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<p class=MsoNormal><font size=2 face=Arial><span style='font-size:11.0pt;
font-family:Arial'>Dear Wien2k users, <o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:11.0pt;
font-family:Arial'>We have compiled Wien2k_11.1 with the following parallel
options <o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:11.0pt;
font-family:Arial'>setenv USE_REMOTE 1<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:11.0pt;
font-family:Arial'>setenv MPI_REMOTE 1<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:11.0pt;
font-family:Arial'>setenv WIEN_GRANULARITY 1<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:11.0pt;
font-family:Arial'>setenv WIEN_MPIRUN "mpirun -np _NP_ -machinefile _HOSTS_
_EXEC_"<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:11.0pt;
font-family:Arial'><o:p> </o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:11.0pt;
font-family:Arial'>The k-point parallel start up script is given by <o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:11.0pt;
font-family:Arial'>#!/bin/bash<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:11.0pt;
font-family:Arial'>#<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:11.0pt;
font-family:Arial'># RJ: Startup for Wien2k-kpoint parallel conforming with
Grid Engine<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:11.0pt;
font-family:Arial'># parallel environment interface<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:11.0pt;
font-family:Arial'>#<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:11.0pt;
font-family:Arial'># usage: start_kpoint.sh <pe_hostfile><o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:11.0pt;
font-family:Arial'>#<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:11.0pt;
font-family:Arial'>PeHostfile2Wien2kMachineFile()<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:11.0pt;
font-family:Arial'>{<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:11.0pt;
font-family:Arial'> cat $1 | while read line; do<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:11.0pt;
font-family:Arial'> # echo $line<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:11.0pt;
font-family:Arial'> host=`echo $line|cut -f1 -d" "|cut -f1 -d"."`<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:11.0pt;
font-family:Arial'> nslots=`echo $line|cut -f2 -d" "`<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:11.0pt;
font-family:Arial'> # add here code to map regular hostnames into IB
hostnames<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:11.0pt;
font-family:Arial'> for ((i=0; i < $nslots; i=i+1)); do<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:11.0pt;
font-family:Arial'> echo 1:i$host<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:11.0pt;
font-family:Arial'> done<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:11.0pt;
font-family:Arial'> done<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:11.0pt;
font-family:Arial'> echo 'granularity:1'<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:11.0pt;
font-family:Arial'> echo 'extrafine:1'<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:11.0pt;
font-family:Arial'>}<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:11.0pt;
font-family:Arial'><o:p> </o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:11.0pt;
font-family:Arial'># useful to control parameters passed to us<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:11.0pt;
font-family:Arial'>echo $*<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:11.0pt;
font-family:Arial'><o:p> </o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:11.0pt;
font-family:Arial'>SLEEPTIME=5<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:11.0pt;
font-family:Arial'>RETRIES=10<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:11.0pt;
font-family:Arial'><o:p> </o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:11.0pt;
font-family:Arial'>me=`basename $0`<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:11.0pt;
font-family:Arial'><o:p> </o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:11.0pt;
font-family:Arial'># test number of args<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:11.0pt;
font-family:Arial'>if [ $# -lt 1 ]; then<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:11.0pt;
font-family:Arial'> echo "$me: got wrong number of arguments" >&2<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:11.0pt;
font-family:Arial'> exit 1<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:11.0pt;
font-family:Arial'>fi<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:11.0pt;
font-family:Arial'><o:p> </o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:11.0pt;
font-family:Arial'># get arguments<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:11.0pt;
font-family:Arial'>pe_hostfile=$1<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:11.0pt;
font-family:Arial'><o:p> </o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:11.0pt;
font-family:Arial'># ensure pe_hostfile is readable<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:11.0pt;
font-family:Arial'>if [ ! -r $pe_hostfile ]; then<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:11.0pt;
font-family:Arial'> echo "$me: can't read $pe_hostfile" >&2<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:11.0pt;
font-family:Arial'> exit 1<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:11.0pt;
font-family:Arial'>fi<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:11.0pt;
font-family:Arial'># create machine-file<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:11.0pt;
font-family:Arial'># remove column with number of slots per queue<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:11.0pt;
font-family:Arial'># mpi does not support them in this form<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:11.0pt;
font-family:Arial'>machines="$TMPDIR/machines.wien2k-kpoint"<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:11.0pt;
font-family:Arial'>pwdir=`pwd`<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:11.0pt;
font-family:Arial'>PeHostfile2Wien2kMachineFile $pe_hostfile >> $machines<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:11.0pt;
font-family:Arial'>cat $machines<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:11.0pt;
font-family:Arial'>hostname<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:11.0pt;
font-family:Arial'>#scp $machines nx0:$pwdir/machines<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:11.0pt;
font-family:Arial'><o:p> </o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:11.0pt;
font-family:Arial'>The SGE job script is given by <o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:11.0pt;
font-family:Arial'>#!/bin/bash<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:11.0pt;
font-family:Arial'>#<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:11.0pt;
font-family:Arial'>#$ -cwd<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:11.0pt;
font-family:Arial'>#$ -j y<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:11.0pt;
font-family:Arial'>#$ -S /bin/bash<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:11.0pt;
font-family:Arial'>#$ -V<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:11.0pt;
font-family:Arial'>#$ -pe kpoint 2-<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:11.0pt;
font-family:Arial'><o:p> </o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:11.0pt;
font-family:Arial'># RJ: Script to run Wien2k-kpoint parallel job thru SGE<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:11.0pt;
font-family:Arial'># use kpoint PE<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:11.0pt;
font-family:Arial'><o:p> </o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:11.0pt;
font-family:Arial'>#echo "Hostname: "<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:11.0pt;
font-family:Arial'>#hostname<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:11.0pt;
font-family:Arial'><o:p> </o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:11.0pt;
font-family:Arial'>#echo "No. of Slots"<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:11.0pt;
font-family:Arial'>#echo $NSLOTS<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:11.0pt;
font-family:Arial'><o:p> </o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:11.0pt;
font-family:Arial'># machines.wien2k-kpoint would be created by<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:11.0pt;
font-family:Arial'># start_kpoint.sh PE script at $TMPDIR<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:11.0pt;
font-family:Arial'>echo "Wien2k Machine file $TMPDIR/machines"<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:11.0pt;
font-family:Arial'>mf=`cat $TMPDIR/machines.wien2k-kpoint`<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:11.0pt;
font-family:Arial'>echo $mf<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:11.0pt;
font-family:Arial'><o:p> </o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:11.0pt;
font-family:Arial'>cp $TMPDIR/machines.wien2k-kpoint .machines<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:11.0pt;
font-family:Arial'><o:p> </o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:11.0pt;
font-family:Arial'># RJ: command for kpoint parallel run<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:11.0pt;
font-family:Arial'>runsp_lapw -cc 0.0001 -ec 0.00001 -in1ef -i 200 –p<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:11.0pt;
font-family:Arial'>Now, we have 12 processors in 1 node. <o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:11.0pt;
font-family:Arial'>When we do <o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:11.0pt;
font-family:Arial'>Qsub –pe kpoint 12 kpoint.sh <o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:11.0pt;
font-family:Arial'>The script works <o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:11.0pt;
font-family:Arial'>But when we do <o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:11.0pt;
font-family:Arial'>Qsub –pe kpoint 16 kpoint.sh<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:11.0pt;
font-family:Arial'><o:p> </o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:11.0pt;
font-family:Arial'>It doesn’t<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:11.0pt;
font-family:Arial'><o:p> </o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:11.0pt;
font-family:Arial'>Can anybody suggest what the problem is and if any changes
in the job script is required <o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:11.0pt;
font-family:Arial'><o:p> </o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:11.0pt;
font-family:Arial'>Thanks in advance <o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:11.0pt;
font-family:Arial'>Suddhasattwa <o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:11.0pt;
font-family:Arial'><o:p> </o:p></span></font></p>
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