JobTypes and Types layered relationships. Could it be more flexible?

[victorsndvg]

JobTypes can currently describe how the applications are called depending on the underlying (software) layers used for running them.

The involved layers we have identified are (based on our experience):

• Workload manager (e.g. Slurm)
• Process manager (e.g. Openmpi)
• Container technology (e.g. Singularity)
• Software call (e.g. echo hola)

Currently, workload managers types like Slurm or Torque describe how a batch script is submitted. In addition, a SingularityJob type describes how to call a singularity container inside workload manager. In particular, a SingularityJob type always use mpirun as a process manager, but I think is not always mandatory (e.g. a sequential singularity job). Finally, a particular software call is also expressed through a command job option.

In my opinion, the top (workload manager) and bottom ("software-call") layers of the hierarchy are mandatory. I think the other layers could be optional and interrelated in order to express (in a more flexible way) the requirements and execution mode of every application. As a suggestion, a contained_in relationship could express this kind of hierarchical structures.

As a(n) (simplified) example, the following options could be acceptable:

• srun command
• srun [mpirun] command
• srun [singularity] command
• srun [mpirun] [singularity] command

This flexibility could be expressed by a blueprint like the following example:

    computational_resources:
        type: hpc.nodes.WorkloadManager
        properties:
           ...

    mpi:
        type: hpc.nodes.MPIJob
        properties:
            job_options: 
                modules:
                    - openmpi
                    ...
                flags:
                    - '--mca orte_tmpdir_base /tmp '
                    - '--mca pmix_server_usock_connections 1'
        relationships:
            - type: contained_in  #job_managed_by_wm
              target: computational_resources

    container:
        type: hpc.nodes.SingularityJob
        properties:
            job_options: 
                modules:
                    - singularity
                    ...
        relationships:
            - type: contained_in 
              target: mpi

    software:
        type: hpc.nodes.ShellJob
        properties:
            job_options: 
                command: 'flow inputfile outputfile'
        relationships:
            - type: contained_in 
              target: container

Even if we though about other container solutions (docker), or single-node parallel jobs, we can interchange MPI+container-contained_in relationships, avoiding the MPI-vendor-and-version matching inside and outside the container in some cases:

• srun [singularity | docker] [mpirun] command

To think

[emepetres]

@victorsndvg it is not clear to me how mpi type could exist standalone, I mean: How it would be used with an SRUN/SBATCH job, without container?

[victorsndvg]

Taking as a base point that workload manager and software are mandatory. What I mean is not the MPI library, but the MPI process manager. One can use mpirun, mpiexec, (from intelmpi, openmpi, mpich, etc.) or srun (from slurm) as process manager inside a sbatch script or not.

The orchestrator can take advantage of containers to provide portable workflows, but it can also use locally installed software from the HPC modules system.

A sequential job does not need to spawn processes (don't need mpirun). The following example illustrate it:

...
#SBATCH -N 1 
#SBATCH -n 1
#SBATCH --ntasks-per-node=1

singularity exec opm.simg flow input output

A parallel MPI job needs to be called by a process manager (e.g. mpirun). The tool to run can be containerized or not. The following example illustrate it:

...
#SBATCH -N 2
#SBATCH -n 48
#SBATCH --ntasks-per-node=24

module load gcc openmpi paraview
mpirun paraview --serve inputdata

In addition, other future important point is the support of other container technologies. Usage of mpirun within a docker container is different.
With singularity: mpirun singularity ...
With docker: docker run mpirun ...

[emepetres]

how mpi flags woud be attached to a sbatch script?

[victorsndvg]

Really don't know if I understand the question. I figure out you mean in the blueprint example of the first post.

This example:

    mpi:
        type: hpc.nodes.MPIJob
        properties:
            job_options: 
                modules:
                    - openmpi
                    ...
                flags:
                    - '--mca orte_tmpdir_base /tmp '
                    - '--mca pmix_server_usock_connections 1'
        relationships:
            - type: contained_in  #job_managed_by_wm
              target: computational_resources

Should be translated like this (e.g inside a sbatch script):

module load openmpi
mpirun --mca orte_tmpdir_base /tmp --mca pmix_server_usock_connections 1 ...

This particular example avoids the dependence of the MPI containers with the /scratch directory at FT2

Instead of adding generic flags job_option, it can be mapped to other options like tmpdir, etc. But every vendor has its own flags and it is a hard work to identify and map all of them