[DFTB-Plus-User] error with ELSI solvers
Bálint Aradi
aradi at uni-bremen.de
Mon Feb 7 22:01:08 CET 2022
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>
> >
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> >
> >
> > --
> > 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/>>
> >
> > _______________________________________________
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> <mailto:DFTB-Plus-User at mailman.zfn.uni-bremen.de>>
> >
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> <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/>
>
> _______________________________________________
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> <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/
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