Author: lahiru
Date: Mon Oct 7 21:22:26 2013
New Revision: 1530072
URL: http://svn.apache.org/r1530072
Log:
fixing issues in ssh authentication.
Modified:
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/job/JobDescriptor.java
airavata/sandbox/gsissh/src/main/java/org/apache/airavata/gsi/ssh/impl/PBSCluster.java
airavata/sandbox/gsissh/src/main/java/org/apache/airavata/gsi/ssh/util/SSHUtils.java
airavata/sandbox/gsissh/src/main/resources/PBSTemplate.xslt
airavata/sandbox/gsissh/src/test/java/org/apache/airavata/gsi/ssh/impl/DefaultSSHApiTest.java
airavata/sandbox/gsissh/src/test/java/org/apache/airavata/gsi/ssh/impl/VanilaSSHTest.java
Modified:
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=1530072&r1=1530071&r2=1530072&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/api/Cluster.java
Mon Oct 7 21:22:26 2013
@@ -63,9 +63,17 @@ public interface Cluster {
*
* @param rFile remote file location
* @param lFile local file path of the file which needs to copy to remote
location
+ * @return the successful remote file path of the transfer
* @throws SSHApiException throws exception during error
*/
- public void scpTo(String rFile, String lFile) throws SSHApiException;
+ public String scpTo(String rFile, String lFile) throws SSHApiException;
+
+ /**
+ * This will create directories in computing resources
+ * @param directoryPath the full qualified path for the directory user
wants to create
+ * @throws SSHApiException throws during error
+ */
+ public void makeDirectory(String directoryPath) throws SSHApiException;
/**
* This will get the job description of a job which is there in the cluster
Modified:
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/JobDescriptor.java?rev=1530072&r1=1530071&r2=1530072&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/JobDescriptor.java
Mon Oct 7 21:22:26 2013
@@ -119,7 +119,8 @@ public class JobDescriptor {
* @param minutes
*/
public void setMaxWallTime(String minutes) {
-
this.getJobDescriptorDocument().getJobDescriptor().setMaxWallTime(minutes);
+ this.getJobDescriptorDocument().getJobDescriptor().setMaxWallTime(
+ CommonUtils.maxWallTimeCalculator(Integer.parseInt(minutes)));
}
Modified:
airavata/sandbox/gsissh/src/main/java/org/apache/airavata/gsi/ssh/impl/PBSCluster.java
URL:
http://svn.apache.org/viewvc/airavata/sandbox/gsissh/src/main/java/org/apache/airavata/gsi/ssh/impl/PBSCluster.java?rev=1530072&r1=1530071&r2=1530072&view=diff
==============================================================================
---
airavata/sandbox/gsissh/src/main/java/org/apache/airavata/gsi/ssh/impl/PBSCluster.java
(original)
+++
airavata/sandbox/gsissh/src/main/java/org/apache/airavata/gsi/ssh/impl/PBSCluster.java
Mon Oct 7 21:22:26 2013
@@ -260,7 +260,8 @@ public class PBSCluster implements Clust
Source text = new StreamSource(new
ByteArrayInputStream(jobDescriptor.toXML().getBytes()));
transformer.transform(text, new StreamResult(results));
- log.debug("generated PBS:" + results.toString());
+ System.out.println(results.toString());
+// log.debug("generated PBS:" + results.toString());
// creating a temporary file using pbs script generated above
int number = new SecureRandom().nextInt();
@@ -455,9 +456,9 @@ public class PBSCluster implements Clust
return jobDescriptor;
}
- public void scpTo(String rFile, String lFile) throws SSHApiException {
+ public String scpTo(String rFile, String lFile) throws SSHApiException {
try {
- SSHUtils.scpTo(rFile, lFile, session);
+ return SSHUtils.scpTo(rFile, lFile, session);
} catch (IOException e) {
throw new SSHApiException("Failed during scping local file:" +
lFile + " to remote file "
+ serverInfo.getHost() + ":rFile", e);
@@ -467,6 +468,18 @@ public class PBSCluster implements Clust
}
}
+ public void makeDirectory(String directoryPath) throws SSHApiException {
+ try {
+ SSHUtils.makeDirectory(directoryPath, session);
+ } catch (IOException e) {
+ throw new SSHApiException("Failed during creating directory:" +
directoryPath + " to remote file "
+ + serverInfo.getHost() + ":rFile", e);
+ } catch (JSchException e) {
+ throw new SSHApiException("Failed during creating directory :" +
directoryPath + " to remote file "
+ + serverInfo.getHost() + ":rFile", e);
+ }
+ }
+
//
// public String submitAsyncJob(Job jobDescriptor, JobSubmissionListener
listener) throws SSHApiException {
//// final Cluster cluster = this;
Modified:
airavata/sandbox/gsissh/src/main/java/org/apache/airavata/gsi/ssh/util/SSHUtils.java
URL:
http://svn.apache.org/viewvc/airavata/sandbox/gsissh/src/main/java/org/apache/airavata/gsi/ssh/util/SSHUtils.java?rev=1530072&r1=1530071&r2=1530072&view=diff
==============================================================================
---
airavata/sandbox/gsissh/src/main/java/org/apache/airavata/gsi/ssh/util/SSHUtils.java
(original)
+++
airavata/sandbox/gsissh/src/main/java/org/apache/airavata/gsi/ssh/util/SSHUtils.java
Mon Oct 7 21:22:26 2013
@@ -196,7 +196,7 @@ public class SSHUtils {
channel.disconnect();
session.disconnect();
- int i = lFile.lastIndexOf("\\");
+ int i = lFile.lastIndexOf(File.separator);
String substring = lFile.substring(i + 1);
return rFile + File.separator + substring;
}
@@ -273,7 +273,7 @@ public class SSHUtils {
out.close();
channel.disconnect();
- int i = lFile.lastIndexOf("\\");
+ int i = lFile.lastIndexOf(File.separator);
String substring = lFile.substring(i + 1);
return rFile + File.separator + substring;
}
@@ -281,7 +281,7 @@ public class SSHUtils {
public static Session makeDirectory(String path, Session session) throws
IOException, JSchException, SSHApiException {
// exec 'scp -t rfile' remotely
- String command = "mkdir " + path;
+ String command = "mkdir -p " + path;
Channel channel = session.openChannel("exec");
CommandOutput commandOutput = new SystemCommandOutput();
((ChannelExec) channel).setCommand(command);
@@ -306,9 +306,6 @@ public class SSHUtils {
commandOutput.onOutput(channel);
channel.disconnect();
- session.disconnect();
-
- channel.disconnect();
return session;
}
Modified: airavata/sandbox/gsissh/src/main/resources/PBSTemplate.xslt
URL:
http://svn.apache.org/viewvc/airavata/sandbox/gsissh/src/main/resources/PBSTemplate.xslt?rev=1530072&r1=1530071&r2=1530072&view=diff
==============================================================================
--- airavata/sandbox/gsissh/src/main/resources/PBSTemplate.xslt (original)
+++ airavata/sandbox/gsissh/src/main/resources/PBSTemplate.xslt Mon Oct 7
21:22:26 2013
@@ -10,32 +10,46 @@
<xsl:template match="/ns:JobDescriptor">
#! /bin/sh
# PBS batch job script built by Globus job manager
-#
- <xsl:if test="shellName != @xsl:nil">
+# <xsl:choose>
+ <xsl:when test="ns:shellName">
##PBS -S <xsl:value-of select="ns:shellName"/>
- </xsl:if>
- <xsl:if test="queueName != @xsl:nil">
+ </xsl:when></xsl:choose>
+ <xsl:choose>
+ <xsl:when test="ns:queueName">
#PBS -q <xsl:value-of select="ns:queueName"/>
- </xsl:if>
- <xsl:if test="mailOptions != @xsl:nil">
+ </xsl:when>
+ </xsl:choose>
+ <xsl:choose>
+ <xsl:when test="ns:mailOptions">
#PBS -m <xsl:value-of select="ns:mailOptions"/>
- </xsl:if>
-<xsl:if test="acountString != @xsl:nil">
+ </xsl:when>
+ </xsl:choose>
+ <xsl:choose>
+<xsl:when test="ns:acountString">
#PBS -A <xsl:value-of select="ns:acountString"/>
- </xsl:if>
- <xsl:if test="maxWallTime != @xsl:nil">
+ </xsl:when>
+ </xsl:choose>
+ <xsl:choose>
+ <xsl:when test="ns:maxWallTime">
#PBS -l walltime=<xsl:value-of select="ns:maxWallTime"/>
- </xsl:if>
- <xsl:if test="standardOutFile != @xsl:nil">
+ </xsl:when>
+ </xsl:choose>
+ <xsl:choose>
+ <xsl:when test="ns:standardOutFile">
#PBS -o <xsl:value-of select="ns:standardOutFile"/>
- </xsl:if>
- <xsl:if test="standardOutFile != @xsl:nil">
+ </xsl:when>
+ </xsl:choose>
+ <xsl:choose>
+ <xsl:when test="ns:standardOutFile">
#PBS -e <xsl:value-of select="ns:standardErrorFile"/>
- </xsl:if>
- <xsl:if test="(nodes != @xsl:nil) and (processesPerNode != @xsl:nil)">
+ </xsl:when>
+ </xsl:choose>
+ <xsl:choose>
+ <xsl:when test="(ns:nodes) and (ns:processesPerNode)">
#PBS -l nodes=<xsl:value-of select="ns:nodes"/>:ppn=<xsl:value-of
select="ns:processesPerNode"/>
<xsl:text>
</xsl:text>
- </xsl:if>
+ </xsl:when>
+ </xsl:choose>
<xsl:for-each select="ns:exports/ns:name">
<xsl:value-of select="."/>=<xsl:value-of
select="./@value"/><xsl:text>
</xsl:text>
export<xsl:text> </xsl:text><xsl:value-of select="."/>
@@ -45,7 +59,8 @@ export<xsl:text> </xsl:text><xsl:value
<xsl:value-of select="."/><xsl:text> </xsl:text>
</xsl:for-each>
cd <xsl:text> </xsl:text><xsl:value-of
select="ns:workingDirectory"/><xsl:text>
</xsl:text>
-<xsl:value-of select="ns:jobSubmitterCommand"/><xsl:text>
</xsl:text><xsl:value-of select="ns:executablePath"/><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>
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=1530072&r1=1530071&r2=1530072&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
Mon Oct 7 21:22:26 2013
@@ -162,7 +162,7 @@ public class DefaultSSHApiTest {
jobDescriptor.setNodes(1);
jobDescriptor.setProcessesPerNode(1);
jobDescriptor.setQueueName("normal");
- jobDescriptor.setMaxWallTime("1:00:00");
+ jobDescriptor.setMaxWallTime("60");
jobDescriptor.setAcountString("sds128");
List<String> inputs = new ArrayList<String>();
inputs.add("Hello World");
@@ -245,7 +245,7 @@ public class DefaultSSHApiTest {
jobDescriptor.setNodes(1);
jobDescriptor.setProcessesPerNode(100);
jobDescriptor.setQueueName("normal");
- jobDescriptor.setMaxWallTime("1:00:00");
+ jobDescriptor.setMaxWallTime("60");
jobDescriptor.setAcountString("sds128");
List<String> inputs = new ArrayList<String>();
inputs.add("Hello World");
@@ -270,7 +270,7 @@ public class DefaultSSHApiTest {
ServerInfo serverInfo = new ServerInfo("ogce", "trestles.sdsc.edu");
- Cluster pbsCluster = new PBSCluster(serverInfo, authenticationInfo,
"/opt/torque/bin1/");
+ Cluster pbsCluster = new PBSCluster(serverInfo, authenticationInfo,
"/opt/torque/bin/");
// Execute command
@@ -378,7 +378,7 @@ public class DefaultSSHApiTest {
jobDescriptor.setStandardErrorFile(workingDirectory + File.separator +
"application.err");
jobDescriptor.setNodes(1);
jobDescriptor.setProcessesPerNode(1);
- jobDescriptor.setMaxWallTime("1:00:00");
+ jobDescriptor.setMaxWallTime("60");
jobDescriptor.setQueueName("normal");
jobDescriptor.setAcountString("sds128");
List<String> inputs = new ArrayList<String>();
Modified:
airavata/sandbox/gsissh/src/test/java/org/apache/airavata/gsi/ssh/impl/VanilaSSHTest.java
URL:
http://svn.apache.org/viewvc/airavata/sandbox/gsissh/src/test/java/org/apache/airavata/gsi/ssh/impl/VanilaSSHTest.java?rev=1530072&r1=1530071&r2=1530072&view=diff
==============================================================================
---
airavata/sandbox/gsissh/src/test/java/org/apache/airavata/gsi/ssh/impl/VanilaSSHTest.java
(original)
+++
airavata/sandbox/gsissh/src/test/java/org/apache/airavata/gsi/ssh/impl/VanilaSSHTest.java
Mon Oct 7 21:22:26 2013
@@ -21,7 +21,6 @@
package org.apache.airavata.gsi.ssh.impl;
-import com.jcraft.jsch.UserInfo;
import org.apache.airavata.gsi.ssh.api.*;
import org.apache.airavata.gsi.ssh.api.authentication.AuthenticationInfo;
import org.apache.airavata.gsi.ssh.api.job.JobDescriptor;
@@ -32,10 +31,11 @@ import org.testng.AssertJUnit;
import org.testng.annotations.BeforeTest;
import org.testng.annotations.Test;
-import javax.swing.*;
import java.io.File;
import java.util.ArrayList;
+import java.util.Date;
import java.util.List;
+import java.util.UUID;
/**
* User: AmilaJ ([email protected])
@@ -56,10 +56,10 @@ public class VanilaSSHTest {
this.hostName = "bigred2.uits.iu.edu";
System.setProperty("my.ssh.user", "lginnali");
- System.setProperty("my.ssh.user.password","");
-// System.setProperty("my.ssh.user","i want to be free");
+ System.setProperty("my.ssh.user.password", "");
this.userName = System.getProperty("my.ssh.user");
this.password = System.getProperty("my.ssh.user.password");
+ System.setProperty("basedir",
"/Users/lahirugunathilake/work/airavata/sandbox/gsissh");
// this.passPhrase = System.getProperty("my.ssh.user.pass.phrase");
if (this.userName == null || this.password == null) {
@@ -72,7 +72,7 @@ public class VanilaSSHTest {
@Test
- public void testSimpleCommand1() throws Exception{
+ public void testSimpleCommand1() throws Exception {
System.out.println("Starting vanila SSH test ....");
@@ -94,7 +94,7 @@ public class VanilaSSHTest {
}
@Test
- public void testSimpleCommand2() throws Exception{
+ public void testSimpleCommand2() throws Exception {
System.out.println("Starting vanila SSH test ....");
@@ -120,17 +120,34 @@ public class VanilaSSHTest {
}
@Test
- public void testSimplePBSJob() throws Exception{
+ public void testSimplePBSJob() throws Exception {
AuthenticationInfo authenticationInfo = new
DefaultPasswordAuthenticationInfo(this.password);
- // Server info
+ // Server info
ServerInfo serverInfo = new ServerInfo(this.userName, this.hostName);
Cluster pbsCluster = new PBSCluster(serverInfo, authenticationInfo,
"/opt/torque/torque-4.2.3.1/bin/");
+ String date = new Date().toString();
+ date = date.replaceAll(" ", "_");
+ date = date.replaceAll(":", "_");
- // Execute command
+ String pomFile = System.getProperty("basedir") + File.separator +
"pom.xml";
+
+ // Constructing theworking directory for demonstration and creating
directories in the remote
+ // resource
String workingDirectory = File.separator + "N" + File.separator + "u"
+ File.separator +
- "lginnali" + File.separator + "BigRed2" + File.separator +
"myjob";
+ "lginnali" + File.separator + "BigRed2";
+ workingDirectory = workingDirectory + File.separator
+ + date + "_" + UUID.randomUUID();
+ pbsCluster.makeDirectory(workingDirectory);
+ Thread.sleep(1000);
+ pbsCluster.makeDirectory(workingDirectory + File.separator + "inputs");
+ Thread.sleep(1000);
+ pbsCluster.makeDirectory(workingDirectory + File.separator +
"outputs");
+
+
+ // doing file transfer to the remote resource
+ String s = pbsCluster.scpTo(workingDirectory + File.separator +
"inputs", pomFile);
// constructing the job object
JobDescriptor jobDescriptor = new JobDescriptor();
jobDescriptor.setWorkingDirectory(workingDirectory);
@@ -147,7 +164,7 @@ public class VanilaSSHTest {
jobDescriptor.setMaxWallTime("5");
jobDescriptor.setJobSubmitter("aprun -n 1");
List<String> inputs = new ArrayList<String>();
- inputs.add("Hello World");
+ inputs.add(s);
jobDescriptor.setInputValues(inputs);
//finished construction of job object
System.out.println(jobDescriptor.toXML());
