polartoolkit
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mdtanker
Kernel crashing with certain plotting elements
Describe the bug
I've been experiencing lots of crashing of kernel with certain aspects of maps.plot_grd, mostly with hist=True or even with show_region. It appears to be an issue with some dependency. I can reliably recreate the crash with the below code:
from polartoolkit import fetch, maps, profiles, regions
import os
os.environ["POLARTOOLKIT_HEMISPHERE"] = "south"
ibcso = fetch.ibcso(
layer="bed",
region=(-40e3, 110e3, -1600e3, -1400e3),
)
fig = maps.plot_grd(
ibcso,
show_region=(-40e3, 110e3, -1600e3, -1400e3),
fig_height=10,
title="Bathymetry",
hist=True,
cmap="rain",
reverse_cpt=True,
cbar_label="elevation (m)",
robust=True,
)
fig.savefig("ibcso_bed.png", dpi=300)
double free or corruption (out)
Aborted (core dumped)
The main differences between the environment that works and the one that doesn't seems to be:
- good env has cartopy 0.24, bad env doesn't have cartopy
- good env has geopandas 1.0.1, bad env has 0.14.4
- good env has zarr 2.18.7, bad env has 3.0.7
Fails with this environment:
_openmp_mutex 4.5 3_kmp_llvm conda-forge
adjusttext 1.3.0 pyhd8ed1ab_0 conda-forge
affine 2.4.0 pyhd8ed1ab_1 conda-forge
aiobotocore 2.21.1 pyhd8ed1ab_0 conda-forge
aiohappyeyeballs 2.6.1 pyhd8ed1ab_0 conda-forge
aiohttp 3.11.18 py312h178313f_0 conda-forge
aioitertools 0.12.0 pyhd8ed1ab_1 conda-forge
aiosignal 1.3.2 pyhd8ed1ab_0 conda-forge
alembic 1.15.2 pyhd8ed1ab_0 conda-forge
alsa-lib 1.2.14 hb9d3cd8_0 conda-forge
anyio 4.9.0 pyh29332c3_0 conda-forge
aom 3.9.1 hac33072_0 conda-forge
argon2-cffi 23.1.0 pyhd8ed1ab_1 conda-forge
argon2-cffi-bindings 21.2.0 py312h66e93f0_5 conda-forge
arrow 1.3.0 pyhd8ed1ab_1 conda-forge
astroid 3.3.9 py312h7900ff3_0 conda-forge
asttokens 3.0.0 pyhd8ed1ab_1 conda-forge
async-lru 2.0.5 pyh29332c3_0 conda-forge
attr 2.5.1 h166bdaf_1 conda-forge
attrs 25.3.0 pyh71513ae_0 conda-forge
aws-c-auth 0.9.0 h094d708_2 conda-forge
aws-c-cal 0.8.9 hada3f3f_0 conda-forge
aws-c-common 0.12.2 hb9d3cd8_0 conda-forge
aws-c-compression 0.3.1 hc2d532b_4 conda-forge
aws-c-event-stream 0.5.4 h8170a11_5 conda-forge
aws-c-http 0.9.5 hca9d837_2 conda-forge
aws-c-io 0.18.0 h7b13e6b_1 conda-forge
aws-c-mqtt 0.12.3 h773eac8_2 conda-forge
aws-c-s3 0.7.15 h46af1f8_1 conda-forge
aws-c-sdkutils 0.2.3 hc2d532b_4 conda-forge
aws-checksums 0.2.5 hc2d532b_1 conda-forge
aws-crt-cpp 0.32.4 h7d42c6f_0 conda-forge
aws-sdk-cpp 1.11.510 h5b777a2_5 conda-forge
azure-core-cpp 1.14.0 h5cfcd09_0 conda-forge
azure-identity-cpp 1.10.0 h113e628_0 conda-forge
azure-storage-blobs-cpp 12.13.0 h3cf044e_1 conda-forge
azure-storage-common-cpp 12.8.0 h736e048_1 conda-forge
azure-storage-files-datalake-cpp 12.12.0 ha633028_1 conda-forge
babel 2.17.0 pyhd8ed1ab_0 conda-forge
beautifulsoup4 4.13.4 pyha770c72_0 conda-forge
bleach 6.2.0 pyh29332c3_4 conda-forge
bleach-with-css 6.2.0 h82add2a_4 conda-forge
blosc 1.21.6 he440d0b_1 conda-forge
bokeh 3.7.2 pyhd8ed1ab_1 conda-forge
botocore 1.37.1 pyge310_1234567_0 conda-forge
boule 0.5.0 pyhd8ed1ab_1 conda-forge
bounded-pool-executor 0.0.3 pyhd8ed1ab_0 conda-forge
branca 0.8.1 pyhd8ed1ab_0 conda-forge
brotli 1.1.0 hb9d3cd8_2 conda-forge
brotli-bin 1.1.0 hb9d3cd8_2 conda-forge
brotli-python 1.1.0 py312h2ec8cdc_2 conda-forge
bzip2 1.0.8 h4bc722e_7 conda-forge
c-ares 1.34.5 hb9d3cd8_0 conda-forge
ca-certificates 2025.1.31 hbd8a1cb_1 conda-forge
cached-property 1.5.2 hd8ed1ab_1 conda-forge
cached_property 1.5.2 pyha770c72_1 conda-forge
cairo 1.18.4 h3394656_0 conda-forge
certifi 2025.1.31 pyhd8ed1ab_0 conda-forge
cf_xarray 0.10.5 pyhd8ed1ab_0 conda-forge
cffi 1.17.1 py312h06ac9bb_0 conda-forge
cfgv 3.3.1 pyhd8ed1ab_1 conda-forge
cftime 1.6.4 py312hc0a28a1_1 conda-forge
charset-normalizer 3.4.1 pyhd8ed1ab_0 conda-forge
choclo 0.3.2 pyhd8ed1ab_0 conda-forge
click 8.1.8 pyh707e725_0 conda-forge
click-plugins 1.1.1 pyhd8ed1ab_1 conda-forge
cligj 0.7.2 pyhd8ed1ab_2 conda-forge
cloudpickle 3.1.1 pyhd8ed1ab_0 conda-forge
cmocean 4.0.3 pyhd8ed1ab_1 conda-forge
colorama 0.4.6 pyhd8ed1ab_1 conda-forge
colorlog 6.9.0 pyh707e725_1 conda-forge
colorspacious 1.1.2 pyhecae5ae_1 conda-forge
comm 0.2.2 pyhd8ed1ab_1 conda-forge
contourpy 1.3.2 py312h68727a3_0 conda-forge
cpython 3.12.10 py312hd8ed1ab_0 conda-forge
crc32c 2.7.1 py312h66e93f0_1 conda-forge
cuda-crt-tools 12.8.93 ha770c72_3 conda-forge
cuda-cudart 12.8.90 h5888daf_1 conda-forge
cuda-cudart_linux-64 12.8.90 h3f2d84a_1 conda-forge
cuda-cuobjdump 12.8.90 hbd13f7d_1 conda-forge
cuda-cupti 12.8.90 h5888daf_1 conda-forge
cuda-nvcc-tools 12.8.93 he02047a_3 conda-forge
cuda-nvdisasm 12.8.90 hbd13f7d_1 conda-forge
cuda-nvrtc 12.8.93 h5888daf_1 conda-forge
cuda-nvtx 12.8.90 h5888daf_1 conda-forge
cuda-nvvm-tools 12.8.93 he02047a_3 conda-forge
cuda-version 12.8 h5d125a7_3 conda-forge
cudnn 9.8.0.87 h81d5506_1 conda-forge
curl 8.13.0 h332b0f4_0 conda-forge
cycler 0.12.1 pyhd8ed1ab_1 conda-forge
cyrus-sasl 2.1.27 h54b06d7_7 conda-forge
cytoolz 1.0.1 py312h66e93f0_0 conda-forge
dask 2025.4.0 pyhd8ed1ab_0 conda-forge
dask-core 2025.4.0 pyhd8ed1ab_0 conda-forge
dav1d 1.2.1 hd590300_0 conda-forge
dbus 1.13.6 h5008d03_3 conda-forge
dcw-gmt 2.2.0 ha770c72_0 conda-forge
debugpy 1.8.14 py312h2ec8cdc_0 conda-forge
decorator 5.2.1 pyhd8ed1ab_0 conda-forge
defusedxml 0.7.1 pyhd8ed1ab_0 conda-forge
deprecated 1.2.18 pyhd8ed1ab_0 conda-forge
deprecation 2.1.0 pyh9f0ad1d_0 conda-forge
dill 0.4.0 pyhd8ed1ab_0 conda-forge
distlib 0.3.9 pyhd8ed1ab_1 conda-forge
distributed 2025.4.0 pyhd8ed1ab_0 conda-forge
docrep 0.3.2 pyh44b312d_0 conda-forge
donfig 0.8.1.post1 pyhd8ed1ab_1 conda-forge
double-conversion 3.3.1 h5888daf_0 conda-forge
earthaccess 0.12.0 pyhd8ed1ab_1 conda-forge
esmf 8.8.1 nompi_h4441c20_0 conda-forge
esmpy 8.8.1 pyhecae5ae_0 conda-forge
et_xmlfile 2.0.0 pyhd8ed1ab_1 conda-forge
exceptiongroup 1.2.2 pyhd8ed1ab_1 conda-forge
executing 2.1.0 pyhd8ed1ab_1 conda-forge
expat 2.7.0 h5888daf_0 conda-forge
fftw 3.3.10 nompi_hf1063bd_110 conda-forge
filelock 3.18.0 pyhd8ed1ab_0 conda-forge
fiona 1.10.1 py312h02b19dd_3 conda-forge
folium 0.19.5 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 h77eed37_3 conda-forge
fontconfig 2.15.0 h7e30c49_1 conda-forge
fonts-conda-ecosystem 1 0 conda-forge
fonts-conda-forge 1 0 conda-forge
fonttools 4.57.0 py312h178313f_0 conda-forge
fqdn 1.5.1 pyhd8ed1ab_1 conda-forge
freetype 2.13.3 ha770c72_1 conda-forge
freexl 2.0.0 h9dce30a_2 conda-forge
frozenlist 1.5.0 py312h178313f_1 conda-forge
fsspec 2025.3.2 pyhd8ed1ab_0 conda-forge
future 1.0.0 pyhd8ed1ab_2 conda-forge
geopandas 0.14.4 pyhd8ed1ab_0 conda-forge
geopandas-base 0.14.4 pyha770c72_0 conda-forge
geos 3.13.1 h97f6797_0 conda-forge
geotiff 1.7.4 h3551947_0 conda-forge
gflags 2.2.2 h5888daf_1005 conda-forge
ghostscript 10.04.0 h5888daf_0 conda-forge
giflib 5.2.2 hd590300_0 conda-forge
gl2ps 1.4.2 hae5d5c5_1 conda-forge
glew 2.1.0 h9c3ff4c_2 conda-forge
glog 0.7.1 hbabe93e_0 conda-forge
gmp 6.3.0 hac33072_2 conda-forge
gmpy2 2.1.5 py312h7201bc8_3 conda-forge
gmt 6.5.0 h8300b2c_8 conda-forge
graphite2 1.3.13 h59595ed_1003 conda-forge
greenlet 3.2.0 py312h2ec8cdc_0 conda-forge
gshhg-gmt 2.3.7 ha770c72_1003 conda-forge
h11 0.14.0 pyhd8ed1ab_1 conda-forge
h2 4.2.0 pyhd8ed1ab_0 conda-forge
harfbuzz 11.1.0 h3beb420_0 conda-forge
harmonica 0.7.0 pyhd8ed1ab_1 conda-forge
hdf4 4.2.15 h2a13503_7 conda-forge
hdf5 1.14.3 nompi_h2d575fe_109 conda-forge
hpack 4.1.0 pyhd8ed1ab_0 conda-forge
httpcore 1.0.7 pyh29332c3_1 conda-forge
httpx 0.28.1 pyhd8ed1ab_0 conda-forge
hyperframe 6.1.0 pyhd8ed1ab_0 conda-forge
icu 75.1 he02047a_0 conda-forge
identify 2.6.10 pyhd8ed1ab_0 conda-forge
idna 3.10 pyhd8ed1ab_1 conda-forge
importlib-metadata 8.6.1 pyha770c72_0 conda-forge
importlib-resources 6.5.2 pyhd8ed1ab_0 conda-forge
importlib_resources 6.5.2 pyhd8ed1ab_0 conda-forge
iniconfig 2.0.0 pyhd8ed1ab_1 conda-forge
invert4geom 0.13.0 pyhd8ed1ab_0 conda-forge
ipykernel 6.29.5 pyh3099207_0 conda-forge
ipython 9.1.0 pyhfb0248b_0 conda-forge
ipython_pygments_lexers 1.1.1 pyhd8ed1ab_0 conda-forge
ipywidgets 8.1.6 pyhd8ed1ab_0 conda-forge
isoduration 20.11.0 pyhd8ed1ab_1 conda-forge
isort 6.0.1 pyhd8ed1ab_0 conda-forge
jedi 0.19.2 pyhd8ed1ab_1 conda-forge
jinja2 3.1.6 pyhd8ed1ab_0 conda-forge
jmespath 1.0.1 pyhd8ed1ab_1 conda-forge
joblib 1.4.2 pyhd8ed1ab_1 conda-forge
json-c 0.18 h6688a6e_0 conda-forge
json5 0.12.0 pyhd8ed1ab_0 conda-forge
jsoncpp 1.9.6 hf42df4d_1 conda-forge
jsonpointer 3.0.0 py312h7900ff3_1 conda-forge
jsonschema 4.23.0 pyhd8ed1ab_1 conda-forge
jsonschema-specifications 2024.10.1 pyhd8ed1ab_1 conda-forge
jsonschema-with-format-nongpl 4.23.0 hd8ed1ab_1 conda-forge
jupyter-lsp 2.2.5 pyhd8ed1ab_1 conda-forge
jupyter_client 8.6.3 pyhd8ed1ab_1 conda-forge
jupyter_core 5.7.2 pyh31011fe_1 conda-forge
jupyter_events 0.12.0 pyh29332c3_0 conda-forge
jupyter_server 2.15.0 pyhd8ed1ab_0 conda-forge
jupyter_server_terminals 0.5.3 pyhd8ed1ab_1 conda-forge
jupyterlab 4.4.1 pyhd8ed1ab_0 conda-forge
jupyterlab_execute_time 3.2.0 pyhd8ed1ab_1 conda-forge
jupyterlab_pygments 0.3.0 pyhd8ed1ab_2 conda-forge
jupyterlab_server 2.27.3 pyhd8ed1ab_1 conda-forge
jupyterlab_widgets 3.0.14 pyhd8ed1ab_0 conda-forge
keyutils 1.6.1 h166bdaf_0 conda-forge
kiwisolver 1.4.8 py312h84d6215_0 conda-forge
kneebow 1.0.2 pypi_0 pypi
krb5 1.21.3 h659f571_0 conda-forge
lcms2 2.17 h717163a_0 conda-forge
ld_impl_linux-64 2.43 h712a8e2_4 conda-forge
lerc 4.0.0 h0aef613_1 conda-forge
libabseil 20250127.1 cxx17_hbbce691_0 conda-forge
libaec 1.1.3 h59595ed_0 conda-forge
libarchive 3.7.7 h75ea233_4 conda-forge
libarrow 19.0.1 h27f8bab_8_cpu conda-forge
libarrow-acero 19.0.1 hcb10f89_8_cpu conda-forge
libarrow-dataset 19.0.1 hcb10f89_8_cpu conda-forge
libarrow-substrait 19.0.1 h1bed206_8_cpu conda-forge
libavif16 1.2.1 hbb36593_2 conda-forge
libblas 3.9.0 31_hfdb39a5_mkl conda-forge
libbrotlicommon 1.1.0 hb9d3cd8_2 conda-forge
libbrotlidec 1.1.0 hb9d3cd8_2 conda-forge
libbrotlienc 1.1.0 hb9d3cd8_2 conda-forge
libcap 2.75 h39aace5_0 conda-forge
libcblas 3.9.0 31_h372d94f_mkl conda-forge
libclang-cpp20.1 20.1.3 default_h1df26ce_0 conda-forge
libclang13 20.1.3 default_he06ed0a_0 conda-forge
libcrc32c 1.1.2 h9c3ff4c_0 conda-forge
libcublas 12.8.4.1 h9ab20c4_1 conda-forge
libcudss 0.5.0.16 h14340ca_1 conda-forge
libcufft 11.3.3.83 h5888daf_1 conda-forge
libcufile 1.13.1.3 h628e99a_1 conda-forge
libcups 2.3.3 h4637d8d_4 conda-forge
libcurand 10.3.9.90 h9ab20c4_1 conda-forge
libcurl 8.13.0 h332b0f4_0 conda-forge
libcusolver 11.7.3.90 h9ab20c4_1 conda-forge
libcusparse 12.5.8.93 h5888daf_1 conda-forge
libde265 1.0.15 h00ab1b0_0 conda-forge
libdeflate 1.23 h86f0d12_0 conda-forge
libdrm 2.4.124 hb9d3cd8_0 conda-forge
libedit 3.1.20250104 pl5321h7949ede_0 conda-forge
libegl 1.7.0 ha4b6fd6_2 conda-forge
libev 4.33 hd590300_2 conda-forge
libevent 2.1.12 hf998b51_1 conda-forge
libexpat 2.7.0 h5888daf_0 conda-forge
libffi 3.4.6 h2dba641_1 conda-forge
libfreetype 2.13.3 ha770c72_1 conda-forge
libfreetype6 2.13.3 h48d6fc4_1 conda-forge
libgcc 14.2.0 h767d61c_2 conda-forge
libgcc-ng 14.2.0 h69a702a_2 conda-forge
libgcrypt-lib 1.11.0 hb9d3cd8_2 conda-forge
libgdal-core 3.10.2 h05269f4_1 conda-forge
libgdal-jp2openjpeg 3.10.2 ha1d2769_1 conda-forge
libgfortran 14.2.0 h69a702a_2 conda-forge
libgfortran-ng 14.2.0 h69a702a_2 conda-forge
libgfortran5 14.2.0 hf1ad2bd_2 conda-forge
libgl 1.7.0 ha4b6fd6_2 conda-forge
libglib 2.84.1 h2ff4ddf_0 conda-forge
libglu 9.0.3 h03adeef_0 conda-forge
libglvnd 1.7.0 ha4b6fd6_2 conda-forge
libglx 1.7.0 ha4b6fd6_2 conda-forge
libgoogle-cloud 2.36.0 hc4361e1_1 conda-forge
libgoogle-cloud-storage 2.36.0 h0121fbd_1 conda-forge
libgpg-error 1.54 hbd13f7d_0 conda-forge
libgrpc 1.71.0 h8e591d7_1 conda-forge
libheif 1.19.7 gpl_hc18d805_100 conda-forge
libhwloc 2.11.2 default_h0d58e46_1001 conda-forge
libiconv 1.18 h4ce23a2_1 conda-forge
libjpeg-turbo 3.1.0 hb9d3cd8_0 conda-forge
libkml 1.3.0 hf539b9f_1021 conda-forge
liblapack 3.9.0 31_hc41d3b0_mkl conda-forge
libllvm20 20.1.3 he9d0ab4_0 conda-forge
liblzma 5.8.1 hb9d3cd8_0 conda-forge
libmagma 2.8.0 h566cb83_2 conda-forge
libnetcdf 4.9.2 nompi_h00e09a9_116 conda-forge
libnghttp2 1.64.0 h161d5f1_0 conda-forge
libnl 3.11.0 hb9d3cd8_0 conda-forge
libnsl 2.0.1 hd590300_0 conda-forge
libntlm 1.8 hb9d3cd8_0 conda-forge
libnvjitlink 12.8.93 h5888daf_1 conda-forge
libogg 1.3.5 h4ab18f5_0 conda-forge
libopentelemetry-cpp 1.20.0 hd1b1c89_0 conda-forge
libopentelemetry-cpp-headers 1.20.0 ha770c72_0 conda-forge
libparquet 19.0.1 h081d1f1_8_cpu conda-forge
libpciaccess 0.18 hd590300_0 conda-forge
libpng 1.6.47 h943b412_0 conda-forge
libpq 17.4 h27ae623_1 conda-forge
libprotobuf 5.29.3 h501fc15_1 conda-forge
libre2-11 2024.07.02 hba17884_3 conda-forge
librttopo 1.1.0 hd718a1a_18 conda-forge
libsodium 1.0.20 h4ab18f5_0 conda-forge
libspatialindex 2.1.0 he57a185_0 conda-forge
libspatialite 5.1.0 h366e088_13 conda-forge
libsqlite 3.49.1 hee588c1_2 conda-forge
libssh2 1.11.1 hf672d98_0 conda-forge
libstdcxx 14.2.0 h8f9b012_2 conda-forge
libstdcxx-ng 14.2.0 h4852527_2 conda-forge
libsystemd0 257.4 h4e0b6ca_1 conda-forge
libtheora 1.1.1 h4ab18f5_1006 conda-forge
libthrift 0.21.0 h0e7cc3e_0 conda-forge
libtiff 4.7.0 hd9ff511_4 conda-forge
libtorch 2.6.0 cuda126_mkl_h9fa54b4_302 conda-forge
libudev1 257.4 hbe16f8c_1 conda-forge
libutf8proc 2.10.0 h4c51ac1_0 conda-forge
libuuid 2.38.1 h0b41bf4_0 conda-forge
libuv 1.50.0 hb9d3cd8_0 conda-forge
libvorbis 1.3.7 h9c3ff4c_0 conda-forge
libwebp-base 1.5.0 h851e524_0 conda-forge
libxcb 1.17.0 h8a09558_0 conda-forge
libxcrypt 4.4.36 hd590300_1 conda-forge
libxkbcommon 1.8.1 hc4a0caf_0 conda-forge
libxml2 2.13.7 h4bc477f_1 conda-forge
libzip 1.11.2 h6991a6a_0 conda-forge
libzlib 1.3.1 hb9d3cd8_2 conda-forge
llvm-openmp 20.1.3 h024ca30_0 conda-forge
llvmlite 0.44.0 py312h374181b_1 conda-forge
locket 1.0.0 pyhd8ed1ab_0 conda-forge
loguru 0.7.2 py312h7900ff3_2 conda-forge
lz4 4.3.3 py312hf0f0c11_2 conda-forge
lz4-c 1.10.0 h5888daf_1 conda-forge
lzo 2.10 hd590300_1001 conda-forge
mako 1.3.10 pyhd8ed1ab_0 conda-forge
mapclassify 2.8.1 pyhd8ed1ab_1 conda-forge
markupsafe 3.0.2 py312h178313f_1 conda-forge
matplotlib-base 3.10.1 py312hd3ec401_0 conda-forge
matplotlib-inline 0.1.7 pyhd8ed1ab_1 conda-forge
mccabe 0.7.0 pyhd8ed1ab_1 conda-forge
minizip 4.0.9 h05a5f5f_0 conda-forge
mistune 3.1.3 pyh29332c3_0 conda-forge
mkl 2024.2.2 ha957f24_16 conda-forge
more-itertools 10.7.0 pyhd8ed1ab_0 conda-forge
mpc 1.3.1 h24ddda3_1 conda-forge
mpfr 4.2.1 h90cbb55_3 conda-forge
mpmath 1.3.0 pyhd8ed1ab_1 conda-forge
msgpack-python 1.1.0 py312h68727a3_0 conda-forge
multidict 6.4.3 py312h178313f_0 conda-forge
multimethod 2.0 pyhd8ed1ab_0 conda-forge
munkres 1.1.4 pyh9f0ad1d_0 conda-forge
mysql-common 9.2.0 h266115a_0 conda-forge
mysql-libs 9.2.0 he0572af_0 conda-forge
narwhals 1.35.0 pyh29332c3_0 conda-forge
nbclient 0.10.2 pyhd8ed1ab_0 conda-forge
nbconvert-core 7.16.6 pyh29332c3_0 conda-forge
nbformat 5.10.4 pyhd8ed1ab_1 conda-forge
nccl 2.26.2.1 ha44e49d_1 conda-forge
ncurses 6.5 h2d0b736_3 conda-forge
nest-asyncio 1.6.0 pyhd8ed1ab_1 conda-forge
netcdf-fortran 4.6.1 nompi_h22f9119_108 conda-forge
netcdf4 1.7.2 nompi_py312h21d6d8e_101 conda-forge
networkx 3.4.2 pyh267e887_2 conda-forge
nlohmann_json 3.12.0 h3f2d84a_0 conda-forge
nodeenv 1.9.1 pyhd8ed1ab_1 conda-forge
notebook-shim 0.2.4 pyhd8ed1ab_1 conda-forge
numba 0.61.2 py312h2e6246c_0 conda-forge
numba-progress 1.1.0 pyhd8ed1ab_0 conda-forge
numcodecs 0.15.1 py312hf9745cd_0 conda-forge
numpy 2.2.5 py312h72c5963_0 conda-forge
openjpeg 2.5.3 h5fbd93e_0 conda-forge
openldap 2.6.9 he970967_0 conda-forge
openpyxl 3.1.5 py312h710cb58_1 conda-forge
openssl 3.5.0 h7b32b05_0 conda-forge
optree 0.15.0 py312h68727a3_0 conda-forge
optuna 4.3.0 pyhd8ed1ab_0 conda-forge
orc 2.1.1 h17f744e_1 conda-forge
overrides 7.7.0 pyhd8ed1ab_1 conda-forge
packaging 25.0 pyh29332c3_1 conda-forge
pandas 2.2.3 py312hf9745cd_3 conda-forge
pandocfilters 1.5.0 pyhd8ed1ab_0 conda-forge
parso 0.8.4 pyhd8ed1ab_1 conda-forge
partd 1.4.2 pyhd8ed1ab_0 conda-forge
patsy 1.0.1 pyhd8ed1ab_1 conda-forge
pcre 8.45 h9c3ff4c_0 conda-forge
pcre2 10.44 hba22ea6_2 conda-forge
pexpect 4.9.0 pyhd8ed1ab_1 conda-forge
pickleshare 0.7.5 pyhd8ed1ab_1004 conda-forge
pillow 11.1.0 py312h80c1187_0 conda-forge
pip 25.0.1 pyh8b19718_0 conda-forge
pixman 0.44.2 h29eaf8c_0 conda-forge
pkgutil-resolve-name 1.3.10 pyhd8ed1ab_2 conda-forge
platformdirs 4.3.7 pyh29332c3_0 conda-forge
plotly 6.0.1 pyhd8ed1ab_0 conda-forge
pluggy 1.5.0 pyhd8ed1ab_1 conda-forge
polartoolkit 0.7.1 pyhd8ed1ab_0 conda-forge
pooch 1.8.2 pyhd8ed1ab_1 conda-forge
pqdm 0.2.0 pyhd8ed1ab_1 conda-forge
pre-commit 4.2.0 pyha770c72_0 conda-forge
proj 9.5.1 h0054346_0 conda-forge
prometheus-cpp 1.3.0 ha5d0236_0 conda-forge
prometheus_client 0.21.1 pyhd8ed1ab_0 conda-forge
prompt-toolkit 3.0.51 pyha770c72_0 conda-forge
propcache 0.3.1 py312h178313f_0 conda-forge
psutil 7.0.0 py312h66e93f0_0 conda-forge
pthread-stubs 0.4 hb9d3cd8_1002 conda-forge
ptyprocess 0.7.0 pyhd8ed1ab_1 conda-forge
pugixml 1.15 h3f63f65_0 conda-forge
pure_eval 0.2.3 pyhd8ed1ab_1 conda-forge
pyarrow 19.0.1 py312h7900ff3_0 conda-forge
pyarrow-core 19.0.1 py312h01725c0_0_cpu conda-forge
pybind11 2.13.6 pyh1ec8472_2 conda-forge
pybind11-global 2.13.6 pyh415d2e4_2 conda-forge
pycparser 2.22 pyh29332c3_1 conda-forge
pygments 2.19.1 pyhd8ed1ab_0 conda-forge
pygmt 0.15.0 pyhd8ed1ab_0 conda-forge
pykdtree 1.4.1 py312hc0a28a1_0 conda-forge
pylint 3.3.6 pyh29332c3_0 conda-forge
pyogrio 0.10.0 py312h02b19dd_1 conda-forge
pyparsing 3.2.3 pyhd8ed1ab_1 conda-forge
pyproj 3.7.1 py312he630544_0 conda-forge
pysocks 1.7.1 pyha55dd90_7 conda-forge
pytest 8.3.5 pyhd8ed1ab_0 conda-forge
python 3.12.10 h9e4cc4f_0_cpython conda-forge
python-cmr 0.13.0 pyhff2d567_1 conda-forge
python-dateutil 2.9.0.post0 pyhff2d567_1 conda-forge
python-dotenv 1.1.0 pyh29332c3_1 conda-forge
python-fastjsonschema 2.21.1 pyhd8ed1ab_0 conda-forge
python-json-logger 2.0.7 pyhd8ed1ab_0 conda-forge
python-tzdata 2025.2 pyhd8ed1ab_0 conda-forge
python_abi 3.12 7_cp312 conda-forge
pytorch 2.6.0 cuda126_mkl_py312_h9a1f04f_302 conda-forge
pytz 2025.2 pyhd8ed1ab_0 conda-forge
pyvista 0.45.0 pyhd8ed1ab_1 conda-forge
pyyaml 6.0.2 py312h178313f_2 conda-forge
pyzmq 26.4.0 py312hbf22597_0 conda-forge
qhull 2020.2 h434a139_5 conda-forge
qt6-main 6.8.3 h6441bc3_2 conda-forge
rasterio 1.4.3 py312h8cae83d_0 conda-forge
rav1e 0.6.6 he8a937b_2 conda-forge
rdma-core 57.0 h5888daf_0 conda-forge
re2 2024.07.02 h9925aae_3 conda-forge
readline 8.2 h8c095d6_2 conda-forge
referencing 0.36.2 pyh29332c3_0 conda-forge
requests 2.32.3 pyhd8ed1ab_1 conda-forge
rfc3339-validator 0.1.4 pyhd8ed1ab_1 conda-forge
rfc3986-validator 0.1.1 pyh9f0ad1d_0 conda-forge
rioxarray 0.19.0 pyhd8ed1ab_0 conda-forge
rpds-py 0.24.0 py312h3b7be25_0 conda-forge
rtree 1.4.0 pyh11ca60a_1 conda-forge
s2n 1.5.16 hba75a32_1 conda-forge
s3fs 2025.3.2 pyhd8ed1ab_0 conda-forge
scikit-learn 1.6.1 py312h7a48858_0 conda-forge
scipy 1.15.2 py312ha707e6e_0 conda-forge
scooby 0.10.0 pyhd8ed1ab_1 conda-forge
seaborn 0.13.2 hd8ed1ab_3 conda-forge
seaborn-base 0.13.2 pyhd8ed1ab_3 conda-forge
send2trash 1.8.3 pyh0d859eb_1 conda-forge
setuptools 79.0.0 pyhff2d567_0 conda-forge
shapely 2.1.0 py312h21f5128_0 conda-forge
six 1.17.0 pyhd8ed1ab_0 conda-forge
sleef 3.8 h1b44611_0 conda-forge
snappy 1.2.1 h8bd8927_1 conda-forge
sniffio 1.3.1 pyhd8ed1ab_1 conda-forge
snuggs 1.4.7 pyhd8ed1ab_2 conda-forge
sortedcontainers 2.4.0 pyhd8ed1ab_1 conda-forge
soupsieve 2.5 pyhd8ed1ab_1 conda-forge
sparse 0.16.0 pyh1646c32_0 conda-forge
sqlalchemy 2.0.40 py312h66e93f0_0 conda-forge
sqlite 3.49.1 h9eae976_2 conda-forge
stack_data 0.6.3 pyhd8ed1ab_1 conda-forge
statsmodels 0.14.4 py312hc0a28a1_0 conda-forge
svt-av1 3.0.2 h5888daf_0 conda-forge
sympy 1.13.3 pyh2585a3b_105 conda-forge
synthetic_bathymetry_inversion 0.0.1 pypi_0 pypi
tbb 2021.13.0 hceb3a55_1 conda-forge
tblib 3.1.0 pyhd8ed1ab_0 conda-forge
terminado 0.18.1 pyh0d859eb_0 conda-forge
threadpoolctl 3.6.0 pyhecae5ae_0 conda-forge
tinycss2 1.4.0 pyhd8ed1ab_0 conda-forge
tinynetrc 1.3.1 pyhd8ed1ab_0 conda-forge
tk 8.6.13 noxft_h4845f30_101 conda-forge
tomli 2.2.1 pyhd8ed1ab_1 conda-forge
tomlkit 0.13.2 pyha770c72_1 conda-forge
toolz 1.0.0 pyhd8ed1ab_1 conda-forge
tornado 6.4.2 py312h66e93f0_0 conda-forge
tqdm 4.67.1 pyhd8ed1ab_1 conda-forge
traitlets 5.14.3 pyhd8ed1ab_1 conda-forge
trame 3.8.2 pyhd8ed1ab_0 conda-forge
trame-client 3.7.1 pyhd8ed1ab_0 conda-forge
trame-server 3.4.0 pyhd8ed1ab_0 conda-forge
triton 3.2.0 cuda126py312h5a3d8a8_1 conda-forge
types-python-dateutil 2.9.0.20241206 pyhd8ed1ab_0 conda-forge
typing-extensions 4.13.2 h0e9735f_0 conda-forge
typing_extensions 4.13.2 pyh29332c3_0 conda-forge
typing_utils 0.1.0 pyhd8ed1ab_1 conda-forge
tzdata 2025b h78e105d_0 conda-forge
ukkonen 1.0.1 py312h68727a3_5 conda-forge
unicodedata2 16.0.0 py312h66e93f0_0 conda-forge
uri-template 1.3.0 pyhd8ed1ab_1 conda-forge
uriparser 0.9.8 hac33072_0 conda-forge
urllib3 2.4.0 pyhd8ed1ab_0 conda-forge
utfcpp 4.0.6 h005c6e1_0 conda-forge
verde 1.8.1 pyhd8ed1ab_0 conda-forge
virtualenv 20.30.0 pyhd8ed1ab_0 conda-forge
vtk-base 9.3.1 qt_py312h6cb585f_216 conda-forge
wayland 1.23.1 h3e06ad9_0 conda-forge
wcwidth 0.2.13 pyhd8ed1ab_1 conda-forge
webcolors 24.11.1 pyhd8ed1ab_0 conda-forge
webencodings 0.5.1 pyhd8ed1ab_3 conda-forge
websocket-client 1.8.0 pyhd8ed1ab_1 conda-forge
wheel 0.45.1 pyhd8ed1ab_1 conda-forge
widgetsnbextension 4.0.14 pyhd8ed1ab_0 conda-forge
wrapt 1.17.2 py312h66e93f0_0 conda-forge
wslink 2.3.3 pyhd8ed1ab_0 conda-forge
x265 3.5 h924138e_3 conda-forge
xarray 2025.3.1 pyhd8ed1ab_0 conda-forge
xcb-util 0.4.1 hb711507_2 conda-forge
xcb-util-cursor 0.1.5 hb9d3cd8_0 conda-forge
xcb-util-image 0.4.0 hb711507_2 conda-forge
xcb-util-keysyms 0.4.1 hb711507_0 conda-forge
xcb-util-renderutil 0.3.10 hb711507_0 conda-forge
xcb-util-wm 0.4.2 hb711507_0 conda-forge
xerces-c 3.2.5 h988505b_2 conda-forge
xesmf 0.8.9 pyhd8ed1ab_0 conda-forge
xkeyboard-config 2.43 hb9d3cd8_0 conda-forge
xorg-libice 1.1.2 hb9d3cd8_0 conda-forge
xorg-libsm 1.2.6 he73a12e_0 conda-forge
xorg-libx11 1.8.12 h4f16b4b_0 conda-forge
xorg-libxau 1.0.12 hb9d3cd8_0 conda-forge
xorg-libxcomposite 0.4.6 hb9d3cd8_2 conda-forge
xorg-libxcursor 1.2.3 hb9d3cd8_0 conda-forge
xorg-libxdamage 1.1.6 hb9d3cd8_0 conda-forge
xorg-libxdmcp 1.1.5 hb9d3cd8_0 conda-forge
xorg-libxext 1.3.6 hb9d3cd8_0 conda-forge
xorg-libxfixes 6.0.1 hb9d3cd8_0 conda-forge
xorg-libxi 1.8.2 hb9d3cd8_0 conda-forge
xorg-libxrandr 1.5.4 hb9d3cd8_0 conda-forge
xorg-libxrender 0.9.12 hb9d3cd8_0 conda-forge
xorg-libxt 1.3.1 hb9d3cd8_0 conda-forge
xorg-libxtst 1.2.5 hb9d3cd8_3 conda-forge
xorg-libxxf86vm 1.1.6 hb9d3cd8_0 conda-forge
xrft 1.0.1 pyhd8ed1ab_1 conda-forge
xyzservices 2025.1.0 pyhd8ed1ab_0 conda-forge
yaml 0.2.5 h7f98852_2 conda-forge
yarl 1.20.0 py312h178313f_0 conda-forge
zarr 3.0.7 pyhd8ed1ab_0 conda-forge
zeromq 4.3.5 h3b0a872_7 conda-forge
zict 3.0.0 pyhd8ed1ab_1 conda-forge
zipp 3.21.0 pyhd8ed1ab_1 conda-forge
zlib 1.3.1 hb9d3cd8_2 conda-forge
zstandard 0.23.0 py312h66e93f0_1 conda-forge
zstd 1.5.7 hb8e6e7a_2 conda-forge
Updating the bad environment's geopandas version to 1.0.1 didn't fix the issue.
Downgrading the bad environments's zarr version to 2.18.7 didn't fix the issue.
Running the code WORKS with an environment created with the below commands:
mamba create --name test_env --channel conda-forge pygmt geopandas cartopy
Installing Polartoolkit locally:
pip install -e .
Running the code FAILS with an environment created with the below commands :
mamba env create --file environment.yml --name test_env
Where environement.yml is defined below.
and installing polartoolkit locally:
pip install -e .
name: test_env
channels:
- conda-forge
- nodefaults
dependencies:
- python=3.12
- invert4geom>=0.13
- geopandas>=1.0
- cartopy
- ipykernel
Running the code FAILS with an environment created with the below commands:
mamba create --name test_env --channel conda-forge pygmt geopandas cartopy invert4geom
Installing Polartoolkit locally:
pip install -e .
Manually updating geopandas
mamba install geopandas=1.0
Running the code WORKS with an environment created with the below commands :
mamba env create --file environment.yml --name test_env
Where environement.yml is defined below.
and installing polartoolkit locally:
pip install -e .
name: test_env
channels:
- conda-forge
- nodefaults
dependencies:
- python=3.12
- geopandas
- pygmt
- pyogrio
- esmpy
- xesmf
- cmocean
- jupyterlab_execute_time
- adjusttext
- boule
- shapely
- ipykernel
- pre-commit
- pylint
- pytest
- pip
- pip:
- kneebow
From the above tests, it seems the issue happens when geopandas is installed AFTER polartoolkit. In future versions, when geopandas version is restricted to >=1, this shouldn't be an issue as the correct geopandas version will be installed through installing polartoolkit.
This still seems to be an issue. I seem to reliably fix it by uninstall Geopandas and PolarToolkit, then installing Geopandas first (with mamba), then separately installing PolarToolkit. I'll need to test this more to confirm this works.
With some additional testing, it seems the (or an additional) cause of the segfault is when pytorch is installed. This may be related to this and this, which found the package pyinterp to cause seg faulting issues with PyGMT.
Comparing the working environment with the broken one (with pytorch installed), the packages installed for pytorch include:
- cpython
- filelock
- gmp
- gmpy2
- libhwloc
- libtorch
- libuv
- llvm-openmp
- mkl
- mpc
- mpfr
- mpmath
- optree
- pybind11
- pybind11-global
- sleef
- sympy
- tbb
I individually included these packages, which showed the error resulted specifically from libtorch
To see specifically what is causes the seg fault, I've tested each of the plotting functions in PolarToolkit with a working and broken environment, created as below:
Working: mamba env create polartoolkit --name ptk_working
Broken: mamba env create polartoolkit libtorch --name ptk_error
The code below runs without error for the environment, but with the broken environment, I've commented which plotting functions cause errors.
from polartoolkit import fetch, maps, regions
ice_thickness = fetch.bedmap3(
layer="ice_thickness",
region=regions.amery_ice_shelf,
)
fig = maps.Figure(
hemisphere="south",
reg=regions.amery_ice_shelf,
)
# these commands work fine
fig.add_coast()
fig.add_gridlines()
fig.add_faults()
fig.add_modis()
fig.add_simple_basemap()
fig.add_scalebar()
fig.add_north_arrow()
fig.add_grid(ice_thickness, colorbar=False)
# these commands produce the below error:
# double free or corruption (out) Aborted (core dumped)
fig.add_inset()
fig.add_box((1630e3, 2360e3, 530e3, 900e3))
fig.add_points(
points=fetch.ghf(points=True, version="burton-johnson-2020"),
colorbar=False,
)
fig.add_colorbar(grid=ice_thickness, hist=True)
# this command produce the below error:
# Segmentation fault (core dumped)
fig.add_imagery()
fig.show()
Related to #https://github.com/GenericMappingTools/pygmt/issues/4038, which found the error to be from the combination of gmt 6.5.0 and liblapack installed from mkl, which can possibly avoided if the package nomkl is a dependency.
Not an issue if using gmt 6.6.0, so this can be closed. If someone requires gmt 6.5.0, open an issue in gmt to back fix this.