Niflheim

This page describes the necessary steps for installing gpaw and dacapo programs.

On the server

  • configure external repositories

  • if not yet done, configure rpmbuild,

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

    mkdir /home/dulak-server/rpm/external; cd /home/dulak-server/rpm/external
  • install-external-packages

  • comment out temporarily the exclude line in edit /etc/yum.conf,

  • and install additional atrpms packages:

    yumdownloader --resolve --enablerepo=atrpms fftw2 fftw2-devel fftw2-static netcdf netcdf-devel netcdf-static
    yum localinstall *
  • and from epel:

    yumdownloader --resolve --enablerepo=epel fftw3 fftw3-devel fftw fftw-devel fftw-static
    yumdownloader --resolve --enablerepo=epel python-matplotlib python-docutils
    yumdownloader --resolve --enablerepo=epel atlas-devel python-pygments scipy
    yum localinstall *
    . /etc/profile.d/modules.sh
  • uncomment the exclude line in edit /etc/yum.conf,

  • Skip this step if not installing on "dulak-server":

    cp -p ~/${FYS_PLATFORM}/RPMS/external/* /home/dulak-server/rpm/external

It's time to build custom RPMS

As root:

cd ~/rpmbuild/SPECS

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

mkdir /home/dulak-server/rpm/campos

Build ase

On systems other than EL5 start directly with building campos-ase3.

On EL5, you need to build more packages:

Build dacapo

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,

Niflheim: Building_a_Cluster_-_Tutorial/installing_software (last edited 2011-04-13 10:24:36 by MarcinDulak)