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conda-forge / cudatoolkit-dev-feedstock

A conda-smithy repository for cudatoolkit-dev.
BSD 3-Clause "New" or "Revised" License
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Unable to install package due to libxml2.so.2 #78

Open killerkaos opened 8 months ago

killerkaos commented 8 months ago

Solution to issue cannot be found in the documentation.

Issue

Hi I am trying to instal cudatoolkit-dev from conda-forge and after two days of trial and error, I am still having the same issue. I get the following error

*stderr: ./cuda-installer: error while loading shared libraries: libxml2.so.2: cannot open shared object file: No such file or directory*

I install first conda install pytorch torchvision torchaudio pytorch-cuda=11.7 cuda-toolkit -c 'nvidia/label/cuda-11.7.0' -c pytorch -c nvidia -y

Then conda install -c conda-forge cudatoolkit-dev

I have installed manually libxml2 via conda install, while activated the environment. Still no effect. I have a feeling it has nothing to do with the dependency. I tried so many times thinking it was the sequential error, but it's not.

Full error is as follows `ERROR conda.core.link:_execute(945): An error occurred while installing package 'conda-forge::cudatoolkit-dev-11.7.0-h1de0b5d_6'. Rolling back transaction: done LinkError: post-link script failed for package conda-forge::cudatoolkit-dev-11.7.0-h1de0b5d_6 location of failed script: /root/miniconda/envs/vicuna-matata/bin/.cudatoolkit-dev-post-link.sh ==> script messages <==

==> script output <== stdout: Running Post installation downloading https://developer.download.nvidia.com/compute/cuda/11.7.0/local_installers/cuda_11.7.0_515.43.04_linux.run to /root/miniconda/envs/vicuna-matata/pkgs/cudatoolkit-dev/cuda_11.7.0_515.43.04_linux.run Extracting on Linux stderr: ./cuda-installer: error while loading shared libraries: libxml2.so.2: cannot open shared object file: No such file or directory Traceback (most recent call last): File "/root/miniconda/envs/vicuna-matata/bin/cudatoolkit-dev-post-install.py", line 311, in _main() File "/root/miniconda/envs/vicuna-matata/bin/cudatoolkit-dev-post-install.py", line 307, in _main extractor.extract() File "/root/miniconda/envs/vicuna-matata/bin/cudatoolkit-dev-post-install.py", line 135, in extract subprocess.run(cmd, env=os.environ.copy(), check=True) File "/root/miniconda/envs/vicuna-matata/lib/python3.10/subprocess.py", line 526, in run raise CalledProcessError(retcode, process.args, subprocess.CalledProcessError: Command '['/root/miniconda/envs/vicuna-matata/pkgs/cudatoolkit-dev/cuda_11.7.0_515.43.04_linux.run', '--silent', '--toolkit', '--toolkitpath=/tmp/tmpm21ydnnj', '--override']' returned non-zero exit status 127. return code: 1 ()` Executing all inside a docker container with base Linuxserver.io ubuntu, updated with wget, git, sudo and screen, as well as gcc-9 and g++-9 ### Installed packages ```shell # packages in environment at /root/miniconda/envs/vicuna-matata: # # Name Version Build Channel _libgcc_mutex 0.1 main _openmp_mutex 5.1 1_gnu blas 1.0 mkl brotli-python 1.0.9 py310h6a678d5_7 bzip2 1.0.8 h7b6447c_0 ca-certificates 2023.12.12 h06a4308_0 certifi 2023.11.17 py310h06a4308_0 cffi 1.16.0 py310h5eee18b_0 charset-normalizer 3.3.2 pypi_0 pypi cryptography 41.0.7 py310hdda0065_0 cuda-cccl 11.7.58 hc415cf5_0 nvidia/label/cuda-11.7.0 cuda-command-line-tools 11.7.0 0 nvidia/label/cuda-11.7.0 cuda-compiler 11.7.0 0 nvidia/label/cuda-11.7.0 cuda-cudart 11.7.60 h9538e0e_0 nvidia/label/cuda-11.7.0 cuda-cudart-dev 11.7.60 h6a7c232_0 nvidia/label/cuda-11.7.0 cuda-cuobjdump 11.7.50 h28cc80a_0 nvidia/label/cuda-11.7.0 cuda-cupti 11.7.50 hb6f9eaf_0 nvidia/label/cuda-11.7.0 cuda-cuxxfilt 11.7.50 hb365495_0 nvidia/label/cuda-11.7.0 cuda-documentation 11.7.50 0 nvidia/label/cuda-11.7.0 cuda-driver-dev 11.7.60 0 nvidia/label/cuda-11.7.0 cuda-gdb 11.7.50 h4a0ac72_0 nvidia/label/cuda-11.7.0 cuda-libraries 11.7.0 0 nvidia/label/cuda-11.7.0 cuda-libraries-dev 11.7.0 0 nvidia/label/cuda-11.7.0 cuda-memcheck 11.7.50 hc446b2b_0 nvidia/label/cuda-11.7.0 cuda-nsight 11.7.50 0 nvidia/label/cuda-11.7.0 cuda-nsight-compute 11.7.0 0 nvidia/label/cuda-11.7.0 cuda-nvcc 11.7.64 0 nvidia/label/cuda-11.7.0 cuda-nvdisasm 11.7.50 h5bd0695_0 nvidia/label/cuda-11.7.0 cuda-nvml-dev 11.7.50 h3af1343_0 nvidia/label/cuda-11.7.0 cuda-nvprof 11.7.50 h7a2404d_0 nvidia/label/cuda-11.7.0 cuda-nvprune 11.7.50 h7add7b4_0 nvidia/label/cuda-11.7.0 cuda-nvrtc 11.7.50 hd0285e0_0 nvidia/label/cuda-11.7.0 cuda-nvrtc-dev 11.7.50 heada363_0 nvidia/label/cuda-11.7.0 cuda-nvtx 11.7.50 h05b0816_0 nvidia/label/cuda-11.7.0 cuda-nvvp 11.7.50 hd2289d5_0 nvidia/label/cuda-11.7.0 cuda-runtime 11.7.0 0 nvidia/label/cuda-11.7.0 cuda-sanitizer-api 11.7.50 hb424887_0 nvidia/label/cuda-11.7.0 cuda-toolkit 11.7.0 0 nvidia/label/cuda-11.7.0 cuda-tools 11.7.0 0 nvidia/label/cuda-11.7.0 cuda-visual-tools 11.7.0 0 nvidia/label/cuda-11.7.0 ffmpeg 4.3 hf484d3e_0 pytorch filelock 3.13.1 py310h06a4308_0 freetype 2.12.1 h4a9f257_0 fsspec 2023.12.2 pypi_0 pypi gds-tools 1.3.0.44 0 nvidia/label/cuda-11.7.0 giflib 5.2.1 h5eee18b_3 gmp 6.2.1 h295c915_3 gmpy2 2.1.2 py310heeb90bb_0 gnutls 3.6.15 he1e5248_0 icu 73.1 h6a678d5_0 idna 3.6 pypi_0 pypi intel-openmp 2023.1.0 hdb19cb5_46306 jinja2 3.1.3 pypi_0 pypi jpeg 9e h5eee18b_1 lame 3.100 h7b6447c_0 lcms2 2.12 h3be6417_0 ld_impl_linux-64 2.38 h1181459_1 lerc 3.0 h295c915_0 libcublas 11.10.1.25 he442b6f_0 nvidia/label/cuda-11.7.0 libcublas-dev 11.10.1.25 h0c8ac2b_0 nvidia/label/cuda-11.7.0 libcufft 10.7.2.50 h80a1efe_0 nvidia/label/cuda-11.7.0 libcufft-dev 10.7.2.50 h59a5ac8_0 nvidia/label/cuda-11.7.0 libcufile 1.3.0.44 0 nvidia/label/cuda-11.7.0 libcufile-dev 1.3.0.44 0 nvidia/label/cuda-11.7.0 libcurand 10.2.10.50 heec50f7_0 nvidia/label/cuda-11.7.0 libcurand-dev 10.2.10.50 hd49a9cd_0 nvidia/label/cuda-11.7.0 libcusolver 11.3.5.50 hcab339c_0 nvidia/label/cuda-11.7.0 libcusolver-dev 11.3.5.50 hc6eba6f_0 nvidia/label/cuda-11.7.0 libcusparse 11.7.3.50 h6aaafad_0 nvidia/label/cuda-11.7.0 libcusparse-dev 11.7.3.50 hc644b96_0 nvidia/label/cuda-11.7.0 libdeflate 1.17 h5eee18b_1 libffi 3.4.4 h6a678d5_0 libgcc-ng 11.2.0 h1234567_1 libgomp 11.2.0 h1234567_1 libiconv 1.16 h7f8727e_2 libidn2 2.3.4 h5eee18b_0 libjpeg-turbo 2.0.0 h9bf148f_0 pytorch libnpp 11.7.3.21 h3effbd9_0 nvidia/label/cuda-11.7.0 libnpp-dev 11.7.3.21 hb6476a9_0 nvidia/label/cuda-11.7.0 libnvjpeg 11.7.2.34 hfe236c7_0 nvidia/label/cuda-11.7.0 libnvjpeg-dev 11.7.2.34 h2e48410_0 nvidia/label/cuda-11.7.0 libpng 1.6.39 h5eee18b_0 libstdcxx-ng 11.2.0 h1234567_1 libtasn1 4.19.0 h5eee18b_0 libtiff 4.5.1 h6a678d5_0 libunistring 0.9.10 h27cfd23_0 libuuid 1.41.5 h5eee18b_0 libwebp 1.3.2 h11a3e52_0 libwebp-base 1.3.2 h5eee18b_0 libxml2 2.10.4 hf1b16e4_1 llvm-openmp 14.0.6 h9e868ea_0 lz4-c 1.9.4 h6a678d5_0 markupsafe 2.1.3 py310h5eee18b_0 mkl 2023.1.0 h213fc3f_46344 mkl-service 2.4.0 py310h5eee18b_1 mkl_fft 1.3.8 py310h5eee18b_0 mkl_random 1.2.4 py310hdb19cb5_0 mpc 1.1.0 h10f8cd9_1 mpfr 4.0.2 hb69a4c5_1 mpmath 1.3.0 py310h06a4308_0 ncurses 6.4 h6a678d5_0 nettle 3.7.3 hbbd107a_1 networkx 3.2.1 pypi_0 pypi nsight-compute 2022.2.0.13 0 nvidia/label/cuda-11.7.0 numpy 1.26.3 py310h5f9d8c6_0 numpy-base 1.26.3 py310hb5e798b_0 nvidia-cublas-cu12 12.1.3.1 pypi_0 pypi nvidia-cuda-cupti-cu12 12.1.105 pypi_0 pypi nvidia-cuda-nvrtc-cu12 12.1.105 pypi_0 pypi nvidia-cuda-runtime-cu12 12.1.105 pypi_0 pypi nvidia-cudnn-cu12 8.9.2.26 pypi_0 pypi nvidia-cufft-cu12 11.0.2.54 pypi_0 pypi nvidia-curand-cu12 10.3.2.106 pypi_0 pypi nvidia-cusolver-cu12 11.4.5.107 pypi_0 pypi nvidia-cusparse-cu12 12.1.0.106 pypi_0 pypi nvidia-nccl-cu12 2.18.1 pypi_0 pypi nvidia-nvjitlink-cu12 12.3.101 pypi_0 pypi nvidia-nvtx-cu12 12.1.105 pypi_0 pypi openh264 2.1.1 h4ff587b_0 openjpeg 2.4.0 h3ad879b_0 openssl 3.0.12 h7f8727e_0 pillow 10.2.0 pypi_0 pypi pip 23.3.1 py310h06a4308_0 pycparser 2.21 pyhd3eb1b0_0 pyopenssl 23.2.0 py310h06a4308_0 pysocks 1.7.1 py310h06a4308_0 python 3.10.13 h955ad1f_0 pytorch 2.1.2 py3.10_cpu_0 pytorch pytorch-cuda 11.7 h778d358_5 pytorch pytorch-mutex 1.0 cpu pytorch pyyaml 6.0.1 py310h5eee18b_0 readline 8.2 h5eee18b_0 requests 2.31.0 py310h06a4308_0 setuptools 68.2.2 py310h06a4308_0 sqlite 3.41.2 h5eee18b_0 sympy 1.12 py310h06a4308_0 tbb 2021.8.0 hdb19cb5_0 tk 8.6.12 h1ccaba5_0 torch 2.1.2 pypi_0 pypi torchaudio 2.1.2 pypi_0 pypi torchvision 0.16.2 pypi_0 pypi triton 2.1.0 pypi_0 pypi typing_extensions 4.9.0 py310h06a4308_0 tzdata 2023d h04d1e81_0 urllib3 2.1.0 pypi_0 pypi wheel 0.41.2 py310h06a4308_0 xz 5.4.5 h5eee18b_0 yaml 0.2.5 h7b6447c_0 zlib 1.2.13 h5eee18b_0 zstd 1.5.5 hc292b87_0 ``` ### Environment info ```shell active environment : vicuna-matata active env location : /root/miniconda/envs/vicuna-matata shell level : 2 user config file : /root/.condarc populated config files : conda version : 23.11.0 conda-build version : not installed python version : 3.11.5.final.0 solver : libmamba (default) virtual packages : __archspec=1=haswell __conda=23.11.0=0 __cuda=12.2=0 __glibc=2.35=0 __linux=6.1.64=0 __unix=0=0 base environment : /root/miniconda (writable) conda av data dir : /root/miniconda/etc/conda conda av metadata url : None channel URLs : https://repo.anaconda.com/pkgs/main/linux-64 https://repo.anaconda.com/pkgs/main/noarch https://repo.anaconda.com/pkgs/r/linux-64 https://repo.anaconda.com/pkgs/r/noarch package cache : /root/miniconda/pkgs /root/.conda/pkgs envs directories : /root/miniconda/envs /root/.conda/envs platform : linux-64 user-agent : conda/23.11.0 requests/2.31.0 CPython/3.11.5 Linux/6.1.64-Unraid ubuntu/22.04.2 glibc/2.35 solver/libmamba conda-libmamba-solver/23.12.0 libmambapy/1.5.3 UID:GID : 0:0 netrc file : None offline mode : False ```
killerkaos commented 8 months ago

I installed outside of the conda environment (not base), in the main ubuntu, and it worked

PRawal671 commented 6 months ago

I installed outside of the conda environment (not base), in the main ubuntu, and it worked

Could you please elaborate? I am facing the same error as you but using mamba to install (mamba install conda-forge::cudatoolkit-dev).