New issue 726: Segmentation fault after a rockstar script fails on a multi particle mass dataset https://bitbucket.org/yt_analysis/yt/issue/726/segmentation-fault-after-a-ro... Nathan Goldbaum: I just tried running the rockstar halo finder on a multi-mass particle dataset and triggered a segmentation fault after the script failed: ``` #! goldbaum at ROUS in ~/Documents/test ○ mpirun -np 4 python test.py --parallel yt : [INFO ] 2013-11-16 22:29:44,695 Global parallel computation enabled: 0 / 4 yt : [INFO ] 2013-11-16 22:29:44,695 Global parallel computation enabled: 1 / 4 yt : [INFO ] 2013-11-16 22:29:44,695 Global parallel computation enabled: 2 / 4 yt : [INFO ] 2013-11-16 22:29:44,695 Global parallel computation enabled: 3 / 4 P000 yt : [INFO ] 2013-11-16 22:29:45,322 Parameters: current_time = 645.817072369 P000 yt : [INFO ] 2013-11-16 22:29:45,322 Parameters: domain_dimensions = [64 64 64] P000 yt : [INFO ] 2013-11-16 22:29:45,325 Parameters: domain_left_edge = [ 0. 0. 0.] P000 yt : [INFO ] 2013-11-16 22:29:45,326 Parameters: domain_right_edge = [ 1. 1. 1.] P000 yt : [INFO ] 2013-11-16 22:29:45,326 Parameters: cosmological_simulation = 1 P000 yt : [INFO ] 2013-11-16 22:29:45,327 Parameters: current_redshift = 0.00139308806408 P000 yt : [INFO ] 2013-11-16 22:29:45,327 Parameters: omega_lambda = 0.7 P000 yt : [INFO ] 2013-11-16 22:29:45,327 Parameters: omega_matter = 0.3 P000 yt : [INFO ] 2013-11-16 22:29:45,327 Parameters: hubble_constant = 0.71 P000 yt : [WARNING ] 2013-11-16 22:29:45,327 The citation for the Rockstar halo finder can be found at P000 yt : [WARNING ] 2013-11-16 22:29:45,327 http://adsabs.harvard.edu/abs/2013ApJ...762..109B P000 yt : [INFO ] 2013-11-16 22:29:45,327 Rockstar is using 1 readers and 2 writers P000 yt : [INFO ] 2013-11-16 22:29:45,333 Starting 'Parsing Hierarchy' P001 yt : [WARNING ] 2013-11-16 22:29:45,327 The citation for the Rockstar halo finder can be found at P001 yt : [WARNING ] 2013-11-16 22:29:45,327 http://adsabs.harvard.edu/abs/2013ApJ...762..109B P001 yt : [INFO ] 2013-11-16 22:29:45,328 Rockstar is using 1 readers and 2 writers P001 yt : [INFO ] 2013-11-16 22:29:45,333 Starting 'Parsing Hierarchy' P002 yt : [WARNING ] 2013-11-16 22:29:45,327 The citation for the Rockstar halo finder can be found at P002 yt : [WARNING ] 2013-11-16 22:29:45,327 http://adsabs.harvard.edu/abs/2013ApJ...762..109B P002 yt : [INFO ] 2013-11-16 22:29:45,328 Rockstar is using 1 readers and 2 writers P002 yt : [INFO ] 2013-11-16 22:29:45,333 Starting 'Parsing Hierarchy' P003 yt : [WARNING ] 2013-11-16 22:29:45,356 The citation for the Rockstar halo finder can be found at P003 yt : [WARNING ] 2013-11-16 22:29:45,356 http://adsabs.harvard.edu/abs/2013ApJ...762..109B P003 yt : [INFO ] 2013-11-16 22:29:45,356 Rockstar is using 1 readers and 2 writers P003 yt : [INFO ] 2013-11-16 22:29:45,363 Starting 'Parsing Hierarchy' P001 yt : [INFO ] 2013-11-16 22:29:45,443 Finishing 'Parsing Hierarchy' P000 yt : [INFO ] 2013-11-16 22:29:45,445 Finishing 'Parsing Hierarchy' P002 yt : [INFO ] 2013-11-16 22:29:45,450 Finishing 'Parsing Hierarchy' P003 yt : [INFO ] 2013-11-16 22:29:45,473 Finishing 'Parsing Hierarchy' P000 yt : [INFO ] 2013-11-16 22:29:45,515 Gathering a field list (this may take a moment.) P000 yt : [INFO ] 2013-11-16 22:29:45,628 Adding unknown field ('io', 'particle_position_y') to list of fields P000 yt : [INFO ] 2013-11-16 22:29:45,629 Adding unknown field ('io', 'particle_index') to list of fields P000 yt : [INFO ] 2013-11-16 22:29:45,629 Adding unknown field ('io', 'creation_time') to list of fields P000 yt : [INFO ] 2013-11-16 22:29:45,629 Adding unknown field ('io', 'dynamical_time') to list of fields P000 yt : [INFO ] 2013-11-16 22:29:45,629 Adding unknown field ('io', 'particle_position_z') to list of fields P000 yt : [INFO ] 2013-11-16 22:29:45,629 Adding unknown field ('io', 'particle_position_x') to list of fields P000 yt : [INFO ] 2013-11-16 22:29:45,630 Adding unknown field ('io', 'metallicity_fraction') to list of fields P000 yt : [INFO ] 2013-11-16 22:29:45,630 Adding unknown field ('io', 'particle_velocity_z') to list of fields P000 yt : [INFO ] 2013-11-16 22:29:45,630 Adding unknown field ('io', 'particle_mass') to list of fields P000 yt : [INFO ] 2013-11-16 22:29:45,630 Adding unknown field ('io', 'particle_velocity_y') to list of fields P000 yt : [INFO ] 2013-11-16 22:29:45,630 Adding unknown field ('io', 'particle_type') to list of fields P000 yt : [INFO ] 2013-11-16 22:29:45,630 Adding unknown field ('io', 'particle_velocity_x') to list of fields Traceback (most recent call last): File "test.py", line 8, in <module> rh = RockstarHaloFinder(ts) File "/Users/goldbaum/Documents/yt-3.0/yt/analysis_modules/halo_finding/rockstar/rockstar.py", line 216, in __init__ p = self._setup_parameters(ts) File "/Users/goldbaum/Documents/yt-3.0/yt/analysis_modules/halo_finding/rockstar/rockstar.py", line 237, in _setup_parameters ptype) yt.utilities.exceptions.YTRockstarMultiMassNotSupported: Particle type 'all' has minimum mass 1.000e+09 and maximum mass 7.820e+11. Multi-mass particles are not currently supported. [ROUS:67873] *** Process received signal *** [ROUS:67873] Signal: Segmentation fault: 11 (11) [ROUS:67873] Signal code: Address not mapped (1) [ROUS:67873] Failing at address: 0x10 [ROUS:67873] [ 0] 2 libsystem_platform.dylib 0x00007fff944c15aa _sigtramp + 26 [ROUS:67873] [ 1] 3 ??? 0x00000001101adb30 0x0 + 4565162800 [ROUS:67873] [ 2] 4 Python 0x000000010fbfa4fd PyObject_Call + 101 [ROUS:67873] [ 3] 5 MPI.so 0x00000001108ea33f __pyx_getprop_6mpi4py_3MPI_4Comm_rank + 63 [ROUS:67873] [ 4] 6 Python 0x000000010fc0a475 getset_get + 58 [ROUS:67873] [ 5] 7 Python 0x000000010fc2a197 _PyObject_GenericGetAttrWithDict + 216 [ROUS:67873] [ 6] 8 Python 0x000000010fc724e3 PyEval_EvalFrameEx + 7320 [ROUS:67873] [ 7] 9 Python 0x000000010fc70721 PyEval_EvalCodeEx + 1638 [ROUS:67873] [ 8] 10 Python 0x000000010fc17caa function_call + 336 [ROUS:67873] [ 9] 11 Python 0x000000010fbfa4fd PyObject_Call + 101 [ROUS:67873] [10] 12 Python 0x000000010fbfa68d call_function_tail + 72 [ROUS:67873] [11] 13 Python 0x000000010fbfa622 PyObject_CallFunction + 195 [ROUS:67873] [12] 14 Python 0x000000010fc2a197 _PyObject_GenericGetAttrWithDict + 216 [ROUS:67873] [13] 15 Python 0x000000010fc724e3 PyEval_EvalFrameEx + 7320 [ROUS:67873] [14] 16 Python 0x000000010fc76aaf fast_function + 182 [ROUS:67873] [15] 17 Python 0x000000010fc73919 PyEval_EvalFrameEx + 12494 [ROUS:67873] [16] 18 Python 0x000000010fc76aaf fast_function + 182 [ROUS:67873] [17] 19 Python 0x000000010fc73919 PyEval_EvalFrameEx + 12494 [ROUS:67873] [18] 20 Python 0x000000010fc70721 PyEval_EvalCodeEx + 1638 [ROUS:67873] [19] 21 Python 0x000000010fc17caa function_call + 336 [ROUS:67873] [20] 22 Python 0x000000010fbfa4fd PyObject_Call + 101 [ROUS:67873] [21] 23 Python 0x000000010fc04f2f instancemethod_call + 174 [ROUS:67873] [22] 24 Python 0x000000010fbfa4fd PyObject_Call + 101 [ROUS:67873] [23] 25 Python 0x000000010fc76274 PyEval_CallObjectWithKeywords + 93 [ROUS:67873] [24] 26 Python 0x000000010fc3fe04 slot_tp_del + 80 [ROUS:67873] [25] 27 Python 0x000000010fc43f83 subtype_dealloc + 286 [ROUS:67873] [26] 28 Python 0x000000010fc16385 frame_dealloc + 110 [ROUS:67873] [27] 29 Python 0x000000010fc9578a tb_dealloc + 101 [ROUS:67873] [28] 30 Python 0x000000010fc95771 tb_dealloc + 76 [ROUS:67873] [29] 31 Python 0x000000010fc26cbf insertdict_by_entry + 242 [ROUS:67873] *** End of error message *** -------------------------------------------------------------------------- mpirun noticed that process rank 1 with PID 67873 on node ROUS exited on signal 11 (Segmentation fault: 11). -------------------------------------------------------------------------- ``` Test script is here: ``` #! from yt.mods import * from yt.analysis_modules.halo_finding.rockstar.api import RockstarHaloFinder import glob as glob ds = load("Enzo_64/DD0043/data0043") ts = TimeSeriesData([ds]) rh = RockstarHaloFinder(ts) rh.run() ```