-ignis-export and ignis-export scripts for copying IgnisHPC out of co…

…ntainer

-ignis-submit can now run outside of the submitter container
-future implementation of udocker has been dropper from slurm
-new slurm dockerfile to extract ignis-slurm from a container
-docker scheduler important fixes

Dockerfiles/driver-builder/Dockerfile

@@ -14,7 +14,7 @@ RUN export DEBIAN_FRONTEND=noninteractive && \
 
 ENV GRADLE_VERSION=7.2
 RUN \
-	mkdir -p /tmp/gradle && \ 
+	mkdir -p /tmp/gradle && \
 	cd /tmp/gradle && \
 	wget https://services.gradle.org/distributions/gradle-${GRADLE_VERSION}-bin.zip -O src.zip && \
 	unzip src && \
@@ -38,4 +38,8 @@ RUN mkdir ${IGNIS_HOME}/lib/java && \
 	rm -fr /tmp/backend
 
 COPY ${RELPATH}driver-install.sh ${IGNIS_HOME}/common
-RUN chmod +x ${IGNIS_HOME}/common/driver-install.sh 
+COPY ${RELPATH}ignis-export ${IGNIS_HOME}/bin
+COPY ${RELPATH}ignis-export-all ${IGNIS_HOME}/bin
+RUN chmod +x ${IGNIS_HOME}/common/driver-install.sh && \
+    chmod +x ${IGNIS_HOME}/bin/ignis-export && \
+    chmod +x ${IGNIS_HOME}/bin/ignis-export-all

Dockerfiles/driver-builder/ignis-export

@@ -0,0 +1,13 @@
+#!/bin/bash
+
+if [ $# -ne 1 ]
+    then echo "usage ignis-export <out-folder>"
+    exit
+fi
+
+cd "$1"
+mkdir -p ignis/lib
+cp -R ${IGNIS_HOME}/bin ignis/
+cp -R ${IGNIS_HOME}/etc ignis/
+cp -R  ${IGNIS_HOME}/backend ignis/
+cp -R ${IGNIS_HOME}/lib/java ignis/lib/

Dockerfiles/driver-builder/ignis-export-all

@@ -0,0 +1,10 @@
+#!/bin/bash
+
+if [ $# -ne 1 ]
+    then echo "usage ignis-export-all <out-folder>"
+    exit
+fi
+
+cd "$1"
+mkdir -p ignis
+cp -R ${IGNIS_HOME}/* ignis/

Dockerfiles/slurm-submitter/Dockerfile

@@ -0,0 +1,9 @@
+
+ARG REGISTRY=""
+ARG NAMESPACE="ignishpc/"
+ARG TAG=""
+FROM ${REGISTRY}${NAMESPACE}common${TAG}
+ARG RELPATH=""
+
+COPY ${RELPATH}ignis-slurm ${IGNIS_HOME}/bin
+RUN chmod +x ${IGNIS_HOME}/bin/ignis-slurm

Dockerfiles/slurm-submitter/ignis-slurm

@@ -0,0 +1,7 @@
+#!/bin/bash
+#script is inside IGNIS_HOME so if it is not set, we can discover it.
+if [[ -z "${IGNIS_HOME}" ]]; then
+  export IGNIS_HOME=$(builtin cd $(dirname "$0"); cd ..; pwd)
+fi
+
+exec ${IGNIS_HOME}/backend/jre/bin/java -cp "${IGNIS_HOME}/lib/java/*" org.ignis.submitter.SlurmSubmit "$@"

Dockerfiles/submitter/Dockerfile

@@ -7,13 +7,12 @@ ARG RELPATH=""
 
 RUN ${IGNIS_HOME}/common/driver-install.sh && \
 	rm -fR ${IGNIS_HOME}/common && \
-	rm -f ${IGNIS_HOME}/bin/* && \
 	export DEBIAN_FRONTEND=noninteractive && \
 	apt update && \
 	apt install -y --no-install-recommends \
 		git \
 		wget \
-		unzip \ 
+		unzip \
 		python3 \
 		python3-distutils && \
 	rm -rf /var/lib/apt/lists/* && \

Dockerfiles/submitter/ignis-submit

@@ -1,2 +1,7 @@
 #!/bin/bash
+#script is inside IGNIS_HOME so if it is not set, we can discover it.
+if [[ -z "${IGNIS_HOME}" ]]; then
+  export IGNIS_HOME=$(builtin cd $(dirname "$0"); cd ..; pwd)
+fi
+
 exec ${IGNIS_HOME}/backend/jre/bin/java -cp "${IGNIS_HOME}/lib/java/*" org.ignis.submitter.Submit "$@"

backend/src/main/java/org/ignis/backend/Main.java

@@ -48,6 +48,7 @@ public static void main(String[] args) {
 
         LOGGER.info("Loading environment variables");
         props.fromEnv(System.getenv());
+        String home = props.getString(IKeys.HOME);
 
         if (props.contains(IKeys.OPTIONS)) {//Submit user options
             try {
@@ -57,6 +58,8 @@ public static void main(String[] args) {
             }
             props.rmProperty(IKeys.OPTIONS);
         }
+        //Submitter home may be different so we ignore it.
+        props.setProperty(IKeys.HOME, home);
 
         LOGGER.info("Loading configuration file");
         try {

backend/src/main/java/org/ignis/backend/cluster/IExecutor.java

@@ -28,7 +28,10 @@
 import org.ignis.rpc.executor.*;
 import org.ignis.scheduler.model.IPort;
 
-import java.util.*;
+import java.util.HashMap;
+import java.util.HashSet;
+import java.util.Map;
+import java.util.Set;
 
 /**
  * @author César Pomar

backend/src/main/java/org/ignis/backend/cluster/tasks/container/IContainerCreateTask.java

@@ -128,6 +128,7 @@ public void run(ITaskContext context) throws IgnisException {
                         try {
                             scheduler.destroyExecutorInstances(stopped);
                         } catch (ISchedulerException ex) {
+                            LOGGER.warn(log() + ex);
                         }
                     } else {
                         for (int i = 0; i < stoppedIndex.size(); i++) {

backend/src/main/java/org/ignis/backend/cluster/tasks/executor/IExecutorDestroyTask.java

@@ -50,7 +50,7 @@ public void run(ITaskContext context) throws IgnisException {
                     "; do sleep 1; done\" || kill -9 " + executor.getPid();
             executor.getContainer().getTunnel().execute(killScript, false);
         } catch (IgnisException ex) {
-            LOGGER.warn(log() + ex.toString());
+            LOGGER.warn(log() + ex);
         }
         executor.setPid(-1);
         LOGGER.info(log() + "Executor destroyed");

etc/ignis.conf

@@ -10,7 +10,7 @@ ignis.debug=false
 #ignis.job.worker=
 #DFS
 #ignis.dfs.id=
-#ignis.dfs.home=
+ignis.dfs.home=/media/dfs
 #SCHEDULER
 #ignis.scheduler.url=
 #ignis.scheduler.type=