This page describes the necessary steps for installing of dl160 On the server ------------- Install external packages ========================= As root: - create yum repository definitions (do **not** enable them):: # atrpms echo '[atrpms]' > /etc/yum.repos.d/atrpms.repo echo 'name=name=CentOS $releasever - $basearch - ATrpms' >> /etc/yum.repos.d/atrpms.repo echo 'baseurl=http://dl.atrpms.net/el$releasever-$basearch/atrpms/stable' >> /etc/yum.repos.d/atrpms.repo echo '#baseurl=http://mirrors.ircam.fr/pub/atrpms/el$releasever-$basearch/atrpms/stable' >> /etc/yum.repos.d/atrpms.repo echo 'gpgkey=http://ATrpms.net/RPM-GPG-KEY.atrpms' >> /etc/yum.repos.d/atrpms.repo echo 'gpgcheck=1' >> /etc/yum.repos.d/atrpms.repo echo 'enabled=0' >> /etc/yum.repos.d/atrpms.repo # epel echo '[epel]' > /etc/yum.repos.d/epel.repo echo 'name=name=CentOS $releasever - $basearch - EPEL' >> /etc/yum.repos.d/epel.repo echo 'baseurl=http://download.fedora.redhat.com/pub/epel/$releasever/$basearch' >> /etc/yum.repos.d/epel.repo echo 'gpgkey=http://download.fedora.redhat.com/pub/epel/RPM-GPG-KEY-EPEL' >> /etc/yum.repos.d/epel.repo echo 'gpgcheck=1' >> /etc/yum.repos.d/epel.repo echo 'enabled=0' >> /etc/yum.repos.d/epel.repo - install, as root:: yum install yum-utils # /var directories must be created yum search --enablerepo=atrpms arpack-devel yum search --enablerepo=epel jmol - configure rpmbuild: - use the following ~rpmbuild/.rpmmacros:: %disttag el5.fys %packager rpmbuild@fysik.dtu.dk %distribution Fysik RPMS %vendor Fysik RPMS %_signature gpg %_gpg_path ~/.gnupg %_gpg_name Fysik RPMS #%_topdir /home/camp/rpmbuild/AMD-Opteron %_topdir /home/camp/rpmbuild/Intel-Nehalem %_rpmdir %{_topdir}/RPMS %_srcrpmdir %{_topdir}/SRPMS %_svndir /home/camp/rpmbuild/rpmbuild %_specdir %{_svndir}/SPECS %_sourcedir %{_svndir}/SOURCES %_rpmfilename %%{NAME}-%%{VERSION}-%%{RELEASE}.%%{ARCH}.rpm #%_tmppath %{_topdir} %_tmppath /tmp/rpmbuild %_builddir %{_tmppath}/BUILD %niflheim 1 - as rpmbuild create directories:: mkdir -p ~/Intel-Nehalem/RPMS mkdir -p ~/Intel-Nehalem/SRPMS mkdir -p ~/Intel-Nehalem/BUILD mkdir -p ~/Intel-Nehalem/SPECS # needed only by openmpi mkdir -p ~/Intel-Nehalem/SOURCES # needed only by openmpi mkdir -p /tmp/rpmbuild/BUILD - install official packages, as rpmbuild:: cd ~/Intel-Nehalem/RPMS yumdownloader --resolve gcc-gfortran gcc43-c++ gcc43-gfortran blas-devel lapack-devel python-devel yumdownloader --resolve gnuplot libXi-devel xorg-x11-fonts-100dpi pexpect tetex-latex tkinter qt-devel yumdownloader --resolve openmpi openmpi-devel openmpi-libs compat-dapl libibverbs librdmacm openib yum localinstall * # as root - install `atrpms` packages, as rpmbuild (``vtk-python`` is currently unavailable 16 Apr 2009):: ~/Intel-Nehalem/RPMS yumdownloader --resolve --enablerepo=atrpms vtk-python arpack-devel graphviz wget http://ATrpms.net/RPM-GPG-KEY.atrpms rpm --import RPM-GPG-KEY.atrpms # as root yum localinstall * # as root - install the packages from `epel`, as rpmbuild:: ~/Intel-Nehalem/RPMS yumdownloader --resolve --enablerepo=epel jmol yumdownloader --resolve --enablerepo=epel environment-modules suitesparse-devel wget http://download.fedora.redhat.com/pub/epel/RPM-GPG-KEY-EPEL rpm --import RPM-GPG-KEY-EPEL # as root yum localinstall * # as root source /etc/profile.d/modules.sh - remove default openmpi:: yum remove openmpi openmpi-libs - edit ``/etc/yum.conf`` so it contains:: exclude=netcdf-* netcdf3-* fftw-* fftw2-* fftw3-* python-numeric openmpi-* It's time to build custom RPMS ============================== As rpmbuild:: cd ~/rpmbuild/SPECS Build a custom openmpi, using torque support:: export rpmtopdir=${HOME}/Intel-Nehalem # set this to _topdir value from ~/.rpmmacros wget http://www.open-mpi.org/software/ompi/v1.3/downloads/openmpi-1.3.2.tar.bz2 \ -O ~/rpmbuild/SOURCES/openmpi-1.3.2.tar.bz2 sh ./buildrpm-1.3.2-1.gfortran.sh ../SOURCES/openmpi-1.3.2.tar.bz2 2>&1 | tee buildrpm-1.3.2-1.gfortran.sh.log.Intel-Nehalem sh ./buildrpm-1.3.2-1.gfortran43.sh ../SOURCES/openmpi-1.3.2.tar.bz2 2>&1 | tee buildrpm-1.3.2-1.gfortran43.sh.log.Intel-Nehalem sh ./buildrpm-1.3.2-1.pathscale.sh ../SOURCES/openmpi-1.3.2.tar.bz2 2>&1 | tee buildrpm-1.3.2-1.pathscale.sh.log.Intel-Nehalem rpm -ivh ~/RPMS/*/openmpi-*.rpm If scripts that contain **ALL** build/install/uninstall commands (``global_install.sh`` and ``global_uninstall.sh``) need to be created, every time after an RPM is successfully built, do:: grep -v "#\!" install.sh >> ~/Intel-Nehalem/global_install.sh cat uninstall.sh ~/Intel-Nehalem/global_uninstall.sh | grep -v "#\!" >> ~/Intel-Nehalem/global_uninstall.sh.tmp && mv -f ~/Intel-Nehalem/global_uninstall.sh.tmp ~/Intel-Nehalem/global_uninstall.sh # ignore "cat: .../global_uninstall.sh: No such ..." error when running first time **Note** that `global_uninstall.sh` won't remove built RPM files, just will uninstall the packages. Build the following for dacapo: - `campos-dacapo-pseudopotentials `_:: python campos_installer.py --machine='dulak-cluster' --create_scripts campos-dacapo-pseudopotentials - `rasmol `_:: python campos_installer.py --machine='dulak-cluster' --create_scripts RasMol cp ~/RPMS/*/RasMol-*.rpm /home/dulak-server/rpm/campos - `gnuplot-py `_:: python campos_installer.py --machine='dulak-cluster' --create_scripts gnuplot-py cp ~/RPMS/*/gnuplot-py-*.rpm /home/dulak-server/rpm/campos if you use modules:: module load gnuplot-py echo "module load gnuplot-py" >> ~/global_install.sh otherwise logout and login again! - `cblas `_:: python campos_installer.py --machine='dulak-cluster' --create_scripts cblas cp ~/RPMS/*/cblas-*.rpm /home/dulak-server/rpm/campos - `python-numeric `_ (we must install **24.2** version, and we keep the default version):: cd rpm -e --nodeps python-numeric yumdownloader --resolve --disableexcludes=main python-numeric cp python-numeric-*.rpm /home/dulak-server/rpm/external # **Skip this step if not installing on "dulak-server"** cd ~/rpmbuild/SPECS python campos_installer.py --machine='dulak-cluster' --create_scripts python-numeric cp ~/RPMS/*/python-numeric-*.rpm /home/dulak-server/rpm/campos **Note**: (16 Apr 2009) currently Numeric's `test.py` results in (we ignore this error):: glibc detected *** python: free(): invalid next size (normal): 0x09aee970 *** If you use modules:: module load python-numeric echo "module load python-numeric" >> ~/global_install.sh otherwise logout and login again! After installing python-numeric make a very rough check:: python -c "import lapack_lite" ldd `rpm -ql python-numeric | grep lapack_lite.so` ldd `rpm -ql python-numeric | grep _dotblas.so` and reinstall the default version:: rpm -ivh --oldpackage ~/python-numeric-*.rpm - `ScientificPython `_:: python campos_installer.py --machine='dulak-cluster' --create_scripts ScientificPython cp ~/RPMS/*/ScientificPython-*.rpm /home/dulak-server/rpm/campos - `campos-ase2 `_:: python campos_installer.py --machine='dulak-cluster' --create_scripts campos-ase2 cp ~/RPMS/*/campos-ase2-*.rpm /home/dulak-server/rpm/campos - `campos-dacapo-python `_:: python campos_installer.py --machine='dulak-cluster' --create_scripts campos-dacapo-python - `campos-dacapo `_:: python campos_installer.py --machine='dulak-cluster' --create_scripts --compiler=gfortran43 campos-dacapo cp ~/RPMS/*/campos-dacapo-*.rpm /home/dulak-server/rpm/campos logout and login again! build following for gpaw: - `campos-gpaw-setups `_:: python campos_installer.py --machine='dulak-cluster' --create_scripts campos-gpaw-setups - `campos-ase3 `_:: python campos_installer.py --machine='dulak-cluster' --create_scripts campos-ase3 cp ~/RPMS/*/campos-ase3-*.rpm /home/dulak-server/rpm/campos - `campos-gpaw `_:: python campos_installer.py --machine='dulak-cluster' --create_scripts --compiler=gfortran43 campos-gpaw cp ~/RPMS/*/campos-gpaw-*.rpm /home/dulak-server/rpm/campos logout and login again! Testing packages ================ Test `dacapo` installation (as **normal** user!). If you use modules:: module load openmpi module load campos-dacapo-pseudopotentials module load python-numeric module load campos-dacapo-python module load ScientificPython module load gnuplot-py module load RasMol module load campos-ase2 module load campos-dacapo ulimit -s 65000 # dacapo needs a large stack Test with (make sure that `/scratch/$USER` exists):: cp -r `rpm -ql campos-dacapo-python | grep "share/campos-dacapo-python$"` /tmp cd /tmp/campos-dacapo-python/Tests python test.py 2>&1 | tee test.log It can take up to 1 day. Please consider disabling these "long" tests in `test.py`:: tests.remove('../Examples/Wannier-ethylene.py') tests.remove('../Examples/Wannier-Pt4.py') tests.remove('../Examples/Wannier-Ptwire.py') tests.remove('../Examples/Wannier-Fe-bcc.py') tests.remove('../Examples/transport_1dmodel.py') **Note** all `vtk` related tests will fail. Test `gpaw` installation (as **normal** user!): If you use modules:: module load openmpi module load campos-ase3 module load campos-gpaw-setups module load campos-gpaw Test with:: cp -r `rpm -ql campos-gpaw | grep "share/campos-gpaw/test$"` /tmp/test.gpaw.$$ cd /tmp/test.gpaw.* python test.py 2>&1 | tee test.log It takes about 20 minutes. On "Golden Client" ------------------ Login, as root, to the "Golden Client":: ssh n001 Enable nfs mount of the `server` home directory - follow 'Enable nfs mount on the "Golden Client"' from `configuring NFS `_. After this do:: cd /home/dulak-server/rpm/campos rpm -ivh campos-dacapo-2* If getting:: package example_package.el5.i386 is already installed remove these packages with:: rpm -e --nodeps example_package to allow the installation to proceed. Make sure that both python-numeric versions are installed:: rpm -q python-numeric This command will show a list of packages that need to be installed to fulfill `dacapo` dependencies. All these packages should be already under ``/home/dulak-server/rpm``. Remember to test the `dacapo` and `gpaw` installations on the "Golden Client" too. If you are installing workstation only, your setup is ready for testing - go to `benchmarking and maintenance `_. If you are building a cluster go **back** to `installing and configuring systemimager `_,