Updating branch

apptainer/README.md

@@ -0,0 +1,52 @@
+## Apptainer images
+
+Apptainer is a container platform designed to run complex applications on HPC clusters. The steps below were tested in Ubuntu 24.04.1 LTS.
+
+### Installing Apptainer
+
+Apptainer may be installed with the following instructions (there are issues with previous versions of Apptainer in Ubuntu 24):
+````
+sudo apt update
+sudo apt install -y wget
+cd /tmp
+wget https://github.com/apptainer/apptainer/releases/download/v1.3.6/apptainer_1.3.6_amd64.deb
+sudo apt install -y ./apptainer_1.3.6_amd64.deb
+````
+
+### Building Apptainer images
+
+In spyro, the Apptainer image is based on the [Docker image](../docker/). Converting from Docker to Apptainer is more productive because Apptainer does not support image layers by design. Then, it is necessary to rerun all the instructions of the definition file when creating Apptainer images even when just one instruction is added (for example, for testing purposes).
+````
+export IMAGE_ID=$(sudo docker images -q devtag:1.0)
+sudo docker save $IMAGE_ID -o devimg.tar
+sudo chown $USER:$USER devimg.tar
+sudo apptainer build devimg.sif docker-archive://devimg.tar
+````
+
+### Running Apptainer images
+
+Before running the Apptainer image, it is necessary to create an [overlay filesystem](https://docs.sylabs.io/guides/3.6/user-guide/persistent_overlays.html) because the SIF container is read only and spyro requires writing to the filesystem.
+````
+apptainer overlay create --size 1024 /tmp/ext3_overlay.img
+````
+
+To execute the image in interactive mode:
+````
+apptainer shell --overlay /tmp/ext3_overlay.img -e devimg.sif
+````
+
+To execute the image in batch mode:
+````
+apptainer run  --overlay /tmp/ext3_overlay.img -e devimg.sif <script>
+````
+
+### Running on Mintrop
+
+In order to run code with Apptainer on Mintrop, you may add the following lines to your Slurm script:
+````
+module load apptainer
+apptainer overlay create --size 1024 /tmp/ext3_overlay.img
+apptainer run  --overlay /tmp/ext3_overlay.img -e devimg.sif ./example.sh
+````
+
+where the script [example.sh](./example.sh) is provided in this directory to show how spyro code could be called.

apptainer/example.sh

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+#!/usr/bin/env bash
+
+. /home/firedrake/firedrake/bin/activate
+python3 -m pytest ../test

docker/Dockerfile

@@ -28,10 +28,9 @@ RUN . /home/firedrake/firedrake/bin/activate; pip install git+https://github.com
 
 FROM spyro_base AS spyro_development
 
-# For notebook development
-RUN . /home/firedrake/firedrake/bin/activate; pip3 install notebook
-EXPOSE 8888
+# Profiling tools
+RUN . /home/firedrake/firedrake/bin/activate; pip3 install -U memory_profiler
 
-RUN . /home/firedrake/firedrake/bin/activate; pip3 install pytest
+RUN . /home/firedrake/firedrake/bin/activate; pip3 install pytest pytest-cov
 WORKDIR /home/firedrake
 RUN echo "/home/firedrake/shared/spyro" >> /home/firedrake/firedrake/lib/python3.12/site-packages/shared.pth

docker/README.md

@@ -21,8 +21,8 @@ docker run -it runtag:1.0
 
 The Dockerfile may also be used to create a development environment. First, clone the git repository and then build the development image:
 ````
-git clone https://github.com/Olender/spyro-1.git
-cd spyro-1
+git clone git@github.com:NDF-Poli-USP/spyro.git
+cd spyro
 git checkout <your_branch>
 docker build -t devtag:1.0 -f docker/Dockerfile --target spyro_development docker
 ````