Docker updates (#711)

* Update dockerfiles - Rebase to a python image based on Debian bookworm - Update runtime requirements (mainly for lavavu) - Modify bash script to allow switching between mpi implementation & change of base image * Remove pawsey files Can be built with the previous commit (8048d4c) * Update CHANGES.md
underworldcode · Feb 3, 2025 · ca6fa46 · ca6fa46
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diff --git a/CHANGES.md b/CHANGES.md
@@ -10,6 +10,7 @@ New:
 
 Changes:
 * UWGeodynamics - 'ressources' folder is now 'resources' (but previous name is still supported).
+* Modify docker building script to allow changing MPI implementation. 
 
 Fixes:
 * Update UWGeoTutorials.rst #693.

diff --git a/docs/development/docker/docker-builder.sh b/docs/development/docker/docker-builder.sh
@@ -7,54 +7,81 @@ set -e
 #   - mpi and lavavu dockers are automatically generated via github actions
 #   - petsc and underworld2 must be created by runn the following script.
 
-UBUNTU_VERSION=24.04
-PYTHON_VERSION=3.12
+PYTHON_VERSION=3.11
 OMPI_VERSION=4.1.4
+MPICH_VERSION=3.4.3
 PETSC_VERSION=3.22.2
 
+MPI_IMPLEMENTATION=opmi
+
+BASE_IMAGE="python:$PYTHON_VERSION-slim-bookworm"
+
+#### x86 images can be built on mac arm architecture using rosetta
 ARCH=$(uname -m)
-echo "Will build docker image locally for architecture type: $ARCH"
+echo "Will build docker image locally for architecture type: $ARCH, with mpi implementation: $MPI_IMPLEMENTATION"
 echo "************************************************************\n"
 
-# Get the ubuntu image
-podman pull ubuntu:$UBUNTU_VERSION
+
+# Get the base image
+podman pull $BASE_IMAGE
 
 ## The mpi and lavavu images should be automatically made via github actions
-podman build . \
-  --rm --squash-all \
-  -f ./docs/development/docker/mpi/Dockerfile.openmpi \
-  --build-arg UBUNTU_VERSION=$UBUNTU_VERSION \
-  --build-arg OMPI_VERSION=$OMPI_VERSION \
-  -t underworldcode/openmpi:$OMPI_VERSION-$ARCH
+
+if [ "$MPI_IMPLEMENTATION" = "MPICH" ]
+then
+  ## Default is openmpi, but can be switched to mpich
+  podman build . \
+    --rm --squash-all \
+    -f ./docs/development/docker/mpi/Dockerfile.mpich \
+    --build-arg BASE_IMAGE=$BASE_IMAGE \
+    --build-arg PYTHON_VERSION=$PYTHON_VERSION \
+    --build-arg MPICH_VERSION=$MPICH_VERSION \
+    -t underworldcode/mpich:$MPICH_VERSION-$ARCH
+
+  MPI_IMAGE=underworldcode/mpich:$MPICH_VERSION-$ARCH
+  mpi_lowercase="mpich"
+else
+  podman build . \
+    --rm --squash-all \
+    -f ./docs/development/docker/mpi/Dockerfile.openmpi \
+    --build-arg BASE_IMAGE=$BASE_IMAGE \
+    --build-arg PYTHON_VERSION=$PYTHON_VERSION \
+    --build-arg OMPI_VERSION=$OMPI_VERSION \
+    -t underworldcode/openmpi:$OMPI_VERSION-$ARCH
+
+  MPI_IMAGE=underworldcode/openmpi:$OMPI_VERSION-$ARCH
+  mpi_lowercase="ompi"
+fi
 
 podman build . \
   --rm --squash-all \
   -f ./docs/development/docker/lavavu/Dockerfile \
-  --build-arg UBUNTU_VERSION=$UBUNTU_VERSION \
+  --build-arg BASE_IMAGE=$BASE_IMAGE \
   --build-arg PYTHON_VERSION=$PYTHON_VERSION \
   -t underworldcode/lavavu:$ARCH
 
 podman build . \
   --rm --squash-all \
   -f ./docs/development/docker/petsc/Dockerfile \
-  --build-arg MPI_IMAGE="underworldcode/openmpi:$OMPI_VERSION-$ARCH" \
-  --build-arg UBUNTU_VERSION=$UBUNTU_VERSION \
+  --build-arg BASE_IMAGE=$BASE_IMAGE \
+  --build-arg MPI_IMAGE=$MPI_IMAGE \
   --build-arg PYTHON_VERSION=$PYTHON_VERSION \
   --build-arg PETSC_VERSION=$PETSC_VERSION \
-  -t underworldcode/petsc:$PETSC_VERSION-$ARCH
+  -t underworldcode/petsc-$mpi_lowercase:$PETSC_VERSION-$ARCH
 
 ### don't use pull here as we want the petsc image above
 podman build . \
   --rm --squash-all \
-  --build-arg UBUNTU_VERSION=$UBUNTU_VERSION \
+  --build-arg BASE_IMAGE=$BASE_IMAGE \
   --build-arg PYTHON_VERSION=$PYTHON_VERSION \
-  --build-arg PETSC_IMAGE="underworldcode/petsc:$PETSC_VERSION-$ARCH" \
+  --build-arg PETSC_IMAGE="underworldcode/petsc-$mpi_lowercase:$PETSC_VERSION-$ARCH" \
   --build-arg LAVAVU_IMAGE="underworldcode/lavavu:$ARCH" \
   -f ./docs/development/docker/underworld2/Dockerfile \
-  -t underworldcode/underworld2:2.16.0b-$ARCH
+  -t underworldcode/underworld2-$mpi_lowercase:2.16.0b-$ARCH
+
 
-#docker push underworldcode/petsc:3.19.4-$ARCH 
-#docker push underworldcode/underworld2:2.15.0b-$ARCH
+#docker push underworldcode/petsc-$mpi_lowercase:$PETSC_VERSION-$ARCH
+#docker push underworldcode/underworld2-$mpi_lowercase:2.16.0b-$ARCH
 
 #### if updates for both arm64 and x86_64 build manifest, ie
 # docker manifest create underworldcode/petsc:3.18.1 \
@@ -64,3 +91,20 @@ podman build . \
 # docker manifest push underworldcode/petsc:3.18.1
 #
 # in future this should be automated
+
+
+
+## How to use image on HPC with singularity/apptainer
+
+### save the docker image
+# podman save -o underworld2-$mpi_lowercase-2.16.0b-$ARCH.tar underworldcode/underworld2-$mpi_lowercase:2.16.0b-$ARCH
+### upload to hpc
+# scp underworld2-$mpi_lowercase-2.16.0b-$ARCH.tar [email protected]:/path/to/store/container
+### extract using singularity/apptainer on HPC
+# module load singularity...
+# singularity build underworld2-mpich-2.16.0b-x86_64.sif docker-archive://underworld2-mpich-2.16.0b-x86_64.tar
+
+
+### Some good resources for using containers on HPC:
+# (1) checking mpi is using system install not container
+# https://pawseysc.github.io/containers-astro-python-workshop/3.hpc/index.html
diff --git a/docs/development/docker/lavavu/Dockerfile b/docs/development/docker/lavavu/Dockerfile
@@ -1,11 +1,10 @@
-ARG UBUNTU_VERSION="24.04"
 ARG PYTHON_VERSION="3.12"
+ARG BASE_IMAGE="python:$PYTHON_VERSION-slim-bookworm"
 
-FROM ubuntu:${UBUNTU_VERSION} as base_runtime
+FROM ${BASE_IMAGE} as base_runtime
 LABEL maintainer="https://github.com/underworldcode/"
 
 # need to repeat ARGS after every FROM 
-ARG UBUNTU_VERSION
 ARG PYTHON_VERSION
 
 ENV LANG=C.UTF-8
@@ -33,11 +32,13 @@ RUN mkdir ${VIRTUAL_ENV} \
 # install runtime requirements
 RUN apt-get update -qq \
 &&  DEBIAN_FRONTEND=noninteractive apt-get install -yq --no-install-recommends \
-        python3-minimal \
-        python3-venv \
-        python3-pip \
-        libpng16-16t64 \
-        libjpeg8 \
+        # python3-minimal \
+        # python3-venv \
+        # python3-pip \
+        # libpng16-16t64 \
+        libpng16-16 \
+        #libjpeg8 \
+        libjpeg-dev \
         libtiff-dev \ 
         libglu1-mesa-dev \
         libosmesa6 \
@@ -53,15 +54,14 @@ RUN apt-get update -qq \
 
 FROM base_runtime AS build_base
 
-ARG UBUNTU_VERSION
 ARG PYTHON_VERSION
 
 # install build requirements
 RUN apt-get update -qq 
 RUN DEBIAN_FRONTEND=noninteractive apt-get install -yq --no-install-recommends \
         build-essential \
-        python3-setuptools \
-        libpython${PYTHON_VERSION}-dev \ 
+        # python3-setuptools \
+        # libpython${PYTHON_VERSION}-dev \ 
         libpng-dev \
         libjpeg-dev \
         libtiff-dev \
@@ -76,14 +76,14 @@ RUN DEBIAN_FRONTEND=noninteractive apt-get install -yq --no-install-recommends \
         cmake \
         libopenblas-dev \
         libz-dev \
-        gcc \
-        python3-full
+        gcc
+        # python3-full
 
 
 # lavavu
 # create a virtualenv to put new python modules
 USER $NB_USER
-RUN /usr/bin/python3 -m venv --system-site-packages ${VIRTUAL_ENV}
+RUN python3 -m venv --system-site-packages ${VIRTUAL_ENV}
 RUN pip3 install -U setuptools  \
 &&  pip3 install --no-cache-dir \
         "numpy<2" \
@@ -101,7 +101,7 @@ COPY --from=build_base /usr/local /usr/local
 # ENV LD_LIBRARY_PATH=$LD_LIBRARY_PATH:/usr/local/lib/x86_64-linux-gnu/
 # Record Python packages, but only record system packages! 
 # Not venv packages, which will be copied directly in.
-RUN PYTHONPATH= /usr/bin/pip3 freeze >/opt/requirements.txt
+RUN PYTHONPATH= pip3 freeze >/opt/requirements.txt
 # Record manually install apt packages.
 RUN apt-mark showmanual >/opt/installed.txt
 

diff --git a/docs/development/docker/mpi/Dockerfile.mpich b/docs/development/docker/mpi/Dockerfile.mpich
@@ -14,9 +14,10 @@
 #####################################################################
 
 ARG MPICH_VERSION="3.4.3"
-ARG UBUNTU_VERSION="24.04"
+ARG PYTHON_VERSION="3.12"
+ARG BASE_IMAGE="python:${PYTHON_VERSION}-slim-bookworm"
 
-FROM ubuntu:${UBUNTU_VERSION} as runtime
+FROM ${BASE_IMAGE} as runtime
 LABEL maintainer="https://github.com/underworldcode/"
 
 ################
@@ -46,7 +47,12 @@ FROM runtime as build
 
 ARG MPICH_VERSION
 # Build options for Dockerfile
-ARG MPICH_CONFIGURE_OPTIONS="--enable-fast=all,O3 --prefix=/usr/local --with-device=ch4:ofi FFLAGS=-fallow-argument-mismatch FCFLAGS=-fallow-argument-mismatch"
+# ARG MPICH_CONFIGURE_OPTIONS="--enable-fast=all,O3 --prefix=/usr/local --with-device=ch4:ofi FFLAGS=-fallow-argument-mismatch FCFLAGS=-fallow-argument-mismatch"
+
+### pawsey config from pawsey base image
+### from https://quay.io/repository/pawsey/mpich-base/manifest/sha256:ca1cf20a4f1a8793ec794b7f927a03289f4ad449b51bc821ac98c5a269ea5e8a
+ARG MPICH_CONFIGURE_OPTIONS="--enable-fast=all,O3 --enable-fortran --enable-romio --prefix=/usr/local --with-device=ch4:ofi CC=gcc CXX=g++ FC=gfortran FFLAGS=-fallow-argument-mismatch"
+
 ARG MPICH_MAKE_OPTIONS="-j4"
 
 RUN apt-get update -qq \

diff --git a/docs/development/docker/mpi/Dockerfile.openmpi b/docs/development/docker/mpi/Dockerfile.openmpi
@@ -15,9 +15,10 @@
 
 # https://docs.docker.com/engine/reference/builder/#understand-how-arg-and-from-interact
 ARG OMPI_VERSION=4.1.4
-ARG UBUNTU_VERSION=24.04
+ARG PYTHON_VERSION="3.12"
+ARG BASE_IMAGE="python:$PYTHON_VERSION-slim-bookworm"
 
-FROM ubuntu:${UBUNTU_VERSION} as runtime
+FROM ${BASE_IMAGE} as runtime
 LABEL maintainer="https://github.com/underworldcode/"
 
 ################

diff --git a/docs/development/docker/pawsey/mpich.dockerfile b/docs/development/docker/pawsey/mpich.dockerfile