-bash-4.1$ sudo ./install_sct ******************************* * Welcome to SCT installation * ******************************* Checking OS type and version... Linux closrvdevipp002 2.6.32-754.35.1.el6.x86_64 #1 SMP Wed Sep 16 06:48:01 EDT 2020 x86_64 x86_64 x86_64 GNU/Linux Checking requirements... OK! SCT version ......... 5.3.0 Installation type ... package Operating system .... linux (unknown) Shell config ........ /root/.bashrc To improve user experience and fix bugs, the SCT development team is using a report system to automatically receive crash reports and errors from users. These reports are anonymous. Do you agree to help us improve SCT? [y]es/[n]o: n --> Crash reports will not be sent. SCT will be installed here: [/root/sct_5.3.0] Do you agree? [y]es/[n]o: n Choose install directory. Warning! Give full path (e.g. /usr/django/sct_v3.0): /mnt/algo/sct_5.3.0 WARNING: Directory already exists. Files will be overwritten. Do you want to add the sct_* scripts to your PATH environment? [y]es/[n]o: n Copying source files from /mnt/algo/spinalcordtoolbox-5.3.0 to /mnt/algo/sct_5.3.0 ........................................................................................................................................................................................................................................................................................................................................................................................................................................... Removing sct and isct softlink from /mnt/algo/sct_5.3.0/bin Installing conda... rm -rf /mnt/algo/sct_5.3.0/python mkdir -p /mnt/algo/sct_5.3.0/python wget -O /tmp/tmp.u4KfRc9Cwz/miniconda.sh https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh --2021-06-06 12:58:56-- https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh Resolving repo.anaconda.com... 104.16.130.3, 104.16.131.3, 2606:4700::6810:8203, ... Connecting to repo.anaconda.com|104.16.130.3|:443... connected. HTTP request sent, awaiting response... 200 OK Length: 94235922 (90M) [application/x-sh] Saving to: “/tmp/tmp.u4KfRc9Cwz/miniconda.sh” 100%[=========================================================================================================================================================================>] 94,235,922 32.1M/s in 2.8s 2021-06-06 12:58:59 (32.1 MB/s) - “/tmp/tmp.u4KfRc9Cwz/miniconda.sh” saved [94235922/94235922] bash /tmp/tmp.u4KfRc9Cwz/miniconda.sh -p /mnt/algo/sct_5.3.0/python -b -f PREFIX=/mnt/algo/sct_5.3.0/python Unpacking payload ... Extracting : requests-2.24.0-py_0.conda: 94%|█████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████▌ | 34/36 [00:23<00:03, 1.73s/it]noCollecting package metadata (current_repodata.json): done Solving environment: done ## Package Plan ## environment location: /mnt/algo/sct_5.3.0/python added / updated specs: - _libgcc_mutex==0.1=main - brotlipy==0.7.0=py38h27cfd23_1003 - ca-certificates==2020.10.14=0 - certifi==2020.6.20=pyhd3eb1b0_3 - cffi==1.14.3=py38h261ae71_2 - chardet==3.0.4=py38h06a4308_1003 - conda-package-handling==1.7.2=py38h03888b9_0 - conda==4.9.2=py38h06a4308_0 - cryptography==3.2.1=py38h3c74f83_1 - idna==2.10=py_0 - ld_impl_linux-64==2.33.1=h53a641e_7 - libedit==3.1.20191231=h14c3975_1 - libffi==3.3=he6710b0_2 - libgcc-ng==9.1.0=hdf63c60_0 - libstdcxx-ng==9.1.0=hdf63c60_0 - ncurses==6.2=he6710b0_1 - openssl==1.1.1h=h7b6447c_0 - pip==20.2.4=py38h06a4308_0 - pycosat==0.6.3=py38h7b6447c_1 - pycparser==2.20=py_2 - pyopenssl==19.1.0=pyhd3eb1b0_1 - pysocks==1.7.1=py38h06a4308_0 - python==3.8.5=h7579374_1 - readline==8.0=h7b6447c_0 - requests==2.24.0=py_0 - ruamel_yaml==0.15.87=py38h7b6447c_1 - setuptools==50.3.1=py38h06a4308_1 - six==1.15.0=py38h06a4308_0 - sqlite==3.33.0=h62c20be_0 - tk==8.6.10=hbc83047_0 - tqdm==4.51.0=pyhd3eb1b0_0 - urllib3==1.25.11=py_0 - wheel==0.35.1=pyhd3eb1b0_0 - xz==5.2.5=h7b6447c_0 - yaml==0.2.5=h7b6447c_0 - zlib==1.2.11=h7b6447c_3 The following NEW packages will be INSTALLED: _libgcc_mutex pkgs/main/linux-64::_libgcc_mutex-0.1-main brotlipy pkgs/main/linux-64::brotlipy-0.7.0-py38h27cfd23_1003 ca-certificates pkgs/main/linux-64::ca-certificates-2020.10.14-0 certifi pkgs/main/noarch::certifi-2020.6.20-pyhd3eb1b0_3 cffi pkgs/main/linux-64::cffi-1.14.3-py38h261ae71_2 chardet pkgs/main/linux-64::chardet-3.0.4-py38h06a4308_1003 conda pkgs/main/linux-64::conda-4.9.2-py38h06a4308_0 conda-package-han~ pkgs/main/linux-64::conda-package-handling-1.7.2-py38h03888b9_0 cryptography pkgs/main/linux-64::cryptography-3.2.1-py38h3c74f83_1 idna pkgs/main/noarch::idna-2.10-py_0 ld_impl_linux-64 pkgs/main/linux-64::ld_impl_linux-64-2.33.1-h53a641e_7 libedit pkgs/main/linux-64::libedit-3.1.20191231-h14c3975_1 libffi pkgs/main/linux-64::libffi-3.3-he6710b0_2 libgcc-ng pkgs/main/linux-64::libgcc-ng-9.1.0-hdf63c60_0 libstdcxx-ng pkgs/main/linux-64::libstdcxx-ng-9.1.0-hdf63c60_0 ncurses pkgs/main/linux-64::ncurses-6.2-he6710b0_1 openssl pkgs/main/linux-64::openssl-1.1.1h-h7b6447c_0 pip pkgs/main/linux-64::pip-20.2.4-py38h06a4308_0 pycosat pkgs/main/linux-64::pycosat-0.6.3-py38h7b6447c_1 pycparser pkgs/main/noarch::pycparser-2.20-py_2 pyopenssl pkgs/main/noarch::pyopenssl-19.1.0-pyhd3eb1b0_1 pysocks pkgs/main/linux-64::pysocks-1.7.1-py38h06a4308_0 python pkgs/main/linux-64::python-3.8.5-h7579374_1 readline pkgs/main/linux-64::readline-8.0-h7b6447c_0 requests pkgs/main/noarch::requests-2.24.0-py_0 ruamel_yaml pkgs/main/linux-64::ruamel_yaml-0.15.87-py38h7b6447c_1 setuptools pkgs/main/linux-64::setuptools-50.3.1-py38h06a4308_1 six pkgs/main/linux-64::six-1.15.0-py38h06a4308_0 sqlite pkgs/main/linux-64::sqlite-3.33.0-h62c20be_0 tk pkgs/main/linux-64::tk-8.6.10-hbc83047_0 tqdm pkgs/main/noarch::tqdm-4.51.0-pyhd3eb1b0_0 urllib3 pkgs/main/noarch::urllib3-1.25.11-py_0 wheel pkgs/main/noarch::wheel-0.35.1-pyhd3eb1b0_0 xz pkgs/main/linux-64::xz-5.2.5-h7b6447c_0 yaml pkgs/main/linux-64::yaml-0.2.5-h7b6447c_0 zlib pkgs/main/linux-64::zlib-1.2.11-h7b6447c_3 Preparing transaction: done Executing transaction: done installation finished. Collecting package metadata (current_repodata.json): done Solving environment: done ==> WARNING: A newer version of conda exists. <== current version: 4.9.2 latest version: 4.10.1 Please update conda by running $ conda update -n base -c defaults conda ## Package Plan ## environment location: /mnt/algo/sct_5.3.0/python/envs/venv_sct added / updated specs: - python=3.6 The following packages will be downloaded: package | build ---------------------------|----------------- ca-certificates-2021.5.25 | h06a4308_1 112 KB certifi-2021.5.30 | py36h06a4308_0 139 KB openssl-1.1.1k | h27cfd23_0 2.5 MB pip-21.1.1 | py36h06a4308_0 1.8 MB python-3.6.13 | hdb3f193_0 29.7 MB readline-8.1 | h27cfd23_0 362 KB setuptools-52.0.0 | py36h06a4308_0 724 KB sqlite-3.35.4 | hdfb4753_0 981 KB wheel-0.36.2 | pyhd3eb1b0_0 33 KB ------------------------------------------------------------ Total: 36.4 MB The following NEW packages will be INSTALLED: _libgcc_mutex pkgs/main/linux-64::_libgcc_mutex-0.1-main ca-certificates pkgs/main/linux-64::ca-certificates-2021.5.25-h06a4308_1 certifi pkgs/main/linux-64::certifi-2021.5.30-py36h06a4308_0 ld_impl_linux-64 pkgs/main/linux-64::ld_impl_linux-64-2.33.1-h53a641e_7 libffi pkgs/main/linux-64::libffi-3.3-he6710b0_2 libgcc-ng pkgs/main/linux-64::libgcc-ng-9.1.0-hdf63c60_0 libstdcxx-ng pkgs/main/linux-64::libstdcxx-ng-9.1.0-hdf63c60_0 ncurses pkgs/main/linux-64::ncurses-6.2-he6710b0_1 openssl pkgs/main/linux-64::openssl-1.1.1k-h27cfd23_0 pip pkgs/main/linux-64::pip-21.1.1-py36h06a4308_0 python pkgs/main/linux-64::python-3.6.13-hdb3f193_0 readline pkgs/main/linux-64::readline-8.1-h27cfd23_0 setuptools pkgs/main/linux-64::setuptools-52.0.0-py36h06a4308_0 sqlite pkgs/main/linux-64::sqlite-3.35.4-hdfb4753_0 tk pkgs/main/linux-64::tk-8.6.10-hbc83047_0 wheel pkgs/main/noarch::wheel-0.36.2-pyhd3eb1b0_0 xz pkgs/main/linux-64::xz-5.2.5-h7b6447c_0 zlib pkgs/main/linux-64::zlib-1.2.11-h7b6447c_3 Downloading and Extracting Packages ca-certificates-2021 | 112 KB | ######################################################################################################################################################################## | 100% certifi-2021.5.30 | 139 KB | ######################################################################################################################################################################## | 100% wheel-0.36.2 | 33 KB | ######################################################################################################################################################################## | 100% sqlite-3.35.4 | 981 KB | ######################################################################################################################################################################## | 100% pip-21.1.1 | 1.8 MB | ######################################################################################################################################################################## | 100% readline-8.1 | 362 KB | ######################################################################################################################################################################## | 100% setuptools-52.0.0 | 724 KB | ######################################################################################################################################################################## | 100% python-3.6.13 | 29.7 MB | ######################################################################################################################################################################## | 100% openssl-1.1.1k | 2.5 MB | ######################################################################################################################################################################## | 100% Preparing transaction: done Verifying transaction: done Executing transaction: done # # To activate this environment, use # # $ conda activate venv_sct # # To deactivate an active environment, use # # $ conda deactivate Installing Python dependencies... Using requirements-freeze.txt (release installation) Looking in links: https://download.pytorch.org/whl/cpu/torch_stable.html Ignoring torch: markers 'sys_platform == "darwin"' don't match your environment Ignoring torchvision: markers 'sys_platform == "darwin"' don't match your environment Collecting absl-py==0.12.0 Using cached absl_py-0.12.0-py3-none-any.whl (129 kB) Collecting appdirs==1.4.4 Using cached appdirs-1.4.4-py2.py3-none-any.whl (9.6 kB) Collecting attrs==20.3.0 Using cached attrs-20.3.0-py2.py3-none-any.whl (49 kB) Collecting bids-neuropoly==0.2 Using cached bids_neuropoly-0.2-py3-none-any.whl (3.1 kB) Collecting bids-validator==1.7.1 Using cached bids_validator-1.7.1-py2.py3-none-any.whl (19 kB) Collecting bleach==1.5.0 Using cached bleach-1.5.0-py2.py3-none-any.whl (17 kB) Collecting cachetools==4.2.1 Using cached cachetools-4.2.1-py3-none-any.whl (12 kB) Collecting certifi==2020.12.5 Using cached certifi-2020.12.5-py2.py3-none-any.whl (147 kB) Collecting cffi==1.14.5 Using cached cffi-1.14.5-cp36-cp36m-manylinux1_x86_64.whl (401 kB) Collecting cfgv==3.2.0 Using cached cfgv-3.2.0-py2.py3-none-any.whl (7.3 kB) Collecting chardet==4.0.0 Using cached chardet-4.0.0-py2.py3-none-any.whl (178 kB) Collecting click==7.1.2 Using cached click-7.1.2-py2.py3-none-any.whl (82 kB) Collecting colored==1.4.2 Using cached colored-1.4.2-py3-none-any.whl Collecting coverage==5.5 Using cached coverage-5.5-cp36-cp36m-manylinux2010_x86_64.whl (240 kB) Collecting cryptography==3.4.7 Using cached cryptography-3.4.7-cp36-abi3-manylinux2010_x86_64.whl (3.1 MB) Collecting csv-diff==1.1 Using cached csv_diff-1.1-py3-none-any.whl (12 kB) Collecting cycler==0.10.0 Using cached cycler-0.10.0-py2.py3-none-any.whl (6.5 kB) Collecting decorator==4.4.2 Using cached decorator-4.4.2-py2.py3-none-any.whl (9.2 kB) Collecting dictdiffer==0.8.1 Using cached dictdiffer-0.8.1-py2.py3-none-any.whl (16 kB) Collecting dipy==1.4.0 Using cached dipy-1.4.0-cp36-cp36m-manylinux2010_x86_64.whl (7.7 MB) Collecting distlib==0.3.1 Using cached distlib-0.3.1-py2.py3-none-any.whl (335 kB) Collecting docopt==0.6.2 Using cached docopt-0.6.2-py2.py3-none-any.whl Collecting docutils==0.17.1 Using cached docutils-0.17.1-py2.py3-none-any.whl (575 kB) Collecting filelock==3.0.12 Using cached filelock-3.0.12-py3-none-any.whl (7.6 kB) Collecting future==0.18.2 Using cached future-0.18.2-py3-none-any.whl Collecting futures==3.1.1 Using cached futures-3.1.1-py3-none-any.whl (2.8 kB) Collecting google-auth==1.29.0 Using cached google_auth-1.29.0-py2.py3-none-any.whl (142 kB) Collecting google-auth-oauthlib==0.4.4 Using cached google_auth_oauthlib-0.4.4-py2.py3-none-any.whl (18 kB) Collecting grpcio==1.37.0 Using cached grpcio-1.37.0-cp36-cp36m-manylinux2010_x86_64.whl (4.1 MB) Collecting h5py==2.10.0 Using cached h5py-2.10.0-cp36-cp36m-manylinux1_x86_64.whl (2.9 MB) Collecting html5lib==0.9999999 Using cached html5lib-0.9999999-py3-none-any.whl Collecting identify==2.2.4 Using cached identify-2.2.4-py2.py3-none-any.whl (98 kB) Collecting idna==2.10 Using cached idna-2.10-py2.py3-none-any.whl (58 kB) Collecting imageio==2.9.0 Using cached imageio-2.9.0-py3-none-any.whl (3.3 MB) Collecting importlib-metadata==4.0.1 Using cached importlib_metadata-4.0.1-py3-none-any.whl (16 kB) Collecting importlib-resources==5.1.2 Using cached importlib_resources-5.1.2-py3-none-any.whl (25 kB) Collecting iniconfig==1.1.1 Using cached iniconfig-1.1.1-py2.py3-none-any.whl (5.0 kB) Collecting ivadomed==2.7.4 Using cached ivadomed-2.7.4-py3-none-any.whl (155 kB) Collecting joblib==1.0.1 Using cached joblib-1.0.1-py3-none-any.whl (303 kB) Collecting jsonpointer==2.1 Using cached jsonpointer-2.1-py2.py3-none-any.whl (7.4 kB) Collecting Keras==2.1.5 Using cached Keras-2.1.5-py2.py3-none-any.whl (334 kB) Collecting kiwisolver==1.3.1 Using cached kiwisolver-1.3.1-cp36-cp36m-manylinux1_x86_64.whl (1.1 MB) Collecting Markdown==3.3.4 Using cached Markdown-3.3.4-py3-none-any.whl (97 kB) Collecting matplotlib==3.3.4 Using cached matplotlib-3.3.4-cp36-cp36m-manylinux1_x86_64.whl (11.5 MB) Collecting mock==4.0.3 Using cached mock-4.0.3-py3-none-any.whl (28 kB) Collecting networkx==2.5.1 Using cached networkx-2.5.1-py3-none-any.whl (1.6 MB) Collecting nibabel==3.2.1 Using cached nibabel-3.2.1-py3-none-any.whl (3.3 MB) Collecting nodeenv==1.6.0 Using cached nodeenv-1.6.0-py2.py3-none-any.whl (21 kB) Collecting num2words==0.5.10 Using cached num2words-0.5.10-py3-none-any.whl (101 kB) Collecting numpy==1.19.5 Using cached numpy-1.19.5-cp36-cp36m-manylinux2010_x86_64.whl (14.8 MB) Collecting oauthlib==3.1.0 Using cached oauthlib-3.1.0-py2.py3-none-any.whl (147 kB) Collecting onnxruntime==1.4.0 Using cached onnxruntime-1.4.0-cp36-cp36m-manylinux2010_x86_64.whl (4.4 MB) Collecting packaging==20.9 Using cached packaging-20.9-py2.py3-none-any.whl (40 kB) Collecting pandas==1.1.5 Using cached pandas-1.1.5-cp36-cp36m-manylinux1_x86_64.whl (9.5 MB) Collecting patsy==0.5.1 Using cached patsy-0.5.1-py2.py3-none-any.whl (231 kB) Collecting Pillow==8.2.0 Using cached Pillow-8.2.0-cp36-cp36m-manylinux1_x86_64.whl (3.0 MB) Collecting pluggy==0.13.1 Using cached pluggy-0.13.1-py2.py3-none-any.whl (18 kB) Collecting pre-commit==2.10.1 Using cached pre_commit-2.10.1-py2.py3-none-any.whl (185 kB) Collecting protobuf==3.15.8 Using cached protobuf-3.15.8-cp36-cp36m-manylinux1_x86_64.whl (1.0 MB) Collecting psutil==5.8.0 Using cached psutil-5.8.0-cp36-cp36m-manylinux2010_x86_64.whl (291 kB) Collecting py==1.10.0 Using cached py-1.10.0-py2.py3-none-any.whl (97 kB) Collecting pyasn1==0.4.8 Using cached pyasn1-0.4.8-py2.py3-none-any.whl (77 kB) Collecting pyasn1-modules==0.2.8 Using cached pyasn1_modules-0.2.8-py2.py3-none-any.whl (155 kB) Collecting pybids==0.13 Using cached pybids-0.13-py3-none-any.whl (3.2 MB) Collecting pycparser==2.20 Using cached pycparser-2.20-py2.py3-none-any.whl (112 kB) Collecting pyOpenSSL==20.0.1 Using cached pyOpenSSL-20.0.1-py2.py3-none-any.whl (54 kB) Collecting pyparsing==2.4.7 Using cached pyparsing-2.4.7-py2.py3-none-any.whl (67 kB) Collecting PyQt5==5.11.3 Using cached PyQt5-5.11.3-5.11.2-cp35.cp36.cp37.cp38-abi3-manylinux1_x86_64.whl (117.8 MB) Collecting PyQt5-sip==4.19.19 Using cached PyQt5_sip-4.19.19-cp36-cp36m-manylinux1_x86_64.whl (67 kB) Collecting pytest==6.2.3 Using cached pytest-6.2.3-py3-none-any.whl (280 kB) Collecting pytest-console-scripts==1.1.0 Using cached pytest_console_scripts-1.1.0-py3-none-any.whl Collecting pytest-cov==2.11.1 Using cached pytest_cov-2.11.1-py2.py3-none-any.whl (20 kB) Collecting pytest-ordering==0.6 Using cached pytest_ordering-0.6-py3-none-any.whl (4.6 kB) Collecting python-dateutil==2.8.1 Using cached python_dateutil-2.8.1-py2.py3-none-any.whl (227 kB) Collecting pytz==2021.1 Using cached pytz-2021.1-py2.py3-none-any.whl (510 kB) Collecting PyWavelets==1.1.1 Using cached PyWavelets-1.1.1-cp36-cp36m-manylinux1_x86_64.whl (4.4 MB) Collecting PyYAML==5.4.1 Using cached PyYAML-5.4.1-cp36-cp36m-manylinux1_x86_64.whl (640 kB) Collecting raven==6.10.0 Using cached raven-6.10.0-py2.py3-none-any.whl (284 kB) Collecting requests==2.25.1 Using cached requests-2.25.1-py2.py3-none-any.whl (61 kB) Collecting requests-oauthlib==1.3.0 Using cached requests_oauthlib-1.3.0-py2.py3-none-any.whl (23 kB) Collecting requirements-parser==0.2.0 Using cached requirements_parser-0.2.0-py3-none-any.whl Collecting rsa==4.7.2 Using cached rsa-4.7.2-py3-none-any.whl (34 kB) Collecting scikit-image==0.17.2 Using cached scikit_image-0.17.2-cp36-cp36m-manylinux1_x86_64.whl (12.4 MB) Collecting scikit-learn==0.24.1 Using cached scikit_learn-0.24.1-cp36-cp36m-manylinux2010_x86_64.whl (22.2 MB) Collecting scipy==1.5.4 Using cached scipy-1.5.4-cp36-cp36m-manylinux1_x86_64.whl (25.9 MB) Collecting seaborn==0.11.1 Using cached seaborn-0.11.1-py3-none-any.whl (285 kB) Collecting six==1.15.0 Using cached six-1.15.0-py2.py3-none-any.whl (10 kB) Collecting sphinx-jsonschema==1.16.8 Using cached sphinx_jsonschema-1.16.8-py3-none-any.whl Collecting SQLAlchemy==1.3.24 Using cached SQLAlchemy-1.3.24-cp36-cp36m-manylinux2010_x86_64.whl (1.3 MB) Collecting tensorboard==2.5.0 Using cached tensorboard-2.5.0-py3-none-any.whl (6.0 MB) Collecting tensorboard-data-server==0.6.0 Using cached tensorboard_data_server-0.6.0-py3-none-manylinux2010_x86_64.whl (3.9 MB) Collecting tensorboard-plugin-wit==1.8.0 Using cached tensorboard_plugin_wit-1.8.0-py3-none-any.whl (781 kB) Collecting tensorflow==1.5.0 Using cached tensorflow-1.5.0-cp36-cp36m-manylinux1_x86_64.whl (44.4 MB) Collecting threadpoolctl==2.1.0 Using cached threadpoolctl-2.1.0-py3-none-any.whl (12 kB) Collecting tifffile==2020.9.3 Using cached tifffile-2020.9.3-py3-none-any.whl (148 kB) Collecting toml==0.10.2 Using cached toml-0.10.2-py2.py3-none-any.whl (16 kB) Collecting tqdm==4.60.0 Using cached tqdm-4.60.0-py2.py3-none-any.whl (75 kB) Collecting transforms3d==0.3.1 Using cached transforms3d-0.3.1-py3-none-any.whl Collecting typing-extensions==3.7.4.3 Using cached typing_extensions-3.7.4.3-py3-none-any.whl (22 kB) Collecting urllib3==1.26.4 Using cached urllib3-1.26.4-py2.py3-none-any.whl (153 kB) Collecting virtualenv==20.4.4 Using cached virtualenv-20.4.4-py2.py3-none-any.whl (7.2 MB) Collecting Werkzeug==1.0.1 Using cached Werkzeug-1.0.1-py2.py3-none-any.whl (298 kB) Collecting wquantiles==0.5 Using cached wquantiles-0.5-py3-none-any.whl Collecting xlwt==1.3.0 Using cached xlwt-1.3.0-py2.py3-none-any.whl (99 kB) Collecting zipp==3.4.1 Using cached zipp-3.4.1-py3-none-any.whl (5.2 kB) Collecting torch==1.5.0+cpu Using cached https://download.pytorch.org/whl/cpu/torch-1.5.0%2Bcpu-cp36-cp36m-linux_x86_64.whl (127.3 MB) Collecting torchvision==0.6.0+cpu Using cached https://download.pytorch.org/whl/cpu/torchvision-0.6.0%2Bcpu-cp36-cp36m-linux_x86_64.whl (5.7 MB) Requirement already satisfied: setuptools>=40.3.0 in ./python/envs/venv_sct/lib/python3.6/site-packages (from google-auth==1.29.0->-r requirements-freeze.txt (line 27)) (52.0.0.post20210125) Requirement already satisfied: wheel>=0.26 in ./python/envs/venv_sct/lib/python3.6/site-packages (from tensorboard==2.5.0->-r requirements-freeze.txt (line 90)) (0.36.2) Collecting tensorflow-tensorboard<1.6.0,>=1.5.0 Using cached tensorflow_tensorboard-1.5.1-py3-none-any.whl (3.0 MB) Installing collected packages: zipp, urllib3, typing-extensions, six, pyparsing, pyasn1, idna, chardet, certifi, rsa, requests, pytz, python-dateutil, pyasn1-modules, packaging, oauthlib, numpy, importlib-metadata, docopt, cachetools, toml, SQLAlchemy, scipy, requests-oauthlib, pycparser, py, pluggy, Pillow, patsy, pandas, num2words, nibabel, kiwisolver, iniconfig, importlib-resources, html5lib, google-auth, future, filelock, distlib, decorator, cycler, click, bids-validator, attrs, appdirs, Werkzeug, virtualenv, torch, tifffile, threadpoolctl, tensorboard-plugin-wit, tensorboard-data-server, PyYAML, PyWavelets, pytest, pybids, protobuf, nodeenv, networkx, mock, matplotlib, Markdown, jsonpointer, joblib, imageio, identify, grpcio, google-auth-oauthlib, docutils, dictdiffer, cfgv, cffi, bleach, absl-py, tqdm, torchvision, tensorflow-tensorboard, tensorboard, sphinx-jsonschema, seaborn, scikit-learn, scikit-image, pytest-ordering, pytest-console-scripts, PyQt5-sip, pre-commit, onnxruntime, h5py, csv-diff, cryptography, coverage, bids-neuropoly, xlwt, wquantiles, transforms3d, tensorflow, requirements-parser, raven, pytest-cov, PyQt5, pyOpenSSL, psutil, Keras, ivadomed, futures, dipy, colored Attempting uninstall: certifi Found existing installation: certifi 2021.5.30 Uninstalling certifi-2021.5.30: Successfully uninstalled certifi-2021.5.30 Successfully installed Keras-2.1.5 Markdown-3.3.4 Pillow-8.2.0 PyQt5-5.11.3 PyQt5-sip-4.19.19 PyWavelets-1.1.1 PyYAML-5.4.1 SQLAlchemy-1.3.24 Werkzeug-1.0.1 absl-py-0.12.0 appdirs-1.4.4 attrs-20.3.0 bids-neuropoly-0.2 bids-validator-1.7.1 bleach-1.5.0 cachetools-4.2.1 certifi-2020.12.5 cffi-1.14.5 cfgv-3.2.0 chardet-4.0.0 click-7.1.2 colored-1.4.2 coverage-5.5 cryptography-3.4.7 csv-diff-1.1 cycler-0.10.0 decorator-4.4.2 dictdiffer-0.8.1 dipy-1.4.0 distlib-0.3.1 docopt-0.6.2 docutils-0.17.1 filelock-3.0.12 future-0.18.2 futures-3.1.1 google-auth-1.29.0 google-auth-oauthlib-0.4.4 grpcio-1.37.0 h5py-2.10.0 html5lib-0.9999999 identify-2.2.4 idna-2.10 imageio-2.9.0 importlib-metadata-4.0.1 importlib-resources-5.1.2 iniconfig-1.1.1 ivadomed-2.7.4 joblib-1.0.1 jsonpointer-2.1 kiwisolver-1.3.1 matplotlib-3.3.4 mock-4.0.3 networkx-2.5.1 nibabel-3.2.1 nodeenv-1.6.0 num2words-0.5.10 numpy-1.19.5 oauthlib-3.1.0 onnxruntime-1.4.0 packaging-20.9 pandas-1.1.5 patsy-0.5.1 pluggy-0.13.1 pre-commit-2.10.1 protobuf-3.15.8 psutil-5.8.0 py-1.10.0 pyOpenSSL-20.0.1 pyasn1-0.4.8 pyasn1-modules-0.2.8 pybids-0.13 pycparser-2.20 pyparsing-2.4.7 pytest-6.2.3 pytest-console-scripts-1.1.0 pytest-cov-2.11.1 pytest-ordering-0.6 python-dateutil-2.8.1 pytz-2021.1 raven-6.10.0 requests-2.25.1 requests-oauthlib-1.3.0 requirements-parser-0.2.0 rsa-4.7.2 scikit-image-0.17.2 scikit-learn-0.24.1 scipy-1.5.4 seaborn-0.11.1 six-1.15.0 sphinx-jsonschema-1.16.8 tensorboard-2.5.0 tensorboard-data-server-0.6.0 tensorboard-plugin-wit-1.8.0 tensorflow-1.5.0 tensorflow-tensorboard-1.5.1 threadpoolctl-2.1.0 tifffile-2020.9.3 toml-0.10.2 torch-1.5.0+cpu torchvision-0.6.0+cpu tqdm-4.60.0 transforms3d-0.3.1 typing-extensions-3.7.4.3 urllib3-1.26.4 virtualenv-20.4.4 wquantiles-0.5 xlwt-1.3.0 zipp-3.4.1 WARNING: Running pip as root will break packages and permissions. You should install packages reliably by using venv: https://pip.pypa.io/warnings/venv Found existing installation: tensorflow-tensorboard 1.5.1 Uninstalling tensorflow-tensorboard-1.5.1: Successfully uninstalled tensorflow-tensorboard-1.5.1 WARNING: Running pip as root will break packages and permissions. You should install packages reliably by using venv: https://pip.pypa.io/warnings/venv Found existing installation: tensorboard 2.5.0 Uninstalling tensorboard-2.5.0: Successfully uninstalled tensorboard-2.5.0 WARNING: Running pip as root will break packages and permissions. You should install packages reliably by using venv: https://pip.pypa.io/warnings/venv Collecting tensorboard Using cached tensorboard-2.5.0-py3-none-any.whl (6.0 MB) Requirement already satisfied: werkzeug>=0.11.15 in ./python/envs/venv_sct/lib/python3.6/site-packages (from tensorboard) (1.0.1) Requirement already satisfied: grpcio>=1.24.3 in ./python/envs/venv_sct/lib/python3.6/site-packages (from tensorboard) (1.37.0) Requirement already satisfied: numpy>=1.12.0 in ./python/envs/venv_sct/lib/python3.6/site-packages (from tensorboard) (1.19.5) Requirement already satisfied: wheel>=0.26 in ./python/envs/venv_sct/lib/python3.6/site-packages (from tensorboard) (0.36.2) Requirement already satisfied: setuptools>=41.0.0 in ./python/envs/venv_sct/lib/python3.6/site-packages (from tensorboard) (52.0.0.post20210125) Requirement already satisfied: tensorboard-plugin-wit>=1.6.0 in ./python/envs/venv_sct/lib/python3.6/site-packages (from tensorboard) (1.8.0) Requirement already satisfied: tensorboard-data-server<0.7.0,>=0.6.0 in ./python/envs/venv_sct/lib/python3.6/site-packages (from tensorboard) (0.6.0) Requirement already satisfied: requests<3,>=2.21.0 in ./python/envs/venv_sct/lib/python3.6/site-packages (from tensorboard) (2.25.1) Requirement already satisfied: google-auth-oauthlib<0.5,>=0.4.1 in ./python/envs/venv_sct/lib/python3.6/site-packages (from tensorboard) (0.4.4) Requirement already satisfied: markdown>=2.6.8 in ./python/envs/venv_sct/lib/python3.6/site-packages (from tensorboard) (3.3.4) Requirement already satisfied: absl-py>=0.4 in ./python/envs/venv_sct/lib/python3.6/site-packages (from tensorboard) (0.12.0) Requirement already satisfied: protobuf>=3.6.0 in ./python/envs/venv_sct/lib/python3.6/site-packages (from tensorboard) (3.15.8) Requirement already satisfied: google-auth<2,>=1.6.3 in ./python/envs/venv_sct/lib/python3.6/site-packages (from tensorboard) (1.29.0) Requirement already satisfied: six in ./python/envs/venv_sct/lib/python3.6/site-packages (from absl-py>=0.4->tensorboard) (1.15.0) Requirement already satisfied: pyasn1-modules>=0.2.1 in ./python/envs/venv_sct/lib/python3.6/site-packages (from google-auth<2,>=1.6.3->tensorboard) (0.2.8) Requirement already satisfied: cachetools<5.0,>=2.0.0 in ./python/envs/venv_sct/lib/python3.6/site-packages (from google-auth<2,>=1.6.3->tensorboard) (4.2.1) Requirement already satisfied: rsa<5,>=3.1.4 in ./python/envs/venv_sct/lib/python3.6/site-packages (from google-auth<2,>=1.6.3->tensorboard) (4.7.2) Requirement already satisfied: requests-oauthlib>=0.7.0 in ./python/envs/venv_sct/lib/python3.6/site-packages (from google-auth-oauthlib<0.5,>=0.4.1->tensorboard) (1.3.0) Requirement already satisfied: importlib-metadata in ./python/envs/venv_sct/lib/python3.6/site-packages (from markdown>=2.6.8->tensorboard) (4.0.1) Requirement already satisfied: pyasn1<0.5.0,>=0.4.6 in ./python/envs/venv_sct/lib/python3.6/site-packages (from pyasn1-modules>=0.2.1->google-auth<2,>=1.6.3->tensorboard) (0.4.8) Requirement already satisfied: idna<3,>=2.5 in ./python/envs/venv_sct/lib/python3.6/site-packages (from requests<3,>=2.21.0->tensorboard) (2.10) Requirement already satisfied: urllib3<1.27,>=1.21.1 in ./python/envs/venv_sct/lib/python3.6/site-packages (from requests<3,>=2.21.0->tensorboard) (1.26.4) Requirement already satisfied: certifi>=2017.4.17 in ./python/envs/venv_sct/lib/python3.6/site-packages (from requests<3,>=2.21.0->tensorboard) (2020.12.5) Requirement already satisfied: chardet<5,>=3.0.2 in ./python/envs/venv_sct/lib/python3.6/site-packages (from requests<3,>=2.21.0->tensorboard) (4.0.0) Requirement already satisfied: oauthlib>=3.0.0 in ./python/envs/venv_sct/lib/python3.6/site-packages (from requests-oauthlib>=0.7.0->google-auth-oauthlib<0.5,>=0.4.1->tensorboard) (3.1.0) Requirement already satisfied: zipp>=0.5 in ./python/envs/venv_sct/lib/python3.6/site-packages (from importlib-metadata->markdown>=2.6.8->tensorboard) (3.4.1) Requirement already satisfied: typing-extensions>=3.6.4 in ./python/envs/venv_sct/lib/python3.6/site-packages (from importlib-metadata->markdown>=2.6.8->tensorboard) (3.7.4.3) Installing collected packages: tensorboard Successfully installed tensorboard-2.5.0 WARNING: Running pip as root will break packages and permissions. You should install packages reliably by using venv: https://pip.pypa.io/warnings/venv Installing spinalcordtoolbox... Obtaining file:///mnt/algo/sct_5.3.0 Installing collected packages: spinalcordtoolbox Running setup.py develop for spinalcordtoolbox Successfully installed spinalcordtoolbox-5.3.0 WARNING: Running pip as root will break packages and permissions. You should install packages reliably by using venv: https://pip.pypa.io/warnings/venv Creating launchers for Python scripts... Installing binaries... sct_download_data -d binaries_linux -o /mnt/algo/sct_5.3.0/bin -k -- Spinal Cord Toolbox (5.3.0) sct_download_data -d binaries_linux -o /mnt/algo/sct_5.3.0/bin -k -- Trying URL: https://osf.io/cs6zt/?action=download Downloading: 20200801_sct_binaries_linux.tar.gz Status: 100%|█████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████| 78.2M/78.2M [00:02<00:00, 32.3MB/s] Creating temporary folder (/tmp/sct-20210606130400.278636-3qfsjs9x) Unzip data to: /tmp/sct-20210606130400.278636-3qfsjs9x Removing temporary folders... Done! All requirements installed! Installing data... rm -rf /mnt/algo/sct_5.3.0/data mkdir -p /mnt/algo/sct_5.3.0/data sct_download_data -d PAM50 -o /mnt/algo/sct_5.3.0/data/PAM50 -- Spinal Cord Toolbox (5.3.0) sct_download_data -d PAM50 -o /mnt/algo/sct_5.3.0/data/PAM50 -- Removing existing destination folder '/mnt/algo/sct_5.3.0/data/PAM50' Trying URL: https://github.com/sct-data/PAM50/releases/download/r20201104/PAM50-r20201104.zip Retrying (Retry(total=2, connect=None, read=None, redirect=None, status=None)) after connection broken by 'SSLError(SSLError(1, '[SSL: CERTIFICATE_VERIFY_FAILED] certificate verify failed (_ssl.c:852)'),)': /269508010/0a8f1980-1e1c-11eb-84b0-fa146c143d89?X-Amz-Algorithm=AWS4-HMAC-SHA256&X-Amz-Credential=AKIAIWNJYAX4CSVEH53A%2F20210606%2Fus-east-1%2Fs3%2Faws4_request&X-Amz-Date=20210606T200404Z&X-Amz-Expires=300&X-Amz-Signature=1efc1d9363803537dee13f262c09a1c905fc7d32e01bb17a5aaca61d4cfafebf&X-Amz-SignedHeaders=host&actor_id=0&key_id=0&repo_id=269508010&response-content-disposition=attachment%3B%20filename%3DPAM50-r20201104.zip&response-content-type=application%2Foctet-stream Retrying (Retry(total=1, connect=None, read=None, redirect=None, status=None)) after connection broken by 'SSLError(SSLError(1, '[SSL: CERTIFICATE_VERIFY_FAILED] certificate verify failed (_ssl.c:852)'),)': /269508010/0a8f1980-1e1c-11eb-84b0-fa146c143d89?X-Amz-Algorithm=AWS4-HMAC-SHA256&X-Amz-Credential=AKIAIWNJYAX4CSVEH53A%2F20210606%2Fus-east-1%2Fs3%2Faws4_request&X-Amz-Date=20210606T200404Z&X-Amz-Expires=300&X-Amz-Signature=1efc1d9363803537dee13f262c09a1c905fc7d32e01bb17a5aaca61d4cfafebf&X-Amz-SignedHeaders=host&actor_id=0&key_id=0&repo_id=269508010&response-content-disposition=attachment%3B%20filename%3DPAM50-r20201104.zip&response-content-type=application%2Foctet-stream Retrying (Retry(total=0, connect=None, read=None, redirect=None, status=None)) after connection broken by 'SSLError(SSLError(1, '[SSL: CERTIFICATE_VERIFY_FAILED] certificate verify failed (_ssl.c:852)'),)': /269508010/0a8f1980-1e1c-11eb-84b0-fa146c143d89?X-Amz-Algorithm=AWS4-HMAC-SHA256&X-Amz-Credential=AKIAIWNJYAX4CSVEH53A%2F20210606%2Fus-east-1%2Fs3%2Faws4_request&X-Amz-Date=20210606T200404Z&X-Amz-Expires=300&X-Amz-Signature=1efc1d9363803537dee13f262c09a1c905fc7d32e01bb17a5aaca61d4cfafebf&X-Amz-SignedHeaders=host&actor_id=0&key_id=0&repo_id=269508010&response-content-disposition=attachment%3B%20filename%3DPAM50-r20201104.zip&response-content-type=application%2Foctet-stream Link download error, trying next mirror (error was: HTTPSConnectionPool(host='github-releases.githubusercontent.com', port=443): Max retries exceeded with url: /269508010/0a8f1980-1e1c-11eb-84b0-fa146c143d89?X-Amz-Algorithm=AWS4-HMAC-SHA256&X-Amz-Credential=AKIAIWNJYAX4CSVEH53A%2F20210606%2Fus-east-1%2Fs3%2Faws4_request&X-Amz-Date=20210606T200404Z&X-Amz-Expires=300&X-Amz-Signature=1efc1d9363803537dee13f262c09a1c905fc7d32e01bb17a5aaca61d4cfafebf&X-Amz-SignedHeaders=host&actor_id=0&key_id=0&repo_id=269508010&response-content-disposition=attachment%3B%20filename%3DPAM50-r20201104.zip&response-content-type=application%2Foctet-stream (Caused by SSLError(SSLError(1, '[SSL: CERTIFICATE_VERIFY_FAILED] certificate verify failed (_ssl.c:852)'),))) Trying URL: https://osf.io/download/5fa21326a5bb9d00610a5a21/ Downloading: PAM50-r20201104.zip Status: 100%|█████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████| 70.9M/70.9M [00:02<00:00, 25.7MB/s] Creating temporary folder (/tmp/sct-20210606130413.576737-_p_p4syt) Unzip data to: /tmp/sct-20210606130413.576737-_p_p4syt Removing temporary folders... Done! sct_download_data -d gm_model -o /mnt/algo/sct_5.3.0/data/gm_model -- Spinal Cord Toolbox (5.3.0) sct_download_data -d gm_model -o /mnt/algo/sct_5.3.0/data/gm_model -- Removing existing destination folder '/mnt/algo/sct_5.3.0/data/gm_model' Trying URL: https://osf.io/ugscu/?action=download Downloading: 20160922_gm_model.zip Status: 100%|█████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████| 10.3M/10.3M [00:00<00:00, 19.6MB/s] Creating temporary folder (/tmp/sct-20210606130416.500044-1jb44nbj) Unzip data to: /tmp/sct-20210606130416.500044-1jb44nbj Removing temporary folders... Done! sct_download_data -d optic_models -o /mnt/algo/sct_5.3.0/data/optic_models -- Spinal Cord Toolbox (5.3.0) sct_download_data -d optic_models -o /mnt/algo/sct_5.3.0/data/optic_models -- Removing existing destination folder '/mnt/algo/sct_5.3.0/data/optic_models' Trying URL: https://github.com/sct-data/optic_models/releases/download/r20170413/20170413_optic_models.zip Retrying (Retry(total=2, connect=None, read=None, redirect=None, status=None)) after connection broken by 'SSLError(SSLError(1, '[SSL: CERTIFICATE_VERIFY_FAILED] certificate verify failed (_ssl.c:852)'),)': /269512426/d1a71900-a6b2-11ea-86a6-5e4fd8fa6cf8?X-Amz-Algorithm=AWS4-HMAC-SHA256&X-Amz-Credential=AKIAIWNJYAX4CSVEH53A%2F20210606%2Fus-east-1%2Fs3%2Faws4_request&X-Amz-Date=20210606T200417Z&X-Amz-Expires=300&X-Amz-Signature=437cd772620ac5ed052c5075da0cb12150182926708de4955a5c0660cecf8cec&X-Amz-SignedHeaders=host&actor_id=0&key_id=0&repo_id=269512426&response-content-disposition=attachment%3B%20filename%3D20170413_optic_models.zip&response-content-type=application%2Foctet-stream Retrying (Retry(total=1, connect=None, read=None, redirect=None, status=None)) after connection broken by 'SSLError(SSLError(1, '[SSL: CERTIFICATE_VERIFY_FAILED] certificate verify failed (_ssl.c:852)'),)': /269512426/d1a71900-a6b2-11ea-86a6-5e4fd8fa6cf8?X-Amz-Algorithm=AWS4-HMAC-SHA256&X-Amz-Credential=AKIAIWNJYAX4CSVEH53A%2F20210606%2Fus-east-1%2Fs3%2Faws4_request&X-Amz-Date=20210606T200417Z&X-Amz-Expires=300&X-Amz-Signature=437cd772620ac5ed052c5075da0cb12150182926708de4955a5c0660cecf8cec&X-Amz-SignedHeaders=host&actor_id=0&key_id=0&repo_id=269512426&response-content-disposition=attachment%3B%20filename%3D20170413_optic_models.zip&response-content-type=application%2Foctet-stream Retrying (Retry(total=0, connect=None, read=None, redirect=None, status=None)) after connection broken by 'SSLError(SSLError(1, '[SSL: CERTIFICATE_VERIFY_FAILED] certificate verify failed (_ssl.c:852)'),)': /269512426/d1a71900-a6b2-11ea-86a6-5e4fd8fa6cf8?X-Amz-Algorithm=AWS4-HMAC-SHA256&X-Amz-Credential=AKIAIWNJYAX4CSVEH53A%2F20210606%2Fus-east-1%2Fs3%2Faws4_request&X-Amz-Date=20210606T200417Z&X-Amz-Expires=300&X-Amz-Signature=437cd772620ac5ed052c5075da0cb12150182926708de4955a5c0660cecf8cec&X-Amz-SignedHeaders=host&actor_id=0&key_id=0&repo_id=269512426&response-content-disposition=attachment%3B%20filename%3D20170413_optic_models.zip&response-content-type=application%2Foctet-stream Link download error, trying next mirror (error was: HTTPSConnectionPool(host='github-releases.githubusercontent.com', port=443): Max retries exceeded with url: /269512426/d1a71900-a6b2-11ea-86a6-5e4fd8fa6cf8?X-Amz-Algorithm=AWS4-HMAC-SHA256&X-Amz-Credential=AKIAIWNJYAX4CSVEH53A%2F20210606%2Fus-east-1%2Fs3%2Faws4_request&X-Amz-Date=20210606T200417Z&X-Amz-Expires=300&X-Amz-Signature=437cd772620ac5ed052c5075da0cb12150182926708de4955a5c0660cecf8cec&X-Amz-SignedHeaders=host&actor_id=0&key_id=0&repo_id=269512426&response-content-disposition=attachment%3B%20filename%3D20170413_optic_models.zip&response-content-type=application%2Foctet-stream (Caused by SSLError(SSLError(1, '[SSL: CERTIFICATE_VERIFY_FAILED] certificate verify failed (_ssl.c:852)'),))) Trying URL: https://osf.io/g4fwn/?action=download Downloading: 20170413_optic_models.zip Status: 100%|█████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████| 17.7k/17.7k [00:00<00:00, 40.5MB/s] Creating temporary folder (/tmp/sct-20210606130423.235578-lil3fng2) Unzip data to: /tmp/sct-20210606130423.235578-lil3fng2 Removing temporary folders... Done! sct_download_data -d pmj_models -o /mnt/algo/sct_5.3.0/data/pmj_models -- Spinal Cord Toolbox (5.3.0) sct_download_data -d pmj_models -o /mnt/algo/sct_5.3.0/data/pmj_models -- Removing existing destination folder '/mnt/algo/sct_5.3.0/data/pmj_models' Trying URL: https://github.com/sct-data/pmj_models/releases/download/r20170922/20170922_pmj_models.zip Retrying (Retry(total=2, connect=None, read=None, redirect=None, status=None)) after connection broken by 'SSLError(SSLError(1, '[SSL: CERTIFICATE_VERIFY_FAILED] certificate verify failed (_ssl.c:852)'),)': /269512441/d53aa000-a6b2-11ea-9182-91a66682fc4b?X-Amz-Algorithm=AWS4-HMAC-SHA256&X-Amz-Credential=AKIAIWNJYAX4CSVEH53A%2F20210606%2Fus-east-1%2Fs3%2Faws4_request&X-Amz-Date=20210606T200424Z&X-Amz-Expires=300&X-Amz-Signature=5990e2d2554a74b37d311744a4dd30d96360e6cbe45b1aa6c5d1e1e1116f9c27&X-Amz-SignedHeaders=host&actor_id=0&key_id=0&repo_id=269512441&response-content-disposition=attachment%3B%20filename%3D20170922_pmj_models.zip&response-content-type=application%2Foctet-stream Retrying (Retry(total=1, connect=None, read=None, redirect=None, status=None)) after connection broken by 'SSLError(SSLError(1, '[SSL: CERTIFICATE_VERIFY_FAILED] certificate verify failed (_ssl.c:852)'),)': /269512441/d53aa000-a6b2-11ea-9182-91a66682fc4b?X-Amz-Algorithm=AWS4-HMAC-SHA256&X-Amz-Credential=AKIAIWNJYAX4CSVEH53A%2F20210606%2Fus-east-1%2Fs3%2Faws4_request&X-Amz-Date=20210606T200424Z&X-Amz-Expires=300&X-Amz-Signature=5990e2d2554a74b37d311744a4dd30d96360e6cbe45b1aa6c5d1e1e1116f9c27&X-Amz-SignedHeaders=host&actor_id=0&key_id=0&repo_id=269512441&response-content-disposition=attachment%3B%20filename%3D20170922_pmj_models.zip&response-content-type=application%2Foctet-stream Retrying (Retry(total=0, connect=None, read=None, redirect=None, status=None)) after connection broken by 'SSLError(SSLError(1, '[SSL: CERTIFICATE_VERIFY_FAILED] certificate verify failed (_ssl.c:852)'),)': /269512441/d53aa000-a6b2-11ea-9182-91a66682fc4b?X-Amz-Algorithm=AWS4-HMAC-SHA256&X-Amz-Credential=AKIAIWNJYAX4CSVEH53A%2F20210606%2Fus-east-1%2Fs3%2Faws4_request&X-Amz-Date=20210606T200424Z&X-Amz-Expires=300&X-Amz-Signature=5990e2d2554a74b37d311744a4dd30d96360e6cbe45b1aa6c5d1e1e1116f9c27&X-Amz-SignedHeaders=host&actor_id=0&key_id=0&repo_id=269512441&response-content-disposition=attachment%3B%20filename%3D20170922_pmj_models.zip&response-content-type=application%2Foctet-stream Link download error, trying next mirror (error was: HTTPSConnectionPool(host='github-releases.githubusercontent.com', port=443): Max retries exceeded with url: /269512441/d53aa000-a6b2-11ea-9182-91a66682fc4b?X-Amz-Algorithm=AWS4-HMAC-SHA256&X-Amz-Credential=AKIAIWNJYAX4CSVEH53A%2F20210606%2Fus-east-1%2Fs3%2Faws4_request&X-Amz-Date=20210606T200424Z&X-Amz-Expires=300&X-Amz-Signature=5990e2d2554a74b37d311744a4dd30d96360e6cbe45b1aa6c5d1e1e1116f9c27&X-Amz-SignedHeaders=host&actor_id=0&key_id=0&repo_id=269512441&response-content-disposition=attachment%3B%20filename%3D20170922_pmj_models.zip&response-content-type=application%2Foctet-stream (Caused by SSLError(SSLError(1, '[SSL: CERTIFICATE_VERIFY_FAILED] certificate verify failed (_ssl.c:852)'),))) Trying URL: https://osf.io/4gufr/?action=download Downloading: 20170922_pmj_models.zip Status: 100%|█████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████| 8.87k/8.87k [00:00<00:00, 28.8MB/s] Creating temporary folder (/tmp/sct-20210606130428.734063-8ncwssq3) Unzip data to: /tmp/sct-20210606130428.734063-8ncwssq3 Removing temporary folders... Done! sct_download_data -d deepseg_sc_models -o /mnt/algo/sct_5.3.0/data/deepseg_sc_models -- Spinal Cord Toolbox (5.3.0) sct_download_data -d deepseg_sc_models -o /mnt/algo/sct_5.3.0/data/deepseg_sc_models -- Removing existing destination folder '/mnt/algo/sct_5.3.0/data/deepseg_sc_models' Trying URL: https://github.com/sct-data/deepseg_sc_models/releases/download/r20180610/20180610_deepseg_sc_models.zip Retrying (Retry(total=2, connect=None, read=None, redirect=None, status=None)) after connection broken by 'SSLError(SSLError(1, '[SSL: CERTIFICATE_VERIFY_FAILED] certificate verify failed (_ssl.c:852)'),)': /269512502/01eeb780-a6b3-11ea-9981-90d94324f01a?X-Amz-Algorithm=AWS4-HMAC-SHA256&X-Amz-Credential=AKIAIWNJYAX4CSVEH53A%2F20210606%2Fus-east-1%2Fs3%2Faws4_request&X-Amz-Date=20210606T200429Z&X-Amz-Expires=300&X-Amz-Signature=41498af1cc9d1be97b4f246944ebee5611ca0429972ae5a423e039a32871e634&X-Amz-SignedHeaders=host&actor_id=0&key_id=0&repo_id=269512502&response-content-disposition=attachment%3B%20filename%3D20180610_deepseg_sc_models.zip&response-content-type=application%2Foctet-stream Retrying (Retry(total=1, connect=None, read=None, redirect=None, status=None)) after connection broken by 'SSLError(SSLError(1, '[SSL: CERTIFICATE_VERIFY_FAILED] certificate verify failed (_ssl.c:852)'),)': /269512502/01eeb780-a6b3-11ea-9981-90d94324f01a?X-Amz-Algorithm=AWS4-HMAC-SHA256&X-Amz-Credential=AKIAIWNJYAX4CSVEH53A%2F20210606%2Fus-east-1%2Fs3%2Faws4_request&X-Amz-Date=20210606T200429Z&X-Amz-Expires=300&X-Amz-Signature=41498af1cc9d1be97b4f246944ebee5611ca0429972ae5a423e039a32871e634&X-Amz-SignedHeaders=host&actor_id=0&key_id=0&repo_id=269512502&response-content-disposition=attachment%3B%20filename%3D20180610_deepseg_sc_models.zip&response-content-type=application%2Foctet-stream Retrying (Retry(total=0, connect=None, read=None, redirect=None, status=None)) after connection broken by 'SSLError(SSLError(1, '[SSL: CERTIFICATE_VERIFY_FAILED] certificate verify failed (_ssl.c:852)'),)': /269512502/01eeb780-a6b3-11ea-9981-90d94324f01a?X-Amz-Algorithm=AWS4-HMAC-SHA256&X-Amz-Credential=AKIAIWNJYAX4CSVEH53A%2F20210606%2Fus-east-1%2Fs3%2Faws4_request&X-Amz-Date=20210606T200429Z&X-Amz-Expires=300&X-Amz-Signature=41498af1cc9d1be97b4f246944ebee5611ca0429972ae5a423e039a32871e634&X-Amz-SignedHeaders=host&actor_id=0&key_id=0&repo_id=269512502&response-content-disposition=attachment%3B%20filename%3D20180610_deepseg_sc_models.zip&response-content-type=application%2Foctet-stream Link download error, trying next mirror (error was: HTTPSConnectionPool(host='github-releases.githubusercontent.com', port=443): Max retries exceeded with url: /269512502/01eeb780-a6b3-11ea-9981-90d94324f01a?X-Amz-Algorithm=AWS4-HMAC-SHA256&X-Amz-Credential=AKIAIWNJYAX4CSVEH53A%2F20210606%2Fus-east-1%2Fs3%2Faws4_request&X-Amz-Date=20210606T200429Z&X-Amz-Expires=300&X-Amz-Signature=41498af1cc9d1be97b4f246944ebee5611ca0429972ae5a423e039a32871e634&X-Amz-SignedHeaders=host&actor_id=0&key_id=0&repo_id=269512502&response-content-disposition=attachment%3B%20filename%3D20180610_deepseg_sc_models.zip&response-content-type=application%2Foctet-stream (Caused by SSLError(SSLError(1, '[SSL: CERTIFICATE_VERIFY_FAILED] certificate verify failed (_ssl.c:852)'),))) Trying URL: https://osf.io/avf97/?action=download Downloading: 20180610_deepseg_sc_models.zip Status: 100%|█████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████| 58.7M/58.7M [00:02<00:00, 28.1MB/s] Creating temporary folder (/tmp/sct-20210606130436.434084-3wi8n59v) Unzip data to: /tmp/sct-20210606130436.434084-3wi8n59v Removing temporary folders... Done! sct_download_data -d deepseg_gm_models -o /mnt/algo/sct_5.3.0/data/deepseg_gm_models -- Spinal Cord Toolbox (5.3.0) sct_download_data -d deepseg_gm_models -o /mnt/algo/sct_5.3.0/data/deepseg_gm_models -- Removing existing destination folder '/mnt/algo/sct_5.3.0/data/deepseg_gm_models' Trying URL: https://github.com/sct-data/deepseg_gm_models/releases/download/r20180205/20180205_deepseg_gm_models.zip Retrying (Retry(total=2, connect=None, read=None, redirect=None, status=None)) after connection broken by 'SSLError(SSLError(1, '[SSL: CERTIFICATE_VERIFY_FAILED] certificate verify failed (_ssl.c:852)'),)': /269512458/dc61ae00-a6b2-11ea-8d5b-d92b61cea5cf?X-Amz-Algorithm=AWS4-HMAC-SHA256&X-Amz-Credential=AKIAIWNJYAX4CSVEH53A%2F20210606%2Fus-east-1%2Fs3%2Faws4_request&X-Amz-Date=20210606T200438Z&X-Amz-Expires=300&X-Amz-Signature=3a64f90ee36d085254999196aaa64f17e0eebf5ee9841f310eb8f203fe6a3b2c&X-Amz-SignedHeaders=host&actor_id=0&key_id=0&repo_id=269512458&response-content-disposition=attachment%3B%20filename%3D20180205_deepseg_gm_models.zip&response-content-type=application%2Foctet-stream Retrying (Retry(total=1, connect=None, read=None, redirect=None, status=None)) after connection broken by 'SSLError(SSLError(1, '[SSL: CERTIFICATE_VERIFY_FAILED] certificate verify failed (_ssl.c:852)'),)': /269512458/dc61ae00-a6b2-11ea-8d5b-d92b61cea5cf?X-Amz-Algorithm=AWS4-HMAC-SHA256&X-Amz-Credential=AKIAIWNJYAX4CSVEH53A%2F20210606%2Fus-east-1%2Fs3%2Faws4_request&X-Amz-Date=20210606T200438Z&X-Amz-Expires=300&X-Amz-Signature=3a64f90ee36d085254999196aaa64f17e0eebf5ee9841f310eb8f203fe6a3b2c&X-Amz-SignedHeaders=host&actor_id=0&key_id=0&repo_id=269512458&response-content-disposition=attachment%3B%20filename%3D20180205_deepseg_gm_models.zip&response-content-type=application%2Foctet-stream Retrying (Retry(total=0, connect=None, read=None, redirect=None, status=None)) after connection broken by 'SSLError(SSLError(1, '[SSL: CERTIFICATE_VERIFY_FAILED] certificate verify failed (_ssl.c:852)'),)': /269512458/dc61ae00-a6b2-11ea-8d5b-d92b61cea5cf?X-Amz-Algorithm=AWS4-HMAC-SHA256&X-Amz-Credential=AKIAIWNJYAX4CSVEH53A%2F20210606%2Fus-east-1%2Fs3%2Faws4_request&X-Amz-Date=20210606T200438Z&X-Amz-Expires=300&X-Amz-Signature=3a64f90ee36d085254999196aaa64f17e0eebf5ee9841f310eb8f203fe6a3b2c&X-Amz-SignedHeaders=host&actor_id=0&key_id=0&repo_id=269512458&response-content-disposition=attachment%3B%20filename%3D20180205_deepseg_gm_models.zip&response-content-type=application%2Foctet-stream Link download error, trying next mirror (error was: HTTPSConnectionPool(host='github-releases.githubusercontent.com', port=443): Max retries exceeded with url: /269512458/dc61ae00-a6b2-11ea-8d5b-d92b61cea5cf?X-Amz-Algorithm=AWS4-HMAC-SHA256&X-Amz-Credential=AKIAIWNJYAX4CSVEH53A%2F20210606%2Fus-east-1%2Fs3%2Faws4_request&X-Amz-Date=20210606T200438Z&X-Amz-Expires=300&X-Amz-Signature=3a64f90ee36d085254999196aaa64f17e0eebf5ee9841f310eb8f203fe6a3b2c&X-Amz-SignedHeaders=host&actor_id=0&key_id=0&repo_id=269512458&response-content-disposition=attachment%3B%20filename%3D20180205_deepseg_gm_models.zip&response-content-type=application%2Foctet-stream (Caused by SSLError(SSLError(1, '[SSL: CERTIFICATE_VERIFY_FAILED] certificate verify failed (_ssl.c:852)'),))) Trying URL: https://osf.io/b9y4x/?action=download Downloading: 20180205_deepseg_gm_models.zip Status: 100%|█████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████| 2.28M/2.28M [00:00<00:00, 6.31MB/s] Creating temporary folder (/tmp/sct-20210606130443.223710-rjyhnjup) Unzip data to: /tmp/sct-20210606130443.223710-rjyhnjup Removing temporary folders... Done! sct_download_data -d deepseg_lesion_models -o /mnt/algo/sct_5.3.0/data/deepseg_lesion_models -- Spinal Cord Toolbox (5.3.0) sct_download_data -d deepseg_lesion_models -o /mnt/algo/sct_5.3.0/data/deepseg_lesion_models -- Removing existing destination folder '/mnt/algo/sct_5.3.0/data/deepseg_lesion_models' Trying URL: https://github.com/sct-data/deepseg_lesion_models/releases/download/r20180613/20180613_deepseg_lesion_models.zip Retrying (Retry(total=2, connect=None, read=None, redirect=None, status=None)) after connection broken by 'SSLError(SSLError(1, '[SSL: CERTIFICATE_VERIFY_FAILED] certificate verify failed (_ssl.c:852)'),)': /269512694/12069700-a6b3-11ea-97f9-12f63cbbc4b7?X-Amz-Algorithm=AWS4-HMAC-SHA256&X-Amz-Credential=AKIAIWNJYAX4CSVEH53A%2F20210606%2Fus-east-1%2Fs3%2Faws4_request&X-Amz-Date=20210606T200444Z&X-Amz-Expires=300&X-Amz-Signature=040d87c6816dd22e7b53b3cc35fc17e7abfb0af6a54dd2bc990fb4707a7ef585&X-Amz-SignedHeaders=host&actor_id=0&key_id=0&repo_id=269512694&response-content-disposition=attachment%3B%20filename%3D20180613_deepseg_lesion_models.zip&response-content-type=application%2Foctet-stream Retrying (Retry(total=1, connect=None, read=None, redirect=None, status=None)) after connection broken by 'SSLError(SSLError(1, '[SSL: CERTIFICATE_VERIFY_FAILED] certificate verify failed (_ssl.c:852)'),)': /269512694/12069700-a6b3-11ea-97f9-12f63cbbc4b7?X-Amz-Algorithm=AWS4-HMAC-SHA256&X-Amz-Credential=AKIAIWNJYAX4CSVEH53A%2F20210606%2Fus-east-1%2Fs3%2Faws4_request&X-Amz-Date=20210606T200444Z&X-Amz-Expires=300&X-Amz-Signature=040d87c6816dd22e7b53b3cc35fc17e7abfb0af6a54dd2bc990fb4707a7ef585&X-Amz-SignedHeaders=host&actor_id=0&key_id=0&repo_id=269512694&response-content-disposition=attachment%3B%20filename%3D20180613_deepseg_lesion_models.zip&response-content-type=application%2Foctet-stream Retrying (Retry(total=0, connect=None, read=None, redirect=None, status=None)) after connection broken by 'SSLError(SSLError(1, '[SSL: CERTIFICATE_VERIFY_FAILED] certificate verify failed (_ssl.c:852)'),)': /269512694/12069700-a6b3-11ea-97f9-12f63cbbc4b7?X-Amz-Algorithm=AWS4-HMAC-SHA256&X-Amz-Credential=AKIAIWNJYAX4CSVEH53A%2F20210606%2Fus-east-1%2Fs3%2Faws4_request&X-Amz-Date=20210606T200444Z&X-Amz-Expires=300&X-Amz-Signature=040d87c6816dd22e7b53b3cc35fc17e7abfb0af6a54dd2bc990fb4707a7ef585&X-Amz-SignedHeaders=host&actor_id=0&key_id=0&repo_id=269512694&response-content-disposition=attachment%3B%20filename%3D20180613_deepseg_lesion_models.zip&response-content-type=application%2Foctet-stream Link download error, trying next mirror (error was: HTTPSConnectionPool(host='github-releases.githubusercontent.com', port=443): Max retries exceeded with url: /269512694/12069700-a6b3-11ea-97f9-12f63cbbc4b7?X-Amz-Algorithm=AWS4-HMAC-SHA256&X-Amz-Credential=AKIAIWNJYAX4CSVEH53A%2F20210606%2Fus-east-1%2Fs3%2Faws4_request&X-Amz-Date=20210606T200444Z&X-Amz-Expires=300&X-Amz-Signature=040d87c6816dd22e7b53b3cc35fc17e7abfb0af6a54dd2bc990fb4707a7ef585&X-Amz-SignedHeaders=host&actor_id=0&key_id=0&repo_id=269512694&response-content-disposition=attachment%3B%20filename%3D20180613_deepseg_lesion_models.zip&response-content-type=application%2Foctet-stream (Caused by SSLError(SSLError(1, '[SSL: CERTIFICATE_VERIFY_FAILED] certificate verify failed (_ssl.c:852)'),))) Trying URL: https://osf.io/eg7v9/?action=download Downloading: 20180613_deepseg_lesion_models.zip Status: 100%|█████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████| 16.0M/16.0M [00:00<00:00, 16.9MB/s] Creating temporary folder (/tmp/sct-20210606130450.763164-mqi_oj5t) Unzip data to: /tmp/sct-20210606130450.763164-mqi_oj5t Removing temporary folders... Done! sct_download_data -d c2c3_disc_models -o /mnt/algo/sct_5.3.0/data/c2c3_disc_models -- Spinal Cord Toolbox (5.3.0) sct_download_data -d c2c3_disc_models -o /mnt/algo/sct_5.3.0/data/c2c3_disc_models -- Removing existing destination folder '/mnt/algo/sct_5.3.0/data/c2c3_disc_models' Trying URL: https://github.com/sct-data/c2c3_disc_models/releases/download/r20190117/20190117_c2c3_disc_models.zip Retrying (Retry(total=2, connect=None, read=None, redirect=None, status=None)) after connection broken by 'SSLError(SSLError(1, '[SSL: CERTIFICATE_VERIFY_FAILED] certificate verify failed (_ssl.c:852)'),)': /269512401/ce139200-a6b2-11ea-891a-29457fa7b011?X-Amz-Algorithm=AWS4-HMAC-SHA256&X-Amz-Credential=AKIAIWNJYAX4CSVEH53A%2F20210606%2Fus-east-1%2Fs3%2Faws4_request&X-Amz-Date=20210606T200451Z&X-Amz-Expires=300&X-Amz-Signature=03eefc2cde42ee75504c45246ba5351041588f486b3fc21440e98ed36ecc8341&X-Amz-SignedHeaders=host&actor_id=0&key_id=0&repo_id=269512401&response-content-disposition=attachment%3B%20filename%3D20190117_c2c3_disc_models.zip&response-content-type=application%2Foctet-stream Retrying (Retry(total=1, connect=None, read=None, redirect=None, status=None)) after connection broken by 'SSLError(SSLError(1, '[SSL: CERTIFICATE_VERIFY_FAILED] certificate verify failed (_ssl.c:852)'),)': /269512401/ce139200-a6b2-11ea-891a-29457fa7b011?X-Amz-Algorithm=AWS4-HMAC-SHA256&X-Amz-Credential=AKIAIWNJYAX4CSVEH53A%2F20210606%2Fus-east-1%2Fs3%2Faws4_request&X-Amz-Date=20210606T200451Z&X-Amz-Expires=300&X-Amz-Signature=03eefc2cde42ee75504c45246ba5351041588f486b3fc21440e98ed36ecc8341&X-Amz-SignedHeaders=host&actor_id=0&key_id=0&repo_id=269512401&response-content-disposition=attachment%3B%20filename%3D20190117_c2c3_disc_models.zip&response-content-type=application%2Foctet-stream Retrying (Retry(total=0, connect=None, read=None, redirect=None, status=None)) after connection broken by 'SSLError(SSLError(1, '[SSL: CERTIFICATE_VERIFY_FAILED] certificate verify failed (_ssl.c:852)'),)': /269512401/ce139200-a6b2-11ea-891a-29457fa7b011?X-Amz-Algorithm=AWS4-HMAC-SHA256&X-Amz-Credential=AKIAIWNJYAX4CSVEH53A%2F20210606%2Fus-east-1%2Fs3%2Faws4_request&X-Amz-Date=20210606T200451Z&X-Amz-Expires=300&X-Amz-Signature=03eefc2cde42ee75504c45246ba5351041588f486b3fc21440e98ed36ecc8341&X-Amz-SignedHeaders=host&actor_id=0&key_id=0&repo_id=269512401&response-content-disposition=attachment%3B%20filename%3D20190117_c2c3_disc_models.zip&response-content-type=application%2Foctet-stream Link download error, trying next mirror (error was: HTTPSConnectionPool(host='github-releases.githubusercontent.com', port=443): Max retries exceeded with url: /269512401/ce139200-a6b2-11ea-891a-29457fa7b011?X-Amz-Algorithm=AWS4-HMAC-SHA256&X-Amz-Credential=AKIAIWNJYAX4CSVEH53A%2F20210606%2Fus-east-1%2Fs3%2Faws4_request&X-Amz-Date=20210606T200451Z&X-Amz-Expires=300&X-Amz-Signature=03eefc2cde42ee75504c45246ba5351041588f486b3fc21440e98ed36ecc8341&X-Amz-SignedHeaders=host&actor_id=0&key_id=0&repo_id=269512401&response-content-disposition=attachment%3B%20filename%3D20190117_c2c3_disc_models.zip&response-content-type=application%2Foctet-stream (Caused by SSLError(SSLError(1, '[SSL: CERTIFICATE_VERIFY_FAILED] certificate verify failed (_ssl.c:852)'),))) Trying URL: https://osf.io/t97ap/?action=download Downloading: 20190117_c2c3_disc_models.zip Status: 100%|█████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████| 8.94k/8.94k [00:00<00:00, 29.5MB/s] Creating temporary folder (/tmp/sct-20210606130456.505333-pmqjzirs) Unzip data to: /tmp/sct-20210606130456.505333-pmqjzirs Removing temporary folders... Done! Link download error, trying next mirror (error was: HTTPSConnectionPool(host='github-releases.githubusercontent.com', port=443): Max retries exceeded with url: /276185670/cbeef880-bae3-11ea-94c1-5638f6070d8c?X-Amz-Algorithm=AWS4-HMAC-SHA256&X-Amz-Credential=AKIAIWNJYAX4CSVEH53A%2F20210606%2Fus-east-1%2Fs3%2Faws4_request&X-Amz-Date=20210606T200457Z&X-Amz-Expires=300&X-Amz-Signature=99e3c49ab05e89767f14bdfd12e34aa24a08a3e3ed74fb4f593e33e3590dd175&X-Amz-SignedHeaders=host&actor_id=0&key_id=0&repo_id=276185670&response-content-disposition=attachment%3B%20filename%3Dr20200622_t2star_sc.zip&response-content-type=application%2Foctet-stream (Caused by SSLError(SSLError(1, '[SSL: CERTIFICATE_VERIFY_FAILED] certificate verify failed (_ssl.c:852)'),))) Status: 100%|█████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████| 18.0M/18.0M [00:00<00:00, 24.1MB/s] Not adding /mnt/algo/sct_5.3.0 to $PATH. You can always add it later or call SCT functions with full path /mnt/algo/sct_5.3.0/bin/sct_xxx Validate installation... -- Spinal Cord Toolbox (5.3.0) sct_check_dependencies -- SCT info: - version: 5.3.0 - path: /mnt/algo/sct_5.3.0 OS: linux (Linux-2.6.32-754.35.1.el6.x86_64-x86_64-with-redhat-6.10-Santiago) CPU cores: Available: 2, Used by ITK functions: 2 RAM: Total: 11912MB, Used: 3498MB, Available: 8165MB Check Python executable.............................[OK] Using bundled python 3.6.13 |Anaconda, Inc.| (default, Feb 23 2021, 21:15:04) [GCC 7.3.0] at /mnt/algo/sct_5.3.0/python/envs/venv_sct/bin/python Check if data are installed.........................[OK] Check if colored is installed.......................[OK] (1.4.2) Check if dipy is installed..........................[OK] (1.4.0) Check if futures is installed.......................[OK] Check if h5py is installed..........................[OK] (2.10.0) Check if Keras (2.1.5) is installed.................[FAIL] Traceback (most recent call last): File "/mnt/algo/sct_5.3.0/python/envs/venv_sct/lib/python3.6/site-packages/tensorflow/python/pywrap_tensorflow.py", line 58, in from tensorflow.python.pywrap_tensorflow_internal import * File "/mnt/algo/sct_5.3.0/python/envs/venv_sct/lib/python3.6/site-packages/tensorflow/python/pywrap_tensorflow_internal.py", line 28, in _pywrap_tensorflow_internal = swig_import_helper() File "/mnt/algo/sct_5.3.0/python/envs/venv_sct/lib/python3.6/site-packages/tensorflow/python/pywrap_tensorflow_internal.py", line 24, in swig_import_helper _mod = imp.load_module('_pywrap_tensorflow_internal', fp, pathname, description) File "/mnt/algo/sct_5.3.0/python/envs/venv_sct/lib/python3.6/imp.py", line 243, in load_module return load_dynamic(name, filename, file) File "/mnt/algo/sct_5.3.0/python/envs/venv_sct/lib/python3.6/imp.py", line 343, in load_dynamic return _load(spec) ImportError: /lib64/libc.so.6: version `GLIBC_2.17' not found (required by /mnt/algo/sct_5.3.0/python/envs/venv_sct/lib/python3.6/site-packages/tensorflow/python/_pywrap_tensorflow_internal.so) Failed to load the native TensorFlow runtime. See https://www.tensorflow.org/install/install_sources#common_installation_problems for some common reasons and solutions. Include the entire stack trace above this error message when asking for help. Check if ivadomed is installed......................Traceback (most recent call last): File "/mnt/algo/sct_5.3.0/spinalcordtoolbox/scripts/sct_check_dependencies.py", line 347, in main(sys.argv[1:]) File "/mnt/algo/sct_5.3.0/spinalcordtoolbox/scripts/sct_check_dependencies.py", line 271, in main module = module_import(module_name, suppress_stderr) File "/mnt/algo/sct_5.3.0/spinalcordtoolbox/scripts/sct_check_dependencies.py", line 109, in module_import module = importlib.import_module(module_name) File "/mnt/algo/sct_5.3.0/python/envs/venv_sct/lib/python3.6/importlib/__init__.py", line 126, in import_module return _bootstrap._gcd_import(name[level:], package, level) File "", line 994, in _gcd_import File "", line 971, in _find_and_load File "", line 955, in _find_and_load_unlocked File "", line 665, in _load_unlocked File "", line 678, in exec_module File "", line 219, in _call_with_frames_removed File "/mnt/algo/sct_5.3.0/python/envs/venv_sct/lib/python3.6/site-packages/ivadomed/__init__.py", line 1, in from .utils import __version__, __ivadomed_dir__ File "/mnt/algo/sct_5.3.0/python/envs/venv_sct/lib/python3.6/site-packages/ivadomed/utils.py", line 7, in import torch File "/mnt/algo/sct_5.3.0/python/envs/venv_sct/lib/python3.6/site-packages/torch/__init__.py", line 135, in _load_global_deps() File "/mnt/algo/sct_5.3.0/python/envs/venv_sct/lib/python3.6/site-packages/torch/__init__.py", line 93, in _load_global_deps ctypes.CDLL(lib_path, mode=ctypes.RTLD_GLOBAL) File "/mnt/algo/sct_5.3.0/python/envs/venv_sct/lib/python3.6/ctypes/__init__.py", line 348, in __init__ self._handle = _dlopen(self._name, mode) OSError: /lib64/libc.so.6: version `GLIBC_2.14' not found (required by /mnt/algo/sct_5.3.0/python/envs/venv_sct/lib/python3.6/site-packages/torch/lib/libgomp-7c85b1e2.so.1) Installation validation Failed! Installation failed! Please copy the output of this Terminal (starting with the command install_sct) and upload it as a .txt attachment in a new topic on SCT's forum: --> http://forum.spinalcordmri.org/c/sct