feat: Add support for the docker backend (#1)

* feat: add support for the docker backend Signed-off-by: Vassilis Vassiliadis <[email protected]> * docs: add an example to run a small-scale experiment using docker/podman Signed-off-by: Vassilis Vassiliadis <[email protected]> --------- Signed-off-by: Vassilis Vassiliadis <[email protected]>
st4sd · Aug 1, 2023 · 85244f5 · 85244f5
1 parent f06d38c
commit 85244f5
Show file tree

Hide file tree

Showing 5 changed files with 86 additions and 1 deletion.
diff --git a/README.md b/README.md
@@ -32,6 +32,8 @@ rest_uid = api.api_experiment_start("nanopore-geometry-experiment", payload)
 
 **Note**: The [example notebook](nanopore-geometry-experiment.ipynb) shows a full example.
 
+**Note**: You can also run a small scale experiment using docker/podman. See our example [here](docker-example/README.md).
+
 ## Help and Support
 
 Please feel free to create an issue and alert the maintainers listed in the [MAINTAINERS.md](MAINTAINERS.md) page.

diff --git a/conf/flowir_package.yaml b/conf/flowir_package.yaml
@@ -98,6 +98,9 @@ variables:
       numberOfNanopores: 3
       probeRadius_A: 1.4
       zeo_memory: '2Gi'
+  docker:
+    global:
+      numberOfNanopores: 1
 
 blueprint:
   openshift:
@@ -106,6 +109,11 @@ blueprint:
         config:
           walltime: 14400.0
           backend: kubernetes
+  docker:
+    global:
+      resourceManager:
+        config:
+          backend: docker
 
 environments:
   default:
@@ -162,6 +170,8 @@ components:
       kubernetes:
         image: quay.io/st4sd/community-applications/raspa-source-mdlab:latest
         cpuUnitsPerCore: 0.25
+      docker:
+        image: quay.io/st4sd/community-applications/raspa-source-mdlab:latest
     resourceRequest:
       memory: 512Mi
     workflowAttributes:
@@ -181,7 +191,8 @@ components:
     resourceManager:
       kubernetes:
         image: quay.io/st4sd/community-applications/geometry-mdlab:latest
-        cpuUnitsPerCore: 1.0
+      docker:
+        image: quay.io/st4sd/community-applications/geometry-mdlab:latest
     resourceRequest:
       memory: '%(zeo_memory)s'
     workflowAttributes:
@@ -203,6 +214,8 @@ components:
       kubernetes:
         image: quay.io/st4sd/community-applications/geometry-mdlab:latest
         cpuUnitsPerCore: 0.25
+      docker:
+        image: quay.io/st4sd/community-applications/geometry-mdlab:latest
     resourceRequest:
       memory: 256Mi
 
@@ -220,6 +233,8 @@ components:
       kubernetes:
         image: quay.io/st4sd/community-applications/geometry-mdlab:latest
         cpuUnitsPerCore: 0.25
+      docker:
+        image: quay.io/st4sd/community-applications/geometry-mdlab:latest
     resourceRequest:
       memory: 256Mi
 
@@ -236,6 +251,8 @@ components:
       kubernetes:
         image: quay.io/st4sd/community-applications/geometry-mdlab:latest
         cpuUnitsPerCore: 0.25
+      docker:
+        image: quay.io/st4sd/community-applications/geometry-mdlab:latest
     resourceRequest:
       memory: 256Mi
     workflowAttributes:
@@ -249,5 +266,6 @@ output:
 
 platforms:
   - openshift
+  - docker
 
 version: 1.0.0
diff --git a/docker-example/README.md b/docker-example/README.md
@@ -0,0 +1,36 @@
+# Run nanopore-geometry-experiment using the Docker backend of ST4SD
+
+## Prerequisites
+
+1. A recent version of python 3 - [python 3.7+](https://www.python.org/downloads/)
+2. The [docker](https://docs.docker.com/get-docker/) container runtime
+3. The [git](https://git-scm.com/book/en/v2/Getting-Started-Installing-Git) command-line utility
+
+
+## Instructions
+
+You can try out the experiment on your laptop by:
+
+1. creating a python virtual environment, activating it, and installing the python module `st4sd-runtime-core`
+2. cloning this repository
+3. launching the experiment
+
+
+For example:
+
+```bash
+#!/usr/bin/env sh
+
+# Download virtual experiment
+git clone https://github.com/st4sd/nanopore-geometry-experiment.git
+
+# Setup ST4SD runtime-core
+python3 -m venv --copies venv
+. venv/bin/activate
+python3 -m pip install "st4sd-runtime-core"
+
+# Run experiment
+./nanopore-geometry-experiment/docker-example/run.sh
+```
+
+**Note**: Make sure you run the `git clone` command in a directory that `docker` (or `podman`) can mount later when you execute the experiment.
diff --git a/docker-example/cif_files.dat b/docker-example/cif_files.dat
@@ -0,0 +1 @@
+CoRE2019/GUJVOX_clean
diff --git a/docker-example/run.sh b/docker-example/run.sh
@@ -0,0 +1,28 @@
+#!/usr/bin/env sh
+cd $(dirname ${0})/..
+
+docker_like_location=""
+if ! which docker >/dev/null; then
+    echo "The docker command is not available on this system, will try to use podman" >&2
+
+    if location=$(which podman); then 
+        docker_like_location="--dockerExecutableOverride=${location}"
+        echo "Podman located at ${location}" >&2
+    else
+        echo "No docker or podman command on this system - aborting" >&2
+        exit 2
+    fi
+fi
+
+# Run experiment
+echo "Executing the experiment ..." >&2
+elaunch.py --failSafeDelays=no ${docker_like_location} -l40 \
+    --instanceName nanopore-geometry-experiment \
+    --manifest manifest.yaml \
+    --input docker-example/cif_files.dat \
+    --platform docker conf/flowir_package.yaml
+
+# See outputs of experiment
+echo "\n\nMeasured properties are:" >&2
+output_dir=$(ls -td nanopore-geometry-experiment*.instance | head -1)
+cat "${output_dir}/output/properties.csv"