Hi Heejoon, Good Catch. Did you do a composer update in the airavata-php-gateway folder once you did a clone? This will pull the required dependencies into the vendor folder.
Suresh > On Jan 4, 2016, at 3:32 AM, Heejoon Chae <[email protected]> wrote: > > Hi, Supun, > > I got this error when I locally try to open > > 'http://localhost/test/airavata-php-gateway/public/index.php > <http://localhost/test/airavata-php-gateway/public/index.php>' on latest PGA > cloned from 'https://github.com/apache/airavata-php-gateway > <https://github.com/apache/airavata-php-gateway>' > > It seems there is no 'vendor' folder which I guess previous version had. > > Thank you, > Heejoon. > > On Mon, Jan 4, 2016 at 12:06 PM, Supun Nakandala <[email protected] > <mailto:[email protected]>> wrote: > In the current version navigation link to the previous home page was removed. > Instead a new landing page is shown. But the link to previous home page > <server-root>/public/home will take you the previous home page. > > On Sun, Jan 3, 2016 at 9:39 PM, Heejoon Chae <[email protected] > <mailto:[email protected]>> wrote: > Hi, > > For some reasons, I cannot see the main page of recent version of PGA. > Is current one being in the middle of update or do I need to set it up > differently? > > After clone from https://github.com/apache/airavata-php-gateway > <https://github.com/apache/airavata-php-gateway>, > I only set the app/config/pga_config.php.template to pga_config.php as I set > before. > > I also checked previous version of PGA that I deployed couple of months ago > and it is working correctly. > > Thank you, > Heejoon. > > On Sun, Jan 3, 2016 at 4:52 PM, Heejoon Chae <[email protected] > <mailto:[email protected]>> wrote: > Okay, I upgraded from 'https://github.com/apache/airavata-php-gateway > <https://github.com/apache/airavata-php-gateway>'. > > Please make the name as 'biovlab_snu'. Should this set to admin user name? > > Customizing the theme is good addition :) > > Thank you, > Heejoon. > > On Sun, Jan 3, 2016 at 4:08 PM, Suresh Marru <[email protected] > <mailto:[email protected]>> wrote: > 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] >> <mailto:[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 >>> >> >> > > > > > > > -- > Thank you > Supun Nakandala > Dept. Computer Science and Engineering > University of Moratuwa > > <???? 린샷 2016-01-04 오후 5.27.14.png>
