Hi Heejoon, Yes please upgrade PGA as well. As well as the default name will not work, pick a name for your gateway. We can assist you in customizing the theme for your gateway. You can look at this as a example of a customized theme - https://seagrid.org/ <https://seagrid.org/>
Suresh > On Jan 2, 2016, at 5:19 PM, Heejoon Chae <[email protected]> wrote: > > Hi Suresh, > > Should I use latest PGA as well? I only updated Airavata server recently. I > am currently using identity server hosted by SciGaP. > > Is the name of gateway written in this section? > /** > * PGA Gateway ID > */ > 'gateway-id' => 'php_reference_gateway', > > or > > /** > * Tenant Domain > */ > 'tenant-domain' => 'master.airavata', > > /** > * Tenant admin's username > */ > 'admin-username' => 'master', > > /** > * Tenant admin's password > */ > 'admin-password' => 'master', > > > By the way, I have admin permission with default ID 'master' if the admin you > mentioned is same as this. > > Briefly, I am using locally hosted lastest Airavata server with 1 or 2 month > old locally running PGA, and use identity server hosted by SciGaP. I > registered own computing resource locally with SLURM job submission interface. > > Thank you! > Heejoon. > > > On Sun, Jan 3, 2016 at 12:02 AM, Suresh Marru <[email protected] > <mailto:[email protected]>> wrote: > Hi Heejoon, > > If you have latest Airavata (master), then you can use the user interface in > PGA to create credential store tokens. Only admins can register tokens. Are > you using your own identity server or the one hosted by SciGaP? Can you > briefly tell what is the name of your gateway so we can set up a tenant for > you and make you an admin for it. > > Suresh > >> On Jan 2, 2016, at 3:29 AM, Heejoon Chae <[email protected] >> <mailto:[email protected]>> wrote: >> >> Hi, >> >> I have succeeded to build recent version. Now I have compiled class located >> at >> >> 'org/apache/airavata/credential/store/store/impl/db/SSHCredentialTest.class' >> >> How can I run that to generate credential token? >> >> I tried 'java >> org/apache/airavata/credential/store/store/impl/db/SSHCredentialTest', but >> it says >> >> ############################################################################################# >> [heechae@biobrainpool test-classes]$ java >> org/apache/airavata/credential/store/store/impl/db/SSHCredentialTest >> Error: A JNI error has occurred, please check your installation and try again >> Exception in thread "main" java.lang.NoClassDefFoundError: >> org/apache/airavata/common/exception/ApplicationSettingsException >> at java.lang.Class.getDeclaredMethods0(Native Method) >> at java.lang.Class.privateGetDeclaredMethods(Class.java:2701) >> at java.lang.Class.privateGetMethodRecursive(Class.java:3048) >> at java.lang.Class.getMethod0(Class.java:3018) >> at java.lang.Class.getMethod(Class.java:1784) >> at >> sun.launcher.LauncherHelper.validateMainClass(LauncherHelper.java:544) >> at sun.launcher.LauncherHelper.checkAndLoadMain(LauncherHelper.java:526) >> Caused by: java.lang.ClassNotFoundException: >> org.apache.airavata.common.exception.ApplicationSettingsException >> at java.net.URLClassLoader.findClass(URLClassLoader.java:381) >> at java.lang.ClassLoader.loadClass(ClassLoader.java:424) >> at sun.misc.Launcher$AppClassLoader.loadClass(Launcher.java:331) >> at java.lang.ClassLoader.loadClass(ClassLoader.java:357) >> ... 7 more >> ############################################################################################ >> >> >> it seems it cannot find dependent classes. >> >> I manually copied all required classes to same location and tried to run, >> but at the end I still got >> >> ############################################################################################## >> Exception in thread "main" java.lang.NoClassDefFoundError: >> org/slf4j/LoggerFactory >> at org.apache.airavata.common.utils.DBUtil.<clinit>(DBUtil.java:43) >> at >> org.apache.airavata.credential.store.store.impl.db.SSHCredentialTest.main(SSHCredentialTest.java:50) >> Caused by: java.lang.ClassNotFoundException: org.slf4j.LoggerFactory >> at java.net.URLClassLoader.findClass(URLClassLoader.java:381) >> at java.lang.ClassLoader.loadClass(ClassLoader.java:424) >> at sun.misc.Launcher$AppClassLoader.loadClass(Launcher.java:331) >> at java.lang.ClassLoader.loadClass(ClassLoader.java:357) >> ... 2 more >> ############################################################################################## >> >> Thanks, >> Heejoon. >> >> On Tue, Dec 22, 2015 at 10:34 AM, Supun Nakandala <[email protected] >> <mailto:[email protected]>> wrote: >> The build should work fine now. >> >> On Mon, Dec 21, 2015 at 8:17 PM, Heejoon Chae <[email protected] >> <mailto:[email protected]>> wrote: >> Unfortunately, the compile fails at certain point, >> >> [INFO] >> ------------------------------------------------------------------------ >> [INFO] BUILD FAILURE >> [INFO] >> ------------------------------------------------------------------------ >> [INFO] Total time: 7:41.368s >> [INFO] Finished at: Tue Dec 22 10:05:36 KST 2015 >> [INFO] Final Memory: 95M/3073M >> [INFO] >> ------------------------------------------------------------------------ >> [ERROR] Failed to execute goal >> org.apache.maven.plugins:maven-compiler-plugin:3.1:compile (default-compile) >> on project airavata-client-samples: Compilation failure: Compilation failure: >> [ERROR] >> /data/project/mcpg/airavata/test/airavata/airavata-api/airavata-client-sdks/java-client-samples/src/main/java/org/apache/airavata/client/samples/CancelExperiments.java:[63,55] >> incompatible types: java.lang.String cannot be converted to >> org.apache.airavata.model.security.AuthzToken >> [ERROR] >> /data/project/mcpg/airavata/test/airavata/airavata-api/airavata-client-sdks/java-client-samples/src/main/java/org/apache/airavata/client/samples/DataManagerSample.java:[38,65] >> incompatible types: java.lang.String cannot be converted to >> org.apache.airavata.model.security.AuthzToken >> [ERROR] >> /data/project/mcpg/airavata/test/airavata/airavata-api/airavata-client-sdks/java-client-samples/src/main/java/org/apache/airavata/client/tools/RegisterSampleApplications.java:[193,81] >> incompatible types: java.lang.String cannot be converted to >> org.apache.airavata.model.security.AuthzToken >> >> Thanks, >> Heejoon. >> >> On Tue, Dec 22, 2015 at 10:02 AM, Heejoon Chae <[email protected] >> <mailto:[email protected]>> wrote: >> Sorry, I found my JAVA_HOME set to different location even I use java 1.8. >> >> Now it seems building goes correctly! >> >> Thank you! >> Heejoon. >> >> On Tue, Dec 22, 2015 at 9:56 AM, Heejoon Chae <[email protected] >> <mailto:[email protected]>> wrote: >> Yes. I am using java 1.8 >> >> [heechae@biobrainpool airavata]$ which java >> /packages/jdk1.8.0_65/bin/java >> >> Thanks, >> Heejoon. >> >> On Tue, Dec 22, 2015 at 9:46 AM, Chathuri Wimalasena <[email protected] >> <mailto:[email protected]>> wrote: >> Hi Heejoon, >> >> I hope you are using java 1.8. >> >> Thanks.. >> Chathuri >> >> On Mon, Dec 21, 2015 at 7:08 PM, Heejoon Chae <[email protected] >> <mailto:[email protected]>> wrote: >> Hi, Supun, >> >> Thank you for fixing that. I updated and do mvn clean install. >> I got some errors like, >> >> INFO] BUILD FAILURE >> [INFO] >> ------------------------------------------------------------------------ >> [INFO] Total time: 7.754s >> [INFO] Finished at: Tue Dec 22 09:05:21 KST 2015 >> [INFO] Final Memory: 36M/1931M >> [INFO] >> ------------------------------------------------------------------------ >> [ERROR] Failed to execute goal >> org.apache.maven.plugins:maven-compiler-plugin:3.1:compile (default-compile) >> on project airavata-data-models: Fatal error compiling: invalid target >> release: 1.8 -> [Help 1] >> [ERROR] >> [ERROR] To see the full stack trace of the errors, re-run Maven with the -e >> switch. >> [ERROR] Re-run Maven using the -X switch to enable full debug logging. >> [ERROR] >> [ERROR] For more information about the errors and possible solutions, please >> read the following articles: >> [ERROR] [Help 1] >> http://cwiki.apache.org/confluence/display/MAVEN/MojoExecutionException >> <http://cwiki.apache.org/confluence/display/MAVEN/MojoExecutionException> >> [ERROR] >> [ERROR] After correcting the problems, you can resume the build with the >> command >> [ERROR] mvn <goals> -rf :airavata-data-models >> >> Thanks, >> Heejoon. >> >> On Tue, Dec 22, 2015 at 12:35 AM, Supun Nakandala <[email protected] >> <mailto:[email protected]>> wrote: >> Hi Heejoon, >> >> There was an issue in the pom files and I fixed it now. Can you check >> whether your build is working now >> >> On Sun, Dec 20, 2015 at 7:52 PM, Heejoon Chae <[email protected] >> <mailto:[email protected]>> wrote: >> I got following as well, >> >> [INFO] Scanning for projects... >> [ERROR] The build could not read 2 projects -> [Help 1] >> [ERROR] >> [ERROR] The project org.apache.airavata:data-manager-cpi:0.16-SNAPSHOT >> (/data/project/mcpg/airavata/test/airavata/modules/data-manager/data-manager-cpi/pom.xml) >> has 1 error >> [ERROR] Non-resolvable parent POM: Could not find artifact >> org.apache.airavata:airavata:pom:0.16-SNAPSHOT and 'parent.relativePath' >> points at wrong local POM @ line 5, column 13 -> [Help 2] >> [ERROR] >> [ERROR] The project org.apache.airavata:data-manager-core:0.16-SNAPSHOT >> (/data/project/mcpg/airavata/test/airavata/modules/data-manager/data-manager-core/pom.xml) >> has 1 error >> [ERROR] Non-resolvable parent POM: Could not find artifact >> org.apache.airavata:airavata:pom:0.16-SNAPSHOT and 'parent.relativePath' >> points at wrong local POM @ line 5, column 13 -> [Help 2] >> [ERROR] >> [ERROR] To see the full stack trace of the errors, re-run Maven with the -e >> switch. >> [ERROR] Re-run Maven using the -X switch to enable full debug logging. >> [ERROR] >> [ERROR] For more information about the errors and possible solutions, please >> read the following articles: >> [ERROR] [Help 1] >> http://cwiki.apache.org/confluence/display/MAVEN/ProjectBuildingException >> <http://cwiki.apache.org/confluence/display/MAVEN/ProjectBuildingException> >> [ERROR] [Help 2] >> http://cwiki.apache.org/confluence/display/MAVEN/UnresolvableModelException >> <http://cwiki.apache.org/confluence/display/MAVEN/UnresolvableModelException> >> >> Thanks, >> Heejoon. >> >> On Mon, Dec 21, 2015 at 9:48 AM, Chathuri Wimalasena <[email protected] >> <mailto:[email protected]>> wrote: >> Instead of building only credential store module, could you build from >> airavata source root. Credential store module depends on >> airavata-server-configuration and other jars. That should resolve your >> issue.. >> >> Thanks. >> Chathuri >> >> On Sun, Dec 20, 2015 at 7:45 PM, Heejoon Chae <[email protected] >> <mailto:[email protected]>> wrote: >> Hi, Chathuri, >> >> Thank you for the explanation. >> >> I cloned the git and tried to compile credential-store with 'mvn clean >> install -Dmaven.test.skip=true' with mvn 3.0 and java 8 but got following >> errors. >> >> >> ############################################################################################################### >> Downloaded: >> http://repo1.maven.org/maven2/org/apache/derby/derbyclient/10.11.1.1/derbyclient-10.11.1.1.jar >> >> <http://repo1.maven.org/maven2/org/apache/derby/derbyclient/10.11.1.1/derbyclient-10.11.1.1.jar> >> (571 KB at 2.8 KB/sec) >> [INFO] >> ------------------------------------------------------------------------ >> [INFO] BUILD FAILURE >> [INFO] >> ------------------------------------------------------------------------ >> [INFO] Total time: 3:53.576s >> [INFO] Finished at: Mon Dec 21 09:38:34 KST 2015 >> [INFO] Final Memory: 11M/1931M >> [INFO] >> ------------------------------------------------------------------------ >> [ERROR] Failed to execute goal on project airavata-credential-store: Could >> not resolve dependencies for project >> org.apache.airavata:airavata-credential-store:jar:0.16-SNAPSHOT: The >> following artifacts could not be resolved: >> org.apache.airavata:airavata-credential-store-stubs:jar:0.16-SNAPSHOT, >> org.apache.airavata:airavata-server-configuration:jar:0.16-SNAPSHOT, >> org.apache.airavata:airavata-commons:jar:0.16-SNAPSHOT: Could not find >> artifact >> org.apache.airavata:airavata-credential-store-stubs:jar:0.16-SNAPSHOT in >> apache.snapshots (http://repository.apache.org/snapshots >> <http://repository.apache.org/snapshots>) -> [Help 1] >> [ERROR] >> [ERROR] To see the full stack trace of the errors, re-run Maven with the -e >> switch. >> [ERROR] Re-run Maven using the -X switch to enable full debug logging. >> [ERROR] >> [ERROR] For more information about the errors and possible solutions, please >> read the following articles: >> [ERROR] [Help 1] >> http://cwiki.apache.org/confluence/display/MAVEN/DependencyResolutionException >> >> <http://cwiki.apache.org/confluence/display/MAVEN/DependencyResolutionException> >> ############################################################################################################### >> >> Any suggestion? >> >> Thanks, >> Heejoon. >> >> On Fri, Dec 18, 2015 at 9:29 PM, Chathuri Wimalasena <[email protected] >> <mailto:[email protected]>> wrote: >> Hi Heejoon, >> >> You need to set up a valid credential store token in the credential store >> (experiment-catalog database has tables related to credential store). Same >> credential store token needs to be set in gateway profiles. This token is >> used when airavata ssh to resource, input staging and all the remote >> connections with the resource. Credential store token is the identifier for >> SSH credential object which contains valid SSH keys. Refer this code >> https://github.com/apache/airavata/blob/master/modules/credential-store/credential-store-service/src/test/java/org/apache/airavata/credential/store/store/impl/db/SSHCredentialTest.java >> >> <https://github.com/apache/airavata/blob/master/modules/credential-store/credential-store-service/src/test/java/org/apache/airavata/credential/store/store/impl/db/SSHCredentialTest.java>. >> There are API methods to generate SSH keys as well. You can use any of the >> two methods. >> >> Thanks.. >> Chathuri >> >> >> >> On Fri, Dec 18, 2015 at 12:02 AM, Heejoon Chae <[email protected] >> <mailto:[email protected]>> wrote: >> Hi, Suresh, >> >> Thank you for the help. It correctly parses the email. >> >> Now I have another error caused by 'credential token' as below, >> >> ERROR] expId: ttt_d0a8ca90-46b3-4225-add7-c29207130fc8, processId: >> PROCESS_273f058f-a0bc-400b-9a82-5d71246c8fa8, taskId: >> TASK_fc9dd43b-f0ea-4e6c-bd92-c5daa698257b type: DATA_STAGING,:- output >> staging failed, reason: Provided credential store token is not valid. Please >> provide the correct credential store token >> [INFO] expId: ttt_d0a8ca90-46b3-4225-add7-c29207130fc8, processId: >> PROCESS_273f058f-a0bc-400b-9a82-5d71246c8fa8 :- Process status changed >> FAILED -> FAILED >> [INFO] Publishing status to rabbitmq... >> [ERROR] GFac Worker throws an exception >> org.apache.airavata.gfac.core.GFacException: Error while staging output data >> at >> org.apache.airavata.gfac.impl.GFacEngineImpl.outputDataStaging(GFacEngineImpl.java:478) >> at >> org.apache.airavata.gfac.impl.GFacEngineImpl.runProcessOutflow(GFacEngineImpl.java:393) >> at >> org.apache.airavata.gfac.impl.GFacWorker.runProcessOutflow(GFacWorker.java:172) >> at org.apache.airavata.gfac.impl.GFacWorker.run(GFacWorker.java:105) >> 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:745) >> >> I actually set 'false' for storing credential in the >> 'airavata-server.properties' file as bellow >> >> start.credential.store=false >> >> but it seems still they are active. >> >> Thank you, >> Heejoon. >> >> On Fri, Dec 18, 2015 at 12:42 AM, Suresh Marru <[email protected] >> <mailto:[email protected]>> wrote: >> Hi Heejoon, >> >> You will need to configure your email within gfac-config.yaml (you will find >> it in the bin directory). >> >> If you can add your email to: >> >> - jobManagerType: SLURM >> commandOutputParser: org.apache.airavata.gfac.impl.job.SlurmOutputParser >> emailParser: org.apache.airavata.gfac.monitor.email.parser.SLURMEmailParser >> resourceEmailAddresses: >> - SDSC Admin <[email protected] >> <mailto:[email protected]>> # comet >> - [email protected] >> <mailto:[email protected]> # stampede >> - [email protected] <mailto:[email protected]> >> >> >> Thanks, >> Suresh >> >> > On Dec 16, 2015, at 6:33 PM, Heejoon Chae <[email protected] >> > <mailto:[email protected]>> wrote: >> > >> > Hi, Suresh, >> > >> > I am using one month old version of PGA and Airavata server. Both were >> > recent version at that time. >> > >> > apache-airavata-server-0.16-SNAPSHOT >> > >> > Thank you, >> > Heejoon. >> > >> > >> > >> > On Thu, Dec 17, 2015 at 8:28 AM, Suresh Marru <[email protected] >> > <mailto:[email protected]>> wrote: >> > Hi Heejoon, >> > >> > Are you using Airavata 0.15 or 0.16 for this purpose? >> > >> > Suresh >> > >> >> On Dec 16, 2015, at 5:38 PM, Heejoon Chae <[email protected] >> >> <mailto:[email protected]>> wrote: >> >> >> >> Hi, >> >> >> >> I have succeeded run job with SLURM. >> >> >> >> Now, the job monitoring through email causes some errors as bellow. >> >> >> >> It seems the Airavata server correctly log in the email account and bring >> >> email list, but it could not parse it correctly. >> >> >> >> ################################################################################# >> >> [ERROR] [EJM]: Error parsing email message >> >> =====================================> >> >> org.apache.airavata.common.exception.AiravataException: [EJM]: Couldn't >> >> identify Resource job manager type from address [email protected] >> >> <mailto:[email protected]> >> >> at >> >> org.apache.airavata.gfac.monitor.email.EmailBasedMonitor.getJobMonitorType(EmailBasedMonitor.java:160) >> >> at >> >> org.apache.airavata.gfac.monitor.email.EmailBasedMonitor.parse(EmailBasedMonitor.java:144) >> >> at >> >> org.apache.airavata.gfac.monitor.email.EmailBasedMonitor.processMessages(EmailBasedMonitor.java:239) >> >> at >> >> org.apache.airavata.gfac.monitor.email.EmailBasedMonitor.run(EmailBasedMonitor.java:208) >> >> at java.lang.Thread.run(Thread.java:745) >> >> [ERROR] FROM: [email protected] <mailto:[email protected]> >> >> [ERROR] TO: [email protected] <mailto:[email protected]> >> >> [ERROR] SUBJECT: SLURM Job_id=116 Name=A1514598207 Ended, Run time >> >> 00:00:01, COMPLETED, ExitCode 0 >> >> ################################################################################# >> >> >> >> Thank you, >> >> Heejoon. >> > >> > >> >> >> >> >> >> >> >> >> >> -- >> Thank you >> Supun Nakandala >> Dept. Computer Science and Engineering >> University of Moratuwa >> >> >> >> >> >> >> >> >> -- >> Thank you >> Supun Nakandala >> Dept. Computer Science and Engineering >> University of Moratuwa >> > >
