[Pw_forum] XSpectra can not run
hi, all, I'm a newcomer to the QE world. I want to do some XAS calculations with XSpectra. So I followed the steps in the file run_example_diamond, got the pseudopotential, finished the scf calculation, generated the core state (C.wfc put in the working directory). Well, when I tried to run xspectra.x with the example input file, e. g., diamond.xspectra_fermi.in, I found xspectra.x does not exist (why hasn't it been compiled with all the other QE modules?). So I came to the XSpetra directory and ran make, it came up with some error message that some .o files under ../GIPAW were required. I hd to go to ../GIPAW and ran make. This time it seemed working. Then I went back to XSpectra/ and ran make. It came up with some warning like xspectra.f90(431): remark #8290: Recommended relationship between field width 'W' and the number of fractional digits 'D' in this edit descriptor is 'W>=D+3'. WRITE (stdout,'(a,1x,3(f10.8, 1x))') 'xepsilon(:)=', (xepsilon(i),i=1,3) -^ ### but still generated the xspectra.x executable. The problem came when I ran xspectra.xdiamond.xspectra_fermi.out, with the following error: ### forrtl: severe (174): SIGSEGV, segmentation fault occurred Image PCRoutineLineSource xspectra.x 00674016 fft_types_mp_fft_ 568 fft_types.f90 xspectra.x 00646F8E stick_set_mp_psti 224 stick_set.f90 xspectra.x 0046B8AA data_structure_62 data_structure.f90 xspectra.x 004569D7 allocate_fft_ 38 allocate_fft.f90 xspectra.x 00431A55 read_file_xspectr 231 read_file_xspectra.f90 xspectra.x 00405C13 MAIN__371 xspectra.f90 xspectra.x 004050FC Unknown Unknown Unknown libc.so.6 7F71CF6F4D8E Unknown Unknown Unknown xspectra.x 00404FF9 Unknown Unknown Unknown ## My input file is: &input_xspectra calculation='fermi_level', prefix='diamond', outdir='./', xread_wf=.true., / &plot / &pseudos filecore='./C.wfc', / &cut_occ / 4 4 4 0 0 0 What's wrong with my compilation? I'm using ifort V.12 with MKL and under a Linux64 system. The compilation of pw.x and many other executables are ok. Sorry for this long post. Any help will be greatly appreciated! best regards Yu Zhang
[Pw_forum] XSpectra can not run
On Apr 7, 2011, at 18:56 , Yu Zhang wrote: > (why hasn't it been compiled with all the other QE modules?) $ make to install, type at the shell prompt: ./configure make target where target is one of the following: pw basic code for scf, structure optimization, MD cp CP code: CP MD with ultrasoft pseudopotentials ph phonon code neb code for Nudged Elastic Band method tddfpt time dependent dft code pp postprocessing programs gammaGamma-only version of phonon code pwcond ballistic conductance d3 third-order derivatives vdw vdW calculation gipawmagnetic response (NMR, EPR, ...) w90 Maximally localised Wannier Functions want Quantum Transport with Wannier functions plumed Patch for calculating free-energy paths with pw or cp gww GW with Wannier Functions yamboelectronic excitations with plane waves toolsmisc tools for data analysis ld1 utilities for pseudopotential generation upf utilities for pseudopotential conversion xspectra X-ray core-hole spectroscopy calculations pwallsame as "make pw ph pp gamma pwcond d3 tools" all same as "make pwall cp ld1 upf tddfpt" As you can see, some specialized code are not compiled by "make all" > So I came to the XSpetra directory and ran make "make xspectra" should be run from the root QE directory > xspectra.f90(431): remark #8290: Recommended relationship between > field > width 'W' and the number of fractional digits 'D' in this edit > descriptor is 'W>=D+3'. this is completely irrelevant > forrtl: severe (174): SIGSEGV, segmentation fault occurred does it work for the provided example? > I'm using ifort V.12 with MKL and under a Linux64 system. v.12.0.2 should work; v.12.0.0 doesn't P. --- Paolo Giannozzi, Dept of Chemistry&Physics&Environment, Univ. Udine, via delle Scienze 208, 33100 Udine, Italy Phone +39-0432-558216, fax +39-0432-558222
[Pw_forum] XSpectra can not run
hi, Paolo, Thank you very much for your help. I deleted *.o and *.x under /GIPAW and /Xspectra and then ran make gipaw and make xspectra in the QE root directory, as you suggested. No error found in compilation. Well, when I ran xspectra.xdiamond.xspectra_fermi.out again, I saw the same error as before. diamond.xspectra_fermi.in is from the example file. What should I do next? My intel fortran is V 12.0.3. Many thanks again! best regards Yu Zhang On 2011?04?07? 10:53, Paolo Giannozzi wrote: > On Apr 7, 2011, at 18:56 , Yu Zhang wrote: > >> (why hasn't it been compiled with all the other QE modules?) > $ make > to install, type at the shell prompt: > ./configure > make target > where target is one of the following: > pw basic code for scf, structure optimization, MD > cp CP code: CP MD with ultrasoft pseudopotentials > ph phonon code > neb code for Nudged Elastic Band method > tddfpt time dependent dft code > pp postprocessing programs > gammaGamma-only version of phonon code > pwcond ballistic conductance > d3 third-order derivatives > vdw vdW calculation > gipawmagnetic response (NMR, EPR, ...) > w90 Maximally localised Wannier Functions > want Quantum Transport with Wannier functions > plumed Patch for calculating free-energy paths with pw or cp > gww GW with Wannier Functions > yamboelectronic excitations with plane waves > toolsmisc tools for data analysis > ld1 utilities for pseudopotential generation > upf utilities for pseudopotential conversion > xspectra X-ray core-hole spectroscopy calculations > pwallsame as "make pw ph pp gamma pwcond d3 tools" > all same as "make pwall cp ld1 upf tddfpt" > > > As you can see, some specialized code are not compiled > by "make all" > >> So I came to the XSpetra directory and ran make > "make xspectra" should be run from the root QE directory > >> xspectra.f90(431): remark #8290: Recommended relationship between >> field >> width 'W' and the number of fractional digits 'D' in this edit >> descriptor is 'W>=D+3'. > this is completely irrelevant > >> forrtl: severe (174): SIGSEGV, segmentation fault occurred > does it work for the provided example? > >> I'm using ifort V.12 with MKL and under a Linux64 system. > v.12.0.2 should work; v.12.0.0 doesn't > > P. > --- > Paolo Giannozzi, Dept of Chemistry&Physics&Environment, > Univ. Udine, via delle Scienze 208, 33100 Udine, Italy > Phone +39-0432-558216, fax +39-0432-558222 > > > > > ___ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum >
[Pw_forum] XSpectra can not run
On Apr 7, 2011, at 20:26 , Yu Zhang wrote: > What should I do next? answer the following question: >> does it work for the provided example? P. --- Paolo Giannozzi, Dept of Chemistry&Physics&Environment, Univ. Udine, via delle Scienze 208, 33100 Udine, Italy Phone +39-0432-558216, fax +39-0432-558222
[Pw_forum] XSpectra can not run
hi, Paolo, I run run_example_diamond from the XSpectra example directory and the program stops at the XAS fermi level calculation step and produces the same error. Sorry for not mention this before. Thanks. Yu Zhang On 2011?04?07? 12:55, Paolo Giannozzi wrote: > On Apr 7, 2011, at 20:26 , Yu Zhang wrote: > >> What should I do next? > answer the following question: > >>> does it work for the provided example? > P. > --- > Paolo Giannozzi, Dept of Chemistry&Physics&Environment, > Univ. Udine, via delle Scienze 208, 33100 Udine, Italy > Phone +39-0432-558216, fax +39-0432-558222 > > > > > ___ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum >
[Pw_forum] XSpectra can not run
On Thu, 2011-04-07 at 14:25 -0700, Yu Zhang wrote: > I run run_example_diamond from the XSpectra example directory and the > program stops at the XAS fermi level calculation step and produces the > same error. Sorry for not mention this before. replace read-file_xspectra.f90 with the attached version P. -- Paolo Giannozzi, IOM-Democritos and University of Udine, Italy -- next part -- A non-text attachment was scrubbed... Name: read_file_xspectra.f90 Type: text/x-fortran Size: 12641 bytes Desc: not available Url : http://www.democritos.it/pipermail/pw_forum/attachments/20110408/8bd504f0/attachment.bin
[Pw_forum] XSpectra can not run
hi, Paolo, This really solves my problem! Thank you very much. Could you please explain briefly what the cause of the problem is? best regards Yu Zhang On 2011?04?08? 02:36, Paolo Giannozzi wrote: > On Thu, 2011-04-07 at 14:25 -0700, Yu Zhang wrote: > >> I run run_example_diamond from the XSpectra example directory and the >> program stops at the XAS fermi level calculation step and produces the >> same error. Sorry for not mention this before. > replace read-file_xspectra.f90 with the attached version > > P. > > > ___ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum -- next part -- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110408/6ebbb68e/attachment-0001.htm
[Pw_forum] XSpectra can not run
On Apr 8, 2011, at 20:49 , Yu Zhang wrote: > This really solves my problem! Thank you very much. you should thank Matteo Calandra, not me > Could you please explain briefly what the cause of the problem is? the problem is that some recent changes to the initialization of FFT grids, G-vectors, and other basic stuff, had not been propagated to that particular routine. I had forgotten that XSpectra uses a different routine to read the data file from all other QE codes. Just an overlook. Paolo --- Paolo Giannozzi, Dept of Chemistry&Physics&Environment, Univ. Udine, via delle Scienze 208, 33100 Udine, Italy Phone +39-0432-558216, fax +39-0432-558222
[Pw_forum] XSpectra can not run
hi, Paolo, Thank Matteo and you very much! Well, I got some similar reading error when I tried to do XSpectra calculation with my own input file. Could you please see the post http://www.democritos.it/pipermail/pw_forum/2011-April/020020.html for me (I apologize if you've already seen it)? Thank you very much! best wishes Yu Zhang On 04/08/2011 12:18, Paolo Giannozzi wrote: > On Apr 8, 2011, at 20:49 , Yu Zhang wrote: > >> This really solves my problem! Thank you very much. > you should thank Matteo Calandra, not me > >> Could you please explain briefly what the cause of the problem is? > the problem is that some recent changes to the initialization of FFT > grids, G-vectors, and other basic stuff, had not been propagated > to that particular routine. I had forgotten that XSpectra uses a > different routine to read the data file from all other QE codes. > Just an overlook. > > Paolo > --- > Paolo Giannozzi, Dept of Chemistry&Physics&Environment, > Univ. Udine, via delle Scienze 208, 33100 Udine, Italy > Phone +39-0432-558216, fax +39-0432-558222 > > > > > ___ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum >
[Pw_forum] XSpectra can not run
> hi, Paolo, > Thank Matteo and you very much! Well, I got some similar reading > error when I tried to do XSpectra calculation with my own input file. > Could you please see the post > http://www.democritos.it/pipermail/pw_forum/2011-April/020020.html > for me (I apologize if you've already seen it)? Thank you very much! > best wishes > Yu Zhang > Dear Yu Zhang, I think the problem is that some of your pseudopotentials do not have gipaw reconstruction inside. In principle this is needed only for the absorbing atom, but for the moment the code requires that all the pseudo do have gipaw reconstruction. I have to modify this as soon as I have some time. Th second problem is that xspectra does not work with the Gamma only version of the code. So you should run both the scf and xspectra not with K_POINTS gamma but with K_POINTS automatic 1 1 1 0 0 0 It should then work. M. > On 04/08/2011 12:18, Paolo Giannozzi wrote: >> On Apr 8, 2011, at 20:49 , Yu Zhang wrote: >> >>> This really solves my problem! Thank you very much. >> you should thank Matteo Calandra, not me >> >>> Could you please explain briefly what the cause of the problem is? >> the problem is that some recent changes to the initialization of FFT >> grids, G-vectors, and other basic stuff, had not been propagated >> to that particular routine. I had forgotten that XSpectra uses a >> different routine to read the data file from all other QE codes. >> Just an overlook. >> >> Paolo >> --- >> Paolo Giannozzi, Dept of Chemistry&Physics&Environment, >> Univ. Udine, via delle Scienze 208, 33100 Udine, Italy >> Phone +39-0432-558216, fax +39-0432-558222 >> >> >> >> >> ___ >> Pw_forum mailing list >> Pw_forum at pwscf.org >> http://www.democritos.it/mailman/listinfo/pw_forum >> > > > > -- > > Message: 2 > Date: Mon, 11 Apr 2011 17:15:33 -0500 > From: "Nichols A. Romero" > Subject: Re: [Pw_forum] I/O performance on BG/P systems > To: PWSCF Forum > Cc: Gabriele Sclauzero > Message-ID: > Content-Type: text/plain; charset=ISO-8859-1 > > Gabriele, > > A couple of other technical details that I am remembering: > 1. The BG/P at ANL has 1 I/O node per 64 nodes, 8 I/O nodes per mid-plane > 2. The bottleneck of writing multiple files per MPI tasks does not > become serious > until about 8+ racks. > > On Mon, Apr 11, 2011 at 3:50 PM, Gabriele Sclauzero > wrote: >> Dear Paolo and Nichols, >> ?? ?as a follow up, I had a brief meeting with the sysadmin of our local >> BGP. It looks like the timings I was reporting actually correspond to the >> maximum I/O throughput of that specific rack, which depends on the number of >> I/O nodes present on the rack itself (in that case, 4 I/O nodes per >> midplane, each of them capable of 350 MB/s, corresponding to 1.7 GB/s for >> that midplane). >> In the example I was reporting: >> ?? ? davcio ??: ??1083.30s?CPU ??1083.30s WALL ( ?38 calls) >> I've been running on just 128 nodes (512 cores in VN mode), therefore I had >> only one I/O node (1 midplane = 4 x 128 nodes, for the non-BG/P-ers). Now, >> the total size of the .wfc files was around 9200 MB, which cannot be written >> in less than 9200/350 = 26.3 sec, according to the figures that the >> sysadmins gave me. >> In my case the timings give:?1083.30s/38=28.5s, which is close to the >> theoretical maximum. >> I will perform more testing and I will take into consideration the >> suggestion of Nichols about the number of files per node. In our machine we >> have one rack with 16 I/O nodes per midplane, I will try to see if the I/O >> performance scales accordingly. >> As a side effect, I met a problem in the timing procedure. I found very >> different davcio timings (i.e. 3 orders of magnitude!) for two jobs where >> the size of the wavefunctions differed by a factor 2 only (the jobs?have >> been executed on the same rack and with the same number of processors and >> same parallelization scheme). >> The sysadmins replied that I/O bandwidth measured in the?fastest case is not >> attainable on BG/P, and should be imputed to an inaccurate measurement of >> cputime/walltime. >> I'm going to investigate this anyway. >> I'm not aware of anyone working on MPI I/O porting. >> Thanks so far for your suggestions, >> >> >> Gabriele >> >> >> Il giorno 11/apr/2011, alle ore 20.02, Nichols A. Romero ha scritto: >> >> Sorry for not replying earlier, but I missed this e-mail due to the >> APS March Meeting. >> >> The GPFS file system on BG/P does a poor job at handling writes to more than >> one file per node. My guess is that Gabriele was running QE in either dual >> or VN mode (2 and 4 MPI tasks per node, respectively). So on BG/P, >> you basically >> want to write one file per node (which GPFS is designed to handle) or >> one big file >> using MPI-I/O. >> >> At ANL, we are thinking about re-writing some of the I/O >> using parallel I/O (e.g. HDF5, Parallel NetCDF). The simple
