[QE-users] Segmentation fault in qe-7.3 with DFT+U
Kazume NISHIDATE
nisidate at iwate-u.ac.jp
Wed Jun 5 12:46:55 CEST 2024
Dear Angus Gentles,
Just a note.
You should check the source file 'Modules/parameters.f90'.
It is sates that
> INTEGER, PARAMETER :: ntypx = 10
> !! max number of different types of atom
> INTEGER, PARAMETER :: nsx = ntypx
so you can handle up to 10 different kinds of atom.
However, you specify the ntype as
> ntyp = 20
in your input file, and this is two times larger than the default
value.
I think, you should try to re-compile QE with increasing the value of
ntypx in the 'Modules/parameters.f90'. And then, you can calculate
your system without the limitation of the 'ntype'.
> 2024/06/05 17:05、Angus Gentles via users <users at lists.quantum-espresso.org>のメール:
>
> Dear all,
>
> I am getting a segmentation fault error when using DFT+U calculations as below.
>
> [n3511-027:2614825] 127 more processes have sent help message help-mpi-btl-openib.txt / error in device init
> [n3511-027:2614825] Set MCA parameter "orte_base_help_aggregate" to 0 to see all help / error messages
> [n3511-027:2614833:0:2614833] Caught signal 11 (Segmentation fault: address not mapped to object at address 0xffffffff80a1adb8)
> ==== backtrace (tid:2614833) ====
> 0 /lib64/libucs.so.0(ucs_handle_error+0x2dc) [0x14bef008cedc]
> 1 /lib64/libucs.so.0(+0x2b0bc) [0x14bef008d0bc]
> 2 /lib64/libucs.so.0(+0x2b28a) [0x14bef008d28a]
> 3 /home/fs71766/waldhoer02/data/tools/vsc5/base_libs/install/openmpi-4.1.1/lib/libmpi.so.40(MPI_Bcast+0x58) [0x14bf04d4e598]
> 4 /gpfs/opt/sw/vsc4/VSC/x86_64/glibc-2.17/skylake/intel/oneapi/mkl/2022.0.1/lib/intel64/libmkl_blacs_openmpi_lp64.so.2(MKLMPI_Bcast+0xdd) [0x14bf0c5a6dfd]
> 5 /gpfs/opt/sw/vsc4/VSC/x86_64/glibc-2.17/skylake/intel/oneapi/mkl/2022.0.1/lib/intel64/libmkl_scalapack_lp64.so.2(PB_CpgemmMPI+0x1097) [0x14bf0c1bbad7]
> 6 /gpfs/opt/sw/vsc4/VSC/x86_64/glibc-2.17/skylake/intel/oneapi/mkl/2022.0.1/lib/intel64/libmkl_scalapack_lp64.so.2(pdgemm_+0xda7) [0x14bf0c21ff07]
> 7 /gpfs/opt/sw/vsc4/VSC/x86_64/glibc-2.17/skylake/intel/oneapi/mkl/2022.0.1/lib/intel64/libmkl_scalapack_lp64.so.2(pdlaed1_+0x7cd) [0x14bf0bcc6dbd]
> 8 /gpfs/opt/sw/vsc4/VSC/x86_64/glibc-2.17/skylake/intel/oneapi/mkl/2022.0.1/lib/intel64/libmkl_scalapack_lp64.so.2(pdlaed0_+0x9a1) [0x14bf0bcc6551]
> 9 /gpfs/opt/sw/vsc4/VSC/x86_64/glibc-2.17/skylake/intel/oneapi/mkl/2022.0.1/lib/intel64/libmkl_scalapack_lp64.so.2(pdstedc_+0x639) [0x14bf0bcd0f19]
> 10 /gpfs/opt/sw/vsc4/VSC/x86_64/glibc-2.17/skylake/intel/oneapi/mkl/2022.0.1/lib/intel64/libmkl_scalapack_lp64.so.2(mkl_pzheevd0_+0xf99) [0x14bf0bf377c9]
> 11 /gpfs/opt/sw/vsc4/VSC/x86_64/glibc-2.17/skylake/intel/oneapi/mkl/2022.0.1/lib/intel64/libmkl_scalapack_lp64.so.2(mkl_pzheevdm_+0xb99) [0x14bf0bf36379]
> 12 /gpfs/opt/sw/vsc4/VSC/x86_64/glibc-2.17/skylake/intel/oneapi/mkl/2022.0.1/lib/intel64/libmkl_scalapack_lp64.so.2(pzheevd_+0x3ca) [0x14bf0bf3553a]
> 13 pw.x() [0xbb9d5a]
> 14 pw.x() [0xb9bb82]
> 15 pw.x() [0x71de4b]
> 16 pw.x() [0x5a03a9]
> 17 pw.x() [0x5a47c4]
> 18 pw.x() [0x412a44]
> 19 pw.x() [0x41caf9]
> 20 pw.x() [0x4f955b]
> 21 pw.x() [0x40688c]
> 22 pw.x() [0x4065cd]
> 23 /lib64/libc.so.6(__libc_start_main+0xe5) [0x14bf033d8d85]
> 24 pw.x() [0x40660e]
> =================================
>
> Program received signal SIGSEGV: Segmentation fault - invalid memory reference.
>
> Backtrace for this error:
> #0 0x14bf033ecb4f in ???
> #1 0x14bf04d4e598 in ompi_comm_invalid
> at ../../../../ompi/communicator/communicator.h:341
> #2 0x14bf04d4e598 in PMPI_Bcast
> at /home/fs71766/waldhoer02/data/tools/vsc5/base_libs/build/openmpi-4.1.1/ompi/mpi/c/profile/pbcast.c:72
> #3 0x14bf0c5a6dfc in ???
> #4 0x14bf0c1bbad6 in ???
> #5 0x14bf0c21ff06 in ???
> #6 0x14bf0bcc6dbc in ???
> #7 0x14bf0bcc6550 in ???
> #8 0x14bf0bcd0f18 in ???
> #9 0x14bf0bf377c8 in ???
> #10 0x14bf0bf36378 in ???
> #11 0x14bf0bf35539 in ???
> #12 0xbb9d59 in __zhpev_module_MOD_pzheevd_drv
> at /home/fs71287/gentles/tools/sc-qe-7.3/LAXlib/zhpev_drv.f90:1562
> #13 0xb9bb81 in laxlib_pcdiaghg_
> at /home/fs71287/gentles/tools/sc-qe-7.3/LAXlib/cdiaghg.f90:587
> #14 0x71de4a in pcegterg_
> at /home/fs71287/gentles/tools/sc-qe-7.3/KS_Solvers/Davidson/cegterg.f90:944
> #15 0x5a03a8 in diag_bands_k
> at /home/fs71287/gentles/tools/sc-qe-7.3/PW/src/c_bands.f90:1030
> #16 0x5a03a8 in diag_bands_
> at /home/fs71287/gentles/tools/sc-qe-7.3/PW/src/c_bands.f90:322
> #17 0x5a47c3 in c_bands_
> at /home/fs71287/gentles/tools/sc-qe-7.3/PW/src/c_bands.f90:132
> #18 0x412a43 in electrons_scf_
> at /home/fs71287/gentles/tools/sc-qe-7.3/PW/src/electrons.f90:689
> #19 0x41caf8 in electrons_
> at /home/fs71287/gentles/tools/sc-qe-7.3/PW/src/electrons.f90:192
> #20 0x4f955a in run_pwscf_
> at /home/fs71287/gentles/tools/sc-qe-7.3/PW/src/run_pwscf.f90:189
> #21 0x40688b in pwscf
> at /home/fs71287/gentles/tools/sc-qe-7.3/PW/src/pwscf.f90:85
> #22 0x4065cc in main
> at /home/fs71287/gentles/tools/sc-qe-7.3/PW/src/pwscf.f90:40
>
> I have been using 128 atom supercells with DFT+U calculations, Using InGaAsSb. The version is qe-7.3. I have seen a few previous versions having similar problems, but I am not sure if their fixes will be a appropriate given the changes in the DFT+U codes. It seems to be a problem with loading the environment. I am using supercomputers with 128 processors. The input file is:
>
> &CONTROL
> calculation = 'vc-relax',
> disk_io = 'low',
> etot_conv_thr = 1d-05,
> forc_conv_thr = 0.001,
> outdir = './tmp_In0.0Ga1.0As0.75Sb0.25_4x4x4',
> prefix = 'In0.0Ga1.0As0.75Sb0.25_4x4x4',
> pseudo_dir = '/home/fs71287/gentles/data/pseudos/',
> restart_mode = 'from_scratch',
> verbosity = 'low',
> /
> &SYSTEM
> celldm(1) = 43.6265,
> degauss = 0.0001,
> ecutwfc = 100,
> ibrav = 2,
> lspinorb = .TRUE.,
> nat = 128,
> nbnd = 1792,
> noncolin = .TRUE.,
> ntyp = 20,
> occupations = 'smearing',
> /
> &ELECTRONS
> conv_thr = 1d-05,
> mixing_beta = 0.65,
> /
> &IONS
> /
> &CELL
> cell_dofree = 'ibrav',
> /
> ATOMIC_SPECIES
> As1 74.9216 As.pbe.NC-FR.standard.v0.4.UPF
> As0 74.9216 As.pbe.NC-FR.standard.v0.4.UPF
> As2 74.9216 As.pbe.NC-FR.standard.v0.4.UPF
> As3 74.9216 As.pbe.NC-FR.standard.v0.4.UPF
> As4 74.9216 As.pbe.NC-FR.standard.v0.4.UPF
> Ga1 69.7230 Ga.pbe.NC-FR.standard.v0.4.UPF
> Ga0 69.7230 Ga.pbe.NC-FR.standard.v0.4.UPF
> Ga2 69.7230 Ga.pbe.NC-FR.standard.v0.4.UPF
> Ga3 69.7230 Ga.pbe.NC-FR.standard.v0.4.UPF
> Ga4 69.7230 Ga.pbe.NC-FR.standard.v0.4.UPF
> In1 114.8180 In.pbe.NC-FR.standard.v0.4.UPF
> In0 114.8180 In.pbe.NC-FR.standard.v0.4.UPF
> In2 114.8180 In.pbe.NC-FR.standard.v0.4.UPF
> In3 114.8180 In.pbe.NC-FR.standard.v0.4.UPF
> In4 114.8180 In.pbe.NC-FR.standard.v0.4.UPF
> Sb1 121.7600 Sb.pbe.NC-FR.standard.v0.4.UPF
> Sb0 121.7600 Sb.pbe.NC-FR.standard.v0.4.UPF
> Sb2 121.7600 Sb.pbe.NC-FR.standard.v0.4.UPF
> Sb3 121.7600 Sb.pbe.NC-FR.standard.v0.4.UPF
> Sb4 121.7600 Sb.pbe.NC-FR.standard.v0.4.UPF
> ATOMIC_POSITIONS crystal
> Ga4 0.000000 0.000000 0.000000
> As4 0.062500 0.062500 0.062500
> Ga3 0.000000 0.000000 0.250000
> As4 0.062500 0.062500 0.312500
> Ga4 0.000000 0.000000 0.500000
> As4 0.062500 0.062500 0.562500
> Ga4 0.000000 0.000000 0.750000
> As4 0.062500 0.062500 0.812500
> Ga4 0.000000 0.250000 0.000000
> As4 0.062500 0.312500 0.062500
> Ga4 0.000000 0.250000 0.250000
> As4 0.062500 0.312500 0.312500
> Ga2 0.000000 0.250000 0.500000
> Sb4 0.062500 0.312500 0.562500
> Ga2 0.000000 0.250000 0.750000
> As4 0.062500 0.312500 0.812500
> Ga4 0.000000 0.500000 0.000000
> As4 0.062500 0.562500 0.062500
> Ga4 0.000000 0.500000 0.250000
> As4 0.062500 0.562500 0.312500
> Ga1 0.000000 0.500000 0.500000
> Sb4 0.062500 0.562500 0.562500
> Ga3 0.000000 0.500000 0.750000
> As4 0.062500 0.562500 0.812500
> Ga4 0.000000 0.750000 0.000000
> As4 0.062500 0.812500 0.062500
> Ga2 0.000000 0.750000 0.250000
> Sb4 0.062500 0.812500 0.312500
> Ga2 0.000000 0.750000 0.500000
> As4 0.062500 0.812500 0.562500
> Ga4 0.000000 0.750000 0.750000
> As4 0.062500 0.812500 0.812500
> Ga4 0.250000 0.000000 0.000000
> As4 0.312500 0.062500 0.062500
> Ga3 0.250000 0.000000 0.250000
> As4 0.312500 0.062500 0.312500
> Ga4 0.250000 0.000000 0.500000
> As4 0.312500 0.062500 0.562500
> Ga4 0.250000 0.000000 0.750000
> As4 0.312500 0.062500 0.812500
> Ga3 0.250000 0.250000 0.000000
> As4 0.312500 0.312500 0.062500
> Ga4 0.250000 0.250000 0.250000
> As4 0.312500 0.312500 0.312500
> Ga2 0.250000 0.250000 0.500000
> Sb4 0.312500 0.312500 0.562500
> Ga2 0.250000 0.250000 0.750000
> Sb4 0.312500 0.312500 0.812500
> Ga4 0.250000 0.500000 0.000000
> As4 0.312500 0.562500 0.062500
> Ga4 0.250000 0.500000 0.250000
> As4 0.312500 0.562500 0.312500
> Ga1 0.250000 0.500000 0.500000
> Sb4 0.312500 0.562500 0.562500
> Ga2 0.250000 0.500000 0.750000
> As4 0.312500 0.562500 0.812500
> Ga4 0.250000 0.750000 0.000000
> As4 0.312500 0.812500 0.062500
> Ga2 0.250000 0.750000 0.250000
> Sb4 0.312500 0.812500 0.312500
> Ga2 0.250000 0.750000 0.500000
> As4 0.312500 0.812500 0.562500
> Ga4 0.250000 0.750000 0.750000
> As4 0.312500 0.812500 0.812500
> Ga4 0.500000 0.000000 0.000000
> As4 0.562500 0.062500 0.062500
> Ga3 0.500000 0.000000 0.250000
> As4 0.562500 0.062500 0.312500
> Ga4 0.500000 0.000000 0.500000
> As4 0.562500 0.062500 0.562500
> Ga4 0.500000 0.000000 0.750000
> As4 0.562500 0.062500 0.812500
> Ga3 0.500000 0.250000 0.000000
> As4 0.562500 0.312500 0.062500
> Ga4 0.500000 0.250000 0.250000
> As4 0.562500 0.312500 0.312500
> Ga2 0.500000 0.250000 0.500000
> Sb4 0.562500 0.312500 0.562500
> Ga1 0.500000 0.250000 0.750000
> Sb4 0.562500 0.312500 0.812500
> Ga4 0.500000 0.500000 0.000000
> As4 0.562500 0.562500 0.062500
> Ga3 0.500000 0.500000 0.250000
> Sb4 0.562500 0.562500 0.312500
> Ga0 0.500000 0.500000 0.500000
> Sb4 0.562500 0.562500 0.562500
> Ga2 0.500000 0.500000 0.750000
> As4 0.562500 0.562500 0.812500
> Ga4 0.500000 0.750000 0.000000
> As4 0.562500 0.812500 0.062500
> Ga1 0.500000 0.750000 0.250000
> Sb4 0.562500 0.812500 0.312500
> Ga2 0.500000 0.750000 0.500000
> As4 0.562500 0.812500 0.562500
> Ga4 0.500000 0.750000 0.750000
> As4 0.562500 0.812500 0.812500
> Ga4 0.750000 0.000000 0.000000
> As4 0.812500 0.062500 0.062500
> Ga3 0.750000 0.000000 0.250000
> As4 0.812500 0.062500 0.312500
> Ga4 0.750000 0.000000 0.500000
> As4 0.812500 0.062500 0.562500
> Ga4 0.750000 0.000000 0.750000
> As4 0.812500 0.062500 0.812500
> Ga3 0.750000 0.250000 0.000000
> As4 0.812500 0.312500 0.062500
> Ga4 0.750000 0.250000 0.250000
> As4 0.812500 0.312500 0.312500
> Ga2 0.750000 0.250000 0.500000
> Sb4 0.812500 0.312500 0.562500
> Ga1 0.750000 0.250000 0.750000
> Sb4 0.812500 0.312500 0.812500
> Ga4 0.750000 0.500000 0.000000
> As4 0.812500 0.562500 0.062500
> Ga3 0.750000 0.500000 0.250000
> As4 0.812500 0.562500 0.312500
> Ga1 0.750000 0.500000 0.500000
> Sb4 0.812500 0.562500 0.562500
> Ga2 0.750000 0.500000 0.750000
> As4 0.812500 0.562500 0.812500
> Ga4 0.750000 0.750000 0.000000
> As4 0.812500 0.812500 0.062500
> Ga2 0.750000 0.750000 0.250000
> Sb4 0.812500 0.812500 0.312500
> Ga2 0.750000 0.750000 0.500000
> As4 0.812500 0.812500 0.562500
> Ga4 0.750000 0.750000 0.750000
> As4 0.812500 0.812500 0.812500
> K_POINTS automatic
> 3 3 3 0 0 0
>
> HUBBARD (atomic)
> U In0-5p -2.24
> U Ga0-4p -2.04
> U As0-4p 4.02
> U Sb0-5p 4.43
> U In1-5p -2.2575000000000003
> U Ga1-4p -2.39
> U As1-4p 4.5424999999999995
> U Sb1-5p 4.7825
> U In2-5p -2.2750000000000004
> U Ga2-4p -2.74
> U As2-4p 5.0649999999999995
> U Sb2-5p 5.135
> U In3-5p -2.2925
> U Ga3-4p -3.09
> U As3-4p 5.5875
> U Sb3-5p 5.4875
> U In4-5p -2.31
> U Ga4-4p -3.44
> U As4-4p 6.11
> U Sb4-5p 5.84
>
> The output file gets through several optimisation steps and then stalls at an scf iteration, as below:
>
> Number of occupied Hubbard levels = 615.3045
>
> total cpu time spent up to now is 166039.0 secs
>
> total energy = -22879.33720322 Ry
> estimated scf accuracy < 0.00963404 Ry
>
> iteration # 2 ecut= 100.00 Ry beta= 0.65
> Davidson diagonalization with overlap
> ethr = 5.38E-07, avg # of iterations = 6.0
>
> total cpu time spent up to now is 172245.2 secs
>
> total energy = -22879.33685019 Ry
> estimated scf accuracy < 0.03584310 Ry
>
> iteration # 3 ecut= 100.00 Ry beta= 0.65
> Davidson diagonalization with overlap
>
> I am relatively confident that this isn't a problem with the memory of the computer being overcome. I get problems on smaller cells and bands calculations. Any help is appreciated.
>
>
> With kind regards, I am
> Angus Gentles
> ams-OSRAM
> Intitute of Microelectronics, TU Wien
>
>
> _______________________________________________
> The Quantum ESPRESSO community stands by the Ukrainian
> people and expresses its concerns about the devastating
> effects that the Russian military offensive has on their
> country and on the free and peaceful scientific, cultural,
> and economic cooperation amongst peoples
> _______________________________________________
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> users mailing list users at lists.quantum-espresso.org
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西館数芽
Kazume NISHIDATE Ph.D
Department of Systems Innovation Engineering,
Graduate School of Science and Engineering, Iwate University
4-3-5 Ueda, Morioka, Iwate, 020-8551 JAPAN
Phone:+81-19-621-6391
kazume.nishidate at gmail.com, nisidate at iwate-u.ac.jp
https://sites.google.com/site/nisidatelab/
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