Dear Prof. Peter Blaha, Thank your for your reply!
Best, On Wed, Nov 9, 2011 at 12:23 AM, Peter Blaha <pblaha at theochem.tuwien.ac.at>wrote: > The problem is the following: > > When doing a scf calculation (run_lapw -p), the > x lapw1 -p step will use the .machines file > for parallelization (usually created on the fly by the PBS job), > but at the same time it will create automatically a > .processes file, which will be used for parallelization > of the later steps of an scf (lapwso, lapw2). > > This scheme allows to modify the .machines file DURING a running > scf calculation. > > Thus what you have to do is modify your PBS script and create instead of > the .machines file the .processes file. > > Just examine an existing file, its content should be clear from that. > > Am 08.11.2011 12:07, schrieb Bin Shao: > >> Dear all, >> >> 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 >> 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 >> 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 >> new job run in the new nodes, but it actually run in the old nodes. >> >> The following is the script to submit jobs: >> >> # setting up local SCRATCH >> #setenv SCRATCH /tmp/$PBS_JOBID >> >> # creating .machines >> cat $PBS_NODEFILE > .machines_current >> set aa=`wc .machines_current` >> echo '#' > .machines >> >> # run lapw1/2 using k-point parallel >> set i=1 >> while ($i <= $aa[1]) >> echo -n '1:' >> .machines >> # head -$i .machines_current |tail -1 >> .machines >> set nn = `head -$i .machines_current |tail -1` >> echo $nn >> .machines >> # echo -n '1:' >> .machines >> # echo $nn >> .machines >> # rsh $nn mkdir -p $SCRATCH >> @ i++ >> end >> echo 'granularity:1' >>.machines >> echo 'extrafine:1' >>.machines >> >> # setup $delay and $sleepy >> setenv LAPW_DELAY 1 >> setenv LAPW_SLEEPY 1 >> >> # Wien2k command >> runsp_lapw -p -i 100 -ec 0.000001 -NI (scf) >> ------------------------------**------------------------------** >> ----------------- >> # Wien2k command >> x lapwso -up -p -c (nonscf) >> x lapw2 -up -p -so -c >> x lapw2 -dn -p -so -c >> >> So how can I submit the new job (nonscf) to a different nodes? >> >> Thank you in advanced. Any suggestion will be appreciated! >> >> Best regards, >> >> -- >> Bin Shao, Ph.D. Candidate >> College of Information Technical Science, Nankai University >> 94 Weijin Rd. Nankai Dist. Tianjin 300071, China >> Email: bshao at mail.nankai.edu.cn <mailto:bshao at >> mail.nankai.edu.**cn<bshao at mail.nankai.edu.cn> >> > >> >> >> >> ______________________________**_________________ >> Wien mailing list >> Wien at zeus.theochem.tuwien.ac.**at <Wien at zeus.theochem.tuwien.ac.at> >> http://zeus.theochem.tuwien.**ac.at/mailman/listinfo/wien<http://zeus.theochem.tuwien.ac.at/mailman/listinfo/wien> >> > > -- > ------------------------------**----------- > Peter Blaha > Inst. Materials Chemistry, TU Vienna > Getreidemarkt 9, A-1060 Vienna, Austria > Tel: +43-1-5880115671 > Fax: +43-1-5880115698 > email: pblaha at theochem.tuwien.ac.at > ------------------------------**----------- > ______________________________**_________________ > Wien mailing list > Wien at zeus.theochem.tuwien.ac.**at <Wien at zeus.theochem.tuwien.ac.at> > http://zeus.theochem.tuwien.**ac.at/mailman/listinfo/wien<http://zeus.theochem.tuwien.ac.at/mailman/listinfo/wien> > -- Bin Shao, Ph.D. Candidate College of Information Technical Science, Nankai University 94 Weijin Rd. Nankai Dist. Tianjin 300071, China Email: bshao at mail.nankai.edu.cn -------------- next part -------------- An HTML attachment was scrubbed... URL: <http://zeus.theochem.tuwien.ac.at/pipermail/wien/attachments/20111109/afdcf6ae/attachment.htm>