Closed nico-canta closed 1 year ago
Logfiles from GitLab pipeline #158523 (:white_check_mark:) have been uploaded here!
Status and direct links:
todo: add tox and tox-conda in the setup.py (only in the conda installation)
In tox.ini
I added some features based on tox-conda
. Since the CI is all green, I assume tox-conda is ignored when running on BB5. Is this the case?
Logfiles from GitLab pipeline #158666 (:white_check_mark:) have been uploaded here!
Status and direct links:
Can you elaborate on the issue you encounter with test_petsc_installation
? To me it looks like a conda issue, not related to tox.
Logfiles from GitLab pipeline #158877 (:white_check_mark:) have been uploaded here!
Status and direct links:
Logfiles from GitLab pipeline #158886 (:white_check_mark:) have been uploaded here!
Status and direct links:
At the moment there are two things I'm not very convinced:
tox
on bb5 doesn't work because it cannot install petsc4py using pip. EDIT: It worksEXTRA_MODULES:
unstable:gcc
unstable:hpe-mpi
unstable:petsc
unstable:py-petsc4py
but importing modules inside a virtual environment doesn't seem a great idea.
So... overall, I'm not sure we should still keep using tox
. Or maybe we could move to tox-conda and use it on bb5 and for our CI.
I wanted to discuss this in next meeting. Of course, if this is not a priority we can keep it as it is, as far as it is working fine.
@tristan0x please disregard the previous comments. I found the problem.
For some unknown reasons pass_env = *
in tox.ini
is not working (in my venv, in my local machine).
Next week I'm gonna investigate why I have this problem.
@tristan0x please disregard the previous comments. I found the problem. For some unknown reasons
pass_env = *
intox.ini
is not working (in my venv, in my local machine). Next week I'm gonna investigate why I have this problem.
I found the reason for the strange behavior. Activating a conda environment on top of another environment messes everything up.
Anyway. The error persists:
E ModuleNotFoundError: No module named 'mpi4py'
Honestly, I expected this error, since mpi4py
is not in the dependencies. But now I'm not sure I did everything the way you did. @tristan0x Can you please let me know all the steps you did?
In any case, this work will be useful because the errors that I'm experiencing right now are potential errors for the Astrovascpy users. So, I will improve the readme file.
Here is the list of conda packages I have installed:
$ conda list
# Name Version Build Channel
blosc2 2.2.9 pypi_0 pypi
boltons 23.0.0 py311hca03da5_0
brotlipy 0.7.0 py311h80987f9_1002
bzip2 1.0.8 h620ffc9_4
c-ares 1.19.0 h80987f9_0
ca-certificates 2023.08.22 hca03da5_0
cached-property 1.5.2 pypi_0 pypi
cachetools 5.3.1 pypi_0 pypi
certifi 2023.7.22 py311hca03da5_0
cffi 1.15.1 py311h80987f9_3
chardet 5.2.0 pypi_0 pypi
charset-normalizer 2.0.4 pyhd3eb1b0_0
click 8.1.7 pypi_0 pypi
colorama 0.4.6 pypi_0 pypi
conda 23.9.0 py311hca03da5_0
conda-content-trust 0.1.3 py311hca03da5_0
conda-libmamba-solver 23.7.0 pyhd8ed1ab_0 conda-forge
conda-package-handling 2.2.0 pyh38be061_0 conda-forge
conda-package-streaming 0.9.0 pyhd8ed1ab_0 conda-forge
contourpy 1.1.1 pypi_0 pypi
coverage 7.3.2 pypi_0 pypi
cryptography 39.0.1 py311h834c97f_2
cycler 0.12.0 pypi_0 pypi
cython 3.0.3 pypi_0 pypi
distlib 0.3.7 pypi_0 pypi
fftw 3.3.10 mpi_openmpi_haef8dc3_8 conda-forge
filelock 3.12.4 pypi_0 pypi
fmt 9.1.0 h48ca7d4_0
fonttools 4.43.1 pypi_0 pypi
gmp 6.2.1 h9f76cd9_0 conda-forge
h5py 3.9.0 pypi_0 pypi
hdf5 1.14.2 mpi_openmpi_ha832a9f_0 conda-forge
hypre 2.28.0 mpi_openmpi_haba3941_0 conda-forge
icu 68.1 hc377ac9_0
idna 3.4 py311hca03da5_0
iniconfig 2.0.0 pypi_0 pypi
jinja2 3.1.2 pypi_0 pypi
jsonpatch 1.32 pyhd3eb1b0_0
jsonpointer 2.1 pyhd3eb1b0_0
kiwisolver 1.4.5 pypi_0 pypi
krb5 1.20.1 hf3e1bf2_1
libaec 1.1.2 h13dd4ca_1 conda-forge
libarchive 3.6.2 h62fee54_2
libblas 3.9.0 18_osxarm64_openblas conda-forge
libcblas 3.9.0 18_osxarm64_openblas conda-forge
libcurl 8.2.1 h3e2b118_0
libcxx 16.0.6 h4653b0c_0 conda-forge
libedit 3.1.20221030 h80987f9_0
libev 4.33 h1a28f6b_1
libexpat 2.5.0 hb7217d7_1 conda-forge
libffi 3.4.4 hca03da5_0
libgfortran 5.0.0 13_2_0_hd922786_1 conda-forge
libgfortran5 13.2.0 hf226fd6_1 conda-forge
libiconv 1.16 h1a28f6b_2
liblapack 3.9.0 18_osxarm64_openblas conda-forge
libmamba 1.4.1 h1c5506f_1
libmambapy 1.4.1 py311h1c5506f_1
libnghttp2 1.52.0 h62f6fdd_1
libopenblas 0.3.24 openmp_hd76b1f2_0 conda-forge
libsolv 0.7.22 h98b2900_0
libsonata 0.1.23 pypi_0 pypi
libsqlite 3.43.0 hb31c410_0 conda-forge
libssh2 1.10.0 h02f6b3c_2
libxml2 2.10.3 h372ba2a_0
libzlib 1.2.13 h53f4e23_5 conda-forge
llvm-openmp 17.0.2 h1c12783_0 conda-forge
lz4-c 1.9.4 h313beb8_0
markupsafe 2.1.3 pypi_0 pypi
matplotlib 3.8.0 pypi_0 pypi
metis 5.1.0 h13dd4ca_1007 conda-forge
mock 5.1.0 pypi_0 pypi
morphio 3.3.6 pypi_0 pypi
mpfr 4.2.0 he09a6ba_0 conda-forge
mpi 1.0 openmpi conda-forge
mpi4py 3.1.4 py311h01356f8_1 conda-forge
msgpack 1.0.7 pypi_0 pypi
mumps-include 5.2.1 hce30654_11 conda-forge
mumps-mpi 5.2.1 h51c74a9_11 conda-forge
ncurses 6.4 h313beb8_0
ndindex 1.7 pypi_0 pypi
networkx 3.1 pypi_0 pypi
numexpr 2.8.7 pypi_0 pypi
numpy 1.26.0 py311hb8f3215_0 conda-forge
openmpi 4.1.6 h4971d84_100 conda-forge
openssl 3.1.3 h53f4e23_0 conda-forge
packaging 23.2 pypi_0 pypi
pandas 1.5.3 pypi_0 pypi
parmetis 4.0.3 h6eb5794_1005 conda-forge
pcre2 10.37 h37e8eca_1
petsc 3.20.0 real_h0603ae5_100 conda-forge
petsc4py 3.20.0 real_h01487f0_100 conda-forge
pillow 10.0.1 pypi_0 pypi
pip 23.2.1 py311hca03da5_0
platformdirs 3.11.0 pypi_0 pypi
pluggy 1.3.0 pypi_0 pypi
psutil 5.9.5 pypi_0 pypi
ptscotch 6.0.9 h1aec651_2 conda-forge
py-cpuinfo 9.0.0 pypi_0 pypi
pybind11-abi 4 hd3eb1b0_1
pycosat 0.6.4 py311h80987f9_0
pycparser 2.21 pyhd3eb1b0_0
pyopenssl 23.0.0 py311hca03da5_0
pyparsing 3.1.1 pypi_0 pypi
pyproject-api 1.6.1 pypi_0 pypi
pysocks 1.7.1 py311hca03da5_0
pytest 7.4.2 pypi_0 pypi
pytest-click 1.1.0 pypi_0 pypi
pytest-cov 4.1.0 pypi_0 pypi
pytest-html 4.0.2 pypi_0 pypi
pytest-metadata 3.0.0 pypi_0 pypi
python 3.11.5 h47c9636_0_cpython conda-forge
python-dateutil 2.8.2 pypi_0 pypi
python.app 3 py311h80987f9_0
python_abi 3.11 4_cp311 conda-forge
pytz 2023.3.post1 pypi_0 pypi
pyyaml 6.0.1 pypi_0 pypi
readline 8.2 h1a28f6b_0
reproc 14.2.4 hc377ac9_1
reproc-cpp 14.2.4 hc377ac9_1
requests 2.29.0 py311hca03da5_0
ruamel.yaml 0.17.21 py311h80987f9_0
scalapack 2.2.0 h515df86_1 conda-forge
scipy 1.11.3 pypi_0 pypi
scotch 6.0.9 h7537618_2 conda-forge
seaborn 0.13.0 pypi_0 pypi
setuptools 67.8.0 py311hca03da5_0
six 1.16.0 pyhd3eb1b0_1
sqlite 3.41.2 h80987f9_0
suitesparse 5.10.1 h7cd81ec_1 conda-forge
superlu 5.2.2 hc615359_0 conda-forge
superlu_dist 7.2.0 hfdb8677_0 conda-forge
tables 3.9.1.dev0 pypi_0 pypi
tbb 2021.10.0 h1995070_1 conda-forge
tk 8.6.12 hb8d0fd4_0
toolz 0.12.0 py311hca03da5_0
tox 4.11.3 pypi_0 pypi
tqdm 4.65.0 py311hb6e6a13_0
trimesh 3.23.5 pypi_0 pypi
truststore 0.8.0 pyhd8ed1ab_0 conda-forge
tzdata 2023c h04d1e81_0
urllib3 1.26.16 py311hca03da5_0
vascpy 0.1.1 pypi_0 pypi
virtualenv 20.24.5 pypi_0 pypi
vtk 9.2.6 pypi_0 pypi
wheel 0.38.4 py311hca03da5_0
xz 5.4.2 h80987f9_0
yaml 0.2.5 h3422bc3_2 conda-forge
yaml-cpp 0.7.0 hc377ac9_1
zlib 1.2.13 h53f4e23_5 conda-forge
zstandard 0.19.0 py311h80987f9_0
zstd 1.5.5 hd90d995_0
And the Python packages installed with pip from conda:
$ $CONDA_PREFIX/bin/pip
Package Version
----------------------- ------------
blosc2 2.2.9
boltons 23.0.0
brotlipy 0.7.0
cached-property 1.5.2
cachetools 5.3.1
certifi 2023.7.22
cffi 1.15.1
chardet 5.2.0
charset-normalizer 2.0.4
click 8.1.7
colorama 0.4.6
conda 23.9.0
conda-content-trust 0.1.3
conda-libmamba-solver 23.7.0
conda-package-handling 2.2.0
conda_package_streaming 0.9.0
contourpy 1.1.1
coverage 7.3.2
cryptography 39.0.1
cycler 0.12.0
Cython 3.0.3
distlib 0.3.7
filelock 3.12.4
fonttools 4.43.1
h5py 3.9.0
idna 3.4
iniconfig 2.0.0
Jinja2 3.1.2
jsonpatch 1.32
jsonpointer 2.1
kiwisolver 1.4.5
libmambapy 1.4.1
libsonata 0.1.23
MarkupSafe 2.1.3
matplotlib 3.8.0
mock 5.1.0
MorphIO 3.3.6
mpi4py 3.1.4
msgpack 1.0.7
ndindex 1.7
networkx 3.1
numexpr 2.8.7
numpy 1.26.0
packaging 23.2
pandas 1.5.3
petsc4py 3.20.0
Pillow 10.0.1
pip 23.2.1
platformdirs 3.11.0
pluggy 1.3.0
psutil 5.9.5
py-cpuinfo 9.0.0
pycosat 0.6.4
pycparser 2.21
pyOpenSSL 23.0.0
pyparsing 3.1.1
pyproject-api 1.6.1
PySocks 1.7.1
pytest 7.4.2
pytest-click 1.1.0
pytest-cov 4.1.0
pytest-html 4.0.2
pytest-metadata 3.0.0
python-dateutil 2.8.2
pytz 2023.3.post1
PyYAML 6.0.1
requests 2.29.0
ruamel.yaml 0.17.21
scipy 1.11.3
seaborn 0.13.0
setuptools 67.8.0
six 1.16.0
tables 3.9.1.dev0
toolz 0.12.0
tox 4.11.3
tqdm 4.65.0
trimesh 3.23.5
truststore 0.8.0
urllib3 1.26.16
vascpy 0.1.1
virtualenv 20.24.5
vtk 9.2.6
wheel 0.38.4
zstandard 0.19.0
A way to force tox
to see the conda Python packages is to force the PYTHONPATH
environment variable.
For instance, you can execute in your shell the output of the following command:
$CONDA_PREFIX/bin/python3 -c "import sys; print('export PYTHONPATH={}'.format(';'.join(sys.path)))"
then, you may clean the previous tox environments (rm -rf .tox
), and run tox
again
Logfiles from GitLab pipeline #159423 (:white_check_mark:) have been uploaded here!
Status and direct links:
Logfiles from GitLab pipeline #159435 (:white_check_mark:) have been uploaded here!
Status and direct links:
Logfiles from GitLab pipeline #159444 (:no_entry:) have been uploaded here!
Status and direct links:
Logfiles from GitLab pipeline #159473 (:white_check_mark:) have been uploaded here!
Status and direct links:
Logfiles from GitLab pipeline #159476 (:white_check_mark:) have been uploaded here!
Status and direct links:
I tried to run tox locally. Since locally the venv is managed by anaconda, I used tox-conda. The following two tests failed:
With this PR we are solving these 2 errors.
Interesting question:
Why within the same tox environment, solve_linear calculates 2 different results?