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--- doku:gpaw [2014/04/09 13:24] – markus
+++ doku:gpaw [2014/08/27 11:26] – jz
@@ Line 1: / Line 1: @@
-===== GPAW =====
+a:2:{s:7:"current";a:9:{s:4:"date";a:2:{s:7:"created";i:1396952157;s:8:"modified";i:1397050095;}s:4:"user";s:0:"";s:7:"creator";s:0:"";s:11:"last_change";a:7:{s:4:"date";i:1397050095;s:2:"ip";s:14:"128.131.35.162";s:4:"type";s:1:"E";s:2:"id";s:9:"doku:gpaw";s:4:"user";s:6:"markus";s:3:"sum";s:0:"";s:5:"extra";s:0:"";}s:11:"contributor";a:1:{s:6:"markus";s:13:"Stoehr Markus";}s:5:"title";s:4:"GPAW";s:11:"description";a:2:{s:15:"tableofcontents";a:1:{i:0;a:4:{s:3:"hid";s:4:"gpaw";s:5:"title";s:4:"GPAW";s:4:"type";s:2:"ul";s:5:"level";i:2;}}s:8:"abstract";s:264:"GPAW
-=== 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: 11364 ; ase: 3440
-  * gpaw-setups-0.9.9672
-  * numpy-1.6.2
-  * MPI Version: impi-4.1.x
+	*  gpaw (?): 11253 ; ase (?): 3547
-  * FFTW from INTEL MKL
+	*  gpaw 0.10.0: 11364 ; ase 3.8.1: 3440
-  * files: {{:doku:gpaw:sl65:site.cfg.numpy.sl65_icc_mkl.txt}}, {{:doku:gpaw:sl65:install_gpaw_vsc_sl65.sh}},  {{:doku:gpaw:sl65:customize_sl65_icc_mkl.py}}, {{:doku:gpaw:sl65:config.py}}
+	*  gpaw-setups-0.9.9672
+	*  numpy-1.6.2";}s:8:"relation";a:2:{s:5:"media";a:14:{s:46:"doku:gpaw:sl65:site.cfg.numpy.sl65_icc_mkl.txt";b:1;s:39:"doku:gpaw:sl65:install_gpaw_vsc_sl65.sh";b:1;s:40:"doku:gpaw:sl65:customize_sl65_icc_mkl.py";b:1;s:24:"doku:gpaw:sl65:config.py";b:1;s:41:"doku:gpaw:site.cfg.numpy.sl64_icc_mkl.txt";b:1;s:34:"doku:gpaw:install_gpaw_vsc_sl64.sh";b:1;s:35:"doku:gpaw:customize_sl64_icc_mkl.py";b:1;s:19:"doku:gpaw:config.py";b:1;s:33:"doku:gpaw:site.cfg.numpy.vsc1.txt";b:1;s:31:"doku:gpaw:install_gpaw_vsc_x.sh";b:1;s:31:"doku:gpaw:customize_vsc1_icc.py";b:1;s:33:"doku:gpaw:site.cfg.numpy.vsc2.txt";b:1;s:31:"doku:gpaw:customize_vsc2_icc.py";b:1;s:24:"doku:gpaw:config.qmmm.py";b:1;}s:10:"firstimage";s:0:"";}s:8:"internal";a:2:{s:5:"cache";b:1;s:3:"toc";b:1;}}s:10:"persistent";a:5:{s:4:"date";a:2:{s:7:"created";i:1396952157;s:8:"modified";i:1397050095;}s:4:"user";s:0:"";s:7:"creator";s:0:"";s:11:"last_change";a:7:{s:4:"date";i:1397050095;s:2:"ip";s:14:"128.131.35.162";s:4:"type";s:1:"E"
-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:
-  * gpaw: svn checkout https://svn.fysik.dtu.dk/projects/gpaw/trunk gpaw -r 10428
-  * ase: svn checkout https://svn.fysik.dtu.dk/projects/ase/trunk ase -r 2801
-  * gpaw-setups-0.8.7929
-  * numpy-1.6.2
-  * MPI Version: impi-4.1.0.024
-  * FFTW from INTEL MKL
-  * files: {{:doku:gpaw:site.cfg.numpy.sl64_icc_mkl.txt}}, {{:doku:gpaw:install_gpaw_vsc_sl64.sh}},  {{:doku:gpaw:customize_sl64_icc_mkl.py}}, {{:doku:gpaw:config.py}}
-  * 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:
-  * gpaw: svn checkout https://svn.fysik.dtu.dk/projects/gpaw/trunk gpaw -r 9616
-  * ase: svn checkout https://svn.fysik.dtu.dk/projects/ase/trunk ase -r 2801
-  * gpaw-setups-0.8.7929
-  * numpy-1.6.2
-  * MPI Version: mvapich2_intel_qlc-1.6 ; qlogic MPI did not work
-  * FFTW from INTEL MKL
-  * files: {{:doku:gpaw:site.cfg.numpy.vsc1.txt}}, {{:doku:gpaw:install_gpaw_vsc_x.sh}}, {{:doku:gpaw:customize_vsc1_icc.py}}, {{:doku:gpaw:config.py}}
-=== Settings VSC-2 scientific linux 6.1 (old) ===
-Following Versions of GPAW and ASE were used:
-  * gpaw: svn checkout https://svn.fysik.dtu.dk/projects/gpaw/trunk gpaw -r 9616
-  * ase: svn checkout https://svn.fysik.dtu.dk/projects/ase/trunk ase -r 2801
-  * gpaw-setups-0.8.7929
-  * numpy-1.6.2
-  * MPI Version: intel_mpi_intel64-4.0.3.008
-  * FFTW from INTEL MKL
-  * files: {{:doku:gpaw:site.cfg.numpy.vsc2.txt}}, {{:doku:gpaw:install_gpaw_vsc_x.sh}}, {{:doku:gpaw:customize_vsc2_icc.py}}, {{:doku:gpaw:config.py}}
-=== 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 'install_gpaw_*.sh'.
-  * Execute install_gpaw_*.sh
-   <code>
-   bash install_gpaw_*.sh all
-   </code>
-  * Testing of GPAW:
-<code>
-gpaw-python <DIR_TO_GPAW_INST_BIN>/gpaw-test
-</code>
-For certain problems an assert statement in
-<code>
-~/gpaw_inst_latest/lib64/python2.6/site-packages/gpaw/wavefunctions/lcao.py
-</code>
-has to be commented out (approx line 239):
-<code>
-#assert abs(c_n.imag).max() < 1e-14
-</code>
-=== running gpaw jobs ===
-Job submission on VSC-1 (on VSC-2 also mpich8, mpich4 can be used instead)
-<code>
-#!/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 "$NSLOTS / $NSLOTS_PER_NODE_AVAILABLE * $NSLOTS_PER_NODE_USED" | bc  `
-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/machines >> $TMPDIR/tmp
-done
-sort $TMPDIR/tmp  > $TMPDIR/myhosts
-cat $TMPDIR/myhosts
-mpirun -machinefile $TMPDIR/myhosts -np $NSLOTS_REDUCED gpaw-python static.py --domain=None --band=1 --sl_default=4,4,64
-</code>
-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.