loading system configuration loading override configuration from /zhome/89/0/38697/mxtest/mctest/../mccodelib/mcxtrace-test/McXtrace-1.x_CPU_MPICC/mccode_config.json INFO: Using directory: "1" INFO: Regenerating c-file: Airport_scannerII.c Warning: Component Origin=Progress_bar(string profile) definition parameter may be changed into a setting parameter to avoid warnings at compile time. Warning: Component source1=Source_flat(string spectrum_file) definition parameter may be changed into a setting parameter to avoid warnings at compile time. Warning: Component emon=E_monitor(string filename) definition parameter may be changed into a setting parameter to avoid warnings at compile time. CFLAGS= INFO: Recompiling: ./Airport_scannerII.out mccode-r.c: In function ‘sighandler’: mccode-r.c:3830:5: warning: implicit declaration of function ‘kill’; did you mean ‘ceill’? [-Wimplicit-function-declaration] WARNING: Ignoring invalid parameter: "Airport_scannerII.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 'Airport_scannerII' (/zhome/89/0/38697/xTESTS/2022-12-01/McXtrace-1.x_CPU_MPICC_1e7/Airport_scannerII/Airport_scannerII.instr): running on 10 nodes (master is 'n-62-29-31', MPI version 3.1). [Airport_scannerII] Initialize Opening input file '/zhome/89/0/38697/McXtrace/mcxtrace/1.x-dev/tools/Python/mxrun/../mccodelib/../../../data/book.txt' (Table_Read_Offset) Loading geometry file (OFF/PLY): book.ply Number of vertices: 2853 [Airport_scannerII] Initialize Number of polygons: 5722 [Airport_scannerII] Initialize Warning: Neither xwidth, yheight or zdepth are defined. The file-defined (non-scaled) geometry the OFF geometry book.ply will be applied! Bounding box dimensions for geometry book.ply: Length=0.239599 (100.000%) Width= 0.029804 (100.000%) Depth= 0.164529 (100.000%) sample_scan: Volume[1], material='book.txt' geometry='book.ply' Opening input file '/zhome/89/0/38697/McXtrace/mcxtrace/1.x-dev/tools/Python/mxrun/../mccodelib/../../../data/h2o2.dat' (Table_Read_Offset) Loading geometry file (OFF/PLY): h2o2.ply Number of vertices: 406 Number of polygons: 808 Warning: Neither xwidth, yheight or zdepth are defined. The file-defined (non-scaled) geometry the OFF geometry h2o2.ply will be applied! Bounding box dimensions for geometry h2o2.ply: Length=0.126295 (100.000%) Width= 0.046911 (100.000%) Depth= 0.090087 (100.000%) sample_scan: Volume[2], material='h2o2.dat' geometry='h2o2.ply' Opening input file '/zhome/89/0/38697/McXtrace/mcxtrace/1.x-dev/tools/Python/mxrun/../mccodelib/../../../data/H2O.txt' (Table_Read_Offset) Loading geometry file (OFF/PLY): water.ply Number of vertices: 818 Number of polygons: 1632 sample_scan: Volume[1], material='book.txt' geometry='book.ply' Warning: Neither xwidth, yheight or zdepth are defined. The file-defined (non-scaled) geometry the OFF geometry water.ply will be applied! Bounding box dimensions for geometry water.ply: Length=0.066238 (100.000%) Width= 0.058313 (100.000%) Depth= 0.217547 (100.000%) sample_scan: Volume[3], material='H2O.txt' geometry='water.ply' [Airport_scannerII] Initialize sample_scan: Volume[1], material='book.txt' geometry='book.ply' [Airport_scannerII] Initialize Opening input file '/zhome/89/0/38697/McXtrace/mcxtrace/1.x-dev/tools/Python/mxrun/../mccodelib/../../../data/ethanol.txt' (Table_Read_Offset) Loading geometry file (OFF/PLY): whiskey.ply sample_scan: Volume[2], material='h2o2.dat' geometry='h2o2.ply' Number of vertices: 616 sample_scan: Volume[2], material='h2o2.dat' geometry='h2o2.ply' Number of polygons: 1228 Warning: Neither xwidth, yheight or zdepth are defined. The file-defined (non-scaled) geometry the OFF geometry whiskey.ply will be applied! Bounding box dimensions for geometry whiskey.ply: Length=0.082601 (100.000%) Width= 0.076881 (100.000%) Depth= 0.141927 (100.000%) sample_scan: Volume[4], material='ethanol.txt' geometry='whiskey.ply' Opening input file '/zhome/89/0/38697/McXtrace/mcxtrace/1.x-dev/tools/Python/mxrun/../mccodelib/../../../data/Cu.txt' (Table_Read_Offset) sample_scan: Volume[3], material='H2O.txt' geometry='water.ply' Loading geometry file (OFF/PLY): wire.ply sample_scan: Volume[3], material='H2O.txt' geometry='water.ply' sample_scan: Volume[1], material='book.txt' geometry='book.ply' sample_scan: Volume[1], material='book.txt' geometry='book.ply' Number of vertices: 2584 sample_scan: Volume[4], material='ethanol.txt' geometry='whiskey.ply' sample_scan: Volume[4], material='ethanol.txt' geometry='whiskey.ply' [Airport_scannerII] Initialize sample_scan: Volume[2], material='h2o2.dat' geometry='h2o2.ply' Number of polygons: 5438 sample_scan: Volume[2], material='h2o2.dat' geometry='h2o2.ply' [Airport_scannerII] Initialize [Airport_scannerII] Initialize Warning: Neither xwidth, yheight or zdepth are defined. The file-defined (non-scaled) geometry the OFF geometry wire.ply will be applied! Bounding box dimensions for geometry wire.ply: Length=0.173456 (100.000%) Width= 0.078031 (100.000%) Depth= 0.145752 (100.000%) sample_scan: Volume[5], material='Cu.txt' geometry='wire.ply' sample_scan: Volume[3], material='H2O.txt' geometry='water.ply' sample_scan: Volume[3], material='H2O.txt' geometry='water.ply' Opening input file '/zhome/89/0/38697/McXtrace/mcxtrace/1.x-dev/tools/Python/mxrun/../mccodelib/../../../data/Al.txt' (Table_Read_Offset) Loading geometry file (OFF/PLY): luggage.off sample_scan: Volume[4], material='ethanol.txt' geometry='whiskey.ply' sample_scan: Volume[4], material='ethanol.txt' geometry='whiskey.ply' Number of vertices: 37707 sample_scan: Volume[5], material='Cu.txt' geometry='wire.ply' sample_scan: Volume[5], material='Cu.txt' geometry='wire.ply' sample_scan: Volume[1], material='book.txt' geometry='book.ply' sample_scan: Volume[1], material='book.txt' geometry='book.ply' sample_scan: Volume[1], material='book.txt' geometry='book.ply' sample_scan: Volume[2], material='h2o2.dat' geometry='h2o2.ply' sample_scan: Volume[2], material='h2o2.dat' geometry='h2o2.ply' sample_scan: Volume[2], material='h2o2.dat' geometry='h2o2.ply' sample_scan: Volume[5], material='Cu.txt' geometry='wire.ply' sample_scan: Volume[5], material='Cu.txt' geometry='wire.ply' sample_scan: Volume[3], material='H2O.txt' geometry='water.ply' [Airport_scannerII] Initialize sample_scan: Volume[3], material='H2O.txt' geometry='water.ply' sample_scan: Volume[3], material='H2O.txt' geometry='water.ply' sample_scan: Volume[4], material='ethanol.txt' geometry='whiskey.ply' sample_scan: Volume[4], material='ethanol.txt' geometry='whiskey.ply' sample_scan: Volume[1], material='book.txt' geometry='book.ply' Number of polygons: 84521 [Airport_scannerII] Initialize sample_scan: Volume[4], material='ethanol.txt' geometry='whiskey.ply' sample_scan: Volume[2], material='h2o2.dat' geometry='h2o2.ply' sample_scan: Volume[3], material='H2O.txt' geometry='water.ply' sample_scan: Volume[5], material='Cu.txt' geometry='wire.ply' sample_scan: Volume[5], material='Cu.txt' geometry='wire.ply' sample_scan: Volume[1], material='book.txt' geometry='book.ply' sample_scan: Volume[5], material='Cu.txt' geometry='wire.ply' sample_scan: Volume[2], material='h2o2.dat' geometry='h2o2.ply' sample_scan: Volume[4], material='ethanol.txt' geometry='whiskey.ply' sample_scan: Volume[3], material='H2O.txt' geometry='water.ply' sample_scan: Volume[4], material='ethanol.txt' geometry='whiskey.ply' sample_scan: Volume[5], material='Cu.txt' geometry='wire.ply' sample_scan: Volume[5], material='Cu.txt' geometry='wire.ply' Warning: Neither xwidth, yheight or zdepth are defined. The file-defined (non-scaled) geometry the OFF geometry luggage.off will be applied! Bounding box dimensions for geometry luggage.off: Length=0.324186 (100.000%) Width= 0.260044 (100.000%) Depth= 0.540097 (100.000%) sample_scan: Volume[6], material='Al.txt' geometry='luggage.off' sample_scan: Volume[6], material='Al.txt' geometry='luggage.off' sample_scan: Volume[6], material='Al.txt' geometry='luggage.off' sample_scan: Volume[6], material='Al.txt' geometry='luggage.off' sample_scan: Volume[6], material='Al.txt' geometry='luggage.off' sample_scan: Volume[6], material='Al.txt' geometry='luggage.off' sample_scan: Volume[6], material='Al.txt' geometry='luggage.off' sample_scan: Volume[6], material='Al.txt' geometry='luggage.off' sample_scan: Volume[6], material='Al.txt' geometry='luggage.off' sample_scan: Volume[6], material='Al.txt' geometry='luggage.off' [n-62-29-31:03057] 9 more processes have sent help message help-mpi-btl-openib.txt / ib port not selected [n-62-29-31:03057] Set MCA parameter "orte_base_help_aggregate" to 0 to see all help / error messages [n-62-29-31:03057] 9 more processes have sent help message help-mpi-btl-openib.txt / error in device init Trace ETA 16.6667 [min] % 1 Trace ETA 16.6667 [min] % 1 Trace ETA 16.6667 [min] % 1 Trace ETA 16.6667 [min] % 1 Trace ETA 14.1 [min] % 1 Trace ETA 14.1 [min] % 1 Trace ETA 16.6667 [min] % 1 Trace ETA 14.1 [min] % 1 Trace ETA 14.1 [min] % 1 Trace ETA 14.1 [min] % 1 2 2 2 2 2 2 2 2 2 2 3 3 3 3 3 3 3 3 3 3 4 4 4 4 4 4 4 4 4 4 5 5 5 5 5 5 5 5 5 5 6 6 6 6 6 6 6 6 6 6 7 7 7 7 7 7 7 8 8 7 8 8 7 8 7 9 9 9 9 9 8 8 8 8 8 10 10 10 10 10 9 9 9 9 9 11 11 11 11 11 10 10 10 10 10 12 12 12 12 12 11 11 11 11 13 11 13 13 13 13 12 12 14 12 12 14 14 14 12 14 13 15 15 13 15 15 13 15 13 13 16 16 16 16 14 16 14 14 14 14 17 17 17 17 17 15 15 15 15 15 18 18 18 18 18 16 16 16 16 16 19 19 19 19 19 17 17 17 20 20 17 20 20 20 17 18 18 21 21 21 21 18 21 18 18 19 22 22 22 22 19 22 19 19 19 23 23 23 23 20 23 20 20 20 20 24 24 24 24 24 21 21 21 21 25 21 25 25 25 25 22 22 22 22 26 26 26 26 22 26 23 23 23 27 23 27 27 27 27 23 24 24 28 24 28 28 28 24 28 24 25 25 29 29 29 25 29 29 25 25 26 30 26 30 30 30 30 26 26 26 27 31 31 31 27 31 31 27 27 27 32 28 32 32 32 28 32 28 28 28 33 33 33 29 33 33 29 29 29 29 34 34 34 34 30 34 30 30 30 35 35 35 30 35 35 31 31 31 36 31 36 36 36 36 31 32 32 37 37 32 37 37 32 37 32 33 38 33 38 38 38 38 33 33 33 34 39 39 39 34 39 39 34 34 34 40 35 40 40 40 40 35 35 35 41 41 41 35 36 41 41 36 36 42 36 42 42 42 42 37 36 37 43 37 43 43 37 43 43 38 37 38 44 44 44 38 44 44 38 39 38 45 39 45 45 45 45 39 39 40 46 39 46 46 46 40 46 40 40 47 41 47 47 47 40 47 41 41 48 41 48 48 42 48 48 41 42 49 42 49 49 42 49 49 43 42 43 50 50 50 43 50 50 43 44 43 51 44 51 51 51 51 44 44 45 52 52 44 52 45 52 52 45 45 46 53 53 53 53 53 45 46 46 54 46 54 47 54 54 54 46 47 47 55 55 55 47 55 48 55 47 48 56 56 56 48 56 56 48 49 49 57 48 57 57 57 57 49 49 50 58 58 58 50 49 58 58 50 50 51 59 59 59 59 51 59 50 51 60 52 51 60 60 60 60 52 51 52 61 61 61 53 52 61 61 53 52 62 62 53 62 62 54 53 62 54 63 53 63 63 54 63 63 55 54 64 55 64 64 54 64 64 55 56 55 65 65 65 56 65 65 55 56 57 66 56 66 66 66 66 57 56 57 67 58 67 57 67 67 67 58 57 68 58 68 59 68 58 68 68 59 69 58 69 69 59 60 69 69 59 70 60 70 70 59 70 60 70 61 60 71 71 61 71 71 71 60 61 62 61 72 72 72 62 72 72 61 62 63 73 62 73 73 73 73 63 62 63 64 74 63 74 74 74 74 64 63 75 65 64 75 75 64 75 75 65 64 76 66 65 76 76 65 76 76 66 77 65 77 67 66 77 66 77 77 67 78 78 66 78 68 67 78 78 67 68 79 79 79 67 69 68 79 79 68 80 69 80 80 68 70 80 80 69 69 81 70 81 81 81 81 71 69 70 70 82 82 82 71 82 82 72 70 71 83 71 83 83 83 72 83 73 84 71 72 84 84 72 84 84 73 85 74 85 72 85 73 73 85 85 74 86 86 75 86 73 74 86 86 74 87 75 87 87 76 87 87 74 75 75 88 88 88 76 88 77 88 75 76 89 76 89 89 77 89 89 78 90 76 77 90 90 77 90 90 78 79 91 91 78 91 77 78 91 91 79 92 80 92 92 79 78 92 92 79 93 80 93 81 93 93 93 80 79 80 94 94 81 94 82 94 94 81 95 80 81 95 95 82 95 83 95 96 82 96 81 96 82 96 96 83 84 97 97 97 83 82 83 97 97 84 85 98 98 98 84 98 83 98 84 99 85 86 99 99 99 99 85 84 85 Finally [Airport_scannerII: 1]. Time: 14.1667 [min] Warning: 305 events were removed in Component[7] psd2=PSD_monitor() (negative time, miss next components, rounding errors, Nan, Inf). 86 87 Finally [Airport_scannerII: 1]. Time: 14.2167 [min] Warning: 273 events were removed in Component[7] psd2=PSD_monitor() (negative time, miss next components, rounding errors, Nan, Inf). Finally [Airport_scannerII: 1]. Time: 14.2167 [min] Warning: 288 events were removed in Component[7] psd2=PSD_monitor() (negative time, miss next components, rounding errors, Nan, Inf). 86 85 86 88 87 87 86 87 89 88 88 87 88 90 89 89 88 89 91 90 90 89 90 92 91 91 90 91 93 92 92 91 92 94 93 93 92 93 95 94 94 93 94 96 95 95 94 95 97 96 96 95 96 98 97 97 96 97 99 98 98 97 98 99 99 98 99 Finally [Airport_scannerII: 1]. Time: 16.6 [min] Finally [Airport_scannerII: 1]. Time: 16.6 [min] Warning: 289 events were removed in Component[7] psd2=PSD_monitor() (negative time, miss next components, rounding errors, Nan, Inf). Warning: 289 events were removed in Component[7] psd2=PSD_monitor() (negative time, miss next components, rounding errors, Nan, Inf). Finally [Airport_scannerII: 1]. Time: 16.6333 [min] Warning: 308 events were removed in Component[7] psd2=PSD_monitor() (negative time, miss next components, rounding errors, Nan, Inf). Finally [Airport_scannerII: 1]. Time: 16.6333 [min] Warning: 323 events were removed in Component[7] psd2=PSD_monitor() (negative time, miss next components, rounding errors, Nan, Inf). 99 Save [Airport_scannerII] Detector: psd0_I=0.00103488 psd0_ERR=3.27258e-07 psd0_N=1e+07 "psd0.dat" Finally [Airport_scannerII: 1]. Time: 16.7833 [min] Warning: 298 events were removed in Component[7] psd2=PSD_monitor() (negative time, miss next components, rounding errors, Nan, Inf). Detector: emon_I=0.00103488 emon_ERR=3.27258e-07 emon_N=1e+07 "emon.dat" Detector: psd2_I=0.000629446 psd2_ERR=2.5105e-07 psd2_N=7.65585e+06 "psd2.dat" Finally [Airport_scannerII: 1]. Time: 16.7833 [min] Warning: 289 events were removed in Component[7] psd2=PSD_monitor() (negative time, miss next components, rounding errors, Nan, Inf). Detector: psd_far_I=1.09961e-05 psd_far_ERR=3.13196e-08 psd_far_N=306633 "psdfar.dat" Finally [Airport_scannerII: 1]. Time: 16.7833 [min] Warning: 291 events were removed in Component[7] psd2=PSD_monitor() (negative time, miss next components, rounding errors, Nan, Inf). INFO: Placing instr file copy /zhome/89/0/38697/xTESTS/2022-12-01/McXtrace-1.x_CPU_MPICC_1e7/Airport_scannerII/Airport_scannerII.instr in dataset 1