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doku:gpaw [2014/04/09 13:25] – markus | doku:gpaw [2014/08/27 11:26] – jz | ||
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- | ===== GPAW ===== | + | a: |
- | === Settings Scientific linux 6.5 (VSC 1+2) === | + | Settings Scientific linux 6.5 (VSC 1+2) |
- | Following Revisions of GPAW and ASE were used: | + | |
- | * gpaw: 11253 ; ase: 3547 | + | Following Revisions of GPAW and ASE were used, specify the revisions in install_gpaw_vsc_sl65.sh: |
- | * gpaw 0.10.0: 11364 ; ase 3.8.1: 3440 | + | |
- | * gpaw-setups-0.9.9672 | + | |
- | * numpy-1.6.2 | + | |
- | | + | * gpaw (?): 11253 ; ase (?): 3547 |
- | * FFTW from INTEL MKL | + | * gpaw 0.10.0: 11364 ; ase 3.8.1: 3440 |
- | | + | * |
- | + | * | |
- | Notes: | + | |
- | * The library '' | + | |
- | * In customize_sl65_icc_mkl.py '' | + | |
- | * In config.py '' | + | |
- | + | ||
- | === Settings Scientific linux 6.4 (VSC 1+2) === | + | |
- | Following Versions of GPAW and ASE were used: | + | |
- | * gpaw: svn checkout https:// | + | |
- | * ase: svn checkout https:// | + | |
- | * gpaw-setups-0.8.7929 | + | |
- | * numpy-1.6.2 | + | |
- | + | ||
- | * MPI Version: impi-4.1.0.024 | + | |
- | * FFTW from INTEL MKL | + | |
- | * files: {{: | + | |
- | + | ||
- | * With Scientific Linux 6.4 the header file '/ | + | |
- | + | ||
- | === Settings VSC-1 centos 5.7 (old) === | + | |
- | Following Versions of GPAW and ASE were used: | + | |
- | * gpaw: svn checkout https:// | + | |
- | * ase: svn checkout https:// | + | |
- | * gpaw-setups-0.8.7929 | + | |
- | * numpy-1.6.2 | + | |
- | + | ||
- | * MPI Version: mvapich2_intel_qlc-1.6 | + | |
- | * FFTW from INTEL MKL | + | |
- | * files: {{: | + | |
- | + | ||
- | + | ||
- | + | ||
- | + | ||
- | === Settings VSC-2 scientific linux 6.1 (old) === | + | |
- | Following Versions of GPAW and ASE were used: | + | |
- | * gpaw: svn checkout https:// | + | |
- | * ase: svn checkout https:// | + | |
- | * gpaw-setups-0.8.7929 | + | |
- | * numpy-1.6.2 | + | |
- | + | ||
- | * MPI Version: intel_mpi_intel64-4.0.3.008 | + | |
- | * FFTW from INTEL MKL | + | |
- | * files: {{: | + | |
- | + | ||
- | === Settings gpaw qmmm version === | + | |
- | As other versions, but with special config file: | + | |
- | * {{:doku:gpaw:config.qmmm.py}} | + | |
- | * use other config files for specific cluster / OS | + | |
- | + | ||
- | === 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 ' | + | |
- | * Execute install_gpaw_*.sh | + | |
- | < | + | |
- | bash install_gpaw_*.sh all | + | |
- | </ | + | |
- | * Testing of GPAW: | + | |
- | < | + | |
- | gpaw-python < | + | |
- | </ | + | |
- | + | ||
- | + | ||
- | For certain problems an assert statement in | + | |
- | < | + | |
- | ~/ | + | |
- | </ | + | |
- | + | ||
- | has to be commented out (approx line 239): | + | |
- | < | + | |
- | #assert abs(c_n.imag).max() < 1e-14 | + | |
- | </ | + | |
- | + | ||
- | === running gpaw jobs === | + | |
- | Job submission on VSC-1 (on VSC-2 also mpich8, mpich4 can be used instead) | + | |
- | < | + | |
- | #!/bin/sh | + | |
- | #$ -N Cl5_4x4x1 | + | |
- | #$ -pe mpich 256 | + | |
- | #$ -V | + | |
- | export OMP_NUM_THREADS=1 | + | |
- | NSLOTS_PER_NODE_AVAILABLE=8 | + | |
- | NSLOTS_PER_NODE_USED=4 | + | |
- | NSLOTS_REDUCED=`echo | + | |
- | + | ||
- | echo "starting run with $NSLOTS_REDUCED processes; $NSLOTS_PER_NODE_USED per node" | + | |
- | for i in `seq 1 $NSLOTS_PER_NODE_USED` | + | |
- | do | + | |
- | uniq $TMPDIR/ | + | |
- | done | + | |
- | + | ||
- | sort $TMPDIR/ | + | |
- | cat $TMPDIR/ | + | |
- | + | ||
- | mpirun -machinefile $TMPDIR/ | + | |
- | + | ||
- | </ | + | |
- | + | ||
- | Significant speed up is seen 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. | + |