INFO: Using directory: "1" INFO: Using existing c-file: ./NBI_Lab_TOMO.c INFO: Using existing binary: ./NBI_Lab_TOMO.out WARNING: Ignoring invalid parameter: "mxrun" WARNING: Ignoring invalid parameter: "NBI_Lab_TOMO.instr" INFO: === INFO: Using system default number of mpirun -np processes -------------------------------------------------------------------------- By default, for Open MPI 4.0 and later, infiniband ports on a device are not used by default. The intent is to use UCX for these devices. You can override this policy by setting the btl_openib_allow_ib MCA parameter to true. Local host: n-62-29-12 Local adapter: mlx4_0 Local port: 1 -------------------------------------------------------------------------- -------------------------------------------------------------------------- WARNING: There was an error initializing an OpenFabrics device. Local host: n-62-29-12 Local device: mlx4_0 -------------------------------------------------------------------------- Simulation 'NBI_Lab_TOMO' (/zhome/89/0/38697/xTESTS/2022-03-01/McXtrace-1.x_CPU_MPICC_5e7/NBI_Lab_TOMO/NBI_Lab_TOMO.instr): running on 10 nodes (master is 'n-62-29-34', MPI version 3.1). [NBI_Lab_TOMO] Initialize Opening input file '/zhome/89/0/38697/McXtrace/mcxtrace/1.x-dev/tools/Python/mxrun/../mccodelib/../../../data/spectrumU50_th5.dat' (Table_Read_Offset) Source_pt(source) Integrated intensity radiated is 1.39838e+14 pht/s Source_pt(source) E0!=0 -> assuming intensity spectrum is parametrized by energy [keV] Opening input file '/zhome/89/0/38697/McXtrace/mcxtrace/1.x-dev/tools/Python/mxrun/../mccodelib/../../../data/Be.txt' (Table_Read_Offset) [NBI_Lab_TOMO] Initialize WARNING: (Table_Rebin): Rebinning table from Be.txt would exceed 1M rows. Skipping. [NBI_Lab_TOMO] Initialize filter_Be: Rebinning material data (Be.txt) for faster tracing...done Opening input file '/zhome/89/0/38697/McXtrace/mcxtrace/1.x-dev/tools/Python/mxrun/../mccodelib/../../../data/Al.txt' (Table_Read_Offset) [NBI_Lab_TOMO] Initialize WARNING: (Table_Rebin): Rebinning table from Al.txt would exceed 1M rows. Skipping. filterAl: Rebinning material data (Al.txt) for faster tracing...done Loading geometry file (OFF/PLY): king.off [NBI_Lab_TOMO] Initialize Source_pt(source) Integrated intensity radiated is 1.39838e+14 pht/s Source_pt(source) E0!=0 -> assuming intensity spectrum is parametrized by energy [keV] Source_pt(source) Integrated intensity radiated is 1.39838e+14 pht/s Source_pt(source) E0!=0 -> assuming intensity spectrum is parametrized by energy [keV] Source_pt(source) Integrated intensity radiated is 1.39838e+14 pht/s Source_pt(source) E0!=0 -> assuming intensity spectrum is parametrized by energy [keV] Source_pt(source) Integrated intensity radiated is 1.39838e+14 pht/s Source_pt(source) E0!=0 -> assuming intensity spectrum is parametrized by energy [keV] Number of vertices: 7192 WARNING: (Table_Rebin): Rebinning table from Be.txt would exceed 1M rows. Skipping. filter_Be: Rebinning material data (Be.txt) for faster tracing...done WARNING: (Table_Rebin): Rebinning table from Be.txt would exceed 1M rows. Skipping. WARNING: (Table_Rebin): Rebinning table from Be.txt would exceed 1M rows. Skipping. filter_Be: Rebinning material data (Be.txt) for faster tracing...done filter_Be: Rebinning material data (Be.txt) for faster tracing...done WARNING: (Table_Rebin): Rebinning table from Al.txt would exceed 1M rows. Skipping. filterAl: Rebinning material data (Al.txt) for faster tracing...done WARNING: (Table_Rebin): Rebinning table from Be.txt would exceed 1M rows. Skipping. filter_Be: Rebinning material data (Be.txt) for faster tracing...done [NBI_Lab_TOMO] Initialize filterAl: Rebinning material data (Al.txt) for faster tracing...done WARNING: (Table_Rebin): Rebinning table from Al.txt would exceed 1M rows. Skipping. WARNING: (Table_Rebin): Rebinning table from Al.txt would exceed 1M rows. Skipping. filterAl: Rebinning material data (Al.txt) for faster tracing...done WARNING: (Table_Rebin): Rebinning table from Al.txt would exceed 1M rows. Skipping. filterAl: Rebinning material data (Al.txt) for faster tracing...done [NBI_Lab_TOMO] Initialize [NBI_Lab_TOMO] Initialize Source_pt(source) Integrated intensity radiated is 1.39838e+14 pht/s Source_pt(source) E0!=0 -> assuming intensity spectrum is parametrized by energy [keV] Source_pt(source) Integrated intensity radiated is 1.39838e+14 pht/s Source_pt(source) E0!=0 -> assuming intensity spectrum is parametrized by energy [keV] Source_pt(source) Integrated intensity radiated is 1.39838e+14 pht/s Source_pt(source) E0!=0 -> assuming intensity spectrum is parametrized by energy [keV] WARNING: (Table_Rebin): Rebinning table from Be.txt would exceed 1M rows. Skipping. filter_Be: Rebinning material data (Be.txt) for faster tracing...done WARNING: (Table_Rebin): Rebinning table from Al.txt would exceed 1M rows. Skipping. filterAl: Rebinning material data (Al.txt) for faster tracing...done WARNING: (Table_Rebin): Rebinning table from Be.txt would exceed 1M rows. Skipping. filter_Be: Rebinning material data (Be.txt) for faster tracing...done WARNING: (Table_Rebin): Rebinning table from Be.txt would exceed 1M rows. Skipping. filter_Be: Rebinning material data (Be.txt) for faster tracing...done WARNING: (Table_Rebin): Rebinning table from Al.txt would exceed 1M rows. Skipping. WARNING: (Table_Rebin): Rebinning table from Al.txt would exceed 1M rows. Skipping. filterAl: Rebinning material data (Al.txt) for faster tracing...done filterAl: Rebinning material data (Al.txt) for faster tracing...done [NBI_Lab_TOMO] Initialize Source_pt(source) Integrated intensity radiated is 1.39838e+14 pht/s Source_pt(source) E0!=0 -> assuming intensity spectrum is parametrized by energy [keV] WARNING: (Table_Rebin): Rebinning table from Be.txt would exceed 1M rows. Skipping. filter_Be: Rebinning material data (Be.txt) for faster tracing...done WARNING: (Table_Rebin): Rebinning table from Al.txt would exceed 1M rows. Skipping. filterAl: Rebinning material data (Al.txt) for faster tracing...done [NBI_Lab_TOMO] Initialize Source_pt(source) Integrated intensity radiated is 1.39838e+14 pht/s Source_pt(source) E0!=0 -> assuming intensity spectrum is parametrized by energy [keV] WARNING: (Table_Rebin): Rebinning table from Be.txt would exceed 1M rows. Skipping. filter_Be: Rebinning material data (Be.txt) for faster tracing...done WARNING: (Table_Rebin): Rebinning table from Al.txt would exceed 1M rows. Skipping. filterAl: Rebinning material data (Al.txt) for faster tracing...done Number of polygons: 14380 Warning: Aspect ratio of the geometry king.off was modified. If you want to keep the original proportions, specifiy only one of the dimensions. Bounding box dimensions for geometry king.off: Length=0.015000 (0.047%) Width= 0.015000 (0.047%) Depth= 0.015000 (0.024%) Opening input file '/zhome/89/0/38697/McXtrace/mcxtrace/1.x-dev/tools/Python/mxrun/../mccodelib/../../../data/Glass.dat' (Table_Read_Offset) king: Rebinning material data (Glass.dat) for faster tracing...done king: Rebinning material data (Glass.dat) for faster tracing...done king: Rebinning material data (Glass.dat) for faster tracing...done filter_air: Rebinning material data (FilterAir_1mm.dat) for faster tracing...done filter_Al: Rebinning material data (Al.txt) for faster tracing...done WARNING: (Table_Rebin): Rebinning table from Al.txt would exceed 1M rows. Skipping. king: Rebinning material data (Glass.dat) for faster tracing...done king: Rebinning material data (Glass.dat) for faster tracing...done filter_air: Rebinning material data (FilterAir_1mm.dat) for faster tracing...done filter_Al: Rebinning material data (Al.txt) for faster tracing...done WARNING: (Table_Rebin): Rebinning table from Al.txt would exceed 1M rows. Skipping. king: Rebinning material data (Glass.dat) for faster tracing...done king: Rebinning material data (Glass.dat) for faster tracing...done king: Rebinning material data (Glass.dat) for faster tracing...done filter_air: Rebinning material data (FilterAir_1mm.dat) for faster tracing...done WARNING: (Table_Rebin): Rebinning table from Al.txt would exceed 1M rows. Skipping. filter_Al: Rebinning material data (Al.txt) for faster tracing...done king: Rebinning material data (Glass.dat) for faster tracing...done Opening input file '/zhome/89/0/38697/McXtrace/mcxtrace/1.x-dev/tools/Python/mxrun/../mccodelib/../../../data/FilterAir_1mm.dat' (Table_Read_Offset) filter_air: Rebinning material data (FilterAir_1mm.dat) for faster tracing...done filter_air: Rebinning material data (FilterAir_1mm.dat) for faster tracing...done filter_Al: Rebinning material data (Al.txt) for faster tracing...done WARNING: (Table_Rebin): Rebinning table from Al.txt would exceed 1M rows. Skipping. WARNING: (Table_Rebin): Rebinning table from Al.txt would exceed 1M rows. Skipping. filter_Al: Rebinning material data (Al.txt) for faster tracing...done king: Rebinning material data (Glass.dat) for faster tracing...done filter_air: Rebinning material data (FilterAir_1mm.dat) for faster tracing...done WARNING: (Table_Rebin): Rebinning table from Al.txt would exceed 1M rows. Skipping. filter_Al: Rebinning material data (Al.txt) for faster tracing...done filter_air: Rebinning material data (FilterAir_1mm.dat) for faster tracing...done filter_Al: Rebinning material data (Al.txt) for faster tracing...done WARNING: (Table_Rebin): Rebinning table from Al.txt would exceed 1M rows. Skipping. filter_air: Rebinning material data (FilterAir_1mm.dat) for faster tracing...done filter_Al: Rebinning material data (Al.txt) for faster tracing...done WARNING: (Table_Rebin): Rebinning table from Al.txt would exceed 1M rows. Skipping. filter_air: Rebinning material data (FilterAir_1mm.dat) for faster tracing...done WARNING: (Table_Rebin): Rebinning table from Al.txt would exceed 1M rows. Skipping. filter_Al: Rebinning material data (Al.txt) for faster tracing...done Opening input file '/zhome/89/0/38697/McXtrace/mcxtrace/1.x-dev/tools/Python/mxrun/../mccodelib/../../../data/Si.txt' (Table_Read_Offset) filter_air: Rebinning material data (FilterAir_1mm.dat) for faster tracing...done WARNING: (Table_Rebin): Rebinning table from Al.txt would exceed 1M rows. Skipping. filter_Al: Rebinning material data (Al.txt) for faster tracing...done [n-62-29-34:15796] 9 more processes have sent help message help-mpi-btl-openib.txt / ib port not selected [n-62-29-34:15796] Set MCA parameter "orte_base_help_aggregate" to 0 to see all help / error messages [n-62-29-34:15796] 9 more processes have sent help message help-mpi-btl-openib.txt / error in device init Trace ETA 7.96667 [min] % 2 Trace ETA 8.25 [min] % 2 Trace ETA 8.03333 [min] % 2 Trace ETA 8.03333 [min] % 2 Trace ETA 8.33333 [min] % 2 Trace ETA 8.4 [min] % 2 Trace ETA 7.83333 [min] % 2 Trace ETA 7.9 [min] % 2 Trace ETA 7.96667 [min] % 2 Trace ETA 7.9 [min] % 2 12 12 12 12 12 12 12 12 12 12 22 22 22 22 22 22 22 22 22 22 32 32 32 32 32 32 32 32 32 32 42 42 42 42 42 42 42 42 42 42 52 52 52 52 52 52 52 52 52 52 62 62 62 62 62 62 62 62 62 62 72 72 72 72 72 72 72 72 72 72 82 82 82 82 82 82 82 82 82 82 92 92 92 92 92 92 92 92 92 92 Finally [NBI_Lab_TOMO: 1]. Time: 7.63333 [min] Finally [NBI_Lab_TOMO: 1]. Time: 7.7 [min] Finally [NBI_Lab_TOMO: 1]. Time: 7.71667 [min] Finally [NBI_Lab_TOMO: 1]. Time: 7.71667 [min] Finally [NBI_Lab_TOMO: 1]. Time: 8.11667 [min] Save [NBI_Lab_TOMO] Finally [NBI_Lab_TOMO: 1]. Time: 8.21667 [min] Detector: emon0_I=2.42715e+15 emon0_ERR=6.92378e+11 emon0_N=5e+07 "emon0.dat" Finally [NBI_Lab_TOMO: 1]. Time: 8.21667 [min] Detector: emonef_I=2.16923e+14 emonef_ERR=5.77513e+10 emonef_N=3.01666e+07 "emon0ef.dat" Detector: e_mon1_I=3.73147e+12 e_mon1_ERR=6.93375e+09 e_mon1_N=794041 "emon1.dat" Finally [NBI_Lab_TOMO: 1]. Time: 8.23333 [min] Finally [NBI_Lab_TOMO: 1]. Time: 8.23333 [min] Detector: Detector_Si_I=3.88293e+13 Detector_Si_ERR=8.22947e+09 Detector_Si_N=4.99869e+07 "detector_Si.dat" Detector: e_mon2_I=4.61902e+11 e_mon2_ERR=8.3751e+08 e_mon2_N=781381 "emon2.dat" Finally [NBI_Lab_TOMO: 1]. Time: 8.23333 [min] INFO: Placing instr file copy /zhome/89/0/38697/xTESTS/2022-03-01/McXtrace-1.x_CPU_MPICC_5e7/NBI_Lab_TOMO/NBI_Lab_TOMO.instr in dataset 1 loading system configuration loading override configuration from /zhome/89/0/38697/mxtest/mctest/../mccodelib/mcxtrace-test/McXtrace-1.x_CPU_MPICC/mccode_config.json