Merge pull request #3748 from LBNL-UCB-STI/inm/gcp-running-jupyter-bu…

…gfix GCP: running jupyter bugfixes
LBNL-UCB-STI · May 10, 2023 · 910538e · 910538e
2 parents 9dcf153 + d650b3c
commit 910538e
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Showing 3 changed files with 23 additions and 13 deletions.
diff --git a/gcp/build.gradle b/gcp/build.gradle
@@ -68,7 +68,7 @@ tasks.register('deployToGCE') {
 }
 
 tasks.register("jupyterGCE") {
-    doLast {
+    doFirst {
         project.ext."runJupyter" = "true"
         project.ext."runBeam" = "false"
         project.ext."beamConfigs" = ""
@@ -88,11 +88,11 @@ tasks.register("jupyterGCE") {
         if (!project.hasProperty("shutdownBehaviour")) {
             project.ext."shutdownBehaviour" = "stop"
         }
-
-        dependsOn ':gcp:deployToGCE'
     }
 }
 
+jupyterGCE.finalizedBy(deployToGCE)
+
 static HttpResponse makeJsonPostRequest(String functionUrl, String requestBody) {
     GoogleCredentials credentials = GoogleCredentials.getApplicationDefault();
     IdTokenCredentials tokenCredential =

diff --git a/gcp/src/main/bash/cloud-init.sh b/gcp/src/main/bash/cloud-init.sh
@@ -123,36 +123,39 @@ EOF
 echo "$start_json"
 curl -X POST "https://ca4ircx74d.execute-api.us-east-2.amazonaws.com/production/spreadsheet" -H "Content-Type:application/json" --data "$start_json"
 
+set -x
+
 ./gradlew assemble
 
 if [ "${RUN_JUPYTER,,}" = "true" ]; then
-
+  echo "Running Jupyter"
   export GOOGLE_API_KEY="$GOOGLE_API_KEY"
 
-  set -x
   if [ -n "$JUPYTER_TOKEN" ] && [ -n "$JUPYTER_IMAGE" ]
-  then sudo ./gradlew jupyterStart -Puser=root -PjupyterToken="$JUPYTER_TOKEN" -PjupyterImage="$JUPYTER_IMAGE"
+  then ./gradlew jupyterStart -Puser=root -PjupyterToken="$JUPYTER_TOKEN" -PjupyterImage="$JUPYTER_IMAGE"
   elif [ -n "$JUPYTER_TOKEN" ]
-  then sudo ./gradlew jupyterStart -Puser=root -PjupyterToken="$JUPYTER_TOKEN"
+  then ./gradlew jupyterStart -Puser=root -PjupyterToken="$JUPYTER_TOKEN"
   elif [ -n "$JUPYTER_IMAGE" ]
-  then sudo ./gradlew jupyterStart -Puser=root -PjupyterImage="$JUPYTER_IMAGE"
-  else sudo ./gradlew jupyterStart -Puser=root
+  then ./gradlew jupyterStart -Puser=root -PjupyterImage="$JUPYTER_IMAGE"
+  else ./gradlew jupyterStart -Puser=root
   fi
-  set +x
 
+  # somehow there are not enough permissions for gradle lock file if jupyter was run before
+  sudo chmod -R 777 .
 else
   echo "NOT going to start jupyter. [RUN_JUPYTER ('${RUN_JUPYTER,,}') not equal to 'true']"
 fi
 
-
 if [ "${RUN_BEAM,,}" = "true" ]; then
   echo "Running BEAM"
   export GOOGLE_API_KEY="$GOOGLE_API_KEY"
+
   ./gradlew --stacktrace :run -PappArgs="['--config', '$BEAM_CONFIG']" -PmaxRAM="$MAX_RAM"g
 else
   echo "NOT going to start BEAM. [RUN_BEAM ('${RUN_BEAM,,}') not equal to 'true']"
 fi
 
+set +x
 
 # copy to bucket
 storage_url=""
@@ -194,16 +197,22 @@ if [ -d "$finalPath" ]; then
       health_metrics="$health_metrics, $metric:$count"
     done < $simulation_health_analysis_output_file
     health_metrics="{$(echo "$health_metrics" | cut -c3-)}"
-    echo "$health_metrics"
+    echo "Health Metrics: $health_metrics"
     if [ "${STORAGE_PUBLISH,,}" != "false" ]; then
       gsutil cp "$simulation_health_analysis_output_file" "gs://beam-core-outputs/$finalPath/$simulation_health_analysis_output_file"
     fi
     curl -H "Authorization:Bearer $SLACK_TOKEN" -F file=@$simulation_health_analysis_output_file -F initial_comment="Beam Health Analysis" -F channels="$SLACK_CHANNEL" "https://slack.com/api/files.upload"
 fi
 
 
+if [ "${RUN_BEAM,,}" != "true" ] && [ "${RUN_JUPYTER,,}" = "true" ]; then
+  final_status="Jupyter Instance"
+else
+  final_status=$(check_simulation_result)
+fi
+
+
 #Slack message
-final_status=$(check_simulation_result)
 bye_msg=$(cat <<EOF
 Run Completed
 Run Name **$RUN_NAME**

diff --git a/gcp/src/main/python/deploy_beam/main.py b/gcp/src/main/python/deploy_beam/main.py
@@ -93,6 +93,7 @@ def create_beam_instance(request):
     startup_script = """
 #!/bin/sh
 CLOUD_INIT_SCRIPT_URL=$(curl http://metadata/computeMetadata/v1/instance/attributes/cloud_init_script_url -H "Metadata-Flavor: Google")
+sudo chown -R clu:clu /home/clu
 sudo -u clu bash -c "cd; wget $CLOUD_INIT_SCRIPT_URL"
 sudo -u clu bash -c "cd; chmod 755 cloud-init.sh"
 sudo -u clu bash -c "cd; ./cloud-init.sh &> cloud-init-output.log"