Author: lahiru
Date: Thu Sep 5 21:04:37 2013
New Revision: 1520424
URL: http://svn.apache.org/r1520424
Log:
major changes to api implementation.
Added:
airavata/sandbox/gsissh/src/main/java/org/apache/airavata/gsi/ssh/api/Cluster.java
airavata/sandbox/gsissh/src/main/java/org/apache/airavata/gsi/ssh/api/CommandExecutor.java
airavata/sandbox/gsissh/src/main/java/org/apache/airavata/gsi/ssh/api/job/Job.java
- copied, changed from r1520111,
airavata/sandbox/gsissh/src/main/java/org/apache/airavata/gsi/ssh/api/job/JobDescriptor.java
airavata/sandbox/gsissh/src/main/java/org/apache/airavata/gsi/ssh/impl/DefaultCluster.java
- copied, changed from r1519854,
airavata/sandbox/gsissh/src/main/java/org/apache/airavata/gsi/ssh/api/Cluster.java
airavata/sandbox/gsissh/src/test/resources/sleep.pbs
airavata/sandbox/gsissh/src/test/resources/test.pbs
Removed:
airavata/sandbox/gsissh/src/main/java/org/apache/airavata/gsi/ssh/api/SSHApi.java
airavata/sandbox/gsissh/src/main/java/org/apache/airavata/gsi/ssh/api/SSHApiFactory.java
airavata/sandbox/gsissh/src/main/java/org/apache/airavata/gsi/ssh/api/job/JobDescriptor.java
airavata/sandbox/gsissh/src/main/java/org/apache/airavata/gsi/ssh/impl/DefaultSSHApi.java
Modified:
airavata/sandbox/gsissh/src/main/java/org/apache/airavata/gsi/ssh/api/AuthenticationInfo.java
airavata/sandbox/gsissh/src/main/java/org/apache/airavata/gsi/ssh/api/Core.java
airavata/sandbox/gsissh/src/main/java/org/apache/airavata/gsi/ssh/impl/DefaultJobSubmissionListener.java
airavata/sandbox/gsissh/src/main/java/org/apache/airavata/gsi/ssh/impl/MyProxyAuthenticationInfo.java
airavata/sandbox/gsissh/src/main/java/org/apache/airavata/gsi/ssh/listener/JobSubmissionListener.java
airavata/sandbox/gsissh/src/main/resources/gsissh.properties
airavata/sandbox/gsissh/src/test/java/org/apache/airavata/gsi/ssh/config/SCPToTest.java
airavata/sandbox/gsissh/src/test/java/org/apache/airavata/gsi/ssh/impl/DefaultSSHApiTest.java
Modified:
airavata/sandbox/gsissh/src/main/java/org/apache/airavata/gsi/ssh/api/AuthenticationInfo.java
URL:
http://svn.apache.org/viewvc/airavata/sandbox/gsissh/src/main/java/org/apache/airavata/gsi/ssh/api/AuthenticationInfo.java?rev=1520424&r1=1520423&r2=1520424&view=diff
==============================================================================
---
airavata/sandbox/gsissh/src/main/java/org/apache/airavata/gsi/ssh/api/AuthenticationInfo.java
(original)
+++
airavata/sandbox/gsissh/src/main/java/org/apache/airavata/gsi/ssh/api/AuthenticationInfo.java
Thu Sep 5 21:04:37 2013
@@ -25,13 +25,26 @@ package org.apache.airavata.gsi.ssh.api;
* Time: 3:38 PM
*/
+import apple.awt.ClientPropertyApplicator;
import org.ietf.jgss.GSSCredential;
+import java.util.Properties;
+
/**
* Authentication data. Could be MyProxy user name, password, could be
GSSCredentials
* or could be SSH keys.
*/
-public interface AuthenticationInfo {
+public abstract class AuthenticationInfo {
+
+ public Properties properties = new Properties();
+
+ public abstract GSSCredential getCredentials() throws SecurityException;
+
+ public Properties getProperties() {
+ return properties;
+ }
- GSSCredential getCredentials() throws SecurityException;
+ public void setProperties(Properties properties) {
+ this.properties = properties;
+ }
}
Added:
airavata/sandbox/gsissh/src/main/java/org/apache/airavata/gsi/ssh/api/Cluster.java
URL:
http://svn.apache.org/viewvc/airavata/sandbox/gsissh/src/main/java/org/apache/airavata/gsi/ssh/api/Cluster.java?rev=1520424&view=auto
==============================================================================
---
airavata/sandbox/gsissh/src/main/java/org/apache/airavata/gsi/ssh/api/Cluster.java
(added)
+++
airavata/sandbox/gsissh/src/main/java/org/apache/airavata/gsi/ssh/api/Cluster.java
Thu Sep 5 21:04:37 2013
@@ -0,0 +1,85 @@
+/*
+ *
+ * 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 (the
+ * "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.
+ *
+*/
+package org.apache.airavata.gsi.ssh.api;
+
+import com.jcraft.jsch.Session;
+import org.apache.airavata.gsi.ssh.api.job.Job;
+import org.apache.airavata.gsi.ssh.listener.JobSubmissionListener;
+
+
+public interface Cluster {
+
+ /**
+ * This will submit a job to the cluster with a given pbs file and some
parameters
+ *
+ * @param pbsFilePath
+ * @param workingDirectory
+ * @return
+ * @throws SSHApiException
+ */
+ public String submitAsyncJobWithPBS(String pbsFilePath, String
workingDirectory) throws SSHApiException;
+
+ /**
+ * This will submit the given job and not performing any monitoring
+ *
+ * @param jobDescriptor
+ * @return
+ * @throws SSHApiException
+ */
+ public String submitAsyncJob(Job jobDescriptor) throws SSHApiException;
+
+ /**
+ * This will get all the information about the cluster and store them as
parameters
+ * So that api user can extract required information about the cluster
+ *
+ * @return
+ * @throws SSHApiException
+ */
+ public Cluster loadCluster() throws SSHApiException;
+
+ /**
+ * This will copy the lFile to rFile location in configured cluster
+ *
+ * @param rFile
+ * @param lFile
+ * @return
+ * @throws SSHApiException
+ */
+ public Session scpTo(String rFile, String lFile) throws SSHApiException;
+
+ /**
+ * submit a job and register the listener so that status changes will be
triggers
+ * and appropricate action implemented in the JobSubmissionListener will
get invoked
+ *
+ * @param jobDescriptor
+ * @param listener
+ * @return
+ * @throws SSHApiException
+ */
+ public String submitAsyncJob(Job jobDescriptor, JobSubmissionListener
listener) throws SSHApiException;
+
+ /**
+ * @param jobID
+ * @return
+ * @throws SSHApiException
+ */
+ public Job getJobById(String jobID) throws SSHApiException;
+}
Added:
airavata/sandbox/gsissh/src/main/java/org/apache/airavata/gsi/ssh/api/CommandExecutor.java
URL:
http://svn.apache.org/viewvc/airavata/sandbox/gsissh/src/main/java/org/apache/airavata/gsi/ssh/api/CommandExecutor.java?rev=1520424&view=auto
==============================================================================
---
airavata/sandbox/gsissh/src/main/java/org/apache/airavata/gsi/ssh/api/CommandExecutor.java
(added)
+++
airavata/sandbox/gsissh/src/main/java/org/apache/airavata/gsi/ssh/api/CommandExecutor.java
Thu Sep 5 21:04:37 2013
@@ -0,0 +1,170 @@
+/*
+ *
+ * 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 (the
+ * "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.
+ *
+*/
+package org.apache.airavata.gsi.ssh.api;
+
+import com.jcraft.jsch.*;
+import org.apache.airavata.gsi.ssh.config.ConfigReader;
+import org.apache.airavata.gsi.ssh.jsch.ExtendedJSch;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
+
+public class CommandExecutor {
+ static {
+ JSch.setConfig("gssapi-with-mic.x509",
"org.apache.airavata.gsi.ssh.GSSContextX509");
+ JSch.setConfig("userauth.gssapi-with-mic",
"com.jcraft.jsch.UserAuthGSSAPIWithMICGSSCredentials");
+
+ }
+
+ private static final Logger log =
LoggerFactory.getLogger(CommandExecutor.class);
+ public static final String X509_CERT_DIR = "X509_CERT_DIR";
+
+ /**
+ * This will execute the given command with given session and session is
not closed at the end.
+ *
+ * @param commandInfo
+ * @param session
+ * @param commandOutput
+ * @throws SSHApiException
+ */
+ public static Session executeCommand(CommandInfo commandInfo, Session
session,
+ CommandOutput commandOutput) throws
SSHApiException {
+
+ String command = commandInfo.getCommand();
+
+ Channel channel = null;
+ try {
+ if (!session.isConnected()) {
+ session.connect();
+ }
+ channel = session.openChannel("exec");
+ ((ChannelExec) channel).setCommand(command);
+ } catch (JSchException e) {
+ session.disconnect();
+
+ throw new SSHApiException("Unable to execute command - ", e);
+ }
+
+ channel.setInputStream(null);
+ ((ChannelExec) channel).setErrStream(commandOutput.getStandardError());
+
+ try {
+ channel.connect();
+ } catch (JSchException e) {
+
+ channel.disconnect();
+ session.disconnect();
+
+ throw new SSHApiException("Unable to retrieve command output.
Command - " + command, e);
+ }
+
+ commandOutput.onOutput(channel);
+ //Only disconnecting the channel, session can be reused
+ channel.disconnect();
+ return session;
+ }
+
+ /**
+ * This will not reuse any session, it will create the session and close
it at the end
+ *
+ * @param commandInfo Encapsulated information about command. E.g
:- executable name
+ * parameters etc ...
+ * @param serverInfo The SSHing server information.
+ * @param authenticationInfo Security data needs to be communicated with
remote server.
+ * @param commandOutput The output of the command.
+ * @throws SSHApiException
+ */
+ public static void executeCommand(CommandInfo commandInfo, ServerInfo
serverInfo,
+ AuthenticationInfo authenticationInfo,
+ CommandOutput commandOutput,
ConfigReader configReader) throws SSHApiException {
+ System.setProperty(X509_CERT_DIR, (String)
authenticationInfo.getProperties().get("X509_CERT_DIR"));
+ JSch jsch = new ExtendedJSch();
+
+ log.info("Connecting to server - " + serverInfo.getHost() + ":" +
serverInfo.getPort() + " with user name - "
+ + serverInfo.getUserName());
+
+ Session session = null;
+
+ try {
+ session = jsch.getSession(serverInfo.getUserName(),
serverInfo.getHost(), serverInfo.getPort());
+ } catch (JSchException e) {
+ throw new SSHApiException("An exception occurred while creating
SSH session." +
+ "Connecting server - " + serverInfo.getHost() + ":" +
serverInfo.getPort() +
+ " connecting user name - "
+ + serverInfo.getUserName(), e);
+ }
+
+ java.util.Properties config = configReader.getProperties();
+ session.setConfig(config);
+
+ // Not a good way, but we dont have any choice
+ if (session instanceof ExtendedSession) {
+ ((ExtendedSession)
session).setAuthenticationInfo(authenticationInfo);
+ }
+
+ try {
+ session.connect();
+ } catch (JSchException e) {
+ throw new SSHApiException("An exception occurred while connecting
to server." +
+ "Connecting server - " + serverInfo.getHost() + ":" +
serverInfo.getPort() +
+ " connecting user name - "
+ + serverInfo.getUserName(), e);
+ }
+
+ String command = commandInfo.getCommand();
+
+ Channel channel = null;
+ try {
+ channel = session.openChannel("exec");
+ ((ChannelExec) channel).setCommand(command);
+ } catch (JSchException e) {
+ session.disconnect();
+
+ throw new SSHApiException("Unable to execute command - " + command
+
+ " on server - " + serverInfo.getHost() + ":" +
serverInfo.getPort() +
+ " connecting user name - "
+ + serverInfo.getUserName(), e);
+ }
+
+
+ channel.setInputStream(null);
+ ((ChannelExec) channel).setErrStream(commandOutput.getStandardError());
+
+ try {
+ channel.connect();
+ } catch (JSchException e) {
+
+ channel.disconnect();
+ session.disconnect();
+
+ throw new SSHApiException("Unable to retrieve command output.
Command - " + command +
+ " on server - " + serverInfo.getHost() + ":" +
serverInfo.getPort() +
+ " connecting user name - "
+ + serverInfo.getUserName(), e);
+ }
+
+ commandOutput.onOutput(channel);
+
+ channel.disconnect();
+ session.disconnect();
+ }
+
+
+}
Modified:
airavata/sandbox/gsissh/src/main/java/org/apache/airavata/gsi/ssh/api/Core.java
URL:
http://svn.apache.org/viewvc/airavata/sandbox/gsissh/src/main/java/org/apache/airavata/gsi/ssh/api/Core.java?rev=1520424&r1=1520423&r2=1520424&view=diff
==============================================================================
---
airavata/sandbox/gsissh/src/main/java/org/apache/airavata/gsi/ssh/api/Core.java
(original)
+++
airavata/sandbox/gsissh/src/main/java/org/apache/airavata/gsi/ssh/api/Core.java
Thu Sep 5 21:04:37 2013
@@ -20,10 +20,10 @@
*/
package org.apache.airavata.gsi.ssh.api;
-import org.apache.airavata.gsi.ssh.api.job.JobDescriptor;
+import org.apache.airavata.gsi.ssh.api.job.Job;
public class Core {
- private JobDescriptor job;
+ private Job job;
private String id;
public Core(String id) {
@@ -45,11 +45,11 @@ public class Core {
/**
* @return job running on the core
*/
- public JobDescriptor getJob() {
+ public Job getJob() {
return job;
}
- public void setJob(JobDescriptor job) {
+ public void setJob(Job job) {
this.job = job;
}
Copied:
airavata/sandbox/gsissh/src/main/java/org/apache/airavata/gsi/ssh/api/job/Job.java
(from r1520111,
airavata/sandbox/gsissh/src/main/java/org/apache/airavata/gsi/ssh/api/job/JobDescriptor.java)
URL:
http://svn.apache.org/viewvc/airavata/sandbox/gsissh/src/main/java/org/apache/airavata/gsi/ssh/api/job/Job.java?p2=airavata/sandbox/gsissh/src/main/java/org/apache/airavata/gsi/ssh/api/job/Job.java&p1=airavata/sandbox/gsissh/src/main/java/org/apache/airavata/gsi/ssh/api/job/JobDescriptor.java&r1=1520111&r2=1520424&rev=1520424&view=diff
==============================================================================
---
airavata/sandbox/gsissh/src/main/java/org/apache/airavata/gsi/ssh/api/job/JobDescriptor.java
(original)
+++
airavata/sandbox/gsissh/src/main/java/org/apache/airavata/gsi/ssh/api/job/Job.java
Thu Sep 5 21:04:37 2013
@@ -30,22 +30,22 @@ import java.util.List;
* This class define a job with required parameters, based on this
configuration API is generating a Pbs script and
* submit the job to the computing resource
*/
-public class JobDescriptor {
+public class Job {
private JobDescriptorDocument jobDescriptionDocument;
- public JobDescriptor() {
+ public Job() {
jobDescriptionDocument = JobDescriptorDocument.Factory.newInstance();
jobDescriptionDocument.addNewJobDescriptor();
}
- public JobDescriptor(JobDescriptorDocument jobDescriptorDocument) {
+ public Job(JobDescriptorDocument jobDescriptorDocument) {
this.jobDescriptionDocument = jobDescriptorDocument;
}
- public JobDescriptor(CommandOutput commandOutput) {
+ public Job(CommandOutput commandOutput) {
jobDescriptionDocument = JobDescriptorDocument.Factory.newInstance();
jobDescriptionDocument.addNewJobDescriptor();
}
@@ -59,11 +59,11 @@ public class JobDescriptor {
return this.jobDescriptionDocument;
}
- public static JobDescriptor fromXML(String xml)
+ public static Job fromXML(String xml)
throws XmlException {
JobDescriptorDocument parse = JobDescriptorDocument.Factory
.parse(xml);
- JobDescriptor jobDescriptor = new JobDescriptor(parse);
+ Job jobDescriptor = new Job(parse);
return jobDescriptor;
}
Copied:
airavata/sandbox/gsissh/src/main/java/org/apache/airavata/gsi/ssh/impl/DefaultCluster.java
(from r1519854,
airavata/sandbox/gsissh/src/main/java/org/apache/airavata/gsi/ssh/api/Cluster.java)
URL:
http://svn.apache.org/viewvc/airavata/sandbox/gsissh/src/main/java/org/apache/airavata/gsi/ssh/impl/DefaultCluster.java?p2=airavata/sandbox/gsissh/src/main/java/org/apache/airavata/gsi/ssh/impl/DefaultCluster.java&p1=airavata/sandbox/gsissh/src/main/java/org/apache/airavata/gsi/ssh/api/Cluster.java&r1=1519854&r2=1520424&rev=1520424&view=diff
==============================================================================
---
airavata/sandbox/gsissh/src/main/java/org/apache/airavata/gsi/ssh/api/Cluster.java
(original)
+++
airavata/sandbox/gsissh/src/main/java/org/apache/airavata/gsi/ssh/impl/DefaultCluster.java
Thu Sep 5 21:04:37 2013
@@ -18,15 +18,472 @@
* under the License.
*
*/
-package org.apache.airavata.gsi.ssh.api;
+package org.apache.airavata.gsi.ssh.impl;
-public class Cluster {
+import com.jcraft.jsch.*;
+import org.apache.airavata.gsi.ssh.api.*;
+import org.apache.airavata.gsi.ssh.api.job.Job;
+import org.apache.airavata.gsi.ssh.config.ConfigReader;
+import org.apache.airavata.gsi.ssh.jsch.ExtendedJSch;
+import org.apache.airavata.gsi.ssh.listener.JobSubmissionListener;
+import org.apache.commons.io.FileUtils;
+import org.apache.commons.io.FilenameUtils;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
+
+import javax.xml.transform.*;
+import javax.xml.transform.stream.StreamResult;
+import javax.xml.transform.stream.StreamSource;
+import java.io.*;
+import java.security.SecureRandom;
+import java.util.ArrayList;
+
+public class DefaultCluster implements Cluster {
+ static {
+ JSch.setConfig("gssapi-with-mic.x509",
"org.apache.airavata.gsi.ssh.GSSContextX509");
+ JSch.setConfig("userauth.gssapi-with-mic",
"com.jcraft.jsch.UserAuthGSSAPIWithMICGSSCredentials");
+
+ }
+
+ private static final Logger log =
LoggerFactory.getLogger(DefaultCluster.class);
+ public static final String X509_CERT_DIR = "X509_CERT_DIR";
+ public static final String POLLING_FREQUENCEY = "polling.frequency";
+ public static final String SSH_SESSION_TIMEOUT = "ssh.session.timeout";
private Machine[] Nodes;
-/**
- *
- * @return cluster Nodes as array of machines
- */
+
+ private ServerInfo serverInfo;
+
+ private AuthenticationInfo authenticationInfo;
+
+ private Session session;
+
+ private static JSch jSch;
+
+ private ConfigReader configReader;
+
+ public DefaultCluster(ServerInfo serverInfo, AuthenticationInfo
authenticationInfo) throws SSHApiException {
+
+ this.serverInfo = serverInfo;
+
+ this.authenticationInfo = authenticationInfo;
+
+ System.setProperty(X509_CERT_DIR, (String)
authenticationInfo.getProperties().get(X509_CERT_DIR));
+
+ try {
+ this.configReader = new ConfigReader();
+ } catch (IOException e) {
+ throw new SSHApiException("Unable to load system configurations.",
e);
+ }
+ this.jSch = new ExtendedJSch();
+
+ log.info("Connecting to server - " + serverInfo.getHost() + ":" +
serverInfo.getPort() + " with user name - "
+ + serverInfo.getUserName());
+
+ try {
+ session = jSch.getSession(serverInfo.getUserName(),
serverInfo.getHost(), serverInfo.getPort());
+
session.setTimeout(Integer.parseInt(configReader.getConfiguration(SSH_SESSION_TIMEOUT)));
+ } catch (JSchException e) {
+ throw new SSHApiException("An exception occurred while creating
SSH session." +
+ "Connecting server - " + serverInfo.getHost() + ":" +
serverInfo.getPort() +
+ " connecting user name - "
+ + serverInfo.getUserName(), e);
+ }
+
+ java.util.Properties config = this.configReader.getProperties();
+ session.setConfig(config);
+
+ // Not a good way, but we dont have any choice
+ if (session instanceof ExtendedSession) {
+ ((ExtendedSession)
session).setAuthenticationInfo(authenticationInfo);
+ }
+
+ try {
+ session.connect();
+ } catch (JSchException e) {
+ throw new SSHApiException("An exception occurred while connecting
to server." +
+ "Connecting server - " + serverInfo.getHost() + ":" +
serverInfo.getPort() +
+ " connecting user name - "
+ + serverInfo.getUserName(), e);
+ }
+ System.out.println(session.isConnected());
+ }
+
+
+
+ public String submitAsyncJobWithPBS(String pbsFilePath, String
workingDirectory) throws SSHApiException {
+
+ this.scpTo(workingDirectory, pbsFilePath);
+
+ // since this is a constant we do not ask users to fill this
+ RawCommandInfo rawCommandInfo = new
RawCommandInfo("/opt/torque/bin/qsub " +
+ workingDirectory + File.separator +
FilenameUtils.getName(pbsFilePath));
+
+ StandardOutReader jobIDReaderCommandOutput = new StandardOutReader();
+ CommandExecutor.executeCommand(rawCommandInfo, this.session,
jobIDReaderCommandOutput);
+
+ //Check whether pbs submission is successful or not, if it failed
throw and exception in submitJob method
+ // with the error thrown in qsub command
+ if (jobIDReaderCommandOutput.getErrorifAvailable().equals("")) {
+ return jobIDReaderCommandOutput.getStdOutput();
+ } else {
+ throw new
SSHApiException(jobIDReaderCommandOutput.getStandardError().toString());
+ }
+ }
+
+ public String submitAsyncJob(Job jobDescriptor) throws SSHApiException {
+ TransformerFactory factory = TransformerFactory.newInstance();
+ String xsltPath = "src" + File.separator + "main" + File.separator +
"resources" + File.separator + "PBSTemplate.xslt";
+ Source xslt = new StreamSource(new File(xsltPath));
+ Transformer transformer = null;
+ StringWriter results = new StringWriter();
+ File tempPBSFile = null;
+ try {
+ // generate the pbs script using xslt
+ transformer = factory.newTransformer(xslt);
+ Source text = new StreamSource(new
ByteArrayInputStream(jobDescriptor.toXML().getBytes()));
+ transformer.transform(text, new StreamResult(results));
+
+ log.info("generated PBS:" + results.toString());
+
+ // creating a temporary file using pbs script generated above
+ int number = new SecureRandom().nextInt();
+ number = (number < 0 ? -number : number);
+
+ tempPBSFile = new File(Integer.toString(number) + ".pbs");
+ FileUtils.writeStringToFile(tempPBSFile, results.toString());
+
+ //reusing submitAsyncJobWithPBS method to submit a job
+
+ String jobID =
this.submitAsyncJobWithPBS(tempPBSFile.getAbsolutePath(),
+ jobDescriptor.getWorkingDirectory());
+ log.info("Job has successfully submitted, JobID : " + jobID);
+ return jobID.replace("\n", "");
+ } catch (TransformerConfigurationException e) {
+ throw new SSHApiException("Error parsing PBS transformation", e);
+ } catch (TransformerException e) {
+ throw new SSHApiException("Error generating PBS script", e);
+ } catch (IOException e) {
+ throw new SSHApiException("An exception occurred while connecting
to server." +
+ "Connecting server - " + serverInfo.getHost() + ":" +
serverInfo.getPort() +
+ " connecting user name - "
+ + serverInfo.getUserName(), e);
+ } finally {
+ tempPBSFile.delete();
+ }
+ }
+
+
+ public Cluster loadCluster() throws SSHApiException {
+ RawCommandInfo rawCommandInfo = new
RawCommandInfo("/opt/torque/bin/qnodes");
+
+ StandardOutReader stdOutReader = new StandardOutReader();
+ CommandExecutor.executeCommand(rawCommandInfo, this.getSession(),
stdOutReader);
+ if (!stdOutReader.getErrorifAvailable().equals("")) {
+ throw new
SSHApiException(stdOutReader.getStandardError().toString());
+ }
+ String result = stdOutReader.getStdOutput();
+ String[] Nodes = result.split("\n");
+ String[] line;
+ String header, value;
+ Machine Node;
+ Core[] Cores = null;
+ ArrayList<Machine> Machines = new ArrayList<Machine>();
+ int i = 0;
+ while (i < Nodes.length) {
+ Node = new Machine();
+ Node.setName(Nodes[i]);
+ i++;
+
+ while (i < Nodes.length) {
+ if (!Nodes[i].startsWith(" ")) {
+ i++;
+ break;
+ }
+
+ line = Nodes[i].split("=");
+ header = line[0].trim();
+ value = line[1].trim();
+
+ if ("state".equals(header))
+ Node.setState(value);
+ else if ("np".equals(header)) {
+ Node.setNp(value);
+ int np = Integer.parseInt(Node.getNp());
+ Cores = new Core[np];
+ for (int n = 0; n < np; n++) {
+ Cores[n] = new Core("" + n);
+ }
+ } else if ("ntype".equals(header))
+ Node.setNtype(value);
+ else if ("jobs".equals(header)) {
+ String[] jobs = value.split(", ");
+ Job jo = new Job();
+ //Job[] Jobs = new Job[jobs.length];
+ for (int j = 0; j < jobs.length; j++) {
+ String[] c = jobs[j].split("/");
+ String Jid = c[1];
+ jo = this.getJobById(Jid);
+ int core = Integer.parseInt(c[0]);
+ Cores[core].setJob(jo);
+
+ }
+
+
+ }
+ i++;
+ }
+ Node.setCores(Cores);
+ Machines.add(Node);
+ }
+ this.setNodes(Machines.toArray(new Machine[Machines.size()]));
+ return this;
+ }
+
+ public Job getJobById(String jobID) throws SSHApiException {
+ RawCommandInfo rawCommandInfo = new
RawCommandInfo("/opt/torque/bin/qstat -f " + jobID);
+
+ StandardOutReader stdOutReader = new StandardOutReader();
+ CommandExecutor.executeCommand(rawCommandInfo,this.getSession(),
stdOutReader);
+ if (!stdOutReader.getErrorifAvailable().equals("")) {
+ throw new
SSHApiException(stdOutReader.getStandardError().toString());
+ }
+ String result = stdOutReader.getStdOutput();
+ String[] info = result.split("\n");
+ Job jobDescriptor = new Job();
+ String header = "";
+ String value = "";
+ String[] line;
+ for (int i = 0; i < info.length; i++) {
+ if (info[i].contains("=")) {
+ line = info[i].split("=", 2);
+ } else {
+ line = info[i].split(":", 2);
+ }
+ if (line.length >= 2) {
+ header = line[0].trim();
+ log.debug("Header = " + header);
+ value = line[1].trim();
+ log.debug("value = " + value);
+
+ if (header.equals("Variable_List")) {
+ while (info[i + 1].startsWith("\t")) {
+ value += info[i + 1];
+ i++;
+ }
+ value = value.replaceAll("\t", "");
+ jobDescriptor.setVariableList(value);
+ } else if ("Job Id".equals(header)) {
+ jobDescriptor.setJobID(value);
+ } else if ("Job_Name".equals(header)) {
+ jobDescriptor.setJobName(value);
+ } else if ("Account_Name".equals(header)) {
+ jobDescriptor.setAcountString(value);
+ } else if ("job_state".equals(header)) {
+ jobDescriptor.setStatus(value);
+ } else if ("Job_Owner".equals(header)) {
+ jobDescriptor.setOwner(value);
+ } else if ("resources_used.cput".equals(header)) {
+ jobDescriptor.setUsedCPUTime(value);
+ } else if ("resources_used.mem".equals(header)) {
+ jobDescriptor.setUsedMemory(value);
+ } else if ("resources_used.walltime".equals(header)) {
+ jobDescriptor.setEllapsedTime(value);
+ } else if ("job_state".equals(header)) {
+ jobDescriptor.setStatus(value);
+ } else if ("queue".equals(header))
+ jobDescriptor.setQueueName(value);
+ else if ("ctime".equals(header)) {
+ jobDescriptor.setCTime(value);
+ } else if ("qtime".equals(header)) {
+ jobDescriptor.setQTime(value);
+ } else if ("mtime".equals(header)) {
+ jobDescriptor.setMTime(value);
+ } else if ("start_time".equals(header)) {
+ jobDescriptor.setSTime(value);
+ } else if ("comp_time".equals(header)) {
+ jobDescriptor.setCompTime(value);
+ } else if ("exec_host".equals(header)) {
+ jobDescriptor.setExecuteNode(value);
+ } else if ("Output_Path".equals(header)) {
+ if (info[i + 1].contains("=") || info[i + 1].contains(":"))
+ jobDescriptor.setStandardOutFile(value);
+ else {
+ jobDescriptor.setStandardOutFile(value + info[i +
1].trim());
+ i++;
+ }
+ } else if ("Error_Path".equals(header)) {
+ if (info[i + 1].contains("=") || info[i + 1].contains(":"))
+ jobDescriptor.setStandardErrorFile(value);
+ else {
+ String st = info[i + 1].trim();
+ jobDescriptor.setStandardErrorFile(value + st);
+ i++;
+ }
+
+ } else if ("submit_args".equals(header)) {
+ while (i + 1 < info.length) {
+ if (info[i + 1].startsWith("\t")) {
+ value += info[i + 1];
+ i++;
+ } else
+ break;
+ }
+ value = value.replaceAll("\t", "");
+ jobDescriptor.setSubmitArgs(value);
+ }
+ }
+ }
+ return jobDescriptor;
+ }
+
+ public Session scpTo(String rFile, String lFile) throws SSHApiException {
+ FileInputStream fis = null;
+ String prefix = null;
+ if (new File(lFile).isDirectory()) {
+ prefix = lFile + File.separator;
+ }
+ boolean ptimestamp = true;
+ try {
+ // exec 'scp -t rfile' remotely
+ String command = "scp " + (ptimestamp ? "-p" : "") + " -t " +
rFile;
+ Channel channel = session.openChannel("exec");
+ ((ChannelExec) channel).setCommand(command);
+
+ // get I/O streams for remote scp
+ OutputStream out = channel.getOutputStream();
+ InputStream in = channel.getInputStream();
+
+ channel.connect();
+
+ if (checkAck(in) != 0) {
+ System.exit(0);
+ }
+
+ File _lfile = new File(lFile);
+
+ if (ptimestamp) {
+ command = "T " + (_lfile.lastModified() / 1000) + " 0";
+ // The access time should be sent here,
+ // but it is not accessible with JavaAPI ;-<
+ command += (" " + (_lfile.lastModified() / 1000) + " 0\n");
+ out.write(command.getBytes());
+ out.flush();
+ if (checkAck(in) != 0) {
+ System.exit(0);
+ }
+ }
+
+ // send "C0644 filesize filename", where filename should not
include '/'
+ long filesize = _lfile.length();
+ command = "C0644 " + filesize + " ";
+ if (lFile.lastIndexOf('/') > 0) {
+ command += lFile.substring(lFile.lastIndexOf('/') + 1);
+ } else {
+ command += lFile;
+ }
+ command += "\n";
+ out.write(command.getBytes());
+ out.flush();
+ if (checkAck(in) != 0) {
+ System.exit(0);
+ }
+
+ // send a content of lFile
+ fis = new FileInputStream(lFile);
+ byte[] buf = new byte[1024];
+ while (true) {
+ int len = fis.read(buf, 0, buf.length);
+ if (len <= 0) break;
+ out.write(buf, 0, len); //out.flush();
+ }
+ fis.close();
+ fis = null;
+ // send '\0'
+ buf[0] = 0;
+ out.write(buf, 0, 1);
+ out.flush();
+ if (checkAck(in) != 0) {
+ System.exit(0);
+ }
+ out.close();
+ // We are not disconnecting the session
+// session.disconnect();
+ channel.disconnect();
+ } catch (Exception e) {
+ log.error(e.getMessage());
+ throw new SSHApiException("Error occured during file transfer
operation: " + e);
+ }
+ return session;
+ }
+
+
+ static int checkAck(InputStream in) throws IOException {
+ int b = in.read();
+ if (b == 0) return b;
+ if (b == -1) return b;
+
+ if (b == 1 || b == 2) {
+ StringBuffer sb = new StringBuffer();
+ int c;
+ do {
+ c = in.read();
+ sb.append((char) c);
+ }
+ while (c != '\n');
+ if (b == 1) { // error
+ System.out.print(sb.toString());
+ }
+ if (b == 2) { // fatal error
+ System.out.print(sb.toString());
+ }
+ }
+ return b;
+ }
+
+ public String submitAsyncJob(Job jobDescriptor, JobSubmissionListener
listener) throws SSHApiException {
+ String jobID = this.submitAsyncJob(jobDescriptor);
+ try {
+
Thread.sleep(Long.parseLong(configReader.getConfiguration(POLLING_FREQUENCEY)));
+ } catch (InterruptedException e) {
+ log.error("Error during job status monitoring");
+ throw new SSHApiException("Error during job status monitoring", e);
+ }
+ // Get the job status first
+ Job jobById = this.getJobById(jobID);
+
+ while (!jobById.getStatus().equals(JobStatus.C.toString())) {
+ if
(!jobById.getStatus().equals(listener.getJobStatus().toString())) {
+
listener.setJobStatus(JobStatus.fromString(jobById.getStatus()));
+ listener.statusChanged(jobById);
+ }
+ try {
+
Thread.sleep(Long.parseLong(configReader.getConfiguration(POLLING_FREQUENCEY)));
+ } catch (InterruptedException e) {
+ log.error("Error during job status monitoring");
+ throw new SSHApiException("Error during job status
monitoring", e);
+ }
+ jobById = this.getJobById(jobID);
+ }
+ listener.statusChanged(jobById);
+ return null; //To change body of implemented methods use File |
Settings | File Templates.
+ }
+
+ public void setServerInfo(ServerInfo serverInfo) {
+ this.serverInfo = serverInfo;
+ }
+
+ public void setAuthenticationInfo(AuthenticationInfo authenticationInfo) {
+ this.authenticationInfo = authenticationInfo;
+ }
+
+ public void setSession(Session session) {
+ this.session = session;
+ }
+
+ /**
+ * @return cluster Nodes as array of machines
+ */
public Machine[] getNodes() {
return Nodes;
}
@@ -35,4 +492,20 @@ public class Cluster {
this.Nodes = Nodes;
}
+ public ServerInfo getServerInfo() {
+ return serverInfo;
+ }
+
+ public AuthenticationInfo getAuthenticationInfo() {
+ return authenticationInfo;
+ }
+
+ /**
+ * This gaurantee to return a valid session
+ *
+ * @return
+ */
+ public Session getSession() {
+ return this.session;
+ }
}
Modified:
airavata/sandbox/gsissh/src/main/java/org/apache/airavata/gsi/ssh/impl/DefaultJobSubmissionListener.java
URL:
http://svn.apache.org/viewvc/airavata/sandbox/gsissh/src/main/java/org/apache/airavata/gsi/ssh/impl/DefaultJobSubmissionListener.java?rev=1520424&r1=1520423&r2=1520424&view=diff
==============================================================================
---
airavata/sandbox/gsissh/src/main/java/org/apache/airavata/gsi/ssh/impl/DefaultJobSubmissionListener.java
(original)
+++
airavata/sandbox/gsissh/src/main/java/org/apache/airavata/gsi/ssh/impl/DefaultJobSubmissionListener.java
Thu Sep 5 21:04:37 2013
@@ -21,12 +21,12 @@
package org.apache.airavata.gsi.ssh.impl;
import org.apache.airavata.gsi.ssh.api.SSHApiException;
-import org.apache.airavata.gsi.ssh.api.job.JobDescriptor;
+import org.apache.airavata.gsi.ssh.api.job.Job;
import org.apache.airavata.gsi.ssh.listener.JobSubmissionListener;
public class DefaultJobSubmissionListener extends JobSubmissionListener {
- public void statusChanged(JobDescriptor jobDescriptor) throws
SSHApiException {
+ public void statusChanged(Job jobDescriptor) throws SSHApiException {
System.out.println("Job status has changed : " +
jobDescriptor.getStatus());
}
}
Modified:
airavata/sandbox/gsissh/src/main/java/org/apache/airavata/gsi/ssh/impl/MyProxyAuthenticationInfo.java
URL:
http://svn.apache.org/viewvc/airavata/sandbox/gsissh/src/main/java/org/apache/airavata/gsi/ssh/impl/MyProxyAuthenticationInfo.java?rev=1520424&r1=1520423&r2=1520424&view=diff
==============================================================================
---
airavata/sandbox/gsissh/src/main/java/org/apache/airavata/gsi/ssh/impl/MyProxyAuthenticationInfo.java
(original)
+++
airavata/sandbox/gsissh/src/main/java/org/apache/airavata/gsi/ssh/impl/MyProxyAuthenticationInfo.java
Thu Sep 5 21:04:37 2013
@@ -26,14 +26,17 @@ import org.globus.myproxy.MyProxy;
import org.globus.myproxy.MyProxyException;
import org.ietf.jgss.GSSCredential;
+import java.util.Properties;
+
/**
* User: AmilaJ ([email protected])
* Date: 8/14/13
* Time: 5:22 PM
*/
-public class MyProxyAuthenticationInfo implements AuthenticationInfo {
+public class MyProxyAuthenticationInfo extends AuthenticationInfo {
+ public static final String X509_CERT_DIR = "X509_CERT_DIR";
private String userName;
private String password;
private String myProxyUrl;
@@ -41,12 +44,13 @@ public class MyProxyAuthenticationInfo i
private int lifeTime;
public MyProxyAuthenticationInfo(String userName, String password, String
myProxyUrl, int myProxyPort,
- int life) {
+ int life, String certificatePath) {
this.userName = userName;
this.password = password;
this.myProxyUrl = myProxyUrl;
this.myProxyPort = myProxyPort;
this.lifeTime = life;
+ properties.setProperty(X509_CERT_DIR, certificatePath);
}
public String getUserName() {
@@ -89,7 +93,7 @@ public class MyProxyAuthenticationInfo i
this.lifeTime = lifeTime;
}
- public GSSCredential getCredentials() throws SecurityException{
+ public GSSCredential getCredentials() throws SecurityException {
return getMyProxyCredentials();
}
@@ -101,4 +105,6 @@ public class MyProxyAuthenticationInfo i
throw new SecurityException("Error getting proxy credentials", e);
}
}
+
+
}
Modified:
airavata/sandbox/gsissh/src/main/java/org/apache/airavata/gsi/ssh/listener/JobSubmissionListener.java
URL:
http://svn.apache.org/viewvc/airavata/sandbox/gsissh/src/main/java/org/apache/airavata/gsi/ssh/listener/JobSubmissionListener.java?rev=1520424&r1=1520423&r2=1520424&view=diff
==============================================================================
---
airavata/sandbox/gsissh/src/main/java/org/apache/airavata/gsi/ssh/listener/JobSubmissionListener.java
(original)
+++
airavata/sandbox/gsissh/src/main/java/org/apache/airavata/gsi/ssh/listener/JobSubmissionListener.java
Thu Sep 5 21:04:37 2013
@@ -21,7 +21,7 @@
package org.apache.airavata.gsi.ssh.listener;
import org.apache.airavata.gsi.ssh.api.SSHApiException;
-import org.apache.airavata.gsi.ssh.api.job.JobDescriptor;
+import org.apache.airavata.gsi.ssh.api.job.Job;
import org.apache.airavata.gsi.ssh.impl.JobStatus;
/**
@@ -40,7 +40,7 @@ public abstract class JobSubmissionListe
* @param jobDescriptor
* @throws SSHApiException
*/
- public abstract void statusChanged(JobDescriptor jobDescriptor) throws
SSHApiException;
+ public abstract void statusChanged(Job jobDescriptor) throws
SSHApiException;
public JobStatus getJobStatus() {
return jobStatus;
Modified: airavata/sandbox/gsissh/src/main/resources/gsissh.properties
URL:
http://svn.apache.org/viewvc/airavata/sandbox/gsissh/src/main/resources/gsissh.properties?rev=1520424&r1=1520423&r2=1520424&view=diff
==============================================================================
--- airavata/sandbox/gsissh/src/main/resources/gsissh.properties (original)
+++ airavata/sandbox/gsissh/src/main/resources/gsissh.properties Thu Sep 5
21:04:37 2013
@@ -1,3 +1,5 @@
# Specifies system level configurations as a key/value pairs.
-StrictHostKeyChecking=no
\ No newline at end of file
+StrictHostKeyChecking=no
+polling.frequency=60000
+ssh.session.timeout=360000
\ No newline at end of file
Modified:
airavata/sandbox/gsissh/src/test/java/org/apache/airavata/gsi/ssh/config/SCPToTest.java
URL:
http://svn.apache.org/viewvc/airavata/sandbox/gsissh/src/test/java/org/apache/airavata/gsi/ssh/config/SCPToTest.java?rev=1520424&r1=1520423&r2=1520424&view=diff
==============================================================================
---
airavata/sandbox/gsissh/src/test/java/org/apache/airavata/gsi/ssh/config/SCPToTest.java
(original)
+++
airavata/sandbox/gsissh/src/test/java/org/apache/airavata/gsi/ssh/config/SCPToTest.java
Thu Sep 5 21:04:37 2013
@@ -64,7 +64,7 @@ public class SCPToTest {
// Create authentication
AuthenticationInfo authenticationInfo
= new MyProxyAuthenticationInfo(myProxyUserName,
myProxyPassword, "myproxy.teragrid.org",
- 7512, 17280000);
+ 7512, 17280000,certificateLocation);
ServerInfo serverInfo = new ServerInfo("ogce" ,"trestles.sdsc.edu");
SCPTo scpTo = new
SCPTo(serverInfo,authenticationInfo,this.certificateLocation,new
ConfigReader());
scpTo.scpTo(rFilePath, lFilePath);
Modified:
airavata/sandbox/gsissh/src/test/java/org/apache/airavata/gsi/ssh/impl/DefaultSSHApiTest.java
URL:
http://svn.apache.org/viewvc/airavata/sandbox/gsissh/src/test/java/org/apache/airavata/gsi/ssh/impl/DefaultSSHApiTest.java?rev=1520424&r1=1520423&r2=1520424&view=diff
==============================================================================
---
airavata/sandbox/gsissh/src/test/java/org/apache/airavata/gsi/ssh/impl/DefaultSSHApiTest.java
(original)
+++
airavata/sandbox/gsissh/src/test/java/org/apache/airavata/gsi/ssh/impl/DefaultSSHApiTest.java
Thu Sep 5 21:04:37 2013
@@ -22,7 +22,8 @@
package org.apache.airavata.gsi.ssh.impl;
import org.apache.airavata.gsi.ssh.api.*;
-import org.apache.airavata.gsi.ssh.api.job.JobDescriptor;
+import org.apache.airavata.gsi.ssh.api.job.Job;
+import org.apache.airavata.gsi.ssh.config.ConfigReader;
import org.testng.AssertJUnit;
import org.testng.annotations.BeforeTest;
import org.testng.annotations.Test;
@@ -46,11 +47,12 @@ public class DefaultSSHApiTest {
private String certificateLocation;
private String pbsFilePath;
private String workingDirectory;
+ private String jobID;
@BeforeTest
public void setUp() throws Exception {
-// System.setProperty("myproxy.user", "ogce");
-// System.setProperty("myproxy.password", "");
+ System.setProperty("myproxy.user", "ogce");
+ System.setProperty("myproxy.password", "Jdas7wph");
System.setProperty("basedir",
"/Users/lahirugunathilake/work/airavata/sandbox/gsissh");
myProxyUserName = System.getProperty("myproxy.user");
myProxyPassword = System.getProperty("myproxy.password");
@@ -83,7 +85,7 @@ public class DefaultSSHApiTest {
// Create authentication
AuthenticationInfo authenticationInfo
= new MyProxyAuthenticationInfo(myProxyUserName,
myProxyPassword, "myproxy.teragrid.org",
- 7512, 17280000);
+ 7512, 17280000,certificateLocation);
// Create command
CommandInfo commandInfo = new RawCommandInfo("/bin/ls");
@@ -94,58 +96,32 @@ public class DefaultSSHApiTest {
// Output
CommandOutput commandOutput = new SystemCommandOutput();
- // Get the API
- SSHApi sshApi = SSHApiFactory.createSSHApi(this.certificateLocation);
-
// Execute command
- sshApi.executeCommand(commandInfo, serverInfo, authenticationInfo,
commandOutput);
+ CommandExecutor.executeCommand(commandInfo, serverInfo,
authenticationInfo, commandOutput, new ConfigReader());
}
- @Test
- public void testSubmitSimpleCommand() throws Exception {
- // Create authentication
- AuthenticationInfo authenticationInfo
- = new MyProxyAuthenticationInfo(myProxyUserName,
myProxyPassword, "myproxy.teragrid.org",
- 7512, 17280000);
-
- // Create command
- CommandInfo commandInfo = new RawCommandInfo("/opt/torque/bin/qsub
/home/ogce/test.pbs");
-
- // Server info
- ServerInfo serverInfo = new ServerInfo("ogce", "trestles.sdsc.edu");
-
- // Output
- CommandOutput commandOutput = new SystemCommandOutput();
-
- // Get the API
- SSHApi sshApi = SSHApiFactory.createSSHApi(this.certificateLocation);
-
- // Execute command
- sshApi.executeCommand(commandInfo, serverInfo, authenticationInfo,
commandOutput);
- }
@Test
public void testSubmitAsyncJobWithPBS() throws Exception {
// Create authentication
AuthenticationInfo authenticationInfo
= new MyProxyAuthenticationInfo(myProxyUserName,
myProxyPassword, "myproxy.teragrid.org",
- 7512, 17280000);
+ 7512, 17280000,certificateLocation);
// Server info
ServerInfo serverInfo = new ServerInfo("ogce", "trestles.sdsc.edu");
- // Get the API
- SSHApi sshApi = SSHApiFactory.createSSHApi(this.certificateLocation);
+ Cluster trestles = new DefaultCluster(serverInfo, authenticationInfo);
// Execute command
System.out.println("Target PBS file path: " + workingDirectory);
System.out.println("Local PBS File path: " + pbsFilePath);
- JobDescriptor jobDescriptor = new JobDescriptor();
+ Job jobDescriptor = new Job();
//Here we give working directory as a file name to replace the file,
to allow multiple test runs with the same
//file name
jobDescriptor.setWorkingDirectory(workingDirectory);
- String jobID = sshApi.submitAsyncJobWithPBS(serverInfo,
authenticationInfo, pbsFilePath, jobDescriptor);
+ String jobID = trestles.submitAsyncJobWithPBS(pbsFilePath,
workingDirectory);
System.out.println("JobID returned : " + jobID);
}
@@ -154,20 +130,20 @@ public class DefaultSSHApiTest {
// Create authentication
AuthenticationInfo authenticationInfo
= new MyProxyAuthenticationInfo(myProxyUserName,
myProxyPassword, "myproxy.teragrid.org",
- 7512, 17280000);
+ 7512, 17280000,certificateLocation);
// Server info
ServerInfo serverInfo = new ServerInfo("ogce", "trestles.sdsc.edu");
- // Get the API
- SSHApi sshApi = SSHApiFactory.createSSHApi(this.certificateLocation);
+ Cluster trestles = new DefaultCluster(serverInfo, authenticationInfo);
+
// Execute command
System.out.println("Target PBS file path: " + workingDirectory);
System.out.println("Local PBS File path: " + pbsFilePath);
String workingDirectory = File.separator + "home" + File.separator +
"ogce" + File.separator + "gsissh";
- JobDescriptor jobDescriptor = new JobDescriptor();
+ Job jobDescriptor = new Job();
jobDescriptor.setWorkingDirectory(workingDirectory);
jobDescriptor.setShellName("/bin/bash");
jobDescriptor.setJobName("GSI_SSH_SLEEP_JOB");
@@ -184,12 +160,12 @@ public class DefaultSSHApiTest {
inputs.add("Hello World");
jobDescriptor.setInputValues(inputs);
System.out.println(jobDescriptor.toXML());
- String jobID = sshApi.submitAsyncJob(serverInfo, authenticationInfo,
jobDescriptor);
+ jobID = trestles.submitAsyncJob(jobDescriptor);
System.out.println("JobID returned : " + jobID);
// Cluster cluster = sshApi.getCluster(serverInfo, authenticationInfo);
Thread.sleep(1000);
- JobDescriptor jobById = sshApi.getJobById(serverInfo,
authenticationInfo, jobID);
+ Job jobById = trestles.getJobById(jobID);
AssertJUnit.assertEquals(jobById.getJobId(), jobID);
System.out.println(jobById.getAcountString());
System.out.println(jobById.getAllEnvExport());
@@ -211,43 +187,10 @@ public class DefaultSSHApiTest {
}
- @Test
- public void testGetJob() throws Exception {
- // Create authentication
- AuthenticationInfo authenticationInfo
- = new MyProxyAuthenticationInfo(myProxyUserName,
myProxyPassword, "myproxy.teragrid.org",
- 7512, 17280000);
-
- // Server info
- ServerInfo serverInfo = new ServerInfo("ogce", "trestles.sdsc.edu");
- // Get the API
- SSHApi sshApi = SSHApiFactory.createSSHApi(this.certificateLocation);
-
- // Execute command
- String jobID = "1584791.trestles-fe1.sdsc.edu";
- JobDescriptor jobById = sshApi.getJobById(serverInfo,
authenticationInfo, jobID);
- System.out.println(jobById.getAcountString());
- System.out.println(jobById.getAllEnvExport());
- System.out.println(jobById.getCompTime());
- System.out.println(jobById.getExecutablePath());
- System.out.println(jobById.getEllapsedTime());
- System.out.println(jobById.getQueueName());
- System.out.println(jobById.getExecuteNode());
- System.out.println(jobById.getJobName());
- System.out.println(jobById.getCTime());
- System.out.println(jobById.getSTime());
- System.out.println(jobById.getMTime());
- System.out.println(jobById.getCompTime());
- System.out.println(jobById.getOwner());
- System.out.println(jobById.getQTime());
- System.out.println(jobById.getUsedCPUTime());
- System.out.println(jobById.getUsedMemory());
-
- }
@Test
- public void testGetCluster()throws Exception{
+ public void testGetCluster() throws Exception {
// AuthenticationInfo authenticationInfo
// = new MyProxyAuthenticationInfo(myProxyUserName,
myProxyPassword, "myproxy.teragrid.org",
// 7512, 17280000);
@@ -270,20 +213,18 @@ public class DefaultSSHApiTest {
// Create authentication
AuthenticationInfo authenticationInfo
= new MyProxyAuthenticationInfo(myProxyUserName,
myProxyPassword, "myproxy.teragrid.org",
- 7512, 17280000);
+ 7512, 17280000,certificateLocation);
// Server info
ServerInfo serverInfo = new ServerInfo("ogce", "trestles.sdsc.edu");
-
- // Get the API
- SSHApi sshApi = SSHApiFactory.createSSHApi(this.certificateLocation);
+ Cluster trestles = new DefaultCluster(serverInfo, authenticationInfo);
// Execute command
System.out.println("Target PBS file path: " + workingDirectory);
System.out.println("Local PBS File path: " + pbsFilePath);
String workingDirectory = File.separator + "home" + File.separator +
"ogce" + File.separator + "gsissh";
- JobDescriptor jobDescriptor = new JobDescriptor();
+ Job jobDescriptor = new Job();
jobDescriptor.setWorkingDirectory(workingDirectory);
jobDescriptor.setShellName("/bin/bash");
jobDescriptor.setJobName("GSI_SSH_SLEEP_JOB");
@@ -301,36 +242,36 @@ public class DefaultSSHApiTest {
jobDescriptor.setInputValues(inputs);
System.out.println(jobDescriptor.toXML());
try {
- String jobID = sshApi.submitAsyncJob(serverInfo,
authenticationInfo, jobDescriptor);
+ String jobID = trestles.submitAsyncJob(jobDescriptor);
System.out.println("JobID returned : " + jobID);
} catch (SSHApiException e) {
System.out.println(e.getMessage());
}
}
-@Test
+ @Test
public void testSubmitAsyncJobWithListener() throws Exception {
// Create authentication
AuthenticationInfo authenticationInfo
= new MyProxyAuthenticationInfo(myProxyUserName,
myProxyPassword, "myproxy.teragrid.org",
- 7512, 17280000);
+ 7512, 17280000,certificateLocation);
// Server info
ServerInfo serverInfo = new ServerInfo("ogce", "trestles.sdsc.edu");
- // Get the API
- SSHApi sshApi = SSHApiFactory.createSSHApi(this.certificateLocation);
+ Cluster trestles = new DefaultCluster(serverInfo, authenticationInfo);
+
// Execute command
System.out.println("Target PBS file path: " + workingDirectory);
System.out.println("Local PBS File path: " + pbsFilePath);
String workingDirectory = File.separator + "home" + File.separator +
"ogce" + File.separator + "gsissh";
- JobDescriptor jobDescriptor = new JobDescriptor();
+ Job jobDescriptor = new Job();
jobDescriptor.setWorkingDirectory(workingDirectory);
jobDescriptor.setShellName("/bin/bash");
jobDescriptor.setJobName("GSI_SSH_SLEEP_JOB");
- jobDescriptor.setExecutablePath("/bin/sleep");
+ jobDescriptor.setExecutablePath("/bin/echo");
jobDescriptor.setAllEnvExport(true);
jobDescriptor.setMailOptions("n");
jobDescriptor.setStandardOutFile(workingDirectory + File.separator +
"application.out");
@@ -340,10 +281,10 @@ public class DefaultSSHApiTest {
jobDescriptor.setMaxWallTime("1:00:00");
jobDescriptor.setAcountString("sds128");
List<String> inputs = new ArrayList<String>();
- inputs.add("10000");
+ inputs.add("Hello World !!");
jobDescriptor.setInputValues(inputs);
System.out.println(jobDescriptor.toXML());
- sshApi.submitAsyncJob(serverInfo, authenticationInfo,
jobDescriptor,new DefaultJobSubmissionListener());
+ trestles.submitAsyncJob(jobDescriptor, new
DefaultJobSubmissionListener());
}
}
Added: airavata/sandbox/gsissh/src/test/resources/sleep.pbs
URL:
http://svn.apache.org/viewvc/airavata/sandbox/gsissh/src/test/resources/sleep.pbs?rev=1520424&view=auto
==============================================================================
--- airavata/sandbox/gsissh/src/test/resources/sleep.pbs (added)
+++ airavata/sandbox/gsissh/src/test/resources/sleep.pbs Thu Sep 5 21:04:37
2013
@@ -0,0 +1,14 @@
+#!/bin/bash
+# Grid Engine batch job script built by Globus job manager
+
+#$ -S /bin/bash
+#$ -V
+#$ -pe 1way 32
+#$ -m n
+#$ -q normal
+#$ -A <ACCOUNT>
+#$ -l h_rt=0:60:00
+#$ -o application.stdout
+#$ -e application.stderr
+#PBS -N GSI_SSH_SLEEP_JOB
+/bin/sleep 60
Added: airavata/sandbox/gsissh/src/test/resources/test.pbs
URL:
http://svn.apache.org/viewvc/airavata/sandbox/gsissh/src/test/resources/test.pbs?rev=1520424&view=auto
==============================================================================
--- airavata/sandbox/gsissh/src/test/resources/test.pbs (added)
+++ airavata/sandbox/gsissh/src/test/resources/test.pbs Thu Sep 5 21:04:37 2013
@@ -0,0 +1,10 @@
+#!/bin/bash
+#PBS -q normal
+#PBS -A sds128
+#PBS -l nodes=1:ppn=1
+#PBS -l walltime=00:00:01
+#PBS -o job_output
+#PBS -N GSI_SSH_JOB
+#PBS -V
+
+/bin/date
