surface (5.4.2) crashes on very large (16 GB) grid

Added by Gregory 3 months ago

Attempting to process a large dataset, surface runs for six hours and then traps. Possible 64-bit problem?
Mac Pro late 2013 OSX 10.11.6, 128 GB memory, not all of which is used. Smaller grids execute normally.

5095 ttys005 638:33.61 /Applications/GMT-5.4.2.app/Contents/Resources/bin/gmt surface -V -Z1.25 x512_blockmedian_r.xyz -T.5 -A0.50 -R0/360/-45/0 -r -Gx512.grd -I0.001953125 -bi3

surface: Provides 3, expects 3-column binary data
surface: Grid domain: W: 0 E: 360 S: -90 N: -45 n_columns: 184320 n_rows: 23040 [pixel registration]
surface: Processing input table data
surface: Input 3 columns via binary records using format ddd
surface: Minimum value of your dataset x,y,z at: surface: 187.505905151 -70.3606567383 -9.12985038757
surface: Maximum value of your dataset x,y,z at: surface: 39.4090232849 -84.6712493896 7.02735805511
surface: LS plane determined: z = -0.825341 + (-2.8224e-06 * col) + (-1.20333e-05 * row)
surface: Grid Mode Iteration Max Change Conv Limit Total Iterations
surface: 4608 D 1 -2.22959773634 4.83853675421e-08 1
surface: 1536 I 5240 1.39037688964e-07 1.45156102626e-07 5241
surface: 1536 D 1 -2.22959773634 1.45156102626e-07 5242
surface: 512 I 24054 4.33379122696e-07 4.35468307879e-07 29296
surface: 512 D 2 2.44667531415e-08 4.35468307879e-07 29298
surface: 256 I 62443 8.68502283957e-07 8.70936615757e-07 91741
surface: 256 D 7 2.0080175922e-07 8.70936615757e-07 91748
surface: 128 I 64000 8.40152799729e-06 1.74187323151e-06 155748
surface: 128 D 9 2.65463638675e-07 1.74187323151e-06 155757
surface: 64 I 32000 3.2891032307e-05 3.48374646303e-06 187757
surface: 64 D 11 2.14462316366e-06 3.48374646303e-06 187768
surface: 32 I 16000 6.36366143738e-05 6.96749292606e-06 203768
surface: 32 D 47 6.04954202682e-06 6.96749292606e-06 203815
surface: 16 I 8000 0.00014593421727 1.39349858521e-05 211815
surface: 16 D 129 1.39076998007e-05 1.39349858521e-05 211944
surface: 8 I 4000 0.000327907408884 2.78699717042e-05 215944
surface: 8 D 271 2.71266201582e-05 2.78699717042e-05 216215
surface: 4 I 2000 0.000665688454029 5.57399434085e-05 218215
ERROR: Caught signal number 11 (Segmentation fault) at
0 libgmt.5.4.2.dylib 0x000000010d3c3ff1 iterate + 2625
1 ? 0x0000000000000000 0x0 + 0
Stack backtrace:
0 libgmt.5.4.2.dylib 0x000000010d172f33 sig_handler + 579
1 libsystem_platform.dylib 0x00007fff950aa52a _sigtramp + 26
2 ?
0x0000000000000000 0x0 + 0
3 libgmt.5.4.2.dylib 0x000000010d3c1125 GMT_surface + 17541
4 libgmt.5.4.2.dylib 0x000000010d181fa0 GMT_Call_Module + 272
5 gmt 0x000000010d16416a main + 1290
6 libdyld.dylib 0x00007fff83aaf5ad start + 1
7 ??? 0x000000000000000c 0x0 + 12

PhysMem: 92G used (5320M wired), 36G unused. VM: 819G vsize, 535M framework vsize, 27898(0) swapins, 250886(0) swapouts.