Re-build container

In case of new versions for one of the three models, the container will need to be updated.

Update Docker

Steps:

• Save the files under MultiMalModPy/dependencies
• Modify the Dockerfile.rocky8 as needed, i.e. by updating the version to install
• Download and install Docker from https://app.docker.com/ (requires to create an account)
• Navigate to MultiMalModPy/dependencies, assuming you are already at the repository root:

  cd dependencies
  

• In terminal run (including the dot):

  docker build -f Dockerfile.rocky8 -t emod:rocky8 .
  

  This takes around 60 minutes.
• View all docker images to veriy its completion

  docker images
  

• Optional, save docker file to specific location (note it is already existing on your local machine) This is only required when the container should be moved to another machine. Also this step takes quite long for an image of size ~3.7GB.

  docker save -o emod_rocky8.tar emod:rocky8
  

HPC (singularity)

Steps:

• Modify the Singularity.recipe as needed, i.e. by updating the version to install

• Log into Quest and load the singularity modules

  module load singularity
  

• Authenticate against the remote builder. Will request that you create a token and copy the token in order to authenticate.

  • Create an account and generate access token under https://cloud.sylabs.io/auth/tokens
  • Then run in terminal:

    singularity remote login
    

• Build the container using the remote builder

  singularity build --remote emod-with-om-46-R-4.4.1.sif Singularity.recipe
  

Understanding where things are in the container

• OpenMalaria: The container currently only has v46.0 and it lives in the container here:

  /openmalaria-schema-46.0/build
  

  • Any future Open Malaria XX.X would live in the container here:

    /openmalaria-schema-XX.X/build
    

• EMOD: The emodpy_om virtual environment lives here:

  /opt/envs/emodpy_om
  

• malariasimulation: The R executable, required for malariasimulation, can be found here

  /opt/R/4.4.1/bin/R
  

Invoking the container (developer mode)

• Set things in manifest.py

  OPENMALARIA_venv = f'\n\nexport PATH=/openmalaria-schema-46.0/build/:$PATH\n'
  EMOD_venv = f'source /opt/envs/emodpy_om/bin/activate'
  

• Run launch_sim_test.py with the container Note the <YOUR DIRECTORY> at the end of the line. Replace this with the location of the image.

  module purge
  module load singularity
  singularity exec -B /etc/passwd -B /etc/slurm -B `which sbatch ` -B `which srun ` -B `which sacct ` -B `which scontrol ` -B `which salloc ` -B `which scancel ` -B `which squeue ` -B /usr/lib64/slurm/ -B /usr/lib64/liblua-5.1.so -B /usr/lib64/liblua-5.1.so:/usr/lib64/liblua.so -B /usr/lib64/libjson-c.so.2 -B /usr/lib64/libjson-c.so.2.0.1 -B /usr/lib64/libmunge.so.2 -B /usr/lib64/libmunge.so.2.0.0 -B /usr/lib64/libpmi2.so -B /usr/lib64/libpmi2.so.0 -B /usr/lib64/libpmi2.so.0.0.0 -B /usr/lib64/libpmi.so -B /usr/lib64/libpmi.so.0 -B /usr/lib64/libpmi.so.0.0.0 -B /usr/local/pmix -B /usr/local/hwloc -B /usr/local/ucx-1.13.0 -B /usr/local/ucx-1.10.0 -B /usr/local/ucx-1.8.1 -B /usr/local/spack -B /usr/local/spack_v20d1 -B /usr/local/libevent/ -B /run -B /projects -B /scratch --writable-tmpfs /<YOUR DIRECTORY>/emod-with-om-46-R-4.4.1.sif /opt/envs/emodpy_om/bin/python3 launch_sim.py --models EMOD --test
  

These instructions were provided by Northwestern Research IT and the format adapted for the online documentation.