ValueError: cannot set WRITEABLE flag to True of this array

[cradesto]

Problem description

We are trying to install TARDIS from the scratch following the description on
https://tardis-sn.github.io/tardis/installation.html

After that we are trying to run example notebook
docs/models/examples/run_simple_example.ipynb

And we fall into the error
ValueError: cannot set WRITEABLE flag to True of this array
on step 3:
#TARDIS now uses the data in the data repo
sim = run_tardis('tardis_example.yml')

We are thinking that this error is connected with this issue
pandas-dev/pandas#24839
But we cannot either downgrade numpy version
or upgrade pytables version as recommended on the page
pandas-dev/pandas#24839.

[chvogl]

The same problem occurs for @manolis07gr (see #976).

[manolis07gr]

Hi @chvogl - sounds good. I am also here with the same issue as the one described by @cradesto. Thank you for looking into it - we are excited to get your help.

[chvogl]

What are the versions of numpy and pytables that you are using @cradesto, @manolis07gr?

[manolis07gr]

@chvogl I am using 1.17.4 for NumPy and 3.4.4 for Tables:

print(numpy.version)
1.17.4
print(tables.version)
3.4.4

[chvogl]

@manolis07gr, as suggested by @cradesto you might try to downgrade numpy. I currently use 1.15.4 (conda install numpy=1.15.4) and the same version of pytables as you.

[manolis07gr]

@chvogl just did but I get a new error now:
Traceback (most recent call last):
File "example.py", line 6, in
sim = run_tardis('tardis_example.yml')
File "/anaconda3/envs/tardis/lib/python3.6/site-packages/tardis_sn-3.0.dev3356-py3.6-macosx-10.9-x86_64.egg/tardis/base.py", line 24, in run_tardis
from tardis.simulation import Simulation
File "/anaconda3/envs/tardis/lib/python3.6/site-packages/tardis_sn-3.0.dev3356-py3.6-macosx-10.9-x86_64.egg/tardis/simulation/init.py", line 1, in
from tardis.simulation.base import Simulation
File "/anaconda3/envs/tardis/lib/python3.6/site-packages/tardis_sn-3.0.dev3356-py3.6-macosx-10.9-x86_64.egg/tardis/simulation/base.py", line 8, in
from tardis.montecarlo import MontecarloRunner
File "/anaconda3/envs/tardis/lib/python3.6/site-packages/tardis_sn-3.0.dev3356-py3.6-macosx-10.9-x86_64.egg/tardis/montecarlo/init.py", line 1, in
from tardis.montecarlo.base import *
File "/anaconda3/envs/tardis/lib/python3.6/site-packages/tardis_sn-3.0.dev3356-py3.6-macosx-10.9-x86_64.egg/tardis/montecarlo/base.py", line 13, in
from tardis.montecarlo import montecarlo, packet_source
File "init.pxd", line 918, in init tardis.montecarlo.montecarlo
ValueError: numpy.ufunc size changed, may indicate binary incompatibility. Expected 216 from C header, got 192 from PyObject

[chvogl]

There a numerous issues that deal with this problem e.g. scikit-learn-contrib/hdbscan#272. Upgrading to numpy=1.16.1 might solve the problem.

[chvogl]

It might also be a good idea to redo the TARDIS installation (since the problem seems to occur in compiled cython code). Use git clean -dfx to remove all compiled files and rerun python setup.py install.

[GeronimoChen]

I remember I used this command to solve the problem, referring to (pandas-dev/pandas#24839 (comment)):

pip install -e git+https://github.com/PyTables/PyTables@492ee2f#egg=tables

I am not sure whether this problem depends on OS, because I was installing tardis on both my laptop (ubuntu 19.10) and a supercomputer (centos), and the compatible pandas/numpy seems to be different.
Also, my environment (on ubuntu 19.10) is like this:

name: tardis
channels:

• conda-forge
• defaults
  dependencies:
• _libgcc_mutex=0.1=main
• alabaster=0.7.12=py_0
• asn1crypto=0.24.0=py36_1003
• astropy=3.2.1=py36h516909a_0
• atomicwrites=1.3.0=py_0
• attrs=19.1.0=py_0
• babel=2.7.0=py_0
• backcall=0.1.0=py_0
• blas=1.1=openblas
• bleach=3.1.0=py_0
• blosc=1.17.0=he1b5a44_0
• boost-cpp=1.66.0=1
• bzip2=1.0.8=h516909a_0
• ca-certificates=2019.6.16=hecc5488_0
• cairo=1.16.0=h18b612c_1001
• certifi=2019.6.16=py36_1
• cffi=1.12.3=py36h8022711_0
• chardet=3.0.4=py36_1003
• codecov=2.0.15=py_1
• commonmark=0.9.0=py_0
• coverage=4.5.4=py36h516909a_0
• cryptography=2.7=py36h72c5cf5_0
• cycler=0.10.0=py_1
• cython=0.29.13=py36he1b5a44_0
• dbus=1.13.6=he372182_0
• decorator=4.4.0=py_0
• defusedxml=0.5.0=py_1
• docopt=0.6.2=py_1
• docutils=0.15.2=py36_0
• entrypoints=0.3=py36_1000
• expat=2.2.5=he1b5a44_1003
• fontconfig=2.13.1=he4413a7_1000
• freetype=2.10.0=he983fc9_1
• future=0.17.1=py36_1000
• gettext=0.19.8.1=hc5be6a0_1002
• git-lfs=2.8.0=0
• glib=2.58.3=h6f030ca_1002
• graphite2=1.3.13=hf484d3e_1000
• graphviz=2.38.0=hf68f40c_1011
• gst-plugins-base=1.14.5=h0935bb2_0
• gstreamer=1.14.5=h36ae1b5_0
• h5py=2.8.0=py36h470a237_0
• harfbuzz=2.4.0=h37c48d4_1
• hdf5=1.10.1=2
• icu=58.2=hf484d3e_1000
• idna=2.8=py36_1000
• imagesize=1.1.0=py_0
• importlib_metadata=0.18=py36_0
• ipykernel=5.1.2=py36h5ca1d4c_0
• ipython=7.7.0=py36h5ca1d4c_0
• ipython_genutils=0.2.0=py_1
• ipywidgets=7.5.1=py_0
• jedi=0.15.1=py36_0
• jinja2=2.10.1=py_0
• jpeg=9c=h14c3975_1001
• jsonschema=3.0.2=py36_0
• jupyter=1.0.0=py_2
• jupyter_client=5.3.1=py_0
• jupyter_console=6.0.0=py_0
• jupyter_core=4.4.0=py_0
• kiwisolver=1.1.0=py36hc9558a2_0
• latexcodec=1.0.7=py_0
• libblas=3.8.0=12_openblas
• libcblas=3.8.0=12_openblas
• libffi=3.2.1=he1b5a44_1006
• libgcc=7.2.0=h69d50b8_2
• libgcc-ng=9.1.0=hdf63c60_0
• libgfortran=3.0.0=1
• libgfortran-ng=7.3.0=hdf63c60_0
• libiconv=1.15=h516909a_1005
• liblapack=3.8.0=12_openblas
• libopenblas=0.3.7=h6e990d7_1
• libpng=1.6.37=hed695b0_0
• libsodium=1.0.17=h516909a_0
• libstdcxx-ng=9.1.0=hdf63c60_0
• libtiff=4.0.10=h57b8799_1003
• libtool=2.4.6=h14c3975_1002
• libuuid=2.32.1=h14c3975_1000
• libxcb=1.13=h14c3975_1002
• libxml2=2.9.9=h13577e0_2
• llvmlite=0.28.0=py36hdbcaa40_0
• lz4-c=1.8.3=he1b5a44_1001
• lzo=2.10=h14c3975_1000
• markupsafe=1.1.1=py36h14c3975_0
• matplotlib=3.1.1=py36_0
• matplotlib-base=3.1.1=py36hfd891ef_0
• mistune=0.8.4=py36h14c3975_1000
• moab=4.9.1=3
• more-itertools=7.2.0=py_0
• mpi=1.0=mpich
• mpich=3.2.1=hc99cbb1_1014
• nbconvert=5.6.0=py_0
• nbformat=4.4.0=py_1
• nbsphinx=0.4.2=py_0
• ncurses=6.1=hf484d3e_1002
• networkx=2.3=py_0
• notebook=6.0.0=py36_0
• numba=0.43.1=py36hf2d7682_0
• numexpr=2.7.0=py36hb3f55d8_0
• numpydoc=0.9.1=py_0
• openblas=0.2.20=8
• openssl=1.1.1c=h516909a_0
• oset=0.1.3=py_1
• packaging=19.0=py_0
• pandas=0.24.2=py36hb3f55d8_0
• pandoc=2.7.3=0
• pandocfilters=1.4.2=py_1
• pango=1.40.14=he7ab937_1005
• parso=0.5.1=py_0
• pbr=5.4.2=py_0
• pcre=8.41=hf484d3e_1003
• pexpect=4.7.0=py36_0
• pickleshare=0.7.5=py36_1000
• pip=19.2.2=py36_0
• pixman=0.38.0=h516909a_1003
• pluggy=0.12.0=py_0
• prometheus_client=0.7.1=py_0
• prompt_toolkit=2.0.9=py_0
• psutil=5.6.3=py36h516909a_0
• pthread-stubs=0.4=h14c3975_1001
• ptyprocess=0.6.0=py_1001
• py=1.8.0=py_0
• pybtex=0.22.2=py36_0
• pybtex-docutils=0.2.1=py36_1000
• pycparser=2.19=py36_1
• pygments=2.4.2=py_0
• pygraphviz=1.5=py36h516909a_1001
• pyne=0.5.11=py36_blas_openblas_0
• pyopenssl=19.0.0=py36_0
• pyparsing=2.4.2=py_0
• pyqt=5.9.2=py36hcca6a23_2
• pyrsistent=0.15.4=py36h516909a_0
• pysocks=1.7.0=py36_0
• pytest=5.1.0=py36_0
• pytest-arraydiff=0.3=py_0
• pytest-astropy=0.5.0=py_0
• pytest-cov=2.7.1=py_0
• pytest-doctestplus=0.3.0=py_0
• pytest-html=1.22.0=py_0
• pytest-metadata=1.8.0=py_0
• pytest-openfiles=0.4.0=py_0
• pytest-remotedata=0.3.1=py_0
• python=3.6.7=h357f687_1005
• python-dateutil=2.8.0=py_0
• pytz=2019.2=py_0
• pyyaml=5.1.2=py36h516909a_0
• pyzmq=18.0.2=py36h1768529_2
• qt=5.9.7=h52cfd70_2
• qtconsole=4.5.3=py_0
• readline=8.0=hf8c457e_0
• recommonmark=0.6.0=py_0
• requests=2.22.0=py36_1
• scipy=1.1.0=py36_blas_openblash7943236_201
• send2trash=1.5.0=py_0
• setuptools=41.0.1=py36_0
• sip=4.19.8=py36hf484d3e_1000
• six=1.12.0=py36_1000
• snowballstemmer=1.9.0=py_0
• sphinx=2.1.2=py_0
• sphinx_bootstrap_theme=0.6.4=py_0
• sphinx_rtd_theme=0.4.3=py_0
• sphinxcontrib-apidoc=0.3.0=py_1
• sphinxcontrib-applehelp=1.0.1=py_0
• sphinxcontrib-bibtex=0.4.2=py_0
• sphinxcontrib-devhelp=1.0.1=py_0
• sphinxcontrib-htmlhelp=1.0.2=py_0
• sphinxcontrib-jsmath=1.0.1=py_0
• sphinxcontrib-qthelp=1.0.2=py_0
• sphinxcontrib-serializinghtml=1.1.1=py_0
• sqlite=3.29.0=hcee41ef_0
• terminado=0.8.2=py36_0
• testpath=0.4.2=py_1001
• tk=8.6.9=hed695b0_1002
• tornado=6.0.3=py36h516909a_0
• tqdm=4.33.0=py_0
• traitlets=4.3.2=py36_1000
• urllib3=1.25.3=py36_0
• wcwidth=0.1.7=py_1
• webencodings=0.5.1=py_1
• wheel=0.33.4=py36_0
• widgetsnbextension=3.5.1=py36_0
• xorg-kbproto=1.0.7=h14c3975_1002
• xorg-libice=1.0.10=h516909a_0
• xorg-libsm=1.2.3=h84519dc_1000
• xorg-libx11=1.6.8=h516909a_0
• xorg-libxau=1.0.9=h14c3975_0
• xorg-libxdmcp=1.1.3=h516909a_0
• xorg-libxext=1.3.4=h516909a_0
• xorg-libxpm=3.5.12=h14c3975_1002
• xorg-libxrender=0.9.10=h516909a_1002
• xorg-libxt=1.1.5=h516909a_1003
• xorg-renderproto=0.11.1=h14c3975_1002
• xorg-xextproto=7.3.0=h14c3975_1002
• xorg-xproto=7.0.31=h14c3975_1007
• xz=5.2.4=h14c3975_1001
• yaml=0.1.7=h14c3975_1001
• zeromq=4.3.2=he1b5a44_2
• zipp=0.5.2=py_0
• zlib=1.2.11=h516909a_1005
• zstd=1.4.0=h3b9ef0a_0
• pip:
  • bqplot==0.12.0
  • numpy==1.16.0
  • tardis-sn==3.0.dev3354
  • traittypes==0.2.1
    prefix: /home/gesa/anaconda3/envs/tardis

[manolis07gr]

Hi @chvogl, I now get a new error:

Traceback (most recent call last):
File "example.py", line 1, in
from tardis import run_tardis
File "/anaconda3/envs/tardis/lib/python3.6/site-packages/tardis_sn-3.0.dev3357-py3.6-macosx-10.9-x86_64.egg/tardis/init.py", line 11, in
from tardis.io.util import yaml_load_config_file as yaml_load
File "/anaconda3/envs/tardis/lib/python3.6/site-packages/tardis_sn-3.0.dev3357-py3.6-macosx-10.9-x86_64.egg/tardis/io/init.py", line 2, in
from tardis.io.model_reader import read_simple_ascii_density, read_simple_ascii_abundances, read_density_file
File "/anaconda3/envs/tardis/lib/python3.6/site-packages/tardis_sn-3.0.dev3357-py3.6-macosx-10.9-x86_64.egg/tardis/io/model_reader.py", line 8, in
from pyne import nucname
ImportError: cannot import name 'nucname'

[chvogl]

@manolis07gr, could you please run
from tardis.montecarlo import montecarlo, packet_source
to make sure that the numpy problem does not occur anymore.
What is the pyne version you are using?

[manolis07gr]

@chvogl - I managed to reinstall pyne and numba on my conda tardis environment and things now run smoothly for this quickstart test - thank you so much for your patience and help! I am sure I may be reaching out again soon when I try to run my own application. Thanks again.

[chvogl]

@manolis07gr, that is great. Happy to help!

[wkerzendorf]

@cradesto download the newest environment file - it should now work.