Migrate eCLM image to ubuntu:24.04

README.md

@@ -9,7 +9,7 @@ Run `docker pull <repository>:<tag>` to retrieve the desired image.
 | Image | Version |         `docker pull` command         |     Usage guide    |
 |:-----:|:-------:|:-------------------------------------:|:------------------:|
 | CLM5  |   0.4   | `docker pull hpscterrsys/clm5:latest` | [link][clm5-usage] |
-| eCLM  |   0.1   | `docker pull hpscterrsys/eclm:latest` | [link][eclm-usage] |
+| eCLM  |   0.2   | `docker pull hpscterrsys/eclm:latest` | [link][eclm-usage] |
 
 
 [HPSCTerrSys DockerHub repository]: https://hub.docker.com/u/hpscterrsys

eclm/Dockerfile

@@ -1,67 +1,62 @@
 # escape=`
-FROM centos:8.4.2105
+FROM ubuntu:24.04
 
-# Image metadata for documentation purposes. Has no effect on docker build behavior.
-LABEL `
-    org.label-schema.schema-version="1.0" `
-    org.label-schema.name="eCLM" `
-    org.label-schema.version="0.1" `
-    org.label-schema.vendor="IBG-3" `
-    org.label-schema.license="GPLv2" `
-    org.label-schema.build-date="2021-09-27" `
-    eclm.version.major="alpha" `
-    eclm.env.compiler="GCC" `
-    eclm.env.compiler.version="8.4.1-1" `
-    eclm.env.mpi="OpenMPI" `
-    eclm.env.mpi.version="4.0.5" `
-    eclm.env.cmake.version="3.18.2" `
-    eclm.env.pnetcdf.version="1.12.1" `
-    eclm.env.netcdf-c.version="4.7.0" `
-    eclm.env.netcdf-fortran.version="4.5.2"
+#
+# TODO: Specify image metadata following OCI format spec: https://github.com/opencontainers/image-spec/blob/main/spec.md
+#
+# LABEL ...
 
-# Install required packages from base repo
-RUN dnf update -y `
-    && dnf group install -y "Development Tools" `
-    && dnf install -y glibc-langpack-en libcurl-devel `
-                      man-db man-pages passwd sudo vim wget which tree `
-                      python39 python39-pip cmake`
-                      epel-release `
-    && dnf config-manager --set-enabled powertools `
-    `
-# Install required packages from EPEL and SCL repos
-    && dnf install -y hdf5-devel lapack-devel openssl-devel `
-                      openmpi openmpi-devel `
-                      netcdf-devel netcdf-fortran netcdf-fortran-devel `
-    && dnf clean all `
-    `
-# Add python symlinks to /usr/local
-    && python3 -m pip install --upgrade pip `
-    && ln -s /usr/bin/python3 /usr/local/bin/python
 
+# Download compiler toolchain and libraries
+RUN <<EOF
+export DEBIAN_FRONTEND=noninteractive
+apt-get update
+apt-get install -y sudo nano git wget tree cmake python3.12 pip nco
+apt-get install -y gfortran g++ openmpi-bin libopenmpi-dev liblapack-dev libblas-dev
+apt-get install -y libxml++2.6-dev libhdf5-openmpi-dev libhdf5-openmpi-hl-fortran-100t64 hdf5-helpers
+EOF
+
+# Build prep
+ENV VER_NETCDF_C="4.9.2"
+ENV VER_NETCDF_F90="4.6.1"
+ENV VER_PNETCDF="1.14.0"
+ENV CC=mpicc FC=mpifort CXX=mpicxx
+ENV TMP=/tmp/bld
+ENV INSTALL_PREFIX=/usr/local
+ENV MAKEFLAGS=-j8
+
+RUN <<EOF
+# Install netCDF
+mkdir -p $TMP && cd $TMP
+wget -c https://github.com/Unidata/netcdf-c/archive/refs/tags/v${VER_NETCDF_C}.tar.gz
+tar zxf v${VER_NETCDF_C}.tar.gz
+cd netcdf-c-${VER_NETCDF_C}
+CPPFLAGS=-I/usr/include/hdf5/openmpi LDFLAGS=-L/usr/lib/x86_64-linux-gnu/hdf5/openmpi ./configure --prefix=${INSTALL_PREFIX}
+make install
+EOF
+
+RUN <<EOF
+# Install netCDF Fortran
+cd $TMP
+wget -c https://github.com/Unidata/netcdf-fortran/archive/refs/tags/v${VER_NETCDF_F90}.tar.gz
+tar zxf v${VER_NETCDF_F90}.tar.gz
+cd netcdf-fortran-${VER_NETCDF_F90}
+./configure --prefix=${INSTALL_PREFIX}
+make install
+EOF
+
+RUN <<EOF
 # Install PnetCDF
-ENV PATH="/usr/lib64/openmpi/bin:${PATH}"
-RUN mkdir -vp /tmp/bld `
-    && cd /tmp/bld `
-    && wget -c https://github.com/Parallel-NetCDF/PnetCDF/archive/checkpoint.1.12.1.tar.gz `
-    && tar zxf checkpoint.1.12.1.tar.gz `
-    && cd PnetCDF-checkpoint.1.12.1 `
-    && autoreconf -i `
-    && ./configure --prefix=/usr/local && make -j && make install `
-    && cd / && rm -rf /tmp/bld
+cd $TMP
+wget -c https://github.com/Parallel-NetCDF/PnetCDF/archive/checkpoint.${VER_PNETCDF}.tar.gz
+tar zxf checkpoint.${VER_PNETCDF}.tar.gz
+cd PnetCDF-checkpoint.${VER_PNETCDF}
+autoreconf -i
+./configure --prefix=${INSTALL_PREFIX}
+make install
+cd / && rm -rvf $TMP
+EOF
 
-# Add user account
-RUN groupadd -g 1555 clm5docker `
-    && useradd clmuser -g clm5docker`
-    && echo clm5 | passwd --stdin clmuser `
-    && usermod -aG wheel clmuser `
-    && rm /run/nologin `
-    `
-# Set default envs
-    && echo "export PATH=/usr/lib64/openmpi/bin:/home/clmuser/.local/bin:$PATH" >> /home/clmuser/.bash_profile `
-    && echo "export PKG_CONFIG_PATH=/usr/local/lib/pkgconfig:/usr/lib64/pkgconfig" >> /home/clmuser/.bash_profile `
-    && echo "export CC=mpicc" >> /home/clmuser/.bash_profile `
-    && echo "export FC=mpifort" >> /home/clmuser/.bash_profile `
-    && echo "alias ll='ls -phAlv'" >> /home/clmuser/.bash_profile
-USER clmuser
-WORKDIR /home/clmuser
+USER root
+WORKDIR /root
 CMD ["/bin/bash","-l"]

eclm/Dockerfile_dev

@@ -0,0 +1,32 @@
+# escape=`
+FROM hpscterrsys/eclm:0.2
+
+#
+# TODO: Specify image metadata following OCI format spec: https://github.com/opencontainers/image-spec/blob/main/spec.md
+#
+# LABEL ...
+
+
+# Install dev tools
+RUN <<EOF
+export DEBIAN_FRONTEND=noninteractive
+apt-get update
+apt-get install -y vim gdb
+EOF
+
+# Dev environment presets
+USER root
+WORKDIR /root
+RUN <<EOF
+echo "export CC=mpicc FC=mpif90 CXX=mpicxx"                    >> .bash_profile
+echo "export OMPI_ALLOW_RUN_AS_ROOT=1"                         >> .bash_profile
+echo "export OMPI_ALLOW_RUN_AS_ROOT_CONFIRM=1"                 >> .bash_profile
+echo "export PIP_BREAK_SYSTEM_PACKAGES=1"                      >> .bash_profile
+echo "export CMAKE_INSTALL_PREFIX=/root/.local"                >> .bash_profile
+echo "export LD_LIBRARY_PATH=/usr/local/lib:/root/.local/lib"  >> .bash_profile
+echo "export PATH=${PATH}:/root/.local/bin"                    >> .bash_profile
+echo "export SW=/root/.local"                                  >> .bash_profile
+echo "export EDITOR=vim"                                       >> .bash_profile
+mkdir -vp .local/{bin,lib}
+EOF
+CMD ["/bin/bash","-l"]

eclm/README.md

@@ -1,17 +1,83 @@
-## Manual build steps
+# eCLM Docker Build Guide
 
-1. Build Docker image
+This guide requires [Podman](https://docs.podman.io/en/v4.6.1/index.html). If you're on Debian/Ubuntu, run
 
 ```sh
-IMG_VERSION="0.1"
-docker build --tag hpscterrsys/eclm:latest --tag hpscterrsys/eclm:$IMG_VERSION .
+sudo apt update
+sudo apt-get install -y podman
 ```
 
-2. Commit image to DockerHub
+Otherwise, head over to the [Podman install guide](http://podman.io/docs/installation) and follow the instructions
+specific to your system.
+
+## Building the eCLM container
+
+> [!NOTE]
+> This section is only relevant for developers who have push access rights to the [HPSCTerrSys DockerHub](https://hub.docker.com/u/hpscterrsys).
+
+1. Build eCLM base image.
+
+```sh
+podman build --tag hpscterrsys/eclm:latest --tag hpscterrsys/eclm:0.2 .
+```
+
+2. Push eCLM base image to DockerHub.
+
+```sh
+podman login --username $USER docker.io
+podman push hpscterrsys/eclm:latest
+podman push hpscterrsys/eclm:0.2
+```
+
+3. Build eCLM dev image.
+
+```sh
+podman build --tag hpscterrsys/eclm:latest-dev --tag hpscterrsys/eclm:0.2-dev -f Dockerfile_dev
+```
+
+4. Push eCLM dev image to DockerHub.
+
+```sh
+podman push hpscterrsys/eclm:latest-dev
+podman push hpscterrsys/eclm:0.2-dev
+podman logout
+```
+
+## Using the container image for local development
+
+First we configure file sharing between the host machine and the container image. Decide which
+local folder you'd like to expose to the container image, then save its full path to `WORKDIR`:
 
 ```sh
-docker login
-docker push hpscterrsys/eclm:latest
-docker push hpscterrsys/eclm:$IMG_VERSION
-docker logout
+WORKDIR=/home/user/shared_folder
 ```
+
+Then create a container named `eclm-dev`.
+
+```sh
+podman run --name eclm-dev -it -v ${WORKDIR}:/root/$(basename ${WORKDIR}) hpscterrsys/eclm:latest-dev
+```
+
+The command above will also start `eclm-dev`. Verify that everything works by running these commands:
+
+```sh
+root@e06d13d06436:~# pwd                  # $HOME directory
+/root
+root@e06d13d06436:~# ls                   # Should see your WORKDIR here
+shared_folder
+root@e06d13d06436:~# echo $CC $FC $CXX    # Preset compilers in this dev image
+mpicc mpif90 mpicxx
+```
+
+If the container has been stopped, simply run `podman start -ai eclm-dev` to restart it. `podman run` is only done once, *i.e.* during
+container creation. It's also important to know these commands:
+
+- `podman ps -a`: list created containers
+- `podman images`: list downloaded images
+- `podman rm`: Delete existing container
+- `podman rmi`: Delete existing image
+
+The mentioned `podman` commands are sufficient to manage your local `eclm-dev` image. For more information regarding `podman` usage, visit the [Podman tutorial](https://docs.podman.io/en/v4.6.1/Tutorials.html).
+
+
+