subject:"\[jira\] \[Commented\] \(AIRAVATA\-2621\) SSH port provided in compute resource registration is not considered for cluster SSH communication"

[jira] [Commented] (AIRAVATA-2621) SSH port provided in compute resource registration is not considered for cluster SSH communication

2018-02-22 Thread ASF subversion and git services (JIRA)


[ 
https://issues.apache.org/jira/browse/AIRAVATA-2621?page=com.atlassian.jira.plugin.system.issuetabpanels:comment-tabpanel=16373069#comment-16373069
 ] 

ASF subversion and git services commented on AIRAVATA-2621:
---

Commit 6c1478c906fd0f1b209b5b0d2eb2317a68ed549d in airavata's branch 
refs/heads/develop from dimuthu.upeks...@gmail.com
[ https://gitbox.apache.org/repos/asf?p=airavata.git;h=6c1478c ]

Fixing AIRAVATA-2621


> SSH port provided in compute resource registration is not considered for 
> cluster SSH communication
> --
>
> Key: AIRAVATA-2621
> URL: https://issues.apache.org/jira/browse/AIRAVATA-2621
> Project: Airavata
>  Issue Type: Bug
>  Components: GFac
>Affects Versions: 0.18
> Environment: https://hpcgateway.gsu.edu/
> https://scigap.org/
>Reporter: Eroma
>Assignee: Dimuthu Upeksha
>Priority: Major
> Fix For: 0.18
>
>
> 1. Added a specific port for job submissions (15022)
> 2. But when submitting jobs, for environment creation, the gfac is using the 
> default 22 port, not the specified one in scigap.org for hpclogin.gsu.edu.
> 3. log messages in airavata log
> 2017-12-19 11:13:18,996 [pool-7-thread-2] INFO  
> o.a.airavata.gfac.impl.Factory 
> process_id=PROCESS_3b471b3b-5b4e-4b6d-a66e-554652a390d2, 
> token_id=35da840b-63d5-4cbf-b9ce-3005cd94d961, 
> experiment_id=NWChem2_a38ac303-666f-4dea-9b4c-7bffe0f97dd7, 
> gateway_id=georgiastate - Initialize a new SSH session for 
> :airavata_hpclogin.gsu.edu_22_35da840b-63d5-4cbf-b9ce-3005cd94d961
> 2017-12-19 11:15:26,272 [pool-7-thread-2] ERROR o.a.a.gfac.core.GFacException 
> process_id=PROCESS_3b471b3b-5b4e-4b6d-a66e-554652a390d2, 
> token_id=35da840b-63d5-4cbf-b9ce-3005cd94d961, 
> experiment_id=NWChem2_a38ac303-666f-4dea-9b4c-7bffe0f97dd7, 
> gateway_id=georgiastate - JSch initialization error
> com.jcraft.jsch.JSchException: java.net.ConnectException: Connection timed 
> out (Connection timed out)
> at com.jcraft.jsch.Util.createSocket(Util.java:349)
> at com.jcraft.jsch.Session.connect(Session.java:215)
> at com.jcraft.jsch.Session.connect(Session.java:183)
> at 
> org.apache.airavata.gfac.impl.Factory.getSSHSession(Factory.java:542)
> at 
> org.apache.airavata.gfac.impl.HPCRemoteCluster.getSshSession(HPCRemoteCluster.java:138)
> at 
> org.apache.airavata.gfac.impl.HPCRemoteCluster.getSession(HPCRemoteCluster.java:315)
> at 
> org.apache.airavata.gfac.impl.HPCRemoteCluster.makeDirectory(HPCRemoteCluster.java:242)
> at 
> org.apache.airavata.gfac.impl.task.EnvironmentSetupTask.execute(EnvironmentSetupTask.java:51)
> at 
> org.apache.airavata.gfac.impl.GFacEngineImpl.executeTask(GFacEngineImpl.java:814)
> at 
> org.apache.airavata.gfac.impl.GFacEngineImpl.configureWorkspace(GFacEngineImpl.java:553)
> at 
> org.apache.airavata.gfac.impl.GFacEngineImpl.executeTaskListFrom(GFacEngineImpl.java:324)
> at 
> org.apache.airavata.gfac.impl.GFacEngineImpl.executeProcess(GFacEngineImpl.java:286)
> at 
> org.apache.airavata.gfac.impl.GFacWorker.executeProcess(GFacWorker.java:227)
> at org.apache.airavata.gfac.impl.GFacWorker.run(GFacWorker.java:86)
> at 
> org.apache.airavata.common.logging.MDCUtil.lambda$wrapWithMDC$0(MDCUtil.java:40)
> at 
> java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142)
> at 
> java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617)
> at java.lang.Thread.run(Thread.java:748)
> Caused by: java.net.ConnectException: Connection timed out (Connection timed 
> out)
> at java.net.PlainSocketImpl.socketConnect(Native Method)
> at 
> java.net.AbstractPlainSocketImpl.doConnect(AbstractPlainSocketImpl.java:350)
> at 
> java.net.AbstractPlainSocketImpl.connectToAddress(AbstractPlainSocketImpl.java:206)
> at 
> java.net.AbstractPlainSocketImpl.connect(AbstractPlainSocketImpl.java:188)
> at java.net.SocksSocketImpl.connect(SocksSocketImpl.java:392)
> at java.net.Socket.connect(Socket.java:589)
> at java.net.Socket.connect(Socket.java:538)
> at java.net.Socket.(Socket.java:434)
> at java.net.Socket.(Socket.java:211)
> at com.jcraft.jsch.Util.createSocket(Util.java:343)
> ... 17 common frames omitted
> ?NWChem2_a38ac303-666f-4dea-9b4c-7bffe0f97dd7



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[jira] [Commented] (AIRAVATA-2621) SSH port provided in compute resource registration is not considered for cluster SSH communication

2018-01-19 Thread ASF subversion and git services (JIRA)


[ 
https://issues.apache.org/jira/browse/AIRAVATA-2621?page=com.atlassian.jira.plugin.system.issuetabpanels:comment-tabpanel=16332515#comment-16332515
 ] 

ASF subversion and git services commented on AIRAVATA-2621:
---

Commit f13c17fe41bfdd1a4c8e35a88ab16f534190b523 in airavata's branch 
refs/heads/AIRAVATA-2620 from dimuthu.upeks...@gmail.com
[ https://gitbox.apache.org/repos/asf?p=airavata.git;h=f13c17f ]

Fixing AIRAVATA-2621


> SSH port provided in compute resource registration is not considered for 
> cluster SSH communication
> --
>
> Key: AIRAVATA-2621
> URL: https://issues.apache.org/jira/browse/AIRAVATA-2621
> Project: Airavata
>  Issue Type: Bug
>  Components: GFac
>Affects Versions: 0.18
> Environment: https://hpcgateway.gsu.edu/
> https://scigap.org/
>Reporter: Eroma
>Assignee: Dimuthu Upeksha
>Priority: Major
> Fix For: 0.18
>
>
> 1. Added a specific port for job submissions (15022)
> 2. But when submitting jobs, for environment creation, the gfac is using the 
> default 22 port, not the specified one in scigap.org for hpclogin.gsu.edu.
> 3. log messages in airavata log
> 2017-12-19 11:13:18,996 [pool-7-thread-2] INFO  
> o.a.airavata.gfac.impl.Factory 
> process_id=PROCESS_3b471b3b-5b4e-4b6d-a66e-554652a390d2, 
> token_id=35da840b-63d5-4cbf-b9ce-3005cd94d961, 
> experiment_id=NWChem2_a38ac303-666f-4dea-9b4c-7bffe0f97dd7, 
> gateway_id=georgiastate - Initialize a new SSH session for 
> :airavata_hpclogin.gsu.edu_22_35da840b-63d5-4cbf-b9ce-3005cd94d961
> 2017-12-19 11:15:26,272 [pool-7-thread-2] ERROR o.a.a.gfac.core.GFacException 
> process_id=PROCESS_3b471b3b-5b4e-4b6d-a66e-554652a390d2, 
> token_id=35da840b-63d5-4cbf-b9ce-3005cd94d961, 
> experiment_id=NWChem2_a38ac303-666f-4dea-9b4c-7bffe0f97dd7, 
> gateway_id=georgiastate - JSch initialization error
> com.jcraft.jsch.JSchException: java.net.ConnectException: Connection timed 
> out (Connection timed out)
> at com.jcraft.jsch.Util.createSocket(Util.java:349)
> at com.jcraft.jsch.Session.connect(Session.java:215)
> at com.jcraft.jsch.Session.connect(Session.java:183)
> at 
> org.apache.airavata.gfac.impl.Factory.getSSHSession(Factory.java:542)
> at 
> org.apache.airavata.gfac.impl.HPCRemoteCluster.getSshSession(HPCRemoteCluster.java:138)
> at 
> org.apache.airavata.gfac.impl.HPCRemoteCluster.getSession(HPCRemoteCluster.java:315)
> at 
> org.apache.airavata.gfac.impl.HPCRemoteCluster.makeDirectory(HPCRemoteCluster.java:242)
> at 
> org.apache.airavata.gfac.impl.task.EnvironmentSetupTask.execute(EnvironmentSetupTask.java:51)
> at 
> org.apache.airavata.gfac.impl.GFacEngineImpl.executeTask(GFacEngineImpl.java:814)
> at 
> org.apache.airavata.gfac.impl.GFacEngineImpl.configureWorkspace(GFacEngineImpl.java:553)
> at 
> org.apache.airavata.gfac.impl.GFacEngineImpl.executeTaskListFrom(GFacEngineImpl.java:324)
> at 
> org.apache.airavata.gfac.impl.GFacEngineImpl.executeProcess(GFacEngineImpl.java:286)
> at 
> org.apache.airavata.gfac.impl.GFacWorker.executeProcess(GFacWorker.java:227)
> at org.apache.airavata.gfac.impl.GFacWorker.run(GFacWorker.java:86)
> at 
> org.apache.airavata.common.logging.MDCUtil.lambda$wrapWithMDC$0(MDCUtil.java:40)
> at 
> java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142)
> at 
> java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617)
> at java.lang.Thread.run(Thread.java:748)
> Caused by: java.net.ConnectException: Connection timed out (Connection timed 
> out)
> at java.net.PlainSocketImpl.socketConnect(Native Method)
> at 
> java.net.AbstractPlainSocketImpl.doConnect(AbstractPlainSocketImpl.java:350)
> at 
> java.net.AbstractPlainSocketImpl.connectToAddress(AbstractPlainSocketImpl.java:206)
> at 
> java.net.AbstractPlainSocketImpl.connect(AbstractPlainSocketImpl.java:188)
> at java.net.SocksSocketImpl.connect(SocksSocketImpl.java:392)
> at java.net.Socket.connect(Socket.java:589)
> at java.net.Socket.connect(Socket.java:538)
> at java.net.Socket.(Socket.java:434)
> at java.net.Socket.(Socket.java:211)
> at com.jcraft.jsch.Util.createSocket(Util.java:343)
> ... 17 common frames omitted
> ?NWChem2_a38ac303-666f-4dea-9b4c-7bffe0f97dd7



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[jira] [Commented] (AIRAVATA-2621) SSH port provided in compute resource registration is not considered for cluster SSH communication

2018-01-18 Thread ASF GitHub Bot (JIRA)


[ 
https://issues.apache.org/jira/browse/AIRAVATA-2621?page=com.atlassian.jira.plugin.system.issuetabpanels:comment-tabpanel=16331047#comment-16331047
 ] 

ASF GitHub Bot commented on AIRAVATA-2621:
--

machristie closed pull request #160: Fixing AIRAVATA-2621
URL: https://github.com/apache/airavata/pull/160
 
 
   

This is a PR merged from a forked repository.
As GitHub hides the original diff on merge, it is displayed below for
the sake of provenance:

As this is a foreign pull request (from a fork), the diff is supplied
below (as it won't show otherwise due to GitHub magic):

diff --git 
a/modules/gfac/gfac-core/src/main/java/org/apache/airavata/gfac/core/context/ProcessContext.java
 
b/modules/gfac/gfac-core/src/main/java/org/apache/airavata/gfac/core/context/ProcessContext.java
index 6ca29e35e7..2dad12bce0 100644
--- 
a/modules/gfac/gfac-core/src/main/java/org/apache/airavata/gfac/core/context/ProcessContext.java
+++ 
b/modules/gfac/gfac-core/src/main/java/org/apache/airavata/gfac/core/context/ProcessContext.java
@@ -43,6 +43,7 @@
 import org.apache.airavata.model.status.ProcessStatus;
 import org.apache.airavata.model.task.TaskModel;
 import org.apache.airavata.registry.cpi.AppCatalog;
+import org.apache.airavata.registry.cpi.AppCatalogException;
 import org.apache.airavata.registry.cpi.ExperimentCatalog;
 import org.apache.curator.framework.CuratorFramework;
 import org.slf4j.Logger;
@@ -620,7 +621,44 @@ private ComputationalResourceSchedulingModel 
getProcessCRSchedule() {
}
}
 
-   public ServerInfo getComputeResourceServerInfo(){
+   public ServerInfo getComputeResourceServerInfo() throws GFacException {
+
+   if (this.jobSubmissionProtocol  == JobSubmissionProtocol.SSH) {
+   Optional 
firstJobSubmissionIface = getComputeResourceDescription()
+   .getJobSubmissionInterfaces().stream()
+   .filter(iface -> 
iface.getJobSubmissionProtocol() == JobSubmissionProtocol.SSH)
+   .findFirst();
+
+   if (firstJobSubmissionIface.isPresent()) {
+
+   try {
+SSHJobSubmission sshJobSubmission = 
appCatalog.getComputeResource()
+
.getSSHJobSubmission(firstJobSubmissionIface.get().getJobSubmissionInterfaceId());
+
+   String alternateHostName = 
sshJobSubmission.getAlternativeSSHHostName();
+   String hostName = !(alternateHostName 
== null || alternateHostName.length() == 0) ? alternateHostName :
+   
getComputeResourceDescription().getHostName();
+
+   if (sshJobSubmission.getSshPort() > 0) {
+return new ServerInfo(
+getComputeResourceLoginUserName(),
+hostName,
+getComputeResourceCredentialToken(),
+sshJobSubmission.getSshPort());
+} else {
+return new ServerInfo(
+getComputeResourceLoginUserName(),
+hostName,
+getComputeResourceCredentialToken());
+}
+
+   } catch (AppCatalogException e) {
+   throw new GFacException("Failed to 
fetch ssh job submission for interface " +
+
firstJobSubmissionIface.get().getJobSubmissionInterfaceId(), e);
+   }
+   }
+   }
+
return new ServerInfo(getComputeResourceLoginUserName(),
getComputeResourceDescription().getHostName(),
getComputeResourceCredentialToken());
diff --git 
a/modules/gfac/gfac-impl/src/main/java/org/apache/airavata/gfac/impl/Factory.java
 
b/modules/gfac/gfac-impl/src/main/java/org/apache/airavata/gfac/impl/Factory.java
index 37848e73ba..5ef22e1a63 100644
--- 
a/modules/gfac/gfac-impl/src/main/java/org/apache/airavata/gfac/impl/Factory.java
+++ 
b/modules/gfac/gfac-impl/src/main/java/org/apache/airavata/gfac/impl/Factory.java
@@ -22,12 +22,7 @@
 import com.google.common.cache.Cache;
 import com.google.common.cache.CacheBuilder;
 import com.google.common.cache.RemovalListener;
-import com.jcraft.jsch.Channel;
-import com.jcraft.jsch.ChannelExec;
-import com.jcraft.jsch.JSch;
-import com.jcraft.jsch.JSchException;
-import com.jcraft.jsch.Session;
-import com.jcraft.jsch.UserInfo;
+import com.jcraft.jsch.*;
 import org.apache.airavata.common.exception.AiravataException;
 import org.apache.airavata.common.exception.ApplicationSettingsException;
 import

[jira] [Commented] (AIRAVATA-2621) SSH port provided in compute resource registration is not considered for cluster SSH communication

2018-01-18 Thread ASF GitHub Bot (JIRA)


[ 
https://issues.apache.org/jira/browse/AIRAVATA-2621?page=com.atlassian.jira.plugin.system.issuetabpanels:comment-tabpanel=16331046#comment-16331046
 ] 

ASF GitHub Bot commented on AIRAVATA-2621:
--

machristie commented on issue #160: Fixing AIRAVATA-2621
URL: https://github.com/apache/airavata/pull/160#issuecomment-358756007
 
 
   I merged this manually.


This is an automated message from the Apache Git Service.
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For queries about this service, please contact Infrastructure at:
us...@infra.apache.org


> SSH port provided in compute resource registration is not considered for 
> cluster SSH communication
> --
>
> Key: AIRAVATA-2621
> URL: https://issues.apache.org/jira/browse/AIRAVATA-2621
> Project: Airavata
>  Issue Type: Bug
>  Components: GFac
>Affects Versions: 0.18
> Environment: https://hpcgateway.gsu.edu/
> https://scigap.org/
>Reporter: Eroma
>Assignee: Dimuthu Upeksha
>Priority: Major
> Fix For: 0.18
>
>
> 1. Added a specific port for job submissions (15022)
> 2. But when submitting jobs, for environment creation, the gfac is using the 
> default 22 port, not the specified one in scigap.org for hpclogin.gsu.edu.
> 3. log messages in airavata log
> 2017-12-19 11:13:18,996 [pool-7-thread-2] INFO  
> o.a.airavata.gfac.impl.Factory 
> process_id=PROCESS_3b471b3b-5b4e-4b6d-a66e-554652a390d2, 
> token_id=35da840b-63d5-4cbf-b9ce-3005cd94d961, 
> experiment_id=NWChem2_a38ac303-666f-4dea-9b4c-7bffe0f97dd7, 
> gateway_id=georgiastate - Initialize a new SSH session for 
> :airavata_hpclogin.gsu.edu_22_35da840b-63d5-4cbf-b9ce-3005cd94d961
> 2017-12-19 11:15:26,272 [pool-7-thread-2] ERROR o.a.a.gfac.core.GFacException 
> process_id=PROCESS_3b471b3b-5b4e-4b6d-a66e-554652a390d2, 
> token_id=35da840b-63d5-4cbf-b9ce-3005cd94d961, 
> experiment_id=NWChem2_a38ac303-666f-4dea-9b4c-7bffe0f97dd7, 
> gateway_id=georgiastate - JSch initialization error
> com.jcraft.jsch.JSchException: java.net.ConnectException: Connection timed 
> out (Connection timed out)
> at com.jcraft.jsch.Util.createSocket(Util.java:349)
> at com.jcraft.jsch.Session.connect(Session.java:215)
> at com.jcraft.jsch.Session.connect(Session.java:183)
> at 
> org.apache.airavata.gfac.impl.Factory.getSSHSession(Factory.java:542)
> at 
> org.apache.airavata.gfac.impl.HPCRemoteCluster.getSshSession(HPCRemoteCluster.java:138)
> at 
> org.apache.airavata.gfac.impl.HPCRemoteCluster.getSession(HPCRemoteCluster.java:315)
> at 
> org.apache.airavata.gfac.impl.HPCRemoteCluster.makeDirectory(HPCRemoteCluster.java:242)
> at 
> org.apache.airavata.gfac.impl.task.EnvironmentSetupTask.execute(EnvironmentSetupTask.java:51)
> at 
> org.apache.airavata.gfac.impl.GFacEngineImpl.executeTask(GFacEngineImpl.java:814)
> at 
> org.apache.airavata.gfac.impl.GFacEngineImpl.configureWorkspace(GFacEngineImpl.java:553)
> at 
> org.apache.airavata.gfac.impl.GFacEngineImpl.executeTaskListFrom(GFacEngineImpl.java:324)
> at 
> org.apache.airavata.gfac.impl.GFacEngineImpl.executeProcess(GFacEngineImpl.java:286)
> at 
> org.apache.airavata.gfac.impl.GFacWorker.executeProcess(GFacWorker.java:227)
> at org.apache.airavata.gfac.impl.GFacWorker.run(GFacWorker.java:86)
> at 
> org.apache.airavata.common.logging.MDCUtil.lambda$wrapWithMDC$0(MDCUtil.java:40)
> at 
> java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142)
> at 
> java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617)
> at java.lang.Thread.run(Thread.java:748)
> Caused by: java.net.ConnectException: Connection timed out (Connection timed 
> out)
> at java.net.PlainSocketImpl.socketConnect(Native Method)
> at 
> java.net.AbstractPlainSocketImpl.doConnect(AbstractPlainSocketImpl.java:350)
> at 
> java.net.AbstractPlainSocketImpl.connectToAddress(AbstractPlainSocketImpl.java:206)
> at 
> java.net.AbstractPlainSocketImpl.connect(AbstractPlainSocketImpl.java:188)
> at java.net.SocksSocketImpl.connect(SocksSocketImpl.java:392)
> at java.net.Socket.connect(Socket.java:589)
> at java.net.Socket.connect(Socket.java:538)
> at java.net.Socket.(Socket.java:434)
> at java.net.Socket.(Socket.java:211)
> at com.jcraft.jsch.Util.createSocket(Util.java:343)
> ... 17 common frames omitted
> ?NWChem2_a38ac303-666f-4dea-9b4c-7bffe0f97dd7



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[jira] [Commented] (AIRAVATA-2621) SSH port provided in compute resource registration is not considered for cluster SSH communication

2018-01-18 Thread ASF subversion and git services (JIRA)


[ 
https://issues.apache.org/jira/browse/AIRAVATA-2621?page=com.atlassian.jira.plugin.system.issuetabpanels:comment-tabpanel=16331030#comment-16331030
 ] 

ASF subversion and git services commented on AIRAVATA-2621:
---

Commit f13c17fe41bfdd1a4c8e35a88ab16f534190b523 in airavata's branch 
refs/heads/master from dimuthu.upeks...@gmail.com
[ https://gitbox.apache.org/repos/asf?p=airavata.git;h=f13c17f ]

Fixing AIRAVATA-2621


> SSH port provided in compute resource registration is not considered for 
> cluster SSH communication
> --
>
> Key: AIRAVATA-2621
> URL: https://issues.apache.org/jira/browse/AIRAVATA-2621
> Project: Airavata
>  Issue Type: Bug
>  Components: GFac
>Affects Versions: 0.18
> Environment: https://hpcgateway.gsu.edu/
> https://scigap.org/
>Reporter: Eroma
>Assignee: Dimuthu Upeksha
>Priority: Major
> Fix For: 0.18
>
>
> 1. Added a specific port for job submissions (15022)
> 2. But when submitting jobs, for environment creation, the gfac is using the 
> default 22 port, not the specified one in scigap.org for hpclogin.gsu.edu.
> 3. log messages in airavata log
> 2017-12-19 11:13:18,996 [pool-7-thread-2] INFO  
> o.a.airavata.gfac.impl.Factory 
> process_id=PROCESS_3b471b3b-5b4e-4b6d-a66e-554652a390d2, 
> token_id=35da840b-63d5-4cbf-b9ce-3005cd94d961, 
> experiment_id=NWChem2_a38ac303-666f-4dea-9b4c-7bffe0f97dd7, 
> gateway_id=georgiastate - Initialize a new SSH session for 
> :airavata_hpclogin.gsu.edu_22_35da840b-63d5-4cbf-b9ce-3005cd94d961
> 2017-12-19 11:15:26,272 [pool-7-thread-2] ERROR o.a.a.gfac.core.GFacException 
> process_id=PROCESS_3b471b3b-5b4e-4b6d-a66e-554652a390d2, 
> token_id=35da840b-63d5-4cbf-b9ce-3005cd94d961, 
> experiment_id=NWChem2_a38ac303-666f-4dea-9b4c-7bffe0f97dd7, 
> gateway_id=georgiastate - JSch initialization error
> com.jcraft.jsch.JSchException: java.net.ConnectException: Connection timed 
> out (Connection timed out)
> at com.jcraft.jsch.Util.createSocket(Util.java:349)
> at com.jcraft.jsch.Session.connect(Session.java:215)
> at com.jcraft.jsch.Session.connect(Session.java:183)
> at 
> org.apache.airavata.gfac.impl.Factory.getSSHSession(Factory.java:542)
> at 
> org.apache.airavata.gfac.impl.HPCRemoteCluster.getSshSession(HPCRemoteCluster.java:138)
> at 
> org.apache.airavata.gfac.impl.HPCRemoteCluster.getSession(HPCRemoteCluster.java:315)
> at 
> org.apache.airavata.gfac.impl.HPCRemoteCluster.makeDirectory(HPCRemoteCluster.java:242)
> at 
> org.apache.airavata.gfac.impl.task.EnvironmentSetupTask.execute(EnvironmentSetupTask.java:51)
> at 
> org.apache.airavata.gfac.impl.GFacEngineImpl.executeTask(GFacEngineImpl.java:814)
> at 
> org.apache.airavata.gfac.impl.GFacEngineImpl.configureWorkspace(GFacEngineImpl.java:553)
> at 
> org.apache.airavata.gfac.impl.GFacEngineImpl.executeTaskListFrom(GFacEngineImpl.java:324)
> at 
> org.apache.airavata.gfac.impl.GFacEngineImpl.executeProcess(GFacEngineImpl.java:286)
> at 
> org.apache.airavata.gfac.impl.GFacWorker.executeProcess(GFacWorker.java:227)
> at org.apache.airavata.gfac.impl.GFacWorker.run(GFacWorker.java:86)
> at 
> org.apache.airavata.common.logging.MDCUtil.lambda$wrapWithMDC$0(MDCUtil.java:40)
> at 
> java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142)
> at 
> java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617)
> at java.lang.Thread.run(Thread.java:748)
> Caused by: java.net.ConnectException: Connection timed out (Connection timed 
> out)
> at java.net.PlainSocketImpl.socketConnect(Native Method)
> at 
> java.net.AbstractPlainSocketImpl.doConnect(AbstractPlainSocketImpl.java:350)
> at 
> java.net.AbstractPlainSocketImpl.connectToAddress(AbstractPlainSocketImpl.java:206)
> at 
> java.net.AbstractPlainSocketImpl.connect(AbstractPlainSocketImpl.java:188)
> at java.net.SocksSocketImpl.connect(SocksSocketImpl.java:392)
> at java.net.Socket.connect(Socket.java:589)
> at java.net.Socket.connect(Socket.java:538)
> at java.net.Socket.(Socket.java:434)
> at java.net.Socket.(Socket.java:211)
> at com.jcraft.jsch.Util.createSocket(Util.java:343)
> ... 17 common frames omitted
> ?NWChem2_a38ac303-666f-4dea-9b4c-7bffe0f97dd7



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[jira] [Commented] (AIRAVATA-2621) SSH port provided in compute resource registration is not considered for cluster SSH communication

2018-01-18 Thread ASF subversion and git services (JIRA)


[ 
https://issues.apache.org/jira/browse/AIRAVATA-2621?page=com.atlassian.jira.plugin.system.issuetabpanels:comment-tabpanel=16331021#comment-16331021
 ] 

ASF subversion and git services commented on AIRAVATA-2621:
---

Commit f13c17fe41bfdd1a4c8e35a88ab16f534190b523 in airavata's branch 
refs/heads/develop from dimuthu.upeks...@gmail.com
[ https://gitbox.apache.org/repos/asf?p=airavata.git;h=f13c17f ]

Fixing AIRAVATA-2621


> SSH port provided in compute resource registration is not considered for 
> cluster SSH communication
> --
>
> Key: AIRAVATA-2621
> URL: https://issues.apache.org/jira/browse/AIRAVATA-2621
> Project: Airavata
>  Issue Type: Bug
>  Components: GFac
>Affects Versions: 0.18
> Environment: https://hpcgateway.gsu.edu/
> https://scigap.org/
>Reporter: Eroma
>Assignee: Dimuthu Upeksha
>Priority: Major
> Fix For: 0.18
>
>
> 1. Added a specific port for job submissions (15022)
> 2. But when submitting jobs, for environment creation, the gfac is using the 
> default 22 port, not the specified one in scigap.org for hpclogin.gsu.edu.
> 3. log messages in airavata log
> 2017-12-19 11:13:18,996 [pool-7-thread-2] INFO  
> o.a.airavata.gfac.impl.Factory 
> process_id=PROCESS_3b471b3b-5b4e-4b6d-a66e-554652a390d2, 
> token_id=35da840b-63d5-4cbf-b9ce-3005cd94d961, 
> experiment_id=NWChem2_a38ac303-666f-4dea-9b4c-7bffe0f97dd7, 
> gateway_id=georgiastate - Initialize a new SSH session for 
> :airavata_hpclogin.gsu.edu_22_35da840b-63d5-4cbf-b9ce-3005cd94d961
> 2017-12-19 11:15:26,272 [pool-7-thread-2] ERROR o.a.a.gfac.core.GFacException 
> process_id=PROCESS_3b471b3b-5b4e-4b6d-a66e-554652a390d2, 
> token_id=35da840b-63d5-4cbf-b9ce-3005cd94d961, 
> experiment_id=NWChem2_a38ac303-666f-4dea-9b4c-7bffe0f97dd7, 
> gateway_id=georgiastate - JSch initialization error
> com.jcraft.jsch.JSchException: java.net.ConnectException: Connection timed 
> out (Connection timed out)
> at com.jcraft.jsch.Util.createSocket(Util.java:349)
> at com.jcraft.jsch.Session.connect(Session.java:215)
> at com.jcraft.jsch.Session.connect(Session.java:183)
> at 
> org.apache.airavata.gfac.impl.Factory.getSSHSession(Factory.java:542)
> at 
> org.apache.airavata.gfac.impl.HPCRemoteCluster.getSshSession(HPCRemoteCluster.java:138)
> at 
> org.apache.airavata.gfac.impl.HPCRemoteCluster.getSession(HPCRemoteCluster.java:315)
> at 
> org.apache.airavata.gfac.impl.HPCRemoteCluster.makeDirectory(HPCRemoteCluster.java:242)
> at 
> org.apache.airavata.gfac.impl.task.EnvironmentSetupTask.execute(EnvironmentSetupTask.java:51)
> at 
> org.apache.airavata.gfac.impl.GFacEngineImpl.executeTask(GFacEngineImpl.java:814)
> at 
> org.apache.airavata.gfac.impl.GFacEngineImpl.configureWorkspace(GFacEngineImpl.java:553)
> at 
> org.apache.airavata.gfac.impl.GFacEngineImpl.executeTaskListFrom(GFacEngineImpl.java:324)
> at 
> org.apache.airavata.gfac.impl.GFacEngineImpl.executeProcess(GFacEngineImpl.java:286)
> at 
> org.apache.airavata.gfac.impl.GFacWorker.executeProcess(GFacWorker.java:227)
> at org.apache.airavata.gfac.impl.GFacWorker.run(GFacWorker.java:86)
> at 
> org.apache.airavata.common.logging.MDCUtil.lambda$wrapWithMDC$0(MDCUtil.java:40)
> at 
> java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142)
> at 
> java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617)
> at java.lang.Thread.run(Thread.java:748)
> Caused by: java.net.ConnectException: Connection timed out (Connection timed 
> out)
> at java.net.PlainSocketImpl.socketConnect(Native Method)
> at 
> java.net.AbstractPlainSocketImpl.doConnect(AbstractPlainSocketImpl.java:350)
> at 
> java.net.AbstractPlainSocketImpl.connectToAddress(AbstractPlainSocketImpl.java:206)
> at 
> java.net.AbstractPlainSocketImpl.connect(AbstractPlainSocketImpl.java:188)
> at java.net.SocksSocketImpl.connect(SocksSocketImpl.java:392)
> at java.net.Socket.connect(Socket.java:589)
> at java.net.Socket.connect(Socket.java:538)
> at java.net.Socket.(Socket.java:434)
> at java.net.Socket.(Socket.java:211)
> at com.jcraft.jsch.Util.createSocket(Util.java:343)
> ... 17 common frames omitted
> ?NWChem2_a38ac303-666f-4dea-9b4c-7bffe0f97dd7



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[jira] [Commented] (AIRAVATA-2621) SSH port provided in compute resource registration is not considered for cluster SSH communication

2018-01-18 Thread ASF subversion and git services (JIRA)


[ 
https://issues.apache.org/jira/browse/AIRAVATA-2621?page=com.atlassian.jira.plugin.system.issuetabpanels:comment-tabpanel=16331023#comment-16331023
 ] 

ASF subversion and git services commented on AIRAVATA-2621:
---

Commit 0f25c2f1dcb3f58a31cfad631d19bfbef714a349 in airavata's branch 
refs/heads/develop from [~marcuschristie]
[ https://gitbox.apache.org/repos/asf?p=airavata.git;h=0f25c2f ]

Merge branch 'AIRAVATA-2621-bugfix' into develop

Fixes AIRAVATA-2621 and AIRAVATA-2624


> SSH port provided in compute resource registration is not considered for 
> cluster SSH communication
> --
>
> Key: AIRAVATA-2621
> URL: https://issues.apache.org/jira/browse/AIRAVATA-2621
> Project: Airavata
>  Issue Type: Bug
>  Components: GFac
>Affects Versions: 0.18
> Environment: https://hpcgateway.gsu.edu/
> https://scigap.org/
>Reporter: Eroma
>Assignee: Dimuthu Upeksha
>Priority: Major
> Fix For: 0.18
>
>
> 1. Added a specific port for job submissions (15022)
> 2. But when submitting jobs, for environment creation, the gfac is using the 
> default 22 port, not the specified one in scigap.org for hpclogin.gsu.edu.
> 3. log messages in airavata log
> 2017-12-19 11:13:18,996 [pool-7-thread-2] INFO  
> o.a.airavata.gfac.impl.Factory 
> process_id=PROCESS_3b471b3b-5b4e-4b6d-a66e-554652a390d2, 
> token_id=35da840b-63d5-4cbf-b9ce-3005cd94d961, 
> experiment_id=NWChem2_a38ac303-666f-4dea-9b4c-7bffe0f97dd7, 
> gateway_id=georgiastate - Initialize a new SSH session for 
> :airavata_hpclogin.gsu.edu_22_35da840b-63d5-4cbf-b9ce-3005cd94d961
> 2017-12-19 11:15:26,272 [pool-7-thread-2] ERROR o.a.a.gfac.core.GFacException 
> process_id=PROCESS_3b471b3b-5b4e-4b6d-a66e-554652a390d2, 
> token_id=35da840b-63d5-4cbf-b9ce-3005cd94d961, 
> experiment_id=NWChem2_a38ac303-666f-4dea-9b4c-7bffe0f97dd7, 
> gateway_id=georgiastate - JSch initialization error
> com.jcraft.jsch.JSchException: java.net.ConnectException: Connection timed 
> out (Connection timed out)
> at com.jcraft.jsch.Util.createSocket(Util.java:349)
> at com.jcraft.jsch.Session.connect(Session.java:215)
> at com.jcraft.jsch.Session.connect(Session.java:183)
> at 
> org.apache.airavata.gfac.impl.Factory.getSSHSession(Factory.java:542)
> at 
> org.apache.airavata.gfac.impl.HPCRemoteCluster.getSshSession(HPCRemoteCluster.java:138)
> at 
> org.apache.airavata.gfac.impl.HPCRemoteCluster.getSession(HPCRemoteCluster.java:315)
> at 
> org.apache.airavata.gfac.impl.HPCRemoteCluster.makeDirectory(HPCRemoteCluster.java:242)
> at 
> org.apache.airavata.gfac.impl.task.EnvironmentSetupTask.execute(EnvironmentSetupTask.java:51)
> at 
> org.apache.airavata.gfac.impl.GFacEngineImpl.executeTask(GFacEngineImpl.java:814)
> at 
> org.apache.airavata.gfac.impl.GFacEngineImpl.configureWorkspace(GFacEngineImpl.java:553)
> at 
> org.apache.airavata.gfac.impl.GFacEngineImpl.executeTaskListFrom(GFacEngineImpl.java:324)
> at 
> org.apache.airavata.gfac.impl.GFacEngineImpl.executeProcess(GFacEngineImpl.java:286)
> at 
> org.apache.airavata.gfac.impl.GFacWorker.executeProcess(GFacWorker.java:227)
> at org.apache.airavata.gfac.impl.GFacWorker.run(GFacWorker.java:86)
> at 
> org.apache.airavata.common.logging.MDCUtil.lambda$wrapWithMDC$0(MDCUtil.java:40)
> at 
> java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142)
> at 
> java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617)
> at java.lang.Thread.run(Thread.java:748)
> Caused by: java.net.ConnectException: Connection timed out (Connection timed 
> out)
> at java.net.PlainSocketImpl.socketConnect(Native Method)
> at 
> java.net.AbstractPlainSocketImpl.doConnect(AbstractPlainSocketImpl.java:350)
> at 
> java.net.AbstractPlainSocketImpl.connectToAddress(AbstractPlainSocketImpl.java:206)
> at 
> java.net.AbstractPlainSocketImpl.connect(AbstractPlainSocketImpl.java:188)
> at java.net.SocksSocketImpl.connect(SocksSocketImpl.java:392)
> at java.net.Socket.connect(Socket.java:589)
> at java.net.Socket.connect(Socket.java:538)
> at java.net.Socket.(Socket.java:434)
> at java.net.Socket.(Socket.java:211)
> at com.jcraft.jsch.Util.createSocket(Util.java:343)
> ... 17 common frames omitted
> ?NWChem2_a38ac303-666f-4dea-9b4c-7bffe0f97dd7



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[jira] [Commented] (AIRAVATA-2621) SSH port provided in compute resource registration is not considered for cluster SSH communication

2018-01-18 Thread ASF subversion and git services (JIRA)


[ 
https://issues.apache.org/jira/browse/AIRAVATA-2621?page=com.atlassian.jira.plugin.system.issuetabpanels:comment-tabpanel=16331024#comment-16331024
 ] 

ASF subversion and git services commented on AIRAVATA-2621:
---

Commit 0f25c2f1dcb3f58a31cfad631d19bfbef714a349 in airavata's branch 
refs/heads/develop from [~marcuschristie]
[ https://gitbox.apache.org/repos/asf?p=airavata.git;h=0f25c2f ]

Merge branch 'AIRAVATA-2621-bugfix' into develop

Fixes AIRAVATA-2621 and AIRAVATA-2624


> SSH port provided in compute resource registration is not considered for 
> cluster SSH communication
> --
>
> Key: AIRAVATA-2621
> URL: https://issues.apache.org/jira/browse/AIRAVATA-2621
> Project: Airavata
>  Issue Type: Bug
>  Components: GFac
>Affects Versions: 0.18
> Environment: https://hpcgateway.gsu.edu/
> https://scigap.org/
>Reporter: Eroma
>Assignee: Dimuthu Upeksha
>Priority: Major
> Fix For: 0.18
>
>
> 1. Added a specific port for job submissions (15022)
> 2. But when submitting jobs, for environment creation, the gfac is using the 
> default 22 port, not the specified one in scigap.org for hpclogin.gsu.edu.
> 3. log messages in airavata log
> 2017-12-19 11:13:18,996 [pool-7-thread-2] INFO  
> o.a.airavata.gfac.impl.Factory 
> process_id=PROCESS_3b471b3b-5b4e-4b6d-a66e-554652a390d2, 
> token_id=35da840b-63d5-4cbf-b9ce-3005cd94d961, 
> experiment_id=NWChem2_a38ac303-666f-4dea-9b4c-7bffe0f97dd7, 
> gateway_id=georgiastate - Initialize a new SSH session for 
> :airavata_hpclogin.gsu.edu_22_35da840b-63d5-4cbf-b9ce-3005cd94d961
> 2017-12-19 11:15:26,272 [pool-7-thread-2] ERROR o.a.a.gfac.core.GFacException 
> process_id=PROCESS_3b471b3b-5b4e-4b6d-a66e-554652a390d2, 
> token_id=35da840b-63d5-4cbf-b9ce-3005cd94d961, 
> experiment_id=NWChem2_a38ac303-666f-4dea-9b4c-7bffe0f97dd7, 
> gateway_id=georgiastate - JSch initialization error
> com.jcraft.jsch.JSchException: java.net.ConnectException: Connection timed 
> out (Connection timed out)
> at com.jcraft.jsch.Util.createSocket(Util.java:349)
> at com.jcraft.jsch.Session.connect(Session.java:215)
> at com.jcraft.jsch.Session.connect(Session.java:183)
> at 
> org.apache.airavata.gfac.impl.Factory.getSSHSession(Factory.java:542)
> at 
> org.apache.airavata.gfac.impl.HPCRemoteCluster.getSshSession(HPCRemoteCluster.java:138)
> at 
> org.apache.airavata.gfac.impl.HPCRemoteCluster.getSession(HPCRemoteCluster.java:315)
> at 
> org.apache.airavata.gfac.impl.HPCRemoteCluster.makeDirectory(HPCRemoteCluster.java:242)
> at 
> org.apache.airavata.gfac.impl.task.EnvironmentSetupTask.execute(EnvironmentSetupTask.java:51)
> at 
> org.apache.airavata.gfac.impl.GFacEngineImpl.executeTask(GFacEngineImpl.java:814)
> at 
> org.apache.airavata.gfac.impl.GFacEngineImpl.configureWorkspace(GFacEngineImpl.java:553)
> at 
> org.apache.airavata.gfac.impl.GFacEngineImpl.executeTaskListFrom(GFacEngineImpl.java:324)
> at 
> org.apache.airavata.gfac.impl.GFacEngineImpl.executeProcess(GFacEngineImpl.java:286)
> at 
> org.apache.airavata.gfac.impl.GFacWorker.executeProcess(GFacWorker.java:227)
> at org.apache.airavata.gfac.impl.GFacWorker.run(GFacWorker.java:86)
> at 
> org.apache.airavata.common.logging.MDCUtil.lambda$wrapWithMDC$0(MDCUtil.java:40)
> at 
> java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142)
> at 
> java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617)
> at java.lang.Thread.run(Thread.java:748)
> Caused by: java.net.ConnectException: Connection timed out (Connection timed 
> out)
> at java.net.PlainSocketImpl.socketConnect(Native Method)
> at 
> java.net.AbstractPlainSocketImpl.doConnect(AbstractPlainSocketImpl.java:350)
> at 
> java.net.AbstractPlainSocketImpl.connectToAddress(AbstractPlainSocketImpl.java:206)
> at 
> java.net.AbstractPlainSocketImpl.connect(AbstractPlainSocketImpl.java:188)
> at java.net.SocksSocketImpl.connect(SocksSocketImpl.java:392)
> at java.net.Socket.connect(Socket.java:589)
> at java.net.Socket.connect(Socket.java:538)
> at java.net.Socket.(Socket.java:434)
> at java.net.Socket.(Socket.java:211)
> at com.jcraft.jsch.Util.createSocket(Util.java:343)
> ... 17 common frames omitted
> ?NWChem2_a38ac303-666f-4dea-9b4c-7bffe0f97dd7



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[jira] [Commented] (AIRAVATA-2621) SSH port provided in compute resource registration is not considered for cluster SSH communication

2018-01-18 Thread ASF GitHub Bot (JIRA)


[ 
https://issues.apache.org/jira/browse/AIRAVATA-2621?page=com.atlassian.jira.plugin.system.issuetabpanels:comment-tabpanel=16331002#comment-16331002
 ] 

ASF GitHub Bot commented on AIRAVATA-2621:
--

machristie commented on issue #160: Fixing AIRAVATA-2621
URL: https://github.com/apache/airavata/pull/160#issuecomment-358750296
 
 
   Looks good, @DImuthuUpe . I'm going to pull these commits into a branch off 
master and merge them into develop and master.


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> SSH port provided in compute resource registration is not considered for 
> cluster SSH communication
> --
>
> Key: AIRAVATA-2621
> URL: https://issues.apache.org/jira/browse/AIRAVATA-2621
> Project: Airavata
>  Issue Type: Bug
>  Components: GFac
>Affects Versions: 0.18
> Environment: https://hpcgateway.gsu.edu/
> https://scigap.org/
>Reporter: Eroma
>Assignee: Dimuthu Upeksha
>Priority: Major
> Fix For: 0.18
>
>
> 1. Added a specific port for job submissions (15022)
> 2. But when submitting jobs, for environment creation, the gfac is using the 
> default 22 port, not the specified one in scigap.org for hpclogin.gsu.edu.
> 3. log messages in airavata log
> 2017-12-19 11:13:18,996 [pool-7-thread-2] INFO  
> o.a.airavata.gfac.impl.Factory 
> process_id=PROCESS_3b471b3b-5b4e-4b6d-a66e-554652a390d2, 
> token_id=35da840b-63d5-4cbf-b9ce-3005cd94d961, 
> experiment_id=NWChem2_a38ac303-666f-4dea-9b4c-7bffe0f97dd7, 
> gateway_id=georgiastate - Initialize a new SSH session for 
> :airavata_hpclogin.gsu.edu_22_35da840b-63d5-4cbf-b9ce-3005cd94d961
> 2017-12-19 11:15:26,272 [pool-7-thread-2] ERROR o.a.a.gfac.core.GFacException 
> process_id=PROCESS_3b471b3b-5b4e-4b6d-a66e-554652a390d2, 
> token_id=35da840b-63d5-4cbf-b9ce-3005cd94d961, 
> experiment_id=NWChem2_a38ac303-666f-4dea-9b4c-7bffe0f97dd7, 
> gateway_id=georgiastate - JSch initialization error
> com.jcraft.jsch.JSchException: java.net.ConnectException: Connection timed 
> out (Connection timed out)
> at com.jcraft.jsch.Util.createSocket(Util.java:349)
> at com.jcraft.jsch.Session.connect(Session.java:215)
> at com.jcraft.jsch.Session.connect(Session.java:183)
> at 
> org.apache.airavata.gfac.impl.Factory.getSSHSession(Factory.java:542)
> at 
> org.apache.airavata.gfac.impl.HPCRemoteCluster.getSshSession(HPCRemoteCluster.java:138)
> at 
> org.apache.airavata.gfac.impl.HPCRemoteCluster.getSession(HPCRemoteCluster.java:315)
> at 
> org.apache.airavata.gfac.impl.HPCRemoteCluster.makeDirectory(HPCRemoteCluster.java:242)
> at 
> org.apache.airavata.gfac.impl.task.EnvironmentSetupTask.execute(EnvironmentSetupTask.java:51)
> at 
> org.apache.airavata.gfac.impl.GFacEngineImpl.executeTask(GFacEngineImpl.java:814)
> at 
> org.apache.airavata.gfac.impl.GFacEngineImpl.configureWorkspace(GFacEngineImpl.java:553)
> at 
> org.apache.airavata.gfac.impl.GFacEngineImpl.executeTaskListFrom(GFacEngineImpl.java:324)
> at 
> org.apache.airavata.gfac.impl.GFacEngineImpl.executeProcess(GFacEngineImpl.java:286)
> at 
> org.apache.airavata.gfac.impl.GFacWorker.executeProcess(GFacWorker.java:227)
> at org.apache.airavata.gfac.impl.GFacWorker.run(GFacWorker.java:86)
> at 
> org.apache.airavata.common.logging.MDCUtil.lambda$wrapWithMDC$0(MDCUtil.java:40)
> at 
> java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142)
> at 
> java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617)
> at java.lang.Thread.run(Thread.java:748)
> Caused by: java.net.ConnectException: Connection timed out (Connection timed 
> out)
> at java.net.PlainSocketImpl.socketConnect(Native Method)
> at 
> java.net.AbstractPlainSocketImpl.doConnect(AbstractPlainSocketImpl.java:350)
> at 
> java.net.AbstractPlainSocketImpl.connectToAddress(AbstractPlainSocketImpl.java:206)
> at 
> java.net.AbstractPlainSocketImpl.connect(AbstractPlainSocketImpl.java:188)
> at java.net.SocksSocketImpl.connect(SocksSocketImpl.java:392)
> at java.net.Socket.connect(Socket.java:589)
> at java.net.Socket.connect(Socket.java:538)
> at java.net.Socket.(Socket.java:434)
> at java.net.Socket.(Socket.java:211)
> at com.jcraft.jsch.Util.createSocket(Util.java:343)
> ... 17 common frames omitted
> ?NWChem2_a38ac303-666f-4dea-9b4c-7bffe0f97dd7



--
This

[jira] [Commented] (AIRAVATA-2621) SSH port provided in compute resource registration is not considered for cluster SSH communication

2018-01-17 Thread Eroma (JIRA)


[ 
https://issues.apache.org/jira/browse/AIRAVATA-2621?page=com.atlassian.jira.plugin.system.issuetabpanels:comment-tabpanel=16329210#comment-16329210
 ] 

Eroma commented on AIRAVATA-2621:
-

Changing status of the Jira to RESOLVED on behalf of [~dimuthuupe]

> SSH port provided in compute resource registration is not considered for 
> cluster SSH communication
> --
>
> Key: AIRAVATA-2621
> URL: https://issues.apache.org/jira/browse/AIRAVATA-2621
> Project: Airavata
>  Issue Type: Bug
>  Components: GFac
>Affects Versions: 0.18
> Environment: https://hpcgateway.gsu.edu/
> https://scigap.org/
>Reporter: Eroma
>Assignee: Dimuthu Upeksha
>Priority: Major
> Fix For: 0.18
>
>
> 1. Added a specific port for job submissions (15022)
> 2. But when submitting jobs, for environment creation, the gfac is using the 
> default 22 port, not the specified one in scigap.org for hpclogin.gsu.edu.
> 3. log messages in airavata log
> 2017-12-19 11:13:18,996 [pool-7-thread-2] INFO  
> o.a.airavata.gfac.impl.Factory 
> process_id=PROCESS_3b471b3b-5b4e-4b6d-a66e-554652a390d2, 
> token_id=35da840b-63d5-4cbf-b9ce-3005cd94d961, 
> experiment_id=NWChem2_a38ac303-666f-4dea-9b4c-7bffe0f97dd7, 
> gateway_id=georgiastate - Initialize a new SSH session for 
> :airavata_hpclogin.gsu.edu_22_35da840b-63d5-4cbf-b9ce-3005cd94d961
> 2017-12-19 11:15:26,272 [pool-7-thread-2] ERROR o.a.a.gfac.core.GFacException 
> process_id=PROCESS_3b471b3b-5b4e-4b6d-a66e-554652a390d2, 
> token_id=35da840b-63d5-4cbf-b9ce-3005cd94d961, 
> experiment_id=NWChem2_a38ac303-666f-4dea-9b4c-7bffe0f97dd7, 
> gateway_id=georgiastate - JSch initialization error
> com.jcraft.jsch.JSchException: java.net.ConnectException: Connection timed 
> out (Connection timed out)
> at com.jcraft.jsch.Util.createSocket(Util.java:349)
> at com.jcraft.jsch.Session.connect(Session.java:215)
> at com.jcraft.jsch.Session.connect(Session.java:183)
> at 
> org.apache.airavata.gfac.impl.Factory.getSSHSession(Factory.java:542)
> at 
> org.apache.airavata.gfac.impl.HPCRemoteCluster.getSshSession(HPCRemoteCluster.java:138)
> at 
> org.apache.airavata.gfac.impl.HPCRemoteCluster.getSession(HPCRemoteCluster.java:315)
> at 
> org.apache.airavata.gfac.impl.HPCRemoteCluster.makeDirectory(HPCRemoteCluster.java:242)
> at 
> org.apache.airavata.gfac.impl.task.EnvironmentSetupTask.execute(EnvironmentSetupTask.java:51)
> at 
> org.apache.airavata.gfac.impl.GFacEngineImpl.executeTask(GFacEngineImpl.java:814)
> at 
> org.apache.airavata.gfac.impl.GFacEngineImpl.configureWorkspace(GFacEngineImpl.java:553)
> at 
> org.apache.airavata.gfac.impl.GFacEngineImpl.executeTaskListFrom(GFacEngineImpl.java:324)
> at 
> org.apache.airavata.gfac.impl.GFacEngineImpl.executeProcess(GFacEngineImpl.java:286)
> at 
> org.apache.airavata.gfac.impl.GFacWorker.executeProcess(GFacWorker.java:227)
> at org.apache.airavata.gfac.impl.GFacWorker.run(GFacWorker.java:86)
> at 
> org.apache.airavata.common.logging.MDCUtil.lambda$wrapWithMDC$0(MDCUtil.java:40)
> at 
> java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142)
> at 
> java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617)
> at java.lang.Thread.run(Thread.java:748)
> Caused by: java.net.ConnectException: Connection timed out (Connection timed 
> out)
> at java.net.PlainSocketImpl.socketConnect(Native Method)
> at 
> java.net.AbstractPlainSocketImpl.doConnect(AbstractPlainSocketImpl.java:350)
> at 
> java.net.AbstractPlainSocketImpl.connectToAddress(AbstractPlainSocketImpl.java:206)
> at 
> java.net.AbstractPlainSocketImpl.connect(AbstractPlainSocketImpl.java:188)
> at java.net.SocksSocketImpl.connect(SocksSocketImpl.java:392)
> at java.net.Socket.connect(Socket.java:589)
> at java.net.Socket.connect(Socket.java:538)
> at java.net.Socket.(Socket.java:434)
> at java.net.Socket.(Socket.java:211)
> at com.jcraft.jsch.Util.createSocket(Util.java:343)
> ... 17 common frames omitted
> ?NWChem2_a38ac303-666f-4dea-9b4c-7bffe0f97dd7



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[jira] [Commented] (AIRAVATA-2621) SSH port provided in compute resource registration is not considered for cluster SSH communication

2018-01-17 Thread Dimuthu Upeksha (JIRA)


[ 
https://issues.apache.org/jira/browse/AIRAVATA-2621?page=com.atlassian.jira.plugin.system.issuetabpanels:comment-tabpanel=16329205#comment-16329205
 ] 

Dimuthu Upeksha commented on AIRAVATA-2621:
---

Fix will look for the SSHJobSumission instances for a compute resource if the 
job submission protocol is SSH. If it can find an instance, it will override 
the the host name an port of the ServerInfo bean with the alternateHostName and 
the port of the SSHJobSubmission instance.

> SSH port provided in compute resource registration is not considered for 
> cluster SSH communication
> --
>
> Key: AIRAVATA-2621
> URL: https://issues.apache.org/jira/browse/AIRAVATA-2621
> Project: Airavata
>  Issue Type: Bug
>  Components: GFac
>Affects Versions: 0.18
> Environment: https://hpcgateway.gsu.edu/
> https://scigap.org/
>Reporter: Eroma
>Assignee: Dimuthu Upeksha
>Priority: Major
> Fix For: 0.18
>
>
> 1. Added a specific port for job submissions (15022)
> 2. But when submitting jobs, for environment creation, the gfac is using the 
> default 22 port, not the specified one in scigap.org for hpclogin.gsu.edu.
> 3. log messages in airavata log
> 2017-12-19 11:13:18,996 [pool-7-thread-2] INFO  
> o.a.airavata.gfac.impl.Factory 
> process_id=PROCESS_3b471b3b-5b4e-4b6d-a66e-554652a390d2, 
> token_id=35da840b-63d5-4cbf-b9ce-3005cd94d961, 
> experiment_id=NWChem2_a38ac303-666f-4dea-9b4c-7bffe0f97dd7, 
> gateway_id=georgiastate - Initialize a new SSH session for 
> :airavata_hpclogin.gsu.edu_22_35da840b-63d5-4cbf-b9ce-3005cd94d961
> 2017-12-19 11:15:26,272 [pool-7-thread-2] ERROR o.a.a.gfac.core.GFacException 
> process_id=PROCESS_3b471b3b-5b4e-4b6d-a66e-554652a390d2, 
> token_id=35da840b-63d5-4cbf-b9ce-3005cd94d961, 
> experiment_id=NWChem2_a38ac303-666f-4dea-9b4c-7bffe0f97dd7, 
> gateway_id=georgiastate - JSch initialization error
> com.jcraft.jsch.JSchException: java.net.ConnectException: Connection timed 
> out (Connection timed out)
> at com.jcraft.jsch.Util.createSocket(Util.java:349)
> at com.jcraft.jsch.Session.connect(Session.java:215)
> at com.jcraft.jsch.Session.connect(Session.java:183)
> at 
> org.apache.airavata.gfac.impl.Factory.getSSHSession(Factory.java:542)
> at 
> org.apache.airavata.gfac.impl.HPCRemoteCluster.getSshSession(HPCRemoteCluster.java:138)
> at 
> org.apache.airavata.gfac.impl.HPCRemoteCluster.getSession(HPCRemoteCluster.java:315)
> at 
> org.apache.airavata.gfac.impl.HPCRemoteCluster.makeDirectory(HPCRemoteCluster.java:242)
> at 
> org.apache.airavata.gfac.impl.task.EnvironmentSetupTask.execute(EnvironmentSetupTask.java:51)
> at 
> org.apache.airavata.gfac.impl.GFacEngineImpl.executeTask(GFacEngineImpl.java:814)
> at 
> org.apache.airavata.gfac.impl.GFacEngineImpl.configureWorkspace(GFacEngineImpl.java:553)
> at 
> org.apache.airavata.gfac.impl.GFacEngineImpl.executeTaskListFrom(GFacEngineImpl.java:324)
> at 
> org.apache.airavata.gfac.impl.GFacEngineImpl.executeProcess(GFacEngineImpl.java:286)
> at 
> org.apache.airavata.gfac.impl.GFacWorker.executeProcess(GFacWorker.java:227)
> at org.apache.airavata.gfac.impl.GFacWorker.run(GFacWorker.java:86)
> at 
> org.apache.airavata.common.logging.MDCUtil.lambda$wrapWithMDC$0(MDCUtil.java:40)
> at 
> java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142)
> at 
> java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617)
> at java.lang.Thread.run(Thread.java:748)
> Caused by: java.net.ConnectException: Connection timed out (Connection timed 
> out)
> at java.net.PlainSocketImpl.socketConnect(Native Method)
> at 
> java.net.AbstractPlainSocketImpl.doConnect(AbstractPlainSocketImpl.java:350)
> at 
> java.net.AbstractPlainSocketImpl.connectToAddress(AbstractPlainSocketImpl.java:206)
> at 
> java.net.AbstractPlainSocketImpl.connect(AbstractPlainSocketImpl.java:188)
> at java.net.SocksSocketImpl.connect(SocksSocketImpl.java:392)
> at java.net.Socket.connect(Socket.java:589)
> at java.net.Socket.connect(Socket.java:538)
> at java.net.Socket.(Socket.java:434)
> at java.net.Socket.(Socket.java:211)
> at com.jcraft.jsch.Util.createSocket(Util.java:343)
> ... 17 common frames omitted
> ?NWChem2_a38ac303-666f-4dea-9b4c-7bffe0f97dd7



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[jira] [Commented] (AIRAVATA-2621) SSH port provided in compute resource registration is not considered for cluster SSH communication

2018-01-17 Thread ASF GitHub Bot (JIRA)


[ 
https://issues.apache.org/jira/browse/AIRAVATA-2621?page=com.atlassian.jira.plugin.system.issuetabpanels:comment-tabpanel=16328963#comment-16328963
 ] 

ASF GitHub Bot commented on AIRAVATA-2621:
--

DImuthuUpe opened a new pull request #160: Fixing AIRAVATA-2621
URL: https://github.com/apache/airavata/pull/160
 
 
   


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> SSH port provided in compute resource registration is not considered for 
> cluster SSH communication
> --
>
> Key: AIRAVATA-2621
> URL: https://issues.apache.org/jira/browse/AIRAVATA-2621
> Project: Airavata
>  Issue Type: Bug
>  Components: GFac
>Affects Versions: 0.18
> Environment: https://hpcgateway.gsu.edu/
> https://scigap.org/
>Reporter: Eroma
>Assignee: Suresh Marru
>Priority: Major
> Fix For: 0.18
>
>
> 1. Added a specific port for job submissions (15022)
> 2. But when submitting jobs, for environment creation, the gfac is using the 
> default 22 port, not the specified one in scigap.org for hpclogin.gsu.edu.
> 3. log messages in airavata log
> 2017-12-19 11:13:18,996 [pool-7-thread-2] INFO  
> o.a.airavata.gfac.impl.Factory 
> process_id=PROCESS_3b471b3b-5b4e-4b6d-a66e-554652a390d2, 
> token_id=35da840b-63d5-4cbf-b9ce-3005cd94d961, 
> experiment_id=NWChem2_a38ac303-666f-4dea-9b4c-7bffe0f97dd7, 
> gateway_id=georgiastate - Initialize a new SSH session for 
> :airavata_hpclogin.gsu.edu_22_35da840b-63d5-4cbf-b9ce-3005cd94d961
> 2017-12-19 11:15:26,272 [pool-7-thread-2] ERROR o.a.a.gfac.core.GFacException 
> process_id=PROCESS_3b471b3b-5b4e-4b6d-a66e-554652a390d2, 
> token_id=35da840b-63d5-4cbf-b9ce-3005cd94d961, 
> experiment_id=NWChem2_a38ac303-666f-4dea-9b4c-7bffe0f97dd7, 
> gateway_id=georgiastate - JSch initialization error
> com.jcraft.jsch.JSchException: java.net.ConnectException: Connection timed 
> out (Connection timed out)
> at com.jcraft.jsch.Util.createSocket(Util.java:349)
> at com.jcraft.jsch.Session.connect(Session.java:215)
> at com.jcraft.jsch.Session.connect(Session.java:183)
> at 
> org.apache.airavata.gfac.impl.Factory.getSSHSession(Factory.java:542)
> at 
> org.apache.airavata.gfac.impl.HPCRemoteCluster.getSshSession(HPCRemoteCluster.java:138)
> at 
> org.apache.airavata.gfac.impl.HPCRemoteCluster.getSession(HPCRemoteCluster.java:315)
> at 
> org.apache.airavata.gfac.impl.HPCRemoteCluster.makeDirectory(HPCRemoteCluster.java:242)
> at 
> org.apache.airavata.gfac.impl.task.EnvironmentSetupTask.execute(EnvironmentSetupTask.java:51)
> at 
> org.apache.airavata.gfac.impl.GFacEngineImpl.executeTask(GFacEngineImpl.java:814)
> at 
> org.apache.airavata.gfac.impl.GFacEngineImpl.configureWorkspace(GFacEngineImpl.java:553)
> at 
> org.apache.airavata.gfac.impl.GFacEngineImpl.executeTaskListFrom(GFacEngineImpl.java:324)
> at 
> org.apache.airavata.gfac.impl.GFacEngineImpl.executeProcess(GFacEngineImpl.java:286)
> at 
> org.apache.airavata.gfac.impl.GFacWorker.executeProcess(GFacWorker.java:227)
> at org.apache.airavata.gfac.impl.GFacWorker.run(GFacWorker.java:86)
> at 
> org.apache.airavata.common.logging.MDCUtil.lambda$wrapWithMDC$0(MDCUtil.java:40)
> at 
> java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142)
> at 
> java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617)
> at java.lang.Thread.run(Thread.java:748)
> Caused by: java.net.ConnectException: Connection timed out (Connection timed 
> out)
> at java.net.PlainSocketImpl.socketConnect(Native Method)
> at 
> java.net.AbstractPlainSocketImpl.doConnect(AbstractPlainSocketImpl.java:350)
> at 
> java.net.AbstractPlainSocketImpl.connectToAddress(AbstractPlainSocketImpl.java:206)
> at 
> java.net.AbstractPlainSocketImpl.connect(AbstractPlainSocketImpl.java:188)
> at java.net.SocksSocketImpl.connect(SocksSocketImpl.java:392)
> at java.net.Socket.connect(Socket.java:589)
> at java.net.Socket.connect(Socket.java:538)
> at java.net.Socket.(Socket.java:434)
> at java.net.Socket.(Socket.java:211)
> at com.jcraft.jsch.Util.createSocket(Util.java:343)
> ... 17 common frames omitted
> ?NWChem2_a38ac303-666f-4dea-9b4c-7bffe0f97dd7



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[jira] [Commented] (AIRAVATA-2621) SSH port provided in compute resource registration is not considered for cluster SSH communication

[jira] [Commented] (AIRAVATA-2621) SSH port provided in compute resource registration is not considered for cluster SSH communication

[jira] [Commented] (AIRAVATA-2621) SSH port provided in compute resource registration is not considered for cluster SSH communication

[jira] [Commented] (AIRAVATA-2621) SSH port provided in compute resource registration is not considered for cluster SSH communication

[jira] [Commented] (AIRAVATA-2621) SSH port provided in compute resource registration is not considered for cluster SSH communication

[jira] [Commented] (AIRAVATA-2621) SSH port provided in compute resource registration is not considered for cluster SSH communication

[jira] [Commented] (AIRAVATA-2621) SSH port provided in compute resource registration is not considered for cluster SSH communication

[jira] [Commented] (AIRAVATA-2621) SSH port provided in compute resource registration is not considered for cluster SSH communication

[jira] [Commented] (AIRAVATA-2621) SSH port provided in compute resource registration is not considered for cluster SSH communication

[jira] [Commented] (AIRAVATA-2621) SSH port provided in compute resource registration is not considered for cluster SSH communication

[jira] [Commented] (AIRAVATA-2621) SSH port provided in compute resource registration is not considered for cluster SSH communication

[jira] [Commented] (AIRAVATA-2621) SSH port provided in compute resource registration is not considered for cluster SSH communication

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