Segmentation fault during `run_pycurv.py`

[m-albert]

Hi,

I'm occasionally getting segmentation faults while running python run_pycurv.py config.yml ${i}.surface.vtp as part of the configurable pipeline. However, the meshes created during python segmentation_to_meshes.py config.yml look good judging by visual inspection.

Before going into debugging, I was wondering whether this is would perhaps be a known problem and whether there'd be some go-to parameters / things to look out for for avoiding the seg faults?

Thanks!

[GenevieveBuckley]

I've also experienced the same problem recently.

No advice yet, I haven't figured out what is different this time compared to the last time I tried to use this (quite some time ago)

[GenevieveBuckley]

This issue https://github.com/GrotjahnLab/surface_morphometrics/issues/24 from two weeks ago has the suggestion to try:

• increasing the amount of memory available (eg: close all other programs)
• reduce the max_triangles variable

[m-albert]

Thanks Genevieve!

I had missed that issue and will try the two suggestions and report back.

[m-albert]

Okay, so even with a lot of available memory (128GB) and max_triangles=50000 (a third of the default value) I'm getting the segmentation faults. Also SLURM reported that only ~300MB were used by the failed jobs.

The segmentation faults appear just after the curvature warnings:

2024-07-01 14:50:19.936 (   4.617s) [    7F03A9204740]      vtkCurvatures.cxx:379   WARN| vtkCurvatures (0x55ebe9fac7f0): The Gaussian or mean curvature at point 26255 have a large computation error... The maximum curvature is likely off.
2024-07-01 14:50:19.936 (   4.617s) [    7F03A9204740]      vtkCurvatures.cxx:379   WARN| vtkCurvatures (0x55ebe9fac7f0): The Gaussian or mean curvature at point 26256 have a large computation error... The maximum curvature is likely off.
2024-07-01 14:50:19.936 (   4.617s) [    7F03A9204740]      vtkCurvatures.cxx:379   WARN| vtkCurvatures (0x55ebe9fac7f0): The Gaussian or mean curvature at point 26257 have a large computation error... The maximum curvature is likely off.
2024-07-01 14:50:19.936 (   4.617s) [    7F03A9204740]      vtkCurvatures.cxx:379   WARN| vtkCurvatures (0x55ebe9fac7f0): The Gaussian or mean curvature at point 26258 have a large computation error... The maximum curvature is likely off.
2024-07-01 14:50:19.936 (   4.617s) [    7F03A9204740]      vtkCurvatures.cxx:379   WARN| vtkCurvatures (0x55ebe9fac7f0): The Gaussian or mean curvature at point 26259 have a large computation error... The maximum curvature is likely off.
srun: error: maestro-1016: task 0: Segmentation fault

I've experienced segmentation faults before when using vtk in combination with meshes, but I don't remember to have found a solution or pattern to when the problem occurred. I wouldn't be surprised if it correlated with meshes sometimes having weird properties like intersecting faces and such...

[bbarad]

So it looks like the input surfaces I was making are malformed vtk files some of the time. Something is wrong with this new meshing protocol - I am working on it. In the mean time, try turning "ultrafine" off in the config. I'll hopefully have a fix in the next couple days - we are now reproducibly getting this issue in-house which of course makes it much easier for me to fix!

[m-albert]

Thanks a lot for looking into this @bbarad! Happy to help with any testing from 15/7 on.

[GenevieveBuckley]

Thanks for working on a fix! I am also very happy to help test things.

[bbarad]

I've narrowed things down to a new issue with either pymeshlab's ply writer, vtk's ply reader, or vtk's vtp writer (seems least likely!). The VTP file that gets fed into pycurv etc is malformed - paraview can't load it either. Would either of you mind sharing a pip freeze of your environment that is causing segfaults?

[bbarad]

OK - I've narrowed it down to just VTK operations, as the ply file that is generated seems to work perfectly with other analysis.

[bbarad]

Disregard that - any VTK that I make from one of these ply files won't work. Seems to be coming from the pymeshlab side...

[GenevieveBuckley]

Would either of you mind sharing a pip freeze of your environment that is causing segfaults?

pip freeze (click to expand)

``` anyio==4.4.0 argon2-cffi==23.1.0 argon2-cffi-bindings==21.2.0 arrow==1.3.0 asttokens @ file:///home/conda/feedstock_root/build_artifacts/asttokens_1698341106958/work async-lru==2.0.4 attrs==23.2.0 Babel==2.15.0 beautifulsoup4==4.12.3 bleach==6.1.0 certifi @ file:///home/conda/feedstock_root/build_artifacts/certifi_1718025014955/work/certifi cffi @ file:///home/conda/feedstock_root/build_artifacts/cffi_1696001742886/work charset-normalizer==3.3.2 click==8.1.7 cloudpickle==3.0.0 comm==0.2.2 cycler @ file:///home/conda/feedstock_root/build_artifacts/cycler_1696677705766/work debugpy==1.8.2 decorator @ file:///home/conda/feedstock_root/build_artifacts/decorator_1641555617451/work defusedxml==0.7.1 dill==0.3.8 doit==0.36.0 exceptiongroup @ file:///home/conda/feedstock_root/build_artifacts/exceptiongroup_1704921103267/work executing @ file:///home/conda/feedstock_root/build_artifacts/executing_1698579936712/work fastjsonschema==2.20.0 fqdn==1.5.1 future==1.0.0 h11==0.14.0 httpcore==1.0.5 httpx==0.27.0 idna==3.7 imageio==2.34.2 importlib_metadata==8.0.0 iniconfig==2.0.0 ipykernel==6.29.4 ipython @ file:///home/conda/feedstock_root/build_artifacts/ipython_1701831663892/work ipywidgets==8.1.3 isoduration==20.11.0 jedi @ file:///home/conda/feedstock_root/build_artifacts/jedi_1696326070614/work Jinja2==3.1.4 joblib==1.4.2 json5==0.9.25 jsonpointer==3.0.0 jsonschema==4.22.0 jsonschema-specifications==2023.12.1 jupyter==1.0.0 jupyter-console==6.6.3 jupyter-events==0.10.0 jupyter-lsp==2.2.5 jupyter_client==8.6.2 jupyter_core==5.7.2 jupyter_server==2.14.1 jupyter_server_terminals==0.5.3 jupyterlab==4.2.3 jupyterlab_pygments==0.3.0 jupyterlab_server==2.27.2 jupyterlab_widgets==3.0.11 kiwisolver @ file:///home/conda/feedstock_root/build_artifacts/kiwisolver_1695379916629/work lazy_loader==0.4 MarkupSafe==2.1.5 matplotlib @ file:///home/conda/feedstock_root/build_artifacts/matplotlib-suite_1610582847402/work matplotlib-inline @ file:///home/conda/feedstock_root/build_artifacts/matplotlib-inline_1713250518406/work mistune==3.0.2 -e git+https://github.com/ccpem/mrcfile.git@2e2be7b7e09382caf1f1c37965bd2087a8746110#egg=mrcfile multiprocess==0.70.16 nbclient==0.10.0 nbconvert==7.16.4 nbformat==5.10.4 nest-asyncio==1.6.0 networkx==3.2.1 nibabel==5.2.1 notebook==7.2.1 notebook_shim==0.2.4 numpy @ file:///home/conda/feedstock_root/build_artifacts/numpy_1707225342954/work/dist/numpy-1.26.4-cp39-cp39-linux_x86_64.whl#sha256=c799942b5898f6e6c60264d1663a6469a475290e758c654aeeb78e2596463abd overrides==7.7.0 packaging @ file:///home/conda/feedstock_root/build_artifacts/packaging_1718189413536/work pandas @ file:///home/conda/feedstock_root/build_artifacts/pandas_1715897627815/work pandocfilters==1.5.1 parso @ file:///home/conda/feedstock_root/build_artifacts/parso_1712320355065/work pathos==0.3.2 patsy==0.5.6 pexpect @ file:///home/conda/feedstock_root/build_artifacts/pexpect_1706113125309/work pickleshare @ file:///home/conda/feedstock_root/build_artifacts/pickleshare_1602536217715/work pillow @ file:///home/conda/feedstock_root/build_artifacts/pillow_1718833722821/work platformdirs==4.2.2 pluggy==1.5.0 ply @ file:///home/conda/feedstock_root/build_artifacts/ply_1712242996588/work pox==0.3.4 ppft==1.7.6.8 prometheus_client==0.20.0 prompt_toolkit @ file:///home/conda/feedstock_root/build_artifacts/prompt-toolkit_1718047967974/work psutil==6.0.0 ptyprocess @ file:///home/conda/feedstock_root/build_artifacts/ptyprocess_1609419310487/work/dist/ptyprocess-0.7.0-py2.py3-none-any.whl pure-eval @ file:///home/conda/feedstock_root/build_artifacts/pure_eval_1642875951954/work pycairo==1.26.0 pycparser @ file:///home/conda/feedstock_root/build_artifacts/pycparser_1711811537435/work pycurv @ git+https://github.com/kalemaria/pycurv.git@6dd72f64455b3c8abfa0a152ab54894a27043080 Pygments @ file:///home/conda/feedstock_root/build_artifacts/pygments_1714846767233/work PyGObject==3.48.2 pymeshlab==2023.12.post1 pyparsing @ file:///home/conda/feedstock_root/build_artifacts/pyparsing_1709721012883/work PyQt5==5.15.9 PyQt5-sip==12.12.2 pytest==8.2.2 python-dateutil @ file:///home/conda/feedstock_root/build_artifacts/python-dateutil_1709299778482/work python-json-logger==2.0.7 pyto @ git+https://github.com/vladanl/Pyto.git@5cd9c556fee69a270dae5257c7dc78288c934a2c pytz @ file:///home/conda/feedstock_root/build_artifacts/pytz_1706886791323/work PyYAML==6.0.1 pyzmq==26.0.3 qtconsole==5.5.2 QtPy==2.4.1 referencing==0.35.1 requests==2.32.3 rfc3339-validator==0.1.4 rfc3986-validator==0.1.1 rpds-py==0.18.1 scikit-image==0.24.0 scikit-learn==1.5.0 scipy @ file:///home/conda/feedstock_root/build_artifacts/scipy-split_1716470218293/work/dist/scipy-1.13.1-cp39-cp39-linux_x86_64.whl#sha256=e6696cb8683d94467891b7648e068a3970f6bc0a1b3c1aa7f9bc89458eafd2f0 Send2Trash==1.8.3 sip @ file:///home/conda/feedstock_root/build_artifacts/sip_1697300422453/work six @ file:///home/conda/feedstock_root/build_artifacts/six_1620240208055/work sniffio==1.3.1 soupsieve==2.5 stack-data @ file:///home/conda/feedstock_root/build_artifacts/stack_data_1669632077133/work statsmodels==0.14.2 terminado==0.18.1 threadpoolctl==3.5.0 tifffile==2024.6.18 tinycss2==1.3.0 toml @ file:///home/conda/feedstock_root/build_artifacts/toml_1604308577558/work tomli @ file:///home/conda/feedstock_root/build_artifacts/tomli_1644342247877/work tornado @ file:///home/conda/feedstock_root/build_artifacts/tornado_1717722887379/work traitlets @ file:///home/conda/feedstock_root/build_artifacts/traitlets_1713535121073/work types-python-dateutil==2.9.0.20240316 typing_extensions @ file:///home/conda/feedstock_root/build_artifacts/typing_extensions_1717802530399/work tzdata @ file:///home/conda/feedstock_root/build_artifacts/python-tzdata_1707747584337/work uri-template==1.3.0 urllib3==2.2.2 vtk==9.3.0 wcwidth @ file:///home/conda/feedstock_root/build_artifacts/wcwidth_1704731205417/work webcolors==24.6.0 webencodings==0.5.1 websocket-client==1.8.0 widgetsnbextension==4.0.11 zipp==3.19.2 zstandard==0.22.0 ```

conda list (click to expand)

``` # packages in environment at /home/supervisor/miniforge3/envs/morphometrics: # # Name Version Build Channel _libgcc_mutex 0.1 conda_forge conda-forge _openmp_mutex 4.5 2_gnu conda-forge _x86_64-microarch-level 1 2_x86_64 conda-forge alsa-lib 1.2.12 h4ab18f5_0 conda-forge anyio 4.4.0 pypi_0 pypi argon2-cffi 23.1.0 pypi_0 pypi argon2-cffi-bindings 21.2.0 pypi_0 pypi arrow 1.3.0 pypi_0 pypi asttokens 2.4.1 pyhd8ed1ab_0 conda-forge async-lru 2.0.4 pypi_0 pypi at-spi2-atk 2.38.0 h0630a04_3 conda-forge at-spi2-core 2.40.3 h0630a04_0 conda-forge atk-1.0 2.38.0 h04ea711_2 conda-forge attr 2.5.1 h166bdaf_1 conda-forge attrs 23.2.0 pypi_0 pypi babel 2.15.0 pypi_0 pypi beautifulsoup4 4.12.3 pypi_0 pypi bleach 6.1.0 pypi_0 pypi bzip2 1.0.8 hd590300_5 conda-forge ca-certificates 2024.6.2 hbcca054_0 conda-forge cairo 1.18.0 hbb29018_2 conda-forge cairomm-1.16 1.16.2 h7e731d7_1 conda-forge certifi 2024.6.2 pyhd8ed1ab_0 conda-forge cffi 1.16.0 py39h7a31438_0 conda-forge charset-normalizer 3.3.2 pypi_0 pypi click 8.1.7 pypi_0 pypi cloudpickle 3.0.0 pypi_0 pypi comm 0.2.2 pypi_0 pypi cycler 0.12.1 pyhd8ed1ab_0 conda-forge dbus 1.13.6 h5008d03_3 conda-forge debugpy 1.8.2 pypi_0 pypi decorator 5.1.1 pyhd8ed1ab_0 conda-forge defusedxml 0.7.1 pypi_0 pypi dill 0.3.8 pypi_0 pypi doit 0.36.0 pypi_0 pypi epoxy 1.5.10 h166bdaf_1 conda-forge exceptiongroup 1.2.0 pyhd8ed1ab_2 conda-forge executing 2.0.1 pyhd8ed1ab_0 conda-forge expat 2.6.2 h59595ed_0 conda-forge fastjsonschema 2.20.0 pypi_0 pypi 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_2 conda-forge fontconfig 2.14.2 h14ed4e7_0 conda-forge fonts-conda-ecosystem 1 0 conda-forge fonts-conda-forge 1 0 conda-forge fqdn 1.5.1 pypi_0 pypi freetype 2.12.1 h267a509_2 conda-forge fribidi 1.0.10 h36c2ea0_0 conda-forge future 1.0.0 pypi_0 pypi gdk-pixbuf 2.42.12 hb9ae30d_0 conda-forge gettext 0.22.5 h59595ed_2 conda-forge gettext-tools 0.22.5 h59595ed_2 conda-forge glib 2.80.2 h8a4344b_1 conda-forge glib-tools 2.80.2 h73ef956_1 conda-forge gmp 6.3.0 hac33072_2 conda-forge graph-tool 2.70 py39hf2e61fb_100 conda-forge graph-tool-base 2.70 py39h9e6c721_100 conda-forge graphite2 1.3.13 h59595ed_1003 conda-forge gst-plugins-base 1.24.5 hbaaba92_0 conda-forge gstreamer 1.24.5 haf2f30d_0 conda-forge gtk3 3.24.42 h6d40eaa_0 conda-forge h11 0.14.0 pypi_0 pypi harfbuzz 8.5.0 hfac3d4d_0 conda-forge hicolor-icon-theme 0.17 ha770c72_2 conda-forge httpcore 1.0.5 pypi_0 pypi httpx 0.27.0 pypi_0 pypi icu 73.2 h59595ed_0 conda-forge idna 3.7 pypi_0 pypi imageio 2.34.2 pypi_0 pypi importlib-metadata 8.0.0 pypi_0 pypi iniconfig 2.0.0 pypi_0 pypi ipykernel 6.29.4 pypi_0 pypi ipython 8.18.1 pyh707e725_3 conda-forge ipywidgets 8.1.3 pypi_0 pypi isoduration 20.11.0 pypi_0 pypi jedi 0.19.1 pyhd8ed1ab_0 conda-forge jinja2 3.1.4 pypi_0 pypi joblib 1.4.2 pypi_0 pypi json5 0.9.25 pypi_0 pypi jsonpointer 3.0.0 pypi_0 pypi jsonschema 4.22.0 pypi_0 pypi jsonschema-specifications 2023.12.1 pypi_0 pypi jupyter 1.0.0 pypi_0 pypi jupyter-client 8.6.2 pypi_0 pypi jupyter-console 6.6.3 pypi_0 pypi jupyter-core 5.7.2 pypi_0 pypi jupyter-events 0.10.0 pypi_0 pypi jupyter-lsp 2.2.5 pypi_0 pypi jupyter-server 2.14.1 pypi_0 pypi jupyter-server-terminals 0.5.3 pypi_0 pypi jupyterlab 4.2.3 pypi_0 pypi jupyterlab-pygments 0.3.0 pypi_0 pypi jupyterlab-server 2.27.2 pypi_0 pypi jupyterlab-widgets 3.0.11 pypi_0 pypi keyutils 1.6.1 h166bdaf_0 conda-forge kiwisolver 1.4.5 py39h7633fee_1 conda-forge krb5 1.21.2 h659d440_0 conda-forge lame 3.100 h166bdaf_1003 conda-forge lazy-loader 0.4 pypi_0 pypi lcms2 2.16 hb7c19ff_0 conda-forge ld_impl_linux-64 2.40 hf3520f5_7 conda-forge lerc 4.0.0 h27087fc_0 conda-forge libasprintf 0.22.5 h661eb56_2 conda-forge libasprintf-devel 0.22.5 h661eb56_2 conda-forge libblas 3.9.0 22_linux64_openblas conda-forge libboost 1.84.0 hba137d9_3 conda-forge libboost-python 1.84.0 py39h85c637f_3 conda-forge libcap 2.69 h0f662aa_0 conda-forge libcblas 3.9.0 22_linux64_openblas conda-forge libclang-cpp15 15.0.7 default_h127d8a8_5 conda-forge libclang13 18.1.8 default_h6ae225f_0 conda-forge libcups 2.3.3 h4637d8d_4 conda-forge libdeflate 1.20 hd590300_0 conda-forge libedit 3.1.20191231 he28a2e2_2 conda-forge libevent 2.1.12 hf998b51_1 conda-forge libexpat 2.6.2 h59595ed_0 conda-forge libffi 3.4.2 h7f98852_5 conda-forge libflac 1.4.3 h59595ed_0 conda-forge libgcc-ng 13.2.0 h77fa898_13 conda-forge libgcrypt 1.10.3 hd590300_0 conda-forge libgettextpo 0.22.5 h59595ed_2 conda-forge libgettextpo-devel 0.22.5 h59595ed_2 conda-forge libgfortran-ng 13.2.0 h69a702a_13 conda-forge libgfortran5 13.2.0 h3d2ce59_13 conda-forge libgirepository 1.80.1 h003a4f0_0 conda-forge libglib 2.80.2 h8a4344b_1 conda-forge libgomp 13.2.0 h77fa898_13 conda-forge libgpg-error 1.49 h4f305b6_0 conda-forge libiconv 1.17 hd590300_2 conda-forge libjpeg-turbo 3.0.0 hd590300_1 conda-forge liblapack 3.9.0 22_linux64_openblas conda-forge libllvm15 15.0.7 hb3ce162_4 conda-forge libllvm18 18.1.8 hc9dba70_0 conda-forge libnsl 2.0.1 hd590300_0 conda-forge libogg 1.3.4 h7f98852_1 conda-forge libopenblas 0.3.27 pthreads_h413a1c8_0 conda-forge libopus 1.3.1 h7f98852_1 conda-forge libpng 1.6.43 h2797004_0 conda-forge libpq 16.3 ha72fbe1_0 conda-forge librsvg 2.58.1 hadf69e7_0 conda-forge libsndfile 1.2.2 hc60ed4a_1 conda-forge libsqlite 3.46.0 hde9e2c9_0 conda-forge libstdcxx-ng 13.2.0 hc0a3c3a_13 conda-forge libsystemd0 255 h3516f8a_1 conda-forge libtiff 4.6.0 h1dd3fc0_3 conda-forge libuuid 2.38.1 h0b41bf4_0 conda-forge libvorbis 1.3.7 h9c3ff4c_0 conda-forge libwebp-base 1.4.0 hd590300_0 conda-forge libxcb 1.16 hd590300_0 conda-forge libxcrypt 4.4.36 hd590300_1 conda-forge libxkbcommon 1.7.0 h2c5496b_1 conda-forge libxml2 2.12.7 hc051c1a_1 conda-forge libzlib 1.3.1 h4ab18f5_1 conda-forge lz4-c 1.9.4 hcb278e6_0 conda-forge markupsafe 2.1.5 pypi_0 pypi matplotlib 3.3.3 py39hf3d152e_0 conda-forge matplotlib-base 3.3.3 py39h2fa2bec_0 conda-forge matplotlib-inline 0.1.7 pyhd8ed1ab_0 conda-forge mistune 3.0.2 pypi_0 pypi mpg123 1.32.6 h59595ed_0 conda-forge mrcfile 1.5.0.dev0 dev_0 multiprocess 0.70.16 pypi_0 pypi mysql-common 8.3.0 hf1915f5_4 conda-forge mysql-libs 8.3.0 hca2cd23_4 conda-forge nbclient 0.10.0 pypi_0 pypi nbconvert 7.16.4 pypi_0 pypi nbformat 5.10.4 pypi_0 pypi ncurses 6.5 h59595ed_0 conda-forge nest-asyncio 1.6.0 pypi_0 pypi networkx 3.2.1 pypi_0 pypi nibabel 5.2.1 pypi_0 pypi notebook 7.2.1 pypi_0 pypi notebook-shim 0.2.4 pypi_0 pypi nspr 4.35 h27087fc_0 conda-forge nss 3.101 h593d115_0 conda-forge numpy 1.26.4 py39h474f0d3_0 conda-forge openjpeg 2.5.2 h488ebb8_0 conda-forge openssl 3.3.1 h4ab18f5_0 conda-forge overrides 7.7.0 pypi_0 pypi packaging 24.1 pyhd8ed1ab_0 conda-forge pandas 2.2.2 py39hfc16268_1 conda-forge pandocfilters 1.5.1 pypi_0 pypi pango 1.54.0 h84a9a3c_0 conda-forge parso 0.8.4 pyhd8ed1ab_0 conda-forge pathlib 1.0.1 py39hf3d152e_7 conda-forge pathos 0.3.2 pypi_0 pypi patsy 0.5.6 pypi_0 pypi pcre2 10.44 h0f59acf_0 conda-forge pexpect 4.9.0 pyhd8ed1ab_0 conda-forge pickleshare 0.7.5 py_1003 conda-forge pillow 10.3.0 py39h16a7006_1 conda-forge pip 24.0 pyhd8ed1ab_0 conda-forge pixman 0.43.2 h59595ed_0 conda-forge platformdirs 4.2.2 pypi_0 pypi pluggy 1.5.0 pypi_0 pypi ply 3.11 pyhd8ed1ab_2 conda-forge pox 0.3.4 pypi_0 pypi ppft 1.7.6.8 pypi_0 pypi prometheus-client 0.20.0 pypi_0 pypi prompt-toolkit 3.0.47 pyha770c72_0 conda-forge psutil 6.0.0 pypi_0 pypi pthread-stubs 0.4 h36c2ea0_1001 conda-forge ptyprocess 0.7.0 pyhd3deb0d_0 conda-forge pulseaudio-client 17.0 hb77b528_0 conda-forge pure_eval 0.2.2 pyhd8ed1ab_0 conda-forge pycairo 1.26.0 py39hc92de75_0 conda-forge pycparser 2.22 pyhd8ed1ab_0 conda-forge pycurv 2.0.0 pypi_0 pypi pygments 2.18.0 pyhd8ed1ab_0 conda-forge pygobject 3.48.2 py39hb25b1be_0 conda-forge pymeshlab 2023.12.post1 pypi_0 pypi pyparsing 3.1.2 pyhd8ed1ab_0 conda-forge pyqt 5.15.9 py39h52134e7_5 conda-forge pyqt5-sip 12.12.2 py39h3d6467e_5 conda-forge pytest 8.2.2 pypi_0 pypi python 3.9.19 h0755675_0_cpython conda-forge python-dateutil 2.9.0 pyhd8ed1ab_0 conda-forge python-json-logger 2.0.7 pypi_0 pypi python-tzdata 2024.1 pyhd8ed1ab_0 conda-forge python_abi 3.9 4_cp39 conda-forge pyto 1.9.2 pypi_0 pypi pytz 2024.1 pyhd8ed1ab_0 conda-forge pyyaml 6.0.1 pypi_0 pypi pyzmq 26.0.3 pypi_0 pypi qt-main 5.15.8 ha2b5568_22 conda-forge qtconsole 5.5.2 pypi_0 pypi qtpy 2.4.1 pypi_0 pypi readline 8.2 h8228510_1 conda-forge referencing 0.35.1 pypi_0 pypi requests 2.32.3 pypi_0 pypi rfc3339-validator 0.1.4 pypi_0 pypi rfc3986-validator 0.1.1 pypi_0 pypi rpds-py 0.18.1 pypi_0 pypi scikit-image 0.24.0 pypi_0 pypi scikit-learn 1.5.0 pypi_0 pypi scipy 1.13.1 py39haf93ffa_0 conda-forge send2trash 1.8.3 pypi_0 pypi setuptools 70.1.0 pyhd8ed1ab_0 conda-forge sigcpp-3.0 3.6.0 h59595ed_0 conda-forge sip 6.7.12 py39h3d6467e_0 conda-forge six 1.16.0 pyh6c4a22f_0 conda-forge sniffio 1.3.1 pypi_0 pypi soupsieve 2.5 pypi_0 pypi sparsehash 2.0.4 hcb278e6_1 conda-forge stack_data 0.6.2 pyhd8ed1ab_0 conda-forge statsmodels 0.14.2 pypi_0 pypi terminado 0.18.1 pypi_0 pypi threadpoolctl 3.5.0 pypi_0 pypi tifffile 2024.6.18 pypi_0 pypi tinycss2 1.3.0 pypi_0 pypi tk 8.6.13 noxft_h4845f30_101 conda-forge toml 0.10.2 pyhd8ed1ab_0 conda-forge tomli 2.0.1 pyhd8ed1ab_0 conda-forge tornado 6.4.1 py39hd3abc70_0 conda-forge traitlets 5.14.3 pyhd8ed1ab_0 conda-forge types-python-dateutil 2.9.0.20240316 pypi_0 pypi typing_extensions 4.12.2 pyha770c72_0 conda-forge tzdata 2024a h0c530f3_0 conda-forge uri-template 1.3.0 pypi_0 pypi urllib3 2.2.2 pypi_0 pypi vtk 9.3.0 pypi_0 pypi wayland 1.23.0 h5291e77_0 conda-forge wcwidth 0.2.13 pyhd8ed1ab_0 conda-forge webcolors 24.6.0 pypi_0 pypi webencodings 0.5.1 pypi_0 pypi websocket-client 1.8.0 pypi_0 pypi wheel 0.43.0 pyhd8ed1ab_1 conda-forge widgetsnbextension 4.0.11 pypi_0 pypi xcb-util 0.4.1 hb711507_2 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 xkeyboard-config 2.42 h4ab18f5_0 conda-forge xorg-compositeproto 0.4.2 h7f98852_1001 conda-forge xorg-damageproto 1.2.1 h7f98852_1002 conda-forge xorg-fixesproto 5.0 h7f98852_1002 conda-forge xorg-inputproto 2.3.2 h7f98852_1002 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 1.8.9 hb711507_1 conda-forge xorg-libxau 1.0.11 hd590300_0 conda-forge xorg-libxcomposite 0.4.6 h0b41bf4_1 conda-forge xorg-libxcursor 1.2.0 h0b41bf4_1 conda-forge xorg-libxdamage 1.1.5 h7f98852_1 conda-forge xorg-libxdmcp 1.1.3 h7f98852_0 conda-forge xorg-libxext 1.3.4 h0b41bf4_2 conda-forge xorg-libxfixes 5.0.3 h7f98852_1004 conda-forge xorg-libxi 1.7.10 h7f98852_0 conda-forge xorg-libxinerama 1.1.5 h27087fc_0 conda-forge xorg-libxrandr 1.5.2 h7f98852_1 conda-forge xorg-libxrender 0.9.11 hd590300_0 conda-forge xorg-libxtst 1.2.3 h7f98852_1002 conda-forge xorg-randrproto 1.5.0 h7f98852_1001 conda-forge xorg-recordproto 1.14.2 h7f98852_1002 conda-forge xorg-renderproto 0.11.1 h7f98852_1002 conda-forge xorg-util-macros 1.19.3 h7f98852_0 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 zipp 3.19.2 pypi_0 pypi zlib 1.3.1 h4ab18f5_1 conda-forge zstandard 0.22.0 py39h81c9582_1 conda-forge zstd 1.5.6 ha6fb4c9_0 conda-forge ```

[GenevieveBuckley]

Sadly, setting "ultrafine: false" did not help.

[bbarad]

Yeah, I can't get anything from meshlab or pymeshlab through with any settings on the workstation. Works fine on my laptop of course... Just a matter of identifying the difference now!

On Mon, Jul 8, 2024 at 6:03 PM Genevieve Buckley @.***> wrote:

Sadly, setting "ultrafine: false" did not help.

— Reply to this email directly, view it on GitHub https://github.com/GrotjahnLab/surface_morphometrics/issues/27#issuecomment-2215919365, or unsubscribe https://github.com/notifications/unsubscribe-auth/ABKJDT4XU54DTRRNMXLZEJDZLMZFTAVCNFSM6AAAAABJ7Q2VWKVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDEMJVHEYTSMZWGU . You are receiving this because you were mentioned.Message ID: @.***>

[GenevieveBuckley]

You said you have a reproducible example now, would it help to share that so we can both be looking at the same thing?

[Kathir-66]

Although I not running on a HPC. Some of the tomograms succesfully run the run_pycurv.py step and some don't. So I will also share my pip freeze and conda list

I am using the surface_morphometrics-1.0beta1 version

pip freeze

``` absl-py==2.0.0 alabaster==0.7.16 annotated-types==0.7.0 app-model==0.2.7 appdirs==1.4.4 asteval==0.9.32 asttokens==2.4.1 astunparse==1.6.3 attrs==23.2.0 Babel==2.15.0 build==1.2.1 cachetools==5.3.2 cachey==0.2.1 certifi @ file:///croot/certifi_1717618050233/work/certifi cffi @ file:///croot/cffi_1714483155441/work click==8.1.7 cloudpickle==3.0.0 comm==0.2.2 contourpy==1.2.0 cryoCAT==0.2.0 cycler==0.12.1 dask==2024.5.1 debugpy==1.8.1 decorator==5.1.1 dill==0.3.8 distlib==0.3.8 docstring_parser==0.16 docutils==0.21.2 doit==0.36.0 emfile==0.3.0 exceptiongroup==1.2.1 executing==2.0.1 filelock==3.13.1 fire==0.5.0 flatbuffers==23.5.26 fonttools==4.45.1 freetype-py==2.4.0 fsspec==2024.5.0 future==1.0.0 gast==0.5.4 google-auth==2.23.4 google-auth-oauthlib==1.0.0 google-pasta==0.2.0 grpcio==1.59.3 h5py==3.10.0 HeapDict==1.0.1 hsluv==5.0.4 imageio==2.33.0 imagesize==1.4.1 importlib-metadata==6.8.0 importlib-resources==6.1.1 in-n-out==0.2.1 iniconfig==2.0.0 ipykernel==6.29.4 ipython==8.18.1 jedi==0.19.1 Jinja2==3.1.4 joblib==1.3.2 jsonschema==4.22.0 jsonschema-specifications==2023.12.1 jupyter_client==8.6.2 jupyter_core==5.7.2 keras==2.14.0 kiwisolver==1.4.5 lazy_loader==0.3 libclang==16.0.6 lmfit==1.2.2 locket==1.0.0 magicgui==0.8.2 Markdown==3.5.1 markdown-it-py==3.0.0 MarkupSafe==2.1.3 matplotlib==3.8.2 matplotlib-inline==0.1.7 mdurl==0.1.2 ml-dtypes==0.2.0 mpi4py_mpich==3.1.5 mrcfile==1.4.3 multiprocess==0.70.16 napari==0.4.19.post1 napari-console==0.0.9 -e git+ssh://git@gitlab.mpcdf.mpg.de/mpibr/scic/napari-particle-extraction.git@a70184f1ec570e1801a4e3d49894648736e0c604#egg=napari_particle_extraction napari-plugin-engine==0.2.0 napari-svg==0.1.10 nest-asyncio==1.6.0 networkx==3.2.1 nibabel==5.2.1 npe2==0.7.5 numpy==1.23.5 numpydoc==1.7.0 nvidia-cublas-cu11==11.11.3.6 nvidia-cublas-cu12==12.5.2.13 nvidia-cuda-cupti-cu11==11.8.87 nvidia-cuda-nvcc-cu11==11.8.89 nvidia-cuda-runtime-cu11==11.8.89 nvidia-cudnn-cu11==8.7.0.84 nvidia-cudnn-cu12==9.1.1.17 nvidia-cufft-cu11==10.9.0.58 nvidia-curand-cu11==10.3.0.86 nvidia-cusolver-cu11==11.4.1.48 nvidia-cusparse-cu11==11.7.5.86 nvidia-nccl-cu11==2.16.5 oauthlib==3.2.2 opt-einsum==3.3.0 packaging==24.0 pandas @ file:///home/conda/feedstock_root/build_artifacts/pandas_1715897627815/work parso==0.8.4 partd==1.4.2 pathlib==1.0.1 pathos==0.3.2 patsy==0.5.6 pexpect==4.9.0 Pillow==10.1.0 Pint==0.23 platformdirs==4.1.0 pluggy==1.5.0 ply==3.11 pooch==1.8.1 pox==0.3.4 ppft==1.7.6.8 prompt_toolkit==3.0.45 protobuf==4.25.1 psutil==5.9.8 psygnal==0.11.1 ptyprocess==0.7.0 pure-eval==0.2.2 pyarrow==15.0.2 pyasn1==0.5.1 pyasn1-modules==0.3.0 pycairo==1.23.0 pyconify==0.1.6 pycparser @ file:///tmp/build/80754af9/pycparser_1636541352034/work pycurv @ git+https://github.com/kalemaria/pycurv.git@6dd72f64455b3c8abfa0a152ab54894a27043080 pydantic-compat==0.1.2 pydantic_core==2.18.2 Pygments==2.18.0 PyGObject==3.48.2 pymeshlab==2022.2.post3 PyOpenGL==3.1.7 pyparsing==3.1.1 pyproject_hooks==1.1.0 PyQt5==5.15.10 PyQt5-Qt5==5.15.2 PyQt5-sip==12.13.0 pytest==8.2.1 python-dateutil==2.8.2 pyto @ git+https://github.com/vladanl/Pyto.git@5cd9c556fee69a270dae5257c7dc78288c934a2c pytz==2024.1 PyWavelets==1.5.0 PyYAML==6.0.1 pyzmq==26.0.3 qtconsole==5.5.2 QtPy==2.4.1 referencing==0.35.1 requests-oauthlib==1.3.1 rich==13.7.1 rpds-py==0.18.1 rsa==4.9 scikit-image==0.22.0 scikit-learn==1.4.1.post1 scipy==1.11.4 seaborn==0.13.2 shellingham==1.5.4 sip @ file:///croot/sip_1698675935381/work six==1.16.0 snowballstemmer==2.2.0 Sphinx==7.3.7 sphinxcontrib-applehelp==1.0.8 sphinxcontrib-devhelp==1.0.6 sphinxcontrib-htmlhelp==2.0.5 sphinxcontrib-jsmath==1.0.1 sphinxcontrib-qthelp==1.0.7 sphinxcontrib-serializinghtml==1.1.10 stack-data==0.6.3 starfile==0.5.6 statsmodels==0.14.2 superqt==0.6.6 tabulate==0.9.0 tensorboard==2.14.1 tensorboard-data-server==0.7.2 tensorflow==2.14.1 tensorflow-estimator==2.14.0 tensorflow-io-gcs-filesystem==0.34.0 tensorrt==8.5.3.1 termcolor==2.3.0 threadpoolctl==3.4.0 tifffile==2023.9.26 toml @ file:///tmp/build/80754af9/toml_1616166611790/work tomli==2.0.1 tomli_w==1.0.0 tornado==6.4 traitlets==5.14.3 typer==0.12.3 typing_extensions==4.8.0 tzdata==2024.1 uncertainties==3.1.7 virtualenv==20.25.0 vispy==0.14.2 vtk==9.3.0 wcwidth==0.2.13 Werkzeug==3.0.1 wrapt==1.14.1 zipp==3.17.0 zstandard @ file:///croot/zstandard_1714677652653/work ```

conda list

# packages in environment at /opt/local/software/miniconda/envs/morphometrics: # # Name Version Build Channel _libgcc_mutex 0.1 conda_forge conda-forge _openmp_mutex 4.5 2_gnu conda-forge _x86_64-microarch-level 4 2_skylake_avx512 conda-forge alsa-lib 1.2.12 h4ab18f5_0 conda-forge at-spi2-atk 2.38.0 h0630a04_3 conda-forge at-spi2-core 2.40.3 h0630a04_0 conda-forge atk-1.0 2.38.0 h04ea711_2 conda-forge attr 2.5.1 h166bdaf_1 conda-forge blas 1.0 openblas bzip2 1.0.8 h5eee18b_6 ca-certificates 2024.3.11 h06a4308_0 cairo 1.18.0 h3faef2a_0 conda-forge cairomm-1.16 1.16.2 h7e731d7_1 conda-forge certifi 2024.6.2 py39h06a4308_0 cffi 1.16.0 py39h5eee18b_1 click 8.1.7 pypi_0 pypi cloudpickle 3.0.0 pypi_0 pypi cycler 0.11.0 pyhd3eb1b0_0 dbus 1.13.18 hb2f20db_0 dill 0.3.8 pypi_0 pypi doit 0.36.0 pypi_0 pypi epoxy 1.5.10 h166bdaf_1 conda-forge exceptiongroup 1.2.1 pypi_0 pypi expat 2.6.2 h6a678d5_0 font-ttf-dejavu-sans-mono 2.37 hd3eb1b0_0 font-ttf-inconsolata 2.001 hcb22688_0 font-ttf-source-code-pro 2.030 hd3eb1b0_0 font-ttf-ubuntu 0.83 h8b1ccd4_0 fontconfig 2.14.2 h14ed4e7_0 conda-forge fonts-anaconda 1 h8fa9717_0 fonts-conda-ecosystem 1 hd3eb1b0_0 freetype 2.12.1 h4a9f257_0 fribidi 1.0.10 h7b6447c_0 future 1.0.0 pypi_0 pypi gdk-pixbuf 2.42.12 hb9ae30d_0 conda-forge gettext 0.22.5 h59595ed_2 conda-forge gettext-tools 0.22.5 h59595ed_2 conda-forge glib 2.80.2 hf974151_0 conda-forge glib-tools 2.80.2 hb6ce0ca_0 conda-forge gmp 6.3.0 h59595ed_1 conda-forge graph-tool 2.69 py39h3a7ffd6_400 conda-forge graph-tool-base 2.69 py39hc4a2bb6_400 conda-forge graphite2 1.3.14 h295c915_1 gst-plugins-base 1.24.4 h9ad1361_0 conda-forge gstreamer 1.24.4 haf2f30d_0 conda-forge gtk3 3.24.42 h6d40eaa_0 conda-forge harfbuzz 8.5.0 hfac3d4d_0 conda-forge hicolor-icon-theme 0.17 h06a4308_2 icu 73.2 h59595ed_0 conda-forge imageio 2.34.1 pypi_0 pypi importlib-metadata 7.1.0 pypi_0 pypi iniconfig 2.0.0 pypi_0 pypi keyutils 1.6.1 h166bdaf_0 conda-forge kiwisolver 1.4.4 py39h6a678d5_0 krb5 1.21.2 h659d440_0 conda-forge lame 3.100 h7b6447c_0 lazy-loader 0.4 pypi_0 pypi lcms2 2.16 hb7c19ff_0 conda-forge ld_impl_linux-64 2.38 h1181459_1 lerc 4.0.0 h27087fc_0 conda-forge libasprintf 0.22.5 h661eb56_2 conda-forge libasprintf-devel 0.22.5 h661eb56_2 conda-forge libboost 1.84.0 h8013b2b_2 conda-forge libboost-python 1.84.0 py39h85c637f_3 conda-forge libcap 2.69 h0f662aa_0 conda-forge libclang-cpp15 15.0.7 default_h127d8a8_5 conda-forge libclang13 18.1.4 default_h5d6823c_0 conda-forge libcups 2.3.3 h4637d8d_4 conda-forge libdeflate 1.20 hd590300_0 conda-forge libedit 3.1.20230828 h5eee18b_0 libevent 2.1.12 hdbd6064_1 libexpat 2.6.2 h59595ed_0 conda-forge libffi 3.4.4 h6a678d5_1 libflac 1.4.3 h59595ed_0 conda-forge libgcc-ng 13.2.0 h77fa898_7 conda-forge libgcrypt 1.10.3 hd590300_0 conda-forge libgettextpo 0.22.5 h59595ed_2 conda-forge libgettextpo-devel 0.22.5 h59595ed_2 conda-forge libgfortran-ng 11.2.0 h00389a5_1 libgfortran5 11.2.0 h1234567_1 libgirepository 1.80.1 h003a4f0_0 conda-forge libglib 2.80.2 hf974151_0 conda-forge libgomp 13.2.0 h77fa898_7 conda-forge libgpg-error 1.49 h4f305b6_0 conda-forge libiconv 1.17 hd590300_2 conda-forge libjpeg-turbo 3.0.0 hd590300_1 conda-forge libllvm15 15.0.7 hb3ce162_4 conda-forge libllvm18 18.1.4 h2448989_0 conda-forge libnsl 2.0.1 hd590300_0 conda-forge libogg 1.3.5 h27cfd23_1 libopenblas 0.3.21 h043d6bf_0 libopus 1.3.1 h7b6447c_0 libpng 1.6.43 h2797004_0 conda-forge libpq 16.3 ha72fbe1_0 conda-forge librsvg 2.58.0 hadf69e7_1 conda-forge libsndfile 1.2.2 hc60ed4a_1 conda-forge libsqlite 3.46.0 hde9e2c9_0 conda-forge libstdcxx-ng 13.2.0 hc0a3c3a_7 conda-forge libsystemd0 255 h3516f8a_1 conda-forge libtiff 4.6.0 h1dd3fc0_3 conda-forge libuuid 2.38.1 h0b41bf4_0 conda-forge libvorbis 1.3.7 h7b6447c_0 libwebp-base 1.3.2 h5eee18b_0 libxcb 1.15 h7f8727e_0 libxcrypt 4.4.36 hd590300_1 conda-forge libxkbcommon 1.7.0 h662e7e4_0 conda-forge libxml2 2.12.7 hc051c1a_1 conda-forge libzlib 1.2.13 h4ab18f5_6 conda-forge lz4-c 1.9.4 h6a678d5_1 matplotlib 3.3.3 py39hf3d152e_0 conda-forge matplotlib-base 3.3.3 py39h2fa2bec_0 conda-forge mpg123 1.32.6 h59595ed_0 conda-forge mrcfile 1.5.0 pypi_0 pypi multiprocess 0.70.16 pypi_0 pypi mysql-common 8.3.0 hf1915f5_4 conda-forge mysql-libs 8.3.0 hca2cd23_4 conda-forge ncurses 6.5 h59595ed_0 conda-forge networkx 3.2.1 pypi_0 pypi nibabel 5.2.1 pypi_0 pypi nspr 4.35 h6a678d5_0 nss 3.100 hca3bf56_0 conda-forge numpy 1.26.4 py39heeff2f4_0 numpy-base 1.26.4 py39h8a23956_0 openjpeg 2.5.2 h488ebb8_0 conda-forge openssl 3.3.1 h4ab18f5_0 conda-forge packaging 23.2 py39h06a4308_0 pandas 2.2.2 py39hfc16268_1 conda-forge pango 1.54.0 h84a9a3c_0 conda-forge pathlib 1.0.1 py39hf3d152e_7 conda-forge pathos 0.3.2 pypi_0 pypi pcre2 10.43 hcad00b1_0 conda-forge pillow 10.3.0 py39h90c7501_0 conda-forge pip 24.0 pyhd8ed1ab_0 conda-forge pixman 0.43.2 h59595ed_0 conda-forge pluggy 1.5.0 pypi_0 pypi ply 3.11 py39h06a4308_0 pox 0.3.4 pypi_0 pypi ppft 1.7.6.8 pypi_0 pypi pulseaudio-client 17.0 hb77b528_0 conda-forge pybind11-abi 4 hd3eb1b0_1 pycairo 1.23.0 py39hd1222b9_0 pycparser 2.21 pyhd3eb1b0_0 pycurv 2.0.0 pypi_0 pypi pygobject 3.48.2 py39hb25b1be_0 conda-forge pymeshlab 2022.2.post3 pypi_0 pypi pyparsing 3.0.9 py39h06a4308_0 pyqt 5.15.9 py39h52134e7_5 conda-forge pyqt5-sip 12.12.2 py39h3d6467e_5 conda-forge pytest 8.2.2 pypi_0 pypi python 3.9.19 h0755675_0_cpython conda-forge python-dateutil 2.9.0post0 py39h06a4308_2 python-tzdata 20

[bbarad]

I am actually running into my problems with the example data, which shows its really generic. Its happening with or without the new ultrafine sampling, so I don't believe thats the issue. I've attached the ply and surface.vtp files. What's odd is that both of these seem to work fine on my m1 mac but not on my ubuntu workstations... Surfaces.zip

[Kathir-66]

The issue always occurs to me when I am running it on the Inner mitochondria membrane and always works with the OMM without any issues!

But wow, were you able to find a workaround or a solution that could work?