[Wien] (no subject)
Dear Wien2k users and developers, I am trying the supercell calculations, l created the supercell structure file and replaced one of the atom with Bi. I have some query regarding this, how to replace an atom with particular valency (Bi+5. Bi+3). Please help me regarding this. Thanking you ___ 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] warning: !!! Bravais lattice has changed.
Dear all In doing the initialization of As element in the trigonal symmetry, space group number is 166 with a=b= 3.76 and c=10.5480 alpha and beta = 90 and gamma = 120 (Information from WWW-MINCRYST) atomic positions are 0.0 0.0 0.226 I am getting warning: !!! Bravais lattice has changed. Space group has changed to 12 (C 2/m), while I have used 166 (R-3m) space group. Why I am getting this error. ___ 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
Re: [Wien] warning: !!! Bravais lattice has changed.
Hi, you can find some informations in the answers to this question (at the very bottom of the page): https://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/msg09208.html On Thu, 29 May 2014, sonusha...@iitmandi.ac.in wrote: Dear all In doing the initialization of As element in the trigonal symmetry, space group number is 166 with a=b= 3.76 and c=10.5480 alpha and beta = 90 and gamma = 120 (Information from WWW-MINCRYST) atomic positions are 0.0 0.0 0.226 I am getting warning: !!! Bravais lattice has changed. Space group has changed to 12 (C 2/m), while I have used 166 (R-3m) space group. Why I am getting this error. ___ 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
[Wien] Dear Wien2k users and developers
I am making structure file of BiFeO3 space group R3 with lattice parameters a=b =5.5805 and c= 13.8763 (Angstrom) with angles alpha= beta = 90 gamma = 120 ( degree) during initialization i got an error. if i accept gmax value reduces to gmin in LSTAR. please help me how can strucure file can be made with above said space group. ERROR !!! RMT( 3)=2.0 AND RMT( 5)=2.0 SUMS TO 4.0 GT NNN-DIST= 2.26055 ERROR !!! RMT( 3)=2.0 AND RMT( 3)=2.0 SUMS TO 4.0 GT NNN-DIST= 2.32636 ERROR !!! RMT( 3)=2.0 AND RMT( 1)=2.0 SUMS TO 4.0 GT NNN-DIST= 2.34990 ERROR !!! RMT( 3)=2.0 AND RMT( 2)=2.0 SUMS TO 4.0 GT NNN-DIST= 2.97626 ERROR !!! RMT( 3)=2.0 AND RMT( 6)=2.0 SUMS TO 4.0 GT NNN-DIST= 3.96941 ERROR !!! RMT( 4)=2.0 AND RMT( 2)=2.0 SUMS TO 4.0 GT NNN-DIST= 2.34990 ERROR !!! RMT( 4)=2.0 AND RMT( 4)=2.0 SUMS TO 4.0 GT NNN-DIST= 2.94645 ERROR !!! RMT( 4)=2.0 AND RMT( 1)=2.0 SUMS TO 4.0 GT NNN-DIST= 2.97626 ERROR !!! RMT( 4)=2.0 AND RMT( 5)=2.0 SUMS TO 4.0 GT NNN-DIST= 3.13382 ERROR !!! RMT( 5)=2.0 AND RMT( 2)=2.0 SUMS TO 4.0 GT NNN-DIST= 0.86519 ERROR !!! RMT( 6)=2.0 AND RMT( 3)=2.0 SUMS TO 4.0 GT NNN-DIST= 3.96941 NN ENDS 0.1u 0.0s 0:00.13 100.0% 0+0k 0+320io 0pf+0w atom Z RMT-max RMT 1 83.0 1.20 0.47 2 83.0 0.47 0.47 3 26.0 1.14 1.14 4 26.0 1.14 1.14 5 8.0 0.39 0.39 6 8.0 1.82 0.39 Do you want to accept these radii; discard them; or rerun setRmt (a/d/r): *Best Regards* *Mian Fayyaz Ahmad* *PhD Research Scholar* *Magnetophotonics Research Lab.* *Department of Physics* *Sungkyunkwan University* *Suwon,440-746* * Republic of Korea* *Cell# +821059295956* ___ 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] (no subject)
Dear ALl I am doing the initialization and got this problem 13 SELECT ENERGY to separate core and valence states: recommended: -6.0 Ry (check how much core charge leaks out of MT-sphere) ALTERNATIVELY: specify charge localization (between 0.97 and 1.0) to select core state -9.8 :WARNING: 0.111 Sr CORE electrons leak out of MT-sphere :WARNING: touch .lcore and run scf-cycle with core density superposition :WARNING: Or: rerun lstart with lower E-core separation energy :WARNING: 0.111 Sr CORE electrons leak out of MT-sphere :WARNING: touch .lcore and run scf-cycle with core density superposition :WARNING: Or: rerun lstart with lower E-core separation energy :WARNING: 0.648 Ce CORE electrons leak out of MT-sphere :WARNING: touch .lcore and run scf-cycle with core density superposition :WARNING: Or: rerun lstart with lower E-core separation energy :WARNING: 0.648 Ce CORE electrons leak out of MT-sphere :WARNING: touch .lcore and run scf-cycle with core density superposition :WARNING: Or: rerun lstart with lower E-core separation energy :WARNING: 0.021 N CORE electrons leak out of MT-sphere :WARNING: touch .lcore and run scf-cycle with core density superposition :WARNING: Or: rerun lstart with lower E-core separation energy :WARNING: 0.021 N CORE electrons leak out of MT-sphere :WARNING: touch .lcore and run scf-cycle with core density superposition :WARNING: Or: rerun lstart with lower E-core separation energy :WARNING: 0.021 N CORE electrons leak out of MT-sphere :WARNING: touch .lcore and run scf-cycle with core density superposition :WARNING: Or: rerun lstart with lower E-core separation energy :WARNING: 0.021 N CORE electrons leak out of MT-sphere :WARNING: touch .lcore and run scf-cycle with core density superposition :WARNING: Or: rerun lstart with lower E-core separation energy :WARNING: 0.021 N CORE electrons leak out of MT-sphere :WARNING: touch .lcore and run scf-cycle with core density superposition :WARNING: Or: rerun lstart with lower E-core separation energy :WARNING: 0.021 N CORE electrons leak out of MT-sphere :WARNING: touch .lcore and run scf-cycle with core density superposition :WARNING: Or: rerun lstart with lower E-core separation energy :WARNING: 0.021 N CORE electrons leak out of MT-sphere :WARNING: touch .lcore and run scf-cycle with core density superposition :WARNING: Or: rerun lstart with lower E-core separation energy :WARNING: 0.021 N CORE electrons leak out of MT-sphere :WARNING: touch .lcore and run scf-cycle with core density superposition :WARNING: Or: rerun lstart with lower E-core separation energy :WARNING: 0.021 N CORE electrons leak out of MT-sphere :WARNING: touch .lcore and run scf-cycle with core density superposition :WARNING: Or: rerun lstart with lower E-core separation energy :WARNING: 0.021 N CORE electrons leak out of MT-sphere :WARNING: touch .lcore and run scf-cycle with core density superposition :WARNING: Or: rerun lstart with lower E-core separation energy :WARNING: 0.021 N CORE electrons leak out of MT-sphere :WARNING: touch .lcore and run scf-cycle with core density superposition :WARNING: Or: rerun lstart with lower E-core separation energy :WARNING: 0.021 N CORE electrons leak out of MT-sphere :WARNING: touch .lcore and run scf-cycle with core density superposition :WARNING: Or: rerun lstart with lower E-core separation energy :WARNING: 0.021 N CORE electrons leak out of MT-sphere :WARNING: touch .lcore and run scf-cycle with core density superposition :WARNING: Or: rerun lstart with lower E-core separation energy :WARNING: 0.021 N CORE electrons leak out of MT-sphere :WARNING: touch .lcore and run scf-cycle with core density superposition :WARNING: Or: rerun lstart with lower E-core separation energy LSTART ENDS 1.448u 0.044s 0:07.05 20.9% 0+0k 0+16064io 0pf+0w ERROR !!! nstop,iter,tets,test 28 1 9.99939225290E-009 nstop,iter,tets,test 28 1 9.99939225290E-009 nstop,iter,tets,test 28 1 9.99939225290E-009 nstop,iter,tets,test 28 1 9.99939225290E-009 nstop,iter,tets,test 28 1 9.99939225290E-009 nstop,iter,tets,test 28 1 9.99939225290E-009 nstop,iter,tets,test 28 1 9.99939225290E-009 nstop,iter,tets,test 28 1 9.99939225290E-009 nstop,iter,tets,test 28 1 9.99939225290E-009 nstop,iter,tets,test 28 1 9.99939225290E-009 nstop,iter,tets,test 28 1 9.99939225290E-009 nstop,iter,tets,test 28 1 9.99939225290E-009 nstop,iter,tets,test 28 1 9.99939225290E-009 nstop,iter,tets,test 28 1 9.99939225290E-009 nstop,iter,tets,test 28 1 9.99939225290E-009 nstop,iter,tets,test 28 1 9.99939225290E-009
Re: [Wien] Dear Wien2k users and developers
The problem is that spheres overlap which is forbidden. I don't think that your case.struct file is ok. Be aware that the values for a, b and c in case.struct are always in bohr. unit=ang in case.struct is only for the w2web interface. On Thu, 29 May 2014, Mian Fayyaz Ahmad wrote: I am making structure file of BiFeO3 space group R3 with lattice parameters a=b =5.5805 and c= 13.8763 (Angstrom) with angles alpha= beta = 90 gamma = 120 ( degree) during initialization i got an error. if i accept gmax value reduces to gmin in LSTAR. please help me how can strucure file can be made with above said space group. ERROR !!! RMT( 3)=2.0 AND RMT( 5)=2.0 SUMS TO 4.0 GT NNN-DIST= 2.26055 ERROR !!! RMT( 3)=2.0 AND RMT( 3)=2.0 SUMS TO 4.0 GT NNN-DIST= 2.32636 ERROR !!! RMT( 3)=2.0 AND RMT( 1)=2.0 SUMS TO 4.0 GT NNN-DIST= 2.34990 ERROR !!! RMT( 3)=2.0 AND RMT( 2)=2.0 SUMS TO 4.0 GT NNN-DIST= 2.97626 ERROR !!! RMT( 3)=2.0 AND RMT( 6)=2.0 SUMS TO 4.0 GT NNN-DIST= 3.96941 ERROR !!! RMT( 4)=2.0 AND RMT( 2)=2.0 SUMS TO 4.0 GT NNN-DIST= 2.34990 ERROR !!! RMT( 4)=2.0 AND RMT( 4)=2.0 SUMS TO 4.0 GT NNN-DIST= 2.94645 ERROR !!! RMT( 4)=2.0 AND RMT( 1)=2.0 SUMS TO 4.0 GT NNN-DIST= 2.97626 ERROR !!! RMT( 4)=2.0 AND RMT( 5)=2.0 SUMS TO 4.0 GT NNN-DIST= 3.13382 ERROR !!! RMT( 5)=2.0 AND RMT( 2)=2.0 SUMS TO 4.0 GT NNN-DIST= 0.86519 ERROR !!! RMT( 6)=2.0 AND RMT( 3)=2.0 SUMS TO 4.0 GT NNN-DIST= 3.96941 NN ENDS 0.1u 0.0s 0:00.13 100.0% 0+0k 0+320io 0pf+0w atom Z RMT-max RMT 1 83.0 1.20 0.47 2 83.0 0.47 0.47 3 26.0 1.14 1.14 4 26.0 1.14 1.14 5 8.0 0.39 0.39 6 8.0 1.82 0.39 Do you want to accept these radii; discard them; or rerun setRmt (a/d/r): Best Regards Mian Fayyaz AhmadPhD Research Scholar Magnetophotonics Research Lab. Department of Physics Sungkyunkwan University Suwon,440-746 Republic of Korea Cell# +821059295956 ___ 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
Re: [Wien] (no subject)
Your RMT spheres are too small, such that there is quite big core leakage. If possible, choose larger RMT spheres. On Thu, 29 May 2014, sikandar azam wrote: Dear ALl I am doing the initialization and got this problem 13 SELECT ENERGY to separate core and valence states: recommended: -6.0 Ry (check how much core charge leaks out of MT-sphere) ALTERNATIVELY: specify charge localization (between 0.97 and 1.0) to select core state -9.8 :WARNING: 0.111 Sr CORE electrons leak out of MT-sphere :WARNING: touch .lcore and run scf-cycle with core density superposition :WARNING: Or: rerun lstart with lower E-core separation energy :WARNING: 0.111 Sr CORE electrons leak out of MT-sphere :WARNING: touch .lcore and run scf-cycle with core density superposition :WARNING: Or: rerun lstart with lower E-core separation energy :WARNING: 0.648 Ce CORE electrons leak out of MT-sphere :WARNING: touch .lcore and run scf-cycle with core density superposition :WARNING: Or: rerun lstart with lower E-core separation energy :WARNING: 0.648 Ce CORE electrons leak out of MT-sphere :WARNING: touch .lcore and run scf-cycle with core density superposition :WARNING: Or: rerun lstart with lower E-core separation energy :WARNING: 0.021 N CORE electrons leak out of MT-sphere :WARNING: touch .lcore and run scf-cycle with core density superposition :WARNING: Or: rerun lstart with lower E-core separation energy :WARNING: 0.021 N CORE electrons leak out of MT-sphere :WARNING: touch .lcore and run scf-cycle with core density superposition :WARNING: Or: rerun lstart with lower E-core separation energy :WARNING: 0.021 N CORE electrons leak out of MT-sphere :WARNING: touch .lcore and run scf-cycle with core density superposition :WARNING: Or: rerun lstart with lower E-core separation energy :WARNING: 0.021 N CORE electrons leak out of MT-sphere :WARNING: touch .lcore and run scf-cycle with core density superposition :WARNING: Or: rerun lstart with lower E-core separation energy :WARNING: 0.021 N CORE electrons leak out of MT-sphere :WARNING: touch .lcore and run scf-cycle with core density superposition :WARNING: Or: rerun lstart with lower E-core separation energy :WARNING: 0.021 N CORE electrons leak out of MT-sphere :WARNING: touch .lcore and run scf-cycle with core density superposition :WARNING: Or: rerun lstart with lower E-core separation energy :WARNING: 0.021 N CORE electrons leak out of MT-sphere :WARNING: touch .lcore and run scf-cycle with core density superposition :WARNING: Or: rerun lstart with lower E-core separation energy :WARNING: 0.021 N CORE electrons leak out of MT-sphere :WARNING: touch .lcore and run scf-cycle with core density superposition :WARNING: Or: rerun lstart with lower E-core separation energy :WARNING: 0.021 N CORE electrons leak out of MT-sphere :WARNING: touch .lcore and run scf-cycle with core density superposition :WARNING: Or: rerun lstart with lower E-core separation energy :WARNING: 0.021 N CORE electrons leak out of MT-sphere :WARNING: touch .lcore and run scf-cycle with core density superposition :WARNING: Or: rerun lstart with lower E-core separation energy :WARNING: 0.021 N CORE electrons leak out of MT-sphere :WARNING: touch .lcore and run scf-cycle with core density superposition :WARNING: Or: rerun lstart with lower E-core separation energy :WARNING: 0.021 N CORE electrons leak out of MT-sphere :WARNING: touch .lcore and run scf-cycle with core density superposition :WARNING: Or: rerun lstart with lower E-core separation energy :WARNING: 0.021 N CORE electrons leak out of MT-sphere :WARNING: touch .lcore and run scf-cycle with core density superposition :WARNING: Or: rerun lstart with lower E-core separation energy :WARNING: 0.021 N CORE electrons leak out of MT-sphere :WARNING: touch .lcore and run scf-cycle with core density superposition :WARNING: Or: rerun lstart with lower E-core separation energy LSTART ENDS 1.448u 0.044s 0:07.05 20.9% 0+0k 0+16064io 0pf+0w ERROR !!! nstop,iter,tets,test 28 1 9.99939225290E-009 nstop,iter,tets,test 28 1 9.99939225290E-009 nstop,iter,tets,test 28 1 9.99939225290E-009 nstop,iter,tets,test 28 1 9.99939225290E-009 nstop,iter,tets,test 28 1 9.99939225290E-009 nstop,iter,tets,test 28 1 9.99939225290E-009 nstop,iter,tets,test 28 1 9.99939225290E-009 nstop,iter,tets,test 28 1 9.99939225290E-009 nstop,iter,tets,test 28 1 9.99939225290E-009 nstop,iter,tets,test 28 1 9.99939225290E-009 nstop,iter,tets,test 28 1 9.99939225290E-009 nstop,iter,tets,test 28 1 9.99939225290E-009 nstop,iter,tets,test 28 1 9.99939225290E-009
Re: [Wien] Wien2k stopped working
Problems such as this are hard to help with remotely. It looks like something has gone wrong at the system level, and my guess is that it has one of two sources: a. Something has gone wrong with your account/directories. It could be as simple as your time allocation has expired, your password has been hacked or your .bashrc file has got corrupted. Check the basics, e.g. you can create a file, compile a simple program etc. While this is unlikely, you never know. b. There have been OS changes of some sort. Many sys_admins assume that users just employ the software that is provided, often using modules, and this is not compatible with how Wien2k runs. It may be that they have removed some of the libraries that you linked Wien2k against, changed how the nodes list is provided to you (which may break Machines2W). For instance, the overwriting of OMP_NUM_THREADS implies to me that someone has decided that of course you want to run using openmpi, which at least at the moment is not useful to you. (I know PB wants to change this, so sometime this statement may change.) Try some diagnostics to try and work out what has happened, for instance: * Compile something like hello world both mpi and non-mpi versions, then run it in a simple job. * Write a small script to interrogate the environment when you start a job, e.g. using commands such as ldd $WIENROOT/lapw1_mpi, env | grep -e MPI -e MKL as well as obvious ones such as ulimit, echo $PATH etc. * Check the cluster web-page, maybe they announced some changes. * Use ifort --version and similar, as well as which mpirun and similar -- maybe new. * If you know a friendly sys_admin ask them for general info. It is good to nurture someone. Of course, all of this may be totally wrong and you may have already sorted things out. On Wed, May 28, 2014 at 8:23 AM, Luis Ogando lcoda...@gmail.com wrote: Dear Wien2k community, I have Wien2k 13.1 installed in a SGI cluster using ifort, icc and Open MPI. The installation was a hard work (I would like to thank again the help from Prof. Lawrence Marks), but after all I have used Wien2k without problems for several months. I performed the first step of a long calculation and saved it in a different directory. When I tried the next step in the original directory, Wien2k crashed. After some tests, I decided to reinitialize the calculation from the beginning (in other words, to repeat the first step). To my surprise, I did not succeed even in this case and I would like to know if someone has faced such an unexpected problem. Please, find below some of the output files that I consider the most relevant ones. Finally, I would like to stress some points: 1) lapw0 stops after more or less 7 minutes, but it took about 2 hours in the successful calculation. 2) lapw1 stops after 5 seconds without generating the case.energy_* files and case.dayfile does not contain the time statistic for each processor. 3) OMP_NUM_THREADS=12 is overwritten by the system (in my .bashrc I have OMP_NUM_THREADS=1), but even when I export this variable equal to 1 in the submission script, I get the same crash. Thank you very much for your attention, Luis === :log file (init_lapw) options: Wed Apr 2 14:07:30 BRT 2014 (x_lapw) nn -f InPzb15InPwurt3-V2 Wed Apr 2 14:07:46 BRT 2014 (x) nn Wed Apr 2 14:08:03 BRT 2014 (x) sgroup Wed Apr 2 14:08:23 BRT 2014 (x) symmetry Wed Apr 2 14:08:48 BRT 2014 (x) lstart Wed Apr 2 14:09:38 BRT 2014 (x) kgen Wed Apr 2 14:09:58 BRT 2014 (x) dstart -c -p (initso_lapw) options: Tue May 27 16:07:00 BRT 2014 (x) Machines2W (run_lapw) options: -p -NI -ec 0.0001 -cc 0.0001 -i 150 -it Tue May 27 16:07:00 BRT 2014 (x) lapw0 -p Tue May 27 16:14:10 BRT 2014 (x) lapw1 -it -p -c Tue May 27 16:14:15 BRT 2014 (x) lapw2 -p -c === case.dayfile Calculating InPzb15InPwurt3-V2 in /home/ice/proj/proj546/ogando/Wien/Calculos/InP/InPzbInPwurt/15camadasZB+3WZ/InPzb15InPwurt3-V2 on r1i0n15 with PID 6538 using WIEN2k_13.1 (Release 17/6/2013) in /home/ice/proj/proj546/ogando/Wien/Executaveis-13-OpenMPI start (Tue May 27 16:07:00 BRT 2014) with lapw0 (150/99 to go) cycle 1 (Tue May 27 16:07:00 BRT 2014) (150/99 to go) lapw0 -p (16:07:00) starting parallel lapw0 at Tue May 27 16:07:00 BRT 2014 .machine0 : 12 processors 2540.314u 12.204s 7:09.36 594.4% 0+0k 180672+52736io 5pf+0w lapw1 -it -p -c (16:14:10) starting parallel lapw1 at Tue May 27 16:14:10 BRT 2014 - starting parallel LAPW1 jobs at Tue May 27 16:14:10 BRT 2014 running LAPW1 in parallel mode (using .machines) 12 number_of_parallel_jobs r1i0n15(1) r1i0n15(1) r1i0n15(1) r1i0n15(1) r1i0n15(1) r1i0n15(1) r1i0n15(1) r1i0n15(1) r1i0n15(1) r1i0n15(1) r1i0n15(1) r1i0n15(1)Summary of lapw1para: r1i0n15 k=1
Re: [Wien] Dear Wien2k users and developers
An additional comment: Spacegroup 146_R3 is an R spacegroup lattice [http://www.mail-archive.com/wien%40zeus.theochem.tuwien.ac.at/msg05554.html]. You should make sure that all your atomic positions are rhombohedral and nonequivalent. On 5/29/2014 3:58 AM, t...@theochem.tuwien.ac.at wrote: The problem is that spheres overlap which is forbidden. I don't think that your case.struct file is ok. Be aware that the values for a, b and c in case.struct are always in bohr. unit=ang in case.struct is only for the w2web interface. On Thu, 29 May 2014, Mian Fayyaz Ahmad wrote: I am making structure file of BiFeO3 space group R3 with lattice parameters a=b =5.5805 and c= 13.8763 (Angstrom) with angles alpha= beta = 90 gamma = 120 ( degree) during initialization i got an error. if i accept gmax value reduces to gmin in LSTAR. please help me how can strucure file can be made with above said space group. ERROR !!! RMT( 3)=2.0 AND RMT( 5)=2.0 SUMS TO 4.0 GT NNN-DIST= 2.26055 ERROR !!! RMT( 3)=2.0 AND RMT( 3)=2.0 SUMS TO 4.0 GT NNN-DIST= 2.32636 ERROR !!! RMT( 3)=2.0 AND RMT( 1)=2.0 SUMS TO 4.0 GT NNN-DIST= 2.34990 ERROR !!! RMT( 3)=2.0 AND RMT( 2)=2.0 SUMS TO 4.0 GT NNN-DIST= 2.97626 ERROR !!! RMT( 3)=2.0 AND RMT( 6)=2.0 SUMS TO 4.0 GT NNN-DIST= 3.96941 ERROR !!! RMT( 4)=2.0 AND RMT( 2)=2.0 SUMS TO 4.0 GT NNN-DIST= 2.34990 ERROR !!! RMT( 4)=2.0 AND RMT( 4)=2.0 SUMS TO 4.0 GT NNN-DIST= 2.94645 ERROR !!! RMT( 4)=2.0 AND RMT( 1)=2.0 SUMS TO 4.0 GT NNN-DIST= 2.97626 ERROR !!! RMT( 4)=2.0 AND RMT( 5)=2.0 SUMS TO 4.0 GT NNN-DIST= 3.13382 ERROR !!! RMT( 5)=2.0 AND RMT( 2)=2.0 SUMS TO 4.0 GT NNN-DIST= 0.86519 ERROR !!! RMT( 6)=2.0 AND RMT( 3)=2.0 SUMS TO 4.0 GT NNN-DIST= 3.96941 NN ENDS 0.1u 0.0s 0:00.13 100.0% 0+0k 0+320io 0pf+0w atom Z RMT-max RMT 1 83.0 1.20 0.47 2 83.0 0.47 0.47 3 26.0 1.14 1.14 4 26.0 1.14 1.14 5 8.0 0.39 0.39 6 8.0 1.82 0.39 Do you want to accept these radii; discard them; or rerun setRmt (a/d/r): Best Regards Mian Fayyaz AhmadPhD Research Scholar Magnetophotonics Research Lab. Department of Physics Sungkyunkwan University Suwon,440-746 Republic of Korea Cell# +821059295956 ___ 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
Re: [Wien] warning: !!! Bravais lattice has changed.
(0.0,0.0,0.226) appears to be in hexagonal coordinates. Did you enter the atomic position in StructGen as rhombohedral [http://www.mail-archive.com/wien%40zeus.theochem.tuwien.ac.at/msg05554.html]? On 5/29/2014 12:37 AM, sonusha...@iitmandi.ac.in wrote: Dear all In doing the initialization of As element in the trigonal symmetry, space group number is 166 with a=b= 3.76 and c=10.5480 alpha and beta = 90 and gamma = 120 (Information from WWW-MINCRYST) atomic positions are 0.0 0.0 0.226 I am getting warning: !!! Bravais lattice has changed. Space group has changed to 12 (C 2/m), while I have used 166 (R-3m) space group. Why I am getting this error. ___ 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
Re: [Wien] Wien2k stopped working
Dear Prof. Marks, Thank you very much for your comments. I suspect that sys_adm changed something they assumed harmless for users. I will follow your suggestions. All the best, Luis 2014-05-29 10:19 GMT-03:00 Laurence Marks l-ma...@northwestern.edu: Problems such as this are hard to help with remotely. It looks like something has gone wrong at the system level, and my guess is that it has one of two sources: a. Something has gone wrong with your account/directories. It could be as simple as your time allocation has expired, your password has been hacked or your .bashrc file has got corrupted. Check the basics, e.g. you can create a file, compile a simple program etc. While this is unlikely, you never know. b. There have been OS changes of some sort. Many sys_admins assume that users just employ the software that is provided, often using modules, and this is not compatible with how Wien2k runs. It may be that they have removed some of the libraries that you linked Wien2k against, changed how the nodes list is provided to you (which may break Machines2W). For instance, the overwriting of OMP_NUM_THREADS implies to me that someone has decided that of course you want to run using openmpi, which at least at the moment is not useful to you. (I know PB wants to change this, so sometime this statement may change.) Try some diagnostics to try and work out what has happened, for instance: * Compile something like hello world both mpi and non-mpi versions, then run it in a simple job. * Write a small script to interrogate the environment when you start a job, e.g. using commands such as ldd $WIENROOT/lapw1_mpi, env | grep -e MPI -e MKL as well as obvious ones such as ulimit, echo $PATH etc. * Check the cluster web-page, maybe they announced some changes. * Use ifort --version and similar, as well as which mpirun and similar -- maybe new. * If you know a friendly sys_admin ask them for general info. It is good to nurture someone. Of course, all of this may be totally wrong and you may have already sorted things out. On Wed, May 28, 2014 at 8:23 AM, Luis Ogando lcoda...@gmail.com wrote: Dear Wien2k community, I have Wien2k 13.1 installed in a SGI cluster using ifort, icc and Open MPI. The installation was a hard work (I would like to thank again the help from Prof. Lawrence Marks), but after all I have used Wien2k without problems for several months. I performed the first step of a long calculation and saved it in a different directory. When I tried the next step in the original directory, Wien2k crashed. After some tests, I decided to reinitialize the calculation from the beginning (in other words, to repeat the first step). To my surprise, I did not succeed even in this case and I would like to know if someone has faced such an unexpected problem. Please, find below some of the output files that I consider the most relevant ones. Finally, I would like to stress some points: 1) lapw0 stops after more or less 7 minutes, but it took about 2 hours in the successful calculation. 2) lapw1 stops after 5 seconds without generating the case.energy_* files and case.dayfile does not contain the time statistic for each processor. 3) OMP_NUM_THREADS=12 is overwritten by the system (in my .bashrc I have OMP_NUM_THREADS=1), but even when I export this variable equal to 1 in the submission script, I get the same crash. Thank you very much for your attention, Luis === :log file (init_lapw) options: Wed Apr 2 14:07:30 BRT 2014 (x_lapw) nn -f InPzb15InPwurt3-V2 Wed Apr 2 14:07:46 BRT 2014 (x) nn Wed Apr 2 14:08:03 BRT 2014 (x) sgroup Wed Apr 2 14:08:23 BRT 2014 (x) symmetry Wed Apr 2 14:08:48 BRT 2014 (x) lstart Wed Apr 2 14:09:38 BRT 2014 (x) kgen Wed Apr 2 14:09:58 BRT 2014 (x) dstart -c -p (initso_lapw) options: Tue May 27 16:07:00 BRT 2014 (x) Machines2W (run_lapw) options: -p -NI -ec 0.0001 -cc 0.0001 -i 150 -it Tue May 27 16:07:00 BRT 2014 (x) lapw0 -p Tue May 27 16:14:10 BRT 2014 (x) lapw1 -it -p -c Tue May 27 16:14:15 BRT 2014 (x) lapw2 -p -c === case.dayfile Calculating InPzb15InPwurt3-V2 in /home/ice/proj/proj546/ogando/Wien/Calculos/InP/InPzbInPwurt/15camadasZB+3WZ/InPzb15InPwurt3-V2 on r1i0n15 with PID 6538 using WIEN2k_13.1 (Release 17/6/2013) in /home/ice/proj/proj546/ogando/Wien/Executaveis-13-OpenMPI start (Tue May 27 16:07:00 BRT 2014) with lapw0 (150/99 to go) cycle 1 (Tue May 27 16:07:00 BRT 2014) (150/99 to go) lapw0 -p (16:07:00) starting parallel lapw0 at Tue May 27 16:07:00 BRT 2014 .machine0 : 12 processors 2540.314u 12.204s 7:09.36 594.4% 0+0k 180672+52736io 5pf+0w lapw1 -it -p -c (16:14:10) starting parallel lapw1 at Tue May 27
Re: [Wien] Yes, the sys_adm changed somethings
The wonders of sys_admins! A very, very strange decision; I assume that someone was abusing the system which led to the change. You are going to have to change many things, not just your options. The first thing to do it find out what will work to launch a task on another node without doing a login. It may be that you can use rsh or something else since (I assume) ssh is forbidden. Hopefully there is something you can use and just change the variable remote uses in lapwXpara, i.e. something like in parallel_options setenv remote Some Command. If there is nothing, or they are less than helpful, you are going to have to use something similar to pbsh in SRC_mpiutil/mpi_examples as a replacement for ssh. This uses mpirun (any flavor should work although options may change) to create a csh on a remote node, in effect a login-free ssh. (It can in fact be better than ssh since that has some bugs when things go wrong.) I assume that they have not broken the conventional mpi launching of tasks on remote nodes. You may also need to do some more convolutions. For instance, on one cluster I use ssh can be badly broken so in parallel_options I have (impi version) setenv WIEN_MPIRUN mpirun -bootstrap-exec $WIENROOT/hopen -n _NP_ -machinefile _HOSTS_ _EXEC_ with hopen the file: #!/bin/bash a=`echo $@ | sed -e 's/-x -q//'` /software/mpi/openmpi-1.7.2-intel2013.2/bin/mpirun -np 1 --host $a This uses openmpi to launch an mpi task for impi (Intel's version) instead of ssh. Note that it edits the input string to change some things from impi to openmpi options, which you may need to do as well. On Thu, May 29, 2014 at 2:24 PM, Luis Ogando lcoda...@gmail.com wrote: Hi Gavin and Prof. Marks, The system administrators answered me and ,yes, they changed somethings: 1) The users are no more allowed to log in the nodes where jobs are run. 2) The run of interactive remote jobs (from other nodes in the nodes where jobs are run) is now forbidden. In other words, the interactive access (login) and remote execution of commands are now forbidden. Do I have to change my parallel_options file because of this ?? All the best, Luis 2014-05-29 14:25 GMT-03:00 Gavin Abo gs...@crimson.ua.edu: Dear Luis, A few comments off the mailing list. I agree with Prof. Marks that this problem is hard to help with remotely. I suppose it is okay, but in your :log file, I find it a little strange that you have initso_lapw, but it is not a -so (spin orbit) calculation that you are running. I haven't used -it for any calculations recently. I doubt it causes the problem, but you might try without it to see if it makes any difference. Is it just this calculation that does not work? Or other calculations with and without -p that do not run? The first error message that I see is grep: .processes: No such file or directory. This likely means that there is no .processes file, when there is expected to be one. I believe the .processes file is create by lapw1para_lapw. It looks like the .processes file is created from an 'awk' of the .machines file. I see no error message for awk, so awk should be installed on the system. However, it would be best to check that it is installed and working in a terminal with the command: awk -W version I'm not familiar with Machines2W, but if I understand correctly, this is creating the .machines file for your system. If I had the same problem, I would first try to open the .machines file in the directory InPzb15InPwurt3-V2 of the current calculation with a text editor to check if it looks okay or not. Then, I would try to compare it to the .machines file of an earlier calculation that worked. It might be a little helpful (but not a lot) for your current problem, but it is noted that in $WIENROOT/lapw1para_lapw, you could change line 61 from: set debug = 0 to set debug = 1 to get some debug information for lapw1para_lapw. Kind regards, Gavin On 5/29/2014 7:19 AM, Laurence Marks wrote: Problems such as this are hard to help with remotely. It looks like something has gone wrong at the system level, and my guess is that it has one of two sources: a. Something has gone wrong with your account/directories. It could be as simple as your time allocation has expired, your password has been hacked or your .bashrc file has got corrupted. Check the basics, e.g. you can create a file, compile a simple program etc. While this is unlikely, you never know. b. There have been OS changes of some sort. Many sys_admins assume that users just employ the software that is provided, often using modules, and this is not compatible with how Wien2k runs. It may be that they have removed some of the libraries that you linked Wien2k against, changed how the nodes list is provided to you (which may break Machines2W). For instance, the overwriting of OMP_NUM_THREADS implies to me that someone has decided that of course you want to
