This page contains a guide for building and using OpenIFS 48r1 at model version 48R1.1 in a linux based container using Docker.
While this page focuses on the containerised installation, the details presented can be used as a recipe for the underlying dependencies required to install and run OpenIFS 48r1 on a linux system.
If you have access to ATOS hpc2020 and are planning to run OpenIFS on that system please refer to OpenIFS 48r1 - Getting Started (ATOS hpc2020).
Contents:
Creation of a docker build directory
The first step is to make a directory from which the OpenIFS container can be created and cd into that directory, e.g.
mkdir <openifs-docker-build-dir> cd <openifs-docker-build-dir>
Once inside the <openifs-docker-build-dir> clone or branch from the git repository with the OpenIFS release package, e.g.
git clone --single-branch --branch release ssh://git@git.ecmwf.int/oifs/openifs-48r1.1.git
- Please note that currently access to this repository is restricted to a limited number of users only.
- It is important that the OpenIFS package in the docker build directory is a fresh clone/branch, i.e., not built on your local system.
Once OpenIFS 48r1 has been extracted to your <openifs-docker-build-dir> , then copy the Dockerfile from the release to <openifs-docker-build-dir>
cp <openifs-docker-build-dir>/openifs-48r1.1/scripts/docker/gcc-docker-48r1.1/Dockerfile <openifs-docker-build-dir>/.
This cp step is important because the Dockerfile and the OpenIFS release, i.e., openifs-48r1.1, need to be in the same directory to build the container (see the openifs-48r1.1/scripts/docker/gcc-docker-48r1.1/Dockerfile)
Build the OpenIFS docker image
The following command builds the docker image
docker build --tag "openifs-48r1.1" .
Note the trailing '.' to build in the current dir, which is required.
This command runs the build process for the OpenIFS image using gcc:11.2.0-bullseye as the base image, which is a debian Linux distribution with gcc 11.2 (at the time of writing, similar to the gcc on the ATOS). After downloading the image, the Dockerfile installs the following software
apt install -y git && \
apt install -y cmake && \
apt install -y python3 python3-ruamel.yaml python3-yaml python3-venv && \
apt install -y libomp-dev && \
apt install -y libboost-dev libboost-date-time-dev libboost-filesystem-dev libboost-serialization-dev libboost-program-options-dev&& \
apt install -y netcdf-bin libnetcdf-dev libnetcdff-dev && \
apt install -y libatlas-base-dev && \
apt install -y liblapack-dev && \
apt install -y libeigen3-dev && \
apt install -y bison && \
apt install -y flex && \
apt install -y vim && \
apt install -y wget bc
Once these packages are installed, open-mpi is downloaded and built, the openifs user is created and the openifs-48r1.1 directory is copied to the image.
On a Macbook pro (M1) the initial build of the container, takes about 5 minutes. If you decide to change the Dockerfile following a build, you can just execute the same command and, depending on what you change, subsequent builds can be a lot quicker.
- At the time of writing open-mpi is downloaded and built as part of the image creation. This is quite slow, so in the future we will investigate the use of a standard library
- If a fresh build is required but an image has already been built, then execute the following command, which is the same as above but with no-cache
docker build --no-cache --tag "openifs-48r1.1" .
- The tag name does not need to be provided but it is useful for identifying images.
Running OpenIFS-test using the docker image
Once a build has completed, the image can be checked by typing docker images , e.g.,
docker images REPOSITORY TAG IMAGE ID CREATED SIZE openifs-48r1.1 latest f72ea92f010f 5 hours ago 2.15GB
And the container can be run using the following
docker run -it 'openifs-48r1.1'
This command will open an interactive session in the new container, in which the entry directory is the openifs-48r1.1 directory, e.g.
docker run -it 'openifs-48r1.1' OpenIFS environment variables are: ------------------------------------------------------ OIFS_CYCLE=48r1 OIFS_DATA_DIR=/perm/openifs/oifs_data/48r1/48r1 OIFS_HOME=/home/openifs/openifs-48r1.1 OIFS_LOGFILE=/home/openifs/openifs-48r1.1/oifs_test_log.txt openifs@d1bd89ccc47f:~/openifs-48r1.1$ ls CHANGES COPYING NOTICE arch ifs-source oifs-config.edit_me.sh scripts CITE LICENSE README bundle.yml ifs-test openifs-bundle
- In the above code block the openifs config (
oifs-config.edit_me.sh) is sourced automatically so the container has the correct environment for OpenIFS
Once inside the container, the openifs-test.sh script can be run, e.g.,
openifs@d1bd89ccc47f:~/openifs-48r1.1$ ./scripts/openifs-test.sh -cbt -s docker
where :
-c will clean the directory (not necessary for a fresh image or new container)
-b will configure the bundle and build OpenIFS, i.e.,
- the OpenIFS double and single precision master executables (ifsMASTER.DP and ifsMASTER.SP, respectively) , which are used to run 3-D OpenIFS. The executables are located in
$OIFS_HOME/build/bin. - the double and single precision Single Column Model (SCM) executables (MASTER_scm.DP and MASTER_scm.SP, respectively), which are used to run the SCM derived from OpenIFS. The executables are located in
$OIFS_HOME/build/bin.
-t will run the ifs-test
- 21 3-D OpenIFS forecast-only tests with and without chemistry
- 1 SCM test (based on TWP-ICE)
-s docker defines the system as docker, which makes the script use the correct build commands
On a Macbook pro (M1) the build of OpenIFS, takes about 10 minutes, while successful completion of ifstest takes just over 3 minutes.
Notes about containers
Exiting the container
- The container can be exited by typing
exitfrom the active container. Once exited all data and changes made within the container will be lost. Hence, if necessary, it is important to- Push any code changes back to a repo
- If data is required either set-up a data volume or copy the data back to a local machine, using
docker cp
Check for existing containers, stopping, restarting
Executing docker run will always create a new container, hence we recommend