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

Differences between revisions 1 and 398 (spanning 397 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):

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 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 (epel, atrpms).
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 el 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 el repos

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
# 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 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

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: 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

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 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):

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-mkllibdev, intel-mkllib), and build mkl compatibility package (only on thul):

cd ~/rpmbuild/SOURCES
export mkl=10.1.3.027
mkdir ${mkl}
cp -rp /opt/intel/mkl/${mkl}/lib ${mkl}
cp -rp /opt/intel/mkl/${mkl}/doc ${mkl}
tar zcf intel-redist-mkl-${mkl}.tar.gz ${mkl}

cd ~/rpmbuild/SPECS
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.

openmpi

Build a custom openmpi, using torque support:

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.open64.4.2.1.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.4.4.0.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, 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. 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:
blas_version=1.26
. fys.set.gfortran.default.sh

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

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:

. 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

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.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

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.0.99.1.2.sh)

On Niflheim build the following RPMS::

   . fys.build.python-matplotlib.0.99.1.2.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

# 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-1.tar.gz

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

campos-dacapo-python

Requires campos-ase2.

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

campos-dacapo

Note that FC's 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.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
# 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-11.85.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:

. 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.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.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.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.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.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.blacs.1.1.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.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.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.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.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.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.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.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.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.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.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.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 build the following RPMS:

. 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

#
# 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

# 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:

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

. fys.build.Asap.sh

# only on thul
. fys.set.Niflheim.Asap.3.2.6.ifort.11.0.openmpi.1.3.3.sh

. fys.build.Asap.sh

abinit

Note this package is not relocatable!

abinit-pseudopotentials-1.tar.gz

abinit pseudopotentials

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

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

. 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

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.3.2.1.448.default.sh
. fys.set.atlas.default.sh

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

On Niflheim build the following RPMS:

. 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

. 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

. 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.1.0.0.sh)

On Niflheim build the following RPMS:

. fys.build.elk-species.1.0.0.sh

elk

On a custom system build the following RPMS:

. fys.set.gfortran.default.sh
. 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.blas.acml.4.3.0_mp.sh
. fys.set.lapack.acml.sh

(thread_mode=mp && . fys.build.elk.1.0.0.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.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/.

On a custom system build the following RPMS:

# Compile with VASP TST library: http://theory.cm.utexas.edu/vtsttools/downloads/
tst=false # or true

. fys.set.vasp.5.2.default.sh

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

On Niflheim build the following RPMS:

# Compile with VASP TST library: http://theory.cm.utexas.edu/vtsttools/downloads/
tst=false # or true

. fys.set.Niflheim.vasp.5.2.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

. fys.set.Niflheim.vasp.5.2.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".
. fys.set.Niflheim.vasp.5.2.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
. fys.set.Niflheim.vasp.5.2.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.

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

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.

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

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

version_svn=82
cd ~/rpmbuild/SOURCES && python cmr_release.py
cd ~/rpmbuild/SPECS
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

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 1 as of 2009-06-06 12:05:58 → 
  Size: 11167
  Editor: MarcinDulak
  Comment:
+   ← Revision 398 as of 2010-08-04 10:59:26 → ⇥
  Size: 79335
  Editor: MarcinDulak
  Comment: new cmr
-Deletions are marked like this.
+Additions are marked like this.
 Line 1:
-This page describes the necessary steps for installing
`gpaw <https://wiki.fysik.dtu.dk/gpaw>`_ and `dacapo <https://wiki.fysik.dtu.dk/dacapo>`_ programs.

On the server
-------------
+## page was renamed from Building a Cluster - Tutorial/test dl160
.. _32H2O.xyz: attachment:32H2O.xyz

This page below describes:

- configuration of the `fys` yum repository,

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


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

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

.. Contents::

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

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

- 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 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 (epel, atrpms).

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

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

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

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

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

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

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

On RedHat Enterprise Linux or CentOS, as root:

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

 - `ATrpms <http://atrpms.net/>`_:

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

       enabled=0

   - fast way::

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

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

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

       enabled=0

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

- 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
-Line 10:
+Line 163:
-As root:

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

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

   yum install yum-utils

- if not yet done, go to `configuring rpmbuild <Building_a_Cluster_-_Tutorial/configuring_rpmbuild>`_,

- **Skip this step if not installing on "dulak-server"**: create the ``/home/dulak-server/rpm/external`` directory (to keep external RPMS)::

   mkdir /home/dulak-server/rpm/external; cd /home/dulak-server/rpm/external

- install official packages::

   yumdownloader --resolve gcc-gfortran gcc43-c++ gcc43-gfortran blas-devel lapack-devel python-devel
+- 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
   # el5 packages
   yumdownloader --resolve emacs binutils-devel glib-devel libstdc++-devel
   yumdownloader --resolve gcc-gfortran blas-devel lapack-devel python-devel python-sphinx
-Line 45:
+Line 174:
-   yum localinstall *

- install `atrpms` packages (``vtk-python`` is currently unavailable 16 Apr 2009)::

   yumdownloader --resolve --enablerepo=atrpms vtk-python fftw2 fftw2-devel netcdf netcdf-devel arpack-devel graphviz
+   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 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
-Line 51:
+Line 187:
-   rpm --import RPM-GPG-KEY.atrpms
   yum localinstall *

- install the packages from `epel`::

   yumdownloader --resolve --enablerepo=epel fftw3 fftw3-devel python-matplotlib python-docutils jmol
+   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
-Line 59:
+Line 196:
-   rpm --import RPM-GPG-KEY-EPEL
   yum localinstall *
   source /etc/profile.d/modules.sh
+   rpm --import RPM-GPG-KEY-EPEL # as root
   yum localinstall * # as root

- on Niflheim **only**: remove default openmpi::

   yum remove openmpi openmpi-libs
-Line 65:
+Line 205:
-   exclude=netcdf-* netcdf3-* fftw-* fftw2-* fftw3-* python-numeric openmpi-*
+   exclude=netcdf-* netcdf3-* fftw-* fftw2-* fftw3-* python-numeric openmpi-* libgfortran4* gcc4* libstdc++4* libgomp-* ScientificPython-*
-Line 70:
+Line 210:
-As root::

 cd ~/rpmbuild/SPECS

**Skip this step if not installing on "dulak-server"**: create the ``/home/dulak-server/rpm/campos`` directory (to keep custom built RPMS)::

  mkdir /home/dulak-server/rpm/campos

Preferably build a custom openmpi, using the latest gcc/gfortran and torque support::

  wget http://www.open-mpi.org/software/ompi/v1.3/downloads/openmpi-1.3.1.tar.bz2 \
       -O ~/rpmbuild/SOURCES/openmpi-1.3.1.tar.bz2
  export rpmtopdir=${HOME} # set this to _topdir value from ~/.rpmmacros
  sh ./buildrpm-1.3.1-1.gfortran.sh ../SOURCES/openmpi-1.3.1.tar.bz2 2>&1 | tee buildrpm-1.3.1-1.gfortran.sh.log
  rpm -ivh ~/RPMS/*/openmpi-*.rpm
  cp ~/RPMS/*/openmpi-*.rpm /home/dulak-server/rpm/campos

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

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

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

Build the following for dacapo:
   
- `campos-dacapo-pseudopotentials <https://wiki.fysik.dtu.dk/niflheim/Cluster_software_-_RPMS#campos-dacapo-pseudopotentials>`_::

    python campos_installer.py --machine='dulak-cluster' --create_scripts campos-dacapo-pseudopotentials

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

    python campos_installer.py --machine='dulak-cluster' --create_scripts RasMol
    cp ~/RPMS/*/RasMol-*.rpm /home/dulak-server/rpm/campos

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

    python campos_installer.py --machine='dulak-cluster' --create_scripts gnuplot-py
    cp ~/RPMS/*/gnuplot-py-*.rpm /home/dulak-server/rpm/campos

  if you use modules::
+compilers and tools
-------------------

open64
++++++

Install (on the login and computes nodes) `Install Open64 Compiler Suite <http://www.open64.net/>`_ RPM (available under `~rpmbuild/${FYS_PLATFORM}/RPMS/external/prefix`),
and deploy module file under ` ~rpmbuild/modulefiles/${FYS_PLATFORM}/open64`.
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 <http://www.g95.org/>`_ RPM (available under `~rpmbuild/${FYS_PLATFORM}/RPMS/external/prefix`),
and deploy module file under ` ~rpmbuild/modulefiles/${FYS_PLATFORM}/g95`.
Install using **--relocate** option::

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

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

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

intel
+++++

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**: 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

**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 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``)::

    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-mkllibdev`, `intel-mkllib`), and build mkl compatibility package (only on **thul**)::

  cd ~/rpmbuild/SOURCES
  export mkl=10.1.3.027
  mkdir ${mkl}
  cp -rp /opt/intel/mkl/${mkl}/lib ${mkl}
  cp -rp /opt/intel/mkl/${mkl}/doc ${mkl}
  tar zcf intel-redist-mkl-${mkl}.tar.gz ${mkl}

  cd ~/rpmbuild/SPECS
  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**.

openmpi
-------

Build a custom openmpi, using torque support::

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

  Build the following RPMS::

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

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

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

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

    . fys.build.acml.sh
    #
    . fys.set.Niflheim.open64.4.2.1.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.4.4.0.sh

    . fys.build.acml.sh

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

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

    . fys.build.acml.sh


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

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

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

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

  Download 32H2O.xyz_

goto
----

  `GotoBLAS <http://www.tacc.utexas.edu/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.
  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::

    blas_version=1.26
    . fys.set.gfortran.default.sh

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

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

    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

  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

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::

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

     . fys.build.numpy.1.3.0.sh

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

     . fys.build.numpy.1.3.0.sh

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

     . fys.build.numpy.1.3.0.sh

  After installing python-numeric make a very rough check:

  - is using modules::

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

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

      . /etc/profile.d/numpy.sh

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

  **Required by campos-ase2**.

  On a custom system build the following RPMS::

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

  On Niflheim build the following RPMS::

     . fys.build.gnuplot-py.1.8.sh

  If using modules::
-Line 115:
+Line 722:
-    echo "module load gnuplot-py" >> ~/global_install.sh

  otherwise logout and login again!

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

    python campos_installer.py --machine='dulak-cluster' --create_scripts cblas
    cp ~/RPMS/*/cblas-*.rpm /home/dulak-server/rpm/campos

- `python-numeric <https://wiki.fysik.dtu.dk/niflheim/Cluster_software_-_RPMS#python-numeric>`_ (we must install **24.2** version, and we keep the default version)::

    cd
    rpm -e --nodeps python-numeric
+  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
-Line 129:
+Line 739:
-    cp python-numeric-*.rpm /home/dulak-server/rpm/external # **Skip this step if not installing on "dulak-server"**
-Line 131:
+Line 740:
-    python campos_installer.py --machine='dulak-cluster' --create_scripts python-numeric
    cp ~/RPMS/*/python-numeric-*.rpm /home/dulak-server/rpm/campos
+  On a custom system build the following RPMS::

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

    . fys.build.Numeric.24.2.sh

  On Niflheim build the following RPMS::

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

     . fys.build.Numeric.24.2.sh
-Line 138:
+Line 760:
-  If you use modules::

    module load python-numeric
    echo "module load python-numeric" >> ~/global_install.sh

  otherwise logout and login again!

  After installing python-numeric make a very rough check::

    python -c "import lapack_lite"
    ldd `rpm -ql python-numeric | grep lapack_lite.so`
    ldd `rpm -ql python-numeric | grep _dotblas.so`
+  After installing python-numeric make a very rough check:

  - is using modules::

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

  - else::

      . /etc/profile.d/python-numeric.sh
      python -c "import lapack_lite"
      ldd `rpm -ql python-numeric | grep lapack_lite.so`
      ldd `rpm -ql python-numeric | grep _dotblas.so`
-Line 153:
+Line 780:
-    rpm -ivh --oldpackage ~/python-numeric-*.rpm

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

    python campos_installer.py --machine='dulak-cluster' --create_scripts ScientificPython
    cp ~/RPMS/*/ScientificPython-*.rpm /home/dulak-server/rpm/campos

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

    python campos_installer.py --machine='dulak-cluster' --create_scripts campos-ase2
    cp ~/RPMS/*/campos-ase2-*.rpm /home/dulak-server/rpm/campos

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

    python campos_installer.py --machine='dulak-cluster' --create_scripts campos-dacapo-python

- `campos-dacapo <https://wiki.fysik.dtu.dk/niflheim/Cluster_software_-_RPMS#id17>`_::

    python campos_installer.py --machine='dulak-cluster' --create_scripts --compiler=gfortran43 campos-dacapo
    cp ~/RPMS/*/campos-dacapo-*.rpm /home/dulak-server/rpm/campos

  logout and login again!

build following for gpaw:

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

    python campos_installer.py --machine='dulak-cluster' --create_scripts campos-gpaw-setups

- `campos-ase3 <https://wiki.fysik.dtu.dk/niflheim/Cluster_software_-_RPMS#campos-ase3>`_::

    python campos_installer.py --machine='dulak-cluster' --create_scripts campos-ase3
    cp ~/RPMS/*/campos-ase3-*.rpm /home/dulak-server/rpm/campos

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

    python campos_installer.py --machine='dulak-cluster' --create_scripts --compiler=gfortran43 campos-gpaw
    cp ~/RPMS/*/campos-gpaw-*.rpm /home/dulak-server/rpm/campos

  logout and login again!
+    rpm -ivh --oldpackage ~/${FYS_PLATFORM}/RPMS/external/python-numeric-23.*.rpm

netcdf
------

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

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

  On a custom system build the following RPMS::

    . fys.set.gfortran.default.sh

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

  On Niflheim build the following RPMS::

     . fys.set.Niflheim.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


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.0.99.1.2.sh)

  On Niflheim build the following RPMS::

     . fys.build.python-matplotlib.0.99.1.2.sh

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

 On a custom system build the following RPMS::

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

  On Niflheim build the following RPMS::

     . fys.build.ase2.2.3.13.sh

fftw2
-----

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

  On a custom system build the following RPMS::

    . fys.set.fftw2.default.sh

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

  On Niflheim build the following RPMS::

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

    . fys.build.fftw2.2.1.5.sh

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

    . fys.build.fftw2.2.1.5.sh

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

    . fys.build.fftw2.2.1.5.sh

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

    . fys.build.fftw2.2.1.5.sh

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

    . fys.build.fftw2.2.1.5.sh

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

campos-dacapo-pseudopotentials-1.tar.gz_

  On a custom system build the following RPMS::

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

  On Niflheim build the following RPMS::

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

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

  **Requires campos-ase2**.

  On a custom system build the following RPMS::

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

  On Niflheim build the following RPMS::

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

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

  Note that FC's 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.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
    # 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-11.85.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::

    . fys.build.ase3.sh

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

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

blacs
-----

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

 On a custom system build the following RPMS::

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

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

 On Niflheim build the following RPMS::

    . fys.set.Niflheim.gfortran.4.1.2.sh
    . fys.set.Niflheim.openmpi.1.3.3.sh

    . fys.build.blacs.sh

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

    . fys.build.blacs.sh

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

    . fys.build.blacs.sh

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

    . fys.build.blacs.sh

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

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

    . fys.build.blacs.sh

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

    . fys.build.blacs.sh

scalapack
---------

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

 On a custom system build the following RPMS::

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

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

 On Niflheim build the following RPMS::

    . fys.set.Niflheim.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.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.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.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.blacs.1.1.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.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.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.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.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.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.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.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.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.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.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.sh

PDSYEVRnew
----------

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


  On Niflheim build the following RPMS::

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

     . fys.build.PDSYEVRnew.sh

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

     . fys.build.PDSYEVRnew.sh

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

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

  On a custom system build the following RPMS::

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

  On Niflheim build the following RPMS::

    . fys.build.gpaw-setups.sh

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

  On a custom system build the following RPMS::

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

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

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

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

  On Niflheim build the following RPMS::

    . 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

    #
    # 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

    # 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::

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

    . fys.build.Asap.sh

    # only on thul
    . fys.set.Niflheim.Asap.3.2.6.ifort.11.0.openmpi.1.3.3.sh

    . fys.build.Asap.sh

abinit
------

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

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

abinit-pseudopotentials-1.tar.gz_

- abinit pseudopotentials

  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

- abinit

  `abinit <http://www.abinit.org/>`_ is a Density Functional Theory (DFT) package with pseudopotentials and a planewave basis.

  On a custom system build the following RPMS::

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

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

  On Niflheim build the following RPMS::

    . fys.set.Niflheim.abinit.5.4.4p.gfortran43.4.3.2.openmpi.1.3.3.acml.4.3.0.acml.4.3.0.fftw3.sh

    . fys.build.abinit.5.4.4p.sh

siesta
------

.. _siesta-pseudopotentials-2.tar.gz: attachment:siesta-pseudopotentials-2.tar.gz

siesta-pseudopotentials-2.tar.gz_

- siesta pseudopotentials

  Build the following RPMS::

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

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

- siesta

  `siesta <http://www.nanotec.es/products/siesta.php>`_ (Spanish Initiative for Electronic Simulations with Thousands of Atoms)
  is both a method and its computer program implementation, to perform electronic structure calculations and ab initio molecular dynamics simulations of molecules and solids.

  Build the following RPMS::

    cd ~/rpmbuild/SPECS

    major_version=2
    version1=0

    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 <http://www.quantum-espresso.org/>`_

- espresso pseudopotentials

  On a custom system build the following RPMS::

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

  On Niflheim build the following RPMS::

    . fys.build.espresso_pp.sh

- espresso

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

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

  On a custom system build the following RPMS::

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

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

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

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

  On Niflheim build the following RPMS::

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

    . fys.build.espresso.sh

yambo
-----

- yambo

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

  On a custom system build the following RPMS::

    . fys.set.yambo.3.2.1.448.default.sh
    . fys.set.atlas.default.sh

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

  On Niflheim build the following RPMS::

    . 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

    . 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

    . fys.build.yambo.sh

elk
---

`elk <http://elk.sourceforge.net/>`_

- elk species

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

  On a custom system build the following RPMS::

    (default_version_usage="--with default_version" && modules_usage="--without modules" && . fys.build.elk-species.1.0.0.sh)

  On Niflheim build the following RPMS::

    . fys.build.elk-species.1.0.0.sh

- elk

  On a custom system build the following RPMS::

    . fys.set.gfortran.default.sh
    . 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.blas.acml.4.3.0_mp.sh
    . fys.set.lapack.acml.sh
    
    (thread_mode=mp && . fys.build.elk.1.0.0.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
-------

- octopus

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

  On a custom system build the following RPMS::

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

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

  On Niflheim build the following RPMS::

    . fys.set.Niflheim.gfortran43.4.3.2.sh
    . fys.set.Niflheim.openmpi.1.3.3.sh
    . fys.set.Niflheim.netcdf4.4.0.1.sh
    . fys.set.Niflheim.fftw3.3.2.1.sh
    . fys.set.blas.acml.4.3.0.sh
    . fys.set.lapack.acml.sh
    . fys.set.gsl.default.sh
    . fys.set.arpack.default.sh
    
    . fys.build.octopus.3.2.0.sh

TAU
---

- pdtoolkit

  `Program Database Toolkit <http://www.cs.uoregon.edu/research/pdt/>`_ is a framework for analyzing source code written in several programming languages
  and for making rich program knowledge accessible to developers of static and dynamic analysis tools. PDT is required by TAU.

  On a custom system build the following RPMS::

    . fys.set.gfortran.default.sh

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

  On Niflheim build the following RPMS::

    . fys.set.Niflheim.gfortran.4.1.2.sh
    
    . fys.build.pdtoolkit.sh
    #
    . fys.set.Niflheim.gfortran43.4.3.2.sh
    
    . fys.build.pdtoolkit.sh

- tau

  `TAU Performance System® <http://www.cs.uoregon.edu/research/tau/>`_ is a portable profiling and tracing toolkit
  for performance analysis of parallel programs written in Fortran, C, C++, Java, Python.

  On a custom system build the following RPMS::

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

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

  On Niflheim build the following RPMS::

    pdtoolkit_version=3.15

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

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

vasp
----

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

- vasp potentials

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

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

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

  On a custom system build the following RPMS::

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

  On Niflheim build the following RPMS::

    . fys.build.vasp-potpaw.sh

- vasp

  `vasp <http://cms.mpi.univie.ac.at/vasp/>`_. Download ``vasp.5.X.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/.

  On a custom system build the following RPMS::

    # Compile with VASP TST library: http://theory.cm.utexas.edu/vtsttools/downloads/
    tst=false # or true

    . fys.set.vasp.5.2.default.sh

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

  On Niflheim build the following RPMS::

    # Compile with VASP TST library: http://theory.cm.utexas.edu/vtsttools/downloads/
    tst=false # or true

    . fys.set.Niflheim.vasp.5.2.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

    . fys.set.Niflheim.vasp.5.2.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".
    . fys.set.Niflheim.vasp.5.2.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
    . fys.set.Niflheim.vasp.5.2.ifort.11.1.openmpi.1.3.3.acml.4.4.0.acml.4.4.0.fftw3.sh

    . fys.build.vasp.sh

exciting
--------

- exciting species

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

  On a custom system build the following RPMS::

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

  On Niflheim build the following RPMS::

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

- exciting

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

    could not find ParserDetails.ini

  do as root::

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

  On a custom system build the following RPMS::

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

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

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

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

  On Niflheim build the following RPMS::

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

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

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

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

fleur
-----

- fleur

  `fleur <http://www.flapw.de/>`_. Download the source to ``~/rpmbuild/SOURCES``.

  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

gulp
----

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

- gulp

  `gulp <https://www.ivec.org/gulp/>`_. Download ``gulp.3.4.source.tar.gz`` ``~/rpmbuild/SOURCES``.

  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

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

  version_svn=82
  cd ~/rpmbuild/SOURCES && python cmr_release.py
  cd ~/rpmbuild/SPECS
  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
-Line 197:
+Line 2394:
+**Note** this section is outdated.
-Line 201:
+Line 2400:
-   module load openmpi
   module load campos-dacapo-pseudopotentials
   module load python-numeric
   module load campos-dacapo-python
   module load ScientificPython
   module load gnuplot-py
   module load RasMol
   module load campos-ase2
   module load campos-dacapo
   ulimit -s 65000 # dacapo needs a large stack
+   module load campos-dacapo # fulfill all dependencies requested by module
   ulimit -s 500000 # dacapo needs a large stack
-Line 233:
+Line 2424:
-   module load openmpi
   module load campos-ase3
   module load campos-gpaw-setups
   module load campos-gpaw
+  module load campos-gpaw # fulfill all dependencies requested by module
-Line 245:
+Line 2433:
-On "Golden Client"
------------------

Login, as root, to the "Golden Client"::

 ssh n001

Enable nfs mount of the `server` home directory
- follow 'Enable nfs mount on the "Golden Client"' from `configuring NFS <Building_a_Cluster_-_Tutorial/configuring_NFS>`_.
After this do::

 cd /home/dulak-server/rpm/campos

 rpm -ivh campos-dacapo-2*

If getting::

  package example_package.el5.i386 is already installed

remove these packages with::

  rpm -e --nodeps example_package

to allow the installation to proceed.

Make sure that both python-numeric versions are installed::

  rpm -q python-numeric

This command will show a list of packages that need to be installed to fulfill `dacapo` dependencies.
All these packages should be already under ``/home/dulak-server/rpm``.
Remember to test the `dacapo` and `gpaw` installations on the "Golden Client" too.

If you are installing workstation only, your setup is ready for testing - go to `benchmarking and maintenance <Building_a_Cluster_-_Tutorial/benchmarking_and_maintenance>`_.

If you are building a cluster go **back** to `installing and configuring systemimager <Building_a_Cluster_-_Tutorial/installing_and_configuring_systemimager>`_,