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<title>Re: [Wien] Problem in run_phonon script</title>
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<p class=MsoNormal><font size=2 face="Times New Roman"><span style='font-size:
11.0pt'>Dear <st1:GivenName w:st="on">Gerhard</st1:GivenName>, <o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 face="Times New Roman"><span style='font-size:
11.0pt'>I had to wait for my turn in the queuing job submission to check if the
same error comes <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'>My job file now looks like (as per your suggestion)<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 face="Times New Roman"><span style='font-size:
11.0pt'>#!/bin/csh -f<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'>set file=ABr2_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'>foreach i ( \<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 face="Times New Roman"><span style='font-size:
11.0pt'> 1 \<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 face="Times New Roman"><span style='font-size:
11.0pt'> 2 \<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 face="Times New Roman"><span style='font-size:
11.0pt'> 3 \<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 face="Times New Roman"><span style='font-size:
11.0pt'> 4 \<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 face="Times New Roman"><span style='font-size:
11.0pt'> 5 \<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 face="Times New Roman"><span style='font-size:
11.0pt'> 6 \<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 face="Times New Roman"><span style='font-size:
11.0pt'> 7 \<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 face="Times New Roman"><span style='font-size:
11.0pt'> 8 \<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 face="Times New Roman"><span style='font-size:
11.0pt'> 9 \<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 face="Times New Roman"><span style='font-size:
11.0pt'> 10 \<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 face="Times New Roman"><span style='font-size:
11.0pt'> 11 \<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 face="Times New Roman"><span style='font-size:
11.0pt'> 12 \<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 face="Times New Roman"><span style='font-size:
11.0pt'> 13 \<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 face="Times New Roman"><span style='font-size:
11.0pt'> 14 \<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 face="Times New Roman"><span style='font-size:
11.0pt'> 15 \<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 face="Times New Roman"><span style='font-size:
11.0pt'> 16 \<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 face="Times New Roman"><span style='font-size:
11.0pt'> 17 \<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 face="Times New Roman"><span style='font-size:
11.0pt'> 18 \<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'> cd case_$i<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 face="Times New Roman"><span style='font-size:
11.0pt'> echo running case_$i<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'># select other options if necessary<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 -I -i 200 -cc 0.0001 -fc 0.1 -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'># select other save-name if necessary<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 face="Times New Roman"><span style='font-size:
11.0pt'> save_lapw case_${i}_gga_rkm8.00_12000k<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 face="Times New Roman"><span style='font-size:
11.0pt'> cd ..<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 face="Times New Roman"><span style='font-size:
11.0pt'>end<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'>Surprisingly, the same error comes <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 pasting the script file which was generated <o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 face="Times New Roman"><span style='font-size:
11.0pt'>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'>1:ibnx79 1:ibnx79 1:ibnx79 1:ibnx79 1:ibnx107 1:ibnx107 1:ibnx107 1:ibnx107
1:ib<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 face="Times New Roman"><span style='font-size:
11.0pt'>nx107 1:ibnx107 1:ibnx107 1:ibnx107 1:ibnx63 1:ibnx63 1:ibnx63 1:ibnx20
granular<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 face="Times New Roman"><span style='font-size:
11.0pt'>ity:1 extrafine:1<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 face="Times New Roman"><span style='font-size:
11.0pt'>Too many (‘s.<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'>This time as well, it is “(“ rather than “/”<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'>Thanks wand waiting for your suggestions <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>
<div>
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face="Times New Roman"><span style='font-size:12.0pt'>
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<p class=MsoNormal><b><font size=2 face=Tahoma><span style='font-size:10.0pt;
font-family:Tahoma;font-weight:bold'>From:</span></font></b><font size=2
face=Tahoma><span style='font-size:10.0pt;font-family:Tahoma'>
wien-bounces@zeus.theochem.tuwien.ac.at
[mailto:wien-bounces@zeus.theochem.tuwien.ac.at] <b><span style='font-weight:
bold'>On Behalf Of </span></b><st2:PersonName w:st="on"><st1:GivenName w:st="on">Gerhard</st1:GivenName>
<st1:Sn w:st="on">Fecher</st1:Sn></st2:PersonName><br>
<b><span style='font-weight:bold'>Sent:</span></b> Monday, January 03, 2011
1:13 PM<br>
<b><span style='font-weight:bold'>To:</span></b> <st2:PersonName w:st="on"><st1:GivenName
w:st="on">A</st1:GivenName> <st1:middlename w:st="on">Mailing list</st1:middlename>
<st1:middlename w:st="on">for</st1:middlename> <st1:middlename w:st="on">WIEN2k</st1:middlename>
<st1:Sn w:st="on">users</st1:Sn></st2:PersonName><br>
<b><span style='font-weight:bold'>Subject:</span></b> Re: [<st1:Sn w:st="on">Wien</st1:Sn>]
Problem in run_phonon script</span></font><o:p></o:p></p>
</div>
<p class=MsoNormal><font size=3 face="Times New Roman"><span style='font-size:
12.0pt'><o:p> </o:p></span></font></p>
<p><font size=2 face="Times New Roman"><span style='font-size:10.0pt'>The error
message is just wrong it is Too many \'s and not Too many (‘s.<br>
The problem is in the run_phonon job file<br>
for some reason the template creates \\ instead of \<br>
<br>
replace:<br>
foreach i ( \\<br>
1 \\<br>
2 \\<br>
etc.<br>
<br>
by:<br>
foreach i ( \<br>
1 \<br>
2 \<br>
etc<br>
<br>
<br>
<br>
<br>
Ciao<br>
Gerhard<br>
<br>
====================================<br>
<st2:PersonName w:st="on"><st1:title w:st="on">Dr.</st1:title> <st1:GivenName
w:st="on">Gerhard</st1:GivenName> <st1:middlename w:st="on">H.</st1:middlename>
<st1:Sn w:st="on">Fecher</st1:Sn></st2:PersonName><br>
Institut of Inorganic and Analytical Chemistry<br>
<st2:PersonName w:st="on"><st1:GivenName w:st="on">Johannes</st1:GivenName> <st1:Sn
w:st="on">Gutenberg</st1:Sn></st2:PersonName> - University<br>
55099 <st2:City w:st="on"><st2:place w:st="on">Mainz</st2:place></st2:City><br>
________________________________________<br>
Von: wien-bounces@zeus.theochem.tuwien.ac.at
[wien-bounces@zeus.theochem.tuwien.ac.at]&quot; im Auftrag von &quot;<st2:PersonName
w:st="on"><st1:GivenName w:st="on">Ghosh</st1:GivenName> <st1:Sn w:st="on">SUDDHASATTWA</st1:Sn></st2:PersonName>
[ssghosh@igcar.gov.in]<br>
Gesendet: Montag, 3. Januar 2011 08:29<br>
Bis: 'A Mailing list for WIEN2k users'<br>
Betreff: [<st1:Sn w:st="on">Wien</st1:Sn>] Problem in run_phonon script<br>
<br>
Dear <st2:PersonName w:st="on"><st1:title w:st="on">Dr.</st1:title> <st1:Sn
w:st="on">Blaha</st1:Sn></st2:PersonName>,<br>
I am running k point parallel in Wien2k using the following job script<br>
<br>
#!/bin/bash<br>
#<br>
#$ -cwd<br>
#$ -j y<br>
#$ -S /bin/bash<br>
#$ -V<br>
<br>
# RJ: Script to run Wien2k-kpoint parallel job thru SGE<br>
# Use kpoint PE<br>
<br>
#hc=`cat $PE_HOSTFILE`<br>
#echo "-------------------------"<br>
#echo "Contents of $PE_HOSTFILE :"<br>
#echo $hc<br>
#echo "-------------------------"<br>
#echo "Hostname: "<br>
#hostname<br>
#echo "No. of Slots"<br>
#echo $NSLOTS<br>
<br>
echo "Wien2k Machine file TMPDIR/machines"<br>
mf=`cat $TMPDIR/machines.wien2k-kpoint`<br>
echo $mf<br>
<br>
cp $TMPDIR/machines.wien2k-kpoint .machines<br>
<br>
# RJ: command for kpoint parallel run<br>
run_phonon<br>
<br>
<br>
The script works very well (some 50-80 jobs have been completed) when I use<br>
#!/bin/bash<br>
#<br>
#$ -cwd<br>
#$ -j y<br>
#$ -S /bin/bash<br>
#$ -V<br>
<br>
# RJ: Script to run Wien2k-kpoint parallel job thru SGE<br>
# Use kpoint PE<br>
<br>
#hc=`cat $PE_HOSTFILE`<br>
#echo "-------------------------"<br>
#echo "Contents of $PE_HOSTFILE :"<br>
#echo $hc<br>
#echo "-------------------------"<br>
#echo "Hostname: "<br>
#hostname<br>
#echo "No. of Slots"<br>
#echo $NSLOTS<br>
<br>
echo "Wien2k Machine file TMPDIR/machines"<br>
mf=`cat $TMPDIR/machines.wien2k-kpoint`<br>
echo $mf<br>
<br>
cp $TMPDIR/machines.wien2k-kpoint .machines<br>
<br>
# RJ: command for kpoint parallel run<br>
Run_lapw –cc 0.0001 –ec 0.0001 –in1ef –p<br>
<br>
<br>
The job is submitted by<br>
qsub –pe kpoint 6 kpoint.sh<br>
Where kpoint.sh is the job script file<br>
<br>
When I replace wih run_phonon, the job is submitted but suddenly
disappears!!!!!!<br>
<br>
<br>
I checked the script files and noted the following<br>
<br>
Wien2k machine file TMPDIR/machines<br>
1:ibnx79 1:ibnx79 1:ibnx79 1:ibnx79 1:ibnx79 1:ibnx79 1:ibnx79 granularity:1
extrafine:1<br>
Too many (‘s.<br>
<br>
<br>
Can any body tell me what is the issue here?<br>
There are no issues with the script file as I have been using this for quite
some time<br>
<br>
Suddhasattwa<br>
<br>
<br>
<br>
<br>
_______________________________________________<br>
<st1:Sn w:st="on">Wien</st1:Sn> mailing list<br>
Wien@zeus.theochem.tuwien.ac.at<br>
<a href="http://zeus.theochem.tuwien.ac.at/mailman/listinfo/wien">http://zeus.theochem.tuwien.ac.at/mailman/listinfo/wien</a></span></font>
<o:p></o:p></p>
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<p class=avgcert color="#000000"><font size=3 face="Times New Roman"><span
style='font-size:12.0pt'>No virus found in this message.<br>
Checked by AVG - <a href="http://www.avg.com">www.avg.com</a><br>
Version: 10.0.1170 / Virus Database: 1435/3355 - Release Date: 01/02/11<o:p></o:p></span></font></p>
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