[Wannier] No seedname_u.mat output + segmentation fault
Payden Brown
plbrown5 at asu.edu
Thu Apr 27 01:14:42 CEST 2023
Sorry! The error message was lost. Here it is:
*TACC: Starting up job 5423502 *
*TACC: Starting parallel tasks... *
*[c121-002:267668:0:267668] Caught signal 11 (Segmentation fault: address
not mapped to object at address 0x4)*
*[c121-002:267670:0:267670] Caught signal 11 (Segmentation fault: address
not mapped to object at address 0x4)*
*[c121-002:267677:0:267677] Caught signal 11 (Segmentation fault: address
not mapped to object at address 0x4)*
*[c121-002:267679:0:267679] Caught signal 11 (Segmentation fault: address
not mapped to object at address 0x4)*
*[c121-002:267681:0:267681] Caught signal 11 (Segmentation fault: address
not mapped to object at address 0x4)*
*[c121-002:267673:0:267673] Caught signal 11 (Segmentation fault: address
not mapped to object at address 0x4)*
*[c121-002:267672:0:267672] Caught signal 11 (Segmentation fault: address
not mapped to object at address 0x4)*
*[c121-002:267669:0:267669] Caught signal 11 (Segmentation fault: address
not mapped to object at address 0x4)*
*==== backtrace (tid: 267668) ====*
* 0 0x00000000004c7c73 w90_wannierise_mp_wann_write_xyz_() ???:0*
* 1 0x00000000004af265 w90_wannierise_mp_wann_main_() ???:0*
* 2 0x000000000040509e MAIN__() ???:0*
* 3 0x0000000000404a12 main() ???:0*
* 4 0x0000000000022555 __libc_start_main() ???:0*
* 5 0x0000000000404929 _start() ???:0*
*=================================*
*==== backtrace (tid: 267670) ====*
* 0 0x00000000004c7c73 w90_wannierise_mp_wann_write_xyz_() ???:0*
* 1 0x00000000004af265 w90_wannierise_mp_wann_main_() ???:0*
* 2 0x000000000040509e MAIN__() ???:0*
* 3 0x0000000000404a12 main() ???:0*
* 4 0x0000000000022555 __libc_start_main() ???:0*
* 5 0x0000000000404929 _start() ???:0*
*=================================*
*==== backtrace (tid: 267677) ====*
* 0 0x00000000004c7c73 w90_wannierise_mp_wann_write_xyz_() ???:0*
* 1 0x00000000004af265 w90_wannierise_mp_wann_main_() ???:0*
* 2 0x000000000040509e MAIN__() ???:0*
* 3 0x0000000000404a12 main() ???:0*
* 4 0x0000000000022555 __libc_start_main() ???:0*
* 5 0x0000000000404929 _start() ???:0*
*=================================*
*==== backtrace (tid: 267681) ====*
* 0 0x00000000004c7c73 w90_wannierise_mp_wann_write_xyz_() ???:0*
* 1 0x00000000004af265 w90_wannierise_mp_wann_main_() ???:0*
* 2 0x000000000040509e MAIN__() ???:0*
* 3 0x0000000000404a12 main() ???:0*
* 4 0x0000000000022555 __libc_start_main() ???:0*
* 5 0x0000000000404929 _start() ???:0*
*=================================*
*==== backtrace (tid: 267669) ====*
* 0 0x00000000004c7c73 w90_wannierise_mp_wann_write_xyz_() ???:0*
* 1 0x00000000004af265 w90_wannierise_mp_wann_main_() ???:0*
* 2 0x000000000040509e MAIN__() ???:0*
* 3 0x0000000000404a12 main() ???:0*
* 4 0x0000000000022555 __libc_start_main() ???:0*
* 5 0x0000000000404929 _start() ???:0*
*=================================*
*==== backtrace (tid: 267673) ====*
* 0 0x00000000004c7c73 w90_wannierise_mp_wann_write_xyz_() ???:0*
* 1 0x00000000004af265 w90_wannierise_mp_wann_main_() ???:0*
* 2 0x000000000040509e MAIN__() ???:0*
* 3 0x0000000000404a12 main() ???:0*
* 4 0x0000000000022555 __libc_start_main() ???:0*
* 5 0x0000000000404929 _start() ???:0*
*=================================*
*==== backtrace (tid: 267672) ====*
* 0 0x00000000004c7c73 w90_wannierise_mp_wann_write_xyz_() ???:0*
* 1 0x00000000004af265 w90_wannierise_mp_wann_main_() ???:0*
* 2 0x000000000040509e MAIN__() ???:0*
* 3 0x0000000000404a12 main() ???:0*
* 4 0x0000000000022555 __libc_start_main() ???:0*
* 5 0x0000000000404929 _start() ???:0*
*=================================*
*==== backtrace (tid: 267679) ====*
* 0 0x00000000004c7c73 w90_wannierise_mp_wann_write_xyz_() ???:0*
* 1 0x00000000004af265 w90_wannierise_mp_wann_main_() ???:0*
* 2 0x000000000040509e MAIN__() ???:0*
* 3 0x0000000000404a12 main() ???:0*
* 4 0x0000000000022555 __libc_start_main() ???:0*
* 5 0x0000000000404929 _start() ???:0*
*=================================*
*forrtl: severe (174): SIGSEGV, segmentation fault occurred*
*Image PC Routine Line Source
*
*wannier90.x 000000000055C5BA Unknown Unknown
Unknown*
*libpthread-2.17.s 00002AB2D3AFF630 Unknown Unknown
Unknown*
*wannier90.x 00000000004C7C73 Unknown Unknown
Unknown*
*wannier90.x 00000000004AF265 Unknown Unknown
Unknown*
*wannier90.x 000000000040509E Unknown Unknown
Unknown*
*wannier90.x 0000000000404A12 Unknown Unknown
Unknown*
*libc-2.17.so <http://libc-2.17.so> 00002AB2D5B5A555
__libc_start_main Unknown Unknown*
*wannier90.x 0000000000404929 Unknown Unknown
Unknown*
*forrtl: severe (174): SIGSEGV, segmentation fault occurred*
*Image PC Routine Line Source
*
*wannier90.x 000000000055C5BA Unknown Unknown
Unknown*
*libpthread-2.17.s 00002B45C5251630 Unknown Unknown
Unknown*
*wannier90.x 00000000004C7C73 Unknown Unknown
Unknown*
*wannier90.x 00000000004AF265 Unknown Unknown
Unknown*
*wannier90.x 000000000040509E Unknown Unknown
Unknown*
*wannier90.x 0000000000404A12 Unknown Unknown
Unknown*
*libc-2.17.so <http://libc-2.17.so> 00002B45C72AC555
__libc_start_main Unknown Unknown*
*wannier90.x 0000000000404929 Unknown Unknown
Unknown*
*forrtl: severe (174): SIGSEGV, segmentation fault occurred*
*Image PC Routine Line Source
*
*wannier90.x 000000000055C5BA Unknown Unknown
Unknown*
*libpthread-2.17.s 00002AD8C43D6630 Unknown Unknown
Unknown*
*wannier90.x 00000000004C7C73 Unknown Unknown
Unknown*
*wannier90.x 00000000004AF265 Unknown Unknown
Unknown*
*wannier90.x 000000000040509E Unknown Unknown
Unknown*
*wannier90.x 0000000000404A12 Unknown Unknown
Unknown*
*libc-2.17.so <http://libc-2.17.so> 00002AD8C6431555
__libc_start_main Unknown Unknown*
*wannier90.x 0000000000404929 Unknown Unknown
Unknown*
*forrtl: severe (174): SIGSEGV, segmentation fault occurred*
*Image PC Routine Line Source
*
*wannier90.x 000000000055C5BA Unknown Unknown
Unknown*
*libpthread-2.17.s 00002B5E3EA5E630 Unknown Unknown
Unknown*
*wannier90.x 00000000004C7C73 Unknown Unknown
Unknown*
*wannier90.x 00000000004AF265 Unknown Unknown
Unknown*
*wannier90.x 000000000040509E Unknown Unknown
Unknown*
*wannier90.x 0000000000404A12 Unknown Unknown
Unknown*
*libc-2.17.so <http://libc-2.17.so> 00002B5E40AB9555
__libc_start_main Unknown Unknown*
*wannier90.x 0000000000404929 Unknown Unknown
Unknown*
*forrtl: severe (174): SIGSEGV, segmentation fault occurred*
*Image PC Routine Line Source
*
*wannier90.x 000000000055C5BA Unknown Unknown
Unknown*
*libpthread-2.17.s 00002B9771B42630 Unknown Unknown
Unknown*
*wannier90.x 00000000004C7C73 Unknown Unknown
Unknown*
*wannier90.x 00000000004AF265 Unknown Unknown
Unknown*
*wannier90.x 000000000040509E Unknown Unknown
Unknown*
*wannier90.x 0000000000404A12 Unknown Unknown
Unknown*
*libc-2.17.so <http://libc-2.17.so> 00002B9773B9D555
__libc_start_main Unknown Unknown*
*wannier90.x 0000000000404929 Unknown Unknown
Unknown*
*forrtl: severe (174): SIGSEGV, segmentation fault occurred*
*Image PC Routine Line Source
*
*wannier90.x 000000000055C5BA Unknown Unknown
Unknown*
*libpthread-2.17.s 00002B67D277E630 Unknown Unknown
Unknown*
*wannier90.x 00000000004C7C73 Unknown Unknown
Unknown*
*wannier90.x 00000000004AF265 Unknown Unknown
Unknown*
*wannier90.x 000000000040509E Unknown Unknown
Unknown*
*wannier90.x 0000000000404A12 Unknown Unknown
Unknown*
*libc-2.17.so <http://libc-2.17.so> 00002B67D47D9555
__libc_start_main Unknown Unknown*
*wannier90.x 0000000000404929 Unknown Unknown
Unknown*
*forrtl: severe (174): SIGSEGV, segmentation fault occurred*
*Image PC Routine Line Source
*
*wannier90.x 000000000055C5BA Unknown Unknown
Unknown*
*libpthread-2.17.s 00002AF7E5406630 Unknown Unknown
Unknown*
*wannier90.x 00000000004C7C73 Unknown Unknown
Unknown*
*wannier90.x 00000000004AF265 Unknown Unknown
Unknown*
*wannier90.x 000000000040509E Unknown Unknown
Unknown*
*wannier90.x 0000000000404A12 Unknown Unknown
Unknown*
*libc-2.17.so <http://libc-2.17.so> 00002AF7E7461555
__libc_start_main Unknown Unknown*
*wannier90.x 0000000000404929 Unknown Unknown
Unknown*
*forrtl: severe (174): SIGSEGV, segmentation fault occurred*
*Image PC Routine Line Source
*
*wannier90.x 000000000055C5BA Unknown Unknown
Unknown*
*libpthread-2.17.s 00002B81C2B60630 Unknown Unknown
Unknown*
*wannier90.x 00000000004C7C73 Unknown Unknown
Unknown*
*wannier90.x 00000000004AF265 Unknown Unknown
Unknown*
*wannier90.x 000000000040509E Unknown Unknown
Unknown*
*wannier90.x 0000000000404A12 Unknown Unknown
Unknown*
*libc-2.17.so <http://libc-2.17.so> 00002B81C4BBB555
__libc_start_main Unknown Unknown*
*wannier90.x 0000000000404929 Unknown Unknown
Unknown*
*===================================================================================*
*= BAD TERMINATION OF ONE OF YOUR APPLICATION PROCESSES*
*= RANK 0 PID 267667 RUNNING AT c121-002*
*= KILLED BY SIGNAL: 9 (Killed)*
*===================================================================================*
*===================================================================================*
*= BAD TERMINATION OF ONE OF YOUR APPLICATION PROCESSES*
*= RANK 4 PID 267671 RUNNING AT c121-002*
*= KILLED BY SIGNAL: 9 (Killed)*
*===================================================================================*
*===================================================================================*
*= BAD TERMINATION OF ONE OF YOUR APPLICATION PROCESSES*
*= RANK 7 PID 267674 RUNNING AT c121-002*
*= KILLED BY SIGNAL: 9 (Killed)*
*===================================================================================*
*===================================================================================*
*= BAD TERMINATION OF ONE OF YOUR APPLICATION PROCESSES*
*= RANK 8 PID 267675 RUNNING AT c121-002*
*= KILLED BY SIGNAL: 9 (Killed)*
*===================================================================================*
*===================================================================================*
*= BAD TERMINATION OF ONE OF YOUR APPLICATION PROCESSES*
*= RANK 9 PID 267676 RUNNING AT c121-002*
*= KILLED BY SIGNAL: 9 (Killed)*
*===================================================================================*
*===================================================================================*
*= BAD TERMINATION OF ONE OF YOUR APPLICATION PROCESSES*
*= RANK 11 PID 267678 RUNNING AT c121-002*
*= KILLED BY SIGNAL: 9 (Killed)*
*===================================================================================*
*===================================================================================*
*= BAD TERMINATION OF ONE OF YOUR APPLICATION PROCESSES*
*= RANK 13 PID 267680 RUNNING AT c121-002*
*= KILLED BY SIGNAL: 9 (Killed)*
*===================================================================================*
*===================================================================================*
*= BAD TERMINATION OF ONE OF YOUR APPLICATION PROCESSES*
*= RANK 15 PID 267682 RUNNING AT c121-002*
*= KILLED BY SIGNAL: 9 (Killed)*
*===================================================================================*
*TACC: MPI job exited with code: 255 *
*TACC: Shutdown complete. Exiting.*
On Tue, Apr 25, 2023 at 6:18 PM Payden Brown <plbrown5 at asu.edu> wrote:
> Hello all,
>
> I am trying to run wannier90.x in parallel on PbWO4. At first, I was
> running into a segmentation fault failure at iteration ~300 out of 5000
> iterations. Thinking it could be a stack or memory issue, I changed the
> soft ulimit to unlimited and I am using the "optimisation=0" setting for
> memory optimization.
> When looking at pbwo4.wout, now the "wannierise" calculation runs all 5000
> iterations and it gets to the final WF state, then either stops while
> pbwo4_centres.xyz is being written or finishes writing and then stops
> without outputting pbwo4_u.mat. When I check the job output it still says
> there are segmentation faults. I am new to using wannier90 so I don't know
> if there is an obvious or common fix to this issue. I don't know if the
> issue is with my input or how I compiled. Description of system and input
> files below:
>
> System: TACC Frontera compiled with intel19 and the make.inc.ifort file.
> I'm using the MKL library and modified the mkl libpath in make.inc.ifort to
> point to the right location. No issues when compiling and "wannier90.x -pp"
> runs without any issues too.
>
> contents of pbwo4.win (1000 kpoints are truncated):
> begin projections
> random
> end projections
> guiding_centres=true
>
> num_bands = 16
> num_wann = 16
>
> iprint = 2
> dis_num_iter = 500
> dis_win_max = 9.0
> dis_froz_max = 9.0
> dis_conv_tol = 1.0d-9
> dis_conv_window = 20
>
> num_iter = 5000
> conv_tol = 1.0d-9
> conv_window = 20
> mp_grid = 10 10 10
>
> begin unit_cell_cart
> Ang
> 0.0000000000000000 5.6128862829189758 0.0000000000000000
> 4.9874188999999998 0.0000000000000000 0.0000000000000000
> 0.0000000000000000 -4.2185204449493545 -12.9777995413697234
> end unit_cell_cart
>
> write_u_matrices = .true.
> write_xyz = .true.
>
> #restart = plot
> BANDS_PLOT = TRUE
> BANDS_PLOT_FORMAT = gnuplot
> BANDS_NUM_POINTS = 100
>
> BEGIN KPOINT_PATH
> G 0.000 0.000 0.000 Z 0.000 0.500 0.000
> Z 0.000 0.500 0.000 D 0.000 0.500 0.500
> D 0.000 0.500 0.500 B 0.000 0.000 0.500
> B 0.000 0.000 0.500 G 0.000 0.000 0.000
> G 0.000 0.000 0.000 A -0.500 0.000 0.500
> A -0.500 0.000 0.500 E -0.500 0.500 0.500
> E -0.500 0.500 0.500 Z 0.000 0.500 0.000
> Z 0.000 0.500 0.000 C -0.500 0.500 0.000
> C -0.500 0.500 0.000 Y -0.500 0.000 0.000
> Y -0.500 0.000 0.000 G 0.000 0.000 0.000
> END KPOINT_PATH
>
> begin atoms_frac
> Pb 0.1679799000000000 0.3033784899999999 0.6510552800000000
> Pb 0.8320201000000000 0.8033784900000001 0.8489447200000000
> Pb 0.8320201000000000 0.6966215100000001 0.3489447200000000
> Pb 0.1679799000000000 0.1966215100000001 0.1510552800000000
> W 0.6119139800000002 0.7507408600000001 0.5773005600000001
> W 0.3880860199999998 0.2507408600000001 0.9226994399999999
> W 0.3880860199999998 0.2492591399999999 0.4226994399999999
> W 0.6119139800000002 0.7492591399999999 0.0773005600000001
> O 0.7282079600000000 0.4559118599999999 0.5179289499999999
> O 0.2717920400000000 0.9559118600000001 0.9820710500000001
> O 0.2717920400000000 0.5440881400000001 0.4820710500000001
> O 0.7282079600000000 0.0440881400000001 0.0179289499999999
> O 0.3917558500000000 0.0565561700000001 0.5614836900000000
> O 0.6082441500000000 0.5565561700000001 0.9385163100000000
> O 0.6082441500000000 0.9434438299999999 0.4385163100000000
> O 0.3917558500000000 0.4434438299999999 0.0614836900000000
> O 0.9097576700000001 0.8854765500000000 0.6490210500000000
> O 0.0902423299999999 0.3854765500000000 0.8509789500000000
> O 0.0902423299999999 0.1145234500000000 0.3509789500000000
> O 0.9097576700000001 0.6145234500000000 0.1490210500000000
> O 0.5403943700000000 0.6068396200000001 0.6868019599999999
> O 0.4596056300000000 0.1068396200000001 0.8131980400000001
> O 0.4596056300000000 0.3931603799999999 0.3131980400000001
> O 0.5403943700000000 0.8931603799999999 0.1868019599999999
> end atoms_frac
>
> begin kpoints
> 0.00000000 0.00000000 0.00000000
> 0.00000000 0.00000000 0.10000000
> 0.00000000 0.00000000 0.20000000
> 0.00000000 0.00000000 0.30000000
> .
> .
> .
> Error messages:
>
> [image: Screen Shot 2023-04-25 at 1.42.05 PM.png]
> [image: Screen Shot 2023-04-25 at 1.42.26 PM.png]
>
> Your help and suggestions are very much appreciated,
> Payden
>
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