[DFTB-Plus-User] DFTB-Plus-User Digest, Vol 58, Issue 11
Ben Hourahine
benjamin.hourahine at strath.ac.uk
Sat Jun 22 21:25:50 CEST 2019
Hello David,
If possible use an optimized blas instead of the reference one, as this
makes a big difference in performance.
You might be better off using a serial compiled binary and 2 threads on
each of the 4 images (if with a thread aware blas/lapack).
Yes, sorry, had picked up 8 cores and mistakenly thought that was the
number of images (is 4 enough for REMD?).
Regards
Ben
On 22/06/2019 17:34, David Furman wrote:
> Hi Ben,
>
> 1. I use libblas-dev 3.6.0 (This implementation is the Fortran 77
> reference implementation found at netlib)
> 2. I run each instance from the same shell, 'echo $OMP_NUM_THREADS'
> yields: 1
> 3. Yes it is the correct context. I try to run a Replica-Exchange MD
> using 4 replicas. As far as I know, i-pi distributes the replicas to
> clients (DFTB+ in this case) so that I can run 4 concurrent replicas.
> Since I have a relatively large system in terms of number of atoms,
> each replica takes a significant amount of time. Hence I was thinking
> of parallelizing each replica on 2 or more MPI cores (i.e. parallelize
> each DFTB+ instance). But, then I encounter this weird "bottleneck".
> Regarding your suggestion: I'm not sure how running 8 serial instances
> is of help in my case.
>
> I appreciate your help!
>
>
>
> On Sat, Jun 22, 2019 at 2:54 PM
> <dftb-plus-user-request at mailman.zfn.uni-bremen.de
> <mailto:dftb-plus-user-request at mailman.zfn.uni-bremen.de>> wrote:
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> Today's Topics:
>
> 1. Possible bug in DFTB+ with MPI (David Furman)
> 2. Re: problem with installation (Farzad Molani)
> 3. Re: Possible bug in DFTB+ with MPI (Ben Hourahine)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Sat, 22 Jun 2019 14:41:01 +0100
> From: David Furman <sirok4 at gmail.com <mailto:sirok4 at gmail.com>>
> To: dftb-plus-user at mailman.zfn.uni-bremen.de
> <mailto:dftb-plus-user at mailman.zfn.uni-bremen.de>
> Subject: [DFTB-Plus-User] Possible bug in DFTB+ with MPI
> Message-ID:
>
> <CADtBuo94A729tJFsTW5ev69sEs4qVNM=qOXkjMKFTS8_f1N8pg at mail.gmail.com
> <mailto:qOXkjMKFTS8_f1N8pg at mail.gmail.com>>
> Content-Type: text/plain; charset="utf-8"
>
> Hi all,
> I have a question concerning the running of DFTB+ with MPI. There
> seems to
> be a problem when running more than one DFTB+ instance (with MPI
> parallelization) on the same system.
>
> When I run 4 instances (separate folders) of dftb+ with 2 cores
> each (i.e.
> 8 cores in total):
> mpirun.openmpi -np 2 dftb+, each %CPU usage drops to 50%.
>
> This is the 'top' output:
> ========================================================
> 35426 user 20 0 423384 40404 18248 R 50.5 0.0 0:37.69
> dftb+
> 35434 user 20 0 423080 39720 18248 R 50.2 0.0 0:05.70
> dftb+
> 35396 user 20 0 422044 38660 17644 R 49.8 0.0 1:21.35
> dftb+
> 35402 user 20 0 423384 40460 18304 R 49.8 0.0 1:09.54
> dftb+
> 35403 user 20 0 422044 38872 17848 R 49.8 0.0 1:16.15
> dftb+
> 35427 user 20 0 422044 39048 18032 R 49.8 0.0 0:32.93
> dftb+
> 35435 user 20 0 421732 38164 17716 R 49.8 0.0 0:09.07
> dftb+
> 35395 user 20 0 423384 40360 18204 R 49.5 0.0 1:13.18
> dftb+
> =========================================================
>
> Whereas, when I run one instance with 8 cores, the efficiency is
> 100% as
> expected:
>
> =========================================================
> 35837 user 20 0 441868 35196 19112 R 100.3 0.0 0:04.90
> dftb+
> 35828 user 20 0 442580 35676 19120 R 100.0 0.0 0:04.83
> dftb+
> 35829 user 20 0 442544 36024 19432 R 100.0 0.0 0:04.91
> dftb+
> 35830 user 20 0 441912 35356 19360 R 100.0 0.0 0:04.91
> dftb+
> 35831 user 20 0 441688 35048 19304 R 100.0 0.0 0:04.90
> dftb+
> 35833 user 20 0 441904 35656 19500 R 100.0 0.0 0:04.91
> dftb+
> 35841 user 20 0 441516 34824 19076 R 100.0 0.0 0:04.89
> dftb+
> 35843 user 20 0 441224 34456 18868 R 99.7 0.0 0:04.89
> dftb+
> =========================================================
>
> I run both cases with OMP_NUM_THREADS=1.
> with open-mpi 1.10.2 and gcc 5.4.0.
>
> Could anyone give a hint about what is wrong?
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> ------------------------------
>
> Message: 2
> Date: Sat, 22 Jun 2019 21:42:46 +0800
> From: Farzad Molani <f.molani at gmail.com <mailto:f.molani at gmail.com>>
> To: "User list for DFTB+ related questions"
> <dftb-plus-user at mailman.zfn.uni-bremen.de
> <mailto:dftb-plus-user at mailman.zfn.uni-bremen.de>>
> Subject: Re: [DFTB-Plus-User] problem with installation
> Message-ID:
>
> <CAJY0Q+obk-e8iUOJ_986DS4tWpWG4kAZ99a=6qNstswS0myifg at mail.gmail.com
> <mailto:6qNstswS0myifg at mail.gmail.com>>
> Content-Type: text/plain; charset="utf-8"
>
> I know, but I don't know how can I unstall arpack?
> The package downloaded and now I need help to install it.
> Please note that, I don't permit to login as a root.
>
> On Saturday, June 22, 2019, RICCARDO ROZZA
> <rozza.riccardo at studium.unict.it
> <mailto:rozza.riccardo at studium.unict.it>>
> wrote:
>
> > Dear Farzad,
> >
> > It seems that you need to install the arpack library (ld: cannot
> find
> > -larpack).
> > All the best,
> >
> > Riccardo.
> >
> > On 22 Jun 2019, at 10:01, Farzad Molani <f.molani at gmail.com
> <mailto:f.molani at gmail.com>> wrote:
> >
> >
> > Dear DFTB users,
> > I want to install the newest version of DFTB+. The source and
> executable
> > files from http://www.dftbplus.org/download/dftb-stable/ have been
> > downloaded and untarred. I try to install the software based on
> > instructions on INSTALL.rst, but I got the following error after
> the make.
> > .
> > .
> > .
> > .
> > w.o dispuffdata.o inputdata.o pmlocalisation.o repcont.o repspline.o
> > reppoly.o xlbomd.o extlagrangian.o linresp.o linrespgrad.o qm.o
> > linrespcommon.o arpack.o eigensolver.o typegeometry.o simplemixer.o
> > numderivs2.o potentials.o thirdorder.o charges.o dftbplusu.o
> geoopt.o
> > steepdesc.o gdiis.o orbitalequiv.o broydenmixer.o stress.o etemp.o
> > hermite.o factorial.o intrinsicpr.o mixer.o andersonmixer.o
> > elecconstraints.o angmomentum.o eigenvects.o parser.o hsdutils2.o
> > unitconversion.o oldcompat.o typegeometryhsd.o oldskdata.o
> densitymatrix.o
> > populations.o repulsive.o spinorbit.o forces.o
> -L/home/fmolani/DFTB+/
> > dftbplus-18.2/_build/external/xmlf90 -lxmlf90
> -L/home/fmolani/DFTB+/
> > dftbplus-18.2/_build/external/fsockets -lfsockets
> > -L/apps/intel/2015/composer_xe_2015.3.187/mkl/lib/intel64
> > -lmkl_intel_lp64 -lmkl_intel_thread -lmkl_core -larpack -liomp5
> > ld: cannot find -larpack
> > make[1]: *** [dftb+] Error 1
> > make[1]: Leaving directory `/home/fmolani/DFTB+/dftbplus-
> > 18.2/_build/prog/dftb+'
> > make: *** [dftb+] Error 2
> >
> > I would appreciate to help me to solve the problem.
> > Best regards, Farzad
> > --
> > Farzad Molani
> > Postdoctoral Research Fellow
> > School of Pharmaceutical Science and Technology
> > Tianjin University
> > Building 24, Room A205
> > 92 Weijin Road, Nankai District
> >
> <https://www.google.com/maps/search/92+Weijin+Road,+Nankai+District+%0D%0A+P.+R.+China?entry=gmail&source=g>
> > P. R. China
> >
> <https://www.google.com/maps/search/92+Weijin+Road,+Nankai+District+%0D%0A+P.+R.+China?entry=gmail&source=g>
> > Tel.: +8617526526420
> > Email: f.molani at gmail.com <mailto:f.molani at gmail.com> and
> f.molani at tju.edu.cn <mailto:f.molani at tju.edu.cn>
> > <fmolani at dena.kntu.ac.ir <mailto:fmolani at dena.kntu.ac.ir>>
> >
> >
> > --
> > Farzad Molani
> > Postdoctoral Research Fellow
> > School of Pharmaceutical Science and Technology
> > Tianjin University
> > Building 24, Room A205
> > 92 Weijin Road, Nankai District
> >
> <https://www.google.com/maps/search/92+Weijin+Road,+Nankai+District+%0D%0A+P.+R.+China?entry=gmail&source=g>
> > P. R. China
> >
> <https://www.google.com/maps/search/92+Weijin+Road,+Nankai+District+%0D%0A+P.+R.+China?entry=gmail&source=g>
> > Tel.: +8617526526420
> > Email: f.molani at gmail.com <mailto:f.molani at gmail.com> and
> f.molani at tju.edu.cn <mailto:f.molani at tju.edu.cn>
> > <fmolani at dena.kntu.ac.ir <mailto:fmolani at dena.kntu.ac.ir>>
> > _______________________________________________
> > 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
> >
> >
> >
>
> --
> Farzad Molani
> Postdoctoral Research Fellow
> School of Pharmaceutical Science and Technology
> Tianjin University
> Building 24, Room A205
> 92 Weijin Road, Nankai District
> P. R. China
> Tel.: +8617526526420
> Email: f.molani at gmail.com <mailto:f.molani at gmail.com> and
> f.molani at tju.edu.cn <mailto:f.molani at tju.edu.cn>
> <fmolani at dena.kntu.ac.ir <mailto:fmolani at dena.kntu.ac.ir>>
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> ------------------------------
>
> Message: 3
> Date: Sat, 22 Jun 2019 14:54:40 +0100
> From: Ben Hourahine <benjamin.hourahine at strath.ac.uk
> <mailto:benjamin.hourahine at strath.ac.uk>>
> To: dftb-plus-user at mailman.zfn.uni-bremen.de
> <mailto:dftb-plus-user at mailman.zfn.uni-bremen.de>
> Subject: Re: [DFTB-Plus-User] Possible bug in DFTB+ with MPI
> Message-ID: <16da7e6a-92dd-2184-7a98-067e751cdb14 at strath.ac.uk
> <mailto:16da7e6a-92dd-2184-7a98-067e751cdb14 at strath.ac.uk>>
> Content-Type: text/plain; charset="utf-8"
>
> Hello David,
>
> thoughts so far:
>
> 1) Which blas are you using? Sometimes openBlas steals extra
> threads, is
> your top output shown with thread reporting enabled (H)?
>
> 2) Are you definitely getting the OMP_NUM_THREADS shell variable
> to each
> of the instances?
>
> 3) If this is related to the i-PI mailing list question, is there any
> reason not to run 8 serial instances with 1 thread each? The MPI
> parallelism overhead on just one process is probably not worth it.
>
> Regards
>
> Ben
>
> On 22/06/2019 14:41, David Furman wrote:
> > Hi all,
> > I have a question concerning the running of DFTB+ with MPI. There
> > seems to be a problem when running more than one DFTB+ instance
> (with
> > MPI parallelization) on the same system.
> >
> > When I run 4 instances (separate folders) of dftb+ with 2 cores each
> > (i.e. 8 cores in total):
> > mpirun.openmpi -np 2 dftb+, each %CPU usage drops to 50%.
> >
> > This is the 'top' output:
> > ========================================================
> > 35426 user 20 0 423384 40404 18248 R 50.5 0.0
> 0:37.69 dftb+
> > 35434 user 20 0 423080 39720 18248 R 50.2 0.0
> 0:05.70 dftb+
> > 35396 user 20 0 422044 38660 17644 R 49.8 0.0
> 1:21.35 dftb+
> > 35402 user 20 0 423384 40460 18304 R 49.8 0.0
> 1:09.54 dftb+
> > 35403 user 20 0 422044 38872 17848 R 49.8 0.0
> 1:16.15 dftb+
> > 35427 user 20 0 422044 39048 18032 R 49.8 0.0
> 0:32.93 dftb+
> > 35435 user 20 0 421732 38164 17716 R 49.8 0.0
> 0:09.07 dftb+
> > 35395 user 20 0 423384 40360 18204 R 49.5 0.0
> 1:13.18 dftb+
> > =========================================================
> >
> > Whereas, when I run one instance with 8 cores, the efficiency is
> 100%
> > as expected:
> >
> > =========================================================
> > 35837 user 20 0 441868 35196 19112 R 100.3 0.0
> 0:04.90 dftb+
> > 35828 user 20 0 442580 35676 19120 R 100.0 0.0
> 0:04.83 dftb+
> > 35829 user 20 0 442544 36024 19432 R 100.0 0.0
> 0:04.91 dftb+
> > 35830 user 20 0 441912 35356 19360 R 100.0 0.0
> 0:04.91 dftb+
> > 35831 user 20 0 441688 35048 19304 R 100.0 0.0
> 0:04.90 dftb+
> > 35833 user 20 0 441904 35656 19500 R 100.0 0.0
> 0:04.91 dftb+
> > 35841 user 20 0 441516 34824 19076 R 100.0 0.0
> 0:04.89 dftb+
> > 35843 user 20 0 441224 34456 18868 R 99.7 0.0
> 0:04.89 dftb+
> > =========================================================
> >
> > I run both cases with OMP_NUM_THREADS=1.
> > with open-mpi 1.10.2 and gcc 5.4.0.
> >
> > Could anyone give a hint about what is wrong?
> >
> >
> > _______________________________________________
> > 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
>
> --
> Dr. B. Hourahine, Senior lecturer
> SUPA, Department of Physics,
> University of Strathclyde,
> John Anderson Building,
> 107 Rottenrow, Glasgow G4 0NG, UK.
> +44 141 548 2325, benjamin.hourahine at strath.ac.uk
> <mailto:benjamin.hourahine at strath.ac.uk>
>
> The Department is a partner in SUPA, the Scottish
> Universities Physics Alliance
>
> The University of Strathclyde is a charitable body,
> registered in Scotland, number SC015263
>
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> Subject: Digest Footer
>
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> ------------------------------
>
> End of DFTB-Plus-User Digest, Vol 58, Issue 11
> **********************************************
>
>
>
> --
> David Furman, PhD, MRSC**Herchel Smith Research Fellow Department of
> Chemistry University of Cambridge Lensfield Road CB2 1EW
>
> _______________________________________________
> 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. B. Hourahine, Senior lecturer
SUPA, Department of Physics,
University of Strathclyde,
John Anderson Building,
107 Rottenrow, Glasgow G4 0NG, UK.
+44 141 548 2325, benjamin.hourahine at strath.ac.uk
The Department is a partner in SUPA, the Scottish
Universities Physics Alliance
The University of Strathclyde is a charitable body,
registered in Scotland, number SC015263
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