Add support for OCI containers

Update the configure-eda.sh script to install rootless docker for compute nodes.

Add playbook and script to configure users to run rootless docker.

Resolves #29

docs/containers.md

@@ -0,0 +1,109 @@
+# Containers
+
+Slurm supports [running jobs in unprivileged OCI containers](https://slurm.schedmd.com/containers.html).
+OCI is the [Open Container Initiative](https://opencontainers.org/), an open governance structure with the purpose of creating open industry standards around container formats and runtimes.
+
+I'm going to document how to add OCI support to your EDA Slurm cluster.
+Note that most EDA tools are not containerized and that some won't run in containers and that some may run in a container, but not correctly.
+I recommend following the guidance of your EDA vendor and consult with them.
+
+I've seen a couple of main motivations for using containers for EDA tools.
+The first is because orchestration tools like Kubernetes and AWS Batch require jobs to run in containers.
+The other is to have more flexibility managing the run time environment of the tools.
+Since the EDA tools themselves aren't containerized, the container is usually used to manage file system mounts and packages that are used by the tools.
+If new packages are required by a new tool, then it is easy to update and distribute a new version of the container.
+
+## Compute node configuration
+
+The compute node must be configured to use an unprivileged container runtime.
+We'll show how to install and configure rootless Docker.
+
+The following directions have been automated in the [creation of a custom EDA compute node AMI](custom-amis.md).
+
+First, [install the latest Docker from the Docker yum repo](https://docs.docker.com/engine/install/rhel/).
+
+Next, [configure Docker to run rootless](https://docs.docker.com/engine/security/rootless/).
+
+Configure subuid and subgid.
+
+Each user that will run Docker must have an entry in `/etc/subuid` and `/etc/subgid`.
+
+## Per user configuration
+
+You must configure docker to use a non-NFS storage location for storing images.
+
+`~/.config/docker/daemon.json`:
+
+```
+{
+    "data-root": "/var/tmp/${USER}/containers/storage"
+}
+```
+
+## Create OCI Bundle
+
+Each container requires an [OCI bundle](https://slurm.schedmd.com/containers.html#bundle).
+
+The bundle directories can be stored on NFS and shared between users.
+For example, you could create an oci-bundles directory on your shared file system.
+
+This shows how to create an ubuntu bundle.
+You can do this as root with the docker service running, but it would be better to run
+it using rootless Docker.
+
+```
+export OCI_BUNDLES_DIR=~/oci-bundles
+export IMAGE_NAME=ubuntu
+export BUNDLE_NAME=ubuntu
+mkdir -p $OCI_BUNDLES_DIR
+cd $OCI_BUNDLES_DIR
+mkdir -p $BUNDLE_NAME
+cd $BUNDLE_NAME
+docker pull $IMAGE_NAME
+docker export $(docker create $IMAGE_NAME) > $BUNDLE_NAME.tar
+mkdir rootfs
+tar -C rootfs -xf $IMAGE_NAME.tar
+runc spec --rootless
+runc run containerid
+```
+
+The same process works for Rocky Linux 8.
+
+```
+export OCI_BUNDLES_DIR=~/oci-bundles
+export IMAGE_NAME=rockylinux:8
+export BUNDLE_NAME=rockylinux8
+mkdir -p $OCI_BUNDLES_DIR
+cd $OCI_BUNDLES_DIR
+mkdir -p $BUNDLE_NAME
+cd $BUNDLE_NAME
+docker pull $IMAGE_NAME
+docker export $(docker create $IMAGE_NAME) > $BUNDLE_NAME.tar
+mkdir rootfs
+tar -C rootfs -xf $BUNDLE_NAME.tar
+runc spec --rootless
+runc run containerid2
+```
+
+## Test the bundle locally
+
+```
+export OCI_BUNDLES_DIR=~/oci-bundles
+export BUNDLE_NAME=rockylinux8
+cd $OCI_BUNDLES_DIR/$BUNDLE_NAME
+runc spec --rootless
+runc run containerid2
+```
+
+## Run a bundle on Slurm
+
+```
+export OCI_BUNDLES_DIR=~/oci-bundles
+export BUNDLE_NAME=rockylinux8
+
+srun -p interactive --container $OCI_BUNDLES_DIR/$BUNDLE_NAME --pty hostname
+
+srun -p interactive --container $OCI_BUNDLES_DIR/$BUNDLE_NAME --pty bash
+
+sbatch -p interactive --container $OCI_BUNDLES_DIR/$BUNDLE_NAME --wrap hostname
+```

mkdocs.yml

@@ -15,6 +15,7 @@ nav:
   - 'job_preemption.md'
   - 'rest_api.md'
   - 'onprem.md'
+  - 'containers.md'
  # - 'federation.md'
   - 'delete-cluster.md'
  # - 'implementation.md'

source/cdk/cdk_slurm_stack.py

@@ -1199,11 +1199,13 @@ def create_parallel_cluster_assets(self):
         # Additions or deletions to the list should be reflected in config_scripts in on_head_node_start.sh.
         files_to_upload = [
             'config/bin/configure-eda.sh',
+            'config/bin/configure-rootless-docker.sh',
             'config/bin/create_or_update_users_groups_json.sh',
             'config/bin/create_users_groups_json.py',
             'config/bin/create_users_groups_json_configure.sh',
             'config/bin/create_users_groups_json_deconfigure.sh',
             'config/bin/create_users_groups.py',
+            'config/bin/install-rootless-docker.sh',
             'config/bin/on_head_node_start.sh',
             'config/bin/on_head_node_configured.sh',
             'config/bin/on_head_node_updated.sh',
@@ -1477,6 +1479,7 @@ def create_parallel_cluster_lambdas(self):
                 'ConfigureEdaScriptS3Url': self.custom_action_s3_urls['config/bin/configure-eda.sh'],
                 'ErrorSnsTopicArn': self.config.get('ErrorSnsTopicArn', ''),
                 'ImageBuilderSecurityGroupId': self.imagebuilder_sg.security_group_id,
+                'InstallDockerScriptS3Url': self.custom_action_s3_urls['config/bin/install-rootless-docker.sh'],
                 'ParallelClusterVersion': self.config['slurm']['ParallelClusterConfig']['Version'],
                 'Region': self.cluster_region,
                 'SubnetId': self.config['SubnetId'],

source/resources/lambdas/CreateBuildFiles/CreateBuildFiles.py

@@ -217,6 +217,23 @@ def lambda_handler(event, context):
                             Body   = build_file_content
                         )
 
+                    # Image with rootless Docker installed
+                    template_vars['ImageName'] = f"parallelcluster-{parallelcluster_version_name}-docker-{distribution}-{version}-{architecture}".replace('_', '-')
+                    template_vars['ComponentS3Url'] = environ['InstallDockerScriptS3Url']
+                    build_file_s3_key = f"{assets_base_key}/config/build-files/{template_vars['ImageName']}.yml"
+                    if requestType == 'Delete':
+                        response = s3_client.delete_object(
+                            Bucket = assets_bucket,
+                            Key    = build_file_s3_key
+                        )
+                    else:
+                        build_file_content = build_file_template.render(**template_vars)
+                        s3_client.put_object(
+                            Bucket = assets_bucket,
+                            Key    = build_file_s3_key,
+                            Body   = build_file_content
+                        )
+
                     # Image with EDA packages
                     template_vars['ImageName'] = f"parallelcluster-{parallelcluster_version_name}-eda-{distribution}-{version}-{architecture}".replace('_', '-')
                     template_vars['ComponentS3Url'] = environ['ConfigureEdaScriptS3Url']

source/resources/parallel-cluster/config/bin/configure-eda.sh

@@ -88,4 +88,6 @@ ansible-playbook $PLAYBOOKS_PATH/eda_tools.yml \
     -i inventories/local.yml \
     -e @$ANSIBLE_PATH/ansible_head_node_vars.yml
 
-popd
+ansible-playbook $PLAYBOOKS_PATH/install-rootless-docker.yml \
+    -i inventories/local.yml \
+    -e @$ANSIBLE_PATH/ansible_head_node_vars.yml

source/resources/parallel-cluster/config/bin/configure-rootless-docker.sh

@@ -0,0 +1,86 @@
+#!/bin/bash -ex
+# Copyright Amazon.com, Inc. or its affiliates. All Rights Reserved.
+# SPDX-License-Identifier: MIT-0
+
+# Configure rootless docker for user.
+# The slurm config directory must exist
+
+script=$0
+script_name=$(basename $script)
+
+# Jinja2 template variables
+assets_bucket={{assets_bucket}}
+assets_base_key={{assets_base_key}}
+export AWS_DEFAULT_REGION={{Region}}
+ClusterName={{ClusterName}}
+ErrorSnsTopicArn={{ErrorSnsTopicArn}}
+playbooks_s3_url={{playbooks_s3_url}}
+
+# Notify user of errors
+function on_exit {
+    rc=$?
+    set +e
+    if [[ $rc -ne 0 ]] && [[ ":$ErrorSnsTopicArn" != ":" ]]; then
+        tmpfile=$(mktemp)
+        echo "See log files for more info:
+    /var/lib/amazon/toe/TOE_*
+    grep PCImageBuilderEDA /var/log/messages | less" > $tmpfile
+        aws --region $AWS_DEFAULT_REGION sns publish --topic-arn $ErrorSnsTopicArn --subject "${ClusterName} configure-rootless-docker.sh failed" --message file://$tmpfile
+        rm $tmpfile
+    fi
+}
+trap on_exit EXIT
+
+# Redirect all IO to /var/log/messages and then echo to stderr
+exec 1> >(logger -s -t configure-rootless-docker) 2>&1
+
+# Install ansible
+if ! yum list installed ansible &> /dev/null; then
+    yum install -y ansible || amazon-linux-extras install -y ansible2
+fi
+
+external_login_node_config_dir=/opt/slurm/${ClusterName}/config
+if [ -e $external_login_node_config_dir ]; then
+    config_dir=$external_login_node_config_dir
+else
+    config_dir=/opt/slurm/config
+fi
+config_bin_dir=$config_dir/bin
+ANSIBLE_PATH=$config_dir/ansible
+PLAYBOOKS_PATH=$ANSIBLE_PATH/playbooks
+PLAYBOOKS_ZIP_PATH=$ANSIBLE_PATH/playbooks.zip
+
+if ! [ -e $external_login_node_config_dir ]; then
+    mkdir -p $config_bin_dir
+
+    ansible_head_node_vars_yml_s3_url="s3://$assets_bucket/$assets_base_key/config/ansible/ansible_head_node_vars.yml"
+    ansible_compute_node_vars_yml_s3_url="s3://$assets_bucket/$assets_base_key/config/ansible/ansible_compute_node_vars.yml"
+    ansible_external_login_node_vars_yml_s3_url="s3://$assets_bucket/$assets_base_key/config/ansible/ansible_external_login_node_vars.yml"
+
+    # Download ansible playbooks
+    aws s3 cp $playbooks_s3_url ${PLAYBOOKS_ZIP_PATH}.new
+    if ! [ -e $PLAYBOOKS_ZIP_PATH ] || ! diff -q $PLAYBOOKS_ZIP_PATH ${PLAYBOOKS_ZIP_PATH}.new; then
+        mv $PLAYBOOKS_ZIP_PATH.new $PLAYBOOKS_ZIP_PATH
+        rm -rf $PLAYBOOKS_PATH
+        mkdir -p $PLAYBOOKS_PATH
+        pushd $PLAYBOOKS_PATH
+        yum -y install unzip
+        unzip $PLAYBOOKS_ZIP_PATH
+        chmod -R 0700 $ANSIBLE_PATH
+        popd
+    fi
+
+    aws s3 cp $ansible_head_node_vars_yml_s3_url /opt/slurm/config/ansible/ansible_head_node_vars.yml
+
+    aws s3 cp $ansible_compute_node_vars_yml_s3_url /opt/slurm/config/ansible/ansible_compute_node_vars.yml
+
+    aws s3 cp $ansible_external_login_node_vars_yml_s3_url /opt/slurm/config/ansible/ansible_external_login_node_vars.yml
+fi
+
+pushd $PLAYBOOKS_PATH
+
+ansible-playbook $PLAYBOOKS_PATH/configure-rootless-docker.yml \
+    -i inventories/local.yml \
+    -e @$ANSIBLE_PATH/ansible_external_login_node_vars.yml
+
+popd

source/resources/parallel-cluster/config/bin/install-rootless-docker.sh

@@ -0,0 +1,91 @@
+#!/bin/bash -ex
+# Copyright Amazon.com, Inc. or its affiliates. All Rights Reserved.
+# SPDX-License-Identifier: MIT-0
+
+# This script calls an ansible playbook that installs rootless docker on a compute node.
+# It has 2 different use cases:
+#   * To build ParallelCluster AMIs
+#   * To install docker on VDIs or other login nodes using a ParallellCluster.
+# The location of the config directory is different for those 2 use cases.
+# For an AMI build, the config directory and scripts will not exist and must be downloaded from S3.
+# For a login node, the playbooks and scripts will already exist.
+
+script=$0
+script_name=$(basename $script)
+
+# Jinja2 template variables
+assets_bucket={{assets_bucket}}
+assets_base_key={{assets_base_key}}
+export AWS_DEFAULT_REGION={{Region}}
+ClusterName={{ClusterName}}
+ErrorSnsTopicArn={{ErrorSnsTopicArn}}
+playbooks_s3_url={{playbooks_s3_url}}
+
+# Notify user of errors
+function on_exit {
+    rc=$?
+    set +e
+    if [[ $rc -ne 0 ]] && [[ ":$ErrorSnsTopicArn" != ":" ]]; then
+        tmpfile=$(mktemp)
+        echo "See log files for more info:
+    /var/lib/amazon/toe/TOE_*
+    grep PCImageBuilderEDA /var/log/messages | less" > $tmpfile
+        aws --region $AWS_DEFAULT_REGION sns publish --topic-arn $ErrorSnsTopicArn --subject "${ClusterName} install-rootless-docker.sh failed" --message file://$tmpfile
+        rm $tmpfile
+    fi
+}
+trap on_exit EXIT
+
+# Redirect all IO to /var/log/messages and then echo to stderr
+exec 1> >(logger -s -t install-rootless-docker) 2>&1
+
+# Install ansible
+if ! yum list installed ansible &> /dev/null; then
+    yum install -y ansible || amazon-linux-extras install -y ansible2
+fi
+
+external_login_node_config_dir=/opt/slurm/${ClusterName}/config
+if [ -e $external_login_node_config_dir ]; then
+    config_dir=$external_login_node_config_dir
+else
+    config_dir=/opt/slurm/config
+fi
+config_bin_dir=$config_dir/bin
+ANSIBLE_PATH=$config_dir/ansible
+PLAYBOOKS_PATH=$ANSIBLE_PATH/playbooks
+PLAYBOOKS_ZIP_PATH=$ANSIBLE_PATH/playbooks.zip
+
+if ! [ -e $external_login_node_config_dir ]; then
+    mkdir -p $config_bin_dir
+
+    ansible_head_node_vars_yml_s3_url="s3://$assets_bucket/$assets_base_key/config/ansible/ansible_head_node_vars.yml"
+    ansible_compute_node_vars_yml_s3_url="s3://$assets_bucket/$assets_base_key/config/ansible/ansible_compute_node_vars.yml"
+    ansible_external_login_node_vars_yml_s3_url="s3://$assets_bucket/$assets_base_key/config/ansible/ansible_external_login_node_vars.yml"
+
+    # Download ansible playbooks
+    aws s3 cp $playbooks_s3_url ${PLAYBOOKS_ZIP_PATH}.new
+    if ! [ -e $PLAYBOOKS_ZIP_PATH ] || ! diff -q $PLAYBOOKS_ZIP_PATH ${PLAYBOOKS_ZIP_PATH}.new; then
+        mv $PLAYBOOKS_ZIP_PATH.new $PLAYBOOKS_ZIP_PATH
+        rm -rf $PLAYBOOKS_PATH
+        mkdir -p $PLAYBOOKS_PATH
+        pushd $PLAYBOOKS_PATH
+        yum -y install unzip
+        unzip $PLAYBOOKS_ZIP_PATH
+        chmod -R 0700 $ANSIBLE_PATH
+        popd
+    fi
+
+    aws s3 cp $ansible_head_node_vars_yml_s3_url /opt/slurm/config/ansible/ansible_head_node_vars.yml
+
+    aws s3 cp $ansible_compute_node_vars_yml_s3_url /opt/slurm/config/ansible/ansible_compute_node_vars.yml
+
+    aws s3 cp $ansible_external_login_node_vars_yml_s3_url /opt/slurm/config/ansible/ansible_external_login_node_vars.yml
+fi
+
+pushd $PLAYBOOKS_PATH
+
+ansible-playbook $PLAYBOOKS_PATH/install-rootless-docker.yml \
+    -i inventories/local.yml \
+    -e @$ANSIBLE_PATH/ansible_compute_node_vars.yml
+
+popd

source/resources/parallel-cluster/config/bin/on_head_node_start.sh

@@ -64,11 +64,13 @@ users_groups_json_s3_url="s3://$assets_bucket/$assets_base_key/config/users_grou
 # Download all of the config scripts
 config_scripts=(\
     configure-eda.sh \
+    configure-rootless-docker.sh \
     create_or_update_users_groups_json.sh \
     create_users_groups_json.py \
     create_users_groups_json_configure.sh \
     create_users_groups_json_deconfigure.sh \
     create_users_groups.py \
+    install-rootless-docker.sh \
     on_head_node_start.sh \
     on_head_node_configured.sh \
     on_head_node_updated.sh \

source/resources/playbooks/ParallelClusterComputeNode.yml

@@ -10,3 +10,4 @@
     - security_updates
     - bug_fixes
     - ParallelClusterComputeNode
+    - install-rootless-docker

source/resources/playbooks/configure-rootless-docker.yml

@@ -0,0 +1,8 @@
+---
+- name: Configure rootless docker for user
+  hosts:
+    - ExternalLoginNode
+  become_user: root
+  become: yes
+  roles:
+    - configure-rootless-docker

source/resources/playbooks/install-rootless-docker.yml

@@ -0,0 +1,8 @@
+---
+- name: Install rootless docker for OCI containers
+  hosts:
+    - ParallelClusterComputeNode
+  become_user: root
+  become: yes
+  roles:
+    - install-rootless-docker

source/resources/playbooks/roles/ParallelClusterHeadNode/files/opt/slurm/etc/oci.conf

@@ -0,0 +1,6 @@
+EnvExclude="^(SLURM_CONF|SLURM_CONF_SERVER)="
+RunTimeEnvExclude="^(SLURM_CONF|SLURM_CONF_SERVER)="
+RunTimeQuery="runc --rootless=true --root=/run/user/%U/ state %n.%u.%j.%s.%t"
+RunTimeKill="runc --rootless=true --root=/run/user/%U/ kill -a %n.%u.%j.%s.%t"
+RunTimeDelete="runc --rootless=true --root=/run/user/%U/ delete --force %n.%u.%j.%s.%t"
+RunTimeRun="runc --rootless=true --root=/run/user/%U/ run %n.%u.%j.%s.%t -b