Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Jump to bottom

Segmentation fault using phy template-gui params.py #1320

Open
FabianMunozSilva opened this issue Dec 17, 2024 · 2 comments
Open

Segmentation fault using phy template-gui params.py #1320

FabianMunozSilva opened this issue Dec 17, 2024 · 2 comments

Comments

@FabianMunozSilva
Copy link

Hi Evereyone,
I just started with Kilosort, and it is working but when I run
phy template-gui params.py --debug
14:44:52.938 [D] init:68 Start capturing exceptions.
14:44:52.963 [D] model:619 Loading spike clusters.
14:44:52.983 [D] model:692 Loading templates.
14:44:52.992 [D] model:724 Templates are dense.
14:44:52.992 [W] model:667 Skipping spike waveforms that do not exist, they will be extracted on the fly from the raw data as needed.
14:44:52.992 [D] model:730 Loading the whitening matrix.
14:44:52.992 [D] model:737 Loading the inverse of the whitening matrix.
14:44:52.993 [D] model:766 Loading features.
14:44:52.994 [D] model:781 Features are sparse.
14:44:52.994 [D] model:803 Loading template features.
14:44:52.995 [D] model:530 Load spike_detection_templates.npy.
14:44:52.996 [D] model:530 Load spike_positions.npy.
14:44:52.996 [D] model:504 Load cluster_Amplitude.tsv.
14:44:52.997 [D] model:504 Load cluster_group.tsv.
14:44:52.998 [D] model:504 Load cluster_ContamPct.tsv.
14:44:52.999 [D] model:504 Load cluster_KSLabel.tsv.
14:44:53.141 [D] context:100 Initialize joblib cache dir at /home/vpflab/Documents/K4/kilosort4/.phy.
14:44:53.141 [D] context:101 Reducing the size of the cache if needed.
14:44:53.142 [D] base:102 Add filter high_pass.
14:44:53.142 [D] config:31 Load config file /home/vpflab/.phy/phy_config.py.
14:44:53.142 [D] plugin:146 Loading 0 plugins.
14:44:53.143 [D] context:209 The file /home/vpflab/Documents/K4/kilosort4/.phy/new_cluster_id.pkl doesn't exist.
14:44:53.158 [D] context:185 Save data to /home/vpflab/Documents/K4/kilosort4/.phy/spikes_per_cluster.pkl.
14:44:53.190 [D] gui:463 Creating GUI.
14:44:53.195 [D] state:46 Load /home/vpflab/.phy/TemplateGUI/state.json for GUIState.
Segmentation fault (core dumped)
I’ve reviewed previous posts but haven’t found a solution to my problem. I can run phy trace-gui params.py, so I suspect the issue is related to the graphical interface. However, I’m unsure how to resolve it.
For reference, I’m using Ubuntu 24.04.1 LTS.
Any guidance would be greatly appreciated!
Thanks in advance
Fabian
@FabianMunozSilva
Copy link
Author

I change the python from 3.9 to 3.12 in environment.yml installation and I can see the GUI but I can not see the traces I have this message
15:18:46.798 [W] gui:671 Could not create view TemplateFeatureView.
dict_keys([<class 'numpy.ndarray'>, <class 'bytes'>, <class 'OpenGL.converters.c_int_Array_1'>])

@ilsedippenaar
Copy link

ilsedippenaar commented Dec 20, 2024 •
edited
Loading

Hi! I'm running into a similar problem, also on Ubuntu 24.04.1. I ran these installation steps:

conda create -n phy2 -y python=3.11
conda activate phy2
conda install -c conda-forge libstdcxx-ng  # needed to allow MESA-LOADER to find iris and swrast shared libraries
pip install git+https://github.com/cortex-lab/phy.git

I also needed to update conda to >24 to avoid needing to mess with LD_PRELOAD in order to pull a more recent C library for the iris_dri.so and swrast_dri.so binaries. After doing all of that, I experience what's described above (Phy launches, but no traces displayed). However, in my case, Phy throws a lot of Exception in paintGL: Attempt to retrieve context when no valid context errors.

If I try installing with conda env update environment.yml --prune, I get a host of version errors or missing package errors (e.g., libiconv, libicuuc) with Glib version mismatches as well.

Weirdly, Phy does work perfectly well on a different computer running Ubuntu 24.04.1 but that computer has a GPU. In that case, I didn't need to update libstdcxx-ng, but I did need to install directly from environment.yml. In case it's helpful, I've copied the full frozen environment from that computer below, but there are still plenty of version conflicts when I install on the first computer.

environment.yml 
name: phy2
channels:
  - conda-forge
  - defaults
dependencies:
  - _libgcc_mutex=0.1=conda_forge
  - _openmp_mutex=4.5=2_gnu
  - alsa-lib=1.2.13=hb9d3cd8_0
  - asttokens=3.0.0=pyhd8ed1ab_1
  - attr=2.5.1=h166bdaf_1
  - aws-c-auth=0.8.0=hb921021_15
  - aws-c-cal=0.8.1=h1a47875_3
  - aws-c-common=0.10.6=hb9d3cd8_0
  - aws-c-compression=0.3.0=h4e1184b_5
  - aws-c-event-stream=0.5.0=h7959bf6_11
  - aws-c-http=0.9.2=hefd7a92_4
  - aws-c-io=0.15.3=h831e299_5
  - aws-c-mqtt=0.11.0=h11f4f37_12
  - aws-c-s3=0.7.7=hf454442_0
  - aws-c-sdkutils=0.2.1=h4e1184b_4
  - aws-checksums=0.2.2=h4e1184b_4
  - aws-crt-cpp=0.29.7=hd92328a_7
  - aws-sdk-cpp=1.11.458=hc430e4a_4
  - azure-core-cpp=1.14.0=h5cfcd09_0
  - azure-identity-cpp=1.10.0=h113e628_0
  - azure-storage-blobs-cpp=12.13.0=h3cf044e_1
  - azure-storage-common-cpp=12.8.0=h736e048_1
  - azure-storage-files-datalake-cpp=12.12.0=ha633028_1
  - bokeh=3.6.2=pyhd8ed1ab_1
  - brotli=1.1.0=hb9d3cd8_2
  - brotli-bin=1.1.0=hb9d3cd8_2
  - brotli-python=1.1.0=py311hfdbb021_2
  - bzip2=1.0.8=h5eee18b_6
  - c-ares=1.34.4=hb9d3cd8_0
  - ca-certificates=2024.12.14=hbcca054_0
  - cached-property=1.5.2=hd8ed1ab_1
  - cached_property=1.5.2=pyha770c72_1
  - cairo=1.18.2=h3394656_1
  - certifi=2024.12.14=pyhd8ed1ab_0
  - cffi=1.17.1=py311hf29c0ef_0
  - charset-normalizer=3.4.0=pyhd8ed1ab_1
  - click=8.1.7=unix_pyh707e725_1
  - cloudpickle=3.1.0=pyhd8ed1ab_1
  - colorama=0.4.6=pyhd8ed1ab_1
  - comm=0.2.2=pyhd8ed1ab_1
  - contourpy=1.3.1=py311hd18a35c_0
  - cycler=0.12.1=pyhd8ed1ab_1
  - cyrus-sasl=2.1.27=h54b06d7_7
  - cython=3.0.11=py311h55d416d_3
  - cytoolz=1.0.1=py311h9ecbd09_0
  - dask=2024.12.1=pyhd8ed1ab_0
  - dask-core=2024.12.1=pyhd8ed1ab_0
  - dask-expr=1.1.21=pyhd8ed1ab_0
  - dbus=1.13.6=h5008d03_3
  - debugpy=1.8.11=py311hfdbb021_0
  - decorator=5.1.1=pyhd8ed1ab_1
  - distributed=2024.12.1=pyhd8ed1ab_0
  - double-conversion=3.3.0=h59595ed_0
  - exceptiongroup=1.2.2=pyhd8ed1ab_1
  - executing=2.1.0=pyhd8ed1ab_1
  - expat=2.6.4=h5888daf_0
  - font-ttf-dejavu-sans-mono=2.37=hab24e00_0
  - font-ttf-inconsolata=3.000=h77eed37_0
  - font-ttf-source-code-pro=2.038=h77eed37_0
  - font-ttf-ubuntu=0.83=h77eed37_3
  - fontconfig=2.15.0=h7e30c49_1
  - fonts-conda-ecosystem=1=0
  - fonts-conda-forge=1=0
  - fonttools=4.55.3=py311h2dc5d0c_0
  - freetype=2.12.1=h267a509_2
  - fsspec=2024.10.0=pyhd8ed1ab_1
  - gettext=0.22.5=he02047a_3
  - gettext-tools=0.22.5=he02047a_3
  - gflags=2.2.2=h5888daf_1005
  - giflib=5.2.2=hd590300_0
  - git=2.47.1=pl5321h59d505e_0
  - glib=2.82.2=h44428e9_0
  - glib-tools=2.82.2=h4833e2c_0
  - glog=0.7.1=hbabe93e_0
  - graphite2=1.3.13=h59595ed_1003
  - gst-plugins-base=1.24.7=h0a52356_0
  - gstreamer=1.24.7=hf3bb09a_0
  - h2=4.1.0=pyhd8ed1ab_1
  - h5py=3.12.1=nompi_py311hb639ac4_102
  - harfbuzz=9.0.0=hda332d3_1
  - hdf5=1.14.3=nompi_h2d575fe_108
  - hpack=4.0.0=pyhd8ed1ab_1
  - hyperframe=6.0.1=pyhd8ed1ab_1
  - icu=75.1=he02047a_0
  - idna=3.10=pyhd8ed1ab_1
  - importlib-metadata=8.5.0=pyha770c72_1
  - iniconfig=2.0.0=pyhd8ed1ab_1
  - ipykernel=6.29.5=pyh3099207_0
  - ipython=8.30.0=pyh707e725_0
  - jedi=0.19.2=pyhd8ed1ab_1
  - jinja2=3.1.4=pyhd8ed1ab_1
  - joblib=1.4.2=pyhd8ed1ab_1
  - jupyter_client=8.6.3=pyhd8ed1ab_1
  - jupyter_core=5.7.2=pyh31011fe_1
  - keyutils=1.6.1=h166bdaf_0
  - kiwisolver=1.4.7=py311hd18a35c_0
  - krb5=1.21.3=h659f571_0
  - lame=3.100=h166bdaf_1003
  - lcms2=2.16=hb7c19ff_0
  - ld_impl_linux-64=2.40=h12ee557_0
  - lerc=4.0.0=h27087fc_0
  - libabseil=20240722.0=cxx17_h5888daf_1
  - libaec=1.1.3=h59595ed_0
  - libarrow=18.1.0=h44a453e_6_cpu
  - libarrow-acero=18.1.0=hcb10f89_6_cpu
  - libarrow-dataset=18.1.0=hcb10f89_6_cpu
  - libarrow-substrait=18.1.0=h3ee7192_6_cpu
  - libasprintf=0.22.5=he8f35ee_3
  - libasprintf-devel=0.22.5=he8f35ee_3
  - libblas=3.9.0=26_linux64_openblas
  - libbrotlicommon=1.1.0=hb9d3cd8_2
  - libbrotlidec=1.1.0=hb9d3cd8_2
  - libbrotlienc=1.1.0=hb9d3cd8_2
  - libcap=2.71=h39aace5_0
  - libcblas=3.9.0=26_linux64_openblas
  - libclang-cpp19.1=19.1.5=default_hb5137d0_0
  - libclang13=19.1.5=default_h9c6a7e4_0
  - libcrc32c=1.1.2=h9c3ff4c_0
  - libcups=2.3.3=h4637d8d_4
  - libcurl=8.11.1=h332b0f4_0
  - libdeflate=1.23=h4ddbbb0_0
  - libdrm=2.4.124=hb9d3cd8_0
  - libedit=3.1.20191231=he28a2e2_2
  - libegl=1.7.0=ha4b6fd6_2
  - libev=4.33=hd590300_2
  - libevent=2.1.12=hf998b51_1
  - libexpat=2.6.4=h5888daf_0
  - libffi=3.4.4=h6a678d5_1
  - libflac=1.4.3=h59595ed_0
  - libgcc=14.2.0=h77fa898_1
  - libgcc-ng=14.2.0=h69a702a_1
  - libgcrypt-lib=1.11.0=hb9d3cd8_2
  - libgettextpo=0.22.5=he02047a_3
  - libgettextpo-devel=0.22.5=he02047a_3
  - libgfortran=14.2.0=h69a702a_1
  - libgfortran5=14.2.0=hd5240d6_1
  - libgl=1.7.0=ha4b6fd6_2
  - libglib=2.82.2=h2ff4ddf_0
  - libglvnd=1.7.0=ha4b6fd6_2
  - libglx=1.7.0=ha4b6fd6_2
  - libgomp=14.2.0=h77fa898_1
  - libgoogle-cloud=2.32.0=h804f50b_0
  - libgoogle-cloud-storage=2.32.0=h0121fbd_0
  - libgpg-error=1.51=hbd13f7d_1
  - libgrpc=1.67.1=hc2c308b_0
  - libiconv=1.17=hd590300_2
  - libjpeg-turbo=3.0.0=hd590300_1
  - liblapack=3.9.0=26_linux64_openblas
  - libllvm19=19.1.6=ha7bfdaf_0
  - liblzma=5.6.3=hb9d3cd8_1
  - libnghttp2=1.64.0=h161d5f1_0
  - libnsl=2.0.1=hd590300_0
  - libntlm=1.4=h7f98852_1002
  - libogg=1.3.5=h4ab18f5_0
  - libopenblas=0.3.28=pthreads_h94d23a6_1
  - libopengl=1.7.0=ha4b6fd6_2
  - libopus=1.3.1=h7f98852_1
  - libparquet=18.1.0=h081d1f1_6_cpu
  - libpciaccess=0.18=hd590300_0
  - libpng=1.6.44=hadc24fc_0
  - libpq=17.2=h3b95a9b_1
  - libprotobuf=5.28.2=h5b01275_0
  - libre2-11=2024.07.02=hbbce691_1
  - libsndfile=1.2.2=hc60ed4a_1
  - libsodium=1.0.20=h4ab18f5_0
  - libsqlite=3.47.2=hee588c1_0
  - libssh2=1.11.1=hf672d98_0
  - libstdcxx=14.2.0=hc0a3c3a_1
  - libstdcxx-ng=14.2.0=h4852527_1
  - libsystemd0=256.9=h0b6a36f_2
  - libthrift=0.21.0=h0e7cc3e_0
  - libtiff=4.7.0=hd9ff511_3
  - libutf8proc=2.9.0=hb9d3cd8_1
  - libuuid=2.38.1=h0b41bf4_0
  - libvorbis=1.3.7=h9c3ff4c_0
  - libwebp=1.4.0=h2c329e2_0
  - libwebp-base=1.4.0=hd590300_0
  - libxcb=1.17.0=h8a09558_0
  - libxcrypt=4.4.36=hd590300_1
  - libxkbcommon=1.7.0=h2c5496b_1
  - libxml2=2.13.5=h8d12d68_1
  - libxslt=1.1.39=h76b75d6_0
  - libzlib=1.3.1=hb9d3cd8_2
  - locket=1.0.0=pyhd8ed1ab_0
  - lz4=4.3.3=py311h8c6ae76_2
  - lz4-c=1.10.0=h5888daf_1
  - markupsafe=3.0.2=py311h2dc5d0c_1
  - matplotlib=3.10.0=py311h38be061_0
  - matplotlib-base=3.10.0=py311h2b939e6_0
  - matplotlib-inline=0.1.7=pyhd8ed1ab_1
  - mpg123=1.32.9=hc50e24c_0
  - msgpack-python=1.1.0=py311hd18a35c_0
  - munkres=1.1.4=pyh9f0ad1d_0
  - mysql-common=9.0.1=h266115a_3
  - mysql-libs=9.0.1=he0572af_3
  - ncurses=6.5=he02047a_1
  - nest-asyncio=1.6.0=pyhd8ed1ab_1
  - nspr=4.36=h5888daf_0
  - nss=3.107=hdf54f9c_0
  - numpy=1.26.4=py311h64a7726_0
  - openjpeg=2.5.3=h5fbd93e_0
  - openldap=2.6.9=he970967_0
  - openssl=3.4.0=hb9d3cd8_0
  - orc=2.0.3=h97ab989_1
  - packaging=24.2=pyhd8ed1ab_2
  - pandas=2.2.3=py311h7db5c69_1
  - parso=0.8.4=pyhd8ed1ab_1
  - partd=1.4.2=pyhd8ed1ab_0
  - pcre2=10.44=hba22ea6_2
  - perl=5.32.1=7_hd590300_perl5
  - pexpect=4.9.0=pyhd8ed1ab_1
  - pickleshare=0.7.5=pyhd8ed1ab_1004
  - pillow=11.0.0=py311h49e9ac3_0
  - pip=24.3.1=pyh8b19718_2
  - pixman=0.44.2=h29eaf8c_0
  - platformdirs=4.3.6=pyhd8ed1ab_1
  - pluggy=1.5.0=pyhd8ed1ab_1
  - ply=3.11=pyhd8ed1ab_3
  - prompt-toolkit=3.0.48=pyha770c72_1
  - psutil=6.1.0=py311h9ecbd09_0
  - pthread-stubs=0.4=hb9d3cd8_1002
  - ptyprocess=0.7.0=pyhd8ed1ab_1
  - pulseaudio-client=17.0=hb77b528_0
  - pure_eval=0.2.3=pyhd8ed1ab_1
  - pyarrow=18.1.0=py311h38be061_0
  - pyarrow-core=18.1.0=py311h4854187_0_cpu
  - pycparser=2.22=pyh29332c3_1
  - pygments=2.18.0=pyhd8ed1ab_1
  - pyopengl=3.1.6=pyhd8ed1ab_2
  - pyparsing=3.2.0=pyhd8ed1ab_2
  - pyqt=5.15.9=py311hf0fb5b6_5
  - pyqt5-sip=12.12.2=py311hb755f60_5
  - pyqtwebengine=5.15.9=py311hd529140_5
  - pyside6=6.8.1=py311h9053184_0
  - pysocks=1.7.1=pyha55dd90_7
  - pytest=8.3.4=pyhd8ed1ab_1
  - python=3.11.11=h9e4cc4f_1_cpython
  - python-dateutil=2.9.0.post0=pyhff2d567_1
  - python-tzdata=2024.2=pyhd8ed1ab_1
  - python_abi=3.11=5_cp311
  - pytz=2024.1=pyhd8ed1ab_0
  - pyyaml=6.0.2=py311h9ecbd09_1
  - pyzmq=26.2.0=py311h7deb3e3_3
  - qhull=2020.2=h434a139_5
  - qt-main=5.15.15=h796de64_1
  - qt-webengine=5.15.15=hd04a301_1
  - qt6-main=6.8.1=h9d28a51_0
  - qtconsole=5.6.1=pyhd8ed1ab_1
  - qtconsole-base=5.6.1=pyha770c72_1
  - qtpy=2.4.2=pyhdecd6ff_0
  - re2=2024.07.02=h77b4e00_1
  - readline=8.2=h5eee18b_0
  - requests=2.32.3=pyhd8ed1ab_1
  - responses=0.25.3=pyhd8ed1ab_1
  - s2n=1.5.10=hb5b8611_0
  - scikit-learn=1.6.0=py311h57cc02b_0
  - scipy=1.14.1=py311he9a78e4_2
  - setuptools=75.1.0=py311h06a4308_0
  - sip=6.7.12=py311hb755f60_0
  - six=1.17.0=pyhd8ed1ab_0
  - snappy=1.2.1=h8bd8927_1
  - sortedcontainers=2.4.0=pyhd8ed1ab_0
  - stack_data=0.6.3=pyhd8ed1ab_1
  - tblib=3.0.0=pyhd8ed1ab_1
  - threadpoolctl=3.5.0=pyhc1e730c_0
  - tk=8.6.13=noxft_h4845f30_101
  - toml=0.10.2=pyhd8ed1ab_1
  - tomli=2.2.1=pyhd8ed1ab_1
  - toolz=1.0.0=pyhd8ed1ab_1
  - tornado=6.4.2=py311h9ecbd09_0
  - traitlets=5.14.3=pyhd8ed1ab_1
  - types-pyyaml=6.0.12.20240917=pyhd8ed1ab_1
  - typing_extensions=4.12.2=pyha770c72_1
  - tzdata=2024b=h04d1e81_0
  - unicodedata2=15.1.0=py311h9ecbd09_1
  - urllib3=2.2.3=pyhd8ed1ab_1
  - wayland=1.23.1=h3e06ad9_0
  - wcwidth=0.2.13=pyhd8ed1ab_1
  - wheel=0.44.0=py311h06a4308_0
  - xcb-util=0.4.1=hb711507_2
  - xcb-util-cursor=0.1.5=hb9d3cd8_0
  - xcb-util-image=0.4.0=hb711507_2
  - xcb-util-keysyms=0.4.1=hb711507_0
  - xcb-util-renderutil=0.3.10=hb711507_0
  - xcb-util-wm=0.4.2=hb711507_0
  - xkeyboard-config=2.43=hb9d3cd8_0
  - xorg-libice=1.1.2=hb9d3cd8_0
  - xorg-libsm=1.2.5=he73a12e_0
  - xorg-libx11=1.8.10=h4f16b4b_1
  - xorg-libxau=1.0.12=hb9d3cd8_0
  - xorg-libxcomposite=0.4.6=hb9d3cd8_2
  - xorg-libxcursor=1.2.3=hb9d3cd8_0
  - xorg-libxdamage=1.1.6=hb9d3cd8_0
  - xorg-libxdmcp=1.1.5=hb9d3cd8_0
  - xorg-libxext=1.3.6=hb9d3cd8_0
  - xorg-libxfixes=6.0.1=hb9d3cd8_0
  - xorg-libxi=1.8.2=hb9d3cd8_0
  - xorg-libxrandr=1.5.4=hb9d3cd8_0
  - xorg-libxrender=0.9.12=hb9d3cd8_0
  - xorg-libxtst=1.2.5=hb9d3cd8_3
  - xorg-libxxf86vm=1.1.6=hb9d3cd8_0
  - xorg-xf86vidmodeproto=2.3.1=hb9d3cd8_1005
  - xyzservices=2024.9.0=pyhd8ed1ab_1
  - yaml=0.2.5=h7f98852_2
  - zeromq=4.3.5=h3b0a872_7
  - zict=3.0.0=pyhd8ed1ab_1
  - zipp=3.21.0=pyhd8ed1ab_1
  - zstandard=0.23.0=py311hbc35293_1
  - zstd=1.5.6=ha6fb4c9_0
  - pip:
      - colorcet==3.1.0
      - ghp-import==2.1.0
      - markdown==3.7
      - mergedeep==1.3.4
      - mkdocs==1.6.1
      - mkdocs-get-deps==0.2.0
      - mtscomp==1.0.2
      - pathspec==0.12.1
      - phy==2.0b5
      - phylib==2.6.0
      - pyyaml-env-tag==0.1
      - tqdm==4.67.1
      - watchdog==6.0.0

Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Assignees
No one assigned
Labels
None yet
Projects
None yet
Milestone
No milestone
Development

No branches or pull requests
2 participants
@ilsedippenaar @FabianMunozSilva