Compute¶

In order to actually execute Transformations to obtain free energy estimates, you must deploy compute services to resources suitable for executing these types of calculations. This document details how to do this on several different types of compute resources.

There currently exists a single implementation of an alchemiscale compute service: the SynchronousComputeService. Other variants will likely be created in the future, optimized for different use cases. This documentation will expand over time as these variants become available; for now, it assumes use of this variant.

In all cases, you will need to define a configuration file for your compute services to consume on startup. A template for this file can be found here; replace $ALCHEMISCALE_VERSION with the version tag, e.g. v0.1.4, you have deployed for your server:

https://raw.githubusercontent.com/OpenFreeEnergy/alchemiscale/$ALCHEMISCALE_VERSION/devtools/configs/synchronous-compute-settings.yaml

Single-host¶

To deploy a compute service (or multiple services) to a single host, we recommend one of two routes:

installing all dependencies in a conda/mamba environment
running the services as Docker containers, with all dependencies baked in

Deploying with conda/mamba¶

To deploy via conda/mamba, first create an environment (we recommend mamba for its performance):

mamba env create -n alchemiscale-compute-$ALCHEMISCALE_VERSION \
                 -f https://raw.githubusercontent.com/OpenFreeEnergy/alchemiscale/$ALCHEMISCALE_VERSION/devtools/conda-envs/alchemiscale-compute.yml

Once created, activate the environment in your current shell:

conda activate alchemiscale-compute-$ALCHEMISCALE_VERSION

Then start a compute service, assuming your configuration file is in the current working directory, with:

alchemiscale compute synchronous -c synchronous-compute-settings.yaml

Deploying with Docker¶

Assuming your configuration file is in the current working directory, to deploy with Docker, you might use:

docker run --gpus all \
           --rm \
           -v $(pwd):/mnt ghcr.io/OpenFreeEnergy/alchemiscale-compute:$ALCHEMISCALE_VERSION \
           compute synchronous -c /mnt/synchronous-compute-settings.yaml

See the official Docker documentation on GPU use for details on how to specify individual GPUs for each container you launch. It may also make sense to apply constraints to the number of CPUs available to each container to avoid oversubscription.

HPC cluster¶

To deploy compute services to an HPC cluster, we recommend submitting them as individual jobs to the HPC cluster’s scheduler. Different clusters feature different schedulers (e.g. SLURM, LSF, TORQUE/PBS, etc.), and vary widely in their hardware and queue configurations. You will need to tailor your specific approach to the constraints of the cluster you are targeting.

The following is an example of the content of a script submitted to an HPC cluster. We have omitted queuing system-specific options and flags, and certain environment variables (e.g. JOBID, JOBINDEX) should be tailored to those presented by the queuing system. Note that for this case we’ve made use of a conda/mamba-based deployment, detailed above in Deploying with conda/mamba:

# don't limit stack size
ulimit -s unlimited

# make scratch space (path will be HPC system dependent)
ALCHEMISCALE_SCRATCH=/scratch/${USER}/${JOBID}-${JOBINDEX}
mkdir -p $ALCHEMISCALE_SCRATCH

# activate environment
conda activate alchemiscale-compute-$ALCHEMISCALE_VERSION

# create a YAML file with specific substitutions
# each service in this job can share the same config
envsubst < settings.yaml > configs/settings.${JOBID}-${JOBINDEX}.yaml

# start up a single service
alchemiscale compute synchronous -c configs/settings.${JOBID}-${JOBINDEX}.yaml

# remove scratch space
rm -r $ALCHEMISCALE_SCRATCH

The envsubst line in particular will make a config specific to this job, with environment variable substitutions. A subset of options used in the config file are given below:

---
# options for service initialization
init:

  # Filesystem path to use for `ProtocolDAG` `shared` space.
  shared_basedir: "/scratch/${USER}/${JOBID}-${JOBINDEX}/shared"

  # Filesystem path to use for `ProtocolUnit` `scratch` space.
  scratch_basedir: "/scratch/${USER}/${JOBID}-${JOBINDEX}/scratch"

  # Path to file for logging output; if not set, logging will only go to
  # STDOUT.
  logfile: /home/${USER}/logs/service.${JOBID}.log

# options for service execution
start:

  # Max number of Tasks to execute before exiting. If `null`, the service will
  # have no task limit.
  max_tasks: 1

  # Max number of seconds to run before exiting. If `null`, the service will
  # have no time limit.
  max_time: 300

For HPC job-based execution, we recommend limiting the number of Tasks the compute service executes to a small number, preferrably 1, and setting a time limit beyond which the compute service will shut down. With this configuration, when a compute service comes up and claims a Task, it will have nearly the full walltime of its job to execute it. Any compute service that fails to claim a Task will shut itself down, and the job will exit, avoiding waste and a scenario where a Task is claimed without enough walltime left on the job to complete it.

Kubernetes cluster¶

To deploy compute services to a Kubernetes (“k8s”) cluster, we make use of a similar approach to deployment with Docker detailed above in Deploying with Docker. We define a k8s Deployment featuring a single container spec as the file compute-services.yaml:

apiVersion: apps/v1
kind: Deployment
metadata:
  name: alchemiscale-synchronouscompute
  labels:
    app: alchemiscale-synchronouscompute
spec:
  replicas: 1
  selector:
    matchLabels:
      app: alchemiscale-synchronouscompute
  template:
    metadata:
      labels:
        app: alchemiscale-synchronouscompute
    spec:
      containers:
      - name: alchemiscale-synchronous-container
        image: ghcr.io/OpenFreeEnergy/alchemiscale-compute:$ALCHEMISCALE_VERSION
        args: ["compute", "synchronous", "-c", "/mnt/settings/synchronous-compute-settings.yaml"]
        resources:
          limits:
            cpu: 2
            memory: 12Gi
            ephemeral-storage: 48Gi
            nvidia.com/gpu: 1
          requests:
            cpu: 2
            memory: 12Gi
            ephemeral-storage: 48Gi
        volumeMounts:
          - name: alchemiscale-compute-settings-yaml
            mountPath: "/mnt/settings"
            readOnly: true
        env:
          - name: OPENMM_CPU_THREADS
            value: "2"
      volumes:
        - name: alchemiscale-compute-settings-yaml
          secret:
            secretName: alchemiscale-compute-settings-yaml

This assumes our configuration file has been defined as a secret in the cluster. Assuming the file is in the current working directory, we can add it as a secret with:

kubectl create secret generic alchemiscale-compute-settings-yaml \
                              --from-file=synchronous-compute-settings.yaml

Then we can then deploy the compute services with:

kubectl apply -f compute-services.yaml

To scale up the number of compute services on the cluster, increase replicas to the number desired, and re-run the kubectl apply command above.

A more complete example of this type of deployment can be found in alchemiscale-k8s.