[yt-dev] Issue #726: Segmentation fault after a rockstar script fails on a multi particle mass dataset (yt_analysis/yt)
Nathan Goldbaum
issues-reply at bitbucket.org
Sat Nov 16 22:35:03 PST 2013
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-rockstar-script
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()
```
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