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

Differences between revisions 385 and 523 (spanning 138 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 385 as of 2010-05-11 20:52:49 → 
  Size: 78350
  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 24:
-We host a yum repository, which contains RPM packages of our software for the following systems: el (RedHat Enterprise Linux, or CentOS), fc (Fedora):
+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):
-Line 32:
+Line 33:
+  **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).
-Line 33:
+Line 38:
-  Moreover on a fc system you do not need to include any external repositories (epel, atrpms).
+  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>`_
-Line 39:
+Line 48:
-  **Note**: on el `configure external el repositories <https://wiki.fysik.dtu.dk/niflheim/Cluster_software_-_RPMS#configure-external-el-repos>`_
+  **Note**: on el `configure external repositories <https://wiki.fysik.dtu.dk/niflheim/Cluster_software_-_RPMS#configure-external-repos>`_
-Line 43:
+Line 52:
-Line 48:
+Line 56:
-      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
+    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
-Line 61:
+Line 69:
-Configure external el repos
===========================
+  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!!!
-Line 108:
+Line 130:
-Line 114:
+Line 137:
-    svn co https://svn.fysik.dtu.dk/projects/rpmbuild/trunk rpmbuild
+    svn co https://svn.fysik.dtu.dk/projects/rpmbuild/trunk ~/rpmbuild
-Line 121:
+Line 144:
+   **Note**: if installing on a system different than el5 edit the `rpm_platform` and `egg_info` variables.
-Line 161:
+Line 186:
-   yumdownloader --resolve texlive-latex emacs-auctex tex-preview
+   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
-Line 164:
+Line 194:
-   yumdownloader --resolve gcc-gfortran blas-devel lapack-devel python-devel
+   yumdownloader --resolve gcc-gfortran blas-devel lapack-devel python-devel python-sphinx
-Line 171:
+Line 201:
-   yumdownloader --resolve gcc43-c++ gcc43-gfortran
+   yumdownloader --resolve perl-XML-SAX # for exciting
   yumdownloader --resolve ImageMagick # for ASE3

   yumdownloader --resolve gcc43-c++ gcc43-gfortran # only on EL5 == 5.2
-Line 198:
+Line 230:
-   exclude=netcdf-* netcdf3-* fftw-* fftw2-* fftw3-* python-numeric openmpi-* libgfortran4* gcc4* libstdc++4* libgomp-*
+   exclude=netcdf-* netcdf3-* fftw-* fftw2-* fftw3-* python-numeric openmpi-* libgfortran4* gcc4* libstdc++4* libgomp-* ScientificPython-*
-Line 240:
+Line 272:
-Install icc/ifort compilers (only on the login nodes, packages available under `/home/data/Intel` with restricted access), install (using ``rpm -ivh``) 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**)::

  cd ~/rpmbuild/SPECS
  rpmbuild -bb ${modules_usage} intel-redist.spec
+**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 ${modules_usage} --with major_version=2011 --with version1=1 --with version2=107 intel-redist.spec
-Line 273:
+Line 302:
-  cp /scratch/rpmbuild/intel-11.1.046/11.1.046-1.intel64.${disttag} ~rpmbuild/modulefiles/${FYS_PLATFORM}/ifort
+  cp /scratch/rpmbuild/intel-2011.1.107/2011.1.107-1.intel64${disttag} ~rpmbuild/modulefiles/${FYS_PLATFORM}/ifort
-Line 275:
+Line 304:
-  ln -s 11.1.046-1.intel64.${disttag} 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 287:
+Line 376:
-- install RPMS (on the login and computes 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``)::
+- 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``)::
-Line 315:
+Line 404:
-- provide the module file `~rpmbuild/modulefiles/${FYS_PLATFORM}/ifort/10.1.015-1.intel64.${disttag}`::
+- provide the module file `~rpmbuild/modulefiles/${FYS_PLATFORM}/ifort/10.1.015-1.intel64${disttag}`::
-Line 331:
+Line 420:
-    ln -s 10.1.015-1.intel64.${disttag} 10.1-1
+    ln -s 10.1.015-1.intel64${disttag} 10.1-1
-Line 341:
+Line 430:
-Install mkl RPMS (`intel-mkl`, `intel-mkllibdev`, `intel-mkllib`), and build mkl compatibility package (only on **thul**)::
+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 344:
+Line 438:
-  export mkl=10.1.3.027
+  export mkl=10.3.3.174
-Line 347:
+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 350:
+Line 445:
-  cd ~/rpmbuild/SPECS
+  cd ~/rpmbuild/SPECS # as rpmbuild
  rpmbuild -bb --with version1=3 --with version2=3 --with version3=174 ${modules_usage} --with platform=intel64 intel-redist-mkl.spec
  # **Warning**: mkl < 10.3 uses em64t
-Line 359:
+Line 456:
-  cp /tmp/intel-mkl-${mkl}/${mkl}-1.${disttag}.em64t ~rpmbuild/modulefiles/${FYS_PLATFORM}/mkl
+  cp /tmp/intel-mkl-${mkl}/${mkl}-1${disttag}.em64t ~rpmbuild/modulefiles/${FYS_PLATFORM}/mkl
-Line 361:
+Line 458:
-  ln -s ${mkl}-1.${disttag}.em64t 10.1p-027
+  ln -s ${mkl}-1${disttag}.em64t 10.1p-027
-Line 378:
+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 .
-Line 383:
+Line 487:
+  # 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 402:
+Line 517:
-  rpm -ivh --nodeps --oldpackage ~rpmbuild/${FYS_PLATFORM}/RPMS/openmpi-1.3.3-1.${disttag}.ifort.11.1.x86_64.rpm
+  rpm -ivh --nodeps --oldpackage ~rpmbuild/${FYS_PLATFORM}/RPMS/openmpi-1.3.3-1${disttag}.ifort.11.1.x86_64.rpm
-Line 433:
+Line 548:
-    #
    . fys.set.Niflheim.open64.4.2.1.sh
    . fys.set.blas.acml.4.3.0.sh

    . fys.build.acml.sh
-Line 455:
+Line 565:
-Line 491:
+Line 602:
-  `GotoBLAS <http://www.tacc.utexas.edu/resources/software/#blas>`_ contains optimized BLAS libraries,
  and is available for academic community after registration. Does not work in Intel Nehalem.

  Download **GotoBLAS-1.26.tar.gz** (**Warning** outdated release of GotoBLAS is no longer available) and  **GotoBLAS2-1.23.tar.gz** (supports Nehalem) to ~/rpmbuild/SOURCES.
+  `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.
-Line 501:
+Line 611:
-    blas_version=1.26
-Line 504:
+Line 613:
-    (rpm_prefix=/usr && . fys.build.goto.sh)
+    (rpm_prefix=/usr && . fys.build.goto2.sh)
-Line 508:
+Line 617:
+    . 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 538:
+Line 668:
-  GotoBLAS2::

    . 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
-Line 671:
+Line 785:
+     module load python-setuptools
     module load python-nose
-Line 689:
+Line 806:
-      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}
+      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}
-Line 757:
+Line 874:
-      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}
+      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}.${lapack_version}
-Line 761:
+Line 878:
-      ldd `rpm -ql python-numeric-24.2-4.${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}.${lapack_version} | grep _dotblas.so`
+      ldd `rpm -ql python-numeric-24.2-4${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`
-Line 775:
+Line 892:
+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
-Line 793:
+Line 964:
+     #
     . 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
    #
-Line 827:
+Line 1006:
+     # 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
-Line 872:
+Line 1101:
-  On Niflheim build the following RPMS::

     . fys.build.docutils.0.5.sh

  If using modules::
+ On Niflheim build the following RPMS::

    . fys.build.docutils.0.5.sh

 If using modules::
-Line 880:
+Line 1109:
-  else, if not using the default "/usr" prefix::
+ else, if not using the default "/usr" prefix::
-Line 891:
+Line 1120:
-  On Niflheim build the following RPMS::

     . fys.build.pytz.2008g.sh

  If using modules::
+ On Niflheim build the following RPMS::

    . fys.build.pytz.2008g.sh

 If using modules::
-Line 899:
+Line 1128:
-  else, if not using the default "/usr" prefix::
+ else, if not using the default "/usr" prefix::
-Line 910:
+Line 1139:
-  On Niflheim build the following RPMS::

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

  If using modules::
+ On Niflheim build the following RPMS::

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

 If using modules::
-Line 918:
+Line 1147:
-  else, if not using the default "/usr" prefix::
+ else, if not using the default "/usr" prefix::
-Line 927:
+Line 1156:
-    (rpm_prefix=/usr && . fys.build.python-matplotlib.0.99.1.2.sh)

  On Niflheim build the following RPMS::

     . fys.build.python-matplotlib.0.99.1.2.sh
+    (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
-Line 940:
+Line 1174:
-  On Niflheim build the following RPMS::

     . fys.build.ase2.2.3.13.sh
+ On Niflheim build the following RPMS::

    . fys.build.ase2.2.3.13.sh
-Line 981:
+Line 1215:
+    #
    . fys.set.Niflheim.open64.4.2.4.sh

    . fys.build.fftw2.2.1.5.sh
-Line 989:
+Line 1228:
-  **Note** this package is **not** relocatable!

.. _campos-dacapo-pseudopotentials-1.tar.gz: attachment:campos-dacapo-pseudopotentials-1.tar.gz

campos-dacapo-pseudopotentials-1.tar.gz_
+  **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
-Line 1019:
+Line 1256:
-  Note that FC's fftw version 3 is incompatible with `dacapo`.
+  **Note**: fftw version 3 is incompatible with `dacapo`.
-Line 1046:
+Line 1283:
+    #
    . 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
    #
-Line 1124:
+Line 1369:
+    #
    . 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
-Line 1242:
+Line 1495:
-    cd ~/rpmbuild/SOURCES&& wget http://ftp.gnu.org/pub/gnu/auctex/auctex-11.85.tar.gz
+    cd ~/rpmbuild/SOURCES&& wget http://ftp.gnu.org/pub/gnu/auctex/auctex-11.86.tar.gz
-Line 1256:
+Line 1509:
+    module load NUMPY
-Line 1264:
+Line 1518:
-    release=${major_version}.${version1}.${version2}.${version_svn}/1.${disttag}.python${python_version}
+    release=${major_version}.${version1}.${version2}.${version_svn}/1${disttag}.python${python_version}
-Line 1269:
+Line 1523:
-    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${python_version} \
+    rm /home/camp/rpmbuild/Intel-Nehalem-el5/RPMS/campos-ase3-${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} \
-Line 1289:
+Line 1543:
+    . fys.set.Niflheim.open64.4.2.4.sh
    . fys.set.Niflheim.openmpi.1.4.3.sh

    . fys.build.blacs.sh

    # older builds
    #
-Line 1317:
+Line 1578:
-Line 1346:
+Line 1608:
+    #
    . 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

    #
-Line 1352:
+Line 1652:
-    . fys.build.scalapack.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
-Line 1361:
+Line 1670:
-    . fys.build.scalapack.sh
+    . fys.build.scalapack.1.8.0.sh
-Line 1370:
+Line 1679:
-    . fys.build.scalapack.sh
+    . fys.build.scalapack.1.8.0.sh

    # old old builds
-Line 1379:
+Line 1689:
-    . fys.build.scalapack.sh
+    . fys.build.scalapack.1.8.0.sh
-Line 1388:
+Line 1699:
-    . fys.build.scalapack.sh
+    . fys.build.scalapack.1.8.0.sh
-Line 1397:
+Line 1708:
-    . fys.build.scalapack.sh
+    . fys.build.scalapack.1.8.0.sh
-Line 1407:
+Line 1718:
-    . fys.build.scalapack.sh
+    . fys.build.scalapack.1.8.0.sh
-Line 1416:
+Line 1727:
-    . fys.build.scalapack.sh
+    . fys.build.scalapack.1.8.0.sh
-Line 1426:
+Line 1737:
-    . fys.build.scalapack.sh
+    . fys.build.scalapack.1.8.0.sh
-Line 1435:
+Line 1746:
-    . fys.build.scalapack.sh
+    . fys.build.scalapack.1.8.0.sh
-Line 1443:
+Line 1754:
-    . fys.build.scalapack.sh
+    . fys.build.scalapack.1.8.0.sh
-Line 1451:
+Line 1762:
-    . fys.build.scalapack.sh
+    . fys.build.scalapack.1.8.0.sh
-Line 1460:
+Line 1771:
-    . fys.build.scalapack.sh
+    . fys.build.scalapack.1.8.0.sh
-Line 1469:
+Line 1780:
-    . fys.build.scalapack.sh
+    . fys.build.scalapack.1.8.0.sh
-Line 1529:
+Line 1840:
-  On Niflheim build the following RPMS::
+  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
    #
-Line 1620:
+Line 1950:
-    #
    # 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.goto2.1.13.sh
    . fys.set.Niflheim.blacs.1.1.sh
    . fys.set.Niflheim.scalapack.1.8.0.sh

    . fys.build.gpaw.sh
-Line 1714:
+Line 2032:
+    #
    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
-Line 1715:
+Line 2045:
+    module load ASE3
-Line 1720:
+Line 2051:
-    . fys.set.Niflheim.Asap.3.2.6.ifort.11.0.openmpi.1.3.3.sh
+    module load ASE3
    module load ifort/11.1-1
    . fys.set.Niflheim.Asap.3.2.6.ifort.11.1.openmpi.1.3.3.sh
-Line 1727:
+Line 2060:
-  **Note** this package is **not** relocatable!

.. _abinit-pseudopotentials-1.tar.gz: attachment:abinit-pseudopotentials-1.tar.gz

abinit-pseudopotentials-1.tar.gz_
-Line 1735:
+Line 2062:
-  On a custom system build the following RPMS::

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

  On Niflheim build the following RPMS::

    . fys.build.abinit-pseudopotentials.1.sh
+  **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
-Line 1757:
+Line 2088:
+    hdf=none
-Line 1801:
+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 1804:
+Line 2136:
-    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
+    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
-Line 1808:
+Line 2140:
-    blacsdir=/opt/blacs/1.1/24.${disttag_network}.${compiler}.${compiler_version}.openmpi.${openmpi_version}/lib64
+    blacsdir=/opt/blacs/1.1/24${disttag_network}.${compiler}.${compiler_version}.openmpi.${openmpi_version}/lib64
-Line 1810:
+Line 2142:
-    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}
+    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}
-Line 1869:
+Line 2201:
+    # 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
-Line 1880:
+Line 2216:
-    . fys.set.yambo.3.2.1.448.default.sh
+    . fys.set.yambo.default.sh
-Line 1887:
+Line 2223:
+    # 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
    #
-Line 1888:
+Line 2230:
+    hdf=none
-Line 1893:
+Line 2236:
+    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
-Line 1907:
+Line 2262:
-    (default_version_usage="--with default_version" && modules_usage="--without modules" && . fys.build.elk-species.1.0.0.sh)

  On Niflheim build the following RPMS::

    . fys.build.elk-species.1.0.0.sh
+    (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
-Line 1918:
+Line 2273:
-    . fys.set.atlas.default.sh

    (rpm_prefix=/usr && thread_mode=mp && . fys.build.elk.1.0.0.sh)

  On Niflheim build the following RPMS::

    . fys.set.Niflheim.gfortran43.4.3.2.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
-Line 1928:
+Line 2287:
-    (thread_mode=mp && . fys.build.elk.1.0.0.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)
-Line 1954:
+Line 2328:
-             --with prefix=/opt/vtkdata/5.4.2/1.${disttag} vtkdata.spec
+             --with prefix=/opt/vtkdata/5.4.2/1${disttag} vtkdata.spec
-Line 1968:
+Line 2342:
-    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
+    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
-Line 1980:
+Line 2354:
-                   --with prefix=/opt/vtk/5.4.2/1.${disttag_network}.${compiler}.${compiler_version}.python${python_version}.openmpi.${openmpi_version} vtk.spec
+                   --with prefix=/opt/vtk/5.4.2/1${disttag_network}.${compiler}.${compiler_version}.python${python_version}.openmpi.${openmpi_version} vtk.spec
-Line 2093:
+Line 2467:
-  `vasp <http://cms.mpi.univie.ac.at/vasp/>`_. Download ``vasp.5.X.tar.gz`` and  ``vasp.5.lib.tar.gz`` to ``~/rpmbuild/SOURCES``.
  Optionally download also ``vtstcode.tar.gz`` from http://theory.cm.utexas.edu/vtsttools/downloads/.
+  `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.
-Line 2099:
+Line 2473:
+    hdf=none
-Line 2100:
+Line 2475:
-    if [ "$tst" == "false" ];
    then
       vasp_tst='.'
    else
       vasp_tst='.tst.'
    fi

    . fys.set.gfortran.default.sh
    . fys.set.openmpi.default.sh
    . fys.set.netcdf.default.sh
    . fys.set.fftw3.default.sh
    . fys.set.blas.default.sh
    . fys.set.lapack.default.sh
    blacs=none
    scalapack=none
    major_version=5
    version1=2
    release=1.${disttag_network}${vasp_tst}${compiler}.${compiler_version}.openmpi.${openmpi_version}.${blas}.${blas_version}.${lapack}.${lapack_version}.${fftw}
+    . fys.set.vasp.5.2.11.default.sh
-Line 2123:
+Line 2482:
+    # gfortran 4.1.2 is the only of our compilers that works! MD 6 Oct 2011
-Line 2124:
+Line 2484:
+    hdf=none
-Line 2126:
+Line 2487:
-    . fys.set.Niflheim.vasp.5.2.gfortran.4.1.2.openmpi.1.3.3.acml.4.0.1.acml.4.0.1.sh
+    . 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
-Line 2131:
+Line 2492:
-    . fys.set.Niflheim.vasp.5.2.gfortran43.4.3.2.openmpi.1.3.3.acml.4.3.0.acml.4.3.0.sh
+    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
-Line 2136:
+Line 2499:
-    . fys.set.Niflheim.vasp.5.2.open64.4.2.3.openmpi.1.3.3.acml.4.4.0.acml.4.4.0.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
-Line 2175:
+Line 2551:
+    # 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)
-Line 2199:
+Line 2584:
-  Build the following RPMS::

    cd ~/rpmbuild/SPECS

    major_version=25
    version1=g
    if [ "$version1" == "None" ];
    then
       fleur_version=${major_version}
    else
       fleur_version=${major_version}.${version1}
    fi

    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
    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 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/fleur/${fleur_version}/${release} fleur.spec

    module load g95 # only on fjorm

    compiler=g95 # only on fjorm
    compiler_version=0.91
    compiler_libdir=/opt/g95/0.91/lib/gcc-lib/x86_64-unknown-linux-gnu/4.0.3
    compiler_bindir=/opt/g95/0.91/bin
    blas=blas
    blas_version=3.0.37.el5
    blasdir=/usr/lib64
    lapack=lapack
    lapack_version=${blas_version}
    lapackdir=/usr/lib64
    openmpi_version=1.3.3
    ompi_libdir=/opt/openmpi/${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}.${compiler_version}/bin
    blacs=none
    scalapack=none
    release=1.${disttag_network}.${compiler}.${compiler_version}.${thread_mode}.openmpi.${openmpi_version}.${blas}.${blas_version}.${lapack}.${lapack_version}

    !rpmbuild # as rpmbuild above

    module load ifort # only on thul

    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
    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}
    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=mkl
    blacsdir=${blasdir}
    scalapack=mkl
    scalapackdir=${blasdir}
    release=1.${disttag_network}.${compiler}.${compiler_version}.${thread_mode}.openmpi.${openmpi_version}.${blas}.${blas_version}.${lapack}.${lapack_version}

    !rpmbuild # as rpmbuild above
+  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
-Line 2300:
+Line 2609:
-  Build the following RPMS::

    major_version=3
    version1=4

    cd ~/rpmbuild/SPECS
    thread_mode=nomp

    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}.${compiler_version}.${thread_mode}.${blas}.${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 thread_mode=${thread_mode} --with parallel=1 \
                   ${modules_usage} --with default_version=1 \
                   --with system=${rpm_platform} \
                   --with prefix=/opt/gulp/${major_version}.${version1}/${release} gulp.spec

    # multithreaded
    thread_mode=mp
    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}/${compiler}64_${thread_mode}/lib
    lapack=acml
    lapack_version=4.3.0
    lapackdir=/opt/${lapack}/${lapack_version}/${compiler}64_${thread_mode}/lib
    release=1.${disttag}.${compiler}.${compiler_version}.${thread_mode}.${blas}.${blas_version}.${lapack}.${lapack_version}

    !rpmbuild # as rpmbuild above
+  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)
-Line 2363:
+Line 2644:
-  version_svn=51
+  # if needed, create tar file
-Line 2366:
+Line 2647:
-  rpmbuild -bb --with version_svn=${version_svn} \
               ${default_version_usage} ${modules_usage} --with cmr_repository="/home/niflheim/repository/db" \
               --with prefix=/opt/cmr/${version_svn}/1.${disttag}.python${python_version} cmr.spec
+  . fys.build.cmr.sh