Set up read-only container image store on NFS

src/Dockerfile

@@ -11,3 +11,8 @@ RUN groupadd -g $GID $HOST_USER && adduser --gid $GID -u $UID --gecos "" \
   --disabled-password $HOST_USER && \
 adduser $HOST_USER sudo && groupadd -g 1338 docker && adduser $HOST_USER docker && \
 ssed -i '/^%sudo/s/ALL$/NOPASSWD:ALL/' /etc/sudoers
+
+# Update containerimages.conf in case of the file is modified manually.
+# On slurm worker, they should be same. On controller, it might be different if user adds new images to the conf file before running setup.sh.
+RUN rm /usr/local/share/slurm_gcp_docker/src/containerimages.conf
+COPY containerimages.conf /usr/local/share/slurm_gcp_docker/src/

src/containerimages.conf

@@ -0,0 +1,7 @@
+
+## List of images to be pulled to /mnt/nfs/clust_containers. Start line with "=".
+
+=gcr.io/broad-getzlab-workflows/cga_production_pipeline:v0.1
+=gcr.io/broad-getzlab-workflows/base_image
+=chipstewart/pcawg_full:3
+

src/prefect_config.toml

@@ -0,0 +1,12 @@
+
+## This file will be read when prefect is imported
+
+additionalimagestores = ["/mnt/nfs/clust_containers"]
+backend = "server"
+
+# output_dir_stem = "/mnt/nfs/workspace"
+# use_podman = true
+#
+# [canine_backend_conf]
+# type = "LocalDocker"
+

src/provision_server.py

@@ -80,7 +80,7 @@ def print_conf(D, path):
 	# Slurm conf. file cgroup.conf and boto conf can be copied-as is
 	# (other conf. files will need editing below)
 	subprocess.check_call(
-	  "cp {CPR}/conf/cgroup.conf /mnt/nfs/clust_conf/slurm; cp {CPR}/conf/boto.conf /mnt/nfs/clust_conf/misc".format(
+	  "cp {CPR}/conf/cgroup.conf /mnt/nfs/clust_conf/slurm; cp {CPR}/conf/boto.conf /mnt/nfs/clust_conf/misc; cp {CPR}/src/containerimages.conf /mnt/nfs/clust_conf/misc/containerimages.conf".format(
 	    CPR = shlex.quote(CLUST_PROV_ROOT)
 	  ),
 	  shell = True
@@ -144,6 +144,13 @@ def print_conf(D, path):
 
 	print_conf(C, "/mnt/nfs/clust_conf/slurm/slurmdbd.conf")
 
+        #
+        # Pull readonly container images. If those images already exist, it should be fast.
+        subprocess.check_call("""
+            cat /mnt/nfs/clust_conf/misc/containerimages.conf | grep '^=' | sed 's/^=//' | xargs -L1 sudo podman --root /mnt/nfs/clust_containers pull
+            """, shell=True, executable = '/bin/bash'
+        )
+
 	#
 	# start Slurm controller
 	print("Checking for running Slurm controller ... ")

src/setup.sh

@@ -13,6 +13,10 @@ IVERSION=$(tr . - <<< $VERSION)
 
 ./generate_container_host_image.py -i slurm-gcp-docker-${IVERSION}-`git rev-parse --short HEAD`-$USER
 
+# copy prefect config, this will be read by prefect when it is imported
+mkdir -p ~/.prefect
+cp prefect_config.toml ~/.prefect/config.toml
+
 sudo docker build -t broadinstitute/slurm_gcp_docker:$VERSION \
   -t broadinstitute/slurm_gcp_docker:latest \
   --build-arg HOST_USER=$USER --build-arg UID=$UID --build-arg GID=$(id -g) .