diff --git a/env/export_pip-r.sh b/env/export_pip-r.sh index 042563e1..9ec14c61 100644 --- a/env/export_pip-r.sh +++ b/env/export_pip-r.sh @@ -48,21 +48,23 @@ echo "Exporting versions from $2..." echo "#" } > $1 -pip_cmd="python --version && pip list --format=freeze --no-color --all --disable-pip-version-check --no-input" +pip_cmd="python --version && pip list --format=freeze --no-color --disable-pip-version-check --no-input" if [ "${2/#.sif}" != "$2" ] then # singularity - cmd="singularity exec $2 /bin/bash -c '$pip_cmd'" + cmd=("singularity" "exec" "$2" "/bin/bash" -c "$pip_cmd") + clean_cmd="singularity exec $2 /bin/bash -c '$pip_cmd'" else # docker - cmd="docker run --entrypoint /bin/bash $2 -c '$pip_cmd'" + clean_cmd="docker run --rm -u : --entrypoint /bin/bash $2 -c '$pip_cmd'" + cmd=("docker" "run" --rm -u "$(id -u):$(id -g)" --entrypoint /bin/bash "$2" -c "$pip_cmd") fi { echo "# Which ran the following command:" - echo "# $cmd" + echo "# $clean_cmd" echo "#" } >> $1 -out=$($cmd) +out=$("${cmd[@]}") hardware=$(echo "$out" | grep "torch==" | cut -d"+" -f2) pyversion=$(echo "$out" | head -n 1 | cut -d" " -f2) { diff --git a/requirements.cpu.txt b/requirements.cpu.txt new file mode 100644 index 00000000..fe88cd9e --- /dev/null +++ b/requirements.cpu.txt @@ -0,0 +1,104 @@ +# +# This file is autogenerated by kueglerd from deepmi/fastsurfer:cpu-v2.3.0 +# by the following command from FastSurfer: +# +# ./requirements.cpu.txt deepmi/fastsurfer:cpu-v2.3.0 +# +# Which ran the following command: +# docker run --rm -u : --entrypoint /bin/bash deepmi/fastsurfer:cpu-v2.3.0 -c 'python --version && pip list --format=freeze --no-color --disable-pip-version-check --no-input' +# +# +# Image was configured for cpu using python version 3.10.14 +# +--extra-index-url https://download.pytorch.org/whl/cpu + +# Python 3.10.14 +absl-py==2.1.0 +Brotli==1.1.0 +cached-property==1.5.2 +certifi==2024.7.4 +cffi==1.17.0 +charset-normalizer==3.3.2 +click==8.1.7 +colorama==0.4.6 +contourpy==1.2.1 +cycler==0.12.1 +Deprecated==1.2.14 +filelock==3.15.4 +fonttools==4.53.1 +fsspec==2024.6.1 +grpcio==1.62.2 +h2==4.1.0 +h5py==3.11.0 +hpack==4.0.0 +humanize==4.10.0 +hyperframe==6.0.1 +idna==3.8 +imagecodecs==2024.6.1 +imageio==2.35.1 +importlib_metadata==8.4.0 +importlib_resources==6.4.4 +Jinja2==3.1.4 +joblib==1.4.2 +kiwisolver==1.4.5 +lapy==1.1.0 +lazy_loader==0.4 +Markdown==3.6 +markdown-it-py==3.0.0 +MarkupSafe==2.1.5 +matplotlib==3.9.2 +mdurl==0.1.2 +mpmath==1.3.0 +munkres==1.1.4 +networkx==3.3 +nibabel==5.2.1 +numpy==1.26.4 +packaging==24.1 +pandas==2.2.2 +pillow==10.4.0 +pip==24.2 +plotly==5.23.0 +protobuf==4.25.3 +psutil==6.0.0 +pycparser==2.22 +Pygments==2.18.0 +pyparsing==3.1.4 +PySide6==6.7.2 +PySocks==1.7.1 +python-dateutil==2.9.0 +pytz==2024.1 +PyWavelets==1.7.0 +PyYAML==6.0.2 +requests==2.32.3 +rich==13.8.0 +scikit-image==0.24.0 +scikit-learn==1.5.1 +scikit-sparse==0.4.14 +scipy==1.14.1 +setuptools==72.2.0 +shellingham==1.5.4 +shiboken6==6.7.2 +SimpleITK==2.4.0 +six==1.16.0 +sympy==1.13.2 +tenacity==9.0.0 +tensorboard==2.17.1 +tensorboard-data-server==0.7.0 +threadpoolctl==3.5.0 +tifffile==2024.8.24 +torch==2.4.0+cpu +torchio==0.19.9 +torchvision==0.19.0+cpu +tornado==6.4.1 +tqdm==4.66.5 +typer==0.12.5 +typing_extensions==4.12.2 +tzdata==2024.1 +unicodedata2==15.1.0 +urllib3==2.2.2 +Werkzeug==3.0.4 +wheel==0.44.0 +wrapt==1.16.0 +yacs==0.1.8 +zipp==3.20.0 +zstandard==0.23.0 diff --git a/requirements.txt b/requirements.txt index 4ee513bf..f168f221 100644 --- a/requirements.txt +++ b/requirements.txt @@ -1,210 +1,117 @@ # -# This file is autogenerated by pip-compile with Python 3.10 -# by the following command: +# This file is autogenerated by kueglerd from deepmi/fastsurfer:cu124-v2.3.0 +# by the following command from FastSurfer: # -# pip-compile requirements.in +# ./requirements.txt deepmi/fastsurfer:cu124-v2.3.0 # ---extra-index-url https://download.pytorch.org/whl/cu117 +# Which ran the following command: +# docker run --rm -u : --entrypoint /bin/bash deepmi/fastsurfer:cu124-v2.3.0 -c 'python --version && pip list --format=freeze --no-color --disable-pip-version-check --no-input' +# +# +# Image was configured for cu124 using python version 3.10.14 +# +--extra-index-url https://download.pytorch.org/whl/cu124 -absl-py==2.0.0 - # via tensorboard -cachetools==5.3.2 - # via google-auth -certifi==2023.7.22 - # via requests +# Python 3.10.14 +absl-py==2.1.0 +Brotli==1.1.0 +cached-property==1.5.2 +certifi==2024.7.4 +cffi==1.17.0 charset-normalizer==3.3.2 - # via requests click==8.1.7 - # via torchio -cmake==3.27.7 - # via triton -contourpy==1.2.0 - # via matplotlib +colorama==0.4.6 +contourpy==1.2.1 cycler==0.12.1 - # via matplotlib -deprecated==1.2.14 - # via torchio -filelock==3.13.1 - # via - # torch - # triton -fonttools==4.44.3 - # via matplotlib -google-auth==2.23.4 - # via - # google-auth-oauthlib - # tensorboard -google-auth-oauthlib==1.0.0 - # via tensorboard -grpcio==1.59.2 - # via tensorboard -h5py==3.7.0 - # via -r requirements.in -humanize==4.8.0 - # via torchio -idna==3.4 - # via requests -imageio==2.32.0 - # via scikit-image -jinja2==3.1.2 - # via torch -joblib==1.3.2 - # via scikit-learn +Deprecated==1.2.14 +filelock==3.15.4 +fonttools==4.53.1 +fsspec==2024.6.1 +grpcio==1.62.2 +h2==4.1.0 +h5py==3.11.0 +hpack==4.0.0 +humanize==4.10.0 +hyperframe==6.0.1 +idna==3.8 +imagecodecs==2024.6.1 +imageio==2.35.1 +importlib_metadata==8.4.0 +importlib_resources==6.4.4 +Jinja2==3.1.4 +joblib==1.4.2 kiwisolver==1.4.5 - # via matplotlib -lapy==1.0.1 - # via -r requirements.in -lit==17.0.5 - # via triton -markdown==3.5.1 - # via tensorboard -markupsafe==2.1.3 - # via - # jinja2 - # werkzeug -matplotlib==3.7.1 - # via -r requirements.in +lapy==1.1.0 +lazy_loader==0.4 +Markdown==3.6 +markdown-it-py==3.0.0 +MarkupSafe==2.1.5 +matplotlib==3.9.2 +mdurl==0.1.2 mpmath==1.3.0 - # via sympy -networkx==3.2.1 - # via - # scikit-image - # torch -nibabel==5.1.0 - # via - # -r requirements.in - # lapy - # torchio -numpy==1.25.0 - # via - # -r requirements.in - # contourpy - # h5py - # imageio - # lapy - # matplotlib - # nibabel - # pandas - # pywavelets - # scikit-image - # scikit-learn - # scipy - # tensorboard - # tifffile - # torchio - # torchvision -oauthlib==3.2.2 - # via requests-oauthlib -packaging==23.2 - # via - # matplotlib - # nibabel - # plotly - # scikit-image -pandas==1.5.3 - # via -r requirements.in -pillow==10.0.1 - # via - # -r requirements.in - # imageio - # matplotlib - # scikit-image - # torchvision -plotly==5.18.0 - # via lapy -protobuf==4.25.1 - # via tensorboard -psutil==5.9.6 - # via lapy -pyasn1==0.5.0 - # via - # pyasn1-modules - # rsa -pyasn1-modules==0.3.0 - # via google-auth -pyparsing==3.1.1 - # via matplotlib -python-dateutil==2.8.2 - # via - # -r requirements.in - # matplotlib - # pandas -pytz==2023.3.post1 - # via pandas -pywavelets==1.4.1 - # via scikit-image -pyyaml==6.0 - # via - # -r requirements.in - # yacs -requests==2.31.0 - # via - # requests-oauthlib - # tensorboard - # torchvision -requests-oauthlib==1.3.1 - # via google-auth-oauthlib -rsa==4.9 - # via google-auth -scikit-image==0.19.3 - # via -r requirements.in -scikit-learn==1.2.2 - # via -r requirements.in -scipy==1.10.1 - # via - # -r requirements.in - # lapy - # scikit-image - # scikit-learn - # torchio -simpleitk==2.2.1 - # via - # -r requirements.in - # torchio +munkres==1.1.4 +networkx==3.3 +nibabel==5.2.1 +numpy==1.26.4 +nvidia-cublas-cu12==12.4.2.65 +nvidia-cuda-cupti-cu12==12.4.99 +nvidia-cuda-nvrtc-cu12==12.4.99 +nvidia-cuda-runtime-cu12==12.4.99 +nvidia-cudnn-cu12==9.1.0.70 +nvidia-cufft-cu12==11.2.0.44 +nvidia-curand-cu12==10.3.5.119 +nvidia-cusolver-cu12==11.6.0.99 +nvidia-cusparse-cu12==12.3.0.142 +nvidia-nccl-cu12==2.20.5 +nvidia-nvjitlink-cu12==12.4.99 +nvidia-nvtx-cu12==12.4.99 +packaging==24.1 +pandas==2.2.2 +pillow==10.4.0 +pip==24.2 +plotly==5.23.0 +protobuf==4.25.3 +psutil==6.0.0 +pycparser==2.22 +Pygments==2.18.0 +pyparsing==3.1.4 +PySide6==6.7.2 +PySocks==1.7.1 +python-dateutil==2.9.0 +pytz==2024.1 +PyWavelets==1.7.0 +PyYAML==6.0.2 +requests==2.32.3 +rich==13.7.1 +scikit-image==0.24.0 +scikit-learn==1.5.1 +scikit-sparse==0.4.14 +scipy==1.14.1 +setuptools==72.2.0 +shellingham==1.5.4 +shiboken6==6.7.2 +SimpleITK==2.4.0 six==1.16.0 - # via python-dateutil -sympy==1.12 - # via torch -tenacity==8.2.3 - # via plotly -tensorboard==2.12.1 - # via -r requirements.in -tensorboard-data-server==0.7.2 - # via tensorboard -tensorboard-plugin-wit==1.8.1 - # via tensorboard -threadpoolctl==3.2.0 - # via scikit-learn -tifffile==2023.9.26 - # via scikit-image -torch==2.0.1+cu117 - # via - # -r requirements.in - # torchio - # torchvision - # triton -torchio==0.18.83 - # via -r requirements.in -torchvision==0.15.2+cu117 - # via -r requirements.in -tqdm==4.65.0 - # via - # -r requirements.in - # torchio -triton==2.0.0 - # via torch -typing-extensions==4.8.0 - # via torch -urllib3==2.1.0 - # via requests -werkzeug==3.0.1 - # via tensorboard -wheel==0.41.3 - # via tensorboard +sympy==1.13.2 +tenacity==9.0.0 +tensorboard==2.17.1 +tensorboard-data-server==0.7.0 +threadpoolctl==3.5.0 +tifffile==2024.8.24 +torch==2.4.0+cu124 +torchio==0.19.9 +torchvision==0.19.0+cu124 +tornado==6.4.1 +tqdm==4.66.5 +triton==3.0.0 +typer==0.12.5 +typing_extensions==4.12.2 +tzdata==2024.1 +unicodedata2==15.1.0 +urllib3==2.2.2 +Werkzeug==3.0.4 +wheel==0.44.0 wrapt==1.16.0 - # via deprecated yacs==0.1.8 - # via -r requirements.in - -# The following packages are considered to be unsafe in a requirements file: -# setuptools +zipp==3.20.0 +zstandard==0.23.0 diff --git a/requirements_cpu.txt b/requirements_cpu.txt deleted file mode 100644 index 2e342b12..00000000 --- a/requirements_cpu.txt +++ /dev/null @@ -1,201 +0,0 @@ -# -# This file is autogenerated by pip-compile with Python 3.10 -# by the following command: -# -# pip-compile --output-file=requirements_cpu.txt requirements.in -# ---extra-index-url https://download.pytorch.org/whl/cpu - -absl-py==2.0.0 - # via tensorboard -cachetools==5.3.2 - # via google-auth -certifi==2023.7.22 - # via requests -charset-normalizer==3.3.2 - # via requests -click==8.1.7 - # via torchio -contourpy==1.2.0 - # via matplotlib -cycler==0.12.1 - # via matplotlib -deprecated==1.2.14 - # via torchio -filelock==3.13.1 - # via torch -fonttools==4.44.3 - # via matplotlib -google-auth==2.23.4 - # via - # google-auth-oauthlib - # tensorboard -google-auth-oauthlib==1.0.0 - # via tensorboard -grpcio==1.59.2 - # via tensorboard -h5py==3.7.0 - # via -r requirements.in -humanize==4.8.0 - # via torchio -idna==3.4 - # via requests -imageio==2.32.0 - # via scikit-image -jinja2==3.1.2 - # via torch -joblib==1.3.2 - # via scikit-learn -kiwisolver==1.4.5 - # via matplotlib -lapy==1.0.1 - # via -r requirements.in -markdown==3.5.1 - # via tensorboard -markupsafe==2.1.3 - # via - # jinja2 - # werkzeug -matplotlib==3.7.1 - # via -r requirements.in -mpmath==1.3.0 - # via sympy -networkx==3.2.1 - # via - # scikit-image - # torch -nibabel==5.1.0 - # via - # -r requirements.in - # lapy - # torchio -numpy==1.25.0 - # via - # -r requirements.in - # contourpy - # h5py - # imageio - # lapy - # matplotlib - # nibabel - # pandas - # pywavelets - # scikit-image - # scikit-learn - # scipy - # tensorboard - # tifffile - # torchio - # torchvision -oauthlib==3.2.2 - # via requests-oauthlib -packaging==23.2 - # via - # matplotlib - # nibabel - # plotly - # scikit-image -pandas==1.5.3 - # via -r requirements.in -pillow==10.0.1 - # via - # -r requirements.in - # imageio - # matplotlib - # scikit-image - # torchvision -plotly==5.18.0 - # via lapy -protobuf==4.25.1 - # via tensorboard -psutil==5.9.6 - # via lapy -pyasn1==0.5.0 - # via - # pyasn1-modules - # rsa -pyasn1-modules==0.3.0 - # via google-auth -pyparsing==3.1.1 - # via matplotlib -python-dateutil==2.8.2 - # via - # -r requirements.in - # matplotlib - # pandas -pytz==2023.3.post1 - # via pandas -pywavelets==1.4.1 - # via scikit-image -pyyaml==6.0 - # via - # -r requirements.in - # yacs -requests==2.31.0 - # via - # requests-oauthlib - # tensorboard - # torchvision -requests-oauthlib==1.3.1 - # via google-auth-oauthlib -rsa==4.9 - # via google-auth -scikit-image==0.19.3 - # via -r requirements.in -scikit-learn==1.2.2 - # via -r requirements.in -scipy==1.10.1 - # via - # -r requirements.in - # lapy - # scikit-image - # scikit-learn - # torchio -simpleitk==2.2.1 - # via - # -r requirements.in - # torchio -six==1.16.0 - # via python-dateutil -sympy==1.12 - # via torch -tenacity==8.2.3 - # via plotly -tensorboard==2.12.1 - # via -r requirements.in -tensorboard-data-server==0.7.2 - # via tensorboard -tensorboard-plugin-wit==1.8.1 - # via tensorboard -threadpoolctl==3.2.0 - # via scikit-learn -tifffile==2023.9.26 - # via scikit-image -torch==2.0.1+cpu - # via - # -r requirements.in - # torchio - # torchvision -torchio==0.18.83 - # via -r requirements.in -torchvision==0.15.2+cpu - # via -r requirements.in -tqdm==4.65.0 - # via - # -r requirements.in - # torchio -typing-extensions==4.8.0 - # via torch -urllib3==2.1.0 - # via requests -werkzeug==3.0.1 - # via tensorboard -wheel==0.41.3 - # via tensorboard -wrapt==1.16.0 - # via deprecated -yacs==0.1.8 - # via -r requirements.in - -# The following packages are considered to be unsafe in a requirements file: -# setuptools