[Wien] MBJ fails to produce gap unto 0.6 for VO2 M1 phase
Dear Experts, I am doing some calculations for VO2 M1 phase. To get the correct band gap value, I applied MBJ. But, I am getting zero gap. To get the gap, I increased the c value. with such large c value, there is no sign of convergence of my calculation. I appreciate if experts have any comments and suggestions. Regards Wasim ___ 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] Problems of out of memory in parallel jobs
I suggest that you talk to a sysadmin to get some clarification. In particular, see if this is just memory, or a combination of memory and file space. From what I can see it is probably memory, but there seems to be some flexibility in how it is configured. One other possibility is a memory leak. What mpi are you using? N.B., I would be a bit concerned that srun is not working for you. Talk to a sysadmin, you might be running outside/around your memory allocation. Two relevant sources: https://community.pivotal.io/s/article/the-application-crashes-with-the-message-cgroup-out-of-memory?language=en_US https://bugs.schedmd.com/show_bug.cgi?id=2614 On Mon, May 11, 2020 at 10:55 AM MA Weiliang wrote: > Dear Wien users, > > The wien2k 18.2 I used is compiled in a share memory cluster with intel > compiler 2019, mkl 2019 and impi 2019. Because ‘srun' cannot get a correct > parallel calculation in the system, I commented the line of "#setenv > WIEN_MPIRUN "srun -K -N_nodes_ -n_NP_ -r_offset_ _PINNING_ _EXEC_” in the > parallel_options file and used the second choice "mpirun='mpirun -np _NP_ > _EXEC_”. > > Parallel jobs go well in scf cycles. But when I increase k points (about > 5000) to calculate DOS, the lapw1 crashed with the cgroup out-of-memory > handler halfway. That is very strange. With same parameters, job runs well > with single core. > > The similar problem is encountered on nlvdw_mpi step. I also increase > memory up to 50G for this less than 10 atoms cell, but it still didn’t work. > > *[Parallel job output:]* > *starting parallel lapw1 at lun. mai 11 16:24:48 CEST 2020* > *-> starting parallel LAPW1 jobs at lun. mai 11 16:24:48 CEST 2020* > *running LAPW1 in parallel mode (using .machines)* > *1 number_of_parallel_jobs* > *[1] 12604* > *[1] + Done ( cd $PWD; $t $ttt; rm -f > .lock_$lockfile[$p] ) >> .time1_$loop* > * lame25 lame25 lame25 lame25 lame25 lame25 lame25 lame25(5038) > 4641.609u 123.862s 10:00.69 793.3% 0+0k 489064+2505080io 7642pf+0w* > * Summary of lapw1para:* > * lame25k=0 user=0 wallclock=0* > *** LAPW1 crashed!* > *4643.674u 126.539s 10:03.50 790.4% 0+0k 490512+2507712io 7658pf+0w* > *error: command /home/mcsete/work/wma/Package/wien2k.18n/lapw1para > lapw1.def failed* > *slurmstepd: error: Detected 1 oom-kill event(s) in step 86112.batch > cgroup. Some of your processes may have been killed by the cgroup > out-of-memory handler.* > > *[Single mode output: ]* > * LAPW1 END* > *11651.205u 178.664s 3:23:49.07 96.7%0+0k 19808+22433688io 26pf+0w* > > Do you have any ideas? Thank you in advance! > > Best regards, > Liang > ___ > Wien mailing list > Wien@zeus.theochem.tuwien.ac.at > > https://urldefense.com/v3/__http://zeus.theochem.tuwien.ac.at/mailman/listinfo/wien__;!!Dq0X2DkFhyF93HkjWTBQKhk!FzOfv9gey6e2nE6BL116Cgoy1UpRBalprajLfQ67QqwAytt0uPXPCtFoozTIGaBYJjay5Q$ > SEARCH the MAILING-LIST at: > https://urldefense.com/v3/__http://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/index.html__;!!Dq0X2DkFhyF93HkjWTBQKhk!FzOfv9gey6e2nE6BL116Cgoy1UpRBalprajLfQ67QqwAytt0uPXPCtFoozTIGaAW3twYHA$ > -- Professor Laurence Marks Department of Materials Science and Engineering Northwestern University www.numis.northwestern.edu Corrosion in 4D: www.numis.northwestern.edu/MURI Co-Editor, Acta Cryst A "Research is to see what everybody else has seen, and to think what nobody else has thought" Albert Szent-Gyorgi ___ 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] Problems of out of memory in parallel jobs
Dear Wien users, The wien2k 18.2 I used is compiled in a share memory cluster with intel compiler 2019, mkl 2019 and impi 2019. Because ‘srun' cannot get a correct parallel calculation in the system, I commented the line of "#setenv WIEN_MPIRUN "srun -K -N_nodes_ -n_NP_ -r_offset_ _PINNING_ _EXEC_” in the parallel_options file and used the second choice "mpirun='mpirun -np _NP_ _EXEC_”. Parallel jobs go well in scf cycles. But when I increase k points (about 5000) to calculate DOS, the lapw1 crashed with the cgroup out-of-memory handler halfway. That is very strange. With same parameters, job runs well with single core. The similar problem is encountered on nlvdw_mpi step. I also increase memory up to 50G for this less than 10 atoms cell, but it still didn’t work. [Parallel job output:] starting parallel lapw1 at lun. mai 11 16:24:48 CEST 2020 -> starting parallel LAPW1 jobs at lun. mai 11 16:24:48 CEST 2020 running LAPW1 in parallel mode (using .machines) 1 number_of_parallel_jobs [1] 12604 [1] + Done ( cd $PWD; $t $ttt; rm -f .lock_$lockfile[$p] ) >> .time1_$loop lame25 lame25 lame25 lame25 lame25 lame25 lame25 lame25(5038) 4641.609u 123.862s 10:00.69 793.3% 0+0k 489064+2505080io 7642pf+0w Summary of lapw1para: lame25k=0 user=0 wallclock=0 ** LAPW1 crashed! 4643.674u 126.539s 10:03.50 790.4% 0+0k 490512+2507712io 7658pf+0w error: command /home/mcsete/work/wma/Package/wien2k.18n/lapw1para lapw1.def failed slurmstepd: error: Detected 1 oom-kill event(s) in step 86112.batch cgroup. Some of your processes may have been killed by the cgroup out-of-memory handler. [Single mode output: ] LAPW1 END 11651.205u 178.664s 3:23:49.07 96.7%0+0k 19808+22433688io 26pf+0w Do you have any ideas? Thank you in advance! Best regards, Liang ___ 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] Characters of atoms in the fold2bloch bands.
Hi Artem, what you describe sounds very interesting. It will be a QTL-resolved unfolded band structure. Are you doing calculations with SOC? Thanks Oleg On 2020-05-10 8:51 p.m., Артем Тарасов wrote: Hello Oleg, I’m sorry for that my question was not enough clear. Now I will try to describe my situation in terms of lapw1, lapw2 and fold2bloch output files. After completion of "lapw1 -band" I got eigenvalues of energy for all states in k-vectors that listed in case.klist_band. Then I can use the "lapw2 -qtl" procedure to find out the contribution of each atom of an unit cell in all (E,k)-states that were calculated by lapw1. Thus, I obtain the table with columns: k-vector, Energy, сontribution (of an atom or its orbital). If I apply fold2bloch on eigenstates in case.vector, I obtain the case.f2b file with columns: k-vector, Energy, the spectral Bloch weight. So I was trying to identify a total contribution of selected atoms in each state listed in case.f2b. To be honest, I think that I resolved this problem because I have obtained realistic results for my tests. I had examined the code of the fold2bloch procedure and have found that each k-vector in the original case.klist_band file transforms to some number of k-vector in the case.f2b file and this number is determined by the size of supercell (for example 1 k-vector of the 4x4x1 cell transforms to 16 new k-vectors). So to resolve my problem I just multiply the spectral Bloch weights that match these 16 k-vectors with the same energy eigenvalues on the value of an atomic сontribution for the folded (E,k)-state. Then I do this operation for all spectral Bloch weights of the unfolded (E,k)-states. I suppose that my procedure is quite acceptable and I get good results with it. When I tell about atomic contributions I mean partial charges, of course. Sincerely yours, Artem Tarasov Department of Solid State Electronics Saint Petersburg State University. ___ 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
