Repository: airavata Updated Branches: refs/heads/master 0df74e911 -> 72f3524f7 Fixing more issues with push monitoring Project: http://git-wip-us.apache.org/repos/asf/airavata/repo Commit: http://git-wip-us.apache.org/repos/asf/airavata/commit/aaba6d6e Tree: http://git-wip-us.apache.org/repos/asf/airavata/tree/aaba6d6e Diff: http://git-wip-us.apache.org/repos/asf/airavata/diff/aaba6d6e Branch: refs/heads/master Commit: aaba6d6ec687ee132c6166f1ee7efa75b73b0d83 Parents: 21c9a92 Author: lahiru Authored: Thu Sep 25 17:02:56 2014 -0400 Committer: lahiru Committed: Thu Sep 25 17:02:56 2014 -0400 ---------------------------------------------------------------------- .../airavata/client/samples/CreateLaunchExperiment.java | 10 ++++++---- .../server/src/main/resources/PBSTemplate.xslt | 3 ++- .../server/src/main/resources/SGETemplate.xslt | 6 +++--- .../server/src/main/resources/SLURMTemplate.xslt | 5 +++-- .../apache/airavata/gfac/server/GfacServerHandler.java | 7 ++++--- .../apache/airavata/gfac/gsissh/util/GFACGSISSHUtils.java | 1 + .../gfac/monitor/impl/pull/qstat/HPCPullMonitor.java | 8 -------- .../monitor/impl/push/amqp/SimpleJobFinishConsumer.java | 4 +++- .../org/apache/airavata/gfac/ssh/util/GFACSSHUtils.java | 1 + .../apache/airavata/gsi/ssh/api/job/JobDescriptor.java | 10 ++++++++++ .../src/main/resources/schemas/PBSJobDescriptor.xsd | 1 + 11 files changed, 34 insertions(+), 22 deletions(-) ---------------------------------------------------------------------- http://git-wip-us.apache.org/repos/asf/airavata/blob/aaba6d6e/airavata-api/airavata-client-sdks/java-client-samples/src/main/java/org/apache/airavata/client/samples/CreateLaunchExperiment.java ---------------------------------------------------------------------- diff --git a/airavata-api/airavata-client-sdks/java-client-samples/src/main/java/org/apache/airavata/client/samples/CreateLaunchExperiment.java b/airavata-api/airavata-client-sdks/java-client-samples/src/main/java/org/apache/airavata/client/samples/CreateLaunchExperiment.java index a3dd336..bbfc873 100644 --- a/airavata-api/airavata-client-sdks/java-client-samples/src/main/java/org/apache/airavata/client/samples/CreateLaunchExperiment.java +++ b/airavata-api/airavata-client-sdks/java-client-samples/src/main/java/org/apache/airavata/client/samples/CreateLaunchExperiment.java @@ -46,7 +46,7 @@ public class CreateLaunchExperiment { private static final String DEFAULT_USER = "default.registry.user"; private static final String DEFAULT_GATEWAY = "default.registry.gateway"; private static Airavata.Client airavataClient; - private static String echoAppId = "Echo_c6e6aaac-7d9d-44fc-aba2-63b5100528e8"; + private static String echoAppId = "Echo_38c5ad74-3a27-46d3-963b-d63f1c37b194"; private static String wrfAppId = "WRF_5f097c9c-7066-49ec-aed7-4e39607b3adc"; private static String amberAppId = "Amber_89906be6-5678-49a6-9d04-a0604fbdef2e"; @@ -56,13 +56,14 @@ public class CreateLaunchExperiment { private static String br2HostName = "bigred2.uits.iu.edu"; public static void main(String[] args) { - try { + for (int i = 0; i < 1; i++) + try { airavataClient = AiravataClientFactory.createAiravataClient(THRIFT_SERVER_HOST, THRIFT_SERVER_PORT); System.out.println("API version is " + airavataClient.getAPIVersion()); // registerApplications(); // run this only the first time // final String expId = createExperimentForSSHHost(airavata); -// final String expId = createEchoExperimentForTrestles(airavataClient); + final String expId = createEchoExperimentForTrestles(airavataClient); // final String expId = createEchoExperimentForStampede(airavataClient); // final String expId = createExperimentEchoForLocalHost(airavataClient); // final String expId = createExperimentWRFTrestles(airavataClient); @@ -74,7 +75,8 @@ public class CreateLaunchExperiment { // System.out.println("Experiment ID : " + expId); // updateExperiment(airavata, expId); -// launchExperiment(airavataClient, expId); + launchExperiment(airavataClient, expId); + // System.out.println(expId); } catch (Exception e) { logger.error("Error while connecting with server", e.getMessage()); http://git-wip-us.apache.org/repos/asf/airavata/blob/aaba6d6e/modules/configuration/server/src/main/resources/PBSTemplate.xslt ---------------------------------------------------------------------- diff --git a/modules/configuration/server/src/main/resources/PBSTemplate.xslt b/modules/configuration/server/src/main/resources/PBSTemplate.xslt index 5c266f4..ca02d79 100644 --- a/modules/configuration/server/src/main/resources/PBSTemplate.xslt +++ b/modules/configuration/server/src/main/resources/PBSTemplate.xslt @@ -8,6 +8,7 @@ + " #! /bin/sh # PBS batch job submission script generated by Apache Airavata # @@ -74,7 +75,7 @@ cd -~/rabbitmq-java-client-bin-3.3.5/runjava.sh com.rabbitmq.examples.SimpleProducer amqp:// , +~/rabbitmq-java-client-bin-3.3.5/runjava.sh com.rabbitmq.examples.SimpleProducer amqp:// , \ No newline at end of file http://git-wip-us.apache.org/repos/asf/airavata/blob/aaba6d6e/modules/configuration/server/src/main/resources/SGETemplate.xslt ---------------------------------------------------------------------- diff --git a/modules/configuration/server/src/main/resources/SGETemplate.xslt b/modules/configuration/server/src/main/resources/SGETemplate.xslt index bcf8948..d2bf871 100644 --- a/modules/configuration/server/src/main/resources/SGETemplate.xslt +++ b/modules/configuration/server/src/main/resources/SGETemplate.xslt @@ -8,7 +8,8 @@ -#! /bin/bash + " + #! /bin/bash # Grid Engine batch job script built by Apache Airavata # @@ -73,7 +74,6 @@ cd -~/rabbitmq-java-client-bin-3.3.5/runjava.sh com.rabbitmq.examples.SimpleProducer amqp:// , + ~/rabbitmq-java-client-bin-3.3.5/runjava.sh com.rabbitmq.examples.SimpleProducer amqp:// , - \ No newline at end of file http://git-wip-us.apache.org/repos/asf/airavata/blob/aaba6d6e/modules/configuration/server/src/main/resources/SLURMTemplate.xslt ---------------------------------------------------------------------- diff --git a/modules/configuration/server/src/main/resources/SLURMTemplate.xslt b/modules/configuration/server/src/main/resources/SLURMTemplate.xslt index 4444ec2..b494cc0 100644 --- a/modules/configuration/server/src/main/resources/SLURMTemplate.xslt +++ b/modules/configuration/server/src/main/resources/SLURMTemplate.xslt @@ -8,7 +8,8 @@ - + " + #! @@ -69,7 +70,7 @@ cd -~/rabbitmq-java-client-bin-3.3.5/runjava.sh com.rabbitmq.examples.SimpleProducer amqp:// , + ~/rabbitmq-java-client-bin-3.3.5/runjava.sh com.rabbitmq.examples.SimpleProducer amqp:// , \ No newline at end of file http://git-wip-us.apache.org/repos/asf/airavata/blob/aaba6d6e/modules/gfac/airavata-gfac-service/src/main/java/org/apache/airavata/gfac/server/GfacServerHandler.java ---------------------------------------------------------------------- diff --git a/modules/gfac/airavata-gfac-service/src/main/java/org/apache/airavata/gfac/server/GfacServerHandler.java b/modules/gfac/airavata-gfac-service/src/main/java/org/apache/airavata/gfac/server/GfacServerHandler.java index f7c3cb8..3d86dff 100644 --- a/modules/gfac/airavata-gfac-service/src/main/java/org/apache/airavata/gfac/server/GfacServerHandler.java +++ b/modules/gfac/airavata-gfac-service/src/main/java/org/apache/airavata/gfac/server/GfacServerHandler.java @@ -63,7 +63,7 @@ public class GfacServerHandler implements GfacService.Iface, Watcher{ private boolean connected = false; - private static Integer mutex = new Integer(-1); + private static Integer mutex = -1; private MonitorPublisher publisher; @@ -153,8 +153,9 @@ public class GfacServerHandler implements GfacService.Iface, Watcher{ } else if(state == Event.KeeperState.Expired || state == Event.KeeperState.Disconnected){ try { - zk = new ZooKeeper(AiravataZKUtils.getZKhostPort(),6000,this); - synchronized(mutex){ + mutex = -1; + zk = new ZooKeeper(AiravataZKUtils.getZKhostPort(), 6000, this); + synchronized (mutex) { mutex.wait(); // waiting for the syncConnected event } storeServerConfig(); http://git-wip-us.apache.org/repos/asf/airavata/blob/aaba6d6e/modules/gfac/gfac-gsissh/src/main/java/org/apache/airavata/gfac/gsissh/util/GFACGSISSHUtils.java ---------------------------------------------------------------------- diff --git a/modules/gfac/gfac-gsissh/src/main/java/org/apache/airavata/gfac/gsissh/util/GFACGSISSHUtils.java b/modules/gfac/gfac-gsissh/src/main/java/org/apache/airavata/gfac/gsissh/util/GFACGSISSHUtils.java index dcdbb4d..40784df 100644 --- a/modules/gfac/gfac-gsissh/src/main/java/org/apache/airavata/gfac/gsissh/util/GFACGSISSHUtils.java +++ b/modules/gfac/gfac-gsissh/src/main/java/org/apache/airavata/gfac/gsissh/util/GFACGSISSHUtils.java @@ -115,6 +115,7 @@ public class GFACGSISSHUtils { JobDescriptor jobDescriptor = new JobDescriptor(); // this is common for any application descriptor jobDescriptor.setCallBackIp(ServerSettings.getIp()); + jobDescriptor.setCallBackPort(ServerSettings.getSetting(org.apache.airavata.common.utils.Constants.GFAC_SERVER_PORT, "8950")); jobDescriptor.setInputDirectory(app.getInputDataDirectory()); jobDescriptor.setOutputDirectory(app.getOutputDataDirectory()); jobDescriptor.setExecutablePath(app.getExecutableLocation()); http://git-wip-us.apache.org/repos/asf/airavata/blob/aaba6d6e/modules/gfac/gfac-monitor/src/main/java/org/apache/airavata/gfac/monitor/impl/pull/qstat/HPCPullMonitor.java ---------------------------------------------------------------------- diff --git a/modules/gfac/gfac-monitor/src/main/java/org/apache/airavata/gfac/monitor/impl/pull/qstat/HPCPullMonitor.java b/modules/gfac/gfac-monitor/src/main/java/org/apache/airavata/gfac/monitor/impl/pull/qstat/HPCPullMonitor.java index bac27bf..b588894 100644 --- a/modules/gfac/gfac-monitor/src/main/java/org/apache/airavata/gfac/monitor/impl/pull/qstat/HPCPullMonitor.java +++ b/modules/gfac/gfac-monitor/src/main/java/org/apache/airavata/gfac/monitor/impl/pull/qstat/HPCPullMonitor.java @@ -243,14 +243,6 @@ public class HPCPullMonitor extends PullMonitor { " 3 times, so skip this Job from Monitor"); iMonitorID.setLastMonitored(new Timestamp((new Date()).getTime())); completedJobs.put(iMonitorID.getJobName(), iMonitorID); - try { - logger.error("Launching outflow handlers to check output are genereated or not"); - gfac.invokeOutFlowHandlers(iMonitorID.getJobExecutionContext()); - } catch (GFacException e) { - publisher.publish(new TaskStatusChangeRequest(new TaskIdentity(iMonitorID.getExperimentID(), iMonitorID.getWorkflowNodeID(), - iMonitorID.getTaskID()), TaskState.FAILED)); - logger.info(e.getLocalizedMessage(), e); - } } else { // Evey iMonitorID.setLastMonitored(new Timestamp((new Date()).getTime())); http://git-wip-us.apache.org/repos/asf/airavata/blob/aaba6d6e/modules/gfac/gfac-monitor/src/main/java/org/apache/airavata/gfac/monitor/impl/push/amqp/SimpleJobFinishConsumer.java ---------------------------------------------------------------------- diff --git a/modules/gfac/gfac-monitor/src/main/java/org/apache/airavata/gfac/monitor/impl/push/amqp/SimpleJobFinishConsumer.java b/modules/gfac/gfac-monitor/src/main/java/org/apache/airavata/gfac/monitor/impl/push/amqp/SimpleJobFinishConsumer.java index 3a6aae7..64f8d21 100644 --- a/modules/gfac/gfac-monitor/src/main/java/org/apache/airavata/gfac/monitor/impl/push/amqp/SimpleJobFinishConsumer.java +++ b/modules/gfac/gfac-monitor/src/main/java/org/apache/airavata/gfac/monitor/impl/push/amqp/SimpleJobFinishConsumer.java @@ -24,6 +24,8 @@ import com.rabbitmq.client.Channel; import com.rabbitmq.client.Connection; import com.rabbitmq.client.ConnectionFactory; import com.rabbitmq.client.QueueingConsumer; +import org.apache.airavata.common.utils.Constants; +import org.apache.airavata.common.utils.ServerSettings; import org.slf4j.Logger; import org.slf4j.LoggerFactory; @@ -40,8 +42,8 @@ public class SimpleJobFinishConsumer { public void listen() { try { + String queueName = ServerSettings.getSetting(Constants.GFAC_SERVER_PORT, "8950"); String uri = "amqp://localhost"; - String queueName = "SimpleQueue"; ConnectionFactory connFactory = new ConnectionFactory(); connFactory.setUri(uri); http://git-wip-us.apache.org/repos/asf/airavata/blob/aaba6d6e/modules/gfac/gfac-ssh/src/main/java/org/apache/airavata/gfac/ssh/util/GFACSSHUtils.java ---------------------------------------------------------------------- diff --git a/modules/gfac/gfac-ssh/src/main/java/org/apache/airavata/gfac/ssh/util/GFACSSHUtils.java b/modules/gfac/gfac-ssh/src/main/java/org/apache/airavata/gfac/ssh/util/GFACSSHUtils.java index d5dd97b..8235725 100644 --- a/modules/gfac/gfac-ssh/src/main/java/org/apache/airavata/gfac/ssh/util/GFACSSHUtils.java +++ b/modules/gfac/gfac-ssh/src/main/java/org/apache/airavata/gfac/ssh/util/GFACSSHUtils.java @@ -96,6 +96,7 @@ public class GFACSSHUtils { JobDescriptor jobDescriptor = new JobDescriptor(); // this is common for any application descriptor jobDescriptor.setCallBackIp(ServerSettings.getIp()); + jobDescriptor.setCallBackPort(ServerSettings.getSetting(org.apache.airavata.common.utils.Constants.GFAC_SERVER_PORT, "8950")); jobDescriptor.setInputDirectory(app.getInputDataDirectory()); jobDescriptor.setOutputDirectory(app.getOutputDataDirectory()); jobDescriptor.setExecutablePath(app.getExecutableLocation()); http://git-wip-us.apache.org/repos/asf/airavata/blob/aaba6d6e/tools/gsissh/src/main/java/org/apache/airavata/gsi/ssh/api/job/JobDescriptor.java ---------------------------------------------------------------------- diff --git a/tools/gsissh/src/main/java/org/apache/airavata/gsi/ssh/api/job/JobDescriptor.java b/tools/gsissh/src/main/java/org/apache/airavata/gsi/ssh/api/job/JobDescriptor.java index 3890a09..9a0639b 100644 --- a/tools/gsissh/src/main/java/org/apache/airavata/gsi/ssh/api/job/JobDescriptor.java +++ b/tools/gsissh/src/main/java/org/apache/airavata/gsi/ssh/api/job/JobDescriptor.java @@ -399,8 +399,18 @@ public class JobDescriptor { this.jobDescriptionDocument.getJobDescriptor().setCallBackIp(ip); } + public void setCallBackPort(String ip){ + this.jobDescriptionDocument.getJobDescriptor().setCallBackPort(ip); + } + + public String getCallBackIp(){ return this.jobDescriptionDocument.getJobDescriptor().getCallBackIp(); } + public String getCallBackPort(){ + return this.jobDescriptionDocument.getJobDescriptor().getCallBackPort(); + } + + } http://git-wip-us.apache.org/repos/asf/airavata/blob/aaba6d6e/tools/gsissh/src/main/resources/schemas/PBSJobDescriptor.xsd ---------------------------------------------------------------------- diff --git a/tools/gsissh/src/main/resources/schemas/PBSJobDescriptor.xsd b/tools/gsissh/src/main/resources/schemas/PBSJobDescriptor.xsd index a9917bc..7749769 100644 --- a/tools/gsissh/src/main/resources/schemas/PBSJobDescriptor.xsd +++ b/tools/gsissh/src/main/resources/schemas/PBSJobDescriptor.xsd @@ -57,6 +57,7 @@ +