This version is outdated by a newer approved version.DiffThis version (2014/08/27 11:14) is a draft.
Approvals: 0/1

This is an old revision of the document!

GPAW

Settings Scientific linux 6.5 (VSC 1+2)

Following Revisions of GPAW and ASE were used, specify the revisions in install_gpaw_vsc_sl65.sh:

  • gpaw (?): 11253 ; ase (?): 3547
  • gpaw 0.10.0: 11364 ; ase 3.8.1: 3440
  • gpaw-setups-0.9.9672
  • numpy-1.6.2

Notes:

  • The library libxc had to be installed.
  • In customize_sl65_icc_mkl.py extra_link_args += ['-lxc'] had to be added.
  • In config.py mpicompiler = 'mpiicc' needed to be set.

Settings Scientific linux 6.4 (VSC 1+2)

Following Versions of GPAW and ASE were used:

  • With Scientific Linux 6.4 the header file '/usr/include/python2.6/modsupport.h' makes some Problems, for compiling gpaw some RedHat specific lines at the bottom of the file had to be commented out

Settings VSC-1 centos 5.7 (old)

Following Versions of GPAW and ASE were used:

Settings VSC-2 scientific linux 6.1 (old)

Following Versions of GPAW and ASE were used:

Settings gpaw qmmm version

As other versions, but with special config file:

Installation procedure

  • For installing download the following files from one of the settings sections above to a directory of your choice
  • After downloading edit file 'install_gpaw_*.sh'.
  • Execute install_gpaw_*.sh
   bash install_gpaw_*.sh all
  • Testing of GPAW:
gpaw-python <DIR_TO_GPAW_INST_BIN>/gpaw-test

For certain problems an assert statement in 

~/gpaw_inst_latest/lib64/python2.6/site-packages/gpaw/wavefunctions/lcao.py

has to be commented out (approx line 239): 

#assert abs(c_n.imag).max() < 1e-14

running gpaw jobs

Job submission using all cores on the compute nodes (VSC1 and VSC2)
#!/bin/sh
#$ -N Cl5_4x4x1
#$ -pe mpich 256
#$ -V

mpirun -machinefile $TMPDIR/machines -np $NSLOTS gpaw-python static.py --domain=None --band=1 --sl_default=4,4,64
Job submission using half of the cores on the compute nodes on VSC 2
#!/bin/sh
#$ -N Cl5_4x4x1
#$ -pe mpich8 256
#$ -V

mpirun -machinefile $TMPDIR/machines -np $NSLOTS_REDUCED gpaw-python static.py --domain=None --band=1 --sl_default=4,4,64

Significant speed up is seen in our test case when –sl_default is set. First two parameters for the BLACS grid should be similar in size to get an optimal memory distribution on the nodes.

  • doku/gpaw.1409138063.txt.gz
  • Last modified: 2014/08/27 11:14
  • by markus