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| Deletions are marked like this. | Additions are marked like this. |
| Line 1607: | Line 1607: |
| compiler=gfortran43 compiler_version=4.3.2 compiler_libdir=/usr/lib64 compiler_bindir=/usr/bin |
compiler=pathscale # only on fjorm compiler_version=3.2 compiler_libdir=/opt/pathscale/lib/3.2 compiler_bindir=/opt/pathscale/bin |
| Line 1617: | Line 1617: |
| compiler=open64 # only on fjorm compiler_version=4.2.1 compiler_libdir=/opt/open64/4.2.1/lib/gcc-lib/x86_64-open64-linux/4.2.1 compiler_bindir=/opt/open64/4.2.1/bin openmpi_version=1.3.3 ompi_libdir=/opt/openmpi/${openmpi_version}-1.${disttag}.${compiler}.${compiler_version}/lib64 ompi_includedir=/opt/openmpi/${openmpi_version}-1.${disttag}.${compiler}.${compiler_version}/include ompi_bindir=/opt/openmpi/${openmpi_version}-1.${disttag}.${compiler}.${compiler_version}/bin release=1.${disttag}.${compiler}.${compiler_version}.python2.4.openmpi.${openmpi_version} |
module load ifort/11.0-1 |
| Line 1642: | Line 1633: |
| --with prefix=/opt/campos-asap/3.2.0/${release} campos-asap.spec | --with prefix=/opt/campos-asap3/3.2.0/${release} campos-asap.spec |
This page describes the necessary steps for installing the login nodes fjorm or thul.
Warning: el5 installs often 32-bit versions of packages on 64-bit machines. Please verify that 64-bit versions are installed, otherwise run the corresponding yum install package again.
Install external packages
As root:
create yum repository definitions (do not enable them):
# atrpms echo '[atrpms]' > /etc/yum.repos.d/atrpms.repo echo 'name=CentOS $releasever - $basearch - ATrpms' >> /etc/yum.repos.d/atrpms.repo echo 'baseurl=http://dl.atrpms.net/el$releasever-$basearch/atrpms/stable' >> /etc/yum.repos.d/atrpms.repo echo '#baseurl=http://mirrors.ircam.fr/pub/atrpms/el$releasever-$basearch/atrpms/stable' >> /etc/yum.repos.d/atrpms.repo echo 'gpgkey=http://ATrpms.net/RPM-GPG-KEY.atrpms' >> /etc/yum.repos.d/atrpms.repo echo 'gpgcheck=1' >> /etc/yum.repos.d/atrpms.repo echo 'enabled=0' >> /etc/yum.repos.d/atrpms.repo # epel echo '[epel]' > /etc/yum.repos.d/epel.repo echo 'name=CentOS $releasever - $basearch - EPEL' >> /etc/yum.repos.d/epel.repo echo 'baseurl=http://download.fedora.redhat.com/pub/epel/$releasever/$basearch' >> /etc/yum.repos.d/epel.repo echo 'gpgkey=http://download.fedora.redhat.com/pub/epel/RPM-GPG-KEY-EPEL' >> /etc/yum.repos.d/epel.repo echo 'gpgcheck=1' >> /etc/yum.repos.d/epel.repo echo 'enabled=0' >> /etc/yum.repos.d/epel.repo
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 (as rpmbuild):
enable modules - add to ~/.bashrc:
if [ -r "/home/camp/modulefiles.sh" ]; then source /home/camp/modulefiles.sh fiset the FYS_PLATFORM variable:
export FYS_PLATFORM=Intel-Nehalem-el5 # thul export FYS_PLATFORM=AMD-Opteron-el5 # fjorm
Note that this variable will be set automatically by /home/camp/modulefiles.sh after the environment-modules package is installed.
use the following ~rpmbuild/.rpmmacros:
%disttag el5.fys %packager rpmbuild@fysik.dtu.dk %distribution Fysik RPMS %vendor Fysik RPMS <rpm@fysik.dtu.dk> %_signature gpg %_gpg_path ~/.gnupg %_gpg_name Fysik RPMS %_topdir /home/camp/rpmbuild/%(echo $FYS_PLATFORM) %_rpmdir %{_topdir}/RPMS %_srcrpmdir %{_topdir}/SRPMS %_svndir /home/camp/rpmbuild/rpmbuild %_specdir %{_svndir}/SPECS %_sourcedir %{_svndir}/SOURCES %_rpmfilename %%{NAME}-%%{VERSION}-%%{RELEASE}.%%{ARCH}.rpm %_builddir /scratch/rpmbuild %_tmppath %{_topdir}/BUILD # no debuginfo %debug_package %{nil} # don't strip (this does not fully work) # https://bugzilla.redhat.com/show_bug.cgi?id=219731 %define __strip /bin/true %niflheim 1as rpmbuild create directories:
mkdir -p ~/${FYS_PLATFORM}/RPMS mkdir -p ~/${FYS_PLATFORM}/SRPMS mkdir -p ~/${FYS_PLATFORM}/BUILD mkdir -p ~/${FYS_PLATFORM}/SPECS # needed only by openmpi mkdir -p ~/${FYS_PLATFORM}/SOURCES # needed only by openmpi
install official packages, as rpmbuild:
cd ~/${FYS_PLATFORM}/RPMS mkdir external; cd external yumdownloader --resolve gcc-gfortran gcc43-c++ gcc43-gfortran blas-devel lapack-devel python-devel yumdownloader --resolve gnuplot libXi-devel xorg-x11-fonts-100dpi pexpect tetex-latex tkinter qt-devel yumdownloader --resolve openmpi openmpi-devel openmpi-libs compat-dapl libibverbs librdmacm openib yumdownloader --resolve pygtk2-devel gtk2-devel tk-devel agg ghostscript libtiff-devel yumdownloader --resolve libX11-devel libXext-devel openmotif openmotif-devel gd-devel libXpm-devel yum localinstall * # as rootinstall atrpms packages, as rpmbuild (vtk-python is currently unavailable 16 Apr 2009):
cd ~/${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 rootinstall the packages from epel, as rpmbuild:
~/${FYS_PLATFORM}/RPMS/external yumdownloader --resolve --enablerepo=epel jmol gsl-devel yumdownloader --resolve --enablerepo=epel environment-modules suitesparse-devel wget http://download.fedora.redhat.com/pub/epel/RPM-GPG-KEY-EPEL rpm --import RPM-GPG-KEY-EPEL # as root yum localinstall * # as rootremove default openmpi:
yum remove openmpi openmpi-libs
edit /etc/yum.conf so it contains:
exclude=netcdf-* netcdf3-* fftw-* fftw2-* fftw3-* python-numeric openmpi-*
logout and login (as rpmbuild) again to activate modules settings from ~/.bashrc.
It's time to build custom RPMS
As rpmbuild:
cd ~/rpmbuild/SPECS
Install Install Open64 Compiler Suite RPM, and deploy module file under ` ~rpmbuild/modulefiles/${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
Note that 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
Install icc/ifort compilers, install only the following packages from l_cproc_p_11.1.046_intel64:
intel-cproc046-11.1-1.x86_64.rpm intel-cproidb046-11.1-1.x86_64.rpm intel-cprolib046-11.1-1.x86_64.rpm intel-cprolibdev046-11.1-1.x86_64.rpm intel-cprotbblib046-11.1-1.noarch.rpm intel-cprotbblibdev046-11.1-1.noarch.rpm intel-cprocsdk046-11.1-1.noarch.rpm intel-cproidbsdk046-11.1-1.noarch.rpm
and from l_cprof_p_11.1.046_intel64:
intel-cprof046-11.1-1.x86_64.rpm intel-cproflib046-11.1-1.x86_64.rpm intel-cprofsdk046-11.1-1.noarch.rpm
, enable them (only on thul):
. /opt/intel/Compiler/11.1/046/bin/intel64/ifortvars_intel64.sh . /opt/intel/Compiler/11.1/046/bin/intel64/iccvars_intel64.sh
Build intel compatibility packages (only on thul):
rpmbuild -bb --with modules intel-redist.spec
Note: do not install the resulting RPMS on the login node. They need to be installed only on compute nodes. 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/${FYS_PLATFORM}/ifort
cp /scratch/rpmbuild/intel-11.1.046/11.1.046-1.intel64.el5.fys ~rpmbuild/modulefiles/${FYS_PLATFORM}/ifort
cd ~rpmbuild/modulefiles/${FYS_PLATFORM}/ifort
ln -s 11.1.046-1.intel64.el5.fys 11.1-1Note: the above module file should contain at least:
prepend-path LD_LIBRARY_PATH /opt/intel/Compiler/11.1/046/lib/intel64 prepend-path PATH /opt/intel/Compiler/11.1/046/bin/intel64 prepend-path MANPATH /opt/intel/Compiler/11.1/046/man
Install mkl, 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 ${mkl}
cd ~/rpmbuild/SPECS
rpmbuild -bb --with version1=1 --with version2=3 --with version3=027 --with modules intel-redist-mkl.specNote: do not install the resulting RPM on the login node. It needs to be installed only on compute nodes. On the login node only the module file needs to be deployed under ~rpmbuild/modulefiles, as rpmbuild. Note that this directory is available as svn checkout at https://svn.fysik.dtu.dk/projects/modulefiles/trunk. Here is what need to be done for a new version of the package:
mkdir ~rpmbuild/modulefiles/${FYS_PLATFORM}/mkl
cp /tmp/intel-mkl-${mkl}/${mkl}-1.el5.fys.em64t ~rpmbuild/modulefiles/${FYS_PLATFORM}/mkl
cd ~rpmbuild/modulefiles/${FYS_PLATFORM}/mkl
ln -s ${mkl}-1.el5.fys.em64t 10.1p-027Note: the above module file should contain at least:
prepend-path LD_LIBRARY_PATH /opt/intel/mkl/10.1.3.027/lib/em64t
Moreover: intel-*intel64* RPMS need to be installed with --nodeps, so move them into a special directory:
mkdir -p ~/${FYS_PLATFORM}/RPMS/nodeps
mv ~/${FYS_PLATFORM}/RPMS/intel-*intel64* ~/${FYS_PLATFORM}/RPMS/nodepsBuild 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.aLogout and login as rpmbuild.
Build a custom openmpi, using torque support:
export rpmtopdir=${HOME}/${FYS_PLATFORM} # set this to _topdir value from ~/.rpmmacros
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.${FYS_PLATFORM}
sh ./buildrpm-1.3.3-1.ifort.sh ../SOURCES/openmpi-1.3.3.tar.bz2 2>&1 | tee buildrpm-1.3.3-1.ifort.sh.log.${FYS_PLATFORM} # thul only
module load open64 # 24 June 2009: build fails on Nehalem with *configure: error: TM support requested but not found. Aborting*
sh ./buildrpm-1.3.3-1.open64.sh ../SOURCES/openmpi-1.3.3.tar.bz2 2>&1 | tee buildrpm-1.3.3-1.open64.sh.log.${FYS_PLATFORM}Note: intel openmpi needs to be installed ignoring dependencies:
rpm -ivh --nodeps --oldpackage ~rpmbuild/${FYS_PLATFORM}/RPMS/openmpi-1.3.3-1.el5.fys.ifort.11.1.x86_64.rpmIf scripts that contain ALL build/install/uninstall commands (global_install.sh and global_uninstall.sh) need to be created, every time after an RPM is successfully built, do:
grep -v "#\!" install.sh >> ~/${FYS_PLATFORM}/global_install.sh
cat uninstall.sh ~/${FYS_PLATFORM}/global_uninstall.sh | grep -v "#\!" >> ~/${FYS_PLATFORM}/global_uninstall.sh.tmp && mv -f ~/${FYS_PLATFORM}/global_uninstall.sh.tmp ~/${FYS_PLATFORM}/global_uninstall.sh
# ignore "cat: .../global_uninstall.sh: No such ..." error when running first timeNote that global_uninstall.sh won't remove built RPM files, just will uninstall the packages.
Build the following for dacapo:
set the disttag variable for convenience:
export disttag="el5.fys" modules=1
acml
AMD Core Math Library contains optimized BLAS and LAPACK libraries for AMD opteron processors (work also on intel), and is available for download after registration.
Build the following RPMS:
version1=0 version2=1 compiler=gfortran version1=0 version2=1 compiler=pathscale version1=1 version2=0 compiler=gfortran43 # fjorm only version1=1 version2=0 compiler=pathscale version1=2 version2=0 compiler=gfortran43 version1=2 version2=0 compiler=pathscale version1=2 version2=0 compiler=ifort # thul only version1=3 version2=0 compiler=gfortran43 version1=3 version2=0 compiler=open64 # fjorm only version1=3 version2=0 compiler=ifort # thul only rpmbuild -bb --with compiler=${compiler} --with version1=${version1} --with version2=${version1} \ --with modules=${modules} --with default_version acml.specNote 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()-t0Download 32H2O.xyz
goto (only on fjorm).
GotoBLAS contains optimized BLAS libraries, and is available for academic community after registration.
Download GotoBLAS-1.26.tar.gz to ~/rpmbuild/SOURCES. The default build process searches your $PATH for available compilers. Priority order is PathScale, PGI, Intel, gfortran, g95 and g77, therefore setting compilers explicitly is needed. Build RPMS (on the target compute node!) using the following command:
blas_version=1.26 compiler=gfortran compiler_version=4.1.2 compiler_libdir=/usr/lib64 compiler_bindir=/usr/bin compiler=gfortran43 compiler_version=4.3.2 compiler_libdir=/usr/lib64 compiler_bindir=/usr/bin compiler=pathscale compiler_version=3.2 compiler_libdir=/opt/pathscale/lib/3.2 compiler_bindir=/opt/pathscale/bin compiler=open64 # only on fjorm compiler_version=4.2.1 compiler_libdir=/opt/open64/4.2.1/lib/gcc-lib/x86_64-open64-linux/4.2.1 compiler_bindir=/opt/open64/4.2.1/bin rpmbuild --bb --with compiler=${compiler} --with compiler_version=${compiler_version} \ --with compiler_libdir=${compiler_libdir} --with compiler_bindir=${compiler_bindir} \ --with modules=${modules} --with default_version=1 \ --with prefix=/opt/goto/${blas_version}/1.${disttag}.${compiler}.${compiler_version}.smp goto.specNote - 1.26 version fails on Nehalem with:
../../../param.h:1195:21: error: division by zero in #if
atlas
Build the following RPMS:
cd ~/rpmbuild/SOURCES&& wget http://downloads.sourceforge.net/project/math-atlas/Stable/3.8.3/atlas3.8.3.tar.bz2 cd ~/rpmbuild/SPECS blas_version=3.8.3 compiler=gfortran compiler_version=4.1.2 compiler_libdir=/usr/lib64 compiler_bindir=/usr/bin compiler=gfortran43 compiler_version=4.3.2 compiler_libdir=/usr/lib64 compiler_bindir=/usr/bin rpmbuild --bb --with compiler=${compiler} --with compiler_version=${compiler_version} \ --with compiler_libdir=${compiler_libdir} --with compiler_bindir=${compiler_bindir} \ --with modules=${modules} --with default_version=1 \ --with prefix=/opt/atlas/${blas_version}/1.${disttag}.${compiler}.${compiler_version} atlas.specNote: - 3.8.3 version fails on Opteron with open64 with:
/scratch/rpmbuild/ATLAS/RpmObjs/..//CONFIG/src/backend/comptestC.c:5: undefined reference to `__pathscale_malloc_alg'
campos-dacapo-pseudopotentials
campos-dacapo-pseudopotentials-1.tar.gz
Build the following RPMS:
cd ~/rpmbuild/SOURCES&& wget --no-check-certificate \ "https://wiki.fysik.dtu.dk/dacapo/Installation?action=AttachFile&do=get&target=campos-dacapo-pseudopotentials-1.tar.gz" \ -O campos-dacapo-pseudopotentials-1.tar.gz cd ~/rpmbuild/SPECS rpmbuild -bb --with modules --with default_version campos-dacapo-pseudopotentials.spec
rasmol
Note that rasmol is built for 32bit architecture, so make sure that your system fulfills "BuildRequires" for both 64 and 32bit:
rpmbuild --nobuild RasMol.spec
Build the following RPMS:
cd ~/rpmbuild/SOURCES&& wget http://downloads.sourceforge.net/openrasmol/RasMol_2.7.3.tar.gz cd ~/rpmbuild/SPECS rpmbuild -bb --with modules --with default_version --with prefix=/opt/RasMol/2.7.3/3.${disttag} RasMol.speccblas
Build the following RPMS:
cd ~/rpmbuild/SOURCES&& wget http://www.netlib.org/blas/blast-forum/cblas.tgz cd ~/rpmbuild/SPECS compiler=gfortran compiler_version=4.1.2 blas=blas blas_version=3.0.37.el5 blasdir=/usr/lib64 compiler=gfortran compiler_version=4.1.2 blas=acml blas_version=4.0.1 blasdir=/opt/${blas}/${blas_version}/${compiler}64/lib rpmbuild --bb --with compiler=${compiler} --with compiler_version=${compiler_version} \ --with blas=${blas} --with blas_version=${blas_version} --with blasdir=${blasdir} \ --with modules=${modules} --with default_version=1 \ --with prefix=/opt/cblas/2.23.3/1.${disttag}.${compiler}.${compiler_version}.${blas}.${blas_version} cblas.specpython-setuptools
Build the following RPMS:
cd ~/rpmbuild/SOURCES&& wget http://pypi.python.org/packages/source/s/setuptools/setuptools-0.6c9.tar.gz cd ~/rpmbuild/SPECS rpmbuild -bb --with modules --with default_version --with prefix=/opt/python-setuptools/0.6c9/1.${disttag}.python2.4 python-setuptools.specpython-nose
Build the following RPMS:
cd ~/rpmbuild/SOURCES&& wget http://somethingaboutorange.com/mrl/projects/nose/nose-0.10.4.tar.gz cd ~/rpmbuild/SPECS rpmbuild -bb --with modules --with default_version --with prefix=/opt/python-nose/0.10.4/1.${disttag}.python2.4 python-nose.spec module load python-setuptools module load python-nosenumpy
Note: Standard (unoptimized) numpy for EL4 can be found at Scientific Linux (example given for i386):
wget ftp://ftp.scientificlinux.org/linux/scientific/4x/i386/SL/RPMS/numpy-1.0.4-1.i386.rpm wget --no-check-certificate https://www.scientificlinux.org/documentation/gpg/RPM-GPG-KEY-dawson rpm --import RPM-GPG-KEY-dawson yum localinstall numpy-1.0.4-1.i386.rpm
and for EL5 at http://fedoraproject.org/wiki/EPEL/FAQ#howtouse.
Build the following RPMS:
cd ~/rpmbuild/SOURCES&& wget http://downloads.sourceforge.net/project/numpy/NumPy/1.3.0/numpy-1.3.0.tar.gz cd ~/rpmbuild/SPECS compiler=gfortran # Aug 6 2009: causes problems to gpaw cg2.py test compiler_version=4.1.2 compiler_libdir=/usr/lib64 compiler_bindir=/usr/bin blas=blas blas_version=3.0.37.el5 blasdir=/usr/lib64 lapack=lapack lapack_version=3.0.37.el5 lapackdir=/usr/lib64 cblas_prefix=/opt/cblas/2.23.3/1.${disttag}.${compiler}.${compiler_version}.${blas}.${blas_version} release=1.${disttag}.${compiler}.${compiler_version}.python2.4.${blas}.${blas_version}.${lapack}.${lapack_version} compiler=gfortran compiler_version=4.1.2 compiler_libdir=/usr/lib64 compiler_bindir=/usr/bin blas=acml blas_version=4.0.1 blasdir=/opt/${blas}/${blas_version}/${compiler}64/lib lapack=acml lapack_version=4.0.1 lapackdir=/opt/${blas}/${blas_version}/${compiler}64/lib cblas_prefix=none # dotblas fails with acml release=1.${disttag}.${compiler}.${compiler_version}.python2.4.${blas}.${blas_version}.${lapack}.${lapack_version} compiler=gfortran # only on thul compiler_version=4.1.2 compiler_libdir=/usr/lib64 compiler_bindir=/usr/bin blas=mkl blas_version=10.1.3.027 blasdir=/opt/intel/mkl/10.1.3.027/lib/em64t lapack=mkl_lapack lapack_version=10.1.3.027 lapackdir=/opt/intel/mkl/10.1.3.027/lib/em64t cblas_prefix=/opt/intel/mkl/10.1.3.027 release=1.${disttag}.${compiler}.${compiler_version}.python2.4.${blas}.${blas_version}.${lapack}.${lapack_version} rpmbuild --bb --with cblas_prefix=${cblas_prefix} \ --with blas=${blas} --with blas_version=${blas_version} --with blasdir=${blasdir} \ --with compiler=${compiler} --with compiler_version=${compiler_version} \ --with compiler_bindir=${compiler_bindir} --with compiler_libdir=${compiler_libdir} \ --with lapack=${lapack} --with lapack_version=${lapack_version} --with lapackdir=${lapackdir} \ --with modules=${modules} --with default_version=1 \ --with prefix=/opt/numpy/1.3.0/${release} numpy.specTest with:
module load cblas-blas-gfortran64/2.23.3-1.el5.fys.gfortran.4.1.2.blas.3.0.37.el5 module load numpy/1.3.0-1.el5.fys.gfortran.4.1.2.python2.4.blas.3.0.37.el5.lapack.3.0.37.el5 python -c "import numpy; from numpy.core.multiarray import dot; b = numpy.ones(13, numpy.complex); dot(b, b)" python -c "import numpy; numpy.test()" module unload numpy/1.3.0-1.el5.fys.gfortran.4.1.2.python2.4.blas.3.0.37.el5.lapack.3.0.37.el5 module load acml-gfortran64/4.0.1-1.el5.fys module load numpy/1.3.0-1.el5.fys.gfortran.4.1.2.python2.4.acml.4.0.1.acml.4.0.1 python -c "import numpy; from numpy.core.multiarray import dot; b = numpy.ones(13, numpy.complex); dot(b, b)" python -c "import numpy; numpy.test()" module unload numpy/1.3.0-1.el5.fys.gfortran.4.1.2.python2.4.acml.4.0.1.acml.4.0.1 module unload acml-gfortran64/4.0.1-1.el5.fys
Load the default numpy:
module load numpy/1.3.0-1.el5.fys.gfortran.4.1.2.python2.4.acml.4.0.1.acml.4.0.1
gnuplot-py
Build the following RPMS:
cd ~/rpmbuild/SOURCES&& wget http://downloads.sourceforge.net/gnuplot-py/gnuplot-py-1.8.tar.gz cd ~/rpmbuild/SPECS rpmbuild -bb --with modules --with default_version --with prefix=/opt/gnuplot-py/1.8.1/1.${disttag}.python2.4 gnuplot-py.spec module load gnuplot-pypython-numeric
We must install 24.2 version, and we keep the default version. Build the following RPMS:
cd ~/rpmbuild/SOURCES&& wget http://downloads.sourceforge.net/numpy/Numeric-24.2.tar.gz cd ~/rpmbuild/SPECS cd ~/${FYS_PLATFORM}/RPMS/external rpm -e --nodeps python-numeric # as root yumdownloader --resolve --disableexcludes=main python-numeric cd ~/rpmbuild/SPECS compiler=gfortran compiler_version=4.1.2 compiler_libdir=/usr/lib64 compiler_bindir=/usr/bin blas=blas blas_version=3.0.37.el5 blasdir=/usr/lib64 lapack=lapack lapack_version=3.0.37.el5 lapackdir=/usr/lib64 cblas_prefix=/opt/cblas/2.23.3/1.${disttag}.${compiler}.${compiler_version}.${blas}.${blas_version} release=1.${disttag}.${compiler}.${compiler_version}.python2.4.${blas}.${blas_version}.${lapack}.${lapack_version} compiler=gfortran compiler_version=4.1.2 compiler_libdir=/usr/lib64 compiler_bindir=/usr/bin blas=acml blas_version=4.0.1 blasdir=/opt/${blas}/${blas_version}/${compiler}64/lib lapack=acml lapack_version=4.0.1 lapackdir=/opt/${blas}/${blas_version}/${compiler}64/lib cblas_prefix=/opt/cblas/2.23.3/1.${disttag}.${compiler}.${compiler_version}.${blas}.${blas_version} release=1.${disttag}.${compiler}.${compiler_version}.python2.4.${blas}.${blas_version}.${lapack}.${lapack_version} rpmbuild --bb --with cblas_prefix=${cblas_prefix} \ --with blas=${blas} --with blas_version=${blas_version} --with blasdir=${blasdir} \ --with compiler=${compiler} --with compiler_version=${compiler_version} \ --with compiler_bindir=${compiler_bindir} --with compiler_libdir=${compiler_libdir} \ --with lapack=${lapack} --with lapack_version=${lapack_version} --with lapackdir=${lapackdir} \ --with modules=${modules} --with default_version=1 \ --with prefix=/opt/python-numeric/24.2/${release} python-numeric.specNote: (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 cblas-blas-gfortran64/2.23.3-1.el5.fys.gfortran.4.1.2.blas.3.0.37.el5 module load python-numeric/24.2-4.el5.fys.gfortran.4.1.2.python2.4.blas.3.0.37.el5.lapack.3.0.37.el5 python -c "import lapack_lite" ldd `rpm -ql python-numeric-24.2-4.el5.fys.gfortran.4.1.2.python2.4.blas.3.0.37.el5.lapack.3.0.37.el5 | grep lapack_lite.so` ldd `rpm -ql python-numeric-24.2-4.el5.fys.gfortran.4.1.2.python2.4.blas.3.0.37.el5.lapack.3.0.37.el5 | grep _dotblas.so` module unload python-numeric/24.2-4.el5.fys.gfortran.4.1.2.python2.4.blas.3.0.37.el5.lapack.3.0.37.el5 module load acml-gfortran64/4.0.1-1.el5.fys module load cblas-acml-gfortran64/2.23.3-1.el5.fys.gfortran.4.1.2.acml.4.0.1 module load python-numeric/24.2-4.el5.fys.gfortran.4.1.2.python2.4.acml.4.0.1.acml.4.0.1 python -c "import lapack_lite" ldd `rpm -ql python-numeric-24.2-4.el5.fys.gfortran.4.1.2.python2.4.acml.4.0.1.acml.4.0.1 | grep lapack_lite.so` ldd `rpm -ql python-numeric-24.2-4.el5.fys.gfortran.4.1.2.python2.4.acml.4.0.1.acml.4.0.1 | grep _dotblas.so` module unload python-numeric/24.2-4.el5.fys.gfortran.4.1.2.python2.4.acml.4.0.1.acml.4.0.1 module unload acml-gfortran64/4.0.1-1.el5.fys
and reinstall the default version:
rpm -ivh --oldpackage ~rpmbuild/${FYS_PLATFORM}/RPMS/external/python-numeric-23.*.rpmload the default Numeric version:
module load acml-gfortran64/4.0.1-1.el5.fys module load cblas-acml-gfortran64/2.23.3-1.el5.fys.gfortran.4.1.2.acml.4.0.1 module load python-numeric/24.2-4.el5.fys.gfortran.4.1.2.python2.4.acml.4.0.1.acml.4.0.1
netcdf
NetCDF (network Common Data Form) is an interface for array-oriented data access and a library that provides an implementation of the interface. The NetCDF library also defines a machine-independent format for representing scientific data.
We prefer version 3.6.1 or higher (note that version 3.6.2 has fortran interface in libnetcdff.a).
Build the following RPMS:
cd ~/rpmbuild/SOURCES&& wget http://www.unidata.ucar.edu/downloads/netcdf/ftp/netcdf-4.0.1.tar.gz cd ~/rpmbuild/SPECS compiler=gfortran compiler_version=4.1.2 compiler_libdir=/usr/lib64 compiler_bindir=/usr/bin compiler=gfortran43 compiler_version=4.3.2 compiler_libdir=/usr/lib64 compiler_bindir=/usr/bin compiler=pathscale # only on fjorm compiler_version=3.2 compiler_libdir=/opt/pathscale/lib/3.2 compiler_bindir=/opt/pathscale/bin compiler=ifort # only on thul compiler_version=11.0 compiler_libdir=/opt/intel/Compiler/11.0/083/lib/intel64 compiler_bindir=/opt/intel/Compiler/11.0/083/bin/intel64 compiler=open64 # only on fjorm compiler_version=4.2.1 compiler_libdir=/opt/open64/4.2.1/lib/gcc-lib/x86_64-open64-linux/4.2.1 compiler_bindir=/opt/open64/4.2.1/bin rpmbuild --bb --with compiler=${compiler} --with compiler_version=${compiler_version} \ --with compiler_bindir=${compiler_bindir} \ --with compiler_libdir=${compiler_libdir} \ --with modules=${modules} --with default_version=1 \ --with prefix=/opt/netcdf4/4.0.1/1.${disttag}.${compiler}.${compiler_version} netcdf4.specScientificPython
Build the following RPMS:
cd ~/rpmbuild/SOURCES&& wget https://sourcesup.cru.fr/frs/download.php/2234/ScientificPython-2.6.2.tar.gz cd ~/rpmbuild/SOURCES&& wget https://sourcesup.cru.fr/frs/download.php/2234/ScientificPython-2.8.tar.gz cd ~/rpmbuild/SPECS compiler=gfortran compiler_version=4.1.2 compiler_libdir=/usr/lib64 compiler_bindir=/usr/bin netcdf=netcdf4 netcdf_includedir=/opt/${netcdf}/4.0.1/1.${disttag}.${compiler}.${compiler_version}/include netcdf_libdir=/opt/${netcdf}/4.0.1/1.${disttag}.${compiler}.${compiler_version}/lib64 openmpi_version=1.3.3 ompi_libdir=/opt/openmpi/${openmpi_version}-1.${disttag}.${compiler}.${compiler_version}/lib64 ompi_includedir=/opt/openmpi/${openmpi_version}-1.${disttag}.${compiler}.${compiler_version}/include ompi_bindir=/opt/openmpi/${openmpi_version}-1.${disttag}.${compiler}.${compiler_version}/bin rpmbuild --bb --with Numeric_includedir=none --with numpy=numpy \ --with compiler=${compiler} --with compiler_version=${compiler_version} \ --with netcdf=${netcdf} --with netcdf_includedir=${netcdf_includedir} --with netcdf_libdir=${netcdf_libdir} \ --with modules=${modules} --with default_version=1 \ --with prefix=/opt/ScientificPython/2.8/1.${disttag}.${compiler}.${compiler_version}.python2.4.serial_version.only.numpy ScientificPython.spec rpmbuild --bb --with numpy=numeric \ --with compiler=${compiler} --with compiler_version=${compiler_version} \ --with netcdf=${netcdf} --with netcdf_includedir=${netcdf_includedir} --with netcdf_libdir=${netcdf_libdir} \ --with modules=${modules} --with default_version=1 \ --with parallel=1 --with openmpi=openmpi --with openmpi_version=${openmpi_version} \ --with ompi_libdir=${ompi_libdir} --with ompi_includedir=${ompi_includedir} --with ompi_bindir=${ompi_bindir} \ --with prefix=/opt/ScientificPython/2.6.2/1.${disttag}.${compiler}.${compiler_version}.python2.4.openmpi.${openmpi_version}.numeric ScientificPython.specpython-docutils
Build the following RPMS:
cd ~/rpmbuild/SOURCES&& wget http://downloads.sourceforge.net/project/docutils/docutils/0.5/docutils-0.5.tar.gz cd ~/rpmbuild/SPECS rpmbuild -bb --with modules --with default_version --with prefix=/opt/python-docutils/0.5/1.${disttag}.python2.4 python-docutils.specpytz
Build the following RPMS:
cd ~/rpmbuild/SOURCES&& wget http://pypi.python.org/packages/source/p/pytz/pytz-2008g.tar.gz cd ~/rpmbuild/SPECS rpmbuild -bb --with modules --with default_version --with prefix=/opt/pytz/2008g/1.${disttag}.python2.4 pytz.specpython-dateutil
Build the following RPMS:
cd ~/rpmbuild/SOURCES&& wget http://pypi.python.org/packages/source/p/python-dateutil/python-dateutil-1.4.1.tar.gz cd ~/rpmbuild/SPECS rpmbuild -bb --with modules --with default_version --with prefix=/opt/python-dateutil/1.4.1/3.${disttag}.python2.4 python-dateutil.specpython-matplotlib
Build the following RPMS:
cd ~/rpmbuild/SOURCES&& wget http://downloads.sourceforge.net/project/matplotlib/matplotlib/matplotlib-0.98.5/matplotlib-0.98.5.3.tar.gz cd ~/rpmbuild/SPECS module load pytz module load python-docutils module load python-dateutil rpmbuild -bb --with modules --with default_version --with prefix=/opt/python-matplotlib/0.98.5.3/1.${disttag}.python2.4 python-matplotlib.speccampos-ase2
Build the following RPMS:
cd ~/rpmbuild/SOURCES&& wget --no-check-certificate \ "https://wiki.fysik.dtu.dk/ase2/Download?action=AttachFile&do=get&target=campos-ase-2.3.13.tar.gz" \ -O campos-ase-2.3.13.tar.gz cd ~/rpmbuild/SPECS rpmbuild -bb --with modules --with default_version --with prefix=/opt/campos-ase2/2.3.13/1.${disttag}.python2.4 campos-ase2.speccampos-dacapo-python
Build the following RPMS:
cd ~/rpmbuild/SOURCES&& wget --no-check-certificate \ "https://wiki.fysik.dtu.dk/dacapo/Installation?action=AttachFile&do=get&target=Dacapo-0.9.4.tar.gz" \ -O Dacapo-0.9.4.tar.gz cd ~/rpmbuild/SPECS rpmbuild -bb --with modules --with default_version --with prefix=/opt/campos-dacapo-python/0.9.4/1.${disttag}.python2.4 campos-dacapo-python.specfftw2
We use version 2.1.5.
Build the following RPMS:
cd ~/rpmbuild/SOURCES&& wget http://www.fftw.org/fftw-2.1.5.tar.gz cd ~/rpmbuild/SPECS compiler=gfortran compiler_version=4.1.2 compiler_libdir=/usr/lib64 compiler_bindir=/usr/bin compiler=gfortran43 compiler_version=4.3.2 compiler_libdir=/usr/lib64 compiler_bindir=/usr/bin compiler=pathscale # only on fjorm compiler_version=3.2 compiler_libdir=/opt/pathscale/lib/3.2 compiler_bindir=/opt/pathscale/bin # Note: 24 June 2009: ifort fails to build static fftw2 compiler=ifort # only on thul compiler_version=11.0 compiler_libdir=/opt/intel/Compiler/11.0/083/lib/intel64 compiler_bindir=/opt/intel/Compiler/11.0/083/bin/intel64 compiler=open64 # only on fjorm compiler_version=4.2.1 compiler_libdir=/opt/open64/4.2.1/lib/gcc-lib/x86_64-open64-linux/4.2.1 compiler_bindir=/opt/open64/4.2.1/bin rpmbuild --bb --with compiler=${compiler} --with compiler_version=${compiler_version} \ --with compiler_bindir=${compiler_bindir} \ --with compiler_libdir=${compiler_libdir} \ --with modules=${modules} --with default_version=1 \ --with prefix=/opt/fftw2/2.1.5/12.${disttag}.${compiler}.${compiler_version} fftw2.speccampos-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 won netcdf should work).
Build the following RPMS:
cd ~/rpmbuild/SOURCES&& wget --no-check-certificate \ "https://wiki.fysik.dtu.dk/dacapo/Installation?action=AttachFile&do=get&target=campos-dacapo-2.7.16.tar.gz" \ -O campos-dacapo-2.7.16.tar.gz cd ~/rpmbuild/SPECS compiler=gfortran43 compiler_version=4.3.2 compiler_libdir=/usr/lib64 compiler_bindir=/usr/bin blas=acml blas_version=4.3.0 blasdir=/opt/${blas}/${blas_version}/${compiler}64/lib lapack=acml lapack_version=4.3.0 lapackdir=/opt/${lapack}/${lapack_version}/${compiler}64/lib fftw=fftw2 fftw_libdir=/opt/${fftw}/2.1.5/12.${disttag}.${compiler}.${compiler_version}/lib64 netcdf=netcdf4 netcdf_includedir=/opt/${netcdf}/4.0.1/1.${disttag}.${compiler}.${compiler_version}/include netcdf_libdir=/opt/${netcdf}/4.0.1/1.${disttag}.${compiler}.${compiler_version}/lib64 openmpi_version=1.3.3 ompi_libdir=/opt/openmpi/${openmpi_version}-1.${disttag}.${compiler}.${compiler_version}/lib64 ompi_includedir=/opt/openmpi/${openmpi_version}-1.${disttag}.${compiler}.${compiler_version}/include ompi_bindir=/opt/openmpi/${openmpi_version}-1.${disttag}.${compiler}.${compiler_version}/bin release=1.${disttag}.${compiler}.${compiler_version}.openmpi.${openmpi_version}.${blas}.${blas_version}.${lapack}.${lapack_version}.${fftw} compiler=pathscale compiler_version=3.2 compiler_libdir=/opt/pathscale/lib/3.2 compiler_bindir=/opt/pathscale/bin blas=acml blas_version=4.0.1 blasdir=/opt/${blas}/${blas_version}/${compiler}64/lib lapack=acml lapack_version=4.0.1 lapackdir=/opt/${lapack}/${lapack_version}/${compiler}64/lib fftw=fftw2 fftw_libdir=/opt/${fftw}/2.1.5/12.${disttag}.${compiler}.${compiler_version}/lib64 netcdf=netcdf4 netcdf_includedir=/opt/${netcdf}/4.0.1/1.${disttag}.${compiler}.${compiler_version}/include netcdf_libdir=/opt/${netcdf}/4.0.1/1.${disttag}.${compiler}.${compiler_version}/lib64 openmpi_version=1.3.3 ompi_libdir=/opt/openmpi/${openmpi_version}-1.${disttag}.${compiler}.${compiler_version}/lib64 ompi_includedir=/opt/openmpi/${openmpi_version}-1.${disttag}.${compiler}.${compiler_version}/include ompi_bindir=/opt/openmpi/${openmpi_version}-1.${disttag}.${compiler}.${compiler_version}/bin release=1.${disttag}.${compiler}.${compiler_version}.openmpi.${openmpi_version}.${blas}.${blas_version}.${lapack}.${lapack_version}.${fftw} compiler=gfortran compiler_version=4.1.2 compiler_libdir=/usr/lib64 compiler_bindir=/usr/bin blas=blas blas_version=3.0.37.el5 blasdir=/usr/lib64 lapack=lapack lapack_version=3.0.37.el5 lapackdir=/usr/lib64 fftw=fftw2 fftw_libdir=/opt/${fftw}/2.1.5/12.${disttag}.${compiler}.${compiler_version}/lib64 netcdf=netcdf4 netcdf_includedir=/opt/${netcdf}/4.0.1/1.${disttag}.${compiler}.${compiler_version}/include netcdf_libdir=/opt/${netcdf}/4.0.1/1.${disttag}.${compiler}.${compiler_version}/lib64 openmpi_version=1.3.3 ompi_libdir=/opt/openmpi/${openmpi_version}-1.${disttag}.${compiler}.${compiler_version}/lib64 ompi_includedir=/opt/openmpi/${openmpi_version}-1.${disttag}.${compiler}.${compiler_version}/include ompi_bindir=/opt/openmpi/${openmpi_version}-1.${disttag}.${compiler}.${compiler_version}/bin release=1.${disttag}.${compiler}.${compiler_version}.openmpi.${openmpi_version}.${blas}.${blas_version}.${lapack}.${lapack_version}.${fftw} rpmbuild --bb --with blas=${blas} --with blas_version=${blas_version} --with blasdir=${blasdir} \ --with compiler=${compiler} --with compiler_version=${compiler_version} \ --with compiler_bindir=${compiler_bindir} --with compiler_libdir=${compiler_libdir} \ --with fftw=${fftw} --with fftw_libdir=${fftw_libdir} \ --with lapack=${lapack} --with lapack_version=${lapack_version} --with lapackdir=${lapackdir} \ --with netcdf=${netcdf} --with netcdf_includedir=${netcdf_includedir} --with netcdf_libdir=${netcdf_libdir} \ --with modules=${modules} --with default_version=1 \ --with parallel=1 --with openmpi=openmpi --with openmpi_version=${openmpi_version} \ --with ompi_libdir=${ompi_libdir} --with ompi_includedir=${ompi_includedir} --with ompi_bindir=${ompi_bindir} \ --with prefix=/opt/campos-dacapo/2.7.16/${release} campos-dacapo.specOptional builds:
compiler=ifort # only on thul # multinode jobs fail compiler_version=11.0 compiler_libdir=/opt/intel/Compiler/11.0/083/lib/intel64 compiler_bindir=/opt/intel/Compiler/11.0/083/bin/intel64 blas=mkl blas_version=10.1.3.027 blasdir=/opt/intel/${blas}/${blas_version}/lib/em64t lapack=mkl_lapack lapack_version=${blas_version} lapackdir=${blasdir} fftw=mkl fftw_libdir=${blasdir} netcdf=netcdf4 netcdf_includedir=/opt/${netcdf}/4.0.1/1.${disttag}.${compiler}.${compiler_version}/include netcdf_libdir=/opt/${netcdf}/4.0.1/1.${disttag}.${compiler}.${compiler_version}/lib64 openmpi_version=1.3.3 ompi_libdir=/opt/openmpi/${openmpi_version}-1.${disttag}.${compiler}.${compiler_version}/lib64 ompi_includedir=/opt/openmpi/${openmpi_version}-1.${disttag}.${compiler}.${compiler_version}/include ompi_bindir=/opt/openmpi/${openmpi_version}-1.${disttag}.${compiler}.${compiler_version}/bin release=1.${disttag}.${compiler}.${compiler_version}.openmpi.${openmpi_version}.${blas}.${blas_version}.${lapack}.${lapack_version}.${fftw} compiler=gfortran43 # only on thul compiler_version=4.3.2 compiler_libdir=/usr/lib64 compiler_bindir=/usr/bin blas=mkl blas_version=10.1.3.027 blasdir=/opt/intel/${blas}/${blas_version}/lib/em64t lapack=mkl_lapack lapack_version=${blas_version} lapackdir=${blasdir} fftw=mkl fftw_libdir=${blasdir} netcdf=netcdf4 netcdf_includedir=/opt/${netcdf}/4.0.1/1.${disttag}.${compiler}.${compiler_version}/include netcdf_libdir=/opt/${netcdf}/4.0.1/1.${disttag}.${compiler}.${compiler_version}/lib64 openmpi_version=1.3.3 ompi_libdir=/opt/openmpi/${openmpi_version}-1.${disttag}.${compiler}.${compiler_version}/lib64 ompi_includedir=/opt/openmpi/${openmpi_version}-1.${disttag}.${compiler}.${compiler_version}/include ompi_bindir=/opt/openmpi/${openmpi_version}-1.${disttag}.${compiler}.${compiler_version}/bin release=1.${disttag}.${compiler}.${compiler_version}.openmpi.${openmpi_version}.${blas}.${blas_version}.${lapack}.${lapack_version}.${fftw} compiler=open64 # only on fjorm compiler_version=4.2.1 compiler_libdir=/opt/open64/4.2.1/lib/gcc-lib/x86_64-open64-linux/4.2.1 compiler_bindir=/opt/open64/4.2.1/bin blas=acml blas_version=4.3.0 blasdir=/opt/${blas}/${blas_version}/${compiler}64/lib lapack=acml lapack_version=4.3.0 lapackdir=/opt/${lapack}/${lapack_version}/${compiler}64/lib fftw=fftw2 fftw_libdir=/opt/${fftw}/2.1.5/12.${disttag}.${compiler}.${compiler_version}/lib64 netcdf=netcdf4 netcdf_includedir=/opt/${netcdf}/4.0.1/1.${disttag}.${compiler}.${compiler_version}/include netcdf_libdir=/opt/${netcdf}/4.0.1/1.${disttag}.${compiler}.${compiler_version}/lib64 openmpi_version=1.3.3 ompi_libdir=/opt/openmpi/${openmpi_version}-1.${disttag}.${compiler}.${compiler_version}/lib64 ompi_includedir=/opt/openmpi/${openmpi_version}-1.${disttag}.${compiler}.${compiler_version}/include ompi_bindir=/opt/openmpi/${openmpi_version}-1.${disttag}.${compiler}.${compiler_version}/bin release=1.${disttag}.${compiler}.${compiler_version}.openmpi.${openmpi_version}.${blas}.${blas_version}.${lapack}.${lapack_version}.${fftw} compiler=gfortran43 compiler_version=4.3.2 compiler_libdir=/usr/lib64 compiler_bindir=/usr/bin blas=goto blas_version=1.26 blasdir=/opt/${blas}/${blas_version}/1.${disttag}.${compiler}.${compiler_version}.smp/lib64 lapack=acml lapack_version=4.3.0 lapackdir=/opt/${lapack}/${lapack_version}/${compiler}64/lib fftw=fftw2 fftw_libdir=/opt/${fftw}/2.1.5/12.${disttag}.${compiler}.${compiler_version}/lib64 netcdf=netcdf4 netcdf_includedir=/opt/${netcdf}/4.0.1/1.${disttag}.${compiler}.${compiler_version}/include netcdf_libdir=/opt/${netcdf}/4.0.1/1.${disttag}.${compiler}.${compiler_version}/lib64 openmpi_version=1.3.3 ompi_libdir=/opt/openmpi/${openmpi_version}-1.${disttag}.${compiler}.${compiler_version}/lib64 ompi_includedir=/opt/openmpi/${openmpi_version}-1.${disttag}.${compiler}.${compiler_version}/include ompi_bindir=/opt/openmpi/${openmpi_version}-1.${disttag}.${compiler}.${compiler_version}/bin release=1.${disttag}.${compiler}.${compiler_version}.openmpi.${openmpi_version}.${blas}.${blas_version}.${lapack}.${lapack_version}.${fftw} compiler=open64 # only on fjorm compiler_version=4.2.1 compiler_libdir=/opt/open64/4.2.1/lib/gcc-lib/x86_64-open64-linux/4.2.1 compiler_bindir=/opt/open64/4.2.1/bin blas=goto blas_version=1.26 blasdir=/opt/${blas}/${blas_version}/1.${disttag}.${compiler}.${compiler_version}.smp/lib64 lapack=acml lapack_version=4.3.0 lapackdir=/opt/${lapack}/${lapack_version}/${compiler}64/lib fftw=fftw2 fftw_libdir=/opt/${fftw}/2.1.5/12.${disttag}.${compiler}.${compiler_version}/lib64 netcdf=netcdf4 netcdf_includedir=/opt/${netcdf}/4.0.1/1.${disttag}.${compiler}.${compiler_version}/include netcdf_libdir=/opt/${netcdf}/4.0.1/1.${disttag}.${compiler}.${compiler_version}/lib64 openmpi_version=1.3.3 ompi_libdir=/opt/openmpi/${openmpi_version}-1.${disttag}.${compiler}.${compiler_version}/lib64 ompi_includedir=/opt/openmpi/${openmpi_version}-1.${disttag}.${compiler}.${compiler_version}/include ompi_bindir=/opt/openmpi/${openmpi_version}-1.${disttag}.${compiler}.${compiler_version}/bin release=1.${disttag}.${compiler}.${compiler_version}.openmpi.${openmpi_version}.${blas}.${blas_version}.${lapack}.${lapack_version}.${fftw}
Build following for gpaw
fftw3
Build the following RPMS:
cd ~/rpmbuild/SOURCES&& wget ftp://ftp.fftw.org/pub/fftw/fftw-3.2.1.tar.gz cd ~/rpmbuild/SPECS compiler=gfortran compiler_version=4.1.2 compiler_libdir=/usr/lib64 compiler_bindir=/usr/bin compiler=gfortran43 compiler_version=4.3.2 compiler_libdir=/usr/lib64 compiler_bindir=/usr/bin rpmbuild --bb --with major_version=3 --with version1=2 --with version2=1 \ --with compiler=${compiler} --with compiler_version=${compiler_version} \ --with compiler_bindir=${compiler_bindir} \ --with compiler_libdir=${compiler_libdir} \ --with modules=${modules} --with default_version=1 \ --with prefix=/opt/fftw3/3.2.1/12.${disttag}.${compiler}.${compiler_version} fftw2.specscipy
Build the following RPMS:
cd ~/rpmbuild/SOURCES&& wget http://downloads.sourceforge.net/project/scipy/scipy/0.7.0/scipy-0.7.0.tar.gz cd ~/rpmbuild/SPECS module load numpy/1.3.0-1.el5.fys.gfortran.4.1.2.python2.4.blas.3.0.37.el5.lapack.3.0.37.el5 compiler=gfortran compiler_version=4.1.2 compiler_libdir=/usr/lib64 compiler_bindir=/usr/bin blas=blas blas_version=3.0.37.el5 blasdir=/usr/lib64 lapack=lapack lapack_version=3.0.37.el5 lapackdir=/usr/lib64 fftw=fftw3 fftw_libdir=/opt/${fftw}/3.2.1/12.${disttag}.${compiler}.${compiler_version}/lib64 cblas_prefix=/opt/cblas/2.23.3/1.${disttag}.${compiler}.${compiler_version}.${blas}.${blas_version} release=1.${disttag}.${compiler}.${compiler_version}.python2.4.${blas}.${blas_version}.${lapack}.${lapack_version} compiler=gfortran compiler_version=4.1.2 compiler_libdir=/usr/lib64 compiler_bindir=/usr/bin blas=acml blas_version=4.0.1 blasdir=/opt/${blas}/${blas_version}/${compiler}64/lib lapack=acml lapack_version=4.0.1 lapackdir=/opt/${blas}/${blas_version}/${compiler}64/lib fftw=fftw3 fftw_libdir=/opt/${fftw}/3.2.1/12.${disttag}.${compiler}.${compiler_version}/lib64 cblas_prefix=/opt/cblas/2.23.3/1.${disttag}.${compiler}.${compiler_version}.${blas}.${blas_version} release=1.${disttag}.${compiler}.${compiler_version}.python2.4.${blas}.${blas_version}.${lapack}.${lapack_version} rpmbuild --bb --with cblas_prefix=${cblas_prefix} \ --with blas=${blas} --with blas_version=${blas_version} --with blasdir=${blasdir} \ --with compiler=${compiler} --with compiler_version=${compiler_version} \ --with compiler_bindir=${compiler_bindir} --with compiler_libdir=${compiler_libdir} \ --with lapack=${lapack} --with lapack_version=${lapack_version} --with lapackdir=${lapackdir} \ --with ufsparse_libdir=/usr/lib64 --with ufsparse_includedir=/usr/include/suitesparse \ --with fftw=${fftw} --with fftw_libdir=${fftw_libdir} \ --with modules=${modules} --with default_version=1 \ --with prefix=/opt/scipy/0.7.0/${release} scipy.speccampos-gpaw-setups
Build the following RPMS:
cd ~/rpmbuild/SOURCES&& wget --no-check-certificate "http://wiki.fysik.dtu.dk/stuff/gpaw-setups-0.5.3574.tar.gz" cd ~/rpmbuild/SPECS rpmbuild -bb --with default_version --with modules campos-gpaw-setups.spec
povray
Build the following RPMS:
cd ~/rpmbuild/SOURCES&& wget http://www.povray.org/redirect/www.povray.org/ftp/pub/povray/Official/Unix/povray-3.6.tar.bz2 mv povray-3.6.tar.bz2 povray-3.6.1.tar.bz2 cd ~/rpmbuild/SPECS rpmbuild -bb --with modules --with default_version --with prefix=/opt/povray/3.6.1/3.${disttag} povray.specpython-jinja2
Build the following RPMS:
cd ~/rpmbuild/SOURCES&& wget http://pypi.python.org/packages/source/J/Jinja2/Jinja2-2.1.1.tar.gz cd ~/rpmbuild/SPECS rpmbuild -bb --with modules --with default_version --with prefix=/opt/python-jinja2/2.1.1/1.${disttag}.python2.4 python-jinja2.specpython-pygments
Build the following RPMS:
cd ~/rpmbuild/SOURCES&& wget http://pypi.python.org/packages/source/P/Pygments/Pygments-1.0.tar.gz cd ~/rpmbuild/SPECS rpmbuild -bb --with modules --with default_version --with prefix=/opt/python-pygments/1.0/1.${disttag}.python2.4 python-pygments.specbabel
Build the following RPMS:
cd ~/rpmbuild/SOURCES&& wget http://ftp.edgewall.com/pub/babel/Babel-0.9.4.tar.bz2 cd ~/rpmbuild/SPECS rpmbuild -bb --with modules --with default_version --with prefix=/opt/babel/0.9.4/1.${disttag}.python2.4 babel.specpython-sphinx
Build the following RPMS:
cd ~/rpmbuild/SOURCES&& wget http://pypi.python.org/packages/source/S/Sphinx/Sphinx-0.6.1.tar.gz cd ~/rpmbuild/SPECS module load python-jinja2 rpmbuild -bb --with modules --with default_version --with prefix=/opt/python-sphinx/0.6.1/1.${disttag}.python2.4 python-sphinx.speccampos-ase3
Build the following RPMS:
cd ~/rpmbuild/SOURCES&& wget --no-check-certificate \ "https://wiki.fysik.dtu.dk/ase-files/python-ase-3.1.0.846.tar.gz" \ -O python-ase-3.1.0.846.tar.gz cd ~/rpmbuild/SPECS rpmbuild -bb --with modules --with default_version --with prefix=/opt/campos-ase3/3.1.0.846/1.${disttag}.python2.4 campos-ase3.specSnapshot package is built with, e.g.:
version1=2 version2=0 version_svn=1066 release=3.${version1}.${version2}.${version_svn}/1.${disttag}.python2.4 rpmbuild -bb --with version1=${version1} --with version2=${version2} --with version_svn=${version_svn} --with keep_install=1 \ --with modules --with default_version \ --with prefix=/home/camp/rpmbuild/opt/Intel-Nehalem-el5/campos-ase3/${release} campos-ase3.spec rm /home/camp/rpmbuild/Intel-Nehalem-el5/RPMS/campos-ase3-3.2.0.1066-1.el5.fys.python2.4.x86_64.rpm dir=~/Intel-Nehalem-el5/BUILD/campos-ase3-3.${version1}.${version2}.${version_svn}-1.${disttag}.python2.4-root ln -s ${dir}/etc/modulefiles/campos-ase3/3.${version1}.${version2}.${version_svn}-1.${disttag}.python2.4 \ ~/Intel-Nehalem-el5/modulefiles.testing/campos-ase3 ln -s ${dir}/home/camp/rpmbuild/opt/Intel-Nehalem-el5/campos-ase3/3.${version1}.${version2}.${version_svn} ~/opt/Intel-Nehalem-el5/campos-ase3blacs
BLACS is used by ScaLapack.
Build the following RPMS:
cd ~/rpmbuild/SOURCES wget http://www.netlib.org/blacs/mpiblacs.tgz wget http://www.netlib.org/blacs/blacstester.tgz 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}.${compiler}.${compiler_version}/lib64 ompi_includedir=/opt/openmpi/${openmpi_version}-1.${disttag}.${compiler}.${compiler_version}/include ompi_bindir=/opt/openmpi/${openmpi_version}-1.${disttag}.${compiler}.${compiler_version}/bin compiler=gfortran43 compiler_version=4.3.2 compiler_libdir=/usr/lib64 compiler_bindir=/usr/bin openmpi_version=1.3.3 ompi_libdir=/opt/openmpi/${openmpi_version}-1.${disttag}.${compiler}.${compiler_version}/lib64 ompi_includedir=/opt/openmpi/${openmpi_version}-1.${disttag}.${compiler}.${compiler_version}/include ompi_bindir=/opt/openmpi/${openmpi_version}-1.${disttag}.${compiler}.${compiler_version}/bin compiler=pathscale compiler_version=3.2 compiler_libdir=/opt/pathscale/lib/3.2 compiler_bindir=/opt/pathscale/bin openmpi_version=1.3.3 ompi_libdir=/opt/openmpi/${openmpi_version}-1.${disttag}.${compiler}.${compiler_version}/lib64 ompi_includedir=/opt/openmpi/${openmpi_version}-1.${disttag}.${compiler}.${compiler_version}/include ompi_bindir=/opt/openmpi/${openmpi_version}-1.${disttag}.${compiler}.${compiler_version}/bin compiler=open64 compiler_version=4.2.1 compiler_libdir=/opt/open64/4.2.1/lib/gcc-lib/x86_64-open64-linux/4.2.1 compiler_bindir=/opt/open64/4.2.1/bin openmpi_version=1.3.3 ompi_libdir=/opt/openmpi/${openmpi_version}-1.${disttag}.${compiler}.${compiler_version}/lib64 ompi_includedir=/opt/openmpi/${openmpi_version}-1.${disttag}.${compiler}.${compiler_version}/include ompi_bindir=/opt/openmpi/${openmpi_version}-1.${disttag}.${compiler}.${compiler_version}/bin rpmbuild --bb --with compiler=${compiler} --with compiler_version=${compiler_version} \ --with compiler_bindir=${compiler_bindir} --with compiler_libdir=${compiler_libdir} \ --with modules=${modules} --with default_version=1 \ --with parallel=1 --with openmpi=openmpi --with openmpi_version=${openmpi_version} \ --with ompi_libdir=${ompi_libdir} --with ompi_includedir=${ompi_includedir} --with ompi_bindir=${ompi_bindir} \ --with prefix=/opt/blacs/1.1/24.${disttag}.${compiler}.${compiler_version}.openmpi.${openmpi_version} blacs.specscalapack
Build the following RPMS:
cd ~/rpmbuild/SOURCES&& wget http://www.netlib.org/scalapack/scalapack-1.8.0.tgz cd ~/rpmbuild/SPECS compiler=gfortran43 compiler_version=4.3.2 compiler_libdir=/usr/lib64 compiler_bindir=/usr/bin blas=acml blas_version=4.3.0 blasdir=/opt/${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.${disttag}.${compiler}.${compiler_version}/lib64 ompi_includedir=/opt/openmpi/${openmpi_version}-1.${disttag}.${compiler}.${compiler_version}/include ompi_bindir=/opt/openmpi/${openmpi_version}-1.${disttag}.${compiler}.${compiler_version}/bin release=1.${disttag}.${compiler}.${compiler_version}.openmpi.${openmpi_version}.${blas}.${blas_version}.${lapack}.${lapack_version} compiler=gfortran43 compiler_version=4.3.2 compiler_libdir=/usr/lib64 compiler_bindir=/usr/bin blas=goto blas_version=1.26 blasdir=/opt/${blas}/${blas_version}/1.${disttag}.${compiler}.${compiler_version}.smp/lib64 lapack=acml lapack_version=4.3.0 lapackdir=/opt/${lapack}/${lapack_version}/${compiler}64/lib openmpi_version=1.3.3 ompi_libdir=/opt/openmpi/${openmpi_version}-1.${disttag}.${compiler}.${compiler_version}/lib64 ompi_includedir=/opt/openmpi/${openmpi_version}-1.${disttag}.${compiler}.${compiler_version}/include ompi_bindir=/opt/openmpi/${openmpi_version}-1.${disttag}.${compiler}.${compiler_version}/bin release=1.${disttag}.${compiler}.${compiler_version}.openmpi.${openmpi_version}.${blas}.${blas_version}.${lapack}.${lapack_version} compiler=open64 compiler_version=4.2.1 compiler_libdir=/opt/open64/4.2.1/lib/gcc-lib/x86_64-open64-linux/4.2.1 compiler_bindir=/opt/open64/4.2.1/bin blas=acml blas_version=4.3.0 blasdir=/opt/${blas}/${blas_version}/${compiler}64/lib lapack=acml lapack_version=4.3.0 lapackdir=/opt/${lapack}/${lapack_version}/${compiler}64/lib openmpi_version=1.3.3 ompi_libdir=/opt/openmpi/${openmpi_version}-1.${disttag}.${compiler}.${compiler_version}/lib64 ompi_includedir=/opt/openmpi/${openmpi_version}-1.${disttag}.${compiler}.${compiler_version}/include ompi_bindir=/opt/openmpi/${openmpi_version}-1.${disttag}.${compiler}.${compiler_version}/bin release=1.${disttag}.${compiler}.${compiler_version}.openmpi.${openmpi_version}.${blas}.${blas_version}.${lapack}.${lapack_version} compiler=open64 compiler_version=4.2.1 compiler_libdir=/opt/open64/4.2.1/lib/gcc-lib/x86_64-open64-linux/4.2.1 compiler_bindir=/opt/open64/4.2.1/bin blas=goto blas_version=1.26 blasdir=/opt/${blas}/${blas_version}/1.${disttag}.${compiler}.${compiler_version}.smp/lib64 lapack=acml lapack_version=4.3.0 lapackdir=/opt/${lapack}/${lapack_version}/${compiler}64/lib openmpi_version=1.3.3 ompi_libdir=/opt/openmpi/${openmpi_version}-1.${disttag}.${compiler}.${compiler_version}/lib64 ompi_includedir=/opt/openmpi/${openmpi_version}-1.${disttag}.${compiler}.${compiler_version}/include ompi_bindir=/opt/openmpi/${openmpi_version}-1.${disttag}.${compiler}.${compiler_version}/bin release=1.${disttag}.${compiler}.${compiler_version}.openmpi.${openmpi_version}.${blas}.${blas_version}.${lapack}.${lapack_version} compiler=pathscale compiler_version=3.2 compiler_libdir=/opt/pathscale/lib/3.2 compiler_bindir=/opt/pathscale/bin blas=acml blas_version=4.0.1 blasdir=/opt/${blas}/${blas_version}/${compiler}64/lib lapack=acml lapack_version=4.0.1 lapackdir=/opt/${lapack}/${lapack_version}/${compiler}64/lib openmpi_version=1.3.3 ompi_libdir=/opt/openmpi/${openmpi_version}-1.${disttag}.${compiler}.${compiler_version}/lib64 ompi_includedir=/opt/openmpi/${openmpi_version}-1.${disttag}.${compiler}.${compiler_version}/include ompi_bindir=/opt/openmpi/${openmpi_version}-1.${disttag}.${compiler}.${compiler_version}/bin release=1.${disttag}.${compiler}.${compiler_version}.openmpi.${openmpi_version}.${blas}.${blas_version}.${lapack}.${lapack_version} compiler=gfortran43 compiler_version=4.3.2 compiler_libdir=/usr/lib64 compiler_bindir=/usr/bin blas=blas blas_version=3.0.37.el5 blasdir=/usr/lib64 lapack=lapack lapack_version=3.0.37.el5 lapackdir=/usr/lib64 openmpi_version=1.3.3 ompi_libdir=/opt/openmpi/${openmpi_version}-1.${disttag}.${compiler}.${compiler_version}/lib64 ompi_includedir=/opt/openmpi/${openmpi_version}-1.${disttag}.${compiler}.${compiler_version}/include ompi_bindir=/opt/openmpi/${openmpi_version}-1.${disttag}.${compiler}.${compiler_version}/bin release=1.${disttag}.${compiler}.${compiler_version}.openmpi.${openmpi_version}.${blas}.${blas_version}.${lapack}.${lapack_version} compiler=gfortran compiler_version=4.1.2 compiler_libdir=/usr/lib64 compiler_bindir=/usr/bin blas=blas blas_version=3.0.37.el5 blasdir=/usr/lib64 lapack=lapack lapack_version=3.0.37.el5 lapackdir=/usr/lib64 openmpi_version=1.3.3 ompi_libdir=/opt/openmpi/${openmpi_version}-1.${disttag}.${compiler}.${compiler_version}/lib64 ompi_includedir=/opt/openmpi/${openmpi_version}-1.${disttag}.${compiler}.${compiler_version}/include ompi_bindir=/opt/openmpi/${openmpi_version}-1.${disttag}.${compiler}.${compiler_version}/bin release=1.${disttag}.${compiler}.${compiler_version}.openmpi.${openmpi_version}.${blas}.${blas_version}.${lapack}.${lapack_version} rpmbuild --bb --with blacs=blacs --with blacsdir=/opt/blacs/1.1/24.${disttag}.${compiler}.${compiler_version}.openmpi.${openmpi_version}/lib64 \ --with blas=${blas} --with blas_version=${blas_version} --with blasdir=${blasdir} \ --with compiler=${compiler} --with compiler_version=${compiler_version} \ --with compiler_bindir=${compiler_bindir} --with compiler_libdir=${compiler_libdir} \ --with lapack=${lapack} --with lapack_version=${lapack_version} --with lapackdir=${lapackdir} \ --with modules=${modules} --with default_version=1 \ --with parallel=1 --with openmpi=openmpi --with openmpi_version=${openmpi_version} \ --with ompi_libdir=${ompi_libdir} --with ompi_includedir=${ompi_includedir} --with ompi_bindir=${ompi_bindir} \ --with prefix=/opt/scalapack/1.8.0/${release} scalapack.speccampos-gpaw
Build the following RPMS:
cd ~/rpmbuild/SOURCES&& wget --no-check-certificate \ "https://wiki.fysik.dtu.dk/gpaw-files/gpaw-0.5.3667.tar.gz" \ -O gpaw-0.5.3667.tar.gz cd ~/rpmbuild/SPECS compiler=gfortran43 # only on fjorm compiler_version=4.3.2 compiler_libdir=/usr/lib64 compiler_bindir=/usr/bin blas=goto blas_version=1.26 blasdir=/opt/${blas}/${blas_version}/1.${disttag}.${compiler}.${compiler_version}.smp/lib64 lapack=acml lapack_version=4.3.0 lapackdir=/opt/${lapack}/${lapack_version}/${compiler}64/lib openmpi_version=1.3.3 ompi_libdir=/opt/openmpi/${openmpi_version}-1.${disttag}.${compiler}.${compiler_version}/lib64 ompi_includedir=/opt/openmpi/${openmpi_version}-1.${disttag}.${compiler}.${compiler_version}/include ompi_bindir=/opt/openmpi/${openmpi_version}-1.${disttag}.${compiler}.${compiler_version}/bin blacs=blacs blacsdir=/opt/blacs/1.1/24.${disttag}.${compiler}.${compiler_version}.openmpi.${openmpi_version}/lib64 scalapack=scalapack scalapackdir=/opt/scalapack/1.8.0/1.${disttag}.${compiler}.${compiler_version}.openmpi.${openmpi_version}.${blas}.${blas_version}.${lapack}.${lapack_version}/lib64 release=1.${disttag}.${compiler}.${compiler_version}.python2.4.without_ase.openmpi.${openmpi_version}.${blas}.${blas_version}.${lapack}.${lapack_version} compiler=pathscale # only on fjorm # note --with sl_second_underscore=1 is necessary for rpmbuild compiler_version=3.2 compiler_libdir=/opt/pathscale/lib/3.2 compiler_bindir=/opt/pathscale/bin blas=goto blas_version=1.26 blasdir=/opt/${blas}/${blas_version}/1.${disttag}.${compiler}.${compiler_version}.smp/lib64 lapack=acml lapack_version=4.0.1 lapackdir=/opt/${lapack}/${lapack_version}/${compiler}64/lib openmpi_version=1.3.3 ompi_libdir=/opt/openmpi/${openmpi_version}-1.${disttag}.${compiler}.${compiler_version}/lib64 ompi_includedir=/opt/openmpi/${openmpi_version}-1.${disttag}.${compiler}.${compiler_version}/include ompi_bindir=/opt/openmpi/${openmpi_version}-1.${disttag}.${compiler}.${compiler_version}/bin blacs=blacs blacsdir=/opt/blacs/1.1/24.${disttag}.${compiler}.${compiler_version}.openmpi.${openmpi_version}/lib64 scalapack=scalapack #scalapackdir=/opt/scalapack/1.8.0/1.${disttag}.${compiler}.${compiler_version}.openmpi.${openmpi_version}.${blas}.${blas_version}.${lapack}.${lapack_version}/lib64 scalapackdir=/opt/scalapack/1.8.0/1.${disttag}.${compiler}.${compiler_version}.openmpi.${openmpi_version}.acml.4.0.1.${lapack}.${lapack_version}/lib64 release=1.${disttag}.${compiler}.${compiler_version}.python2.4.without_ase.openmpi.${openmpi_version}.${blas}.${blas_version}.${lapack}.${lapack_version} compiler=gfortran43 compiler_version=4.3.2 compiler_libdir=/usr/lib64 compiler_bindir=/usr/bin blas=blas blas_version=3.0.37.el5 blasdir=/usr/lib64 lapack=lapack lapack_version=3.0.37.el5 lapackdir=/usr/lib64 openmpi_version=1.3.3 ompi_libdir=/opt/openmpi/${openmpi_version}-1.${disttag}.${compiler}.${compiler_version}/lib64 ompi_includedir=/opt/openmpi/${openmpi_version}-1.${disttag}.${compiler}.${compiler_version}/include ompi_bindir=/opt/openmpi/${openmpi_version}-1.${disttag}.${compiler}.${compiler_version}/bin blacs=blacs blacsdir=/opt/blacs/1.1/24.${disttag}.${compiler}.${compiler_version}.openmpi.${openmpi_version}/lib64 scalapack=scalapack scalapackdir=/opt/scalapack/1.8.0/1.${disttag}.${compiler}.${compiler_version}.openmpi.${openmpi_version}.${blas}.${blas_version}.${lapack}.${lapack_version}/lib64 release=1.${disttag}.${compiler}.${compiler_version}.python2.4.without_ase.openmpi.${openmpi_version}.${blas}.${blas_version}.${lapack}.${lapack_version} rpmbuild --bb --with blas=${blas} --with blas_version=${blas_version} --with blasdir=${blasdir} \ --with compiler=${compiler} --with compiler_version=${compiler_version} \ --with compiler_bindir=${compiler_bindir} --with compiler_libdir=${compiler_libdir} \ --with lapack=${lapack} --with lapack_version=${lapack_version} --with lapackdir=${lapackdir} \ --with modules=${modules} --with default_version=1 \ --with parallel=1 --with openmpi=openmpi --with openmpi_version=${openmpi_version} \ --with ompi_libdir=${ompi_libdir} --with ompi_includedir=${ompi_includedir} --with ompi_bindir=${ompi_bindir} \ --with blacs=${blacs} --with blacsdir=${blacsdir} \ --with scalapack=${scalapack} --with scalapackdir=${scalapackdir} \ --with prefix=/opt/campos-gpaw/0.5.3667/${release} campos-gpaw.specNote: open64 compiler fails with:
/usr/bin/ld: /opt/open64/4.2.1/lib/gcc-lib/x86_64-open64-linux/4.2.1/libmv.a(vcos.o): relocation R_X86_64_32S against `a local symbol' can not be used when making a shared object; recompile with -fPIC /opt/open64/4.2.1/lib/gcc-lib/x86_64-open64-linux/4.2.1/libmv.a: could not read symbols: Bad value
Optional builds:
compiler=gfortran compiler_version=4.1.2 compiler_libdir=/usr/lib64 compiler_bindir=/usr/bin blas=blas blas_version=3.0.37.el5 blasdir=/usr/lib64 lapack=lapack lapack_version=3.0.37.el5 lapackdir=/usr/lib64 openmpi_version=1.3.3 ompi_libdir=/opt/openmpi/${openmpi_version}-1.${disttag}.${compiler}.${compiler_version}/lib64 ompi_includedir=/opt/openmpi/${openmpi_version}-1.${disttag}.${compiler}.${compiler_version}/include ompi_bindir=/opt/openmpi/${openmpi_version}-1.${disttag}.${compiler}.${compiler_version}/bin blacs=blacs blacsdir=/opt/blacs/1.1/24.${disttag}.${compiler}.${compiler_version}.openmpi.${openmpi_version}/lib64 scalapack=scalapack scalapackdir=/opt/scalapack/1.8.0/1.${disttag}.${compiler}.${compiler_version}.openmpi.${openmpi_version}.${blas}.${blas_version}.${lapack}.${lapack_version}/lib64 release=1.${disttag}.${compiler}.${compiler_version}.python2.4.without_ase.openmpi.${openmpi_version}.${blas}.${blas_version}.${lapack}.${lapack_version} compiler=gfortran43 # fails on thul compiler_version=4.3.2 compiler_libdir=/usr/lib64 compiler_bindir=/usr/bin blas=acml blas_version=4.3.0 blasdir=/opt/${blas}/${blas_version}/${compiler}64/lib lapack=acml lapack_version=4.3.0 lapackdir=/opt/${lapack}/${lapack_version}/${compiler}64/lib openmpi_version=1.3.3 ompi_libdir=/opt/openmpi/${openmpi_version}-1.${disttag}.${compiler}.${compiler_version}/lib64 ompi_includedir=/opt/openmpi/${openmpi_version}-1.${disttag}.${compiler}.${compiler_version}/include ompi_bindir=/opt/openmpi/${openmpi_version}-1.${disttag}.${compiler}.${compiler_version}/bin blacs=blacs blacsdir=/opt/blacs/1.1/24.${disttag}.${compiler}.${compiler_version}.openmpi.${openmpi_version}/lib64 scalapack=scalapack scalapackdir=/opt/scalapack/1.8.0/1.${disttag}.${compiler}.${compiler_version}.openmpi.${openmpi_version}.${blas}.${blas_version}.${lapack}.${lapack_version}/lib64 release=1.${disttag}.${compiler}.${compiler_version}.python2.4.without_ase.openmpi.${openmpi_version}.${blas}.${blas_version}.${lapack}.${lapack_version} compiler=gfortran compiler_version=4.1.2 compiler_libdir=/usr/lib64 compiler_bindir=/usr/bin blas=blas blas_version=4.0.1 blasdir=/opt/${blas}/${blas_version}/${compiler}64/lib lapack=acml lapack_version=4.0.1 lapackdir=/opt/${blas}/${lapack_version}/${compiler}64/lib openmpi_version=1.3.3 ompi_libdir=/opt/openmpi/${openmpi_version}-1.${disttag}.${compiler}.${compiler_version}/lib64 ompi_includedir=/opt/openmpi/${openmpi_version}-1.${disttag}.${compiler}.${compiler_version}/include ompi_bindir=/opt/openmpi/${openmpi_version}-1.${disttag}.${compiler}.${compiler_version}/bin blacs=blacs blacsdir=/opt/blacs/1.1/24.${disttag}.${compiler}.${compiler_version}.openmpi.${openmpi_version}/lib64 scalapack=scalapack scalapackdir=/opt/scalapack/1.8.0/1.${disttag}.${compiler}.${compiler_version}.openmpi.${openmpi_version}.${blas}.${blas_version}.${lapack}.${lapack_version}/lib64 release=1.${disttag}.${compiler}.${compiler_version}.python2.4.without_ase.openmpi.${openmpi_version}.${blas}.${blas_version}.${lapack}.${lapack_version} compiler=ifort # fails on thul compiler_version=11.0 compiler_libdir=/opt/intel/Compiler/11.0/083/lib/intel64 compiler_bindir=/opt/intel/Compiler/11.0/083/bin/intel64 blas=mkl blas_version=10.1.3.027 blasdir=/opt/intel/${blas}/${blas_version}/lib/em64t lapack=mkl_lapack lapack_version=10.1.3.027 lapackdir=${blasdir} openmpi_version=1.3.3 ompi_libdir=/opt/openmpi/${openmpi_version}-1.${disttag}.${compiler}.${compiler_version}/lib64 ompi_includedir=/opt/openmpi/${openmpi_version}-1.${disttag}.${compiler}.${compiler_version}/include ompi_bindir=/opt/openmpi/${openmpi_version}-1.${disttag}.${compiler}.${compiler_version}/bin blacs=mkl blacsdir=${blasdir} scalapack=mkl scalapackdir=${blasdir} release=1.${disttag}.${compiler}.${compiler_version}.python2.4.without_ase.openmpi.${openmpi_version}.${blas}.${blas_version}.${lapack}.${lapack_version} compiler=gfortran43 # only on thul # fails on thul compiler_version=4.3.2 compiler_libdir=/usr/lib64 compiler_bindir=/usr/bin blas=mkl blas_version=10.1.3.027 blasdir=/opt/intel/${blas}/${blas_version}/lib/em64t lapack=mkl_lapack lapack_version=10.1.3.027 lapackdir=${blasdir} openmpi_version=1.3.3 ompi_libdir=/opt/openmpi/${openmpi_version}-1.${disttag}.${compiler}.${compiler_version}/lib64 ompi_includedir=/opt/openmpi/${openmpi_version}-1.${disttag}.${compiler}.${compiler_version}/include ompi_bindir=/opt/openmpi/${openmpi_version}-1.${disttag}.${compiler}.${compiler_version}/bin blacs=mkl blacsdir=${blasdir} scalapack=mkl scalapackdir=${blasdir} release=1.${disttag}.${compiler}.${compiler_version}.python2.4.without_ase.openmpi.${openmpi_version}.${blas}.${blas_version}.${lapack}.${lapack_version} compiler=gfortran43 # only on thul compiler_version=4.3.2 compiler_libdir=/usr/lib64 compiler_bindir=/usr/bin blas=mkl blas_version=10.2.1.017 blasdir=/opt/intel/${blas}/${blas_version}/lib/em64t lapack=mkl_lapack lapack_version=10.2.1.017 lapackdir=${blasdir} openmpi_version=1.3.3 ompi_libdir=/opt/openmpi/${openmpi_version}-1.${disttag}.${compiler}.${compiler_version}/lib64 ompi_includedir=/opt/openmpi/${openmpi_version}-1.${disttag}.${compiler}.${compiler_version}/include ompi_bindir=/opt/openmpi/${openmpi_version}-1.${disttag}.${compiler}.${compiler_version}/bin blacs=mkl blacsdir=${blasdir} scalapack=mkl scalapackdir=${blasdir} release=1.${disttag}.${compiler}.${compiler_version}.python2.4.without_ase.openmpi.${openmpi_version}.${blas}.${blas_version}.${lapack}.${lapack_version}
Build the following for Asap
Asap
Build the following RPMS:
cd ~/rpmbuild/SOURCES&& wget "http://dcwww.camp.dtu.dk/campos/download/Asap-3.2.0.tar.gz" cd ~/rpmbuild/SPECS compiler=pathscale # only on fjorm compiler_version=3.2 compiler_libdir=/opt/pathscale/lib/3.2 compiler_bindir=/opt/pathscale/bin openmpi_version=1.3.3 ompi_libdir=/opt/openmpi/${openmpi_version}-1.${disttag}.${compiler}.${compiler_version}/lib64 ompi_includedir=/opt/openmpi/${openmpi_version}-1.${disttag}.${compiler}.${compiler_version}/include ompi_bindir=/opt/openmpi/${openmpi_version}-1.${disttag}.${compiler}.${compiler_version}/bin release=1.${disttag}.${compiler}.${compiler_version}.python2.4.openmpi.${openmpi_version} module load ifort/11.0-1 compiler=ifort # only 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 openmpi_version=1.3.3 ompi_libdir=/opt/openmpi/${openmpi_version}-1.${disttag}.${compiler}.${compiler_version}/lib64 ompi_includedir=/opt/openmpi/${openmpi_version}-1.${disttag}.${compiler}.${compiler_version}/include ompi_bindir=/opt/openmpi/${openmpi_version}-1.${disttag}.${compiler}.${compiler_version}/bin release=1.${disttag}.${compiler}.${compiler_version}.python2.4.openmpi.${openmpi_version} rpmbuild --bb --with compiler=${compiler} --with compiler_version=${compiler_version} \ --with compiler_bindir=${compiler_bindir} --with compiler_libdir=${compiler_libdir} \ --with modules=${modules} --with default_version=1 \ --with parallel=1 --with openmpi=openmpi --with openmpi_version=${openmpi_version} \ --with ompi_libdir=${ompi_libdir} --with ompi_includedir=${ompi_includedir} --with ompi_bindir=${ompi_bindir} \ --with prefix=/opt/campos-asap3/3.2.0/${release} campos-asap.spec
Build the following for abinit
abinit-pseudopotentials-1.tar.gz
abinit 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=abinit-pseudopotentials-1.tar.gz" \ -O abinit-pseudopotentials-1.tar.gz cd ~/rpmbuild/SPECS rpmbuild -bb --with modules --with default_version abinit-pseudopotentials.spec
abinit
abinit is a Density Functional Theory (DFT) package with pseudopotentials and a planewave basis.
Build the following RPMS:
cd ~/rpmbuild/SOURCES&& wget ftp://ftp.abinit.org/pub/abinitio/ABINIT_v5.4.4/abinit-5.4.4p.tar.gz cd ~/rpmbuild/SPECS compiler=gfortran43 compiler_version=4.3.2 compiler_libdir=/usr/lib64 compiler_bindir=/usr/bin blas=acml blas_version=4.3.0 blasdir=/opt/${blas}/${blas_version}/${compiler}64/lib lapack=acml lapack_version=4.3.0 lapackdir=/opt/${lapack}/${lapack_version}/${compiler}64/lib fftw=fftw3 fftw_libdir=/opt/${fftw}/3.2.1/12.${disttag}.${compiler}.${compiler_version}/lib64 netcdf=netcdf4 netcdf_includedir=/opt/${netcdf}/4.0.1/1.${disttag}.${compiler}.${compiler_version}/include netcdf_libdir=/opt/${netcdf}/4.0.1/1.${disttag}.${compiler}.${compiler_version}/lib64 openmpi_version=1.3.3 ompi_libdir=/opt/openmpi/${openmpi_version}-1.${disttag}.${compiler}.${compiler_version}/lib64 ompi_includedir=/opt/openmpi/${openmpi_version}-1.${disttag}.${compiler}.${compiler_version}/include ompi_bindir=/opt/openmpi/${openmpi_version}-1.${disttag}.${compiler}.${compiler_version}/bin release=1.${disttag}.${compiler}.${compiler_version}.openmpi.${openmpi_version}.${blas}.${blas_version}.${lapack}.${lapack_version}.${fftw} rpmbuild --bb --with blas=${blas} --with blas_version=${blas_version} --with blasdir=${blasdir} \ --with compiler=${compiler} --with compiler_version=${compiler_version} \ --with compiler_bindir=${compiler_bindir} --with compiler_libdir=${compiler_libdir} \ --with fftw=${fftw} --with fftw_libdir=${fftw_libdir} \ --with lapack=${lapack} --with lapack_version=${lapack_version} --with lapackdir=${lapackdir} \ --with netcdf=${netcdf} --with netcdf_includedir=${netcdf_includedir} --with netcdf_libdir=${netcdf_libdir} \ --with modules=${modules} --with default_version=1 \ --with parallel=1 --with openmpi=openmpi --with openmpi_version=${openmpi_version} \ --with ompi_libdir=${ompi_libdir} --with ompi_includedir=${ompi_includedir} --with ompi_bindir=${ompi_bindir} \ --with prefix=/opt/abinit/5.4.4p/${release} abinit.spec
Build the following for espresso
espresso pseudopotentials
Build the following RPMS:
cd ~/rpmbuild/SOURCES&& wget http://www.quantum-espresso.org/pseudo/espresso_pp.tar.gz cd ~/rpmbuild/SPECS rpmbuild -bb --with modules --with default_version espresso_pp.spec
espresso
Build the following RPMS:
cd ~/rpmbuild/SOURCES&& wget http://www.pwscf.org/downloads/PWversion/4.0.5/espresso-4.0.5.tar.gz cd ~/rpmbuild/SPECS compiler=gfortran43 compiler_version=4.3.2 compiler_libdir=/usr/lib64 compiler_bindir=/usr/bin blas=acml blas_version=4.3.0 blasdir=/opt/${blas}/${blas_version}/${compiler}64/lib lapack=acml lapack_version=4.3.0 lapackdir=/opt/${lapack}/${lapack_version}/${compiler}64/lib fftw=fftw3 fftw_libdir=/opt/${fftw}/3.2.1/12.${disttag}.${compiler}.${compiler_version}/lib64 netcdf=netcdf4 netcdf_includedir=/opt/${netcdf}/4.0.1/1.${disttag}.${compiler}.${compiler_version}/include netcdf_libdir=/opt/${netcdf}/4.0.1/1.${disttag}.${compiler}.${compiler_version}/lib64 openmpi_version=1.3.3 ompi_libdir=/opt/openmpi/${openmpi_version}-1.${disttag}.${compiler}.${compiler_version}/lib64 ompi_includedir=/opt/openmpi/${openmpi_version}-1.${disttag}.${compiler}.${compiler_version}/include ompi_bindir=/opt/openmpi/${openmpi_version}-1.${disttag}.${compiler}.${compiler_version}/bin blacs=blacs blacsdir=/opt/blacs/1.1/24.${disttag}.${compiler}.${compiler_version}.openmpi.${openmpi_version}/lib64 scalapack=scalapack scalapackdir=/opt/scalapack/1.8.0/1.${disttag}.${compiler}.${compiler_version}.openmpi.${openmpi_version}.${blas}.${blas_version}.${lapack}.${lapack_version}/lib64 release=1.${disttag}.${compiler}.${compiler_version}.openmpi.${openmpi_version}.${blas}.${blas_version}.${lapack}.${lapack_version}.${fftw} rpmbuild --bb --with blas=${blas} --with blas_version=${blas_version} --with blasdir=${blasdir} \ --with compiler=${compiler} --with compiler_version=${compiler_version} \ --with compiler_bindir=${compiler_bindir} --with compiler_libdir=${compiler_libdir} \ --with fftw=${fftw} --with fftw_libdir=${fftw_libdir} \ --with lapack=${lapack} --with lapack_version=${lapack_version} --with lapackdir=${lapackdir} \ --with netcdf=${netcdf} --with netcdf_includedir=${netcdf_includedir} --with netcdf_libdir=${netcdf_libdir} \ --with modules=${modules} --with default_version=1 \ --with parallel=1 --with openmpi=openmpi --with openmpi_version=${openmpi_version} \ --with ompi_libdir=${ompi_libdir} --with ompi_includedir=${ompi_includedir} --with ompi_bindir=${ompi_bindir} \ --with blacs=${blacs} --with blacsdir=${blacsdir} \ --with scalapack=${scalapack} --with scalapackdir=${scalapackdir} \ --with prefix=/opt/espresso/4.0.5/${release} espresso.spec
Build the following for yambo
yambo
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.
Build the following RPMS:
cd ~/rpmbuild/SOURCES&& wget "http://www.yambo-code.org/counter/click.php?id=26" cd ~/rpmbuild/SPECS compiler=gfortran43 compiler_version=4.3.2 compiler_libdir=/usr/lib64 compiler_bindir=/usr/bin blas=acml blas_version=4.3.0 blasdir=/opt/${blas}/${blas_version}/${compiler}64/lib lapack=acml lapack_version=4.3.0 lapackdir=/opt/${lapack}/${lapack_version}/${compiler}64/lib fftw=fftw3 fftw_libdir=/opt/${fftw}/3.2.1/12.${disttag}.${compiler}.${compiler_version}/lib64 netcdf=netcdf4 netcdf_includedir=/opt/${netcdf}/4.0.1/1.${disttag}.${compiler}.${compiler_version}/include netcdf_libdir=/opt/${netcdf}/4.0.1/1.${disttag}.${compiler}.${compiler_version}/lib64 openmpi_version=1.3.3 ompi_libdir=/opt/openmpi/${openmpi_version}-1.${disttag}.${compiler}.${compiler_version}/lib64 ompi_includedir=/opt/openmpi/${openmpi_version}-1.${disttag}.${compiler}.${compiler_version}/include ompi_bindir=/opt/openmpi/${openmpi_version}-1.${disttag}.${compiler}.${compiler_version}/bin blacs=blacs blacsdir=/opt/blacs/1.1/24.${disttag}.${compiler}.${compiler_version}.openmpi.${openmpi_version}/lib64 scalapack=scalapack scalapackdir=/opt/scalapack/1.8.0/1.${disttag}.${compiler}.${compiler_version}.openmpi.${openmpi_version}.${blas}.${blas_version}.${lapack}.${lapack_version}/lib64 release=1.${disttag}.${compiler}.${compiler_version}.openmpi.${openmpi_version}.${blas}.${blas_version}.${lapack}.${lapack_version}.${fftw} rpmbuild --bb --with blas=${blas} --with blas_version=${blas_version} --with blasdir=${blasdir} \ --with compiler=${compiler} --with compiler_version=${compiler_version} \ --with compiler_bindir=${compiler_bindir} --with compiler_libdir=${compiler_libdir} \ --with fftw=${fftw} --with fftw_libdir=${fftw_libdir} \ --with lapack=${lapack} --with lapack_version=${lapack_version} --with lapackdir=${lapackdir} \ --with netcdf=${netcdf} --with netcdf_includedir=${netcdf_includedir} --with netcdf_libdir=${netcdf_libdir} \ --with modules=${modules} --with default_version=1 \ --with parallel=1 --with openmpi=openmpi --with openmpi_version=${openmpi_version} \ --with ompi_libdir=${ompi_libdir} --with ompi_includedir=${ompi_includedir} --with ompi_bindir=${ompi_bindir} \ --with blacs=${blacs} --with blacsdir=${blacsdir} \ --with scalapack=${scalapack} --with scalapackdir=${scalapackdir} \ --with iotkdir=/opt/espresso/4.0.5/${release}/share/espresso/iotk \ --with prefix=/opt/yambo/3.2.1.448/${release} yambo.spec
Build the folowing for elk
elk species
Build the following RPMS:
cd ~/rpmbuild/SOURCES&& wget http://downloads.sourceforge.net/project/elk/elk/0.9.262/elk-0.9.262.tgz cd ~/rpmbuild/SPECS rpmbuild -bb --with modules --with default_version elk-species.spec
elk
Build the following RPMS:
cd ~/rpmbuild/SOURCES&& wget http://downloads.sourceforge.net/project/elk/elk/0.9.262/elk-0.9.262.tgz cd ~/rpmbuild/SPECS compiler=gfortran43 compiler_version=4.3.2 compiler_libdir=/usr/lib64 compiler_bindir=/usr/bin blas=acml blas_version=4.3.0 blasdir=/opt/${blas}/${blas_version}/${compiler}64/lib lapack=acml lapack_version=4.3.0 lapackdir=/opt/${lapack}/${lapack_version}/${compiler}64/lib release=1.${disttag}.${compiler}.${compiler_version}.openmp.${blas}.${blas_version}.${lapack}.${lapack_version} compiler=gfortran43 compiler_version=4.3.2 compiler_libdir=/usr/lib64 compiler_bindir=/usr/bin blas=blas blas_version=3.0.37.el5 blasdir=/usr/lib64 lapack=lapack lapack_version=3.0.37.el5 lapackdir=/usr/lib64 release=1.${disttag}.${compiler}.${compiler_version}.openmp.${blas}.${blas_version}.${lapack}.${lapack_version} rpmbuild --bb --with blas=${blas} --with blas_version=${blas_version} --with blasdir=${blasdir} \ --with compiler=${compiler} --with compiler_version=${compiler_version} \ --with compiler_bindir=${compiler_bindir} --with compiler_libdir=${compiler_libdir} \ --with lapack=${lapack} --with lapack_version=${lapack_version} --with lapackdir=${lapackdir} \ --with modules=${modules} --with default_version=1 \ --with parallel=1 \ --with prefix=/opt/elk/0.9.262/${release} elk.spec
Build the following for vtk
cmake
Build the following RPMS:
cd ~/rpmbuild/SOURCES&& wget http://www.cmake.org/files/v2.6/cmake-2.6.4.tar.gz cd ~/rpmbuild/SOURCES&& wget "http://downloads.sourceforge.net/project/xmlrpc-c/Xmlrpc-c Super Stable/1.06.35/xmlrpc-c-1.06.35.tgz" cd ~/rpmbuild/SPECS rpmbuild -bb --with bootstrap --without gui cmake.spec # install the resulting RPM rpmbuild -bb xmlrpc-c.spec # install the resulting RPM rpm -e cmake rpmbuild -bb --without gui cmake.spec # install the resulting RPM
vtkdata
Build the following RPMS:
cd ~/rpmbuild/SOURCES&& wget http://www.vtk.org/files/release/5.4/vtkdata-5.4.2.tar.gz cd ~/rpmbuild/SPECS rpmbuild -bb --with version1=4 --with version2=2 --with modules=1 --with default_version=1 \ --with prefix=/opt/vtkdata/5.4.2/1.${disttag} vtkdata.specvtk
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}.${compiler}.${compiler_version}/lib64 ompi_includedir=/opt/openmpi/${openmpi_version}-1.${disttag}.${compiler}.${compiler_version}/include ompi_bindir=/opt/openmpi/${openmpi_version}-1.${disttag}.${compiler}.${compiler_version}/bin rpmbuild -bb --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 modules=${modules} --with default_version=1 \ --with parallel=1 --with openmpi=openmpi --with openmpi_version=${openmpi_version} \ --with ompi_libdir=${ompi_libdir} --with ompi_includedir=${ompi_includedir} --with ompi_bindir=${ompi_bindir} \ --with prefix=/opt/vtk/5.4.2/1.${disttag}.${compiler}.${compiler_version}.python2.4.openmpi.${openmpi_version} vtk.spec
Build the following for octopus
octopus
Build the following RPMS:
cd ~/rpmbuild/SOURCES&& wget "http://www.tddft.org/programs/octopus/down.php?file=3.1.0/octopus-3.1.0.tar.gz" cd ~/rpmbuild/SPECS compiler=gfortran43 compiler_version=4.3.2 compiler_libdir=/usr/lib64 compiler_bindir=/usr/bin blas=acml blas_version=4.3.0 blasdir=/opt/${blas}/${blas_version}/${compiler}64/lib lapack=acml lapack_version=4.3.0 lapackdir=/opt/${lapack}/${lapack_version}/${compiler}64/lib fftw=fftw3 fftw_libdir=/opt/${fftw}/3.2.1/12.${disttag}.${compiler}.${compiler_version}/lib64 netcdf=netcdf4 netcdf_includedir=/opt/${netcdf}/4.0.1/1.${disttag}.${compiler}.${compiler_version}/include netcdf_libdir=/opt/${netcdf}/4.0.1/1.${disttag}.${compiler}.${compiler_version}/lib64 openmpi_version=1.3.3 ompi_libdir=/opt/openmpi/${openmpi_version}-1.${disttag}.${compiler}.${compiler_version}/lib64 ompi_includedir=/opt/openmpi/${openmpi_version}-1.${disttag}.${compiler}.${compiler_version}/include ompi_bindir=/opt/openmpi/${openmpi_version}-1.${disttag}.${compiler}.${compiler_version}/bin gsl_libdir=/usr/lib64 gsl_includedir=/usr/include/gsl gsl_bindir=/usr/bin arpack=arpack arpackdir=/usr/lib64 release=1.${disttag}.${compiler}.${compiler_version}.openmpi.${openmpi_version}.${blas}.${blas_version}.${lapack}.${lapack_version}.${fftw} rpmbuild --bb --with blas=${blas} --with blas_version=${blas_version} --with blasdir=${blasdir} \ --with compiler=${compiler} --with compiler_version=${compiler_version} \ --with compiler_bindir=${compiler_bindir} --with compiler_libdir=${compiler_libdir} \ --with fftw=${fftw} --with fftw_libdir=${fftw_libdir} \ --with lapack=${lapack} --with lapack_version=${lapack_version} --with lapackdir=${lapackdir} \ --with netcdf=${netcdf} --with netcdf_includedir=${netcdf_includedir} --with netcdf_libdir=${netcdf_libdir} \ --with modules=${modules} --with default_version=1 \ --with parallel=1 --with openmpi=openmpi --with openmpi_version=${openmpi_version} \ --with ompi_libdir=${ompi_libdir} --with ompi_includedir=${ompi_includedir} --with ompi_bindir=${ompi_bindir} \ --with arpack=${arpack} --with arpackdir=${arpackdir} \ --with gsl_libdir=${gsl_libdir} --with gsl_includedir=${gsl_includedir} --with gsl_bindir=${gsl_bindir} \ --with prefix=/opt/octopus/3.1.0/${release} octopus.spec
Testing packages
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.
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. 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,