[Wien] How to apply LSDA+U
Dear You can apply DFT+U within WIEN2k. Please see the userguide, section 7.2 ORB (orbital potentials). Good luck. Ricardo > Hello Dear WIEN2k users; > I'm using WIEN2k_09, and I want to apply LSDA+U in my calculation. But I > don't know how I can do it and where I should put the Hubbard potential. > Please consult me. > Thanks > ___ > Wien mailing list > Wien at zeus.theochem.tuwien.ac.at > http://zeus.theochem.tuwien.ac.at/mailman/listinfo/wien > -- - Dr. Ricardo Faccio Prof. Adjunto de F?sica Mail: Cryssmat-Lab., C?tedra de F?sica, DETEMA Facultad de Qu?mica, Universidad de la Rep?blica Av. Gral. Flores 2124, C.C. 1157 C.P. 11800, Montevideo, Uruguay. E-mail: rfaccio at fq.edu.uy Phone: 598 2 924 98 59 598 2 929 06 48 Fax: 598 2 9241906 Web: http://cryssmat.fq.edu.uy/ricardo/ricardo.htm
[Wien] OS bug/inconveniece with mkl thread/mpi conflicts
Setting OMP_NUM_THREAD lets you select to use multithreading or not. A slight modification of our example script on the WIEN2k faq page can even accounts for this and automatically span on eg. 8 core only 4 mpi processes (when OMP_NUM_THREAD=2). Am 15.03.2011 15:31, schrieb Laurence Marks: > This is an informational report of an issue that can arise with Wien2k > leading to poor performance. I came across it when experimenting with > the "procs=XX" option in msub/qsub with XX=64 as an alternative to the > more standard "nodes=X:ppn=Y". > > In an scf cycle lapwdm and (with the next release) mixer always use > lapack routines (and maybe some others) which by default with mkl are > multithreaded and use multiple cores. For a mpi run with lapw0: > specified lapw0, lapw1 and lapw2 all use mpi. A issue can arise with > msub/qsub (and perhaps other) if the number of cores mkl uses is > larger than what has been allocated and there are other mpi tasks > running on the same node. Then the performance of lapwdm can be bad; > in one case rather than taking 30 seconds it took 14 minutes. > > I am not sure if this is something "fixable" in WIen2k, and there are > ways in qsub/msub to avoid it using nodes=X:ppn=Y. However, procs=XX > is "nice" as Wien2k in mpi does not really need factors of 2 > cores/node (I've tested this) and can fit in the gaps. > > N.B., running without mpi and using nodes=X:ppn=1 could also run into > the same problem. > -- P.Blaha -- Peter BLAHA, Inst.f. Materials Chemistry, TU Vienna, A-1060 Vienna Phone: +43-1-58801-15671 FAX: +43-1-58801-15698 Email: blaha at theochem.tuwien.ac.atWWW: http://info.tuwien.ac.at/theochem/ --
[Wien] OS bug/inconveniece with mkl thread/mpi conflicts
Even better (in my opinion this should be in /etc/bashrc) export MKL_NUM_THREADS=1 OMP_NUM_THREADS=1 export MKL_DOMAIN_NUM_THREADS="MKL_VML=1, MKL_ALL=1" if [ "$PBS_NODEFILE" != "" ] ; then mkln=`grep -e $HOSTNAME $PBS_NODEFILE | wc -l` export MKL_NUM_THREADS=$mkln OMP_NUM_THREADS=$mkln export MKL_DYNAMIC=FALSE export MKL_DOMAIN_NUM_THREADS="MKL_VML=$mkln, MKL_ALL=$mkln" fi Edit as appropriate for other shells. On Tue, Mar 15, 2011 at 10:59 AM, Laurence Marks wrote: > Agreed. Or use something like (in parallel_options, 1 k-point only, > could be generalized) > > set a=`grep -e "1:" .machines | grep -v lapw0 | cut -f 3 -d: | cut -c 1-2` > setenv MKL_NUM_THREADS $a > setenv OMP_NUM_THREADS $a > > or > set a=`grep -e $HOSTNAME $PBS_NODEFILE | wc -l` > > My opinion is that this should be set at the OS level with > MKL_NUM_THREADS etc set by msub/qsub or similar. I've seen problems > due to other processes (not mine) using more threads than they should. > > On Tue, Mar 15, 2011 at 10:35 AM, Peter Blaha > wrote: >> Setting OMP_NUM_THREAD lets you select to use multithreading or not. >> >> A slight modification of our example script on the WIEN2k faq page >> can even accounts for this and automatically span on eg. 8 core only >> 4 mpi processes (when OMP_NUM_THREAD=2). >> >> >> Am 15.03.2011 15:31, schrieb Laurence Marks: >>> >>> This is an informational report of an issue that can arise with Wien2k >>> leading to poor performance. I came across it when experimenting with >>> the "procs=XX" option in msub/qsub with XX=64 as an alternative to the >>> more standard "nodes=X:ppn=Y". >>> >>> In an scf cycle lapwdm and (with the next release) mixer always use >>> lapack routines (and maybe some others) which by default with mkl are >>> multithreaded and use multiple cores. For a mpi run with lapw0: >>> specified lapw0, lapw1 and lapw2 all use mpi. A issue can arise with >>> msub/qsub (and perhaps other) if the number of cores mkl uses is >>> larger than what has been allocated and there are other mpi tasks >>> running on the same node. Then the performance of lapwdm can be bad; >>> in one case rather than taking 30 seconds it took 14 minutes. >>> >>> I am not sure if this is something "fixable" in WIen2k, and there are >>> ways in qsub/msub to avoid it using nodes=X:ppn=Y. However, procs=XX >>> is "nice" as Wien2k in mpi does not really need factors of 2 >>> cores/node (I've tested this) and can fit in the gaps. >>> >>> N.B., running without mpi and using nodes=X:ppn=1 could also run into >>> the same problem. >>> >> >> -- >> >> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ?P.Blaha >> -- >> Peter BLAHA, Inst.f. Materials Chemistry, TU Vienna, A-1060 Vienna >> Phone: +43-1-58801-15671 ? ? ? ? ? ? FAX: +43-1-58801-15698 >> Email: blaha at theochem.tuwien.ac.at ? ?WWW: >> http://info.tuwien.ac.at/theochem/ >> -- >> ___ >> Wien mailing list >> Wien at zeus.theochem.tuwien.ac.at >> http://zeus.theochem.tuwien.ac.at/mailman/listinfo/wien >> > > > > -- > Laurence Marks > Department of Materials Science and Engineering > MSE Rm 2036 Cook Hall > 2220 N Campus Drive > Northwestern University > Evanston, IL 60208, USA > Tel: (847) 491-3996 Fax: (847) 491-7820 > email: L-marks at northwestern dot edu > Web: www.numis.northwestern.edu > Chair, Commission on Electron Crystallography of IUCR > www.numis.northwestern.edu/ > Electron crystallography is the branch of science that uses electron > scattering and imaging to study the structure of matter. > -- Laurence Marks Department of Materials Science and Engineering MSE Rm 2036 Cook Hall 2220 N Campus Drive Northwestern University Evanston, IL 60208, USA Tel: (847) 491-3996 Fax: (847) 491-7820 email: L-marks at northwestern dot edu Web: www.numis.northwestern.edu Chair, Commission on Electron Crystallography of IUCR www.numis.northwestern.edu/ Electron crystallography is the branch of science that uses electron scattering and imaging to study the structure of matter.
[Wien] OS bug/inconveniece with mkl thread/mpi conflicts
Agreed. Or use something like (in parallel_options, 1 k-point only, could be generalized) set a=`grep -e "1:" .machines | grep -v lapw0 | cut -f 3 -d: | cut -c 1-2` setenv MKL_NUM_THREADS $a setenv OMP_NUM_THREADS $a or set a=`grep -e $HOSTNAME $PBS_NODEFILE | wc -l` My opinion is that this should be set at the OS level with MKL_NUM_THREADS etc set by msub/qsub or similar. I've seen problems due to other processes (not mine) using more threads than they should. On Tue, Mar 15, 2011 at 10:35 AM, Peter Blaha wrote: > Setting OMP_NUM_THREAD lets you select to use multithreading or not. > > A slight modification of our example script on the WIEN2k faq page > can even accounts for this and automatically span on eg. 8 core only > 4 mpi processes (when OMP_NUM_THREAD=2). > > > Am 15.03.2011 15:31, schrieb Laurence Marks: >> >> This is an informational report of an issue that can arise with Wien2k >> leading to poor performance. I came across it when experimenting with >> the "procs=XX" option in msub/qsub with XX=64 as an alternative to the >> more standard "nodes=X:ppn=Y". >> >> In an scf cycle lapwdm and (with the next release) mixer always use >> lapack routines (and maybe some others) which by default with mkl are >> multithreaded and use multiple cores. For a mpi run with lapw0: >> specified lapw0, lapw1 and lapw2 all use mpi. A issue can arise with >> msub/qsub (and perhaps other) if the number of cores mkl uses is >> larger than what has been allocated and there are other mpi tasks >> running on the same node. Then the performance of lapwdm can be bad; >> in one case rather than taking 30 seconds it took 14 minutes. >> >> I am not sure if this is something "fixable" in WIen2k, and there are >> ways in qsub/msub to avoid it using nodes=X:ppn=Y. However, procs=XX >> is "nice" as Wien2k in mpi does not really need factors of 2 >> cores/node (I've tested this) and can fit in the gaps. >> >> N.B., running without mpi and using nodes=X:ppn=1 could also run into >> the same problem. >> > > -- > > ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ?P.Blaha > -- > Peter BLAHA, Inst.f. Materials Chemistry, TU Vienna, A-1060 Vienna > Phone: +43-1-58801-15671 ? ? ? ? ? ? FAX: +43-1-58801-15698 > Email: blaha at theochem.tuwien.ac.at ? ?WWW: > http://info.tuwien.ac.at/theochem/ > -- > ___ > Wien mailing list > Wien at zeus.theochem.tuwien.ac.at > http://zeus.theochem.tuwien.ac.at/mailman/listinfo/wien > -- Laurence Marks Department of Materials Science and Engineering MSE Rm 2036 Cook Hall 2220 N Campus Drive Northwestern University Evanston, IL 60208, USA Tel: (847) 491-3996 Fax: (847) 491-7820 email: L-marks at northwestern dot edu Web: www.numis.northwestern.edu Chair, Commission on Electron Crystallography of IUCR www.numis.northwestern.edu/ Electron crystallography is the branch of science that uses electron scattering and imaging to study the structure of matter.
[Wien] OS bug/inconveniece with mkl thread/mpi conflicts
This is an informational report of an issue that can arise with Wien2k leading to poor performance. I came across it when experimenting with the "procs=XX" option in msub/qsub with XX=64 as an alternative to the more standard "nodes=X:ppn=Y". In an scf cycle lapwdm and (with the next release) mixer always use lapack routines (and maybe some others) which by default with mkl are multithreaded and use multiple cores. For a mpi run with lapw0: specified lapw0, lapw1 and lapw2 all use mpi. A issue can arise with msub/qsub (and perhaps other) if the number of cores mkl uses is larger than what has been allocated and there are other mpi tasks running on the same node. Then the performance of lapwdm can be bad; in one case rather than taking 30 seconds it took 14 minutes. I am not sure if this is something "fixable" in WIen2k, and there are ways in qsub/msub to avoid it using nodes=X:ppn=Y. However, procs=XX is "nice" as Wien2k in mpi does not really need factors of 2 cores/node (I've tested this) and can fit in the gaps. N.B., running without mpi and using nodes=X:ppn=1 could also run into the same problem. -- Laurence Marks Department of Materials Science and Engineering MSE Rm 2036 Cook Hall 2220 N Campus Drive Northwestern University Evanston, IL 60208, USA Tel: (847) 491-3996 Fax: (847) 491-7820 email: L-marks at northwestern dot edu Web: www.numis.northwestern.edu Chair, Commission on Electron Crystallography of IUCR www.numis.northwestern.edu/ Electron crystallography is the branch of science that uses electron scattering and imaging to study the structure of matter.
