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From Lahiru Gunathilake <lginn...@indiana.edu>
Subject Re: [SciGaP-Dev] CIPRES-Airavata integration proposal]]
Date Wed, 23 Jul 2014 17:56:51 GMT

On Jul 23, 2014, at 1:49 PM, K Yoshimoto wrote:

> 
> Hi, just following up on this query.  Could someone send a step-by-step
> on registering a new app and using it in an experiment?  
Look at this class RegisterSampleApplications, Suresh is working on the experiment creation code and soon it will be committed.
> Is there
> a way to specify that an app runs on the login node rather than in
> batch?
If you register the same host as a non-hpc resource then it will be like a norma exec otherwise we create a PBS script and submit the job to the job-manager.
>  Also, could someone point me to the Take 1 integration code
> that Saminda developed?
No idea about this.
> 
> Kenneth
> 
> On Fri, Jul 18, 2014 at 01:28:00PM -0700, K Yoshimoto wrote:
>> 
>> I can registerApplicationModule.php now.  registerApplicationInterface.php
>> fails, even when I comment out the disable().  What is the proper way
>> to put in a new Application?  Is there a way to specify an application
>> that runs directly on the submit node, rather than through a batch job?
>> 
>> On Fri, Jul 18, 2014 at 12:24:08PM -0400, Lahiru Gunathilake wrote:
>>> My plan is to use jobname to filter monitoring with an OR condition.
>>> Meantime I can experiment the two phase way of job submission where I can
>>> set the job Id.
>>> 
>>> 
>>> 
>>> 
>>> On Fri, Jul 18, 2014 at 12:12 PM, Lahiru Gunathilake <glahiru@gmail.com>
>>> wrote:
>>> 
>>>> Verifying valid submit host (login4)...OK
>>>>>>> --> Verifying valid jobname...OK
>>>>>>> --> Enforcing max jobs per user...OK
>>>>>>> --> Verifying availability of your home dir (/home1/01437/ogce)...OK
>>>>>>> --> Verifying availability of your work dir (/work/01437/ogce)...OK
>>>>>>> --> Verifying availability of your scratch dir (/scratch/01437/ogce)...OK
>>>>>>> --> Verifying valid ssh keys...OK
>>>>>>> --> Verifying access to desired queue (normal)...OK
>>>>>>> --> Verifying job request is within current queue limits...OK
>>>>>>> --> Checking available allocation (TG-STA110014S)...
>>>> 
>>>> Reason for the in interesting state is above output doesn't have the job Id returned. This is a known issue. We will provide a fix to this issue very soon.
>>>> 
>>>> 
>>>> 
>>>> On Fri, Jul 18, 2014 at 12:07 PM, K Yoshimoto <kenneth@sdsc.edu> wrote:
>>>> 
>>>>> 
>>>>> Sending to dev@airavata.org also.
>>>>> 
>>>>>> 
>>>>>> On 7/16/14, 4:22 PM, K Yoshimoto wrote:
>>>>>>> I got the hello, world experiment to run! I also modified
>>>>>>> createExperiment.php to play with different inputs.  That worked
>>>>>>> fine.
>>>>>>> 
>>>>>>> I was trying to create a new application with
>>>>>>> registerApplicationModule.php
>>>>>>> but got an error:
>>>>>>> 
>>>>>>> php registerApplicationModule.php pwd 1.0 'print working directory'
>>>>>>> Airavata System Exception: Error while adding application module.
>>>>>>> More info : org.airavata.appcatalog.cpi.AppCatalogException:
>>>>>>> <openjpa-2.2.0-r422266:1244990 fatal general error>
>>>>>>> org.apache.openjpa.persistence.PersistenceException: The last packet
>>>>>>> successfully received from the server was 197,463,645 milliseconds
>>>>>>> ago.  The last packet sent successfully to the server was 197,463,646
>>>>>>> milliseconds ago. is longer than the server configured value of
>>>>>>> 'wait_timeout'. You should consider either expiring and/or testing
>>>>>>> connection validity before use in your application, increasing the
>>>>>>> server configured values for client timeouts, or using the
>>>>>>> Connector/J connection property 'autoReconnect=true' to avoid this
>>>>>>> problem.
>>>>>>> FailedObject: pwd_64d83246-dd86-40ab-9890-5c0492766dcc
>>>>>>> [org.apache.openjpa.util.StringId] [java.lang.String]
>>>>>>> 
>>>>>>> On Thu, Jul 10, 2014 at 02:55:21PM -0700, K Yoshimoto wrote:
>>>>>>>> Okay, now I'm getting a really interesting job status: "UNKNOWN".
>>>>>>>> 
>>>>>>>> 
>>>>>>>> john@anya
>>>>> :/media/mdhpss/scigap/phpclientsamples/airavata/airavata-api/airavata-client-sdks/airavata-php-sdk/src/main/resources/php-cli-samples$
>>>>>>>> php getExperimentStatus.php
>>>>>>>> kennethexp4_5855ec6f-651b-4e01-83d0-67fb5b852eb1
>>>>>>>> experiment status = LAUNCHED
>>>>>>>> <br>
>>>>>>>> john@anya
>>>>> :/media/mdhpss/scigap/phpclientsamples/airavata/airavata-api/airavata-client-sdks/airavata-php-sdk/src/main/resources/php-cli-samples$
>>>>>>>> php getExperimentStatus.php
>>>>>>>> kennethexp4_5855ec6f-651b-4e01-83d0-67fb5b852eb1
>>>>>>>> experiment status = LAUNCHED
>>>>>>>> <br>
>>>>>>>> john@anya
>>>>> :/media/mdhpss/scigap/phpclientsamples/airavata/airavata-api/airavata-client-sdks/airavata-php-sdk/src/main/resources/php-cli-samples$
>>>>>>>> php getExperimentStatus.php
>>>>>>>> kennethexp4_5855ec6f-651b-4e01-83d0-67fb5b852eb1
>>>>>>>> experiment status = UNKNOWN
>>>>>>>> <br>
>>>>>>>> john@anya
>>>>> :/media/mdhpss/scigap/phpclientsamples/airavata/airavata-api/airavata-client-sdks/airavata-php-sdk/src/main/resources/php-cli-samples$
>>>>>>>> php getExperimentStatus.php
>>>>>>>> kennethexp4_5855ec6f-651b-4e01-83d0-67fb5b852eb1
>>>>>>>> experiment status = UNKNOWN
>>>>>>>> <br>
>>>>>>>> john@anya
>>>>> :/media/mdhpss/scigap/phpclientsamples/airavata/airavata-api/airavata-client-sdks/airavata-php-sdk/src/main/resources/php-cli-samples$
>>>>>>>> 
>>>>>>>> 
>>>>>>>> On Thu, Jul 10, 2014 at 05:37:12PM -0400, Raminderjeet Singh wrote:
>>>>>>>>> I reported it already to TACC and working with them to get it
>>>>>>>>> resolved.
>>>>>>>>> This is an occasional issue. If you submit new job it will work.
>>>>>>>>> 
>>>>>>>>> Thanks
>>>>>>>>> Raminder
>>>>>>>>> 
>>>>>>>>> 
>>>>>>>>> 
>>>>>>>>> 
>>>>>>>>> On Thu, Jul 10, 2014 at 5:15 PM, K Yoshimoto <kenneth@sdsc.edu>
>>>>> wrote:
>>>>>>>>> 
>>>>>>>>>> I'm getting FAILED with stampede. Maybe allocation check fails?
>>>>>>>>>> 
>>>>>>>>>> php getExperiment.php
>>>>>>>>>> kennethexp4_9acfe7f5-70ad-423e-9eee-602c09bc8ae4
>>>>>>>>>> 
>>>>>>>>>> ...
>>>>>>>>>>    [12]=>
>>>>>>>>>> object(Airavata\Model\Workspace\Experiment\ErrorDetails)#74 (9) {
>>>>>>>>>>      ["errorID"]=>
>>>>>>>>>>      string(4) "1077"
>>>>>>>>>>      ["creationTime"]=>
>>>>>>>>>>      int(1405026660866)
>>>>>>>>>>      ["actualErrorMessage"]=>
>>>>>>>>>>      string(792) "Error submitting the job to host
>>>>>>>>>> stampede.tacc.xsede.org message:
>>>>>>>>>> -----------------------------------------------------------------
>>>>>>>>>>              Welcome to the Stampede Supercomputer
>>>>>>>>>> -----------------------------------------------------------------
>>>>>>>>>> 
>>>>>>>>>> --> Verifying valid submit host (login4)...OK
>>>>>>>>>> --> Verifying valid jobname...OK
>>>>>>>>>> --> Enforcing max jobs per user...OK
>>>>>>>>>> --> Verifying availability of your home dir (/home1/01437/ogce)...OK
>>>>>>>>>> --> Verifying availability of your work dir (/work/01437/ogce)...OK
>>>>>>>>>> --> Verifying availability of your scratch dir
>>>>>>>>>> (/scratch/01437/ogce)...OK
>>>>>>>>>> --> Verifying valid ssh keys...OK
>>>>>>>>>> --> Verifying access to desired queue (normal)...OK
>>>>>>>>>> --> Verifying job request is within current queue limits...OK
>>>>>>>>>> --> Checking available allocation (TG-STA110014S)..."
>>>>>>>>>>      ["userFriendlyMessage"]=>
>>>>>>>>>>      NULL
>>>>>>>>>>      ["errorCategory"]=>
>>>>>>>>>>      int(6)
>>>>>>>>>>      ["transientOrPersistent"]=>
>>>>>>>>>>      bool(false)
>>>>>>>>>>      ["correctiveAction"]=>
>>>>>>>>>>      int(1)
>>>>>>>>>>      ["actionableGroup"]=>
>>>>>>>>>>      int(2)
>>>>>>>>>>      ["rootCauseErrorIdList"]=>
>>>>>>>>>>      NULL
>>>>>>>>>>    }
>>>>>>>>>>    [13]=>
>>>>>>>>>> object(Airavata\Model\Workspace\Experiment\ErrorDetails)#75 (9) {
>>>>>>>>>>      ["errorID"]=>
>>>>>>>>>>      string(4) "1078"
>>>>>>>>>>      ["creationTime"]=>
>>>>>>>>>>      int(1405026660866)
>>>>>>>>>>      ["actualErrorMessage"]=>
>>>>>>>>>>      string(792) "Error submitting the job to host
>>>>>>>>>> stampede.tacc.xsede.org message:
>>>>>>>>>> -----------------------------------------------------------------
>>>>>>>>>>              Welcome to the Stampede Supercomputer
>>>>>>>>>> -----------------------------------------------------------------
>>>>>>>>>> 
>>>>>>>>>> --> Verifying valid submit host (login4)...OK
>>>>>>>>>> --> Verifying valid jobname...OK
>>>>>>>>>> --> Enforcing max jobs per user...OK
>>>>>>>>>> --> Verifying availability of your home dir (/home1/01437/ogce)...OK
>>>>>>>>>> --> Verifying availability of your work dir (/work/01437/ogce)...OK
>>>>>>>>>> --> Verifying availability of your scratch dir
>>>>>>>>>> (/scratch/01437/ogce)...OK
>>>>>>>>>> --> Verifying valid ssh keys...OK
>>>>>>>>>> --> Verifying access to desired queue (normal)...OK
>>>>>>>>>> --> Verifying job request is within current queue limits...OK
>>>>>>>>>> --> Checking available allocation (TG-STA110014S)..."
>>>>>>>>>>      ["userFriendlyMessage"]=>
>>>>>>>>>>      NULL
>>>>>>>>>>      ["errorCategory"]=>
>>>>>>>>>>      int(6)
>>>>>>>>>>      ["transientOrPersistent"]=>
>>>>>>>>>>      bool(false)
>>>>>>>>>>      ["correctiveAction"]=>
>>>>>>>>>>      int(1)
>>>>>>>>>>      ["actionableGroup"]=>
>>>>>>>>>>      int(2)
>>>>>>>>>>      ["rootCauseErrorIdList"]=>
>>>>>>>>>>      NULL
>>>>>>>>>>    }
>>>>>>>>>>    [14]=>
>>>>>>>>>> object(Airavata\Model\Workspace\Experiment\ErrorDetails)#76 (9) {
>>>>>>>>>>      ["errorID"]=>
>>>>>>>>>>      string(4) "1079"
>>>>>>>>>>      ["creationTime"]=>
>>>>>>>>>>      int(1405026660866)
>>>>>>>>>>      ["actualErrorMessage"]=>
>>>>>>>>>>      string(792) "Error submitting the job to host
>>>>>>>>>> stampede.tacc.xsede.org message:
>>>>>>>>>> -----------------------------------------------------------------
>>>>>>>>>>              Welcome to the Stampede Supercomputer
>>>>>>>>>> -----------------------------------------------------------------
>>>>>>>>>> 
>>>>>>>>>> --> Verifying valid submit host (login4)...OK
>>>>>>>>>> --> Verifying valid jobname...OK
>>>>>>>>>> --> Enforcing max jobs per user...OK
>>>>>>>>>> --> Verifying availability of your home dir (/home1/01437/ogce)...OK
>>>>>>>>>> --> Verifying availability of your work dir (/work/01437/ogce)...OK
>>>>>>>>>> --> Verifying availability of your scratch dir
>>>>>>>>>> (/scratch/01437/ogce)...OK
>>>>>>>>>> --> Verifying valid ssh keys...OK
>>>>>>>>>> --> Verifying access to desired queue (normal)...OK
>>>>>>>>>> --> Verifying job request is within current queue limits...OK
>>>>>>>>>> --> Checking available allocation (TG-STA110014S)..."
>>>>>>>>>>      ["userFriendlyMessage"]=>
>>>>>>>>>>      NULL
>>>>>>>>>>      ["errorCategory"]=>
>>>>>>>>>>      int(6)
>>>>>>>>>>      ["transientOrPersistent"]=>
>>>>>>>>>>      bool(false)
>>>>>>>>>>      ["correctiveAction"]=>
>>>>>>>>>>      int(1)
>>>>>>>>>>      ["actionableGroup"]=>
>>>>>>>>>>      int(2)
>>>>>>>>>>      ["rootCauseErrorIdList"]=>
>>>>>>>>>>      NULL
>>>>>>>>>>    }
>>>>>>>>>>    [15]=>
>>>>>>>>>> object(Airavata\Model\Workspace\Experiment\ErrorDetails)#77 (9) {
>>>>>>>>>>      ["errorID"]=>
>>>>>>>>>>      string(4) "1080"
>>>>>>>>>>      ["creationTime"]=>
>>>>>>>>>>      int(1405026660866)
>>>>>>>>>>      ["actualErrorMessage"]=>
>>>>>>>>>>      string(792) "Error submitting the job to host
>>>>>>>>>> stampede.tacc.xsede.org message:
>>>>>>>>>> -----------------------------------------------------------------
>>>>>>>>>>              Welcome to the Stampede Supercomputer
>>>>>>>>>> -----------------------------------------------------------------
>>>>>>>>>> 
>>>>>>>>>> --> Verifying valid submit host (login4)...OK
>>>>>>>>>> --> Verifying valid jobname...OK
>>>>>>>>>> --> Enforcing max jobs per user...OK
>>>>>>>>>> --> Verifying availability of your home dir (/home1/01437/ogce)...OK
>>>>>>>>>> --> Verifying availability of your work dir (/work/01437/ogce)...OK
>>>>>>>>>> --> Verifying availability of your scratch dir
>>>>>>>>>> (/scratch/01437/ogce)...OK
>>>>>>>>>> --> Verifying valid ssh keys...OK
>>>>>>>>>> --> Verifying access to desired queue (normal)...OK
>>>>>>>>>> --> Verifying job request is within current queue limits...OK
>>>>>>>>>> --> Checking available allocation (TG-STA110014S)..."
>>>>>>>>>>      ["userFriendlyMessage"]=>
>>>>>>>>>>      NULL
>>>>>>>>>>      ["errorCategory"]=>
>>>>>>>>>>      int(6)
>>>>>>>>>>      ["transientOrPersistent"]=>
>>>>>>>>>>      bool(false)
>>>>>>>>>>      ["correctiveAction"]=>
>>>>>>>>>>      int(1)
>>>>>>>>>>      ["actionableGroup"]=>
>>>>>>>>>>      int(2)
>>>>>>>>>>      ["rootCauseErrorIdList"]=>
>>>>>>>>>>      NULL
>>>>>>>>>>    }
>>>>>>>>>>  }
>>>>>>>>>> }
>>>>>>>>>> 
>>>>>>>>>> On Thu, Jul 10, 2014 at 08:53:06PM +0000, Singh, Raminder jeet wrote:
>>>>>>>>>>> We setup a new database on Tuesday. Everything created after that
>>>>>>>>>>> should
>>>>>>>>>> exist.
>>>>>>>>>>> Thanks
>>>>>>>>>>> Raminder
>>>>>>>>>>> 
>>>>>>>>>>> On Jul 10, 2014, at 4:47 PM, K Yoshimoto <kenneth@sdsc.edu> wrote:
>>>>>>>>>>> 
>>>>>>>>>>>> Thanks, Raminder.  Did the old experiment, project and user get
>>>>>>>>>>>> wiped out or should they still be there?
>>>>>>>>>>>> 
>>>>>>>>>>>> On Thu, Jul 10, 2014 at 08:38:24PM +0000, Singh, Raminder jeet
>>>>>>>>>>>> wrote:
>>>>>>>>>>>>> Hi Kenneth,
>>>>>>>>>>>>> 
>>>>>>>>>>>>> Create and launch should work now. I added default values for
>>>>>>>>>> applicationid and hostid in createExperiment for Echo application on
>>>>>>>>>> Stampede. I updated launchExperiment with a valid airavata token for
>>>>>>>>>> experiment to work well. Please let me know if you face any other
>>>>>>>>>> issue. I
>>>>>>>>>> am also in process of testing other scripts.
>>>>>>>>>>>>> Thanks
>>>>>>>>>>>>> Raminder
>>>>>>>>>>>>> 
>>>>>>>>>>>>> On Jul 10, 2014, at 4:04 PM, Marlon Pierce <marpierc@iu.edu>
>>>>>>>>>>>>> wrote:
>>>>>>>>>>>>> 
>>>>>>>>>>>>>> There is a bug in script (API changed). Raminder is working to
>>>>>>>>>>>>>> fix
>>>>>>>>>> it now.
>>>>>>>>>>>>>> Marlon
>>>>>>>>>>>>>> 
>>>>>>>>>>>>>> On 7/10/14, 3:57 PM, K Yoshimoto wrote:
>>>>>>>>>>>>>>> I launched another one, and it's still in LAUNCHED.
>>>>>>>>>>>>>>> Is there a way for the gateway developer to retrieve
>>>>>>>>>>>>>>> a job id?
>>>>>>>>>>>>>>> 
>>>>>>>>>>>>>>> john@anya
>>>>> :/media/mdhpss/scigap/phpclientsamples/airavata/airavata-api/airavata-client-sdks/airavata-php-sdk/src/main/resources/php-cli-samples$
>>>>>>>>>>>>>>> 
>>>>>>>>>> php getExperimentStatus.php
>>>>>>>>>> kennethexp2_f161f3a5-04a8-4ee9-862c-918e383e852d
>>>>>>>>>>>>>>> experiment status = LAUNCHED
>>>>>>>>>>>>>>> <br>
>>>>>>>>>>>>>>> john@anya
>>>>> :/media/mdhpss/scigap/phpclientsamples/airavata/airavata-api/airavata-client-sdks/airavata-php-sdk/src/main/resources/php-cli-samples$
>>>>>>>>>>>>>>> 
>>>>>>>>>> php getExperimentStatus.php
>>>>>>>>>> kennethexp2_f161f3a5-04a8-4ee9-862c-918e383e852d
>>>>>>>>>>>>>>> experiment status = LAUNCHED
>>>>>>>>>>>>>>> <br>
>>>>>>>>>>>>>>> john@anya
>>>>> :/media/mdhpss/scigap/phpclientsamples/airavata/airavata-api/airavata-client-sdks/airavata-php-sdk/src/main/resources/php-cli-samples$
>>>>>>>>>>>>>>> 
>>>>>>>>>> php getExperiment.php
>>>>>>>>>> kennethexp2_f161f3a5-04a8-4ee9-862c-918e383e852d
>>>>>>>>>>>>>>> object(Airavata\Model\Workspace\Experiment\Experiment)#6 (18) {
>>>>>>>>>>>>>>> ["experimentID"]=>
>>>>>>>>>>>>>>> string(48) "kennethexp2_f161f3a5-04a8-4ee9-862c-918e383e852d"
>>>>>>>>>>>>>>> ["projectID"]=>
>>>>>>>>>>>>>>> string(48) "kennethtest_721c9e67-846d-4081-b1db-a573e198ec01"
>>>>>>>>>>>>>>> ["creationTime"]=>
>>>>>>>>>>>>>>> int(1405021121026)
>>>>>>>>>>>>>>> ["userName"]=>
>>>>>>>>>>>>>>> string(7) "kenneth"
>>>>>>>>>>>>>>> ["name"]=>
>>>>>>>>>>>>>>> string(11) "kennethexp2"
>>>>>>>>>>>>>>> ["description"]=>
>>>>>>>>>>>>>>> NULL
>>>>>>>>>>>>>>> ["applicationId"]=>
>>>>>>>>>>>>>>> string(11) "SimpleEcho2"
>>>>>>>>>>>>>>> ["applicationVersion"]=>
>>>>>>>>>>>>>>> NULL
>>>>>>>>>>>>>>> ["workflowTemplateId"]=>
>>>>>>>>>>>>>>> NULL
>>>>>>>>>>>>>>> ["workflowTemplateVersion"]=>
>>>>>>>>>>>>>>> NULL
>>>>>>>>>>>>>>> ["userConfigurationData"]=>
>>>>>>>>>>>>>>> 
>>>>>>>>>> object(Airavata\Model\Workspace\Experiment\UserConfigurationData)#7
>>>>> (7)
>>>>>>>>>> {
>>>>>>>>>>>>>>> ["airavataAutoSchedule"]=>
>>>>>>>>>>>>>>>   bool(false)
>>>>>>>>>>>>>>>   ["overrideManualScheduledParams"]=>
>>>>>>>>>>>>>>>   bool(false)
>>>>>>>>>>>>>>>   ["shareExperimentPublicly"]=>
>>>>>>>>>>>>>>>   bool(false)
>>>>>>>>>>>>>>>   ["computationalResourceScheduling"]=>
>>>>>>>>>>>>>>> 
>>>>> 
>>>>>>>>>> object(Airavata\Model\Workspace\Experiment\ComputationalResourceScheduling)#8
>>>>>>>>>> (9) {
>>>>>>>>>>>>>>> ["resourceHostId"]=>
>>>>>>>>>>>>>>>     string(17) "trestles.sdsc.edu"
>>>>>>>>>>>>>>>     ["totalCPUCount"]=>
>>>>>>>>>>>>>>>     int(1)
>>>>>>>>>>>>>>>     ["nodeCount"]=>
>>>>>>>>>>>>>>>     int(1)
>>>>>>>>>>>>>>>     ["numberOfThreads"]=>
>>>>>>>>>>>>>>>     int(0)
>>>>>>>>>>>>>>>     ["queueName"]=>
>>>>>>>>>>>>>>>     string(6) "normal"
>>>>>>>>>>>>>>>     ["wallTimeLimit"]=>
>>>>>>>>>>>>>>>     int(15)
>>>>>>>>>>>>>>>     ["jobStartTime"]=>
>>>>>>>>>>>>>>>     int(566815272)
>>>>>>>>>>>>>>>     ["totalPhysicalMemory"]=>
>>>>>>>>>>>>>>>     int(0)
>>>>>>>>>>>>>>>     ["computationalProjectAccount"]=>
>>>>>>>>>>>>>>>     NULL
>>>>>>>>>>>>>>>   }
>>>>>>>>>>>>>>>   ["advanceInputDataHandling"]=>
>>>>>>>>>>>>>>>   NULL
>>>>>>>>>>>>>>>   ["advanceOutputDataHandling"]=>
>>>>>>>>>>>>>>>   NULL
>>>>>>>>>>>>>>>   ["qosParams"]=>
>>>>>>>>>>>>>>>   NULL
>>>>>>>>>>>>>>> }
>>>>>>>>>>>>>>> ["workflowExecutionInstanceId"]=>
>>>>>>>>>>>>>>> NULL
>>>>>>>>>>>>>>> ["experimentInputs"]=>
>>>>>>>>>>>>>>> array(1) {
>>>>>>>>>>>>>>>   [0]=>
>>>>>>>>>>>>>>> object(Airavata\Model\Workspace\Experiment\DataObjectType)#9 (4)
>>>>>>>>>> {
>>>>>>>>>>>>>>>     ["key"]=>
>>>>>>>>>>>>>>>     string(10) "echo_input"
>>>>>>>>>>>>>>>     ["value"]=>
>>>>>>>>>>>>>>>     string(23) "echo_output=Hello World"
>>>>>>>>>>>>>>>     ["type"]=>
>>>>>>>>>>>>>>>     int(0)
>>>>>>>>>>>>>>>     ["metaData"]=>
>>>>>>>>>>>>>>>     NULL
>>>>>>>>>>>>>>>   }
>>>>>>>>>>>>>>> }
>>>>>>>>>>>>>>> ["experimentOutputs"]=>
>>>>>>>>>>>>>>> array(1) {
>>>>>>>>>>>>>>>   [0]=>
>>>>>>>>>>>>>>> object(Airavata\Model\Workspace\Experiment\DataObjectType)#10
>>>>>>>>>> (4) {
>>>>>>>>>>>>>>>     ["key"]=>
>>>>>>>>>>>>>>>     string(11) "echo_output"
>>>>>>>>>>>>>>>     ["value"]=>
>>>>>>>>>>>>>>>     string(0) ""
>>>>>>>>>>>>>>>     ["type"]=>
>>>>>>>>>>>>>>>     int(0)
>>>>>>>>>>>>>>>     ["metaData"]=>
>>>>>>>>>>>>>>>     NULL
>>>>>>>>>>>>>>>   }
>>>>>>>>>>>>>>> }
>>>>>>>>>>>>>>> ["experimentStatus"]=>
>>>>>>>>>>>>>>> object(Airavata\Model\Workspace\Experiment\ExperimentStatus)#11
>>>>>>>>>> (2) {
>>>>>>>>>>>>>>> ["experimentState"]=>
>>>>>>>>>>>>>>>   int(3)
>>>>>>>>>>>>>>>   ["timeOfStateChange"]=>
>>>>>>>>>>>>>>>   int(1405021142702)
>>>>>>>>>>>>>>> }
>>>>>>>>>>>>>>> ["stateChangeList"]=>
>>>>>>>>>>>>>>> array(1) {
>>>>>>>>>>>>>>>   [0]=>
>>>>>>>>>>>>>>> 
>>>>>>>>>> object(Airavata\Model\Workspace\Experiment\WorkflowNodeStatus)#12
>>>>>>>>>> (2) {
>>>>>>>>>>>>>>> ["workflowNodeState"]=>
>>>>>>>>>>>>>>>     int(7)
>>>>>>>>>>>>>>>     ["timeOfStateChange"]=>
>>>>>>>>>>>>>>>     int(1405021142334)
>>>>>>>>>>>>>>>   }
>>>>>>>>>>>>>>> }
>>>>>>>>>>>>>>> ["workflowNodeDetailsList"]=>
>>>>>>>>>>>>>>> array(1) {
>>>>>>>>>>>>>>>   [0]=>
>>>>>>>>>>>>>>> 
>>>>>>>>>> object(Airavata\Model\Workspace\Experiment\WorkflowNodeDetails)#13
>>>>>>>>>> (10) {
>>>>>>>>>>>>>>> ["nodeInstanceId"]=>
>>>>>>>>>>>>>>>     string(51)
>>>>>>>>>> "IDontNeedaNode_320649b3-450b-4bdb-89cf-70a95ccb817e"
>>>>>>>>>>>>>>> ["creationTime"]=>
>>>>>>>>>>>>>>>     int(1405021142316)
>>>>>>>>>>>>>>>     ["nodeName"]=>
>>>>>>>>>>>>>>>     string(14) "IDontNeedaNode"
>>>>>>>>>>>>>>>     ["executionUnit"]=>
>>>>>>>>>>>>>>>     int(1)
>>>>>>>>>>>>>>>     ["executionUnitData"]=>
>>>>>>>>>>>>>>>     NULL
>>>>>>>>>>>>>>>     ["nodeInputs"]=>
>>>>>>>>>>>>>>>     array(0) {
>>>>>>>>>>>>>>>     }
>>>>>>>>>>>>>>>     ["nodeOutputs"]=>
>>>>>>>>>>>>>>>     array(0) {
>>>>>>>>>>>>>>>     }
>>>>>>>>>>>>>>>     ["workflowNodeStatus"]=>
>>>>>>>>>>>>>>> 
>>>>>>>>>> object(Airavata\Model\Workspace\Experiment\WorkflowNodeStatus)#14
>>>>>>>>>> (2) {
>>>>>>>>>>>>>>> ["workflowNodeState"]=>
>>>>>>>>>>>>>>>       int(7)
>>>>>>>>>>>>>>>       ["timeOfStateChange"]=>
>>>>>>>>>>>>>>>       int(1405021142334)
>>>>>>>>>>>>>>>     }
>>>>>>>>>>>>>>>     ["taskDetailsList"]=>
>>>>>>>>>>>>>>>     array(1) {
>>>>>>>>>>>>>>>       [0]=>
>>>>>>>>>>>>>>> object(Airavata\Model\Workspace\Experiment\TaskDetails)#15
>>>>>>>>>> (14) {
>>>>>>>>>>>>>>>         ["taskID"]=>
>>>>>>>>>>>>>>>         string(51)
>>>>>>>>>> "IDontNeedaNode_c2f6d21f-cd12-45c3-814f-a9c903fa5bde"
>>>>>>>>>>>>>>> ["creationTime"]=>
>>>>>>>>>>>>>>>         NULL
>>>>>>>>>>>>>>>         ["applicationId"]=>
>>>>>>>>>>>>>>>         string(11) "SimpleEcho2"
>>>>>>>>>>>>>>>         ["applicationVersion"]=>
>>>>>>>>>>>>>>>         NULL
>>>>>>>>>>>>>>>         ["applicationDeploymentId"]=>
>>>>>>>>>>>>>>>         NULL
>>>>>>>>>>>>>>>         ["applicationInputs"]=>
>>>>>>>>>>>>>>>         array(1) {
>>>>>>>>>>>>>>>           [0]=>
>>>>>>>>>>>>>>> 
>>>>>>>>>> object(Airavata\Model\Workspace\Experiment\DataObjectType)#16 (4) {
>>>>>>>>>>>>>>>             ["key"]=>
>>>>>>>>>>>>>>>             string(10) "echo_input"
>>>>>>>>>>>>>>>             ["value"]=>
>>>>>>>>>>>>>>>             string(23) "echo_output=Hello World"
>>>>>>>>>>>>>>>             ["type"]=>
>>>>>>>>>>>>>>>             int(0)
>>>>>>>>>>>>>>>             ["metaData"]=>
>>>>>>>>>>>>>>>             NULL
>>>>>>>>>>>>>>>           }
>>>>>>>>>>>>>>>         }
>>>>>>>>>>>>>>>         ["applicationOutputs"]=>
>>>>>>>>>>>>>>>         array(1) {
>>>>>>>>>>>>>>>           [0]=>
>>>>>>>>>>>>>>> 
>>>>>>>>>> object(Airavata\Model\Workspace\Experiment\DataObjectType)#17 (4) {
>>>>>>>>>>>>>>>             ["key"]=>
>>>>>>>>>>>>>>>             string(11) "echo_output"
>>>>>>>>>>>>>>>             ["value"]=>
>>>>>>>>>>>>>>>             string(0) ""
>>>>>>>>>>>>>>>             ["type"]=>
>>>>>>>>>>>>>>>             int(0)
>>>>>>>>>>>>>>>             ["metaData"]=>
>>>>>>>>>>>>>>>             NULL
>>>>>>>>>>>>>>>           }
>>>>>>>>>>>>>>>         }
>>>>>>>>>>>>>>>         ["taskScheduling"]=>
>>>>>>>>>>>>>>> 
>>>>> 
>>>>>>>>>> object(Airavata\Model\Workspace\Experiment\ComputationalResourceScheduling)#18
>>>>>>>>>> (9) {
>>>>>>>>>>>>>>> ["resourceHostId"]=>
>>>>>>>>>>>>>>>           string(17) "trestles.sdsc.edu"
>>>>>>>>>>>>>>>           ["totalCPUCount"]=>
>>>>>>>>>>>>>>>           int(1)
>>>>>>>>>>>>>>>           ["nodeCount"]=>
>>>>>>>>>>>>>>>           int(1)
>>>>>>>>>>>>>>>           ["numberOfThreads"]=>
>>>>>>>>>>>>>>>           int(0)
>>>>>>>>>>>>>>>           ["queueName"]=>
>>>>>>>>>>>>>>>           string(6) "normal"
>>>>>>>>>>>>>>>           ["wallTimeLimit"]=>
>>>>>>>>>>>>>>>           int(15)
>>>>>>>>>>>>>>>           ["jobStartTime"]=>
>>>>>>>>>>>>>>>           int(566815272)
>>>>>>>>>>>>>>>           ["totalPhysicalMemory"]=>
>>>>>>>>>>>>>>>           int(0)
>>>>>>>>>>>>>>>           ["computationalProjectAccount"]=>
>>>>>>>>>>>>>>>           NULL
>>>>>>>>>>>>>>>         }
>>>>>>>>>>>>>>>         ["advancedInputDataHandling"]=>
>>>>>>>>>>>>>>>         NULL
>>>>>>>>>>>>>>>         ["advancedOutputDataHandling"]=>
>>>>>>>>>>>>>>>         NULL
>>>>>>>>>>>>>>>         ["taskStatus"]=>
>>>>>>>>>>>>>>> object(Airavata\Model\Workspace\Experiment\TaskStatus)#19
>>>>>>>>>> (2) {
>>>>>>>>>>>>>>> ["executionState"]=>
>>>>>>>>>>>>>>>           int(12)
>>>>>>>>>>>>>>>           ["timeOfStateChange"]=>
>>>>>>>>>>>>>>>           int(1405021142382)
>>>>>>>>>>>>>>>         }
>>>>>>>>>>>>>>>         ["jobDetailsList"]=>
>>>>>>>>>>>>>>>         array(0) {
>>>>>>>>>>>>>>>         }
>>>>>>>>>>>>>>>         ["dataTransferDetailsList"]=>
>>>>>>>>>>>>>>>         array(0) {
>>>>>>>>>>>>>>>         }
>>>>>>>>>>>>>>>         ["errors"]=>
>>>>>>>>>>>>>>>         array(0) {
>>>>>>>>>>>>>>>         }
>>>>>>>>>>>>>>>       }
>>>>>>>>>>>>>>>     }
>>>>>>>>>>>>>>>     ["errors"]=>
>>>>>>>>>>>>>>>     array(0) {
>>>>>>>>>>>>>>>     }
>>>>>>>>>>>>>>>   }
>>>>>>>>>>>>>>> }
>>>>>>>>>>>>>>> ["errors"]=>
>>>>>>>>>>>>>>> NULL
>>>>>>>>>>>>>>> }
>>>>>>>>>>>>>>> 
>>>>>>>>>>>>>>> john@anya
>>>>> 
>>>>>>>>>> :/media/mdhpss/scigap/phpclientsamples/airavata/airavata-api/airavata-client-sdks/airavata-php-sdk/src/main/resources/php-cli-samples$
>>>>>>>>>> 
>>>>>>>>>>>>>>> On Thu, Jul 10, 2014 at 03:32:03PM -0400, Marlon Pierce wrote:
>>>>>>>>>>>>>>>> Yes, probably a casualty of our updates.
>>>>>>>>>>>>>>>> 
>>>>>>>>>>>>>>>> Marlon
>>>>>>>>>>>>>>>> 
>>>>>>>>>>>>>>>> On 7/10/14, 3:19 PM, K Yoshimoto wrote:
>>>>>>>>>>>>>>>>> I launched a test experiment yesterday, but it hasn't
>>>>>>>>>>>>>>>>> changed from
>>>>>>>>>>>>>>>>> LAUNCHED status.  Should it go into running fairly quickly?
>>>>>>>>>>>>>>>>> 
>>>>>>>>>>>>>>>>> php getExperimentStatus.php
>>>>>>>>>>>>>>>>> kennethexp1_5497b1a2-721e-4690-9e4c-e0f24693c5c1
>>>>>>>>>>>>>>>>> experiment status = LAUNCHED
>>>>>>>>>>>>>>>>> <br>
>>>>>>>>>>>>>>>>> 
>>>>>>>>>>>>>>>>> 
>>>>>>>>>>>>>>>>> On Thu, Jul 10, 2014 at 06:03:12AM -0400, Marlon Pierce wrote:
>>>>>>>>>>>>>>>>>> He'll still need his classpath set properly to run them
>>>>>>>>>>>>>>>>>> from the
>>>>>>>>>> command
>>>>>>>>>>>>>>>>>> line.  Do we have instructions for this?
>>>>>>>>>>>>>>>>>> 
>>>>>>>>>>>>>>>>>> Also, the lowest level pom.xml file is
>>>>>>>>>>>>>>>>>> 
>>>>> 
>>>>>>>>>> airavata/airavata-api//airavata-client-sdks/java-client-samples/pom.xml
>>>>>>>>>> 
>>>>>>>>>>>>>>>>>> so that is where to run "mvn clean install" if recompiling
>>>>>>>>>>>>>>>>>> after
>>>>>>>>>> making
>>>>>>>>>>>>>>>>>> changes.
>>>>>>>>>>>>>>>>>> 
>>>>>>>>>>>>>>>>>> Or use an IDE to manage recompiles, I guess.
>>>>>>>>>>>>>>>>>> 
>>>>>>>>>>>>>>>>>> Marlon
>>>>>>>>>>>>>>>>>> 
>>>>>>>>>>>>>>>>>> On 7/9/14, 9:01 PM, Suresh Marru wrote:
>>>>>>>>>>>>>>>>>>> Hi Kenneth,
>>>>>>>>>>>>>>>>>>> 
>>>>>>>>>>>>>>>>>>> Airavata uses Maven as the build system. Once you checkout
>>>>>>>>>> Airavata, you
>>>>>>>>>>>>>>>>>>> should be able to build "mvn clean install
>>>>>>>>>>>>>>>>>>> -DskipTests=true -f
>>>>> 
>>>>>>>>>>>>>>>>>>> airavata-api/airavata-client-sdks/java-client-samples/pom.xml"
>>>>>>>>>>>>>>>>>>> 
>>>>>>>>>>>>>>>>>>> 
>>>>>>>>>>>>>>>>>>> If you are building from git master, you may need to
>>>>>>>>>>>>>>>>>>> build the
>>>>>>>>>> whole of
>>>>>>>>>>>>>>>>>>> airavata repo. Alternatively, users are provided with
>>>>>>>>>>>>>>>>>>> binaries.
>>>>>>>>>> And
>>>>>>>>>>>>>>>>>>> changes to samples with release versions can be build
>>>>>>>>>>>>>>>>>>> without
>>>>>>>>>> having to
>>>>>>>>>>>>>>>>>>> build the whole repo.
>>>>>>>>>>>>>>>>>>> 
>>>>>>>>>>>>>>>>>>> As an example, if you modify samples within
>>>>>>>>>>>>>>>>>>> https://github.com/apache/airavata/tree/airavata-0.12 you
>>>>>>>>>>>>>>>>>>> can
>>>>>>>>>> just go to
>>>>> 
>>>>>>>>>> airavata/airavata-api/airavata-client-sdks/java-client-samples/src/main/java/org/apache/airavata/client/samples
>>>>>>>>>> 
>>>>>>>>>> and build just the changed samples by running mvn clean install
>>>>>>>>>> -DskipTests=true.
>>>>>>>>>>>>>>>>>>> Long story short, release artifacts are published to maven
>>>>>>>>>> central, so
>>>>>>>>>>>>>>>>>>> building a module will pull the artifacts from maven central
>>>>>>>>>> repo -
>>>>>>>>>>>>>>>>>>> 
>>>>> http://search.maven.org/#search%7Cga%7C1%7Capache%20airavata
>>>>>>>>>>>>>>>>>>> 
>>>>>>>>>>>>>>>>>>> Suresh
>>>>>>>>>>>>>>>>>>> 
>>>>>>>>>>>>>>>>>>> 
>>>>>>>>>>>>>>>>>>> On Jul 9, 2014, at 7:38 PM, K Yoshimoto <kenneth@sdsc.edu>
>>>>>>>>>> wrote:
>>>>>>>>>>>>>>>>>>>> Another question:  is there a Makefile for the java
>>>>>>>>>>>>>>>>>>>> examples?
>>>>>>>>>>>>>>>>>>>> 
>>>>>>>>>>>>>>>>>>>> 
>>>>> 
>>>>>>>>>> airavata/airavata-api/airavata-client-sdks/java-client-samples/src/main/java/org/apache/airavata/client/samples
>>>>>>>>>> 
>>>>>>>>>>>>>>>>>>>> 
>>>>>>>>>>>>>>>>>>>> On Wed, Jul 09, 2014 at 04:32:21PM -0400, Suresh Marru
>>>>>>>>>>>>>>>>>>>> wrote:
>>>>>>>>>>>>>>>>>>>>> Hi Kenneth,
>>>>>>>>>>>>>>>>>>>>> 
>>>>>>>>>>>>>>>>>>>>> I changed the script names to patch the API function
>>>>>>>>>>>>>>>>>>>>> names.
>>>>>>>>>> So it is
>>>>>>>>>>>>>>>>>>>>> now
>>>>>>>>>>>>>>>>>>>>> - registerComputeResource.php
>>>>>>>>>>>>>>>>>>>>> 
>>>>>>>>>>>>>>>>>>>>> I am going to finish up the Wiki articles [1] will
>>>>>>>>>>>>>>>>>>>>> describe
>>>>>>>>>> all the
>>>>>>>>>>>>>>>>>>>>> functions you can do and available samples.
>>>>>>>>>>>>>>>>>>>>> 
>>>>>>>>>>>>>>>>>>>>> Suresh
>>>>>>>>>>>>>>>>>>>>> [1] -
>>>>>>>>>>>>>>>>>>>>> 
>>>>>>>>>> 
>>>>> https://cwiki.apache.org/confluence/display/AIRAVATA/Airavata+API+PHP+Client+Samples
>>>>>>>>>> 
>>>>>>>>>>>>>>>>>>>>> On Jul 9, 2014, at 4:25 PM, K Yoshimoto <kenneth@sdsc.edu
>>>>>> 
>>>>>>>>>> wrote:
>>>>>>>>>>>>>>>>>>>>>> I did a git pull, and add-compute-resource.php does
>>>>>>>>>>>>>>>>>>>>>> not seem
>>>>>>>>>>>>>>>>>>>>>> to be there anymore.  Should it still be available?
>>>>>>>>>>>>>>>>>>>>>> 
>>>>>>>>>>>>>>>>>>>>>> On Thu, Jul 03, 2014 at 01:34:18PM -0700, K Yoshimoto
>>>>>>>>>>>>>>>>>>>>>> wrote:
>>>>>>>>>>>>>>>>>>>>>>> Thanks, Marlon and Suresh.  I'll poke through the app
>>>>>>>>>> catalog api
>>>>>>>>>>>>>>>>>>>>>>> and try out the examples in the new README next week.
>>>>>>>>>>>>>>>>>>>>>>> 
>>>>>>>>>>>>>>>>>>>>>>> Kenneth
>>>>>>>>>>>>>>>>>>>>>>> 
>>>>>>>>>>>>>>>>>>>>>>> On Thu, Jul 03, 2014 at 04:19:21PM -0400, Marlon Pierce
>>>>>>>>>> wrote:
>>>>>>>>>>>>>>>>>>>>>>>> In short, though, if a script in this directory is
>>>>>>>>>>>>>>>>>>>>>>>> not in
>>>>>>>>>> the
>>>>>>>>>>>>>>>>>>>>>>>> README, it is using the App Catalog part of the API.
>>>>>>>>>>>>>>>>>>>>>>>> add-compute-resource.php does some of what you are
>>>>>>>>>>>>>>>>>>>>>>>> looking
>>>>>>>>>> for
>>>>>>>>>>>>>>>>>>>>>>>> below. I'll make some quick updates to the readme.
>>>>>>>>>>>>>>>>>>>>>>>> 
>>>>>>>>>>>>>>>>>>>>>>>> Marlon
>>>>>>>>>>>>>>>>>>>>>>>> 
>>>>>>>>>>>>>>>>>>>>>>>> On 7/3/14, 4:06 PM, Suresh Marru wrote:
>>>>>>>>>>>>>>>>>>>>>>>>> Hi Kenneth,
>>>>>>>>>>>>>>>>>>>>>>>>> 
>>>>>>>>>>>>>>>>>>>>>>>>> I plan to modify the README to describe the use cases
>>>>>>>>>> including the
>>>>>>>>>>>>>>>>>>>>>>>>> one you mention below. Will try to get all that done
>>>>>>>>>> before Monday.
>>>>>>>>>>>>>>>>>>>>>>>>> Suresh
>>>>>>>>>>>>>>>>>>>>>>>>> 
>>>>>>>>>>>>>>>>>>>>>>>>> On Jul 3, 2014, at 4:04 PM, Marlon Pierce <
>>>>>>>>>> marpierc@iu.edu> wrote:
>>>>>>>>>>>>>>>>>>>>>>>>>> Hi Kenneth--
>>>>>>>>>>>>>>>>>>>>>>>>>> 
>>>>>>>>>>>>>>>>>>>>>>>>>> At the API level, those are part of the Application
>>>>>>>>>> Catalog.  At
>>>>>>>>>>>>>>>>>>>>>>>>>> the implementation level, they are done by GFAC
>>>>>>>>>>>>>>>>>>>>>>>>>> plugins
>>>>>>>>>> (GSI-SSH
>>>>>>>>>>>>>>>>>>>>>>>>>> plugin in this case).   These are new (not yet in the
>>>>>>>>>> README), may
>>>>>>>>>>>>>>>>>>>>>>>>>> be missing some examples.
>>>>>>>>>>>>>>>>>>>>>>>>>> 
>>>>>>>>>>>>>>>>>>>>>>>>>> Marlon
>>>>>>>>>>>>>>>>>>>>>>>>>> 
>>>>>>>>>>>>>>>>>>>>>>>>>> On 7/3/14, 3:45 PM, K Yoshimoto wrote:
>>>>>>>>>>>>>>>>>>>>>>>>>>> Are there methods in the API for creating working
>>>>>>>>>>>>>>>>>>>>>>>>>>> dirs
>>>>>>>>>> on the
>>>>>>>>>>>>>>>>>>>>>>>>>>> compute resource, staging input data, and running
>>>>>>>>>> submit wrapper
>>>>>>>>>>>>>>>>>>>>>>>>>>> scripts?
>>>>>>>>>>>>>>>>>>>>>>>>>>> 
>>>>>>>>>>>>>>>>>>>>>>>>>>> I'm looking at:
>>>>>>>>>>>>>>>>>>>>>>>>>>> 
>>>>>>>>>> 
>>>>> https://github.com/SciGaP/Airavata-PHP-Client-Samples/blob/master/client-samples/README-PHP-CLI-Examples.txt
>>>>>>>>>> 
>>>>>>>>>>>>>>>>>>>>>>>>>>> and browsing through:
>>>>>>>>>>>>>>>>>>>>>>>>>>> 
>>>>> 
>>>>>>>>>> airavata/airavata-api/airavata-client-sdks/airavata-php-sdk/src/main/resources/lib/Airavata/API/Airavata.php
>>>>>>>>>> 
>>>>>>>>>>>>>>>>>>>>>>>>>>> but it looks like the interactions with the compute
>>>>>>>>>> resource are
>>>>>>>>>>>>>>>>>>>>>>>>>>> deeper
>>>>>>>>>>>>>>>>>>>>>>>>>>> down...
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>>>> 
>>>> 
>>>> --
>>>> System Analyst Programmer
>>>> PTI Lab
>>>> Indiana University
>>>> 
>>> 
>>> 
>>> 
>>> -- 
>>> System Analyst Programmer
>>> PTI Lab
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