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<p class=MsoNormal><font size=2 face="Times New Roman"><span style='font-size:
11.0pt'>Dear <st2:PersonName w:st="on"><st1:title w:st="on">Dr.</st1:title> <st1:Sn
w:st="on">Blaha</st1:Sn></st2:PersonName>, <o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 face="Times New Roman"><span style='font-size:
11.0pt'>I am running k point parallel in Wien2k using the following job script <o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 face="Times New Roman"><span style='font-size:
11.0pt'><o:p> </o:p></span></font></p>
<p class=MsoNormal><font size=2 face="Times New Roman"><span style='font-size:
11.0pt'>#!/bin/bash<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 face="Times New Roman"><span style='font-size:
11.0pt'>#<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 face="Times New Roman"><span style='font-size:
11.0pt'>#$ -cwd<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 face="Times New Roman"><span style='font-size:
11.0pt'>#$ -j y<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 face="Times New Roman"><span style='font-size:
11.0pt'>#$ -S /bin/bash<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 face="Times New Roman"><span style='font-size:
11.0pt'>#$ -V<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 face="Times New Roman"><span style='font-size:
11.0pt'><o:p> </o:p></span></font></p>
<p class=MsoNormal><font size=2 face="Times New Roman"><span style='font-size:
11.0pt'># RJ: Script to run Wien2k-kpoint parallel job thru SGE<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 face="Times New Roman"><span style='font-size:
11.0pt'># Use kpoint PE<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 face="Times New Roman"><span style='font-size:
11.0pt'><o:p> </o:p></span></font></p>
<p class=MsoNormal><font size=2 face="Times New Roman"><span style='font-size:
11.0pt'>#hc=`cat $PE_HOSTFILE`<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 face="Times New Roman"><span style='font-size:
11.0pt'>#echo "-------------------------"<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 face="Times New Roman"><span style='font-size:
11.0pt'>#echo "Contents of $PE_HOSTFILE :"<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 face="Times New Roman"><span style='font-size:
11.0pt'>#echo $hc<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 face="Times New Roman"><span style='font-size:
11.0pt'>#echo "-------------------------"<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 face="Times New Roman"><span style='font-size:
11.0pt'>#echo "Hostname: "<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 face="Times New Roman"><span style='font-size:
11.0pt'>#hostname<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 face="Times New Roman"><span style='font-size:
11.0pt'>#echo "No. of Slots"<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 face="Times New Roman"><span style='font-size:
11.0pt'>#echo $NSLOTS<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 face="Times New Roman"><span style='font-size:
11.0pt'><o:p> </o:p></span></font></p>
<p class=MsoNormal><font size=2 face="Times New Roman"><span style='font-size:
11.0pt'>echo "Wien2k Machine file TMPDIR/machines"<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 face="Times New Roman"><span style='font-size:
11.0pt'>mf=`cat $TMPDIR/machines.wien2k-kpoint`<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 face="Times New Roman"><span style='font-size:
11.0pt'>echo $mf<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 face="Times New Roman"><span style='font-size:
11.0pt'><o:p> </o:p></span></font></p>
<p class=MsoNormal><font size=2 face="Times New Roman"><span style='font-size:
11.0pt'>cp $TMPDIR/machines.wien2k-kpoint .machines<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 face="Times New Roman"><span style='font-size:
11.0pt'><o:p> </o:p></span></font></p>
<p class=MsoNormal><font size=2 face="Times New Roman"><span style='font-size:
11.0pt'># RJ: command for kpoint parallel run<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 face="Times New Roman"><span style='font-size:
11.0pt'>run_phonon<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 face="Times New Roman"><span style='font-size:
11.0pt'><o:p> </o:p></span></font></p>
<p class=MsoNormal><font size=2 face="Times New Roman"><span style='font-size:
11.0pt'><o:p> </o:p></span></font></p>
<p class=MsoNormal><font size=2 face="Times New Roman"><span style='font-size:
11.0pt'>The script works very well (some 50-80 jobs have been completed) when I
use <o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 face="Times New Roman"><span style='font-size:
11.0pt'>#!/bin/bash<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 face="Times New Roman"><span style='font-size:
11.0pt'>#<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 face="Times New Roman"><span style='font-size:
11.0pt'>#$ -cwd<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 face="Times New Roman"><span style='font-size:
11.0pt'>#$ -j y<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 face="Times New Roman"><span style='font-size:
11.0pt'>#$ -S /bin/bash<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 face="Times New Roman"><span style='font-size:
11.0pt'>#$ -V<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 face="Times New Roman"><span style='font-size:
11.0pt'><o:p> </o:p></span></font></p>
<p class=MsoNormal><font size=2 face="Times New Roman"><span style='font-size:
11.0pt'># RJ: Script to run Wien2k-kpoint parallel job thru SGE<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 face="Times New Roman"><span style='font-size:
11.0pt'># Use kpoint PE<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 face="Times New Roman"><span style='font-size:
11.0pt'><o:p> </o:p></span></font></p>
<p class=MsoNormal><font size=2 face="Times New Roman"><span style='font-size:
11.0pt'>#hc=`cat $PE_HOSTFILE`<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 face="Times New Roman"><span style='font-size:
11.0pt'>#echo "-------------------------"<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 face="Times New Roman"><span style='font-size:
11.0pt'>#echo "Contents of $PE_HOSTFILE :"<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 face="Times New Roman"><span style='font-size:
11.0pt'>#echo $hc<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 face="Times New Roman"><span style='font-size:
11.0pt'>#echo "-------------------------"<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 face="Times New Roman"><span style='font-size:
11.0pt'>#echo "Hostname: "<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 face="Times New Roman"><span style='font-size:
11.0pt'>#hostname<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 face="Times New Roman"><span style='font-size:
11.0pt'>#echo "No. of Slots"<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 face="Times New Roman"><span style='font-size:
11.0pt'>#echo $NSLOTS<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 face="Times New Roman"><span style='font-size:
11.0pt'><o:p> </o:p></span></font></p>
<p class=MsoNormal><font size=2 face="Times New Roman"><span style='font-size:
11.0pt'>echo "Wien2k Machine file TMPDIR/machines"<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 face="Times New Roman"><span style='font-size:
11.0pt'>mf=`cat $TMPDIR/machines.wien2k-kpoint`<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 face="Times New Roman"><span style='font-size:
11.0pt'>echo $mf<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 face="Times New Roman"><span style='font-size:
11.0pt'><o:p> </o:p></span></font></p>
<p class=MsoNormal><font size=2 face="Times New Roman"><span style='font-size:
11.0pt'>cp $TMPDIR/machines.wien2k-kpoint .machines<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 face="Times New Roman"><span style='font-size:
11.0pt'><o:p> </o:p></span></font></p>
<p class=MsoNormal><font size=2 face="Times New Roman"><span style='font-size:
11.0pt'># RJ: command for kpoint parallel run<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 face="Times New Roman"><span style='font-size:
11.0pt'>Run_lapw –cc 0.0001 –ec 0.0001 –in1ef –p <o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 face="Times New Roman"><span style='font-size:
11.0pt'><o:p> </o:p></span></font></p>
<p class=MsoNormal><font size=2 face="Times New Roman"><span style='font-size:
11.0pt'><o:p> </o:p></span></font></p>
<p class=MsoNormal><font size=2 face="Times New Roman"><span style='font-size:
11.0pt'>The job is submitted by <o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 face="Times New Roman"><span style='font-size:
11.0pt'>qsub –pe kpoint 6 kpoint.sh <o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 face="Times New Roman"><span style='font-size:
11.0pt'>Where kpoint.sh is the job script file <o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 face="Times New Roman"><span style='font-size:
11.0pt'><o:p> </o:p></span></font></p>
<p class=MsoNormal><font size=2 face="Times New Roman"><span style='font-size:
11.0pt'>When I replace wih run_phonon, the job is submitted but <b><span
style='font-weight:bold'>suddenly disappears!!!!!!</span></b><o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 face="Times New Roman"><span style='font-size:
11.0pt'><o:p> </o:p></span></font></p>
<p class=MsoNormal><font size=2 face="Times New Roman"><span style='font-size:
11.0pt'><o:p> </o:p></span></font></p>
<p class=MsoNormal><font size=2 face="Times New Roman"><span style='font-size:
11.0pt'>I checked the script files and noted the following <o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 face="Times New Roman"><span style='font-size:
11.0pt'><o:p> </o:p></span></font></p>
<p class=MsoNormal><b><font size=2 face="Times New Roman"><span
style='font-size:11.0pt;font-weight:bold'>Wien2k machine file TMPDIR/machines<o:p></o:p></span></font></b></p>
<p class=MsoNormal><b><font size=2 face="Times New Roman"><span
style='font-size:11.0pt;font-weight:bold'>1:ibnx79 1:ibnx79 1:ibnx79 1:ibnx79 1:ibnx79
1:ibnx79 1:ibnx79 granularity:1 extrafine:1 <o:p></o:p></span></font></b></p>
<p class=MsoNormal><b><font size=2 face="Times New Roman"><span
style='font-size:11.0pt;font-weight:bold'>Too many (‘s.<o:p></o:p></span></font></b></p>
<p class=MsoNormal><b><font size=2 face="Times New Roman"><span
style='font-size:11.0pt;font-weight:bold'><o:p> </o:p></span></font></b></p>
<p class=MsoNormal><font size=2 face="Times New Roman"><span style='font-size:
11.0pt'><o:p> </o:p></span></font></p>
<p class=MsoNormal><font size=2 face="Times New Roman"><span style='font-size:
11.0pt'>Can any body tell me what is the issue here?<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 face="Times New Roman"><span style='font-size:
11.0pt'>There are no issues with the script file as I have been using this for
quite some time <o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 face="Times New Roman"><span style='font-size:
11.0pt'><o:p> </o:p></span></font></p>
<p class=MsoNormal><font size=2 face="Times New Roman"><span style='font-size:
11.0pt'>Suddhasattwa <o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 face="Times New Roman"><span style='font-size:
11.0pt'><o:p> </o:p></span></font></p>
<p class=MsoNormal><font size=2 face="Times New Roman"><span style='font-size:
11.0pt'><o:p> </o:p></span></font></p>
<p class=MsoNormal><font size=2 face="Times New Roman"><span style='font-size:
11.0pt'><o:p> </o:p></span></font></p>
<p class=MsoNormal><font size=2 face="Times New Roman"><span style='font-size:
11.0pt'><o:p> </o:p></span></font></p>
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