[jira] [Resolved] (AIRAVATA-2878) Continuous integration for Django portal
[ https://issues.apache.org/jira/browse/AIRAVATA-2878?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Marcus Christie resolved AIRAVATA-2878. --- Resolution: Fixed > Continuous integration for Django portal > > > Key: AIRAVATA-2878 > URL: https://issues.apache.org/jira/browse/AIRAVATA-2878 > Project: Airavata > Issue Type: Story >Reporter: Marcus Christie >Assignee: Marcus Christie >Priority: Major > > Travis or Jenkins configuration to run linter, build JS code, run tests, etc. > on each commit. -- This message was sent by Atlassian JIRA (v7.6.3#76005)
[jira] [Commented] (AIRAVATA-2878) Continuous integration for Django portal
[ https://issues.apache.org/jira/browse/AIRAVATA-2878?page=com.atlassian.jira.plugin.system.issuetabpanels:comment-tabpanel=16624199#comment-16624199 ] ASF subversion and git services commented on AIRAVATA-2878: --- Commit eb2eb610a078eecdca09a4b7dd74f860e8af1d28 in airavata-django-portal's branch refs/heads/master from [~marcuschristie] [ https://gitbox.apache.org/repos/asf?p=airavata-django-portal.git;h=eb2eb61 ] AIRAVATA-2878 Add JS build, Travis badge > Continuous integration for Django portal > > > Key: AIRAVATA-2878 > URL: https://issues.apache.org/jira/browse/AIRAVATA-2878 > Project: Airavata > Issue Type: Story >Reporter: Marcus Christie >Assignee: Marcus Christie >Priority: Major > > Travis or Jenkins configuration to run linter, build JS code, run tests, etc. > on each commit. -- This message was sent by Atlassian JIRA (v7.6.3#76005)
[jira] [Commented] (AIRAVATA-2878) Continuous integration for Django portal
[ https://issues.apache.org/jira/browse/AIRAVATA-2878?page=com.atlassian.jira.plugin.system.issuetabpanels:comment-tabpanel=16624186#comment-16624186 ] ASF subversion and git services commented on AIRAVATA-2878: --- Commit 970a34b0f124c8692447a9e4fc6ba98216d1e402 in airavata-django-portal's branch refs/heads/master from [~marcuschristie] [ https://gitbox.apache.org/repos/asf?p=airavata-django-portal.git;h=970a34b ] AIRAVATA-2878 Removing 3.7, failed to install in Travis > Continuous integration for Django portal > > > Key: AIRAVATA-2878 > URL: https://issues.apache.org/jira/browse/AIRAVATA-2878 > Project: Airavata > Issue Type: Story >Reporter: Marcus Christie >Assignee: Marcus Christie >Priority: Major > > Travis or Jenkins configuration to run linter, build JS code, run tests, etc. > on each commit. -- This message was sent by Atlassian JIRA (v7.6.3#76005)
[jira] [Commented] (AIRAVATA-2878) Continuous integration for Django portal
[ https://issues.apache.org/jira/browse/AIRAVATA-2878?page=com.atlassian.jira.plugin.system.issuetabpanels:comment-tabpanel=16624150#comment-16624150 ] ASF subversion and git services commented on AIRAVATA-2878: --- Commit 395b6973e9597b2fe8c2bd5ab35b4903e49c in airavata-django-portal's branch refs/heads/master from [~marcuschristie] [ https://gitbox.apache.org/repos/asf?p=airavata-django-portal.git;h=395 ] AIRAVATA-2878 Travis configuration > Continuous integration for Django portal > > > Key: AIRAVATA-2878 > URL: https://issues.apache.org/jira/browse/AIRAVATA-2878 > Project: Airavata > Issue Type: Story >Reporter: Marcus Christie >Assignee: Marcus Christie >Priority: Major > > Travis or Jenkins configuration to run linter, build JS code, run tests, etc. > on each commit. -- This message was sent by Atlassian JIRA (v7.6.3#76005)
[jira] [Commented] (AIRAVATA-2876) Django: Application Editor (Module/Interface/Deployments)
[ https://issues.apache.org/jira/browse/AIRAVATA-2876?page=com.atlassian.jira.plugin.system.issuetabpanels:comment-tabpanel=16624039#comment-16624039 ] ASF subversion and git services commented on AIRAVATA-2876: --- Commit 3c86d7b214a3fd9f1b6b3bb672b6ec30ccb50b3e in airavata-django-portal's branch refs/heads/master from [~marcuschristie] [ https://gitbox.apache.org/repos/asf?p=airavata-django-portal.git;h=3c86d7b ] AIRAVATA-2876 Remove Vuex store, load all modules in dashboard > Django: Application Editor (Module/Interface/Deployments) > - > > Key: AIRAVATA-2876 > URL: https://issues.apache.org/jira/browse/AIRAVATA-2876 > Project: Airavata > Issue Type: Story >Reporter: Marcus Christie >Assignee: Marcus Christie >Priority: Major > > TODO > * [x] Guard against unloading browser page when there are unsaved changes > * [x] Only allow admins to edit applications and interfaces (need to guard > this on the backend as well) > * [x] Use normal sharing rules to control who can edit a deployment > * [ ] white background for application editor (custom background color based > on current route?) > * [ ] enum selector component would be generally useful > * [x] ordered list serializer field that orders output by a numeric field (on > read) and updates that numeric field (on write) > * [x] CommandObjects editor and SetEnvPaths editor > * [ ] transitions on input and output fields? (we now have synthetic keys for > them) > * [x] Do we really need the Vuex store? Maybe just have > ApplicationEditorContainer handle this logic in a simpler way > * [x] load a list of all application modules instead of only "accessible" > modules > * [x] fix setting id when saving module, interface, etc. > (registry-refactoring regression) > * [x] delete application > * [x] add sharing button to app deployment editor > * [x] deployments aren't listed if there is no GroupResourceProfile for that > compute resource. Maybe only allow creating a deployment for compute > resources in GroupResourceProfiles? Or list deployments irrespective of > GroupResourceProfile? -- This message was sent by Atlassian JIRA (v7.6.3#76005)
[jira] [Commented] (AIRAVATA-2876) Django: Application Editor (Module/Interface/Deployments)
[ https://issues.apache.org/jira/browse/AIRAVATA-2876?page=com.atlassian.jira.plugin.system.issuetabpanels:comment-tabpanel=16624040#comment-16624040 ] ASF subversion and git services commented on AIRAVATA-2876: --- Commit 35c6da847de2b8d3da74b1a042f2a1a6c861fe57 in airavata-django-portal's branch refs/heads/master from [~marcuschristie] [ https://gitbox.apache.org/repos/asf?p=airavata-django-portal.git;h=35c6da8 ] AIRAVATA-2876 Removing previous app editor implementation > Django: Application Editor (Module/Interface/Deployments) > - > > Key: AIRAVATA-2876 > URL: https://issues.apache.org/jira/browse/AIRAVATA-2876 > Project: Airavata > Issue Type: Story >Reporter: Marcus Christie >Assignee: Marcus Christie >Priority: Major > > TODO > * [x] Guard against unloading browser page when there are unsaved changes > * [x] Only allow admins to edit applications and interfaces (need to guard > this on the backend as well) > * [x] Use normal sharing rules to control who can edit a deployment > * [ ] white background for application editor (custom background color based > on current route?) > * [ ] enum selector component would be generally useful > * [x] ordered list serializer field that orders output by a numeric field (on > read) and updates that numeric field (on write) > * [x] CommandObjects editor and SetEnvPaths editor > * [ ] transitions on input and output fields? (we now have synthetic keys for > them) > * [x] Do we really need the Vuex store? Maybe just have > ApplicationEditorContainer handle this logic in a simpler way > * [x] load a list of all application modules instead of only "accessible" > modules > * [x] fix setting id when saving module, interface, etc. > (registry-refactoring regression) > * [x] delete application > * [x] add sharing button to app deployment editor > * [x] deployments aren't listed if there is no GroupResourceProfile for that > compute resource. Maybe only allow creating a deployment for compute > resources in GroupResourceProfiles? Or list deployments irrespective of > GroupResourceProfile? -- This message was sent by Atlassian JIRA (v7.6.3#76005)
[jira] [Updated] (AIRAVATA-2876) Django: Application Editor (Module/Interface/Deployments)
[ https://issues.apache.org/jira/browse/AIRAVATA-2876?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Marcus Christie updated AIRAVATA-2876: -- Description: TODO * [x] Guard against unloading browser page when there are unsaved changes * [x] Only allow admins to edit applications and interfaces (need to guard this on the backend as well) * [x] Use normal sharing rules to control who can edit a deployment * [ ] white background for application editor (custom background color based on current route?) * [ ] enum selector component would be generally useful * [x] ordered list serializer field that orders output by a numeric field (on read) and updates that numeric field (on write) * [x] CommandObjects editor and SetEnvPaths editor * [ ] transitions on input and output fields? (we now have synthetic keys for them) * [x] Do we really need the Vuex store? Maybe just have ApplicationEditorContainer handle this logic in a simpler way * [x] load a list of all application modules instead of only "accessible" modules * [x] fix setting id when saving module, interface, etc. (registry-refactoring regression) * [x] delete application * [x] add sharing button to app deployment editor * [x] deployments aren't listed if there is no GroupResourceProfile for that compute resource. Maybe only allow creating a deployment for compute resources in GroupResourceProfiles? Or list deployments irrespective of GroupResourceProfile? was: TODO * [x] Guard against unloading browser page when there are unsaved changes * [x] Only allow admins to edit applications and interfaces (need to guard this on the backend as well) * [x] Use normal sharing rules to control who can edit a deployment * [ ] white background for application editor (custom background color based on current route?) * [ ] enum selector component would be generally useful * [x] ordered list serializer field that orders output by a numeric field (on read) and updates that numeric field (on write) * [x] CommandObjects editor and SetEnvPaths editor * [ ] transitions on input and output fields? (we now have synthetic keys for them) * [ ] Do we really need the Vuex store? Maybe just have ApplicationEditorContainer handle this logic in a simpler way * [x] load a list of all application modules instead of only "accessible" modules * [x] fix setting id when saving module, interface, etc. (registry-refactoring regression) * [x] delete application * [x] add sharing button to app deployment editor * [x] deployments aren't listed if there is no GroupResourceProfile for that compute resource. Maybe only allow creating a deployment for compute resources in GroupResourceProfiles? Or list deployments irrespective of GroupResourceProfile? > Django: Application Editor (Module/Interface/Deployments) > - > > Key: AIRAVATA-2876 > URL: https://issues.apache.org/jira/browse/AIRAVATA-2876 > Project: Airavata > Issue Type: Story >Reporter: Marcus Christie >Assignee: Marcus Christie >Priority: Major > > TODO > * [x] Guard against unloading browser page when there are unsaved changes > * [x] Only allow admins to edit applications and interfaces (need to guard > this on the backend as well) > * [x] Use normal sharing rules to control who can edit a deployment > * [ ] white background for application editor (custom background color based > on current route?) > * [ ] enum selector component would be generally useful > * [x] ordered list serializer field that orders output by a numeric field (on > read) and updates that numeric field (on write) > * [x] CommandObjects editor and SetEnvPaths editor > * [ ] transitions on input and output fields? (we now have synthetic keys for > them) > * [x] Do we really need the Vuex store? Maybe just have > ApplicationEditorContainer handle this logic in a simpler way > * [x] load a list of all application modules instead of only "accessible" > modules > * [x] fix setting id when saving module, interface, etc. > (registry-refactoring regression) > * [x] delete application > * [x] add sharing button to app deployment editor > * [x] deployments aren't listed if there is no GroupResourceProfile for that > compute resource. Maybe only allow creating a deployment for compute > resources in GroupResourceProfiles? Or list deployments irrespective of > GroupResourceProfile? -- This message was sent by Atlassian JIRA (v7.6.3#76005)
[jira] [Resolved] (AIRAVATA-2405) Keycloak: search for users with a given role
[ https://issues.apache.org/jira/browse/AIRAVATA-2405?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Marcus Christie resolved AIRAVATA-2405. --- Resolution: Fixed > Keycloak: search for users with a given role > > > Key: AIRAVATA-2405 > URL: https://issues.apache.org/jira/browse/AIRAVATA-2405 > Project: Airavata > Issue Type: Bug > Components: PGA PHP Web Gateway >Reporter: Marcus Christie >Assignee: Marcus Christie >Priority: Major > Fix For: 0.18 > > > In PGA, admins can search for users that have a selected role. > It would be good to implement this in IamAdminServices in the backend and > then call that from PGA. -- This message was sent by Atlassian JIRA (v7.6.3#76005)
[jira] [Resolved] (AIRAVATA-2505) Update Airavata to Thrift 0.10.0
[ https://issues.apache.org/jira/browse/AIRAVATA-2505?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Marcus Christie resolved AIRAVATA-2505. --- Resolution: Fixed > Update Airavata to Thrift 0.10.0 > > > Key: AIRAVATA-2505 > URL: https://issues.apache.org/jira/browse/AIRAVATA-2505 > Project: Airavata > Issue Type: Improvement >Reporter: Marcus Christie >Assignee: Marcus Christie >Priority: Major > > We need Thrift 0.10.0 to generate Python 3 compatible stubs. -- This message was sent by Atlassian JIRA (v7.6.3#76005)
[jira] [Resolved] (AIRAVATA-2629) Factor out Loading overlay from admin app
[ https://issues.apache.org/jira/browse/AIRAVATA-2629?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Marcus Christie resolved AIRAVATA-2629. --- Resolution: Fixed > Factor out Loading overlay from admin app > - > > Key: AIRAVATA-2629 > URL: https://issues.apache.org/jira/browse/AIRAVATA-2629 > Project: Airavata > Issue Type: Sub-task >Reporter: Marcus Christie >Assignee: Marcus Christie >Priority: Major > > Move the Loading component that Eldho created to the common UI module. -- This message was sent by Atlassian JIRA (v7.6.3#76005)
[jira] [Resolved] (AIRAVATA-2631) File download in experiment summary
[ https://issues.apache.org/jira/browse/AIRAVATA-2631?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Marcus Christie resolved AIRAVATA-2631. --- Resolution: Fixed > File download in experiment summary > --- > > Key: AIRAVATA-2631 > URL: https://issues.apache.org/jira/browse/AIRAVATA-2631 > Project: Airavata > Issue Type: Sub-task >Reporter: Marcus Christie >Assignee: Marcus Christie >Priority: Major > > TODO > - [x] move upload and download views to the *api* app > - [x] add the download url to the DataProductSerializer so it is available in > the API. However, only add the URL if the data product file exists on the > that server. > - [x] remove the experiment id query parameter > - [x] make sure experiment directory is world writeable > - [x] download icon > - [x] return proper 404 when not found > - [x] fix: output files not listed for download > - [x] upload/download service in *api* app -- This message was sent by Atlassian JIRA (v7.6.3#76005)
[jira] [Resolved] (AIRAVATA-2614) Experiment list page
[ https://issues.apache.org/jira/browse/AIRAVATA-2614?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Marcus Christie resolved AIRAVATA-2614. --- Resolution: Fixed > Experiment list page > > > Key: AIRAVATA-2614 > URL: https://issues.apache.org/jira/browse/AIRAVATA-2614 > Project: Airavata > Issue Type: Sub-task >Reporter: Marcus Christie >Assignee: Marcus Christie >Priority: Major > > TODO > * (/) implement backed searchExperiments ViewSet/Serializer with pagination > * (/) implement list UI > * (/) color code experiment statuses > * (/) add View and Edit links > * (/) display application name > * display compute resource name > -- This message was sent by Atlassian JIRA (v7.6.3#76005)
[jira] [Updated] (AIRAVATA-2631) File download in experiment summary
[ https://issues.apache.org/jira/browse/AIRAVATA-2631?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Marcus Christie updated AIRAVATA-2631: -- Description: TODO - [x] move upload and download views to the *api* app - [x] add the download url to the DataProductSerializer so it is available in the API. However, only add the URL if the data product file exists on the that server. - [x] remove the experiment id query parameter - [x] make sure experiment directory is world writeable - [x] download icon - [x] return proper 404 when not found - [x] fix: output files not listed for download - [x] upload/download service in *api* app was: TODO - [x] move upload and download views to the *api* app - [x] add the download url to the DataProductSerializer so it is available in the API. However, only add the URL if the data product file exists on the that server. - [x] remove the experiment id query parameter - [x] make sure experiment directory is world writeable - [x] download icon - [x] return proper 404 when not found - [x] fix: output files not listed for download - [ ] upload/download service in *api* app > File download in experiment summary > --- > > Key: AIRAVATA-2631 > URL: https://issues.apache.org/jira/browse/AIRAVATA-2631 > Project: Airavata > Issue Type: Sub-task >Reporter: Marcus Christie >Assignee: Marcus Christie >Priority: Major > > TODO > - [x] move upload and download views to the *api* app > - [x] add the download url to the DataProductSerializer so it is available in > the API. However, only add the URL if the data product file exists on the > that server. > - [x] remove the experiment id query parameter > - [x] make sure experiment directory is world writeable > - [x] download icon > - [x] return proper 404 when not found > - [x] fix: output files not listed for download > - [x] upload/download service in *api* app -- This message was sent by Atlassian JIRA (v7.6.3#76005)
[jira] [Resolved] (AIRAVATA-2803) Experiment Statistics in Admin Dashboard is not displaying any statistics
[ https://issues.apache.org/jira/browse/AIRAVATA-2803?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Marcus Christie resolved AIRAVATA-2803. --- Resolution: Fixed > Experiment Statistics in Admin Dashboard is not displaying any statistics > - > > Key: AIRAVATA-2803 > URL: https://issues.apache.org/jira/browse/AIRAVATA-2803 > Project: Airavata > Issue Type: Bug > Components: PGA PHP Web Gateway >Affects Versions: 0.18 > Environment: https://pga.group-based-auth.scigap.org/ >Reporter: Eroma >Assignee: Marcus Christie >Priority: Major > Fix For: 0.18 > > Attachments: Screen Shot 2018-06-04 at 1.52.59 PM.png > > > Experiment statistics are not displaying any experiments, not even the > categorization. Even if experiments are not available for the selected period > the categorization (Total experiments, Created, Running, etc) those > categories should have listed with the selected period. There is no such. -- This message was sent by Atlassian JIRA (v7.6.3#76005)
[jira] [Resolved] (AIRAVATA-2671) Users with gateway-read-only role cannot view compute resources.
[ https://issues.apache.org/jira/browse/AIRAVATA-2671?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Marcus Christie resolved AIRAVATA-2671. --- Resolution: Fixed > Users with gateway-read-only role cannot view compute resources. > - > > Key: AIRAVATA-2671 > URL: https://issues.apache.org/jira/browse/AIRAVATA-2671 > Project: Airavata > Issue Type: Bug > Components: Application Catalog, PGA PHP Web Gateway >Affects Versions: 0.18 > Environment: https://dev.seagrid.org >Reporter: Eroma >Assignee: Marcus Christie >Priority: Major > Attachments: Screen Shot 2018-02-05 at 4.22.41 PM.png > > > When clicked on a resource from Compute Resources --> Browse throws an > exception. > User is not authenticated or authorized. > -- This message was sent by Atlassian JIRA (v7.6.3#76005)
[jira] [Resolved] (AIRAVATA-2502) In gateways CILogon is enabled, it to be the main login mechanism
[ https://issues.apache.org/jira/browse/AIRAVATA-2502?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Marcus Christie resolved AIRAVATA-2502. --- Resolution: Fixed > In gateways CILogon is enabled, it to be the main login mechanism > - > > Key: AIRAVATA-2502 > URL: https://issues.apache.org/jira/browse/AIRAVATA-2502 > Project: Airavata > Issue Type: Improvement > Components: PGA PHP Web Gateway >Affects Versions: 0.17 > Environment: https://sciencegateway.usd.edu >Reporter: Eroma >Assignee: Marcus Christie >Priority: Major > Fix For: 0.18 > > > 1. CILogon to be the more focused login to use > 2. First option: Users to have clear indication ‘Login with USD credentials” > and directly take them to USD without needing to select the institute. > 3. Second option: “Login with other institute credentials” This for other > users login to gateway. Here there should be list of institutes to select and > login. > 4. Third option: Create or log in with a local gateway account. -- This message was sent by Atlassian JIRA (v7.6.3#76005)
[jira] [Resolved] (AIRAVATA-2628) After the email verification link is used successfully if the user clicks on it again another mail will be sent with another link.
[ https://issues.apache.org/jira/browse/AIRAVATA-2628?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Marcus Christie resolved AIRAVATA-2628. --- Resolution: Fixed > After the email verification link is used successfully if the user clicks on > it again another mail will be sent with another link. > --- > > Key: AIRAVATA-2628 > URL: https://issues.apache.org/jira/browse/AIRAVATA-2628 > Project: Airavata > Issue Type: Bug > Components: Keycloak Authentication, PGA PHP Web Gateway >Affects Versions: 0.18 >Reporter: Eroma >Assignee: Marcus Christie >Priority: Minor > > 1. User receives an email for email verification. > 2. He uses it successfully and verifies the account. > 3. Goes and click on the email verification link again > 4. Irrespective of using the previous successfully and account is enabled and > email is verified another link is sent to the user. > 5. Once the email is verified verification link should not be sent to the > user. -- This message was sent by Atlassian JIRA (v7.6.3#76005)
[jira] [Resolved] (AIRAVATA-2814) Error: "PersistenceException: Table "PROJECT" has a foreign key to table "USERS" that has not been generated."
[
https://issues.apache.org/jira/browse/AIRAVATA-2814?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel
]
Marcus Christie resolved AIRAVATA-2814.
---
Resolution: Fixed
> Error: "PersistenceException: Table "PROJECT" has a foreign key to table
> "USERS" that has not been generated."
> --
>
> Key: AIRAVATA-2814
> URL: https://issues.apache.org/jira/browse/AIRAVATA-2814
> Project: Airavata
> Issue Type: Bug
>Reporter: Marcus Christie
>Assignee: Marcus Christie
>Priority: Major
>
> This error occurs in the logs when the API server starts up.
> Stacktrace:
> {noformat}
> 2018-06-06 16:22:34,167 [pool-9-thread-2] ERROR
> o.a.a.r.a.s.h.RegistryServerHandler - default
> java.lang.RuntimeException: Failed to get Experiment Catalog EntityManager
> at
> org.apache.airavata.registry.core.repositories.expcatalog.ExpCatAbstractRepository.execute(ExpCatAbstractRepository.java:95)
> at
> org.apache.airavata.registry.core.repositories.expcatalog.ExpCatAbstractRepository.get(ExpCatAbstractRepository.java:49)
> at
> org.apache.airavata.registry.core.repositories.expcatalog.ExpCatAbstractRepository.isExists(ExpCatAbstractRepository.java:87)
> at
> org.apache.airavata.registry.core.repositories.expcatalog.GatewayRepository.isGatewayExist(GatewayRepository.java:99)
> at
> org.apache.airavata.registry.api.service.handler.RegistryServerHandler.isGatewayExistInternal(RegistryServerHandler.java:4165)
> at
> org.apache.airavata.registry.api.service.handler.RegistryServerHandler.getGatewayResourceProfile(RegistryServerHandler.java:1966)
> at
> org.apache.airavata.registry.api.RegistryService$Processor$getGatewayResourceProfile.getResult(RegistryService.java:17795)
> at
> org.apache.airavata.registry.api.RegistryService$Processor$getGatewayResourceProfile.getResult(RegistryService.java:17779)
> at org.apache.thrift.ProcessFunction.process(ProcessFunction.java:39)
> at org.apache.thrift.TBaseProcessor.process(TBaseProcessor.java:39)
> at
> org.apache.thrift.server.TThreadPoolServer$WorkerProcess.run(TThreadPoolServer.java:286)
> at
> java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142)
> at
> java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617)
> at java.lang.Thread.run(Thread.java:748)
> Caused by: org.apache.openjpa.persistence.PersistenceException: Table
> "PROJECT" has a foreign key to table "USERS" that has not been generated.
> You must run the schema generator on all inter-related tables at once.
> at org.apache.openjpa.jdbc.meta.MappingTool.record(MappingTool.java:559)
> at org.apache.openjpa.jdbc.meta.MappingTool.record(MappingTool.java:455)
> at
> org.apache.openjpa.jdbc.kernel.JDBCBrokerFactory.synchronizeMappings(JDBCBrokerFactory.java:160)
> at
> org.apache.openjpa.jdbc.kernel.JDBCBrokerFactory.synchronizeMappings(JDBCBrokerFactory.java:164)
> at
> org.apache.openjpa.jdbc.kernel.JDBCBrokerFactory.newBrokerImpl(JDBCBrokerFactory.java:122)
> at
> org.apache.openjpa.kernel.AbstractBrokerFactory.newBroker(AbstractBrokerFactory.java:209)
> at
> org.apache.openjpa.kernel.DelegatingBrokerFactory.newBroker(DelegatingBrokerFactory.java:156)
> at
> org.apache.openjpa.persistence.EntityManagerFactoryImpl.createEntityManager(EntityManagerFactoryImpl.java:227)
> at
> org.apache.openjpa.persistence.EntityManagerFactoryImpl.createEntityManager(EntityManagerFactoryImpl.java:154)
> at
> org.apache.openjpa.persistence.EntityManagerFactoryImpl.createEntityManager(EntityManagerFactoryImpl.java:60)
> at
> org.apache.airavata.registry.core.utils.JPAUtil.ExpCatalogJPAUtils.getEntityManager(ExpCatalogJPAUtils.java:71)
> at
> org.apache.airavata.registry.core.repositories.expcatalog.ExpCatAbstractRepository.execute(ExpCatAbstractRepository.java:93)
> ... 13 common frames omitted
> {noformat}
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[jira] [Resolved] (AIRAVATA-2839) GroupResourceProfile: require unique login username or unique allocation number
[ https://issues.apache.org/jira/browse/AIRAVATA-2839?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Marcus Christie resolved AIRAVATA-2839. --- Resolution: Fixed > GroupResourceProfile: require unique login username or unique allocation > number > --- > > Key: AIRAVATA-2839 > URL: https://issues.apache.org/jira/browse/AIRAVATA-2839 > Project: Airavata > Issue Type: Story >Reporter: Marcus Christie >Assignee: Marcus Christie >Priority: Major > > The GatewayResourceProfile has ComputeResourcePreferences that are now used > to specify default values for compute resources, but a GroupResourceProfile's > GroupComputeResourcePreferences should be used for the actual > authentication/allocation charged for the job. > This means that a GroupResourceProfile's GroupComputeResourcePreference > should either specify: > * a different loginUserName > * or an allocationProjectNumber > from the corresponding ComputeResourcePreference in the > GatewayResourceProfile. This way a GroupResourceProfile can't accidentally > use the account specified in a GatewayResourceProfile > ComputeResourcePreference. > The main use case for this is that a gateway admin can create a > ComputeResourcePreference with a loginUserName and credential store token > that handles logging in to the compute resource and then a user can create a > GroupComputeResourcePreference that essentially only needs to specify an > allocation number (well, and the user would need to authorize that > loginUserName to be able to use the allocation, depending on the compute > resource's policy). -- This message was sent by Atlassian JIRA (v7.6.3#76005)
[jira] [Resolved] (AIRAVATA-2841) SEAGrid users not getting account verification email on organization email
[ https://issues.apache.org/jira/browse/AIRAVATA-2841?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Marcus Christie resolved AIRAVATA-2841. --- Resolution: Fixed > SEAGrid users not getting account verification email on organization email > -- > > Key: AIRAVATA-2841 > URL: https://issues.apache.org/jira/browse/AIRAVATA-2841 > Project: Airavata > Issue Type: Bug > Components: PGA PHP Web Gateway >Affects Versions: 0.18 >Reporter: Eroma >Assignee: Marcus Christie >Priority: Critical > Fix For: 0.18 > > > Steps > # Gave IU email in seagrid gateway and didnt receive the account > verification email. > # When given gmail address the user gets verification email on time > # Tried the same in testdrive gateway using IU email and received the > verification email on time. > # Seem to happen only in seagrid gateway. > # Sent a separate test email from the PGA email and IU mail got the test > mail. > # Checked the mail on 'junk' folder and not there either. -- This message was sent by Atlassian JIRA (v7.6.3#76005)
[jira] [Resolved] (AIRAVATA-2586) Create Ansible version of Django portal deploy
[ https://issues.apache.org/jira/browse/AIRAVATA-2586?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Marcus Christie resolved AIRAVATA-2586. --- Resolution: Fixed > Create Ansible version of Django portal deploy > -- > > Key: AIRAVATA-2586 > URL: https://issues.apache.org/jira/browse/AIRAVATA-2586 > Project: Airavata > Issue Type: Sub-task >Reporter: Marcus Christie >Assignee: Marcus Christie >Priority: Major > -- This message was sent by Atlassian JIRA (v7.6.3#76005)
[jira] [Created] (AIRAVATA-2880) Create Ansible role to setup a Django portal server
Marcus Christie created AIRAVATA-2880: - Summary: Create Ansible role to setup a Django portal server Key: AIRAVATA-2880 URL: https://issues.apache.org/jira/browse/AIRAVATA-2880 Project: Airavata Issue Type: Sub-task Reporter: Marcus Christie Assignee: Marcus Christie Django deploy role is done, now we need a role to setup a webserver for Django deployments: see https://github.com/apache/airavata/blob/develop/dev-tools/ansible/roles/django_setup/tasks/main.yml -- This message was sent by Atlassian JIRA (v7.6.3#76005)
[jira] [Resolved] (AIRAVATA-2847) Crating new application failed with application interface and deployment details with no reason.
[ https://issues.apache.org/jira/browse/AIRAVATA-2847?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Marcus Christie resolved AIRAVATA-2847. --- Resolution: Fixed > Crating new application failed with application interface and deployment > details with no reason. > > > Key: AIRAVATA-2847 > URL: https://issues.apache.org/jira/browse/AIRAVATA-2847 > Project: Airavata > Issue Type: Bug > Components: Django Portal >Reporter: Eroma >Assignee: Marcus Christie >Priority: Blocker > > Clicked adding new application. > # Was able to save Details tab. > # Saving both Interface and deployment tabs failed with 'Saving Application > Interface Failed' and 'Saving Application Deployment Failed' without any > reason or error code whats wrong. > # I was adding them looking at an existing Gromacs application and nothing > was wrong with details provided. > # For application interface see errors [1] in the console. For deployment > also see similar error > [1] > POST https://django.seagrid.org/api/new/application/interface 400 (Bad > Request) > post @ utils.js:41 > saveApplicationInterface @ app_interface.js:188 > (anonymous) @ vuex.esm.js:704 > E.dispatch @ vuex.esm.js:426 > E.dispatch @ vuex.esm.js:332 > r.dispatch @ vuex.esm.js:634 > n.(anonymous function) @ vuex.esm.js:880 > saveFn @ TabActionConsole.vue:37 > e @ vue.esm.js:2027 > t._withTask.t._withTask @ vue.esm.js:1826 > TabActionConsole.vue:51 Failure Value Bad Request > TabActionConsole.vue:59 Failure Bad Request -- This message was sent by Atlassian JIRA (v7.6.3#76005)
[jira] [Resolved] (AIRAVATA-2846) Cannot creare STDOUT and STDERR outputs in application interface
[ https://issues.apache.org/jira/browse/AIRAVATA-2846?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Marcus Christie resolved AIRAVATA-2846. --- Resolution: Fixed > Cannot creare STDOUT and STDERR outputs in application interface > > > Key: AIRAVATA-2846 > URL: https://issues.apache.org/jira/browse/AIRAVATA-2846 > Project: Airavata > Issue Type: Bug > Components: Django Portal >Reporter: Eroma >Assignee: Marcus Christie >Priority: Blocker > > When creating outputs, the types STDOUT and STDERR are not available. Only > String, integer float and URI was there. -- This message was sent by Atlassian JIRA (v7.6.3#76005)
[jira] [Resolved] (AIRAVATA-2848) In adding application, in Deployments tab, the field 'Application Module' is not required
[ https://issues.apache.org/jira/browse/AIRAVATA-2848?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Marcus Christie resolved AIRAVATA-2848. --- Resolution: Fixed > In adding application, in Deployments tab, the field 'Application Module' is > not required > - > > Key: AIRAVATA-2848 > URL: https://issues.apache.org/jira/browse/AIRAVATA-2848 > Project: Airavata > Issue Type: Bug > Components: Django Portal >Reporter: Eroma >Assignee: Marcus Christie >Priority: Blocker > > # First in application deployment tab the module field should be a list to > select from. > # Secondly now that we have brought the create application steps under > single form with tabs do we even need this field? > # We are not using the 'module' name anymore. -- This message was sent by Atlassian JIRA (v7.6.3#76005)
[jira] [Resolved] (AIRAVATA-2770) registry-refactoring: ids not set correctly for application module, application interface
[ https://issues.apache.org/jira/browse/AIRAVATA-2770?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Marcus Christie resolved AIRAVATA-2770. --- Resolution: Fixed Fixed in AIRAVATA-2876 > registry-refactoring: ids not set correctly for application module, > application interface > - > > Key: AIRAVATA-2770 > URL: https://issues.apache.org/jira/browse/AIRAVATA-2770 > Project: Airavata > Issue Type: Sub-task >Reporter: Marcus Christie >Assignee: Marcus Christie >Priority: Major > > A new application module with name "Protein structure" was created with id > "Protein structure", should have been the name + UUID. > A new application interface was created with id DO_NOT_SET_AT_CLIENTS, should > have been name + UUID. -- This message was sent by Atlassian JIRA (v7.6.3#76005)
[jira] [Resolved] (AIRAVATA-2849) Couldn't find a method to add multiple deployments in to application
[ https://issues.apache.org/jira/browse/AIRAVATA-2849?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Marcus Christie resolved AIRAVATA-2849. --- Resolution: Fixed > Couldn't find a method to add multiple deployments in to application > > > Key: AIRAVATA-2849 > URL: https://issues.apache.org/jira/browse/AIRAVATA-2849 > Project: Airavata > Issue Type: Bug > Components: Django Portal >Reporter: Eroma >Assignee: Marcus Christie >Priority: Blocker > > I couldn't locate a method (button, link) to add multiple deployments of an > application. -- This message was sent by Atlassian JIRA (v7.6.3#76005)
[jira] [Resolved] (AIRAVATA-2386) Fix issues with email monitoring
[ https://issues.apache.org/jira/browse/AIRAVATA-2386?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Dimuthu Upeksha resolved AIRAVATA-2386. --- Resolution: Fixed New job monitors are running based on a state model so the ordering of the emails are not relevant. https://github.com/apache/airavata/tree/develop/modules/job-monitor/email-monitor > Fix issues with email monitoring > > > Key: AIRAVATA-2386 > URL: https://issues.apache.org/jira/browse/AIRAVATA-2386 > Project: Airavata > Issue Type: Task > Components: Airavata System, GFac >Affects Versions: 0.17 >Reporter: Eroma >Assignee: Dimuthu Upeksha >Priority: Major > Fix For: 0.18 > > Attachments: jobstatus.ps > > > There are few issues with email monitoring and the task is to collect them > and fix. -- This message was sent by Atlassian JIRA (v7.6.3#76005)
[jira] [Resolved] (AIRAVATA-2689) Distributed email clients to improve email monitoring
[ https://issues.apache.org/jira/browse/AIRAVATA-2689?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Dimuthu Upeksha resolved AIRAVATA-2689. --- Resolution: Fixed Fixed as a part of new helix implementation. Job monitors were taken out from the core execution logic. https://github.com/apache/airavata/tree/develop/modules/job-monitor/email-monitor > Distributed email clients to improve email monitoring > -- > > Key: AIRAVATA-2689 > URL: https://issues.apache.org/jira/browse/AIRAVATA-2689 > Project: Airavata > Issue Type: New Feature >Reporter: Dimuthu Upeksha >Assignee: Dimuthu Upeksha >Priority: Major > Labels: HackIllinois2018 > > Once Airavata submits a job to a compute resource, scheduler in compute > resource sends emails about the status of the job. Content in the email is > different to each application type so we have written a set of parsers [2] > which can extract correct information form email messages. Airavata has an > email monitoring system which reads those emails, parse them and perform > necessary actions depending on the content of the emails. However this email > monitoring system is tightly coupled into the task execution engine so we > can't easily replicate it to have high availability. > Idea is to come up with a standalone email monitoring client that reads > emails from a given email account, parse them and convert it into a standard > message format. Once the message is parsed into the known message format, put > it in to a queue ( rabbitmq, kafka) in order to be consumed by task execution > engine. There are few non functional requirements > # To improve the availability, we need to have more than one monitoring > client to be running at a given time. However we need to make sure only > exactly one client consumes a given email. So we need the coordination among > email clients > # In future, this will be deployed as a micro service, so final packaging > should be compatible with docker > Current email monitor implementation is this [1]. Set of parsers available > depending on the application [2] > [1] > [https://github.com/apache/airavata/blob/master/modules/gfac/gfac-impl/src/main/java/org/apache/airavata/gfac/monitor/email/EmailBasedMonitor.java] > [2] > https://github.com/apache/airavata/tree/master/modules/gfac/gfac-impl/src/main/java/org/apache/airavata/gfac/monitor/email/parser -- This message was sent by Atlassian JIRA (v7.6.3#76005)
[jira] [Commented] (AIRAVATA-2876) Django: Application Editor (Module/Interface/Deployments)
[ https://issues.apache.org/jira/browse/AIRAVATA-2876?page=com.atlassian.jira.plugin.system.issuetabpanels:comment-tabpanel=16623955#comment-16623955 ] ASF subversion and git services commented on AIRAVATA-2876: --- Commit e4978b0c1081edcff759951bbc99b7dad22991a9 in airavata-django-portal's branch refs/heads/master from [~marcuschristie] [ https://gitbox.apache.org/repos/asf?p=airavata-django-portal.git;h=e4978b0 ] AIRAVATA-2876 Rename deployment_id to deploymentId > Django: Application Editor (Module/Interface/Deployments) > - > > Key: AIRAVATA-2876 > URL: https://issues.apache.org/jira/browse/AIRAVATA-2876 > Project: Airavata > Issue Type: Story >Reporter: Marcus Christie >Assignee: Marcus Christie >Priority: Major > > TODO > * [x] Guard against unloading browser page when there are unsaved changes > * [x] Only allow admins to edit applications and interfaces (need to guard > this on the backend as well) > * [x] Use normal sharing rules to control who can edit a deployment > * [ ] white background for application editor (custom background color based > on current route?) > * [ ] enum selector component would be generally useful > * [x] ordered list serializer field that orders output by a numeric field (on > read) and updates that numeric field (on write) > * [x] CommandObjects editor and SetEnvPaths editor > * [ ] transitions on input and output fields? (we now have synthetic keys for > them) > * [ ] Do we really need the Vuex store? Maybe just have > ApplicationEditorContainer handle this logic in a simpler way > * [x] load a list of all application modules instead of only "accessible" > modules > * [x] fix setting id when saving module, interface, etc. > (registry-refactoring regression) > * [x] delete application > * [x] add sharing button to app deployment editor > * [x] deployments aren't listed if there is no GroupResourceProfile for that > compute resource. Maybe only allow creating a deployment for compute > resources in GroupResourceProfiles? Or list deployments irrespective of > GroupResourceProfile? -- This message was sent by Atlassian JIRA (v7.6.3#76005)
[jira] [Commented] (AIRAVATA-2876) Django: Application Editor (Module/Interface/Deployments)
[ https://issues.apache.org/jira/browse/AIRAVATA-2876?page=com.atlassian.jira.plugin.system.issuetabpanels:comment-tabpanel=16623956#comment-16623956 ] ASF subversion and git services commented on AIRAVATA-2876: --- Commit 1539cd49650f0f4863ae3db730bfd1c4e90b0f63 in airavata-django-portal's branch refs/heads/master from [~marcuschristie] [ https://gitbox.apache.org/repos/asf?p=airavata-django-portal.git;h=1539cd4 ] AIRAVATA-2876 Navigate to route with save error > Django: Application Editor (Module/Interface/Deployments) > - > > Key: AIRAVATA-2876 > URL: https://issues.apache.org/jira/browse/AIRAVATA-2876 > Project: Airavata > Issue Type: Story >Reporter: Marcus Christie >Assignee: Marcus Christie >Priority: Major > > TODO > * [x] Guard against unloading browser page when there are unsaved changes > * [x] Only allow admins to edit applications and interfaces (need to guard > this on the backend as well) > * [x] Use normal sharing rules to control who can edit a deployment > * [ ] white background for application editor (custom background color based > on current route?) > * [ ] enum selector component would be generally useful > * [x] ordered list serializer field that orders output by a numeric field (on > read) and updates that numeric field (on write) > * [x] CommandObjects editor and SetEnvPaths editor > * [ ] transitions on input and output fields? (we now have synthetic keys for > them) > * [ ] Do we really need the Vuex store? Maybe just have > ApplicationEditorContainer handle this logic in a simpler way > * [x] load a list of all application modules instead of only "accessible" > modules > * [x] fix setting id when saving module, interface, etc. > (registry-refactoring regression) > * [x] delete application > * [x] add sharing button to app deployment editor > * [x] deployments aren't listed if there is no GroupResourceProfile for that > compute resource. Maybe only allow creating a deployment for compute > resources in GroupResourceProfiles? Or list deployments irrespective of > GroupResourceProfile? -- This message was sent by Atlassian JIRA (v7.6.3#76005)
[jira] [Commented] (AIRAVATA-2876) Django: Application Editor (Module/Interface/Deployments)
[ https://issues.apache.org/jira/browse/AIRAVATA-2876?page=com.atlassian.jira.plugin.system.issuetabpanels:comment-tabpanel=16623957#comment-16623957 ] ASF subversion and git services commented on AIRAVATA-2876: --- Commit b176d64fae8e69a95a1ca65d2ac19d6709736ea6 in airavata-django-portal's branch refs/heads/master from [~marcuschristie] [ https://gitbox.apache.org/repos/asf?p=airavata-django-portal.git;h=b176d64 ] AIRAVATA-2876 Display success message when application saved > Django: Application Editor (Module/Interface/Deployments) > - > > Key: AIRAVATA-2876 > URL: https://issues.apache.org/jira/browse/AIRAVATA-2876 > Project: Airavata > Issue Type: Story >Reporter: Marcus Christie >Assignee: Marcus Christie >Priority: Major > > TODO > * [x] Guard against unloading browser page when there are unsaved changes > * [x] Only allow admins to edit applications and interfaces (need to guard > this on the backend as well) > * [x] Use normal sharing rules to control who can edit a deployment > * [ ] white background for application editor (custom background color based > on current route?) > * [ ] enum selector component would be generally useful > * [x] ordered list serializer field that orders output by a numeric field (on > read) and updates that numeric field (on write) > * [x] CommandObjects editor and SetEnvPaths editor > * [ ] transitions on input and output fields? (we now have synthetic keys for > them) > * [ ] Do we really need the Vuex store? Maybe just have > ApplicationEditorContainer handle this logic in a simpler way > * [x] load a list of all application modules instead of only "accessible" > modules > * [x] fix setting id when saving module, interface, etc. > (registry-refactoring regression) > * [x] delete application > * [x] add sharing button to app deployment editor > * [x] deployments aren't listed if there is no GroupResourceProfile for that > compute resource. Maybe only allow creating a deployment for compute > resources in GroupResourceProfiles? Or list deployments irrespective of > GroupResourceProfile? -- This message was sent by Atlassian JIRA (v7.6.3#76005)
[jira] [Resolved] (AIRAVATA-2750) Helix Participant is not picking up tasks after a restart
[
https://issues.apache.org/jira/browse/AIRAVATA-2750?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel
]
Dimuthu Upeksha resolved AIRAVATA-2750.
---
Resolution: Fixed
> Helix Participant is not picking up tasks after a restart
> -
>
> Key: AIRAVATA-2750
> URL: https://issues.apache.org/jira/browse/AIRAVATA-2750
> Project: Airavata
> Issue Type: Bug
> Components: helix implementation
>Reporter: Dimuthu Upeksha
>Assignee: Dimuthu Upeksha
>Priority: Major
>
> Helix Participant was restarted due to an OOM issue then it did not pickup
> any task. By changing the participant name fixed that. Controller log
>
> 2018-04-11 19:17:41,850 [GenericHelixController-event_process] DEBUG
> o.a.helix.task.JobRebalancer - All partitions: [0] taskAssignment:
> \{helixparticipant=[]} excludedInstances: []
> 2018-04-11 19:17:41,850 [GenericHelixController-event_process] DEBUG
> o.a.helix.task.JobRebalancer - Throttle tasks to be assigned to instance
> helixparticipant using limitation: Job Concurrent Task(1), Participant Max
> Task(40). Remaining capacity -8.
> 2018-04-11 19:17:41,859 [GenericHelixController-event_process] DEBUG
> o.a.helix.task.JobRebalancer - Job
> Workflow_of_process_PROCESS_e14813b1-a93b-47c8-9faa-634b3cdf47b7-POST-f9e7f2c1-e3af-4f46-8740-b71289e23270_TASK_70f5baae-6e11-4448-9962-e7a964cdff37
> new assignment []
> 2018-04-11 19:17:41,859 [GenericHelixController-event_process] DEBUG
> o.a.h.c.s.BestPossibleStateCalcStage - Processing
> resource:Workflow_of_process_PROCESS_c3fa99be-557a-4c25-bbb7-d4bada5d0ede-PRE-06933b15-fb89-48b9-8501-3bd4a20a1a5f_TASK_ab90e04f-a4d6-4ead-b81c-f021748f4179
> 2018-04-11 19:17:41,859 [GenericHelixController-event_process] DEBUG
> o.a.h.c.s.BestPossibleStateCalcStage - resource
> Workflow_of_process_PROCESS_c3fa99be-557a-4c25-bbb7-d4bada5d0ede-PRE-06933b15-fb89-48b9-8501-3bd4a20a1a5f_TASK_ab90e04f-a4d6-4ead-b81c-f021748f4179
> use idealStateRebalancer org.apache.helix.task.JobRebalancer
> 2018-04-11 19:17:41,859 [GenericHelixController-event_process] DEBUG
> o.a.helix.task.JobRebalancer - Computer Best Partition for job:
> Workflow_of_process_PROCESS_c3fa99be-557a-4c25-bbb7-d4bada5d0ede-PRE-06933b15-fb89-48b9-8501-3bd4a20a1a5f_TASK_ab90e04f-a4d6-4ead-b81c-f021748f4179
> 2018-04-11 19:17:41,860 [GenericHelixController-event_process] DEBUG
> o.a.helix.task.JobRebalancer - All partitions: [0] taskAssignment:
> \{helixparticipant=[]} excludedInstances: []
> 2018-04-11 19:17:41,861 [GenericHelixController-event_process] DEBUG
> o.a.helix.task.JobRebalancer - Throttle tasks to be assigned to instance
> helixparticipant using limitation: Job Concurrent Task(1), Participant Max
> Task(40). Remaining capacity -8.
> 2018-04-11 19:17:41,871 [GenericHelixController-event_process] DEBUG
> o.a.helix.task.JobRebalancer - Job
> Workflow_of_process_PROCESS_c3fa99be-557a-4c25-bbb7-d4bada5d0ede-PRE-06933b15-fb89-48b9-8501-3bd4a20a1a5f_TASK_ab90e04f-a4d6-4ead-b81c-f021748f4179
> new assignment []
> 2018-04-11 19:17:41,872 [GenericHelixController-event_process] DEBUG
> o.a.h.c.s.BestPossibleStateCalcStage - Processing
> resource:Workflow_of_process_PROCESS_5b71bc64-49f9-4bf5-801d-359dc35f58ef-POST-54334da3-d6b8-4d9f-b956-9fd943290d66_TASK_0f141d85-8633-470e-81bb-5158bf8e2ad9
> 2018-04-11 19:17:41,872 [GenericHelixController-event_process] DEBUG
> o.a.h.c.s.BestPossibleStateCalcStage - resource
> Workflow_of_process_PROCESS_5b71bc64-49f9-4bf5-801d-359dc35f58ef-POST-54334da3-d6b8-4d9f-b956-9fd943290d66_TASK_0f141d85-8633-470e-81bb-5158bf8e2ad9
> use idealStateRebalancer org.apache.helix.task.JobRebalancer
> 2018-04-11 19:17:41,872 [GenericHelixController-event_process] DEBUG
> o.a.helix.task.JobRebalancer - Computer Best Partition for job:
> Workflow_of_process_PROCESS_5b71bc64-49f9-4bf5-801d-359dc35f58ef-POST-54334da3-d6b8-4d9f-b956-9fd943290d66_TASK_0f141d85-8633-470e-81bb-5158bf8e2ad9
> 2018-04-11 19:17:41,873 [GenericHelixController-event_process] DEBUG
> o.a.helix.task.JobRebalancer - All partitions: [0] taskAssignment:
> \{helixparticipant=[]} excludedInstances: []
> 2018-04-11 19:17:41,873 [GenericHelixController-event_process] DEBUG
> o.a.helix.task.JobRebalancer - Throttle tasks to be assigned to instance
> helixparticipant using limitation: Job Concurrent Task(1), Participant Max
> Task(40). Remaining capacity -8.
> 2018-04-11 19:17:41,884 [GenericHelixController-event_process] DEBUG
> o.a.helix.task.JobRebalancer - Job
> Workflow_of_process_PROCESS_5b71bc64-49f9-4bf5-801d-359dc35f58ef-POST-54334da3-d6b8-4d9f-b956-9fd943290d66_TASK_0f141d85-8633-470e-81bb-5158bf8e2ad9
> new assignment []
> 2018-04-11 19:17:41,884 [GenericHelixController-event_process] DEBUG
> o.a.h.c.s.BestPossibleStateCalcStage - Processing
>
[jira] [Closed] (AIRAVATA-2783) Gateway output file (.tar.gz) not existing when staging out but in real it exists in the working directory
[ https://issues.apache.org/jira/browse/AIRAVATA-2783?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Dimuthu Upeksha closed AIRAVATA-2783. - Resolution: Fixed Closed as this is no longer an issue as we are deprecating gfac > Gateway output file (.tar.gz) not existing when staging out but in real it > exists in the working directory > -- > > Key: AIRAVATA-2783 > URL: https://issues.apache.org/jira/browse/AIRAVATA-2783 > Project: Airavata > Issue Type: Bug > Components: GFac >Affects Versions: 0.17 >Reporter: Eroma >Assignee: Dimuthu Upeksha >Priority: Major > Fix For: 0.17 > > > # Once the job is completed and email was sent, job updated with status. > # Output file transfer initiates. > # When tried to transfer .tar.gz getting error [1] > # In real the tar.gz files exists in the working directory and it is brought > back in ARCHIVE. > [1] > 2018-05-07 02:50:25,808 [pool-11-thread-2276] INFO > o.a.a.g.i.t.SCPDataStageTask - Fetching output files for wildcard *.tar.gz > in path > /oasis/scratch/comet/svuser/temp_project/simvascular_workdirs/PROCESS_548730f9-2a6b-4d4a-a6c7-7b1556895c97 > 2018-05-07 02:50:26,196 [pool-11-thread-2276] WARN > o.a.[a.g.impl|http://a.g.impl/].HPCRemoteCluster - No matching file found > for extension: *.tar.gz in the > /oasis/scratch/comet/svuser/temp_project/simvascular_workdirs/PROCESS_548730f9-2a6b-4d4a-a6c7-7b1556895c97 > directory > 2018-05-07 02:50:26,196 [pool-11-thread-2276] INFO > o.a.a.g.i.t.SCPDataStageTask - File names that matched with wildcard > *.tar.gz : [] -- This message was sent by Atlassian JIRA (v7.6.3#76005)
[jira] [Resolved] (AIRAVATA-2786) Job COMPLETED but experiment failed with error message "unknown error occurred when initializing ..... "
[ https://issues.apache.org/jira/browse/AIRAVATA-2786?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Dimuthu Upeksha resolved AIRAVATA-2786. --- Resolution: Fixed > Job COMPLETED but experiment failed with error message "unknown error > occurred when initializing . " > > > Key: AIRAVATA-2786 > URL: https://issues.apache.org/jira/browse/AIRAVATA-2786 > Project: Airavata > Issue Type: Bug >Reporter: Eroma >Assignee: Dimuthu Upeksha >Priority: Major > > Job completed and stderr is stagged out. > But experiment failed with error [1] > > [1] > org.apache.airavata.helix.impl.task.TaskOnFailException: Error Code : > 897327b3-d45c-4f9a-a0c8-4f9a8a323ca0, Task > TASK_7c95f237-5002-4fac-9c5d-c9f5a8ac2c6e failed due to Unknown error while > running task TASK_7c95f237-5002-4fac-9c5d-c9f5a8ac2c6e, Error occurred while > initializing the task TASK_7c95f237-5002-4fac-9c5d-c9f5a8ac2c6e of experiment > Test1-US-Jetstream-iteration:26_8b7fe60e-cd90-498c-83b5-29776c3f0855 at > org.apache.airavata.helix.impl.task.AiravataTask.onFail(AiravataTask.java:102) > at > org.apache.airavata.helix.impl.task.AiravataTask.onRun(AiravataTask.java:313) > at org.apache.airavata.helix.core.AbstractTask.run(AbstractTask.java:82) at > org.apache.helix.task.TaskRunner.run(TaskRunner.java:71) at > java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:511) at > java.util.concurrent.FutureTask.run(FutureTask.java:266) at > java.util.concurrent.ScheduledThreadPoolExecutor$ScheduledFutureTask.access$201(ScheduledThreadPoolExecutor.java:180) > at > java.util.concurrent.ScheduledThreadPoolExecutor$ScheduledFutureTask.run(ScheduledThreadPoolExecutor.java:293) > at > java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1149) > at > java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:624) > at java.lang.Thread.run(Thread.java:748) Caused by: > org.apache.airavata.helix.impl.task.TaskOnFailException: Error occurred while > initializing the task TASK_7c95f237-5002-4fac-9c5d-c9f5a8ac2c6e of experiment > Test1-US-Jetstream-iteration:26_8b7fe60e-cd90-498c-83b5-29776c3f0855 at > org.apache.airavata.helix.impl.task.AiravataTask.loadContext(AiravataTask.java:379) > at > org.apache.airavata.helix.impl.task.AiravataTask.onRun(AiravataTask.java:307) > ... 9 more Caused by: RegistryServiceException(message:Error while retrieving > application interface. More info : > org.apache.airavata.registry.cpi.AppCatalogException: > org.apache.openjpa.persistence.InvalidStateException: Can only perform > operation while a transaction is active.) at > org.apache.airavata.registry.api.RegistryService$getApplicationInterface_result$getApplicationInterface_resultStandardScheme.read(RegistryService.java) > at > org.apache.airavata.registry.api.RegistryService$getApplicationInterface_result$getApplicationInterface_resultStandardScheme.read(RegistryService.java) > at > org.apache.airavata.registry.api.RegistryService$getApplicationInterface_result.read(RegistryService.java) > at org.apache.thrift.TServiceClient.receiveBase(TServiceClient.java:89) at > org.apache.airavata.registry.api.RegistryService$Client.recv_getApplicationInterface(RegistryService.java:4686) > at > org.apache.airavata.registry.api.RegistryService$Client.getApplicationInterface(RegistryService.java:4673) > at > org.apache.airavata.helix.impl.task.TaskContext$TaskContextBuilder.build(TaskContext.java:763) > at > org.apache.airavata.helix.impl.task.AiravataTask.loadContext(AiravataTask.java:374) > ... 10 more -- This message was sent by Atlassian JIRA (v7.6.3#76005)
[jira] [Resolved] (AIRAVATA-2784) Airavata unable to connect with the compute resource, comet.sdsc.edu
[ https://issues.apache.org/jira/browse/AIRAVATA-2784?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Dimuthu Upeksha resolved AIRAVATA-2784. --- Resolution: Fixed > Airavata unable to connect with the compute resource, comet.sdsc.edu > > > Key: AIRAVATA-2784 > URL: https://issues.apache.org/jira/browse/AIRAVATA-2784 > Project: Airavata > Issue Type: Bug > Components: GFac >Affects Versions: 0.17 >Reporter: Eroma >Assignee: Dimuthu Upeksha >Priority: Major > Fix For: 0.17 > > > # When the data staging out task was initialted the host was unreachable. > # Hence the data staging was not carried out. > # Error messages in log [1] > > [1] > 2018-05-07 13:41:31,486 [pool-11-thread-2311] INFO > o.a.a.g.c.context.TaskContext - expId: > AC2_post_25_rtot_TAC_0013_ratio_056_sp_62b8889f-1a9e-4abc-bd71-030839773109, > processId: PROCESS_c91901c1-1d91-4249-88da-a5c0a6245965, taskId: > TASK_26fcbd23-0a58-43fd-a05d-0462f6f23273, type: DATA_STAGING : Task status > changed CREATED -> EXECUTING > 2018-05-07 13:41:31,500 [pool-11-thread-2311] INFO > o.a.airavata.gfac.impl.Factory - Session validation failed, key > :svuser_comet.sdsc.edu_22_f5c9e1fd-acee-43b6-b326-608b18e02aca > 2018-05-07 13:41:31,500 [pool-11-thread-2311] INFO > o.a.airavata.gfac.impl.Factory - Initialize a new SSH session for > :svuser_comet.sdsc.edu_22_f5c9e1fd-acee-43b6-b326-608b18e02aca > 2018-05-07 13:41:34,549 [pool-11-thread-2311] ERROR > o.[a.a.gfac|http://a.a.gfac/].core.GFacException - JSch initialization error > com.jcraft.jsch.JSchException: java.net.NoRouteToHostException: No route to > host (Host unreachable) > 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:537) > at > org.apache.airavata.gfac.impl.task.ArchiveTask.execute(ArchiveTask.java:107) > at > org.apache.airavata.gfac.impl.GFacEngineImpl.executeTask(GFacEngineImpl.java:814) > at > org.apache.airavata.gfac.impl.GFacEngineImpl.outputDataStaging(GFacEngineImpl.java:766) > at > org.apache.airavata.gfac.impl.GFacEngineImpl.executeTaskListFrom(GFacEngineImpl.java:362) > at > org.apache.airavata.gfac.impl.GFacEngineImpl.continueProcess(GFacEngineImpl.java:721) > at > org.apache.airavata.gfac.impl.GFacWorker.continueTaskExecution(GFacWorker.java:196) > at org.apache.airavata.gfac.impl.GFacWorker.run(GFacWorker.java:96) > 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.NoRouteToHostException: No route to host (Host > unreachable) > at java.net.PlainSocketImpl.socketConnect(Native Method) > at > [java.net|http://java.net/].AbstractPlainSocketImpl.doConnect(AbstractPlainSocketImpl.java:350) > /AC2_post_25_rtot_TAC_0013_ratio_056_sp_62b8889f-1a9e-4abc-bd71-030839773109 > at > org.apache.airavata.gfac.impl.GFacEngineImpl.executeTask(GFacEngineImpl.java:814) > at > org.apache.airavata.gfac.impl.GFacEngineImpl.outputDataStaging(GFacEngineImpl.java:766) > at > org.apache.airavata.gfac.impl.GFacEngineImpl.executeTaskListFrom(GFacEngineImpl.java:362) > at > org.apache.airavata.gfac.impl.GFacEngineImpl.continueProcess(GFacEngineImpl.java:721) > at > org.apache.airavata.gfac.impl.GFacWorker.continueTaskExecution(GFacWorker.java:196) > at org.apache.airavata.gfac.impl.GFacWorker.run(GFacWorker.java:96) > 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: java.net.NoRouteToHostException: No > route to host (Host unreachable) > 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:537) > ... 10 common frames omitted > Caused by: java.net.NoRouteToHostException: No route to host (Host > unreachable) > at java.net.PlainSocketImpl.socketConnect(Native Method) > at > [java.net|http://java.net/].AbstractPlainSocketImpl.doConnect(AbstractPlainSocketImpl.java:350) > at >
[jira] [Resolved] (AIRAVATA-2789) Experiment failed with unexpected error in opening a session channel
[ https://issues.apache.org/jira/browse/AIRAVATA-2789?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Dimuthu Upeksha resolved AIRAVATA-2789. --- Resolution: Fixed > Experiment failed with unexpected error in opening a session channel > > > Key: AIRAVATA-2789 > URL: https://issues.apache.org/jira/browse/AIRAVATA-2789 > Project: Airavata > Issue Type: Bug > Components: helix implementation >Affects Versions: 0.17 > Environment: https://staging.ultrascan.scigap.org/ >Reporter: Eroma >Assignee: Dimuthu Upeksha >Priority: Major > Fix For: 0.17 > > > Experiment failed with [1]exp ID: > |Test1-US-LoneStar5-37_dbcb9fd4-4390-4163-a6c8-2bb92de95ed0| > org.apache.airavata.helix.impl.task.TaskOnFailException: Error Code : > 712f954d-8477-4a91-b71e-ad6bd6df6537, Task > TASK_4fff49ba-22e5-4975-b920-3c6756ddb8b8 failed due to Task failed due to > unexpected issue, Opening `session` channel failed: open failed at > org.apache.airavata.helix.impl.task.AiravataTask.onFail(AiravataTask.java:102) > at > org.apache.airavata.helix.impl.task.submission.DefaultJobSubmissionTask.onRun(DefaultJobSubmissionTask.java:221) > at > org.apache.airavata.helix.impl.task.AiravataTask.onRun(AiravataTask.java:311) > at org.apache.airavata.helix.core.AbstractTask.run(AbstractTask.java:82) at > org.apache.helix.task.TaskRunner.run(TaskRunner.java:71) at > java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:511) at > java.util.concurrent.FutureTask.run(FutureTask.java:266) at > java.util.concurrent.ScheduledThreadPoolExecutor$ScheduledFutureTask.access$201(ScheduledThreadPoolExecutor.java:180) > at > java.util.concurrent.ScheduledThreadPoolExecutor$ScheduledFutureTask.run(ScheduledThreadPoolExecutor.java:293) > at > java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1149) > at > java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:624) > at java.lang.Thread.run(Thread.java:748) Caused by: > org.apache.airavata.agents.api.AgentException: Opening `session` channel > failed: open failed at > org.apache.airavata.helix.adaptor.SSHJAgentAdaptor.copyFileTo(SSHJAgentAdaptor.java:155) > at > org.apache.airavata.helix.impl.task.submission.JobSubmissionTask.submitBatchJob(JobSubmissionTask.java:80) > at > org.apache.airavata.helix.impl.task.submission.DefaultJobSubmissionTask.onRun(DefaultJobSubmissionTask.java:81) > ... 10 more Caused by: Opening `session` channel failed: open failed at > net.schmizz.sshj.connection.channel.direct.AbstractDirectChannel.gotOpenFailure(AbstractDirectChannel.java:74) > at > net.schmizz.sshj.connection.channel.direct.AbstractDirectChannel.gotUnknown(AbstractDirectChannel.java:99) > at > net.schmizz.sshj.connection.channel.AbstractChannel.handle(AbstractChannel.java:203) > at > net.schmizz.sshj.connection.ConnectionImpl.handle(ConnectionImpl.java:130) at > net.schmizz.sshj.transport.TransportImpl.handle(TransportImpl.java:500) at > net.schmizz.sshj.transport.Decoder.decode(Decoder.java:102) at > net.schmizz.sshj.transport.Decoder.received(Decoder.java:170) at > net.schmizz.sshj.transport.Reader.run(Reader.java:59) -- This message was sent by Atlassian JIRA (v7.6.3#76005)
[jira] [Resolved] (AIRAVATA-2790) File uploading error due to session channel opening error occurred!
[ https://issues.apache.org/jira/browse/AIRAVATA-2790?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Dimuthu Upeksha resolved AIRAVATA-2790. --- Resolution: Fixed > File uploading error due to session channel opening error occurred! > --- > > Key: AIRAVATA-2790 > URL: https://issues.apache.org/jira/browse/AIRAVATA-2790 > Project: Airavata > Issue Type: Bug > Components: helix implementation >Affects Versions: 0.17 >Reporter: Eroma >Assignee: Dimuthu Upeksha >Priority: Major > Fix For: 0.17 > > > Intermittent error [1] when launching an experiment at file uploading. exp > ID: > |Test1-US-LoneStar5-38_d5273cc4-e4e2-447c-8445-474c00b599ba| > > [1] > org.apache.airavata.helix.impl.task.TaskOnFailException: Error Code : > 63e7ddd0-07d2-4eb2-814e-31f3f8a36c6c, Task > TASK_b44a6620-f1f8-4bc7-bd15-286daa41bcf1 failed due to Failed uploading the > input file to > /scratch/01623/us3/airavata-workingdirs/PROCESS_faad2856-46b2-4dcd-8cfd-8b59fa55343e/ > from local path > /tmp/PROCESS_faad2856-46b2-4dcd-8cfd-8b59fa55343e/temp_inputs/hpcinput-localhost-uslims3_cauma3d-00950.tar, > Opening `session` channel failed: open failed at > org.apache.airavata.helix.impl.task.AiravataTask.onFail(AiravataTask.java:102) > at > org.apache.airavata.helix.impl.task.staging.InputDataStagingTask.onRun(InputDataStagingTask.java:137) > at > org.apache.airavata.helix.impl.task.AiravataTask.onRun(AiravataTask.java:311) > at org.apache.airavata.helix.core.AbstractTask.run(AbstractTask.java:82) at > org.apache.helix.task.TaskRunner.run(TaskRunner.java:71) at > java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:511) at > java.util.concurrent.FutureTask.run(FutureTask.java:266) at > java.util.concurrent.ScheduledThreadPoolExecutor$ScheduledFutureTask.access$201(ScheduledThreadPoolExecutor.java:180) > at > java.util.concurrent.ScheduledThreadPoolExecutor$ScheduledFutureTask.run(ScheduledThreadPoolExecutor.java:293) > at > java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1149) > at > java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:624) > at java.lang.Thread.run(Thread.java:748) Caused by: > org.apache.airavata.agents.api.AgentException: Opening `session` channel > failed: open failed at > org.apache.airavata.helix.adaptor.SSHJAgentAdaptor.copyFileTo(SSHJAgentAdaptor.java:155) > at > org.apache.airavata.helix.impl.task.staging.InputDataStagingTask.onRun(InputDataStagingTask.java:119) > ... 10 more Caused by: Opening `session` channel failed: open failed at > net.schmizz.sshj.connection.channel.direct.AbstractDirectChannel.gotOpenFailure(AbstractDirectChannel.java:74) > at > net.schmizz.sshj.connection.channel.direct.AbstractDirectChannel.gotUnknown(AbstractDirectChannel.java:99) > at > net.schmizz.sshj.connection.channel.AbstractChannel.handle(AbstractChannel.java:203) > at > net.schmizz.sshj.connection.ConnectionImpl.handle(ConnectionImpl.java:130) at > net.schmizz.sshj.transport.TransportImpl.handle(TransportImpl.java:500) at > net.schmizz.sshj.transport.Decoder.decode(Decoder.java:102) at > net.schmizz.sshj.transport.Decoder.received(Decoder.java:170) at > net.schmizz.sshj.transport.Reader.run(Reader.java:59) -- This message was sent by Atlassian JIRA (v7.6.3#76005)
[jira] [Resolved] (AIRAVATA-2792) Staging seagrid fails to submit a job
[ https://issues.apache.org/jira/browse/AIRAVATA-2792?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Dimuthu Upeksha resolved AIRAVATA-2792. --- Resolution: Fixed > Staging seagrid fails to submit a job > - > > Key: AIRAVATA-2792 > URL: https://issues.apache.org/jira/browse/AIRAVATA-2792 > Project: Airavata > Issue Type: Bug > Components: helix implementation >Reporter: Sudhakar Pamidighantam >Assignee: Dimuthu Upeksha >Priority: Major > > org.apache.airavata.helix.impl.task.TaskOnFailException: Error Code : > f32162d3-9409-4ba9-92c3-aee14c8e5fb4, Task > TASK_5bf0a74e-6d0a-48bf-87d1-1af985bd90fc failed due to Failed to setup > environment of task TASK_5bf0a74e-6d0a-48bf-87d1-1af985bd90fc, null at > org.apache.airavata.helix.impl.task.AiravataTask.onFail(AiravataTask.java:102) > at > org.apache.airavata.helix.impl.task.env.EnvSetupTask.onRun(EnvSetupTask.java:53) > at > org.apache.airavata.helix.impl.task.AiravataTask.onRun(AiravataTask.java:311) > at org.apache.airavata.helix.core.AbstractTask.run(AbstractTask.java:82) at > org.apache.helix.task.TaskRunner.run(TaskRunner.java:71) at > java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:511) at > java.util.concurrent.FutureTask.run(FutureTask.java:266) at > java.util.concurrent.ScheduledThreadPoolExecutor$ScheduledFutureTask.access$201(ScheduledThreadPoolExecutor.java:180) > at > java.util.concurrent.ScheduledThreadPoolExecutor$ScheduledFutureTask.run(ScheduledThreadPoolExecutor.java:293) > at > java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1149) > at > java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:624) > at java.lang.Thread.run(Thread.java:748) Caused by: > java.lang.NullPointerException at > org.apache.airavata.helix.impl.task.TaskContext.getComputeResourceCredentialToken(TaskContext.java:422) > at > org.apache.airavata.helix.impl.task.env.EnvSetupTask.onRun(EnvSetupTask.java:45) > ... 10 more -- This message was sent by Atlassian JIRA (v7.6.3#76005)
[jira] [Commented] (AIRAVATA-2826) Helix participant server was stopped and started while experiments are launched and job submissions to Jetstream cluster failed
[ https://issues.apache.org/jira/browse/AIRAVATA-2826?page=com.atlassian.jira.plugin.system.issuetabpanels:comment-tabpanel=16623942#comment-16623942 ] Dimuthu Upeksha commented on AIRAVATA-2826: --- Added job submission retrying logic * [|https://issues.apache.org/jira/secure/AddComment!default.jspa?id=13166404] > Helix participant server was stopped and started while experiments are > launched and job submissions to Jetstream cluster failed > --- > > Key: AIRAVATA-2826 > URL: https://issues.apache.org/jira/browse/AIRAVATA-2826 > Project: Airavata > Issue Type: Bug > Components: helix implementation >Affects Versions: 0.18 > Environment: https://staging.seagrid.org/ >Reporter: Eroma >Assignee: Dimuthu Upeksha >Priority: Major > Fix For: 0.18 > > > # Experiments started launching while helix participant stopped and started. > # When the helix participant was started particularly jobs to Jetstream > failed. > # Job submission failed due to environment set up failed in jetstream with > error [1] > [1] > org.apache.airavata.helix.impl.task.TaskOnFailException: Error Code : > 658d46e9-b08b-46c0-9701-4bf5eeb23134, Task > TASK_f4e3eccf-3e03-4d34-9cf0-7028efd09a40 failed due to Failed to setup > environment of task TASK_f4e3eccf-3e03-4d34-9cf0-7028efd09a40, > net.schmizz.sshj.connection.ConnectionException: [CONNECTION_LOST] Did not > receive any keep-alive response for 25 seconds at > org.apache.airavata.helix.impl.task.AiravataTask.onFail(AiravataTask.java:102) > at > org.apache.airavata.helix.impl.task.env.EnvSetupTask.onRun(EnvSetupTask.java:55) > at > org.apache.airavata.helix.impl.task.AiravataTask.onRun(AiravataTask.java:311) > at org.apache.airavata.helix.core.AbstractTask.run(AbstractTask.java:90) at > org.apache.helix.task.TaskRunner.run(TaskRunner.java:71) at > java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:511) at > java.util.concurrent.FutureTask.run(FutureTask.java:266) at > java.util.concurrent.ScheduledThreadPoolExecutor$ScheduledFutureTask.access$201(ScheduledThreadPoolExecutor.java:180) > at > java.util.concurrent.ScheduledThreadPoolExecutor$ScheduledFutureTask.run(ScheduledThreadPoolExecutor.java:293) > at > java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1149) > at > java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:624) > at java.lang.Thread.run(Thread.java:748) Caused by: > org.apache.airavata.agents.api.AgentException: > net.schmizz.sshj.connection.ConnectionException: [CONNECTION_LOST] Did not > receive any keep-alive response for 25 seconds at > org.apache.airavata.helix.adaptor.SSHJAgentAdaptor.createDirectory(SSHJAgentAdaptor.java:146) > at > org.apache.airavata.helix.impl.task.env.EnvSetupTask.onRun(EnvSetupTask.java:51) > ... 10 more Caused by: net.schmizz.sshj.connection.ConnectionException: > [CONNECTION_LOST] Did not receive any keep-alive response for 25 seconds at > net.schmizz.keepalive.KeepAliveRunner.checkMaxReached(KeepAliveRunner.java:64) > at > net.schmizz.keepalive.KeepAliveRunner.doKeepAlive(KeepAliveRunner.java:56) at > net.schmizz.keepalive.KeepAlive.run(KeepAlive.java:63) -- This message was sent by Atlassian JIRA (v7.6.3#76005)
[jira] [Resolved] (AIRAVATA-2826) Helix participant server was stopped and started while experiments are launched and job submissions to Jetstream cluster failed
[ https://issues.apache.org/jira/browse/AIRAVATA-2826?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Dimuthu Upeksha resolved AIRAVATA-2826. --- Resolution: Fixed > Helix participant server was stopped and started while experiments are > launched and job submissions to Jetstream cluster failed > --- > > Key: AIRAVATA-2826 > URL: https://issues.apache.org/jira/browse/AIRAVATA-2826 > Project: Airavata > Issue Type: Bug > Components: helix implementation >Affects Versions: 0.18 > Environment: https://staging.seagrid.org/ >Reporter: Eroma >Assignee: Dimuthu Upeksha >Priority: Major > Fix For: 0.18 > > > # Experiments started launching while helix participant stopped and started. > # When the helix participant was started particularly jobs to Jetstream > failed. > # Job submission failed due to environment set up failed in jetstream with > error [1] > [1] > org.apache.airavata.helix.impl.task.TaskOnFailException: Error Code : > 658d46e9-b08b-46c0-9701-4bf5eeb23134, Task > TASK_f4e3eccf-3e03-4d34-9cf0-7028efd09a40 failed due to Failed to setup > environment of task TASK_f4e3eccf-3e03-4d34-9cf0-7028efd09a40, > net.schmizz.sshj.connection.ConnectionException: [CONNECTION_LOST] Did not > receive any keep-alive response for 25 seconds at > org.apache.airavata.helix.impl.task.AiravataTask.onFail(AiravataTask.java:102) > at > org.apache.airavata.helix.impl.task.env.EnvSetupTask.onRun(EnvSetupTask.java:55) > at > org.apache.airavata.helix.impl.task.AiravataTask.onRun(AiravataTask.java:311) > at org.apache.airavata.helix.core.AbstractTask.run(AbstractTask.java:90) at > org.apache.helix.task.TaskRunner.run(TaskRunner.java:71) at > java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:511) at > java.util.concurrent.FutureTask.run(FutureTask.java:266) at > java.util.concurrent.ScheduledThreadPoolExecutor$ScheduledFutureTask.access$201(ScheduledThreadPoolExecutor.java:180) > at > java.util.concurrent.ScheduledThreadPoolExecutor$ScheduledFutureTask.run(ScheduledThreadPoolExecutor.java:293) > at > java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1149) > at > java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:624) > at java.lang.Thread.run(Thread.java:748) Caused by: > org.apache.airavata.agents.api.AgentException: > net.schmizz.sshj.connection.ConnectionException: [CONNECTION_LOST] Did not > receive any keep-alive response for 25 seconds at > org.apache.airavata.helix.adaptor.SSHJAgentAdaptor.createDirectory(SSHJAgentAdaptor.java:146) > at > org.apache.airavata.helix.impl.task.env.EnvSetupTask.onRun(EnvSetupTask.java:51) > ... 10 more Caused by: net.schmizz.sshj.connection.ConnectionException: > [CONNECTION_LOST] Did not receive any keep-alive response for 25 seconds at > net.schmizz.keepalive.KeepAliveRunner.checkMaxReached(KeepAliveRunner.java:64) > at > net.schmizz.keepalive.KeepAliveRunner.doKeepAlive(KeepAliveRunner.java:56) at > net.schmizz.keepalive.KeepAlive.run(KeepAlive.java:63) -- This message was sent by Atlassian JIRA (v7.6.3#76005)
[jira] [Resolved] (AIRAVATA-2831) Experiment FAILED with an error on output file staging! But the file referring in the error is actually downloaded and available in storage.
[ https://issues.apache.org/jira/browse/AIRAVATA-2831?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Dimuthu Upeksha resolved AIRAVATA-2831. --- Resolution: Fixed This should be fixed after data staging retrying implementation > Experiment FAILED with an error on output file staging! But the file > referring in the error is actually downloaded and available in storage. > > > Key: AIRAVATA-2831 > URL: https://issues.apache.org/jira/browse/AIRAVATA-2831 > Project: Airavata > Issue Type: Bug > Components: helix implementation >Affects Versions: 0.18 > Environment: https://staging.seagrid.org/ >Reporter: Eroma >Assignee: Dimuthu Upeksha >Priority: Major > Fix For: 0.18 > > > # When experiments were launched and jobs were submitted bot real time > monitoring and email monitoring was stopped. > # Started realtime monitoring and then the job statuses got updated > correctly. > # Then stopped the realtime monitoring and started email monitoing. > # Job statuses got updated correctly but experiment status of some are > FAILED with error [1] > # But the file is already transfered. > # exp ID: SLM005-QEspresso-JS:2_1fec2375-945b-4b21-8157-5e91b1391312 and job > iD: 237.torque-server > [1] > |org.apache.airavata.helix.impl.task.TaskOnFailException: Error Code : > 01ee4646-2139-40b8-840e-348e37b1823f, Task > TASK_f5726ea4-638f-4c41-9904-0b3c766fcaee failed due to Error while checking > the file > /N/SEAGrid_scratch//PROCESS_f0192239-787a-4f8f-b63e-7cb45a837f4a/Quantum_Espresso.stdout > existence, net.schmizz.sshj.connection.ConnectionException: > [CONNECTION_LOST] Did not receive any keep-alive response for 25 seconds at > org.apache.airavata.helix.impl.task.AiravataTask.onFail(AiravataTask.java:102) > at > org.apache.airavata.helix.impl.task.staging.OutputDataStagingTask.onRun(OutputDataStagingTask.java:187) > at > org.apache.airavata.helix.impl.task.AiravataTask.onRun(AiravataTask.java:311) > at org.apache.airavata.helix.core.AbstractTask.run(AbstractTask.java:90) at > org.apache.helix.task.TaskRunner.run(TaskRunner.java:71) at > java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:511) at > java.util.concurrent.FutureTask.run(FutureTask.java:266) at > java.util.concurrent.ScheduledThreadPoolExecutor$ScheduledFutureTask.access$201(ScheduledThreadPoolExecutor.java:180) > at > java.util.concurrent.ScheduledThreadPoolExecutor$ScheduledFutureTask.run(ScheduledThreadPoolExecutor.java:293) > at > java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1149) > at > java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:624) > at java.lang.Thread.run(Thread.java:748) Caused by: > org.apache.airavata.agents.api.AgentException: > net.schmizz.sshj.connection.ConnectionException: [CONNECTION_LOST] Did not > receive any keep-alive response for 25 seconds at > org.apache.airavata.helix.adaptor.SSHJAgentAdaptor.doesFileExist(SSHJAgentAdaptor.java:183) > at > org.apache.airavata.helix.impl.task.staging.DataStagingTask.transferFileToStorage(DataStagingTask.java:141) > at > org.apache.airavata.helix.impl.task.staging.OutputDataStagingTask.onRun(OutputDataStagingTask.java:172) > ... 10 more Caused by: net.schmizz.sshj.connection.ConnectionException: > [CONNECTION_LOST] Did not receive any keep-alive response for 25 seconds at > net.schmizz.keepalive.KeepAliveRunner.checkMaxReached(KeepAliveRunner.java:64) > at > net.schmizz.keepalive.KeepAliveRunner.doKeepAlive(KeepAliveRunner.java:56) at > net.schmizz.keepalive.KeepAlive.run(KeepAlive.java:63)| -- This message was sent by Atlassian JIRA (v7.6.3#76005)
[jira] [Resolved] (AIRAVATA-2833) Several experiments failed at various stages of job submission due to connection lost
[ https://issues.apache.org/jira/browse/AIRAVATA-2833?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Dimuthu Upeksha resolved AIRAVATA-2833. --- Resolution: Fixed Added job submission retrying logic > Several experiments failed at various stages of job submission due to > connection lost > - > > Key: AIRAVATA-2833 > URL: https://issues.apache.org/jira/browse/AIRAVATA-2833 > Project: Airavata > Issue Type: Bug > Components: helix implementation >Affects Versions: 0.18 > Environment: https://staging.seagrid.org/ >Reporter: Eroma >Assignee: Dimuthu Upeksha >Priority: Major > Fix For: 0.18 > > > While submitting a batch of jobs, several failed in a single cluster due to > connection lost. > Experiment has failed at uploading input file, output transfer and creating > archive.tar. Error in log [1]. Anything we could do here? Try again? resubmit > the task? > > > Exi ID: > SLM001-QEspresso-JS:2_d01e50dd-74fe-434a-87b3-e4668b827da5 > SLM001-QEspresso-JS:1_b29c6476-8944-4f6d-8946-b2e9f20b2acf > SLM001-QEspresso-JS:0_cd3d980d-017e-4ebe-91f7-85d1157feb94 > > [1] > org.apache.airavata.helix.impl.task.TaskOnFailException: Error Code : > cc1c8295-e5ec-44bf-b705-eceddfca3b1a, Task > TASK_b6ea333e-7468-4221-8b87-09050d7d053c failed due to Failed uploading the > input file to > /N/SEAGrid_scratch/PROCESS_1694a674-3dd7-4693-868e-b7fd2b8d/ from local > path > /tmp/PROCESS_1694a674-3dd7-4693-868e-b7fd2b8d/temp_inputs/Al.sample1.in, > net.schmizz.sshj.connection.ConnectionException: [CONNECTION_LOST] Did not > receive any keep-alive response for 25 seconds at > org.apache.airavata.helix.impl.task.AiravataTask.onFail(AiravataTask.java:102) > at > org.apache.airavata.helix.impl.task.staging.InputDataStagingTask.onRun(InputDataStagingTask.java:137) > at > org.apache.airavata.helix.impl.task.AiravataTask.onRun(AiravataTask.java:311) > at org.apache.airavata.helix.core.AbstractTask.run(AbstractTask.java:90) at > org.apache.helix.task.TaskRunner.run(TaskRunner.java:71) at > java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:511) at > java.util.concurrent.FutureTask.run(FutureTask.java:266) at > java.util.concurrent.ScheduledThreadPoolExecutor$ScheduledFutureTask.access$201(ScheduledThreadPoolExecutor.java:180) > at > java.util.concurrent.ScheduledThreadPoolExecutor$ScheduledFutureTask.run(ScheduledThreadPoolExecutor.java:293) > at > java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1149) > at > java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:624) > at java.lang.Thread.run(Thread.java:748) Caused by: > org.apache.airavata.agents.api.AgentException: > net.schmizz.sshj.connection.ConnectionException: [CONNECTION_LOST] Did not > receive any keep-alive response for 25 seconds at > org.apache.airavata.helix.adaptor.SSHJAgentAdaptor.copyFileTo(SSHJAgentAdaptor.java:155) > at > org.apache.airavata.helix.impl.task.staging.InputDataStagingTask.onRun(InputDataStagingTask.java:119) > ... 10 more Caused by: net.schmizz.sshj.connection.ConnectionException: > [CONNECTION_LOST] Did not receive any keep-alive response for 25 seconds at > net.schmizz.keepalive.KeepAliveRunner.checkMaxReached(KeepAliveRunner.java:64) > at > net.schmizz.keepalive.KeepAliveRunner.doKeepAlive(KeepAliveRunner.java:56) at > net.schmizz.keepalive.KeepAlive.run(KeepAlive.java:63) -- This message was sent by Atlassian JIRA (v7.6.3#76005)
