Dear Prof. Peter Blaha,<br><br>Thank your for your reply!<br><br>Best,<br><br><div class="gmail_quote">On Wed, Nov 9, 2011 at 12:23 AM, Peter Blaha <span dir="ltr"><<a href="mailto:pblaha@theochem.tuwien.ac.at">pblaha@theochem.tuwien.ac.at</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex;">The problem is the following:<br>
<br>
When doing a scf calculation (run_lapw -p), the<br>
x lapw1 -p step will use the .machines file<br>
for parallelization (usually created on the fly by the PBS job),<br>
but at the same time it will create automatically a<br>
.processes file, which will be used for parallelization<br>
of the later steps of an scf (lapwso, lapw2).<br>
<br>
This scheme allows to modify the .machines file DURING a running<br>
scf calculation.<br>
<br>
Thus what you have to do is modify your PBS script and create instead of<br>
the .machines file the .processes file.<br>
<br>
Just examine an existing file, its content should be clear from that.<br>
<br>
Am 08.11.2011 12:07, schrieb Bin Shao:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div><div></div><div class="h5">
Dear all,<br>
<br>
I use PBS system to submit jobs to a cluster with the K-point parallelization mode. I intend to do a nos-scf calculation (soc) after a scf calculation. In the scf<br>
calculation, the .machines files were created by the script in the wien2k website. Then, I copy the directory including the old .machines files of scf to a new directory to<br>
do the nonscf calculation with the same submitting script, just replacing the scf wien2k command with nonscf one. When I submit the new job, the pbs system shows that the<br>
new job run in the new nodes, but it actually run in the old nodes.<br>
<br>
The following is the script to submit jobs:<br>
<br>
# setting up local SCRATCH<br>
#setenv SCRATCH /tmp/$PBS_JOBID<br>
<br>
# creating .machines<br>
cat $PBS_NODEFILE > .machines_current<br>
set aa=`wc .machines_current`<br>
echo '#' > .machines<br>
<br>
# run lapw1/2 using k-point parallel<br>
set i=1<br>
while ($i <= $aa[1])<br>
echo -n '1:' >> .machines<br>
# head -$i .machines_current |tail -1 >> .machines<br>
set nn = `head -$i .machines_current |tail -1`<br>
echo $nn >> .machines<br>
# echo -n '1:' >> .machines<br>
# echo $nn >> .machines<br>
# rsh $nn mkdir -p $SCRATCH<br>
@ i++<br>
end<br>
echo 'granularity:1' >>.machines<br>
echo 'extrafine:1' >>.machines<br>
<br>
# setup $delay and $sleepy<br>
setenv LAPW_DELAY 1<br>
setenv LAPW_SLEEPY 1<br>
<br>
# Wien2k command<br>
runsp_lapw -p -i 100 -ec 0.000001 -NI (scf)<br>
------------------------------<u></u>------------------------------<u></u>-----------------<br>
# Wien2k command<br>
x lapwso -up -p -c (nonscf)<br>
x lapw2 -up -p -so -c<br>
x lapw2 -dn -p -so -c<br>
<br>
So how can I submit the new job (nonscf) to a different nodes?<br>
<br>
Thank you in advanced. Any suggestion will be appreciated!<br>
<br>
Best regards,<br>
<br>
--<br>
Bin Shao, Ph.D. Candidate<br>
College of Information Technical Science, Nankai University<br>
94 Weijin Rd. Nankai Dist. Tianjin 300071, China<br></div></div>
Email: <a href="mailto:bshao@mail.nankai.edu.cn" target="_blank">bshao@mail.nankai.edu.cn</a> <mailto:<a href="mailto:bshao@mail.nankai.edu.cn" target="_blank">bshao@mail.nankai.edu.<u></u>cn</a>><br>
<br>
<br>
<br>
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</blockquote>
<br>
-- <br>
------------------------------<u></u>-----------<br>
Peter Blaha<br>
Inst. Materials Chemistry, TU Vienna<br>
Getreidemarkt 9, A-1060 Vienna, Austria<br>
Tel: <a href="tel:%2B43-1-5880115671" value="+4315880115671" target="_blank">+43-1-5880115671</a><br>
Fax: <a href="tel:%2B43-1-5880115698" value="+4315880115698" target="_blank">+43-1-5880115698</a><br>
email: <a href="mailto:pblaha@theochem.tuwien.ac.at" target="_blank">pblaha@theochem.tuwien.ac.at</a><br>
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</blockquote></div><br><br clear="all"><br>-- <br>Bin Shao, Ph.D. Candidate<br>College of Information Technical Science, Nankai University<br>94 Weijin Rd. Nankai Dist. Tianjin 300071, China<br>Email: <a href="mailto:bshao@mail.nankai.edu.cn" target="_blank">bshao@mail.nankai.edu.cn</a><br>
<br>