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 <[email protected]> Authored: Fri Mar 7 10:19:33 2014 -0500 Committer: lahiru <[email protected]> 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 (theà "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 (theà "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
