Re: [Wien] Dense mesh calculation
Dear Prof. Blaha, dear All, Thank you for your comments! /SCRATCH directories on the older cluster that I am using are usually quite full (in some cases perhaps can be solved by writing some emails asking people to delete old stuff). New harddisk solution is considered, hopefully will be possible. In any case it's always good to have a solution to use less space. In the meantime (after SCF and doing save_lapw) I reduced emin/emax ranges in in1c and inso and managed to calculate 100x100 mesh overnight on the /SCRATCH space that was available. Best, Lukasz On 2018-08-19 07:16, Peter Blaha wrote: By choosing a local scratch directory (like /scratch or /tmp or ..., this depends on your computers, you can then add -scratch /scratch to all wien2k run or x commands) and using massively k-parallelism (on as many different nodes as possible, you can distribute these large case.vector_xx files on many computers. (PS: otherwise a 2 or 4TB harddisk costs less than 100 $ !!??). The case.vectorso_xx files are not needed for fermi surfaces (but of course they are needed for scf or optics, or ...) and can be reduced in size by selecting emin/emax in case.inso very narrow. Another simple trick to save disk space would be: Start x lapw1 -p -band -up/dn and kill this after a few seconds. Do the same with lapwso. It will prepare a couple of uplapw1_xx.def and case.klist_xx files. Now you run in a small loop (csh syntax): foreach i (1 2 3 4) lapw1c uplapw1_$i.def # or lapw1 , depending on in1 or in1c) lapw1c dnlapw1_$i.def lapwso uplapwso_$i.def rm case.vectorup_$i case.vectordn_$i end This should produce only one vector file at the time and by choosing many cores, you can make them arbitrarily small. Of course, this does not work when you need the vector files for other programs (lapw2, optics, ...) Am 18.08.2018 um 20:18 schrieb pluto: Dear Gavin, Thank you for your comments. This is what I was afraid. I can glue output files by myself, no problem, hopefully they don't change the order of k-points. But one way to solve the disk-space issue would be to write a script that calculates SOC eigenvalues k-point by k-point. Then there would be no large vector files. I am not feeling competent to modify and recompile WIEN2k, but perhaps I am able to solve it by the script. Best, Lukasz On 8/18/2018 3:43 PM, Gavin Abo wrote: From WIEN2k 18.2 UG page 126: WFFIL: standard option, writes wave functions to file case.vector (needed in lapw2) SUPWF: suppresses wave function calculation (faster for testing eigenvalues only) WFPRI: prints eigenvectors to case.output1 and writes case.vector (produces long outputs!) With SUPWF from above, it looks like case.vector* files are not written by lapw1 unless WFFIL or WFPRI are used instead. Since Table 4.3 shows case.vector* files are required for lapwso, it may be that you cannot workaround not using them. As far as I know, there is no built in WIEN2k program to combine the .output* files. That is why the multiple recent and past posts about it, such as: https://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/msg17847.html https://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/msg17829.html https://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/msg00508.html https://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/msg02057.html https://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/msg02055.html (awk) http://www.democritos.it/pipermail/xcrysden/2015-September/001731.html http://www.democritos.it/pipermail/xcrysden/2015-December/001788.html Though, I don't see why you couldn't automate it yourself either using a job script (e.g., by adding the "cat case.outputso_1* > case.output1up" to it), by writing your own script (e.g., bash script containing your run[sp]_lapw and "cat case.outputso_1* > case.output1up" commands), or by modifying the WIEN2k source code. On 8/18/2018 5:07 AM, pluto wrote: Dear All, dear Prof. Blaha, I used SUPWF in case.in1c to limit the size of output files. Then I used: x lapw1 -band -up -p -c x lapw1 -band -dn -p -c x lapwso -up -p -c There are no errors, but lapwso does not seem to calculate eigenvalues. I use 4 parallel cores, so I have 4 output files. Output files without SOC look OK, they contain eigenvalues (files case.output1up_1 to 4, same for dn). But SOC output files (outputso_1 to 4) do not contain any eigenvalues, and I don't see any other output files. Am I doing something wrong? Manual in Table 4.3 says that lapwso needs vector files, which are of course missing here. Is there a way out? Also, is there a way to automatically "glue" output files to have just one large output file? Best, Lukasz ___ Wien mailing list Wien@zeus.theochem.tuwien.ac.at http://zeus.theochem.tuwien.ac.at/mailman/listinfo/wien SEARCH the MAILING-LIST at:
Re: [Wien] Dense mesh calculation
By choosing a local scratch directory (like /scratch or /tmp or ..., this depends on your computers, you can then add -scratch /scratch to all wien2k run or x commands) and using massively k-parallelism (on as many different nodes as possible, you can distribute these large case.vector_xx files on many computers. (PS: otherwise a 2 or 4TB harddisk costs less than 100 $ !!??). The case.vectorso_xx files are not needed for fermi surfaces (but of course they are needed for scf or optics, or ...) and can be reduced in size by selecting emin/emax in case.inso very narrow. Another simple trick to save disk space would be: Start x lapw1 -p -band -up/dn and kill this after a few seconds. Do the same with lapwso. It will prepare a couple of uplapw1_xx.def and case.klist_xx files. Now you run in a small loop (csh syntax): foreach i (1 2 3 4) lapw1c uplapw1_$i.def # or lapw1 , depending on in1 or in1c) lapw1c dnlapw1_$i.def lapwso uplapwso_$i.def rm case.vectorup_$i case.vectordn_$i end This should produce only one vector file at the time and by choosing many cores, you can make them arbitrarily small. Of course, this does not work when you need the vector files for other programs (lapw2, optics, ...) Am 18.08.2018 um 20:18 schrieb pluto: Dear Gavin, Thank you for your comments. This is what I was afraid. I can glue output files by myself, no problem, hopefully they don't change the order of k-points. But one way to solve the disk-space issue would be to write a script that calculates SOC eigenvalues k-point by k-point. Then there would be no large vector files. I am not feeling competent to modify and recompile WIEN2k, but perhaps I am able to solve it by the script. Best, Lukasz On 8/18/2018 3:43 PM, Gavin Abo wrote: From WIEN2k 18.2 UG page 126: WFFIL: standard option, writes wave functions to file case.vector (needed in lapw2) SUPWF: suppresses wave function calculation (faster for testing eigenvalues only) WFPRI: prints eigenvectors to case.output1 and writes case.vector (produces long outputs!) With SUPWF from above, it looks like case.vector* files are not written by lapw1 unless WFFIL or WFPRI are used instead. Since Table 4.3 shows case.vector* files are required for lapwso, it may be that you cannot workaround not using them. As far as I know, there is no built in WIEN2k program to combine the .output* files. That is why the multiple recent and past posts about it, such as: https://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/msg17847.html https://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/msg17829.html https://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/msg00508.html https://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/msg02057.html https://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/msg02055.html (awk) http://www.democritos.it/pipermail/xcrysden/2015-September/001731.html http://www.democritos.it/pipermail/xcrysden/2015-December/001788.html Though, I don't see why you couldn't automate it yourself either using a job script (e.g., by adding the "cat case.outputso_1* > case.output1up" to it), by writing your own script (e.g., bash script containing your run[sp]_lapw and "cat case.outputso_1* > case.output1up" commands), or by modifying the WIEN2k source code. On 8/18/2018 5:07 AM, pluto wrote: Dear All, dear Prof. Blaha, I used SUPWF in case.in1c to limit the size of output files. Then I used: x lapw1 -band -up -p -c x lapw1 -band -dn -p -c x lapwso -up -p -c There are no errors, but lapwso does not seem to calculate eigenvalues. I use 4 parallel cores, so I have 4 output files. Output files without SOC look OK, they contain eigenvalues (files case.output1up_1 to 4, same for dn). But SOC output files (outputso_1 to 4) do not contain any eigenvalues, and I don't see any other output files. Am I doing something wrong? Manual in Table 4.3 says that lapwso needs vector files, which are of course missing here. Is there a way out? Also, is there a way to automatically "glue" output files to have just one large output file? Best, Lukasz ___ 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 -- -- 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:
Re: [Wien] Dense mesh calculation
Dear Gavin, Thank you for your comments. This is what I was afraid. I can glue output files by myself, no problem, hopefully they don't change the order of k-points. But one way to solve the disk-space issue would be to write a script that calculates SOC eigenvalues k-point by k-point. Then there would be no large vector files. I am not feeling competent to modify and recompile WIEN2k, but perhaps I am able to solve it by the script. Best, Lukasz On 8/18/2018 3:43 PM, Gavin Abo wrote: From WIEN2k 18.2 UG page 126: WFFIL: standard option, writes wave functions to file case.vector (needed in lapw2) SUPWF: suppresses wave function calculation (faster for testing eigenvalues only) WFPRI: prints eigenvectors to case.output1 and writes case.vector (produces long outputs!) With SUPWF from above, it looks like case.vector* files are not written by lapw1 unless WFFIL or WFPRI are used instead. Since Table 4.3 shows case.vector* files are required for lapwso, it may be that you cannot workaround not using them. As far as I know, there is no built in WIEN2k program to combine the .output* files. That is why the multiple recent and past posts about it, such as: https://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/msg17847.html https://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/msg17829.html https://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/msg00508.html https://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/msg02057.html https://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/msg02055.html (awk) http://www.democritos.it/pipermail/xcrysden/2015-September/001731.html http://www.democritos.it/pipermail/xcrysden/2015-December/001788.html Though, I don't see why you couldn't automate it yourself either using a job script (e.g., by adding the "cat case.outputso_1* > case.output1up" to it), by writing your own script (e.g., bash script containing your run[sp]_lapw and "cat case.outputso_1* > case.output1up" commands), or by modifying the WIEN2k source code. On 8/18/2018 5:07 AM, pluto wrote: Dear All, dear Prof. Blaha, I used SUPWF in case.in1c to limit the size of output files. Then I used: x lapw1 -band -up -p -c x lapw1 -band -dn -p -c x lapwso -up -p -c There are no errors, but lapwso does not seem to calculate eigenvalues. I use 4 parallel cores, so I have 4 output files. Output files without SOC look OK, they contain eigenvalues (files case.output1up_1 to 4, same for dn). But SOC output files (outputso_1 to 4) do not contain any eigenvalues, and I don't see any other output files. Am I doing something wrong? Manual in Table 4.3 says that lapwso needs vector files, which are of course missing here. Is there a way out? Also, is there a way to automatically "glue" output files to have just one large output file? Best, Lukasz ___ 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 -- Dr. Lukasz Plucinski ___ 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] Dense mesh calculation
From WIEN2k 18.2 UG page 126: WFFIL: standard option, writes wave functions to file case.vector (needed in lapw2) SUPWF: suppresses wave function calculation (faster for testing eigenvalues only) WFPRI: prints eigenvectors to case.output1 and writes case.vector (produces long outputs!) With SUPWF from above, it looks like case.vector* files are not written by lapw1 unless WFFIL or WFPRI are used instead. Since Table 4.3 shows case.vector* files are required for lapwso, it may be that you cannot workaround not using them. As far as I know, there is no built in WIEN2k program to combine the .output* files. That is why the multiple recent and past posts about it, such as: https://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/msg17847.html https://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/msg17829.html https://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/msg00508.html https://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/msg02057.html https://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/msg02055.html (awk) http://www.democritos.it/pipermail/xcrysden/2015-September/001731.html http://www.democritos.it/pipermail/xcrysden/2015-December/001788.html Though, I don't see why you couldn't automate it yourself either using a job script (e.g., by adding the "cat case.outputso_1* > case.output1up" to it), by writing your own script (e.g., bash script containing your run[sp]_lapw and "cat case.outputso_1* > case.output1up" commands), or by modifying the WIEN2k source code. On 8/18/2018 5:07 AM, pluto wrote: Dear All, dear Prof. Blaha, I used SUPWF in case.in1c to limit the size of output files. Then I used: x lapw1 -band -up -p -c x lapw1 -band -dn -p -c x lapwso -up -p -c There are no errors, but lapwso does not seem to calculate eigenvalues. I use 4 parallel cores, so I have 4 output files. Output files without SOC look OK, they contain eigenvalues (files case.output1up_1 to 4, same for dn). But SOC output files (outputso_1 to 4) do not contain any eigenvalues, and I don't see any other output files. Am I doing something wrong? Manual in Table 4.3 says that lapwso needs vector files, which are of course missing here. Is there a way out? Also, is there a way to automatically "glue" output files to have just one large output file? Best, Lukasz ___ 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] Dense mesh calculation
Dear All, dear Prof. Blaha, I used SUPWF in case.in1c to limit the size of output files. Then I used: x lapw1 -band -up -p -c x lapw1 -band -dn -p -c x lapwso -up -p -c There are no errors, but lapwso does not seem to calculate eigenvalues. I use 4 parallel cores, so I have 4 output files. Output files without SOC look OK, they contain eigenvalues (files case.output1up_1 to 4, same for dn). But SOC output files (outputso_1 to 4) do not contain any eigenvalues, and I don't see any other output files. Am I doing something wrong? Manual in Table 4.3 says that lapwso needs vector files, which are of course missing here. Is there a way out? Also, is there a way to automatically "glue" output files to have just one large output file? Best, Lukasz On 6/1/2018 3:39 PM, Peter Blaha wrote: It seems that case.energy files (energyup/dn, energysoup) are not printed when using SUPWF option. Is that correct? Do I need to read eigenvalues from case.output files? Yes. I have another question: Can I limit the energy range when calculating bands for dense k-point mesh (e.g. only get eigenvalues near the Fermi level)? Will it increase the speed per k-point? Try it out for a few k-points. There is a substantial difference when using all eigenvalues against the commonly used 10-20 percent, but the improvement is probably small when reducing it "a bit". Definitely, some steps in the diagonalization are independent on the number of eigenvalues. Regards, Lukasz On 5/15/2018 10:55 AM, Peter Blaha wrote: You can avoid the vector file by an option in case.in1. See UG On 05/15/2018 09:58 AM, Lukasz Plucinski wrote: Dear All, Could you let me know how to avoid saving huge vector files during dense mesh calculations? I am trying to do this for spin-polarized+SOC calculations. Perhaps someone could share a script that would only save eigenvalues? Best, Lukasz ___ 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 -- Dr. Lukasz Plucinski ___ 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] Dense mesh calculation
It seems that case.energy files (energyup/dn, energysoup) are not printed when using SUPWF option. Is that correct? Do I need to read eigenvalues from case.output files? Yes. I have another question: Can I limit the energy range when calculating bands for dense k-point mesh (e.g. only get eigenvalues near the Fermi level)? Will it increase the speed per k-point? Try it out for a few k-points. There is a substantial difference when using all eigenvalues against the commonly used 10-20 percent, but the improvement is probably small when reducing it "a bit". Definitely, some steps in the diagonalization are independent on the number of eigenvalues. Regards, Lukasz On 5/15/2018 10:55 AM, Peter Blaha wrote: You can avoid the vector file by an option in case.in1. See UG On 05/15/2018 09:58 AM, Lukasz Plucinski wrote: Dear All, Could you let me know how to avoid saving huge vector files during dense mesh calculations? I am trying to do this for spin-polarized+SOC calculations. Perhaps someone could share a script that would only save eigenvalues? Best, Lukasz ___ 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.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] Dense mesh calculation
Dear Prof. Blaha, dear All, Thank you for your answer. It seems that case.energy files (energyup/dn, energysoup) are not printed when using SUPWF option. Is that correct? Do I need to read eigenvalues from case.output files? I have another question: Can I limit the energy range when calculating bands for dense k-point mesh (e.g. only get eigenvalues near the Fermi level)? Will it increase the speed per k-point? Regards, Lukasz On 5/15/2018 10:55 AM, Peter Blaha wrote: You can avoid the vector file by an option in case.in1. See UG On 05/15/2018 09:58 AM, Lukasz Plucinski wrote: Dear All, Could you let me know how to avoid saving huge vector files during dense mesh calculations? I am trying to do this for spin-polarized+SOC calculations. Perhaps someone could share a script that would only save eigenvalues? Best, Lukasz ___ 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
Re: [Wien] Dense mesh calculation
You can avoid the vector file by an option in case.in1. See UG On 05/15/2018 09:58 AM, Lukasz Plucinski wrote: Dear All, Could you let me know how to avoid saving huge vector files during dense mesh calculations? I am trying to do this for spin-polarized+SOC calculations. Perhaps someone could share a script that would only save eigenvalues? Best, Lukasz ___ 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
[Wien] Dense mesh calculation
Dear All, Could you let me know how to avoid saving huge vector files during dense mesh calculations? I am trying to do this for spin-polarized+SOC calculations. Perhaps someone could share a script that would only save eigenvalues? Best, Lukasz ___ 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
