[DFTB-Plus-User] error with ELSI solvers
Huy Pham
pchuy1906 at gmail.com
Mon Feb 7 22:45:39 CET 2022
Dear Bálint,
Following your suggestion, I am able to solve the problem. Thanks so much!!!
It was a problem with the ELSI library. Before I used ELSI v2.7.1. With the
latest one (2.8.2), it works perfectly.
Thanks again!
Best,
Huy
On Mon, Feb 7, 2022 at 1:01 PM Bálint Aradi <aradi at uni-bremen.de> wrote:
> Dear Huy,
>
> you probably obtained the non-mpi version (which is the default on
> Conda, if you do not ask for mpi explicitely).
>
> My suggestion would be to create a separate conda environment (e.g.
> dftbplus-mpich or dftbplus-openmpi) for the mpi version, to activate
> that environment and then to download the mpi package into that
> environment:
>
> conda create -n dftbplus-mpich
> conda activate dftbplus-mpich
> conda install 'dftbplus=21.2=mpi_mpich_*'
>
> (or the same with openmpi instead). If you afterwards execute
>
> conda list
>
> to investigate the packages within this environment, you should see
> (among others)
>
> elsi 2.8.2 mpi_mpich_h6ba1590_2
> conda-forge
> dftbplus 21.2 mpi_mpich_h3469437_2
> conda-forge
>
> showing that the mpi-version of dftb+ and also elsi were automatically
> installed.
>
> Best regards,
>
> Bálint
>
>
> On 06.02.22 07:30, Huy Pham wrote:
> > Dear Bálint,
> >
> > Thanks for your suggestion!
> >
> > I have tried with the conda version, but I got an error: "Not compiled
> > with ELSI supported solvers".
> > I am not sure how to get the `correct` one that was compiled with ELSI.
> >
> > Best,
> > Huy
> >
> > On Tue, Feb 1, 2022 at 9:13 AM Bálint Aradi <aradi at uni-bremen.de
> > <mailto:aradi at uni-bremen.de>> wrote:
> >
> > Dear Huy,
> >
> > I have some problems to reproduce the segfault. I've tried your
> example
> > with the Conda openmpi version, as well as with an Intel-compiled
> 21.2.
> > Both were able to cope with your example and went without any
> problems
> > beyond the first total energy calculations (after 14 scc iterations).
> >
> > Could you eventually also try the Conda version, just to exclude,
> that
> > it is not a problem with the building process somehow?
> >
> > Best regards,
> >
> > Bálint
> >
> >
> >
> > On 28.01.22 15:57, Huy Pham wrote:
> > > Dear Bálint,
> > >
> > > Thanks for your quick reply!
> > >
> > > I am able to solve the PEXSI problem following your suggestion.
> But
> > > again after the first SCF, there is an error "segmentation fault
> ".
> > >
> > > Adding "ulimit -s unlimited" before running the exe file doesn't
> > help,
> > > still the same error. Please let me know if you have further
> > > suggestions. Attached are my input files, if you need it.
> > >
> > > Thanks,
> > > Huy
> > >
> > > On Fri, Jan 28, 2022 at 12:12 AM Bálint Aradi
> > <aradi at uni-bremen.de <mailto:aradi at uni-bremen.de>
> > > <mailto:aradi at uni-bremen.de <mailto:aradi at uni-bremen.de>>> wrote:
> > >
> > > Dear Huy,
> > >
> > > For the segfault: Often a limited stack size is the reason
> > (hits me
> > > often). Could you check, whether that is the case? (ulimit -s
> > unlimited)
> > >
> > > As for the PEXSI problem. The error message is generated by
> > the PEXSI
> > > library within ELSI. I am definitely not a PEXSI expert, but
> > having a
> > > quick look at the PEXSI code in ELSI
> > >
> > >
> >
> https://gitlab.com/ElectronicStructureLibrary/elsi-interface/-/blob/master/src/elsi_util.f90#L423
> > <
> https://gitlab.com/ElectronicStructureLibrary/elsi-interface/-/blob/master/src/elsi_util.f90#L423
> >
> > >
> > <
> https://gitlab.com/ElectronicStructureLibrary/elsi-interface/-/blob/master/src/elsi_util.f90#L423
> <
> https://gitlab.com/ElectronicStructureLibrary/elsi-interface/-/blob/master/src/elsi_util.f90#L423
> >>
> > >
> > > suggests, that the product of the number of poles per process
> > > (ProcsPerPole), the number of poles (Poles) and the number of
> > > processors
> > > used to search the Fermi level (muPoints) should be greater
> > or equal
> > > than the number of the MPI processes.
> > >
> > > I hope this helps.
> > >
> > > Best regards,
> > >
> > > BálintBest regards,
> > >
> > > Bálint
> > >
> > >
> > >
> > > On 28.01.22 01:58, Huy Pham wrote:
> > > > Hi All,
> > > >
> > > > I have a problem when running short MD simulation using
> > DFTB plus
> > > with
> > > > different solvers in ELSI. I used the 3ob dataset, the
> > system is a
> > > > molecular crystal (C, H, N, O) with 576 atoms (supercell).
> > > >
> > > > The simulation was fine with ELPA, but if I changed the
> > solver to
> > > OMM or
> > > > NTPoly, the simulations crashed after finishing the first
> SCF.
> > > The error
> > > > is "SIGSEGV, segmentation fault occurred" which is
> > difficult to
> > > track down.
> > > >
> > > > When using PEXSI, the error is below:
> > > > **Error! MPI task 38 in elsi_dm_complex_sparse:
> Number of
> > > MPI tasks
> > > > per pole too small
> > > > **Error! MPI task 270 in elsi_dm_complex_sparse:
> Number of
> > > MPI tasks
> > > > per pole too small
> > > > **Error! MPI task 3 in elsi_dm_complex_sparse:
> Number of
> > > MPI tasks
> > > > per pole too small
> > > > **Error! MPI task 219 in elsi_dm_complex_sparse:
> Number of
> > > MPI tasks
> > > > per pole too small
> > > > I couldn't find any related info in the manual. According
> > to the
> > > error
> > > > message, I have tried to increase the number of MPI tasks,
> > still
> > > waiting
> > > > for the simulation to run. Reducing the number of poles
> > doesn't
> > > help, as
> > > > at some point, the error "Too few PEXSI poles" will happen.
> > > >
> > > > Any suggestion would be appreciated!
> > > >
> > > > Thanks,
> > > > Huy
> > > >
> > > > --
> > > >
> > > > C. Huy Pham, Ph.D.
> > > >
> > > > Staff Scientist
> > > >
> > > > Lawrence Livermore National Laboratory
> > > >
> > > > Physical and Life Sciences Directorate
> > > >
> > > > Materials Science Division, L-287
> > > >
> > > > 7000 East Ave, Livermore, CA 94550
> > > >
> > > > Phone: (925) 422-7881
> > > >
> > > > _______________________________________________
> > > > DFTB-Plus-User mailing list
> > > > DFTB-Plus-User at mailman.zfn.uni-bremen.de
> > <mailto:DFTB-Plus-User at mailman.zfn.uni-bremen.de>
> > > <mailto:DFTB-Plus-User at mailman.zfn.uni-bremen.de
> > <mailto:DFTB-Plus-User at mailman.zfn.uni-bremen.de>>
> > > >
> > >
> >
> https://mailman.zfn.uni-bremen.de/cgi-bin/mailman/listinfo/dftb-plus-user
> > <
> https://mailman.zfn.uni-bremen.de/cgi-bin/mailman/listinfo/dftb-plus-user>
> > >
> > <
> https://mailman.zfn.uni-bremen.de/cgi-bin/mailman/listinfo/dftb-plus-user
> <https://mailman.zfn.uni-bremen.de/cgi-bin/mailman/listinfo/dftb-plus-user
> >>
> > >
> > >
> > > --
> > > Dr. Bálint Aradi
> > > Bremen Center for Computational Materials Science, University
> > of Bremen
> > > http://www.bccms.uni-bremen.de/cms/people/b-aradi/
> > <http://www.bccms.uni-bremen.de/cms/people/b-aradi/>
> > > <http://www.bccms.uni-bremen.de/cms/people/b-aradi/
> > <http://www.bccms.uni-bremen.de/cms/people/b-aradi/>>
> > >
> > > _______________________________________________
> > > DFTB-Plus-User mailing list
> > > DFTB-Plus-User at mailman.zfn.uni-bremen.de
> > <mailto:DFTB-Plus-User at mailman.zfn.uni-bremen.de>
> > > <mailto:DFTB-Plus-User at mailman.zfn.uni-bremen.de
> > <mailto:DFTB-Plus-User at mailman.zfn.uni-bremen.de>>
> > >
> >
> https://mailman.zfn.uni-bremen.de/cgi-bin/mailman/listinfo/dftb-plus-user
> > <
> https://mailman.zfn.uni-bremen.de/cgi-bin/mailman/listinfo/dftb-plus-user>
> > >
> > <
> https://mailman.zfn.uni-bremen.de/cgi-bin/mailman/listinfo/dftb-plus-user
> <https://mailman.zfn.uni-bremen.de/cgi-bin/mailman/listinfo/dftb-plus-user
> >>
> > >
> > >
> > >
> > > --
> > >
> > > C. Huy Pham, Ph.D.
> > >
> > > Staff Scientist
> > >
> > > Lawrence Livermore National Laboratory
> > >
> > > Physical and Life Sciences Directorate
> > >
> > > Materials Science Division, L-287
> > >
> > > 7000 East Ave, Livermore, CA 94550
> > >
> > > Phone: (925) 422-7881
> > >
> > > _______________________________________________
> > > DFTB-Plus-User mailing list
> > > DFTB-Plus-User at mailman.zfn.uni-bremen.de
> > <mailto:DFTB-Plus-User at mailman.zfn.uni-bremen.de>
> > >
> >
> https://mailman.zfn.uni-bremen.de/cgi-bin/mailman/listinfo/dftb-plus-user
> > <
> https://mailman.zfn.uni-bremen.de/cgi-bin/mailman/listinfo/dftb-plus-user>
> >
> >
> > --
> > Dr. Bálint Aradi
> > Bremen Center for Computational Materials Science, University of
> Bremen
> > http://www.bccms.uni-bremen.de/cms/people/b-aradi/
> > <http://www.bccms.uni-bremen.de/cms/people/b-aradi/>
> >
> > _______________________________________________
> > DFTB-Plus-User mailing list
> > DFTB-Plus-User at mailman.zfn.uni-bremen.de
> > <mailto:DFTB-Plus-User at mailman.zfn.uni-bremen.de>
> >
> https://mailman.zfn.uni-bremen.de/cgi-bin/mailman/listinfo/dftb-plus-user
> > <
> https://mailman.zfn.uni-bremen.de/cgi-bin/mailman/listinfo/dftb-plus-user>
> >
> >
> >
> > --
> >
> > C. Huy Pham, Ph.D.
> >
> > Staff Scientist
> >
> > Lawrence Livermore National Laboratory
> >
> > Physical and Life Sciences Directorate
> >
> > Materials Science Division, L-287
> >
> > 7000 East Ave, Livermore, CA 94550
> >
> > Phone: (925) 422-7881
> >
> > _______________________________________________
> > DFTB-Plus-User mailing list
> > DFTB-Plus-User at mailman.zfn.uni-bremen.de
> >
> https://mailman.zfn.uni-bremen.de/cgi-bin/mailman/listinfo/dftb-plus-user
>
>
> --
> Dr. Bálint Aradi
> Bremen Center for Computational Materials Science, University of Bremen
> http://www.bccms.uni-bremen.de/cms/people/b-aradi/
>
> _______________________________________________
> DFTB-Plus-User mailing list
> DFTB-Plus-User at mailman.zfn.uni-bremen.de
> https://mailman.zfn.uni-bremen.de/cgi-bin/mailman/listinfo/dftb-plus-user
>
--
C. Huy Pham, Ph.D.
Staff Scientist
Lawrence Livermore National Laboratory
Physical and Life Sciences Directorate
Materials Science Division, L-287
7000 East Ave, Livermore, CA 94550
Phone: (925) 422-7881
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