Re: [Wien] lapwsopara error
maybe this helps from Wikipedia In computing, a bus error is a fault raised by hardware, notifying an operating system (OS) that a process is trying to access memory that the CPU cannot physically address: an invalid address for the address bus, hence the name. In modern use on most architectures these are much rarer than segmentation faults, which occur primarily due to memory access violations: problems in the logical address or permissions. more is found from google Ciao Gerhard DEEP THOUGHT in D. Adams; Hitchhikers Guide to the Galaxy: "I think the problem, to be quite honest with you, is that you have never actually known what the question is." Dr. Gerhard H. Fecher Institut of Inorganic and Analytical Chemistry Johannes Gutenberg - University 55099 Mainz and Max Planck Institute for Chemical Physics of Solids 01187 Dresden Von: Wien [wien-boun...@zeus.theochem.tuwien.ac.at] im Auftrag von Md. Fhokrul Islam [fis...@hotmail.com] Gesendet: Dienstag, 7. März 2017 12:21 An: A Mailing list for WIEN2k users Betreff: Re: [Wien] lapwsopara error Hi Gavin, You are right, there are .timeso files (but no .stdoutso) for each k-point and the ones that fail to complete have an error message: -cn0130 Bus error Considering that this error occurs due to a specific choice of spin direction, can it be due to software bug? Thanks, Fhokrul From: Wien <wien-boun...@zeus.theochem.tuwien.ac.at> on behalf of Gavin Abo <gs...@crimson.ua.edu> Sent: Tuesday, March 7, 2017 12:52 AM To: A Mailing list for WIEN2k users Subject: Re: [Wien] lapwsopara error For example, in the lapwsopara_lapw file on line 292 there is >& .stdoutso_$loop and on line 297 there is >>.timeso_$loop So, some errors that occur might be redirected into these dot files (which are usually hidden unless ls -a is used or show hidden is selected in a graphic file manager [ http://askubuntu.com/questions/94780/what-are-dot-files ]). So if you [https://cdn.sstatic.net/Sites/askubuntu/img/apple-touch-i...@2.png?v=c492c9229955]<http://askubuntu.com/questions/94780/what-are-dot-files> What are dot-files? - Ask Ubuntu<http://askubuntu.com/questions/94780/what-are-dot-files> askubuntu.com I am having a hard time grasping what dot-files are or what they are for. Are they directories? How do I navigate to them? Thank you! haven't already done so, I suggest also checking the .timeso_* and .stdoutso_* files if they exist. On 3/6/2017 8:04 AM, Peter Blaha wrote: > All this info does not help. > There must be somewhere an info why some of the lapwso calculations > crash. > What is in the error files, or in the STDOUT of your batch job. > > Eventually try to put my lapwso uplapwso_1.def line at the end of > your job, or add ls -als /path-to-vector-file/*vector* > > > > On 03/06/2017 02:29 PM, Md. Fhokrul Islam wrote: >> Hi Prof Blaha, >> >> >> Thank you for your reply. Here is some more info about this calculation. >> >> >> I am using Wien2k16 which is compiled using intel/2017. >> >> >> I have checked the output files from lapw1c which look correct to >> me. Unfortunately, >> >> I couldn't check vector* files since it was in temporary scratch >> directory which are >> >> automatically deleted after the job exits form the queue. But the >> corresponding energyup/dn >> >> files are ok. For each k-point it writes out all eigenvalues for the >> corresponding k-point: >> >> >> (more lines above) >> >> 200.20204200.20204198.22381 0.20204 0.20204 0.20204 0.20204 0.20204 >> 0.20204 0.20204 0.20204 0.20204 0.20204 0.0 >> 0.20204 0.20204 -1.7761.0997.0997.0 >> 0.60204999.0999.0999.0999.0999.0 >> 1.6667E-01 1.6667E-01 5.E-01 1 >> 9481 7160 1.0 >>1 -2.97772569684435 >>2 -2.97708536428630 >>3 -2.97619544771632 >>4 -2.30343486814166 >>. >> So I think lapw1 works fine. But the problem is in lapwso. Here is the >> k-mesh that I am using for 001 (same for 110 direction >> which works fine): >> >> 1 1 1 3 6 1.0 -7.0 1.5 >> 16 k, div: ( 3 3 1) >> 2 1 3 3 6 1.0 >> 3 1 5 3 6 1.0 >> 4 3 1 3 6 1.0 >> 5 3 3 3 6 1.0 >> 6 3 5 3 6 1.0 >> 7 5 1 3
Re: [Wien] lapwsopara error
For example, in the lapwsopara_lapw file on line 292 there is >& .stdoutso_$loop and on line 297 there is >>.timeso_$loop So, some errors that occur might be redirected into these dot files (which are usually hidden unless ls -a is used or show hidden is selected in a graphic file manager [ http://askubuntu.com/questions/94780/what-are-dot-files ]). So if you haven't already done so, I suggest also checking the .timeso_* and .stdoutso_* files if they exist. On 3/6/2017 8:04 AM, Peter Blaha wrote: All this info does not help. There must be somewhere an info why some of the lapwso calculations crash. What is in the error files, or in the STDOUT of your batch job. Eventually try to put my lapwso uplapwso_1.def line at the end of your job, or add ls -als /path-to-vector-file/*vector* On 03/06/2017 02:29 PM, Md. Fhokrul Islam wrote: Hi Prof Blaha, Thank you for your reply. Here is some more info about this calculation. I am using Wien2k16 which is compiled using intel/2017. I have checked the output files from lapw1c which look correct to me. Unfortunately, I couldn't check vector* files since it was in temporary scratch directory which are automatically deleted after the job exits form the queue. But the corresponding energyup/dn files are ok. For each k-point it writes out all eigenvalues for the corresponding k-point: (more lines above) 200.20204200.20204198.22381 0.20204 0.20204 0.20204 0.20204 0.20204 0.20204 0.20204 0.20204 0.20204 0.20204 0.0 0.20204 0.20204 -1.7761.0997.0997.0 0.60204999.0999.0999.0999.0999.0 1.6667E-01 1.6667E-01 5.E-01 1 9481 7160 1.0 1 -2.97772569684435 2 -2.97708536428630 3 -2.97619544771632 4 -2.30343486814166 . So I think lapw1 works fine. But the problem is in lapwso. Here is the k-mesh that I am using for 001 (same for 110 direction which works fine): 1 1 1 3 6 1.0 -7.0 1.5 16 k, div: ( 3 3 1) 2 1 3 3 6 1.0 3 1 5 3 6 1.0 4 3 1 3 6 1.0 5 3 3 3 6 1.0 6 3 5 3 6 1.0 7 5 1 3 6 1.0 8 5 3 3 6 1.0 9 5 5 3 6 1.0 END For k-points 2,3,4, 6 and 9 it created all energyso* and outputso* files correctly. But for the remaining k-points it didn't. The supercell has 135 atoms and it is supposed to write parameters for each atoms for both spins and then write out the energy. But it turns out the file ends after writing the parameters for atoms upto 133 spin 1. Here is how the end of the outputso_1 file looks like (the same for other 3 incomplete files) outputso_1: relativistic lo: 1 0.300 2 4 -0.420088705696323 RLO COEFFICIENT: l,A,B,C 1 10.38893 0.0 -11.18331 ATOMIC PARAMETERS FOR ** SPIN=1 ENERGY PARAMETERS ARE 0.20 0.20 -1.78 0.20 0.20 0.20 0.20 for lo: 0.20 0.20-1.78 999.00 997.00 997.00 0.60 999.00 999.00 999.00 999.00 999.00 energysoup_1 (last few lines): 200.20204200.20204198.22005 0.20204 0.20204 0.20204 0.20204 0.20204 0.20204 0.20204 0.20204 0.20204 0.20204 0.0 0.20204 0.20204 -1.77995999.0997.0997.0 0.60204999.0999.0 0.3999.0999.0 200.20204200.20204198.22192 0.20204 0.20204 0.20204 0.20204 0.20204 0.20204 0.20204 0.20204 0.20204 0.20204 0.0 0.20204 0.20204 -1.77808999.0997.0997.0 0.60204999.0999.0 0.3999.0999.0 Clearly both of these files are incomplete. I think memory is not an issue as I am using about 9GB/core and also have 500 GB disk space available. System doesn't have any symmetry for both in-plane and out-of-plane calculations. By the way, there seems to be a formatting problem in outputso files. After writing out parameters for 99 atoms it places an asterisk in place of atom index as shown in the above. ATOMIC PARAMETERS FOR ** SPIN=1 Kind regards, Fhokrul *From:* Wien <wien-boun...@zeus.theochem.tuwien.ac.at> on behalf of Peter Blaha <pbl...@theochem.tuwien.ac.at> *Sent:* Monday, March 6, 2017 9:54 AM *To:* A Mailing list for WIEN2k users *Subject:* Re: [Wien] lapwsopara error Only you can find the real reason for this problem. You are saying that you can find all 9*2 lapw1 calculations worked ? Check ls -als *scf1* ls -als *energy* ls -als *vector* (are you using SRCATCH ?, the search for the vector files in the correspo
Re: [Wien] lapwsopara error
All this info does not help. There must be somewhere an info why some of the lapwso calculations crash. What is in the error files, or in the STDOUT of your batch job. Eventually try to put my lapwso uplapwso_1.def line at the end of your job, or add ls -als /path-to-vector-file/*vector* On 03/06/2017 02:29 PM, Md. Fhokrul Islam wrote: Hi Prof Blaha, Thank you for your reply. Here is some more info about this calculation. I am using Wien2k16 which is compiled using intel/2017. I have checked the output files from lapw1c which look correct to me. Unfortunately, I couldn't check vector* files since it was in temporary scratch directory which are automatically deleted after the job exits form the queue. But the corresponding energyup/dn files are ok. For each k-point it writes out all eigenvalues for the corresponding k-point: (more lines above) 200.20204200.20204198.22381 0.20204 0.20204 0.20204 0.20204 0.20204 0.20204 0.20204 0.20204 0.20204 0.20204 0.0 0.20204 0.20204 -1.7761.0997.0997.0 0.60204999.0999.0999.0999.0999.0 1.6667E-01 1.6667E-01 5.E-01 1 9481 7160 1.0 1 -2.97772569684435 2 -2.97708536428630 3 -2.97619544771632 4 -2.30343486814166 . So I think lapw1 works fine. But the problem is in lapwso. Here is the k-mesh that I am using for 001 (same for 110 direction which works fine): 1 1 1 3 6 1.0 -7.0 1.5 16 k, div: ( 3 3 1) 2 1 3 3 6 1.0 3 1 5 3 6 1.0 4 3 1 3 6 1.0 5 3 3 3 6 1.0 6 3 5 3 6 1.0 7 5 1 3 6 1.0 8 5 3 3 6 1.0 9 5 5 3 6 1.0 END For k-points 2,3,4, 6 and 9 it created all energyso* and outputso* files correctly. But for the remaining k-points it didn't. The supercell has 135 atoms and it is supposed to write parameters for each atoms for both spins and then write out the energy. But it turns out the file ends after writing the parameters for atoms upto 133 spin 1. Here is how the end of the outputso_1 file looks like (the same for other 3 incomplete files) outputso_1: relativistic lo: 1 0.3002 4 -0.420088705696323 RLO COEFFICIENT: l,A,B,C 1 10.38893 0.0 -11.18331 ATOMIC PARAMETERS FOR ** SPIN=1 ENERGY PARAMETERS ARE 0.20 0.20 -1.78 0.20 0.20 0.20 0.20 for lo: 0.20 0.20-1.78 999.00 997.00 997.00 0.60 999.00 999.00 999.00 999.00 999.00 energysoup_1 (last few lines): 200.20204200.20204198.22005 0.20204 0.20204 0.20204 0.20204 0.20204 0.20204 0.20204 0.20204 0.20204 0.20204 0.0 0.20204 0.20204 -1.77995999.0997.0997.0 0.60204999.0999.0 0.3999.0999.0 200.20204200.20204198.22192 0.20204 0.20204 0.20204 0.20204 0.20204 0.20204 0.20204 0.20204 0.20204 0.20204 0.0 0.20204 0.20204 -1.77808999.0997.0997.0 0.60204999.0999.0 0.3999.0999.0 Clearly both of these files are incomplete. I think memory is not an issue as I am using about 9GB/core and also have 500 GB disk space available. System doesn't have any symmetry for both in-plane and out-of-plane calculations. By the way, there seems to be a formatting problem in outputso files. After writing out parameters for 99 atoms it places an asterisk in place of atom index as shown in the above. ATOMIC PARAMETERS FOR ** SPIN=1 Kind regards, Fhokrul *From:* Wien <wien-boun...@zeus.theochem.tuwien.ac.at> on behalf of Peter Blaha <pbl...@theochem.tuwien.ac.at> *Sent:* Monday, March 6, 2017 9:54 AM *To:* A Mailing list for WIEN2k users *Subject:* Re: [Wien] lapwsopara error Only you can find the real reason for this problem. You are saying that you can find all 9*2 lapw1 calculations worked ? Check ls -als *scf1* ls -als *energy* ls -als *vector* (are you using SRCATCH ?, the search for the vector files in the corresponding scratch directories. If they are all ok and complete, you can try to run lapwso individually for all 9 cases: time lapwso uplapwso_1.defruns specifically the calculation producing the scfsoup_1 and *vectorso*_1 files. Check the corresponding outputso*_1 file, and then check for any error or if the vector/scfso files have been created now. Possible problems: memory ? disk space ? network problems ? Most likely, the 2 directions have different symmetry, and thus requirements.
Re: [Wien] lapwsopara error
Only you can find the real reason for this problem. You are saying that you can find all 9*2 lapw1 calculations worked ? Check ls -als *scf1* ls -als *energy* ls -als *vector* (are you using SRCATCH ?, the search for the vector files in the corresponding scratch directories. If they are all ok and complete, you can try to run lapwso individually for all 9 cases: time lapwso uplapwso_1.defruns specifically the calculation producing the scfsoup_1 and *vectorso*_1 files. Check the corresponding outputso*_1 file, and then check for any error or if the vector/scfso files have been created now. Possible problems: memory ? disk space ? network problems ? Most likely, the 2 directions have different symmetry, and thus requirements. Best regards On 03/06/2017 09:54 AM, Md. Fhokrul Islam wrote: Hi Gerhard, Thanks for your reply. I did full SO initialization for each magnetization direction (M). And just to make sure, I repeated the same calculation twice but each time I got the same error. I understand 9 k-point may not give very accurate anisotropy and I will also test with larger k-mesh but my problem is lapwsopara fails only for M along 001 and as I mentioned for some k-points it couldn't write case.scfso file. Regards, Fhokrul *From:* Wien <wien-boun...@zeus.theochem.tuwien.ac.at> on behalf of Fecher, Gerhard <fec...@uni-mainz.de> *Sent:* Monday, March 6, 2017 8:07 AM *To:* A Mailing list for WIEN2k users *Subject:* Re: [Wien] lapwsopara error From your description, it seems you changed only the case.inso but you did not do a full SO initialisation (symmetso, kgen, etc.), did you ? By the way, calculation of magnetic anisotropy is a matter of brute force with respect to number of k points etc., and I think that 9 k points only are by far not enough. Ciao Gerhard DEEP THOUGHT in D. Adams; Hitchhikers Guide to the Galaxy: "I think the problem, to be quite honest with you, is that you have never actually known what the question is." Dr. Gerhard H. Fecher Institut of Inorganic and Analytical Chemistry Johannes Gutenberg - University 55099 Mainz and Max Planck Institute for Chemical Physics of Solids 01187 Dresden Von: Wien [wien-boun...@zeus.theochem.tuwien.ac.at] im Auftrag von Md. Fhokrul Islam [fis...@hotmail.com] Gesendet: Sonntag, 5. März 2017 22:14 An: A Mailing list for WIEN2k users Betreff: [Wien] lapwsopara error Hi Prof Blaha and Wien2k users, I am trying to do anisotropy calculation of some magnetic impurities in bulk Sb2Se3 topological insulator using force theorem. It works fine if I chose magnetization axis in the xy-plane (1 1 0 in case.inso file) but it crashes when magnetization is along z-axis (0 0 1 in case inso). I tried with two different types of impurity (Mn and Cr) but in both cases I get the same error message: Output file: ** LAPWSO crashed! 51852.372u 93.264s 1:56:04.17 745.8%0+0k 376+11416648io 12pf+0w error: command /pfs/nobackup/home/e/eisfh/SRC/Wien2k_16/lapwsopara -up -c uplapwso.def failed Error file: (15 more lapw1 lines above) LAPW1 END LAPW1 END LAPW1 END LAPWSO END LAPWSO END LAPWSO END LAPWSO END LAPWSO END forrtl: severe (24): end-of-file during read, unit 30, file /pfs/nobackup/home/e/eisfh/WIEN2k/Sb2Te3/Bulk/MAE_FT/001/1Mn/1Mn.energysoup_1 Image PCRoutineLineSource lapw2c 006E4A9C Unknown Unknown Unknown lapw2c 00712E75 Unknown Unknown Unknown lapw2c 00425390 fermi_ 43 fermi_tmp_.F lapw2c 00454D31 MAIN__375 lapw2_tmp_.F lapw2c 0040366E Unknown Unknown Unknown libc-2.23.so 2B2573B34830 __libc_start_main Unknown Unknown lapw2c 00403569 Unknown Unknown Unknown I have checked the the size of case.scfso files and clearly 4 of them are much smaller (I have used 9 k-points for both calculations). I have checked one of the files case.scfso_1 and it is incomplete. It didn't write out energy eigenvalues. The corresponding output files from lapw1, case.scf1up_1 (dn) are fine. So I am not sure what is the problem. Any help will be much appreciated. -rw-r--r-- 1 eisfh folk 15898 Mar 5 17:10 1Mn.scfso_1 -rw-r--r-- 1 eisfh folk 77237 Mar 5 19:04 1Mn.scfso_2 -rw-r--r-- 1 eisfh folk 77349 Mar 5 19:05 1Mn.scfso_3 -rw-r--r-- 1 eisfh folk 77237 Mar 5 18:59 1Mn.scfso_4 -rw-r--r-- 1 eisfh folk 15898 Mar 5 17:10 1Mn.scfso_5 -rw-r--r-- 1 eisfh folk 77237 Mar 5 18:59 1Mn.scfso_6 -rw-r--r-- 1 eisfh folk 15898 Mar 5 17:10 1Mn.scfso_7 -rw-r--r-- 1 eisfh folk 15898 Mar 5 17:10 1Mn.scfso_8 -rw-r--r-- 1 eisfh folk 77250 Mar 5 19:04 1Mn.scf
Re: [Wien] lapwsopara error
>From your description, it seems you changed only the case.inso but you did not >do a full SO initialisation (symmetso, kgen, etc.), did you ? By the way, calculation of magnetic anisotropy is a matter of brute force with respect to number of k points etc., and I think that 9 k points only are by far not enough. Ciao Gerhard DEEP THOUGHT in D. Adams; Hitchhikers Guide to the Galaxy: "I think the problem, to be quite honest with you, is that you have never actually known what the question is." Dr. Gerhard H. Fecher Institut of Inorganic and Analytical Chemistry Johannes Gutenberg - University 55099 Mainz and Max Planck Institute for Chemical Physics of Solids 01187 Dresden Von: Wien [wien-boun...@zeus.theochem.tuwien.ac.at] im Auftrag von Md. Fhokrul Islam [fis...@hotmail.com] Gesendet: Sonntag, 5. März 2017 22:14 An: A Mailing list for WIEN2k users Betreff: [Wien] lapwsopara error Hi Prof Blaha and Wien2k users, I am trying to do anisotropy calculation of some magnetic impurities in bulk Sb2Se3 topological insulator using force theorem. It works fine if I chose magnetization axis in the xy-plane (1 1 0 in case.inso file) but it crashes when magnetization is along z-axis (0 0 1 in case inso). I tried with two different types of impurity (Mn and Cr) but in both cases I get the same error message: Output file: ** LAPWSO crashed! 51852.372u 93.264s 1:56:04.17 745.8%0+0k 376+11416648io 12pf+0w error: command /pfs/nobackup/home/e/eisfh/SRC/Wien2k_16/lapwsopara -up -c uplapwso.def failed Error file: (15 more lapw1 lines above) LAPW1 END LAPW1 END LAPW1 END LAPWSO END LAPWSO END LAPWSO END LAPWSO END LAPWSO END forrtl: severe (24): end-of-file during read, unit 30, file /pfs/nobackup/home/e/eisfh/WIEN2k/Sb2Te3/Bulk/MAE_FT/001/1Mn/1Mn.energysoup_1 Image PCRoutineLineSource lapw2c 006E4A9C Unknown Unknown Unknown lapw2c 00712E75 Unknown Unknown Unknown lapw2c 00425390 fermi_ 43 fermi_tmp_.F lapw2c 00454D31 MAIN__375 lapw2_tmp_.F lapw2c 0040366E Unknown Unknown Unknown libc-2.23.so 2B2573B34830 __libc_start_main Unknown Unknown lapw2c 00403569 Unknown Unknown Unknown I have checked the the size of case.scfso files and clearly 4 of them are much smaller (I have used 9 k-points for both calculations). I have checked one of the files case.scfso_1 and it is incomplete. It didn't write out energy eigenvalues. The corresponding output files from lapw1, case.scf1up_1 (dn) are fine. So I am not sure what is the problem. Any help will be much appreciated. -rw-r--r-- 1 eisfh folk 15898 Mar 5 17:10 1Mn.scfso_1 -rw-r--r-- 1 eisfh folk 77237 Mar 5 19:04 1Mn.scfso_2 -rw-r--r-- 1 eisfh folk 77349 Mar 5 19:05 1Mn.scfso_3 -rw-r--r-- 1 eisfh folk 77237 Mar 5 18:59 1Mn.scfso_4 -rw-r--r-- 1 eisfh folk 15898 Mar 5 17:10 1Mn.scfso_5 -rw-r--r-- 1 eisfh folk 77237 Mar 5 18:59 1Mn.scfso_6 -rw-r--r-- 1 eisfh folk 15898 Mar 5 17:10 1Mn.scfso_7 -rw-r--r-- 1 eisfh folk 15898 Mar 5 17:10 1Mn.scfso_8 -rw-r--r-- 1 eisfh folk 77250 Mar 5 19:04 1Mn.scfso_9 Thanks, Fhokrul ___ 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] lapwsopara error
06.03.2017 01:14, Md. Fhokrul Islam wrote: I am trying to do anisotropy calculation of some magnetic impurities in bulk Sb2Se3 topological insulator using force theorem. It works fine if I chose magnetization axis in the xy-plane (1 1 0 in case.inso file) but it crashes when magnetization is along z-axis (0 0 1 in case inso). I tried with two different types of impurity (Mn and Cr) but in both cases I get the same error message: ** LAPWSO crashed! You have done the initso for _both_ directions, haven't you? That is, two initso's? If so - try to obtain and give us more information, now it's not clear. By the way, in this case I'd prefer to take one and the same structure file for oth calculations with the largest possible set of mutual symmetries. Best wishes Lyudmila Dobysheva -- Phys.-Techn. Institute of Ural Br. of Russian Ac. of Sci. 426001 Izhevsk, ul.Kirova 132 RUSSIA -- Tel.:7(3412) 432045(office), 722529(Fax) E-mail: l...@ftiudm.ru, lyuk...@mail.ru (office) lyuk...@gmail.com (home) Skype: lyuka17 (home), lyuka18 (office) http://ftiudm.ru/content/view/25/103/lang,english/ -- ___ 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
