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talmolab
sleap-label crashes with '[Errno 24] Too many open files'
Bug description
Adding new files often throws an error 'Too many open files' which crashes the session.
Expected behaviour
Adding new videos should add new videos; and leave the session in a sane state (i.e. able to be saved). If there is insufficient memory or other resource, the action should fail with an error and remain in the previous state.
Actual behaviour
An error is thrown which leaves the session unuseable. Closing the session is not clean and actually deletes(!) the previously saved session file.
Your personal set up
SLEAP: 1.3.3 TensorFlow: 2.9.2 Numpy: 1.22.4 Python: 3.9.15 OS: macOS-13.6.6-arm64-arm-64bit
Run on an Apple (M1) laptop with limited RAM, so the issue could be triggered by resource limitations.
Environment packages
# Name Version Build Channel
abseil-cpp 20211102.0 he4e09e4_3 conda-forge
absl-py 1.4.0 pypi_0 pypi
aiohttp 3.9.3 py39h17cfd9d_0 conda-forge
aiosignal 1.3.1 pyhd8ed1ab_0 conda-forge
aom 3.5.0 h7ea286d_0 conda-forge
astunparse 1.6.3 pyhd8ed1ab_0 conda-forge
async-timeout 4.0.3 pyhd8ed1ab_0 conda-forge
attrs 23.2.0 pyh71513ae_0 conda-forge
blinker 1.7.0 pyhd8ed1ab_0 conda-forge
blosc 1.21.5 hc338f07_0 conda-forge
brotli 1.0.9 h1a8c8d9_9 conda-forge
brotli-bin 1.0.9 h1a8c8d9_9 conda-forge
brotli-python 1.0.9 py39h23fbdae_9 conda-forge
brunsli 0.1 h9f76cd9_0 conda-forge
bzip2 1.0.8 h93a5062_5 conda-forge
c-ares 1.26.0 h93a5062_0 conda-forge
c-blosc2 2.13.2 ha57e6be_0 conda-forge
ca-certificates 2024.2.2 hf0a4a13_0 conda-forge
cached-property 1.5.2 hd8ed1ab_1 conda-forge
cached_property 1.5.2 pyha770c72_1 conda-forge
cachetools 5.3.1 pypi_0 pypi
cairo 1.16.0 h73a0509_1014 conda-forge
cattrs 1.1.1 pyhd8ed1ab_0 conda-forge
certifi 2024.2.2 pyhd8ed1ab_0 conda-forge
cffi 1.16.0 py39he153c15_0 conda-forge
cfitsio 4.2.0 h2f961c4_0 conda-forge
charls 2.3.4 hbdafb3b_0 conda-forge
charset-normalizer 3.2.0 pypi_0 pypi
click 8.1.7 unix_pyh707e725_0 conda-forge
contourpy 1.2.0 py39he9de807_0 conda-forge
cryptography 39.0.0 py39haa0b8cc_0 conda-forge
cycler 0.12.1 pyhd8ed1ab_0 conda-forge
dav1d 1.2.1 hb547adb_0 conda-forge
efficientnet 1.0.0 pypi_0 pypi
expat 2.5.0 hb7217d7_1 conda-forge
ffmpeg 4.4.2 gpl_hf318d42_112 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_1 conda-forge
fontconfig 2.14.2 h82840c6_0 conda-forge
fonts-conda-ecosystem 1 0 conda-forge
fonts-conda-forge 1 0 conda-forge
fonttools 4.49.0 py39h17cfd9d_0 conda-forge
freetype 2.12.1 hadb7bae_2 conda-forge
frozenlist 1.4.1 py39h17cfd9d_0 conda-forge
gast 0.4.0 pyh9f0ad1d_0 conda-forge
geos 3.12.1 h965bd2d_0 conda-forge
gettext 0.21.1 h0186832_0 conda-forge
giflib 5.2.1 h1a8c8d9_3 conda-forge
glib 2.78.4 h1059232_0 conda-forge
glib-tools 2.78.4 h1059232_0 conda-forge
gmp 6.3.0 h965bd2d_0 conda-forge
gnutls 3.7.9 hd26332c_0 conda-forge
google-auth 2.23.0 pypi_0 pypi
google-auth-oauthlib 0.4.6 pyhd8ed1ab_0 conda-forge
google-pasta 0.2.0 pyh8c360ce_0 conda-forge
graphite2 1.3.13 h9f76cd9_1001 conda-forge
grpc-cpp 1.46.4 hcaf9be7_3 conda-forge
grpcio 1.58.0 pypi_0 pypi
gst-plugins-base 1.22.9 h09b4b5e_0 conda-forge
gstreamer 1.22.9 h551c6ff_0 conda-forge
h5py 3.8.0 nompi_py39hc9149d8_100 conda-forge
harfbuzz 5.3.0 hddbc195_0 conda-forge
hdf5 1.12.2 nompi_h55deafc_101 conda-forge
hdmf 3.9.0 pypi_0 pypi
icu 70.1 h6b3803e_0 conda-forge
idna 3.4 pypi_0 pypi
image-classifiers 1.0.0 pypi_0 pypi
imagecodecs 2022.9.26 py39hd7f743f_4 conda-forge
imageio 2.34.0 pyh4b66e23_0 conda-forge
imgaug 0.4.0 pyhd8ed1ab_1 conda-forge
imgstore 0.2.9 pypi_0 pypi
importlib-metadata 7.0.1 pyha770c72_0 conda-forge
importlib-resources 6.1.1 pyhd8ed1ab_0 conda-forge
importlib_resources 6.1.1 pyhd8ed1ab_0 conda-forge
jasper 2.0.33 hc3cd1e9_1 conda-forge
joblib 1.3.2 pyhd8ed1ab_0 conda-forge
jpeg 9e h1a8c8d9_3 conda-forge
jsmin 3.0.1 pyhd8ed1ab_0 conda-forge
jsonpickle 1.2 py_0 conda-forge
jsonschema 4.19.0 pypi_0 pypi
jsonschema-specifications 2023.7.1 pypi_0 pypi
jxrlib 1.1 h93a5062_3 conda-forge
keras 2.9.0 pyhd8ed1ab_0 conda-forge
keras-applications 1.0.8 pypi_0 pypi
keras-preprocessing 1.1.2 pyhd8ed1ab_0 conda-forge
kiwisolver 1.4.5 py39hbd775c9_1 conda-forge
krb5 1.20.1 h127bd45_0 conda-forge
lame 3.100 h1a8c8d9_1003 conda-forge
lazy_loader 0.3 pyhd8ed1ab_0 conda-forge
lcms2 2.14 h8193b64_0 conda-forge
lerc 4.0.0 h9a09cb3_0 conda-forge
libabseil 20211102.0 cxx17_h28b99d4_3 conda-forge
libaec 1.1.2 h13dd4ca_1 conda-forge
libavif 0.11.1 h9f83d30_2 conda-forge
libblas 3.9.0 20_osxarm64_openblas conda-forge
libbrotlicommon 1.0.9 h1a8c8d9_9 conda-forge
libbrotlidec 1.0.9 h1a8c8d9_9 conda-forge
libbrotlienc 1.0.9 h1a8c8d9_9 conda-forge
libcblas 3.9.0 20_osxarm64_openblas conda-forge
libclang 16.0.6 pypi_0 pypi
libclang13 14.0.6 default_hc7183e1_1 conda-forge
libcurl 7.87.0 hbe9bab4_0 conda-forge
libcxx 16.0.6 h4653b0c_0 conda-forge
libdeflate 1.14 h1a8c8d9_0 conda-forge
libedit 3.1.20191231 hc8eb9b7_2 conda-forge
libev 4.33 h93a5062_2 conda-forge
libexpat 2.5.0 hb7217d7_1 conda-forge
libffi 3.4.2 h3422bc3_5 conda-forge
libgfortran 5.0.0 13_2_0_hd922786_3 conda-forge
libgfortran5 13.2.0 hf226fd6_3 conda-forge
libglib 2.78.4 h1635a5e_0 conda-forge
libiconv 1.17 h0d3ecfb_2 conda-forge
libidn2 2.3.7 h93a5062_0 conda-forge
liblapack 3.9.0 20_osxarm64_openblas conda-forge
liblapacke 3.9.0 20_osxarm64_openblas conda-forge
libllvm14 14.0.6 hd1a9a77_4 conda-forge
libnghttp2 1.51.0 hd184df1_0 conda-forge
libogg 1.3.4 h27ca646_1 conda-forge
libopenblas 0.3.25 openmp_h6c19121_0 conda-forge
libopencv 4.6.0 py39he1c1adf_3 conda-forge
libopus 1.3.1 h27ca646_1 conda-forge
libpng 1.6.42 h091b4b1_0 conda-forge
libpq 15.1 hbce9e56_3 conda-forge
libprotobuf 3.20.3 hb5ab8b9_0 conda-forge
libsodium 1.0.18 h27ca646_1 conda-forge
libsqlite 3.45.1 h091b4b1_0 conda-forge
libssh2 1.10.0 hb80f160_3 conda-forge
libtasn1 4.19.0 h1a8c8d9_0 conda-forge
libtiff 4.4.0 heb92581_5 conda-forge
libunistring 0.9.10 h3422bc3_0 conda-forge
libvorbis 1.3.7 h9f76cd9_0 conda-forge
libvpx 1.11.0 hc470f4d_3 conda-forge
libwebp-base 1.3.2 hb547adb_0 conda-forge
libxcb 1.13 h9b22ae9_1004 conda-forge
libxml2 2.10.3 h67585b2_4 conda-forge
libxslt 1.1.37 h1bd8bc4_0 conda-forge
libzlib 1.2.13 h53f4e23_5 conda-forge
libzopfli 1.0.3 h9f76cd9_0 conda-forge
llvm-openmp 17.0.6 hcd81f8e_0 conda-forge
lz4-c 1.9.4 hb7217d7_0 conda-forge
markdown 3.4.4 pypi_0 pypi
markdown-it-py 3.0.0 pyhd8ed1ab_0 conda-forge
markupsafe 2.1.3 pypi_0 pypi
matplotlib-base 3.8.3 py39hbab7938_0 conda-forge
mdurl 0.1.2 pyhd8ed1ab_0 conda-forge
multidict 6.0.5 py39h02fc5c5_0 conda-forge
munkres 1.1.4 pyh9f0ad1d_0 conda-forge
mysql-common 8.0.32 hab468bb_0 conda-forge
mysql-libs 8.0.32 hea58576_0 conda-forge
ncurses 6.4 h463b476_2 conda-forge
ndx-pose 0.1.1 pypi_0 pypi
nettle 3.9.1 h40ed0f5_0 conda-forge
networkx 3.2.1 pyhd8ed1ab_0 conda-forge
nixio 1.5.3 pypi_0 pypi
nspr 4.35 hb7217d7_0 conda-forge
nss 3.98 h5ce2875_0 conda-forge
numpy 1.22.4 py39h7df2422_0 conda-forge
oauthlib 3.2.2 pyhd8ed1ab_0 conda-forge
opencv 4.6.0 py39hdf13c20_3 conda-forge
openh264 2.3.1 hb7217d7_2 conda-forge
openjpeg 2.5.0 h5d4e404_1 conda-forge
openssl 1.1.1w h53f4e23_0 conda-forge
opt_einsum 3.3.0 pyhc1e730c_2 conda-forge
p11-kit 0.24.1 h29577a5_0 conda-forge
packaging 23.2 pyhd8ed1ab_0 conda-forge
pandas 2.2.0 py39h47e51b9_0 conda-forge
patsy 0.5.6 pyhd8ed1ab_0 conda-forge
pcre2 10.42 h26f9a81_0 conda-forge
pillow 9.2.0 py39h139752e_3 conda-forge
pip 24.0 pyhd8ed1ab_0 conda-forge
pixman 0.43.2 hebf3989_0 conda-forge
protobuf 3.19.6 pypi_0 pypi
psutil 5.9.8 py39h17cfd9d_0 conda-forge
pthread-stubs 0.4 h27ca646_1001 conda-forge
py-opencv 4.6.0 py39hfa6204d_3 conda-forge
pyasn1 0.5.0 pypi_0 pypi
pyasn1-modules 0.3.0 pyhd8ed1ab_0 conda-forge
pycparser 2.21 pyhd8ed1ab_0 conda-forge
pygments 2.17.2 pyhd8ed1ab_0 conda-forge
pyjwt 2.8.0 pyhd8ed1ab_1 conda-forge
pykalman 0.9.5 py_1 conda-forge
pynwb 2.5.0 pypi_0 pypi
pyopenssl 23.2.0 pyhd8ed1ab_1 conda-forge
pyparsing 3.1.1 pyhd8ed1ab_0 conda-forge
pyside2 5.15.8 py39h0adaba8_2 conda-forge
pysocks 1.7.1 pyha2e5f31_6 conda-forge
python 3.9.15 h2d96c93_0_cpython conda-forge
python-dateutil 2.8.2 pyhd8ed1ab_0 conda-forge
python-flatbuffers 1.12 pyhd8ed1ab_1 conda-forge
python-rapidjson 1.14 py39hf3050f2_0 conda-forge
python-tzdata 2024.1 pyhd8ed1ab_0 conda-forge
python_abi 3.9 4_cp39 conda-forge
pytz 2024.1 pyhd8ed1ab_0 conda-forge
pyu2f 0.1.5 pyhd8ed1ab_0 conda-forge
pywavelets 1.4.1 py39hf4a74a7_1 conda-forge
pyyaml 6.0.1 py39h0f82c59_1 conda-forge
pyzmq 25.1.2 py39he1e2164_0 conda-forge
qimage2ndarray 1.10.0 pypi_0 pypi
qt-main 5.15.8 hfe8d25c_6 conda-forge
qtpy 2.4.1 pyhd8ed1ab_0 conda-forge
re2 2022.06.01 h9a09cb3_1 conda-forge
readline 8.2 h92ec313_1 conda-forge
referencing 0.30.2 pypi_0 pypi
requests 2.31.0 pyhd8ed1ab_0 conda-forge
requests-oauthlib 1.3.1 pyhd8ed1ab_0 conda-forge
rich 13.7.0 pyhd8ed1ab_0 conda-forge
rpds-py 0.10.3 pypi_0 pypi
rsa 4.9 pyhd8ed1ab_0 conda-forge
ruamel-yaml 0.17.32 pypi_0 pypi
ruamel-yaml-clib 0.2.7 pypi_0 pypi
scikit-image 0.22.0 py39hf8cecc8_2 conda-forge
scikit-learn 1.0 py39h12ba089_1 conda-forge
scikit-video 1.1.11 pyh24bf2e0_0 conda-forge
scipy 1.9.0 py39h14896cb_0 conda-forge
seaborn 0.13.2 hd8ed1ab_0 conda-forge
seaborn-base 0.13.2 pyhd8ed1ab_0 conda-forge
segmentation-models 1.0.1 pypi_0 pypi
setuptools 69.1.0 pyhd8ed1ab_0 conda-forge
shapely 2.0.2 py39ha70ab96_1 conda-forge
six 1.15.0 pypi_0 pypi
sleap 1.3.3 pypi_0 pypi
snappy 1.1.10 h17c5cce_0 conda-forge
sqlite 3.45.1 hf2abe2d_0 conda-forge
statsmodels 0.14.1 py39h373d45f_0 conda-forge
svt-av1 1.4.1 h7ea286d_0 conda-forge
tensorboard 2.9.1 pypi_0 pypi
tensorboard-data-server 0.6.1 py39haa0b8cc_4 conda-forge
tensorboard-plugin-wit 1.8.1 pyhd8ed1ab_0 conda-forge
tensorflow 2.9.1 cpu_py39h2839aeb_0 conda-forge
tensorflow-base 2.9.1 cpu_py39ha1ad4ae_0 conda-forge
tensorflow-estimator 2.9.1 cpu_py39h7b621ec_0 conda-forge
tensorflow-hub 0.12.0 pyhca92ed8_0 conda-forge
tensorflow-macos 2.9.2 pypi_0 pypi
tensorflow-metal 0.5.0 pypi_0 pypi
termcolor 2.3.0 pypi_0 pypi
threadpoolctl 3.3.0 pyhc1e730c_0 conda-forge
tifffile 2022.10.10 pyhd8ed1ab_0 conda-forge
tk 8.6.13 h5083fa2_1 conda-forge
typing-extensions 4.9.0 hd8ed1ab_0 conda-forge
typing_extensions 4.9.0 pyha770c72_0 conda-forge
tzdata 2024a h0c530f3_0 conda-forge
tzlocal 5.0.1 pypi_0 pypi
unicodedata2 15.1.0 py39h0f82c59_0 conda-forge
urllib3 1.26.16 pypi_0 pypi
werkzeug 2.3.7 pypi_0 pypi
wheel 0.42.0 pyhd8ed1ab_0 conda-forge
wrapt 1.15.0 pypi_0 pypi
x264 1!164.3095 h57fd34a_2 conda-forge
x265 3.5 hbc6ce65_3 conda-forge
xorg-libxau 1.0.11 hb547adb_0 conda-forge
xorg-libxdmcp 1.1.3 h27ca646_0 conda-forge
xz 5.2.6 h57fd34a_0 conda-forge
yaml 0.2.5 h3422bc3_2 conda-forge
yarl 1.9.4 py39h17cfd9d_0 conda-forge
zeromq 4.3.5 h965bd2d_0 conda-forge
zfp 1.0.1 ha8f4885_0 conda-forge
zipp 3.17.0 pyhd8ed1ab_0 conda-forge
zlib 1.2.13 h53f4e23_5 conda-forge
zlib-ng 2.0.7 h1a8c8d9_0 conda-forge
zstd 1.5.5 h4f39d0f_0 conda-forge
Logs
# paste relevant logs here, if any
Screenshots
How to reproduce
- Open a training package.
- Add new videos.
I can create projects with e.g. 100 files and work with these - the error does not always occur with every session. But removing all of these videos and trying to add 30 different ones causes the crash, so it is also not just the number of videos in the project. I have not yet identified a hard-and-fast limit to the number of videos that are 'too many' (or, indeed, whether it is even the video files that are being referrred to in the error).
Hi @rupertoverall!
Sorry you ran into this issue! Here is a previous issue that was resolved that features your same error, Cannot select videos that are in the project #1660 where they increased the limit of open files allowable by the OS.
Let us know if this works! Best, Mariela
Hi all, I had the same issue and my previously saved sessions (I had two open) were deleted. I still have the predictions and models folders for both but the .slp file containing my many labeled frames have been deleted. Are these files lost permanently and is there any way to build on the models from these projects? I tried to train one of these prior models in a new project and it looks like it's reverted back to the few labels in this new project, this will be quite a loss of effort for me, any recommendations?
Hi @hlanovoi,
In the model folders there are some SLP files which store a cached copy of the labels used to train those models. You can try to open those in the GUI and/or import and merge them into the new project.
Let us know if you need some help with that.
In general, we also strongly recommend saving out new versions of your labels as often as possible by going to File --> Save as... and saving a new version (which SLEAP automatically increments in the filename).
Hello @talmo
Thank you for your reply, so from what it looks like I by going to file-> merge into project I can maybe select one of the files you are talking derived from the model with the most labels.
Within the folder for this model I see: lables_pr.val.slp labels_pr.train.slp labels_gt.val.slp labels_gt.train.slp
Is this the right approach and which one of these is most appropriate to import?
I'm noting this point about file hygiene, thanks so much!
You'd want to import the labels_gt.val.slp and the labels_gt.train.slp, since those contain the ground truth labels used to train.
Cheers,
Talmo