[jira] [Commented] (AIRAVATA-2625) Derive and present Text outputs in Experiment summary
[ https://issues.apache.org/jira/browse/AIRAVATA-2625?page=com.atlassian.jira.plugin.system.issuetabpanels:comment-tabpanel&focusedCommentId=16679338#comment-16679338 ] ASF subversion and git services commented on AIRAVATA-2625: --- Commit 2d84196b073e4f17ff1e5375215efb9f12aa3f90 in airavata's branch refs/heads/master from Dimuthu [ https://gitbox.apache.org/repos/asf?p=airavata.git;h=2d84196 ] Merge pull request #184 from DImuthuUpe/AIRAVATA-2625-FIX Fixing Airavata 2625 : Derive and present Text outputs in Experiment summary > Derive and present Text outputs in Experiment summary > - > > Key: AIRAVATA-2625 > URL: https://issues.apache.org/jira/browse/AIRAVATA-2625 > Project: Airavata > Issue Type: Bug > Components: Airavata System >Affects Versions: 0.18 >Reporter: Eroma >Assignee: Dimuthu Upeksha >Priority: Major > > Currently the available application outputs are in the form of stdout, stderr > and URI (files). Going forward to have text (String, Integer, Float) outputs > directly in the experiment summary. > These text outputs to be displayed as key+value pairs and when defining > should be defined a file to derive from, e.g. stdout > At a given time from a single file one or many of these key+value pairs could > be derived. Also gateway admin can define multiple files to derive multiple > of these values. > These would be displayed to user in experiment summary and in detailed > experiment summary in admin dashboard experiment statistics. > These should also be displayed to any other gateway user it is shared with. -- This message was sent by Atlassian JIRA (v7.6.3#76005)
[jira] [Commented] (AIRAVATA-2625) Derive and present Text outputs in Experiment summary
[ https://issues.apache.org/jira/browse/AIRAVATA-2625?page=com.atlassian.jira.plugin.system.issuetabpanels:comment-tabpanel&focusedCommentId=16679336#comment-16679336 ] ASF subversion and git services commented on AIRAVATA-2625: --- Commit 9c4f74e710e134fa8a74e67d4eb9838e7a4b86f5 in airavata's branch refs/heads/master from dimuthu [ https://gitbox.apache.org/repos/asf?p=airavata.git;h=9c4f74e ] Merge branch 'master' of https://github.com/apache/airavata into AIRAVATA-2625-FIX # Conflicts: # modules/gfac/gfac-impl/src/main/java/org/apache/airavata/gfac/impl/task/SCPDataStageTask.java > Derive and present Text outputs in Experiment summary > - > > Key: AIRAVATA-2625 > URL: https://issues.apache.org/jira/browse/AIRAVATA-2625 > Project: Airavata > Issue Type: Bug > Components: Airavata System >Affects Versions: 0.18 >Reporter: Eroma >Assignee: Dimuthu Upeksha >Priority: Major > > Currently the available application outputs are in the form of stdout, stderr > and URI (files). Going forward to have text (String, Integer, Float) outputs > directly in the experiment summary. > These text outputs to be displayed as key+value pairs and when defining > should be defined a file to derive from, e.g. stdout > At a given time from a single file one or many of these key+value pairs could > be derived. Also gateway admin can define multiple files to derive multiple > of these values. > These would be displayed to user in experiment summary and in detailed > experiment summary in admin dashboard experiment statistics. > These should also be displayed to any other gateway user it is shared with. -- This message was sent by Atlassian JIRA (v7.6.3#76005)
[jira] [Commented] (AIRAVATA-2625) Derive and present Text outputs in Experiment summary
[ https://issues.apache.org/jira/browse/AIRAVATA-2625?page=com.atlassian.jira.plugin.system.issuetabpanels:comment-tabpanel&focusedCommentId=16679337#comment-16679337 ] ASF subversion and git services commented on AIRAVATA-2625: --- Commit 356049e5691817559d78d664a3d37c34475faf4e in airavata's branch refs/heads/master from dimuthu [ https://gitbox.apache.org/repos/asf?p=airavata.git;h=356049e ] Merge branch 'master' into AIRAVATA-2625-FIX > Derive and present Text outputs in Experiment summary > - > > Key: AIRAVATA-2625 > URL: https://issues.apache.org/jira/browse/AIRAVATA-2625 > Project: Airavata > Issue Type: Bug > Components: Airavata System >Affects Versions: 0.18 >Reporter: Eroma >Assignee: Dimuthu Upeksha >Priority: Major > > Currently the available application outputs are in the form of stdout, stderr > and URI (files). Going forward to have text (String, Integer, Float) outputs > directly in the experiment summary. > These text outputs to be displayed as key+value pairs and when defining > should be defined a file to derive from, e.g. stdout > At a given time from a single file one or many of these key+value pairs could > be derived. Also gateway admin can define multiple files to derive multiple > of these values. > These would be displayed to user in experiment summary and in detailed > experiment summary in admin dashboard experiment statistics. > These should also be displayed to any other gateway user it is shared with. -- This message was sent by Atlassian JIRA (v7.6.3#76005)
[jira] [Commented] (AIRAVATA-2625) Derive and present Text outputs in Experiment summary
[ https://issues.apache.org/jira/browse/AIRAVATA-2625?page=com.atlassian.jira.plugin.system.issuetabpanels:comment-tabpanel&focusedCommentId=16551258#comment-16551258 ] Eroma commented on AIRAVATA-2625: - Ran the test cases for the new implementation in [http://149.165.168.200:8008|http://149.165.168.200:8008/] # Add a filed from an existing output (QauntumEspresso.out) file. The complete line which start from the added text is derived and displayed in the experiment summary. (e.g.Bravis: bravais-lattice index = 2.) - PASS # Add multiple fields from the same file to be read from the output file. Each text to derive need to be added as separate outputs in the application interface. Added multiple fields will be displayed in the experiment summary. – PASS # Add multiple fields from different files to read and display in experiment summary. - # Add a text to derive from a single file but it appears in multiple places in the file. All the lines the particular text appears will be displayed. – PASS # Add a text which is in middle of a line as the reading text from one of the input files. – The complete line which the text belong will be derived and displayed. Not staring from the text given and forward but the complete line it appears will be displayed. – PASS # Add a new application (Gaussian) in to application catalog and launch a job. This job does not have text outputs defined to be read from files. Job got launched and submitted successfully. Job completed successfully and all defined outputs transferred to the gateway – PASS # Add a text output to be read from defined file (gaussian.log) in the above new application. Clone the above experiment and submit a new experiment. The new experiment and job completed. The experiment summary displays the defined text outputs. The give text appears in multiple times in the file and all those lines are derived and displayed – PASS # NOTE: If you want to derive multiple text from single file, provide the text separating with commas and no spaces. # Tested in both PBS and SLURM machines. - PASS # Try to read from .tar file. Give a string from a file in the tar. This will not work. In order to read a direct file need to be provided. No errors, exceptions thrown. Simply no text will be derived and displayed. Expected behavior. - PASS > Derive and present Text outputs in Experiment summary > - > > Key: AIRAVATA-2625 > URL: https://issues.apache.org/jira/browse/AIRAVATA-2625 > Project: Airavata > Issue Type: Bug > Components: Airavata System >Affects Versions: 0.18 >Reporter: Eroma >Assignee: Dimuthu Upeksha >Priority: Major > > Currently the available application outputs are in the form of stdout, stderr > and URI (files). Going forward to have text (String, Integer, Float) outputs > directly in the experiment summary. > These text outputs to be displayed as key+value pairs and when defining > should be defined a file to derive from, e.g. stdout > At a given time from a single file one or many of these key+value pairs could > be derived. Also gateway admin can define multiple files to derive multiple > of these values. > These would be displayed to user in experiment summary and in detailed > experiment summary in admin dashboard experiment statistics. > These should also be displayed to any other gateway user it is shared with. -- This message was sent by Atlassian JIRA (v7.6.3#76005)
[jira] [Commented] (AIRAVATA-2625) Derive and present Text outputs in Experiment summary
[ https://issues.apache.org/jira/browse/AIRAVATA-2625?page=com.atlassian.jira.plugin.system.issuetabpanels:comment-tabpanel&focusedCommentId=16549817#comment-16549817 ] Eroma commented on AIRAVATA-2625: - Update to the above test cases. The implementation was changed and with the latest implementation # Value: Should have the name of the file read from. File name should be exactly how it appears in the experiment summary. # Search Query: This field will have the text to read from the file. Any line or lines starting from the text filled here will be displayed in the experiment summary. For multiples comma is used to separate. > Derive and present Text outputs in Experiment summary > - > > Key: AIRAVATA-2625 > URL: https://issues.apache.org/jira/browse/AIRAVATA-2625 > Project: Airavata > Issue Type: Bug > Components: Airavata System >Affects Versions: 0.18 >Reporter: Eroma >Assignee: Dimuthu Upeksha >Priority: Major > > Currently the available application outputs are in the form of stdout, stderr > and URI (files). Going forward to have text (String, Integer, Float) outputs > directly in the experiment summary. > These text outputs to be displayed as key+value pairs and when defining > should be defined a file to derive from, e.g. stdout > At a given time from a single file one or many of these key+value pairs could > be derived. Also gateway admin can define multiple files to derive multiple > of these values. > These would be displayed to user in experiment summary and in detailed > experiment summary in admin dashboard experiment statistics. > These should also be displayed to any other gateway user it is shared with. -- This message was sent by Atlassian JIRA (v7.6.3#76005)
[jira] [Commented] (AIRAVATA-2625) Derive and present Text outputs in Experiment summary
[ https://issues.apache.org/jira/browse/AIRAVATA-2625?page=com.atlassian.jira.plugin.system.issuetabpanels:comment-tabpanel&focusedCommentId=16519499#comment-16519499 ] Eroma commented on AIRAVATA-2625: - Test Environment: [http://149.165.168.200:8008/] Test Cases # Define reading output text from an output file in application interface. - PASS ## Value: Should have the name of the file read from. File name should be exactly how it appears in the experiment summary. ## Allocation Argument: This field will have the text to read from the file. Any line or lines starting from the text filled here will be displayed in the experiment summary. ## If the value is defined incorrectly nothing will be derived and no errors will be displayed. – PASS ## If the file name is incorrect still no errors will be displayed – PASS ## Gateway admin need to make sure both the file to read from and the text is correctly entered in to the application interface. # Add a filed from an existing output (gamess.stdout) file. The complete line which start from the added text is derived and displayed in the experiment summary. (e.g.parsed-out: REPLICATED MEMORY= 100 WORDS (ON EVERY NODE).) - PASS # Add multiple fields from the same file to be read from the output file. Each text to derive need to be added as separate outputs in the application interface. Added multiple fields will be displayed in the experiment summary. – PASS # Add multiple fields from different files to read and display in experiment summary. - PASS # Add a text to derive from a single file but it appears in multiple places in the file. All the lines the particular text appears will be displayed. – PASS # Add a text which is in middle of a line as the reading text from one of the input files. – The complete line which the text belong will be derived and displayed. Not staring from the text given and forward but the complete line it appears will be displayed. – PASS > Derive and present Text outputs in Experiment summary > - > > Key: AIRAVATA-2625 > URL: https://issues.apache.org/jira/browse/AIRAVATA-2625 > Project: Airavata > Issue Type: Bug > Components: Airavata System >Affects Versions: 0.18 >Reporter: Eroma >Assignee: Dimuthu Upeksha >Priority: Major > > Currently the available application outputs are in the form of stdout, stderr > and URI (files). Going forward to have text (String, Integer, Float) outputs > directly in the experiment summary. > These text outputs to be displayed as key+value pairs and when defining > should be defined a file to derive from, e.g. stdout > At a given time from a single file one or many of these key+value pairs could > be derived. Also gateway admin can define multiple files to derive multiple > of these values. > These would be displayed to user in experiment summary and in detailed > experiment summary in admin dashboard experiment statistics. > These should also be displayed to any other gateway user it is shared with. -- This message was sent by Atlassian JIRA (v7.6.3#76005)
[jira] [Commented] (AIRAVATA-2625) Derive and present Text outputs in Experiment summary
[ https://issues.apache.org/jira/browse/AIRAVATA-2625?page=com.atlassian.jira.plugin.system.issuetabpanels:comment-tabpanel&focusedCommentId=16338084#comment-16338084 ] Dimuthu Upeksha commented on AIRAVATA-2625: --- This is might require few changes to output data staging task and there are few restrictions. Because we need to read the file to extract the values, we need to read the file content to the JVM heap. Risk of that is, if we read a large file (several gigs) into the heap, it will cause OOM error and eventually the whole JVM might crash. So we have to come up with a reasonable size cap for the files that are scanned (2 - 5 MB?) and if the file is larger than that, we simply ignore the file and notify the user that output file is too big to scan. > Derive and present Text outputs in Experiment summary > - > > Key: AIRAVATA-2625 > URL: https://issues.apache.org/jira/browse/AIRAVATA-2625 > Project: Airavata > Issue Type: Bug > Components: Airavata System >Affects Versions: 0.18 >Reporter: Eroma >Assignee: Suresh Marru >Priority: Major > > Currently the available application outputs are in the form of stdout, stderr > and URI (files). Going forward to have text (String, Integer, Float) outputs > directly in the experiment summary. > These text outputs to be displayed as key+value pairs and when defining > should be defined a file to derive from, e.g. stdout > At a given time from a single file one or many of these key+value pairs could > be derived. Also gateway admin can define multiple files to derive multiple > of these values. > These would be displayed to user in experiment summary and in detailed > experiment summary in admin dashboard experiment statistics. > These should also be displayed to any other gateway user it is shared with. -- This message was sent by Atlassian JIRA (v7.6.3#76005)
[jira] [Commented] (AIRAVATA-2625) Derive and present Text outputs in Experiment summary
[ https://issues.apache.org/jira/browse/AIRAVATA-2625?page=com.atlassian.jira.plugin.system.issuetabpanels:comment-tabpanel&focusedCommentId=16319052#comment-16319052 ] Eroma commented on AIRAVATA-2625: - Currently there are two gateways (searching SRA and CSBG) who would benefit from this. They have requested for this feature. > Derive and present Text outputs in Experiment summary > - > > Key: AIRAVATA-2625 > URL: https://issues.apache.org/jira/browse/AIRAVATA-2625 > Project: Airavata > Issue Type: Bug > Components: Airavata System >Affects Versions: 0.18 >Reporter: Eroma >Assignee: Suresh Marru > > Currently the available application outputs are in the form of stdout, stderr > and URI (files). Going forward to have text (String, Integer, Float) outputs > directly in the experiment summary. > These text outputs to be displayed as key+value pairs and when defining > should be defined a file to derive from, e.g. stdout > At a given time from a single file one or many of these key+value pairs could > be derived. Also gateway admin can define multiple files to derive multiple > of these values. > These would be displayed to user in experiment summary and in detailed > experiment summary in admin dashboard experiment statistics. > These should also be displayed to any other gateway user it is shared with. -- This message was sent by Atlassian JIRA (v6.4.14#64029)
