Merge pull request #2522 from SCIInstitute/amorris/manylinux-build

Switch Linux build to manylinux_2_28 for GLIBC 2.28 compatibility with HPC clusters

Author: akenmorris

.github/workflows/Dockerfile

@@ -1,31 +1,33 @@
-# Based on old ubuntu to create more compatible binaries
+# Based on manylinux_2_28 (AlmaLinux 8, GLIBC 2.28) for maximum HPC compatibility
+# Binaries built here will run on RHEL/Rocky/Alma 8+, Ubuntu 20.04+, and most HPC clusters
 
 # To build (e.g. for ShapeWorks 6.7):
-#    docker build --progress=plain -t akenmorris/ubuntu-build-box-jammy-sw67 .
+#    docker build --progress=plain -t akenmorris/manylinux-build-box-sw67 .
 # To publish:
-#    docker push akenmorris/ubuntu-build-box-jammy-sw67
+#    docker push akenmorris/manylinux-build-box-sw67
 
-FROM ubuntu:jammy-20250819 AS env
-MAINTAINER akenmorris@gmail.com
+FROM quay.io/pypa/manylinux_2_28_x86_64 AS env
+LABEL maintainer="akenmorris@gmail.com"
 
 # Set environment variables
-ENV PATH=/opt/conda/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin
+ENV PATH=/opt/rh/gcc-toolset-13/root/usr/bin:/opt/conda/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin
 
-ARG DEBIAN_FRONTEND=noninteractive
-ENV TZ=Etc/UTC
+# Enable PowerTools repo for additional development packages
+RUN dnf install -y dnf-plugins-core && dnf config-manager --set-enabled powertools
 
-# Update
-RUN apt-get update -y && apt-get upgrade -y && apt-get dist-upgrade -y && apt-get install build-essential software-properties-common -y && add-apt-repository ppa:ubuntu-toolchain-r/test -y && apt-get update -y
+# Update and install build tools
+# gcc-toolset-13 provides GCC 13 with GLIBCXX_3.4.31, required by conda Qt5/ICU packages.
+# This keeps GLIBC 2.28 for binary compatibility while providing modern C++ library symbols.
+RUN dnf update -y && dnf groupinstall -y "Development Tools" \
+    && dnf install -y gcc-toolset-13-gcc gcc-toolset-13-gcc-c++ gcc-toolset-13-binutils gcc-toolset-13-libstdc++-devel
 
 # Install git and git-lfs
-RUN add-apt-repository ppa:git-core/ppa
-RUN apt-get update
-RUN apt-get install git curl -y
-RUN curl -s https://packagecloud.io/install/repositories/github/git-lfs/script.deb.sh | bash
-RUN apt-get install git-lfs -y
+RUN dnf install -y git curl
+RUN curl -s https://packagecloud.io/install/repositories/github/git-lfs/script.rpm.sh | bash
+RUN dnf install -y git-lfs
 
 # Install other dependencies
-RUN apt-get install rsync freeglut3-dev libgl1-mesa-dev libegl1-mesa zip libcups2 pigz wget ccache -y
+RUN dnf install -y rsync freeglut-devel mesa-libGL-devel mesa-libEGL-devel zip cups-libs pigz wget ccache
 
 # Install conda
 RUN curl https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh -o /tmp/Miniconda3-latest-Linux-x86_64.sh \
@@ -38,6 +40,15 @@ RUN curl https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh -
     && echo ". /opt/conda/etc/profile.d/conda.sh" >> ~/.bashrc \
     && echo "conda activate base" >> ~/.bashrc
 
+# Install modern libstdc++ with GLIBCXX_3.4.30+ required by conda Qt5/ICU packages
+# gcc-toolset-13 only provides static libstdc++, so we use conda-forge's libstdcxx-ng
+RUN /opt/conda/bin/conda install -y -c conda-forge libstdcxx-ng=13 \
+    && LIBSTDCXX=$(ls /opt/conda/lib/libstdc++.so.6.0.* | head -1) \
+    && cp -f "$LIBSTDCXX" /usr/lib64/ \
+    && rm -f /usr/lib64/libstdc++.so.6 \
+    && ln -s $(basename "$LIBSTDCXX") /usr/lib64/libstdc++.so.6 \
+    && ldconfig
+
 # Get and decompress linuxdeployqt, it's complicated to use fuse with docker due to the kernel module
 RUN curl -L -o $HOME/linuxdeployqt.AppImage https://github.com/probonopd/linuxdeployqt/releases/download/5/linuxdeployqt-5-x86_64.AppImage && chmod +x $HOME/linuxdeployqt.AppImage ; cd $HOME ; ./linuxdeployqt.AppImage --appimage-extract
 RUN ln -s /root/squashfs-root/usr/bin/linuxdeployqt /usr/bin

.github/workflows/build-linux-debug.yml

@@ -24,7 +24,7 @@ jobs:
   build:
 
     runs-on: ubuntu-latest
-    container: akenmorris/ubuntu-build-box-jammy-sw67
+    container: akenmorris/manylinux-build-box-sw67
 
     steps:
 
@@ -66,7 +66,7 @@ jobs:
       uses: actions/cache/restore@v3
       with:
         path: /github/home/install
-        key: ${{ runner.os }}-deps-debug-${{ hashFiles('.github/workflows/gha_deps.sh', 'install_shapeworks.sh', 'python_requirements.txt', 'build_dependencies.sh') }}
+        key: ${{ runner.os }}-deps-debug-${{ hashFiles('.github/workflows/Dockerfile', '.github/workflows/gha_deps.sh', 'install_shapeworks.sh', 'python_requirements.txt', 'build_dependencies.sh') }}
 
     - name: Check space3.5
       run: df -h
@@ -107,7 +107,7 @@ jobs:
       uses: actions/cache/save@v3
       with:
         path: /github/home/install
-        key: ${{ runner.os }}-deps-debug-${{ hashFiles('.github/workflows/gha_deps.sh', 'install_shapeworks.sh', 'python_requirements.txt', 'build_dependencies.sh') }}
+        key: ${{ runner.os }}-deps-debug-${{ hashFiles('.github/workflows/Dockerfile', '.github/workflows/gha_deps.sh', 'install_shapeworks.sh', 'python_requirements.txt', 'build_dependencies.sh') }}
 
     - name: Check space5
       run: df -h

.github/workflows/build-linux.yml

@@ -25,7 +25,7 @@ jobs:
   build:
 
     runs-on: ubuntu-latest
-    container: akenmorris/ubuntu-build-box-jammy-sw67
+    container: akenmorris/manylinux-build-box-sw67
 
     steps:
 
@@ -64,7 +64,7 @@ jobs:
       uses: actions/cache/restore@v3
       with:
         path: /github/home/install
-        key: ${{ runner.os }}-deps-${{ hashFiles('.github/workflows/gha_deps.sh', 'install_shapeworks.sh', 'python_requirements.txt', 'build_dependencies.sh') }}
+        key: ${{ runner.os }}-deps-${{ hashFiles('.github/workflows/Dockerfile', '.github/workflows/gha_deps.sh', 'install_shapeworks.sh', 'python_requirements.txt', 'build_dependencies.sh') }}
 
     - name: try import vtk
       shell: bash -l {0}
@@ -81,7 +81,7 @@ jobs:
       uses: actions/cache/save@v3
       with:
         path: /github/home/install
-        key: ${{ runner.os }}-deps-${{ hashFiles('.github/workflows/gha_deps.sh', 'install_shapeworks.sh', 'python_requirements.txt', 'build_dependencies.sh') }}
+        key: ${{ runner.os }}-deps-${{ hashFiles('.github/workflows/Dockerfile', '.github/workflows/gha_deps.sh', 'install_shapeworks.sh', 'python_requirements.txt', 'build_dependencies.sh') }}
 
     - name: Check space4
       run: df -h

.github/workflows/gha_conda.sh

@@ -13,7 +13,7 @@ else
     cd ${GITHUB_WORKSPACE}
 
     # run install
-    source ./install_shapeworks.sh --developer
+    source ./install_shapeworks.sh --developer || exit 1
     conda clean -p -t -y
     pip cache info
     pip cache purge

Libs/Python/CMakeLists.txt

@@ -1,4 +1,5 @@
-pybind11_add_module(shapeworks_py
+# NO_EXTRAS disables LTO which can cause GCC internal compiler errors
+pybind11_add_module(shapeworks_py NO_EXTRAS
   ShapeworksPython.cpp
   PythonAnalyze.cpp
   PythonGroom.cpp

Python/shapeworks/shapeworks/network_analysis.py

@@ -4,7 +4,6 @@
 
 import trimesh
 import itertools
-import open3d as o3d
 import scipy
 import spm1d
 import vtk
@@ -19,6 +18,8 @@
 import shapeworks as sw
 np.random.seed(0)
 
+# open3d is imported lazily when needed (not available on all platforms)
+
 
 class NetworkAnalysis:
     def __init__(self, project):
@@ -85,6 +86,16 @@ def compute_mean_shape(self):
         return mesh_points, mesh_normals, mean_shape, surface
 
     def run(self):
+        # Import open3d here (lazy import - not available on all platforms)
+        try:
+            import open3d as o3d
+        except ImportError:
+            raise ImportError(
+                "open3d is required for network analysis but is not installed. "
+                "This feature may not be available on your platform/Python version. "
+                "Try: pip install open3d-cpu (Linux) or pip install open3d (macOS/Windows)"
+            )
+
         project = self.project
         analyze = self.analyze
         num_pts = analyze.get_num_particles()

Python/shapeworks/shapeworks/network_analysis_figures.py

@@ -10,7 +10,6 @@
 import trimesh
 # import itertools
 # import operator
-import open3d as o3d
 import scipy
 # import spm1d
 import vtk
@@ -24,11 +23,23 @@
 import vedo
 import cv2
 
+# open3d is imported lazily when needed (not available on all platforms)
+
 class NetworkAnalysisFigures:
     def __init__(self, network_analysis):
         self.network_analysis = network_analysis
 
     def run(self):
+        # Import open3d here (lazy import - not available on all platforms)
+        try:
+            import open3d as o3d
+        except ImportError:
+            raise ImportError(
+                "open3d is required for network analysis figures but is not installed. "
+                "This feature may not be available on your platform/Python version. "
+                "Try: pip install open3d-cpu (Linux) or pip install open3d (macOS/Windows)"
+            )
+
         # In[4]:
 
         analyze = self.network_analysis.analyze

Support/package.sh

@@ -138,7 +138,8 @@ else
     linuxdeployqt ShapeWorksStudio -verbose=2
     cd ..
 
-    rm lib/libxcb* lib/libX* lib/libfont* lib/libfreetype*
+    # Keep libfreetype as harfbuzz depends on it (FT_Get_Transform requires freetype 2.11+)
+    rm lib/libxcb* lib/libX* lib/libfont*
     rm -rf geometry-central doc
 fi
 

install_shapeworks.sh

@@ -179,22 +179,34 @@ function install_conda() {
     if ! python -m light_the_torch install torch==2.8.0 torchaudio==2.8.0 torchvision==0.23.0; then return 1; fi
   fi
 
-  # for network analysis
+  # for network analysis (optional - not available on all platforms/Python versions)
   # open3d needs to be installed differently on each platform so it's not part of python_requirements.txt
+  OPEN3D_INSTALLED=NO
   if [[ "$(uname)" == "Linux" ]]; then
-      if ! pip install open3d-cpu==0.19.0;       then return 1; fi
+      if pip install open3d-cpu==0.19.0; then
+        OPEN3D_INSTALLED=YES
+      else
+        echo "WARNING: open3d-cpu could not be installed. Network analysis features will not be available."
+      fi
   elif [[ "$(uname)" == "Darwin" ]]; then
-      if ! pip install open3d==0.19.0;           then return 1; fi
-      
-      if [[ "$(uname -m)" == "arm64" ]]; then
-        pushd $CONDA_PREFIX/lib/python3.12/site-packages/open3d/cpu
-        install_name_tool -change /opt/homebrew/opt/libomp/lib/libomp.dylib @rpath/libomp.dylib pybind.cpython-312-darwin.so
-        install_name_tool -add_rpath @loader_path/../../../ pybind.cpython-312-darwin.so
-        popd
-        ln -sf "$CONDA_PREFIX/lib/libomp.dylib" "$CONDA_PREFIX/lib/python3.12/site-packages/open3d/cpu/../../../libomp.dylib"
+      if pip install open3d==0.19.0; then
+        OPEN3D_INSTALLED=YES
+        if [[ "$(uname -m)" == "arm64" ]]; then
+          pushd $CONDA_PREFIX/lib/python3.12/site-packages/open3d/cpu
+          install_name_tool -change /opt/homebrew/opt/libomp/lib/libomp.dylib @rpath/libomp.dylib pybind.cpython-312-darwin.so
+          install_name_tool -add_rpath @loader_path/../../../ pybind.cpython-312-darwin.so
+          popd
+          ln -sf "$CONDA_PREFIX/lib/libomp.dylib" "$CONDA_PREFIX/lib/python3.12/site-packages/open3d/cpu/../../../libomp.dylib"
+        fi
+      else
+        echo "WARNING: open3d could not be installed. Network analysis features will not be available."
       fi
   else
-      if ! pip install open3d==0.19.0;           then return 1; fi
+      if pip install open3d==0.19.0; then
+        OPEN3D_INSTALLED=YES
+      else
+        echo "WARNING: open3d could not be installed. Network analysis features will not be available."
+      fi
   fi
 
   for package in DataAugmentationUtilsPackage DatasetUtilsPackage MONAILabelPackage DeepSSMUtilsPackage DocumentationUtilsPackage ShapeCohortGenPackage shapeworks ; do