[QE-users] Segmentation fault in qe-7.3 with DFT+U
Kazume NISHIDATE
nisidate at iwate-u.ac.jp
Thu Jun 6 05:52:41 CEST 2024
Dear Angus,
I have been calculating the system using your input file.
No error, no segmentation fault, so far.
test-7.3]$ grep achiev gaaso.out
convergence has been achieved in 10 iterations
convergence has been achieved in 8 iterations
convergence has been achieved in 9 iterations
test-7.3]$ grep bfgs gaaso.out
number of bfgs steps = 0
number of bfgs steps = 1
number of bfgs steps = 2
test-7.3]$ grep '! total energy' gaaso.out
! total energy = -22477.13808906 Ry
! total energy = -22551.10067194 Ry
! total energy = -22646.03611011 Ry
Dear Angus,
It is now the 3rd step in the vc-relaxation process.
Now I will have to stop the calculation since it consumes
very large computer resources.
Here I used the cutoff of 'ecutwfc = 40' since the value 100 Ry you
specified is very large for this test calculation.
Also I used the NC pseudopotentials at the pseudo-dojo.
At what computational step did you encounter the segmentation fault?
Was it at the first scf cycle before entering the vc-relaxation?
> 2024/06/05 20:02、Angus Gentles <Angus.Gentles at ams-osram.com>のメール:
>
> Dear Kazume Nishdate,
>
> I have already changed this in my compilation, its set to 50 in my version. Thanks for the comment though.
>
> Kind regards,
> Angus Gentles
> ams-OSRAM
> Intitute of Microelectronics, TU WienFrom: Kazume NISHIDATE <nisidate at iwate-u.ac.jp>
> Sent: 05 June 2024 12:46 PM
> To: Angus Gentles <Angus.Gentles at ams-osram.com>; Quantum ESPRESSO users Forum <users at lists.quantum-espresso.org>
> Subject: Re: [QE-users] Segmentation fault in qe-7.3 with DFT+U
> [You don't often get email from nisidate at iwate-u.ac.jp. Learn why this is important at https://aka.ms/LearnAboutSenderIdentification ]
>
> 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
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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://eur02.safelinks.protection.outlook.com/?url=https%3A%2F%2Fsites.google.com%2Fsite%2Fnisidatelab%2F&data=05%7C02%7C%7Cdadb2905ea4545a700bc08dc854cd65b%7Cec1ca250c2344d56a76b7dfb9eee0c46%7C0%7C0%7C638531815451870160%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C40000%7C%7C%7C&sdata=06Tb%2FdWAL2rfExfPCGov9qOKWrlp7HOMpaInUF4i%2B0c%3D&reserved=0
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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