Author: lahiru
Date: Mon Oct 7 21:20:10 2013
New Revision: 1530070
URL: http://svn.apache.org/r1530070
Log:
enabling ssh and gsissh in gfac-core.
Added:
airavata/trunk/modules/gfac-core/src/test/java/org/apache/airavata/core/gfac/services/impl/BigRed2Test.java
airavata/trunk/modules/gfac-core/src/test/java/org/apache/airavata/core/gfac/services/impl/GSISSHProviderTest.java
airavata/trunk/modules/gfac-core/src/test/resources/PBSTemplate.xslt
Modified:
airavata/trunk/modules/distribution/airavata-server/src/main/resources/conf/gfac-config.xml
airavata/trunk/modules/gfac-core/src/main/java/org/apache/airavata/gfac/context/security/SSHSecurityContext.java
airavata/trunk/modules/gfac-core/src/main/java/org/apache/airavata/gfac/handler/SCPDirectorySetupHandler.java
airavata/trunk/modules/gfac-core/src/main/java/org/apache/airavata/gfac/handler/SCPInputHandler.java
airavata/trunk/modules/gfac-core/src/main/java/org/apache/airavata/gfac/provider/impl/GSISSHProvider.java
airavata/trunk/modules/gfac-core/src/test/java/org/apache/airavata/core/gfac/services/impl/SSHProviderTest.java
airavata/trunk/modules/gfac-core/src/test/resources/gfac-config.xml
Modified:
airavata/trunk/modules/distribution/airavata-server/src/main/resources/conf/gfac-config.xml
URL:
http://svn.apache.org/viewvc/airavata/trunk/modules/distribution/airavata-server/src/main/resources/conf/gfac-config.xml?rev=1530070&r1=1530069&r2=1530070&view=diff
==============================================================================
---
airavata/trunk/modules/distribution/airavata-server/src/main/resources/conf/gfac-config.xml
(original)
+++
airavata/trunk/modules/distribution/airavata-server/src/main/resources/conf/gfac-config.xml
Mon Oct 7 21:20:10 2013
@@ -24,7 +24,7 @@
<Handler
class="org.apache.airavata.gfac.handler.LocalDirectorySetupHandler"/>
</InHandlers>
</Provider>
- <Provider class="org.apache.airavata.gfac.provider.impl.GramProvider"
host="org.apache.airavata.schemas.gfac.impl.GlobusHostTypeImpl">
+ <Provider class="org.apache.airavata.gfac.provider.impl.GSISSHProvider"
host="org.apache.airavata.schemas.gfac.impl.GlobusHostTypeImpl">
<property name="name" value="value"/>
<InHandlers>
<Handler
class="org.apache.airavata.gfac.handler.GramDirectorySetupHandler">
@@ -78,4 +78,13 @@
<Handler
class="org.apache.airavata.gfac.handler.SCPOutputHandler"/>
</OutHandlers>
</Provider>
+ <Provider class="org.apache.airavata.gfac.provider.impl.GSISSHProvider"
host="org.apache.airavata.schemas.gfac.impl.GsisshHostTypeImpl">
+ <InHandlers>
+ <Handler
class="org.apache.airavata.gfac.handler.SCPDirectorySetupHandler"/>
+ <Handler class="org.apache.airavata.gfac.handler.SCPInputHandler"/>
+ </InHandlers>
+ <OutHandlers>
+ <!--Handler
class="org.apache.airavata.gfac.handler.SCPOutputHandler"/-->
+ </OutHandlers>
+ </Provider>
</GFac>
\ No newline at end of file
Modified:
airavata/trunk/modules/gfac-core/src/main/java/org/apache/airavata/gfac/context/security/SSHSecurityContext.java
URL:
http://svn.apache.org/viewvc/airavata/trunk/modules/gfac-core/src/main/java/org/apache/airavata/gfac/context/security/SSHSecurityContext.java?rev=1530070&r1=1530069&r2=1530070&view=diff
==============================================================================
---
airavata/trunk/modules/gfac-core/src/main/java/org/apache/airavata/gfac/context/security/SSHSecurityContext.java
(original)
+++
airavata/trunk/modules/gfac-core/src/main/java/org/apache/airavata/gfac/context/security/SSHSecurityContext.java
Mon Oct 7 21:20:10 2013
@@ -27,6 +27,7 @@ import net.schmizz.sshj.connection.chann
import net.schmizz.sshj.userauth.keyprovider.KeyProvider;
import org.apache.airavata.gfac.SecurityContext;
+import org.apache.airavata.gsi.ssh.api.Cluster;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
@@ -44,6 +45,8 @@ public class SSHSecurityContext implemen
private SSHClient sshClient;
private Session session;
+ Cluster pbsCluster;
+
public String getUsername() {
return username;
}
@@ -106,4 +109,12 @@ public class SSHSecurityContext implemen
}
return sshClient;
}
+
+ public void setPbsCluster(Cluster pbsCluster) {
+ this.pbsCluster = pbsCluster;
+ }
+
+ public Cluster getPbsCluster() {
+ return pbsCluster;
+ }
}
Modified:
airavata/trunk/modules/gfac-core/src/main/java/org/apache/airavata/gfac/handler/SCPDirectorySetupHandler.java
URL:
http://svn.apache.org/viewvc/airavata/trunk/modules/gfac-core/src/main/java/org/apache/airavata/gfac/handler/SCPDirectorySetupHandler.java?rev=1530070&r1=1530069&r2=1530070&view=diff
==============================================================================
---
airavata/trunk/modules/gfac-core/src/main/java/org/apache/airavata/gfac/handler/SCPDirectorySetupHandler.java
(original)
+++
airavata/trunk/modules/gfac-core/src/main/java/org/apache/airavata/gfac/handler/SCPDirectorySetupHandler.java
Mon Oct 7 21:20:10 2013
@@ -33,6 +33,8 @@ import org.apache.airavata.gfac.Constant
import org.apache.airavata.gfac.GFacException;
import org.apache.airavata.gfac.context.JobExecutionContext;
import org.apache.airavata.gfac.context.security.SSHSecurityContext;
+import org.apache.airavata.gsi.ssh.api.Cluster;
+import org.apache.airavata.gsi.ssh.api.SSHApiException;
import org.apache.airavata.schemas.gfac.ApplicationDeploymentDescriptionType;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
@@ -50,31 +52,13 @@ public class SCPDirectorySetupHandler im
ApplicationDeploymentDescriptionType app =
context.getApplicationContext().getApplicationDeploymentDescription().getType();
Session session = null;
try {
- session =
securityContext.getSession(context.getApplicationContext().getHostDescription().getType().getHostAddress());
-
- StringBuilder commandString = new StringBuilder();
-
- commandString.append("mkdir -p ");
- commandString.append(app.getScratchWorkingDirectory());
- commandString.append(" ; ");
- commandString.append("mkdir -p ");
- commandString.append(app.getStaticWorkingDirectory());
- commandString.append(" ; ");
- commandString.append("mkdir -p ");
- commandString.append(app.getInputDataDirectory());
- commandString.append(" ; ");
- commandString.append("mkdir -p ");
- commandString.append(app.getOutputDataDirectory());
-
- Command cmd = session.exec(commandString.toString());
- cmd.join(Constants.COMMAND_EXECUTION_TIMEOUT,
TimeUnit.SECONDS);
- } catch (ConnectionException e) {
- throw new GFacHandlerException(e.getMessage(), e,
context);
- } catch (TransportException e) {
- throw new GFacHandlerException(e.getMessage(), e,
context);
- } catch (IOException e) {
- throw new GFacHandlerException(e.getMessage(), e,
context);
- } finally {
+ Cluster pbsCluster = securityContext.getPbsCluster();
+ pbsCluster.makeDirectory(app.getScratchWorkingDirectory());
+ pbsCluster.makeDirectory(app.getInputDataDirectory());
+ pbsCluster.makeDirectory(app.getOutputDataDirectory());
+ } catch (SSHApiException e) {
+ throw new GFacHandlerException("Error executing the Handler: " +
SCPDirectorySetupHandler.class,e); //To change body of catch statement use
File | Settings | File Templates.
+ } finally {
securityContext.closeSession(session);
}
}
Modified:
airavata/trunk/modules/gfac-core/src/main/java/org/apache/airavata/gfac/handler/SCPInputHandler.java
URL:
http://svn.apache.org/viewvc/airavata/trunk/modules/gfac-core/src/main/java/org/apache/airavata/gfac/handler/SCPInputHandler.java?rev=1530070&r1=1530069&r2=1530070&view=diff
==============================================================================
---
airavata/trunk/modules/gfac-core/src/main/java/org/apache/airavata/gfac/handler/SCPInputHandler.java
(original)
+++
airavata/trunk/modules/gfac-core/src/main/java/org/apache/airavata/gfac/handler/SCPInputHandler.java
Mon Oct 7 21:20:10 2013
@@ -33,6 +33,8 @@ import org.apache.airavata.gfac.GFacExce
import org.apache.airavata.gfac.context.JobExecutionContext;
import org.apache.airavata.gfac.context.MessageContext;
import org.apache.airavata.gfac.context.security.SSHSecurityContext;
+import org.apache.airavata.gsi.ssh.api.Cluster;
+import org.apache.airavata.gsi.ssh.api.SSHApiException;
import org.apache.airavata.schemas.gfac.ApplicationDeploymentDescriptionType;
import org.apache.airavata.schemas.gfac.URIArrayType;
import org.apache.airavata.schemas.gfac.URIParameterType;
@@ -75,17 +77,21 @@ public class SCPInputHandler implements
}
jobExecutionContext.setInMessageContext(inputNew);
}
- private static String stageInputFiles(JobExecutionContext
context,String paramValue) throws IOException,GFacException{
- ApplicationDeploymentDescriptionType app =
context.getApplicationContext().getApplicationDeploymentDescription().getType();
- SSHSecurityContext securityContext =
(SSHSecurityContext)context.getSecurityContext(SSHSecurityContext.SSH_SECURITY_CONTEXT);
- SCPFileTransfer fileTransfer =
securityContext.getSSHClient().newSCPFileTransfer();
- String remoteFile = app.getInputDataDirectory() +
File.separatorChar + paramValue;
-
- File inputFile = new File(paramValue);
- fileTransfer.upload(inputFile.getAbsolutePath(), remoteFile);
- return remoteFile;
- }
+ private static String stageInputFiles(JobExecutionContext context, String
paramValue) throws IOException, GFacException {
+ SSHSecurityContext securityContext =
(SSHSecurityContext)context.getSecurityContext(SSHSecurityContext.SSH_SECURITY_CONTEXT);
+ Cluster pbsCluster = securityContext.getPbsCluster();
+ ApplicationDeploymentDescriptionType app =
context.getApplicationContext().getApplicationDeploymentDescription().getType();
+ String remoteFile = app.getInputDataDirectory() + File.separatorChar +
paramValue;
+
+ try {
+ return pbsCluster.scpTo(app.getInputDataDirectory(), remoteFile);
+ } catch (SSHApiException e) {
+ throw new GFacHandlerException("Error while input File Staging",
context, e, e.getLocalizedMessage());
+ } finally {
+ return null;
+ }
+ }
public void initProperties(Map<String, String> properties) throws
GFacHandlerException, GFacException {
Modified:
airavata/trunk/modules/gfac-core/src/main/java/org/apache/airavata/gfac/provider/impl/GSISSHProvider.java
URL:
http://svn.apache.org/viewvc/airavata/trunk/modules/gfac-core/src/main/java/org/apache/airavata/gfac/provider/impl/GSISSHProvider.java?rev=1530070&r1=1530069&r2=1530070&view=diff
==============================================================================
---
airavata/trunk/modules/gfac-core/src/main/java/org/apache/airavata/gfac/provider/impl/GSISSHProvider.java
(original)
+++
airavata/trunk/modules/gfac-core/src/main/java/org/apache/airavata/gfac/provider/impl/GSISSHProvider.java
Mon Oct 7 21:20:10 2013
@@ -23,24 +23,17 @@ package org.apache.airavata.gfac.provide
import org.apache.airavata.common.utils.StringUtil;
import org.apache.airavata.commons.gfac.type.ActualParameter;
import org.apache.airavata.commons.gfac.type.MappingFactory;
-import org.apache.airavata.gfac.Constants;
import org.apache.airavata.gfac.GFacException;
-import org.apache.airavata.gfac.RequestData;
import org.apache.airavata.gfac.context.JobExecutionContext;
import org.apache.airavata.gfac.context.MessageContext;
-import org.apache.airavata.gfac.context.security.GSISecurityContext;
+import org.apache.airavata.gfac.context.security.SSHSecurityContext;
import org.apache.airavata.gfac.notification.events.StartExecutionEvent;
import org.apache.airavata.gfac.provider.GFacProvider;
import org.apache.airavata.gfac.provider.GFacProviderException;
-import org.apache.airavata.gsi.ssh.api.AuthenticationInfo;
import org.apache.airavata.gsi.ssh.api.Cluster;
import org.apache.airavata.gsi.ssh.api.SSHApiException;
-import org.apache.airavata.gsi.ssh.api.ServerInfo;
import org.apache.airavata.gsi.ssh.api.job.JobDescriptor;
-import org.apache.airavata.gsi.ssh.impl.DefaultJobSubmissionListener;
-import org.apache.airavata.gsi.ssh.impl.MyProxyAuthenticationInfo;
import org.apache.airavata.gsi.ssh.impl.PBSCluster;
-import org.apache.airavata.gsi.ssh.listener.JobSubmissionListener;
import org.apache.airavata.schemas.gfac.*;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
@@ -65,17 +58,9 @@ public class GSISSHProvider implements G
HpcApplicationDeploymentType app = (HpcApplicationDeploymentType)
jobExecutionContext.getApplicationContext().
getApplicationDeploymentDescription().getType();
try {
-
- GSISecurityContext gssCred = ((GSISecurityContext)
jobExecutionContext.
-
getSecurityContext(GSISecurityContext.GSI_SECURITY_CONTEXT));
- RequestData requestData = gssCred.getRequestData();
- ServerInfo serverInfo = new
ServerInfo(requestData.getMyProxyUserName(), host.getHostAddress(), 22);
- AuthenticationInfo authenticationInfo
- = new
MyProxyAuthenticationInfo(requestData.getMyProxyUserName(),
requestData.getMyProxyPassword(), requestData.getMyProxyServerUrl(),
- 7512, 17280000,
System.getProperty(Constants.TRUSTED_CERTIFICATE_SYSTEM_PROPERTY));
-
+ SSHSecurityContext securityContext = (SSHSecurityContext)
jobExecutionContext.getSecurityContext(SSHSecurityContext.SSH_SECURITY_CONTEXT);
+ Cluster cluster = securityContext.getPbsCluster();
// This installed path is a mandetory field, because this could
change based on the computing resource
- Cluster cluster = new PBSCluster(serverInfo,
authenticationInfo,host.getInstalledParentPath());
JobDescriptor jobDescriptor = new JobDescriptor();
jobDescriptor.setWorkingDirectory(app.getScratchWorkingDirectory());
jobDescriptor.setShellName("/bin/bash");
@@ -89,10 +74,15 @@ public class GSISSHProvider implements G
jobDescriptor.setStandardErrorFile(app.getStandardError());
jobDescriptor.setNodes(app.getNodeCount());
jobDescriptor.setProcessesPerNode(app.getProcessorsPerNode());
-
jobDescriptor.setMaxWallTime(maxWallTimeCalculator(app.getMaxWallTime()));
-
jobDescriptor.setAcountString(app.getProjectAccount().getProjectAccountNumber());
- jobDescriptor.setQueueName(app.getQueue().getQueueName());
- jobDescriptor.setOwner(requestData.getMyProxyUserName());
+ jobDescriptor.setMaxWallTime(String.valueOf(app.getMaxWallTime()));
+ jobDescriptor.setJobSubmitter(app.getJobSubmitterCommand());
+ if (app.getProjectAccount() != null) {
+
jobDescriptor.setAcountString(app.getProjectAccount().getProjectAccountNumber());
+ }
+ if (app.getQueue() != null) {
+ jobDescriptor.setQueueName(app.getQueue().getQueueName());
+ }
+ jobDescriptor.setOwner(((PBSCluster)
cluster).getServerInfo().getUserName());
List<String> inputValues = new ArrayList<String>();
MessageContext input = jobExecutionContext.getInMessageContext();
Map<String, Object> inputs = input.getParameters();
@@ -118,6 +108,7 @@ public class GSISSHProvider implements G
}
jobDescriptor.setInputValues(inputValues);
+ System.out.println(jobDescriptor.toXML());
cluster.submitBatchJob(jobDescriptor);
} catch (SSHApiException e) {
String error = "Error submitting the job to host " +
host.getHostAddress() + e.getMessage();
Added:
airavata/trunk/modules/gfac-core/src/test/java/org/apache/airavata/core/gfac/services/impl/BigRed2Test.java
URL:
http://svn.apache.org/viewvc/airavata/trunk/modules/gfac-core/src/test/java/org/apache/airavata/core/gfac/services/impl/BigRed2Test.java?rev=1530070&view=auto
==============================================================================
---
airavata/trunk/modules/gfac-core/src/test/java/org/apache/airavata/core/gfac/services/impl/BigRed2Test.java
(added)
+++
airavata/trunk/modules/gfac-core/src/test/java/org/apache/airavata/core/gfac/services/impl/BigRed2Test.java
Mon Oct 7 21:20:10 2013
@@ -0,0 +1,204 @@
+/*
+ *
+ * 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.core.gfac.services.impl;
+
+import org.apache.airavata.commons.gfac.type.ActualParameter;
+import org.apache.airavata.commons.gfac.type.ApplicationDescription;
+import org.apache.airavata.commons.gfac.type.HostDescription;
+import org.apache.airavata.commons.gfac.type.ServiceDescription;
+import org.apache.airavata.gfac.GFacAPI;
+import org.apache.airavata.gfac.GFacConfiguration;
+import org.apache.airavata.gfac.GFacException;
+import org.apache.airavata.gfac.SecurityContext;
+import org.apache.airavata.gfac.context.ApplicationContext;
+import org.apache.airavata.gfac.context.JobExecutionContext;
+import org.apache.airavata.gfac.context.MessageContext;
+import org.apache.airavata.gfac.context.security.SSHSecurityContext;
+import org.apache.airavata.gsi.ssh.api.Cluster;
+import org.apache.airavata.gsi.ssh.api.SSHApiException;
+import org.apache.airavata.gsi.ssh.api.ServerInfo;
+import org.apache.airavata.gsi.ssh.api.authentication.AuthenticationInfo;
+import org.apache.airavata.gsi.ssh.impl.PBSCluster;
+import
org.apache.airavata.gsi.ssh.impl.authentication.DefaultPasswordAuthenticationInfo;
+import org.apache.airavata.schemas.gfac.*;
+import org.junit.Before;
+import org.junit.Test;
+
+import java.io.File;
+import java.net.URL;
+import java.util.ArrayList;
+import java.util.Date;
+import java.util.List;
+import java.util.UUID;
+
+public class BigRed2Test {
+ private JobExecutionContext jobExecutionContext;
+
+ private static final String hostAddress = "bigred2";
+ private static final String hostName = "bigred2.uits.iu.edu";
+ private static final String userName = "lginnali";
+ private static final String password = "";
+
+ @Before
+ public void setUp() throws Exception {
+ URL resource =
GramProviderTest.class.getClassLoader().getResource("gfac-config.xml");
+ assert resource != null;
+ System.out.println(resource.getFile());
+ GFacConfiguration gFacConfiguration = GFacConfiguration.create(new
File(resource.getPath()), null, null);
+
+// gFacConfiguration.setMyProxyLifeCycle(3600);
+// gFacConfiguration.setMyProxyServer("myproxy.teragrid.org");
+// gFacConfiguration.setMyProxyUser("*****");
+// gFacConfiguration.setMyProxyPassphrase("*****");
+// gFacConfiguration.setTrustedCertLocation("./certificates");
+// //have to set InFlwo Handlers and outFlowHandlers
+// gFacConfiguration.setInHandlers(Arrays.asList(new String[]
{"org.apache.airavata.gfac.handler.GramDirectorySetupHandler","org.apache.airavata.gfac.handler.GridFTPInputHandler"}));
+// gFacConfiguration.setOutHandlers(Arrays.asList(new String[]
{"org.apache.airavata.gfac.handler.GridFTPOutputHandler"}));
+
+ /*
+ * Host
+ */
+ HostDescription host = new HostDescription(GsisshHostType.type);
+ host.getType().setHostAddress(hostAddress);
+ host.getType().setHostName(hostName);
+ ((GsisshHostType)
host.getType()).setInstalledParentPath("/opt/torque/torque-4.2.3.1/bin/");
+ /*
+ * App
+ */
+ ApplicationDescription appDesc = new
ApplicationDescription(HpcApplicationDeploymentType.type);
+ HpcApplicationDeploymentType app = (HpcApplicationDeploymentType)
appDesc.getType();
+ ApplicationDeploymentDescriptionType.ApplicationName name =
ApplicationDeploymentDescriptionType.ApplicationName.Factory.newInstance();
+ name.setStringValue("EchoLocal");
+ app.setApplicationName(name);
+
+ app.setCpuCount(1);
+ app.setJobType(JobTypeType.SERIAL);
+ app.setNodeCount(1);
+ app.setProcessorsPerNode(1);
+
+ /*
+ * Use bat file if it is compiled on Windows
+ */
+ app.setExecutableLocation("/bin/echo");
+
+ /*
+ * Default tmp location
+ */
+ String tempDir = "~/";
+ String date = (new Date()).toString();
+ date = date.replaceAll(" ", "_");
+ date = date.replaceAll(":", "_");
+
+ tempDir = tempDir + File.separator
+ + "SimpleEcho" + "_" + date + "_" + UUID.randomUUID();
+
+ System.out.println(tempDir);
+ app.setScratchWorkingDirectory(tempDir);
+ app.setStaticWorkingDirectory(tempDir);
+ app.setInputDataDirectory(tempDir + File.separator + "inputData");
+ app.setOutputDataDirectory(tempDir + File.separator + "outputData");
+ app.setStandardOutput(tempDir + File.separator +
app.getApplicationName().getStringValue() + ".stdout");
+ app.setStandardError(tempDir + File.separator +
app.getApplicationName().getStringValue() + ".stderr");
+ app.setMaxWallTime(5);
+ app.setJobSubmitterCommand("aprun -n 1");
+
+
+ /*
+ * Service
+ */
+ ServiceDescription serv = new ServiceDescription();
+ serv.getType().setName("SimpleEcho");
+
+ List<InputParameterType> inputList = new
ArrayList<InputParameterType>();
+
+ InputParameterType input = InputParameterType.Factory.newInstance();
+ input.setParameterName("echo_input");
+ input.setParameterType(StringParameterType.Factory.newInstance());
+ inputList.add(input);
+
+ InputParameterType[] inputParamList = inputList.toArray(new
InputParameterType[inputList
+
+ .size()]);
+ List<OutputParameterType> outputList = new
ArrayList<OutputParameterType>();
+ OutputParameterType output = OutputParameterType.Factory.newInstance();
+ output.setParameterName("echo_output");
+ output.setParameterType(StringParameterType.Factory.newInstance());
+ outputList.add(output);
+
+ OutputParameterType[] outputParamList = outputList
+ .toArray(new OutputParameterType[outputList.size()]);
+
+ serv.getType().setInputParametersArray(inputParamList);
+ serv.getType().setOutputParametersArray(outputParamList);
+
+ jobExecutionContext = new JobExecutionContext(gFacConfiguration,
serv.getType().getName());
+ // Adding security context
+
jobExecutionContext.addSecurityContext(SSHSecurityContext.SSH_SECURITY_CONTEXT,
getSecurityContext(host));
+ ApplicationContext applicationContext = new ApplicationContext();
+ jobExecutionContext.setApplicationContext(applicationContext);
+ applicationContext.setServiceDescription(serv);
+ applicationContext.setApplicationDeploymentDescription(appDesc);
+ applicationContext.setHostDescription(host);
+
+ MessageContext inMessage = new MessageContext();
+ ActualParameter echo_input = new ActualParameter();
+ ((StringParameterType)
echo_input.getType()).setValue("echo_output=hello");
+ inMessage.addParameter("echo_input", echo_input);
+
+
+ jobExecutionContext.setInMessageContext(inMessage);
+
+ MessageContext outMessage = new MessageContext();
+ ActualParameter echo_out = new ActualParameter();
+//
((StringParameterType)echo_input.getType()).setValue("echo_output=hello");
+ outMessage.addParameter("echo_output", echo_out);
+
+ jobExecutionContext.setOutMessageContext(outMessage);
+
+ }
+
+ private SecurityContext getSecurityContext(HostDescription host) {
+ AuthenticationInfo authenticationInfo = new
DefaultPasswordAuthenticationInfo(this.password);
+ // Server info
+ ServerInfo serverInfo = new ServerInfo(this.userName, this.hostName);
+
+ Cluster pbsCluster = null;
+ try {
+ pbsCluster = new PBSCluster(serverInfo, authenticationInfo,
+
((GsisshHostType)host.getType()).getInstalledParentPath());
+ } catch (SSHApiException e) {
+ e.printStackTrace(); //To change body of catch statement use File
| Settings | File Templates.
+ }
+
+
+ SSHSecurityContext sshSecurityContext = new SSHSecurityContext();
+ sshSecurityContext.setPbsCluster(pbsCluster);
+ sshSecurityContext.setUsername(userName);
+ return sshSecurityContext;
+ }
+
+ @Test
+ public void testGramProvider() throws GFacException {
+ GFacAPI gFacAPI = new GFacAPI();
+ gFacAPI.submitJob(jobExecutionContext);
+ }
+
+}
Added:
airavata/trunk/modules/gfac-core/src/test/java/org/apache/airavata/core/gfac/services/impl/GSISSHProviderTest.java
URL:
http://svn.apache.org/viewvc/airavata/trunk/modules/gfac-core/src/test/java/org/apache/airavata/core/gfac/services/impl/GSISSHProviderTest.java?rev=1530070&view=auto
==============================================================================
---
airavata/trunk/modules/gfac-core/src/test/java/org/apache/airavata/core/gfac/services/impl/GSISSHProviderTest.java
(added)
+++
airavata/trunk/modules/gfac-core/src/test/java/org/apache/airavata/core/gfac/services/impl/GSISSHProviderTest.java
Mon Oct 7 21:20:10 2013
@@ -0,0 +1,208 @@
+/*
+ *
+ * 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.core.gfac.services.impl;
+
+import org.apache.airavata.commons.gfac.type.ActualParameter;
+import org.apache.airavata.commons.gfac.type.ApplicationDescription;
+import org.apache.airavata.commons.gfac.type.HostDescription;
+import org.apache.airavata.commons.gfac.type.ServiceDescription;
+import org.apache.airavata.gfac.GFacAPI;
+import org.apache.airavata.gfac.GFacConfiguration;
+import org.apache.airavata.gfac.GFacException;
+import org.apache.airavata.gfac.SecurityContext;
+import org.apache.airavata.gfac.context.ApplicationContext;
+import org.apache.airavata.gfac.context.JobExecutionContext;
+import org.apache.airavata.gfac.context.MessageContext;
+import org.apache.airavata.gfac.context.security.SSHSecurityContext;
+import org.apache.airavata.gsi.ssh.api.Cluster;
+import org.apache.airavata.gsi.ssh.api.SSHApiException;
+import org.apache.airavata.gsi.ssh.api.ServerInfo;
+import org.apache.airavata.gsi.ssh.api.authentication.GSIAuthenticationInfo;
+import org.apache.airavata.gsi.ssh.impl.PBSCluster;
+import
org.apache.airavata.gsi.ssh.impl.authentication.MyProxyAuthenticationInfo;
+import org.apache.airavata.schemas.gfac.*;
+import org.junit.Before;
+import org.junit.Test;
+
+import java.io.File;
+import java.net.URL;
+import java.util.ArrayList;
+import java.util.Date;
+import java.util.List;
+import java.util.UUID;
+
+public class GSISSHProviderTest {
+ private JobExecutionContext jobExecutionContext;
+
+ //FIXME: move job properties to configuration file
+ private static final String hostAddress = "trestles.sdsc.edu";
+ private static final String hostName = "trestles";
+ private static final String myProxyUserName = "ogce";
+ private static final String myProxyPassword = "";
+ private static final String certificateLocation =
"/Users/lahirugunathilake/Downloads/certificates";
+
+ @Before
+ public void setUp() throws Exception {
+ URL resource =
GSISSHProviderTest.class.getClassLoader().getResource("gfac-config.xml");
+ assert resource != null;
+ System.out.println(resource.getFile());
+ GFacConfiguration gFacConfiguration = GFacConfiguration.create(new
File(resource.getPath()), null, null);
+
+// gFacConfiguration.setMyProxyLifeCycle(3600);
+// gFacConfiguration.setMyProxyServer("myproxy.teragrid.org");
+// gFacConfiguration.setMyProxyUser("*****");
+// gFacConfiguration.setMyProxyPassphrase("*****");
+// gFacConfiguration.setTrustedCertLocation("./certificates");
+// //have to set InFlwo Handlers and outFlowHandlers
+// gFacConfiguration.setInHandlers(Arrays.asList(new String[]
{"org.apache.airavata.gfac.handler.GramDirectorySetupHandler","org.apache.airavata.gfac.handler.GridFTPInputHandler"}));
+// gFacConfiguration.setOutHandlers(Arrays.asList(new String[]
{"org.apache.airavata.gfac.handler.GridFTPOutputHandler"}));
+
+ /*
+ * Host
+ */
+ HostDescription host = new HostDescription(GsisshHostType.type);
+ host.getType().setHostAddress(hostAddress);
+ host.getType().setHostName(hostName);
+ ((GsisshHostType)
host.getType()).setInstalledParentPath("/opt/torque/bin/");
+ /*
+ * App
+ */
+ ApplicationDescription appDesc = new
ApplicationDescription(HpcApplicationDeploymentType.type);
+ HpcApplicationDeploymentType app = (HpcApplicationDeploymentType)
appDesc.getType();
+ ApplicationDeploymentDescriptionType.ApplicationName name =
ApplicationDeploymentDescriptionType.ApplicationName.Factory.newInstance();
+ name.setStringValue("EchoLocal");
+ app.setApplicationName(name);
+ ProjectAccountType projectAccountType = app.addNewProjectAccount();
+ projectAccountType.setProjectAccountNumber("sds128");
+
+ QueueType queueType = app.addNewQueue();
+ queueType.setQueueName("normal");
+
+ app.setCpuCount(1);
+ app.setJobType(JobTypeType.SERIAL);
+ app.setNodeCount(1);
+ app.setProcessorsPerNode(1);
+
+ /*
+ * Use bat file if it is compiled on Windows
+ */
+ app.setExecutableLocation("/bin/echo");
+
+ /*
+ * Default tmp location
+ */
+ String tempDir = "/home/ogce/scratch/";
+ String date = (new Date()).toString();
+ date = date.replaceAll(" ", "_");
+ date = date.replaceAll(":", "_");
+
+ tempDir = tempDir + File.separator
+ + "SimpleEcho" + "_" + date + "_" + UUID.randomUUID();
+
+ System.out.println(tempDir);
+ app.setScratchWorkingDirectory(tempDir);
+ app.setStaticWorkingDirectory(tempDir);
+ app.setInputDataDirectory(tempDir + File.separator + "inputData");
+ app.setOutputDataDirectory(tempDir + File.separator + "outputData");
+ app.setStandardOutput(tempDir + File.separator +
app.getApplicationName().getStringValue() + ".stdout");
+ app.setStandardError(tempDir + File.separator +
app.getApplicationName().getStringValue() + ".stderr");
+ app.setMaxWallTime(5);
+
+
+ /*
+ * Service
+ */
+ ServiceDescription serv = new ServiceDescription();
+ serv.getType().setName("SimpleEcho");
+
+ List<InputParameterType> inputList = new
ArrayList<InputParameterType>();
+
+ InputParameterType input = InputParameterType.Factory.newInstance();
+ input.setParameterName("echo_input");
+ input.setParameterType(StringParameterType.Factory.newInstance());
+ inputList.add(input);
+
+ InputParameterType[] inputParamList = inputList.toArray(new
InputParameterType[inputList
+
+ .size()]);
+ List<OutputParameterType> outputList = new
ArrayList<OutputParameterType>();
+ OutputParameterType output = OutputParameterType.Factory.newInstance();
+ output.setParameterName("echo_output");
+ output.setParameterType(StringParameterType.Factory.newInstance());
+ outputList.add(output);
+
+ OutputParameterType[] outputParamList = outputList
+ .toArray(new OutputParameterType[outputList.size()]);
+
+ serv.getType().setInputParametersArray(inputParamList);
+ serv.getType().setOutputParametersArray(outputParamList);
+
+ jobExecutionContext = new JobExecutionContext(gFacConfiguration,
serv.getType().getName());
+ // Adding security context
+
jobExecutionContext.addSecurityContext(SSHSecurityContext.SSH_SECURITY_CONTEXT,
getSecurityContext());
+ ApplicationContext applicationContext = new ApplicationContext();
+ jobExecutionContext.setApplicationContext(applicationContext);
+ applicationContext.setServiceDescription(serv);
+ applicationContext.setApplicationDeploymentDescription(appDesc);
+ applicationContext.setHostDescription(host);
+
+ MessageContext inMessage = new MessageContext();
+ ActualParameter echo_input = new ActualParameter();
+ ((StringParameterType)
echo_input.getType()).setValue("echo_output=hello");
+ inMessage.addParameter("echo_input", echo_input);
+
+
+ jobExecutionContext.setInMessageContext(inMessage);
+
+ MessageContext outMessage = new MessageContext();
+ ActualParameter echo_out = new ActualParameter();
+//
((StringParameterType)echo_input.getType()).setValue("echo_output=hello");
+ outMessage.addParameter("echo_output", echo_out);
+
+ jobExecutionContext.setOutMessageContext(outMessage);
+
+ }
+
+ private SecurityContext getSecurityContext() {
+ GSIAuthenticationInfo authenticationInfo
+ = new MyProxyAuthenticationInfo(myProxyUserName,
myProxyPassword, "myproxy.teragrid.org",
+ 7512, 17280000, certificateLocation);
+
+ // Server info
+ ServerInfo serverInfo = new ServerInfo("ogce", "trestles.sdsc.edu");
+ Cluster pbsCluster = null;
+ try {
+ pbsCluster = new PBSCluster(serverInfo, authenticationInfo,
"/opt/torque/bin/");
+ } catch (SSHApiException e) {
+ e.printStackTrace(); //To change body of catch statement use File
| Settings | File Templates.
+ }
+ SSHSecurityContext sshSecurityContext = new SSHSecurityContext();
+ sshSecurityContext.setPbsCluster(pbsCluster);
+ sshSecurityContext.setUsername(myProxyUserName);
+ return sshSecurityContext;
+ }
+ @Test
+ public void testGramProvider() throws GFacException {
+ GFacAPI gFacAPI = new GFacAPI();
+ gFacAPI.submitJob(jobExecutionContext);
+ }
+
+}
Modified:
airavata/trunk/modules/gfac-core/src/test/java/org/apache/airavata/core/gfac/services/impl/SSHProviderTest.java
URL:
http://svn.apache.org/viewvc/airavata/trunk/modules/gfac-core/src/test/java/org/apache/airavata/core/gfac/services/impl/SSHProviderTest.java?rev=1530070&r1=1530069&r2=1530070&view=diff
==============================================================================
---
airavata/trunk/modules/gfac-core/src/test/java/org/apache/airavata/core/gfac/services/impl/SSHProviderTest.java
(original)
+++
airavata/trunk/modules/gfac-core/src/test/java/org/apache/airavata/core/gfac/services/impl/SSHProviderTest.java
Mon Oct 7 21:20:10 2013
@@ -60,8 +60,8 @@ public class SSHProviderTest {
//have to set InFlwo Handlers and outFlowHandlers
ApplicationContext applicationContext = new ApplicationContext();
HostDescription host = new HostDescription(SSHHostType.type);
- host.getType().setHostName("gw85.iu.xsede.org");
- host.getType().setHostAddress("gw85.iu.xsede.org");
+ host.getType().setHostName("bigred");
+ host.getType().setHostAddress("bigred2.uits.iu.edu");
applicationContext.setHostDescription(host);
/*
* App
@@ -156,9 +156,9 @@ public class SSHProviderTest {
private SSHSecurityContext getSecurityContext() {
SSHSecurityContext context = new SSHSecurityContext();
- context.setUsername("*****");
+ context.setUsername("lginnali");
context.setPrivateKeyLoc("~/.ssh/id_dsa");
- context.setKeyPass("*****");
+ context.setKeyPass("i want to be free");
return context;
}
Added: airavata/trunk/modules/gfac-core/src/test/resources/PBSTemplate.xslt
URL:
http://svn.apache.org/viewvc/airavata/trunk/modules/gfac-core/src/test/resources/PBSTemplate.xslt?rev=1530070&view=auto
==============================================================================
--- airavata/trunk/modules/gfac-core/src/test/resources/PBSTemplate.xslt (added)
+++ airavata/trunk/modules/gfac-core/src/test/resources/PBSTemplate.xslt Mon
Oct 7 21:20:10 2013
@@ -0,0 +1,73 @@
+<!--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">
+#! /bin/sh
+# PBS batch job script built by Globus job manager
+# <xsl:choose>
+ <xsl:when test="ns:shellName">
+##PBS -S <xsl:value-of select="ns:shellName"/>
+ </xsl:when></xsl:choose>
+ <xsl:choose>
+ <xsl:when test="ns:queueName">
+#PBS -q <xsl:value-of select="ns:queueName"/>
+ </xsl:when>
+ </xsl:choose>
+ <xsl:choose>
+ <xsl:when test="ns:mailOptions">
+#PBS -m <xsl:value-of select="ns:mailOptions"/>
+ </xsl:when>
+ </xsl:choose>
+ <xsl:choose>
+<xsl:when test="ns:acountString">
+#PBS -A <xsl:value-of select="ns:acountString"/>
+ </xsl:when>
+ </xsl:choose>
+ <xsl:choose>
+ <xsl:when test="ns:maxWallTime">
+#PBS -l walltime=<xsl:value-of select="ns:maxWallTime"/>
+ </xsl:when>
+ </xsl:choose>
+ <xsl:choose>
+ <xsl:when test="ns:standardOutFile">
+#PBS -o <xsl:value-of select="ns:standardOutFile"/>
+ </xsl:when>
+ </xsl:choose>
+ <xsl:choose>
+ <xsl:when test="ns:standardOutFile">
+#PBS -e <xsl:value-of select="ns:standardErrorFile"/>
+ </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: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="."/>
+<xsl:text>
</xsl:text>
+</xsl:for-each>
+<xsl:for-each select="ns:preJobCommands/ns:command">
+ <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: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:for-each select="ns:postJobCommands/ns:command">
+ <xsl:value-of select="."/><xsl:text> </xsl:text>
+</xsl:for-each>
+
+</xsl:template>
+
+</xsl:stylesheet>
\ No newline at end of file
Modified: airavata/trunk/modules/gfac-core/src/test/resources/gfac-config.xml
URL:
http://svn.apache.org/viewvc/airavata/trunk/modules/gfac-core/src/test/resources/gfac-config.xml?rev=1530070&r1=1530069&r2=1530070&view=diff
==============================================================================
--- airavata/trunk/modules/gfac-core/src/test/resources/gfac-config.xml
(original)
+++ airavata/trunk/modules/gfac-core/src/test/resources/gfac-config.xml Mon Oct
7 21:20:10 2013
@@ -78,4 +78,13 @@
<Handler
class="org.apache.airavata.gfac.handler.SCPOutputHandler"/>
</OutHandlers>
</Provider>
+ <Provider class="org.apache.airavata.gfac.provider.impl.GSISSHProvider"
host="org.apache.airavata.schemas.gfac.impl.GsisshHostTypeImpl">
+ <InHandlers>
+ <Handler
class="org.apache.airavata.gfac.handler.SCPDirectorySetupHandler"/>
+ <Handler class="org.apache.airavata.gfac.handler.SCPInputHandler"/>
+ </InHandlers>
+ <OutHandlers>
+ <!--Handler
class="org.apache.airavata.gfac.handler.SCPOutputHandler"/-->
+ </OutHandlers>
+ </Provider>
</GFac>
\ No newline at end of file
