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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 Dr.Blaha, <o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 face="Times New Roman"><span style='font-size:
11.0pt'>Thank you very much for the kind reply. <o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 face="Times New Roman"><span style='font-size:
11.0pt'>However, I rewrote the phonon script again in the vi editor and it
worked !!!!!!<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 face="Times New Roman"><span style='font-size:
11.0pt'>So the problem is solved….<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 face="Times New Roman"><span style='font-size:
11.0pt'>But<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 face="Times New Roman"><span style='font-size:
11.0pt'>Another problem came….<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 face="Times New Roman"><span style='font-size:
11.0pt'>This is the output I got ( I am pasting a part of it)<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'>> stop error<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 face="Times New Roman"><span style='font-size:
11.0pt'>Fallback to compatibility mode with "old" save_lapw<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 face="Times New Roman"><span style='font-size:
11.0pt'>broyden files deleted, clm*, dmat*, vorb*, vresp*, eece*, scf and
struct files s<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 face="Times New Roman"><span style='font-size:
11.0pt'>aved under case_16_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'>running case_17<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 face="Times New Roman"><span style='font-size:
11.0pt'>forrtl: severe (64): input conversion error, unit 8, file /group5/cg/sghosh/<st1:Sn
w:st="on">WIEN</st1:Sn><o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 face="Times New Roman"><span style='font-size:
11.0pt'>2k/lapw/phonon/UZr2_phonon/case_17/case_17.clmsum<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 face="Times New Roman"><span style='font-size:
11.0pt'>Image PC Routine Line
Source<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'>lapw0 00000000005159B2 Unknown Unknown
Unknown<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 face="Times New Roman"><span style='font-size:
11.0pt'>lapw0 0000000000514944 Unknown Unknown
Unknown<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 face="Times New Roman"><span style='font-size:
11.0pt'>lapw0 00000000004CBE96 Unknown Unknown
Unknown<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 face="Times New Roman"><span style='font-size:
11.0pt'>lapw0 0000000000495FEF Unknown Unknown
Unknown<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 face="Times New Roman"><span style='font-size:
11.0pt'>lapw0 00000000004958CC Unknown Unknown
Unknown<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 face="Times New Roman"><span style='font-size:
11.0pt'>lapw0 00000000004AFECE Unknown Unknown
Unknown<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 face="Times New Roman"><span style='font-size:
11.0pt'>lapw0 00000000004AD519 Unknown Unknown
Unknown<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 face="Times New Roman"><span style='font-size:
11.0pt'>lapw0 0000000000432661 MAIN__ 428
lapw0.F<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 face="Times New Roman"><span style='font-size:
11.0pt'>lapw0 0000000000403782 Unknown Unknown
Unknown<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 face="Times New Roman"><span style='font-size:
11.0pt'>libc.so.6 000000362E01D8A4 Unknown Unknown
Unknown<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 face="Times New Roman"><span style='font-size:
11.0pt'>lapw0 00000000004036A9 Unknown Unknown
Unknown<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'>> stop error<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 face="Times New Roman"><span style='font-size:
11.0pt'>Fallback to compatibility mode with "old" save_lapw<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 face="Times New Roman"><span style='font-size:
11.0pt'>broyden files deleted, clm*, dmat*, vorb*, vresp*, eece*, scf and
struct files s<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 face="Times New Roman"><span style='font-size:
11.0pt'>aved under case_17_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'>running case_18<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 face="Times New Roman"><span style='font-size:
11.0pt'>forrtl: severe (64): input conversion error, unit 8, file /group5/cg/sghosh/<st1:Sn
w:st="on">WIEN</st1:Sn><o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 face="Times New Roman"><span style='font-size:
11.0pt'>2k/lapw/phonon/UZr2_phonon/case_18/case_18.clmsum<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'>Can you please tell me what the issue is?<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 face="Times New Roman"><span style='font-size:
11.0pt'>I have optimized this case before a number of times before..i never
came across this problem.<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>
<div>
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face="Times New Roman"><span style='font-size:12.0pt'>
<hr size=2 width="100%" align=center tabindex=-1>
</span></font></div>
<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">Peter</st1:GivenName>
<st1:Sn w:st="on">Blaha</st1:Sn></st2:PersonName><br>
<b><span style='font-weight:bold'>Sent:</span></b> Tuesday, January 04, 2011
12:25 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'>You are
listing a file named "machines", it should be
".machines"<br>
And I don't think your .machines file is correct (except when the<br>
missing linebreaks are only in the email; each 1:ibnxXX should be in an extra
line!<br>
<br>
Change the foreach line to:<br>
<br>
foreach ( 1 2 3 4 .. 18 )<br>
> foreach i ( \<br>
><br>
> 1 \<br>
><br>
> 2 \<br>
><br>
> 3 \<br>
><br>
> 4 \<br>
><br>
> 5 \<br>
><br>
> 6 \<br>
><br>
> 7 \<br>
><br>
> 8 \<br>
><br>
> 9 \<br>
><br>
> 10 \<br>
><br>
> 11 \<br>
><br>
> 12 \<br>
><br>
> 13 \<br>
><br>
> 14 \<br>
><br>
> 15 \<br>
><br>
> 16 \<br>
><br>
> 17 \<br>
><br>
> 18 \<br>
><br>
> )<br>
><br>
> cd case_$i<br>
><br>
> echo running case_$i<br>
><br>
> #<br>
><br>
> # select other options if necessary<br>
><br>
> run_lapw -I -i 200 -cc 0.0001 -fc 0.1 -p<br>
><br>
> #<br>
><br>
> # select other save-name if necessary<br>
><br>
> save_lapw case_${i}_gga_rkm8.00_12000k<br>
><br>
> cd ..<br>
><br>
> end<br>
><br>
> Surprisingly, the same error comes<br>
><br>
> I am pasting the script file which was generated<br>
><br>
> Wien2k Machine file TMPDIR/machines<br>
><br>
> 1:ibnx79 1:ibnx79 1:ibnx79 1:ibnx79 1:ibnx107 1:ibnx107 1:ibnx107
1:ibnx107 1:ib<br>
><br>
> nx107 1:ibnx107 1:ibnx107 1:ibnx107 1:ibnx63 1:ibnx63 1:ibnx63 1:ibnx20
granular<br>
><br>
> ity:1 extrafine:1<br>
><br>
> Too many (‘s.<br>
><br>
> This time as well, it is “(“ rather than “/”<br>
><br>
> Thanks wand waiting for your suggestions<br>
><br>
> Suddhasattwa<br>
><br>
>
----------------------------------------------------------------------------------------------------------------------------------------------------------------------------<br>
><br>
> *From:*wien-bounces@zeus.theochem.tuwien.ac.at [<a
href="mailto:wien-bounces@zeus.theochem.tuwien.ac.at">mailto:wien-bounces@zeus.theochem.tuwien.ac.at</a>]
*On Behalf Of *<st2:PersonName w:st="on"><st1:GivenName w:st="on">Gerhard</st1:GivenName>
<st1:Sn w:st="on">Fecher</st1:Sn></st2:PersonName><br>
> *Sent:* Monday, January 03, 2011 1:13 PM<br>
> *To:* A Mailing list for WIEN2k users<br>
> *Subject:* Re: [<st1:Sn w:st="on">Wien</st1:Sn>] Problem in run_phonon
script<br>
><br>
> 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">Dr. <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 Dr. Blaha,<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><br>
><br>
>
----------------------------------------------------------------------------------------------------------------------------------------------------------------------------<br>
><br>
> No virus found in this message.<br>
> Checked by AVG - www.avg.com <<a href="http://www.avg.com">http://www.avg.com</a>><br>
> Version: 10.0.1170 / Virus Database: 1435/3355 - Release Date: 01/02/11<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><br>
<br>
--<br>
-----------------------------------------<br>
<st2:PersonName w:st="on"><st1:GivenName w:st="on">Peter</st1:GivenName> <st1:Sn
w:st="on">Blaha</st1:Sn></st2:PersonName><br>
Inst. Materials Chemistry, TU Vienna<br>
Getreidemarkt 9, A-1060 <st2:place w:st="on"><st2:City w:st="on">Vienna</st2:City>,
<st2:country-region w:st="on">Austria</st2:country-region></st2:place><br>
Tel: +43-1-5880115671<br>
Fax: +43-1-5880115698<br>
email: pblaha@theochem.tuwien.ac.at<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>
<div class=MsoNormal align=center style='text-align:center'><font size=3
face="Times New Roman"><span style='font-size:12.0pt'>
<hr size=1 width="100%" noshade color="#aca899" align=center>
</span></font></div>
<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: 1435/3357 - Release Date: 01/03/11<o:p></o:p></span></font></p>
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