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processJob.inc.php
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processJob.inc.php
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<?php
#
# Job management functions : SGE & PMES
#
function execJob ($workDir,$shFile,$queue,$cpus=1,$mem=0) {
logger("Start job submission via SGE");
$queue = (isset($queue)? $queue:$GLOBALS['queueTask']);
$jobname = $_SESSION['User']['id']."#".basename($shFile);
// Start SGE process
$process = new ProcessSGE($shFile,$workDir,$queue,$jobname,$cpus,$mem);
$pid = $process->getPid();
if (!$process->status()){
$_SESSION['errorData']['Error'][]="Job submission failed.<br/>".$process->getFullCommand."<br/>".$process->getErr();
$errMesg = "ERROR: Job submission failed. FullCommand: '".$process->getFullCommand."'. ErrorSGE: '".$process->getErr(). "'";
logger($errMesg);
return array(0,$errMesg);
}
logger("The process $cmd is currently running PID = $pid");
return array($pid,"");
}
function execJobPMES ($cloudName,$data){
logger("Start job submission via PMES");
// Start PMES process
$process = new ProcessPMES($cloudName);
if ($cloudName=="mug-ebi"){
die();
}
if (!$process->listening){
$errMesg = "Job submission failed.<br/>PMES call to '".$process->getServer()."' returned: ".$process->getErr();
$_SESSION['errorData']['Error'][]=$errMesg;
$errMesg.="<br/>Server not listening. TEST_RESPONSE = '".json_encode($process->lastCall)."'";
logger($errMesg);
return array(0,$errMesg);
}
$process->runPMES($data);
$jobid = $process->getJobId();
if ($jobid == "0"){
$errMesg = "Job submission failed.<br/>".json_encode($process->lastCall)."<br/>".$process->getErr();
$_SESSION['errorData']['Error'][]=$errMesg;
return array(0,$errMesg);
}
logger("The process is currently running JOB_ID = $jobid");
return array($jobid,"");
}
# getAllRunningJobs
/*
function getRunningJobs(){
$jobs=Array();
$command = QSTAT." -u www-data | awk '$1 ~ /[0-9]+/ {print $1\"\t\"$5\"\t\"$6 $7}'";
exec($command,$queueJobs);
if (!isset($queueJobs[0]))
return $jobs;
else{
foreach ($queueJobs as $jobLine){
list($pid,$state,$start)=explode("\t",$jobLine);
$cmd = QSTAT. " -j $pid | grep job_name | cut -d: -f2 | tr -d \" \"";
exec($cmd,$jobName);
$jobs[$pid]=Array(
'name'=>$jobName[0],
'start'=>$start,
'state'=>jobStateDicc($state)
);
}
}
return $jobs;
}
*/
function getRunningJobInfo($pid,$launcherType=NULL,$cloudName="local"){
$job=Array();
if (! $pid)
return $job;
// guess launcher
if(!$launcherType){
if (is_numeric($pid))
$launcherType = "SGE";
else
$launcherType = "PMES";
}
// create new jobProcess
if ($launcherType == "SGE"){
$process = new ProcessSGE();
$job = $process->getRunningJobInfo($pid);
}elseif($launcherType == "PMES"){
$process = new ProcessPMES($cloudName);
$job = $process->getRunningJobInfo($pid);
}else{
$_SESSION['errorData']['Error'][]="Cannot monitor job '$pid' of type '$launcher'. Launcher not implemented.";
return $job;
}
// return job info
return $job;
}
function updateLogFromJobInfo($logFile,$pid,$launcherType=NULL,$cloudName="local"){
// guess launcher
if(!$launcherType){
if (is_numeric($pid))
$launcherType = "SGE";
else
$launcherType = "PMES";
}
// if PMES, update log content
if ($launcherType == "PMES"){
$process = new ProcessPMES($cloudName);
$job = $process->getActivityInfo($pid);
if ($job['jobOutputMessage'] || $job['jobErrorMessage'] ){
if (is_file($logFile) || is_dir(dirname($logFile))){
$F = fopen($logFile, "w");
}
if ( !$F ) {
//$_SESSION['errorData']['Warning'][]="Cannot update LOG file '".basename(dirname($logFile))."' ($cloudName). Recently deleted from workspace or not accessible.";
return true;
}
if ($job['jobOutputMessage']){
fwrite($F, "##### STDOUT ###############################\n");
fwrite($F, $job['jobOutputMessage']);
}
if ($job['jobErrorMessage']){
fwrite($F, "##### STDERR ###############################\n");
fwrite($F, $job['jobErrorMessage']);
}
fclose($F);
}else{
// $_SESSION['errorData']['Warning'][]="Cannot update LOG file '".basename(dirname($logFile))."' ($cloudName). Recently deleted from workspace or not accessible";
}
}
return true;
}
function getPidFromOutfile($outfile){
$pid=0;
$SGE_updated = getUserJobs($_SESSION['userId']);
foreach($SGE_updated as $data){
$outs = $data['out'];
if (!is_array($data['out']))
$outs = Array($data['out']);
if (in_array($outfile,$outs))
return $data['_id'];
}
return $pid;
}
// cancel job given its output file
function delJobFromOutfiles($outfiles){
if (!is_array($outfiles)){
$outfiles=Array($outfiles);
}
if (count($outfiles) ==0)
return 1;
$SGE_updated = getUserJobs($_SESSION['userId']);
foreach($outfiles as $outfile){
$pid = getPidFromOutfile($outfile);
if ($pid){
//get dependencies of the selected job
$pids=Array($pid);
$jobInfo = getRunningJobInfo($pid);
if (isset($jobInfo['jid_successor_list'])){
foreach (explode(",",$jobInfo['jid_successor_list']) as $pidSucc ){
$succInfo = getRunningJobInfo($pidSucc);
if($succInfo)
array_push($pids,$pidSucc);
}
}
//foreach job, cancel and delete associated files
foreach($pids as $pid){
//delete job
$ok = delJob($pid);
if (!$ok){
$_SESSION['errorData']['Error'][]= "Cannot delete ".basename($outfile)." task. Unsuccessfully exit of 'deljob' for job $pid.";
continue;
}
//delete job associated files
$files=Array();
$jobType = (isset($SGE_updated[$pid]['log'])?basename($SGE_updated[$pid]['log']):"");
if (preg_match('/^PP_/',$jobType)){
$files[] = $SGE_updated[$pid]['log'];
}else{
if (!is_array($SGE_updated[$pid]['out']))
$files[] =$SGE_updated[$pid]['out'];
else
$files = $SGE_updated[$pid]['out'];
$files[] = $SGE_updated[$pid]['log'];
}
foreach ($files as $fn){
$rfn = $GLOBALS['dataDir']."/$fn";
$ofn = $GLOBALS['filesCol']->findOne(array('_id' => $fn));
if (!empty($ofn)){
$ok = deleteGSFileBNS($fn);
if (!$ok){
$_SESSION['errorData']['SGE'][]= "Job ".basename($outfile)." deleted. But errors occured while cleaning temporal files.";
continue;
}
}
if (is_file($rfn)){
unlink ($rfn);
if (error_get_last())
$_SESSION['errorData']['SGE'][]= "Cannot unlink $rfn". error_get_last()["message"];
}
}
//update pending jobs
//unset($SGE_updated[$pid]);
//delUserJob($_SESSION['userId'],$pid);
}
}else{
$_SESSION['errorData']['SGE'][]= "Cannot find job information for '".basename($outfile)."'. <a href=\"workspace/workspace.php\">[ OK ]</a>";
}
}
return 1;
}
function delJob($pid,$launcherType=NULL,$cloudName="local",$login=NULL){
$job=Array();
if (! $pid)
return false;
// guess launcher
if(!$launcherType){
if (is_numeric($pid))
$launcherType = "SGE";
else
$launcherType = "PMES";
}
// cancel job
$r = false;
if ($launcherType == "SGE"){
$process = new ProcessSGE();
list($r,$msg) = $process->stop($pid);
if (!$r)
$_SESSION['errorData']['Error'][]="Cannot delete $launcherType job [id = $pid].<br/>$msg";
}elseif($launcherType == "PMES"){
$process = new ProcessPMES();
$r= $process->stop($pid);
if (!$r)
$_SESSION['errorData']['Error'][]="Cannot delete $launcherType job [id = $pid].<br/>$msg";
}else{
$_SESSION['errorData']['Error'][]="Cannot delete job of type '$launcherType' [id = $pid]. Launcher not implemented.";
return false;
}
$_SESSION['errorData']['Info'][]="Job successfully cancelled";
logger("JOB $pid FINISHED. HAS BEEN CANCELLED");
log_addFinish($pid,"Job has been cancelled");
// wait to make qdel/terminateActivity effective
sleep(15);
// check job status and register output files, if required
if ($r){
if (!$login){$login = $_SESSION['User']['_id'];}
$filesPending= processPendingFiles($login);
//delUserJob($login,$pid); // directly deleting job entry leds to no output registration!
}else{
$_SESSION['errorData']['Internal Error'][] = "Error while cancelling $launcherType job [id = $pid].<br>Job deleted from the system, but not from user metadata";
return false;
}
return true;
}
/*
function jobStateDicc($state){
$dicc = Array (
'r' => "RUNNING",
't' => "TRANSFERING",
'qw' => "PENDING",
'hqw'=> "HOLD",
'dr' => "DELETING",
'Eqw'=> "ERROR"
);
if ($dicc[$state])
return $dicc[$state];
else
return $state;
}
*/
?>