[jira] [Commented] (AIRAVATA-2624) Sampede2 cluster SSH connectivity issue
[ https://issues.apache.org/jira/browse/AIRAVATA-2624?page=com.atlassian.jira.plugin.system.issuetabpanels:comment-tabpanel=16329510#comment-16329510 ] Eroma commented on AIRAVATA-2624: - Changing the Jira status to RESOLVED on behalf of [~dimuthuupe] > Sampede2 cluster SSH connectivity issue > --- > > Key: AIRAVATA-2624 > URL: https://issues.apache.org/jira/browse/AIRAVATA-2624 > Project: Airavata > Issue Type: Bug > Components: Airavata System, GFac >Affects Versions: 0.18 > Environment: https://seagrid.org >Reporter: Eroma >Assignee: Dimuthu Upeksha >Priority: Major > Fix For: 0.18 > > > Job submission fails at env creation due to JSch initialization error. > Error messages > 2018-01-09 09:46:10,786 [pool-7-thread-15] ERROR > o.a.a.gfac.core.GFacException > process_id=PROCESS_650014f6-fcb6-4680-90ea-898bee373f37, > token_id=3d65bf6d-2c9f-4166-a51b-e76e0022bd3b, > experiment_id=Clone_of_st2molcastest_e2942a34-c9c7-4f04-8ccb-af6fe27e0990, > gateway_id=seagrid - JSch initialization error > com.jcraft.jsch.JSchException: Auth fail > at com.jcraft.jsch.Session.connect(Session.java:512) > 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) > 2018-01-09 09:46:10,786 [pool-7-thread-15] ERROR > o.a.a.g.i.t.EnvironmentSetupTask > process_id=PROCESS_650014f6-fcb6-4680-90ea-898bee373f37, > token_id=3d65bf6d-2c9f-4166-a51b-e76e0022bd3b, > experiment_id=Clone_of_st2molcastest_e2942a34-c9c7-4f04-8ccb-af6fe27e0990, > gateway_id=seagrid - Error while environment setup > org.apache.airavata.gfac.core.GFacException: JSch initialization error > at > org.apache.airavata.gfac.impl.Factory.getSSHSession(Factory.java:545) > 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: com.jcraft.jsch.JSchException: Auth fail > at com.jcraft.jsch.Session.connect(Session.java:512) > at com.jcraft.jsch.Session.connect(Session.java:183) > at > org.apache.airavata.gfac.impl.Factory.getSSHSession(Factory.java:542) > ... 14 common frames omitted > 2018-01-09 09:46:10,786 [pool-7-thread-15] INFO >
[jira] [Comment Edited] (AIRAVATA-2621) SSH port provided in compute resource registration is not considered for cluster SSH communication
[ https://issues.apache.org/jira/browse/AIRAVATA-2621?page=com.atlassian.jira.plugin.system.issuetabpanels:comment-tabpanel=16329417#comment-16329417 ] Eroma edited comment on AIRAVATA-2621 at 1/17/18 9:29 PM: -- Tested in [https://dev.seagrid.org|https://dev.seagrid.org/] # Test connecting via SSH and submitting a job using port 22 (default) defined in the SLURM job submission interface of compute resource. Tested using comet.sdsc.edu - PASS # Test connecting via SSH and submitting a job when no port (0) is defined in the SLURM job submission interface of compute resource. When no port exists system uses port 22 and submits job. Tested using js-169-144.jetstream-cloud.org - PASS # Test connecting via SSH and submitting a job when a different port (15022) is defined in the SLURM job submission interface of compute resource. Tested using AcoRE cluster - PASS # Test connecting via SSH and submitting a job using port 22 (default) defined in the PBS job submission interface of compute resource. Tested using bigred2. - PASS # Test connecting via SSH and submitting a job when no port is defined in the PBS job submission interface of compute resource. Tested using Karst. - PASS # Test connecting via SSH and submitting a job when a different port (15022) is defined in the PBS job submission interface of compute resource. Such cluster does not exists for PBS in the system - N/A # Test experiment and job cancellation when the standard SSH port 22 is being used in SLURM job submission interface of the compute resource. Tested with Stampede2 - PASS # Test experiment and job cancellation when a specific SSH port 15022 is being used in SLURM job submission interface of the compute resource. # Test experiment and job cancellation when no port (0) is defined in the PBS job submission interface of compute resource. Tested using Karst - PASS was (Author: eroma_a): Tested in [https://dev.seagrid.org|https://dev.seagrid.org/] # Test connecting via SSH and submitting a job using port 22 (default) defined in the SLURM job submission interface of compute resource. # Test connecting via SSH and submitting a job when no port (0) is defined in the SLURM job submission interface of compute resource. # Test connecting via SSH and submitting a job when a different port (15022) is defined in the SLURM job submission interface of compute resource. - PASS # Test connecting via SSH and submitting a job using port 22 (default) defined in the PBS job submission interface of compute resource. Tested using bigred2. - PASS # Test connecting via SSH and submitting a job when no port is defined in the PBS job submission interface of compute resource. # Test connecting via SSH and submitting a job when a different port (15022) is defined in the PBS job submission interface of compute resource. # Test experiment and job cancellation when the standard SSH port 22 is being used in SLURM job submission interface of the compute resource. # Test experiment and job cancellation when a specific SSH port 15022 is being used in SLURM job submission interface of the compute resource. # Test experiment and job cancellation when no port (0) is defined in the PBS job submission interface of compute resource. Tested using Karst - PASS > 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:
[jira] [Commented] (AIRAVATA-2624) Sampede2 cluster SSH connectivity issue
[ https://issues.apache.org/jira/browse/AIRAVATA-2624?page=com.atlassian.jira.plugin.system.issuetabpanels:comment-tabpanel=16329304#comment-16329304 ] Dimuthu Upeksha commented on AIRAVATA-2624: --- Fixed in [https://github.com/apache/airavata/commit/dc6ea56eb5435ec3f03d6a8226a44497e7290616] Added UIKeyboardInteractive feature for DefaultUserInfo class to support 2 factor ssh authentication. > Sampede2 cluster SSH connectivity issue > --- > > Key: AIRAVATA-2624 > URL: https://issues.apache.org/jira/browse/AIRAVATA-2624 > Project: Airavata > Issue Type: Bug > Components: Airavata System, GFac >Affects Versions: 0.18 > Environment: https://seagrid.org >Reporter: Eroma >Assignee: Suresh Marru >Priority: Major > Fix For: 0.18 > > > Job submission fails at env creation due to JSch initialization error. > Error messages > 2018-01-09 09:46:10,786 [pool-7-thread-15] ERROR > o.a.a.gfac.core.GFacException > process_id=PROCESS_650014f6-fcb6-4680-90ea-898bee373f37, > token_id=3d65bf6d-2c9f-4166-a51b-e76e0022bd3b, > experiment_id=Clone_of_st2molcastest_e2942a34-c9c7-4f04-8ccb-af6fe27e0990, > gateway_id=seagrid - JSch initialization error > com.jcraft.jsch.JSchException: Auth fail > at com.jcraft.jsch.Session.connect(Session.java:512) > 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) > 2018-01-09 09:46:10,786 [pool-7-thread-15] ERROR > o.a.a.g.i.t.EnvironmentSetupTask > process_id=PROCESS_650014f6-fcb6-4680-90ea-898bee373f37, > token_id=3d65bf6d-2c9f-4166-a51b-e76e0022bd3b, > experiment_id=Clone_of_st2molcastest_e2942a34-c9c7-4f04-8ccb-af6fe27e0990, > gateway_id=seagrid - Error while environment setup > org.apache.airavata.gfac.core.GFacException: JSch initialization error > at > org.apache.airavata.gfac.impl.Factory.getSSHSession(Factory.java:545) > 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: com.jcraft.jsch.JSchException: Auth fail > at com.jcraft.jsch.Session.connect(Session.java:512) > at com.jcraft.jsch.Session.connect(Session.java:183) > at >
[jira] [Resolved] (AIRAVATA-2621) SSH port provided in compute resource registration is not considered for cluster SSH communication
[ https://issues.apache.org/jira/browse/AIRAVATA-2621?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Eroma resolved AIRAVATA-2621. - Resolution: Fixed > 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 message was sent by Atlassian JIRA (v7.6.3#76005)
[jira] [Commented] (AIRAVATA-2621) SSH port provided in compute resource registration is not considered for cluster SSH communication
[ 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 -- This message was sent by Atlassian JIRA (v7.6.3#76005)
[jira] [Commented] (AIRAVATA-2621) SSH port provided in compute resource registration is not considered for cluster SSH communication
[ 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 -- This message was sent by Atlassian JIRA (v7.6.3#76005)
[jira] [Assigned] (AIRAVATA-2621) SSH port provided in compute resource registration is not considered for cluster SSH communication
[ https://issues.apache.org/jira/browse/AIRAVATA-2621?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Eroma reassigned AIRAVATA-2621: --- Assignee: Dimuthu Upeksha (was: Suresh Marru) > 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 message was sent by Atlassian JIRA (v7.6.3#76005)
[jira] [Commented] (AIRAVATA-2621) SSH port provided in compute resource registration is not considered for cluster SSH communication
[ 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 This is an automated message from the Apache Git Service. To respond to the message, please log on GitHub and use the URL above to go to the specific comment. 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: 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 -- This message was sent by Atlassian JIRA (v7.6.3#76005)
