Fixes cluster workflow to work with different container profiles (#486)

# Description

Cluster workflow did not work with the different profiles and introduced
names. This PR fixes the workflow and in addition, introduces additional
checks that the profile can be selected. In detail:

- checks whether a profile can be selected depending on whether a
`.env.$container_profile` exists
- allows for `job` to have multiple arguments, also without a profile,
for all other options, the second argument has to be the profile
- check if a docker image exists before building the singularity image
- check if the path for the singularity image exists on the cluster,
otherwise create it
- check if the path for orbit exists on the cluster, otherwise create it


## Type of change

- Bug fix (non-breaking change which fixes an issue)

## Checklist

- [x] I have run the [`pre-commit` checks](https://pre-commit.com/) with
`./orbit.sh --format`
- [x] I have made corresponding changes to the documentation
- [x] My changes generate no new warnings
- [ ] I have added tests that prove my fix is effective or that my
feature works
- [ ] I have run all the tests with `./orbit.sh --test` and they pass
- [ ] I have updated the changelog and the corresponding version in the
extension's `config/extension.toml` file
- [x] I have added my name to the `CONTRIBUTORS.md` or my name already
exists there

---------
Co-authored-by: Leul Tesfaye <lst26@cornell.edu>
Co-authored-by: Mayank Mittal <12863862+Mayankm96@users.noreply.github.com>

docker/cluster/run_singularity.sh

 #!/bin/bash
 
-echo "(run_singularity.py): Called on compute node with arguments $@"
+echo "(run_singularity.py): Called on compute node with container profile $1 and arguments ${@:2}"
 
 #==
 # Helper functions
@@ -46,19 +46,14 @@ mkdir -p "$CLUSTER_ORBIT_DIR/logs"
 touch "$CLUSTER_ORBIT_DIR/logs/.keep"
 cp -r $CLUSTER_ORBIT_DIR $TMPDIR
 
-# copy singulary image to the compute node
-folder="$TMPDIR/isaac-sim.sif"
-
-# Check if the folder exists
-if [ -d "$folder" ]; then
-    echo "1 (run_singularity.py): Folder was already copied to local SSD."
-else
-    tar -xf $CLUSTER_SIF_PATH/orbit.tar  -C $TMPDIR
-fi
+# copy container to the compute node
+tar -xf $CLUSTER_SIF_PATH/$1.tar  -C $TMPDIR
 
 # execute command in singularity container
+# NOTE: ORBIT_PATH is normally set in `orbit.sh` but we directly call the isaac-sim python because we sync the entire
+# orbit directory to the compute node and remote the symbolic link to isaac-sim
 singularity exec \
-    -B $TMPDIR/docker-isaac-sim/cache/kit:${DOCKER_ISAACSIM_PATH}/kit/cache:rw \
+    -B $TMPDIR/docker-isaac-sim/cache/kit:${DOCKER_ISAACSIM_ROOT_PATH}/kit/cache:rw \
     -B $TMPDIR/docker-isaac-sim/cache/ov:${DOCKER_USER_HOME}/.cache/ov:rw \
     -B $TMPDIR/docker-isaac-sim/cache/pip:${DOCKER_USER_HOME}/.cache/pip:rw \
     -B $TMPDIR/docker-isaac-sim/cache/glcache:${DOCKER_USER_HOME}/.cache/nvidia/GLCache:rw \
@@ -68,8 +63,8 @@ singularity exec \
     -B $TMPDIR/docker-isaac-sim/documents:${DOCKER_USER_HOME}/Documents:rw \
     -B $TMPDIR/orbit:/workspace/orbit:rw \
     -B $CLUSTER_ORBIT_DIR/logs:/workspace/orbit/logs:rw \
-    --nv --writable --containall $TMPDIR/orbit.sif \
-    bash -c "cd /workspace/orbit && /isaac-sim/python.sh ${CLUSTER_PYTHON_EXECUTABLE} $@"
+    --nv --writable --containall $TMPDIR/$1.sif \
+    bash -c "export ORBIT_PATH=/workspace/orbit && cd /workspace/orbit && /isaac-sim/python.sh ${CLUSTER_PYTHON_EXECUTABLE} ${@:2}"
 
 # copy resulting cache files back to host
 cp -r $TMPDIR/docker-isaac-sim $CLUSTER_ISAAC_SIM_CACHE_DIR/..

docker/cluster/submit_job.sh

@@ -17,7 +17,8 @@ cat <<EOT > job.sh
 #SBATCH --mail-user=name@mail
 #SBATCH --job-name="training-$(date +"%Y-%m-%dT%H:%M")"
 
-sh "$1/docker/cluster/run_singularity.sh" "${@:2}"
+# Pass the container profile first to run_singularity.sh, then all arguments intended for the executed script
+sh "$1/docker/cluster/run_singularity.sh" "$2" "${@:3}"
 EOT
 
 sbatch < job.sh

docker/container.sh

@@ -21,13 +21,16 @@ SCRIPT_DIR="$( cd "$( dirname "${BASH_SOURCE[0]}" )" >/dev/null 2>&1 && pwd )"
 print_help () {
     echo -e "\nusage: $(basename "$0") [-h] [run] [start] [stop] -- Utility for handling docker in Orbit."
     echo -e "\noptional arguments:"
-    echo -e "\t-h, --help         Display the help content."
-    echo -e "\tstart              Build the docker image and create the container in detached mode."
-    echo -e "\tenter              Begin a new bash process within an existing orbit container."
-    echo -e "\tcopy               Copy build and logs artifacts from the container to the host machine."
-    echo -e "\tstop               Stop the docker container and remove it."
-    echo -e "\tpush               Push the docker image to the cluster."
-    echo -e "\tjob                Submit a job to the cluster."
+    echo -e "\t-h, --help                  Display the help content."
+    echo -e "\tstart [profile]             Build the docker image and create the container in detached mode."
+    echo -e "\tenter [profile]             Begin a new bash process within an existing orbit container."
+    echo -e "\tcopy [profile]              Copy build and logs artifacts from the container to the host machine."
+    echo -e "\tstop [profile]              Stop the docker container and remove it."
+    echo -e "\tpush [profile]              Push the docker image to the cluster."
+    echo -e "\tjob [profile] [job_args]    Submit a job to the cluster."
+    echo -e "\n"
+    echo -e "[profile] is the optional container profile specification and [job_args] optional arguments specific"
+    echo -e "to the executed script"
     echo -e "\n" >&2
 }
 
@@ -64,12 +67,24 @@ check_docker_version() {
 resolve_image_extension() {
     # If no profile was passed, we default to 'base'
     container_profile=${1:-"base"}
+    # check if the second argument has to be a profile or can be a job argument instead
+    necessary_profile=${2:-true}
 
     # We also default to 'base' if "orbit" is passed
     if [ "$1" == "orbit" ]; then
         container_profile="base"
     fi
 
+    # check if a .env.$container_profile file exists
+    # if the argument is necessary a profile, then the file must exists otherwise an info is printed
+    if [ "$necessary_profile" = true ] && [ ! -f $SCRIPT_DIR/.env.$container_profile ]; then
+        echo "[Error] The profile '$container_profile' has no .env.$container_profile file!" >&2;
+        exit 1
+    elif [ ! -f $SCRIPT_DIR/.env.$container_profile ]; then
+        echo "[INFO] No .env.$container_profile found, assume second argument is no profile! Will use default container!" >&2;
+        container_profile="base"
+    fi
+
     add_profiles="--profile $container_profile"
     # We will need .env.base regardless of profile
     add_envs="--env-file .env.base"
@@ -92,6 +107,24 @@ is_container_running() {
     fi
 }
 
+# Checks if a docker image exists, otherwise prints warning and exists
+check_image_exists() {
+    image_name="$1"
+    if ! docker image inspect $image_name &> /dev/null; then
+        echo "[Error] The '$image_name' image does not exist!" >&2;
+        exit 1
+    fi
+}
+
+# Check if the singularity image exists on the remote host, otherwise print warning and exit
+check_singularity_image_exists() {
+    image_name="$1"
+    if ! ssh "$CLUSTER_LOGIN" "[ -f $CLUSTER_SIF_PATH/$image_name.tar ]"; then
+        echo "[Error] The '$image_name' image does not exist on the remote host $CLUSTER_LOGIN!" >&2;
+        exit 1
+    fi
+}
+
 #==
 # Main
 #==
@@ -111,7 +144,27 @@ fi
 
 # parse arguments
 mode="$1"
-resolve_image_extension $2
+profile_arg="$2" # Capture the second argument as the potential profile argument
+
+# Check mode argument and resolve the container profile
+case $mode in
+    build|start|enter|copy|stop|push)
+        resolve_image_extension "$profile_arg" true
+        ;;
+    job)
+        resolve_image_extension "$profile_arg" false
+        ;;
+    *)
+        # Not recognized mode
+        echo "[Error] Invalid command provided: $mode"
+        print_help
+        exit 1
+        ;;
+esac
+
+# Produces a nice print statement stating which container profile is being used
+echo "[INFO] Using container profile: $container_profile"
+
 # resolve mode
 case $mode in
     start)
@@ -169,43 +222,53 @@ case $mode in
         if ! command -v apptainer &> /dev/null; then
             install_apptainer
         fi
+        # Check if Docker image exists
+        check_image_exists orbit-$container_profile:latest
         # Check if Docker version is greater than 25
         check_docker_version
-        # Check if .env.base file exists
-        if [ -f $SCRIPT_DIR/.env.base ]; then
-            # source env file to get cluster login and path information
-            source $SCRIPT_DIR/.env.base
-            # clear old exports
-            rm -rf /$SCRIPT_DIR/exports
-            mkdir -p /$SCRIPT_DIR/exports
-            # create singularity image
-            # NOTE: we create the singularity image as non-root user to allow for more flexibility. If this causes
-            # issues, remove the --fakeroot flag and open an issue on the orbit repository.
-            cd /$SCRIPT_DIR/exports
-            APPTAINER_NOHTTPS=1 apptainer build --sandbox --fakeroot orbit.sif docker-daemon://orbit:latest
-            # tar image and send to cluster
-            tar -cvf /$SCRIPT_DIR/exports/orbit.tar orbit.sif
-            scp /$SCRIPT_DIR/exports/orbit.tar $CLUSTER_LOGIN:$CLUSTER_SIF_PATH/orbit.tar
-        else
-            echo "[Error]: ".env.base" file not found."
-        fi
+        # source env file to get cluster login and path information
+        source $SCRIPT_DIR/.env.base
+        # make sure exports directory exists
+        mkdir -p /$SCRIPT_DIR/exports
+        # clear old exports for selected profile
+        rm -rf /$SCRIPT_DIR/exports/orbit-$container_profile*
+        # create singularity image
+        # NOTE: we create the singularity image as non-root user to allow for more flexibility. If this causes
+        # issues, remove the --fakeroot flag and open an issue on the orbit repository.
+        cd /$SCRIPT_DIR/exports
+        APPTAINER_NOHTTPS=1 apptainer build --sandbox --fakeroot orbit-$container_profile.sif docker-daemon://orbit-$container_profile:latest
+        # tar image (faster to send single file as opposed to directory with many files)
+        tar -cvf /$SCRIPT_DIR/exports/orbit-$container_profile.tar orbit-$container_profile.sif
+        # make sure target directory exists
+        ssh $CLUSTER_LOGIN "mkdir -p $CLUSTER_SIF_PATH"
+        # send image to cluster
+        scp $SCRIPT_DIR/exports/orbit-$container_profile.tar $CLUSTER_LOGIN:$CLUSTER_SIF_PATH/orbit-$container_profile.tar
         ;;
     job)
-        # Check if .env file exists
-        if [ -f $SCRIPT_DIR/.env.base ]; then
-            # Sync orbit code
-            echo "[INFO] Syncing orbit code..."
-            source $SCRIPT_DIR/.env.base
-            rsync -rh  --exclude="*.git*" --filter=':- .dockerignore'  /$SCRIPT_DIR/.. $CLUSTER_LOGIN:$CLUSTER_ORBIT_DIR
-            # execute job script
-            echo "[INFO] Executing job script..."
-            ssh $CLUSTER_LOGIN "cd $CLUSTER_ORBIT_DIR && sbatch $CLUSTER_ORBIT_DIR/docker/cluster/submit_job.sh" "$CLUSTER_ORBIT_DIR" "${@:2}"
+        source $SCRIPT_DIR/.env.base
+        # Check if singularity image exists on the remote host
+        check_singularity_image_exists orbit-$container_profile
+        # make sure target directory exists
+        ssh $CLUSTER_LOGIN "mkdir -p $CLUSTER_ORBIT_DIR"
+        # Sync orbit code
+        echo "[INFO] Syncing orbit code..."
+        rsync -rh  --exclude="*.git*" --filter=':- .dockerignore'  /$SCRIPT_DIR/.. $CLUSTER_LOGIN:$CLUSTER_ORBIT_DIR
+        # execute job script
+        echo "[INFO] Executing job script..."
+        # check whether the second argument is a profile or a job argument
+        if [ "$profile_arg" == "$container_profile" ] ; then
+            # if the second argument is a profile, we have to shift the arguments
+            echo "[INFO] Arguments passed to job script ${@:3}"
+            ssh $CLUSTER_LOGIN "cd $CLUSTER_ORBIT_DIR && sbatch $CLUSTER_ORBIT_DIR/docker/cluster/submit_job.sh" "$CLUSTER_ORBIT_DIR" "orbit-$container_profile" "${@:3}"
         else
-            echo "[Error]: ".env.base" file not found."
+            # if the second argument is a job argument, we have to shift only one argument
+            echo "[INFO] Arguments passed to job script ${@:2}"
+            ssh $CLUSTER_LOGIN "cd $CLUSTER_ORBIT_DIR && sbatch $CLUSTER_ORBIT_DIR/docker/cluster/submit_job.sh" "$CLUSTER_ORBIT_DIR" "orbit-$container_profile" "${@:2}"
         fi
         ;;
     *)
-        echo "[Error] Invalid argument provided: $1"
+        # Not recognized mode
+        echo "[Error] Invalid command provided: $mode"
         print_help
         exit 1
         ;;

docs/source/deployment/cluster.rst

@@ -91,11 +91,13 @@ To export to a singularity image, execute the following command:
 
 .. code:: bash
 
-    ./docker/container.sh push
+    ./docker/container.sh push [profile]
 
 This command will create a singularity image under ``docker/exports`` directory and
 upload it to the defined location on the cluster. Be aware that creating the singularity
 image can take a while.
+``[profile]`` is an optional argument that specifies the container profile to be used. If no profile is
+specified, the default profile ``base`` will be used.
 
 .. note::
   By default, the singularity image is created without root access by providing the ``--fakeroot`` flag to
@@ -141,13 +143,18 @@ To submit a job on the cluster, the following command can be used:
 
 .. code:: bash
 
-    ./docker/container.sh job "argument1" "argument2" ...
+    ./docker/container.sh job [profile] "argument1" "argument2" ...
 
 This command will copy the latest changes in your code to the cluster and submit a job. Please ensure that
 your Python executable's output is stored under ``orbit/logs`` as this directory will be copied again
 from the compute node to ``CLUSTER_ORBIT_DIR``.
 
-The training arguments anove are passed to the Python executable. As an example, the standard
+``[profile]`` is an optional argument that specifies which singularity image corresponding to the  container profile
+will be used. If no profile is specified, the default profile ``base`` will be used. The profile has be defined
+directlty after the ``job`` command. All other arguments are passed to the Python executable. If no profile is
+defined, all arguments are passed to the Python executable.
+
+The training arguments are passed to the Python executable. As an example, the standard
 ANYmal rough terrain locomotion training can be executed with the following command:
 
 .. code:: bash