Hi all,
first of all thanks for the PyMC3 package, I’ll use it for implementation of Kennedy O’Hagan implementation and it seems like just the right tool.
However, I do have some troubles with current version of PyMC3. As I suspect it is a bug of PyMC3 but rather a wrong usage on my side, I hope this is the right plattform to post this issue.
- PyMC3 Version: 3.4.1-py36_0
- Theano Version: 1.0.2-py36he980bc4_0
- Python Version: 3.6.6
- Operating system: Windows 10 64bit (also tested Ubuntu 18.04 64bit, if traceback needed I’ll reproduce it, getting also an error)
- How did you install PyMC3: conda (full package list of new environment, see below)
I’m trying to run your “simpletest.py” example. Running it with no further adjustmens gives the first traceback. adding cores=1 to the pm.sample method (pm.samle(n, cores=1)) runs smoothly (2nd traceback).
So my (probably valid) assumption is that it is caused by multiprocessing, but what am I doing wrong or missing here? Any help very much appreciated 
Traceback (sorry for german language) is:
(pymc_env) Notes\stuff>python simpletest.py
Auto-assigning NUTS sampler...
Initializing NUTS using jitter+adapt_diag...
Multiprocess sampling (4 chains in 4 jobs)
NUTS: [z_logodds__, x]
You can find the C code in this temporary file: C:\Users\pre\AppData\Local\Temp\theano_compilation_error_i91anzzq
Traceback (most recent call last):
File "D:\Programme\anaconda3\envs\pymc_env\lib\site-packages\joblib\externals\loky\process_executor.py", line 377, in
_process_worker
call_item = call_queue.get(block=True, timeout=timeout)
File "D:\Programme\anaconda3\envs\pymc_env\lib\multiprocessing\queues.py", line 113, in get
return _ForkingPickler.loads(res)
File "D:\Programme\anaconda3\envs\pymc_env\lib\site-packages\theano\compile\function_module.py", line 1082, in _constr
uctor_Function
f = maker.create(input_storage, trustme=True)
File "D:\Programme\anaconda3\envs\pymc_env\lib\site-packages\theano\compile\function_module.py", line 1715, in create
input_storage=input_storage_lists, storage_map=storage_map)
File "D:\Programme\anaconda3\envs\pymc_env\lib\site-packages\theano\gof\link.py", line 699, in make_thunk
storage_map=storage_map)[:3]
File "D:\Programme\anaconda3\envs\pymc_env\lib\site-packages\theano\gof\vm.py", line 1091, in make_all
impl=impl))
File "D:\Programme\anaconda3\envs\pymc_env\lib\site-packages\theano\gof\op.py", line 955, in make_thunk
no_recycling)
File "D:\Programme\anaconda3\envs\pymc_env\lib\site-packages\theano\gof\op.py", line 858, in make_c_thunk
output_storage=node_output_storage)
File "D:\Programme\anaconda3\envs\pymc_env\lib\site-packages\theano\gof\cc.py", line 1217, in make_thunk
keep_lock=keep_lock)
File "D:\Programme\anaconda3\envs\pymc_env\lib\site-packages\theano\gof\cc.py", line 1157, in __compile__
keep_lock=keep_lock)
File "D:\Programme\anaconda3\envs\pymc_env\lib\site-packages\theano\gof\cc.py", line 1620, in cthunk_factory
key=key, lnk=self, keep_lock=keep_lock)
File "D:\Programme\anaconda3\envs\pymc_env\lib\site-packages\theano\gof\cmodule.py", line 1181, in module_from_key
module = lnk.compile_cmodule(location)
File "D:\Programme\anaconda3\envs\pymc_env\lib\site-packages\theano\gof\cc.py", line 1523, in compile_cmodule
preargs=preargs)
File "D:\Programme\anaconda3\envs\pymc_env\lib\site-packages\theano\gof\cmodule.py", line 2391, in compile_str
(status, compile_stderr.replace('\n', '. ')))
Exception: ('The following error happened while compiling the node', Alloc(TensorConstant{(1,) of 0.0}, Shape_i{0}.0), '
\n', 'Compilation failed (return status=3): ', '[Alloc(TensorConstant{(1,) of 0.0}, <TensorType(int64, scalar)>)]')
forrtl: error (200): program aborting due to control-C event
Image PC Routine Line Source
libifcoremd.dll 00007FFC620E94C4 Unknown Unknown Unknown
KERNELBASE.dll 00007FFCCA6C7EDD Unknown Unknown Unknown
KERNEL32.DLL 00007FFCCD4D1FE4 Unknown Unknown Unknown
ntdll.dll 00007FFCCD60F061 Unknown Unknown Unknown
forrtl: error (200): program aborting due to control-C event
Image PC Routine Line Source
libifcoremd.dll 00007FFC620E94C4 Unknown Unknown Unknown
KERNELBASE.dll 00007FFCCA6C7EDD Unknown Unknown Unknown
KERNEL32.DLL 00007FFCCD4D1FE4 Unknown Unknown Unknown
ntdll.dll 00007FFCCD60F061 Unknown Unknown Unknown
forrtl: error (200): program aborting due to control-C event
Image PC Routine Line Source
libifcoremd.dll 00007FFC620E94C4 Unknown Unknown Unknown
KERNELBASE.dll 00007FFCCA6C7EDD Unknown Unknown Unknown
KERNEL32.DLL 00007FFCCD4D1FE4 Unknown Unknown Unknown
ntdll.dll 00007FFCCD60F061 Unknown Unknown Unknown
forrtl: error (200): program aborting due to control-C event
Image PC Routine Line Source
libifcoremd.dll 00007FFC620E94C4 Unknown Unknown Unknown
KERNELBASE.dll 00007FFCCA6C7EDD Unknown Unknown Unknown
KERNEL32.DLL 00007FFCCD4D1FE4 Unknown Unknown Unknown
ntdll.dll 00007FFCCD60F061 Unknown Unknown Unknown
forrtl: error (200): program aborting due to control-C event
Image PC Routine Line Source
libifcoremd.dll 00007FFC620E94C4 Unknown Unknown Unknown
KERNELBASE.dll 00007FFCCA6C7EDD Unknown Unknown Unknown
KERNEL32.DLL 00007FFCCD4D1FE4 Unknown Unknown Unknown
ntdll.dll 00007FFCCD60F061 Unknown Unknown Unknown
FEHLER: Der Prozess "13288" wurde nicht gefunden.
Running it only on single core
(pymc_env) \stuff>python simpletest.py
Auto-assigning NUTS sampler...
Initializing NUTS using jitter+adapt_diag...
Sequential sampling (2 chains in 1 job)
NUTS: [z_logodds__, x]
100%|████████████████████████████████████████████████████████████████████████████| 1500/1500 [00:01<00:00, 1069.47it/s]
100%|████████████████████████████████████████████████████████████████████████████| 1500/1500 [00:00<00:00, 1783.11it/s]
Conda output:
conda create -n pymc_env python=3.6 pymc3
Package Plan
environment location: D:\Programme\anaconda3\envs\pymc_env
added / updated specs:
- pymc3
- python=3.6
The following packages will be downloaded:
package | build
---------------------------|-----------------
python-3.6.6 | hea74fb7_0 21.6 MB
The following NEW packages will be INSTALLED:
blas: 1.0-mkl
ca-certificates: 2018.03.07-0
certifi: 2018.4.16-py36_0
cycler: 0.10.0-py36h009560c_0
freetype: 2.8-h51f8f2c_1
h5py: 2.8.0-py36h3bdd7fb_0
hdf5: 1.10.2-hac2f561_1
icc_rt: 2017.0.4-h97af966_0
icu: 58.2-ha66f8fd_1
intel-openmp: 2018.0.3-0
joblib: 0.12-py36_0
jpeg: 9b-hb83a4c4_2
kiwisolver: 1.0.1-py36h12c3424_0
libgpuarray: 0.7.6-hfa6e2cd_0
libpng: 1.6.34-h79bbb47_0
libpython: 2.1-py36_0
m2w64-binutils: 2.25.1-5
m2w64-bzip2: 1.0.6-6
m2w64-crt-git: 5.0.0.4636.2595836-2
m2w64-gcc: 5.3.0-6
m2w64-gcc-ada: 5.3.0-6
m2w64-gcc-fortran: 5.3.0-6
m2w64-gcc-libgfortran: 5.3.0-6
m2w64-gcc-libs: 5.3.0-7
m2w64-gcc-libs-core: 5.3.0-7
m2w64-gcc-objc: 5.3.0-6
m2w64-gmp: 6.1.0-2
m2w64-headers-git: 5.0.0.4636.c0ad18a-2
m2w64-isl: 0.16.1-2
m2w64-libiconv: 1.14-6
m2w64-libmangle-git: 5.0.0.4509.2e5a9a2-2
m2w64-libwinpthread-git: 5.0.0.4634.697f757-2
m2w64-make: 4.1.2351.a80a8b8-2
m2w64-mpc: 1.0.3-3
m2w64-mpfr: 3.1.4-4
m2w64-pkg-config: 0.29.1-2
m2w64-toolchain: 5.3.0-7
m2w64-tools-git: 5.0.0.4592.90b8472-2
m2w64-windows-default-manifest: 6.4-3
m2w64-winpthreads-git: 5.0.0.4634.697f757-2
m2w64-zlib: 1.2.8-10
mako: 1.0.7-py36he15cdb7_0
markupsafe: 1.0-py36h0e26971_1
matplotlib: 2.2.2-py36h153e9ff_1
mkl: 2018.0.3-1
mkl-service: 1.1.2-py36h57e144c_4
mkl_fft: 1.0.1-py36h452e1ab_0
mkl_random: 1.0.1-py36h9258bd6_0
msys2-conda-epoch: 20160418-1
numpy: 1.14.5-py36h9fa60d3_0
numpy-base: 1.14.5-py36h5c71026_0
openssl: 1.0.2o-h8ea7d77_0
pandas: 0.23.1-py36h830ac7b_0
patsy: 0.5.0-py36_0
pip: 10.0.1-py36_0
pygpu: 0.7.6-py36h452e1ab_0
pymc3: 3.4.1-py36_0
pyparsing: 2.2.0-py36h785a196_1
pyqt: 5.9.2-py36h1aa27d4_0
python: 3.6.6-hea74fb7_0
python-dateutil: 2.7.3-py36_0
pytz: 2018.4-py36_0
qt: 5.9.6-vc14h62aca36_0
scipy: 1.1.0-py36h672f292_0
setuptools: 39.2.0-py36_0
sip: 4.19.8-py36h6538335_0
six: 1.11.0-py36h4db2310_1
sqlite: 3.24.0-h7602738_0
theano: 1.0.2-py36he980bc4_0
tornado: 5.0.2-py36_0
tqdm: 4.23.4-py36_0
vc: 14-h0510ff6_3
vs2015_runtime: 14.0.25123-3
wheel: 0.31.1-py36_0
wincertstore: 0.2-py36h7fe50ca_0
zlib: 1.2.11-h8395fce_2