healpy/pixelfunc.py:654: RuntimeWarning: invalid value encountered in _vec2pix_nest

[mschwamb]

sorcha) mes@bourbon:~/python/sorcha/demo$ sorcha -c PPConfig_test.ini -p sspp_testset_colours.txt -ob sspp_testset_orbits.des -e example_output.csv -pd baseline_v2.0_1yr.db -o ./ -t testrun_e2e -f /home/mes/mambaforge/envs/sorcha/lib/python3.10/site-packages/healpy/pixelfunc.py:654: RuntimeWarning: invalid value encountered in _vec2pix_nest return pixlib._vec2pix_nest(nside, x, y, z)

I've tried to give details about the install and system

DISTRIB_ID=Ubuntu DISTRIB_RELEASE=22.04 DISTRIB_CODENAME=jammy DISTRIB_DESCRIPTION="Ubuntu 22.04.3 LTS" PRETTY_NAME="Ubuntu 22.04.3 LTS" NAME="Ubuntu" VERSION_ID="22.04" VERSION="22.04.3 LTS (Jammy Jellyfish)" VERSION_CODENAME=jammy ID=ubuntu ID_LIKE=debian HOME_URL="https://www.ubuntu.com/" SUPPORT_URL="https://help.ubuntu.com/" BUG_REPORT_URL="https://bugs.launchpad.net/ubuntu/" PRIVACY_POLICY_URL="https://www.ubuntu.com/legal/terms-and-policies/privacy-policy" UBUNTU_CODENAME=jammy

#

Name Version Build Channel

_libgcc_mutex 0.1 conda_forge conda-forge _openmp_mutex 4.5 2_gnu conda-forge ads 0.12.3 py_2 conda-forge affine 2.4.0 pyhd8ed1ab_0 conda-forge alabaster 0.7.13 pypi_0 pypi alsa-lib 1.2.9 hd590300_0 conda-forge aom 3.5.0 h27087fc_0 conda-forge asdf 2.15.1 pyhd8ed1ab_0 conda-forge asdf-astropy 0.4.0 pyhd8ed1ab_1 conda-forge asdf-coordinates-schemas 0.2.0 pyhd8ed1ab_1 conda-forge asdf-standard 1.0.3 pyhd8ed1ab_0 conda-forge asdf-transform-schemas 0.3.0 pyhd8ed1ab_0 conda-forge asdf-unit-schemas 0.1.0 pyhd8ed1ab_0 conda-forge asdf-wcs-schemas 0.1.1 pyhd8ed1ab_0 conda-forge assist 1.1.3 pypi_0 pypi astroid 2.15.6 pypi_0 pypi astropy 5.3.3 py310h1f7b6fc_0 conda-forge astroquery 0.4.6 pyhd8ed1ab_0 conda-forge asttokens 2.4.0 pypi_0 pypi attr 2.5.1 h166bdaf_1 conda-forge attrs 23.1.0 pyh71513ae_1 conda-forge babel 2.12.1 pypi_0 pypi backcall 0.2.0 pypi_0 pypi beautifulsoup4 4.12.2 pyha770c72_0 conda-forge black 23.9.1 pypi_0 pypi bleach 6.0.0 pypi_0 pypi blosc 1.21.5 h0f2a231_0 conda-forge boost-cpp 1.78.0 h6582d0a_3 conda-forge bottleneck 1.3.7 py310h0a54255_0 conda-forge brotli 1.1.0 hd590300_0 conda-forge brotli-bin 1.1.0 hd590300_0 conda-forge brotli-python 1.1.0 py310hc6cd4ac_0 conda-forge brunsli 0.1 h9c3ff4c_0 conda-forge bzip2 1.0.8 h7f98852_4 conda-forge c-ares 1.19.1 hd590300_0 conda-forge c-blosc2 2.10.2 hb4ffafa_0 conda-forge ca-certificates 2023.7.22 hbcca054_0 conda-forge cached-property 1.5.2 hd8ed1ab_1 conda-forge cached_property 1.5.2 pyha770c72_1 conda-forge cairo 1.16.0 hbbf8b49_1016 conda-forge certifi 2023.7.22 pyhd8ed1ab_0 conda-forge cffi 1.15.1 py310h255011f_3 conda-forge cfgv 3.3.1 pyhd8ed1ab_0 conda-forge cfitsio 4.3.0 hbdc6101_0 conda-forge charls 2.4.2 h59595ed_0 conda-forge charset-normalizer 3.2.0 pyhd8ed1ab_0 conda-forge click 8.1.7 unix_pyh707e725_0 conda-forge click-plugins 1.1.1 py_0 conda-forge cligj 0.7.2 pyhd8ed1ab_1 conda-forge colorama 0.4.6 pyhd8ed1ab_0 conda-forge comm 0.1.4 pypi_0 pypi contourpy 1.1.0 py310hd41b1e2_0 conda-forge coverage 7.3.1 py310h2372a71_0 conda-forge cryptography 41.0.3 py310h75e40e8_0 conda-forge cspice 67 h166bdaf_4 conda-forge cycler 0.11.0 pyhd8ed1ab_0 conda-forge dav1d 1.2.1 hd590300_0 conda-forge dbus 1.13.6 h5008d03_3 conda-forge debugpy 1.7.0 pypi_0 pypi decorator 5.1.1 pypi_0 pypi defusedxml 0.7.1 pypi_0 pypi difi 1.2rc3 py_0 moeyensj distlib 0.3.7 pyhd8ed1ab_0 conda-forge docutils 0.18.1 pypi_0 pypi exceptiongroup 1.1.3 pyhd8ed1ab_0 conda-forge executing 1.2.0 pypi_0 pypi expat 2.5.0 hcb278e6_1 conda-forge fastjsonschema 2.18.0 pypi_0 pypi filelock 3.12.3 pyhd8ed1ab_0 conda-forge font-ttf-dejavu-sans-mono 2.37 hab24e00_0 conda-forge font-ttf-inconsolata 3.000 h77eed37_0 conda-forge font-ttf-source-code-pro 2.038 h77eed37_0 conda-forge font-ttf-ubuntu 0.83 hab24e00_0 conda-forge fontconfig 2.14.2 h14ed4e7_0 conda-forge fonts-conda-ecosystem 1 0 conda-forge fonts-conda-forge 1 0 conda-forge fonttools 4.42.1 py310h2372a71_0 conda-forge freetype 2.12.1 hca18f0e_1 conda-forge freexl 1.0.6 h166bdaf_1 conda-forge geos 3.12.0 h59595ed_0 conda-forge geotiff 1.7.1 h22adcc9_11 conda-forge gettext 0.21.1 h27087fc_0 conda-forge giflib 5.2.1 h0b41bf4_3 conda-forge ginga 4.1.0 pyhd8ed1ab_0 conda-forge glib 2.78.0 hfc55251_0 conda-forge glib-tools 2.78.0 hfc55251_0 conda-forge graphite2 1.3.13 h58526e2_1001 conda-forge gst-plugins-base 1.22.5 hf7dbed1_0 conda-forge gstreamer 1.22.5 h98fc4e7_0 conda-forge gtest 1.14.0 h00ab1b0_1 conda-forge gwcs 0.18.3 pyhd8ed1ab_0 conda-forge h5py 3.9.0 nompi_py310ha2ad45a_102 conda-forge harfbuzz 7.3.0 hdb3a94d_0 conda-forge hdf4 4.2.15 h501b40f_6 conda-forge hdf5 1.14.2 nompi_h4f84152_100 conda-forge healpy 1.16.5 py310h09b46ba_1 conda-forge html5lib 1.1 pyh9f0ad1d_0 conda-forge icu 72.1 hcb278e6_0 conda-forge identify 2.5.27 pyhd8ed1ab_0 conda-forge idna 3.4 pyhd8ed1ab_0 conda-forge imagecodecs 2023.9.4 py310hedc1555_0 conda-forge imageio 2.31.1 pyh24c5eb1_0 conda-forge imagesize 1.4.1 pypi_0 pypi importlib-metadata 6.8.0 pyha770c72_0 conda-forge importlib-resources 6.0.1 pyhd8ed1ab_0 conda-forge importlib_metadata 6.8.0 hd8ed1ab_0 conda-forge importlib_resources 6.0.1 pyhd8ed1ab_0 conda-forge iniconfig 2.0.0 pyhd8ed1ab_0 conda-forge ipykernel 6.25.2 pypi_0 pypi ipython 8.15.0 pypi_0 pypi jaraco.classes 3.3.0 pyhd8ed1ab_0 conda-forge jedi 0.19.0 pypi_0 pypi jeepney 0.8.0 pyhd8ed1ab_0 conda-forge jinja2 3.1.2 pypi_0 pypi jmespath 1.0.1 pyhd8ed1ab_0 conda-forge joblib 1.3.2 pyhd8ed1ab_0 conda-forge json-c 0.17 h7ab15ed_0 conda-forge jsonschema 4.19.0 pyhd8ed1ab_1 conda-forge jsonschema-specifications 2023.7.1 pyhd8ed1ab_0 conda-forge jupyter-client 8.3.1 pypi_0 pypi jupyter-core 5.3.1 pypi_0 pypi jupyterlab-pygments 0.2.2 pypi_0 pypi jxrlib 1.1 h7f98852_2 conda-forge kealib 1.5.1 hcd42e92_5 conda-forge keyring 24.2.0 py310hff52083_0 conda-forge keyutils 1.6.1 h166bdaf_0 conda-forge kiwisolver 1.4.5 py310hd41b1e2_0 conda-forge krb5 1.21.2 h659d440_0 conda-forge lame 3.100 h166bdaf_1003 conda-forge lazy-object-proxy 1.9.0 pypi_0 pypi lazy_loader 0.3 pyhd8ed1ab_0 conda-forge lcms2 2.15 haa2dc70_1 conda-forge ld_impl_linux-64 2.40 h41732ed_0 conda-forge lerc 4.0.0 h27087fc_0 conda-forge libabseil 20230802.0 cxx17_h59595ed_3 conda-forge libaec 1.0.6 hcb278e6_1 conda-forge libarchive 3.6.2 h039dbb9_1 conda-forge libavif16 1.0.1 h014f275_1 conda-forge libblas 3.9.0 18_linux64_openblas conda-forge libbrotlicommon 1.1.0 hd590300_0 conda-forge libbrotlidec 1.1.0 hd590300_0 conda-forge libbrotlienc 1.1.0 hd590300_0 conda-forge libcap 2.69 h0f662aa_0 conda-forge libcblas 3.9.0 18_linux64_openblas conda-forge libclang 15.0.7 default_h7634d5b_3 conda-forge libclang13 15.0.7 default_h9986a30_3 conda-forge libcrc32c 1.1.2 h9c3ff4c_0 conda-forge libcups 2.3.3 h4637d8d_4 conda-forge libcurl 8.2.1 hca28451_0 conda-forge libdeflate 1.18 h0b41bf4_0 conda-forge libedit 3.1.20191231 he28a2e2_2 conda-forge libev 4.33 h516909a_1 conda-forge libevent 2.1.12 hf998b51_1 conda-forge libexpat 2.5.0 hcb278e6_1 conda-forge libffi 3.4.2 h7f98852_5 conda-forge libflac 1.4.3 h59595ed_0 conda-forge libgcc-ng 13.2.0 h807b86a_0 conda-forge libgcrypt 1.10.1 h166bdaf_0 conda-forge libgdal 3.7.1 h3d2b3c2_7 conda-forge libgfortran-ng 13.2.0 h69a702a_0 conda-forge libgfortran5 13.2.0 ha4646dd_0 conda-forge libglib 2.78.0 hebfc3b9_0 conda-forge libgomp 13.2.0 h807b86a_0 conda-forge libgoogle-cloud 2.12.0 h8d7e28b_2 conda-forge libgpg-error 1.47 h71f35ed_0 conda-forge libgrpc 1.57.0 ha4d0f93_1 conda-forge libiconv 1.17 h166bdaf_0 conda-forge libjpeg-turbo 2.1.5.1 h0b41bf4_0 conda-forge libkml 1.3.0 h37653c0_1015 conda-forge liblapack 3.9.0 18_linux64_openblas conda-forge libllvm14 14.0.6 hcd5def8_4 conda-forge libllvm15 15.0.7 h5cf9203_3 conda-forge libnetcdf 4.9.2 nompi_h80fb2b6_112 conda-forge libnghttp2 1.52.0 h61bc06f_0 conda-forge libnsl 2.0.0 h7f98852_0 conda-forge libogg 1.3.4 h7f98852_1 conda-forge libopenblas 0.3.24 pthreads_h413a1c8_0 conda-forge libopus 1.3.1 h7f98852_1 conda-forge libpng 1.6.39 h753d276_0 conda-forge libpq 15.4 hfc447b1_0 conda-forge libprotobuf 4.23.4 hf27288f_5 conda-forge librttopo 1.1.0 hb58d41b_14 conda-forge libsndfile 1.2.2 hbc2eb40_0 conda-forge libspatialite 5.0.1 h15f6e67_28 conda-forge libsqlite 3.43.0 h2797004_0 conda-forge libssh2 1.11.0 h0841786_0 conda-forge libstdcxx-ng 13.2.0 h7e041cc_0 conda-forge libsystemd0 254 h3516f8a_0 conda-forge libtiff 4.5.1 h8b53f26_1 conda-forge libuuid 2.38.1 h0b41bf4_0 conda-forge libvorbis 1.3.7 h9c3ff4c_0 conda-forge libwebp-base 1.3.1 hd590300_0 conda-forge libxcb 1.15 h0b41bf4_0 conda-forge libxkbcommon 1.5.0 h5d7e998_3 conda-forge libxml2 2.11.5 h0d562d8_0 conda-forge libzip 1.10.1 h2629f0a_3 conda-forge libzlib 1.2.13 hd590300_5 conda-forge libzopfli 1.0.3 h9c3ff4c_0 conda-forge llvmlite 0.40.1 py310h1b8f574_0 conda-forge lz4-c 1.9.4 hcb278e6_0 conda-forge lzo 2.10 h516909a_1000 conda-forge markupsafe 2.1.3 py310h2372a71_0 conda-forge matplotlib 3.7.2 py310hff52083_0 conda-forge matplotlib-base 3.7.2 py310hf38f957_0 conda-forge matplotlib-inline 0.1.6 pypi_0 pypi mistune 3.0.1 pypi_0 pypi mock 5.1.0 pyhd8ed1ab_0 conda-forge more-itertools 10.1.0 pyhd8ed1ab_0 conda-forge mpg123 1.31.3 hcb278e6_0 conda-forge munkres 1.1.4 pyh9f0ad1d_0 conda-forge mypy-extensions 1.0.0 pypi_0 pypi mysql-common 8.0.33 hf1915f5_4 conda-forge mysql-libs 8.0.33 hca2cd23_4 conda-forge nbclient 0.8.0 pypi_0 pypi nbconvert 7.8.0 pypi_0 pypi nbformat 5.9.2 pypi_0 pypi nbsphinx 0.9.3 pypi_0 pypi ncurses 6.4 hcb278e6_0 conda-forge nest-asyncio 1.5.7 pypi_0 pypi networkx 3.1 pyhd8ed1ab_0 conda-forge nodeenv 1.8.0 pyhd8ed1ab_0 conda-forge nomkl 1.0 h5ca1d4c_0 conda-forge nspr 4.35 h27087fc_0 conda-forge nss 3.92 h1d7d5a4_0 conda-forge numba 0.57.1 py310h0f6aa51_0 conda-forge numexpr 2.8.4 py310hd91493a_101 conda-forge numpy 1.24.3 pypi_0 pypi openjpeg 2.5.0 hfec8fc6_2 conda-forge openssl 3.1.2 hd590300_0 conda-forge packaging 23.1 pyhd8ed1ab_0 conda-forge pandas 2.0.3 pypi_0 pypi pandocfilters 1.5.0 pypi_0 pypi parso 0.8.3 pypi_0 pypi pathspec 0.11.2 pypi_0 pypi pcre2 10.40 hc3806b6_0 conda-forge pexpect 4.8.0 pypi_0 pypi photutils 1.9.0 py310h2372a71_0 conda-forge pickleshare 0.7.5 pypi_0 pypi pillow 10.0.0 py310h582fbeb_0 conda-forge pip 23.2.1 pyhd8ed1ab_0 conda-forge pixman 0.40.0 h36c2ea0_0 conda-forge pkgutil-resolve-name 1.3.10 pyhd8ed1ab_0 conda-forge platformdirs 3.10.0 pyhd8ed1ab_0 conda-forge pluggy 1.3.0 pyhd8ed1ab_0 conda-forge ply 3.11 py_1 conda-forge pooch 1.7.0 pyha770c72_3 conda-forge poppler 23.08.0 hd18248d_0 conda-forge poppler-data 0.4.12 hd8ed1ab_0 conda-forge postgresql 15.4 h8972f4a_0 conda-forge pre-commit 3.4.0 pyha770c72_0 conda-forge proj 9.2.1 ha643af7_0 conda-forge prompt-toolkit 3.0.39 pypi_0 pypi psutil 5.9.5 pypi_0 pypi pthread-stubs 0.4 h36c2ea0_1001 conda-forge ptyprocess 0.7.0 pypi_0 pypi pulseaudio-client 16.1 hb77b528_5 conda-forge pure-eval 0.2.2 pypi_0 pypi py-cpuinfo 9.0.0 pyhd8ed1ab_0 conda-forge pycparser 2.21 pyhd8ed1ab_0 conda-forge pyerfa 2.0.0.3 py310h278f3c1_0 conda-forge pygments 2.16.1 pypi_0 pypi pyparsing 3.0.9 pyhd8ed1ab_0 conda-forge pyqt 5.15.9 py310h04931ad_4 conda-forge pyqt5-sip 12.12.2 py310hc6cd4ac_4 conda-forge pysocks 1.7.1 pyha2e5f31_6 conda-forge pytables 3.8.0 py310h374b01c_3 conda-forge pytest 7.4.2 pyhd8ed1ab_0 conda-forge pytest-benchmark 4.0.0 pyhd8ed1ab_0 conda-forge pytest-cov 4.1.0 pyhd8ed1ab_0 conda-forge pytest-runner 6.0.0 pyhd8ed1ab_0 conda-forge python 3.10.12 hd12c33a_0_cpython conda-forge python-dateutil 2.8.2 pyhd8ed1ab_0 conda-forge python-tzdata 2023.3 pyhd8ed1ab_0 conda-forge python_abi 3.10 3_cp310 conda-forge pytz 2023.3.post1 pyhd8ed1ab_0 conda-forge pyvo 1.4.2 pyhd8ed1ab_0 conda-forge pywavelets 1.4.1 py310h0a54255_0 conda-forge pyyaml 6.0.1 py310h2372a71_0 conda-forge pyzmq 25.1.1 pypi_0 pypi qt-main 5.15.8 h7fe3ca9_15 conda-forge qtpy 2.4.0 pyhd8ed1ab_0 conda-forge rasterio 1.3.8 py310hd227816_0 conda-forge rav1e 0.6.6 he8a937b_2 conda-forge re2 2023.03.02 h8c504da_0 conda-forge readline 8.2 h8228510_1 conda-forge rebound 3.26.3 py310h2372a71_1 conda-forge referencing 0.30.2 pyhd8ed1ab_0 conda-forge requests 2.31.0 pyhd8ed1ab_0 conda-forge rpds-py 0.10.2 py310hcb5633a_0 conda-forge sbpy 0.3.0 pyhd8ed1ab_0 conda-forge scikit-image 0.21.0 py310hc6cd4ac_0 conda-forge scikit-learn 1.3.0 py310hf7d194e_0 conda-forge scipy 1.11.2 py310ha4c1d20_0 conda-forge secretstorage 3.3.3 py310hff52083_1 conda-forge semantic_version 2.10.0 pyhd8ed1ab_0 conda-forge setuptools 68.1.2 pyhd8ed1ab_0 conda-forge shapely 2.0.1 py310h7dcad9a_2 conda-forge sip 6.7.11 py310hc6cd4ac_0 conda-forge six 1.16.0 pyh6c4a22f_0 conda-forge snappy 1.1.10 h9fff704_0 conda-forge snowballstemmer 2.2.0 pypi_0 pypi snuggs 1.4.7 py_0 conda-forge sorcha 0.5.2.dev34+g8fc7e9e pypi_0 pypi soupsieve 2.5 pyhd8ed1ab_1 conda-forge sphinx 6.1.3 pypi_0 pypi sphinx-autoapi 2.0.1 pypi_0 pypi sphinx-rtd-theme 1.2.0 pypi_0 pypi sphinxcontrib-applehelp 1.0.7 pypi_0 pypi sphinxcontrib-devhelp 1.0.5 pypi_0 pypi sphinxcontrib-htmlhelp 2.0.4 pypi_0 pypi sphinxcontrib-jquery 4.1 pypi_0 pypi sphinxcontrib-jsmath 1.0.1 pypi_0 pypi sphinxcontrib-qthelp 1.0.6 pypi_0 pypi sphinxcontrib-serializinghtml 1.1.9 pypi_0 pypi spiceypy 6.0.0 pyhd8ed1ab_0 conda-forge sqlite 3.43.0 h2c6b66d_0 conda-forge stack-data 0.6.2 pypi_0 pypi svt-av1 1.7.0 h59595ed_0 conda-forge synphot 1.2.1 py310h278f3c1_1 conda-forge threadpoolctl 3.2.0 pyha21a80b_0 conda-forge tifffile 2023.8.30 pyhd8ed1ab_0 conda-forge tiledb 2.16.3 h84d19f0_1 conda-forge tinycss2 1.2.1 pypi_0 pypi tk 8.6.12 h27826a3_0 conda-forge toml 0.10.2 pyhd8ed1ab_0 conda-forge tomli 2.0.1 pyhd8ed1ab_0 conda-forge tornado 6.3.3 py310h2372a71_0 conda-forge tqdm 4.66.1 pyhd8ed1ab_0 conda-forge traitlets 5.9.0 pypi_0 pypi typing-extensions 4.7.1 hd8ed1ab_0 conda-forge typing_extensions 4.7.1 pyha770c72_0 conda-forge tzcode 2023c h0b41bf4_0 conda-forge tzdata 2023c h71feb2d_0 conda-forge ukkonen 1.0.1 py310hbf28c38_3 conda-forge unicodedata2 15.0.0 py310h5764c6d_0 conda-forge unidecode 1.3.6 pypi_0 pypi urllib3 2.0.4 pyhd8ed1ab_0 conda-forge virtualenv 20.24.4 pyhd8ed1ab_0 conda-forge wcwidth 0.2.6 pypi_0 pypi webencodings 0.5.1 py_1 conda-forge werkzeug 2.3.7 pyhd8ed1ab_0 conda-forge wheel 0.41.2 pyhd8ed1ab_0 conda-forge wrapt 1.15.0 pypi_0 pypi xcb-util 0.4.0 hd590300_1 conda-forge xcb-util-image 0.4.0 h8ee46fc_1 conda-forge xcb-util-keysyms 0.4.0 h8ee46fc_1 conda-forge xcb-util-renderutil 0.3.9 hd590300_1 conda-forge xcb-util-wm 0.4.1 h8ee46fc_1 conda-forge xerces-c 3.2.4 h8d71039_2 conda-forge xkeyboard-config 2.39 hd590300_0 conda-forge xorg-kbproto 1.0.7 h7f98852_1002 conda-forge xorg-libice 1.1.1 hd590300_0 conda-forge xorg-libsm 1.2.4 h7391055_0 conda-forge xorg-libx11 1.8.6 h8ee46fc_0 conda-forge xorg-libxau 1.0.11 hd590300_0 conda-forge xorg-libxdmcp 1.1.3 h7f98852_0 conda-forge xorg-libxext 1.3.4 h0b41bf4_2 conda-forge xorg-libxrender 0.9.11 hd590300_0 conda-forge xorg-renderproto 0.11.1 h7f98852_1002 conda-forge xorg-xextproto 7.3.0 h0b41bf4_1003 conda-forge xorg-xf86vidmodeproto 2.3.1 h7f98852_1002 conda-forge xorg-xproto 7.0.31 h7f98852_1007 conda-forge xz 5.2.6 h166bdaf_0 conda-forge yaml 0.2.5 h7f98852_2 conda-forge zfp 1.0.0 h27087fc_3 conda-forge zipp 3.16.2 pyhd8ed1ab_0 conda-forge zlib 1.2.13 hd590300_5 conda-forge zlib-ng 2.0.7 h0b41bf4_0 conda-forge zstd 1.5.5 hfc55251_0 conda-forge

what pip thinks is installed

(sorcha) mes@bourbon:~/python/sorcha/demo$ pip list Package Version Editable project location

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ads 0.12.3 affine 2.4.0 alabaster 0.7.13 asdf 2.15.1 asdf-astropy 0.4.0 asdf-coordinates-schemas 0.2.0 asdf-standard 1.0.3 asdf-transform-schemas 0.3.0 asdf-unit-schemas 0.1.0 asdf-wcs-schemas 0.1.1 assist 1.1.3 astroid 2.15.6 astropy 5.3.3 astroquery 0.4.6 asttokens 2.4.0 attrs 23.1.0 Babel 2.12.1 backcall 0.2.0 beautifulsoup4 4.12.2 black 23.9.1 bleach 6.0.0 Bottleneck 1.3.7 Brotli 1.1.0 cached-property 1.5.2 certifi 2023.7.22 cffi 1.15.1 cfgv 3.3.1 charset-normalizer 3.2.0 click 8.1.7 click-plugins 1.1.1 cligj 0.7.2 colorama 0.4.6 comm 0.1.4 contourpy 1.1.0 coverage 7.3.1 cryptography 41.0.3 cycler 0.11.0 debugpy 1.7.0 decorator 5.1.1 defusedxml 0.7.1 difi 1.2rc3 distlib 0.3.7 docutils 0.18.1 exceptiongroup 1.1.3 executing 1.2.0 fastjsonschema 2.18.0 filelock 3.12.3 fonttools 4.42.1 ginga 4.1.0 gwcs 0.18.3 h5py 3.9.0 healpy 0.0.0 html5lib 1.1 identify 2.5.27 idna 3.4 imagecodecs 2023.9.4 imageio 2.31.1 imagesize 1.4.1 importlib-metadata 6.8.0 importlib-resources 6.0.1 iniconfig 2.0.0 ipykernel 6.25.2 ipython 8.15.0 jaraco.classes 3.3.0 jedi 0.19.0 jeepney 0.8.0 Jinja2 3.1.2 jmespath 1.0.1 joblib 1.3.2 jsonschema 4.19.0 jsonschema-specifications 2023.7.1 jupyter_client 8.3.1 jupyter_core 5.3.1 jupyterlab-pygments 0.2.2 keyring 24.2.0 kiwisolver 1.4.5 lazy_loader 0.3 lazy-object-proxy 1.9.0 llvmlite 0.40.1 MarkupSafe 2.1.3 matplotlib 3.7.2 matplotlib-inline 0.1.6 mistune 3.0.1 mock 5.1.0 more-itertools 10.1.0 munkres 1.1.4 mypy-extensions 1.0.0 nbclient 0.8.0 nbconvert 7.8.0 nbformat 5.9.2 nbsphinx 0.9.3 nest-asyncio 1.5.7 networkx 3.1 nodeenv 1.8.0 numba 0.57.1 numexpr 2.8.4 numpy 1.24.3 packaging 23.1 pandas 2.0.3 pandocfilters 1.5.0 parso 0.8.3 pathspec 0.11.2 pexpect 4.8.0 photutils 1.9.0 pickleshare 0.7.5 Pillow 10.0.0 pip 23.2.1 pkgutil_resolve_name 1.3.10 platformdirs 3.10.0 pluggy 1.3.0 ply 3.11 pooch 1.7.0 pre-commit 3.4.0 prompt-toolkit 3.0.39 psutil 5.9.5 ptyprocess 0.7.0 pure-eval 0.2.2 py-cpuinfo 9.0.0 pycparser 2.21 pyerfa 2.0.0.3 Pygments 2.16.1 pyparsing 3.0.9 PyQt5 5.15.9 PyQt5-sip 12.12.2 PySocks 1.7.1 pytest 7.4.2 pytest-benchmark 4.0.0 pytest-cov 4.1.0 pytest-runner 6.0.0 python-dateutil 2.8.2 pytz 2023.3.post1 pyvo 1.4.2 PyWavelets 1.4.1 PyYAML 6.0.1 pyzmq 25.1.1 QtPy 2.4.0 rasterio 1.3.8 rebound 3.26.3 referencing 0.30.2 requests 2.31.0 rpds-py 0.10.2 sbpy 0.3.0 scikit-image 0.21.0 scikit-learn 1.3.0 scipy 1.11.2 SecretStorage 3.3.3 semantic-version 2.10.0 setuptools 68.1.2 shapely 2.0.1 sip 6.7.11 six 1.16.0 snowballstemmer 2.2.0 snuggs 1.4.7 sorcha 0.5.2.dev34+g8fc7e9e /home/mes/python/sorcha soupsieve 2.5 Sphinx 6.1.3 sphinx-autoapi 2.0.1 sphinx-rtd-theme 1.2.0 sphinxcontrib-applehelp 1.0.7 sphinxcontrib-devhelp 1.0.5 sphinxcontrib-htmlhelp 2.0.4 sphinxcontrib-jquery 4.1 sphinxcontrib-jsmath 1.0.1 sphinxcontrib-qthelp 1.0.6 sphinxcontrib-serializinghtml 1.1.9 spiceypy 6.0.0 stack-data 0.6.2 synphot 1.2.1 tables 3.8.0 threadpoolctl 3.2.0 tifffile 2023.8.30 tinycss2 1.2.1 toml 0.10.2 tomli 2.0.1 tornado 6.3.3 tqdm 4.66.1 traitlets 5.9.0 typing_extensions 4.7.1 tzdata 2023.3 ukkonen 1.0.1 unicodedata2 15.0.0 Unidecode 1.3.6 urllib3 2.0.4 virtualenv 20.24.4 wcwidth 0.2.6 webencodings 0.5.1 Werkzeug 2.3.7 wheel 0.41.2 wrapt 1.15.0 zipp 3.16.2

[mschwamb]

I get a seg fault after a few of these warnings are printed to the screen

[matthewholman]

Is there any way for you to capture the arguments to pixlib._vec2pix_nest(nside, x, y, z)?
nside needs to be a power of 2.
I think that x, y, z need to be the components of a unit vector, but I'm not 100% sure.

[mschwamb]

probably, but I don't have the bandwidth tonight to do that to debug. I need to work on teaching stuff/prep.

[matthewholman]

No worries.

[mschwamb]

Hopefully this is something that someone else can take a look at later this week.

[matthewholman]

I checked the healpy.vec2pix function, which calls the underlying c/c++ library. The vector doesn't need to be normalized, but if I call the function with, say, nside=31 rather than nside=32 the kernel dies.

[mschwamb]

Found some time during telecons to put some print statements.

I've got some nans and 000s going into the hp.vec2pix

I'm printing out 64 0.0 0.0 0.0 64 -0.6658602182641752 -0.684449965364213 -0.29691482725878254 64 -0.6525706700492232 -0.6951399317794088 -0.3015493257117757 64 -0.6525706700492232 -0.6951399317794088 -0.3015493257117757 64 -0.6525706700492232 -0.6951399317794088 -0.3015493257117757 64 -0.6525706700492232 -0.6951399317794088 -0.3015493257117757 64 nan nan nan 64 -0.6525706700492232 -0.6951399317794088 -0.3015493257117757 64 -0.6525706700492232 -0.6951399317794088 -0.3015493257117757 64 -0.6525706700492232 -0.6951399317794088 -0.3015493257117757 64 0.0 0.0 0.0

print(nside, rho_hat[0], rho_hat[1], rho_hat[2])

[mschwamb]

I get no nans or zeros being printed out on mac for the same sample test set.

[mschwamb]

But that's not the whole issue. If I take the first object in the demo file, I don't get nans or zero at least from healpy.vec2pix input but I still get a segfault

[matthewholman]

Where in the code are you getting the segfault?

On Tue, Sep 12, 2023 at 8:59 AM Meg Schwamb @.***> wrote:

But that's not the whole issue. If I take the first object in the demo file, I don't get nans or zero at least from healpy.vec2pix input but I still get a segfault

— Reply to this email directly, view it on GitHub https://github.com/dirac-institute/sorcha/issues/618#issuecomment-1715678741, or unsubscribe https://github.com/notifications/unsubscribe-auth/AA5CVWNWIV5CCAPSQEGAVW3X2BMDHANCNFSM6AAAAAA4TZ3ZXU . You are receiving this because you commented.Message ID: @.***>

-- Matthew J. Holman, PhD Senior Astrophysicist Center for Astrophysics | Harvard & Smithsonian 60 Garden Street, MS #51 Cambridge, MA 02138 (617) 496-7775

[mschwamb]

I'm not sure. I don't know how to use a debugger in python with a program of this complexity. So I need some guidance/help pair coding

[mschwamb]

I've figured out how to get pdb running I'll see where I get to

[mschwamb]

Not sure if this helpful but I've gotten with faulthandler

sorcha -c PPConfig_test.ini -p params.txt -ob orbits.txt -e ephemeris_output.csv -pd baseline_v2.0_1yr.db -o ./ -t testrun_e2e -f Fatal Python error: Segmentation fault

Current thread 0x00007f04788ae740 (most recent call first): File "/home/mes/mambaforge/envs/sorcha/lib/python3.10/site-packages/rebound/simulation.py", line 1040 in del File "/home/mes/python/sorcha/src/sorcha/sorcha.py", line 74 in runLSSTSimulation File "/home/mes/python/sorcha/src/sorcha/sorcha.py", line 48 in runAll File "/home/mes/python/sorcha/src/sorcha/sorcha.py", line 464 in main File "/home/mes/mambaforge/envs/sorcha/bin/sorcha", line 8 in

Extension modules: numpy.core._multiarray_umath, numpy.core._multiarray_tests, numpy.linalg._umath_linalg, numpy.fft._pocketfft_internal, numpy.random._common, numpy.random.bit_generator, numpy.random._bounded_integers, numpy.random._mt19937, numpy.random.mtrand, numpy.random._philox, numpy.random._pcg64, numpy.random._sfc64, numpy.random._generator, erfa.ufunc, scipy._lib._ccallback_c, scipy.special._ufuncs_cxx, scipy.special._ufuncs, scipy.special._specfun, scipy.special._comb, scipy.linalg._fblas, scipy.linalg._flapack, scipy.linalg.cython_lapack, scipy.linalg._cythonized_array_utils, scipy.linalg._solve_toeplitz, scipy.linalg._decomp_lu_cython, scipy.linalg._matfuncs_sqrtm_triu, scipy.linalg.cython_blas, scipy.linalg._matfuncs_expm, scipy.linalg._decomp_update, scipy.sparse._sparsetools, _csparsetools, scipy.sparse._csparsetools, scipy.sparse.linalg._isolve._iterative, scipy.sparse.linalg._dsolve._superlu, scipy.sparse.linalg._eigen.arpack._arpack, scipy.sparse.csgraph._tools, scipy.sparse.csgraph._shortest_path, scipy.sparse.csgraph._traversal, scipy.sparse.csgraph._min_spanning_tree, scipy.sparse.csgraph._flow, scipy.sparse.csgraph._matching, scipy.sparse.csgraph._reordering, scipy.linalg._flinalg, scipy.special._ellip_harm_2, scipy.integrate._odepack, scipy.integrate._quadpack, scipy.integrate._vode, scipy.integrate._dop, scipy.integrate._lsoda, scipy.optimize._minpack2, scipy.optimize._group_columns, scipy._lib.messagestream, scipy.optimize._trlib._trlib, numpy.linalg.lapack_lite, scipy.optimize._lbfgsb, _moduleTNC, scipy.optimize._moduleTNC, scipy.optimize._cobyla, scipy.optimize._slsqp, scipy.optimize._minpack, scipy.optimize._lsq.givens_elimination, scipy.optimize._zeros, scipy.optimize.__nnls, scipy.optimize._highs.cython.src._highs_wrapper, scipy.optimize._highs._highs_wrapper, scipy.optimize._highs.cython.src._highs_constants, scipy.optimize._highs._highs_constants, scipy.linalg._interpolative, scipy.optimize._bglu_dense, scipy.optimize._lsap, scipy.spatial._ckdtree, scipy.spatial._qhull, scipy.spatial._voronoi, scipy.spatial._distance_wrap, scipy.spatial._hausdorff, scipy.spatial.transform._rotation, scipy.optimize._direct, astropy.time._parse_times, astropy.table._column_mixins, astropy.table._np_utils, yaml._yaml, astropy.io.ascii.cparser, astropy.utils.xml._iterparser, astropy.io.fits._utils, astropy.io.fits._tiled_compression._compression, astropy.io.votable.tablewriter, astropy.wcs._wcs, scipy.interpolate._fitpack, scipy.interpolate.dfitpack, scipy.interpolate._bspl, scipy.interpolate._ppoly, scipy.interpolate.interpnd, scipy.interpolate._rbfinterp_pythran, scipy.interpolate._rgi_cython, _brotli, astropy.stats._stats, astropy.stats._fast_sigma_clip, bottleneck.move, bottleneck.nonreduce, bottleneck.nonreduce_axis, bottleneck.reduce, astropy.timeseries.periodograms.lombscargle.implementations.cython_impl, astropy.timeseries.periodograms.bls._impl, synphot.synphot_utils, pandas._libs.tslibs.np_datetime, pandas._libs.tslibs.dtypes, pandas._libs.tslibs.base, pandas._libs.tslibs.nattype, pandas._libs.tslibs.timezones, pandas._libs.tslibs.ccalendar, pandas._libs.tslibs.fields, pandas._libs.tslibs.timedeltas, pandas._libs.tslibs.tzconversion, pandas._libs.tslibs.timestamps, pandas._libs.properties, pandas._libs.tslibs.offsets, pandas._libs.tslibs.strptime, pandas._libs.tslibs.parsing, pandas._libs.tslibs.conversion, pandas._libs.tslibs.period, pandas._libs.tslibs.vectorized, pandas._libs.ops_dispatch, pandas._libs.missing, pandas._libs.hashtable, pandas._libs.algos, pandas._libs.interval, pandas._libs.lib, pandas._libs.hashing, pandas._libs.tslib, pandas._libs.ops, numexpr.interpreter, pandas._libs.arrays, pandas._libs.sparse, pandas._libs.reduction, pandas._libs.indexing, pandas._libs.index, pandas._libs.internals, pandas._libs.join, pandas._libs.writers, pandas._libs.window.aggregations, pandas._libs.window.indexers, pandas._libs.reshape, pandas._libs.groupby, pandas._libs.testing, pandas._libs.parsers, pandas._libs.json, numba.core.typeconv._typeconv, numba._helperlib, numba._dynfunc, numba._dispatcher, numba.core.runtime._nrt_python, numba.np.ufunc._internal, numba.experimental.jitclass._box, matplotlib._c_internal_utils, PIL._imaging, matplotlib._path, kiwisolver._cext, matplotlib._image, healpy._healpy_sph_transform_lib, healpy._sphtools, healpy._pixelfunc, healpy._query_disc, healpy._masktools, healpy._hotspots, healpy._line_integral_convolution, _cffi_backend (total: 166) Segmentation fault (core dumped)

[mschwamb]

Got a bit further. uninstalled rebound by conda and reinstalling via pip did not seg fault. It produced no output, but need to check if that object is not observable

[mschwamb]

it was rebound - not sure what but mamba installing rebound caused bad things to happen. uninstalling rebound and pip installing fixed it. no errors.... not sure why this is happening on linux and not osx

At least I have a lot of output need to compare the time files, but it ran through

[mschwamb]

Thanks @matthewholman for the help and nudging... I've debugged my first python code kinda properly (well at least I got to figuring out it was rebound)

[mschwamb]

I hate pip/conda(mamba) interactions so much....