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| also in `~/.bashrc`. - set the following variables for convenience (set it in `~/.bashrc`):: export rpm_platform=el5 export rpmtopdir=${HOME}/${FYS_PLATFORM} # set this to _topdir value from ~/.rpmmacros export disttag="${rpm_platform}.fys" export modules=1 export disttag_network="${rpm_platform}.fys" # for infiniband nodes define #export disttag_network="${rpm_platform}.IB.fys" - logout and login (as rpmbuild) again to the settings from `~/.bashrc`. |
|
| Line 74: | Line 88: |
| %disttag el5.fys | %disttag %(echo $disttag) |
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| #%disttag_network el5.IB.fys | %disttag_network %(echo $disttag_network) |
| Line 158: | Line 172: |
| - set the following variables for convenience (set it in `~/.bashrc`):: export rpmtopdir=${HOME}/${FYS_PLATFORM} # set this to _topdir value from ~/.rpmmacros export disttag="el5.fys" export modules=1 export disttag_network="el5.fys" # for infiniband nodes define #export disttag_network="el5.IB.fys" - logout and login (as rpmbuild) again to the settings from `~/.bashrc`. |
|
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| cp /scratch/rpmbuild/intel-11.1.046/11.1.046-1.intel64.el5.fys ~rpmbuild/modulefiles/${FYS_PLATFORM}/ifort | cp /scratch/rpmbuild/intel-11.1.046/11.1.046-1.intel64.${disttag} ~rpmbuild/modulefiles/${FYS_PLATFORM}/ifort |
| Line 242: | Line 245: |
| ln -s 11.1.046-1.intel64.el5.fys 11.1-1 | ln -s 11.1.046-1.intel64.${disttag} 11.1-1 |
| Line 282: | Line 285: |
| - provide the module file `~rpmbuild/modulefiles/${FYS_PLATFORM}/ifort/10.1.015-1.intel64.el5.fys`:: | - provide the module file `~rpmbuild/modulefiles/${FYS_PLATFORM}/ifort/10.1.015-1.intel64.${disttag}`:: |
| Line 298: | Line 301: |
| ln -s 10.1.015-1.intel64.el5.fys 10.1-1 | ln -s 10.1.015-1.intel64.${disttag} 10.1-1 |
| Line 321: | Line 324: |
| cp /tmp/intel-mkl-${mkl}/${mkl}-1.el5.fys.em64t ~rpmbuild/modulefiles/${FYS_PLATFORM}/mkl | cp /tmp/intel-mkl-${mkl}/${mkl}-1.${disttag}.em64t ~rpmbuild/modulefiles/${FYS_PLATFORM}/mkl |
| Line 323: | Line 326: |
| ln -s ${mkl}-1.el5.fys.em64t 10.1p-027 | ln -s ${mkl}-1.${disttag}.em64t 10.1p-027 |
| Line 365: | Line 368: |
| rpm -ivh --nodeps --oldpackage ~rpmbuild/${FYS_PLATFORM}/RPMS/openmpi-1.3.3-1.el5.fys.ifort.11.1.x86_64.rpm | rpm -ivh --nodeps --oldpackage ~rpmbuild/${FYS_PLATFORM}/RPMS/openmpi-1.3.3-1.${disttag}.ifort.11.1.x86_64.rpm |
| Line 384: | Line 387: |
| command="rpmbuild -bb --with compiler=\${compiler} \ --with major_version=\${major_version} --with version1=\${version1} --with version2=\${version2} \ --with thread_mode=\${thread_mode} --with modules=\${modules} --with default_version acml.spec" |
|
| Line 395: | Line 394: |
| $command | rpmbuild -bb --with compiler=${compiler} \ --with major_version=${major_version} --with version1=${version1} --with version2=${version2} \ --with thread_mode=${thread_mode} --with modules=${modules} --with default_version acml.spec |
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| $command | !rpmbuild # as rpmbuild above |
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| $command | !rpmbuild # as rpmbuild above |
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| $command | !rpmbuild # as rpmbuild above |
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| $command | !rpmbuild # as rpmbuild above |
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| $command | !rpmbuild # as rpmbuild above |
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| $command | !rpmbuild # as rpmbuild above |
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| $command | !rpmbuild # as rpmbuild above |
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| $command | !rpmbuild # as rpmbuild above |
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| $command | !rpmbuild # as rpmbuild above |
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| $command | !rpmbuild # as rpmbuild above |
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| command="rpmbuild --bb --with compiler=\${compiler} --with compiler_version=\${compiler_version} \ --with compiler_libdir=\${compiler_libdir} --with compiler_bindir=\${compiler_bindir} \ --with modules=\${modules} --with default_version=1 \ --with prefix=/opt/goto/\${blas_version}/1.\${disttag}.\${compiler}.\${compiler_version}.smp goto.spec" |
|
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| $command | rpmbuild --bb --with compiler=${compiler} --with compiler_version=${compiler_version} \ --with compiler_libdir=${compiler_libdir} --with compiler_bindir=${compiler_bindir} \ --with modules=${modules} --with default_version=1 \ --with prefix=/opt/goto/${blas_version}/1.${disttag}.${compiler}.${compiler_version}.smp goto.spec |
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| $command | !rpmbuild # as rpmbuild above |
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| $command | !rpmbuild # as rpmbuild above |
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| $command | !rpmbuild # as rpmbuild above |
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| - atlas | atlas ----- |
| Line 551: | Line 553: |
| compiler_libdir=/usr/lib64 compiler_bindir=/usr/bin compiler=gfortran43 compiler_version=4.3.2 |
|
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| compiler=gfortran43 compiler_version=4.3.2 compiler_libdir=/usr/lib64 compiler_bindir=/usr/bin !rpmbuild # as rpmbuild above |
|
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| - campos-dacapo-pseudopotentials | campos-dacapo-pseudopotentials ------------------------------ |
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| - rasmol | rasmol ------ |
| Line 596: | Line 602: |
| - cblas | cblas ----- |
| Line 609: | Line 616: |
| rpmbuild --bb --with compiler=${compiler} --with compiler_version=${compiler_version} \ --with blas=${blas} --with blas_version=${blas_version} --with blasdir=${blasdir} \ --with modules=${modules} --with default_version=1 \ --with prefix=/opt/cblas/2.23.3/1.${disttag}.${compiler}.${compiler_version}.${blas}.${blas_version} cblas.spec |
|
| Line 615: | Line 627: |
| rpmbuild --bb --with compiler=${compiler} --with compiler_version=${compiler_version} \ --with blas=${blas} --with blas_version=${blas_version} --with blasdir=${blasdir} \ --with modules=${modules} --with default_version=1 \ --with prefix=/opt/cblas/2.23.3/1.${disttag}.${compiler}.${compiler_version}.${blas}.${blas_version} cblas.spec - python-setuptools |
!rpmbuild # as rpmbuild above python-setuptools ----------------- |
| Line 629: | Line 639: |
| - python-nose | python-nose ----------- |
| Line 640: | Line 651: |
| - numpy | numpy ----- |
| Line 655: | Line 667: |
compiler=gfortran compiler_version=4.1.2 compiler_libdir=/usr/lib64 compiler_bindir=/usr/bin blas=acml blas_version=4.0.1 blasdir=/opt/${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} rpmbuild --bb --with cblas_prefix=${cblas_prefix} \ --with blas=${blas} --with blas_version=${blas_version} --with blasdir=${blasdir} \ --with compiler=${compiler} --with compiler_version=${compiler_version} \ --with compiler_bindir=${compiler_bindir} --with compiler_libdir=${compiler_libdir} \ --with lapack=${lapack} --with lapack_version=${lapack_version} --with lapackdir=${lapackdir} \ --with modules=${modules} --with default_version=1 \ --with prefix=/opt/numpy/1.3.0/${release} numpy.spec compiler=gfortran # only on thul compiler_version=4.1.2 compiler_libdir=/usr/lib64 compiler_bindir=/usr/bin blas=mkl blas_version=10.1.3.027 blasdir=/opt/intel/mkl/10.1.3.027/lib/em64t lapack=mkl_lapack lapack_version=10.1.3.027 lapackdir=/opt/intel/mkl/10.1.3.027/lib/em64t cblas_prefix=/opt/intel/mkl/10.1.3.027 release=1.${disttag}.${compiler}.${compiler_version}.python2.4.${blas}.${blas_version}.${lapack}.${lapack_version} !rpmbuild # as rpmbuild above |
|
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| 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/${release} numpy.spec |
!rpmbuild # as rpmbuild above |
| Line 722: | Line 738: |
| - gnuplot-py | gnuplot-py ---------- |
| Line 733: | Line 750: |
| - python-numeric | python-numeric -------------- **Warning**: on a 64-bit machine works only with python <= 2.4. |
| Line 759: | Line 779: |
| compiler=gfortran compiler_version=4.1.2 compiler_libdir=/usr/lib64 compiler_bindir=/usr/bin blas=acml blas_version=4.0.1 blasdir=/opt/${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}.${lapack_version} |
|
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compiler=gfortran compiler_version=4.1.2 compiler_libdir=/usr/lib64 compiler_bindir=/usr/bin blas=acml blas_version=4.0.1 blasdir=/opt/${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 # as rpmbuild above |
|
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| - netcdf | netcdf ------ |
| Line 830: | Line 853: |
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 |
|
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| - ScientificPython | compiler=gfortran43 compiler_version=4.3.2 compiler_libdir=/usr/lib64 compiler_bindir=/usr/bin !rpmbuild # as rpmbuild above compiler=pathscale # only on fjorm compiler_version=3.2 compiler_libdir=/opt/pathscale/lib/3.2 compiler_bindir=/opt/pathscale/bin !rpmbuild # as rpmbuild above 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 !rpmbuild # as rpmbuild above 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 # as rpmbuild above ScientificPython ---------------- |
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| - python-docutils | python-docutils --------------- |
| Line 900: | Line 933: |
| - pytz | pytz ---- |
| Line 909: | Line 943: |
| - python-dateutil | python-dateutil --------------- |
| Line 918: | Line 953: |
| - python-matplotlib | python-matplotlib ----------------- |
| Line 935: | Line 971: |
| - campos-ase2 | campos-ase2 ----------- |
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| - campos-dacapo-python | campos-dacapo-python -------------------- |
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| - fftw2 | fftw2 ----- |
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| rpmbuild --bb --with compiler=${compiler} --with compiler_version=${compiler_version} \ --with compiler_bindir=${compiler_bindir} \ --with compiler_libdir=${compiler_libdir} \ --with modules=${modules} --with default_version=1 \ --with prefix=/opt/fftw2/2.1.5/12.${disttag}.${compiler}.${compiler_version} fftw2.spec |
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!rpmbuild # as rpmbuild above |
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!rpmbuild # as rpmbuild above |
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| !rpmbuild # as rpmbuild above |
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| rpmbuild --bb --with compiler=${compiler} --with compiler_version=${compiler_version} \ --with compiler_bindir=${compiler_bindir} \ --with compiler_libdir=${compiler_libdir} \ --with modules=${modules} --with default_version=1 \ --with prefix=/opt/fftw2/2.1.5/12.${disttag}.${compiler}.${compiler_version} fftw2.spec - campos-dacapo |
!rpmbuild # as rpmbuild above campos-dacapo ------------- |
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| however custom build (i.e. with building your won netcdf should work). | however custom build (i.e. with building your own netcdf should work). |
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| rpmbuild --bb --with blas=${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.spec |
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| !rpmbuild # as rpmbuild above |
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!rpmbuild # as rpmbuild above |
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| !rpmbuild # as rpmbuild above |
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| 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.spec |
!rpmbuild # as rpmbuild above |
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| !rpmbuild # as rpmbuild above |
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| !rpmbuild # as rpmbuild above |
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!rpmbuild # as rpmbuild above |
This page describes the necessary steps for installing the login nodes fjorm or thul.
Contents
- Configure external repositories
- Configure rpmbuild
- Install external packages
- It's time to build custom RPMS
- compilers and tools
- openmpi
- acml
- goto
- atlas
- campos-dacapo-pseudopotentials
- rasmol
- cblas
- python-setuptools
- python-nose
- numpy
- gnuplot-py
- python-numeric
- netcdf
- ScientificPython
- python-docutils
- pytz
- python-dateutil
- python-matplotlib
- campos-ase2
- campos-dacapo-python
- fftw2
- campos-dacapo
- Build following for gpaw
- Build the following PDSYEVRnew
- Build the following for Asap
- Build the following for abinit
- Build the following for siesta
- Build the following for espresso
- Build the following for yambo
- Build the following for elk
- Build the following for vtk
- Build the following for octopus
- Build the following for TAU
- Build the following for vasp
- Build the following for exciting
- Build the following for fleur
- Build the following for gulp
- Testing packages
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.
Configure external repositories
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/$basearch' >> /etc/yum.repos.d/epel.repo echo 'gpgkey=http://download.fedora.redhat.com/pub/epel/RPM-GPG-KEY-EPEL' >> /etc/yum.repos.d/epel.repo echo 'gpgcheck=1' >> /etc/yum.repos.d/epel.repo echo 'enabled=0' >> /etc/yum.repos.d/epel.repo
install, as root:
yum install yum-utils wget # /var directories must be created yum search --enablerepo=atrpms arpack-devel yum search --enablerepo=epel jmol
Configure rpmbuild
configure rpmbuild (as rpmbuild):
on Niflheim:
enable modules - add to ~/.bashrc:
if [ -r "/home/camp/modulefiles.sh" ]; then source /home/camp/modulefiles.sh fiset the FYS_PLATFORM variable:
export FYS_PLATFORM=Intel-Nehalem-el5 # thul export FYS_PLATFORM=AMD-Opteron-el5 # fjorm
Note that this variable will be set automatically by /home/camp/modulefiles.sh after the environment-modules package is installed.
on a custom system:
create directory:
mkdir -p /scratch/$USER
set the FYS_PLATFORM variable:
export FYS_PLATFORM=el5
also in ~/.bashrc.
set the following variables for convenience (set it in ~/.bashrc):
export rpm_platform=el5 export rpmtopdir=${HOME}/${FYS_PLATFORM} # set this to _topdir value from ~/.rpmmacros export disttag="${rpm_platform}.fys" export modules=1 export disttag_network="${rpm_platform}.fys" # for infiniband nodes define #export disttag_network="${rpm_platform}.IB.fys"logout and login (as rpmbuild) again to the settings from ~/.bashrc.
use the following ~rpmbuild/.rpmmacros:
%disttag %(echo $disttag) # for Niflheim's infiniband nodes define also: %disttag_network %(echo $disttag_network) %_topdir %(echo $HOME)/rpmbuild/%(echo $FYS_PLATFORM) %_rpmdir %{_topdir}/RPMS %_srcrpmdir %{_topdir}/SRPMS %_svndir %(echo $HOME)/rpmbuild %_specdir %{_svndir}/SPECS %_sourcedir %{_svndir}/SOURCES %_rpmfilename %%{NAME}-%%{VERSION}-%%{RELEASE}.%%{ARCH}.rpm %_builddir /scratch/%(echo $USER) %_tmppath %{_topdir}/BUILD # no debuginfo %debug_package %{nil} # don't strip (this does not fully work) # https://bugzilla.redhat.com/show_bug.cgi?id=219731 %define __strip /bin/true # comment out the remaining lines if not on Niflheim %niflheim 1 %packager rpmbuild@fysik.dtu.dk %distribution Fysik RPMS %vendor Fysik RPMS <rpm@fysik.dtu.dk> %_signature gpg %_gpg_path ~/.gnupg %_gpg_name Fysik RPMScreate and retrieve the rpmbuild project (as rpmbuild user):
cd svn co https://svn.fysik.dtu.dk/projects/rpmbuild/branches/campos_installer rpmbuild
as rpmbuild create directories:
mkdir -p ~/${FYS_PLATFORM}/{RPMS,SRPMS,BUILD} mkdir -p ~/${FYS_PLATFORM}/{SPECS,SOURCES} # needed only by openmpi
Install external packages
download official packages, as rpmbuild:
cd ~/${FYS_PLATFORM}/RPMS mkdir external; cd external yumdownloader --resolve binutils-devel glib-devel libstdc++-devel yumdownloader --resolve gcc-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 xterm yumdownloader --resolve libX11-devel libXext-devel openmotif openmotif-devel gd-devel libXpm-devel yumdownloader --resolve gcc43-c++ gcc43-gfortran yum localinstall * # as rootdownload atrpms packages, as rpmbuild (vtk-python is currently unavailable 16 Apr 2009):
cd ~/${FYS_PLATFORM}/RPMS/external yumdownloader --resolve --enablerepo=atrpms vtk-python arpack-devel graphviz wget http://ATrpms.net/RPM-GPG-KEY.atrpms rpm --import RPM-GPG-KEY.atrpms # as root yum localinstall * # as rootdownload the packages from epel, as rpmbuild:
~/${FYS_PLATFORM}/RPMS/external yumdownloader --resolve --enablerepo=epel jmol gsl-devel python-lxml yumdownloader --resolve --enablerepo=epel environment-modules suitesparse-devel wget http://download.fedora.redhat.com/pub/epel/RPM-GPG-KEY-EPEL rpm --import RPM-GPG-KEY-EPEL # as root yum localinstall * # as rooton Niflheim only: remove default openmpi:
yum remove openmpi openmpi-libs
edit /etc/yum.conf so it contains:
exclude=netcdf-* netcdf3-* fftw-* fftw2-* fftw3-* python-numeric openmpi-* libgfortran4* gcc4* libstdc++4* libgomp-*
It's time to build custom RPMS
compilers and tools
open64
Install (on the login and computes nodes) Install Open64 Compiler Suite RPM, and deploy module file under ` ~rpmbuild/modulefiles/${FYS_PLATFORM}/open64`. Install using --relocate option:
rpm -ivh --relocate "/opt/open64"="/opt/open64/4.2.1" open64-4.2.1-0.x86_64.rpm
The module file is available as svn checkout at https://svn.fysik.dtu.dk/projects/modulefiles/trunk. Note: the module file should contain at least:
prepend-path PATH /opt/open64/4.2.1/lib/gcc-lib/x86_64-open64-linux/4.2.1 prepend-path PATH /opt/open64/4.2.1/bin prepend-path LD_LIBRARY_PATH /opt/open64/4.2.1/lib/gcc-lib/x86_64-open64-linux/4.2.1
g95
Install (on the login and computes nodes) g95 RPM, and deploy module file under ` ~rpmbuild/modulefiles/${FYS_PLATFORM}/g95`. Install using --relocate option:
rpm -ivh --relocate "/usr/local"="/opt/g95/0.91" g95-0.91-4.x86_64.rpm
The module file is available as svn checkout at https://svn.fysik.dtu.dk/projects/modulefiles/trunk. Note: the module file should contain at least (do not add the lib directory to LD_LIBRARY_PATH):
prepend-path PATH /opt/g95/0.91/lib/gcc-lib/x86_64-unknown-linux-gnu/4.0.3 prepend-path PATH /opt/g95/0.91/bin
intel
Install icc/ifort compilers (only on the login nodes, packages available under /home/data/Intel with restricted access), install (using rpm -ivh) only the following packages from l_cproc_p_11.1.046_intel64:
intel-cproc046-11.1-1.x86_64.rpm intel-cproidb046-11.1-1.x86_64.rpm intel-cprolib046-11.1-1.x86_64.rpm intel-cprolibdev046-11.1-1.x86_64.rpm intel-cprotbblib046-11.1-1.noarch.rpm intel-cprotbblibdev046-11.1-1.noarch.rpm intel-cprocsdk046-11.1-1.noarch.rpm intel-cproidbsdk046-11.1-1.noarch.rpm
and from l_cprof_p_11.1.046_intel64:
intel-cprof046-11.1-1.x86_64.rpm intel-cproflib046-11.1-1.x86_64.rpm intel-cprofsdk046-11.1-1.noarch.rpm
, enable them (only on thul):
. /opt/intel/Compiler/11.1/046/bin/intel64/ifortvars_intel64.sh . /opt/intel/Compiler/11.1/046/bin/intel64/iccvars_intel64.sh
Build intel compatibility packages (only on thul):
cd ~/rpmbuild/SPECS rpmbuild -bb --with modules intel-redist.spec
Note: do not install the RPMS generated in the last step on the login node. They need to be installed only on compute nodes. On the login node only the module file needs to be deployed under ~rpmbuild/modulefiles, as rpmbuild. Note that this directory is available as svn checkout at https://svn.fysik.dtu.dk/projects/modulefiles/trunk. Here is what need to be done for a new version of the package:
mkdir ~rpmbuild/modulefiles/${FYS_PLATFORM}/ifort
cp /scratch/rpmbuild/intel-11.1.046/11.1.046-1.intel64.${disttag} ~rpmbuild/modulefiles/${FYS_PLATFORM}/ifort
cd ~rpmbuild/modulefiles/${FYS_PLATFORM}/ifort
ln -s 11.1.046-1.intel64.${disttag} 11.1-1Note: the above module file should contain at least:
prepend-path LD_LIBRARY_PATH /opt/intel/Compiler/11.1/046/lib/intel64 prepend-path LD_LIBRARY_PATH /opt/intel/Compiler/11.1/046/idb/lib/intel64 prepend-path PATH /opt/intel/Compiler/11.1/046/bin/intel64 prepend-path MANPATH : prepend-path MANPATH /opt/intel/Compiler/11.1/046/man
Note: intel changes packaging quite often, here are the installation instructions for the 10.1.015 compilers:
install RPMS (on the login and computes nodes) found in l_cc_p_10.1.015_intel64.tar.gz and l_fc_p_10.1.015_intel64.tar.gz manually (using rpm -ivh):
intel-icce101015-10.1.015-1.em64t.rpm intel-iidbe101015-10.1.015-1.em64t.rpm intel-isubhe101015-10.1.015-1.em64t.rpm intel-iforte101015-10.1.015-1.em64t.rpm
replace the installation path in the scripts (action necessary only on the login node):
files=`grep "<INSTALLDIR>" -r /opt/intel/cce/ | cut -d":" -f 1 | uniq` for file in $files; do echo $file sed -i 's#<INSTALLDIR>#/opt/intel/cce/10.1.015#g' $file done files=`grep "<INSTALLDIR>" -r /opt/intel/fce/ | cut -d":" -f 1 | uniq` for file in $files; do echo $file sed -i 's#<INSTALLDIR>#/opt/intel/fce/10.1.015#g' $file done files=`grep "<INSTALLDIR>" -r /opt/intel/idbe/ | cut -d":" -f 1 | uniq` for file in $files; do echo $file sed -i 's#<INSTALLDIR>#/opt/intel/idbe/10.1.015#g' $file doneprovide the module file ~rpmbuild/modulefiles/${FYS_PLATFORM}/ifort/10.1.015-1.intel64.${disttag}:
prepend-path LD_LIBRARY_PATH /opt/intel/cce/10.1.015/lib prepend-path LD_LIBRARY_PATH /opt/intel/fce/10.1.015/lib prepend-path PATH /opt/intel/cce/10.1.015/bin prepend-path PATH /opt/intel/fce/10.1.015/bin prepend-path PATH /opt/intel/idbe/10.1.015/bin prepend-path MANPATH : prepend-path MANPATH /opt/intel/cce/10.1.015/man prepend-path MANPATH /opt/intel/fce/10.1.015/man prepend-path MANPATH /opt/intel/idbe/10.1.015/man
and the link:
cd ~rpmbuild/modulefiles/${FYS_PLATFORM}/ifort ln -s 10.1.015-1.intel64.${disttag} 10.1-1
intel mkl
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.${disttag}.em64t ~rpmbuild/modulefiles/${FYS_PLATFORM}/mkl
cd ~rpmbuild/modulefiles/${FYS_PLATFORM}/mkl
ln -s ${mkl}-1.${disttag}.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/${mkl}/lib/em64t
ln -s libfftw2xf_intel.a libfftw.aLogout and login as rpmbuild.
openmpi
Build a custom openmpi, using torque support:
wget http://www.open-mpi.org/software/ompi/v1.3/downloads/openmpi-1.3.3.tar.bz2 \
-O ~/rpmbuild/SOURCES/openmpi-1.3.3.tar.bz2
sh ./buildrpm-1.3.3-1.gfortran.sh ../SOURCES/openmpi-1.3.3.tar.bz2 2>&1 | tee buildrpm-1.3.3-1.gfortran.sh.log.${FYS_PLATFORM}
sh ./buildrpm-1.3.3-1.gfortran43.sh ../SOURCES/openmpi-1.3.3.tar.bz2 2>&1 | tee buildrpm-1.3.3-1.gfortran43.sh.log.${FYS_PLATFORM}
sh ./buildrpm-1.3.3-1.pathscale.sh ../SOURCES/openmpi-1.3.3.tar.bz2 2>&1 | tee buildrpm-1.3.3-1.pathscale.sh.log.${FYS_PLATFORM}
sh ./buildrpm-1.3.3-1.ifort.sh ../SOURCES/openmpi-1.3.3.tar.bz2 2>&1 | tee buildrpm-1.3.3-1.ifort.sh.log.${FYS_PLATFORM} # thul only
module load g95
sh ./buildrpm-1.3.3-1.g95.sh ../SOURCES/openmpi-1.3.3.tar.bz2 2>&1 | tee buildrpm-1.3.3-1.g95.sh.log.${FYS_PLATFORM} # fjorm only
module unload g95
module load open64 # 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.${FYS_PLATFORM}
module unload open64Note: intel openmpi needs to be installed ignoring dependencies:
rpm -ivh --nodeps --oldpackage ~rpmbuild/${FYS_PLATFORM}/RPMS/openmpi-1.3.3-1.${disttag}.ifort.11.1.x86_64.rpmIf scripts that contain ALL build/install/uninstall commands (global_install.sh and global_uninstall.sh) need to be created, every time after an RPM is successfully built, do:
grep -v "#\!" install.sh >> ~/${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.
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:
major_version=4 thread_mode=nomp version1=0 version2=1 compiler=gfortran rpmbuild -bb --with compiler=${compiler} \ --with major_version=${major_version} --with version1=${version1} --with version2=${version2} \ --with thread_mode=${thread_mode} --with modules=${modules} --with default_version acml.spec version1=0 version2=1 compiler=pathscale !rpmbuild # as rpmbuild above version1=1 version2=0 compiler=gfortran43 # fjorm only !rpmbuild # as rpmbuild above version1=1 version2=0 compiler=pathscale !rpmbuild # as rpmbuild above version1=2 version2=0 compiler=gfortran43 !rpmbuild # as rpmbuild above version1=2 version2=0 compiler=pathscale !rpmbuild # as rpmbuild above version1=2 version2=0 compiler=ifort # thul only !rpmbuild # as rpmbuild above version1=3 version2=0 compiler=gfortran43 !rpmbuild # as rpmbuild above version1=3 version2=0 compiler=open64 # fjorm only !rpmbuild # as rpmbuild above version1=3 version2=0 compiler=ifort # thul only !rpmbuild # as rpmbuild above thread_mode=mp version1=3 version2=0 compiler=open64 # fjorm only !rpmbuild # as rpmbuild aboveNote 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
GotoBLAS contains optimized BLAS libraries, and is available for academic community after registration. Does not work in Intel Nehalem.
Download GotoBLAS-1.26.tar.gz to ~/rpmbuild/SOURCES. The default build process searches your $PATH for available compilers. Priority order is PathScale, PGI, Intel, gfortran, g95 and g77, therefore setting compilers explicitly is needed. Build RPMS (on the target compute node!) using the following command:
blas_version=1.26 compiler=gfortran compiler_version=4.1.2 compiler_libdir=/usr/lib64 compiler_bindir=/usr/bin rpmbuild --bb --with compiler=${compiler} --with compiler_version=${compiler_version} \ --with compiler_libdir=${compiler_libdir} --with compiler_bindir=${compiler_bindir} \ --with modules=${modules} --with default_version=1 \ --with prefix=/opt/goto/${blas_version}/1.${disttag}.${compiler}.${compiler_version}.smp goto.spec compiler=gfortran43 compiler_version=4.3.2 compiler_libdir=/usr/lib64 compiler_bindir=/usr/bin !rpmbuild # as rpmbuild above compiler=pathscale compiler_version=3.2 compiler_libdir=/opt/pathscale/lib/3.2 compiler_bindir=/opt/pathscale/bin !rpmbuild # as rpmbuild above 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 # as rpmbuild aboveNote - 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 rpmbuild --bb --with compiler=${compiler} --with compiler_version=${compiler_version} \ --with compiler_libdir=${compiler_libdir} --with compiler_bindir=${compiler_bindir} \ --with modules=${modules} --with default_version=1 \ --with prefix=/opt/atlas/${blas_version}/1.${disttag}.${compiler}.${compiler_version} atlas.spec compiler=gfortran43 compiler_version=4.3.2 compiler_libdir=/usr/lib64 compiler_bindir=/usr/bin !rpmbuild # as rpmbuild aboveNote: - 3.8.3 version fails on Opteron with open64 with:
/scratch/rpmbuild/ATLAS/RpmObjs/..//CONFIG/src/backend/comptestC.c:5: undefined reference to `__pathscale_malloc_alg'
campos-dacapo-pseudopotentials
campos-dacapo-pseudopotentials-1.tar.gz
Build the following RPMS:
cd ~/rpmbuild/SOURCES&& wget --no-check-certificate \ "https://wiki.fysik.dtu.dk/dacapo/Installation?action=AttachFile&do=get&target=campos-dacapo-pseudopotentials-1.tar.gz" \ -O campos-dacapo-pseudopotentials-1.tar.gz cd ~/rpmbuild/SPECS rpmbuild -bb --with modules --with default_version campos-dacapo-pseudopotentials.spec
rasmol
Note that rasmol is built for 32bit architecture, so make sure that your system fulfills "BuildRequires" for both 64 and 32bit:
rpmbuild --nobuild RasMol.specBuild the following RPMS:
cd ~/rpmbuild/SOURCES&& wget http://downloads.sourceforge.net/openrasmol/RasMol_2.7.3.tar.gz cd ~/rpmbuild/SPECS rpmbuild -bb --with modules --with default_version --with prefix=/opt/RasMol/2.7.3/3.${disttag} RasMol.spec
cblas
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 rpmbuild --bb --with compiler=${compiler} --with compiler_version=${compiler_version} \ --with blas=${blas} --with blas_version=${blas_version} --with blasdir=${blasdir} \ --with modules=${modules} --with default_version=1 \ --with prefix=/opt/cblas/2.23.3/1.${disttag}.${compiler}.${compiler_version}.${blas}.${blas_version} cblas.spec compiler=gfortran compiler_version=4.1.2 blas=acml blas_version=4.0.1 blasdir=/opt/${blas}/${blas_version}/${compiler}64/lib !rpmbuild # as rpmbuild above
python-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.${disttag}.python2.4 python-setuptools.spec
python-nose
Build the following RPMS:
cd ~/rpmbuild/SOURCES&& wget http://somethingaboutorange.com/mrl/projects/nose/nose-0.10.4.tar.gz cd ~/rpmbuild/SPECS rpmbuild -bb --with modules --with default_version --with prefix=/opt/python-nose/0.10.4/1.${disttag}.python2.4 python-nose.spec module load python-setuptools module load python-nose
numpy
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.rpmand 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 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}.${lapack_version} rpmbuild --bb --with cblas_prefix=${cblas_prefix} \ --with blas=${blas} --with blas_version=${blas_version} --with blasdir=${blasdir} \ --with compiler=${compiler} --with compiler_version=${compiler_version} \ --with compiler_bindir=${compiler_bindir} --with compiler_libdir=${compiler_libdir} \ --with lapack=${lapack} --with lapack_version=${lapack_version} --with lapackdir=${lapackdir} \ --with modules=${modules} --with default_version=1 \ --with prefix=/opt/numpy/1.3.0/${release} numpy.spec 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}.${lapack_version} !rpmbuild # as rpmbuild above compiler=gfortran # Aug 6 2009: causes problems to gpaw cg2.py test compiler_version=4.1.2 compiler_libdir=/usr/lib64 compiler_bindir=/usr/bin blas=blas blas_version=3.0.37.el5 blasdir=/usr/lib64 lapack=lapack lapack_version=3.0.37.el5 lapackdir=/usr/lib64 cblas_prefix=/opt/cblas/2.23.3/1.${disttag}.${compiler}.${compiler_version}.${blas}.${blas_version} release=1.${disttag}.${compiler}.${compiler_version}.python2.4.${blas}.${blas_version}.${lapack}.${lapack_version} !rpmbuild # as rpmbuild aboveTest with:
module load cblas-blas-gfortran64/2.23.3-1.el5.fys.gfortran.4.1.2.blas.3.0.37.el5 module load numpy/1.3.0-1.el5.fys.gfortran.4.1.2.python2.4.blas.3.0.37.el5.lapack.3.0.37.el5 python -c "import numpy; from numpy.core.multiarray import dot; b = numpy.ones(13, numpy.complex); dot(b, b)" python -c "import numpy; numpy.test()" module unload numpy/1.3.0-1.el5.fys.gfortran.4.1.2.python2.4.blas.3.0.37.el5.lapack.3.0.37.el5 module load acml-gfortran64/4.0.1-1.el5.fys module load numpy/1.3.0-1.el5.fys.gfortran.4.1.2.python2.4.acml.4.0.1.acml.4.0.1 python -c "import numpy; from numpy.core.multiarray import dot; b = numpy.ones(13, numpy.complex); dot(b, b)" python -c "import numpy; numpy.test()" module unload numpy/1.3.0-1.el5.fys.gfortran.4.1.2.python2.4.acml.4.0.1.acml.4.0.1 module unload acml-gfortran64/4.0.1-1.el5.fysLoad the default numpy:
module load numpy/1.3.0-1.el5.fys.gfortran.4.1.2.python2.4.acml.4.0.1.acml.4.0.1
gnuplot-py
Build the following RPMS:
cd ~/rpmbuild/SOURCES&& wget http://downloads.sourceforge.net/gnuplot-py/gnuplot-py-1.8.tar.gz cd ~/rpmbuild/SPECS rpmbuild -bb --with modules --with default_version --with prefix=/opt/gnuplot-py/1.8.1/1.${disttag}.python2.4 gnuplot-py.spec module load gnuplot-py
python-numeric
Warning: on a 64-bit machine works only with python <= 2.4.
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}.${lapack_version} rpmbuild --bb --with cblas_prefix=${cblas_prefix} \ --with blas=${blas} --with blas_version=${blas_version} --with blasdir=${blasdir} \ --with compiler=${compiler} --with compiler_version=${compiler_version} \ --with compiler_bindir=${compiler_bindir} --with compiler_libdir=${compiler_libdir} \ --with lapack=${lapack} --with lapack_version=${lapack_version} --with lapackdir=${lapackdir} \ --with modules=${modules} --with default_version=1 \ --with prefix=/opt/python-numeric/24.2/${release} python-numeric.spec 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 # as rpmbuild aboveNote: (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.fysand reinstall the default version:
rpm -ivh --oldpackage ~rpmbuild/${FYS_PLATFORM}/RPMS/external/python-numeric-23.*.rpmload the default Numeric version:
module load acml-gfortran64/4.0.1-1.el5.fys module load cblas-acml-gfortran64/2.23.3-1.el5.fys.gfortran.4.1.2.acml.4.0.1 module load python-numeric/24.2-4.el5.fys.gfortran.4.1.2.python2.4.acml.4.0.1.acml.4.0.1
netcdf
NetCDF (network Common Data Form) is an interface for array-oriented data access and a library that provides an implementation of the interface. The NetCDF library also defines a machine-independent format for representing scientific data.
We prefer version 3.6.1 or higher (note that version 3.6.2 has fortran interface in libnetcdff.a).
Build the following RPMS:
cd ~/rpmbuild/SOURCES&& wget http://www.unidata.ucar.edu/downloads/netcdf/ftp/netcdf-4.0.1.tar.gz cd ~/rpmbuild/SPECS compiler=gfortran compiler_version=4.1.2 compiler_libdir=/usr/lib64 compiler_bindir=/usr/bin rpmbuild --bb --with compiler=${compiler} --with compiler_version=${compiler_version} \ --with compiler_bindir=${compiler_bindir} \ --with compiler_libdir=${compiler_libdir} \ --with modules=${modules} --with default_version=1 \ --with prefix=/opt/netcdf4/4.0.1/1.${disttag}.${compiler}.${compiler_version} netcdf4.spec compiler=gfortran43 compiler_version=4.3.2 compiler_libdir=/usr/lib64 compiler_bindir=/usr/bin !rpmbuild # as rpmbuild above compiler=pathscale # only on fjorm compiler_version=3.2 compiler_libdir=/opt/pathscale/lib/3.2 compiler_bindir=/opt/pathscale/bin !rpmbuild # as rpmbuild above compiler=ifort # only on thul compiler_version=11.0 compiler_libdir=/opt/intel/Compiler/11.0/083/lib/intel64 compiler_bindir=/opt/intel/Compiler/11.0/083/bin/intel64 !rpmbuild # as rpmbuild above compiler=open64 # only on fjorm compiler_version=4.2.1 compiler_libdir=/opt/open64/4.2.1/lib/gcc-lib/x86_64-open64-linux/4.2.1 compiler_bindir=/opt/open64/4.2.1/bin !rpmbuild # as rpmbuild above
ScientificPython
Build the following RPMS:
cd ~/rpmbuild/SOURCES&& wget https://sourcesup.cru.fr/frs/download.php/2234/ScientificPython-2.6.2.tar.gz cd ~/rpmbuild/SOURCES&& wget https://sourcesup.cru.fr/frs/download.php/2234/ScientificPython-2.8.tar.gz cd ~/rpmbuild/SPECS compiler=gfortran compiler_version=4.1.2 compiler_libdir=/usr/lib64 compiler_bindir=/usr/bin netcdf=netcdf4 netcdf_includedir=/opt/${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.${disttag_network}.${compiler}.${compiler_version}/lib64 ompi_includedir=/opt/openmpi/${openmpi_version}-1.${disttag_network}.${compiler}.${compiler_version}/include ompi_bindir=/opt/openmpi/${openmpi_version}-1.${disttag_network}.${compiler}.${compiler_version}/bin rpmbuild --bb --with Numeric_includedir=none --with numpy=numpy \ --with compiler=${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_network}.${compiler}.${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.${disttag_network}.${compiler}.${compiler_version}.python2.4.openmpi.${openmpi_version}.numeric ScientificPython.spec
python-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.${disttag}.python2.4 python-docutils.spec
pytz
Build the following RPMS:
cd ~/rpmbuild/SOURCES&& wget http://pypi.python.org/packages/source/p/pytz/pytz-2008g.tar.gz cd ~/rpmbuild/SPECS rpmbuild -bb --with modules --with default_version --with prefix=/opt/pytz/2008g/1.${disttag}.python2.4 pytz.spec
python-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.${disttag}.python2.4 python-dateutil.spec
python-matplotlib
Build the following RPMS:
cd ~/rpmbuild/SOURCES&& wget http://downloads.sourceforge.net/project/matplotlib/matplotlib/matplotlib-0.99.1/matplotlib-0.99.1.2.tar.gz mv ~/rpmbuild/SOURCES/matplotlib-0.99.1.2.tar.gz ~/rpmbuild/SOURCES/matplotlib-0.99.1.1.tar.gz # naming inconsistent cd ~/rpmbuild/SPECS module load acml-gfortran64/4.0.1-1.el5.fys module load python-setuptools module load python-nose module load numpy/1.3.0-1.el5.fys.gfortran.4.1.2.python2.4.acml.4.0.1.acml.4.0.1 module load pytz module load python-docutils module load python-dateutil rpmbuild -bb --with modules --with default_version --with prefix=/opt/python-matplotlib/0.99.1.1/1.${disttag}.python2.4 python-matplotlib.spec
campos-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.${disttag}.python2.4 campos-ase2.spec
campos-dacapo-python
Build the following RPMS:
cd ~/rpmbuild/SOURCES&& wget --no-check-certificate \ "https://wiki.fysik.dtu.dk/dacapo/Installation?action=AttachFile&do=get&target=Dacapo-0.9.4.tar.gz" \ -O Dacapo-0.9.4.tar.gz cd ~/rpmbuild/SPECS rpmbuild -bb --with modules --with default_version --with prefix=/opt/campos-dacapo-python/0.9.4/1.${disttag}.python2.4 campos-dacapo-python.spec
fftw2
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 rpmbuild --bb --with compiler=${compiler} --with compiler_version=${compiler_version} \ --with compiler_bindir=${compiler_bindir} \ --with compiler_libdir=${compiler_libdir} \ --with modules=${modules} --with default_version=1 \ --with prefix=/opt/fftw2/2.1.5/12.${disttag}.${compiler}.${compiler_version} fftw2.spec compiler=gfortran43 compiler_version=4.3.2 compiler_libdir=/usr/lib64 compiler_bindir=/usr/bin !rpmbuild # as rpmbuild above compiler=pathscale # only on fjorm compiler_version=3.2 compiler_libdir=/opt/pathscale/lib/3.2 compiler_bindir=/opt/pathscale/bin !rpmbuild # as rpmbuild above # 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 !rpmbuild # as rpmbuild above 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 # as rpmbuild above
campos-dacapo
Note that FC's fftw version 3 is incompatible with dacapo.
If you build only a serial version add "--without parallel" to the rpmbuild options. Another useful option is "--without default_version" that does not put /etc/profile.d scripts, nor modules under /opt/modulefiles that allows the package to be relocatable.
Warning: currently (9 Oct 2008) packaging of openmpi on FC8/FC9 requires the following link to be made:
ln -s /usr/include/openmpi/1.2.4-gcc/32/mpif-config.h /usr/include/openmpi/1.2.4-gcc/mpif-config.hWarning: currently (9 Oct 2008) the default build fails for EL4 due to double underlined symbols in the netcdf from ATrpms, however custom build (i.e. with building your own netcdf should work).
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_network}.${compiler}.${compiler_version}/lib64 ompi_includedir=/opt/openmpi/${openmpi_version}-1.${disttag_network}.${compiler}.${compiler_version}/include ompi_bindir=/opt/openmpi/${openmpi_version}-1.${disttag_network}.${compiler}.${compiler_version}/bin release=1.${disttag_network}.${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.spec 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_network}.${compiler}.${compiler_version}/lib64 ompi_includedir=/opt/openmpi/${openmpi_version}-1.${disttag_network}.${compiler}.${compiler_version}/include ompi_bindir=/opt/openmpi/${openmpi_version}-1.${disttag_network}.${compiler}.${compiler_version}/bin release=1.${disttag_network}.${compiler}.${compiler_version}.openmpi.${openmpi_version}.${blas}.${blas_version}.${lapack}.${lapack_version}.${fftw} !rpmbuild # as rpmbuild above compiler=pathscale # only on fjorm compiler_version=3.2 compiler_libdir=/opt/pathscale/lib/3.2 compiler_bindir=/opt/pathscale/bin blas=acml blas_version=4.0.1 blasdir=/opt/${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.${disttag_network}.${compiler}.${compiler_version}/lib64 ompi_includedir=/opt/openmpi/${openmpi_version}-1.${disttag_network}.${compiler}.${compiler_version}/include ompi_bindir=/opt/openmpi/${openmpi_version}-1.${disttag_network}.${compiler}.${compiler_version}/bin release=1.${disttag_network}.${compiler}.${compiler_version}.openmpi.${openmpi_version}.${blas}.${blas_version}.${lapack}.${lapack_version}.${fftw} !rpmbuild # as rpmbuild above 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.${disttag_network}.${compiler}.${compiler_version}/lib64 ompi_includedir=/opt/openmpi/${openmpi_version}-1.${disttag_network}.${compiler}.${compiler_version}/include ompi_bindir=/opt/openmpi/${openmpi_version}-1.${disttag_network}.${compiler}.${compiler_version}/bin release=1.${disttag_network}.${compiler}.${compiler_version}.openmpi.${openmpi_version}.${blas}.${blas_version}.${lapack}.${lapack_version}.${fftw} !rpmbuild # as rpmbuild above 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_network}.${compiler}.${compiler_version}/lib64 ompi_includedir=/opt/openmpi/${openmpi_version}-1.${disttag_network}.${compiler}.${compiler_version}/include ompi_bindir=/opt/openmpi/${openmpi_version}-1.${disttag_network}.${compiler}.${compiler_version}/bin release=1.${disttag_network}.${compiler}.${compiler_version}.openmpi.${openmpi_version}.${blas}.${blas_version}.${lapack}.${lapack_version}.${fftw} !rpmbuild # as rpmbuild aboveOptional builds:
compiler=ifort # only on thul # multinode jobs fail compiler_version=11.0 compiler_libdir=/opt/intel/Compiler/11.0/083/lib/intel64 compiler_bindir=/opt/intel/Compiler/11.0/083/bin/intel64 blas=mkl blas_version=10.1.3.027 blasdir=/opt/intel/${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_network}.${compiler}.${compiler_version}/lib64 ompi_includedir=/opt/openmpi/${openmpi_version}-1.${disttag_network}.${compiler}.${compiler_version}/include ompi_bindir=/opt/openmpi/${openmpi_version}-1.${disttag_network}.${compiler}.${compiler_version}/bin release=1.${disttag_network}.${compiler}.${compiler_version}.openmpi.${openmpi_version}.${blas}.${blas_version}.${lapack}.${lapack_version}.${fftw} !rpmbuild # as rpmbuild above compiler=gfortran43 compiler_version=4.3.2 compiler_libdir=/usr/lib64 compiler_bindir=/usr/bin blas=goto blas_version=1.26 blasdir=/opt/${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.${disttag_network}.${compiler}.${compiler_version}/lib64 ompi_includedir=/opt/openmpi/${openmpi_version}-1.${disttag_network}.${compiler}.${compiler_version}/include ompi_bindir=/opt/openmpi/${openmpi_version}-1.${disttag_network}.${compiler}.${compiler_version}/bin release=1.${disttag_network}.${compiler}.${compiler_version}.openmpi.${openmpi_version}.${blas}.${blas_version}.${lapack}.${lapack_version}.${fftw} !rpmbuild # as rpmbuild above 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_network}.${compiler}.${compiler_version}/lib64 ompi_includedir=/opt/openmpi/${openmpi_version}-1.${disttag_network}.${compiler}.${compiler_version}/include ompi_bindir=/opt/openmpi/${openmpi_version}-1.${disttag_network}.${compiler}.${compiler_version}/bin release=1.${disttag_network}.${compiler}.${compiler_version}.openmpi.${openmpi_version}.${blas}.${blas_version}.${lapack}.${lapack_version}.${fftw} !rpmbuild # as rpmbuild above
Build following for gpaw
fftw3
Build the following RPMS:
cd ~/rpmbuild/SOURCES&& wget ftp://ftp.fftw.org/pub/fftw/fftw-3.2.1.tar.gz cd ~/rpmbuild/SPECS compiler=gfortran compiler_version=4.1.2 compiler_libdir=/usr/lib64 compiler_bindir=/usr/bin compiler=gfortran43 compiler_version=4.3.2 compiler_libdir=/usr/lib64 compiler_bindir=/usr/bin rpmbuild --bb --with major_version=3 --with version1=2 --with version2=1 \ --with compiler=${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.${disttag}.python2.4 python-sphinx.speccampos-ase3
Build the following RPMS:
major_version=3 version1=2 version2=0 version_svn=1121 cd ~/rpmbuild/SOURCES&& wget --no-check-certificate \ "https://wiki.fysik.dtu.dk/ase-files/python-ase-${major_version}.${version1}.${version2}.${version_svn}.tar.gz" \ -O python-ase-${major_version}.${version1}.${version2}.${version_svn}.tar.gz cd ~/rpmbuild/SPECS rpmbuild -bb --with major_version=${major_version} --with version1=${version1} --with version2=${version2} --with version_svn=${version_svn} \ --with modules --with default_version --with prefix=/opt/campos-ase3/${major_version}.${version1}.${version2}.${version_svn}/1.${disttag}.python2.4 campos-ase3.specSnapshot package is built with, e.g.:
major_version=3 version1=2 version2=0 version_svn=1066 release=${major_version}.${version1}.${version2}.${version_svn}/1.${disttag}.python2.4 rpmbuild -bb --with major_version=${major_version} --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-${major_version}.${version1}.${version2}.${version_svn}-1.${disttag}.python2.4-root ln -s ${dir}/etc/modulefiles/campos-ase3/${major_version}.${version1}.${version2}.${version_svn}-1.${disttag}.python2.4 \ ~/Intel-Nehalem-el5/modulefiles.testing/campos-ase3 ln -s ${dir}/home/camp/rpmbuild/opt/Intel-Nehalem-el5/campos-ase3/${major_version}.${version1}.${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.${disttag_network}.${compiler}.${compiler_version}/lib64 ompi_includedir=/opt/openmpi/${openmpi_version}-1.${disttag_network}.${compiler}.${compiler_version}/include ompi_bindir=/opt/openmpi/${openmpi_version}-1.${disttag_network}.${compiler}.${compiler_version}/bin compiler=gfortran43 compiler_version=4.3.2 compiler_libdir=/usr/lib64 compiler_bindir=/usr/bin openmpi_version=1.3.3 ompi_libdir=/opt/openmpi/${openmpi_version}-1.${disttag_network}.${compiler}.${compiler_version}/lib64 ompi_includedir=/opt/openmpi/${openmpi_version}-1.${disttag_network}.${compiler}.${compiler_version}/include ompi_bindir=/opt/openmpi/${openmpi_version}-1.${disttag_network}.${compiler}.${compiler_version}/bin compiler=pathscale compiler_version=3.2 compiler_libdir=/opt/pathscale/lib/3.2 compiler_bindir=/opt/pathscale/bin openmpi_version=1.3.3 ompi_libdir=/opt/openmpi/${openmpi_version}-1.${disttag_network}.${compiler}.${compiler_version}/lib64 ompi_includedir=/opt/openmpi/${openmpi_version}-1.${disttag_network}.${compiler}.${compiler_version}/include ompi_bindir=/opt/openmpi/${openmpi_version}-1.${disttag_network}.${compiler}.${compiler_version}/bin compiler=open64 compiler_version=4.2.1 compiler_libdir=/opt/open64/4.2.1/lib/gcc-lib/x86_64-open64-linux/4.2.1 compiler_bindir=/opt/open64/4.2.1/bin openmpi_version=1.3.3 ompi_libdir=/opt/openmpi/${openmpi_version}-1.${disttag_network}.${compiler}.${compiler_version}/lib64 ompi_includedir=/opt/openmpi/${openmpi_version}-1.${disttag_network}.${compiler}.${compiler_version}/include ompi_bindir=/opt/openmpi/${openmpi_version}-1.${disttag_network}.${compiler}.${compiler_version}/bin rpmbuild --bb --with compiler=${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.${disttag_network}.${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_network}.${compiler}.${compiler_version}/lib64 ompi_includedir=/opt/openmpi/${openmpi_version}-1.${disttag_network}.${compiler}.${compiler_version}/include ompi_bindir=/opt/openmpi/${openmpi_version}-1.${disttag_network}.${compiler}.${compiler_version}/bin release=1.${disttag_network}.${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_network}.${compiler}.${compiler_version}/lib64 ompi_includedir=/opt/openmpi/${openmpi_version}-1.${disttag_network}.${compiler}.${compiler_version}/include ompi_bindir=/opt/openmpi/${openmpi_version}-1.${disttag_network}.${compiler}.${compiler_version}/bin release=1.${disttag_network}.${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_network}.${compiler}.${compiler_version}/lib64 ompi_includedir=/opt/openmpi/${openmpi_version}-1.${disttag_network}.${compiler}.${compiler_version}/include ompi_bindir=/opt/openmpi/${openmpi_version}-1.${disttag_network}.${compiler}.${compiler_version}/bin release=1.${disttag_network}.${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_network}.${compiler}.${compiler_version}/lib64 ompi_includedir=/opt/openmpi/${openmpi_version}-1.${disttag_network}.${compiler}.${compiler_version}/include ompi_bindir=/opt/openmpi/${openmpi_version}-1.${disttag_network}.${compiler}.${compiler_version}/bin release=1.${disttag_network}.${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_network}.${compiler}.${compiler_version}/lib64 ompi_includedir=/opt/openmpi/${openmpi_version}-1.${disttag_network}.${compiler}.${compiler_version}/include ompi_bindir=/opt/openmpi/${openmpi_version}-1.${disttag_network}.${compiler}.${compiler_version}/bin release=1.${disttag_network}.${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_network}.${compiler}.${compiler_version}/lib64 ompi_includedir=/opt/openmpi/${openmpi_version}-1.${disttag_network}.${compiler}.${compiler_version}/include ompi_bindir=/opt/openmpi/${openmpi_version}-1.${disttag_network}.${compiler}.${compiler_version}/bin release=1.${disttag_network}.${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_network}.${compiler}.${compiler_version}/lib64 ompi_includedir=/opt/openmpi/${openmpi_version}-1.${disttag_network}.${compiler}.${compiler_version}/include ompi_bindir=/opt/openmpi/${openmpi_version}-1.${disttag_network}.${compiler}.${compiler_version}/bin release=1.${disttag_network}.${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=atlas blas_version=3.8.3 blasdir=/opt/${blas}/${blas_version}/1.${disttag}.${compiler}.${compiler_version}/lib64 lapack=atlas lapack_version=3.8.3 lapackdir=/opt/${lapack}/${lapack_version}/1.${disttag}.${compiler}.${compiler_version}/lib64 openmpi_version=1.3.3 ompi_libdir=/opt/openmpi/${openmpi_version}-1.${disttag_network}.${compiler}.${compiler_version}/lib64 ompi_includedir=/opt/openmpi/${openmpi_version}-1.${disttag_network}.${compiler}.${compiler_version}/include ompi_bindir=/opt/openmpi/${openmpi_version}-1.${disttag_network}.${compiler}.${compiler_version}/bin release=1.${disttag_network}.${compiler}.${compiler_version}.openmpi.${openmpi_version}.${blas}.${blas_version}.${lapack}.${lapack_version} rpmbuild --bb --with blacs=blacs --with blacsdir=/opt/blacs/1.1/24.${disttag_network}.${compiler}.${compiler_version}.openmpi.${openmpi_version}/lib64 \ --with blas=${blas} --with blas_version=${blas_version} --with blasdir=${blasdir} \ --with compiler=${compiler} --with compiler_version=${compiler_version} \ --with compiler_bindir=${compiler_bindir} --with compiler_libdir=${compiler_libdir} \ --with lapack=${lapack} --with lapack_version=${lapack_version} --with lapackdir=${lapackdir} \ --with modules=${modules} --with default_version=1 \ --with parallel=1 --with openmpi=openmpi --with openmpi_version=${openmpi_version} \ --with ompi_libdir=${ompi_libdir} --with ompi_includedir=${ompi_includedir} --with ompi_bindir=${ompi_bindir} \ --with prefix=/opt/scalapack/1.8.0/${release} scalapack.spec
Build the following PDSYEVRnew
PDSYEVRnew ScaLAPACK's new parallel MRRR algorithm for computing eigenpairs of large real symmetric or complex Hermitian matrices.
Build the following RPMS:
cd ~/rpmbuild/SOURCES&& wget www.cs.berkeley.edu/~voemel/PDSYEVRnew.tar.gz cd ~/rpmbuild/SPECS major_version=1 compiler=gfortran43 # compiler_version=4.3.2 compiler_libdir=/usr/lib64 compiler_bindir=/usr/bin blas=acml blas_version=4.3.0 blasdir=/opt/${blas}/${blas_version}/${compiler}64/lib lapack=acml lapack_version=4.3.0 lapackdir=/opt/${lapack}/${lapack_version}/${compiler}64/lib openmpi_version=1.3.3 ompi_libdir=/opt/openmpi/${openmpi_version}-1.${disttag_network}.${compiler}.${compiler_version}/lib64 ompi_includedir=/opt/openmpi/${openmpi_version}-1.${disttag_network}.${compiler}.${compiler_version}/include ompi_bindir=/opt/openmpi/${openmpi_version}-1.${disttag_network}.${compiler}.${compiler_version}/bin blacs=blacs blacsdir=/opt/blacs/1.1/24.${disttag_network}.${compiler}.${compiler_version}.openmpi.${openmpi_version}/lib64 scalapack=scalapack scalapackdir=/opt/scalapack/1.8.0/1.${disttag_network}.${compiler}.${compiler_version}.openmpi.${openmpi_version}.${blas}.${blas_version}.${lapack}.${lapack_version}/lib64 release=1.${disttag_network}.${compiler}.${compiler_version}.openmpi.${openmpi_version}.${blas}.${blas_version}.${lapack}.${lapack_version} 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_network}.${compiler}.${compiler_version}/lib64 ompi_includedir=/opt/openmpi/${openmpi_version}-1.${disttag_network}.${compiler}.${compiler_version}/include ompi_bindir=/opt/openmpi/${openmpi_version}-1.${disttag_network}.${compiler}.${compiler_version}/bin blacs=blacs blacsdir=/opt/blacs/1.1/24.${disttag_network}.${compiler}.${compiler_version}.openmpi.${openmpi_version}/lib64 scalapack=scalapack scalapackdir=/opt/scalapack/1.8.0/1.${disttag_network}.${compiler}.${compiler_version}.openmpi.${openmpi_version}.${blas}.${blas_version}.${lapack}.${lapack_version}/lib64 release=1.${disttag_network}.${compiler}.${compiler_version}.openmpi.${openmpi_version}.${blas}.${blas_version}.${lapack}.${lapack_version} rpmbuild --bb --with major_version=${major_version} \ --with blas=${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/PDSYEVRnew/${major_version}/${release} PDSYEVRnew.speccampos-gpaw
Build the following RPMS:
major_version=0 version1=6 version_svn=5147 cd ~/rpmbuild/SOURCES&& wget --no-check-certificate \ "https://wiki.fysik.dtu.dk/gpaw-files/gpaw-${major_version}.${version1}.${version_svn}.tar.gz" \ -O gpaw-${major_version}.${version1}.${version_svn}.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 openmpi_version=1.3.3 ompi_libdir=/opt/openmpi/${openmpi_version}-1.${disttag_network}.${compiler}.${compiler_version}/lib64 ompi_includedir=/opt/openmpi/${openmpi_version}-1.${disttag_network}.${compiler}.${compiler_version}/include ompi_bindir=/opt/openmpi/${openmpi_version}-1.${disttag_network}.${compiler}.${compiler_version}/bin blacs=blacs blacsdir=/opt/blacs/1.1/24.${disttag_network}.${compiler}.${compiler_version}.openmpi.${openmpi_version}/lib64 scalapack=scalapack scalapackdir=/opt/scalapack/1.8.0/1.${disttag_network}.${compiler}.${compiler_version}.openmpi.${openmpi_version}.${blas}.${blas_version}.${lapack}.${lapack_version}/lib64 release=1.${disttag_network}.${compiler}.${compiler_version}.python2.4.without_ase.openmpi.${openmpi_version}.${blas}.${blas_version}.${lapack}.${lapack_version} 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_network}.${compiler}.${compiler_version}/lib64 ompi_includedir=/opt/openmpi/${openmpi_version}-1.${disttag_network}.${compiler}.${compiler_version}/include ompi_bindir=/opt/openmpi/${openmpi_version}-1.${disttag_network}.${compiler}.${compiler_version}/bin blacs=blacs blacsdir=/opt/blacs/1.1/24.${disttag_network}.${compiler}.${compiler_version}.openmpi.${openmpi_version}/lib64 scalapack=scalapack scalapackdir=/opt/scalapack/1.8.0/1.${disttag_network}.${compiler}.${compiler_version}.openmpi.${openmpi_version}.${blas}.${blas_version}.${lapack}.${lapack_version}/lib64 release=1.${disttag_network}.${compiler}.${compiler_version}.python2.4.without_ase.openmpi.${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_network}.${compiler}.${compiler_version}/lib64 ompi_includedir=/opt/openmpi/${openmpi_version}-1.${disttag_network}.${compiler}.${compiler_version}/include ompi_bindir=/opt/openmpi/${openmpi_version}-1.${disttag_network}.${compiler}.${compiler_version}/bin blacs=blacs blacsdir=/opt/blacs/1.1/24.${disttag_network}.${compiler}.${compiler_version}.openmpi.${openmpi_version}/lib64 scalapack=scalapack scalapackdir=/opt/scalapack/1.8.0/1.${disttag_network}.${compiler}.${compiler_version}.openmpi.${openmpi_version}.${blas}.${blas_version}.${lapack}.${lapack_version}/lib64 release=1.${disttag_network}.${compiler}.${compiler_version}.python2.4.without_ase.openmpi.${openmpi_version}.${blas}.${blas_version}.${lapack}.${lapack_version} rpmbuild --bb --with major_version=${major_version} --with version1=${version1} --with version_svn=${version_svn} \ --with blas=${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/${major_version}.${version1}.${version_svn}/${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=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_network}.${compiler}.${compiler_version}/lib64 ompi_includedir=/opt/openmpi/${openmpi_version}-1.${disttag_network}.${compiler}.${compiler_version}/include ompi_bindir=/opt/openmpi/${openmpi_version}-1.${disttag_network}.${compiler}.${compiler_version}/bin blacs=blacs blacsdir=/opt/blacs/1.1/24.${disttag_network}.${compiler}.${compiler_version}.openmpi.${openmpi_version}/lib64 scalapack=scalapack #scalapackdir=/opt/scalapack/1.8.0/1.${disttag_network}.${compiler}.${compiler_version}.openmpi.${openmpi_version}.${blas}.${blas_version}.${lapack}.${lapack_version}/lib64 scalapackdir=/opt/scalapack/1.8.0/1.${disttag_network}.${compiler}.${compiler_version}.openmpi.${openmpi_version}.acml.4.0.1.${lapack}.${lapack_version}/lib64 release=1.${disttag_network}.${compiler}.${compiler_version}.python2.4.without_ase.openmpi.${openmpi_version}.${blas}.${blas_version}.${lapack}.${lapack_version} compiler=gfortran43 # problems reported on thul compiler_version=4.3.2 compiler_libdir=/usr/lib64 compiler_bindir=/usr/bin blas=atlas blas_version=3.8.3 blasdir=/opt/${blas}/${blas_version}/1.${disttag}.${compiler}.${compiler_version}/lib64 lapack=atlas lapack_version=3.8.3 lapackdir=/opt/${lapack}/${lapack_version}/1.${disttag}.${compiler}.${compiler_version}/lib64 openmpi_version=1.3.3 ompi_libdir=/opt/openmpi/${openmpi_version}-1.${disttag_network}.${compiler}.${compiler_version}/lib64 ompi_includedir=/opt/openmpi/${openmpi_version}-1.${disttag_network}.${compiler}.${compiler_version}/include ompi_bindir=/opt/openmpi/${openmpi_version}-1.${disttag_network}.${compiler}.${compiler_version}/bin blacs=blacs blacsdir=/opt/blacs/1.1/24.${disttag_network}.${compiler}.${compiler_version}.openmpi.${openmpi_version}/lib64 scalapack=scalapack scalapackdir=/opt/scalapack/1.8.0/1.${disttag_network}.${compiler}.${compiler_version}.openmpi.${openmpi_version}.${blas}.${blas_version}.${lapack}.${lapack_version}/lib64 release=1.${disttag_network}.${compiler}.${compiler_version}.python2.4.without_ase.openmpi.${openmpi_version}.${blas}.${blas_version}.${lapack}.${lapack_version} compiler=gfortran compiler_version=4.1.2 compiler_libdir=/usr/lib64 compiler_bindir=/usr/bin blas=blas blas_version=3.0.37.el5 blasdir=/usr/lib64 lapack=lapack lapack_version=3.0.37.el5 lapackdir=/usr/lib64 openmpi_version=1.3.3 ompi_libdir=/opt/openmpi/${openmpi_version}-1.${disttag_network}.${compiler}.${compiler_version}/lib64 ompi_includedir=/opt/openmpi/${openmpi_version}-1.${disttag_network}.${compiler}.${compiler_version}/include ompi_bindir=/opt/openmpi/${openmpi_version}-1.${disttag_network}.${compiler}.${compiler_version}/bin blacs=blacs blacsdir=/opt/blacs/1.1/24.${disttag_network}.${compiler}.${compiler_version}.openmpi.${openmpi_version}/lib64 scalapack=scalapack scalapackdir=/opt/scalapack/1.8.0/1.${disttag_network}.${compiler}.${compiler_version}.openmpi.${openmpi_version}.${blas}.${blas_version}.${lapack}.${lapack_version}/lib64 release=1.${disttag_network}.${compiler}.${compiler_version}.python2.4.without_ase.openmpi.${openmpi_version}.${blas}.${blas_version}.${lapack}.${lapack_version} compiler=gfortran compiler_version=4.1.2 compiler_libdir=/usr/lib64 compiler_bindir=/usr/bin blas=acml 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_network}.${compiler}.${compiler_version}/lib64 ompi_includedir=/opt/openmpi/${openmpi_version}-1.${disttag_network}.${compiler}.${compiler_version}/include ompi_bindir=/opt/openmpi/${openmpi_version}-1.${disttag_network}.${compiler}.${compiler_version}/bin blacs=blacs blacsdir=/opt/blacs/1.1/24.${disttag_network}.${compiler}.${compiler_version}.openmpi.${openmpi_version}/lib64 scalapack=scalapack scalapackdir=/opt/scalapack/1.8.0/1.${disttag_network}.${compiler}.${compiler_version}.openmpi.${openmpi_version}.${blas}.${blas_version}.${lapack}.${lapack_version}/lib64 release=1.${disttag_network}.${compiler}.${compiler_version}.python2.4.without_ase.openmpi.${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.${disttag_network}.${compiler}.${compiler_version}/lib64 ompi_includedir=/opt/openmpi/${openmpi_version}-1.${disttag_network}.${compiler}.${compiler_version}/include ompi_bindir=/opt/openmpi/${openmpi_version}-1.${disttag_network}.${compiler}.${compiler_version}/bin blacs=mkl blacsdir=${blasdir} scalapack=mkl scalapackdir=${blasdir} release=1.${disttag_network}.${compiler}.${compiler_version}.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_network}.${compiler}.${compiler_version}/lib64 ompi_includedir=/opt/openmpi/${openmpi_version}-1.${disttag_network}.${compiler}.${compiler_version}/include ompi_bindir=/opt/openmpi/${openmpi_version}-1.${disttag_network}.${compiler}.${compiler_version}/bin blacs=mkl blacsdir=${blasdir} scalapack=mkl scalapackdir=${blasdir} release=1.${disttag_network}.${compiler}.${compiler_version}.python2.4.without_ase.openmpi.${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.${disttag_network}.${compiler}.${compiler_version}/lib64 ompi_includedir=/opt/openmpi/${openmpi_version}-1.${disttag_network}.${compiler}.${compiler_version}/include ompi_bindir=/opt/openmpi/${openmpi_version}-1.${disttag_network}.${compiler}.${compiler_version}/bin blacs=mkl blacsdir=${blasdir} scalapack=mkl scalapackdir=${blasdir} release=1.${disttag_network}.${compiler}.${compiler_version}.python2.4.without_ase.openmpi.${openmpi_version}.${blas}.${blas_version}.${lapack}.${lapack_version}
Build the following for Asap
Asap
Build the following RPMS:
major_version=3 version1=2 version2=6 cd ~/rpmbuild/SOURCES&& wget "http://dcwww.camp.dtu.dk/campos/download/Asap-${major_version}.${version1}.${version2}.tar.gz" cd ~/rpmbuild/SPECS module load ASE3 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_network}.${compiler}.${compiler_version}/lib64 ompi_includedir=/opt/openmpi/${openmpi_version}-1.${disttag_network}.${compiler}.${compiler_version}/include ompi_bindir=/opt/openmpi/${openmpi_version}-1.${disttag_network}.${compiler}.${compiler_version}/bin release=1.${disttag_network}.${compiler}.${compiler_version}.python2.4.openmpi.${openmpi_version} compiler=open64 # only on fjorm # 24 Aug 2009 fails 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_network}.${compiler}.${compiler_version}/lib64 ompi_includedir=/opt/openmpi/${openmpi_version}-1.${disttag_network}.${compiler}.${compiler_version}/include ompi_bindir=/opt/openmpi/${openmpi_version}-1.${disttag_network}.${compiler}.${compiler_version}/bin release=1.${disttag_network}.${compiler}.${compiler_version}.python2.4.openmpi.${openmpi_version} 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_network}.${compiler}.${compiler_version}/lib64 ompi_includedir=/opt/openmpi/${openmpi_version}-1.${disttag_network}.${compiler}.${compiler_version}/include ompi_bindir=/opt/openmpi/${openmpi_version}-1.${disttag_network}.${compiler}.${compiler_version}/bin release=1.${disttag_network}.${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_network}.${compiler}.${compiler_version}/lib64 ompi_includedir=/opt/openmpi/${openmpi_version}-1.${disttag_network}.${compiler}.${compiler_version}/include ompi_bindir=/opt/openmpi/${openmpi_version}-1.${disttag_network}.${compiler}.${compiler_version}/bin release=1.${disttag_network}.${compiler}.${compiler_version}.python2.4.openmpi.${openmpi_version} rpmbuild --bb --with major_version=${major_version} --with version1=${version1} --with version2=${version2} \ --with compiler=${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-asap${major_version}/${major_version}.${version1}.${version2}/${release} campos-asap.spec
Build the following for abinit
abinit-pseudopotentials-1.tar.gz
abinit pseudopotentials
Build the following RPMS:
cd ~/rpmbuild/SOURCES&& wget --no-check-certificate \ "https://wiki.fysik.dtu.dk/niflheim/Cluster_software_-_RPMS?action=AttachFile&do=get&target=abinit-pseudopotentials-1.tar.gz" \ -O abinit-pseudopotentials-1.tar.gz cd ~/rpmbuild/SPECS rpmbuild -bb --with modules --with default_version abinit-pseudopotentials.spec
abinit
abinit is a Density Functional Theory (DFT) package with pseudopotentials and a planewave basis.
Build the following RPMS:
cd ~/rpmbuild/SOURCES&& wget ftp://ftp.abinit.org/pub/abinitio/ABINIT_v5.4.4/abinit-5.4.4p.tar.gz cd ~/rpmbuild/SPECS compiler=gfortran43 compiler_version=4.3.2 compiler_libdir=/usr/lib64 compiler_bindir=/usr/bin blas=acml blas_version=4.3.0 blasdir=/opt/${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.${disttag_network}.${compiler}.${compiler_version}/lib64 ompi_includedir=/opt/openmpi/${openmpi_version}-1.${disttag_network}.${compiler}.${compiler_version}/include ompi_bindir=/opt/openmpi/${openmpi_version}-1.${disttag_network}.${compiler}.${compiler_version}/bin release=1.${disttag_network}.${compiler}.${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/${release} abinit.spec
Build the following for siesta
siesta-pseudopotentials-2.tar.gz
siesta pseudopotentials
Build the following RPMS:
cd ~/rpmbuild/SOURCES&& wget --no-check-certificate \ "https://wiki.fysik.dtu.dk/niflheim/Cluster_software_-_RPMS?action=AttachFile&do=get&target=siesta-pseudopotentials-2.tar.gz" \ -O siesta-pseudopotentials-2.tar.gz cd ~/rpmbuild/SPECS rpmbuild -bb --with modules --with default_version siesta-pseudopotentials.spec
siesta
siesta (Spanish Initiative for Electronic Simulations with Thousands of Atoms) is both a method and its computer program implementation, to perform electronic structure calculations and ab initio molecular dynamics simulations of molecules and solids.
Build the following RPMS:
cd ~/rpmbuild/SPECS major_version=2 version1=0 compiler=gfortran43 compiler_version=4.3.2 compiler_libdir=/usr/lib64 compiler_bindir=/usr/bin blas=acml blas_version=4.3.0 blasdir=/opt/${blas}/${blas_version}/${compiler}64/lib lapack=acml lapack_version=4.3.0 lapackdir=/opt/${lapack}/${lapack_version}/${compiler}64/lib netcdf=netcdf4 netcdf_includedir=/opt/${netcdf}/4.0.1/1.${disttag}.${compiler}.${compiler_version}/include netcdf_libdir=/opt/${netcdf}/4.0.1/1.${disttag}.${compiler}.${compiler_version}/lib64 openmpi_version=1.3.3 ompi_libdir=/opt/openmpi/${openmpi_version}-1.${disttag_network}.${compiler}.${compiler_version}/lib64 ompi_includedir=/opt/openmpi/${openmpi_version}-1.${disttag_network}.${compiler}.${compiler_version}/include ompi_bindir=/opt/openmpi/${openmpi_version}-1.${disttag_network}.${compiler}.${compiler_version}/bin blacs=blacs blacsdir=/opt/blacs/1.1/24.${disttag_network}.${compiler}.${compiler_version}.openmpi.${openmpi_version}/lib64 scalapack=scalapack scalapackdir=/opt/scalapack/1.8.0/1.${disttag_network}.${compiler}.${compiler_version}.openmpi.${openmpi_version}.${blas}.${blas_version}.${lapack}.${lapack_version}/lib64 release=1.${disttag_network}.${compiler}.${compiler_version}.openmpi.${openmpi_version}.${blas}.${blas_version}.${lapack}.${lapack_version} rpmbuild --bb --with major_version=${major_version} --with version1=${version1} \ --with blas=${blas} --with blas_version=${blas_version} --with blasdir=${blasdir} \ --with compiler=${compiler} --with compiler_version=${compiler_version} \ --with compiler_bindir=${compiler_bindir} --with compiler_libdir=${compiler_libdir} \ --with lapack=${lapack} --with lapack_version=${lapack_version} --with lapackdir=${lapackdir} \ --with netcdf=${netcdf} --with netcdf_includedir=${netcdf_includedir} --with netcdf_libdir=${netcdf_libdir} \ --with 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=${scalapackdir} \ --with prefix=/opt/siesta${major_version}/${major_version}.${version1}/${release} siesta.spec
Build the following for espresso
espresso pseudopotentials
Build the following RPMS:
cd ~/rpmbuild/SOURCES&& wget http://www.quantum-espresso.org/pseudo/espresso_pp.tar.gz cd ~/rpmbuild/SPECS rpmbuild -bb --with modules --with default_version espresso_pp.spec
espresso
Build the following RPMS:
cd ~/rpmbuild/SOURCES&& wget http://www.pwscf.org/downloads/PWversion/4.0.5/espresso-4.0.5.tar.gz cd ~/rpmbuild/SPECS compiler=gfortran43 compiler_version=4.3.2 compiler_libdir=/usr/lib64 compiler_bindir=/usr/bin blas=acml blas_version=4.3.0 blasdir=/opt/${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.${disttag_network}.${compiler}.${compiler_version}/lib64 ompi_includedir=/opt/openmpi/${openmpi_version}-1.${disttag_network}.${compiler}.${compiler_version}/include ompi_bindir=/opt/openmpi/${openmpi_version}-1.${disttag_network}.${compiler}.${compiler_version}/bin blacs=blacs blacsdir=/opt/blacs/1.1/24.${disttag_network}.${compiler}.${compiler_version}.openmpi.${openmpi_version}/lib64 scalapack=scalapack scalapackdir=/opt/scalapack/1.8.0/1.${disttag_network}.${compiler}.${compiler_version}.openmpi.${openmpi_version}.${blas}.${blas_version}.${lapack}.${lapack_version}/lib64 release=1.${disttag_network}.${compiler}.${compiler_version}.openmpi.${openmpi_version}.${blas}.${blas_version}.${lapack}.${lapack_version}.${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.${disttag_network}.${compiler}.${compiler_version}/lib64 ompi_includedir=/opt/openmpi/${openmpi_version}-1.${disttag_network}.${compiler}.${compiler_version}/include ompi_bindir=/opt/openmpi/${openmpi_version}-1.${disttag_network}.${compiler}.${compiler_version}/bin blacs=blacs blacsdir=/opt/blacs/1.1/24.${disttag_network}.${compiler}.${compiler_version}.openmpi.${openmpi_version}/lib64 scalapack=scalapack scalapackdir=/opt/scalapack/1.8.0/1.${disttag_network}.${compiler}.${compiler_version}.openmpi.${openmpi_version}.${blas}.${blas_version}.${lapack}.${lapack_version}/lib64 release=1.${disttag_network}.${compiler}.${compiler_version}.openmpi.${openmpi_version}.${blas}.${blas_version}.${lapack}.${lapack_version}.${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 following for elk
elk species
Build the following RPMS:
major_version=0 version1=9 version2=278 cd ~/rpmbuild/SOURCES&& wget http://downloads.sourceforge.net/project/elk/elk/${major_version}.${version1}.${version2}/elk-${major_version}.${version1}.${version2}.tgz cd ~/rpmbuild/SPECS rpmbuild -bb --with major_version=${major_version} --with version1=${version1} --with version2=${version2} \ --with modules --with default_version elk-species.specelk
Build the following RPMS:
major_version=0 version1=9 version2=278 cd ~/rpmbuild/SOURCES&& wget http://downloads.sourceforge.net/project/elk/elk/${major_version}.${version1}.${version2}/elk-${major_version}.${version1}.${version2}.tgz cd ~/rpmbuild/SPECS thread_mode=nomp compiler=gfortran43 compiler_version=4.3.2 compiler_libdir=/usr/lib64 compiler_bindir=/usr/bin blas=acml blas_version=4.3.0 blasdir=/opt/${blas}/${blas_version}/${compiler}64/lib lapack=acml lapack_version=4.3.0 lapackdir=/opt/${lapack}/${lapack_version}/${compiler}64/lib release=1.${disttag}.${compiler}.${compiler_version}.${thread_mode}.${blas}.${blas_version}.${lapack}.${lapack_version} compiler=gfortran43 compiler_version=4.3.2 compiler_libdir=/usr/lib64 compiler_bindir=/usr/bin blas=blas blas_version=3.0.37.el5 blasdir=/usr/lib64 lapack=lapack lapack_version=3.0.37.el5 lapackdir=/usr/lib64 release=1.${disttag}.${compiler}.${compiler_version}.${thread_mode}.${blas}.${blas_version}.${lapack}.${lapack_version} # multithreaded thread_mode=mp compiler=gfortran43 compiler_version=4.3.2 compiler_libdir=/usr/lib64 compiler_bindir=/usr/bin blas=acml blas_version=4.3.0 blasdir=/opt/${blas}/${blas_version}/${compiler}64_${thread_mode}/lib lapack=acml lapack_version=4.3.0 lapackdir=/opt/${lapack}/${lapack_version}/${compiler}64_${thread_mode}/lib release=1.${disttag}.${compiler}.${compiler_version}.${thread_mode}.${blas}.${blas_version}.${lapack}.${lapack_version} # multithreaded thread_mode=mp compiler=gfortran43 # only on fjorm # sometimes freezes in threaded mode compiler_version=4.3.2 compiler_libdir=/usr/lib64 compiler_bindir=/usr/bin blas=goto blas_version=1.26 blasdir=/opt/${blas}/${blas_version}/1.${disttag}.${compiler}.${compiler_version}.smp/lib64 lapack=acml lapack_version=4.3.0 lapackdir=/opt/${lapack}/${lapack_version}/${compiler}64_${thread_mode}/lib release=1.${disttag}.${compiler}.${compiler_version}.${thread_mode}.${blas}.${blas_version}.${lapack}.${lapack_version} rpmbuild --bb --with major_version=${major_version} --with version1=${version1} --with version2=${version2} \ --with blas=${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 thread_mode=${thread_mode} --with parallel=1 \ --with prefix=/opt/elk/${major_version}.${version1}.${version2}/${release} elk.spec
Build the following for vtk
cmake
Build the following RPMS:
cd ~/rpmbuild/SOURCES&& wget http://www.cmake.org/files/v2.6/cmake-2.6.4.tar.gz cd ~/rpmbuild/SOURCES&& wget "http://downloads.sourceforge.net/project/xmlrpc-c/Xmlrpc-c Super Stable/1.06.35/xmlrpc-c-1.06.35.tgz" cd ~/rpmbuild/SPECS rpmbuild -bb --with bootstrap --without gui cmake.spec # install the resulting RPM rpmbuild -bb xmlrpc-c.spec # install the resulting RPM rpm -e cmake rpmbuild -bb --without gui cmake.spec # install the resulting RPM
vtkdata
Build the following RPMS:
cd ~/rpmbuild/SOURCES&& wget http://www.vtk.org/files/release/5.4/vtkdata-5.4.2.tar.gz cd ~/rpmbuild/SPECS rpmbuild -bb --with version1=4 --with version2=2 --with modules=1 --with default_version=1 \ --with prefix=/opt/vtkdata/5.4.2/1.${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_network}.${compiler}.${compiler_version}/lib64 ompi_includedir=/opt/openmpi/${openmpi_version}-1.${disttag_network}.${compiler}.${compiler_version}/include ompi_bindir=/opt/openmpi/${openmpi_version}-1.${disttag_network}.${compiler}.${compiler_version}/bin rpmbuild -bb --without qt4 --with version1=4 --with version2=2 \ --with compiler=${compiler} --with compiler_version=${compiler_version} \ --with compiler_bindir=${compiler_bindir} --with compiler_libdir=${compiler_libdir} \ --with 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_network}.${compiler}.${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.${disttag_network}.${compiler}.${compiler_version}/lib64 ompi_includedir=/opt/openmpi/${openmpi_version}-1.${disttag_network}.${compiler}.${compiler_version}/include ompi_bindir=/opt/openmpi/${openmpi_version}-1.${disttag_network}.${compiler}.${compiler_version}/bin gsl_libdir=/usr/lib64 gsl_includedir=/usr/include/gsl gsl_bindir=/usr/bin arpack=arpack arpackdir=/usr/lib64 release=1.${disttag_network}.${compiler}.${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
Build the following for TAU
pdtoolkit
Program Database Toolkit is a framework for analyzing source code written in several programming languages and for making rich program knowledge accessible to developers of static and dynamic analysis tools. PDT is required by TAU.
Build the following RPMS:
cd ~/rpmbuild/SOURCES&& wget http://www.cs.uoregon.edu/research/paracomp/pdtoolkit/Download/pdt_latest.tar.gz mv pdt_latest.tar.gz `tar ztf pdt_latest.tar.gz | head -1 | cut -d "/" -f 2`.tar.gz cd ~/rpmbuild/SPECS major_version=3 version1=14 version2=1 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 version1=${version1} --with version2=${version2} \ --with compiler=${compiler} --with compiler_version=${compiler_version} \ --with compiler_bindir=${compiler_bindir} --with compiler_libdir=${compiler_libdir} \ --with modules=${modules} --with default_version=1 \ --with prefix=/opt/pdtoolkit/${major_version}.${version1}.${version2}/1.${disttag}.${compiler}.${compiler_version}.python2.4 pdtoolkit.spectau
TAU Performance System® is a portable profiling and tracing toolkit for performance analysis of parallel programs written in Fortran, C, C++, Java, Python.
Build the following RPMS:
cd ~/rpmbuild/SOURCES&& wget http://www.cs.uoregon.edu/research/paracomp/tau/tauprofile/dist/tau_latest.tar.gz mv tau_latest.tar.gz `tar ztf tau_latest.tar.gz | head -1 | cut -d "/" -f 1`.tar.gz cd ~/rpmbuild/SPECS major_version=2 version1=18 version2=2p4 module load PDTOOLKIT/3.14.1-1.el5.fys.gfortran.4.1.2.python2.4 pdt_rootdir=${PDTROOT} compiler=gfortran compiler_version=4.1.2 compiler_libdir=/usr/lib64 compiler_bindir=/usr/bin openmpi_version=1.3.3 ompi_libdir=/opt/openmpi/${openmpi_version}-1.${disttag_network}.${compiler}.${compiler_version}/lib64 ompi_includedir=/opt/openmpi/${openmpi_version}-1.${disttag_network}.${compiler}.${compiler_version}/include ompi_bindir=/opt/openmpi/${openmpi_version}-1.${disttag_network}.${compiler}.${compiler_version}/bin release=1.${disttag_network}.${compiler}.${compiler_version}.python2.4.openmpi.${openmpi_version} module load PDTOOLKIT/3.14.1-1.el5.fys.gfortran43.4.3.2.python2.4 pdt_rootdir=${PDTROOT} compiler=gfortran43 compiler_version=4.3.2 compiler_libdir=/usr/lib64 compiler_bindir=/usr/bin openmpi_version=1.3.3 ompi_libdir=/opt/openmpi/${openmpi_version}-1.${disttag_network}.${compiler}.${compiler_version}/lib64 ompi_includedir=/opt/openmpi/${openmpi_version}-1.${disttag_network}.${compiler}.${compiler_version}/include ompi_bindir=/opt/openmpi/${openmpi_version}-1.${disttag_network}.${compiler}.${compiler_version}/bin release=1.${disttag_network}.${compiler}.${compiler_version}.python2.4.openmpi.${openmpi_version} rpmbuild -bb -with version1=${version1} --with version2=${version2} \ --with compiler=${compiler} --with compiler_version=${compiler_version} \ --with compiler_bindir=${compiler_bindir} --with compiler_libdir=${compiler_libdir} \ --with modules=${modules} --with default_version=1 --with pdt_rootdir=${pdt_rootdir} \ --with parallel=1 --with openmpi=openmpi --with openmpi_version=${openmpi_version} \ --with ompi_libdir=${ompi_libdir} --with ompi_includedir=${ompi_includedir} --with ompi_bindir=${ompi_bindir} \ --with prefix=/opt/tau/${major_version}.${version1}.${version2}/${release} tau.spec
Build the following for vasp
Installed with restricted access under vasp UNIX group (needs te be created in advance).
vasp potentials
Download potpaw/potcar.date.tar, potpaw_GGA/potcar.date.tar, and potpaw_PBE/potcar.date.tar to ~/rpmbuild/SOURCES. Create links to the downloaded files so the files are named explicitly with the string date (not the actual dates), for example:
ls -al ~/rpmbuild/SOURCES/potpaw_*potcar.date.tar lrwxrwxrwx 1 rpmbuild campnone 29 Sep 25 17:15 ../SOURCES/potpaw_GGA_potcar.date.tar -> potpaw_GGA/potcar.06Feb03.tar lrwxrwxrwx 1 rpmbuild campnone 29 Sep 25 17:14 ../SOURCES/potpaw_PBE_potcar.date.tar -> potpaw_PBE/potcar.05Feb03.tar lrwxrwxrwx 1 rpmbuild campnone 25 Sep 25 17:14 ../SOURCES/potpaw_potcar.date.tar -> potpaw/potcar.05Feb03.tar
Build the following RPMS:
cd ~/rpmbuild/SPECS rpmbuild -bb --with modules --with default_version vasp-potpaw.spec
vasp
vasp. Download vasp.5.X.tar.gz and vasp.5.lib.tar.gz to ~/rpmbuild/SOURCES. Optionally download also vtstcode.tar.gz from http://theory.cm.utexas.edu/vtsttools/downloads/.
Build the following RPMS:
cd ~/rpmbuild/SPECS major_version=5 version1=2 # Compile with VASP TST library: http://theory.cm.utexas.edu/vtsttools/downloads/ tst=false # or true if [ "$tst" == "false" ]; then vasp_tst='.' else vasp_tst='.tst.' fi 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}/${compiler}64/lib lapack=acml lapack_version=4.0.1 lapackdir=/opt/${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_network}.${compiler}.${compiler_version}/lib64 ompi_includedir=/opt/openmpi/${openmpi_version}-1.${disttag_network}.${compiler}.${compiler_version}/include ompi_bindir=/opt/openmpi/${openmpi_version}-1.${disttag_network}.${compiler}.${compiler_version}/bin blacs=blacs blacsdir=/opt/blacs/1.1/24.${disttag_network}.${compiler}.${compiler_version}.openmpi.${openmpi_version}/lib64 scalapack=scalapack #scalapackdir=/opt/scalapack/1.8.0/1.${disttag_network}.${compiler}.${compiler_version}.openmpi.${openmpi_version}.${blas}.${blas_version}.${lapack}.${lapack_version}/lib64 scalapackdir=/opt/scalapack/1.8.0/1.${disttag_network}.${compiler}.${compiler_version}.openmpi.${openmpi_version}.blas.3.0.37.el5.lapack.3.0.37.el5/lib64 release=1.${disttag_network}${vasp_tst}${compiler}.${compiler_version}.openmpi.${openmpi_version}.${blas}.${blas_version}.${lapack}.${lapack_version}.${fftw} compiler=gfortran43 # 25 Sep 2009: segmentation fault when compiling dipol.f90 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_network}.${compiler}.${compiler_version}/lib64 ompi_includedir=/opt/openmpi/${openmpi_version}-1.${disttag_network}.${compiler}.${compiler_version}/include ompi_bindir=/opt/openmpi/${openmpi_version}-1.${disttag_network}.${compiler}.${compiler_version}/bin blacs=blacs blacsdir=/opt/blacs/1.1/24.${disttag_network}.${compiler}.${compiler_version}.openmpi.${openmpi_version}/lib64 scalapack=scalapack scalapackdir=/opt/scalapack/1.8.0/1.${disttag_network}.${compiler}.${compiler_version}.openmpi.${openmpi_version}.${blas}.${blas_version}.${lapack}.${lapack_version}/lib64 release=1.${disttag_network}${vasp_tst}${compiler}.${compiler_version}.openmpi.${openmpi_version}.${blas}.${blas_version}.${lapack}.${lapack_version}.${fftw} rpmbuild --bb --with tst=${tst} --with major_version=${major_version} --with version1=${version1} \ --with blas=${blas} --with blas_version=${blas_version} --with blasdir=${blasdir} \ --with compiler=${compiler} --with compiler_version=${compiler_version} \ --with compiler_bindir=${compiler_bindir} --with compiler_libdir=${compiler_libdir} \ --with 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=${scalapackdir} \ --with prefix=/opt/vasp/${major_version}.${version1}/${release} vasp.spec
Build the following for exciting
exciting species
Build the following RPMS:
major_version=9 version1=10 version2=None cd ~/rpmbuild/SOURCES&& wget http://static.exciting-code.org/exciting.hydrogen.${major_version}.${version1}.tar.gz cd ~/rpmbuild/SPECS rpmbuild -bb --with major_version=${major_version} --with version1=${version1} --with version2=${version2} \ --with modules --with default_version exciting-species.specexciting
Note: currently (24 Nov 2009) perl-XML-SAX-0.14-5 is broken https://bugzilla.redhat.com/show_bug.cgi?id=438291 on EL5; if exciting's tests complain about:
could not find ParserDetails.ini
do as root:
perl -MXML::SAX -e "XML::SAX->add_parser(q(XML::SAX::PurePerl))->save_parsers()"
Build the following RPMS:
major_version=9 version1=10 version2=None cd ~/rpmbuild/SOURCES&& wget http://static.exciting-code.org/exciting.hydrogen.${major_version}.${version1}.tar.gz cd ~/rpmbuild/SPECS thread_mode=nomp module load g95 # only on fjorm compiler=g95 # only on fjorm compiler_version=0.91 compiler_libdir=/opt/g95/0.91/lib/gcc-lib/x86_64-unknown-linux-gnu/4.0.3 compiler_bindir=/opt/g95/0.91/bin blas=blas blas_version=3.0.37.el5 blasdir=/usr/lib64 lapack=lapack lapack_version=${blas_version} lapackdir=/usr/lib64 openmpi_version=1.3.3 ompi_libdir=/opt/openmpi/${openmpi_version}-1.${disttag_network}.${compiler}.${compiler_version}/lib64 ompi_includedir=/opt/openmpi/${openmpi_version}-1.${disttag_network}.${compiler}.${compiler_version}/include ompi_bindir=/opt/openmpi/${openmpi_version}-1.${disttag_network}.${compiler}.${compiler_version}/bin release=1.${disttag_network}.${compiler}.${compiler_version}.${thread_mode}.openmpi.${openmpi_version}.${blas}.${blas_version}.${lapack}.${lapack_version} module load ifort # only on thul compiler=ifort # only on thul compiler_version=11.0 compiler_libdir=/opt/intel/Compiler/11.0/083/lib/intel64 compiler_bindir=/opt/intel/Compiler/11.0/083/bin/intel64 blas=mkl blas_version=10.1.3.027 blasdir=/opt/intel/${blas}/${blas_version}/lib/em64t lapack=mkl_lapack lapack_version=${blas_version} lapackdir=${blasdir} openmpi_version=1.3.3 ompi_libdir=/opt/openmpi/${openmpi_version}-1.${disttag_network}.${compiler}.${compiler_version}/lib64 ompi_includedir=/opt/openmpi/${openmpi_version}-1.${disttag_network}.${compiler}.${compiler_version}/include ompi_bindir=/opt/openmpi/${openmpi_version}-1.${disttag_network}.${compiler}.${compiler_version}/bin release=1.${disttag_network}.${compiler}.${compiler_version}.${thread_mode}.openmpi.${openmpi_version}.${blas}.${blas_version}.${lapack}.${lapack_version} rpmbuild --bb --with major_version=${major_version} --with version1=${version1} --with version2=${version2} \ --with blas=${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 thread_mode=${thread_mode} --with parallel=1 \ --with parallel=1 --with openmpi=openmpi --with openmpi_version=${openmpi_version} \ --with ompi_libdir=${ompi_libdir} --with ompi_includedir=${ompi_includedir} --with ompi_bindir=${ompi_bindir} \ --with arpack=arpack \ --with prefix=/opt/exciting/${major_version}.${version1}/${release} exciting.spec
Build the following for fleur
fleur
fleur. Download the source to ~/rpmbuild/SOURCES.
Build the following RPMS:
cd ~/rpmbuild/SPECS major_version=25 version1=g if [ "$version1" == "None" ]; then fleur_version=${major_version} else fleur_version=${major_version}.${version1} fi compiler=gfortran43 # compiler_version=4.3.2 compiler_libdir=/usr/lib64 compiler_bindir=/usr/bin blas=acml blas_version=4.3.0 blasdir=/opt/${blas}/${blas_version}/${compiler}64/lib lapack=acml lapack_version=4.3.0 lapackdir=/opt/${lapack}/${lapack_version}/${compiler}64/lib openmpi_version=1.3.3 ompi_libdir=/opt/openmpi/${openmpi_version}-1.${disttag_network}.${compiler}.${compiler_version}/lib64 ompi_includedir=/opt/openmpi/${openmpi_version}-1.${disttag_network}.${compiler}.${compiler_version}/include ompi_bindir=/opt/openmpi/${openmpi_version}-1.${disttag_network}.${compiler}.${compiler_version}/bin blacs=blacs blacsdir=/opt/blacs/1.1/24.${disttag_network}.${compiler}.${compiler_version}.openmpi.${openmpi_version}/lib64 scalapack=scalapack scalapackdir=/opt/scalapack/1.8.0/1.${disttag_network}.${compiler}.${compiler_version}.openmpi.${openmpi_version}.${blas}.${blas_version}.${lapack}.${lapack_version}/lib64 release=1.${disttag_network}.${compiler}.${compiler_version}.openmpi.${openmpi_version}.${blas}.${blas_version}.${lapack}.${lapack_version} module load g95 # only on fjorm compiler=g95 # only on fjorm compiler_version=0.91 compiler_libdir=/opt/g95/0.91/lib/gcc-lib/x86_64-unknown-linux-gnu/4.0.3 compiler_bindir=/opt/g95/0.91/bin blas=blas blas_version=3.0.37.el5 blasdir=/usr/lib64 lapack=lapack lapack_version=${blas_version} lapackdir=/usr/lib64 openmpi_version=1.3.3 ompi_libdir=/opt/openmpi/${openmpi_version}-1.${disttag_network}.${compiler}.${compiler_version}/lib64 ompi_includedir=/opt/openmpi/${openmpi_version}-1.${disttag_network}.${compiler}.${compiler_version}/include ompi_bindir=/opt/openmpi/${openmpi_version}-1.${disttag_network}.${compiler}.${compiler_version}/bin blacs=none scalapack=none release=1.${disttag_network}.${compiler}.${compiler_version}.${thread_mode}.openmpi.${openmpi_version}.${blas}.${blas_version}.${lapack}.${lapack_version} module load ifort # only on thul compiler=ifort # only on thul compiler_version=11.0 compiler_libdir=/opt/intel/Compiler/11.0/083/lib/intel64 compiler_bindir=/opt/intel/Compiler/11.0/083/bin/intel64 blas=mkl blas_version=10.1.3.027 blasdir=/opt/intel/${blas}/${blas_version}/lib/em64t lapack=mkl_lapack lapack_version=${blas_version} lapackdir=${blasdir} openmpi_version=1.3.3 ompi_libdir=/opt/openmpi/${openmpi_version}-1.${disttag_network}.${compiler}.${compiler_version}/lib64 ompi_includedir=/opt/openmpi/${openmpi_version}-1.${disttag_network}.${compiler}.${compiler_version}/include ompi_bindir=/opt/openmpi/${openmpi_version}-1.${disttag_network}.${compiler}.${compiler_version}/bin blacs=mkl blacsdir=${blasdir} scalapack=mkl scalapackdir=${blasdir} release=1.${disttag_network}.${compiler}.${compiler_version}.${thread_mode}.openmpi.${openmpi_version}.${blas}.${blas_version}.${lapack}.${lapack_version} rpmbuild --bb --with major_version=${major_version} --with version1=${version1} \ --with blas=${blas} --with blas_version=${blas_version} --with blasdir=${blasdir} \ --with compiler=${compiler} --with compiler_version=${compiler_version} \ --with compiler_bindir=${compiler_bindir} --with compiler_libdir=${compiler_libdir} \ --with lapack=${lapack} --with lapack_version=${lapack_version} --with lapackdir=${lapackdir} \ --with modules=${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/fleur/${fleur_version}/${release} fleur.spec
Build the following for gulp
Installed with restricted access under gulp UNIX group (needs te be created in advance).
gulp
gulp. Download gulp.3.4.source.tar.gz ~/rpmbuild/SOURCES.
Build the following RPMS:
major_version=3 version1=4 cd ~/rpmbuild/SPECS thread_mode=nomp compiler=gfortran43 compiler_version=4.3.2 compiler_libdir=/usr/lib64 compiler_bindir=/usr/bin blas=acml blas_version=4.3.0 blasdir=/opt/${blas}/${blas_version}/${compiler}64/lib lapack=acml lapack_version=4.3.0 lapackdir=/opt/${lapack}/${lapack_version}/${compiler}64/lib release=1.${disttag}.${compiler}.${compiler_version}.${thread_mode}.${blas}.${blas_version}.${lapack}.${lapack_version} # multithreaded thread_mode=mp compiler=gfortran43 compiler_version=4.3.2 compiler_libdir=/usr/lib64 compiler_bindir=/usr/bin blas=acml blas_version=4.3.0 blasdir=/opt/${blas}/${blas_version}/${compiler}64_${thread_mode}/lib lapack=acml lapack_version=4.3.0 lapackdir=/opt/${lapack}/${lapack_version}/${compiler}64_${thread_mode}/lib release=1.${disttag}.${compiler}.${compiler_version}.${thread_mode}.${blas}.${blas_version}.${lapack}.${lapack_version} rpmbuild --bb --with major_version=${major_version} --with version1=${version1} \ --with blas=${blas} --with blas_version=${blas_version} --with blasdir=${blasdir} \ --with compiler=${compiler} --with compiler_version=${compiler_version} \ --with compiler_bindir=${compiler_bindir} --with compiler_libdir=${compiler_libdir} \ --with lapack=${lapack} --with lapack_version=${lapack_version} --with lapackdir=${lapackdir} \ --with modules=${modules} --with default_version=1 \ --with thread_mode=${thread_mode} --with parallel=1 \ --with prefix=/opt/gulp/${major_version}.${version1}/${release} gulp.spec
Testing packages
Test dacapo installation (as normal user!).
If you use modules:
module load campos-dacapo # fulfill all dependencies requested by module ulimit -s 500000 # dacapo needs a large stack
Test with (make sure that /scratch/$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.