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From Marlon Pierce <marpi...@iu.edu>
Subject Fwd: Re: [SciGaP-Dev] CIPRES-Airavata integration proposal]]
Date Fri, 18 Jul 2014 16:21:09 GMT



-------- Original Message --------
Subject: 	Re: [SciGaP-Dev] CIPRES-Airavata integration proposal]]
Date: 	Fri, 18 Jul 2014 09:07:29 -0700
From: 	K Yoshimoto <kenneth@sdsc.edu>
To: 	<dev@airavata.org>, <dev@scigap.org>



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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