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20 hours ago •
rodluger
rodluger
Starry crashes following Quickstart tutorial
Going through the Quickstart tutorial here (under Computing Light Curves) I get this error when I try to calculate the flux of a system:
time = np.linspace(-0.25, 3.25, 10000)
flux_system = system.flux(time)
Compiling `X`... Done.
You can find the C code in this temporary file: /var/folders/zp/t1q7mq8j2vs68_3mbjscd9qw0000gp/T/theano_compilation_error_qhog32ss
---------------------------------------------------------------------------
Exception Traceback (most recent call last)
File <timed exec>:2
File ~/opt/anaconda3/envs/starry/lib/python3.8/site-packages/starry/kepler.py:1015, in System.flux(self, t, total, integrated)
1005 def flux(self, t, total=True, integrated=False):
1006 """Compute the system flux at times ``t``.
1007
1008 Args:
(...)
1013 from each body.
1014 """
-> 1015 X = self.design_matrix(t)
1017 # Weight the ylms by amplitude
1018 if self._reflected:
1019 # If we're doing reflected light, scale the amplitude of
1020 # each of the secondaries by the amplitude of the primary
1021 # (the illumination source).
File ~/opt/anaconda3/envs/starry/lib/python3.8/site-packages/starry/kepler.py:914, in System.design_matrix(self, t)
895 def design_matrix(self, t):
896 """Compute the system flux design matrix at times ``t``.
897
898 .. note::
(...)
912 the design matrix in units of :py:attr:`time_unit`.
913 """
--> 914 return self.ops.X(
915 self._math.reshape(self._math.to_array_or_tensor(t), [-1])
916 * self._time_factor,
917 self._primary._r,
918 self._primary._m,
919 self._primary._prot,
920 self._primary._t0,
921 self._primary._theta0,
922 self._math.to_array_or_tensor(
923 1.0
924 ), # we treat `amp` seprately in `flux()`
925 getattr(
926 self._primary._map,
927 "_inc",
928 self._math.to_array_or_tensor(0.5 * np.pi),
929 ),
930 getattr(
931 self._primary._map, "_obl", self._math.to_array_or_tensor(0.0)
932 ),
933 getattr(
934 self._primary._map, "fproj", self._math.to_array_or_tensor(0.0)
935 ),
936 self._primary._map._u,
937 self._primary._map._f,
938 self._math.to_array_or_tensor(
939 [sec._r for sec in self._secondaries]
940 ),
941 self._math.to_array_or_tensor(
942 [sec._m for sec in self._secondaries]
943 ),
944 self._math.to_array_or_tensor(
945 [sec._prot for sec in self._secondaries]
946 ),
947 self._math.to_array_or_tensor(
948 [sec._t0 for sec in self._secondaries]
949 ),
950 self._math.to_array_or_tensor(
951 [sec._theta0 for sec in self._secondaries]
952 ),
953 self._get_periods(),
954 self._math.to_array_or_tensor(
955 [sec._ecc for sec in self._secondaries]
956 ),
957 self._math.to_array_or_tensor(
958 [sec._w for sec in self._secondaries]
959 ),
960 self._math.to_array_or_tensor(
961 [sec._Omega for sec in self._secondaries]
962 ),
963 self._math.to_array_or_tensor(
964 [sec._inc for sec in self._secondaries]
965 ),
966 self._math.to_array_or_tensor(
967 np.ones(
968 len(self._secondaries)
969 ) # we treat `amp` seprately in `flux()`
970 ),
971 self._math.to_array_or_tensor(
972 [
973 getattr(
974 sec._map,
975 "_inc",
976 self._math.to_array_or_tensor(0.5 * np.pi),
977 )
978 for sec in self._secondaries
979 ]
980 ),
981 self._math.to_array_or_tensor(
982 [
983 getattr(
984 sec._map, "_obl", self._math.to_array_or_tensor(0.0)
985 )
986 for sec in self._secondaries
987 ]
988 ),
989 self._math.to_array_or_tensor(
990 [sec._map._u for sec in self._secondaries]
991 ),
992 self._math.to_array_or_tensor(
993 [sec._map._f for sec in self._secondaries]
994 ),
995 self._math.to_array_or_tensor(
996 [
997 getattr(
998 sec._map, "_sigr", self._math.to_array_or_tensor(0.0)
999 )
1000 for sec in self._secondaries
1001 ]
1002 ),
1003 )
File ~/opt/anaconda3/envs/starry/lib/python3.8/site-packages/starry/_core/utils.py:161, in autocompile.<locals>.wrapper(instance, *args)
159 with CompileLogMessage(func.__name__):
160 with change_flags(compute_test_value="off"):
--> 161 compiled_func = theano.function(
162 [*dummy_args],
163 func(instance, *dummy_args),
164 on_unused_input="ignore",
165 profile=config.profile,
166 mode=config.mode,
167 )
168 setattr(instance, cname, compiled_func)
170 # Return the compiled version
File ~/opt/anaconda3/envs/starry/lib/python3.8/site-packages/theano/compile/function/__init__.py:337, in function(inputs, outputs, mode, updates, givens, no_default_updates, accept_inplace, name, rebuild_strict, allow_input_downcast, profile, on_unused_input)
331 fn = orig_function(
332 inputs, outputs, mode=mode, accept_inplace=accept_inplace, name=name
333 )
334 else:
335 # note: pfunc will also call orig_function -- orig_function is
336 # a choke point that all compilation must pass through
--> 337 fn = pfunc(
338 params=inputs,
339 outputs=outputs,
340 mode=mode,
341 updates=updates,
342 givens=givens,
343 no_default_updates=no_default_updates,
344 accept_inplace=accept_inplace,
345 name=name,
346 rebuild_strict=rebuild_strict,
347 allow_input_downcast=allow_input_downcast,
348 on_unused_input=on_unused_input,
349 profile=profile,
350 output_keys=output_keys,
351 )
352 return fn
File ~/opt/anaconda3/envs/starry/lib/python3.8/site-packages/theano/compile/function/pfunc.py:524, in pfunc(params, outputs, mode, updates, givens, no_default_updates, accept_inplace, name, rebuild_strict, allow_input_downcast, profile, on_unused_input, output_keys)
519 si = In(
520 variable=sv, value=sv.container, mutable=False, borrow=True, shared=True
521 )
522 inputs.append(si)
--> 524 return orig_function(
525 inputs,
526 cloned_outputs,
527 mode,
528 accept_inplace=accept_inplace,
529 name=name,
530 profile=profile,
531 on_unused_input=on_unused_input,
532 output_keys=output_keys,
533 )
File ~/opt/anaconda3/envs/starry/lib/python3.8/site-packages/theano/compile/function/types.py:1981, in orig_function(inputs, outputs, mode, accept_inplace, name, profile, on_unused_input, output_keys)
1970 m = Maker(
1971 inputs,
1972 outputs,
(...)
1978 name=name,
1979 )
1980 with config.change_flags(compute_test_value="off"):
-> 1981 fn = m.create(defaults)
1982 finally:
1983 t2 = time.time()
File ~/opt/anaconda3/envs/starry/lib/python3.8/site-packages/theano/compile/function/types.py:1836, in FunctionMaker.create(self, input_storage, trustme, storage_map)
1833 start_import_time = theano.link.c.cmodule.import_time
1835 with config.change_flags(traceback__limit=config.traceback__compile_limit):
-> 1836 _fn, _i, _o = self.linker.make_thunk(
1837 input_storage=input_storage_lists, storage_map=storage_map
1838 )
1840 end_linker = time.time()
1842 linker_time = end_linker - start_linker
File ~/opt/anaconda3/envs/starry/lib/python3.8/site-packages/theano/link/basic.py:266, in LocalLinker.make_thunk(self, input_storage, output_storage, storage_map)
265 def make_thunk(self, input_storage=None, output_storage=None, storage_map=None):
--> 266 return self.make_all(
267 input_storage=input_storage,
268 output_storage=output_storage,
269 storage_map=storage_map,
270 )[:3]
File ~/opt/anaconda3/envs/starry/lib/python3.8/site-packages/theano/link/vm.py:1131, in VMLinker.make_all(self, profiler, input_storage, output_storage, storage_map)
1126 thunk_start = time.time()
1127 # no-recycling is done at each VM.__call__ So there is
1128 # no need to cause duplicate c code by passing
1129 # no_recycling here.
1130 thunks.append(
-> 1131 node.op.make_thunk(node, storage_map, compute_map, [], impl=impl)
1132 )
1133 linker_make_thunk_time[node] = time.time() - thunk_start
1134 if not hasattr(thunks[-1], "lazy"):
1135 # We don't want all ops maker to think about lazy Ops.
1136 # So if they didn't specify that its lazy or not, it isn't.
1137 # If this member isn't present, it will crash later.
File ~/opt/anaconda3/envs/starry/lib/python3.8/site-packages/theano/graph/op.py:634, in COp.make_thunk(self, node, storage_map, compute_map, no_recycling, impl)
630 self.prepare_node(
631 node, storage_map=storage_map, compute_map=compute_map, impl="c"
632 )
633 try:
--> 634 return self.make_c_thunk(node, storage_map, compute_map, no_recycling)
635 except (NotImplementedError, MethodNotDefined):
636 # We requested the c code, so don't catch the error.
637 if impl == "c":
File ~/opt/anaconda3/envs/starry/lib/python3.8/site-packages/theano/graph/op.py:600, in COp.make_c_thunk(self, node, storage_map, compute_map, no_recycling)
598 print(f"Disabling C code for {self} due to unsupported float16")
599 raise NotImplementedError("float16")
--> 600 outputs = cl.make_thunk(
601 input_storage=node_input_storage, output_storage=node_output_storage
602 )
603 thunk, node_input_filters, node_output_filters = outputs
605 def rval():
File ~/opt/anaconda3/envs/starry/lib/python3.8/site-packages/theano/link/c/basic.py:1203, in CLinker.make_thunk(self, input_storage, output_storage, storage_map)
1175 """
1176 Compiles this linker's fgraph and returns a function to perform the
1177 computations, as well as lists of storage cells for both the inputs
(...)
1200 first_output = ostor[0].data
1201 """
1202 init_tasks, tasks = self.get_init_tasks()
-> 1203 cthunk, module, in_storage, out_storage, error_storage = self.__compile__(
1204 input_storage, output_storage, storage_map
1205 )
1207 res = _CThunk(cthunk, init_tasks, tasks, error_storage, module)
1208 res.nodes = self.node_order
File ~/opt/anaconda3/envs/starry/lib/python3.8/site-packages/theano/link/c/basic.py:1138, in CLinker.__compile__(self, input_storage, output_storage, storage_map)
1136 input_storage = tuple(input_storage)
1137 output_storage = tuple(output_storage)
-> 1138 thunk, module = self.cthunk_factory(
1139 error_storage,
1140 input_storage,
1141 output_storage,
1142 storage_map,
1143 )
1144 return (
1145 thunk,
1146 module,
(...)
1155 error_storage,
1156 )
File ~/opt/anaconda3/envs/starry/lib/python3.8/site-packages/theano/link/c/basic.py:1634, in CLinker.cthunk_factory(self, error_storage, in_storage, out_storage, storage_map)
1632 for node in self.node_order:
1633 node.op.prepare_node(node, storage_map, None, "c")
-> 1634 module = get_module_cache().module_from_key(key=key, lnk=self)
1636 vars = self.inputs + self.outputs + self.orphans
1637 # List of indices that should be ignored when passing the arguments
1638 # (basically, everything that the previous call to uniq eliminated)
File ~/opt/anaconda3/envs/starry/lib/python3.8/site-packages/theano/link/c/cmodule.py:1191, in ModuleCache.module_from_key(self, key, lnk)
1189 try:
1190 location = dlimport_workdir(self.dirname)
-> 1191 module = lnk.compile_cmodule(location)
1192 name = module.__file__
1193 assert name.startswith(location)
File ~/opt/anaconda3/envs/starry/lib/python3.8/site-packages/theano/link/c/basic.py:1543, in CLinker.compile_cmodule(self, location)
1541 try:
1542 _logger.debug(f"LOCATION {location}")
-> 1543 module = c_compiler.compile_str(
1544 module_name=mod.code_hash,
1545 src_code=src_code,
1546 location=location,
1547 include_dirs=self.header_dirs(),
1548 lib_dirs=self.lib_dirs(),
1549 libs=libs,
1550 preargs=preargs,
1551 )
1552 except Exception as e:
1553 e.args += (str(self.fgraph),)
File ~/opt/anaconda3/envs/starry/lib/python3.8/site-packages/theano/link/c/cmodule.py:2546, in GCC_compiler.compile_str(module_name, src_code, location, include_dirs, lib_dirs, libs, preargs, py_module, hide_symbols)
2542 # We replace '\n' by '. ' in the error message because when Python
2543 # prints the exception, having '\n' in the text makes it more
2544 # difficult to read.
2545 compile_stderr = compile_stderr.replace("\n", ". ")
-> 2546 raise Exception(
2547 f"Compilation failed (return status={status}): {compile_stderr}"
2548 )
2549 elif config.cmodule__compilation_warning and compile_stderr:
2550 # Print errors just below the command line.
2551 print(compile_stderr)
Exception: ('The following error happened while compiling the node', GetClOp(<TensorType(float64, vector)>), '\n', 'Compilation failed (return status=1): In file included from /Users/camu5866/.theano/compiledir_macOS-12.4-arm64-arm-64bit-arm-3.8.15-64/tmpydx46758/mod.cpp:8:. /Users/camu5866/opt/anaconda3/envs/starry/lib/python3.8/site-packages/starry/_core/ops/lib/include/ellip.h:56:5: error: cannot use \'throw\' with exceptions disabled. throw std::runtime_error("Elliptic integral `CEL` ". ^. /Users/camu5866/opt/anaconda3/envs/starry/lib/python3.8/site-packages/starry/_core/ops/lib/include/ellip.h:103:3: error: cannot use \'throw\' with exceptions disabled. throw std::runtime_error("Elliptic integral CEL did not converge.");. ^. /Users/camu5866/opt/anaconda3/envs/starry/lib/python3.8/site-packages/starry/_core/ops/lib/include/ellip.h:132:5: error: cannot use \'throw\' with exceptions disabled. throw std::invalid_argument(. ^. /Users/camu5866/opt/anaconda3/envs/starry/lib/python3.8/site-packages/starry/_core/ops/lib/include/ellip.h:215:5: error: cannot use \'throw\' with exceptions disabled. throw std::runtime_error("Elliptic integral CEL did not converge.");. ^. In file included from /Users/camu5866/.theano/compiledir_macOS-12.4-arm64-arm-64bit-arm-3.8.15-64/tmpydx46758/mod.cpp:9:. /Users/camu5866/opt/anaconda3/envs/starry/lib/python3.8/site-packages/starry/_core/ops/lib/include/limbdark.h:368:5: error: cannot use \'throw\' with exceptions disabled. throw std::runtime_error(. ^. /Users/camu5866/opt/anaconda3/envs/starry/lib/python3.8/site-packages/starry/_core/ops/lib/include/limbdark.h:467:5: error: cannot use \'throw\' with exceptions disabled. throw std::runtime_error(. ^. 6 errors generated.. ', 'FunctionGraph(GetClOp(<TensorType(float64, vector)>))')
Context
I just created a conda environment and installed starry. I had an issue where tqdm wasn't installed with Starry so I also pip installed tqdm.
- Version of starry: '1.2.0'
- Operating system: macOS Monterey, M1 chip, v12.4
- Theano Version: 1.1.2
- Python version & installation method (pip, conda, etc.): Python v3.8.15
(starry) camu5866@CatMsMBP chromatic_fitting % pip list
Package Version
------------------------ -----------
aesara-theano-fallback 0.1.0
anyio 3.6.2
appnope 0.1.3
argon2-cffi 21.3.0
argon2-cffi-bindings 21.2.0
arrow 1.2.3
arviz 0.12.1
astropy 5.2.1
asttokens 2.2.1
attrs 22.2.0
backcall 0.2.0
beautifulsoup4 4.11.1
bleach 5.0.1
bokeh 3.0.3
cachetools 5.2.1
certifi 2022.12.7
cffi 1.15.1
cftime 1.6.2
comm 0.1.2
contourpy 1.0.6
cycler 0.11.0
debugpy 1.6.5
decorator 5.1.1
defusedxml 0.7.1
deprecat 2.1.1
dill 0.3.6
entrypoints 0.4
executing 1.2.0
exoplanet 0.5.3
exoplanet-core 0.1.2
fastjsonschema 2.16.2
fastprogress 1.0.3
filelock 3.9.0
fonttools 4.38.0
fqdn 1.5.1
idna 3.4
importlib-metadata 6.0.0
importlib-resources 5.10.2
ipykernel 6.20.1
ipython 8.8.0
ipython-genutils 0.2.0
ipywidgets 8.0.4
isoduration 20.11.0
jedi 0.18.2
Jinja2 3.1.2
jsonpointer 2.3
jsonschema 4.17.3
jupyter 1.0.0
jupyter_client 7.4.9
jupyter-console 6.4.4
jupyter_core 5.1.3
jupyter-events 0.6.3
jupyter_server 2.0.6
jupyter_server_terminals 0.4.4
jupyterlab-pygments 0.2.2
jupyterlab-widgets 3.0.5
kiwisolver 1.4.4
MarkupSafe 2.1.1
matplotlib 3.6.3
matplotlib-inline 0.1.6
mistune 2.0.4
nbclassic 0.4.8
nbclient 0.7.2
nbconvert 7.2.7
nbformat 5.7.3
nest-asyncio 1.5.6
netCDF4 1.6.2
notebook 6.5.2
notebook_shim 0.2.2
numpy 1.21.6
packaging 23.0
pandas 1.5.2
pandocfilters 1.5.0
parso 0.8.3
patsy 0.5.3
pexpect 4.8.0
pickleshare 0.7.5
Pillow 9.4.0
pip 22.3.1
pkgutil_resolve_name 1.3.10
platformdirs 2.6.2
prometheus-client 0.15.0
prompt-toolkit 3.0.36
psutil 5.9.4
ptyprocess 0.7.0
pure-eval 0.2.2
pycparser 2.21
pyerfa 2.0.0.1
Pygments 2.14.0
pymc3 3.11.5
pymc3-ext 0.1.1
pyparsing 3.0.9
pyrsistent 0.19.3
python-dateutil 2.8.2
python-json-logger 2.0.4
pytz 2022.7
PyYAML 6.0
pyzmq 25.0.0
qtconsole 5.4.0
QtPy 2.3.0
rfc3339-validator 0.1.4
rfc3986-validator 0.1.1
scipy 1.7.3
semver 2.13.0
Send2Trash 1.8.0
setuptools 65.6.3
setuptools-scm 7.1.0
six 1.16.0
sniffio 1.3.0
soupsieve 2.3.2.post1
stack-data 0.6.2
starry 1.2.0
terminado 0.17.1
Theano-PyMC 1.1.2
tinycss2 1.2.1
tomli 2.0.1
tornado 6.2
tqdm 4.64.1
traitlets 5.8.1
typing_extensions 4.4.0
uri-template 1.2.0
wcwidth 0.2.5
webcolors 1.12
webencodings 0.5.1
websocket-client 1.4.2
wheel 0.37.1
widgetsnbextension 4.0.5
wrapt 1.14.1
xarray 2022.12.0
xarray-einstats 0.4.0
xyzservices 2022.9.0
zipp 3.11.0
Additional context Add any other context about the problem here.
