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

Differences between revisions 14 and 16 (spanning 2 versions)

This page describes the necessary steps for installing of dl160

On the server

Install external packages

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, as root:

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

configure rpmbuild:

use the following ~rpmbuild/.rpmmacros:

%disttag        el5.fys

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

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

#%_topdir       /home/camp/rpmbuild/AMD-Opteron
%_topdir        /home/camp/rpmbuild/Intel-Nehalem
%_rpmdir        %{_topdir}/RPMS
%_srcrpmdir     %{_topdir}/SRPMS
%_svndir        /home/camp/rpmbuild/rpmbuild
%_specdir       %{_svndir}/SPECS
%_sourcedir     %{_svndir}/SOURCES
%_rpmfilename   %%{NAME}-%%{VERSION}-%%{RELEASE}.%%{ARCH}.rpm
#%_tmppath      %{_topdir}
%_tmppath       /tmp/rpmbuild
%_builddir      %{_tmppath}/BUILD

# no debuginfo
%debug_package %{nil}

%niflheim       1

as rpmbuild create directories:

mkdir -p ~/Intel-Nehalem/RPMS
mkdir -p ~/Intel-Nehalem/SRPMS
mkdir -p ~/Intel-Nehalem/BUILD
mkdir -p ~/Intel-Nehalem/SPECS # needed only by openmpi
mkdir -p ~/Intel-Nehalem/SOURCES # needed only by openmpi
mkdir -p /tmp/rpmbuild/BUILD

install official packages, as rpmbuild:

cd ~/Intel-Nehalem/RPMS
yumdownloader --resolve gcc-gfortran gcc43-c++ gcc43-gfortran blas-devel lapack-devel python-devel
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
yum localinstall * # as root

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

~/Intel-Nehalem/RPMS
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

install the packages from epel, as rpmbuild:

~/Intel-Nehalem/RPMS
yumdownloader --resolve --enablerepo=epel jmol
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
source /etc/profile.d/modules.sh

remove default openmpi:
```
yum remove openmpi openmpi-libs
```

edit /etc/yum.conf so it contains:

exclude=netcdf-* netcdf3-* fftw-* fftw2-* fftw3-* python-numeric openmpi-*

It's time to build custom RPMS

As rpmbuild:

cd ~/rpmbuild/SPECS

Build a custom openmpi, using torque support:

export rpmtopdir=${HOME}/Intel-Nehalem # set this to _topdir value from ~/.rpmmacros
wget http://www.open-mpi.org/software/ompi/v1.3/downloads/openmpi-1.3.2.tar.bz2 \
     -O ~/rpmbuild/SOURCES/openmpi-1.3.2.tar.bz2
sh ./buildrpm-1.3.2-1.gfortran.sh ../SOURCES/openmpi-1.3.2.tar.bz2 2>&1 | tee buildrpm-1.3.2-1.gfortran.sh.log.Intel-Nehalem
sh ./buildrpm-1.3.2-1.gfortran43.sh ../SOURCES/openmpi-1.3.2.tar.bz2 2>&1 | tee buildrpm-1.3.2-1.gfortran43.sh.log.Intel-Nehalem
sh ./buildrpm-1.3.2-1.pathscale.sh ../SOURCES/openmpi-1.3.2.tar.bz2 2>&1 | tee buildrpm-1.3.2-1.pathscale.sh.log.Intel-Nehalem
rpm -ivh ~/RPMS/*/openmpi-*.rpm

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

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

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

Build the following for dacapo:

set the disttag variable for convenience:
```
export disttag="el5.fys"
```
install icc/ifort compilers,

acml:

rpmbuild -bb --with compiler=gfortran --with version1=0 --with version2=1 --with modules --with default_version acml.spec
rpmbuild -bb --with compiler=pathscale --with version1=0 --with version2=1 --with modules --with default_version acml.spec

rpmbuild -bb --with compiler=gfortran43 --with version1=1 --with version2=0 --with modules --with default_version acml.spec
rpmbuild -bb --with compiler=pathscale --with version1=1 --with version2=0 --with modules --with default_version acml.spec

rpmbuild -bb --with compiler=gfortran43 --with version1=2 --with version2=0 --with modules --with default_version acml.spec
rpmbuild -bb --with compiler=pathscale --with version1=2 --with version2=0 --with modules --with default_version acml.spec
rpmbuild -bb --with compiler=ifort --with version1=2 --with version2=0 --with modules --with default_version acml.spec

goto:

rpmbuild --bb --with compiler=gfortran --with modules=1 --with default_version=1 \
              --with prefix=/opt/goto/1.26/1.${disttag}.gfortran.smp goto.spec
rpmbuild --bb --with compiler=gfortran43 --with modules=1 --with default_version=1 \
              --with prefix=/opt/goto/1.26/1.${disttag}.gfortran43.smp goto.spec
rpmbuild --bb --with compiler=pathscale --with compiler_bindir=/opt/pathscale/bin --with compiler_libdir=/opt/pathscale/lib/3.2 \
              --with modules=1 --with default_version=1 --with prefix=/opt/goto/1.26/1.${disttag}.pathscale.smp goto.spec

Note - 1.26 version fails on Nehalem with:

../../../param.h:1195:21: error: division by zero in #if

campos-dacapo-pseudopotentials:

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

rasmol:

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

cblas:

rpmbuild --bb  --with blas_version=3.0.37.el5 --with modules=1 --with default_version=1 \
               --with prefix=/opt/cblas/2.23.3/1.${disttag}.gfortran.blas.3.0.37.el5 cblas.spec

rpmbuild --bb  --with blas=acml --with blas_version=4.0.1 --with blasdir=/opt/acml/4.0.1/gfortran64/lib \
               --with modules=1 --with default_version=1 --with prefix=/opt/cblas/2.23.3/1.${dist}.gfortran.acml.4.0.1 cblas.spec

python-setuptools:

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

python-nose:

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

numpy:

rpmbuild --bb --with cblas_prefix=none \ # dotblas fails with acml
              --with blas=acml --with blas_version=4.0.1 --with blasdir=/opt/acml/4.0.1/gfortran64/lib \
              --with lapack=acml --with lapackdir=/opt/acml/4.0.1/gfortran64/lib \
              --with compiler=gfortran --with modules=1 --with default_version=1 \
              --with prefix=/opt/numpy/1.3.0/1.${disttag}.gfortran.python2.4.acml.4.0.1.acml numpy.spec

rpmbuild --bb --with cblas_prefix=/opt/cblas/2.23.3/1.${disttag}.gfortran.blas.3.0.37.el5 --with blas_version=3.0.37.el5 \
              --with compiler=gfortran --with modules=1 --with default_version=1 \
              --with prefix=/opt/numpy/1.3.0/1.${disttag}.gfortran.python2.4.blas.3.0.37.el5.lapack numpy.spec

Test with:

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

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

Load the default numpy:

module load numpy/1.3.0-1.el5.fys.gfortran.python2.4.acml.4.0.1.acml

gnuplot-py:

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

module load gnuplot-py

python-numeric (we must install 24.2 version, and we keep the default version):

cd ~/Intel-Nehalem/RPMS
rpm -e --nodeps python-numeric # as root
yumdownloader --resolve --disableexcludes=main python-numeric
cd ~/rpmbuild/SPECS

rpmbuild --bb --with cblas_prefix=/opt/cblas/2.23.3/1.${disttag}.gfortran.acml.4.0.1 \
              --with blas=acml --with blas_version=4.0.1 --with blasdir=/opt/acml/4.0.1/gfortran64/lib \
              --with lapack=acml --with lapackdir=/opt/acml/4.0.1/gfortran64/lib \
              --with compiler=gfortran --with modules=1 --with default_version=1 \
              --with prefix=/opt/python-numeric/24.2/4.${disttag}.gfortran.python2.4.acml.4.0.1.acml python-numeric.spec

rpmbuild --bb --with cblas_prefix=/opt/cblas/2.23.3/1.${disttag}.gfortran.blas.3.0.37.el5 --with blas_version=3.0.37.el5 \
              --with compiler=gfortran --with modules=1 --with default_version=1 \
              --with prefix=/opt/python-numeric/24.2/4.${disttag}.gfortran.python2.4.blas.3.0.37.el5.lapack python-numeric.spec

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:

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

module load acml-gfortran64/4.0.1-1.el5.fys
module load python-numeric/24.2-4.el5.fys.gfortran.python2.4.acml.4.0.1.acml
python -c "import lapack_lite"
ldd `rpm -ql python-numeric-24.2-4.el5.fys.gfortran.python2.4.acml.4.0.1.acml | grep lapack_lite.so`
ldd `rpm -ql python-numeric-24.2-4.el5.fys.gfortran.python2.4.acml.4.0.1.acml | grep _dotblas.so`
module unload python-numeric/24.2-4.el5.fys.gfortran.python2.4.acml.4.0.1.acml
module unload acml-gfortran64/4.0.1-1.el5.fys

and reinstall the default version:

rpm -ivh --oldpackage ~rpmbuild/Intel-Nehalem/RPMS/python-numeric-23.*.rpm

load the default Numeric version:

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

netcdf:

rpmbuild --bb  --with compiler=gfortran --with modules=1 --with default_version=1 \
               --with prefix=/opt/netcdf4/4.0.1/1.gfortran.${disttag} netcdf4.spec
rpmbuild --bb  --with compiler=gfortran43 --with modules=1 --with default_version=1 \
               --with prefix=/opt/netcdf4/4.0.1/1.gfortran43.${disttag} netcdf4.spec
rpmbuild --bb  --with compiler=pathscale --with compiler_bindir=/opt/pathscale/bin --with compiler_libdir=/opt/pathscale/lib/3.2 \
               --with modules=1 --with default_version=1 --with prefix=/opt/netcdf4/4.0.1/1.pathscale.${disttag} netcdf4.spec

ScientificPython:

rpmbuild --bb  --with Numeric_includedir=none --with numpy=numpy --with compiler=gfortran --with netcdf=netcdf4 \
               --with netcdf_includedir=/opt/netcdf4/4.0.1/1.gfortran.${disttag}/include \
               --with netcdf_libdir=/opt/netcdf4/4.0.1/1.gfortran.${disttag}/lib64 \
               --with modules=1 --with default_version=1 \
               --with prefix=/opt/ScientificPython/2.8/1.${disttag}.python2.4.serial_version.numpy ScientificPython.spec

rpmbuild --bb  --with numpy=numeric --with compiler=gfortran --with netcdf=netcdf4 \
               --with netcdf_includedir=/opt/netcdf4/4.0.1/1.gfortran.${disttag}/include \
               --with netcdf_libdir=/opt/netcdf4/4.0.1/1.gfortran.${disttag}/lib64 \
               --with modules=1 --with default_version=1 --with parallel=1 --with openmpi=openmpi \
               --with ompi_bindir=/opt/openmpi/1.3.2-1.gfortran/bin \
               --with ompi_includedir=/opt/openmpi/1.3.2-1.gfortran/include --with ompi_libdir=/opt/openmpi/1.3.2-1.gfortran/lib64 \
               --with prefix=/opt/ScientificPython/2.6.2/1.${disttag}.python2.4.openmpi.numeric ScientificPython.spec

python-docutils:

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

pytz:

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

python-docutils:

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

python-matplotlib:

module load pytz
module load python-docutils
module load python-dateutil
rpmbuild -bb --with modules --with default_version --with prefix=/opt/python-matplotlib/0.98.5.2/1.${disttag}.python2.4 python-matplotlib.spec

campos-ase2:

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

campos-dacapo-python:

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

fftw2:

rpmbuild --bb  --with compiler=gfortran --with default_version=1 --with modules=1 --with prefix=/opt/fftw2/2.1.5/12.gfortran.${disttag} fftw2.spec
rpmbuild --bb  --with compiler=gfortran43 --with default_version=1 --with modules=1 --with prefix=/opt/fftw2/2.1.5/12.gfortran43.${disttag} fftw2.spec
rpmbuild --bb  --with compiler=pathscale --with compiler_bindir=/opt/pathscale/bin --with compiler_libdir=/opt/pathscale/lib/3.2 \
               --with default_version=1 --with modules=1 --with prefix=/opt/fftw2/2.1.5/12.pathscale.${disttag} fftw2.spec

campos-dacapo:

rpmbuild --bb  --with blas=acml --with blas_version=4.2.0 --with blasdir=/opt/acml/4.2.0/gfortran4364/lib \
               --with compiler=gfortran43 --with compiler_bindir=/usr/bin --with compiler_libdir=/usr/lib64 \
               --with fftw=fftw2 --with fftw_libdir=/opt/fftw2/2.1.5/12.gfortran43.${disttag}/lib64 \
               --with lapack=acml --with lapackdir=/opt/acml/4.2.0/gfortran4364/lib --with netcdf=netcdf4 \
               --with netcdf_includedir=/opt/netcdf4/4.0.1/1.gfortran43.${disttag}/include \
               --with netcdf_libdir=/opt/netcdf4/4.0.1/1.gfortran43.${disttag}/lib64 \
               --with modules=1 --with default_version=1 --with parallel=1 --with openmpi=openmpi \
               --with ompi_bindir=/opt/openmpi/1.3.2-1.gfortran43/bin \
               --with ompi_includedir=/opt/openmpi/1.3.2-1.gfortran43/include --with ompi_libdir=/opt/openmpi/1.3.2-1.gfortran43/lib64 \
               --with prefix=/opt/campos-dacapo/2.7.16/1.${disttag}.gfortran43.openmpi.acml.4.2.0.acml campos-dacapo.spec

rpmbuild --bb  --with blas=acml --with blas_version=4.0.1 --with blasdir=/opt/acml/4.0.1/gfortran64/lib \
               --with compiler=gfortran --with compiler_bindir=/usr/bin --with compiler_libdir=/usr/lib64 \
               --with fftw=fftw2 --with fftw_libdir=/opt/fftw2/2.1.5/12.gfortran.${disttag}/lib64 \
               --with lapack=acml --with lapackdir=/opt/acml/4.0.1/gfortran64/lib --with netcdf=netcdf4 \
               --with netcdf_includedir=/opt/netcdf4/4.0.1/1.gfortran.${disttag}/include \
               --with netcdf_libdir=/opt/netcdf4/4.0.1/1.gfortran.${disttag}/lib64 \
               --with modules=1 --with default_version=1 --with parallel=1 --with openmpi=openmpi \
               --with ompi_bindir=/opt/openmpi/1.3.2-1.gfortran/bin \
               --with ompi_includedir=/opt/openmpi/1.3.2-1.gfortran/include --with ompi_libdir=/opt/openmpi/1.3.2-1.gfortran/lib64 \
               --with prefix=/opt/campos-dacapo/2.7.16/1.${disttag}.gfortran.openmpi.acml.4.0.1.acml campos-dacapo.spec

rpmbuild --bb  --with blas=blas --with blas_version=3.0.37.el5 --with blasdir=/usr/lib64 \
               --with compiler=gfortran43 --with compiler_bindir=/usr/bin --with compiler_libdir=/usr/lib64 \
               --with fftw=fftw2 --with fftw_libdir=/opt/fftw2/2.1.5/12.gfortran43.${disttag}/lib64 \
               --with lapack=lapack --with lapackdir=/usr/lib64 --with netcdf=netcdf4 \
               --with netcdf_includedir=/opt/netcdf4/4.0.1/1.gfortran43.${disttag}/include \
               --with netcdf_libdir=/opt/netcdf4/4.0.1/1.gfortran43.${disttag}/lib64 \
               --with modules=1 --with default_version=1 --with parallel=1 --with openmpi=openmpi \
               --with ompi_bindir=/opt/openmpi/1.3.2-1.gfortran43/bin \
               --with ompi_includedir=/opt/openmpi/1.3.2-1.gfortran43/include --with ompi_libdir=/opt/openmpi/1.3.2-1.gfortran43/lib64 \
               --with prefix=/opt/campos-dacapo/2.7.16/1.${disttag}.gfortran43.openmpi.blas.3.0.37.el5.lapack campos-dacapo.spec

rpmbuild --bb  --with blas=blas --with blas_version=3.0.37.el5 --with blasdir=/usr/lib64 \
               --with compiler=gfortran --with compiler_bindir=/usr/bin --with compiler_libdir=/usr/lib64 \
               --with fftw=fftw2 --with fftw_libdir=/opt/fftw2/2.1.5/12.gfortran.${disttag}/lib64 \
               --with lapack=lapack --with lapackdir=/usr/lib64 --with netcdf=netcdf4 \
               --with netcdf_includedir=/opt/netcdf4/4.0.1/1.gfortran.${disttag}/include \
               --with netcdf_libdir=/opt/netcdf4/4.0.1/1.gfortran.${disttag}/lib64 \
               --with modules=1 --with default_version=1 --with parallel=1 --with openmpi=openmpi \
               --with ompi_bindir=/opt/openmpi/1.3.2-1.gfortran/bin \
               --with ompi_includedir=/opt/openmpi/1.3.2-1.gfortran/include --with ompi_libdir=/opt/openmpi/1.3.2-1.gfortran/lib64 \
               --with prefix=/opt/campos-dacapo/2.7.16/1.${disttag}.gfortran.openmpi.blas.3.0.37.el5.lapack campos-dacapo.spec

Build following for gpaw:

fftw3:

rpmbuild --bb --with major_version=3 --with version1=2 --with version2=1 --with compiler=gfortran \
              --with default_version=1 --with modules=1 --with prefix=/opt/fftw3/3.2.1/12.gfortran.${disttag} fftw2.spec
rpmbuild --bb --with major_version=3 --with version1=2 --with version2=1 --with compiler=gfortran43 \
              --with default_version=1 --with modules=1 --with prefix=/opt/fftw3/3.2.1/12.gfortran43.${disttag} fftw2.spec

scipy:

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

rpmbuild --bb --with cblas_prefix=/opt/cblas/2.23.3/1.${disttag}.gfortran.blas.3.0.37.el5 \
              --with blas=blas --with blas_version=3.0.37.el5 --with blasdir=/usrlib64 \
              --with lapack=lapack --with lapackdir=/usr/lib64 \
              --with ufsparse_libdir=/usr/lib64 --with ufsparse_includedir=/usr/include/suitesparse \
              --with fftw_libdir=/opt/fftw3/3.2.1/12.gfortran.${disttag}/lib64 \
              --with compiler=gfortran --with default_version=1 --with modules=1 \
              --with prefix=/opt/scipy/0.7.0/1.${disttag}.gfortran.python2.4.blas.3.0.37.el5.lapack scipy.spec

module unload numpy
module load numpy/1.3.0-1.el5.fys.gfortran.python2.4.acml.4.0.1.acml

rpmbuild --bb --with cblas_prefix=/opt/cblas/2.23.3/1.${disttag}.gfortran.acml.4.0.1 \
              --with blas=acml --with blas_version=4.0.1 --with blasdir=/opt/acml/4.0.1/gfortran64/lib \
              --with lapack=acml --with lapackdir=/opt/acml/4.0.1/gfortran64/lib \
              --with ufsparse_libdir=/usr/lib64 --with ufsparse_includedir=/usr/include/suitesparse \
              --with fftw_libdir=/opt/fftw3/3.2.1/12.gfortran.${disttag}/lib64 \
              --with compiler=gfortran --with default_version=1 --with modules=1 \
              --with prefix=/opt/scipy/0.7.0/1.${disttag}.gfortran.python2.4.acml.4.0.1.acml scipy.spec

campos-gpaw-setups:

rpmbuild -bb --with default_version --with modules campos-gpaw-setups.spec

campos-ase3:

rpmbuild -bb --with modules --with default_version --with prefix=/opt/campos-ase3/3.1.0.846/1.${disttag}.python2.4 campos-ase3.spec

povray:

rpmbuild -bb --with modules --with default_version --with prefix=/opt/povray/3.6.1/3.${disttag} povray.spec

python-jinja2:

rpmbuild -bb --with modules --with default_version --with prefix=/opt/python-jinja2/2.1.1/1.${disttag}.python2.4 python-jinja2.spec

python-pygments:

rpmbuild -bb --with modules --with default_version --with prefix=/opt/python-pygments/1.0/1.${disttag}.python2.4 python-pygments.spec

babel:

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

python-sphinx:

module load python-jinja2
rpmbuild -bb --with modules --with default_version --with prefix=/opt/python-sphinx/0.6.1/1.${disttag}.python2.4 python-sphinx.spec

blacs:

rpmbuild --bb --with compiler=gfortran43 --with compiler_bindir=/usr/bin --with compiler_libdir=/usr/lib64 \
               --with modules=1 --with default_version=1 --with parallel=1 --with openmpi=openmpi \
               --with ompi_bindir=/opt/openmpi/1.3.2-1.gfortran43/bin \
               --with ompi_includedir=/opt/openmpi/1.3.2-1.gfortran43/include --with ompi_libdir=/opt/openmpi/1.3.2-1.gfortran43/lib64 \
               --with prefix=/opt/blacs/1.1/24.${disttag}.gfortran43.openmpi blacs.spec

rpmbuild --bb  --with compiler=gfortran --with compiler_bindir=/usr/bin --with compiler_libdir=/usr/lib64 \
               --with modules=1 --with default_version=1 --with parallel=1 --with openmpi=openmpi \
               --with ompi_bindir=/opt/openmpi/1.3.2-1.gfortran/bin \
               --with ompi_includedir=/opt/openmpi/1.3.2-1.gfortran/include --with ompi_libdir=/opt/openmpi/1.3.2-1.gfortran/lib64 \
               --with prefix=/opt/blacs/1.1/24.${disttag}.gfortran.openmpi blacs.spec

scalapack:

rpmbuild --bb  --with blacs=blacs --with blacsdir=/opt/blacs/1.1/24.${disttag}.gfortran43.openmpi/lib64 \
               --with blas=acml --with blas_version=4.2.0 --with blasdir=/opt/acml/4.2.0/gfortran4364/lib \
               --with compiler=gfortran43 --with compiler_bindir=/usr/bin --with compiler_libdir=/usr/lib64 \
               --with default_version=1 --with modules=1 --with openmpi=openmpi \
               --with lapack=acml --with lapackdir=/opt/acml/4.2.0/gfortran4364/lib \
               --with ompi_bindir=/opt/openmpi/1.3.2-1.gfortran43/bin \
               --with ompi_includedir=/opt/openmpi/1.3.2-1.gfortran43/include --with ompi_libdir=/opt/openmpi/1.3.2-1.gfortran43/lib64 \
               --with prefix=/opt/scalapack/1.8.0/1.${disttag}.gfortran43.openmpi.acml.4.2.0.acml scalapack.spec

rpmbuild --bb  --with blacs=blacs --with blacsdir=/opt/blacs/1.1/24.${disttag}.gfortran.openmpi/lib64 \
               --with blas=acml --with blas_version=4.0.1 --with blasdir=/opt/acml/4.0.1/gfortran64/lib \
               --with compiler=gfortran --with compiler_bindir=/usr/bin --with compiler_libdir=/usr/lib64 \
               --with default_version=1 --with modules=1 --with openmpi=openmpi \
               --with lapack=acml --with lapackdir=/opt/acml/4.0.1/gfortran64/lib \
               --with ompi_bindir=/opt/openmpi/1.3.2-1.gfortran/bin \
               --with ompi_includedir=/opt/openmpi/1.3.2-1.gfortran/include --with ompi_libdir=/opt/openmpi/1.3.2-1.gfortran43/lib \
               --with prefix=/opt/scalapack/1.8.0/1.${disttag}.gfortran.openmpi.acml.4.0.1.acml scalapack.spec

rpmbuild --bb  --with blacs=blacs --with blacsdir=/opt/blacs/1.1/24.${disttag}.gfortran43.openmpi/lib64 \
               --with blas=blas --with blas_version=3.0.37.el5 --with blasdir=/usr/lib64 \
               --with compiler=gfortran43 --with compiler_bindir=/usr/bin --with compiler_libdir=/usr/lib64 \
               --with default_version=1 --with modules=1 --with openmpi=openmpi \
               --with lapack=lapack --with lapackdir=/usr/lib64 \
               --with ompi_bindir=/opt/openmpi/1.3.2-1.gfortran43/bin \
               --with ompi_includedir=/opt/openmpi/1.3.2-1.gfortran43/include --with ompi_libdir=/opt/openmpi/1.3.2-1.gfortran43/lib64 \
               --with prefix=/opt/scalapack/1.8.0/1.${disttag}.gfortran43.openmpi.blas.3.0.37.el5.lapack scalapack.spec

rpmbuild --bb  --with blacs=blacs --with blacsdir=/opt/blacs/1.1/24.${disttag}.gfortran.openmpi/lib64 \
               --with blas=blas --with blas_version=3.0.37.el5 --with blasdir=/usr/lib64 \
               --with compiler=gfortran --with compiler_bindir=/usr/bin --with compiler_libdir=/usr/lib64 \
               --with default_version=1 --with modules=1 --with openmpi=openmpi \
               --with lapack=lapack --with lapackdir=/usr/lib64 \
               --with ompi_bindir=/opt/openmpi/1.3.2-1.gfortran/bin \
               --with ompi_includedir=/opt/openmpi/1.3.2-1.gfortran/include --with ompi_libdir=/opt/openmpi/1.3.2-1.gfortran/lib64 \
               --with prefix=/opt/scalapack/1.8.0/1.${disttag}.gfortran.openmpi.blas.3.0.37.el5.lapack scalapack.spec

campos-gpaw:

rpmbuild --bb  --with blacs=blacs --with blacsdir=/opt/blacs/1.1/24.${disttag}.gfortran.openmpi/lib64 \
               --with blas=acml --with blas_version=4.0.1 --with blasdir=/opt/acml/4.0.1/gfortran64/lib \
               --with cmr_repository=/home/niflheim/repository/db \
               --with compiler=gfortran --with compiler_bindir=/usr/bin --with compiler_libdir=/usr/lib64 \
               --with default_version=1 --with modules=1 \
               --with lapack=acml --with lapackdir=/opt/acml/4.0.1/gfortran64/lib \
               --with ompi_bindir=/opt/openmpi/1.3.2-1.gfortran/bin \
               --with ompi_includedir=/opt/openmpi/1.3.2-1.gfortran/include --with ompi_libdir=/opt/openmpi/1.3.2-1.gfortran/lib64 \
               --with openmpi=openmpi --with parallel=1 \
               --with scalapack=scalapack --with scalapackdir=/opt/scalapack/1.8.0/1.${disttag}.gfortran.openmpi.acml.4.0.1.acml/lib64 \
               --with prefix=/opt/campos-gpaw/0.6.3862/1.${disttag}.gfortran.python2.4.openmpi.acml.4.0.1.acml campos-gpaw.spec

rpmbuild --bb  --with blacs=blacs --with blacsdir=/opt/blacs/1.1/24.${disttag}.gfortran43.openmpi/lib64 \
               --with blas=acml --with blas_version=4.2.0 --with blasdir=/opt/acml/4.2.0/gfortran4364/lib \
               --with cmr_repository=/home/niflheim/repository/db \
               --with compiler=gfortran43 --with compiler_bindir=/usr/bin --with compiler_libdir=/usr/lib64 \
               --with default_version=1 --with modules=1 \
               --with lapack=acml --with lapackdir=/opt/acml/4.2.0/gfortran4364/lib \
               --with ompi_bindir=/opt/openmpi/1.3.2-1.gfortran43/bin \
               --with ompi_includedir=/opt/openmpi/1.3.2-1.gfortran43/include --with ompi_libdir=/opt/openmpi/1.3.2-1.gfortran43/lib64 \
               --with openmpi=openmpi --with parallel=1 \
               --with scalapack=scalapack --with scalapackdir=/opt/scalapack/1.8.0/1.${disttag}.gfortran43.openmpi.acml.4.2.0.acml/lib64 \
               --with prefix=/opt/campos-gpaw/0.6.3862/1.${disttag}.gfortran43.python2.4.openmpi.acml.4.2.0.acml campos-gpaw.spec

Testing packages

Test dacapo installation (as normal user!).

If you use modules:

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

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 openmpi
module load campos-ase3
module load campos-gpaw-setups
module load campos-gpaw

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.

On "Golden Client"

ssh n001

Enable nfs mount of the server home directory - follow 'Enable nfs mount on the "Golden Client"' from 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.

If you are building a cluster go back to installing and configuring systemimager,

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

-  ⇤ ← Revision 14 as of 2009-06-07 11:05:54 → 
  Size: 32274
  Editor: MarcinDulak
  Comment:
+   ← Revision 16 as of 2009-06-10 17:42:49 → ⇥
  Size: 34315
  Editor: MarcinDulak
  Comment:
-Deletions are marked like this.
+Additions are marked like this.
 Line 211:
+    python -c "import numpy; from numpy.core.multiarray import dot; b = numpy.ones(13, numpy.complex); dot(b, b)"
-Line 212:
+Line 213:
-    python -c "import numpy; from numpy.core.multiarray import dot; b = numpy.ones(13, numpy.complex); dot(b, b)"
    module load numpy/1.3.0-1.el5.fys.gfortran.python2.4.blas.3.0.37.el5.lapack
+    module unload numpy/1.3.0-1.el5.fys.gfortran.python2.4.blas.3.0.37.el5.lapack
 Line 217:
+    python -c "import numpy; from numpy.core.multiarray import dot; b = numpy.ones(13, numpy.complex); dot(b, b)"
-Line 218:
+Line 219:
-    python -c "import numpy; from numpy.core.multiarray import dot; b = numpy.ones(13, numpy.complex); dot(b, b)"
 Line 224:
-    module load numpy/1.3.0-1.el5.fys.gfortran.python2.4.blas.3.0.37.el5.lapack
+    module load numpy/1.3.0-1.el5.fys.gfortran.python2.4.acml.4.0.1.acml
 Line 331:
-- fftw::
+- fftw2::
 Line 385:
+- fftw3::

    rpmbuild --bb --with major_version=3 --with version1=2 --with version2=1 --with compiler=gfortran \
                  --with default_version=1 --with modules=1 --with prefix=/opt/fftw3/3.2.1/12.gfortran.${disttag} fftw2.spec
    rpmbuild --bb --with major_version=3 --with version1=2 --with version2=1 --with compiler=gfortran43 \
                  --with default_version=1 --with modules=1 --with prefix=/opt/fftw3/3.2.1/12.gfortran43.${disttag} fftw2.spec

- scipy::

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

    rpmbuild --bb --with cblas_prefix=/opt/cblas/2.23.3/1.${disttag}.gfortran.blas.3.0.37.el5 \
                  --with blas=blas --with blas_version=3.0.37.el5 --with blasdir=/usrlib64 \
                  --with lapack=lapack --with lapackdir=/usr/lib64 \
                  --with ufsparse_libdir=/usr/lib64 --with ufsparse_includedir=/usr/include/suitesparse \
                  --with fftw_libdir=/opt/fftw3/3.2.1/12.gfortran.${disttag}/lib64 \
                  --with compiler=gfortran --with default_version=1 --with modules=1 \
                  --with prefix=/opt/scipy/0.7.0/1.${disttag}.gfortran.python2.4.blas.3.0.37.el5.lapack scipy.spec

    module unload numpy
    module load numpy/1.3.0-1.el5.fys.gfortran.python2.4.acml.4.0.1.acml

    rpmbuild --bb --with cblas_prefix=/opt/cblas/2.23.3/1.${disttag}.gfortran.acml.4.0.1 \
                  --with blas=acml --with blas_version=4.0.1 --with blasdir=/opt/acml/4.0.1/gfortran64/lib \
                  --with lapack=acml --with lapackdir=/opt/acml/4.0.1/gfortran64/lib \
                  --with ufsparse_libdir=/usr/lib64 --with ufsparse_includedir=/usr/include/suitesparse \
                  --with fftw_libdir=/opt/fftw3/3.2.1/12.gfortran.${disttag}/lib64 \
                  --with compiler=gfortran --with default_version=1 --with modules=1 \
                  --with prefix=/opt/scipy/0.7.0/1.${disttag}.gfortran.python2.4.acml.4.0.1.acml scipy.spec