2.4-gcc/mpif-config.h

Warning: currently (9 Oct 2008) the default build fails for EL4 due to double underlined symbols in the netcdf from ATrpms, however custom build (i.e. with building your own netcdf should work).

On a custom system build the following RPMS:

. fys.set.dacapo.default.sh
. fys.set.atlas.default.sh

(rpm_prefix=/usr && . fys.build.dacapo.sh)

# optional build using netlib blas/lapack
. fys.set.dacapo.default.sh

(rpm_prefix=/usr && . fys.build.dacapo.sh)

On Niflheim build the following RPMS:

#
. fys.set.Niflheim.dacapo.2.7.16.open64.4.2.4.openmpi.1.4.3.acml.4.4.0.acml.4.4.0.fftw2.sh
hdf=none

. fys.build.dacapo.sh

# older builds
#
. fys.set.Niflheim.dacapo.2.7.16.gfortran43.4.3.2.openmpi.1.3.3.acml.4.3.0.acml.4.3.0.fftw2.sh

. fys.build.dacapo.sh

# only on fjorm
. fys.set.Niflheim.dacapo.2.7.16.open64.4.2.1.openmpi.1.3.3.acml.4.3.0.acml.4.3.0.fftw2.sh

. fys.build.dacapo.sh

# only on thul
. fys.set.Niflheim.dacapo.2.7.16.gfortran43.4.3.2.openmpi.1.3.3.mkl.10.1.3.027.mkl.10.1.3.027.mkl.sh

. fys.build.dacapo.sh

# optional
. fys.set.Niflheim.gfortran.4.1.2.sh
. fys.set.Nilfheim.openmpi.1.3.3.sh
. fys.set.Niflheim.netcdf4.4.0.1.sh
. fys.set.Niflheim.fftw2.2.1.5.sh
. fys.set.blas.default.sh
. fys.set.lapack.acml.sh

. fys.build.dacapo.sh

# optional
. fys.set.Niflheim.gfortran43.4.3.2.sh
. fys.set.Nilfheim.openmpi.1.3.3.sh
. fys.set.Niflheim.netcdf4.4.0.1.sh
. fys.set.Niflheim.fftw2.2.1.5.sh
. fys.set.blas.acml.4.3.0.sh
. fys.set.lapack.acml.sh
. fys.set.Niflheim.goto.1.26.sh
. fys.set.lapack.acml.sh

. fys.build.dacapo.sh

# optional
. fys.set.Niflheim.open64.4.2.1.sh
. fys.set.Nilfheim.openmpi.1.3.3.sh
. fys.set.Niflheim.netcdf4.4.0.1.sh
. fys.set.Niflheim.fftw2.2.1.5.sh
. fys.set.blas.acml.4.3.0.sh
. fys.set.lapack.acml.sh
. fys.set.Niflheim.goto.1.26.sh
. fys.set.lapack.acml.sh

. fys.build.dacapo.sh

# optional # only on thul # multinode jobs fail
. fys.set.Niflheim.ifort.11.0.sh
. fys.set.Nilfheim.openmpi.1.3.3.sh
. fys.set.Niflheim.netcdf4.4.0.1.sh
. fys.set.Niflheim.mkl.10.1.3.027.sh

. fys.build.dacapo.sh

fftw3

On a custom system build the following RPMS:

. fys.set.fftw3.default.sh

(rpm_prefix=/usr && . fys.build.fftw3.3.2.1.sh)

On Niflheim build the following RPMS:

. fys.set.Niflheim.gfortran.4.1.2.sh

. fys.build.fftw3.3.2.1.sh
#
. fys.set.Niflheim.gfortran43.4.3.2.sh

. fys.build.fftw3.3.2.1.sh
#
. fys.set.Niflheim.open64.4.2.3.sh

. fys.build.fftw3.3.2.1.sh
#
. fys.set.Niflheim.open64.4.2.4.sh

. fys.build.fftw3.3.2.1.sh
# only on thul
. fys.set.Niflheim.ifort.11.1.sh

. fys.build.fftw3.3.2.1.sh

scipy

On a custom system build the following RPMS:

. fys.set.gfortran.default.sh
. fys.set.blas.default.sh
. fys.set.lapack.default.sh
. fys.set.Niflheim.cblas.2.23.3.sh
. fys.set.fftw3.default.sh
. fys.set.suitesparse.default.sh

(rpm_prefix=/usr && . fys.build.scipy.0.7.0.sh)

On Niflheim build the following RPMS:

. fys.set.Niflheim.scipy.0.7.0.gfortran.4.1.2.blas.lapack.cblas.2.23.3.sh

. fys.build.scipy.0.7.0.sh

# optional - not tested!
. fys.set.Niflheim.scipy.0.7.0.gfortran.4.1.2.acml.4.0.1.cblas.2.23.3.sh

. fys.build.scipy.0.7.0.sh

povray

On a custom system build the following RPMS:
(rpm_prefix=/usr && . fys.build.povray.sh)
On Niflheim build the following RPMS:
. fys.build.povray.sh

babel

On a custom system build the following RPMS:
(rpm_prefix=/usr && . fys.build.Babel.0.9.4.sh)
On Niflheim build the following RPMS:
. fys.build.Babel.0.9.4.sh
If using modules:
module load babel
else, if not using the default "/usr" prefix:
. /etc/profile.d/babel.sh

python-jinja2

On a custom system build the following RPMS:
(rpm_prefix=/usr && . fys.build.Jinja2.2.1.1.sh)
On Niflheim build the following RPMS:
. fys.build.Jinja2.2.1.1.sh
If using modules:
module load python-jinja2
else, if not using the default "/usr" prefix:
. /etc/profile.d/python-jinja2.sh

python-pygments

On a custom system build the following RPMS:
(rpm_prefix=/usr && . fys.build.Pygments.1.0.sh)
On Niflheim build the following RPMS:
. fys.build.Pygments.1.0.sh
If using modules:
module load python-pygments
else, if not using the default "/usr" prefix:
. /etc/profile.d/python-pygments.sh

python-sphinx

On a custom system build the following RPMS:
(rpm_prefix=/usr && . fys.build.Sphinx.0.6.1.sh)
On Niflheim build the following RPMS:
. fys.build.Sphinx.0.6.1.sh
If using modules:
module load python-sphinx
else, if not using the default "/usr" prefix:
. /etc/profile.d/python-sphinx.sh

auctex

Build the following RPMS:

cd ~/rpmbuild/SOURCES&& wget http://ftp.gnu.org/pub/gnu/auctex/auctex-11.86.tar.gz
cd ~/rpmbuild/SPECS

rpmbuild -bb auctex.spec

campos-ase3

On a custom system build the following RPMS:

(rpm_prefix=/usr && . fys.build.ase3.sh)

On Niflheim build the following RPMS:

module load NUMPY
. fys.build.ase3.sh

Snapshot package is built with, e.g.:

major_version=3
version1=2
version2=0
version_svn=1066
release=${major_version}.${version1}.${version2}.${version_svn}/1${disttag}.python${python_version}
rpmbuild -bb --with major_version=${major_version} --with version1=${version1} --with version2=${version2} --with version_svn=${version_svn} --with keep_install=1 \
             ${modules_usage} --with default_version -with system=${rpm_platform} \
             --with python_version=${python_version} \
             --with prefix=/home/camp/rpmbuild/opt/Intel-Nehalem-el5/campos-ase3/${release} campos-ase3.spec
rm /home/camp/rpmbuild/Intel-Nehalem-el5/RPMS/campos-ase3-${major_version}.${version1}.${version2}.${version_svn}-1${disttag}.python${python_version}.x86_64.rpm
dir=~/Intel-Nehalem-el5/BUILD/campos-ase3-${major_version}.${version1}.${version2}.${version_svn}-1${disttag}.python${python_version}-root
ln -s ${dir}/etc/modulefiles/campos-ase3/${major_version}.${version1}.${version2}.${version_svn}-1${disttag}.python${python_version} \
   ~/Intel-Nehalem-el5/modulefiles.testing/campos-ase3
ln -s ${dir}/home/camp/rpmbuild/opt/Intel-Nehalem-el5/campos-ase3/${major_version}.${version1}.${version2}.${version_svn} ~/opt/Intel-Nehalem-el5/campos-ase3

blacs

BLACS is used by ScaLapack.

On a custom system build the following RPMS:

. fys.set.gfortran.default.sh
. fys.set.openmpi.default.sh

(rpm_prefix=/usr && . fys.build.blacs.sh)

On Niflheim build the following RPMS:

. fys.set.Niflheim.open64.4.2.4.sh
. fys.set.Niflheim.openmpi.1.4.3.sh

. fys.build.blacs.sh

# older builds
#
. fys.set.Niflheim.gfortran.4.1.2.sh
. fys.set.Niflheim.openmpi.1.3.3.sh

. fys.build.blacs.sh

#
. fys.set.Niflheim.gfortran43.4.3.2.sh
. fys.set.Niflheim.openmpi.1.3.3.sh

. fys.build.blacs.sh

#
. fys.set.Niflheim.pathscale.3.2.sh
. fys.set.Niflheim.openmpi.1.3.3.sh

. fys.build.blacs.sh

#
. fys.set.Niflheim.open64.4.2.1.sh
. fys.set.Niflheim.openmpi.1.3.3.sh

. fys.build.blacs.sh

#
. fys.set.Niflheim.open64.4.2.3.sh
. fys.set.Niflheim.openmpi.1.3.3.sh

. fys.build.blacs.sh

#
. fys.set.Niflheim.ifort.11.0.sh
. fys.set.Niflheim.openmpi.1.3.3.sh

. fys.build.blacs.sh

#
. fys.set.Niflheim.ifort.11.1.sh
. fys.set.Niflheim.openmpi.1.3.3.sh

. fys.build.blacs.sh

scalapack

SCALAPACK.

On a custom system build the following RPMS:

. fys.set.gfortran.default.sh
. fys.set.openmpi.default.sh
. fys.set.blas.default.sh
. fys.set.lapack.default.sh
. fys.set.Niflheim.blacs.1.1.sh

(rpm_prefix=/usr && . fys.build.scalapack.sh)

On Niflheim build the following RPMS:

#
. fys.set.Niflheim.open64.4.2.3.sh
. fys.set.Niflheim.openmpi.1.3.3.sh
. fys.set.blas.acml.4.4.0.sh
. fys.set.lapack.acml.sh
. fys.set.Niflheim.goto2.1.13.sh
. fys.set.Niflheim.blacs.1.1.sh

. fys.build.scalapack.2.0.1.sh
#
. fys.set.Niflheim.open64.4.2.3.sh
. fys.set.Niflheim.openmpi.1.3.3.sh
. fys.set.blas.acml.4.4.0.sh
. fys.set.lapack.acml.sh
. fys.set.Niflheim.blacs.1.1.sh

. fys.build.scalapack.2.0.1.sh

# old builds
. fys.set.Niflheim.open64.4.2.4.sh
. fys.set.Niflheim.openmpi.1.4.3.sh
. fys.set.blas.acml.4.4.0.sh
. fys.set.lapack.acml.sh
. fys.set.Niflheim.blacs.1.1.sh

. fys.build.scalapack.1.8.0.sh

#
. fys.set.Niflheim.open64.4.2.4.sh
. fys.set.Niflheim.openmpi.1.4.3.sh
. fys.set.blas.acml.4.4.0.sh
. fys.set.lapack.acml.sh
. fys.set.Niflheim.goto2.1.13.sh
. fys.set.Niflheim.blacs.1.1.sh

. fys.build.scalapack.1.8.0.sh

#
. fys.set.Niflheim.gfortran.4.1.2.sh
. fys.set.Niflheim.openmpi.1.3.3.sh
. fys.set.blas.default.sh
. fys.set.lapack.default.sh
. fys.set.Niflheim.blacs.1.1.sh

. fys.build.scalapack.1.8.0.sh

#
. fys.set.Niflheim.gfortran.4.1.2.sh
. fys.set.Niflheim.openmpi.1.3.3.sh
. fys.set.blas.acml.4.0.1.sh
. fys.set.lapack.acml.sh
. fys.set.Niflheim.blacs.1.1.sh

. fys.build.scalapack.1.8.0.sh

#
. fys.set.Niflheim.gfortran43.4.3.2.sh
. fys.set.Niflheim.openmpi.1.3.3.sh
. fys.set.blas.default.sh
. fys.set.lapack.default.sh
. fys.set.Niflheim.blacs.1.1.sh

. fys.build.scalapack.1.8.0.sh

#
. fys.set.Niflheim.gfortran43.4.3.2.sh
. fys.set.Niflheim.openmpi.1.3.3.sh
. fys.set.blas.acml.4.4.0.sh
. fys.set.lapack.acml.sh
. fys.set.Niflheim.blacs.1.1.sh

. fys.build.scalapack.1.8.0.sh

# old old builds
#
. fys.set.Niflheim.gfortran43.4.3.2.sh
. fys.set.Niflheim.openmpi.1.3.3.sh
. fys.set.blas.acml.4.3.0.sh
. fys.set.lapack.acml.sh
. fys.set.Niflheim.blacs.1.1.sh

. fys.build.scalapack.1.8.0.sh

#
. fys.set.Niflheim.gfortran43.4.3.2.sh
. fys.set.Niflheim.openmpi.1.3.3.sh
. fys.set.blas.acml.4.4.0.sh
. fys.set.lapack.acml.sh
. fys.set.Niflheim.goto2.1.13.sh
. fys.set.Niflheim.blacs.1.1.sh

. fys.build.scalapack.1.8.0.sh
#
. fys.set.Niflheim.gfortran43.4.3.2.sh
. fys.set.Niflheim.openmpi.1.3.3.sh
. fys.set.blas.acml.4.4.0.sh
. fys.set.lapack.acml.sh
. fys.set.Niflheim.goto.1.26.sh
. fys.set.Niflheim.blacs.1.1.sh

. fys.build.scalapack.1.8.0.sh

#
. fys.set.Niflheim.gfortran43.4.3.2.sh
. fys.set.Niflheim.openmpi.1.3.3.sh
. fys.set.blas.acml.4.3.0.sh
. fys.set.lapack.acml.sh
. fys.set.Niflheim.goto.1.26.sh
. fys.set.Niflheim.blacs.1.1.sh

. fys.build.scalapack.1.8.0.sh

#
. fys.set.Niflheim.open64.4.2.1.sh
. fys.set.Niflheim.openmpi.1.3.3.sh
. fys.set.blas.acml.4.3.0.sh
. fys.set.lapack.acml.sh
. fys.set.Niflheim.blacs.1.1.sh

. fys.build.scalapack.1.8.0.sh

# only on fjorm
. fys.set.Niflheim.open64.4.2.3.sh
. fys.set.Niflheim.openmpi.1.3.3.sh
. fys.set.blas.acml.4.4.0.sh
. fys.set.lapack.acml.sh
. fys.set.Niflheim.goto.1.26.sh
. fys.set.Niflheim.blacs.1.1.sh

. fys.build.scalapack.1.8.0.sh
#
. fys.set.Niflheim.open64.4.2.3.sh
. fys.set.Niflheim.openmpi.1.3.3.sh
. fys.set.blas.acml.4.4.0.sh
. fys.set.lapack.acml.sh
. fys.set.Niflheim.goto2.1.13.sh
. fys.set.Niflheim.blacs.1.1.sh

. fys.build.scalapack.1.8.0.sh
#
. fys.set.Niflheim.open64.4.2.3.sh
. fys.set.Niflheim.openmpi.1.3.3.sh
. fys.set.blas.acml.4.4.0.sh
. fys.set.lapack.acml.sh
. fys.set.Niflheim.blacs.1.1.sh

. fys.build.scalapack.1.8.0.sh

#
. fys.set.Niflheim.gfortran43.4.3.2.sh
. fys.set.Niflheim.openmpi.1.3.3.sh
. fys.set.Niflheim.atlas.3.8.3.sh
. fys.set.Niflheim.blacs.1.1.sh

. fys.build.scalapack.1.8.0.sh

# only on thul
. fys.set.Niflheim.ifort.11.0.sh
. fys.set.Niflheim.openmpi.1.3.3.sh
. fys.set.blas.acml.4.4.0.sh
. fys.set.lapack.acml.sh
. fys.set.Niflheim.blacs.1.1.sh

. fys.build.scalapack.1.8.0.sh

# only on thul
. fys.set.Niflheim.ifort.11.1.sh
. fys.set.Niflheim.openmpi.1.3.3.sh
. fys.set.blas.acml.4.4.0.sh
. fys.set.lapack.acml.sh
. fys.set.Niflheim.blacs.1.1.sh

. fys.build.scalapack.1.8.0.sh

PDSYEVRnew

PDSYEVRnew ScaLAPACK's new parallel MRRR algorithm for computing eigenpairs of large real symmetric or complex Hermitian matrices.

On Niflheim build the following RPMS:

. fys.set.Niflheim.gfortran43.4.3.2.sh
. fys.set.Niflheim.openmpi.1.3.3.sh
. fys.set.blas.acml.4.3.0.sh
. fys.set.lapack.acml.sh
. fys.set.Niflheim.blacs.1.1.sh
. fys.set.Niflheim.scalapack.1.8.0.sh

. fys.build.PDSYEVRnew.sh

#
. fys.set.Niflheim.gfortran43.4.3.2.sh
. fys.set.Niflheim.openmpi.1.3.3.sh
. fys.set.blas.acml.4.3.0.sh
. fys.set.lapack.acml.sh
. fys.set.Niflheim.goto.1.26.sh
. fys.set.Niflheim.blacs.1.1.sh
. fys.set.Niflheim.scalapack.1.8.0.sh

. fys.build.PDSYEVRnew.sh

campos-gpaw-setups

Note this package is not relocatable!

On a custom system build the following RPMS:
(default_version_usage="--with default_version" && modules_usage="--without modules" && . fys.build.gpaw-setups.sh)
On Niflheim build the following RPMS:
. fys.build.gpaw-setups.sh

campos-gpaw

On a custom system build the following RPMS:

# March 3 2010: results in "orthogonalization failed" with EPEL's atlas on el5.x64_64 and i386.
. fys.set.gpaw.default.sh
. fys.set.atlas.default.sh

(rpm_prefix=/usr && . fys.build.gpaw.sh)

# optional build using netlib blas/lapack
. fys.set.gpaw.default.sh

(rpm_prefix=/usr && . fys.build.gpaw.sh)

On Niflheim load first the required modules:

module load ASE3
module load campos-gpaw-setups

and build the following RPMS:

. fys.set.Niflheim.gpaw.0.6.5147.open64.4.2.3.openmpi.1.3.3.acml.4.4.0.acml.4.4.0.sh

. fys.build.gpaw.sh

# older builds
#
. fys.set.Niflheim.gpaw.0.6.5147.open64.4.2.4.openmpi.1.4.3.goto2.1.13.acml.4.4.0.sh

. fys.build.gpaw.sh
#
. fys.set.Niflheim.gpaw.0.6.5147.open64.4.2.3.openmpi.1.3.3.goto2.1.13.acml.4.4.0.sh

. fys.build.gpaw.sh
#
. fys.set.Niflheim.gpaw.0.6.5147.gfortran43.4.3.2.openmpi.1.3.3.acml.4.4.0.acml.4.4.0.sh

. fys.build.gpaw.sh

# only on fjorm
. fys.set.Niflheim.gpaw.0.6.5147.gfortran43.4.3.2.openmpi.1.3.3.goto.1.26.acml.4.4.0.sh

. fys.build.gpaw.sh

Optional builds:

. fys.set.Niflheim.gpaw.0.6.5147.gfortran43.4.3.2.openmpi.1.3.3.acml.4.3.0.acml.4.3.0.sh

. fys.build.gpaw.sh
#
. fys.set.Niflheim.gpaw.0.6.5147.gfortran.4.1.2.openmpi.1.3.3.acml.4.0.1.acml.4.0.1.sh

. fys.build.gpaw.sh

# default gfortran and netlib blas/lapack/scalapack
. fys.set.Niflheim.gpaw.0.6.5147.gfortran.4.1.2.openmpi.1.3.3.acml.4.0.1.acml.4.0.1.sh
. fys.set.blas.default.sh
. fys.set.lapack.default.sh
. fys.set.Niflheim.scalapack.1.8.0.sh

. fys.build.gpaw.sh

# latest gfortran and netlib blas/lapack/scalapack
. fys.set.Niflheim.gpaw.0.6.5147.gfortran43.4.3.2.openmpi.1.3.3.acml.4.3.0.acml.4.3.0.sh
. fys.set.blas.default.sh
. fys.set.lapack.default.sh
. fys.set.Niflheim.scalapack.1.8.0.sh

. fys.build.gpaw.sh

# atlas - gpaw-test fails for diagonalization on fjorm el5 x86_64 18 Jan 2010
. fys.set.Niflheim.gpaw.0.6.5147.gfortran43.4.3.2.openmpi.1.3.3.acml.4.3.0.acml.4.3.0.sh
. fys.set.Niflheim.atlas.3.8.3.sh
. fys.set.Niflheim.scalapack.1.8.0.sh

. fys.build.gpaw.sh

# atlas - gpaw-test fails for diagonalization on fjorm el5 x86_64 18 Jan 2010
. fys.set.Niflheim.gpaw.0.6.5147.gfortran43.4.3.2.openmpi.1.3.3.acml.4.3.0.acml.4.3.0.sh
. fys.set.Niflheim.atlas.3.8.3.sh
. fys.set.Niflheim.scalapack.1.8.0.sh

. fys.build.gpaw.sh

#
. fys.set.Niflheim.gfortran43.4.3.2.sh
. fys.set.Niflheim.openmpi.1.3.3.sh
. fys.set.blas.acml.4.4.0.sh
. fys.set.lapack.acml.sh
. fys.set.Niflheim.goto2.1.13.sh
. fys.set.Niflheim.blacs.1.1.sh
. fys.set.Niflheim.scalapack.1.8.0.sh

. fys.build.gpaw.sh

# only on fjorm
# note gpaw version 0.6 --with sl_init_second_underscore=1 is necessary for rpmbuild
. fys.set.Niflheim.pathscale.3.2.sh
. fys.set.Niflheim.openmpi.1.3.3.sh
. fys.set.blas.acml.4.0.1.sh
. fys.set.lapack.acml.sh
. fys.set.Niflheim.goto.1.26.sh
. fys.set.Niflheim.blacs.1.1.sh
. fys.set.Niflheim.scalapack.1.8.0.sh

. fys.build.gpaw.sh

# only on fjorm
# note gpaw version 0.6 --with sl_init_second_underscore=1 is necessary for rpmbuild
. fys.set.Niflheim.open64.4.2.1.sh
. fys.set.Niflheim.openmpi.1.3.3.sh
. fys.set.blas.acml.4.0.1.sh
. fys.set.lapack.acml.sh
. fys.set.Niflheim.goto.1.26.sh
. fys.set.Niflheim.blacs.1.1.sh
. fys.set.Niflheim.scalapack.1.8.0.sh

. fys.build.gpaw.sh

**Note**: open64 compiler fails with::

/usr/bin/ld: /opt/open64/4.2.1/lib/gcc-lib/x86_64-open64-linux/4.2.1/libmv.a(vcos.o): relocation R_X86_64_32S against `a local symbol' can not be used when making a shared object; recompile with -fPIC
/opt/open64/4.2.1/lib/gcc-lib/x86_64-open64-linux/4.2.1/libmv.a: could not read symbols: Bad value

# only on fjorm
# note gpaw version 0.6 --with sl_init_second_underscore=1 is necessary for rpmbuild
. fys.set.Niflheim.open64.4.2.3.sh
. fys.set.Niflheim.openmpi.1.3.3.sh
. fys.set.blas.acml.4.4.0.sh
. fys.set.lapack.acml.sh
. fys.set.Niflheim.goto.1.26.sh
. fys.set.Niflheim.blacs.1.1.sh
. fys.set.Niflheim.scalapack.1.8.0.sh

. fys.build.gpaw.sh

#
# note gpaw version 0.6 --with sl_init_second_underscore=1 is necessary for rpmbuild
. fys.set.Niflheim.open64.4.2.3.sh
. fys.set.Niflheim.openmpi.1.3.3.sh
. fys.set.blas.acml.4.4.0.sh
. fys.set.lapack.acml.sh
. fys.set.Niflheim.blacs.1.1.sh
. fys.set.Niflheim.scalapack.1.8.0.sh

. fys.build.gpaw.sh

# only on thul
. fys.set.Niflheim.ifort.11.1.sh
. fys.set.Niflheim.openmpi.1.3.3.sh
. fys.set.blas.acml.4.4.0.sh
. fys.set.lapack.acml.sh
. fys.set.Niflheim.blacs.1.1.sh
. fys.set.Niflheim.scalapack.1.8.0.sh

. fys.build.gpaw.sh

# only on thul
. fys.set.Niflheim.ifort.11.0.sh
. fys.set.Niflheim.openmpi.1.3.3.sh
. fys.set.blas.acml.4.4.0.sh
. fys.set.lapack.acml.sh
. fys.set.Niflheim.blacs.1.1.sh
. fys.set.Niflheim.scalapack.1.8.0.sh

. fys.build.gpaw.sh

# only on thul # fails on thul
. fys.set.Niflheim.gfortran43.4.3.2.sh
. fys.set.Niflheim.openmpi.1.3.3.sh
. fys.set.Niflheim.mkl.10.2.4.032.sh

. fys.build.gpaw.sh

# only on thul # fails on thul
. fys.set.Niflheim.gfortran43.4.3.2.sh
. fys.set.Niflheim.openmpi.1.3.3.sh
. fys.set.Niflheim.mkl.10.2.1.017.sh

. fys.build.gpaw.sh

# only on thul # fails on thul
. fys.set.Niflheim.ifort.11.0.sh
. fys.set.Niflheim.openmpi.1.3.3.sh
. fys.set.Niflheim.mkl.10.1.3.027.sh

. fys.build.gpaw.sh

# only on thul # fails on thul
. fys.set.Niflheim.gfortran43.4.3.2.sh
. fys.set.Niflheim.openmpi.1.3.3.sh
. fys.set.Niflheim.mkl.10.1.3.027.sh

. fys.build.gpaw.sh

Asap

On a custom system build the following RPMS:

. fys.set.Asap.default.sh

(rpm_prefix=/usr && . fys.build.Asap.sh)

On Niflheim build the following RPMS:

#
module load ASE3
. fys.set.Niflheim.Asap.3.2.6.open64.4.2.4.openmpi.1.4.3.sh

. fys.build.Asap.sh

#
module load ASE3
. fys.set.Niflheim.Asap.3.2.6.open64.4.2.3.openmpi.1.3.3.sh

. fys.build.Asap.sh

# only on fjorm
module load ASE3
. fys.set.Niflheim.Asap.3.2.6.pathscale.3.2.openmpi.1.3.3.sh

. fys.build.Asap.sh

# only on thul
module load ASE3
module load ifort/11.1-1
. fys.set.Niflheim.Asap.3.2.6.ifort.11.1.openmpi.1.3.3.sh

. fys.build.Asap.sh

abinit

abinit pseudopotentials

Note this package is not relocatable! abinit-pseudopotentials

On a custom system build the following RPMS:
(default_version_usage="--with default_version" && modules_usage="--without modules" && . fys.build.abinit-pseudopotentials.sh)
On Niflheim build the following RPMS:
. fys.build.abinit-pseudopotentials.sh

abinit

abinit is a Density Functional Theory (DFT) package with pseudopotentials and a planewave basis.

On a custom system build the following RPMS:

. fys.set.abinit.5.4.4p.default.sh
. fys.set.atlas.default.sh

(rpm_prefix=/usr && . fys.build.abinit.5.4.4p.sh)

On Niflheim build the following RPMS:

. fys.set.Niflheim.abinit.5.4.4p.gfortran43.4.3.2.openmpi.1.3.3.acml.4.3.0.acml.4.3.0.fftw3.sh
hdf=none

. fys.build.abinit.5.4.4p.sh

siesta

siesta-pseudopotentials-2.tar.gz

siesta pseudopotentials

Build the following RPMS:

cd ~/rpmbuild/SOURCES&& wget --no-check-certificate \
"https://wiki.fysik.dtu.dk/niflheim/Cluster_software_-_RPMS?action=AttachFile&do=get&target=siesta-pseudopotentials-2.tar.gz" \
-O siesta-pseudopotentials-2.tar.gz
cd ~/rpmbuild/SPECS

 rpmbuild -bb ${modules_usage} --with default_version siesta-pseudopotentials.spec

siesta

siesta (Spanish Initiative for Electronic Simulations with Thousands of Atoms) is both a method and its computer program implementation, to perform electronic structure calculations and ab initio molecular dynamics simulations of molecules and solids.

Build the following RPMS:

cd ~/rpmbuild/SPECS

major_version=2
version1=0

compiler=gfortran43
compiler_version=4.3.2
compiler_libdir=/usr/lib64
compiler_bindir=/usr/bin
blas=acml
blas_version=4.3.0
blasdir=/opt/${blas}/${blas_version}/${compiler}64/lib
lapack=acml
lapack_version=4.3.0
lapackdir=/opt/${lapack}/${lapack_version}/${compiler}64/lib
netcdf=netcdf4
netcdf_includedir=/opt/${netcdf}/4.0.1/1${disttag}.${compiler}.${compiler_version}/include
netcdf_libdir=/opt/${netcdf}/4.0.1/1${disttag}.${compiler}.${compiler_version}/lib64
openmpi_version=1.3.3
ompi_libdir=/opt/openmpi/${openmpi_version}-1${disttag_network}.${compiler}.${compiler_version}/lib64
ompi_includedir=/opt/openmpi/${openmpi_version}-1${disttag_network}.${compiler}.${compiler_version}/include
ompi_bindir=/opt/openmpi/${openmpi_version}-1${disttag_network}.${compiler}.${compiler_version}/bin
blacs=blacs
blacsdir=/opt/blacs/1.1/24${disttag_network}.${compiler}.${compiler_version}.openmpi.${openmpi_version}/lib64
scalapack=scalapack
scalapackdir=/opt/scalapack/1.8.0/1${disttag_network}.${compiler}.${compiler_version}.openmpi.${openmpi_version}.${blas}.${blas_version}.${lapack}.${lapack_version}/lib64
release=1${disttag_network}.${compiler}.${compiler_version}.openmpi.${openmpi_version}.${blas}.${blas_version}.${lapack}.${lapack_version}

rpmbuild --bb  --with major_version=${major_version} --with version1=${version1} \
               --with blas=${blas} --with blas_version=${blas_version} --with blasdir=${blasdir} \
               --with compiler=${compiler} --with compiler_version=${compiler_version} \
               --with compiler_bindir=${compiler_bindir} --with compiler_libdir=${compiler_libdir} \
               --with lapack=${lapack} --with lapack_version=${lapack_version} --with lapackdir=${lapackdir} \
               --with netcdf=${netcdf} --with netcdf_includedir=${netcdf_includedir} --with netcdf_libdir=${netcdf_libdir} \
               --with parallel=1 --with openmpi=openmpi --with openmpi_version=${openmpi_version} \
               --with ompi_libdir=${ompi_libdir} --with ompi_includedir=${ompi_includedir} --with ompi_bindir=${ompi_bindir} \
               --with blacs=${blacs} --with blacsdir=${blacsdir} \
               --with scalapack=${scalapack} --with scalapackdir=${scalapackdir} \
               ${modules_usage} --with default_version=1 \
               --with system=${rpm_platform} \
               --with prefix=/opt/siesta${major_version}/${major_version}.${version1}/${release} siesta.spec

espresso

Note this package is not relocatable!

quantum espresso

espresso pseudopotentials

On a custom system build the following RPMS:

(default_version_usage="--with default_version" && modules_usage="--without modules" && . fys.build.espresso_pp.sh)

On Niflheim build the following RPMS:

. fys.build.espresso_pp.sh

espresso

Note March 04 2010: version 4.0.5 does not compile with gfortran >= 4.4 (?)

Note March 04 2010: version 4.1.2 results in and "STOP 1" status for tests if EXX is enabled

On a custom system build the following RPMS:

. fys.set.espresso.4.1.2.default.sh

(rpm_prefix=/usr && . fys.build.espresso.sh)

#  March 06 2010 fc12, el5 with atlas gives for atom-lsda.in: On entry to DSYGVX parameter number 20 had an illegal value
. fys.set.espresso.4.1.2.default.sh
. fys.set.atlas.default.sh

(rpm_prefix=/usr && . fys.build.espresso.sh)

On Niflheim build the following RPMS:

# version used with yambo 3.2.1.426M - enable EXX in the spec file!
. fys.set.Niflheim.espresso.4.0.5.gfortran43.4.3.2.openmpi.1.3.3.acml.4.3.0.acml.4.3.0.sh

. fys.build.espresso.sh

# version 5.0.1
. fys.set.Niflheim.espresso.5.0.1.gfortran43.4.3.2.openmpi.1.3.3.acml.4.3.0.acml.4.3.0.sh
. fys.build.espresso.5.sh

yambo

yambo is a FORTRAN/C code for Many-Body calculations in solid state and molecular physics. Yambo relies on the Kohn-Sham wavefunctions generated by two DFT public codes: abinit, and PWscf. This build creates interfaces to abinit and PWscf.

On a custom system build the following RPMS:

. fys.set.yambo.default.sh
. fys.set.atlas.default.sh

(rpm_prefix=/usr && . fys.build.yambo.sh)

On Niflheim build the following RPMS:

# Nov 15 2010: ETSF compilation part fails with "Error: Symbol 'default_tel' at (1) has no IMPLICIT type": see http://www.yambo-code.org/forum/viewtopic.php?f=1&t=266
. fys.set.Niflheim.yambo.3.2.3.16.gfortran43.4.3.2.openmpi.1.3.3.acml.4.4.0.acml.4.4.0.sh
hdf=none

. fys.build.yambo.sh
#
. fys.set.Niflheim.yambo.3.2.1.448.gfortran43.4.3.2.openmpi.1.3.3.acml.4.3.0.acml.4.3.0.sh
hdf=none

. fys.build.yambo.sh

# special yambo 3.2.1.426M
. fys.set.Niflheim.yambo.3.2.1.426M.gfortran43.4.3.2.openmpi.1.3.3.acml.4.3.0.acml.4.3.0.sh
hdf=none

. fys.build.yambo.sh

yambo NON-GPL

This is a NON-GPL version of yambo.

On Niflheim build the following RPMS:

. fys.set.Niflheim.yambo-ngpl.3.2.3.735M.gfortran43.4.3.2.openmpi.1.3.3.acml.4.4.0.acml.4.4.0.sh
hdf=none

. fys.build.yambo.sh

elk

elk species

Note this package is not relocatable!

On a custom system build the following RPMS:

(default_version_usage="--with default_version" && modules_usage="--without modules" && . fys.build.elk-species.sh)

On Niflheim build the following RPMS:

. fys.build.elk-species.sh

elk

On a custom system build the following RPMS:

. fys.set.gfortran.default.sh
. fys.set.openmpi.default.sh
. fys.set.blas.default.sh
. fys.set.lapack.default.sh

(rpm_prefix=/usr && thread_mode=mp && . fys.build.elk.sh)

On Niflheim build the following RPMS:

# OpenMP with MPI version
. fys.set.Niflheim.gfortran43.4.3.2.sh
. fys.set.Niflheim.openmpi.1.3.3.sh
. fys.set.blas.acml.4.3.0_mp.sh
. fys.set.lapack.acml.sh

(thread_mode=mp && . fys.build.elk.sh)

# OpenMP version
. fys.set.Niflheim.gfortran43.4.3.2.sh
. fys.set.blas.acml.4.3.0_mp.sh
. fys.set.lapack.acml.sh

(thread_mode=mp && . fys.build.elk.sh)

# MPI version
. fys.set.Niflheim.gfortran43.4.3.2.sh
. fys.set.Niflheim.openmpi.1.3.3.sh
. fys.set.blas.acml.4.4.0.sh
. fys.set.lapack.acml.sh

(thread_mode=nomp && . fys.build.elk.sh)

vtk

cmake

Build the following RPMS:

cd ~/rpmbuild/SOURCES&& wget http://www.cmake.org/files/v2.6/cmake-2.6.4.tar.gz
cd ~/rpmbuild/SOURCES&& wget "http://downloads.sourceforge.net/project/xmlrpc-c/Xmlrpc-c Super Stable/1.06.35/xmlrpc-c-1.06.35.tgz"
cd ~/rpmbuild/SPECS

rpmbuild -bb --with bootstrap --without gui cmake.spec  # install the resulting RPM
rpmbuild -bb xmlrpc-c.spec # install the resulting RPM
rpm -e cmake
rpmbuild -bb --without gui cmake.spec # install the resulting RPM

vtkdata

Build the following RPMS:

cd ~/rpmbuild/SOURCES&& wget http://www.vtk.org/files/release/5.4/vtkdata-5.4.2.tar.gz
cd ~/rpmbuild/SPECS

rpmbuild -bb --with version1=4 --with version2=2 ${modules_usage} --with default_version=1 \
         --with prefix=/opt/vtkdata/5.4.2/1${disttag} vtkdata.spec

vtk

Build the following RPMS:

cd ~/rpmbuild/SOURCES&& wget http://www.vtk.org/files/release/5.4/vtk-5.4.2.tar.gz
cd ~/rpmbuild/SPECS

compiler=gfortran
compiler_version=4.1.2
compiler_libdir=/usr/lib64
compiler_bindir=/usr/bin
openmpi_version=1.3.3
ompi_libdir=/opt/openmpi/${openmpi_version}-1${disttag_network}.${compiler}.${compiler_version}/lib64
ompi_includedir=/opt/openmpi/${openmpi_version}-1${disttag_network}.${compiler}.${compiler_version}/include
ompi_bindir=/opt/openmpi/${openmpi_version}-1${disttag_network}.${compiler}.${compiler_version}/bin

rpmbuild -bb   --without qt4 --with version1=4 --with version2=2 \
               --with compiler=${compiler} --with compiler_version=${compiler_version} \
               --with compiler_bindir=${compiler_bindir} --with compiler_libdir=${compiler_libdir} \
               --with parallel=1 --with openmpi=openmpi --with openmpi_version=${openmpi_version} \
               --with ompi_libdir=${ompi_libdir} --with ompi_includedir=${ompi_includedir} --with ompi_bindir=${ompi_bindir} \
               ${modules_usage} --with default_version=1 \
               --with system=${rpm_platform} \
               --with python_version=${python_version} \
               --with prefix=/opt/vtk/5.4.2/1${disttag_network}.${compiler}.${compiler_version}.python${python_version}.openmpi.${openmpi_version} vtk.spec

octopus

Note March 15 2010: gfortran 4.1.2 on el5: Segmentation fault

On a custom system build the following RPMS:

. fys.set.octopus.default.sh
. fys.set.atlas.default.sh

(rpm_prefix=/usr && . fys.build.octopus.3.2.0.sh)

On Niflheim build the following RPMS:

. fys.set.Niflheim.gfortran43.4.3.2.sh
. fys.set.Niflheim.openmpi.1.3.3.sh
. fys.set.Niflheim.netcdf4.4.0.1.sh
. fys.set.Niflheim.fftw3.3.2.1.sh
. fys.set.blas.acml.4.3.0.sh
. fys.set.lapack.acml.sh
. fys.set.gsl.default.sh
. fys.set.arpack.default.sh

. fys.build.octopus.3.2.0.sh

TAU

pdtoolkit

Program Database Toolkit is a framework for analyzing source code written in several programming languages and for making rich program knowledge accessible to developers of static and dynamic analysis tools. PDT is required by TAU.

On a custom system build the following RPMS:
```
. fys.set.gfortran.default.sh

(rpm_prefix=/opt/pdtoolkit && . fys.build.pdtoolkit.sh)
```
On Niflheim build the following RPMS:
```
. fys.set.Niflheim.gfortran.4.1.2.sh

. fys.build.pdtoolkit.sh
#
. fys.set.Niflheim.gfortran43.4.3.2.sh

. fys.build.pdtoolkit.sh
```

tau

TAU Performance System® is a portable profiling and tracing toolkit for performance analysis of parallel programs written in Fortran, C, C++, Java, Python.

On a custom system build the following RPMS:

. fys.set.gfortran.default.sh
. fys.set.openmpi.default.sh

(rpm_prefix=/opt/tau && . fys.build.tau.sh)

On Niflheim build the following RPMS:

pdtoolkit_version=3.15

module purge
unset PDTROOT
. fys.set.Niflheim.gfortran.4.1.2.sh
  module load PDTOOLKIT/${pdtoolkit_version}-1.el5.fys.${compiler}.${compiler_version}.python${python_version}
. fys.set.Niflheim.openmpi.1.3.3.sh

. fys.build.tau.sh
#
module purge
unset PDTROOT
. fys.set.Niflheim.gfortran43.4.3.2.sh
  module load PDTOOLKIT/${pdtoolkit_version}-1.el5.fys.${compiler}.${compiler_version}.python${python_version}
. fys.set.Niflheim.openmpi.1.3.3.sh

. fys.build.tau.sh

vasp

Installed with restricted access under vasp UNIX group (needs te be created in advance).

vasp potentials

Download potpaw/potcar.date.tar, potpaw_GGA/potcar.date.tar, and potpaw_PBE/potcar.date.tar to ~/rpmbuild/SOURCES. Create links to the downloaded files so the files are named explicitly with the string date (not the actual dates), for example:

ls -al ~/rpmbuild/SOURCES/potpaw_*potcar.date.tar
lrwxrwxrwx 1 rpmbuild campnone   29 Sep 25 17:15 ../SOURCES/potpaw_GGA_potcar.date.tar -> potpaw_GGA/potcar.06Feb03.tar
lrwxrwxrwx 1 rpmbuild campnone   29 Sep 25 17:14 ../SOURCES/potpaw_PBE_potcar.date.tar -> potpaw_PBE/potcar.05Feb03.tar
lrwxrwxrwx 1 rpmbuild campnone   25 Sep 25 17:14 ../SOURCES/potpaw_potcar.date.tar -> potpaw/potcar.05Feb03.tar

Note this package is not relocatable!

On a custom system build the following RPMS:

(default_version_usage="--with default_version" && modules_usage="--without modules" && . fys.build.vasp-potpaw.sh)

On Niflheim build the following RPMS:

. fys.build.vasp-potpaw.sh

vasp

vasp. Download vasp.5.X.Y.tar.gz and vasp.5.lib.tar.gz to ~/rpmbuild/SOURCES. Optionally download also vtstcode.tar.gz from http://theory.cm.utexas.edu/vtsttools/download.html.

On a custom system build the following RPMS:

# Compile with VASP TST library: http://theory.cm.utexas.edu/vtsttools/downloads/
hdf=none
tst=false # or true

. fys.set.vasp.5.2.11.default.sh

(rpm_prefix=/usr && . fys.build.vasp.sh)

On Niflheim build the following RPMS:

# gfortran 4.1.2 is the only of our compilers that works! MD 6 Oct 2011
# Compile with VASP TST library: http://theory.cm.utexas.edu/vtsttools/downloads/
hdf=none
tst=false # or true

. fys.set.Niflheim.vasp.5.2.12.gfortran.4.1.2.openmpi.1.3.3.acml.4.0.1.acml.4.0.1.fftw3.sh

. fys.build.vasp.sh
#
# 25 Sep 2009: segmentation fault when compiling dipol.f90
hdf=none
tst=false # or true

. fys.set.Niflheim.vasp.5.2.2.gfortran43.4.3.2.openmpi.1.3.3.acml.4.3.0.acml.4.3.0.fftw3.sh

. fys.build.vasp.sh
#
# 11 May 2010: in dfast.f90"LINCOM" is the name of this program unit, therefore it must not be use associated from module "DFAST".
hdf=none
tst=false # or true

. fys.set.Niflheim.vasp.5.2.2.open64.4.2.3.openmpi.1.3.3.acml.4.4.0.acml.4.4.0.fftw3.sh

. fys.build.vasp.sh
#
# only on thul
# 15 Feb 2011; 6 Oct 2011: forrtl: severe (174): SIGSEGV, segmentation fault occurred during DAV
hdf=none
tst=false # or true

. fys.set.Niflheim.vasp.5.2.12.ifort.11.1.openmpi.1.3.3.acml.4.4.0.acml.4.4.0.fftw3.sh

. fys.build.vasp.sh

exciting

exciting species

Note this package is not relocatable!

On a custom system build the following RPMS:

(default_version_usage="--with default_version" && modules_usage="--without modules" && . fys.build.exciting-species.9.10.sh)

On Niflheim build the following RPMS:

. fys.build.exciting-species.9.10.sh

exciting

Note: currently (24 Nov 2009) perl-XML-SAX-0.14-5 is broken https://bugzilla.redhat.com/show_bug.cgi?id=438291 on EL5; if exciting's tests complain about:

could not find ParserDetails.ini

do as root:

perl -MXML::SAX -e "XML::SAX->add_parser(q(XML::SAX::PurePerl))->save_parsers()"

On a custom system build the following RPMS:

# March 12 2010: build fails on el5 with gfortran 4.1.2 and 4.3.2
. fys.set.gfortran.default.sh
. fys.set.openmpi.default.sh
. fys.set.arpack.default.sh
. fys.set.atlas.default.sh

(rpm_prefix=/usr && thread_mode=nomp && . fys.build.exciting.9.10.sh)

# March 12 2010: build fails on el5 with gfortran 4.1.2 and 4.3.2
. fys.set.gfortran.default.sh
. fys.set.openmpi.default.sh
. fys.set.arpack.default.sh
. fys.set.blas.default.sh
. fys.set.lapack.default.sh

(rpm_prefix=/usr && thread_mode=nomp && . fys.build.exciting.9.10.sh)

On Niflheim build the following RPMS:

# only on fjorm
. fys.set.Niflheim.g95.0.91.sh
. fys.set.Niflheim.openmpi.1.3.3.sh
. fys.set.blas.acml.4.3.0_mp.sh
. fys.set.lapack.acml.sh

(thread_mode=mp && . fys.build.exciting.9.10.sh)

# only on thul
. fys.set.Niflheim.ifort.11.0.sh
. fys.set.Niflheim.openmpi.1.3.3.sh
. fys.set.Niflheim.mkl.10.1.3.027.sh

(thread_mode=nomp && . fys.build.exciting.9.10.sh)

fleur

fleur. Download the source to ~/rpmbuild/SOURCES.

On a custom system build the following RPMS:

. fys.set.fleur.default.sh

(rpm_prefix=/usr && . fys.build.fleur.sh)

On Niflheim build the following RPMS:

. fys.set.Niflheim.fleur.v26b.gfortran43.4.3.2.openmpi.1.3.3.acml.4.4.0.acml.4.4.0.sh

. fys.build.fleur.sh
# only on thul # Sep 04 2010: build fails with forrtl: severe (174): SIGSEGV, segmentation fault occurred
. fys.set.Niflheim.fleur.v26b.ifort.11.0.openmpi.1.3.3.mkl.10.1.3.027.mkl_lapack.10.1.3.027.sh

. fys.build.fleur.sh

gulp

Installed with restricted access under gulp UNIX group (needs te be created in advance).

gulp

gulp. Download gulp.3.4.source.tar.gz ~/rpmbuild/SOURCES.

On a custom system build the following RPMS:

. fys.set.gfortran.default.sh
. fys.set.blas.default.sh
. fys.set.lapack.default.sh

(rpm_prefix=/usr && thread_mode=mp && . fys.build.gulp.sh)

On Niflheim build the following RPMS:

# OpenMP version
. fys.set.Niflheim.gfortran43.4.3.2.sh
. fys.set.blas.acml.4.3.0_mp.sh
. fys.set.lapack.acml.sh

(thread_mode=mp && . fys.build.gulp.sh)

cmr

Computational Materials Repository.

On a custom system build the following RPMS:

(rpm_prefix=/usr && rpmbuild -bb ${default_version_usage} ${modules_usage} cmr.spec)

On Niflheim build the following RPMS:

module load DACAPO
module load GPAW
module unload ASE3
module load ASE3
module load SCIENTIFICPYTHON/2.8

# if needed, create tar file
cd ~/rpmbuild/SOURCES && python cmr_release.py
cd ~/rpmbuild/SPECS
. fys.build.cmr.sh

Testing packages

Note this section is outdated.

Test dacapo installation (as normal user!).

If you use modules:

module load campos-dacapo # fulfill all dependencies requested by module
ulimit -s 500000 # dacapo needs a large stack

Test with (make sure that /scratch/$USER exists):

cp -r `rpm -ql campos-dacapo-python | grep "share/campos-dacapo-python$"` /tmp
cd /tmp/campos-dacapo-python/Tests
python test.py 2>&1 | tee test.log

It can take up to 1 day. Please consider disabling these "long" tests in test.py:

tests.remove('../Examples/Wannier-ethylene.py')
tests.remove('../Examples/Wannier-Pt4.py')
tests.remove('../Examples/Wannier-Ptwire.py')
tests.remove('../Examples/Wannier-Fe-bcc.py')
tests.remove('../Examples/transport_1dmodel.py')

Note all vtk related tests will fail.

Test gpaw installation (as normal user!):

If you use modules:

module load campos-gpaw # fulfill all dependencies requested by module

Test with:

cp -r `rpm -ql campos-gpaw | grep "share/campos-gpaw/test$"` /tmp/test.gpaw.$$
cd /tmp/test.gpaw.*
python test.py 2>&1 | tee test.log

It takes about 20 minutes.

Niflheim: Cluster_software_-_RPMS (last edited 2015-07-02 11:28:20 by OleHolmNielsen)

-  ⇤ ← Revision 105 as of 2009-08-04 08:54:54 → 
  Size: 72596
  Editor: MarcinDulak
  Comment:
+   ← Revision 523 as of 2015-07-02 11:28:20 → ⇥
  Size: 86086
  Editor: OleHolmNielsen
  Comment: http://theory.cm.utexas.edu/vtsttools/download.html
-Deletions are marked like this.
+Additions are marked like this.
 Line 1:
-This page describes the necessary steps for installing the login nodes **fjorm** or **thul**.

Install external packages
=========================

As root:

- create yum repository definitions (do **not** enable them)::

   # atrpms
   echo '[atrpms]' > /etc/yum.repos.d/atrpms.repo
   echo 'name=CentOS $releasever - $basearch - ATrpms' >> /etc/yum.repos.d/atrpms.repo
   echo 'baseurl=http://dl.atrpms.net/el$releasever-$basearch/atrpms/stable' >> /etc/yum.repos.d/atrpms.repo
   echo '#baseurl=http://mirrors.ircam.fr/pub/atrpms/el$releasever-$basearch/atrpms/stable' >> /etc/yum.repos.d/atrpms.repo
   echo 'gpgkey=http://ATrpms.net/RPM-GPG-KEY.atrpms' >> /etc/yum.repos.d/atrpms.repo
   echo 'gpgcheck=1' >> /etc/yum.repos.d/atrpms.repo
   echo 'enabled=0' >> /etc/yum.repos.d/atrpms.repo
   # epel
   echo '[epel]' > /etc/yum.repos.d/epel.repo
   echo 'name=CentOS $releasever - $basearch - EPEL' >> /etc/yum.repos.d/epel.repo
   echo 'baseurl=http://download.fedora.redhat.com/pub/epel/$releasever/$basearch' >> /etc/yum.repos.d/epel.repo
   echo 'gpgkey=http://download.fedora.redhat.com/pub/epel/RPM-GPG-KEY-EPEL' >> /etc/yum.repos.d/epel.repo
   echo 'gpgcheck=1' >> /etc/yum.repos.d/epel.repo
   echo 'enabled=0' >> /etc/yum.repos.d/epel.repo
+## page was renamed from Building a Cluster - Tutorial/test dl160
.. _32H2O.xyz: attachment:32H2O.xyz

This page below describes:

- configuration of the `fys` yum repository,

- the necessary steps to build RPM software packages on a custom RPM-based (currently el, fc) system and the login nodes **fjorm** or **thul**.


**Warning**: campos-dacapo-python_ provides a python interface to campos-dacapo_ Fortran code,
through campos-ase2_.
On a 64-bit machine campos-ase2_ works only with python <= 2.4, due to the unmaintained python-numeric_ package.
Users on modern systems can use instead the campos-ase3_ package and skip installation of any packages related to campos-ase2_.

**Warning**: on 64-bit machines el5 installs often only 32-bit versions of packages.
Please verify that 64-bit versions are installed, otherwise run the corresponding `yum install package` again.

.. Contents::

Configure fys yum repository
============================

We host a yum repository, which contains RPM packages of our software for the following systems: el (RedHat Enterprise Linux, or CentOS), fc (Fedora),
openSUSE (openSUSE):

- configure `fys` yum repository::

    yum -y install yum-utils wget
    cd /etc/yum.repos.d
    wget --no-check-certificate https://svn.fysik.dtu.dk/projects/rpmbuild/trunk/SOURCES/fys_el.repo

  **Note** on a RedHat system the value of $releasever in the `fys_el.repo` file need to be edited manually (changed for example into 5Client, 5Server, etc).

  **Note** on RedHat 6 or clone systems (Scientific Linux, CentOS) the value of $releasever in the `fys_el.repo` file may need to be edited manually (set explicitly to 6).

  **Note** on a Fedora system download `fys_fc.repo` instead, and use `fys_fc` identifier in the command below.
  Moreover on a fc system you do not need to include any external repositories.

  **Note** on an openSUSE system download `fys_openSUSE.repo` instead and save it under `/etc/zypp/repos.d`, and use `fys_openSUSE` identifier in the command below.
  You need to include additional external openSUSE repositories: see
  `configure external repositories <https://wiki.fysik.dtu.dk/niflheim/Cluster_software_-_RPMS#configure-external-repos>`_

- list all packages available in the `fys` yum repository, maybe you need some of them?::

    yum list available --disablerepo=* --enablerepo=fys_el

  **Note**: on el `configure external repositories <https://wiki.fysik.dtu.dk/niflheim/Cluster_software_-_RPMS#configure-external-repos>`_
  as installation of most packages requires enabling `epel` or `atrpms` repositories::

    yum -y install --enablerepo=fys_el,epel,atrpms campos-dacapo
  
  **Note**: most of the `fys` packages are relocatable with the default prefix of `/usr`.
  As an example one installs campos-dacapo into the `/opt/campos-dacapo-2.7.16` prefix as follows::

    mkdir fys && cd fys # fys directory stores downloaded RPMS
    yumdownloader --resolve --enablerepo=fys_el,epel,atrpms campos-dacapo-2.7.16
    mkdir tmp && mv campos-dacapo-2.7.16* tmp
    yum -y localinstall *
    rpm -ivh --relocate "/usr"="/opt/campos-dacapo-2.7.16" tmp/campos-dacapo-*
    mv tmp/campos-dacapo-* . && rmdir tmp

  Have a look at the `/opt/campos-dacapo-2.7.16/share/campos-dacapo/\*.\*sh`
  to see what environment variables need to be set in case of an installation
  into a non-default prefix. There is also a template modulefile
  `/opt/campos-dacapo-2.7.16/share/campos-dacapo/campos-dacapo-2.7.16\*`
  that contains \`prereq\`ired modules (modulefiles surely are different on your system).

  On systems where you don't have root access you can consider downloading RPMS individually and extracting
  the contents of the RPMS, for example::

    mkdir ~/fys && cd ~/fys
    rpm2cpio http://packages/pub/linux/fys/el/5/x86_64/campos-dacapo-pseudopotentials-1-2.el5.fys.noarch.rpm | cpio -idmv

Configure external repos
========================

On openSUSE, as root:

-  enable the packman repository as described at http://opensuse-community.org/Repositories/Packman

-  add `multimedia:/photo` repository, e.g. for opensuse-11.2::

     zypper addrepo --repo http://download.opensuse.org/repositories/multimedia:/photo/openSUSE_11.2/multimedia:photo.repo # python-sphinx is there!!!

On RedHat Enterprise Linux or CentOS, as root:

- create yum repository definitions (do **not** enable them):

 - `ATrpms <http://atrpms.net/>`_:

   - official way: follow `ATrpms installation instructions <http://atrpms.net/install.html>`_ and edit `/etc/yum.repos.d/atrpms.repo`
     so it contains::

       enabled=0

   - fast way::

       echo '[atrpms]' > /etc/yum.repos.d/atrpms.repo
       echo 'name=CentOS $releasever - $basearch - ATrpms' >> /etc/yum.repos.d/atrpms.repo
       echo 'baseurl=http://dl.atrpms.net/el$releasever-$basearch/atrpms/stable' >> /etc/yum.repos.d/atrpms.repo
       echo '#baseurl=http://mirrors.ircam.fr/pub/atrpms/el$releasever-$basearch/atrpms/stable' >> /etc/yum.repos.d/atrpms.repo
       echo 'gpgkey=http://ATrpms.net/RPM-GPG-KEY.atrpms' >> /etc/yum.repos.d/atrpms.repo
       echo 'gpgcheck=1' >> /etc/yum.repos.d/atrpms.repo
       echo 'enabled=0' >> /etc/yum.repos.d/atrpms.repo

 - `EPEL <http://fedoraproject.org/wiki/EPEL>`_:

   - official way: follow `EPEL/FAQ/howtouse <http://fedoraproject.org/wiki/EPEL/FAQ#howtouse>`_ and edit `/etc/yum.repos.d/epel.repo`
     so it contains::

       enabled=0

   - fast way::
   
       echo '[epel]' > /etc/yum.repos.d/epel.repo
       echo 'name=CentOS $releasever - $basearch - EPEL' >> /etc/yum.repos.d/epel.repo
       echo 'baseurl=http://download.fedora.redhat.com/pub/epel/$releasever/$basearch' >> /etc/yum.repos.d/epel.repo
       echo 'gpgkey=http://download.fedora.redhat.com/pub/epel/RPM-GPG-KEY-EPEL' >> /etc/yum.repos.d/epel.repo
       echo 'gpgcheck=1' >> /etc/yum.repos.d/epel.repo
       echo 'enabled=0' >> /etc/yum.repos.d/epel.repo
-Line 28:
+Line 125:
-   yum install yum-utils
+   yum install yum-utils wget
-Line 33:
+Line 130:
-- configure rpmbuild (as rpmbuild):

  - enable modules - add to `~/.bashrc`::

     if [ -r "/home/camp/modulefiles.sh" ]; then
         source /home/camp/modulefiles.sh
+Configure rpmbuild
==================

- create and retrieve the `rpmbuild` project (as **rpmbuild** user)::

    cd
    svn co https://svn.fysik.dtu.dk/projects/rpmbuild/trunk ~/rpmbuild

- include the rpmbuild environment configuration script in `~/.bashrc`:

 - copy the script::

     cp ~/rpmbuild/SOURCES/.bashrc_rpmbuild ~/

   **Note**: if installing on a system different than el5 edit the `rpm_platform` and `egg_info` variables.

 - and add the following to `~/.bashrc`::

     if [ -r "${HOME}/.bashrc_rpmbuild" ]; then
         . ${HOME}/.bashrc_rpmbuild
-Line 41:
+Line 153:
-  - set the `FYS_PLATFORM` variable::

     export FYS_PLATFORM=Intel-Nehalem-el5 # thul
     export FYS_PLATFORM=AMD-Opteron-el5 # fjorm

    **Note** that this variable will be set automatically by `/home/camp/modulefiles.sh` after
    the `environment-modules` package is installed.

  - use the following ~rpmbuild/.rpmmacros::

     %disttag        el5.fys

     %packager       rpmbuild@fysik.dtu.dk
     %distribution   Fysik RPMS
     %vendor         Fysik RPMS <rpm@fysik.dtu.dk>

     %_signature     gpg
     %_gpg_path      ~/.gnupg
     %_gpg_name      Fysik RPMS

     %_topdir        /home/camp/rpmbuild/%(echo $FYS_PLATFORM)
     %_rpmdir        %{_topdir}/RPMS
     %_srcrpmdir     %{_topdir}/SRPMS
     %_svndir        /home/camp/rpmbuild/rpmbuild
     %_specdir       %{_svndir}/SPECS
     %_sourcedir     %{_svndir}/SOURCES
     %_rpmfilename   %%{NAME}-%%{VERSION}-%%{RELEASE}.%%{ARCH}.rpm
     %_builddir      /scratch/rpmbuild
     %_tmppath      %{_topdir}/BUILD

     # no debuginfo
     %debug_package %{nil}

     # don't strip (this does not fully work)
     # https://bugzilla.redhat.com/show_bug.cgi?id=219731
     %define __strip /bin/true

     %niflheim       1

  - as rpmbuild create directories::

     mkdir -p ~/${FYS_PLATFORM}/RPMS
     mkdir -p ~/${FYS_PLATFORM}/SRPMS
     mkdir -p ~/${FYS_PLATFORM}/BUILD
     mkdir -p ~/${FYS_PLATFORM}/SPECS # needed only by openmpi
     mkdir -p ~/${FYS_PLATFORM}/SOURCES # needed only by openmpi

- install official packages, as rpmbuild::
+   **Note** on Niflheim the variables::

       export FYS_PLATFORM=Intel-Nehalem-el5 # thul
       export FYS_PLATFORM=AMD-Opteron-el5 # fjorm

   will be set automatically by `/home/camp/modulefiles.sh`
   if the `environment-modules` package is installed.

- create temporary directory::

   mkdir -p /scratch/$USER

- apply settings from `~/.bashrc` by::

   . ~/.bashrc

- use the following ~rpmbuild/.rpmmacros::

    cp ~/rpmbuild/SOURCES/.rpmmacros ~/

- create directories::

    mkdir -p ~/${FYS_PLATFORM}/{RPMS,SRPMS,BUILD}
    mkdir -p ~/${FYS_PLATFORM}/{SPECS,SOURCES} # needed only by openmpi

Install external packages
=========================

- download official packages, as rpmbuild::
-Line 92:
+Line 185:
-   yumdownloader --resolve gcc-gfortran gcc43-c++ gcc43-gfortran blas-devel lapack-devel python-devel
+   # packages from other distributions
   yumdownloader --resolve texlive-latex emacs-auctex tex-preview # Fedora
   yast -i Modules texlive-latex emacs-auctex # openSUSE
   yast -i python-gtk python-xml python-lxml # openSUSE
   yast -i python-matplotlib python-numpy # openSUSE
   yast -i gcc-fortran gcc44-fortran libgfortran44 # openSUSE-11.2
   yast -i openmpi-devel blas lapack # openSUSE
   # el5 packages
   yumdownloader --resolve emacs binutils-devel glib-devel libstdc++-devel
   yumdownloader --resolve gcc-gfortran blas-devel lapack-devel python-devel python-sphinx
-Line 95:
+Line 197:
-   yumdownloader --resolve pygtk2-devel gtk2-devel tk-devel agg ghostscript libtiff-devel
   yumdownloader --resolve libX11-devel libXext-devel openmotif openmotif-devel
+   yumdownloader --resolve pygtk2-devel gtk2-devel tk-devel agg ghostscript libtiff-devel xterm
   yumdownloader --resolve libX11-devel libXext-devel openmotif openmotif-devel gd-devel libXpm-devel
   yumdownloader --resolve compat-libstdc++-33 # for mathematica
   yumdownloader --resolve MySQL-python # for CMR
   yumdownloader --resolve perl-XML-SAX # for exciting
   yumdownloader --resolve ImageMagick # for ASE3

   yumdownloader --resolve gcc43-c++ gcc43-gfortran # only on EL5 == 5.2
-Line 99:
+Line 207:
-- install `atrpms` packages, as rpmbuild (``vtk-python`` is currently unavailable 16 Apr 2009)::
+- download `atrpms` packages, as rpmbuild (``vtk-python`` is currently unavailable 16 Apr 2009)::
-Line 107:
+Line 215:
-- install the packages from `epel`, as rpmbuild::
+- download the packages from `epel`, as rpmbuild::
-Line 110:
+Line 218:
-   yumdownloader --resolve --enablerepo=epel jmol
+   yumdownloader --resolve --enablerepo=epel jmol gsl-devel python-lxml
-Line 116:
+Line 224:
-- remove default openmpi::
+- on Niflheim **only**: remove default openmpi::
-Line 122:
+Line 230:
-   exclude=netcdf-* netcdf3-* fftw-* fftw2-* fftw3-* python-numeric openmpi-*

- logout and login (as rpmbuild) again to activate modules settings from `~/.bashrc`.
+   exclude=netcdf-* netcdf3-* fftw-* fftw2-* fftw3-* python-numeric openmpi-* libgfortran4* gcc4* libstdc++4* libgomp-* ScientificPython-*
-Line 129:
+Line 235:
-As rpmbuild::

 cd ~/rpmbuild/SPECS

Install `Install Open64 Compiler Suite <http://www.open64.net/>`_ RPM, and deploy module file under ` ~rpmbuild/modulefiles/${FYS_PLATFORM}/open64`.
+compilers and tools
-------------------

open64
++++++

Install (on the login and computes nodes) `Install Open64 Compiler Suite <http://www.open64.net/>`_ RPM (available under `~rpmbuild/${FYS_PLATFORM}/RPMS/external/prefix`),
and deploy module file under ` ~rpmbuild/modulefiles/${FYS_PLATFORM}/open64`.
-Line 138:
+Line 247:
-Note that the module file is available as svn checkout at https://svn.fysik.dtu.dk/projects/modulefiles/trunk.
+The module file is available as svn checkout at https://svn.fysik.dtu.dk/projects/modulefiles/trunk.
-Line 145:
+Line 254:
-Install icc/ifort compilers, install only the following packages from `l_cproc_p_11.1.046_intel64`::

 intel-cproc046-11.1-1.x86_64.rpm
 intel-cproidb046-11.1-1.x86_64.rpm
 intel-cprolib046-11.1-1.x86_64.rpm
 intel-cprolibdev046-11.1-1.x86_64.rpm
 intel-cprotbblib046-11.1-1.noarch.rpm
 intel-cprotbblibdev046-11.1-1.noarch.rpm
 intel-cprocsdk046-11.1-1.noarch.rpm
 intel-cproidbsdk046-11.1-1.noarch.rpm

and from `l_cprof_p_11.1.046_intel64`::

 intel-cprof046-11.1-1.x86_64.rpm
 intel-cproflib046-11.1-1.x86_64.rpm
 intel-cprofsdk046-11.1-1.noarch.rpm

, enable them (only on **thul**)::

 . /opt/intel/Compiler/11.1/046/bin/intel64/ifortvars_intel64.sh
 . /opt/intel/Compiler/11.1/046/bin/intel64/iccvars_intel64.sh

Build intel compatibility packages (only on **thul**)::

  rpmbuild -bb --with modules intel-redist.spec

**Note**: do not install the resulting RPMS on the login node. They need to be installed **only** on compute nodes.
+g95
+++

Install (on the login and computes nodes) `g95 <http://www.g95.org/>`_ RPM (available under `~rpmbuild/${FYS_PLATFORM}/RPMS/external/prefix`),
and deploy module file under ` ~rpmbuild/modulefiles/${FYS_PLATFORM}/g95`.
Install using **--relocate** option::

  rpm -ivh --relocate "/usr/local"="/opt/g95/0.91" g95-0.91-4.x86_64.rpm

The module file is available as svn checkout at https://svn.fysik.dtu.dk/projects/modulefiles/trunk.
**Note**: the module file should contain at least (do **not** add the lib directory to LD_LIBRARY_PATH)::

  prepend-path     PATH /opt/g95/0.91/lib/gcc-lib/x86_64-unknown-linux-gnu/4.0.3
  prepend-path     PATH /opt/g95/0.91/bin

intel
+++++

**Note**: to enable new intell products upgrading of licenses may be necessary, see
http://software.intel.com/en-us/articles/workaround-non-upgraded-serial-numbers-disappear-from-the-intel-registration-center-irc-list/

**Note**: intel changes packaging quite often, here are the installation instructions for the **12.0** compilers:

- install RPMS (**only** on the login node) found in `l_ccompxe_2011.1.107` manually (using ``rpm -ivh``)::

    intel-{compilerpro,idb,idbcdt,ipp,sourcechecker,tbb}*noarch* # exclude intel-compilerpro-common if installed already by mkl
    intel-{compilerpro,idb,ipp,sourcechecker}*x86_64*

  and from `l_fcompxe_2011.1.107`::

    intel-compilerprof*{noarch,x86_64}*

- create a link (only on **thul**)::

    mkdir -p /opt/intel/Compiler/2011.1
    cd /opt/intel/Compiler/2011.1 && ln -s /opt/intel/composerxe-2011.1.107 107

- build intel compatibility packages (only on **thul**)::

    cd ~/rpmbuild/SPECS
    rpmbuild -bb ${modules_usage} --with major_version=2011 --with version1=1 --with version2=107 intel-redist.spec

**Note**: do not install the RPMS generated in the last step on the login node. They need to be installed **only** on compute nodes.
-Line 177:
+Line 302:
-  cp /scratch/rpmbuild/intel-11.1.046/11.1.046-1.intel64.el5.fys ~rpmbuild/modulefiles/${FYS_PLATFORM}/ifort
+  cp /scratch/rpmbuild/intel-2011.1.107/2011.1.107-1.intel64${disttag} ~rpmbuild/modulefiles/${FYS_PLATFORM}/ifort
-Line 179:
+Line 304:
-  ln -s 11.1.046-1.intel64.el5.fys 11.1-1
+  ln -s 2011.1.107-1.intel64${disttag} 12.0-1

**Note**: modify the file so it contains at least::

  setenv INTEL_LICENSE_FILE /opt/intel/licenses

  # generated by intel-redist.spec and installed on compute nodes
  prepend-path    LD_LIBRARY_PATH      /opt/intel/Compiler/2011.1/107/lib/intel64
  # original locations from intel
  prepend-path    LD_LIBRARY_PATH      /opt/intel/composerxe-2011.1.107/compiler/lib/intel64
  prepend-path    LD_LIBRARY_PATH      /opt/intel/composerxe-2011.1.107/debugger/lib/intel64
  prepend-path    PATH                 /opt/intel/composerxe-2011.1.107/bin/intel64
  prepend-path    MANPATH              :
  prepend-path    MANPATH              /opt/intel/composerxe-2011.1.107/man
  # ipp
  prepend-path    PATH                 /opt/intel/composerxe-2011.1.107/ipp/bin/intel64
  prepend-path    LD_LIBRARY_PATH      /opt/intel/composerxe-2011.1.107/ipp/lib/intel64
  # sourcechecker
  prepend-path    PATH                 /opt/intel/composerxe-2011.1.107/bin/sourcechecker/bin/intel64
  prepend-path    LD_LIBRARY_PATH      /opt/intel/composerxe-2011.1.107/bin/sourcechecker/lib/intel64


**Note**: intel changes packaging quite often, here are the installation instructions for the **11.1** compilers:

- install RPMS (**only** on the login node) found in `l_cproc_p_11.1.046_intel64` manually (using ``rpm -ivh``)::

    intel-cproc046-11.1-1.x86_64.rpm
    intel-cproidb046-11.1-1.x86_64.rpm
    intel-cprolib046-11.1-1.x86_64.rpm
    intel-cprolibdev046-11.1-1.x86_64.rpm
    intel-cprotbblib046-11.1-1.noarch.rpm
    intel-cprotbblibdev046-11.1-1.noarch.rpm
    intel-cprocsdk046-11.1-1.noarch.rpm
    intel-cproidbsdk046-11.1-1.noarch.rpm

  and from `l_cprof_p_11.1.046_intel64`::

    intel-cprof046-11.1-1.x86_64.rpm
    intel-cproflib046-11.1-1.x86_64.rpm
    intel-cprofsdk046-11.1-1.noarch.rpm

- enable them (only on **thul**)::

    . /opt/intel/Compiler/11.1/046/bin/intel64/ifortvars_intel64.sh
    . /opt/intel/Compiler/11.1/046/bin/intel64/iccvars_intel64.sh

- build intel compatibility packages as rpmbuild (only on **thul**)::

    cd ~/rpmbuild/SPECS
    rpmbuild -bb ${modules_usage} intel-redist.spec

**Note**: do not install the RPMS generated in the last step on the login node. They need to be installed **only** on compute nodes.
On the login node only the module file needs to be deployed under `~rpmbuild/modulefiles`, as rpmbuild.
Note that this directory is available as svn checkout at https://svn.fysik.dtu.dk/projects/modulefiles/trunk.
Here is what need to be done for a new version of the package::

  mkdir ~rpmbuild/modulefiles/${FYS_PLATFORM}/ifort
  cp /scratch/rpmbuild/intel-11.1.046/11.1.046-1.intel64${disttag} ~rpmbuild/modulefiles/${FYS_PLATFORM}/ifort
  cd ~rpmbuild/modulefiles/${FYS_PLATFORM}/ifort
  ln -s 11.1.046-1.intel64${disttag} 11.1-1 # version < 12
  ln -s 2011.1.107-1.intel64${disttag} 2011.1.107-1
-Line 184:
+Line 369:
+  prepend-path    LD_LIBRARY_PATH      /opt/intel/Compiler/11.1/046/idb/lib/intel64
-Line 185:
+Line 371:
+  prepend-path    MANPATH              :
-Line 187:
+Line 374:
-Install mkl, and build mkl compatibility package (only on **thul**)::
+**Note**: intel changes packaging quite often, here are the installation instructions for the **10.1.015** compilers:

- install RPMS (on the login and compute nodes) found in `l_cc_p_10.1.015_intel64.tar.gz` and `l_fc_p_10.1.015_intel64.tar.gz` manually (using ``rpm -ivh``)::

    intel-icce101015-10.1.015-1.em64t.rpm
    intel-iidbe101015-10.1.015-1.em64t.rpm
    intel-isubhe101015-10.1.015-1.em64t.rpm
    intel-iforte101015-10.1.015-1.em64t.rpm

- replace the installation path in the scripts (action necessary only on the login node)::

   files=`grep "<INSTALLDIR>" -r /opt/intel/cce/ | cut -d":" -f 1 | uniq`
   for file in $files;
   do
       echo $file
       sed -i 's#<INSTALLDIR>#/opt/intel/cce/10.1.015#g' $file
   done
   files=`grep "<INSTALLDIR>" -r /opt/intel/fce/ | cut -d":" -f 1 | uniq`
   for file in $files;
   do
       echo $file
       sed -i 's#<INSTALLDIR>#/opt/intel/fce/10.1.015#g' $file
   done
   files=`grep "<INSTALLDIR>" -r /opt/intel/idbe/ | cut -d":" -f 1 | uniq`
   for file in $files;
   do
       echo $file
       sed -i 's#<INSTALLDIR>#/opt/intel/idbe/10.1.015#g' $file
   done

- provide the module file `~rpmbuild/modulefiles/${FYS_PLATFORM}/ifort/10.1.015-1.intel64${disttag}`::

    prepend-path    LD_LIBRARY_PATH      /opt/intel/cce/10.1.015/lib
    prepend-path    LD_LIBRARY_PATH      /opt/intel/fce/10.1.015/lib

    prepend-path    PATH                 /opt/intel/cce/10.1.015/bin
    prepend-path    PATH                 /opt/intel/fce/10.1.015/bin
    prepend-path    PATH                 /opt/intel/idbe/10.1.015/bin
    prepend-path    MANPATH              :
    prepend-path    MANPATH              /opt/intel/cce/10.1.015/man
    prepend-path    MANPATH              /opt/intel/fce/10.1.015/man
    prepend-path    MANPATH              /opt/intel/idbe/10.1.015/man

  and the link::

    cd ~rpmbuild/modulefiles/${FYS_PLATFORM}/ifort
    ln -s 10.1.015-1.intel64${disttag} 10.1-1

**Moreover**: `intel-*intel64*` RPMS need to be installed with *--nodeps*, so move them into a special directory::

  mkdir -p ~/${FYS_PLATFORM}/RPMS/nodeps
  mv ~/${FYS_PLATFORM}/RPMS/intel-*intel64* ~/${FYS_PLATFORM}/RPMS/nodeps

intel mkl
+++++++++

Install mkl RPMS `intel-mkl-*`, `intel-openmp-*`, `intel-compilerpro-*` (`intel-mkl`, `intel-mkllibdev`, `intel-mkllib` for mkl version < 10.3), and build mkl compatibility package (only on **thul**)::

  # for mkl 10.3, as root
  cd /opt/intel/mkl # packaging of mkl changes again so link is necessary
  ln -s ../composerxe-2011.3.174/mkl/ 10.3.3.174
  ln -s /opt/intel/composerxe-2011.3.174/man 10.3.3.174/man
  # as rpmbuild
-Line 190:
+Line 438:
-  export mkl=10.1.3.027
+  export mkl=10.3.3.174
-Line 193:
+Line 441:
-  cp -rp /opt/intel/mkl/${mkl}/doc ${mkl}
+  cp -rpf /opt/intel/mkl/${mkl}/doc ${mkl} # for mkl < 10.3
  cp -rpf /opt/intel/composerxe-2011.3.174/compiler/lib ${mkl} # for mkl >= 10.3
-Line 196:
+Line 445:
-  cd ~/rpmbuild/SPECS
  rpmbuild -bb --with version1=1 --with version2=3 --with version3=027 --with modules intel-redist-mkl.spec
+  cd ~/rpmbuild/SPECS # as rpmbuild
  rpmbuild -bb --with version1=3 --with version2=3 --with version3=174 ${modules_usage} --with platform=intel64 intel-redist-mkl.spec
  # **Warning**: mkl < 10.3 uses em64t
  rpmbuild -bb --with version1=1 --with version2=3 --with version3=027 ${modules_usage} intel-redist-mkl.spec
-Line 205:
+Line 456:
-  cp /tmp/intel-mkl-${mkl}/${mkl}-1.el5.fys.em64t ~rpmbuild/modulefiles/${FYS_PLATFORM}/mkl
+  cp /tmp/intel-mkl-${mkl}/${mkl}-1${disttag}.em64t ~rpmbuild/modulefiles/${FYS_PLATFORM}/mkl
-Line 207:
+Line 458:
-  ln -s ${mkl}-1.el5.fys.em64t 10.1p-027
+  ln -s ${mkl}-1${disttag}.em64t 10.1p-027
-Line 212:
+Line 463:
-**Moreover**: `intel-*intel64*` RPMS need to be installed with *--nodeps*, so move them into a special directory::

  mkdir -p ~/${FYS_PLATFORM}/RPMS/nodeps
  mv ~/${FYS_PLATFORM}/RPMS/intel-*intel64* ~/${FYS_PLATFORM}/RPMS/nodeps
-Line 229:
+Line 475:
+Unfortunately, from 10.3 version mkl depends on intel libraries located in directories outside of mkl.
This causes troubles for numpy which requires (is there a way to fix that?) all non-standard libraries to be located in one directory.
Therefore one may need to create a link (currently not performed)::

  cd /opt/intel/mkl/10.3.4.191/lib/intel64
  ln -s /opt/intel/composerxe-2011.4.191/compiler/lib/intel64/libiomp5.so .

openmpi
-------
-Line 231:
+Line 487:
-  export rpmtopdir=${HOME}/${FYS_PLATFORM} # set this to _topdir value from ~/.rpmmacros
+  # openmpi-1.4.3
  wget http://www.open-mpi.org/software/ompi/v1.4/downloads/openmpi-1.4.3.tar.bz2 \
       -O ~/rpmbuild/SOURCES/openmpi-1.4.3.tar.bz2
  module load open64/4.2.4-0
  sh ./buildrpm-1.4.3-1.open64.4.2.4.sh ../SOURCES/openmpi-1.4.3.tar.bz2 2>&1 | tee buildrpm-1.4.3-1.open64.4.2.4.sh.log.${FYS_PLATFORM}
  module unload open64/4.2.4-0
  module load ifort/12.0-4
  sh ./buildrpm-1.4.3-1.ifort.12.0.4.sh ../SOURCES/openmpi-1.4.3.tar.bz2 2>&1 | tee buildrpm-1.4.3-1.ifort.12.0.4.sh.log.${FYS_PLATFORM} # thul only
  module unload ifort/12.0-4

  # openmpi-1.3.3
-Line 237:
+Line 503:
-  sh ./buildrpm-1.3.3-1.ifort.sh ../SOURCES/openmpi-1.3.3.tar.bz2 2>&1 | tee buildrpm-1.3.3-1.ifort.sh.log.${FYS_PLATFORM} # thul only
  module load open64 # 24 June 2009: build fails on Nehalem with *configure: error: TM support requested but not found.  Aborting*
  sh ./buildrpm-1.3.3-1.open64.sh ../SOURCES/openmpi-1.3.3.tar.bz2 2>&1 | tee buildrpm-1.3.3-1.open64.sh.log.${FYS_PLATFORM}
+  sh ./buildrpm-1.3.3-1.ifort.11.0.sh ../SOURCES/openmpi-1.3.3.tar.bz2 2>&1 | tee buildrpm-1.3.3-1.ifort.11.0.sh.log.${FYS_PLATFORM} # thul only
  sh ./buildrpm-1.3.3-1.ifort.11.1.sh ../SOURCES/openmpi-1.3.3.tar.bz2 2>&1 | tee buildrpm-1.3.3-1.ifort.11.1.sh.log.${FYS_PLATFORM} # thul only
  module load g95
  sh ./buildrpm-1.3.3-1.g95.sh ../SOURCES/openmpi-1.3.3.tar.bz2 2>&1 | tee buildrpm-1.3.3-1.g95.sh.log.${FYS_PLATFORM} # fjorm only
  module unload g95
  module load open64/4.2.1-0 # 24 June 2009: build fails on Nehalem with *configure: error: TM support requested but not found.  Aborting*
  sh ./buildrpm-1.3.3-1.open64.4.2.1.sh ../SOURCES/openmpi-1.3.3.tar.bz2 2>&1 | tee buildrpm-1.3.3-1.open64.4.2.1.sh.log.${FYS_PLATFORM}
  module unload open64/4.2.1-0
  module load open64/4.2.3-0 # 24 June 2009: build fails on Nehalem with *configure: error: TM support requested but not found.  Aborting*
  sh ./buildrpm-1.3.3-1.open64.4.2.3.sh ../SOURCES/openmpi-1.3.3.tar.bz2 2>&1 | tee buildrpm-1.3.3-1.open64.4.2.3.sh.log.${FYS_PLATFORM}
  module unload open64/4.2.3-0
-Line 243:
+Line 517:
-  rpm -ivh --nodeps --oldpackage ~rpmbuild/${FYS_PLATFORM}/RPMS/openmpi-1.3.3-1.el5.fys.ifort.11.1.x86_64.rpm 

If scripts that contain **ALL** build/install/uninstall commands (``global_install.sh`` and ``global_uninstall.sh``) need to be created,
every time after an RPM is successfully built, do::

    grep -v "#\!" install.sh >> ~/${FYS_PLATFORM}/global_install.sh
    cat uninstall.sh ~/${FYS_PLATFORM}/global_uninstall.sh | grep -v "#\!" >> ~/${FYS_PLATFORM}/global_uninstall.sh.tmp && mv -f ~/${FYS_PLATFORM}/global_uninstall.sh.tmp ~/${FYS_PLATFORM}/global_uninstall.sh
    # ignore "cat: .../global_uninstall.sh: No such ..." error when running first time

**Note** that `global_uninstall.sh` won't remove built RPM files, just will uninstall the packages.

Build the following for dacapo:
-------------------------------

- set the disttag variable for convenience::

   export disttag="el5.fys"
   modules=1

- acml::

    version1=0
    version2=1
    compiler=gfortran

    version1=0
    version2=1
    compiler=pathscale

    version1=1
    version2=0
    compiler=gfortran43 # fjorm only

    version1=1
    version2=0
    compiler=pathscale

    version1=2
    version2=0
    compiler=gfortran43

    version1=2
    version2=0
    compiler=pathscale

    version1=2
    version2=0
    compiler=ifort # thul only

    version1=3
    version2=0
    compiler=gfortran43

    version1=3
    version2=0
    compiler=open64 # fjorm only

    version1=3
    version2=0
    compiler=ifort # thul only

    rpmbuild -bb --with compiler=${compiler} --with version1=${version1} --with version2=${version1} \
                 --with modules=${modules} --with default_version acml.spec

- goto (only on **fjorm**)::
+  rpm -ivh --nodeps --oldpackage ~rpmbuild/${FYS_PLATFORM}/RPMS/openmpi-1.3.3-1${disttag}.ifort.11.1.x86_64.rpm 

acml
----

  **Note** this package is **not** relocatable!

  `AMD Core Math Library <http://developer.amd.com/acml.jsp>`_ contains optimized BLAS and LAPACK libraries
  for AMD opteron processors (work also on intel), and is available for download after registration.

  Build the following RPMS::

    . fys.set.Niflheim.gfortran.4.1.2.sh
    . fys.set.blas.acml.4.0.1.sh

    . fys.build.acml.sh
    #
    . fys.set.Niflheim.pathscale.3.2.sh
    . fys.set.blas.acml.4.0.1.sh

    . fys.build.acml.sh
    #
    . fys.set.Niflheim.gfortran43.4.3.2.sh
    . fys.set.blas.acml.4.3.0.sh

    . fys.build.acml.sh
    #
    . fys.set.Niflheim.gfortran43.4.3.2.sh
    . fys.set.blas.acml.4.3.0_mp.sh

    . fys.build.acml.sh

    #
    . fys.set.Niflheim.gfortran43.4.3.2.sh
    . fys.set.blas.acml.4.4.0.sh

    . fys.build.acml.sh

    #
    . fys.set.Niflheim.ifort.11.0.sh
    . fys.set.blas.acml.4.4.0.sh

    . fys.build.acml.sh
    #
    . fys.set.Niflheim.open64.4.2.3.sh
    . fys.set.blas.acml.4.4.0.sh

    . fys.build.acml.sh



  **Note** problems with `dgemm <http://developer.amd.com/cpu/Libraries/acml/downloads/assets/ReleaseNotes.txt>`_ acml 4.1.0 and 4.2.0 have been reported.
  Moreover campos-dacapo_ built with **acml-4-1-0-pathscale-64bit.tgz** fails with "ZINSC 2 returned info= 2"
  for the following job::

    #!/usr/bin/env python
    from Dacapo import Calculator
    from ASE.IO.xyz import ReadXYZ
    from ASE.Dynamics.Langevin import Langevin

    prefix = 'D'
    atoms = ReadXYZ('32H2O.xyz')
    L = 9.8553729
    atoms.SetUnitCell([L, L, L], fix=True)
    atoms.SetBoundaryConditions(True)
    r = 1
    atoms = atoms.Repeat([r, r, r])
    n = 48 * r
    calc = Calculator(nbands=128 * r**3, planewavecutoff=350,
                      densitycutoff=500, xc='PBE')
    atoms.SetCalculator(calc)

    from time import time
    atoms.GetPotentialEnergy()
    pos=atoms[0].GetCartesianPosition()
    atoms[0].SetCartesianPosition(pos+0.005)
    t0=time()
    atoms.GetPotentialEnergy()
    print time()-t0

  Download 32H2O.xyz_

goto
----

  `GotoBLAS <http://www.tacc.utexas.edu/tacc-projects/gotoblas2/>`_ contains optimized BLAS libraries.

  Download **GotoBLAS-1.26.tar.gz** (**Warning** outdated release of GotoBLAS is no longer available) and  **GotoBLAS2-1.13_bsd.tar.gz** (supports Nehalem) to ~/rpmbuild/SOURCES.
  The default build process searches your $PATH for available compilers.
  Priority order is PathScale, PGI, Intel, gfortran, g95 and g77,
  therefore setting compilers explicitly is needed.

  On a custom system build the following RPMS::

    . fys.set.gfortran.default.sh

    (rpm_prefix=/usr && . fys.build.goto2.sh)

  On Niflheim build RPMS (on the **target** compute node!) using the following command::

    . fys.set.Niflheim.gfortran.4.1.2.sh

    . fys.build.goto2.sh

    #
    . fys.set.Niflheim.gfortran43.4.3.2.sh

    . fys.build.goto2.sh

    #
    . fys.set.Niflheim.open64.4.2.3.sh

    . fys.build.goto2.sh

    #
    . fys.set.Niflheim.open64.4.2.4.sh

    . fys.build.goto2.sh

    # older version of goto
    #
-Line 310:
+Line 639:
-    compiler=gfortran
    compiler_version=4.1.2
    compiler_libdir=/usr/lib64
    compiler_bindir=/usr/bin

    compiler=gfortran43
    compiler_version=4.3.2
    compiler_libdir=/usr/lib64
    compiler_bindir=/usr/bin

    compiler=pathscale
    compiler_version=3.2
    compiler_libdir=/opt/pathscale/lib/3.2
    compiler_bindir=/opt/pathscale/bin

    compiler=open64 # only on fjorm
    compiler_version=4.2.1
    compiler_libdir=/opt/open64/4.2.1/lib/gcc-lib/x86_64-open64-linux/4.2.1
    compiler_bindir=/opt/open64/4.2.1/bin

    rpmbuild --bb --with compiler=${compiler} --with compiler_version=${compiler_version} \
                  --with compiler_libdir=${compiler_libdir} --with compiler_bindir=${compiler_bindir} \
                  --with modules=${modules} --with default_version=1 \
                  --with prefix=/opt/goto/${blas_version}/1.${disttag}.${compiler}.${compiler_version}.smp goto.spec
+    . fys.set.Niflheim.gfortran.4.1.2.sh

    . fys.build.goto.sh

    #
    blas_version=1.26
    . fys.set.Niflheim.gfortran43.4.3.2.sh

    . fys.build.goto.sh

    #
    blas_version=1.26
    . fys.set.Niflheim.pathscale.3.2.sh

    . fys.build.goto.sh
    #
    blas_version=1.26
    . fys.set.Niflheim.open64.4.2.1.sh

    . fys.build.goto.sh
    #
    blas_version=1.26
    . fys.set.Niflheim.open64.4.2.3.sh

    . fys.build.goto.sh
-Line 340:
+Line 669:
-- atlas::
+atlas
-----

  **Note** this package is **not** relocatable!

  On a custom system build the following RPMS::
-Line 343:
+Line 677:
-    compiler=gfortran
    compiler_version=4.1.2
    compiler_libdir=/usr/lib64
    compiler_bindir=/usr/bin

    compiler=gfortran43
    compiler_version=4.3.2
    compiler_libdir=/usr/lib64
    compiler_bindir=/usr/bin

    rpmbuild --bb --with compiler=${compiler} --with compiler_version=${compiler_version} \
                  --with compiler_libdir=${compiler_libdir} --with compiler_bindir=${compiler_bindir} \
                  --with modules=${modules} --with default_version=1 \
                  --with prefix=/opt/atlas/${blas_version}/1.${disttag}.${compiler}.${compiler_version} atlas.spec
+    . fys.set.gfortran.default.sh
    (rpm_prefix=/usr/local/atlas && default_version_usage="--with default_version" && . fys.build.atlas.sh)

  On Niflheim build the following RPMS::

    blas_version=3.8.3
    . fys.set.Niflheim.gfortran.4.1.2.sh

    . fys.build.atlas.sh

    #
    blas_version=3.8.3
    . fys.set.Niflheim.gfortran43.4.3.2.sh

    . fys.build.atlas.sh
-Line 363:
+Line 697:
-- `campos-dacapo-pseudopotentials <https://wiki.fysik.dtu.dk/niflheim/Cluster_software_-_RPMS#campos-dacapo-pseudopotentials>`_::

    rpmbuild -bb --with modules --with default_version campos-dacapo-pseudopotentials.spec

- `rasmol <https://wiki.fysik.dtu.dk/niflheim/Cluster_software_-_RPMS#rasmol>`_::

    rpmbuild -bb --with modules --with default_version --with prefix=/opt/RasMol/2.7.3/3.${disttag} RasMol.spec

- `cblas <https://wiki.fysik.dtu.dk/niflheim/Cluster_software_-_RPMS#cblas>`_::

    compiler=gfortran
    compiler_version=4.1.2
    blas=blas
    blas_version=3.0.37.el5
    blasdir=/usr/lib64

    compiler=gfortran
    compiler_version=4.1.2
    blas=acml
    blas_version=4.0.1
    blasdir=/opt/${blas}/${blas_version}/${compiler}64/lib

    rpmbuild --bb  --with compiler=${compiler} --with compiler_version=${compiler_version} \
                   --with blas=${blas} --with blas_version=${blas_version} --with blasdir=${blasdir} \
                   --with modules=${modules} --with default_version=1 \
                   --with prefix=/opt/cblas/2.23.3/1.${disttag}.${compiler}.${compiler_version}.${blas}.${blas_version} cblas.spec

- python-setuptools::

       rpmbuild -bb --with modules --with default_version --with prefix=/opt/python-setuptools/0.6c9/1.${disttag}.python2.4 python-setuptools.spec

- python-nose::

       rpmbuild -bb --with modules --with default_version --with prefix=/opt/python-nose/0.10.4/1.${disttag}.python2.4 python-nose.spec
       module load python-setuptools
       module load python-nose

- numpy::

    compiler=gfortran
    compiler_version=4.1.2
    compiler_libdir=/usr/lib64
    compiler_bindir=/usr/bin
    blas=blas
    blas_version=3.0.37.el5
    blasdir=/usr/lib64
    lapack=lapack
    lapack_version=3.0.37.el5
    lapackdir=/usr/lib64
    cblas_prefix=/opt/cblas/2.23.3/1.${disttag}.${compiler}.${compiler_version}.${blas}.${blas_version}
    release=1.${disttag}.${compiler}.${compiler_version}.python2.4.${blas}.${blas_version}.${lapack}.${lapack_version}

    compiler=gfortran
    compiler_version=4.1.2
    compiler_libdir=/usr/lib64
    compiler_bindir=/usr/bin
    blas=acml
    blas_version=4.0.1
    blasdir=/opt/${blas}/${blas_version}/${compiler}64/lib
    lapack=acml
    lapack_version=4.0.1
    lapackdir=/opt/${blas}/${blas_version}/${compiler}64/lib
    cblas_prefix=none # dotblas fails with acml
    release=1.${disttag}.${compiler}.${compiler_version}.python2.4.${blas}.${blas_version}.${lapack}.${lapack_version}

    compiler=gfortran # Jun 23 2009: test below fails
    compiler_version=4.1.2
    compiler_libdir=/usr/lib64
    compiler_bindir=/usr/bin
    blas=mkl
    blas_version=10.1.3.027
    blasdir=/opt/intel/mkl/10.1.3.027
    lapack=mkl_lapack
    lapack_version=10.1.3.027
    lapackdir=/opt/intel/mkl/10.1.3.027
    cblas_prefix=/opt/intel/mkl/10.1.3.027
    release=1.${disttag}.${compiler}.${compiler_version}.python2.4.${blas}.${blas_version}.${lapack}.${lapack_version}

    rpmbuild --bb --with cblas_prefix=${cblas_prefix} \
                  --with blas=${blas} --with blas_version=${blas_version} --with blasdir=${blasdir} \
                  --with compiler=${compiler} --with compiler_version=${compiler_version} \
                  --with compiler_bindir=${compiler_bindir} --with compiler_libdir=${compiler_libdir} \
                  --with lapack=${lapack} --with lapack_version=${lapack_version} --with lapackdir=${lapackdir} \
                  --with modules=${modules} --with default_version=1 \
                  --with prefix=/opt/numpy/1.3.0/${release} numpy.spec

  Test with::

    module load cblas-blas-gfortran64/2.23.3-1.el5.fys.gfortran.4.1.2.blas.3.0.37.el5
    module load numpy/1.3.0-1.el5.fys.gfortran.4.1.2.python2.4.blas.3.0.37.el5.lapack.3.0.37.el5
    python -c "import numpy; from numpy.core.multiarray import dot; b = numpy.ones(13, numpy.complex); dot(b, b)"
    python -c "import numpy; numpy.test()"
    module unload numpy/1.3.0-1.el5.fys.gfortran.4.1.2.python2.4.blas.3.0.37.el5.lapack.3.0.37.el5
     
    module load acml-gfortran64/4.0.1-1.el5.fys
    module load numpy/1.3.0-1.el5.fys.gfortran.4.1.2.python2.4.acml.4.0.1.acml.4.0.1
    python -c "import numpy; from numpy.core.multiarray import dot; b = numpy.ones(13, numpy.complex); dot(b, b)"
    python -c "import numpy; numpy.test()"
    module unload numpy/1.3.0-1.el5.fys.gfortran.4.1.2.python2.4.acml.4.0.1.acml.4.0.1
    module unload acml-gfortran64/4.0.1-1.el5.fys

  Load the default numpy::

    module load numpy/1.3.0-1.el5.fys.gfortran.4.1.2.python2.4.blas.3.0.37.el5.lapack.3.0.37.el5

- `gnuplot-py <https://wiki.fysik.dtu.dk/niflheim/Cluster_software_-_RPMS#gnuplot-py>`_::

    rpmbuild -bb --with modules --with default_version --with prefix=/opt/gnuplot-py/1.8.1/1.${disttag}.python2.4 gnuplot-py.spec
+rasmol
------

  **Required by campos-ase2**.

  **Note** that rasmol is built for 32bit architecture, so make sure that your system fulfills "BuildRequires" for both 64 and 32bit::

    rpmbuild --nobuild RasMol.spec

  On a custom system build the following RPMS::

     (rpm_prefix=/usr && . fys.build.RasMol.2.7.3.sh)

  On Niflheim build the following RPMS::

     . fys.build.RasMol.2.7.3.sh

cblas
-----
 
  **Required by campos-ase2**.

  On a custom system build the following RPMS::

    . fys.set.gfortran.default.sh
    . fys.set.blas.default.sh

    (rpm_prefix=/usr && . fys.build.cblas.sh)

  On Niflheim build the following RPMS::

     . fys.set.Niflheim.gfortran.4.1.2.sh
     . fys.set.blas.acml.4.0.1.sh

     . fys.build.cblas.sh

python-setuptools
-----------------

  On a custom system build the following RPMS::

     (rpm_prefix=/usr && . fys.build.setuptools.0.6c9.sh)

  On Niflheim build the following RPMS::

    . fys.build.setuptools.0.6c9.sh

  If using modules::

    module load python-setuptools

  else, if not using the default "/usr" prefix::

    . /etc/profile.d/python-setuptools.sh

python-nose
-----------

  On a custom system build the following RPMS::

     (rpm_prefix=/usr && . fys.build.nose.0.10.4.sh)

  On Niflheim build the following RPMS::

    . fys.build.nose.0.10.4.sh

  If using modules::

    module load python-nose

  else, if not using the default "/usr" prefix::

    . /etc/profile.d/python-nose.sh

numpy
-----

  On a custom system build the following RPMS::

    . fys.set.gfortran.default.sh
    . fys.set.blas.default.sh
    . fys.set.lapack.default.sh
    . fys.set.Niflheim.cblas.2.23.3.sh

     (rpm_prefix=/usr && . fys.build.numpy.1.3.0.sh)

  On Niflheim build the following RPMS::

     module load python-setuptools
     module load python-nose

     . fys.set.Niflheim.numpy.1.3.0.gfortran.4.1.2.acml.4.0.1.cblas.none.sh

     . fys.build.numpy.1.3.0.sh

     # only on thul
     . fys.set.Niflheim.numpy.1.3.0.gfortran.4.1.2.mkl.10.1.3.027.cblas.mkl.10.1.3.027.sh

     . fys.build.numpy.1.3.0.sh

     # building using cblas/acml causes the test below to fail
     . fys.set.Niflheim.numpy.1.3.0.gfortran.4.1.2.acml.4.0.1.cblas.2.23.3.sh

     . fys.build.numpy.1.3.0.sh

  After installing python-numeric make a very rough check:

  - is using modules::

      module load ${blas}-${compiler}64/${blas_version}-1${disttag}
      module load cblas-${blas}-${compiler}64/2.23.3-1${disttag}.${compiler}.${compiler_version}.${blas}.${blas_version}
      module load numpy/1.3.0-1${disttag}.${compiler}.${compiler_version}.python${python_version}.${blas}.${blas_version}.${lapack}.${lapack_version}
      python -c "import numpy; from numpy.core.multiarray import dot; b = numpy.ones(13, numpy.complex); dot(b, b)"
      python -c "import numpy; numpy.test()"

  - else, if not using the default "/usr" prefix::

      . /etc/profile.d/numpy.sh

gnuplot-py
----------

  **Required by campos-ase2**.

  On a custom system build the following RPMS::

     (rpm_prefix=/usr && . fys.build.gnuplot-py.1.8.sh)

  On Niflheim build the following RPMS::

     . fys.build.gnuplot-py.1.8.sh

  If using modules::
-Line 474:
+Line 833:
-- `python-numeric <https://wiki.fysik.dtu.dk/niflheim/Cluster_software_-_RPMS#python-numeric>`_ (we must install **24.2** version, and we keep the default version)::
+  else, if not using the default "/usr" prefix::

    . /etc/profile.d/gnuplot-py.sh

python-numeric
--------------

  **Required by campos-ase2**.

  **Warning**: on a 64-bit machine works only with python <= 2.4.

  We must install **24.2** version, and we keep the default version::
-Line 481:
+Line 851:
-    compiler=gfortran
    compiler_version=4.1.2
    compiler_libdir=/usr/lib64
    compiler_bindir=/usr/bin
    blas=blas
    blas_version=3.0.37.el5
    blasdir=/usr/lib64
    lapack=lapack
    lapack_version=3.0.37.el5
    lapackdir=/usr/lib64
    cblas_prefix=/opt/cblas/2.23.3/1.${disttag}.${compiler}.${compiler_version}.${blas}.${blas_version}
    release=1.${disttag}.${compiler}.${compiler_version}.python2.4.${blas}.${blas_version}.${lapack}.${lapack_version}

    compiler=gfortran
    compiler_version=4.1.2
    compiler_libdir=/usr/lib64
    compiler_bindir=/usr/bin
    blas=acml
    blas_version=4.0.1
    blasdir=/opt/${blas}/${blas_version}/${compiler}64/lib
    lapack=acml
    lapack_version=4.0.1
    lapackdir=/opt/${blas}/${blas_version}/${compiler}64/lib
    cblas_prefix=/opt/cblas/2.23.3/1.${disttag}.${compiler}.${compiler_version}.${blas}.${blas_version}
    release=1.${disttag}.${compiler}.${compiler_version}.python2.4.${blas}.${blas_version}.${lapack}.${lapack_version}

    rpmbuild --bb --with cblas_prefix=${cblas_prefix} \
                  --with blas=${blas} --with blas_version=${blas_version} --with blasdir=${blasdir} \
                  --with compiler=${compiler} --with compiler_version=${compiler_version} \
                  --with compiler_bindir=${compiler_bindir} --with compiler_libdir=${compiler_libdir} \
                  --with lapack=${lapack} --with lapack_version=${lapack_version} --with lapackdir=${lapackdir} \
                  --with modules=${modules} --with default_version=1 \
                  --with prefix=/opt/python-numeric/24.2/${release} python-numeric.spec
+  On a custom system build the following RPMS::

    . fys.set.gfortran.default.sh
    . fys.set.blas.default.sh
    . fys.set.lapack.default.sh
    . fys.set.Niflheim.cblas.2.23.3.sh

    . fys.build.Numeric.24.2.sh

  On Niflheim build the following RPMS::

     . fys.set.Niflheim.Numeric.24.2.gfortran.4.1.2.acml.4.0.1.cblas.2.23.3.sh

     . fys.build.Numeric.24.2.sh
-Line 519:
+Line 870:
-  After installing python-numeric make a very rough check::

    module load python-numeric/24.2-4.el5.fys.gfortran.4.1.2.python2.4.blas.3.0.37.el5.lapack.3.0.37.el5
    python -c "import lapack_lite"
    ldd `rpm -ql python-numeric-24.2-4.el5.fys.gfortran.4.1.2.python2.4.blas.3.0.37.el5.lapack.3.0.37.el5 | grep lapack_lite.so`
    ldd `rpm -ql python-numeric-24.2-4.el5.fys.gfortran.4.1.2.python2.4.blas.3.0.37.el5.lapack.3.0.37.el5 | grep _dotblas.so`
    module unload python-numeric/24.2-4.el5.fys.gfortran.4.1.2.python2.4.blas.3.0.37.el5.lapack.3.0.37.el5

    module load acml-gfortran64/4.0.1-1.el5.fys
    module load python-numeric/24.2-4.el5.fys.gfortran.4.1.2.python2.4.acml.4.0.1.acml.4.0.1
    python -c "import lapack_lite"
    ldd `rpm -ql python-numeric-24.2-4.el5.fys.gfortran.4.1.2.python2.4.acml.4.0.1.acml.4.0.1 | grep lapack_lite.so`
    ldd `rpm -ql python-numeric-24.2-4.el5.fys.gfortran.4.1.2.python2.4.acml.4.0.1.acml.4.0.1 | grep _dotblas.so`
    module unload python-numeric/24.2-4.el5.fys.gfortran.4.1.2.python2.4.acml.4.0.1.acml.4.0.1
    module unload acml-gfortran64/4.0.1-1.el5.fys
+  After installing python-numeric make a very rough check:

  - is using modules::

      module load ${blas}-${compiler}64/${blas_version}-1${disttag}
      module load cblas-${blas}-${compiler}64/2.23.3-1${disttag}.${compiler}.${compiler_version}.${blas}.${blas_version}
      module load python-numeric/24.2-4${disttag}.${compiler}.${compiler_version}.python${python_version}.${blas}.${blas_version}.${lapack}.${lapack_version}
      python -c "import lapack_lite"
      ldd `rpm -ql python-numeric-24.2-4${disttag}.${compiler}.${compiler_version}.python${python_version}.${blas}.${blas_version}.${lapack}.${lapack_version} | grep lapack_lite.so`
      ldd `rpm -ql python-numeric-24.2-4${disttag}.${compiler}.${compiler_version}.python${python_version}.${blas}.${blas_version}.${lapack}.${lapack_version} | grep _dotblas.so`

  - else::

      . /etc/profile.d/python-numeric.sh
      python -c "import lapack_lite"
      ldd `rpm -ql python-numeric | grep lapack_lite.so`
      ldd `rpm -ql python-numeric | grep _dotblas.so`
-Line 537:
+Line 890:
-    rpm -ivh --oldpackage ~rpmbuild/${FYS_PLATFORM}/RPMS/external/python-numeric-23.*.rpm

  load the default `Numeric` version::

    module load acml-gfortran64/4.0.1-1.el5.fys
    module load python-numeric/24.2-4.el5.fys.gfortran.4.1.2.python2.4.acml.4.0.1.acml

- netcdf::

    compiler=gfortran
    compiler_version=4.1.2
    compiler_libdir=/usr/lib64
    compiler_bindir=/usr/bin

    compiler=gfortran43
    compiler_version=4.3.2
    compiler_libdir=/usr/lib64
    compiler_bindir=/usr/bin

    compiler=pathscale # only on fjorm
    compiler_version=3.2
    compiler_libdir=/opt/pathscale/lib/3.2
    compiler_bindir=/opt/pathscale/bin

    compiler=ifort  # only on thul
    compiler_version=11.0
    compiler_libdir=/opt/intel/Compiler/11.0/083/lib/intel64
    compiler_bindir=/opt/intel/Compiler/11.0/083/bin/intel64

    compiler=open64 # only on fjorm
    compiler_version=4.2.1
    compiler_libdir=/opt/open64/4.2.1/lib/gcc-lib/x86_64-open64-linux/4.2.1
    compiler_bindir=/opt/open64/4.2.1/bin

    rpmbuild --bb  --with compiler=${compiler} --with compiler_version=${compiler_version} \
                   --with compiler_bindir=${compiler_bindir} \
                   --with compiler_libdir=${compiler_libdir} \
                   --with modules=${modules} --with default_version=1 \
                   --with prefix=/opt/netcdf4/4.0.1/1.${disttag}.${compiler}.${compiler_version} netcdf4.spec

- `ScientificPython <https://wiki.fysik.dtu.dk/niflheim/Cluster_software_-_RPMS#python-scientific>`_::

    compiler=gfortran
    compiler_version=4.1.2
    compiler_libdir=/usr/lib64
    compiler_bindir=/usr/bin
    netcdf=netcdf4
    netcdf_includedir=/opt/${netcdf}/4.0.1/1.${disttag}.${compiler}.${compiler_version}/include
    netcdf_libdir=/opt/${netcdf}/4.0.1/1.${disttag}.${compiler}.${compiler_version}/lib64
    openmpi_version=1.3.3
    ompi_libdir=/opt/openmpi/${openmpi_version}-1.${disttag}.${compiler}.${compiler_version}/lib64
    ompi_includedir=/opt/openmpi/${openmpi_version}-1.${disttag}.${compiler}.${compiler_version}/include
    ompi_bindir=/opt/openmpi/${openmpi_version}-1.${disttag}.${compiler}.${compiler_version}/bin

    rpmbuild --bb  --with Numeric_includedir=none --with numpy=numpy \
                   --with compiler=${compiler} --with compiler_version=${compiler_version} \
                   --with netcdf=${netcdf} --with netcdf_includedir=${netcdf_includedir} --with netcdf_libdir=${netcdf_libdir} \
                   --with modules=${modules} --with default_version=1 \
                   --with prefix=/opt/ScientificPython/2.8/1.${disttag}.${compiler}.${compiler_version}.python2.4.serial_version.only.numpy ScientificPython.spec

    rpmbuild --bb  --with numpy=numeric \
                   --with compiler=${compiler} --with compiler_version=${compiler_version} \
                   --with netcdf=${netcdf} --with netcdf_includedir=${netcdf_includedir} --with netcdf_libdir=${netcdf_libdir} \
                   --with modules=${modules} --with default_version=1 \
                   --with parallel=1 --with openmpi=openmpi --with openmpi_version=${openmpi_version} \
                   --with ompi_libdir=${ompi_libdir} --with ompi_includedir=${ompi_includedir} --with ompi_bindir=${ompi_bindir} \
                   --with prefix=/opt/ScientificPython/2.6.2/1.${disttag}.${compiler}.${compiler_version}.python2.4.openmpi.${openmpi_version}.numeric ScientificPython.spec

- python-docutils::

    rpmbuild -bb --with modules --with default_version --with prefix=/opt/python-docutils/0.5/1.${disttag}.python2.4 python-docutils.spec

- pytz::

    rpmbuild -bb --with modules --with default_version --with prefix=/opt/pytz/2008g/1.${disttag}.python2.4 pytz.spec

- python-dateutil::

    rpmbuild -bb --with modules --with default_version --with prefix=/opt/python-dateutil/1.4.1/3.${disttag}.python2.4 python-dateutil.spec

- python-matplotlib::
+    rpm -ivh --oldpackage ~/${FYS_PLATFORM}/RPMS/external/python-numeric-23.*.rpm

hdf5
----

  `HDF5 <http://www.hdfgroup.org/HDF5/>`_  is a data model, library, and file format for storing and managing data.

  We prefer version `1.8.6 <http://www.hdfgroup.org/HDF5/release/obtain5.html>`_.

  On a custom system build the following RPMS::

    . fys.set.gfortran.default.sh
    . fys.set.openmpi.default.sh

    (rpm_prefix=/usr && . fys.build.hdf5.sh)

  On Niflheim build the following RPMS::

     # 
     module load open64/4.2.4-0
     . fys.set.Niflheim.open64.4.2.4.sh
     . fys.set.Niflheim.openmpi.1.4.3.sh

     . fys.build.hdf5.1.8.6.sh
     module unload open64/4.2.4-0

     # older builds
     #
     . fys.set.Niflheim.gfortran.4.1.2.sh
     . fys.set.Niflheim.openmpi.1.3.3.sh

     . fys.build.hdf5.1.8.6.sh

     # 
     . fys.set.Niflheim.gfortran43.4.3.2.sh
     . fys.set.Niflheim.openmpi.1.3.3.sh

     . fys.build.hdf5.1.8.6.sh

     # 
     module load open64/4.2.3-0
     . fys.set.Niflheim.open64.4.2.3.sh
     . fys.set.Niflheim.openmpi.1.3.3.sh

     . fys.build.hdf5.1.8.6.sh
     module unload open64/4.2.4-0

     # only on thul
     module load ifort/11.1-1
     . fys.set.Niflheim.ifort.11.1.sh
     . fys.set.Niflheim.openmpi.1.3.3.sh

     . fys.build.hdf5.1.8.6.sh
     module unload ifort/11.1-1


netcdf
------

  `NetCDF <http://www.unidata.ucar.edu/software/netcdf/>`_ (*network Common Data Form*) is an interface for array-oriented 
  data access and a library that provides an implementation of the interface. The *NetCDF* library also defines a 
  machine-independent format for representing scientific data. 

  We prefer version `3.6.1 <http://www.unidata.ucar.edu/software/netcdf/release-notes-3.6.1.html>`_
  or higher (note that version `3.6.2` has fortran interface in libnetcdff.a).

  On a custom system build the following RPMS::

    . fys.set.gfortran.default.sh

    (rpm_prefix=/usr && . fys.build.netcdf4.4.0.1.sh)

  On Niflheim build the following RPMS::

     #
     . fys.set.Niflheim.open64.4.2.4.sh
     . fys.set.Niflheim.netcdf4.4.1.2.sh

     . fys.build.netcdf4.4.1.2.sh

    # older builds
    # 
     . fys.set.Niflheim.gfortran.4.1.2.sh
     . fys.set.Niflheim.netcdf4.4.0.1.sh

     . fys.build.netcdf4.4.0.1.sh

     # 
     . fys.set.Niflheim.gfortran43.4.3.2.sh
     . fys.set.Niflheim.netcdf4.4.0.1.sh

     . fys.build.netcdf4.4.0.1.sh

     # only on fjorm
     . fys.set.Niflheim.pathscale.3.2.sh
     . fys.set.Niflheim.netcdf4.4.0.1.sh

     . fys.build.netcdf4.4.0.1.sh

     # only on thul
     . fys.set.Niflheim.ifort.11.0.sh
     . fys.set.Niflheim.netcdf4.4.0.1.sh

     . fys.build.netcdf4.4.0.1.sh

     # only on fjorm
     . fys.set.Niflheim.open64.4.2.1.sh
     . fys.set.Niflheim.netcdf4.4.0.1.sh

     . fys.build.netcdf4.4.0.1.sh

     #
     . fys.set.Niflheim.open64.4.2.3.sh
     . fys.set.Niflheim.netcdf4.4.0.1.sh

     . fys.build.netcdf4.4.0.1.sh
     # only on thul
     . fys.set.Niflheim.ifort.11.1.sh
     . fys.set.Niflheim.netcdf4.4.0.1.sh

     . fys.build.netcdf4.4.0.1.sh

etsf_io
-------

  `ETSF_IO <http://www.etsf.eu/resources/software/libraries_and_tools>`_
   A library of F90 routines to read/write the ETSF file format has been written.
   It is called ETSF_IO and available under LGPL.

  On a custom system build the following RPMS::

    . fys.set.gfortran.default.sh
    . fys.set.netcdf.default.sh
    . fys.set.hdf5.default.sh

    (. fys.build.etsf_io.sh)

  On Niflheim build the following RPMS::

     # 
     . fys.set.Niflheim.gfortran43.4.3.2.sh
     . fys.set.Niflheim.netcdf4.4.0.1.sh
     hdf=none

     . fys.build.etsf_io.sh

     # Oct 4 2010:  fatal error: gfc_todo: Not Implemented: complex character array constructors
     . fys.set.Niflheim.gfortran.4.1.2.sh
     . fys.set.Niflheim.netcdf4.4.0.1.sh
     hdf=none

     . fys.build.etsf_io.sh

     # Oct 04 2010: tests/group_level failed
     . fys.set.Niflheim.open64.4.2.3.sh
     . fys.set.Niflheim.netcdf4.4.0.1.sh
     hdf=none

     . fys.build.etsf_io.sh

     # Apr 18 2010: tests/group_level failed
     . fys.set.Niflheim.open64.4.2.4.sh
     . fys.set.Niflheim.netcdf4.4.1.2.sh
     hdf=none

     . fys.build.etsf_io.sh

ScientificPython 2.6.2
----------------------

  **Warning**: version 2.6.2 required by `campos-ase2`_. Later versions are needed by `campos-ase3`_.
  **Note** that versions 2.6.2 and >= 2.8 are mutually exclusive if installed in the default "/usr" prefix.

  On a custom system build the following RPMS::

    . fys.set.ScientificPython.2.6.2.default.sh

    (rpm_prefix=/usr && . fys.build.ScientificPython.sh)

  On Niflheim build the following RPMS::

    . fys.set.Niflheim.ScientificPython.2.6.2.gfortran.4.1.2.openmpi.1.3.3.numeric.sh

    . fys.build.ScientificPython.sh

ScientificPython 2.8 or later
-----------------------------

  **Note** that versions 2.6.2 and >= 2.8 are mutually exclusive if installed in the default "/usr" prefix.

  Required by `campos-ase3`_.

  On a custom system build the following RPMS::

    . fys.set.ScientificPython.2.8.default.sh

    (rpm_prefix=/usr && . fys.build.ScientificPython.sh)

  On Niflheim build the following RPMS::

    . fys.set.Niflheim.ScientificPython.2.8.gfortran.4.1.2.serial_version.only.numpy.sh

    . fys.build.ScientificPython.sh

python-docutils
---------------

 On a custom system build the following RPMS::

    (rpm_prefix=/usr && . fys.build.docutils.0.5.sh)

 On Niflheim build the following RPMS::

    . fys.build.docutils.0.5.sh

 If using modules::

    module load python-docutils

 else, if not using the default "/usr" prefix::

    . /etc/profile.d/python-docutils.sh

pytz
----

 On a custom system build the following RPMS::

    (rpm_prefix=/usr && . fys.build.pytz.2008g.sh)

 On Niflheim build the following RPMS::

    . fys.build.pytz.2008g.sh

 If using modules::
-Line 620:
+Line 1127:
+ else, if not using the default "/usr" prefix::

    . /etc/profile.d/pytz.sh

python-dateutil
---------------

 On a custom system build the following RPMS::

    (rpm_prefix=/usr && . fys.build.python-dateutil.1.4.1.sh)

 On Niflheim build the following RPMS::

    . fys.build.python-dateutil.1.4.1.sh

 If using modules::

    module load python-dateutil

 else, if not using the default "/usr" prefix::

    . /etc/profile.d/python-dateutil.sh

python-matplotlib
-----------------

 On a custom system build the following RPMS::

    (rpm_prefix=/usr && . fys.build.python-matplotlib.sh)

 On Niflheim build the following RPMS::

    module load NUMPY
-Line 621:
+Line 1162:
+    module load pytz
-Line 622:
+Line 1164:
-    rpmbuild -bb --with modules --with default_version --with prefix=/opt/python-matplotlib/0.98.5.2/1.${disttag}.python2.4 python-matplotlib.spec

- `campos-ase2 <https://wiki.fysik.dtu.dk/niflheim/Cluster_software_-_RPMS#campos-ase2>`_::

    rpmbuild -bb --with modules --with default_version --with prefix=/opt/campos-ase2/2.3.13/1.${disttag}.python2.4 campos-ase2.spec

- `campos-dacapo-python <https://wiki.fysik.dtu.dk/niflheim/Cluster_software_-_RPMS#campos-dacapo-python>`_::

    rpmbuild -bb --with modules --with default_version --with prefix=/opt/campos-dacapo-python/0.9.4/1.${disttag}.python2.4 campos-dacapo-python.spec

- fftw2::

    compiler=gfortran
    compiler_version=4.1.2
    compiler_libdir=/usr/lib64
    compiler_bindir=/usr/bin

    compiler=gfortran43
    compiler_version=4.3.2
    compiler_libdir=/usr/lib64
    compiler_bindir=/usr/bin

    compiler=pathscale # only on fjorm
    compiler_version=3.2
    compiler_libdir=/opt/pathscale/lib/3.2
    compiler_bindir=/opt/pathscale/bin
+    . fys.build.python-matplotlib.1.0.1.sh

campos-ase2
-----------

 On a custom system build the following RPMS::

    (rpm_prefix=/usr && . fys.build.ase2.2.3.13.sh)

 On Niflheim build the following RPMS::

    . fys.build.ase2.2.3.13.sh

fftw2
-----

  We use version `2.1.5 <http://www.fftw.org/fftw-2.1.5.tar.gz>`_.

  On a custom system build the following RPMS::

    . fys.set.fftw2.default.sh

    (rpm_prefix=/usr && . fys.build.fftw2.2.1.5.sh)

  On Niflheim build the following RPMS::

    . fys.set.Niflheim.gfortran.4.1.2.sh

    . fys.build.fftw2.2.1.5.sh

    #
    . fys.set.Niflheim.gfortran43.4.3.2.sh

    . fys.build.fftw2.2.1.5.sh

    #
    . fys.set.Niflheim.pathscale.3.2.sh

    . fys.build.fftw2.2.1.5.sh

    # only on fjorm
    . fys.set.Niflheim.open64.4.2.1.sh

    . fys.build.fftw2.2.1.5.sh

    #
    . fys.set.Niflheim.open64.4.2.3.sh

    . fys.build.fftw2.2.1.5.sh

    #
    . fys.set.Niflheim.open64.4.2.4.sh

    . fys.build.fftw2.2.1.5.sh
-Line 650:
+Line 1221:
-    compiler=ifort  # only on thul
    compiler_version=11.0
    compiler_libdir=/opt/intel/Compiler/11.0/083/lib/intel64
    compiler_bindir=/opt/intel/Compiler/11.0/083/bin/intel64

    compiler=open64 # only on fjorm
    compiler_version=4.2.1
    compiler_libdir=/opt/open64/4.2.1/lib/gcc-lib/x86_64-open64-linux/4.2.1
    compiler_bindir=/opt/open64/4.2.1/bin

    rpmbuild --bb  --with compiler=${compiler} --with compiler_version=${compiler_version} \
                   --with compiler_bindir=${compiler_bindir} \
                   --with compiler_libdir=${compiler_libdir} \
                   --with modules=${modules} --with default_version=1 \
                   --with prefix=/opt/fftw2/2.1.5/12.${disttag}.${compiler}.${compiler_version} fftw2.spec

- `campos-dacapo <https://wiki.fysik.dtu.dk/niflheim/Cluster_software_-_RPMS#id17>`_::
+    . fys.set.Niflheim.ifort.11.0.sh

    . fys.build.fftw2.2.1.5.sh

campos-dacapo-pseudopotentials
------------------------------

  **Note** this package is **not** relocatable!  `campos-dacapo-pseudopotentials`_

.. _campos-dacapo-pseudopotentials: http://wiki.fysik.dtu.dk/dacapo-files/campos-dacapo-pseudopotentials-2.tar.gz

  On a custom system build the following RPMS::

    (default_version_usage="--with default_version" && modules_usage="--without modules" && . fys.build.dacapo-pseudopotentials.1.sh)

  On Niflheim build the following RPMS::

    . fys.build.dacapo-pseudopotentials.1.sh

campos-dacapo-python
--------------------

  **Requires campos-ase2**.

  On a custom system build the following RPMS::

    (rpm_prefix=/usr && . fys.build.dacapo-python.0.9.4.sh)

  On Niflheim build the following RPMS::

    . fys.build.dacapo-python.0.9.4.sh

campos-dacapo
-------------

  **Note**: fftw version 3 is incompatible with `dacapo`.

  If you build only a serial version add "--without parallel" to the rpmbuild options.
  Another useful option is "--without default_version" that does not put `/etc/profile.d` scripts,
  nor modules under `/opt/modulefiles` that allows the package to be relocatable.

  **Warning**: currently (9 Oct 2008) packaging of openmpi on FC8/FC9 requires the following link to be made::

   ln -s /usr/include/openmpi/1.2.4-gcc/32/mpif-config.h /usr/include/openmpi/1.2.4-gcc/mpif-config.h

  **Warning**: currently (9 Oct 2008) the default build fails for EL4 due to double underlined symbols in the netcdf from `ATrpms`,
  however custom build (i.e. with building your own netcdf should work).

  On a custom system build the following RPMS::

    . fys.set.dacapo.default.sh
    . fys.set.atlas.default.sh

    (rpm_prefix=/usr && . fys.build.dacapo.sh)

    # optional build using netlib blas/lapack
    . fys.set.dacapo.default.sh

    (rpm_prefix=/usr && . fys.build.dacapo.sh)

  On Niflheim build the following RPMS::

    #
    . fys.set.Niflheim.dacapo.2.7.16.open64.4.2.4.openmpi.1.4.3.acml.4.4.0.acml.4.4.0.fftw2.sh
    hdf=none

    . fys.build.dacapo.sh

    # older builds
    #
    . fys.set.Niflheim.dacapo.2.7.16.gfortran43.4.3.2.openmpi.1.3.3.acml.4.3.0.acml.4.3.0.fftw2.sh

    . fys.build.dacapo.sh

    # only on fjorm
    . fys.set.Niflheim.dacapo.2.7.16.open64.4.2.1.openmpi.1.3.3.acml.4.3.0.acml.4.3.0.fftw2.sh

    . fys.build.dacapo.sh

    # only on thul
    . fys.set.Niflheim.dacapo.2.7.16.gfortran43.4.3.2.openmpi.1.3.3.mkl.10.1.3.027.mkl.10.1.3.027.mkl.sh

    . fys.build.dacapo.sh

    # optional
    . fys.set.Niflheim.gfortran.4.1.2.sh
    . fys.set.Nilfheim.openmpi.1.3.3.sh
    . fys.set.Niflheim.netcdf4.4.0.1.sh
    . fys.set.Niflheim.fftw2.2.1.5.sh
    . fys.set.blas.default.sh
    . fys.set.lapack.acml.sh

    . fys.build.dacapo.sh

    # optional
    . fys.set.Niflheim.gfortran43.4.3.2.sh
    . fys.set.Nilfheim.openmpi.1.3.3.sh
    . fys.set.Niflheim.netcdf4.4.0.1.sh
    . fys.set.Niflheim.fftw2.2.1.5.sh
    . fys.set.blas.acml.4.3.0.sh
    . fys.set.lapack.acml.sh
    . fys.set.Niflheim.goto.1.26.sh
    . fys.set.lapack.acml.sh

    . fys.build.dacapo.sh

    # optional
    . fys.set.Niflheim.open64.4.2.1.sh
    . fys.set.Nilfheim.openmpi.1.3.3.sh
    . fys.set.Niflheim.netcdf4.4.0.1.sh
    . fys.set.Niflheim.fftw2.2.1.5.sh
    . fys.set.blas.acml.4.3.0.sh
    . fys.set.lapack.acml.sh
    . fys.set.Niflheim.goto.1.26.sh
    . fys.set.lapack.acml.sh

    . fys.build.dacapo.sh

    # optional # only on thul # multinode jobs fail
    . fys.set.Niflheim.ifort.11.0.sh
    . fys.set.Nilfheim.openmpi.1.3.3.sh
    . fys.set.Niflheim.netcdf4.4.0.1.sh
    . fys.set.Niflheim.mkl.10.1.3.027.sh

    . fys.build.dacapo.sh

fftw3
-----

  On a custom system build the following RPMS::

    . fys.set.fftw3.default.sh

    (rpm_prefix=/usr && . fys.build.fftw3.3.2.1.sh)

  On Niflheim build the following RPMS::

    . fys.set.Niflheim.gfortran.4.1.2.sh

    . fys.build.fftw3.3.2.1.sh
    #
    . fys.set.Niflheim.gfortran43.4.3.2.sh

    . fys.build.fftw3.3.2.1.sh
    #
    . fys.set.Niflheim.open64.4.2.3.sh

    . fys.build.fftw3.3.2.1.sh
    #
    . fys.set.Niflheim.open64.4.2.4.sh

    . fys.build.fftw3.3.2.1.sh
    # only on thul
    . fys.set.Niflheim.ifort.11.1.sh

    . fys.build.fftw3.3.2.1.sh

scipy
-----

 On a custom system build the following RPMS::

    . fys.set.gfortran.default.sh
    . fys.set.blas.default.sh
    . fys.set.lapack.default.sh
    . fys.set.Niflheim.cblas.2.23.3.sh
    . fys.set.fftw3.default.sh
    . fys.set.suitesparse.default.sh

    (rpm_prefix=/usr && . fys.build.scipy.0.7.0.sh)

 On Niflheim build the following RPMS::

    . fys.set.Niflheim.scipy.0.7.0.gfortran.4.1.2.blas.lapack.cblas.2.23.3.sh

    . fys.build.scipy.0.7.0.sh

    # optional - not tested!
    . fys.set.Niflheim.scipy.0.7.0.gfortran.4.1.2.acml.4.0.1.cblas.2.23.3.sh

    . fys.build.scipy.0.7.0.sh

povray
------

  On a custom system build the following RPMS::

    (rpm_prefix=/usr && . fys.build.povray.sh)

  On Niflheim build the following RPMS::

    . fys.build.povray.sh

babel
-----

  On a custom system build the following RPMS::

    (rpm_prefix=/usr && . fys.build.Babel.0.9.4.sh)

  On Niflheim build the following RPMS::

    . fys.build.Babel.0.9.4.sh

  If using modules::

    module load babel

  else, if not using the default "/usr" prefix::

    . /etc/profile.d/babel.sh

python-jinja2
-------------

  On a custom system build the following RPMS::

    (rpm_prefix=/usr && . fys.build.Jinja2.2.1.1.sh)

  On Niflheim build the following RPMS::

    . fys.build.Jinja2.2.1.1.sh

  If using modules::

    module load python-jinja2

  else, if not using the default "/usr" prefix::

    . /etc/profile.d/python-jinja2.sh

python-pygments
---------------

  On a custom system build the following RPMS::

    (rpm_prefix=/usr && . fys.build.Pygments.1.0.sh)

  On Niflheim build the following RPMS::

    . fys.build.Pygments.1.0.sh

  If using modules::

    module load python-pygments

  else, if not using the default "/usr" prefix::

    . /etc/profile.d/python-pygments.sh

python-sphinx
-------------

  On a custom system build the following RPMS::

    (rpm_prefix=/usr && . fys.build.Sphinx.0.6.1.sh)

  On Niflheim build the following RPMS::

    . fys.build.Sphinx.0.6.1.sh

  If using modules::

    module load python-sphinx

  else, if not using the default "/usr" prefix::

    . /etc/profile.d/python-sphinx.sh

auctex
------

  Build the following RPMS::

    cd ~/rpmbuild/SOURCES&& wget http://ftp.gnu.org/pub/gnu/auctex/auctex-11.86.tar.gz
    cd ~/rpmbuild/SPECS

    rpmbuild -bb auctex.spec

campos-ase3
-----------

  On a custom system build the following RPMS::

    (rpm_prefix=/usr && . fys.build.ase3.sh)

  On Niflheim build the following RPMS::

    module load NUMPY
    . fys.build.ase3.sh

  Snapshot package is built with, e.g.::

    major_version=3
    version1=2
    version2=0
    version_svn=1066
    release=${major_version}.${version1}.${version2}.${version_svn}/1${disttag}.python${python_version}
    rpmbuild -bb --with major_version=${major_version} --with version1=${version1} --with version2=${version2} --with version_svn=${version_svn} --with keep_install=1 \
                 ${modules_usage} --with default_version -with system=${rpm_platform} \
                 --with python_version=${python_version} \
                 --with prefix=/home/camp/rpmbuild/opt/Intel-Nehalem-el5/campos-ase3/${release} campos-ase3.spec
    rm /home/camp/rpmbuild/Intel-Nehalem-el5/RPMS/campos-ase3-${major_version}.${version1}.${version2}.${version_svn}-1${disttag}.python${python_version}.x86_64.rpm
    dir=~/Intel-Nehalem-el5/BUILD/campos-ase3-${major_version}.${version1}.${version2}.${version_svn}-1${disttag}.python${python_version}-root
    ln -s ${dir}/etc/modulefiles/campos-ase3/${major_version}.${version1}.${version2}.${version_svn}-1${disttag}.python${python_version} \
       ~/Intel-Nehalem-el5/modulefiles.testing/campos-ase3
    ln -s ${dir}/home/camp/rpmbuild/opt/Intel-Nehalem-el5/campos-ase3/${major_version}.${version1}.${version2}.${version_svn} ~/opt/Intel-Nehalem-el5/campos-ase3

blacs
-----

  `BLACS <http://www.netlib.org/blacs/>`_ is used by ScaLapack.

 On a custom system build the following RPMS::

    . fys.set.gfortran.default.sh
    . fys.set.openmpi.default.sh

    (rpm_prefix=/usr && . fys.build.blacs.sh)

 On Niflheim build the following RPMS::

    . fys.set.Niflheim.open64.4.2.4.sh
    . fys.set.Niflheim.openmpi.1.4.3.sh

    . fys.build.blacs.sh

    # older builds
    #
    . fys.set.Niflheim.gfortran.4.1.2.sh
    . fys.set.Niflheim.openmpi.1.3.3.sh

    . fys.build.blacs.sh

    #
    . fys.set.Niflheim.gfortran43.4.3.2.sh
    . fys.set.Niflheim.openmpi.1.3.3.sh

    . fys.build.blacs.sh

    #
    . fys.set.Niflheim.pathscale.3.2.sh
    . fys.set.Niflheim.openmpi.1.3.3.sh

    . fys.build.blacs.sh

    #
    . fys.set.Niflheim.open64.4.2.1.sh
    . fys.set.Niflheim.openmpi.1.3.3.sh

    . fys.build.blacs.sh

    #
    . fys.set.Niflheim.open64.4.2.3.sh
    . fys.set.Niflheim.openmpi.1.3.3.sh

    . fys.build.blacs.sh

    #
    . fys.set.Niflheim.ifort.11.0.sh
    . fys.set.Niflheim.openmpi.1.3.3.sh

    . fys.build.blacs.sh

    #
    . fys.set.Niflheim.ifort.11.1.sh
    . fys.set.Niflheim.openmpi.1.3.3.sh

    . fys.build.blacs.sh

scalapack
---------

  `SCALAPACK <http://www.netlib.org/scalapack/>`_.

 On a custom system build the following RPMS::

    . fys.set.gfortran.default.sh
    . fys.set.openmpi.default.sh
    . fys.set.blas.default.sh
    . fys.set.lapack.default.sh
    . fys.set.Niflheim.blacs.1.1.sh

    (rpm_prefix=/usr && . fys.build.scalapack.sh)

 On Niflheim build the following RPMS::

    #
    . fys.set.Niflheim.open64.4.2.3.sh
    . fys.set.Niflheim.openmpi.1.3.3.sh
    . fys.set.blas.acml.4.4.0.sh
    . fys.set.lapack.acml.sh
    . fys.set.Niflheim.goto2.1.13.sh
    . fys.set.Niflheim.blacs.1.1.sh

    . fys.build.scalapack.2.0.1.sh
    #
    . fys.set.Niflheim.open64.4.2.3.sh
    . fys.set.Niflheim.openmpi.1.3.3.sh
    . fys.set.blas.acml.4.4.0.sh
    . fys.set.lapack.acml.sh
    . fys.set.Niflheim.blacs.1.1.sh

    . fys.build.scalapack.2.0.1.sh

    # old builds
    . fys.set.Niflheim.open64.4.2.4.sh
    . fys.set.Niflheim.openmpi.1.4.3.sh
    . fys.set.blas.acml.4.4.0.sh
    . fys.set.lapack.acml.sh
    . fys.set.Niflheim.blacs.1.1.sh

    . fys.build.scalapack.1.8.0.sh

    #
    . fys.set.Niflheim.open64.4.2.4.sh
    . fys.set.Niflheim.openmpi.1.4.3.sh
    . fys.set.blas.acml.4.4.0.sh
    . fys.set.lapack.acml.sh
    . fys.set.Niflheim.goto2.1.13.sh
    . fys.set.Niflheim.blacs.1.1.sh

    . fys.build.scalapack.1.8.0.sh

    #
    . fys.set.Niflheim.gfortran.4.1.2.sh
    . fys.set.Niflheim.openmpi.1.3.3.sh
    . fys.set.blas.default.sh
    . fys.set.lapack.default.sh
    . fys.set.Niflheim.blacs.1.1.sh

    . fys.build.scalapack.1.8.0.sh

    #
    . fys.set.Niflheim.gfortran.4.1.2.sh
    . fys.set.Niflheim.openmpi.1.3.3.sh
    . fys.set.blas.acml.4.0.1.sh
    . fys.set.lapack.acml.sh
    . fys.set.Niflheim.blacs.1.1.sh

    . fys.build.scalapack.1.8.0.sh

    #
    . fys.set.Niflheim.gfortran43.4.3.2.sh
    . fys.set.Niflheim.openmpi.1.3.3.sh
    . fys.set.blas.default.sh
    . fys.set.lapack.default.sh
    . fys.set.Niflheim.blacs.1.1.sh

    . fys.build.scalapack.1.8.0.sh

    #
    . fys.set.Niflheim.gfortran43.4.3.2.sh
    . fys.set.Niflheim.openmpi.1.3.3.sh
    . fys.set.blas.acml.4.4.0.sh
    . fys.set.lapack.acml.sh
    . fys.set.Niflheim.blacs.1.1.sh

    . fys.build.scalapack.1.8.0.sh

    # old old builds
    #
    . fys.set.Niflheim.gfortran43.4.3.2.sh
    . fys.set.Niflheim.openmpi.1.3.3.sh
    . fys.set.blas.acml.4.3.0.sh
    . fys.set.lapack.acml.sh
    . fys.set.Niflheim.blacs.1.1.sh

    . fys.build.scalapack.1.8.0.sh

    #
    . fys.set.Niflheim.gfortran43.4.3.2.sh
    . fys.set.Niflheim.openmpi.1.3.3.sh
    . fys.set.blas.acml.4.4.0.sh
    . fys.set.lapack.acml.sh
    . fys.set.Niflheim.goto2.1.13.sh
    . fys.set.Niflheim.blacs.1.1.sh

    . fys.build.scalapack.1.8.0.sh
    #
    . fys.set.Niflheim.gfortran43.4.3.2.sh
    . fys.set.Niflheim.openmpi.1.3.3.sh
    . fys.set.blas.acml.4.4.0.sh
    . fys.set.lapack.acml.sh
    . fys.set.Niflheim.goto.1.26.sh
    . fys.set.Niflheim.blacs.1.1.sh

    . fys.build.scalapack.1.8.0.sh

    #
    . fys.set.Niflheim.gfortran43.4.3.2.sh
    . fys.set.Niflheim.openmpi.1.3.3.sh
    . fys.set.blas.acml.4.3.0.sh
    . fys.set.lapack.acml.sh
    . fys.set.Niflheim.goto.1.26.sh
    . fys.set.Niflheim.blacs.1.1.sh

    . fys.build.scalapack.1.8.0.sh

    #
    . fys.set.Niflheim.open64.4.2.1.sh
    . fys.set.Niflheim.openmpi.1.3.3.sh
    . fys.set.blas.acml.4.3.0.sh
    . fys.set.lapack.acml.sh
    . fys.set.Niflheim.blacs.1.1.sh

    . fys.build.scalapack.1.8.0.sh

    # only on fjorm
    . fys.set.Niflheim.open64.4.2.3.sh
    . fys.set.Niflheim.openmpi.1.3.3.sh
    . fys.set.blas.acml.4.4.0.sh
    . fys.set.lapack.acml.sh
    . fys.set.Niflheim.goto.1.26.sh
    . fys.set.Niflheim.blacs.1.1.sh

    . fys.build.scalapack.1.8.0.sh
    #
    . fys.set.Niflheim.open64.4.2.3.sh
    . fys.set.Niflheim.openmpi.1.3.3.sh
    . fys.set.blas.acml.4.4.0.sh
    . fys.set.lapack.acml.sh
    . fys.set.Niflheim.goto2.1.13.sh
    . fys.set.Niflheim.blacs.1.1.sh

    . fys.build.scalapack.1.8.0.sh
    #
    . fys.set.Niflheim.open64.4.2.3.sh
    . fys.set.Niflheim.openmpi.1.3.3.sh
    . fys.set.blas.acml.4.4.0.sh
    . fys.set.lapack.acml.sh
    . fys.set.Niflheim.blacs.1.1.sh

    . fys.build.scalapack.1.8.0.sh

    #
    . fys.set.Niflheim.gfortran43.4.3.2.sh
    . fys.set.Niflheim.openmpi.1.3.3.sh
    . fys.set.Niflheim.atlas.3.8.3.sh
    . fys.set.Niflheim.blacs.1.1.sh

    . fys.build.scalapack.1.8.0.sh

    # only on thul
    . fys.set.Niflheim.ifort.11.0.sh
    . fys.set.Niflheim.openmpi.1.3.3.sh
    . fys.set.blas.acml.4.4.0.sh
    . fys.set.lapack.acml.sh
    . fys.set.Niflheim.blacs.1.1.sh

    . fys.build.scalapack.1.8.0.sh

    # only on thul
    . fys.set.Niflheim.ifort.11.1.sh
    . fys.set.Niflheim.openmpi.1.3.3.sh
    . fys.set.blas.acml.4.4.0.sh
    . fys.set.lapack.acml.sh
    . fys.set.Niflheim.blacs.1.1.sh

    . fys.build.scalapack.1.8.0.sh

PDSYEVRnew
----------

- `PDSYEVRnew <http://www.cs.berkeley.edu/~voemel/PDSYEVRnew.tar.gz>`_ ScaLAPACK's new parallel MRRR algorithm
  for computing eigenpairs of large real symmetric or complex Hermitian matrices.


  On Niflheim build the following RPMS::

     . fys.set.Niflheim.gfortran43.4.3.2.sh
     . fys.set.Niflheim.openmpi.1.3.3.sh
     . fys.set.blas.acml.4.3.0.sh
     . fys.set.lapack.acml.sh
     . fys.set.Niflheim.blacs.1.1.sh
     . fys.set.Niflheim.scalapack.1.8.0.sh

     . fys.build.PDSYEVRnew.sh

     #
     . fys.set.Niflheim.gfortran43.4.3.2.sh
     . fys.set.Niflheim.openmpi.1.3.3.sh
     . fys.set.blas.acml.4.3.0.sh
     . fys.set.lapack.acml.sh
     . fys.set.Niflheim.goto.1.26.sh
     . fys.set.Niflheim.blacs.1.1.sh
     . fys.set.Niflheim.scalapack.1.8.0.sh

     . fys.build.PDSYEVRnew.sh

campos-gpaw-setups
------------------

  **Note** this package is **not** relocatable!

  On a custom system build the following RPMS::

    (default_version_usage="--with default_version" && modules_usage="--without modules" && . fys.build.gpaw-setups.sh)

  On Niflheim build the following RPMS::

    . fys.build.gpaw-setups.sh

campos-gpaw
-----------

  On a custom system build the following RPMS::

    # March 3 2010: results in "orthogonalization failed" with EPEL's atlas on el5.x64_64 and i386.
    . fys.set.gpaw.default.sh
    . fys.set.atlas.default.sh

    (rpm_prefix=/usr && . fys.build.gpaw.sh)

    # optional build using netlib blas/lapack
    . fys.set.gpaw.default.sh

    (rpm_prefix=/usr && . fys.build.gpaw.sh)

  On Niflheim load first the required modules::

     module load ASE3
     module load campos-gpaw-setups

  and build the following RPMS::

    . fys.set.Niflheim.gpaw.0.6.5147.open64.4.2.3.openmpi.1.3.3.acml.4.4.0.acml.4.4.0.sh

    . fys.build.gpaw.sh

    # older builds
    #
    . fys.set.Niflheim.gpaw.0.6.5147.open64.4.2.4.openmpi.1.4.3.goto2.1.13.acml.4.4.0.sh

    . fys.build.gpaw.sh
    #
    . fys.set.Niflheim.gpaw.0.6.5147.open64.4.2.3.openmpi.1.3.3.goto2.1.13.acml.4.4.0.sh

    . fys.build.gpaw.sh
    #
    . fys.set.Niflheim.gpaw.0.6.5147.gfortran43.4.3.2.openmpi.1.3.3.acml.4.4.0.acml.4.4.0.sh

    . fys.build.gpaw.sh

    # only on fjorm
    . fys.set.Niflheim.gpaw.0.6.5147.gfortran43.4.3.2.openmpi.1.3.3.goto.1.26.acml.4.4.0.sh

    . fys.build.gpaw.sh

  Optional builds::

    . fys.set.Niflheim.gpaw.0.6.5147.gfortran43.4.3.2.openmpi.1.3.3.acml.4.3.0.acml.4.3.0.sh

    . fys.build.gpaw.sh
    #
    . fys.set.Niflheim.gpaw.0.6.5147.gfortran.4.1.2.openmpi.1.3.3.acml.4.0.1.acml.4.0.1.sh

    . fys.build.gpaw.sh

    # default gfortran and netlib blas/lapack/scalapack
    . fys.set.Niflheim.gpaw.0.6.5147.gfortran.4.1.2.openmpi.1.3.3.acml.4.0.1.acml.4.0.1.sh
    . fys.set.blas.default.sh
    . fys.set.lapack.default.sh
    . fys.set.Niflheim.scalapack.1.8.0.sh

    . fys.build.gpaw.sh

    # latest gfortran and netlib blas/lapack/scalapack
    . fys.set.Niflheim.gpaw.0.6.5147.gfortran43.4.3.2.openmpi.1.3.3.acml.4.3.0.acml.4.3.0.sh
    . fys.set.blas.default.sh
    . fys.set.lapack.default.sh
    . fys.set.Niflheim.scalapack.1.8.0.sh

    . fys.build.gpaw.sh

    # atlas - gpaw-test fails for diagonalization on fjorm el5 x86_64 18 Jan 2010
    . fys.set.Niflheim.gpaw.0.6.5147.gfortran43.4.3.2.openmpi.1.3.3.acml.4.3.0.acml.4.3.0.sh
    . fys.set.Niflheim.atlas.3.8.3.sh
    . fys.set.Niflheim.scalapack.1.8.0.sh

    . fys.build.gpaw.sh

    # atlas - gpaw-test fails for diagonalization on fjorm el5 x86_64 18 Jan 2010
    . fys.set.Niflheim.gpaw.0.6.5147.gfortran43.4.3.2.openmpi.1.3.3.acml.4.3.0.acml.4.3.0.sh
    . fys.set.Niflheim.atlas.3.8.3.sh
    . fys.set.Niflheim.scalapack.1.8.0.sh

    . fys.build.gpaw.sh

    #
    . fys.set.Niflheim.gfortran43.4.3.2.sh
    . fys.set.Niflheim.openmpi.1.3.3.sh
    . fys.set.blas.acml.4.4.0.sh
    . fys.set.lapack.acml.sh
    . fys.set.Niflheim.goto2.1.13.sh
    . fys.set.Niflheim.blacs.1.1.sh
    . fys.set.Niflheim.scalapack.1.8.0.sh

    . fys.build.gpaw.sh

    # only on fjorm
    # note gpaw version 0.6 --with sl_init_second_underscore=1 is necessary for rpmbuild
    . fys.set.Niflheim.pathscale.3.2.sh
    . fys.set.Niflheim.openmpi.1.3.3.sh
    . fys.set.blas.acml.4.0.1.sh
    . fys.set.lapack.acml.sh
    . fys.set.Niflheim.goto.1.26.sh
    . fys.set.Niflheim.blacs.1.1.sh
    . fys.set.Niflheim.scalapack.1.8.0.sh

    . fys.build.gpaw.sh

    # only on fjorm
    # note gpaw version 0.6 --with sl_init_second_underscore=1 is necessary for rpmbuild
    . fys.set.Niflheim.open64.4.2.1.sh
    . fys.set.Niflheim.openmpi.1.3.3.sh
    . fys.set.blas.acml.4.0.1.sh
    . fys.set.lapack.acml.sh
    . fys.set.Niflheim.goto.1.26.sh
    . fys.set.Niflheim.blacs.1.1.sh
    . fys.set.Niflheim.scalapack.1.8.0.sh

    . fys.build.gpaw.sh

    **Note**: open64 compiler fails with::

    /usr/bin/ld: /opt/open64/4.2.1/lib/gcc-lib/x86_64-open64-linux/4.2.1/libmv.a(vcos.o): relocation R_X86_64_32S against `a local symbol' can not be used when making a shared object; recompile with -fPIC
    /opt/open64/4.2.1/lib/gcc-lib/x86_64-open64-linux/4.2.1/libmv.a: could not read symbols: Bad value

    # only on fjorm
    # note gpaw version 0.6 --with sl_init_second_underscore=1 is necessary for rpmbuild
    . fys.set.Niflheim.open64.4.2.3.sh
    . fys.set.Niflheim.openmpi.1.3.3.sh
    . fys.set.blas.acml.4.4.0.sh
    . fys.set.lapack.acml.sh
    . fys.set.Niflheim.goto.1.26.sh
    . fys.set.Niflheim.blacs.1.1.sh
    . fys.set.Niflheim.scalapack.1.8.0.sh

    . fys.build.gpaw.sh

    #
    # note gpaw version 0.6 --with sl_init_second_underscore=1 is necessary for rpmbuild
    . fys.set.Niflheim.open64.4.2.3.sh
    . fys.set.Niflheim.openmpi.1.3.3.sh
    . fys.set.blas.acml.4.4.0.sh
    . fys.set.lapack.acml.sh
    . fys.set.Niflheim.blacs.1.1.sh
    . fys.set.Niflheim.scalapack.1.8.0.sh

    . fys.build.gpaw.sh

    # only on thul
    . fys.set.Niflheim.ifort.11.1.sh
    . fys.set.Niflheim.openmpi.1.3.3.sh
    . fys.set.blas.acml.4.4.0.sh
    . fys.set.lapack.acml.sh
    . fys.set.Niflheim.blacs.1.1.sh
    . fys.set.Niflheim.scalapack.1.8.0.sh

    . fys.build.gpaw.sh

    # only on thul
    . fys.set.Niflheim.ifort.11.0.sh
    . fys.set.Niflheim.openmpi.1.3.3.sh
    . fys.set.blas.acml.4.4.0.sh
    . fys.set.lapack.acml.sh
    . fys.set.Niflheim.blacs.1.1.sh
    . fys.set.Niflheim.scalapack.1.8.0.sh

    . fys.build.gpaw.sh

    # only on thul # fails on thul
    . fys.set.Niflheim.gfortran43.4.3.2.sh
    . fys.set.Niflheim.openmpi.1.3.3.sh
    . fys.set.Niflheim.mkl.10.2.4.032.sh

    . fys.build.gpaw.sh

    # only on thul # fails on thul
    . fys.set.Niflheim.gfortran43.4.3.2.sh
    . fys.set.Niflheim.openmpi.1.3.3.sh
    . fys.set.Niflheim.mkl.10.2.1.017.sh

    . fys.build.gpaw.sh

    # only on thul # fails on thul
    . fys.set.Niflheim.ifort.11.0.sh
    . fys.set.Niflheim.openmpi.1.3.3.sh
    . fys.set.Niflheim.mkl.10.1.3.027.sh

    . fys.build.gpaw.sh

    # only on thul # fails on thul
    . fys.set.Niflheim.gfortran43.4.3.2.sh
    . fys.set.Niflheim.openmpi.1.3.3.sh
    . fys.set.Niflheim.mkl.10.1.3.027.sh

    . fys.build.gpaw.sh

Asap
----

  On a custom system build the following RPMS::

    . fys.set.Asap.default.sh

    (rpm_prefix=/usr && . fys.build.Asap.sh)

  On Niflheim build the following RPMS::

    #
    module load ASE3
    . fys.set.Niflheim.Asap.3.2.6.open64.4.2.4.openmpi.1.4.3.sh

    . fys.build.Asap.sh

    #
    module load ASE3
    . fys.set.Niflheim.Asap.3.2.6.open64.4.2.3.openmpi.1.3.3.sh

    . fys.build.Asap.sh

    # only on fjorm
    module load ASE3
    . fys.set.Niflheim.Asap.3.2.6.pathscale.3.2.openmpi.1.3.3.sh

    . fys.build.Asap.sh

    # only on thul
    module load ASE3
    module load ifort/11.1-1
    . fys.set.Niflheim.Asap.3.2.6.ifort.11.1.openmpi.1.3.3.sh

    . fys.build.Asap.sh

abinit
------

- abinit pseudopotentials

  **Note** this package is **not** relocatable! `abinit-pseudopotentials`_

.. _abinit-pseudopotentials: http://wiki.fysik.dtu.dk/abinit-files/abinit-pseudopotentials-2.tar.gz

  On a custom system build the following RPMS::

    (default_version_usage="--with default_version" && modules_usage="--without modules" && . fys.build.abinit-pseudopotentials.sh)

  On Niflheim build the following RPMS::

    . fys.build.abinit-pseudopotentials.sh

- abinit

  `abinit <http://www.abinit.org/>`_ is a Density Functional Theory (DFT) package with pseudopotentials and a planewave basis.

  On a custom system build the following RPMS::

    . fys.set.abinit.5.4.4p.default.sh
    . fys.set.atlas.default.sh

    (rpm_prefix=/usr && . fys.build.abinit.5.4.4p.sh)

  On Niflheim build the following RPMS::

    . fys.set.Niflheim.abinit.5.4.4p.gfortran43.4.3.2.openmpi.1.3.3.acml.4.3.0.acml.4.3.0.fftw3.sh
    hdf=none

    . fys.build.abinit.5.4.4p.sh

siesta
------

.. _siesta-pseudopotentials-2.tar.gz: attachment:siesta-pseudopotentials-2.tar.gz

siesta-pseudopotentials-2.tar.gz_

- siesta pseudopotentials

  Build the following RPMS::

    cd ~/rpmbuild/SOURCES&& wget --no-check-certificate \
    "https://wiki.fysik.dtu.dk/niflheim/Cluster_software_-_RPMS?action=AttachFile&do=get&target=siesta-pseudopotentials-2.tar.gz" \
    -O siesta-pseudopotentials-2.tar.gz
    cd ~/rpmbuild/SPECS

     rpmbuild -bb ${modules_usage} --with default_version siesta-pseudopotentials.spec

- siesta

  `siesta <http://www.nanotec.es/products/siesta.php>`_ (Spanish Initiative for Electronic Simulations with Thousands of Atoms)
  is both a method and its computer program implementation, to perform electronic structure calculations and ab initio molecular dynamics simulations of molecules and solids.

  Build the following RPMS::

    cd ~/rpmbuild/SPECS

    major_version=2
    version1=0
-Line 678:
+Line 2132:
-    fftw=fftw2
    fftw_libdir=/opt/${fftw}/2.1.5/12.${disttag}.${compiler}.${compiler_version}/lib64
-Line 681:
+Line 2133:
-    netcdf_includedir=/opt/${netcdf}/4.0.1/1.${disttag}.${compiler}.${compiler_version}/include
    netcdf_libdir=/opt/${netcdf}/4.0.1/1.${disttag}.${compiler}.${compiler_version}/lib64
+    netcdf_includedir=/opt/${netcdf}/4.0.1/1${disttag}.${compiler}.${compiler_version}/include
    netcdf_libdir=/opt/${netcdf}/4.0.1/1${disttag}.${compiler}.${compiler_version}/lib64
-Line 684:
+Line 2136:
-    ompi_libdir=/opt/openmpi/${openmpi_version}-1.${disttag}.${compiler}.${compiler_version}/lib64
    ompi_includedir=/opt/openmpi/${openmpi_version}-1.${disttag}.${compiler}.${compiler_version}/include
    ompi_bindir=/opt/openmpi/${openmpi_version}-1.${disttag}.${compiler}.${compiler_version}/bin
    release=1.${disttag}.${compiler}.${compiler_version}.openmpi.${openmpi_version}.${blas}.${blas_version}.${lapack}.${lapack_version}.${fftw}

    compiler=pathscale
    compiler_version=3.2
    compiler_libdir=/opt/pathscale/lib/3.2
    compiler_bindir=/opt/pathscale/bin
    blas=acml
    blas_version=4.0.1
    blasdir=/opt/${blas}/${blas_version}/${compiler}64/lib
    lapack=acml
    lapack_version=4.0.1
    lapackdir=/opt/${lapack}/${lapack_version}/${compiler}64/lib
    fftw=fftw2
    fftw_libdir=/opt/${fftw}/2.1.5/12.${disttag}.${compiler}.${compiler_version}/lib64
    netcdf=netcdf4
    netcdf_includedir=/opt/${netcdf}/4.0.1/1.${disttag}.${compiler}.${compiler_version}/include
    netcdf_libdir=/opt/${netcdf}/4.0.1/1.${disttag}.${compiler}.${compiler_version}/lib64
    openmpi_version=1.3.3
    ompi_libdir=/opt/openmpi/${openmpi_version}-1.${disttag}.${compiler}.${compiler_version}/lib64
    ompi_includedir=/opt/openmpi/${openmpi_version}-1.${disttag}.${compiler}.${compiler_version}/include
    ompi_bindir=/opt/openmpi/${openmpi_version}-1.${disttag}.${compiler}.${compiler_version}/bin
    release=1.${disttag}.${compiler}.${compiler_version}.openmpi.${openmpi_version}.${blas}.${blas_version}.${lapack}.${lapack_version}.${fftw}

    compiler=gfortran
    compiler_version=4.1.2
    compiler_libdir=/usr/lib64
    compiler_bindir=/usr/bin
    blas=blas
    blas_version=3.0.37.el5
    blasdir=/usr/lib64
    lapack=lapack
    lapack_version=3.0.37.el5
    lapackdir=/usr/lib64
    fftw=fftw2
    fftw_libdir=/opt/${fftw}/2.1.5/12.${disttag}.${compiler}.${compiler_version}/lib64
    netcdf=netcdf4
    netcdf_includedir=/opt/${netcdf}/4.0.1/1.${disttag}.${compiler}.${compiler_version}/include
    netcdf_libdir=/opt/${netcdf}/4.0.1/1.${disttag}.${compiler}.${compiler_version}/lib64
    openmpi_version=1.3.3
    ompi_libdir=/opt/openmpi/${openmpi_version}-1.${disttag}.${compiler}.${compiler_version}/lib64
    ompi_includedir=/opt/openmpi/${openmpi_version}-1.${disttag}.${compiler}.${compiler_version}/include
    ompi_bindir=/opt/openmpi/${openmpi_version}-1.${disttag}.${compiler}.${compiler_version}/bin
    release=1.${disttag}.${compiler}.${compiler_version}.openmpi.${openmpi_version}.${blas}.${blas_version}.${lapack}.${lapack_version}.${fftw}

    rpmbuild --bb  --with blas=${blas} --with blas_version=${blas_version} --with blasdir=${blasdir} \
+    ompi_libdir=/opt/openmpi/${openmpi_version}-1${disttag_network}.${compiler}.${compiler_version}/lib64
    ompi_includedir=/opt/openmpi/${openmpi_version}-1${disttag_network}.${compiler}.${compiler_version}/include
    ompi_bindir=/opt/openmpi/${openmpi_version}-1${disttag_network}.${compiler}.${compiler_version}/bin
    blacs=blacs
    blacsdir=/opt/blacs/1.1/24${disttag_network}.${compiler}.${compiler_version}.openmpi.${openmpi_version}/lib64
    scalapack=scalapack
    scalapackdir=/opt/scalapack/1.8.0/1${disttag_network}.${compiler}.${compiler_version}.openmpi.${openmpi_version}.${blas}.${blas_version}.${lapack}.${lapack_version}/lib64
    release=1${disttag_network}.${compiler}.${compiler_version}.openmpi.${openmpi_version}.${blas}.${blas_version}.${lapack}.${lapack_version}

    rpmbuild --bb  --with major_version=${major_version} --with version1=${version1} \
                   --with blas=${blas} --with blas_version=${blas_version} --with blasdir=${blasdir} \
-Line 734:
+Line 2149:
-                   --with fftw=${fftw} --with fftw_libdir=${fftw_libdir} \
-Line 737:
+Line 2151:
-                   --with modules=${modules} --with default_version=1 \
-Line 740:
+Line 2153:
-                   --with prefix=/opt/campos-dacapo/2.7.16/${release} campos-dacapo.spec

  Optional builds::

    compiler=ifort # only on thul # multinode jobs fail
    compiler_version=11.0
    compiler_libdir=/opt/intel/Compiler/11.0/083/lib/intel64
    compiler_bindir=/opt/intel/Compiler/11.0/083/bin/intel64
    blas=mkl
    blas_version=10.1.3.027
    blasdir=/opt/intel/${blas}/${blas_version}/lib/em64t
    lapack=mkl_lapack
    lapack_version=${blas_version}
    lapackdir=${blasdir}
    fftw=mkl
    fftw_libdir=${blasdir}
    netcdf=netcdf4
    netcdf_includedir=/opt/${netcdf}/4.0.1/1.${disttag}.${compiler}.${compiler_version}/include
    netcdf_libdir=/opt/${netcdf}/4.0.1/1.${disttag}.${compiler}.${compiler_version}/lib64
    openmpi_version=1.3.3
    ompi_libdir=/opt/openmpi/${openmpi_version}-1.${disttag}.${compiler}.${compiler_version}/lib64
    ompi_includedir=/opt/openmpi/${openmpi_version}-1.${disttag}.${compiler}.${compiler_version}/include
    ompi_bindir=/opt/openmpi/${openmpi_version}-1.${disttag}.${compiler}.${compiler_version}/bin
    release=1.${disttag}.${compiler}.${compiler_version}.openmpi.${openmpi_version}.${blas}.${blas_version}.${lapack}.${lapack_version}.${fftw}

    compiler=gfortran43 # only on thul
    compiler_version=4.3.2
    compiler_libdir=/usr/lib64
    compiler_bindir=/usr/bin
    blas=mkl
    blas_version=10.1.3.027
    blasdir=/opt/intel/${blas}/${blas_version}/lib/em64t
    lapack=mkl_lapack
    lapack_version=${blas_version}
    lapackdir=${blasdir}
    fftw=mkl
    fftw_libdir=${blasdir}
    netcdf=netcdf4
    netcdf_includedir=/opt/${netcdf}/4.0.1/1.${disttag}.${compiler}.${compiler_version}/include
    netcdf_libdir=/opt/${netcdf}/4.0.1/1.${disttag}.${compiler}.${compiler_version}/lib64
    openmpi_version=1.3.3
    ompi_libdir=/opt/openmpi/${openmpi_version}-1.${disttag}.${compiler}.${compiler_version}/lib64
    ompi_includedir=/opt/openmpi/${openmpi_version}-1.${disttag}.${compiler}.${compiler_version}/include
    ompi_bindir=/opt/openmpi/${openmpi_version}-1.${disttag}.${compiler}.${compiler_version}/bin
    release=1.${disttag}.${compiler}.${compiler_version}.openmpi.${openmpi_version}.${blas}.${blas_version}.${lapack}.${lapack_version}.${fftw}

    compiler=open64 # only on fjorm
    compiler_version=4.2.1
    compiler_libdir=/opt/open64/4.2.1/lib/gcc-lib/x86_64-open64-linux/4.2.1
    compiler_bindir=/opt/open64/4.2.1/bin
    blas=acml
    blas_version=4.3.0
    blasdir=/opt/${blas}/${blas_version}/${compiler}64/lib
    lapack=acml
    lapack_version=4.3.0
    lapackdir=/opt/${lapack}/${lapack_version}/${compiler}64/lib
    fftw=fftw2
    fftw_libdir=/opt/${fftw}/2.1.5/12.${disttag}.${compiler}.${compiler_version}/lib64
    netcdf=netcdf4
    netcdf_includedir=/opt/${netcdf}/4.0.1/1.${disttag}.${compiler}.${compiler_version}/include
    netcdf_libdir=/opt/${netcdf}/4.0.1/1.${disttag}.${compiler}.${compiler_version}/lib64
    openmpi_version=1.3.3
    ompi_libdir=/opt/openmpi/${openmpi_version}-1.${disttag}.${compiler}.${compiler_version}/lib64
    ompi_includedir=/opt/openmpi/${openmpi_version}-1.${disttag}.${compiler}.${compiler_version}/include
    ompi_bindir=/opt/openmpi/${openmpi_version}-1.${disttag}.${compiler}.${compiler_version}/bin
    release=1.${disttag}.${compiler}.${compiler_version}.openmpi.${openmpi_version}.${blas}.${blas_version}.${lapack}.${lapack_version}.${fftw}

    compiler=gfortran43
    compiler_version=4.3.2
    compiler_libdir=/usr/lib64
    compiler_bindir=/usr/bin
    blas=goto
    blas_version=1.26
    blasdir=/opt/${blas}/${blas_version}/1.${disttag}.${compiler}.${compiler_version}.smp/lib64
    lapack=acml
    lapack_version=4.3.0
    lapackdir=/opt/${lapack}/${lapack_version}/${compiler}64/lib
    fftw=fftw2
    fftw_libdir=/opt/${fftw}/2.1.5/12.${disttag}.${compiler}.${compiler_version}/lib64
    netcdf=netcdf4
    netcdf_includedir=/opt/${netcdf}/4.0.1/1.${disttag}.${compiler}.${compiler_version}/include
    netcdf_libdir=/opt/${netcdf}/4.0.1/1.${disttag}.${compiler}.${compiler_version}/lib64
    openmpi_version=1.3.3
    ompi_libdir=/opt/openmpi/${openmpi_version}-1.${disttag}.${compiler}.${compiler_version}/lib64
    ompi_includedir=/opt/openmpi/${openmpi_version}-1.${disttag}.${compiler}.${compiler_version}/include
    ompi_bindir=/opt/openmpi/${openmpi_version}-1.${disttag}.${compiler}.${compiler_version}/bin
    release=1.${disttag}.${compiler}.${compiler_version}.openmpi.${openmpi_version}.${blas}.${blas_version}.${lapack}.${lapack_version}.${fftw}

Build following for gpaw:
-------------------------

- fftw3::

    compiler=gfortran
    compiler_version=4.1.2
    compiler_libdir=/usr/lib64
    compiler_bindir=/usr/bin

    compiler=gfortran43
    compiler_version=4.3.2
    compiler_libdir=/usr/lib64
    compiler_bindir=/usr/bin

    rpmbuild --bb  --with major_version=3 --with version1=2 --with version2=1 \
                   --with compiler=${compiler} --with compiler_version=${compiler_version} \
                   --with compiler_bindir=${compiler_bindir} \
                   --with compiler_libdir=${compiler_libdir} \
                   --with modules=${modules} --with default_version=1 \
                   --with prefix=/opt/fftw3/3.2.1/12.${disttag}.${compiler}.${compiler_version} fftw2.spec
- scipy::

    module load numpy/1.3.0-1.el5.fys.gfortran.4.1.2.python2.4.blas.3.0.37.el5.lapack.3.0.37.el5

    compiler=gfortran
    compiler_version=4.1.2
    compiler_libdir=/usr/lib64
    compiler_bindir=/usr/bin
    blas=blas
    blas_version=3.0.37.el5
    blasdir=/usr/lib64
    lapack=lapack
    lapack_version=3.0.37.el5
    lapackdir=/usr/lib64
    fftw=fftw3
    fftw_libdir=/opt/${fftw}/3.2.1/12.${disttag}.${compiler}.${compiler_version}/lib64
    cblas_prefix=/opt/cblas/2.23.3/1.${disttag}.${compiler}.${compiler_version}.${blas}.${blas_version}
    release=1.${disttag}.${compiler}.${compiler_version}.python2.4.${blas}.${blas_version}.${lapack}.${lapack_version}

    compiler=gfortran
    compiler_version=4.1.2
    compiler_libdir=/usr/lib64
    compiler_bindir=/usr/bin
    blas=acml
    blas_version=4.0.1
    blasdir=/opt/${blas}/${blas_version}/${compiler}64/lib
    lapack=acml
    lapack_version=4.0.1
    lapackdir=/opt/${blas}/${blas_version}/${compiler}64/lib
    fftw=fftw3
    fftw_libdir=/opt/${fftw}/3.2.1/12.${disttag}.${compiler}.${compiler_version}/lib64
    cblas_prefix=/opt/cblas/2.23.3/1.${disttag}.${compiler}.${compiler_version}.${blas}.${blas_version}
    release=1.${disttag}.${compiler}.${compiler_version}.python2.4.${blas}.${blas_version}.${lapack}.${lapack_version}

    rpmbuild --bb --with cblas_prefix=${cblas_prefix} \
                  --with blas=${blas} --with blas_version=${blas_version} --with blasdir=${blasdir} \
                  --with compiler=${compiler} --with compiler_version=${compiler_version} \
                  --with compiler_bindir=${compiler_bindir} --with compiler_libdir=${compiler_libdir} \
                  --with lapack=${lapack} --with lapack_version=${lapack_version} --with lapackdir=${lapackdir} \
                  --with ufsparse_libdir=/usr/lib64 --with ufsparse_includedir=/usr/include/suitesparse \
                  --with fftw=${fftw} --with fftw_libdir=${fftw_libdir} \
                  --with modules=${modules} --with default_version=1 \
                  --with prefix=/opt/scipy/0.7.0/${release} scipy.spec

- `campos-gpaw-setups <https://wiki.fysik.dtu.dk/niflheim/Cluster_software_-_RPMS#campos-gpaw-setups>`_::

    rpmbuild -bb --with default_version --with modules campos-gpaw-setups.spec

- povray::

    rpmbuild -bb --with modules --with default_version --with prefix=/opt/povray/3.6.1/3.${disttag} povray.spec

- python-jinja2::

    rpmbuild -bb --with modules --with default_version --with prefix=/opt/python-jinja2/2.1.1/1.${disttag}.python2.4 python-jinja2.spec

- python-pygments::

    rpmbuild -bb --with modules --with default_version --with prefix=/opt/python-pygments/1.0/1.${disttag}.python2.4 python-pygments.spec

- babel::

    rpmbuild -bb --with modules --with default_version --with prefix=/opt/babel/0.9.4/1.${disttag}.python2.4 babel.spec

- python-sphinx::

    module load python-jinja2
    rpmbuild -bb --with modules --with default_version --with prefix=/opt/python-sphinx/0.6.1/1.${disttag}.python2.4 python-sphinx.spec

- `campos-ase3 <https://wiki.fysik.dtu.dk/niflheim/Cluster_software_-_RPMS#campos-ase3>`_::

    rpmbuild -bb --with modules --with default_version --with prefix=/opt/campos-ase3/3.1.0.846/1.${disttag}.python2.4 campos-ase3.spec

  Snapshot package is built with, e.g.::

    version1=2
    version2=0
    version_svn=1066
    release=3.${version1}.${version2}.${version_svn}/1.${disttag}.python2.4
    rpmbuild -bb --with version1=${version1} --with version2=${version2} --with version_svn=${version_svn} --with keep_install=1 \
                 --with modules --with default_version \
                 --with prefix=/home/camp/rpmbuild/opt/Intel-Nehalem-el5/campos-ase3/${release} campos-ase3.spec
    rm /home/camp/rpmbuild/Intel-Nehalem-el5/RPMS/campos-ase3-3.2.0.1066-1.el5.fys.python2.4.x86_64.rpm
    dir=~/Intel-Nehalem-el5/BUILD/campos-ase3-3.${version1}.${version2}.${version_svn}-1.${disttag}.python2.4-root
    ln -s ${dir}/etc/modulefiles/campos-ase3/3.${version1}.${version2}.${version_svn}-1.${disttag}.python2.4 \
       ~/Intel-Nehalem-el5/modulefiles.testing/campos-ase3
    ln -s ${dir}/home/camp/rpmbuild/opt/Intel-Nehalem-el5/campos-ase3/3.${version1}.${version2}.${version_svn} ~/opt/Intel-Nehalem-el5/campos-ase3

- blacs::
+                   --with blacs=${blacs} --with blacsdir=${blacsdir} \
                   --with scalapack=${scalapack} --with scalapackdir=${scalapackdir} \
                   ${modules_usage} --with default_version=1 \
                   --with system=${rpm_platform} \
                   --with prefix=/opt/siesta${major_version}/${major_version}.${version1}/${release} siesta.spec

espresso
--------

  **Note** this package is **not** relocatable!

`quantum espresso <http://www.quantum-espresso.org/>`_

- espresso pseudopotentials

  On a custom system build the following RPMS::

    (default_version_usage="--with default_version" && modules_usage="--without modules" && . fys.build.espresso_pp.sh)

  On Niflheim build the following RPMS::

    . fys.build.espresso_pp.sh

- espresso

  **Note** March 04 2010: version 4.0.5 does not compile with gfortran >= 4.4 (?)

  **Note** March 04 2010: version 4.1.2 results in and "STOP 1" status for tests if EXX is enabled

  On a custom system build the following RPMS::

    . fys.set.espresso.4.1.2.default.sh

    (rpm_prefix=/usr && . fys.build.espresso.sh)

    #  March 06 2010 fc12, el5 with atlas gives for atom-lsda.in: On entry to DSYGVX parameter number 20 had an illegal value
    . fys.set.espresso.4.1.2.default.sh
    . fys.set.atlas.default.sh

    (rpm_prefix=/usr && . fys.build.espresso.sh)

  On Niflheim build the following RPMS::

    # version used with yambo 3.2.1.426M - enable EXX in the spec file!
    . fys.set.Niflheim.espresso.4.0.5.gfortran43.4.3.2.openmpi.1.3.3.acml.4.3.0.acml.4.3.0.sh

    . fys.build.espresso.sh

    # version 5.0.1
    . fys.set.Niflheim.espresso.5.0.1.gfortran43.4.3.2.openmpi.1.3.3.acml.4.3.0.acml.4.3.0.sh
    . fys.build.espresso.5.sh

yambo
-----

- yambo

  `yambo <http://www.yambo-code.org/>`_ is a FORTRAN/C code for Many-Body calculations in solid state and molecular physics.
  Yambo relies on the Kohn-Sham wavefunctions generated by two DFT public codes: abinit, and PWscf.
  This build creates interfaces to abinit and PWscf.

  On a custom system build the following RPMS::

    . fys.set.yambo.default.sh
    . fys.set.atlas.default.sh

    (rpm_prefix=/usr && . fys.build.yambo.sh)

  On Niflheim build the following RPMS::

    # Nov 15 2010: ETSF compilation part fails with "Error: Symbol 'default_tel' at (1) has no IMPLICIT type": see http://www.yambo-code.org/forum/viewtopic.php?f=1&t=266
    . fys.set.Niflheim.yambo.3.2.3.16.gfortran43.4.3.2.openmpi.1.3.3.acml.4.4.0.acml.4.4.0.sh
    hdf=none

    . fys.build.yambo.sh
    #
    . fys.set.Niflheim.yambo.3.2.1.448.gfortran43.4.3.2.openmpi.1.3.3.acml.4.3.0.acml.4.3.0.sh
    hdf=none

    . fys.build.yambo.sh

    # special yambo 3.2.1.426M
    . fys.set.Niflheim.yambo.3.2.1.426M.gfortran43.4.3.2.openmpi.1.3.3.acml.4.3.0.acml.4.3.0.sh
    hdf=none

    . fys.build.yambo.sh

- yambo NON-GPL

  This is a NON-GPL version of yambo.

  On Niflheim build the following RPMS::

    . fys.set.Niflheim.yambo-ngpl.3.2.3.735M.gfortran43.4.3.2.openmpi.1.3.3.acml.4.4.0.acml.4.4.0.sh
    hdf=none

    . fys.build.yambo.sh

elk
---

`elk <http://elk.sourceforge.net/>`_

- elk species

  **Note** this package is **not** relocatable!

  On a custom system build the following RPMS::

    (default_version_usage="--with default_version" && modules_usage="--without modules" && . fys.build.elk-species.sh)

  On Niflheim build the following RPMS::

    . fys.build.elk-species.sh

- elk

  On a custom system build the following RPMS::

    . fys.set.gfortran.default.sh
    . fys.set.openmpi.default.sh
    . fys.set.blas.default.sh
    . fys.set.lapack.default.sh

    (rpm_prefix=/usr && thread_mode=mp && . fys.build.elk.sh)

  On Niflheim build the following RPMS::

    # OpenMP with MPI version
    . fys.set.Niflheim.gfortran43.4.3.2.sh
    . fys.set.Niflheim.openmpi.1.3.3.sh
    . fys.set.blas.acml.4.3.0_mp.sh
    . fys.set.lapack.acml.sh
    
    (thread_mode=mp && . fys.build.elk.sh)

    # OpenMP version
    . fys.set.Niflheim.gfortran43.4.3.2.sh
    . fys.set.blas.acml.4.3.0_mp.sh
    . fys.set.lapack.acml.sh
    
    (thread_mode=mp && . fys.build.elk.sh)

    # MPI version
    . fys.set.Niflheim.gfortran43.4.3.2.sh
    . fys.set.Niflheim.openmpi.1.3.3.sh
    . fys.set.blas.acml.4.4.0.sh
    . fys.set.lapack.acml.sh
    
    (thread_mode=nomp && . fys.build.elk.sh)

vtk
---

- cmake

  Build the following RPMS::

    cd ~/rpmbuild/SOURCES&& wget http://www.cmake.org/files/v2.6/cmake-2.6.4.tar.gz
    cd ~/rpmbuild/SOURCES&& wget "http://downloads.sourceforge.net/project/xmlrpc-c/Xmlrpc-c Super Stable/1.06.35/xmlrpc-c-1.06.35.tgz"
    cd ~/rpmbuild/SPECS

    rpmbuild -bb --with bootstrap --without gui cmake.spec  # install the resulting RPM
    rpmbuild -bb xmlrpc-c.spec # install the resulting RPM
    rpm -e cmake
    rpmbuild -bb --without gui cmake.spec # install the resulting RPM

- vtkdata

  Build the following RPMS::

    cd ~/rpmbuild/SOURCES&& wget http://www.vtk.org/files/release/5.4/vtkdata-5.4.2.tar.gz
    cd ~/rpmbuild/SPECS

    rpmbuild -bb --with version1=4 --with version2=2 ${modules_usage} --with default_version=1 \
             --with prefix=/opt/vtkdata/5.4.2/1${disttag} vtkdata.spec
 
- vtk

  Build the following RPMS::

    cd ~/rpmbuild/SOURCES&& wget http://www.vtk.org/files/release/5.4/vtk-5.4.2.tar.gz
    cd ~/rpmbuild/SPECS
-Line 944:
+Line 2342:
-    ompi_libdir=/opt/openmpi/${openmpi_version}-1.${disttag}.${compiler}.${compiler_version}/lib64
    ompi_includedir=/opt/openmpi/${openmpi_version}-1.${disttag}.${compiler}.${compiler_version}/include
    ompi_bindir=/opt/openmpi/${openmpi_version}-1.${disttag}.${compiler}.${compiler_version}/bin

    compiler=gfortran43
    compiler_version=4.3.2
    compiler_libdir=/usr/lib64
    compiler_bindir=/usr/bin
    openmpi_version=1.3.3
    ompi_libdir=/opt/openmpi/${openmpi_version}-1.${disttag}.${compiler}.${compiler_version}/lib64
    ompi_includedir=/opt/openmpi/${openmpi_version}-1.${disttag}.${compiler}.${compiler_version}/include
    ompi_bindir=/opt/openmpi/${openmpi_version}-1.${disttag}.${compiler}.${compiler_version}/bin

    compiler=pathscale
    compiler_version=3.2
    compiler_libdir=/opt/pathscale/lib/3.2
    compiler_bindir=/opt/pathscale/bin
    openmpi_version=1.3.3
    ompi_libdir=/opt/openmpi/${openmpi_version}-1.${disttag}.${compiler}.${compiler_version}/lib64
    ompi_includedir=/opt/openmpi/${openmpi_version}-1.${disttag}.${compiler}.${compiler_version}/include
    ompi_bindir=/opt/openmpi/${openmpi_version}-1.${disttag}.${compiler}.${compiler_version}/bin

    compiler=open64
    compiler_version=4.2.1
    compiler_libdir=/opt/open64/4.2.1/lib/gcc-lib/x86_64-open64-linux/4.2.1
    compiler_bindir=/opt/open64/4.2.1/bin
    openmpi_version=1.3.3
    ompi_libdir=/opt/openmpi/${openmpi_version}-1.${disttag}.${compiler}.${compiler_version}/lib64
    ompi_includedir=/opt/openmpi/${openmpi_version}-1.${disttag}.${compiler}.${compiler_version}/include
    ompi_bindir=/opt/openmpi/${openmpi_version}-1.${disttag}.${compiler}.${compiler_version}/bin

    rpmbuild --bb  --with compiler=${compiler} --with compiler_version=${compiler_version} \
+    ompi_libdir=/opt/openmpi/${openmpi_version}-1${disttag_network}.${compiler}.${compiler_version}/lib64
    ompi_includedir=/opt/openmpi/${openmpi_version}-1${disttag_network}.${compiler}.${compiler_version}/include
    ompi_bindir=/opt/openmpi/${openmpi_version}-1${disttag_network}.${compiler}.${compiler_version}/bin

    rpmbuild -bb   --without qt4 --with version1=4 --with version2=2 \
                   --with compiler=${compiler} --with compiler_version=${compiler_version} \
-Line 977:
+Line 2349:
-                   --with modules=${modules} --with default_version=1 \
-Line 980:
+Line 2351:
-                   --with prefix=/opt/blacs/1.1/24.${disttag}.${compiler}.${compiler_version}.openmpi.${openmpi_version} blacs.spec

- scalapack::

    compiler=gfortran43
    compiler_version=4.3.2
    compiler_libdir=/usr/lib64
    compiler_bindir=/usr/bin
    blas=acml
    blas_version=4.3.0
    blasdir=/opt/${blas}/${blas_version}/${compiler}64/lib
    lapack=acml
    lapack_version=4.3.0
    lapackdir=/opt/${lapack}/${blas_version}/${compiler}64/lib
    openmpi_version=1.3.3
    ompi_libdir=/opt/openmpi/${openmpi_version}-1.${disttag}.${compiler}.${compiler_version}/lib64
    ompi_includedir=/opt/openmpi/${openmpi_version}-1.${disttag}.${compiler}.${compiler_version}/include
    ompi_bindir=/opt/openmpi/${openmpi_version}-1.${disttag}.${compiler}.${compiler_version}/bin
    release=1.${disttag}.${compiler}.${compiler_version}.openmpi.${openmpi_version}.${blas}.${blas_version}.${lapack}.${lapack_version}

    compiler=open64
    compiler_version=4.2.1
    compiler_libdir=/opt/open64/4.2.1/lib/gcc-lib/x86_64-open64-linux/4.2.1
    compiler_bindir=/opt/open64/4.2.1/bin
    blas=acml
    blas_version=4.3.0
    blasdir=/opt/${blas}/${blas_version}/${compiler}64/lib
    lapack=acml
    lapack_version=4.3.0
    lapackdir=/opt/${lapack}/${blas_version}/${compiler}64/lib
    openmpi_version=1.3.3
    ompi_libdir=/opt/openmpi/${openmpi_version}-1.${disttag}.${compiler}.${compiler_version}/lib64
    ompi_includedir=/opt/openmpi/${openmpi_version}-1.${disttag}.${compiler}.${compiler_version}/include
    ompi_bindir=/opt/openmpi/${openmpi_version}-1.${disttag}.${compiler}.${compiler_version}/bin
    release=1.${disttag}.${compiler}.${compiler_version}.openmpi.${openmpi_version}.${blas}.${blas_version}.${lapack}.${lapack_version}

    compiler=pathscale
    compiler_version=3.2
    compiler_libdir=/opt/pathscale/lib/3.2
    compiler_bindir=/opt/pathscale/bin
    blas=acml
    blas_version=4.3.0
    blasdir=/opt/${blas}/${blas_version}/${compiler}64/lib
    lapack=acml
    lapack_version=4.3.0
    lapackdir=/opt/${lapack}/${blas_version}/${compiler}64/lib
    openmpi_version=1.3.3
    ompi_libdir=/opt/openmpi/${openmpi_version}-1.${disttag}.${compiler}.${compiler_version}/lib64
    ompi_includedir=/opt/openmpi/${openmpi_version}-1.${disttag}.${compiler}.${compiler_version}/include
    ompi_bindir=/opt/openmpi/${openmpi_version}-1.${disttag}.${compiler}.${compiler_version}/bin
    release=1.${disttag}.${compiler}.${compiler_version}.openmpi.${openmpi_version}.${blas}.${blas_version}.${lapack}.${lapack_version}

    compiler=gfortran43
    compiler_version=4.3.2
    compiler_libdir=/usr/lib64
    compiler_bindir=/usr/bin
    blas=blas
    blas_version=3.0.37.el5
    blasdir=/usr/lib64
    lapack=lapack
    lapack_version=3.0.37.el5
    lapackdir=/usr/lib64
    openmpi_version=1.3.3
    ompi_libdir=/opt/openmpi/${openmpi_version}-1.${disttag}.${compiler}.${compiler_version}/lib64
    ompi_includedir=/opt/openmpi/${openmpi_version}-1.${disttag}.${compiler}.${compiler_version}/include
    ompi_bindir=/opt/openmpi/${openmpi_version}-1.${disttag}.${compiler}.${compiler_version}/bin
    release=1.${disttag}.${compiler}.${compiler_version}.openmpi.${openmpi_version}.${blas}.${blas_version}.${lapack}.${lapack_version}

    compiler=gfortran
    compiler_version=4.1.2
    compiler_libdir=/usr/lib64
    compiler_bindir=/usr/bin
    blas=blas
    blas_version=3.0.37.el5
    blasdir=/usr/lib64
    lapack=lapack
    lapack_version=3.0.37.el5
    lapackdir=/usr/lib64
    openmpi_version=1.3.3
    ompi_libdir=/opt/openmpi/${openmpi_version}-1.${disttag}.${compiler}.${compiler_version}/lib64
    ompi_includedir=/opt/openmpi/${openmpi_version}-1.${disttag}.${compiler}.${compiler_version}/include
    ompi_bindir=/opt/openmpi/${openmpi_version}-1.${disttag}.${compiler}.${compiler_version}/bin
    release=1.${disttag}.${compiler}.${compiler_version}.openmpi.${openmpi_version}.${blas}.${blas_version}.${lapack}.${lapack_version}

    rpmbuild --bb  --with blacs=blacs --with blacsdir=/opt/blacs/1.1/24.${disttag}.${compiler}.${compiler_version}.openmpi.${openmpi_version}/lib64 \
                   --with blas=${blas} --with blas_version=${blas_version} --with blasdir=${blasdir} \
                   --with compiler=${compiler} --with compiler_version=${compiler_version} \
                   --with compiler_bindir=${compiler_bindir} --with compiler_libdir=${compiler_libdir} \
                   --with lapack=${lapack} --with lapack_version=${lapack_version} --with lapackdir=${lapackdir} \
                   --with modules=${modules} --with default_version=1 \
                   --with parallel=1 --with openmpi=openmpi --with openmpi_version=${openmpi_version} \
                   --with ompi_libdir=${ompi_libdir} --with ompi_includedir=${ompi_includedir} --with ompi_bindir=${ompi_bindir} \
                   --with prefix=/opt/scalapack/1.8.0/${release} scalapack.spec

- `campos-gpaw <https://wiki.fysik.dtu.dk/niflheim/Cluster_software_-_RPMS#campos-gpaw>`_::

    compiler=gfortran43 # only on fjorm
    compiler_version=4.3.2
    compiler_libdir=/usr/lib64
    compiler_bindir=/usr/bin
    blas=goto
    blas_version=1.26
    blasdir=/opt/${goto}/${blas_version}/1.${disttag}.${compiler}.${compiler_version}.smp/lib64
    lapack=acml
    lapack_version=4.3.0
    lapackdir=/opt/${lapack}/${blas_version}/${compiler}64/lib
    openmpi_version=1.3.3
    ompi_libdir=/opt/openmpi/${openmpi_version}-1.${disttag}.${compiler}.${compiler_version}/lib64
    ompi_includedir=/opt/openmpi/${openmpi_version}-1.${disttag}.${compiler}.${compiler_version}/include
    ompi_bindir=/opt/openmpi/${openmpi_version}-1.${disttag}.${compiler}.${compiler_version}/bin
    blacs=blacs
    blacsdir=/opt/blacs/1.1/24.${disttag}.${compiler}.${compiler_version}.openmpi.${openmpi_version}/lib64
    scalapack=scalapack
    scalapackdir=/opt/scalapack/1.8.0/1.${disttag}.${compiler}.${compiler_version}.openmpi.${openmpi_version}.${blas}.${blas_version}.${lapack}.${lapack_version}/lib64
    release=1.${disttag}.${compiler}.${compiler_version}.python2.4.without_ase.openmpi.${openmpi_version}.${blas}.${blas_version}.${lapack}.${lapack_version}

    compiler=pathscale # only on fjorm
    # note --with sl_second_underscore=1 is necessary for rpmbuild
    compiler_version=3.2
    compiler_libdir=/opt/pathscale/lib/3.2
    compiler_bindir=/opt/pathscale/bin
    blas=goto
    blas_version=1.26
    blasdir=/opt/${goto}/${blas_version}/1.${disttag}.${compiler}.${compiler_version}.smp/lib64
    lapack=acml
    lapack_version=4.3.0
    lapackdir=/opt/${lapack}/${blas_version}/${compiler}64/lib
    openmpi_version=1.3.3
    ompi_libdir=/opt/openmpi/${openmpi_version}-1.${disttag}.${compiler}.${compiler_version}/lib64
    ompi_includedir=/opt/openmpi/${openmpi_version}-1.${disttag}.${compiler}.${compiler_version}/include
    ompi_bindir=/opt/openmpi/${openmpi_version}-1.${disttag}.${compiler}.${compiler_version}/bin
    blacs=blacs
    blacsdir=/opt/blacs/1.1/24.${disttag}.${compiler}.${compiler_version}.openmpi.${openmpi_version}/lib64
    scalapack=scalapack
    scalapackdir=/opt/scalapack/1.8.0/1.${disttag}.${compiler}.${compiler_version}.openmpi.${openmpi_version}.${blas}.${blas_version}.${lapack}.${lapack_version}/lib64
    release=1.${disttag}.${compiler}.${compiler_version}.python2.4.without_ase.openmpi.${openmpi_version}.${blas}.${blas_version}.${lapack}.${lapack_version

    compiler=gfortran43
    compiler_version=4.3.2
    compiler_libdir=/usr/lib64
    compiler_bindir=/usr/bin
    blas=blas
    blas_version=3.0.37.el5
    blasdir=/usr/lib64
    lapack=lapack
    lapack_version=3.0.37.el5
    lapackdir=/usr/lib64
    openmpi_version=1.3.3
    ompi_libdir=/opt/openmpi/${openmpi_version}-1.${disttag}.${compiler}.${compiler_version}/lib64
    ompi_includedir=/opt/openmpi/${openmpi_version}-1.${disttag}.${compiler}.${compiler_version}/include
    ompi_bindir=/opt/openmpi/${openmpi_version}-1.${disttag}.${compiler}.${compiler_version}/bin
    blacs=blacs
    blacsdir=/opt/blacs/1.1/24.${disttag}.${compiler}.${compiler_version}.openmpi.${openmpi_version}/lib64
    scalapack=scalapack
    scalapackdir=/opt/scalapack/1.8.0/1.${disttag}.${compiler}.${compiler_version}.openmpi.${openmpi_version}.${blas}.${blas_version}.${lapack}.${lapack_version}/lib64
    release=1.${disttag}.${compiler}.${compiler_version}.python2.4.without_ase.openmpi.${openmpi_version}.${blas}.${blas_version}.${lapack}.${lapack_version}

    compiler=gfortran
    compiler_version=4.1.2
    compiler_libdir=/usr/lib64
    compiler_bindir=/usr/bin
    blas=blas
    blas_version=3.0.37.el5
    blasdir=/usr/lib64
    lapack=lapack
    lapack_version=3.0.37.el5
    lapackdir=/usr/lib64
    openmpi_version=1.3.3
    ompi_libdir=/opt/openmpi/${openmpi_version}-1.${disttag}.${compiler}.${compiler_version}/lib64
    ompi_includedir=/opt/openmpi/${openmpi_version}-1.${disttag}.${compiler}.${compiler_version}/include
    ompi_bindir=/opt/openmpi/${openmpi_version}-1.${disttag}.${compiler}.${compiler_version}/bin
    blacs=blacs
    blacsdir=/opt/blacs/1.1/24.${disttag}.${compiler}.${compiler_version}.openmpi.${openmpi_version}/lib64
    scalapack=scalapack
    scalapackdir=/opt/scalapack/1.8.0/1.${disttag}.${compiler}.${compiler_version}.openmpi.${openmpi_version}.${blas}.${blas_version}.${lapack}.${lapack_version}/lib64
    release=1.${disttag}.${compiler}.${compiler_version}.python2.4.without_ase.openmpi.${openmpi_version}.${blas}.${blas_version}.${lapack}.${lapack_version}

    rpmbuild --bb  --with blas=${blas} --with blas_version=${blas_version} --with blasdir=${blasdir} \
                   --with compiler=${compiler} --with compiler_version=${compiler_version} \
                   --with compiler_bindir=${compiler_bindir} --with compiler_libdir=${compiler_libdir} \
                   --with lapack=${lapack} --with lapack_version=${lapack_version} --with lapackdir=${lapackdir} \
                   --with modules=${modules} --with default_version=1 \
                   --with parallel=1 --with openmpi=openmpi --with openmpi_version=${openmpi_version} \
                   --with ompi_libdir=${ompi_libdir} --with ompi_includedir=${ompi_includedir} --with ompi_bindir=${ompi_bindir} \
                   --with blacs=${blacs} --with blacsdir=${blacsdir} \
                   --with scalapack=${scalapack} --with scalapackdir=${scalapackdir} \
                   --with prefix=/opt/campos-gpaw/0.5.3667/${release} campos-gpaw.spec

  Optional builds::

    compiler=gfortran43 # fails on thul
    compiler_version=4.3.2
    compiler_libdir=/usr/lib64
    compiler_bindir=/usr/bin
    blas=acml
    blas_version=4.3.0
    blasdir=/opt/${blas}/${blas_version}/${compiler}64/lib
    lapack=acml
    lapack_version=4.3.0
    lapackdir=/opt/${lapack}/${blas_version}/${compiler}64/lib
    openmpi_version=1.3.3
    ompi_libdir=/opt/openmpi/${openmpi_version}-1.${disttag}.${compiler}.${compiler_version}/lib64
    ompi_includedir=/opt/openmpi/${openmpi_version}-1.${disttag}.${compiler}.${compiler_version}/include
    ompi_bindir=/opt/openmpi/${openmpi_version}-1.${disttag}.${compiler}.${compiler_version}/bin
    blacs=blacs
    blacsdir=/opt/blacs/1.1/24.${disttag}.${compiler}.${compiler_version}.openmpi.${openmpi_version}/lib64
    scalapack=scalapack
    scalapackdir=/opt/scalapack/1.8.0/1.${disttag}.${compiler}.${compiler_version}.openmpi.${openmpi_version}.${blas}.${blas_version}.${lapack}.${lapack_version}/lib64
    release=1.${disttag}.${compiler}.${compiler_version}.python2.4.without_ase.openmpi.${openmpi_version}.${blas}.${blas_version}.${lapack}.${lapack_version}

    compiler=gfortran
    compiler_version=4.1.2
    compiler_libdir=/usr/lib64
    compiler_bindir=/usr/bin
    blas=blas
    blas_version=4.0.1
    blasdir=/opt/${blas}/${blas_version}/${compiler}64/lib
    lapack=acml
    lapack_version=4.0.1
    lapackdir=/opt/${blas}/${blas_version}/${compiler}64/lib
    openmpi_version=1.3.3
    ompi_libdir=/opt/openmpi/${openmpi_version}-1.${disttag}.${compiler}.${compiler_version}/lib64
    ompi_includedir=/opt/openmpi/${openmpi_version}-1.${disttag}.${compiler}.${compiler_version}/include
    ompi_bindir=/opt/openmpi/${openmpi_version}-1.${disttag}.${compiler}.${compiler_version}/bin
    blacs=blacs
    blacsdir=/opt/blacs/1.1/24.${disttag}.${compiler}.${compiler_version}.openmpi.${openmpi_version}/lib64
    scalapack=scalapack
    scalapackdir=/opt/scalapack/1.8.0/1.${disttag}.${compiler}.${compiler_version}.openmpi.${openmpi_version}.${blas}.${blas_version}.${lapack}.${lapack_version}/lib64
    release=1.${disttag}.${compiler}.${compiler_version}.python2.4.without_ase.openmpi.${openmpi_version}.${blas}.${blas_version}.${lapack}.${lapack_version}

    compiler=ifort # fails on thul
    compiler_version=11.0
    compiler_libdir=/opt/intel/Compiler/11.0/083/lib/intel64
    compiler_bindir=/opt/intel/Compiler/11.0/083/bin/intel64
    blas=mkl
    blas_version=10.1.3.027
    blasdir=/opt/intel/${blas}/${blas_version}/lib/em64t
    lapack=mkl_lapack
    lapack_version=10.1.3.027
    lapackdir=${blasdir}
    openmpi_version=1.3.3
    ompi_libdir=/opt/openmpi/${openmpi_version}-1.${disttag}.${compiler}.${compiler_version}/lib64
    ompi_includedir=/opt/openmpi/${openmpi_version}-1.${disttag}.${compiler}.${compiler_version}/include
    ompi_bindir=/opt/openmpi/${openmpi_version}-1.${disttag}.${compiler}.${compiler_version}/bin
    blacs=mkl
    blacsdir=${blasdir}
    scalapack=mkl
    scalapackdir=${blasdir}
    release=1.${disttag}.${compiler}.${compiler_version}.python2.4.without_ase.openmpi.${openmpi_version}.${blas}.${blas_version}.${lapack}.${lapack_version}

    compiler=gfortran43 # only on thul # fails on thul
    compiler_version=4.3.2
    compiler_libdir=/usr/lib64
    compiler_bindir=/usr/bin
    blas=mkl
    blas_version=10.1.3.027
    blasdir=/opt/intel/${blas}/${blas_version}/lib/em64t
    lapack=mkl_lapack
    lapack_version=10.1.3.027
    lapackdir=${blasdir}
    openmpi_version=1.3.3
    ompi_libdir=/opt/openmpi/${openmpi_version}-1.${disttag}.${compiler}.${compiler_version}/lib64
    ompi_includedir=/opt/openmpi/${openmpi_version}-1.${disttag}.${compiler}.${compiler_version}/include
    ompi_bindir=/opt/openmpi/${openmpi_version}-1.${disttag}.${compiler}.${compiler_version}/bin
    blacs=mkl
    blacsdir=${blasdir}
    scalapack=mkl
    scalapackdir=${blasdir}
    release=1.${disttag}.${compiler}.${compiler_version}.python2.4.without_ase.openmpi.${openmpi_version}.${blas}.${blas_version}.${lapack}.${lapack_version}

    compiler=gfortran43 # only on thul
    compiler_version=4.3.2
    compiler_libdir=/usr/lib64
    compiler_bindir=/usr/bin
    blas=mkl
    blas_version=10.2.1.017
    blasdir=/opt/intel/${blas}/${blas_version}/lib/em64t
    lapack=mkl_lapack
    lapack_version=10.2.1.017
    lapackdir=${blasdir}
    openmpi_version=1.3.3
    ompi_libdir=/opt/openmpi/${openmpi_version}-1.${disttag}.${compiler}.${compiler_version}/lib64
    ompi_includedir=/opt/openmpi/${openmpi_version}-1.${disttag}.${compiler}.${compiler_version}/include
    ompi_bindir=/opt/openmpi/${openmpi_version}-1.${disttag}.${compiler}.${compiler_version}/bin
    blacs=mkl
    blacsdir=${blasdir}
    scalapack=mkl
    scalapackdir=${blasdir}
    release=1.${disttag}.${compiler}.${compiler_version}.python2.4.without_ase.openmpi.${openmpi_version}.${blas}.${blas_version}.${lapack}.${lapack_version}

Build the following for abinit:
-------------------------------

- abinit pseudopotentials::

     rpmbuild -bb --with modules --with default_version abinit-pseudopotentials.spec

- abinit::

    compiler=gfortran43
    compiler_version=4.3.2
    compiler_libdir=/usr/lib64
    compiler_bindir=/usr/bin
    blas=acml
    blas_version=4.3.0
    blasdir=/opt/${blas}/${blas_version}/${compiler}64/lib
    lapack=acml
    lapack_version=4.3.0
    lapackdir=/opt/${lapack}/${lapack_version}/${compiler}64/lib
    fftw=fftw3
    fftw_libdir=/opt/${fftw}/3.2.1/12.${disttag}.${compiler}.${compiler_version}/lib64
    netcdf=netcdf4
    netcdf_includedir=/opt/${netcdf}/4.0.1/1.${disttag}.${compiler}.${compiler_version}/include
    netcdf_libdir=/opt/${netcdf}/4.0.1/1.${disttag}.${compiler}.${compiler_version}/lib64
    openmpi_version=1.3.3
    ompi_libdir=/opt/openmpi/${openmpi_version}-1.${disttag}.${compiler}.${compiler_version}/lib64
    ompi_includedir=/opt/openmpi/${openmpi_version}-1.${disttag}.${compiler}.${compiler_version}/include
    ompi_bindir=/opt/openmpi/${openmpi_version}-1.${disttag}.${compiler}.${compiler_version}/bin
    release=1.${disttag}.${compiler}.${compiler_version}.openmpi.${openmpi_version}.${blas}.${blas_version}.${lapack}.${lapack_version}.${fftw}

    rpmbuild --bb  --with blas=${blas} --with blas_version=${blas_version} --with blasdir=${blasdir} \
                   --with compiler=${compiler} --with compiler_version=${compiler_version} \
                   --with compiler_bindir=${compiler_bindir} --with compiler_libdir=${compiler_libdir} \
                   --with fftw=${fftw} --with fftw_libdir=${fftw_libdir} \
                   --with lapack=${lapack} --with lapack_version=${lapack_version} --with lapackdir=${lapackdir} \
                   --with netcdf=${netcdf} --with netcdf_includedir=${netcdf_includedir} --with netcdf_libdir=${netcdf_libdir} \
                   --with modules=${modules} --with default_version=1 \
                   --with parallel=1 --with openmpi=openmpi --with openmpi_version=${openmpi_version} \
                   --with ompi_libdir=${ompi_libdir} --with ompi_includedir=${ompi_includedir} --with ompi_bindir=${ompi_bindir} \
                   --with prefix=/opt/abinit/5.4.4p/${release} abinit.spec

Build the following for espresso:
---------------------------------

- espresso pseudopotentials::

     rpmbuild -bb --with modules --with default_version espresso_pp.spec

- espresso::

    compiler=gfortran43
    compiler_version=4.3.2
    compiler_libdir=/usr/lib64
    compiler_bindir=/usr/bin
    blas=acml
    blas_version=4.3.0
    blasdir=/opt/${blas}/${blas_version}/${compiler}64/lib
    lapack=acml
    lapack_version=4.3.0
    lapackdir=/opt/${lapack}/${lapack_version}/${compiler}64/lib
    fftw=fftw3
    fftw_libdir=/opt/${fftw}/3.2.1/12.${disttag}.${compiler}.${compiler_version}/lib64
    netcdf=netcdf4
    netcdf_includedir=/opt/${netcdf}/4.0.1/1.${disttag}.${compiler}.${compiler_version}/include
    netcdf_libdir=/opt/${netcdf}/4.0.1/1.${disttag}.${compiler}.${compiler_version}/lib64
    openmpi_version=1.3.3
    ompi_libdir=/opt/openmpi/${openmpi_version}-1.${disttag}.${compiler}.${compiler_version}/lib64
    ompi_includedir=/opt/openmpi/${openmpi_version}-1.${disttag}.${compiler}.${compiler_version}/include
    ompi_bindir=/opt/openmpi/${openmpi_version}-1.${disttag}.${compiler}.${compiler_version}/bin
    blacs=blacs
    blacsdir=/opt/blacs/1.1/24.${disttag}.${compiler}.${compiler_version}.openmpi.${openmpi_version}/lib64
    scalapack=scalapack
    scalapackdir=/opt/scalapack/1.8.0/1.${disttag}.${compiler}.${compiler_version}.openmpi.${openmpi_version}.${blas}.${blas_version}.${lapack}.${lapack_version}/lib64
    release=1.${disttag}.${compiler}.${compiler_version}.openmpi.${openmpi_version}.${blas}.${blas_version}.${lapack}.${lapack_version}.${fftw}

    rpmbuild --bb  --with blas=${blas} --with blas_version=${blas_version} --with blasdir=${blasdir} \
                   --with compiler=${compiler} --with compiler_version=${compiler_version} \
                   --with compiler_bindir=${compiler_bindir} --with compiler_libdir=${compiler_libdir} \
                   --with fftw=${fftw} --with fftw_libdir=${fftw_libdir} \
                   --with lapack=${lapack} --with lapack_version=${lapack_version} --with lapackdir=${lapackdir} \
                   --with netcdf=${netcdf} --with netcdf_includedir=${netcdf_includedir} --with netcdf_libdir=${netcdf_libdir} \
                   --with modules=${modules} --with default_version=1 \
                   --with parallel=1 --with openmpi=openmpi --with openmpi_version=${openmpi_version} \
                   --with ompi_libdir=${ompi_libdir} --with ompi_includedir=${ompi_includedir} --with ompi_bindir=${ompi_bindir} \
                   --with blacs=${blacs} --with blacsdir=${blacsdir} \
                   --with scalapack=${scalapack} --with scalapackdir=${scalapackdir} \
                   --with prefix=/opt/espresso/4.0.5/${release} espresso.spec

Build the following for yambo:
------------------------------

- yambo::

    compiler=gfortran43
    compiler_version=4.3.2
    compiler_libdir=/usr/lib64
    compiler_bindir=/usr/bin
    blas=acml
    blas_version=4.3.0
    blasdir=/opt/${blas}/${blas_version}/${compiler}64/lib
    lapack=acml
    lapack_version=4.3.0
    lapackdir=/opt/${lapack}/${lapack_version}/${compiler}64/lib
    fftw=fftw3
    fftw_libdir=/opt/${fftw}/3.2.1/12.${disttag}.${compiler}.${compiler_version}/lib64
    netcdf=netcdf4
    netcdf_includedir=/opt/${netcdf}/4.0.1/1.${disttag}.${compiler}.${compiler_version}/include
    netcdf_libdir=/opt/${netcdf}/4.0.1/1.${disttag}.${compiler}.${compiler_version}/lib64
    openmpi_version=1.3.3
    ompi_libdir=/opt/openmpi/${openmpi_version}-1.${disttag}.${compiler}.${compiler_version}/lib64
    ompi_includedir=/opt/openmpi/${openmpi_version}-1.${disttag}.${compiler}.${compiler_version}/include
    ompi_bindir=/opt/openmpi/${openmpi_version}-1.${disttag}.${compiler}.${compiler_version}/bin
    blacs=blacs
    blacsdir=/opt/blacs/1.1/24.${disttag}.${compiler}.${compiler_version}.openmpi.${openmpi_version}/lib64
    scalapack=scalapack
    scalapackdir=/opt/scalapack/1.8.0/1.${disttag}.${compiler}.${compiler_version}.openmpi.${openmpi_version}.${blas}.${blas_version}.${lapack}.${lapack_version}/lib64
    release=1.${disttag}.${compiler}.${compiler_version}.openmpi.${openmpi_version}.${blas}.${blas_version}.${lapack}.${lapack_version}.${fftw}

    rpmbuild --bb  --with blas=${blas} --with blas_version=${blas_version} --with blasdir=${blasdir} \
                   --with compiler=${compiler} --with compiler_version=${compiler_version} \
                   --with compiler_bindir=${compiler_bindir} --with compiler_libdir=${compiler_libdir} \
                   --with fftw=${fftw} --with fftw_libdir=${fftw_libdir} \
                   --with lapack=${lapack} --with lapack_version=${lapack_version} --with lapackdir=${lapackdir} \
                   --with netcdf=${netcdf} --with netcdf_includedir=${netcdf_includedir} --with netcdf_libdir=${netcdf_libdir} \
                   --with modules=${modules} --with default_version=1 \
                   --with parallel=1 --with openmpi=openmpi --with openmpi_version=${openmpi_version} \
                   --with ompi_libdir=${ompi_libdir} --with ompi_includedir=${ompi_includedir} --with ompi_bindir=${ompi_bindir} \
                   --with blacs=${blacs} --with blacsdir=${blacsdir} \
                   --with scalapack=${scalapack} --with scalapackdir=${scalapackdir} \
                   --with iotkdir=/opt/espresso/4.0.5/${release}/share/espresso/iotk \
                   --with prefix=/opt/yambo/3.2.0.315/${release} yambo.spec

Build the folowing for elk:
---------------------------

- elk species::

     rpmbuild -bb --with modules --with default_version elk-species.spec

- elk::

    compiler=gfortran43
    compiler_version=4.3.2
    compiler_libdir=/usr/lib64
    compiler_bindir=/usr/bin
    blas=acml
    blas_version=4.3.0
    blasdir=/opt/${blas}/${blas_version}/${compiler}64/lib
    lapack=acml
    lapack_version=4.3.0
    lapackdir=/opt/${lapack}/${lapack_version}/${compiler}64/lib
    release=1.${disttag}.${compiler}.${compiler_version}.openmp.${blas}.${blas_version}.${lapack}.${lapack_version}

    rpmbuild --bb  --with blas=${blas} --with blas_version=${blas_version} --with blasdir=${blasdir} \
                   --with compiler=${compiler} --with compiler_version=${compiler_version} \
                   --with compiler_bindir=${compiler_bindir} --with compiler_libdir=${compiler_libdir} \
                   --with lapack=${lapack} --with lapack_version=${lapack_version} --with lapackdir=${lapackdir} \
                   --with modules=${modules} --with default_version=1 \
                   --with parallel=1 \
                   --with prefix=/opt/elk/0.9.262/${release} elk.spec

Build the following for vtk:
----------------------------

- cmake::

   rpmbuild -bb --with bootstrap --without gui cmake.spec  # install the resulting RPM
   rpmbuild -bb xmlrpc-c.spec # install the resulting RPM
   rpm -e cmake
   rpmbuild -bb --without gui cmake.spec # install the resulting RPM

- vtkdata::

   cd ~/rpmbuild/SPECS
   rpmbuild -bb --with version1=4 --with version2=2 --with modules=1 --with default_version=1 \
            --with prefix=/opt/vtkdata/5.4.2/1.${disttag} vtkdata.spec

- vtk::

   cd ~/rpmbuild/SPECS
+                   ${modules_usage} --with default_version=1 \
                   --with system=${rpm_platform} \
                   --with python_version=${python_version} \
                   --with prefix=/opt/vtk/5.4.2/1${disttag_network}.${compiler}.${compiler_version}.python${python_version}.openmpi.${openmpi_version} vtk.spec

octopus
-------

- octopus

  **Note** March 15 2010: gfortran 4.1.2 on el5: Segmentation fault

  On a custom system build the following RPMS::

    . fys.set.octopus.default.sh
    . fys.set.atlas.default.sh

    (rpm_prefix=/usr && . fys.build.octopus.3.2.0.sh)

  On Niflheim build the following RPMS::

    . fys.set.Niflheim.gfortran43.4.3.2.sh
    . fys.set.Niflheim.openmpi.1.3.3.sh
    . fys.set.Niflheim.netcdf4.4.0.1.sh
    . fys.set.Niflheim.fftw3.3.2.1.sh
    . fys.set.blas.acml.4.3.0.sh
    . fys.set.lapack.acml.sh
    . fys.set.gsl.default.sh
    . fys.set.arpack.default.sh
    
    . fys.build.octopus.3.2.0.sh

TAU
---

- pdtoolkit

  `Program Database Toolkit <http://www.cs.uoregon.edu/research/pdt/>`_ is a framework for analyzing source code written in several programming languages
  and for making rich program knowledge accessible to developers of static and dynamic analysis tools. PDT is required by TAU.

  On a custom system build the following RPMS::

    . fys.set.gfortran.default.sh

    (rpm_prefix=/opt/pdtoolkit && . fys.build.pdtoolkit.sh)

  On Niflheim build the following RPMS::

    . fys.set.Niflheim.gfortran.4.1.2.sh
    
    . fys.build.pdtoolkit.sh
    #
    . fys.set.Niflheim.gfortran43.4.3.2.sh
    
    . fys.build.pdtoolkit.sh

- tau

  `TAU Performance System® <http://www.cs.uoregon.edu/research/tau/>`_ is a portable profiling and tracing toolkit
  for performance analysis of parallel programs written in Fortran, C, C++, Java, Python.

  On a custom system build the following RPMS::

    . fys.set.gfortran.default.sh
    . fys.set.openmpi.default.sh

    (rpm_prefix=/opt/tau && . fys.build.tau.sh)

  On Niflheim build the following RPMS::

    pdtoolkit_version=3.15

    module purge
    unset PDTROOT
    . fys.set.Niflheim.gfortran.4.1.2.sh
      module load PDTOOLKIT/${pdtoolkit_version}-1.el5.fys.${compiler}.${compiler_version}.python${python_version}
    . fys.set.Niflheim.openmpi.1.3.3.sh

    . fys.build.tau.sh
    #
    module purge
    unset PDTROOT
    . fys.set.Niflheim.gfortran43.4.3.2.sh
      module load PDTOOLKIT/${pdtoolkit_version}-1.el5.fys.${compiler}.${compiler_version}.python${python_version}
    . fys.set.Niflheim.openmpi.1.3.3.sh
    
    . fys.build.tau.sh

vasp
----

Installed with restricted access under `vasp` UNIX group (needs te be created in advance).

- vasp potentials

  Download ``potpaw/potcar.date.tar``, ``potpaw_GGA/potcar.date.tar``, and ``potpaw_PBE/potcar.date.tar``
  to ``~/rpmbuild/SOURCES``. Create links to the downloaded files so the files
  are named explicitly with the string ``date`` (not the actual dates), for example::

    ls -al ~/rpmbuild/SOURCES/potpaw_*potcar.date.tar
    lrwxrwxrwx 1 rpmbuild campnone   29 Sep 25 17:15 ../SOURCES/potpaw_GGA_potcar.date.tar -> potpaw_GGA/potcar.06Feb03.tar
    lrwxrwxrwx 1 rpmbuild campnone   29 Sep 25 17:14 ../SOURCES/potpaw_PBE_potcar.date.tar -> potpaw_PBE/potcar.05Feb03.tar
    lrwxrwxrwx 1 rpmbuild campnone   25 Sep 25 17:14 ../SOURCES/potpaw_potcar.date.tar -> potpaw/potcar.05Feb03.tar

  **Note** this package is **not** relocatable!

  On a custom system build the following RPMS::

    (default_version_usage="--with default_version" && modules_usage="--without modules" && . fys.build.vasp-potpaw.sh)

  On Niflheim build the following RPMS::

    . fys.build.vasp-potpaw.sh

- vasp

  `vasp <http://cms.mpi.univie.ac.at/vasp/>`_. Download ``vasp.5.X.Y.tar.gz`` and  ``vasp.5.lib.tar.gz`` to ``~/rpmbuild/SOURCES``.
  Optionally download also ``vtstcode.tar.gz`` from http://theory.cm.utexas.edu/vtsttools/download.html.

  On a custom system build the following RPMS::

    # Compile with VASP TST library: http://theory.cm.utexas.edu/vtsttools/downloads/
    hdf=none
    tst=false # or true

    . fys.set.vasp.5.2.11.default.sh

    (rpm_prefix=/usr && . fys.build.vasp.sh)

  On Niflheim build the following RPMS::

    # gfortran 4.1.2 is the only of our compilers that works! MD 6 Oct 2011
    # Compile with VASP TST library: http://theory.cm.utexas.edu/vtsttools/downloads/
    hdf=none
    tst=false # or true

    . fys.set.Niflheim.vasp.5.2.12.gfortran.4.1.2.openmpi.1.3.3.acml.4.0.1.acml.4.0.1.fftw3.sh
    
    . fys.build.vasp.sh
    #
    # 25 Sep 2009: segmentation fault when compiling dipol.f90
    hdf=none
    tst=false # or true

    . fys.set.Niflheim.vasp.5.2.2.gfortran43.4.3.2.openmpi.1.3.3.acml.4.3.0.acml.4.3.0.fftw3.sh

    . fys.build.vasp.sh
    #
    # 11 May 2010: in dfast.f90"LINCOM" is the name of this program unit, therefore it must not be use associated from module "DFAST".
    hdf=none
    tst=false # or true

    . fys.set.Niflheim.vasp.5.2.2.open64.4.2.3.openmpi.1.3.3.acml.4.4.0.acml.4.4.0.fftw3.sh

    . fys.build.vasp.sh
    #
    # only on thul
    # 15 Feb 2011; 6 Oct 2011: forrtl: severe (174): SIGSEGV, segmentation fault occurred during DAV
    hdf=none
    tst=false # or true

    . fys.set.Niflheim.vasp.5.2.12.ifort.11.1.openmpi.1.3.3.acml.4.4.0.acml.4.4.0.fftw3.sh

    . fys.build.vasp.sh

exciting
--------

- exciting species

  **Note** this package is **not** relocatable!

  On a custom system build the following RPMS::

    (default_version_usage="--with default_version" && modules_usage="--without modules" && . fys.build.exciting-species.9.10.sh)

  On Niflheim build the following RPMS::

    . fys.build.exciting-species.9.10.sh

- exciting

  **Note**: currently (24 Nov 2009) perl-XML-SAX-0.14-5 is broken `<https://bugzilla.redhat.com/show_bug.cgi?id=438291>`_ on EL5; if exciting's tests complain about::

    could not find ParserDetails.ini

  do as root::

   perl -MXML::SAX -e "XML::SAX->add_parser(q(XML::SAX::PurePerl))->save_parsers()"

  On a custom system build the following RPMS::

    # March 12 2010: build fails on el5 with gfortran 4.1.2 and 4.3.2
    . fys.set.gfortran.default.sh
    . fys.set.openmpi.default.sh
    . fys.set.arpack.default.sh
    . fys.set.atlas.default.sh

    (rpm_prefix=/usr && thread_mode=nomp && . fys.build.exciting.9.10.sh)

    # March 12 2010: build fails on el5 with gfortran 4.1.2 and 4.3.2
    . fys.set.gfortran.default.sh
    . fys.set.openmpi.default.sh
    . fys.set.arpack.default.sh
    . fys.set.blas.default.sh
    . fys.set.lapack.default.sh

    (rpm_prefix=/usr && thread_mode=nomp && . fys.build.exciting.9.10.sh)

  On Niflheim build the following RPMS::

    # only on fjorm
    . fys.set.Niflheim.g95.0.91.sh
    . fys.set.Niflheim.openmpi.1.3.3.sh
    . fys.set.blas.acml.4.3.0_mp.sh
    . fys.set.lapack.acml.sh

    (thread_mode=mp && . fys.build.exciting.9.10.sh)

    # only on thul
    . fys.set.Niflheim.ifort.11.0.sh
    . fys.set.Niflheim.openmpi.1.3.3.sh
    . fys.set.Niflheim.mkl.10.1.3.027.sh

    (thread_mode=nomp && . fys.build.exciting.9.10.sh)

fleur
-----

- fleur

  `fleur <http://www.flapw.de/>`_. Download the source to ``~/rpmbuild/SOURCES``.

  On a custom system build the following RPMS::

    . fys.set.fleur.default.sh

    (rpm_prefix=/usr && . fys.build.fleur.sh)

  On Niflheim build the following RPMS::

    . fys.set.Niflheim.fleur.v26b.gfortran43.4.3.2.openmpi.1.3.3.acml.4.4.0.acml.4.4.0.sh

    . fys.build.fleur.sh
    # only on thul # Sep 04 2010: build fails with forrtl: severe (174): SIGSEGV, segmentation fault occurred
    . fys.set.Niflheim.fleur.v26b.ifort.11.0.openmpi.1.3.3.mkl.10.1.3.027.mkl_lapack.10.1.3.027.sh

    . fys.build.fleur.sh

gulp
----

Installed with restricted access under `gulp` UNIX group (needs te be created in advance).

- gulp

  `gulp <https://www.ivec.org/gulp/>`_. Download ``gulp.3.4.source.tar.gz`` ``~/rpmbuild/SOURCES``.

  On a custom system build the following RPMS::

    . fys.set.gfortran.default.sh
    . fys.set.blas.default.sh
    . fys.set.lapack.default.sh

    (rpm_prefix=/usr && thread_mode=mp && . fys.build.gulp.sh)

  On Niflheim build the following RPMS::

    # OpenMP version
    . fys.set.Niflheim.gfortran43.4.3.2.sh
    . fys.set.blas.acml.4.3.0_mp.sh
    . fys.set.lapack.acml.sh
    
    (thread_mode=mp && . fys.build.gulp.sh)


cmr
---

Computational Materials Repository.

On a custom system build the following RPMS::

  (rpm_prefix=/usr && rpmbuild -bb ${default_version_usage} ${modules_usage} cmr.spec)

On Niflheim build the following RPMS::

  module load DACAPO
  module load GPAW
  module unload ASE3
  module load ASE3
  module load SCIENTIFICPYTHON/2.8

  # if needed, create tar file
  cd ~/rpmbuild/SOURCES && python cmr_release.py
  cd ~/rpmbuild/SPECS
  . fys.build.cmr.sh
-Line 1454:
+Line 2651:
+**Note** this section is outdated.
-Line 1492:
+Line 2691:
-On "Golden Client"
------------------

Login, as root, to the "Golden Client"::

 ssh n001

Enable nfs mount of the `server` home directory
- follow 'Enable nfs mount on the "Golden Client"' from `configuring NFS <Building_a_Cluster_-_Tutorial/configuring_NFS>`_.
After this do::

 cd /home/dulak-server/rpm/campos

 rpm -ivh campos-dacapo-2*

If getting::

  package example_package.el5.i386 is already installed

remove these packages with::

  rpm -e --nodeps example_package

to allow the installation to proceed.

Make sure that both python-numeric versions are installed::

  rpm -q python-numeric

This command will show a list of packages that need to be installed to fulfill `dacapo` dependencies.
All these packages should be already under ``/home/dulak-server/rpm``.
Remember to test the `dacapo` and `gpaw` installations on the "Golden Client" too.

If you are installing workstation only, your setup is ready for testing - go to `benchmarking and maintenance <Building_a_Cluster_-_Tutorial/benchmarking_and_maintenance>`_.

If you are building a cluster go **back** to `installing and configuring systemimager <Building_a_Cluster_-_Tutorial/installing_and_configuring_systemimager>`_,