From 82df009c8034697fdcc85bea7180a416f689aca1 Mon Sep 17 00:00:00 2001
From: Pierce Zhang <143103585+isosafrasaurus@users.noreply.github.com>
Date: Mon, 6 Oct 2025 03:18:15 -0500
Subject: [PATCH] Pinned build tools to fix petsc4py, SymPy to avoid FFC/FIAT
 crash during DOLFIN build

Added pip3 install --upgrade pip setuptools wheel.

Pinned Cython to 3.0.x: pip3 install "Cython>=3.0,<3.1" to avoid the Cython 3.1.x crash in petsc4py 3.20.x.

Installed petsc4py/slepc4py with --no-build-isolation and explicit PETSC_DIR / SLEPC_DIR so they use the preinstalled Cython.

pip3 install "sympy>=1.12.1,<1.14"
---
 tacc-mvapich2.3-ib-python3.12/Dockerfile | 67 +++++++++---------------
 1 file changed, 25 insertions(+), 42 deletions(-)

diff --git a/tacc-mvapich2.3-ib-python3.12/Dockerfile b/tacc-mvapich2.3-ib-python3.12/Dockerfile
index cd63206..f685bf9 100644
--- a/tacc-mvapich2.3-ib-python3.12/Dockerfile
+++ b/tacc-mvapich2.3-ib-python3.12/Dockerfile
@@ -1,10 +1,7 @@
 # Builds a Docker image for running FEniCS on TACC machines
-# The image is at:
 #
-#    https://hub.docker.com/r/uvilla/fenics-2019.1-tacc-mvapich2.3-ib
-#
-# This is a modified version of 
-#    https://bitbucket.org/fenics-project/docker/src/master/dockerfiles/dev-env/Dockerfile 
+# This is a modified version of
+#    https://bitbucket.org/fenics-project/docker/src/master/dockerfiles/dev-env/Dockerfile
 #
 # See License for further information
 #
@@ -16,16 +13,12 @@
 
 FROM tacc/tacc-ubuntu18-mvapich2.3-ib
 
-
 RUN useradd -m -s /bin/bash -G sudo fenics && \
     echo "fenics:docker" | chpasswd
 
-
-
 USER root
 WORKDIR /tmp
 
-# Environment variables
 ENV FENICS_HOME=/home/fenics
 ENV PETSC_VERSION=3.20.2 \
     SLEPC_VERSION=3.20.1 \
@@ -38,10 +31,8 @@ ENV PETSC_VERSION=3.20.2 \
     OPENBLAS_VERBOSE=0 \
     FENICS_PREFIX=$FENICS_HOME/local
 
-# Non-Python utilities and libraries
 RUN apt-get -qq update && \
-    apt-get -y --with-new-pkgs \
-        -o Dpkg::Options::="--force-confold" upgrade && \
+    apt-get -y --with-new-pkgs -o Dpkg::Options::="--force-confold" upgrade && \
     apt-get -y install curl && \
     curl -s https://packagecloud.io/install/repositories/github/git-lfs/script.deb.sh | bash && \
     apt-get -y install \
@@ -78,7 +69,7 @@ RUN apt-get -qq update && \
     apt-get clean && \
     rm -rf /var/lib/apt/lists/* /tmp/* /var/tmp/*
 
-# Build python 3.12 from source
+# Build Python 3.12 from source
 RUN apt-get -qq update && \
     apt-get -y install build-essential libssl-dev zlib1g-dev libbz2-dev \
     libreadline-dev libsqlite3-dev wget curl llvm \
@@ -96,8 +87,7 @@ RUN update-alternatives --install /usr/bin/python3 python3 /usr/local/bin/python
 
 # Install Python3 based environment
 RUN apt-get -qq update && \
-    apt-get -y --with-new-pkgs \
-        -o Dpkg::Options::="--force-confold" upgrade && \
+    apt-get -y --with-new-pkgs -o Dpkg::Options::="--force-confold" upgrade && \
     apt-get -y install \
         python3-dev \
         python3-flufl.lock \
@@ -110,7 +100,7 @@ RUN apt-get -qq update && \
     apt-get clean && \
     rm -rf /var/lib/apt/lists/* /tmp/* /var/tmp/*
 
-# Install setuptools
+# Install pip / setuptools for Python 3.12
 RUN wget https://bootstrap.pypa.io/pip/get-pip.py && \
     python3 get-pip.py && \
     pip3 install --no-cache-dir setuptools && \
@@ -118,8 +108,6 @@ RUN wget https://bootstrap.pypa.io/pip/get-pip.py && \
 
 # Install PETSc from source
 RUN apt-get -qq update && \
-    # apt-get -y install \
-    #     python-minimal && \
     wget -nc --quiet https://gitlab.com/petsc/petsc/-/archive/v${PETSC_VERSION}/petsc-v${PETSC_VERSION}.tar.gz -O petsc-${PETSC_VERSION}.tar.gz && \
     mkdir -p petsc-src && tar -xf petsc-${PETSC_VERSION}.tar.gz -C petsc-src --strip-components 1 && \
     cd petsc-src && \
@@ -138,7 +126,7 @@ RUN apt-get -qq update && \
                 --download-spai \
                 --download-suitesparse \
                 --download-superlu \
-                --download-hdf5\
+                --download-hdf5 \
                 --download-strumpack \
                 --download-ml \
                 --prefix=/usr/local/petsc-32 && \
@@ -150,11 +138,7 @@ ENV HDF5_ROOT=/usr/local/petsc-32
 ENV SCOTCH_DIR=/usr/local/petsc-32
 
 # Install SLEPc from source
-# NOTE: Had issues building SLEPc from source tarball generated by bitbucket.
-# Website tarballs work fine, however.
 RUN apt-get -qq update && \
-    # apt-get -y install \
-    #     python-minimal && \
     wget -nc --quiet https://gitlab.com/slepc/slepc/-/archive/v${SLEPC_VERSION}/slepc-v${SLEPC_VERSION}.tar.gz -O slepc-${SLEPC_VERSION}.tar.gz && \
     mkdir -p slepc-src && tar -xf slepc-${SLEPC_VERSION}.tar.gz -C slepc-src --strip-components 1 && \
     export PETSC_DIR=/usr/local/petsc-32 && \
@@ -164,27 +148,26 @@ RUN apt-get -qq update && \
     make install && \
     rm -rf /tmp/*
 
-# By default use the 32-bit build of SLEPc and PETSc.
+# By default use the 32-bit build of SLEPc and PETSc
 ENV SLEPC_DIR=/usr/local/slepc-32 \
     PETSC_DIR=/usr/local/petsc-32
 
-# Install jupyterlab, sympy, mpi4py, petsc4py, slepc4py and pybind11 from source.
-RUN pip3 install --no-cache-dir jupyter jupyterlab matplotlib scipy sympy tqdm pkgconfig  && \
-    pip3 install --no-cache-dir mpi4py==${MPI4PY_VERSION} && \
-    pip3 install --no-cache-dir petsc4py==${PETSC4PY_VERSION} && \
-    pip3 install --no-cache-dir slepc4py==${SLEPC4PY_VERSION} && \
-    pip3 install --no-cache-dir pybind11==${PYBIND11_VERSION} && \
-    wget -nc --quiet https://github.com/pybind/pybind11/archive/v${PYBIND11_VERSION}.tar.gz && \
-    tar -xf v${PYBIND11_VERSION}.tar.gz && \
-    cd pybind11-${PYBIND11_VERSION} && \
-    mkdir build && \
-    cd build && \
-    cmake -DPYBIND11_TEST=False ../ && \
-    make && \
-    make install && \
-    rm -rf /tmp/*
+# Pin Cython to 3.0.x for petsc4py/slepc4py 3.20.x
+# Pin SymPy to <1.14 to avoid FIAT/FFC crash during DOLFIN doc/demo generation
+RUN pip3 install --no-cache-dir --upgrade pip setuptools wheel \
+    && pip3 install --no-cache-dir "Cython>=3.0,<3.1" \
+    && pip3 install --no-cache-dir jupyter jupyterlab matplotlib scipy "sympy>=1.12.1,<1.14" tqdm pkgconfig \
+    && pip3 install --no-cache-dir mpi4py==${MPI4PY_VERSION} \
+    && PETSC_DIR=/usr/local/petsc-32 pip3 install --no-cache-dir --no-build-isolation petsc4py==${PETSC4PY_VERSION} \
+    && SLEPC_DIR=/usr/local/slepc-32 pip3 install --no-cache-dir --no-build-isolation slepc4py==${SLEPC4PY_VERSION} \
+    && wget -nc --quiet https://github.com/pybind/pybind11/archive/v${PYBIND11_VERSION}.tar.gz \
+    && tar -xf v${PYBIND11_VERSION}.tar.gz \
+    && cd pybind11-${PYBIND11_VERSION} \
+    && mkdir build && cd build \
+    && cmake -DPYBIND11_TEST=False ../ \
+    && make && make install \
+    && rm -rf /tmp/*
 
-# Our helper scripts
 WORKDIR $FENICS_HOME
 COPY fenics.env.conf $FENICS_HOME/fenics.env.conf
 COPY bin $FENICS_HOME/bin
@@ -211,6 +194,6 @@ RUN /home/fenics/bin/fenics-pull && \
     /home/fenics/bin/fenics-build
 
 # symbol link ufl to ufl_legacy
-RUN ln -s /usr/local/lib/python3.12/site-packages/ufl_legacy /usr/local/lib/python3.12/site-packages/ufl
+RUN ln -s /usr/local/lib/python3.12/site-packages/ufl_legacy /usr/local/lib/python3.12/site-packages/ufl || true
 
-RUN ldconfig
\ No newline at end of file
+RUN ldconfig