Repository: airavata Updated Branches: refs/heads/master 2f3da0104 -> bad2c1c0a
http://git-wip-us.apache.org/repos/asf/airavata/blob/bad2c1c0/modules/gfac/gfac-impl/src/main/java/org/apache/airavata/gfac/ssh/provider/impl/SSHProvider.java ---------------------------------------------------------------------- diff --git a/modules/gfac/gfac-impl/src/main/java/org/apache/airavata/gfac/ssh/provider/impl/SSHProvider.java b/modules/gfac/gfac-impl/src/main/java/org/apache/airavata/gfac/ssh/provider/impl/SSHProvider.java index f162fd5..d1b35cd 100644 --- a/modules/gfac/gfac-impl/src/main/java/org/apache/airavata/gfac/ssh/provider/impl/SSHProvider.java +++ b/modules/gfac/gfac-impl/src/main/java/org/apache/airavata/gfac/ssh/provider/impl/SSHProvider.java @@ -21,6 +21,7 @@ package org.apache.airavata.gfac.ssh.provider.impl; +import org.apache.airavata.gfac.core.cluster.RemoteCluster; import org.apache.airavata.registry.cpi.AppCatalogException; import org.apache.airavata.common.exception.AiravataException; import org.apache.airavata.common.exception.ApplicationSettingsException; @@ -29,7 +30,6 @@ import org.apache.airavata.gfac.core.Constants; import org.apache.airavata.gfac.core.GFacException; import org.apache.airavata.gfac.core.JobDescriptor; import org.apache.airavata.gfac.core.SSHApiException; -import org.apache.airavata.gfac.core.cluster.Cluster; import org.apache.airavata.gfac.core.cluster.JobStatus; import org.apache.airavata.gfac.core.context.JobExecutionContext; import org.apache.airavata.gfac.core.context.MessageContext; @@ -73,7 +73,7 @@ import java.util.*; */ public class SSHProvider extends AbstractProvider { private static final Logger log = LoggerFactory.getLogger(SSHProvider.class); - private Cluster cluster; + private RemoteCluster remoteCluster; private String jobID = null; private String taskID = null; // we keep gsisshprovider to support qsub submission incase of hpc scenario with ssh @@ -93,20 +93,20 @@ public class SSHProvider extends AbstractProvider { JobSubmissionProtocol preferredJobSubmissionProtocol = jobExecutionContext.getPreferredJobSubmissionProtocol(); if (preferredJobSubmissionProtocol == JobSubmissionProtocol.SSH && resourceJobManagerType == ResourceJobManagerType.FORK) { jobID = "SSH_" + jobExecutionContext.getHostName() + "_" + Calendar.getInstance().getTimeInMillis(); - cluster = ((SSHSecurityContext) jobExecutionContext.getSecurityContext(hostAddress)).getPbsCluster(); + remoteCluster = ((SSHSecurityContext) jobExecutionContext.getSecurityContext(hostAddress)).getRemoteCluster(); String remoteFile = jobExecutionContext.getWorkingDir() + File.separatorChar + Constants.EXECUTABLE_NAME; details.setJobID(taskID); details.setJobDescription(remoteFile); jobExecutionContext.setJobDetails(details); - // FIXME : Why cluster is passed as null - JobDescriptor jobDescriptor = GFACSSHUtils.createJobDescriptor(jobExecutionContext, cluster); + // FIXME : Why remoteCluster is passed as null + JobDescriptor jobDescriptor = GFACSSHUtils.createJobDescriptor(jobExecutionContext, remoteCluster); details.setJobDescription(jobDescriptor.toXML()); GFacUtils.saveJobStatus(jobExecutionContext, details, JobState.SETUP); log.info(remoteFile); File runscript = createShellScript(jobExecutionContext); - cluster.scpTo(remoteFile, runscript.getAbsolutePath()); + remoteCluster.scpTo(remoteFile, runscript.getAbsolutePath()); } else { hpcType = true; } @@ -130,7 +130,7 @@ public class SSHProvider extends AbstractProvider { RawCommandInfo rawCommandInfo = new RawCommandInfo("/bin/chmod 755 " + executable + "; " + executable); StandardOutReader jobIDReaderCommandOutput = new StandardOutReader(); log.info("Executing RawCommand : " + rawCommandInfo.getCommand()); - CommandExecutor.executeCommand(rawCommandInfo, cluster.getSession(), jobIDReaderCommandOutput); + CommandExecutor.executeCommand(rawCommandInfo, remoteCluster.getSession(), jobIDReaderCommandOutput); String stdOutputString = getOutputifAvailable(jobIDReaderCommandOutput, "Error submitting job to resource"); log.info("stdout=" + stdOutputString); } catch (Exception e) { @@ -143,36 +143,36 @@ public class SSHProvider extends AbstractProvider { String hostAddress = jobExecutionContext.getHostName(); MonitorPublisher monitorPublisher = jobExecutionContext.getMonitorPublisher(); try { - Cluster cluster = null; + RemoteCluster remoteCluster = null; if (jobExecutionContext.getSecurityContext(hostAddress) == null) { GFACSSHUtils.addSecurityContext(jobExecutionContext); } - cluster = ((SSHSecurityContext) jobExecutionContext.getSecurityContext(hostAddress)).getPbsCluster(); - if (cluster == null) { + remoteCluster = ((SSHSecurityContext) jobExecutionContext.getSecurityContext(hostAddress)).getRemoteCluster(); + if (remoteCluster == null) { throw new GFacProviderException("Security context is not set properly"); } else { log.info("Successfully retrieved the Security Context"); } // This installed path is a mandetory field, because this could change based on the computing resource - JobDescriptor jobDescriptor = GFACSSHUtils.createJobDescriptor(jobExecutionContext, cluster); + JobDescriptor jobDescriptor = GFACSSHUtils.createJobDescriptor(jobExecutionContext, remoteCluster); jobDetails.setJobName(jobDescriptor.getJobName()); log.info(jobDescriptor.toXML()); jobDetails.setJobDescription(jobDescriptor.toXML()); - String jobID = cluster.submitBatchJob(jobDescriptor); + String jobID = remoteCluster.submitBatchJob(jobDescriptor); if (jobID != null && !jobID.isEmpty()) { jobDetails.setJobID(jobID); GFacUtils.saveJobStatus(jobExecutionContext, jobDetails, JobState.SUBMITTED); monitorPublisher.publish(new GfacExperimentStateChangeRequest(new MonitorID(jobExecutionContext) , GfacExperimentState.JOBSUBMITTED)); jobExecutionContext.setJobDetails(jobDetails); - if (verifyJobSubmissionByJobId(cluster, jobID)) { + if (verifyJobSubmissionByJobId(remoteCluster, jobID)) { monitorPublisher.publish(new GfacExperimentStateChangeRequest(new MonitorID(jobExecutionContext) , GfacExperimentState.JOBSUBMITTED)); GFacUtils.saveJobStatus(jobExecutionContext, jobDetails, JobState.QUEUED); } } else { jobExecutionContext.setJobDetails(jobDetails); - String verifyJobId = verifyJobSubmission(cluster, jobDetails); + String verifyJobId = verifyJobSubmission(remoteCluster, jobDetails); if (verifyJobId != null && !verifyJobId.isEmpty()) { // JobStatus either changed from SUBMITTED to QUEUED or directly to QUEUED jobID = verifyJobId; @@ -216,16 +216,16 @@ public class SSHProvider extends AbstractProvider { } } - private boolean verifyJobSubmissionByJobId(Cluster cluster, String jobID) throws SSHApiException { - JobStatus status = cluster.getJobStatus(jobID); + private boolean verifyJobSubmissionByJobId(RemoteCluster remoteCluster, String jobID) throws SSHApiException { + JobStatus status = remoteCluster.getJobStatus(jobID); return status != null && status != JobStatus.U; } - private String verifyJobSubmission(Cluster cluster, JobDetails jobDetails) { + private String verifyJobSubmission(RemoteCluster remoteCluster, JobDetails jobDetails) { String jobName = jobDetails.getJobName(); String jobId = null; try { - jobId = cluster.getJobIdByJobName(jobName, cluster.getServerInfo().getUserName()); + jobId = remoteCluster.getJobIdByJobName(jobName, remoteCluster.getServerInfo().getUserName()); } catch (SSHApiException e) { log.error("Error while verifying JobId from JobName"); } @@ -243,8 +243,8 @@ public class SSHProvider extends AbstractProvider { if (!hpcType) { throw new NotImplementedException(); } else { - Cluster cluster = ((SSHSecurityContext) jobExecutionContext.getSecurityContext(hostAddress)).getPbsCluster(); - if (cluster == null) { + RemoteCluster remoteCluster = ((SSHSecurityContext) jobExecutionContext.getSecurityContext(hostAddress)).getRemoteCluster(); + if (remoteCluster == null) { throw new GFacProviderException("Security context is not set properly"); } else { log.info("Successfully retrieved the Security Context"); @@ -256,7 +256,7 @@ public class SSHProvider extends AbstractProvider { } try { if (jobDetails.getJobID() != null) { - if (cluster.cancelJob(jobDetails.getJobID()) != null) { + if (remoteCluster.cancelJob(jobDetails.getJobID()) != null) { // if this operation success without any exceptions, we can assume cancel operation succeeded. GFacUtils.saveJobStatus(jobExecutionContext, jobDetails, JobState.CANCELED); return true; http://git-wip-us.apache.org/repos/asf/airavata/blob/bad2c1c0/modules/gfac/gfac-impl/src/main/java/org/apache/airavata/gfac/ssh/security/SSHSecurityContext.java ---------------------------------------------------------------------- diff --git a/modules/gfac/gfac-impl/src/main/java/org/apache/airavata/gfac/ssh/security/SSHSecurityContext.java b/modules/gfac/gfac-impl/src/main/java/org/apache/airavata/gfac/ssh/security/SSHSecurityContext.java index a624efc..d6464e2 100644 --- a/modules/gfac/gfac-impl/src/main/java/org/apache/airavata/gfac/ssh/security/SSHSecurityContext.java +++ b/modules/gfac/gfac-impl/src/main/java/org/apache/airavata/gfac/ssh/security/SSHSecurityContext.java @@ -27,7 +27,7 @@ import net.schmizz.sshj.connection.channel.direct.Session; import net.schmizz.sshj.userauth.keyprovider.KeyProvider; import org.apache.airavata.gfac.core.SecurityContext; -import org.apache.airavata.gfac.core.cluster.Cluster; +import org.apache.airavata.gfac.core.cluster.RemoteCluster; import org.slf4j.Logger; import org.slf4j.LoggerFactory; @@ -43,7 +43,7 @@ public class SSHSecurityContext implements SecurityContext { private SSHClient sshClient; private Session session; - private Cluster pbsCluster; + private RemoteCluster remoteCluster; public String getUsername() { return username; @@ -108,11 +108,11 @@ public class SSHSecurityContext implements SecurityContext { return sshClient; } - public void setPbsCluster(Cluster pbsCluster) { - this.pbsCluster = pbsCluster; + public void setRemoteCluster(RemoteCluster remoteCluster) { + this.remoteCluster = remoteCluster; } - public Cluster getPbsCluster() { - return this.pbsCluster; + public RemoteCluster getRemoteCluster() { + return this.remoteCluster; } } http://git-wip-us.apache.org/repos/asf/airavata/blob/bad2c1c0/modules/gfac/gfac-impl/src/main/java/org/apache/airavata/gfac/ssh/util/GFACSSHUtils.java ---------------------------------------------------------------------- diff --git a/modules/gfac/gfac-impl/src/main/java/org/apache/airavata/gfac/ssh/util/GFACSSHUtils.java b/modules/gfac/gfac-impl/src/main/java/org/apache/airavata/gfac/ssh/util/GFACSSHUtils.java index 2fba9a9..69c7df4 100644 --- a/modules/gfac/gfac-impl/src/main/java/org/apache/airavata/gfac/ssh/util/GFACSSHUtils.java +++ b/modules/gfac/gfac-impl/src/main/java/org/apache/airavata/gfac/ssh/util/GFACSSHUtils.java @@ -20,6 +20,8 @@ */ package org.apache.airavata.gfac.ssh.util; +import org.apache.airavata.gfac.core.cluster.RemoteCluster; +import org.apache.airavata.gfac.gsi.ssh.impl.HPCRemoteCluster; import org.apache.airavata.registry.cpi.AppCatalog; import org.apache.airavata.registry.cpi.AppCatalogException; import org.apache.airavata.common.exception.ApplicationSettingsException; @@ -30,14 +32,12 @@ import org.apache.airavata.gfac.core.GFacException; import org.apache.airavata.gfac.core.RequestData; import org.apache.airavata.gfac.core.JobDescriptor; import org.apache.airavata.gfac.core.JobManagerConfiguration; -import org.apache.airavata.gfac.core.cluster.Cluster; import org.apache.airavata.gfac.core.cluster.ServerInfo; import org.apache.airavata.gfac.core.context.JobExecutionContext; import org.apache.airavata.gfac.core.context.MessageContext; import org.apache.airavata.gfac.core.handler.GFacHandlerException; import org.apache.airavata.gfac.core.GFacUtils; import org.apache.airavata.gfac.gsi.ssh.impl.GSISSHAbstractCluster; -import org.apache.airavata.gfac.gsi.ssh.impl.PBSCluster; import org.apache.airavata.gfac.gsi.ssh.impl.authentication.DefaultPasswordAuthenticationInfo; import org.apache.airavata.gfac.gsi.ssh.util.CommonUtils; import org.apache.airavata.gfac.ssh.context.SSHAuthWrapper; @@ -66,7 +66,7 @@ import java.util.*; public class GFACSSHUtils { private final static Logger logger = LoggerFactory.getLogger(GFACSSHUtils.class); - public static Map<String, List<Cluster>> clusters = new HashMap<String, List<Cluster>>(); + public static Map<String, List<RemoteCluster>> clusters = new HashMap<String, List<RemoteCluster>>(); public static final String PBS_JOB_MANAGER = "pbs"; public static final String SLURM_JOB_MANAGER = "slurm"; @@ -99,7 +99,7 @@ public class GFACSSHUtils { ServerInfo serverInfo = new ServerInfo(null, jobExecutionContext.getHostName()); - Cluster pbsCluster = null; + RemoteCluster pbsRemoteCluster = null; try { AuthenticationInfo tokenizedSSHAuthInfo = new TokenizedSSHAuthInfo(requestData); String installedParentPath = jobExecutionContext.getResourceJobManager().getJobManagerBinPath(); @@ -132,19 +132,19 @@ public class GFACSSHUtils { } else if (clusters.containsKey(key)) { int i = new Random().nextInt(Integer.MAX_VALUE) % maxClusterCount; if (clusters.get(key).get(i).getSession().isConnected()) { - pbsCluster = clusters.get(key).get(i); + pbsRemoteCluster = clusters.get(key).get(i); } else { clusters.get(key).remove(i); recreate = true; } if (!recreate) { try { - pbsCluster.listDirectory("~/"); // its hard to trust isConnected method, so we try to connect if it works we are good,else we recreate + pbsRemoteCluster.listDirectory("~/"); // its hard to trust isConnected method, so we try to connect if it works we are good,else we recreate } catch (Exception e) { clusters.get(key).remove(i); logger.info("Connection found the connection map is expired, so we create from the scratch"); maxClusterCount++; - recreate = true; // we make the pbsCluster to create again if there is any exception druing connection + recreate = true; // we make the pbsRemoteCluster to create again if there is any exception druing connection } } logger.info("Re-using the same connection used with the connection string:" + key); @@ -169,21 +169,21 @@ public class GFACSSHUtils { } } - pbsCluster = new PBSCluster(serverInfo, tokenizedSSHAuthInfo,jConfig); - List<Cluster> pbsClusters = null; + pbsRemoteCluster = new HPCRemoteCluster(serverInfo, tokenizedSSHAuthInfo,jConfig); + List<RemoteCluster> pbsRemoteClusters = null; if (!(clusters.containsKey(key))) { - pbsClusters = new ArrayList<Cluster>(); + pbsRemoteClusters = new ArrayList<RemoteCluster>(); } else { - pbsClusters = clusters.get(key); + pbsRemoteClusters = clusters.get(key); } - pbsClusters.add(pbsCluster); - clusters.put(key, pbsClusters); + pbsRemoteClusters.add(pbsRemoteCluster); + clusters.put(key, pbsRemoteClusters); } } } catch (Exception e) { throw new GFacException("Error occurred...", e); } - sshSecurityContext.setPbsCluster(pbsCluster); + sshSecurityContext.setRemoteCluster(pbsRemoteCluster); jobExecutionContext.addSecurityContext(jobExecutionContext.getHostName(), sshSecurityContext); } } catch (AppCatalogException e) { @@ -214,7 +214,7 @@ public class GFACSSHUtils { logger.error("Not able to get SSHJobSubmission from registry"); } - Cluster pbsCluster = null; + RemoteCluster pbsRemoteCluster = null; String key=sshAuth.getKey(); boolean recreate = false; synchronized (clusters) { @@ -223,19 +223,19 @@ public class GFACSSHUtils { } else if (clusters.containsKey(key)) { int i = new Random().nextInt(Integer.MAX_VALUE) % maxClusterCount; if (clusters.get(key).get(i).getSession().isConnected()) { - pbsCluster = clusters.get(key).get(i); + pbsRemoteCluster = clusters.get(key).get(i); } else { clusters.get(key).remove(i); recreate = true; } if (!recreate) { try { - pbsCluster.listDirectory("~/"); // its hard to trust isConnected method, so we try to connect if it works we are good,else we recreate + pbsRemoteCluster.listDirectory("~/"); // its hard to trust isConnected method, so we try to connect if it works we are good,else we recreate } catch (Exception e) { clusters.get(key).remove(i); logger.info("Connection found the connection map is expired, so we create from the scratch"); maxClusterCount++; - recreate = true; // we make the pbsCluster to create again if there is any exception druing connection + recreate = true; // we make the pbsRemoteCluster to create again if there is any exception druing connection } } logger.info("Re-using the same connection used with the connection string:" + key); @@ -268,19 +268,19 @@ public class GFACSSHUtils { } } } - pbsCluster = new PBSCluster(sshAuth.getServerInfo(), sshAuth.getAuthenticationInfo(),jConfig); + pbsRemoteCluster = new HPCRemoteCluster(sshAuth.getServerInfo(), sshAuth.getAuthenticationInfo(),jConfig); key = sshAuth.getKey(); - List<Cluster> pbsClusters = null; + List<RemoteCluster> pbsRemoteClusters = null; if (!(clusters.containsKey(key))) { - pbsClusters = new ArrayList<Cluster>(); + pbsRemoteClusters = new ArrayList<RemoteCluster>(); } else { - pbsClusters = clusters.get(key); + pbsRemoteClusters = clusters.get(key); } - pbsClusters.add(pbsCluster); - clusters.put(key, pbsClusters); + pbsRemoteClusters.add(pbsRemoteCluster); + clusters.put(key, pbsRemoteClusters); } } - sshSecurityContext.setPbsCluster(pbsCluster); + sshSecurityContext.setRemoteCluster(pbsRemoteCluster); jobExecutionContext.addSecurityContext(key, sshSecurityContext); } catch (Exception e) { logger.error(e.getMessage(), e); @@ -289,7 +289,7 @@ public class GFACSSHUtils { } - public static JobDescriptor createJobDescriptor(JobExecutionContext jobExecutionContext, Cluster cluster) throws AppCatalogException, ApplicationSettingsException { + public static JobDescriptor createJobDescriptor(JobExecutionContext jobExecutionContext, RemoteCluster remoteCluster) throws AppCatalogException, ApplicationSettingsException { JobDescriptor jobDescriptor = new JobDescriptor(); TaskDetails taskData = jobExecutionContext.getTaskData(); @@ -415,10 +415,10 @@ public class GFACSSHUtils { } jobDescriptor.setInputValues(inputValues); - jobDescriptor.setUserName(((GSISSHAbstractCluster) cluster).getServerInfo().getUserName()); + jobDescriptor.setUserName(((GSISSHAbstractCluster) remoteCluster).getServerInfo().getUserName()); jobDescriptor.setShellName("/bin/bash"); jobDescriptor.setAllEnvExport(true); - jobDescriptor.setOwner(((PBSCluster) cluster).getServerInfo().getUserName()); + jobDescriptor.setOwner(((HPCRemoteCluster) remoteCluster).getServerInfo().getUserName()); ResourceJobManager resourceJobManager = jobExecutionContext.getResourceJobManager(); http://git-wip-us.apache.org/repos/asf/airavata/blob/bad2c1c0/modules/gfac/gfac-impl/src/main/java/org/apache/airavata/gfac/ssh/util/HandleOutputs.java ---------------------------------------------------------------------- diff --git a/modules/gfac/gfac-impl/src/main/java/org/apache/airavata/gfac/ssh/util/HandleOutputs.java b/modules/gfac/gfac-impl/src/main/java/org/apache/airavata/gfac/ssh/util/HandleOutputs.java index 31550fd..890b858 100644 --- a/modules/gfac/gfac-impl/src/main/java/org/apache/airavata/gfac/ssh/util/HandleOutputs.java +++ b/modules/gfac/gfac-impl/src/main/java/org/apache/airavata/gfac/ssh/util/HandleOutputs.java @@ -8,7 +8,7 @@ import java.util.List; import org.apache.airavata.gfac.core.context.JobExecutionContext; import org.apache.airavata.gfac.core.handler.GFacHandlerException; import org.apache.airavata.gfac.core.GFacUtils; -import org.apache.airavata.gfac.core.cluster.Cluster; +import org.apache.airavata.gfac.core.cluster.RemoteCluster; import org.apache.airavata.model.appcatalog.appinterface.DataType; import org.apache.airavata.model.appcatalog.appinterface.OutputDataObjectType; import org.slf4j.Logger; @@ -21,14 +21,14 @@ import org.slf4j.LoggerFactory; public class HandleOutputs { private static final Logger log = LoggerFactory.getLogger(HandleOutputs.class); - public static List<OutputDataObjectType> handleOutputs(JobExecutionContext jobExecutionContext, Cluster cluster) throws GFacHandlerException { + public static List<OutputDataObjectType> handleOutputs(JobExecutionContext jobExecutionContext, RemoteCluster remoteCluster) throws GFacHandlerException { List<OutputDataObjectType> outputArray = new ArrayList<OutputDataObjectType>(); try { String outputDataDir = File.separator + "tmp" + File.separator + jobExecutionContext.getExperimentID(); (new File(outputDataDir)).mkdirs(); List<OutputDataObjectType> outputs = jobExecutionContext.getTaskData().getApplicationOutputs(); - List<String> outputList = cluster.listDirectory(jobExecutionContext.getWorkingDir()); + List<String> outputList = remoteCluster.listDirectory(jobExecutionContext.getWorkingDir()); boolean missingOutput = false; for (OutputDataObjectType output : outputs) { @@ -45,7 +45,7 @@ public class HandleOutputs { if (output.getLocation() == null && !outputList.contains(fileName) && output.isIsRequired()) { missingOutput = true; } else { - cluster.scpFrom(outputFile, outputDataDir); + remoteCluster.scpFrom(outputFile, outputDataDir); String localFile = outputDataDir + File.separator + fileName; jobExecutionContext.addOutputFile(localFile); output.setValue(localFile); @@ -55,7 +55,7 @@ public class HandleOutputs { } else if (DataType.STDOUT == output.getType()) { String downloadFile = jobExecutionContext.getStandardOutput(); String fileName = downloadFile.substring(downloadFile.lastIndexOf(File.separatorChar) + 1, downloadFile.length()); - cluster.scpFrom(downloadFile, outputDataDir); + remoteCluster.scpFrom(downloadFile, outputDataDir); String localFile = outputDataDir + File.separator + fileName; jobExecutionContext.addOutputFile(localFile); jobExecutionContext.setStandardOutput(localFile); @@ -65,7 +65,7 @@ public class HandleOutputs { } else if (DataType.STDERR == output.getType()) { String downloadFile = jobExecutionContext.getStandardError(); String fileName = downloadFile.substring(downloadFile.lastIndexOf(File.separatorChar) + 1, downloadFile.length()); - cluster.scpFrom(downloadFile, outputDataDir); + remoteCluster.scpFrom(downloadFile, outputDataDir); String localFile = outputDataDir + File.separator + fileName; jobExecutionContext.addOutputFile(localFile); jobExecutionContext.setStandardError(localFile); http://git-wip-us.apache.org/repos/asf/airavata/blob/bad2c1c0/modules/gfac/gfac-impl/src/test/java/org/apache/airavata/core/gfac/services/impl/BigRed2TestWithSSHAuth.java ---------------------------------------------------------------------- diff --git a/modules/gfac/gfac-impl/src/test/java/org/apache/airavata/core/gfac/services/impl/BigRed2TestWithSSHAuth.java b/modules/gfac/gfac-impl/src/test/java/org/apache/airavata/core/gfac/services/impl/BigRed2TestWithSSHAuth.java index c83bf6a..65d52c3 100644 --- a/modules/gfac/gfac-impl/src/test/java/org/apache/airavata/core/gfac/services/impl/BigRed2TestWithSSHAuth.java +++ b/modules/gfac/gfac-impl/src/test/java/org/apache/airavata/core/gfac/services/impl/BigRed2TestWithSSHAuth.java @@ -32,12 +32,12 @@ //import org.apache.airavata.gfac.core.context.MessageContext; //import org.apache.airavata.gfac.impl.BetterGfacImpl; //import org.apache.airavata.gfac.ssh.security.SSHSecurityContext; -//import org.apache.airavata.gfac.ssh.api.Cluster; +//import org.apache.airavata.gfac.ssh.api.RemoteCluster; //import org.apache.airavata.gfac.ssh.api.SSHApiException; //import org.apache.airavata.gfac.ssh.api.ServerInfo; //import AuthenticationInfo; //import org.apache.airavata.gfac.ssh.api.job.JobManagerConfiguration; -//import org.apache.airavata.gfac.ssh.impl.PBSCluster; +//import org.apache.airavata.gfac.ssh.impl.HPCRemoteCluster; //import org.apache.airavata.gfac.ssh.impl.authentication.DefaultPasswordAuthenticationInfo; //import org.apache.airavata.gfac.ssh.impl.authentication.DefaultPublicKeyFileAuthentication; //import org.apache.airavata.gfac.ssh.util.CommonUtils; @@ -222,15 +222,15 @@ // // Server info // ServerInfo serverInfo = new ServerInfo(this.userName, this.hostName); // -// Cluster pbsCluster = null; +// RemoteCluster pbsCluster = null; // SSHSecurityContext sshSecurityContext = null; // // JobManagerConfiguration pbsJobManager = CommonUtils.getPBSJobManager(app.getInstalledParentPath()); -// pbsCluster = new PBSCluster(serverInfo, authenticationInfo, pbsJobManager); +// pbsCluster = new HPCRemoteCluster(serverInfo, authenticationInfo, pbsJobManager); // // // sshSecurityContext = new SSHSecurityContext(); -// sshSecurityContext.setPbsCluster(pbsCluster); +// sshSecurityContext.setRemoteCluster(pbsCluster); // sshSecurityContext.setUsername(userName); // sshSecurityContext.setKeyPass(passPhrase); // sshSecurityContext.setPrivateKeyLoc(privateKeyPath); http://git-wip-us.apache.org/repos/asf/airavata/blob/bad2c1c0/modules/gfac/gfac-impl/src/test/java/org/apache/airavata/core/gfac/services/impl/CredentialStoreTest.java ---------------------------------------------------------------------- diff --git a/modules/gfac/gfac-impl/src/test/java/org/apache/airavata/core/gfac/services/impl/CredentialStoreTest.java b/modules/gfac/gfac-impl/src/test/java/org/apache/airavata/core/gfac/services/impl/CredentialStoreTest.java index babbaf7..8158fc5 100644 --- a/modules/gfac/gfac-impl/src/test/java/org/apache/airavata/core/gfac/services/impl/CredentialStoreTest.java +++ b/modules/gfac/gfac-impl/src/test/java/org/apache/airavata/core/gfac/services/impl/CredentialStoreTest.java @@ -37,7 +37,7 @@ //import org.apache.airavata.gfac.ssh.security.TokenizedSSHAuthInfo; //import org.apache.airavata.gfac.ssh.api.SSHApiException; //import org.apache.airavata.gfac.ssh.api.ServerInfo; -//import org.apache.airavata.gfac.ssh.impl.PBSCluster; +//import org.apache.airavata.gfac.ssh.impl.HPCRemoteCluster; //import org.apache.airavata.gfac.ssh.util.CommonUtils; //import org.apache.airavata.registry.api.AiravataRegistry2; //import org.apache.airavata.registry.api.AiravataRegistryFactory; @@ -91,7 +91,7 @@ // SSHCredential credentials = tokenizedSSHAuthInfo.getCredentials(); // ServerInfo serverInfo = new ServerInfo("cgateway", "bigred2.uits.iu.edu"); // -// PBSCluster pbsCluster = new PBSCluster(serverInfo, tokenizedSSHAuthInfo, CommonUtils.getPBSJobManager("/opt/torque/bin/")); +// HPCRemoteCluster pbsCluster = new HPCRemoteCluster(serverInfo, tokenizedSSHAuthInfo, CommonUtils.getPBSJobManager("/opt/torque/bin/")); // Assert.assertNotNull(pbsCluster); // return; // http://git-wip-us.apache.org/repos/asf/airavata/blob/bad2c1c0/modules/gfac/gfac-impl/src/test/java/org/apache/airavata/core/gfac/services/impl/GSISSHProviderTestWithMyProxyAuth.java ---------------------------------------------------------------------- diff --git a/modules/gfac/gfac-impl/src/test/java/org/apache/airavata/core/gfac/services/impl/GSISSHProviderTestWithMyProxyAuth.java b/modules/gfac/gfac-impl/src/test/java/org/apache/airavata/core/gfac/services/impl/GSISSHProviderTestWithMyProxyAuth.java index c1bc393..9891485 100644 --- a/modules/gfac/gfac-impl/src/test/java/org/apache/airavata/core/gfac/services/impl/GSISSHProviderTestWithMyProxyAuth.java +++ b/modules/gfac/gfac-impl/src/test/java/org/apache/airavata/core/gfac/services/impl/GSISSHProviderTestWithMyProxyAuth.java @@ -44,7 +44,7 @@ //import org.apache.airavata.gfac.ssh.api.SSHApiException; //import org.apache.airavata.gfac.ssh.api.ServerInfo; //import GSIAuthenticationInfo; -//import org.apache.airavata.gfac.ssh.impl.PBSCluster; +//import org.apache.airavata.gfac.ssh.impl.HPCRemoteCluster; //import org.apache.airavata.gfac.ssh.impl.authentication.MyProxyAuthenticationInfo; //import org.apache.airavata.gfac.ssh.util.CommonUtils; //import org.apache.airavata.model.appcatalog.appdeployment.ApplicationDeploymentDescription; @@ -211,7 +211,7 @@ // ServerInfo serverInfo = new ServerInfo("ogce", "trestles.sdsc.edu"); // Cluster pbsCluster = null; // try { -// pbsCluster = new PBSCluster(serverInfo, authenticationInfo, CommonUtils.getPBSJobManager(app.getInstalledParentPath())); +// pbsCluster = new HPCRemoteCluster(serverInfo, authenticationInfo, CommonUtils.getPBSJobManager(app.getInstalledParentPath())); // } catch (SSHApiException e) { // e.printStackTrace(); //To change body of catch statement use File | Settings | File Templates. // } http://git-wip-us.apache.org/repos/asf/airavata/blob/bad2c1c0/modules/gfac/gfac-impl/src/test/java/org/apache/airavata/gfac/ssh/impl/DefaultSSHApiTestWithMyProxyAuth.java ---------------------------------------------------------------------- diff --git a/modules/gfac/gfac-impl/src/test/java/org/apache/airavata/gfac/ssh/impl/DefaultSSHApiTestWithMyProxyAuth.java b/modules/gfac/gfac-impl/src/test/java/org/apache/airavata/gfac/ssh/impl/DefaultSSHApiTestWithMyProxyAuth.java index 45d8ca2..4932fcf 100644 --- a/modules/gfac/gfac-impl/src/test/java/org/apache/airavata/gfac/ssh/impl/DefaultSSHApiTestWithMyProxyAuth.java +++ b/modules/gfac/gfac-impl/src/test/java/org/apache/airavata/gfac/ssh/impl/DefaultSSHApiTestWithMyProxyAuth.java @@ -28,7 +28,7 @@ import org.apache.airavata.gfac.core.cluster.RawCommandInfo; import org.apache.airavata.gfac.core.cluster.ServerInfo; import org.apache.airavata.gfac.gsi.ssh.api.CommandExecutor; import org.apache.airavata.gfac.gsi.ssh.config.ConfigReader; -import org.apache.airavata.gfac.gsi.ssh.impl.PBSCluster; +import org.apache.airavata.gfac.gsi.ssh.impl.HPCRemoteCluster; import org.apache.airavata.gfac.gsi.ssh.impl.SystemCommandOutput; import org.apache.airavata.gfac.gsi.ssh.impl.authentication.DefaultPublicKeyAuthentication; import org.apache.commons.io.IOUtils; @@ -38,7 +38,7 @@ import org.slf4j.LoggerFactory; import java.io.*; public class DefaultSSHApiTestWithMyProxyAuth { - private static final Logger log = LoggerFactory.getLogger(PBSCluster.class); + private static final Logger log = LoggerFactory.getLogger(HPCRemoteCluster.class); http://git-wip-us.apache.org/repos/asf/airavata/blob/bad2c1c0/modules/gfac/gfac-impl/src/test/java/org/apache/airavata/gfac/ssh/impl/VanilaTestWithSSHAuth.java ---------------------------------------------------------------------- diff --git a/modules/gfac/gfac-impl/src/test/java/org/apache/airavata/gfac/ssh/impl/VanilaTestWithSSHAuth.java b/modules/gfac/gfac-impl/src/test/java/org/apache/airavata/gfac/ssh/impl/VanilaTestWithSSHAuth.java index 8bc8c66..f262930 100644 --- a/modules/gfac/gfac-impl/src/test/java/org/apache/airavata/gfac/ssh/impl/VanilaTestWithSSHAuth.java +++ b/modules/gfac/gfac-impl/src/test/java/org/apache/airavata/gfac/ssh/impl/VanilaTestWithSSHAuth.java @@ -23,9 +23,9 @@ package org.apache.airavata.gfac.ssh.impl; import org.apache.airavata.gfac.core.JobDescriptor; import org.apache.airavata.gfac.core.authentication.AuthenticationInfo; -import org.apache.airavata.gfac.core.cluster.Cluster; +import org.apache.airavata.gfac.core.cluster.RemoteCluster; import org.apache.airavata.gfac.core.cluster.ServerInfo; -import org.apache.airavata.gfac.gsi.ssh.impl.PBSCluster; +import org.apache.airavata.gfac.gsi.ssh.impl.HPCRemoteCluster; import org.apache.airavata.gfac.gsi.ssh.impl.authentication.DefaultPasswordAuthenticationInfo; import org.apache.airavata.gfac.gsi.ssh.impl.authentication.DefaultPublicKeyFileAuthentication; import org.apache.airavata.gfac.gsi.ssh.util.CommonUtils; @@ -112,7 +112,7 @@ public class VanilaTestWithSSHAuth { } // Server info ServerInfo serverInfo = new ServerInfo(this.userName, this.hostName); - Cluster pbsCluster = new PBSCluster(serverInfo, authenticationInfo, CommonUtils.getPBSJobManager(path)); + RemoteCluster pbsRemoteCluster = new HPCRemoteCluster(serverInfo, authenticationInfo, CommonUtils.getPBSJobManager(path)); String date = new Date().toString(); date = date.replaceAll(" ", "_"); @@ -122,16 +122,16 @@ public class VanilaTestWithSSHAuth { workingDirectory = workingDirectory + File.separator + date + "_" + UUID.randomUUID(); - pbsCluster.makeDirectory(workingDirectory); + pbsRemoteCluster.makeDirectory(workingDirectory); Thread.sleep(1000); - pbsCluster.makeDirectory(workingDirectory + File.separator + "inputs"); + pbsRemoteCluster.makeDirectory(workingDirectory + File.separator + "inputs"); Thread.sleep(1000); - pbsCluster.makeDirectory(workingDirectory + File.separator + "outputs"); + pbsRemoteCluster.makeDirectory(workingDirectory + File.separator + "outputs"); // doing file transfer to the remote resource String remoteLocation = workingDirectory + File.separator + "inputs"; - pbsCluster.scpTo(remoteLocation, pomFile); + pbsRemoteCluster.scpTo(remoteLocation, pomFile); int i = pomFile.lastIndexOf(File.separator); String fileName = pomFile.substring(i + 1); @@ -156,12 +156,12 @@ public class VanilaTestWithSSHAuth { //finished construction of job object System.out.println(jobDescriptor.toXML()); if(hostName.contains("trestles")){ - String jobID = pbsCluster.submitBatchJob(jobDescriptor); + String jobID = pbsRemoteCluster.submitBatchJob(jobDescriptor); System.out.println("JobID returned : " + jobID); -// Cluster cluster = sshApi.getCluster(serverInfo, authenticationInfo); +// RemoteCluster cluster = sshApi.getCluster(serverInfo, authenticationInfo); Thread.sleep(1000); - JobDescriptor jobById = pbsCluster.getJobDescriptorById(jobID); + JobDescriptor jobById = pbsRemoteCluster.getJobDescriptorById(jobID); //printing job data got from previous call AssertJUnit.assertEquals(jobById.getJobId(), jobID); @@ -224,8 +224,8 @@ public class VanilaTestWithSSHAuth { jobDescriptor.setInputValues(inputs); //finished construction of job object System.out.println(jobDescriptor.toXML()); - Cluster pbsCluster = new PBSCluster(CommonUtils.getLSFJobManager("")); - ((PBSCluster) pbsCluster).generateJobScript(jobDescriptor); + RemoteCluster pbsRemoteCluster = new HPCRemoteCluster(CommonUtils.getLSFJobManager("")); + ((HPCRemoteCluster) pbsRemoteCluster).generateJobScript(jobDescriptor); } @Test @@ -240,8 +240,8 @@ public class VanilaTestWithSSHAuth { } // Server info ServerInfo serverInfo = new ServerInfo(this.userName, this.hostName); - Cluster pbsCluster = new PBSCluster(serverInfo, authenticationInfo, CommonUtils.getPBSJobManager(path)); - new PBSCluster(serverInfo, authenticationInfo, CommonUtils.getPBSJobManager(path));; + RemoteCluster pbsRemoteCluster = new HPCRemoteCluster(serverInfo, authenticationInfo, CommonUtils.getPBSJobManager(path)); + new HPCRemoteCluster(serverInfo, authenticationInfo, CommonUtils.getPBSJobManager(path));; String date = new Date().toString(); date = date.replaceAll(" ", "_"); @@ -256,9 +256,9 @@ public class VanilaTestWithSSHAuth { // resource workingDirectory = workingDirectory + File.separator + date + "_" + UUID.randomUUID(); - pbsCluster.makeDirectory(workingDirectory); - pbsCluster.scpTo(workingDirectory, pomFile); + pbsRemoteCluster.makeDirectory(workingDirectory); + pbsRemoteCluster.scpTo(workingDirectory, pomFile); Thread.sleep(1000); - pbsCluster.scpFrom(workingDirectory + File.separator + "pom.xml", (new File(".")).getAbsolutePath()); + pbsRemoteCluster.scpFrom(workingDirectory + File.separator + "pom.xml", (new File(".")).getAbsolutePath()); } } http://git-wip-us.apache.org/repos/asf/airavata/blob/bad2c1c0/modules/gfac/gfac-impl/src/test/java/org/apache/airavata/job/AMQPMonitorTest.java ---------------------------------------------------------------------- diff --git a/modules/gfac/gfac-impl/src/test/java/org/apache/airavata/job/AMQPMonitorTest.java b/modules/gfac/gfac-impl/src/test/java/org/apache/airavata/job/AMQPMonitorTest.java index fc0ea30..f4da3d0 100644 --- a/modules/gfac/gfac-impl/src/test/java/org/apache/airavata/job/AMQPMonitorTest.java +++ b/modules/gfac/gfac-impl/src/test/java/org/apache/airavata/job/AMQPMonitorTest.java @@ -22,16 +22,16 @@ package org.apache.airavata.job; import com.google.common.eventbus.EventBus; import com.google.common.eventbus.Subscribe; +import org.apache.airavata.gfac.core.cluster.RemoteCluster; +import org.apache.airavata.gfac.gsi.ssh.impl.HPCRemoteCluster; import org.apache.airavata.registry.cpi.AppCatalog; import org.apache.aiaravata.application.catalog.data.impl.AppCatalogFactory; import org.apache.airavata.common.utils.MonitorPublisher; import org.apache.airavata.gfac.core.JobDescriptor; import org.apache.airavata.gfac.core.SSHApiException; import org.apache.airavata.gfac.core.authentication.GSIAuthenticationInfo; -import org.apache.airavata.gfac.core.cluster.Cluster; import org.apache.airavata.gfac.core.cluster.ServerInfo; import org.apache.airavata.gfac.core.monitor.MonitorID; -import org.apache.airavata.gfac.gsi.ssh.impl.PBSCluster; import org.apache.airavata.gfac.gsi.ssh.impl.authentication.MyProxyAuthenticationInfo; import org.apache.airavata.gfac.gsi.ssh.util.CommonUtils; import org.apache.airavata.gfac.monitor.impl.push.amqp.AMQPMonitor; @@ -148,8 +148,8 @@ public class AMQPMonitorTest { ServerInfo serverInfo = new ServerInfo("ogce", "login1.stampede.tacc.utexas.edu",2222); - Cluster pbsCluster = new - PBSCluster(serverInfo, authenticationInfo, CommonUtils.getPBSJobManager("/usr/bin/")); + RemoteCluster pbsRemoteCluster = new + HPCRemoteCluster(serverInfo, authenticationInfo, CommonUtils.getPBSJobManager("/usr/bin/")); // Execute command @@ -176,7 +176,7 @@ public class AMQPMonitorTest { jobDescriptor.setInputValues(inputs); //finished construction of job object System.out.println(jobDescriptor.toXML()); - String jobID = pbsCluster.submitBatchJob(jobDescriptor); + String jobID = pbsRemoteCluster.submitBatchJob(jobDescriptor); System.out.println(jobID); try { pushQueue.add(new MonitorID(computeResourceDescription, jobID,null,null,null, "ogce", jobName)); http://git-wip-us.apache.org/repos/asf/airavata/blob/bad2c1c0/modules/gfac/gfac-impl/src/test/java/org/apache/airavata/job/QstatMonitorTestWithMyProxyAuth.java ---------------------------------------------------------------------- diff --git a/modules/gfac/gfac-impl/src/test/java/org/apache/airavata/job/QstatMonitorTestWithMyProxyAuth.java b/modules/gfac/gfac-impl/src/test/java/org/apache/airavata/job/QstatMonitorTestWithMyProxyAuth.java index c405e8c..70727f7 100644 --- a/modules/gfac/gfac-impl/src/test/java/org/apache/airavata/job/QstatMonitorTestWithMyProxyAuth.java +++ b/modules/gfac/gfac-impl/src/test/java/org/apache/airavata/job/QstatMonitorTestWithMyProxyAuth.java @@ -37,7 +37,7 @@ //import org.apache.airavata.gfac.ssh.api.ServerInfo; //import org.apache.airavata.gfac.ssh.api.authentication.GSIAuthenticationInfo; //import org.apache.airavata.gfac.ssh.api.job.JobDescriptor; -//import org.apache.airavata.gfac.ssh.impl.PBSCluster; +//import org.apache.airavata.gfac.ssh.impl.HPCRemoteCluster; //import org.apache.airavata.gfac.ssh.impl.authentication.MyProxyAuthenticationInfo; //import org.apache.airavata.gfac.ssh.util.CommonUtils; //import org.apache.airavata.model.messaging.event.JobStatusChangeEvent; @@ -119,7 +119,7 @@ // ServerInfo serverInfo = new ServerInfo("ogce", hostDescription.getType().getHostAddress()); // // -// Cluster pbsCluster = new PBSCluster(serverInfo, authenticationInfo, CommonUtils.getPBSJobManager("/opt/torque/bin/")); +// Cluster pbsCluster = new HPCRemoteCluster(serverInfo, authenticationInfo, CommonUtils.getPBSJobManager("/opt/torque/bin/")); // // // // Execute command
