To err is human, to make slly name/spelling errors takes a Prof. Yes, I should have written .processes etc, sorry.
On Tue, Jun 4, 2013 at 9:08 AM, Peter Blaha <pbl...@theochem.tuwien.ac.at> wrote: > I guess I also have to add some clarifications, because there is no > .process or .process2 file, .... > > > For parallel calculations the main file of interest is > > .machines > > And this file is used by lapw0para and lapw1para as input. > > However, lapw1para produces > > .processes > > (because you may have more parallel jobs then specified in .machines > (because of "non-integer k-point/core ratio) and in particular because > we allow explicitly to modify .machines during run_lapw (changing the > parallelization by hand for the next iterations in case a machine is > overloaded on a cluster). > > The following parallel scripts (lapwso, lapw2) therefore read from > .processes (and not from .machines). (Also vec2old and vec2pratt need > .processes and this may cause eventually problems, although if you > change the number of cores ot use a non-local $SCRATCH, it cannot do -it > at the very beginning anyway). > > This is (at least to some extend) documented in the UG (search eg. for > processes). > > These are usually the only 2 files of interest for a user. > There are no .process or .process2 files; and other ".machineXX or > .processesXX files are internal only. > > I'm sometimes using PBS-scripts which do generate .processes, but the > easiest thing would be to add a flag to lapw1para, so that it does not > execute lapw1, but just generates the .processes file. > > > > On 06/04/2013 02:42 PM, Laurence Marks 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 >> >> >> > > -- > > 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 _______________________________________________ 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