VASP 6.3.1 with Wannier90 3.1.0: Segmentation fault

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dixiao
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VASP 6.3.1 with Wannier90 3.1.0: Segmentation fault

#1 Post by dixiao » Wed Jul 13, 2022 10:36 pm

For the system I study, the calculation of generating wannier input files always results in segmentation fault:

Code: Select all

 running on   40 total cores
 distrk:  each k-point on   40 cores,    1 groups
 distr:  one band on    1 cores,   40 groups
 vasp.6.3.2 27Jun22 (build Jul 13 2022 13:41:57) complex                        
  
 POSCAR found type information on POSCAR S TiBa
 POSCAR found :  3 types and     120 ions
 Reading from existing POTCAR
 scaLAPACK will be used
 -----------------------------------------------------------------------------
|                                                                             |
|           W    W    AA    RRRRR   N    N  II  N    N   GGGG   !!!           |
|           W    W   A  A   R    R  NN   N  II  NN   N  G    G  !!!           |
|           W    W  A    A  R    R  N N  N  II  N N  N  G       !!!           |
|           W WW W  AAAAAA  RRRRR   N  N N  II  N  N N  G  GGG   !            |
|           WW  WW  A    A  R   R   N   NN  II  N   NN  G    G                |
|           W    W  A    A  R    R  N    N  II  N    N   GGGG   !!!           |
|                                                                             |
|     For optimal performance we recommend to set                             |
|       NCORE = 2 up to number-of-cores-per-socket                            |
|     NCORE specifies how many cores store one orbital (NPAR=cpu/NCORE).      |
|     This setting can greatly improve the performance of VASP for DFT.       |
|     The default, NCORE=1 might be grossly inefficient on modern             |
|     multi-core architectures or massively parallel machines. Do your        |
|     own testing! More info at https://www.vasp.at/wiki/index.php/NCORE      |
|     Unfortunately you need to use the default for GW and RPA                |
|     calculations (for HF NCORE is supported but not extensively tested      |
|     yet).                                                                   |
|                                                                             |
 -----------------------------------------------------------------------------

 Reading from existing POTCAR
 -----------------------------------------------------------------------------
|                                                                             |
|               ----> ADVICE to this user running VASP <----                  |
|                                                                             |
|     You have a (more or less) 'large supercell' and for larger cells it     |
|     might be more efficient to use real-space projection operators.         |
|     Therefore, try LREAL= Auto in the INCAR file.                           |
|     Mind: For very accurate calculation, you might also keep the            |
|     reciprocal projection scheme (i.e. LREAL=.FALSE.).                      |
|                                                                             |
 -----------------------------------------------------------------------------

 LDA part: xc-table for Pade appr. of Perdew
 WARNING: stress and forces are not correct
 POSCAR, INCAR and KPOINTS ok, starting setup
 FFT: planning ... GRIDC
 FFT: planning ... GRID_SOFT
 FFT: planning ... GRID
 WAVECAR not read
 reading imaginary part of occupancies ...
 charge-density read from file: BaTiS3                                  
 entering main loop
       N       E                     dE             d eps       ncg     rms          rms(c)
DAV:   1     0.706176548422E+04    0.70618E+04   -0.31377E+05  5440   0.928E+02
DAV:   2     0.282757103521E+03   -0.67790E+04   -0.63859E+04  5680   0.292E+02
DAV:   3    -0.639582801528E+03   -0.92234E+03   -0.89486E+03  7680   0.106E+02
DAV:   4    -0.725669298874E+03   -0.86086E+02   -0.85848E+02  7880   0.267E+01
DAV:   5    -0.730759312079E+03   -0.50900E+01   -0.50888E+01  7480   0.573E+00
DAV:   6    -0.730880166580E+03   -0.12085E+00   -0.12084E+00  7480   0.110E+00
DAV:   7    -0.730885542291E+03   -0.53757E-02   -0.53755E-02  7560   0.193E-01
DAV:   8    -0.730885620710E+03   -0.78419E-04   -0.78417E-04  7520   0.276E-02
DAV:   9    -0.730885623365E+03   -0.26544E-05   -0.26543E-05  6680   0.459E-03
DAV:  10    -0.730885623480E+03   -0.11524E-06   -0.11481E-06  4880   0.105E-03
 Calling wannier_setup of wannier90 in library mode
 Wannier90 mode
 Computing MMN (overlap matrix elements)
 Computing AMN (projections onto localized orbitals)
[n3298:28134:0:28134] Caught signal 11 (Segmentation fault: Sent by the kernel at address (nil))
[n3298:28142:0:28142] Caught signal 11 (Segmentation fault: Sent by the kernel at address (nil))
[n3298:28144:0:28144] Caught signal 11 (Segmentation fault: Sent by the kernel at address (nil))
[n3298:28164:0:28164] Caught signal 11 (Segmentation fault: Sent by the kernel at address (nil))
[n3298:28132:0:28132] Caught signal 11 (Segmentation fault: Sent by the kernel at address (nil))
[n3298:28150:0:28150] Caught signal 11 (Segmentation fault: Sent by the kernel at address (nil))
[n3298:28141:0:28141] Caught signal 11 (Segmentation fault: Sent by the kernel at address (nil))
[n3298:28146:0:28146] Caught signal 11 (Segmentation fault: Sent by the kernel at address (nil))
[n3298:28135:0:28135] Caught signal 11 (Segmentation fault: Sent by the kernel at address (nil))
[n3298:28133:0:28133] Caught signal 11 (Segmentation fault: Sent by the kernel at address (nil))
[n3298:28158:0:28158] Caught signal 11 (Segmentation fault: Sent by the kernel at address (nil))
[n3298:28149:0:28149] Caught signal 11 (Segmentation fault: Sent by the kernel at address (nil))
[n3298:28136:0:28136] Caught signal 11 (Segmentation fault: Sent by the kernel at address (nil))
==== backtrace (tid:  28134) ====
 0 0x0000000000012b30 .annobin_sigaction.c()  sigaction.c:0
 1 0x0000000000086111 __GI___libc_free()  :0
 2 0x0000000001ebb4b3 for_dealloc_allocatable()  ???:0
 3 0x0000000001e63303 do_deallocate_all()  for_alloc_copy.c:0
 4 0x0000000001e63b29 for_dealloc_all_nocheck()  ???:0
 5 0x00000000014e9c3b mlwf_mp_calc_wannier_trafo_proj_()  ???:0
 6 0x00000000014e79c3 mlwf_mp_mlwf_trafo_run_()  ???:0
 7 0x00000000014c7645 mlwf_mp_mlwf_main_()  ???:0
 8 0x0000000001ccef36 MAIN__()  ???:0
 9 0x000000000041b322 main()  ???:0
10 0x00000000000234a3 __libc_start_main()  ???:0
11 0x000000000041b22e _start()  ???:0
=================================
[n3298:28137:0:28137] Caught signal 11 (Segmentation fault: Sent by the kernel at address (nil))
[n3298:28143:0:28143] Caught signal 11 (Segmentation fault: Sent by the kernel at address (nil))
[n3298:28130:0:28130] Caught signal 11 (Segmentation fault: Sent by the kernel at address (nil))
[n3298:28161:0:28161] Caught signal 11 (Segmentation fault: Sent by the kernel at address (nil))
forrtl: severe (174): SIGSEGV, segmentation fault occurred
Image              PC                Routine            Line        Source             
vasp_std           0000000001E8428A  for__signal_handl     Unknown  Unknown
libpthread-2.28.s  0000146F9CFD2B30  Unknown               Unknown  Unknown
libc-2.28.so       0000146F9C8FF111  cfree                 Unknown  Unknown
vasp_std           0000000001EBB4B3  for_dealloc_alloc     Unknown  Unknown
vasp_std           0000000001E63303  Unknown               Unknown  Unknown
vasp_std           0000000001E63B29  for_dealloc_all_n     Unknown  Unknown
vasp_std           00000000014E9C3B  Unknown               Unknown  Unknown
vasp_std           00000000014E79C3  Unknown               Unknown  Unknown
vasp_std           00000000014C7645  Unknown               Unknown  Unknown
vasp_std           0000000001CCEF36  Unknown               Unknown  Unknown
vasp_std           000000000041B322  Unknown               Unknown  Unknown
libc-2.28.so       0000146F9C89C4A3  __libc_start_main     Unknown  Unknown
vasp_std           000000000041B22E  Unknown               Unknown  Unknown
[n3298:28148:0:28148] Caught signal 11 (Segmentation fault: Sent by the kernel at address (nil))
[n3298:28166:0:28166] Caught signal 11 (Segmentation fault: Sent by the kernel at address (nil))
[n3298:28168:0:28168] Caught signal 11 (Segmentation fault: Sent by the kernel at address (nil))
[n3298:28138:0:28138] Caught signal 11 (Segmentation fault: Sent by the kernel at address (nil))
==== backtrace (tid:  28142) ====
 0 0x0000000000012b30 .annobin_sigaction.c()  sigaction.c:0
 1 0x0000000000086111 __GI___libc_free()  :0
 2 0x0000000001ebb4b3 for_dealloc_allocatable()  ???:0
 3 0x0000000001e63303 do_deallocate_all()  for_alloc_copy.c:0
 4 0x0000000001e63b29 for_dealloc_all_nocheck()  ???:0
 5 0x00000000014e9c3b mlwf_mp_calc_wannier_trafo_proj_()  ???:0
 6 0x00000000014e79c3 mlwf_mp_mlwf_trafo_run_()  ???:0
 7 0x00000000014c7645 mlwf_mp_mlwf_main_()  ???:0
 8 0x0000000001ccef36 MAIN__()  ???:0
 9 0x000000000041b322 main()  ???:0
10 0x00000000000234a3 __libc_start_main()  ???:0
11 0x000000000041b22e _start()  ???:0
=================================
==== backtrace (tid:  28144) ====
 0 0x0000000000012b30 .annobin_sigaction.c()  sigaction.c:0
 1 0x0000000000086111 __GI___libc_free()  :0
 2 0x0000000001ebb4b3 for_dealloc_allocatable()  ???:0
 3 0x0000000001e63303 do_deallocate_all()  for_alloc_copy.c:0
 4 0x0000000001e63b29 for_dealloc_all_nocheck()  ???:0
 5 0x00000000014e9c3b mlwf_mp_calc_wannier_trafo_proj_()  ???:0
 6 0x00000000014e79c3 mlwf_mp_mlwf_trafo_run_()  ???:0
 7 0x00000000014c7645 mlwf_mp_mlwf_main_()  ???:0
 8 0x0000000001ccef36 MAIN__()  ???:0
 9 0x000000000041b322 main()  ???:0
10 0x00000000000234a3 __libc_start_main()  ???:0
11 0x000000000041b22e _start()  ???:0
=================================
[n3298:28139:0:28139] Caught signal 11 (Segmentation fault: Sent by the kernel at address (nil))
[n3298:28140:0:28140] Caught signal 11 (Segmentation fault: Sent by the kernel at address (nil))
[n3298:28151:0:28151] Caught signal 11 (Segmentation fault: Sent by the kernel at address (nil))
[n3298:28156:0:28156] Caught signal 11 (Segmentation fault: Sent by the kernel at address (nil))
[n3298:28131:0:28131] Caught signal 11 (Segmentation fault: Sent by the kernel at address (nil))
forrtl: severe (174): SIGSEGV, segmentation fault occurred
Image              PC                Routine            Line        Source             
vasp_std           0000000001E8428A  for__signal_handl     Unknown  Unknown
libpthread-2.28.s  000014DDE0266B30  Unknown               Unknown  Unknown
libc-2.28.so       000014DDDFB93111  cfree                 Unknown  Unknown
vasp_std           0000000001EBB4B3  for_dealloc_alloc     Unknown  Unknown
vasp_std           0000000001E63303  Unknown               Unknown  Unknown
vasp_std           0000000001E63B29  for_dealloc_all_n     Unknown  Unknown
vasp_std           00000000014E9C3B  Unknown               Unknown  Unknown
vasp_std           00000000014E79C3  Unknown               Unknown  Unknown
vasp_std           00000000014C7645  Unknown               Unknown  Unknown
vasp_std           0000000001CCEF36  Unknown               Unknown  Unknown
vasp_std           000000000041B322  Unknown               Unknown  Unknown
libc-2.28.so       000014DDDFB304A3  __libc_start_main     Unknown  Unknown
vasp_std           000000000041B22E  Unknown               Unknown  Unknown
forrtl: severe (174): SIGSEGV, segmentation fault occurred
Image              PC                Routine            Line        Source             
vasp_std           0000000001E8428A  for__signal_handl     Unknown  Unknown
libpthread-2.28.s  0000152947F21B30  Unknown               Unknown  Unknown
libc-2.28.so       000015294784E111  cfree                 Unknown  Unknown
vasp_std           0000000001EBB4B3  for_dealloc_alloc     Unknown  Unknown
vasp_std           0000000001E63303  Unknown               Unknown  Unknown
vasp_std           0000000001E63B29  for_dealloc_all_n     Unknown  Unknown
vasp_std           00000000014E9C3B  Unknown               Unknown  Unknown
vasp_std           00000000014E79C3  Unknown               Unknown  Unknown
vasp_std           00000000014C7645  Unknown               Unknown  Unknown
vasp_std           0000000001CCEF36  Unknown               Unknown  Unknown
vasp_std           000000000041B322  Unknown               Unknown  Unknown
libc-2.28.so       00001529477EB4A3  __libc_start_main     Unknown  Unknown
vasp_std           000000000041B22E  Unknown               Unknown  Unknown
[n3298:28145:0:28145] Caught signal 11 (Segmentation fault: Sent by the kernel at address (nil))
[n3298:28157:0:28157] Caught signal 11 (Segmentation fault: Sent by the kernel at address (nil))
==== backtrace (tid:  28164) ====
 0 0x0000000000012b30 .annobin_sigaction.c()  sigaction.c:0
 1 0x0000000000086111 __GI___libc_free()  :0
 2 0x0000000001ebb4b3 for_dealloc_allocatable()  ???:0
 3 0x0000000001e63303 do_deallocate_all()  for_alloc_copy.c:0
 4 0x0000000001e63b29 for_dealloc_all_nocheck()  ???:0
 5 0x00000000014e9c3b mlwf_mp_calc_wannier_trafo_proj_()  ???:0
 6 0x00000000014e79c3 mlwf_mp_mlwf_trafo_run_()  ???:0
 7 0x00000000014c7645 mlwf_mp_mlwf_main_()  ???:0
 8 0x0000000001ccef36 MAIN__()  ???:0
 9 0x000000000041b322 main()  ???:0
10 0x00000000000234a3 __libc_start_main()  ???:0
11 0x000000000041b22e _start()  ???:0
=================================
[n3298:28147:0:28147] Caught signal 11 (Segmentation fault: Sent by the kernel at address (nil))
[n3298:28162:0:28162] Caught signal 11 (Segmentation fault: Sent by the kernel at address (nil))
I have attached the input files. I was starting from an existing calculation. To reproduce, change ICHARG from 11 to 2 in INCAR.
You do not have the required permissions to view the files attached to this post.

henrique_miranda
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Re: VASP 6.3.1 with Wannier90 3.1.0: Segmentation fault

#2 Post by henrique_miranda » Thu Jul 14, 2022 11:37 am

I am sorry you are experiencing this issue.
There seems to be an issue in the handling of the exclude_bands tag which I will look into.
I suggest that in the meantime you try re-runing after removing `exclude_bands` from the wannier90.win file.
Note that you will still be able to exclude bands based on the energy using the `dis_froz_min` and `dis_froz_max` tags.

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