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Posted to commits@airavata.apache.org by la...@apache.org on 2014/03/07 16:20:19 UTC
[1/2] git commit: Adding SLURMTEMPLATE to the build- AIRAVATA-1057
Repository: airavata
Updated Branches:
refs/heads/master ccf48b253 -> 4523bd9db
Adding SLURMTEMPLATE to the build- AIRAVATA-1057
Project: http://git-wip-us.apache.org/repos/asf/airavata/repo
Commit: http://git-wip-us.apache.org/repos/asf/airavata/commit/4ecf18e8
Tree: http://git-wip-us.apache.org/repos/asf/airavata/tree/4ecf18e8
Diff: http://git-wip-us.apache.org/repos/asf/airavata/diff/4ecf18e8
Branch: refs/heads/master
Commit: 4ecf18e831892bdd3d7c43d8c8c9acba6f25ecca
Parents: c57378b
Author: lahiru <la...@apache.org>
Authored: Fri Mar 7 10:19:33 2014 -0500
Committer: lahiru <la...@apache.org>
Committed: Fri Mar 7 10:19:33 2014 -0500
----------------------------------------------------------------------
.../monitor/impl/pull/qstat/QstatMonitor.java | 16 +++--
.../src/main/resources/SLURMTemplate.xslt | 69 --------------------
.../src/main/resources/conf/SLURMTemplate.xslt | 69 ++++++++++++++++++++
3 files changed, 80 insertions(+), 74 deletions(-)
----------------------------------------------------------------------
http://git-wip-us.apache.org/repos/asf/airavata/blob/4ecf18e8/modules/airavata-job-monitor/src/main/java/org/apache/airavata/job/monitor/impl/pull/qstat/QstatMonitor.java
----------------------------------------------------------------------
diff --git a/modules/airavata-job-monitor/src/main/java/org/apache/airavata/job/monitor/impl/pull/qstat/QstatMonitor.java b/modules/airavata-job-monitor/src/main/java/org/apache/airavata/job/monitor/impl/pull/qstat/QstatMonitor.java
index fa18db8..3e8475d 100644
--- a/modules/airavata-job-monitor/src/main/java/org/apache/airavata/job/monitor/impl/pull/qstat/QstatMonitor.java
+++ b/modules/airavata-job-monitor/src/main/java/org/apache/airavata/job/monitor/impl/pull/qstat/QstatMonitor.java
@@ -36,6 +36,7 @@ import org.slf4j.LoggerFactory;
import java.sql.Timestamp;
import java.util.Date;
import java.util.HashMap;
+import java.util.Iterator;
import java.util.Map;
import java.util.concurrent.BlockingQueue;
@@ -73,7 +74,7 @@ public class QstatMonitor extends PullMonitor implements Runnable {
try {
startPulling();
// After finishing one iteration of the full queue this thread sleeps 1 second
- Thread.sleep(1000);
+ Thread.sleep(5000);
} catch (Exception e){
// we catch all the exceptions here because no matter what happens we do not stop running this
// thread, but ideally we should report proper error messages, but this is handled in startPulling
@@ -96,8 +97,14 @@ public class QstatMonitor extends PullMonitor implements Runnable {
JobStatus jobStatus = new JobStatus();
while (!this.queue.isEmpty()) {
try {
- take = this.queue.take();
- if (take.getHost().getType() instanceof GsisshHostType) {
+ Iterator<MonitorID> iterator = this.queue.iterator();
+ // no need to check iterator.hasNext because its already checked
+ MonitorID next = iterator.next();
+ // we check whether the job is type of gsissh otherwise we return the job back to the queue
+ // Here we use iterator because it not fair to take the object from the queue unless its
+ // the correct host type,so if its not the right type it will remain in the queue
+ if(next.getHost().getType() instanceof GsisshHostType){
+ take = this.queue.take();
long monitorDiff = 0;
long startedDiff = 0;
if (take.getLastMonitored() != null) {
@@ -136,8 +143,7 @@ public class QstatMonitor extends PullMonitor implements Runnable {
}
}
} else {
- //Qstat doesn't handle other jobs eexcept GsisshHostTypes
- this.queue.put(take);
+ logger.debug("Qstat Monitor doesn't handle non-gsissh hosts");
}
} catch (InterruptedException e) {
if(!this.queue.contains(take)){
http://git-wip-us.apache.org/repos/asf/airavata/blob/4ecf18e8/modules/distribution/airavata-server/src/main/resources/SLURMTemplate.xslt
----------------------------------------------------------------------
diff --git a/modules/distribution/airavata-server/src/main/resources/SLURMTemplate.xslt b/modules/distribution/airavata-server/src/main/resources/SLURMTemplate.xslt
deleted file mode 100644
index 169dbbf..0000000
--- a/modules/distribution/airavata-server/src/main/resources/SLURMTemplate.xslt
+++ /dev/null
@@ -1,69 +0,0 @@
-<!--Licensed to the Apache Software Foundation (ASF) under one or more contributor license agreements. See the NOTICE file
- distributed with this work for additional information regarding copyright ownership. The ASF licenses this file to you under
- the Apache License, Version 2.0 (theÏ "License"); you may not use this file except in compliance with the License. You may
- obtain a copy of the License at http://www.apache.org/licenses/LICENSE-2.0 Unless required by applicable law or agreed to
- in writing, software distributed under the License is distributed on an "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF
- ANY ~ KIND, either express or implied. See the License for the specific language governing permissions and limitations under
- the License. -->
-<xsl:stylesheet version="1.0" xmlns:xsl="http://www.w3.org/1999/XSL/Transform" xmlns:ns="http://airavata.apache.org/gsi/ssh/2012/12">
-<xsl:output method="text" />
-<xsl:template match="/ns:JobDescriptor">
-<xsl:choose>
-<xsl:when test="ns:shellName">
-#!<xsl:value-of select="ns:shellName"/>
- </xsl:when>
- </xsl:choose>
-<xsl:choose>
- <xsl:when test="ns:queueName">
-#SBATCH -p <xsl:value-of select="ns:queueName"/>
- </xsl:when>
- </xsl:choose>
-<xsl:choose>
- <xsl:when test="ns:nodes">
-#SBATCH -n <xsl:value-of select="ns:nodes"/>
- </xsl:when>
- </xsl:choose>
- <xsl:choose>
- <xsl:when test="ns:mailAddress">
-#SBATCH -mail-user=<xsl:value-of select="ns:mailAddress"/>
- </xsl:when>
- </xsl:choose>
- <xsl:choose>
- <xsl:when test="ns:mailType">
-#SBATCH -mail-type=<xsl:value-of select="ns:mailType"/>
- </xsl:when>
- </xsl:choose>
- <xsl:choose>
-<xsl:when test="ns:acountString">
-#SBATCH -A <xsl:value-of select="ns:acountString"/>
- </xsl:when>
- </xsl:choose>
- <xsl:choose>
- <xsl:when test="ns:maxWallTime">
-#SBATCH -t <xsl:value-of select="ns:maxWallTime"/>
- </xsl:when>
- </xsl:choose>
- <xsl:choose>
- <xsl:when test="ns:jobName">
-#SBATCH -J <xsl:value-of select="ns:jobName"/>
- </xsl:when>
- </xsl:choose>
- <xsl:choose>
- <xsl:when test="ns:standardOutFile">
-#SBATCH -o <xsl:value-of select="ns:standardOutFile"/>
- </xsl:when>
- </xsl:choose>
- <xsl:choose>
- <xsl:when test="ns:standardOutFile">
-#SBATCH -e <xsl:value-of select="ns:standardErrorFile"/>
- </xsl:when>
- </xsl:choose>
-cd <xsl:text> </xsl:text><xsl:value-of select="ns:workingDirectory"/><xsl:text>
</xsl:text>
- <xsl:choose><xsl:when test="ns:jobSubmitterCommand">
-<xsl:value-of select="ns:jobSubmitterCommand"/><xsl:text> </xsl:text></xsl:when></xsl:choose><xsl:value-of select="ns:executablePath"/><xsl:text> </xsl:text>
-<xsl:for-each select="ns:inputs/ns:input">
- <xsl:value-of select="."/><xsl:text> </xsl:text>
- </xsl:for-each>
-</xsl:template>
-
-</xsl:stylesheet>
\ No newline at end of file
http://git-wip-us.apache.org/repos/asf/airavata/blob/4ecf18e8/modules/distribution/airavata-server/src/main/resources/conf/SLURMTemplate.xslt
----------------------------------------------------------------------
diff --git a/modules/distribution/airavata-server/src/main/resources/conf/SLURMTemplate.xslt b/modules/distribution/airavata-server/src/main/resources/conf/SLURMTemplate.xslt
new file mode 100644
index 0000000..169dbbf
--- /dev/null
+++ b/modules/distribution/airavata-server/src/main/resources/conf/SLURMTemplate.xslt
@@ -0,0 +1,69 @@
+<!--Licensed to the Apache Software Foundation (ASF) under one or more contributor license agreements. See the NOTICE file
+ distributed with this work for additional information regarding copyright ownership. The ASF licenses this file to you under
+ the Apache License, Version 2.0 (theÏ "License"); you may not use this file except in compliance with the License. You may
+ obtain a copy of the License at http://www.apache.org/licenses/LICENSE-2.0 Unless required by applicable law or agreed to
+ in writing, software distributed under the License is distributed on an "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF
+ ANY ~ KIND, either express or implied. See the License for the specific language governing permissions and limitations under
+ the License. -->
+<xsl:stylesheet version="1.0" xmlns:xsl="http://www.w3.org/1999/XSL/Transform" xmlns:ns="http://airavata.apache.org/gsi/ssh/2012/12">
+<xsl:output method="text" />
+<xsl:template match="/ns:JobDescriptor">
+<xsl:choose>
+<xsl:when test="ns:shellName">
+#!<xsl:value-of select="ns:shellName"/>
+ </xsl:when>
+ </xsl:choose>
+<xsl:choose>
+ <xsl:when test="ns:queueName">
+#SBATCH -p <xsl:value-of select="ns:queueName"/>
+ </xsl:when>
+ </xsl:choose>
+<xsl:choose>
+ <xsl:when test="ns:nodes">
+#SBATCH -n <xsl:value-of select="ns:nodes"/>
+ </xsl:when>
+ </xsl:choose>
+ <xsl:choose>
+ <xsl:when test="ns:mailAddress">
+#SBATCH -mail-user=<xsl:value-of select="ns:mailAddress"/>
+ </xsl:when>
+ </xsl:choose>
+ <xsl:choose>
+ <xsl:when test="ns:mailType">
+#SBATCH -mail-type=<xsl:value-of select="ns:mailType"/>
+ </xsl:when>
+ </xsl:choose>
+ <xsl:choose>
+<xsl:when test="ns:acountString">
+#SBATCH -A <xsl:value-of select="ns:acountString"/>
+ </xsl:when>
+ </xsl:choose>
+ <xsl:choose>
+ <xsl:when test="ns:maxWallTime">
+#SBATCH -t <xsl:value-of select="ns:maxWallTime"/>
+ </xsl:when>
+ </xsl:choose>
+ <xsl:choose>
+ <xsl:when test="ns:jobName">
+#SBATCH -J <xsl:value-of select="ns:jobName"/>
+ </xsl:when>
+ </xsl:choose>
+ <xsl:choose>
+ <xsl:when test="ns:standardOutFile">
+#SBATCH -o <xsl:value-of select="ns:standardOutFile"/>
+ </xsl:when>
+ </xsl:choose>
+ <xsl:choose>
+ <xsl:when test="ns:standardOutFile">
+#SBATCH -e <xsl:value-of select="ns:standardErrorFile"/>
+ </xsl:when>
+ </xsl:choose>
+cd <xsl:text> </xsl:text><xsl:value-of select="ns:workingDirectory"/><xsl:text>
</xsl:text>
+ <xsl:choose><xsl:when test="ns:jobSubmitterCommand">
+<xsl:value-of select="ns:jobSubmitterCommand"/><xsl:text> </xsl:text></xsl:when></xsl:choose><xsl:value-of select="ns:executablePath"/><xsl:text> </xsl:text>
+<xsl:for-each select="ns:inputs/ns:input">
+ <xsl:value-of select="."/><xsl:text> </xsl:text>
+ </xsl:for-each>
+</xsl:template>
+
+</xsl:stylesheet>
\ No newline at end of file
[2/2] git commit: Merge branch 'master' of
https://git-wip-us.apache.org/repos/asf/airavata
Posted by la...@apache.org.
Merge branch 'master' of https://git-wip-us.apache.org/repos/asf/airavata
Project: http://git-wip-us.apache.org/repos/asf/airavata/repo
Commit: http://git-wip-us.apache.org/repos/asf/airavata/commit/4523bd9d
Tree: http://git-wip-us.apache.org/repos/asf/airavata/tree/4523bd9d
Diff: http://git-wip-us.apache.org/repos/asf/airavata/diff/4523bd9d
Branch: refs/heads/master
Commit: 4523bd9db25e6257f674f9a223b3181414fe4f6f
Parents: 4ecf18e ccf48b2
Author: lahiru <la...@apache.org>
Authored: Fri Mar 7 10:20:12 2014 -0500
Committer: lahiru <la...@apache.org>
Committed: Fri Mar 7 10:20:12 2014 -0500
----------------------------------------------------------------------
modules/integration-tests/pom.xml | 144 ++++---
.../apache/airavata/integration/BaseCaseIT.java | 405 +++++++++----------
.../airavata/integration/ForEachCaseIT.java | 32 +-
.../WorkflowIntegrationTestBase.java | 182 +++++----
.../integration/WorkflowSamplesCaseIT.java | 23 +-
.../test/resources/airavata-client.properties | 66 ---
6 files changed, 401 insertions(+), 451 deletions(-)
----------------------------------------------------------------------