Kubernetes-native-launcher

.gitignore

@@ -15,3 +15,7 @@ volumes/
 *.key
 *.pem
 .jwks
+
+# Python
+__pycache__/
+*.pyc

front_end/Dockerfile

@@ -25,7 +25,7 @@ RUN apt-get update && apt-get install -y libmcrypt-dev \
     && docker-php-ext-install gd 
 
 RUN apt-get update && apt-get install gnupg curl
-RUN curl -fsSL https://www.mongodb.org/static/pgp/server-7.0.asc |gpg -o /usr/share/keyrings/mongodb-server-7.0.gpg --dearmor
+RUN curl -fsSL https://pgp.mongodb.com/server-7.0.asc | gpg -o /usr/share/keyrings/mongodb-server-7.0.gpg --dearmor
 RUN echo "deb [ signed-by=/usr/share/keyrings/mongodb-server-7.0.gpg ] http://repo.mongodb.org/apt/debian bookworm/mongodb-org/7.0 main" | tee /etc/apt/sources.list.d/mongodb-org-7.0.list
 RUN apt-get update
 RUN apt-get install -y mongodb-org
@@ -39,9 +39,7 @@ WORKDIR /var/www/html
 ADD openVRE /var/www/html/openVRE
 RUN cd openVRE
 WORKDIR /var/www/html/openVRE
-RUN curl -sS https://getcomposer.org/installer | php -- --install-dir=/usr/local/bin --filename=composer
-RUN composer self-update
-RUN composer update --ignore-platform-req=ext-mongodb --ignore-platform-req=ext-mongodb
+# Dependencies are pre-seeded in ./openVRE/vendor for offline/reproducible builds.
 RUN mkdir logs
 RUN touch logs/application.log
 RUN chmod -R 777 logs/application.log

front_end/openVRE/public/phplib/classes/Tooljob.php

@@ -98,6 +98,7 @@ public function __construct($tool, $execution = "", $project = "", $descrip = ""
 		switch ($this->launcher) {
 			case "SGE":
 			case "docker_SGE":
+			case "kubernetes_native":
 				$this->root_dir_virtual = $GLOBALS['clouds'][$this->cloudName]['dataDir_virtual'] . "/" . $_SESSION['User']['id'];
 				$this->root_dir_mug     = $GLOBALS['clouds'][$this->cloudName]['dataDir_virtual'];
 				$this->pub_dir_virtual  = $GLOBALS['clouds'][$this->cloudName]['pubDir_virtual'];
@@ -1116,6 +1117,19 @@ public function prepareExecution($tool, $metadata, $metadata_pub = [])
 
 					break;
 
+				case "kubernetes_native":
+					$cmd  = $this->setBashCmd_SGE($tool);
+					if (!$cmd) {
+						return 0;
+					}
+
+					$submissionFilename = $this->createSubmitFile_SGE($cmd);
+					if (!is_file($submissionFilename)) {
+						return 0;
+					}
+
+					break;
+
 				case "PMES":
 					$json_data = $this->setPMESrequest($tool);
 					if (!$json_data) {
@@ -1395,6 +1409,10 @@ protected function setBashCommandDockerSge($tool)
 				" --out_metadata "   . $this->stageout_file_virtual .
 				" --log_file "       . $this->log_file_virtual;
 
+			if (isset($this->launcher) && $this->launcher === "kubernetes_native") {
+				return $cmd_vre;
+			}
+
 
 			$cmd =  "docker run --privileged -v /var/run/docker.sock:/var/run/docker.sock -d" .
 				" " . $cmd_envs .
@@ -1788,6 +1806,7 @@ public function submit($tool)
 			case "SGE":
 			case "ega_demo":
 			case "docker_SGE":
+			case "kubernetes_native":
 				return $this->enqueue($tool);
 			case "Slurm_Singularity":
 				return $this->enqueue($tool);
@@ -1808,21 +1827,32 @@ protected function enqueue($tool)
 			return 0;
 		}
 		$jobManager = $launcherInfo['launcher']['job_manager'] 
-                  ?? $tool['infrastructure']['clouds'][$this->cloudName]['launcher'];
+                 ?? $tool['infrastructure']['clouds'][$this->cloudName]['launcher'];
 		$memory = $launcherInfo['memory'] ?? $tool['infrastructure']['memory'];
 		$cpus = $launcherInfo['cpus'] ?? $tool['infrastructure']['cpus'];
 		$queue = $launcherInfo['queue'] ?? $tool['infrastructure']['clouds'][$this->cloudName]['queue'];
-		// error_log("Resolved Parameters: Queue=$queue, CPUs=$cpus, Memory=$memory, jobManager=$jobManager");
+		$jobOptions = array();
+		if ($jobManager === "kubernetes_native") {
+			$jobOptions["image"] = $tool['infrastructure']['container_image'] ?? "";
+			if ($jobOptions["image"] === "") {
+				$_SESSION['errorData']['Error'][] = "Missing infrastructure.container_image for kubernetes_native launcher.";
+				return 0;
+			}
+			$jobOptions["env"] = array();
+			if (isset($tool['infrastructure']['container_env']) && is_array($tool['infrastructure']['container_env'])) {
+				foreach ($tool['infrastructure']['container_env'] as $env_key => $env_value) {
+					$jobOptions["env"][$env_key] = (string)$env_value;
+				}
+			}
+		}
 
-		list($pid, $errMesg) = execJob($this->working_dir, $this->submission_file, $queue, $cpus, $memory,  $this->stdout_file, $this->stderr_file, $jobManager);
+		list($pid, $errMesg) = execJob($this->working_dir, $this->submission_file, $queue, $cpus, $memory,  $this->stdout_file, $this->stderr_file, $jobManager, $this->toolId, $jobOptions);
 		if (!$pid) {
-			//error_log($pid, $errMesg, NULL, $this->toolId, $this->cloudName, "SGE", $cpus, $memory);
-			error_log("Error: $errMesg");
+			log_addError($pid, $errMesg, NULL, $this->toolId, $this->cloudName, $jobManager, $cpus, $memory);
 			$_SESSION['errorData']['Error'][] = "Internal error. Cannot enqueue job.";
 			return 0;
 		}
-		#logger("USER:" . $_SESSION['User']['_id'] . ", ID:" . $_SESSION['User']['id'] . ", LAUNCHER:SGE, TOOL:" . $this->toolId . ", PID:$pid");
-		//error_log("USER:" . $_SESSION['User']['_id'] . ", ID:" . $_SESSION['User']['id'] . ", LAUNCHER:SGE, TOOL:" . $this->toolId . ", PID:$pid");
+		logger("USER:" . $_SESSION['User']['_id'] . ", ID:" . $_SESSION['User']['id'] . ", LAUNCHER:" . $jobManager . ", TOOL:" . $this->toolId . ", PID:$pid");
 		log_addSubmission($pid, $this->toolId, $this->cloudName, $jobManager, $cpus, $memory, $this->working_dir);
 
 		$this->pid = $pid;

front_end/openVRE/public/phplib/processJob.inc.php

@@ -5,7 +5,7 @@
 #
 
 
-function execJob($workDir, $shFile, $queue, $cpus = 1, $mem = 0, $logFile = "job_output.log", $errFile = "job_error.log", $jobManager = "docker_SGE")
+function execJob($workDir, $shFile, $queue, $cpus = 1, $mem = 0, $logFile = "job_output.log", $errFile = "job_error.log", $jobManager = "docker_SGE", $toolId = "", $jobOptions = array())
 {
     logger("Start job submission via $jobManager");
     error_log("DEBUG- execJob: Start job submission via $jobManager");
@@ -33,15 +33,11 @@ function execJob($workDir, $shFile, $queue, $cpus = 1, $mem = 0, $logFile = "job
         $_SESSION['errorData']['Error'][] = "Queue not provided.";
         return [0, "Queue not provided."];
     }
-
+    
 
     $queue   = (isset($queue) ? $queue : $GLOBALS['queueTask']);
     $jobname = $_SESSION['User']['id'] . "#" . basename($shFile);
 
-    //
-    // Start SGE process
-    //$process = new ProcessSGE($shFile, $workDir, $queue, $jobname, $cpus, $mem, $logFile, $errFile);
-
     switch ($jobManager) {
         case "docker_SGE":
             error_log("DEBUG: Submitting job via docker_SGE. Parameters: shFile=$shFile, workDir=$workDir, queue=$queue, jobname=$jobname, cpus=$cpus, mem=$mem, logFile=$logFile, errFile=$errFile");
@@ -52,14 +48,31 @@ function execJob($workDir, $shFile, $queue, $cpus = 1, $mem = 0, $logFile = "job
             error_log("DEBUG: Submitting job via Slurm to $remote_system. Parameters: shFile=$shFile, workDir=$workDir, logFile=$logFile, errFile=$errFile");
             $process = new ProcessSlurm($shFile, $workDir, $logFile, $errFile, $remote_system);
             break;
+        case "kubernetes_native":
+            $schedUrl = getenv("OPENVRE_K8S_SCHEDULER_URL") ?: "";
+            $schedHost = $schedUrl !== ""
+                ? (string)(parse_url($schedUrl, PHP_URL_HOST) ?: "(parse_failed)")
+                : "(not_set)";
+            $k8sNs = getenv("OPENVRE_K8S_NAMESPACE") ?: "(env_unset)";
+            $jobOptKeys = is_array($jobOptions) && count($jobOptions)
+                ? implode(",", array_keys($jobOptions))
+                : "(none)";
+            error_log(
+                "DEBUG: Submitting job via kubernetes_native. Parameters: shFile=$shFile, workDir=$workDir, queue=$queue, "
+                . "jobname=$jobname, cpus=$cpus, mem=$mem, logFile=$logFile, errFile=$errFile, "
+                . "namespace=$k8sNs, scheduler_host=$schedHost, jobOptions_keys=$jobOptKeys"
+            );
+            require_once __DIR__ . "/classes/ProcessK8s.php";
+            $process = new ProcessK8s($shFile, $workDir, $queue, $jobname, $cpus, $mem, $logFile, $errFile, $jobOptions);
+            break;
         default:
             $process = new ProcessSGE($shFile, $workDir, $queue, $jobname, $cpus, $mem, $logFile, $errFile);
-            break;  
+            break;
     }
- 
+
     if (!$process->status()) {
         $_SESSION['errorData']['Error'][] = "Job submission failed.<br/>" . $process->getFullCommand() . "<br/>" . $process->getErr();
-        $errMesg = "ERROR: Job submission failed. FullCommand: '" . $process->getFullCommand() . "'. ErrorSGE: '" . $process->getErr() . "'";
+        $errMesg = "ERROR: Job submission failed. FullCommand: '" . $process->getFullCommand() . "'. ErrorDetail: '" . $process->getErr() . "'";
         logger($errMesg);
         return array(0, $errMesg);
     }
@@ -140,18 +153,30 @@ function getRunningJobInfo($pid, $launcherType = NULL, $cloudName = "local")
 
     // guess launcher
     if (!$launcherType) {
-        if (is_numeric($pid))
+        if (is_numeric($pid)) {
             $launcherType = "SGE";
-        else
+        } elseif (strpos((string)$pid, "-") !== false) {
+            $launcherType = "kubernetes_native";
+        } else {
             $launcherType = "PMES";
+        }
     }
-
     logger("getRunningJobInfo: launcherType = $launcherType");
 
     // create new jobProcess
     if ($launcherType == "SGE" || $launcherType == "docker_SGE") {
         $process = new ProcessSGE();
         $job = $process->getRunningJobInfo($pid);
+    } elseif ($launcherType == "kubernetes_native") {
+        require_once __DIR__ . "/classes/ProcessK8s.php";
+        $process = new ProcessK8s();
+        $job = $process->getRunningJobInfo($pid);
+        $k8sSummary = empty($job)
+            ? "empty (job finished or unknown to scheduler)"
+            : ("keys=" . implode(",", array_keys($job))
+                . (isset($job['state']) ? " state=" . $job['state'] : ""));
+        error_log("DEBUG: getRunningJobInfo kubernetes_native pid=$pid $k8sSummary");
+        logger("getRunningJobInfo (kubernetes_native): pid=$pid $k8sSummary");
     } elseif ($launcherType == "PMES") {
         $process = new ProcessPMES($cloudName);
         $job = $process->getRunningJobInfo($pid);
@@ -164,9 +189,7 @@ function getRunningJobInfo($pid, $launcherType = NULL, $cloudName = "local")
         $_SESSION['errorData']['Error'][] = "Cannot monitor job '$pid' of type '$launcherType'. Launcher not implemented.";
         return $job;
     }
-
     logger("getRunningJobInfo: end processing $pid");
-
     // return job info
     return $job;
 }
@@ -304,6 +327,8 @@ function delJob($pid, $launcherType = NULL, $cloudName = "local", $login = NULL)
     if (!$launcherType) {
         if (is_numeric($pid)) {
             $launcherType = "docker_SGE";
+        } elseif (strpos((string)$pid, "-") !== false) {
+            $launcherType = "kubernetes_native";
         } else {
             $launcherType = "PMES";
         }
@@ -321,6 +346,16 @@ function delJob($pid, $launcherType = NULL, $cloudName = "local", $login = NULL)
             updateLogFromJobInfo($jobInfo['log'], $pid, $launcherType, $cloudName);
             // Add any other file redirection logic here
         }
+    } elseif ($launcherType == "kubernetes_native") {
+        error_log("DEBUG: delJob kubernetes_native pid=$pid calling ProcessK8s::stop");
+        require_once __DIR__ . "/classes/ProcessK8s.php";
+        $processK8s = new ProcessK8s();
+        list($r_sge, $msg_sge) = $processK8s->stop($pid);
+        error_log(
+            "DEBUG: delJob kubernetes_native pid=$pid stop_ok=" . ($r_sge ? "1" : "0")
+            . " msg=" . $msg_sge
+        );
+        logger("delJob (kubernetes_native): pid=$pid stop_ok=" . ($r_sge ? "1" : "0") . " msg=" . $msg_sge);
     } elseif ($launcherType == "PMES") {
         $process = new ProcessPMES();
         $r = $process->stop($pid);

front_end/openVRE/public/phplib/projects.inc.php

@@ -2347,7 +2347,7 @@ function resolvePath_toLocalAbsolutePath($path, $job)
 				$rfn = str_replace($job['root_dir_virtual'], $GLOBALS['dataDir'] . $_SESSION['User']['id'], $path);
 
 				//SGE finds mounted dataDir as root_dir_virtual
-			} elseif ($job['launcher'] == "SGE" || $job['launcher'] == "ega_demo" || $job['launcher'] == "docker_SGE") {
+			} elseif ($job['launcher'] == "SGE" || $job['launcher'] == "ega_demo" || $job['launcher'] == "docker_SGE" || $job['launcher'] == "kubernetes_native") {
 				$rfn = str_replace($job['root_dir_mug'], $GLOBALS['dataDir'], $path);
 			}
 			// direct from file_path
@@ -2380,6 +2380,10 @@ function resolvePath_toLocalAbsolutePath($path, $job)
 		}
 	}
 	//clean slashes
+	if ($rfn === "") {
+		// Keep original absolute path instead of returning empty when launcher mapping is missing.
+		$rfn = $path;
+	}
 	$rfn = preg_replace('#/+#', '/', $rfn);
 
 	//return absolute path

scheduler/.dockerignore

@@ -0,0 +1,12 @@
+.git
+.gitignore
+__pycache__/
+*.pyc
+*.pyo
+*.pyd
+.pytest_cache/
+.mypy_cache/
+.ruff_cache/
+dist/
+build/
+*.egg-info/

scheduler/Dockerfile

@@ -0,0 +1,11 @@
+FROM python:3.11-alpine
+
+WORKDIR /app
+
+COPY app.py /app/app.py
+
+EXPOSE 8080
+
+USER 65534:65534
+
+CMD ["python", "/app/app.py"]