Issue with Colmap Library Dependencies

[DavidTu21]

Dear Authors,

Thank you for your amazing work on this project. I have been testing the code on a sample video, Lego.mp4, and encountered an issue that seems to be related to Colmap. I am using Ubuntu 20.04.5 LTS and have set up a conda virtual environment for the project, following the installation guide you provided.

The first part of the code, which is to '1. extract images from the input video,' executed without any issues. I used the following command:

$bash projects/neuralangelo/scripts/run_ffmpeg.sh ${SEQUENCE} ${PATH_TO_VIDEO} ${DOWNSAMPLE_RATE}) and I could see the extracted images stored in {DATA_PATH}/images_raw, and I got the following output:

ffmpeg version 6.0 Copyright (c) 2000-2023 the FFmpeg developers built with gcc 12.3.0 (conda-forge gcc 12.3.0-0) configuration: --prefix=/home/conda/feedstock_root/build_artifacts/ffmpeg_1687154882217/_h_env_placehold_placehold_placehold_placehold_placehold_pla cehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_plac --cc=/home/conda/f eedstock_root/build_artifacts/ffmpeg_1687154882217/_build_env/bin/x86_64-conda-linux-gnu-cc --cxx=/home/conda/feedstock_root/build_artifacts/ffmpeg_16 87154882217/_build_env/bin/x86_64-conda-linux-gnu-c++ --nm=/home/conda/feedstock_root/build_artifacts/ffmpeg_1687154882217/_build_env/bin/x86_64-conda -linux-gnu-nm --ar=/home/conda/feedstock_root/build_artifacts/ffmpeg_1687154882217/_build_env/bin/x86_64-conda-linux-gnu-ar --disable-doc --disable-op enssl --enable-demuxer=dash --enable-hardcoded-tables --enable-libfreetype --enable-libfontconfig --enable-libopenh264 --enable-libdav1d --enable-gnut ls --enable-libmp3lame --enable-libvpx --enable-libass --enable-pthreads --enable-vaapi --enable-gpl --enable-libx264 --enable-libx265 --enable-libaom --enable-libsvtav1 --enable-libxml2 --enable-pic --enable-shared --disable-static --enable-version3 --enable-zlib --enable-libopus --pkg-config=/home /conda/feedstock_root/build_artifacts/ffmpeg_1687154882217/_build_env/bin/pkg-config libavutil 58. 2.100 / 58. 2.100 libavcodec 60. 3.100 / 60. 3.100 libavformat 60. 3.100 / 60. 3.100 libavdevice 60. 1.100 / 60. 1.100 libavfilter 9. 3.100 / 9. 3.100 libswscale 7. 1.100 / 7. 1.100 libswresample 4. 10.100 / 4. 10.100 libpostproc 57. 1.100 / 57. 1.100 -vsync is deprecated. Use -fps_mode Input #0, mov,mp4,m4a,3gp,3g2,mj2, from 'lego.mp4': Metadata: major_brand : isom minor_version : 512 compatible_brands: isomiso2avc1mp41 encoder : Lavf59.16.100 Duration: 00:00:08.00, start: 0.000000, bitrate: 2181 kb/s Stream #0:0[0x1](und): Video: h264 (High) (avc1 / 0x31637661), yuv420p(progressive), 800x800, 2178 kb/s, 25 fps, 25 tbr, 12800 tbn (default) Metadata: handler_name : VideoHandler vendor_id : [0][0][0][0] Stream mapping: Stream #0:0 -> #0:0 (h264 (native) -> mjpeg (native)) Press [q] to stop, [?] for help [swscaler @ 0x563c38ccb340] deprecated pixel format used, make sure you did set range correctly Output #0, image2, to 'datasets/lego_skip2/raw_images/%06d.jpg': Metadata: major_brand : isom minor_version : 512 compatible_brands: isomiso2avc1mp41 encoder : Lavf60.3.100 Stream #0:0(und): Video: mjpeg, yuvj420p(pc, progressive), 800x800, q=2-31, 200 kb/s, 25 fps, 25 tbn (default) Metadata: handler_name : VideoHandler vendor_id : [0][0][0][0] encoder : Lavc60.3.100 mjpeg Side data: cpb: bitrate max/min/avg: 0/0/200000 buffer size: 0 vbv_delay: N/A frame= 100 fps=0.0 q=2.0 Lsize=N/A time=00:00:07.92 bitrate=N/A speed=62.6x its/s speed=N/A video:7275kB audio:0kB subtitle:0kB other streams:0kB global headers:0kB muxing overhead: unknown

However when I proceed to the second step of running colmap, I saw the error of as below. $ bash projects/neuralangelo/scripts/run_colmap.sh "datasets/lego_skip2" colmap: error while loading shared libraries: libcudart.so.12: cannot open shared object file: No such file or directory colmap: error while loading shared libraries: libcudart.so.12: cannot open shared object file: No such file or directory colmap: error while loading shared libraries: libcudart.so.12: cannot open shared object file: No such file or directory colmap: error while loading shared libraries: libcudart.so.12: cannot open shared object file: No such file or directory

Upon checking the libraries in my virtual environment located at {user_name}/anaconda/envs/neuralangelo/lib, I found that I have 'libcudart.so.11.7.99' and 'libcudart.so.11.7.60', but not 'libcudart.so.12', which seems to be causing the error.

Could you please guide me on how to resolve this issue? I would greatly appreciate your assistance.

Thank you very much for your time and consideration.

P.S. Below are the conda installed packages under this environment: Name Version Build Channel _libgcc_mutex 0.1 conda_forge conda-forge _openmp_mutex 4.5 2_gnu conda-forge absl-py 1.4.0 pypi_0 pypi addict 2.4.0 pypi_0 pypi alsa-lib 1.2.9 hd590300_0 conda-forge ansi2html 1.8.0 pypi_0 pypi anyio 3.7.1 pyhd8ed1ab_0 conda-forge aom 3.5.0 h27087fc_0 conda-forge appdirs 1.4.4 pypi_0 pypi argon2-cffi 23.1.0 pyhd8ed1ab_0 conda-forge argon2-cffi-bindings 21.2.0 py38h0a891b7_3 conda-forge arrow 1.2.3 pyhd8ed1ab_0 conda-forge asttokens 2.2.1 pyhd8ed1ab_0 conda-forge async-lru 2.0.4 pyhd8ed1ab_0 conda-forge attr 2.5.1 h166bdaf_1 conda-forge attrs 23.1.0 pyh71513ae_1 conda-forge babel 2.12.1 pyhd8ed1ab_1 conda-forge backcall 0.2.0 pyh9f0ad1d_0 conda-forge backports 1.0 pyhd8ed1ab_3 conda-forge backports.functools_lru_cache 1.6.5 pyhd8ed1ab_0 conda-forge beautifulsoup4 4.12.2 pyha770c72_0 conda-forge binutils_impl_linux-64 2.36.1 h193b22a_2 conda-forge binutils_linux-64 2.36 hf3e587d_10 conda-forge bleach 6.0.0 pyhd8ed1ab_0 conda-forge blessed 1.19.1 pyhe4f9e05_2 conda-forge boost-cpp 1.78.0 h6582d0a_3 conda-forge brotli-python 1.0.9 py38hfa26641_9 conda-forge bzip2 1.0.8 h7f98852_4 conda-forge c-ares 1.19.1 hd590300_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 cachetools 5.3.1 pypi_0 pypi cairo 1.16.0 hbbf8b49_1016 conda-forge ceres-solver 2.1.0 hf302a74_1 conda-forge certifi 2023.7.22 pyhd8ed1ab_0 conda-forge cffi 1.15.1 py38h4a40e3a_3 conda-forge charset-normalizer 3.2.0 pyhd8ed1ab_0 conda-forge click 8.1.7 pypi_0 pypi cmake 3.26.4 hcfe8598_0 conda-forge colmap 3.8 gpuh32ed341_103 conda-forge colorama 0.4.6 pyhd8ed1ab_0 conda-forge comm 0.1.4 pyhd8ed1ab_0 conda-forge configargparse 1.7 pypi_0 pypi contourpy 1.1.0 pypi_0 pypi cuda-cudart 11.7.99 0 nvidia cuda-cupti 11.7.101 0 nvidia cuda-libraries 11.7.1 0 nvidia cuda-nvrtc 11.7.99 0 nvidia cuda-nvtx 11.7.91 0 nvidia cuda-runtime 11.7.1 0 nvidia cuda-version 12.0 hffde075_2 conda-forge cudatoolkit-dev 11.7.0 h1de0b5d_6 conda-forge cycler 0.11.0 pypi_0 pypi cython 3.0.0 py38h17151c0_0 conda-forge dash 2.12.1 pypi_0 pypi dash-core-components 2.0.0 pypi_0 pypi dash-html-components 2.0.0 pypi_0 pypi dash-table 5.0.0 pypi_0 pypi dav1d 1.2.1 hd590300_0 conda-forge dbus 1.13.6 h5008d03_3 conda-forge debugpy 1.6.8 py38h17151c0_0 conda-forge decorator 5.1.1 pyhd8ed1ab_0 conda-forge defusedxml 0.7.1 pyhd8ed1ab_0 conda-forge diskcache 5.6.1 pyhd8ed1ab_0 conda-forge docker-pycreds 0.4.0 pypi_0 pypi eigen 3.4.0 h00ab1b0_0 conda-forge entrypoints 0.4 pyhd8ed1ab_0 conda-forge exceptiongroup 1.1.3 pyhd8ed1ab_0 conda-forge executing 1.2.0 pyhd8ed1ab_0 conda-forge expat 2.5.0 hcb278e6_1 conda-forge ffmpeg 6.0.0 gpl_hdbbbd96_103 conda-forge filelock 3.12.2 pyhd8ed1ab_0 conda-forge flann 1.9.1 h941a29b_1013 conda-forge flask 2.2.5 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 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 pypi_0 pypi fqdn 1.5.1 pyhd8ed1ab_0 conda-forge freeimage 3.18.0 he1b5a44_0 conda-forge freetype 2.12.1 hca18f0e_1 conda-forge fribidi 1.0.10 h36c2ea0_0 conda-forge future 0.18.3 pypi_0 pypi gcc 8.5.0 h143be6b_10 conda-forge gcc_impl_linux-64 8.5.0 hb55b52c_17 conda-forge gcc_linux-64 8.5.0 h87d5063_10 conda-forge gdown 4.7.1 pyhd8ed1ab_0 conda-forge gettext 0.21.1 h27087fc_0 conda-forge gflags 2.2.2 he1b5a44_1004 conda-forge gitdb 4.0.10 pypi_0 pypi gitpython 3.1.32 pypi_0 pypi glew 2.1.0 h9c3ff4c_2 conda-forge glib 2.76.4 hfc55251_0 conda-forge glib-tools 2.76.4 hfc55251_0 conda-forge glog 0.6.0 h6f12383_0 conda-forge gmp 6.2.1 h58526e2_0 conda-forge gmpy2 2.1.2 py38h793c122_1 conda-forge gnutls 3.7.8 hf3e180e_0 conda-forge google-auth 2.22.0 pypi_0 pypi google-auth-oauthlib 1.0.0 pypi_0 pypi gpustat 1.1.1 pyhd8ed1ab_0 conda-forge graphite2 1.3.13 h58526e2_1001 conda-forge grpcio 1.57.0 pypi_0 pypi gst-plugins-base 1.22.5 hf7dbed1_0 conda-forge gstreamer 1.22.5 h98fc4e7_0 conda-forge gxx_impl_linux-64 8.5.0 hb55b52c_17 conda-forge gxx_linux-64 8.5.0 h82b3ca4_10 conda-forge harfbuzz 7.3.0 hdb3a94d_0 conda-forge hdf5 1.14.1 nompi_h4f84152_100 conda-forge icecream 2.1.3 pypi_0 pypi icu 72.1 hcb278e6_0 conda-forge idna 3.4 pyhd8ed1ab_0 conda-forge imageio 2.31.1 pypi_0 pypi imageio-ffmpeg 0.4.8 pypi_0 pypi importlib-metadata 6.8.0 pyha770c72_0 conda-forge importlib_metadata 6.8.0 hd8ed1ab_0 conda-forge importlib_resources 6.0.1 pyhd8ed1ab_0 conda-forge imutils 0.5.4 pypi_0 pypi ipdb 0.13.13 pypi_0 pypi ipykernel 6.25.1 pyh71e2992_0 conda-forge ipython 8.12.0 pyh41d4057_0 conda-forge ipywidgets 8.1.0 pypi_0 pypi isoduration 20.11.0 pyhd8ed1ab_0 conda-forge itsdangerous 2.1.2 pypi_0 pypi jedi 0.19.0 pyhd8ed1ab_0 conda-forge jinja2 3.1.2 pyhd8ed1ab_1 conda-forge joblib 1.3.2 pypi_0 pypi json5 0.9.14 pyhd8ed1ab_0 conda-forge jsonpointer 2.0 py_0 conda-forge jsonschema 4.19.0 pyhd8ed1ab_1 conda-forge jsonschema-specifications 2023.7.1 pyhd8ed1ab_0 conda-forge jsonschema-with-format-nongpl 4.19.0 pyhd8ed1ab_1 conda-forge jupyter-lsp 2.2.0 pyhd8ed1ab_0 conda-forge jupyter_client 8.3.0 pyhd8ed1ab_0 conda-forge jupyter_core 4.12.0 py38h578d9bd_0 conda-forge jupyter_events 0.7.0 pyhd8ed1ab_2 conda-forge jupyter_server 2.7.1 pyhd8ed1ab_0 conda-forge jupyter_server_terminals 0.4.4 pyhd8ed1ab_1 conda-forge jupyterlab 4.0.5 pyhd8ed1ab_0 conda-forge jupyterlab-widgets 3.0.8 pypi_0 pypi jupyterlab_pygments 0.2.2 pyhd8ed1ab_0 conda-forge jupyterlab_server 2.24.0 pyhd8ed1ab_0 conda-forge k3d 2.15.3 pypi_0 pypi kernel-headers_linux-64 2.6.32 he073ed8_16 conda-forge keyutils 1.6.1 h166bdaf_0 conda-forge kiwisolver 1.4.4 pypi_0 pypi kornia 0.7.0 pypi_0 pypi krb5 1.21.2 h659d440_0 conda-forge lame 3.100 h166bdaf_1003 conda-forge lazy-loader 0.3 pypi_0 pypi lcms2 2.15 haa2dc70_1 conda-forge ld_impl_linux-64 2.36.1 hea4e1c9_2 conda-forge lerc 4.0.0 h27087fc_0 conda-forge libaec 1.0.6 hcb278e6_1 conda-forge libass 0.17.1 hc9aadba_0 conda-forge libblas 3.9.0 17_linux64_openblas conda-forge libcap 2.69 h0f662aa_0 conda-forge libcblas 3.9.0 17_linux64_openblas conda-forge libclang 15.0.7 default_h7634d5b_3 conda-forge libclang13 15.0.7 default_h9986a30_3 conda-forge libcublas 11.10.3.66 0 nvidia libcufft 10.7.2.124 h4fbf590_0 nvidia libcufile 1.5.0.59 hcb278e6_0 conda-forge libcups 2.3.3 h4637d8d_4 conda-forge libcurand 10.3.1.50 hcb278e6_0 conda-forge libcurl 8.2.1 hca28451_0 conda-forge libcusolver 11.4.0.1 0 nvidia libcusparse 11.7.4.91 0 nvidia libdeflate 1.18 h0b41bf4_0 conda-forge libdrm 2.4.114 h166bdaf_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-devel_linux-64 8.5.0 h82e8279_17 conda-forge libgcc-ng 13.1.0 he5830b7_0 conda-forge libgcrypt 1.10.1 h166bdaf_0 conda-forge libgfortran-ng 13.1.0 h69a702a_0 conda-forge libgfortran5 13.1.0 h15d22d2_0 conda-forge libglib 2.76.4 hebfc3b9_0 conda-forge libglu 9.0.0 hac7e632_1002 conda-forge libgomp 13.1.0 he5830b7_0 conda-forge libgpg-error 1.47 h71f35ed_0 conda-forge libhwloc 2.9.2 nocuda_h7313eea_1008 conda-forge libiconv 1.17 h166bdaf_0 conda-forge libidn2 2.3.4 h166bdaf_0 conda-forge libjpeg-turbo 2.1.5.1 h0b41bf4_0 conda-forge liblapack 3.9.0 17_linux64_openblas conda-forge libllvm15 15.0.7 h5cf9203_3 conda-forge libnghttp2 1.52.0 h61bc06f_0 conda-forge libnpp 11.7.4.75 0 nvidia libnsl 2.0.0 h7f98852_0 conda-forge libnvjpeg 11.8.0.2 0 nvidia libogg 1.3.4 h7f98852_1 conda-forge libopenblas 0.3.23 pthreads_h80387f5_0 conda-forge libopus 1.3.1 h7f98852_1 conda-forge libpciaccess 0.17 h166bdaf_0 conda-forge libpng 1.6.39 h753d276_0 conda-forge libpq 15.4 hfc447b1_0 conda-forge libprotobuf 3.20.3 h3eb15da_0 conda-forge libsanitizer 8.5.0 h70fd0c9_17 conda-forge libsndfile 1.2.2 hbc2eb40_0 conda-forge libsodium 1.0.18 h36c2ea0_1 conda-forge libsqlite 3.42.0 h2797004_0 conda-forge libssh2 1.11.0 h0841786_0 conda-forge libstdcxx-devel_linux-64 8.5.0 h82e8279_17 conda-forge libstdcxx-ng 13.1.0 hfd8a6a1_0 conda-forge libsystemd0 254 h3516f8a_0 conda-forge libtasn1 4.19.0 h166bdaf_0 conda-forge libtiff 4.5.1 h8b53f26_0 conda-forge libunistring 0.9.10 h7f98852_0 conda-forge libuuid 2.38.1 h0b41bf4_0 conda-forge libuv 1.44.2 hd590300_1 conda-forge libva 2.19.0 hd590300_0 conda-forge libvorbis 1.3.7 h9c3ff4c_0 conda-forge libvpx 1.13.0 hcb278e6_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 libzlib 1.2.13 hd590300_5 conda-forge lpips 0.1.4 pypi_0 pypi lz4-c 1.9.4 hcb278e6_0 conda-forge markdown 3.4.4 pypi_0 pypi markupsafe 2.1.3 py38h01eb140_0 conda-forge matplotlib 3.7.2 pypi_0 pypi matplotlib-inline 0.1.6 pyhd8ed1ab_0 conda-forge mediapy 1.1.9 pypi_0 pypi metis 5.1.1 h59595ed_0 conda-forge mistune 3.0.1 pyhd8ed1ab_0 conda-forge mpc 1.3.1 hfe3b2da_0 conda-forge mpfr 4.2.0 hb012696_0 conda-forge mpg123 1.31.3 hcb278e6_0 conda-forge mpmath 1.3.0 pyhd8ed1ab_0 conda-forge msgpack 1.0.5 pypi_0 pypi mysql-common 8.0.33 hf1915f5_2 conda-forge mysql-libs 8.0.33 hca2cd23_2 conda-forge nbclient 0.8.0 pyhd8ed1ab_0 conda-forge nbconvert-core 7.7.4 pyhd8ed1ab_0 conda-forge nbformat 5.7.0 pypi_0 pypi ncurses 6.4 hcb278e6_0 conda-forge nest-asyncio 1.5.6 pyhd8ed1ab_0 conda-forge nettle 3.8.1 hc379101_1 conda-forge networkx 3.1 pyhd8ed1ab_0 conda-forge ninja 1.11.1 pypi_0 pypi notebook-shim 0.2.3 pyhd8ed1ab_0 conda-forge nspr 4.35 h27087fc_0 conda-forge nss 3.92 h1d7d5a4_0 conda-forge numpy 1.24.4 py38h59b608b_0 conda-forge nvidia-ml-py 12.535.77 pyhd8ed1ab_0 conda-forge nvidia-ml-py3 7.352.0 pypi_0 pypi oauthlib 3.2.2 pypi_0 pypi open3d 0.17.0 pypi_0 pypi opencv-python-headless 4.8.0.76 pypi_0 pypi openexr 1.3.9 pypi_0 pypi openh264 2.3.1 hcb278e6_2 conda-forge openjpeg 2.5.0 hfec8fc6_2 conda-forge openssl 3.1.2 hd590300_0 conda-forge overrides 7.4.0 pyhd8ed1ab_0 conda-forge p11-kit 0.24.1 hc5aa10d_0 conda-forge packaging 23.1 pyhd8ed1ab_0 conda-forge pandocfilters 1.5.0 pyhd8ed1ab_0 conda-forge parso 0.8.3 pyhd8ed1ab_0 conda-forge pathlib 1.0.1 pypi_0 pypi pathtools 0.1.2 pypi_0 pypi pcre2 10.40 hc3806b6_0 conda-forge pexpect 4.8.0 pyh1a96a4e_2 conda-forge pickleshare 0.7.5 py_1003 conda-forge pillow 10.0.0 py38h885162f_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 plotly 5.16.1 pypi_0 pypi pooch 1.7.0 pyha770c72_3 conda-forge prometheus_client 0.17.1 pyhd8ed1ab_0 conda-forge prompt-toolkit 3.0.39 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[chenhsuanlin]

Hi @DavidTu21, the conda installation guide in the README is for Neuralangelo itself (the PyTorch program) not COLMAP. There is probably some missing dependencies. Please use our provided Docker image or refer to the installation instructions in the official COLMAP website.

[DavidTu21]

Hi @chenhsuanlin thank you very much for your reply! Yes I noticed that there is no colmap in the yaml file, so I installed it via conda install -c conda-forge colmap and that might cause some dependencies errors. I will try the official installation as you suggested and let you know if everything works. Thank you again for your time!

[chenhsuanlin]

No problem! Please feel free to reopen if there are further issues.