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Upgrade Stan/PyStan to v2.19 #137
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Errors similar to what was seen in the past happen here too... [root@0f7bb2cefb83 sampling]# python3 sampling_test.py SamplingTests.test_PyStan
2019-08-07T16:55:24[INFO ] __main__(16) -> PyStanSampling test
2019-08-07T16:55:24[INFO ] morpho.processors.BaseProcessor(50) -> Configure <pystanProcessor>
2019-08-07T16:55:24[DEBUG ] morpho.processors.sampling.PyStanSamplingProcessor(254) -> seed = None
2019-08-07T16:55:24[INFO ] morpho.processors.BaseProcessor(72) -> Run <pystanProcessor>...
/host/Project8/SourceTree/morpho/morpho/processors/sampling/PyStanSamplingProcessor.py:127: ResourceWarning: unclosed file <_io.TextIOWrapper name='model.stan' mode='r+' encoding='UTF-8'>
theModel = open(self.model_code, 'r+').read()
2019-08-07T16:55:24[DEBUG ] morpho.processors.sampling.PyStanSamplingProcessor(138) -> No functions file location given
2019-08-07T16:55:24[DEBUG ] morpho.processors.sampling.PyStanSamplingProcessor(161) -> Import function files: complete
2019-08-07T16:55:24[DEBUG ] morpho.processors.sampling.PyStanSamplingProcessor(177) -> Trying to load cached StanModel
2019-08-07T16:55:24[DEBUG ] morpho.processors.sampling.PyStanSamplingProcessor(180) -> None exists -> creating Stan cache
2019-08-07T16:55:24[DEBUG ] pystan(169) -> Successfully parsed Stan model 'anon_model_add5de6cfa753066e2255c6fea849b7e'.
2019-08-07T16:55:24[INFO ] pystan(242) -> COMPILING THE C++ CODE FOR MODEL anon_model_add5de6cfa753066e2255c6fea849b7e NOW.
E
======================================================================
ERROR: test_PyStan (__main__.SamplingTests)
----------------------------------------------------------------------
Traceback (most recent call last):
File "/host/Project8/SourceTree/morpho/morpho/processors/sampling/PyStanSamplingProcessor.py", line 178, in _stan_cache
self.stanModel = pickle.load(open(cache_fn, 'rb'))
FileNotFoundError: [Errno 2] No such file or directory: './cached-anon_model-add5de6cfa753066e2255c6fea849b7e.pkl'
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "/opt/rh/rh-python36/root/usr/lib64/python3.6/distutils/unixccompiler.py", line 128, in _compile
extra_postargs)
File "/opt/rh/rh-python36/root/usr/lib64/python3.6/distutils/ccompiler.py", line 909, in spawn
spawn(cmd, dry_run=self.dry_run)
File "/opt/rh/rh-python36/root/usr/lib64/python3.6/distutils/spawn.py", line 36, in spawn
_spawn_posix(cmd, search_path, dry_run=dry_run)
File "/opt/rh/rh-python36/root/usr/lib64/python3.6/distutils/spawn.py", line 159, in _spawn_posix
% (cmd, exit_status))
distutils.errors.DistutilsExecError: command 'gcc' failed with exit status 4
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "sampling_test.py", line 34, in test_PyStan
self.assertTrue(pystanProcessor.Run())
File "/host/Project8/SourceTree/morpho/morpho/processors/BaseProcessor.py", line 73, in Run
if not self.InternalRun():
File "/host/Project8/SourceTree/morpho/morpho/processors/sampling/PyStanSamplingProcessor.py", line 271, in InternalRun
self._stan_cache()
File "/host/Project8/SourceTree/morpho/morpho/processors/sampling/PyStanSamplingProcessor.py", line 181, in _stan_cache
self._create_and_save_model(theModel, cache_fn)
File "/host/Project8/SourceTree/morpho/morpho/processors/sampling/PyStanSamplingProcessor.py", line 186, in _create_and_save_model
self.stanModel = pystan.StanModel(model_code=theModel)
File "/opt/rh/rh-python36/root/usr/lib64/python3.6/site-packages/pystan/model.py", line 349, in __init__
build_extension.run()
File "/opt/rh/rh-python36/root/usr/lib64/python3.6/distutils/command/build_ext.py", line 339, in run
self.build_extensions()
File "/opt/rh/rh-python36/root/usr/lib64/python3.6/distutils/command/build_ext.py", line 448, in build_extensions
self._build_extensions_serial()
File "/opt/rh/rh-python36/root/usr/lib64/python3.6/distutils/command/build_ext.py", line 473, in _build_extensions_serial
self.build_extension(ext)
File "/opt/rh/rh-python36/root/usr/lib64/python3.6/distutils/command/build_ext.py", line 533, in build_extension
depends=ext.depends)
File "/opt/rh/rh-python36/root/usr/lib64/python3.6/distutils/ccompiler.py", line 574, in compile
self._compile(obj, src, ext, cc_args, extra_postargs, pp_opts)
File "/opt/rh/rh-python36/root/usr/lib64/python3.6/distutils/unixccompiler.py", line 130, in _compile
raise CompileError(msg)
distutils.errors.CompileError: command 'gcc' failed with exit status 4
----------------------------------------------------------------------
Ran 1 test in 204.963s
FAILED (errors=1) |
Possible solution: switch to python 3.6.5 |
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Is your feature request related to a problem? Please describe.
Access new features such as numerical integration
Describe the solution you'd like
Describe alternatives you've considered
We have had issues with upgrading things as compiled models tend to not run properly, need to reinvestigate this issue.
Additional context
The text was updated successfully, but these errors were encountered: