[QE-users] MPI error in pw.x
Axel Kohlmeyer
akohlmey at gmail.com
Mon Dec 10 13:15:02 CET 2018
a careful look at the error message reveals, that you are running out
of space for MPI communicators for which a fixed maximum number (16k)
seems to be allowed.
this hints at a problem somewhere that communicators are generated
with MPI_Comm_split() and not properly cleared afterwards.
axel.
On Mon, Dec 10, 2018 at 6:53 AM Alex.Durie <alex.durie at open.ac.uk> wrote:
>
> The problem seems to crop up when a minimum of 8 processors are used. As a quick and easily accessible test, I tried it on example08 of the Wannier90 examples with the following command;
>
>
> mpirun -np 8 pw.x -i iron.scf > scf.out
>
>
> and the same problem occurred. I am using PWSCF v.6.3 using the Intel parallel studio 2016 suite. PW was built using all intel compilers, intel MPI and mkl.
>
>
> Many thanks,
>
>
> Alex
>
>
> Date: Sun, 9 Dec 2018 21:26:31 +0100
> From: Paolo Giannozzi <p.giannozzi at gmail.com>
> To: Quantum Espresso users Forum <users at lists.quantum-espresso.org>
> Subject: Re: [QE-users] MPI error in pw.x
> Message-ID:
> <CAPMgbCs0VU+GJZJ_TY3cfX+8pGoRVsuF5LvW0k7+fyB+sBZ2Hg at mail.gmail.com>
> Content-Type: text/plain; charset="utf-8"
>
> If it is not a problem of your compiler or mpi libraries, it can only be
> the usual problem of irreproducibility of results on different processors.
> In order to figure out this, one needs as a strict minimum some information
> on which exact version exhibits the problem, under which exact
> circumstances (e.g. mpirun -np ... ) and an input that can be run in a
> reasonable amount of time on a reasonably small machine.
>
> Paolo
> -
>
> On Sat, Dec 8, 2018 at 9:55 PM Alex.Durie <alex.durie at open.ac.uk> wrote:
>
> > Dear experts,
> >
> > I have been running pw.x with multiple processes quite successfully,
> > however when the number of processes is high enough, such that the space
> > group has more than 7 processes, where the subspace diagonalization no
> > longer uses a serial algorithm, the program crashes abruptly at about the
> > 10th iteration with the following errors;
> >
> > Fatal error in PMPI_Cart_sub: Other MPI error, error stack:
> > PMPI_Cart_sub(242)...................: MPI_Cart_sub(comm=0xc400fcf3,
> > remain_dims=0x7ffe0b27a6e8, comm_new=0x7ffe0b27a640) failed
> > PMPI_Cart_sub(178)...................:
> > MPIR_Comm_split_impl(270)............:
> > MPIR_Get_contextid_sparse_group(1330): Too many communicators (0/16384
> > free on this process; ignore_id=0)
> > Fatal error in PMPI_Cart_sub: Other MPI error, error stack:
> > PMPI_Cart_sub(242)...................: MPI_Cart_sub(comm=0xc400fcf3,
> > remain_dims=0x7ffefaee7ce8, comm_new=0x7ffefaee7c40) failed
> > PMPI_Cart_sub(178)...................:
> > MPIR_Comm_split_impl(270)............:
> > MPIR_Get_contextid_sparse_group(1330): Too many communicators (0/16384
> > free on this process; ignore_id=0)
> > Fatal error in PMPI_Cart_sub: Other MPI error, error stack:
> > PMPI_Cart_sub(242)...................: MPI_Cart_sub(comm=0xc400fcf3,
> > remain_dims=0x7fffc482d168, comm_new=0x7fffc482d0c0) failed
> > PMPI_Cart_sub(178)...................:
> > MPIR_Comm_split_impl(270)............:
> > MPIR_Get_contextid_sparse_group(1330): Too many communicators (0/16384
> > free on this process; ignore_id=0)
> > Fatal error in PMPI_Cart_sub: Other MPI error, error stack:
> > PMPI_Cart_sub(242)...................: MPI_Cart_sub(comm=0xc400fcf3,
> > remain_dims=0x7ffe23a022e8, comm_new=0x7ffe23a02240) failed
> > PMPI_Cart_sub(178)...................:
> > MPIR_Comm_split_impl(270)............:
> > MPIR_Get_contextid_sparse_group(1330): Too many communicators (0/16384
> > free on this process; ignore_id=0)
> > forrtl: error (69): process interrupted (SIGINT)
> > Image PC Routine Line
> > Source
> > pw.x 0000000000EAAC45 Unknown Unknown Unknown
> > pw.x 0000000000EA8867 Unknown Unknown Unknown
> > pw.x 0000000000E3DC64 Unknown Unknown Unknown
> > pw.x 0000000000E3DA76 Unknown Unknown Unknown
> > pw.x 0000000000DC41B6 Unknown Unknown Unknown
> > pw.x 0000000000DCBB2E Unknown Unknown Unknown
> > libpthread.so.0 00002BA339B746D0 Unknown Unknown
> > Unknown
> > libmpi.so.12 00002BA3390A345F Unknown Unknown
> > Unknown
> > libmpi.so.12 00002BA3391AEE39 Unknown Unknown
> > Unknown
> > libmpi.so.12 00002BA3391AEB32 Unknown Unknown
> > Unknown
> > libmpi.so.12 00002BA3390882F9 Unknown Unknown
> > Unknown
> > libmpi.so.12 00002BA339087D5D Unknown Unknown
> > Unknown
> > libmpi.so.12 00002BA339087BDC Unknown Unknown
> > Unknown
> > libmpi.so.12 00002BA339087B0C Unknown Unknown
> > Unknown
> > libmpi.so.12 00002BA339089932 Unknown Unknown
> > Unknown
> > libmpifort.so.12 00002BA338C41B1C Unknown Unknown
> > Unknown
> > pw.x 0000000000BCEE47 bcast_real_ 37
> > mp_base.f90
> > pw.x 0000000000BAF7E4 mp_mp_mp_bcast_rv 395 mp.f90
> > pw.x 0000000000B6E881 pcdiaghg_ 363
> > cdiaghg.f90
> > pw.x 0000000000AF7304 protate_wfc_k_ 256
> > rotate_wfc_k.f90
> > pw.x 0000000000681E82 rotate_wfc_ 64
> > rotate_wfc.f90
> > pw.x 000000000064F519 diag_bands_ 423
> > c_bands.f90
> > pw.x 000000000064CAD4 c_bands_ 99
> > c_bands.f90
> > pw.x 000000000040C014 electrons_scf_ 552
> > electrons.f90
> > pw.x 0000000000408DBD electrons_ 146
> > electrons.f90
> > pw.x 000000000057582B run_pwscf_ 132
> > run_pwscf.f90
> > pw.x 0000000000406AC5 MAIN__ 77
> > pwscf.f90
> > pw.x 000000000040695E Unknown Unknown Unknown
> > libc.so.6 00002BA33A0A5445 Unknown Unknown
> > Unknown
> > pw.x 0000000000406869 Unknown Unknown Unknown
> > forrtl: error (69): process interrupted (SIGINT)
> > Image PC Routine Line
> > Source
> > pw.x 0000000000EAAC45 Unknown Unknown Unknown
> > pw.x 0000000000EA8867 Unknown Unknown Unknown
> > pw.x 0000000000E3DC64 Unknown Unknown Unknown
> > pw.x 0000000000E3DA76 Unknown Unknown Unknown
> > pw.x 0000000000DC41B6 Unknown Unknown Unknown
> > pw.x 0000000000DCBB2E Unknown Unknown Unknown
> > libpthread.so.0 00002B8E527936D0 Unknown Unknown
> > Unknown
> > libmpi.so.12 00002B8E51CC276E Unknown Unknown
> > Unknown
> > libmpi.so.12 00002B8E51DCDE39 Unknown Unknown
> > Unknown
> > libmpi.so.12 00002B8E51DCDB32 Unknown Unknown
> > Unknown
> > libmpi.so.12 00002B8E51CA72F9 Unknown Unknown
> > Unknown
> > libmpi.so.12 00002B8E51CA6D5D Unknown Unknown
> > Unknown
> > libmpi.so.12 00002B8E51CA6BDC Unknown Unknown
> > Unknown
> > libmpi.so.12 00002B8E51CA6B0C Unknown Unknown
> > Unknown
> > libmpi.so.12 00002B8E51CA8932 Unknown Unknown
> > Unknown
> > libmpifort.so.12 00002B8E51860B1C Unknown Unknown
> > Unknown
> > pw.x 0000000000BCEE47 bcast_real_ 37
> > mp_base.f90
> > pw.x 0000000000BAF7E4 mp_mp_mp_bcast_rv 395 mp.f90
> > pw.x 0000000000B6E881 pcdiaghg_ 363
> > cdiaghg.f90
> > pw.x 0000000000AF7304 protate_wfc_k_ 256
> > rotate_wfc_k.f90
> > pw.x 0000000000681E82 rotate_wfc_ 64
> > rotate_wfc.f90
> > pw.x 000000000064F519 diag_bands_ 423
> > c_bands.f90
> > pw.x 000000000064CAD4 c_bands_ 99
> > c_bands.f90
> > pw.x 000000000040C014 electrons_scf_ 552
> > electrons.f90
> > pw.x 0000000000408DBD electrons_ 146
> > electrons.f90
> > pw.x 000000000057582B run_pwscf_ 132
> > run_pwscf.f90
> > pw.x 0000000000406AC5 MAIN__ 77
> > pwscf.f90
> > pw.x 000000000040695E Unknown Unknown Unknown
> > libc.so.6 00002B8E52CC4445 Unknown Unknown
> > Unknown
> > pw.x 0000000000406869 Unknown Unknown Unknown
> > forrtl: error (69): process interrupted (SIGINT)
> > Image PC Routine Line
> > Source
> > pw.x 0000000000EAAC45 Unknown Unknown Unknown
> > pw.x 0000000000EA8867 Unknown Unknown Unknown
> > pw.x 0000000000E3DC64 Unknown Unknown Unknown
> > pw.x 0000000000E3DA76 Unknown Unknown Unknown
> > pw.x 0000000000DC41B6 Unknown Unknown Unknown
> > pw.x 0000000000DCBB2E Unknown Unknown Unknown
> > libpthread.so.0 00002ABAB008D6D0 Unknown Unknown
> > Unknown
> > libmpi.so.12 00002ABAAF5BC45C Unknown Unknown
> > Unknown
> > libmpi.so.12 00002ABAAF6C7E39 Unknown Unknown
> > Unknown
> > libmpi.so.12 00002ABAAF6C7B32 Unknown Unknown
> > Unknown
> > libmpi.so.12 00002ABAAF5A12F9 Unknown Unknown
> > Unknown
> > libmpi.so.12 00002ABAAF5A0D5D Unknown Unknown
> > Unknown
> > libmpi.so.12 00002ABAAF5A0BDC Unknown Unknown
> > Unknown
> > libmpi.so.12 00002ABAAF5A0B0C Unknown Unknown
> > Unknown
> > libmpi.so.12 00002ABAAF5A2932 Unknown Unknown
> > Unknown
> > libmpifort.so.12 00002ABAAF15AB1C Unknown Unknown
> > Unknown
> > pw.x 0000000000BCEE47 bcast_real_ 37
> > mp_base.f90
> > pw.x 0000000000BAF7E4 mp_mp_mp_bcast_rv 395 mp.f90
> > pw.x 0000000000B6E881 pcdiaghg_ 363
> > cdiaghg.f90
> > pw.x 0000000000AF7304 protate_wfc_k_ 256
> > rotate_wfc_k.f90
> > pw.x 0000000000681E82 rotate_wfc_ 64
> > rotate_wfc.f90
> > pw.x 000000000064F519 diag_bands_ 423
> > c_bands.f90
> > pw.x 000000000064CAD4 c_bands_ 99
> > c_bands.f90
> > pw.x 000000000040C014 electrons_scf_ 552
> > electrons.f90
> > pw.x 0000000000408DBD electrons_ 146
> > electrons.f90
> > pw.x 000000000057582B run_pwscf_ 132
> > run_pwscf.f90
> > pw.x 0000000000406AC5 MAIN__ 77
> > pwscf.f90
> > pw.x 000000000040695E Unknown Unknown Unknown
> > libc.so.6 00002ABAB05BE445 Unknown Unknown
> > Unknown
> > pw.x 0000000000406869 Unknown Unknown Unknown
> > forrtl: error (69): process interrupted (SIGINT)
> > Image PC Routine Line
> > Source
> > pw.x 0000000000EAAC45 Unknown Unknown Unknown
> > pw.x 0000000000EA8867 Unknown Unknown Unknown
> > pw.x 0000000000E3DC64 Unknown Unknown Unknown
> > pw.x 0000000000E3DA76 Unknown Unknown Unknown
> > pw.x 0000000000DC41B6 Unknown Unknown Unknown
> > pw.x 0000000000DCBB2E Unknown Unknown Unknown
> > libpthread.so.0 00002ACB4BF866D0 Unknown Unknown
> > Unknown
> > libmpi.so.12 00002ACB4B4B5775 Unknown Unknown
> > Unknown
> > libmpi.so.12 00002ACB4B5C0E39 Unknown Unknown
> > Unknown
> > libmpi.so.12 00002ACB4B5C0B32 Unknown Unknown
> > Unknown
> > libmpi.so.12 00002ACB4B49A2F9 Unknown Unknown
> > Unknown
> > libmpi.so.12 00002ACB4B499D5D Unknown Unknown
> > Unknown
> > libmpi.so.12 00002ACB4B499BDC Unknown Unknown
> > Unknown
> > libmpi.so.12 00002ACB4B499B0C Unknown Unknown
> > Unknown
> > libmpi.so.12 00002ACB4B49B932 Unknown Unknown
> > Unknown
> > libmpifort.so.12 00002ACB4B053B1C Unknown Unknown
> > Unknown
> > pw.x 0000000000BCEE47 bcast_real_ 37
> > mp_base.f90
> > pw.x 0000000000BAF7E4 mp_mp_mp_bcast_rv 395 mp.f90
> > pw.x 0000000000B6E881 pcdiaghg_ 363
> > cdiaghg.f90
> > pw.x 0000000000AF7304 protate_wfc_k_ 256
> > rotate_wfc_k.f90
> > pw.x 0000000000681E82 rotate_wfc_ 64
> > rotate_wfc.f90
> > pw.x 000000000064F519 diag_bands_ 423
> > c_bands.f90
> > pw.x 000000000064CAD4 c_bands_ 99
> > c_bands.f90
> > pw.x 000000000040C014 electrons_scf_ 552
> > electrons.f90
> > pw.x 0000000000408DBD electrons_ 146
> > electrons.f90
> > pw.x 000000000057582B run_pwscf_ 132
> > run_pwscf.f90
> > pw.x 0000000000406AC5 MAIN__ 77
> > pwscf.f90
> > pw.x 000000000040695E Unknown Unknown Unknown
> > libc.so.6 00002ACB4C4B7445 Unknown Unknown
> > Unknown
> > pw.x 0000000000406869 Unknown Unknown Unknown
> >
> > Sample output below
> >
> > Parallel version (MPI), running on 16 processors
> >
> > MPI processes distributed on 1 nodes R & G space division:
> > proc/nbgrp/npool/nimage = 16
> >
> > Reading cobalt.scf Message from routine
> > read_cards : DEPRECATED: no units specified in
> > ATOMIC_POSITIONS card Message
> > from routine read_cards :
> >
> > ATOMIC_POSITIONS: units set to alat
> >
> > Current dimensions of program PWSCF are:
> >
> > Max number of different atomic species (ntypx) = 10
> >
> > Max number of k-points (npk) = 40000
> >
> > Max angular momentum in pseudopotentials (lmaxx) = 3
> >
> > Presently no symmetry can be used with electric field
> >
> >
> > file Co.pz-n-kjpaw_psl.1.0.0.UPF: wavefunction(s) 4S 3D renormalized
> >
> >
> > Subspace diagonalization in iterative solution of the eigenvalue problem:
> >
> > one sub-group per band group will be used
> >
> > scalapack distributed-memory algorithm (size of sub-group: 2* 2 procs)
> >
> >
> > Parallelization info
> >
> > --------------------
> >
> > sticks: dense smooth PW G-vecs: dense smooth PW
> >
> > Min 13 13 4 2449 2449 462
> >
> > Max 14 14 5 2516 2516 527
> >
> > Sum 221 221 69 39945 39945 7777
> >
> > Many thanks,
> >
> > Alex Durie
> > PhD student
> > Open University
> > United Kingdom
> > _______________________________________________
> > users mailing list
> > users at lists.quantum-espresso.org
> > https://lists.quantum-espresso.org/mailman/listinfo/users
>
>
>
> --
> Paolo Giannozzi, Dip. Scienze Matematiche Informatiche e Fisiche,
> Univ. Udine, via delle Scienze 208, 33100 Udine, Italy
> Phone +39-0432-558216, fax +39-0432-558222
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--
Dr. Axel Kohlmeyer akohlmey at gmail.com http://goo.gl/1wk0
College of Science & Technology, Temple University, Philadelphia PA, USA
International Centre for Theoretical Physics, Trieste. Italy.
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