I meant "may not be too hard" to setup a script. Too early in the morning, not enough coffee.
On Tue, Jun 4, 2013 at 7:42 AM, Laurence Marks <l-ma...@northwestern.edu> wrote: > Let me add a couple of clarifications to what Peter suggested, since I > often get caught by the ".process" and ".process2" files. I just did a > quick search of the UG and they do not appear to be described > (suggestion to Peter to add). Their format is somewhat self > explanatory (although they do not seem to be constructed to be very > human readable, i.e. no comments on the right.) > > The shell scripts create these files during a -p run so, for instance, > lapw2 can run in parallel on the same nodes that lapw1 used and > therefore SCRATCH and other files which might only be in temporary > storage are consistent. When you run under PBS or several other > similar job control codes which nodes you use are dynamically > allocated and are then stored within these files. If you now run a > second job or interactive task to do some analysis you are likely to > have a different set of nodes allocated to you which can then create > problems. > > If you are running interactively you can adjust these files for the > nodes that you have. Alternatively you can do a single -p pass > although unfortunately -it might switch to non-iterative because the > setup uses the .process file to cp the old vector file. > > I suspect that it may be too hard to construct a shell script (or csh) > to set these up properly for a given .machines file by extracting the > relevant section from lapw1para, perhaps a good mini project for > someone. > > On Tue, Jun 4, 2013 at 7:04 AM, Peter Blaha > <pbl...@theochem.tuwien.ac.at> wrote: >> -it does not have an effect for lapw2 since there is no diagonalization. >> >> The problem is most likely that you need a proper .processes file to run >> x lapw2 -p. Most PBS-scripts create only .machines and run_lapw >> will then generate later on .processes. >> >> My suggestion: First check if you have the vector files in "case": >> >> cd /home/my_username/wien2k/case >> ls -alsrt *vector* >> >> If they look ok (size and date !!!) >> >> use join_vectorfiles >> >> to combine them to a single "non-parallel" vector and then >> submit x lapw2 -qtl (without -p) >> >> Note: in "QTL-mode", lapw2 always runs only on a single core and the -p >> option is only used to let the code know about the parallel vector files. >> >> >> On 06/04/2013 12:06 PM, Yundi Quan wrote: >>> Thank Stefaan and Michael for your prompt replies. >>> >>> My $SCRATCH file is set to ./ in the .bashrc file. I forgot to mention >>> that I used x lapw2 -qtl -p -it rather than x lapw2 -qtl -p. The >>> option -it tells WIEN2k to use iterative diagonalization, which should >>> not be a problem. In uplapw2_1.def, it says that >>> 10,'./case.vectorup_1', 'unknown','unformatted',9000 >>> >>> I think this line tells lapw2 where to find the vector. But again, ./ >>> seems to mean my home directory rather than my working directory. >>> >>> I tried making a new scratch directory and set the $SCRATCH to that >>> directory as suggested by Michael. I hope it works. >>> >>> >>> >>> Yundi >>> >>> >>> >>> On Tue, Jun 4, 2013 at 2:34 AM, Yundi Quan <yq...@ucdavis.edu> wrote: >>>> >>>> >>>> ---------- Forwarded message ---------- >>>> From: Yundi Quan <quanyu...@gmail.com> >>>> Date: Tue, Jun 4, 2013 at 2:19 AM >>>> Subject: [Wien] scp error >>>> To: A Mailing list for WIEN2k users <wien@zeus.theochem.tuwien.ac.at> >>>> >>>> >>>> Hi, >>>> I'm working on a cluster 8 quadcore nodes. Nodes are called n001, >>>> n002, n003, n004... I use torque PBS queue system. When I submit a job >>>> using a bash file, the default directory is always my home directory. >>>> Therefore, at the beginning of my bash file, I always add a line 'cd >>>> '. This works for scf calculations. >>>> However, when I use x lapw2 -qtl -band -p to calculate the band >>>> structure or x lapw2 -qtl -p to calculate the DOS, I always encounter >>>> the following error message: >>>> scp: .//case.vector_1 not found >>>> scp: .//case.vector_2 not found >>>> ... >>>> >>>> It seems scp is looking for case.vector_1 in my home directory rather >>>> than my working directory, even though I've added the line 'cd >>>> /home/my_username/case' in my bash file. This problem only occurs with >>>> using x lapw2 -qtl -p. I used to do scf calculation in serial and then >>>> use x lapw2 -qtl. But I'm wondering whether there is a workaround. >>>> >>>> >>>> Thanks. >>>> _______________________________________________ >>>> Wien mailing list >>>> Wien@zeus.theochem.tuwien.ac.at >>>> http://zeus.theochem.tuwien.ac.at/mailman/listinfo/wien >>>> SEARCH the MAILING-LIST at: >>>> http://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/index.html >>>> >>> _______________________________________________ >>> Wien mailing list >>> Wien@zeus.theochem.tuwien.ac.at >>> http://zeus.theochem.tuwien.ac.at/mailman/listinfo/wien >>> SEARCH the MAILING-LIST at: >>> http://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/index.html >>> >> >> -- >> >> P.Blaha >> -------------------------------------------------------------------------- >> Peter BLAHA, Inst.f. Materials Chemistry, TU Vienna, A-1060 Vienna >> Phone: +43-1-58801-165300 FAX: +43-1-58801-165982 >> Email: bl...@theochem.tuwien.ac.at WWW: >> http://info.tuwien.ac.at/theochem/ >> -------------------------------------------------------------------------- >> _______________________________________________ >> Wien mailing list >> Wien@zeus.theochem.tuwien.ac.at >> http://zeus.theochem.tuwien.ac.at/mailman/listinfo/wien >> SEARCH the MAILING-LIST at: >> http://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/index.html > > > > -- > Professor Laurence Marks > Department of Materials Science and Engineering > Northwestern University > www.numis.northwestern.edu 1-847-491-3996 > "Research is to see what everybody else has seen, and to think what > nobody else has thought" > Albert Szent-Gyorgi -- Professor Laurence Marks Department of Materials Science and Engineering Northwestern University www.numis.northwestern.edu 1-847-491-3996 "Research is to see what everybody else has seen, and to think what nobody else has thought" Albert Szent-Gyorgi _______________________________________________ Wien mailing list Wien@zeus.theochem.tuwien.ac.at http://zeus.theochem.tuwien.ac.at/mailman/listinfo/wien SEARCH the MAILING-LIST at: http://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/index.html