WIP sample slurm script for batch execution

Author: danv61

vcell-server/src/test/java/cbit/vcell/message/server/htc/slurm/SlurmProxyTest.java

@@ -139,7 +139,35 @@ public String createScriptForNativeSolvers(String simTaskResourcePath, String[]
 
 	public String createScriptForNativeSolversBatch(String simTaskResourcePath, String[] command, String JOB_NAME) throws IOException, XmlParseException, ExpressionException {
 
-		return null;
+		SimulationTask simTask = XmlHelper.XMLToSimTask(readTextFileFromResource(simTaskResourcePath));
+		KeyValue simKey = simTask.getSimKey();
+
+		SlurmProxy slurmProxy = new SlurmProxy(null, "vcell");
+		File subFileExternal = new File("/share/apps/vcell3/htclogs/V_REL_"+simKey+"_0_0.slurm.sub");
+
+		User simOwner = simTask.getSimulation().getVersion().getOwner();
+		final int jobId = simTask.getSimulationJob().getJobIndex();
+
+
+		// TODO: fill here with stuff
+
+
+		String args = null;		// dummy code, replace once we know
+		ExecutableCommand preprocessorCmd = new ExecutableCommand(null, false, false, args);
+		ExecutableCommand solverCmd = new ExecutableCommand(null, false, false, args);
+		ExecutableCommand postprocessorCmd = new ExecutableCommand(null, false, false, args);
+
+		// TODO: more stuff
+
+		ExecutableCommand.Container commandSet = new ExecutableCommand.Container();
+		commandSet.add(preprocessorCmd);
+		commandSet.add(solverCmd);
+		commandSet.add(postprocessorCmd);
+
+		int NUM_CPUs = 1;
+		int MEM_SIZE_MB = 1000;
+		ArrayList<PortableCommand> postProcessingCommands = new ArrayList<>();
+		return slurmProxy.createJobScriptText(JOB_NAME, commandSet, NUM_CPUs, MEM_SIZE_MB, postProcessingCommands, simTask);
 	}
 
 	public String createScriptForJavaSolvers(String simTaskResourcePath, String JOB_NAME) throws IOException, XmlParseException, ExpressionException {
@@ -261,11 +289,17 @@ public void testSimJobScriptLangevin() throws IOException, XmlParseException, Ex
 
 	@Test
 	public void testSimJobScriptLangevinBatch() throws IOException, XmlParseException, ExpressionException {
-
 		String simTaskResourcePath = "slurm_fixtures/langevin/SimID_999999999_0__0.simtask.xml";
 		String JOB_NAME = "V_REL_999999999_0_0";
 
 
+		// TODO: fill here with stuff
+
+
+		String[] command = null;	// dummy to avoid compiler error for "command" variable below
+		String slurmScript = createScriptForNativeSolversBatch(simTaskResourcePath, command, JOB_NAME);
+		String expectedSlurmScript = readTextFileFromResource("slurm_fixtures/langevin/V_REL_999999999_0_0.slurm.sub");
+		Assertions.assertEquals(expectedSlurmScript.trim(), slurmScript.trim());
 	}
 
 

vcell-server/src/test/resources/slurm_fixtures/langevin/V_REL_274672135_0_0.slurm.sub

@@ -44,9 +44,9 @@ container_env+="--env secondary_datadir_external=/share/apps/vcell7/users "
 container_env+="--env htclogdir_external=/share/apps/vcell3/htclogs "
 container_env+="--env softwareVersion=Rel_Version_7.6.0_build_28 "
 container_env+="--env serverid=REL "
-solver_docker_name=ghcr.io/virtualcell/vcell-batch:7.6.0.43
+solver_docker_name=ghcr.io/virtualcell/vcell-batch:7.6.0.43   # should be latest, like 7.7.0.27
 solver_container_prefix="singularity run --containall ${container_bindings} ${container_env} docker://${solver_docker_name}"
-batch_docker_name=ghcr.io/virtualcell/vcell-batch:7.6.0.43
+batch_docker_name=ghcr.io/virtualcell/vcell-batch:7.6.0.43    # 7.7.0.27 or latest
 batch_container_prefix="singularity run --containall ${container_bindings} ${container_env} docker://${batch_docker_name}"