Re: [Wien] Error during NMR calculations
Dear Prof. Peter Blaha and Gavin Abo, Thanks for your response and suggestions! I will try to resolve it. By the way, I have tried NMR calculation on other material (containing 56 atoms) using same way and it works well for NMR calculations in parallel mode. Regards Sandeep On Tue, Sep 11, 2018 at 6:10 PM sandeep Kumar wrote: > Dear Prof. Peter Blaha and WIEN2k Users, > > I got an error when I was trying to calculate the NMR chemical shift of > all atoms in NaCaPO4. The scf finished nicely (in parallel mode), > but when I did "x_nmr_lapw -p " (after "x_nmr_lapw -mode in1 -focus O"), > I got errors. Howver, nmr_q0 was created and I got an errors in LAPW1. > The error was below: > > ** Error in Parallel LAPW1 > ** LAPW1 STOPPED at Tue Sep 11 16:52:39 IDT 2018 > ** check ERROR FILES! > Error in LAPW1 > > and the output details are: > > klist ready > > nmr: klists done > > cd ./nmr_q0 ... x lapw1 -nmr -c -p -scratch ./ > starting parallel lapw1 at Tue Sep 11 08:28:54 IDT 2018 > -> starting parallel LAPW1 jobs at Tue Sep 11 08:28:54 IDT 2018 > running LAPW1 in parallel mode (using .machines) > 6 number_of_parallel_jobs > [1] 659 > [2] 711 > [3] 787 > [4] 863 > [5] 976 > [6] 1051 > exciton10(1) 13730.809u 51.902s 4:03:10.73 94.46% 0+0k 0+0io > 0pf+0w > exciton10(1) 13665.578u 70.931s 8:16:25.69 46.12% 0+0k 0+0io > 0pf+0w > exciton10(1) 4.504u 15.270s 2:27.88 13.37% 0+0k 0+0io 0pf+0w > exciton10(1) 13839.711u 66.818s 8:22:41.08 46.11% 0+0k 0+0io > 0pf+0w > exciton10(1) 13835.693u 70.164s 8:23:41.55 46.01% 0+0k 0+0io > 0pf+0w > exciton10(1) 13437.276u 54.243s 6:43:58.23 55.66% 0+0k 0+0io > 0pf+0w >Summary of lapw1para: >exciton10 k=6 user=68513.6wallclock=2294.88 > ** LAPW1 crashed! > 1.164u 2.922s 8:24:14.40 0.0% 0+0k 27024+1952io 235pf+0w > error: command /home/qnt/sandeep/CODES/WIEN2k_18.1_libxc/lapw1cpara -c > lapw1.def failed > > stop error > > > Please suggest me what should I do in this case. I would be thankful to > you. > > Thanks > > Sandeep > > > -- > Dr. Sandeep Kumar (Postdoctoral Research Fellow) > Institute for Nanotechnology & Advanced Materials, > Department of Chemistry, > Bar-Ilan University, Ramat-Gan 52900, Israel > > -- Dr. Sandeep Kumar (Postdoctoral Research Fellow) Institute for Nanotechnology & Advanced Materials, Department of Chemistry, Bar-Ilan University, Ramat-Gan 52900, Israel ___ 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] Error during NMR calculations
There is almost no information. From the dayfile I can see that the 3rd lapw1 is much shorter than the others: exciton10(1) 4.504u 15.270s 2:27.88 13.37% 0+0k 0+0io 0pf+0w so I expect that this one crashes for what ever reasons (most likely, something like not enough memory, diskspace, communication error, ...) cd nmr_q0 lse and check the error (or output1_* files). If it was a temporary system failure, all you need is to restart the job. On 09/11/2018 05:10 PM, sandeep Kumar wrote: Dear Prof. Peter Blaha and WIEN2k Users, I got an error when I was trying to calculate the NMR chemical shift of all atoms in NaCaPO4. The scf finished nicely (in parallel mode), but when I did "x_nmr_lapw -p " (after "x_nmr_lapw -mode in1 -focus O"), I got errors. Howver, nmr_q0 was created and I got an errors in LAPW1. The error was below: ** Error in Parallel LAPW1 ** LAPW1 STOPPED at Tue Sep 11 16:52:39 IDT 2018 ** check ERROR FILES! Error in LAPW1 and the output details are: klist ready nmr: klists done cd ./nmr_q0 ... x lapw1 -nmr -c -p -scratch ./ starting parallel lapw1 at Tue Sep 11 08:28:54 IDT 2018 -> starting parallel LAPW1 jobs at Tue Sep 11 08:28:54 IDT 2018 running LAPW1 in parallel mode (using .machines) 6 number_of_parallel_jobs [1] 659 [2] 711 [3] 787 [4] 863 [5] 976 [6] 1051 exciton10(1) 13730.809u 51.902s 4:03:10.73 94.46% 0+0k 0+0io 0pf+0w exciton10(1) 13665.578u 70.931s 8:16:25.69 46.12% 0+0k 0+0io 0pf+0w exciton10(1) 4.504u 15.270s 2:27.88 13.37% 0+0k 0+0io 0pf+0w exciton10(1) 13839.711u 66.818s 8:22:41.08 46.11% 0+0k 0+0io 0pf+0w exciton10(1) 13835.693u 70.164s 8:23:41.55 46.01% 0+0k 0+0io 0pf+0w exciton10(1) 13437.276u 54.243s 6:43:58.23 55.66% 0+0k 0+0io 0pf+0w Summary of lapw1para: exciton10 k=6 user=68513.6 wallclock=2294.88 ** LAPW1 crashed! 1.164u 2.922s 8:24:14.40 0.0% 0+0k 27024+1952io 235pf+0w error: command /home/qnt/sandeep/CODES/WIEN2k_18.1_libxc/lapw1cpara -c lapw1.def failed stop error Please suggest me what should I do in this case. I would be thankful to you. Thanks Sandeep -- Dr. Sandeep Kumar (Postdoctoral Research Fellow) Institute for Nanotechnology & Advanced Materials, Department of Chemistry, Bar-Ilan University, Ramat-Gan 52900, Israel ___ 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.atWIEN2k: http://www.wien2k.at WWW: http://www.imc.tuwien.ac.at/TC_Blaha -- ___ 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] Error during NMR calculations
The output below looks like it is from a *.error and case.dayfile. While that is partially informative, it seems insufficient. So I doubt anybody can help you with the given information. I suggest you look further for additional error messages. Usually such an error is accompanied with a forrtl (if WIEN2k was built with the Intel Fortran compiler with the -traceback setting) or mpi error message. The MPI_COMM_WORLD error from mpirun and forrtl: severe (174): SIGSEGV looks like an example of something similar you might find for both at [ https://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/msg01723.html ]. If I recall correctly, those usually seemed to be in the standard error output of the terminal if entering the command directly in the terminal or standard output file if using a queue system. Though, on rare occurrences, I think some error message appeared in other files such as :parallel, .time*, .stdout*, .lapw1para. Refer to reference [11] at [ https://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/msg17970.html ]. There are cases that happen less often were there are no error messages. Check the output files such as the case.output* and case.scf* files. There are sometimes messages like WARNINGS or indicators of problematic data (NaN, ). Also, don't forget about the possibility of compiler issues (as I don't see a mention of what compiler you used) [ https://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/msg17288.html ]. Since lapw1cpara is a symbolic link to the lapw1para_lapw script file, you could also try turning on echo (-x) [or verbose (-v)] by changing the first line temporarily in lapw1para_lapw for example to [ https://docs.oracle.com/cd/E19683-01/816-0210/6m6nb7m71/index.html ]: #!/bin/csh -xf Using that to help debug/troubleshoot is something I got from mailing list archive: https://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/msg17930.html https://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/msg07734.html On 9/11/2018 9:10 AM, sandeep Kumar wrote: Dear Prof. Peter Blaha and WIEN2k Users, I got an error when I was trying to calculate the NMR chemical shift of all atoms in NaCaPO4. The scf finished nicely (in parallel mode), but when I did "x_nmr_lapw -p " (after "x_nmr_lapw -mode in1 -focus O"), I got errors. Howver, nmr_q0 was created and I got an errors in LAPW1. The error was below: ** Error in Parallel LAPW1 ** LAPW1 STOPPED at Tue Sep 11 16:52:39 IDT 2018 ** check ERROR FILES! Error in LAPW1 and the output details are: klist ready nmr: klists done cd ./nmr_q0 ... x lapw1 -nmr -c -p -scratch ./ starting parallel lapw1 at Tue Sep 11 08:28:54 IDT 2018 -> starting parallel LAPW1 jobs at Tue Sep 11 08:28:54 IDT 2018 running LAPW1 in parallel mode (using .machines) 6 number_of_parallel_jobs [1] 659 [2] 711 [3] 787 [4] 863 [5] 976 [6] 1051 exciton10(1) 13730.809u 51.902s 4:03:10.73 94.46% 0+0k 0+0io 0pf+0w exciton10(1) 13665.578u 70.931s 8:16:25.69 46.12% 0+0k 0+0io 0pf+0w exciton10(1) 4.504u 15.270s 2:27.88 13.37% 0+0k 0+0io 0pf+0w exciton10(1) 13839.711u 66.818s 8:22:41.08 46.11% 0+0k 0+0io 0pf+0w exciton10(1) 13835.693u 70.164s 8:23:41.55 46.01% 0+0k 0+0io 0pf+0w exciton10(1) 13437.276u 54.243s 6:43:58.23 55.66% 0+0k 0+0io 0pf+0w Summary of lapw1para: exciton10 k=6 user=68513.6 wallclock=2294.88 ** LAPW1 crashed! 1.164u 2.922s 8:24:14.40 0.0% 0+0k 27024+1952io 235pf+0w error: command /home/qnt/sandeep/CODES/WIEN2k_18.1_libxc/lapw1cpara -c lapw1.def failed stop error Please suggest me what should I do in this case. I would be thankful to you. Thanks Sandeep -- Dr. Sandeep Kumar (Postdoctoral Research Fellow) Institute for Nanotechnology & Advanced Materials, Department of Chemistry, Bar-Ilan University, Ramat-Gan 52900, Israel ___ 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] Error during NMR calculations
Dear Prof. Peter Blaha and WIEN2k Users, I got an error when I was trying to calculate the NMR chemical shift of all atoms in NaCaPO4. The scf finished nicely (in parallel mode), but when I did "x_nmr_lapw -p " (after "x_nmr_lapw -mode in1 -focus O"), I got errors. Howver, nmr_q0 was created and I got an errors in LAPW1. The error was below: ** Error in Parallel LAPW1 ** LAPW1 STOPPED at Tue Sep 11 16:52:39 IDT 2018 ** check ERROR FILES! Error in LAPW1 and the output details are: klist ready nmr: klists done cd ./nmr_q0 ... x lapw1 -nmr -c -p -scratch ./ starting parallel lapw1 at Tue Sep 11 08:28:54 IDT 2018 -> starting parallel LAPW1 jobs at Tue Sep 11 08:28:54 IDT 2018 running LAPW1 in parallel mode (using .machines) 6 number_of_parallel_jobs [1] 659 [2] 711 [3] 787 [4] 863 [5] 976 [6] 1051 exciton10(1) 13730.809u 51.902s 4:03:10.73 94.46% 0+0k 0+0io 0pf+0w exciton10(1) 13665.578u 70.931s 8:16:25.69 46.12% 0+0k 0+0io 0pf+0w exciton10(1) 4.504u 15.270s 2:27.88 13.37% 0+0k 0+0io 0pf+0w exciton10(1) 13839.711u 66.818s 8:22:41.08 46.11% 0+0k 0+0io 0pf+0w exciton10(1) 13835.693u 70.164s 8:23:41.55 46.01% 0+0k 0+0io 0pf+0w exciton10(1) 13437.276u 54.243s 6:43:58.23 55.66% 0+0k 0+0io 0pf+0w Summary of lapw1para: exciton10 k=6 user=68513.6wallclock=2294.88 ** LAPW1 crashed! 1.164u 2.922s 8:24:14.40 0.0% 0+0k 27024+1952io 235pf+0w error: command /home/qnt/sandeep/CODES/WIEN2k_18.1_libxc/lapw1cpara -c lapw1.def failed stop error Please suggest me what should I do in this case. I would be thankful to you. Thanks Sandeep -- Dr. Sandeep Kumar (Postdoctoral Research Fellow) Institute for Nanotechnology & Advanced Materials, Department of Chemistry, Bar-Ilan University, Ramat-Gan 52900, Israel ___ 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] Error During NMR Calculations
Dear Professor Peter Blaha,
I am using WIEN2k 17.1 version to compute the NMR chemical shifts of a
compound. All part of calculations has completed and I also got
case.outputnmt_integ file but there were not written the final NMR chemical
shifts at the end of the file. I got this error:
[1]Exit 41 ( cd $dir; $exec -p $loop >>
nmr.out.${loop} ) >& nmr.err.$loop
forrtl: severe (24): end-of-file during read, unit 57, file
/home/qnt/sandeep/wien_data/C1_test/C1_test.xim_1
Image PCRoutineLineSource
nmrc 004DB159 Unknown Unknown Unknown
nmrc 0045F33F sumpara_ 42
sumpara.f
nmrc 00411C5E MAIN__ 35 nmr.f
nmrc 004046A6 Unknown Unknown Unknown
libc.so.6 00340C81ED1D Unknown Unknown Unknown
nmrc 00404599 Unknown Unknown Unknown
forrtl: severe (24): end-of-file during read, unit 54, file
/home/qnt/sandeep/wien_data/C1_test/C1_test.current_int_x
Image PCRoutineLineSource
nmrc 004D68A6 Unknown Unknown Unknown
nmrc 004300A6 read_current_int_ 80
read_current_tmp_.F
nmrc 0043AD9E integrate_current 34
integrate_current_tmp_.F
nmrc 00411C89 MAIN__ 44 nmr.f
nmrc 004046A6 Unknown Unknown Unknown
libc.so.6 00340C81ED1D Unknown Unknown Unknown
nmrc 00404599 Unknown Unknown Unknown
Please suggest me what should I do? I would be thankful to you.
Waiting eagerly for your reply!
Thanks
Sandeep
--
Dr. Sandeep Kumar, Post-doc
Department of Chemistry,
The Lise Meitner-Minerva Center for Computational Quantum Chemistry &
The Institute for Nanotechnology and Advanced Materials,
Bar-Ilan University, Ramat-Gan 52900, Israel
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