In looking through the outputs, I noticed that in the task list,
applicationId is set correctly, but in the top level of the experiment
structure, applicationId was actually module Id. I updated
experiment to have applicationId. Now, I get an internal server
error.
john@anya:/media/scigap/scigap/javaclient/airavata/airavata-api/thrift-interface-descriptions/gen-py/apache/airavata/api$
./Airavata-remote2 -h localhost:8930 updateExperiment
echoexperiment_4cbf1edf-5769-4129-88eb-3bd42914674b
"experimentModel.ttypes.Experiment(userName='kenneth1',name='echoexperiment',projectID='echoproject_e422632d-f873-4a1e-9290-0c7dc355d3d0',applicationId='testecho_72968890-bf93-4e93-b7a1-b336b813baec')"
None
john@anya:/media/scigap/scigap/javaclient/airavata/airavata-api/thrift-interface-descriptions/gen-py/apache/airavata/api$
./Airavata-remote2 -h localhost:8930 launchExperiment
echoexperiment_4cbf1edf-5769-4129-88eb-3bd42914674b runme Traceback (most
recent call last): File
"./Airavata-remote2", line 291, in <module>
pp.pprint(client.launchExperiment(args[0],args[1],))
File
"/media/scigap/scigap/javaclient/airavata/airavata-api/thrift-interface-descriptions/gen-py/apache/airavata/api/Airavata.py",
line 2474, in launchExperiment
self.recv_launchExperiment()
File
"/media/scigap/scigap/javaclient/airavata/airavata-api/thrift-interface-descriptions/gen-py/apache/airavata/api/Airavata.py",
line 2491, in recv_launchExperiment
raise x
thrift.Thrift.TApplicationException: Internal error processing launchExperiment
john@anya:/media/scigap/scigap/javaclient/airavata/airavata-api/thrift-interface-descriptions/gen-py/apache/airavata/api$
./Airavata-remote2 -h localhost:8930 getAllUserExperiments kenneth1
[ Experiment(userName='kenneth1',
experimentOutputs=[], errors=None, applicationVersion=None,
name='echoexperiment', workflowTemplateId=None,
projectID='echoproject_e422632d-f873-4a1e-9290-0c7dc355d3d0',
stateChangeList=[WorkflowNodeStatus(timeOfStateChange=1415834224364,
workflowNodeState=7), WorkflowNodeStatus(timeOfStateChange=1416425646059,
workflowNodeState=7)], creationTime=1416425627289,
workflowNodeDetailsList=[WorkflowNodeDetails(nodeInstanceId='IDontNeedaNode_c4407bd7-6654-49f1-87b3-5595c1565cb0',
errors=[], nodeName='IDontNeedaNode', nodeOutputs=[], executionUnitData=None,
workflowNodeStatus=WorkflowNodeStatus(timeOfStateChange=1415834224364,
workflowNodeState=7), creationTime=1415834224252, executionUnit=1,
taskDetailsList=[TaskDetails(applicationInputs=[], errors=[],
applicationVersion=None, applicationOutputs=[], applicationDeploymentId=None,
advancedOutputDataHandling=None, creationTime=None, dataTransferDetailsList=[],
taskStatus=TaskStatus(timeOfStateChange=1415834224512, executionState=12),
advancedInputDataHandling=None,
taskID='IDontNeedaNode_713ea733-0784-44e1-a54e-542a042614e7',
jobDetailsList=[], taskScheduling=None,
applicationId='testecho_72968890-bf93-4e93-b7a1-b336b813baec')],
nodeInputs=[]),
WorkflowNodeDetails(nodeInstanceId='IDontNeedaNode_fdca8846-77d8-4230-8ea1-7c2460cd5430',
errors=[], nodeName='IDontNeedaNode', nodeOutputs=[], executionUnitData=None,
workflowNodeStatus=WorkflowNodeStatus(timeOfStateChange=1416425646059,
workflowNodeState=7), creationTime=1416425646033, executionUnit=1,
taskDetailsList=[TaskDetails(applicationInputs=[], errors=[],
applicationVersion=None, applicationOutputs=[], applicationDeploymentId=None,
advancedOutputDataHandling=None, creationTime=None, dataTransferDetailsList=[],
taskStatus=TaskStatus(timeOfStateChange=1416425646154, executionState=12),
advancedInputDataHandling=None,
taskID='IDontNeedaNode_f4094967-8282-4414-a1be-77a3dc5eab40',
jobDetailsList=[], taskScheduling=None,
applicationId='testecho_72968890-bf93-4e93-b7a1-b336b813baec')],
nodeInputs=[])],
experimentID='echoexperiment_4cbf1edf-5769-4129-88eb-3bd42914674b',
workflowTemplateVersion=None, workflowExecutionInstanceId=None,
userConfigurationData=None, experimentInputs=[],
experimentStatus=ExperimentStatus(timeOfStateChange=1415828345114,
experimentState=0),
applicationId='testecho_72968890-bf93-4e93-b7a1-b336b813baec',
description=None)]
john@anya:/media/scigap/scigap/javaclient/airavata/airavata-api/thrift-interface-descriptions/gen-py/apache/airavata/api$
[INFO] Id:echoexperiment_4cbf1edf-5769-4129-88eb-3bd42914674b : Successfully
updated experiment echoexperiment
[ERROR] Error occurred during processing of message.
java.lang.NullPointerException
at
org.apache.airavata.orchestrator.core.validator.impl.SimpleAppDataValidator.validate(SimpleAppDataValidator.java:50)
at
org.apache.airavata.orchestrator.cpi.impl.SimpleOrchestratorImpl.validateExperiment(SimpleOrchestratorImpl.java:120)
at
org.apache.airavata.orchestrator.server.OrchestratorServerHandler.validateExperiment(OrchestratorServerHandler.java:265)
at
org.apache.airavata.orchestrator.cpi.OrchestratorService$Processor$validateExperiment.getResult(OrchestratorService.java:547)
at
org.apache.airavata.orchestrator.cpi.OrchestratorService$Processor$validateExperiment.getResult(OrchestratorService.java:531)
at org.apache.thrift.ProcessFunction.process(ProcessFunction.java:39)
at org.apache.thrift.TBaseProcessor.process(TBaseProcessor.java:39)
at
org.apache.thrift.server.TThreadPoolServer$WorkerProcess.run(TThreadPoolServer.java:225)
at
java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1146)
at
java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:615)
at java.lang.Thread.run(Thread.java:701)
[ERROR] Internal error processing launchExperiment
org.apache.thrift.transport.TTransportException
at
org.apache.thrift.transport.TIOStreamTransport.read(TIOStreamTransport.java:132)
at org.apache.thrift.transport.TTransport.readAll(TTransport.java:84)
at
org.apache.thrift.protocol.TBinaryProtocol.readAll(TBinaryProtocol.java:362)
at
org.apache.thrift.protocol.TBinaryProtocol.readI32(TBinaryProtocol.java:284)
at
org.apache.thrift.protocol.TBinaryProtocol.readMessageBegin(TBinaryProtocol.java:191)
at org.apache.thrift.TServiceClient.receiveBase(TServiceClient.java:69)
at
org.apache.airavata.orchestrator.cpi.OrchestratorService$Client.recv_validateExperiment(OrchestratorService.java:237)
at
org.apache.airavata.orchestrator.cpi.OrchestratorService$Client.validateExperiment(OrchestratorService.java:224)
at
org.apache.airavata.api.server.handler.AiravataServerHandler.launchExperiment(AiravataServerHandler.java:1168)
at
org.apache.airavata.api.Airavata$Processor$launchExperiment.getResult(Airavata.java:7952)
at
org.apache.airavata.api.Airavata$Processor$launchExperiment.getResult(Airavata.java:7936)
at org.apache.thrift.ProcessFunction.process(ProcessFunction.java:39)
at org.apache.thrift.TBaseProcessor.process(TBaseProcessor.java:39)
at
org.apache.thrift.server.TThreadPoolServer$WorkerProcess.run(TThreadPoolServer.java:225)
at
java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1146)
at
java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:615)
at java.lang.Thread.run(Thread.java:701)
On Wed, Nov 19, 2014 at 10:18:50AM -0800, K Yoshimoto wrote:
>
> Outputs are inline below. I think I need to somehow specify the
> execution type in one of the steps. Not sure which step that is...
>
>
> On Wed, Nov 19, 2014 at 12:51:05PM -0500, Lahiru Gunathilake wrote:
> > Hi Kennath,
> >
> > Yes you have to give the application interface Id when you create
> > Experiment. During registration registerApplicationInterface will return
> > the Id. but if you have already registered and you don't have it you have
> > to get all the Applications and find which Application Id you need by
> > comparing the name or some other sensible property you have.
> > Please check following operations.
> >
> > registerApplicationInterface
>
>
> john@anya:/media/scigap/scigap/javaclient/airavata/airavata-api/thrift-interface-descriptions/gen-py/apache/airavata/api$
> ./Airavata-remote2 -h localhost:8930 registerApplicationInterface
> "applicationInterfaceModel.ttypes.ApplicationInterfaceDescription(applicationName='testecho',applicationModules=['test1moduleid_a3eaf9f9-8b55-44d4-a188-e788fb02c100',])"
> 'testecho_72968890-bf93-4e93-b7a1-b336b813baec'
> john@anya:/media/scigap/scigap/javaclient/airavata/airavata-api/thrift-interface-descriptions/gen-py/apache/airavata/api$
>
>
> >
> > getAllApplicationInterfaceNames
>
>
> john@anya:/media/scigap/scigap/javaclient/airavata/airavata-api/thrift-interface-descriptions/gen-py/apache/airavata/api$
> ./Airavata-remote2 -h localhost:8930 getAllApplicationInterfaceNames
> { 'Amber_09c213df-9a16-417d-8483-4671c15f6e48': 'Amber',
> 'Amber_2bc2df9a-8cb5-4d5f-ad28-a4fb6bb70e33': 'Amber',
> 'Amber_ecd8e7b4-ce44-47ab-a2f7-c3acb11b8e36': 'Amber',
> 'AutoDock_730469ef-3ddd-4753-86c4-f9472b805ab5': 'AutoDock',
> 'AutoDock_ba2f7b79-de9c-4de0-9097-d832ad3fb1ee': 'AutoDock',
> 'AutoDock_d3089626-a36f-4ed2-9290-6c7687fa5fb0': 'AutoDock',
> 'ESPRESSO_19505f99-04b2-49bc-b6d1-8a6d9c555404': 'ESPRESSO',
> 'ESPRESSO_7b4e5bce-b878-4556-9f74-0e2609fa9d37': 'ESPRESSO',
> 'ESPRESSO_fa045f70-3ac2-4126-b4a8-2dab1ddd8aee': 'ESPRESSO',
> 'Echo_7c58876f-dda8-4ed8-8807-d93f626388a3': 'Echo',
> 'Echo_8a1c59b7-3cc3-4dff-9b3f-61d60b76a4f6': 'Echo',
> 'Echo_d2fdb22f-bdee-4ea1-80cc-e2aa51797fe4': 'Echo',
> 'GROMACS_08035974-82fc-4b98-82b8-45790bd3a31b': 'GROMACS',
> 'GROMACS_44c214db-83cb-4993-8cf9-e4cfeb57ae47': 'GROMACS',
> 'GROMACS_a141fa43-b3ad-49ef-a138-da047b8c63f9': 'GROMACS',
> 'LAMMPS_a5e8cb34-6a6c-4821-bc2f-00f434218355': 'LAMMPS',
> 'LAMMPS_cf77273d-d947-4985-9f5f-3c5285ae63e1': 'LAMMPS',
> 'LAMMPS_fe3608cc-5399-4e33-88c3-32a7224731d7': 'LAMMPS',
> 'NWChem_82dfa63e-ea05-4247-b3f0-17b327b953d0': 'NWChem',
> 'NWChem_91c6815c-52f0-4c58-885a-6e45561083d1': 'NWChem',
> 'NWChem_c901c844-42e6-4fee-9e70-c597260b34e7': 'NWChem',
> 'Trinity_27112dae-d56a-4af2-830f-d7a98ea6d465': 'Trinity',
> 'Trinity_4aff86b1-fa7d-4e96-b176-392821719f45': 'Trinity',
> 'Trinity_7e8f7763-e9b3-437c-9b54-2f0c9b567137': 'Trinity',
> 'WRF_20e942c1-a23d-4fb5-b748-344c5db8c685': 'WRF',
> 'WRF_2aa3f5a2-81fe-4240-802c-3be124dff371': 'WRF',
> 'WRF_adf13b52-53c1-4fa8-80fe-cdd76c757b86': 'WRF',
> 'testecho_72968890-bf93-4e93-b7a1-b336b813baec': 'testecho'}
> john@anya:/media/scigap/scigap/javaclient/airavata/airavata-api/thrift-interface-descriptions/gen-py/apache/airavata/api$
>
>
> >
> > getAllApplicationInterfaces
>
>
> john@anya:/media/scigap/scigap/javaclient/airavata/airavata-api/thrift-interface-descriptions/gen-py/apache/airavata/api$
> ./Airavata-remote2 -h localhost:8930 getAllApplicationInterfaces
> [ ApplicationInterfaceDescription(applicationName='Echo',
> applicationDesription='A Simple Echo Application',
> applicationInterfaceId='Echo_8a1c59b7-3cc3-4dff-9b3f-61d60b76a4f6',
> applicationInputs=[InputDataObjectType(userFriendlyDescription='A test string
> to Echo', name='Input_to_Echo', value='Hello World',
> applicationArgument=None, standardInput=False, type=0, metaData=None)],
> applicationOutputs=[OutputDataObjectType(type=0, name='Echoed_Output',
> value='')], applicationModules=['Echo_eaf4c259-b421-4a1f-b2fa-05791a09b14d']),
> ApplicationInterfaceDescription(applicationName='Amber',
> applicationDesription='Assisted Model Building with Energy Refinement MD
> Package',
> applicationInterfaceId='Amber_2bc2df9a-8cb5-4d5f-ad28-a4fb6bb70e33',
> applicationInputs=[InputDataObjectType(userFriendlyDescription='Heating up
> the system equilibration stage - 02_Heat.rst', name='Heat_Restart_File',
> value=None, applicationArgument=None, standardInput=False, type=3,
> metaData=None), InputDataObjectType(userFriendlyDescription='Constant
> pressure and temperature for production stage - 03_Prod.in',
> name='Production_Control_File', value=None, applicationArgument=None,
> standardInput=False, type=3, metaData=None),
> InputDataObjectType(userFriendlyDescription='Parameter and Topology
> coordinates - prmtop', name='Parameter_Topology_File', value=None,
> applicationArgument=None, standardInput=False, type=3, metaData=None)],
> applicationOutputs=[OutputDataObjectType(type=3,
> name='AMBER_Execution_Summary', value=None), OutputDataObjectType(type=3,
> name='AMBER_Execution_log', value=None), OutputDataObjectType(type=3,
> name='AMBER_Trajectory_file', value=None), OutputDataObjectType(type=3,
> name='AMBER_Restart_file', value=None)],
> applicationModules=['Amber_8086cc9f-882c-42f8-aa62-c2569da1d621']),
> ApplicationInterfaceDescription(applicationName='AutoDock',
> applicationDesription='AutoDock suite of automated docking tools',
> applicationInterfaceId='AutoDock_ba2f7b79-de9c-4de0-9097-d832ad3fb1ee',
> applicationInputs=[InputDataObjectType(userFriendlyDescription='Heating up
> the system equilibration stage', name='Heat_Restart_File', value=None,
> applicationArgument=None, standardInput=False, type=3, metaData=None),
> InputDataObjectType(userFriendlyDescription='Constant pressure and
> temperature for production stage', name='Production_Control_File',
> value=None, applicationArgument=None, standardInput=False, type=3,
> metaData=None), InputDataObjectType(userFriendlyDescription='Parameter and
> Topology coordinates', name='Parameter_Topology_File', value=None,
> applicationArgument=None, standardInput=False, type=3, metaData=None)],
> applicationOutputs=[OutputDataObjectType(type=0, name='Echoed_Output',
> value='')],
> applicationModules=['AutoDock_756bc6aa-a0c8-4de7-9c76-40828a91d23d']),
> ApplicationInterfaceDescription(applicationName='ESPRESSO',
> applicationDesription='Nanoscale electronic-structure calculations and
> materials modeling',
> applicationInterfaceId='ESPRESSO_19505f99-04b2-49bc-b6d1-8a6d9c555404',
> applicationInputs=[InputDataObjectType(userFriendlyDescription='AI_Metal_Input_File
> - Al.sample.in', name='AI_Primitive_Cell', value=None,
> applicationArgument=None, standardInput=False, type=3, metaData=None),
> InputDataObjectType(userFriendlyDescription='Constant pressure and
> temperature for production stage - Al.pz-vbc.UPF',
> name='AI_Pseudopotential_File', value=None, applicationArgument=None,
> standardInput=False, type=3, metaData=None)],
> applicationOutputs=[OutputDataObjectType(type=3,
> name='ESPRESSO_Execution_Log', value=None), OutputDataObjectType(type=3,
> name='ESPRESSO_WFC_Binary_file', value=None)],
> applicationModules=['ESPRESSO_0580b239-0250-4be7-af52-dc3992fe475c']),
> ApplicationInterfaceDescription(applicationName='GROMACS',
> applicationDesription='GROMACS Molecular Dynamics Package',
> applicationInterfaceId='GROMACS_a141fa43-b3ad-49ef-a138-da047b8c63f9',
> applicationInputs=[InputDataObjectType(userFriendlyDescription='Coordinates
> velocities, molecular topology and simulation parameters -
> pdb1y6l-EM-vacuum.tpr', name='Portable_Input_Binary_File', value=None,
> applicationArgument=None, standardInput=False, type=3, metaData=None),
> InputDataObjectType(userFriendlyDescription='Trajectory Coordinates Molecular
> Structure in Gromos87 format - pdb1y6l-EM-vacuum.gro',
> name='GROMOS_Coordinate_File', value=None, applicationArgument=None,
> standardInput=False, type=3, metaData=None)],
> applicationOutputs=[OutputDataObjectType(type=3,
> name='GROMACS_Execution_Log', value=None), OutputDataObjectType(type=3,
> name='Full_Precision_Trajectory_file', value=None),
> OutputDataObjectType(type=3, name='Portable_Energy_file', value=None)],
> applicationModules=['GROMACS_8d378c73-b61e-4385-8b5e-2afaf98cc6e1']),
> ApplicationInterfaceDescription(applicationName='LAMMPS',
> applicationDesription='Large-scale Atomic/Molecular Massively Parallel
> Simulator',
> applicationInterfaceId='LAMMPS_fe3608cc-5399-4e33-88c3-32a7224731d7',
> applicationInputs=[InputDataObjectType(userFriendlyDescription='Friction
> Simulation Input - in.friction', name='Friction_Simulation_Input',
> value=None, applicationArgument=None, standardInput=False, type=3,
> metaData=None)], applicationOutputs=[OutputDataObjectType(type=3,
> name='LAMMPS_Simulation_Log', value=None)],
> applicationModules=['LAMMPS_c01e5b28-6483-4e14-93f4-a1b027c9334c']),
> ApplicationInterfaceDescription(applicationName='NWChem',
> applicationDesription='Ab initio computational chemistry software package',
> applicationInterfaceId='NWChem_91c6815c-52f0-4c58-885a-6e45561083d1',
> applicationInputs=[InputDataObjectType(userFriendlyDescription='Water
> Molecule Input File - water.nw', name='Water_Molecule_Input', value=None,
> applicationArgument=None, standardInput=False, type=3, metaData=None)],
> applicationOutputs=[OutputDataObjectType(type=3, name='NWChem_Execution_Log',
> value=None)],
> applicationModules=['NWChem_6dee6b36-dd8b-4ab1-84f4-8d39bbbcdf67']),
> ApplicationInterfaceDescription(applicationName='Trinity',
> applicationDesription='de novo reconstruction of transcriptomes from RNA-seq
> data', applicationInterfaceId='Trinity_27112dae-d56a-4af2-830f-d7a98ea6d465',
> applicationInputs=[InputDataObjectType(userFriendlyDescription='RNA-Seq Left
> Library - reads.left.fq', name='RNA_Seq_Left_Input', value=None,
> applicationArgument=None, standardInput=False, type=3, metaData=None),
> InputDataObjectType(userFriendlyDescription='RNA-Seq Right Library -
> reads.right.fq', name='RNA_Seq_Right_Input', value=None,
> applicationArgument=None, standardInput=False, type=3, metaData=None)],
> applicationOutputs=[OutputDataObjectType(type=3,
> name='Trinity_Execution_Log', value=None), OutputDataObjectType(type=3,
> name='Trinity_FASTA_File', value=None)],
> applicationModules=['Trinity_c70e55c0-4a33-4cd7-9a61-d64b0b597aac']),
> ApplicationInterfaceDescription(applicationName='WRF',
> applicationDesription='Weather Research and Forecasting',
> applicationInterfaceId='WRF_20e942c1-a23d-4fb5-b748-344c5db8c685',
> applicationInputs=[InputDataObjectType(userFriendlyDescription='Namelist
> Configuration File - namelist.input', name='Config_Namelist_File',
> value=None, applicationArgument=None, standardInput=False, type=3,
> metaData=None), InputDataObjectType(userFriendlyDescription='Initial
> Conditions File - wrfinput_d01', name='WRF_Initial_Conditions', value=None,
> applicationArgument=None, standardInput=False, type=3, metaData=None),
> InputDataObjectType(userFriendlyDescription='Boundary Conditions File -
> wrfbdy_d01', name='WRF_Boundary_File', value=None, applicationArgument=None,
> standardInput=False, type=3, metaData=None)],
> applicationOutputs=[OutputDataObjectType(type=3, name='WRF_Output',
> value=''), OutputDataObjectType(type=3, name='WRF_Execution_Log', value='')],
> applicationModules=['WRF_c2ff7d21-b5db-4bc4-a843-aacd3949bb76']),
> ApplicationInterfaceDescription(applicationName='Echo',
> applicationDesription='A Simple Echo Application',
> applicationInterfaceId='Echo_d2fdb22f-bdee-4ea1-80cc-e2aa51797fe4',
> applicationInputs=[InputDataObjectType(userFriendlyDescription='A test string
> to Echo', name='Input_to_Echo', value='Hello World',
> applicationArgument=None, standardInput=False, type=0, metaData=None)],
> applicationOutputs=[OutputDataObjectType(type=0, name='Echoed_Output',
> value='')], applicationModules=['Echo_9702c64c-aac6-4af6-846a-419c6fe90a97']),
> ApplicationInterfaceDescription(applicationName='Amber',
> applicationDesription='Assisted Model Building with Energy Refinement MD
> Package',
> applicationInterfaceId='Amber_09c213df-9a16-417d-8483-4671c15f6e48',
> applicationInputs=[InputDataObjectType(userFriendlyDescription='Heating up
> the system equilibration stage - 02_Heat.rst', name='Heat_Restart_File',
> value=None, applicationArgument=None, standardInput=False, type=3,
> metaData=None), InputDataObjectType(userFriendlyDescription='Constant
> pressure and temperature for production stage - 03_Prod.in',
> name='Production_Control_File', value=None, applicationArgument=None,
> standardInput=False, type=3, metaData=None),
> InputDataObjectType(userFriendlyDescription='Parameter and Topology
> coordinates - prmtop', name='Parameter_Topology_File', value=None,
> applicationArgument=None, standardInput=False, type=3, metaData=None)],
> applicationOutputs=[OutputDataObjectType(type=3,
> name='AMBER_Execution_Summary', value=None), OutputDataObjectType(type=3,
> name='AMBER_Execution_log', value=None), OutputDataObjectType(type=3,
> name='AMBER_Trajectory_file', value=None), OutputDataObjectType(type=3,
> name='AMBER_Restart_file', value=None)],
> applicationModules=['Amber_f8751ce1-50be-4a66-a379-435b12fb913c']),
> ApplicationInterfaceDescription(applicationName='AutoDock',
> applicationDesription='AutoDock suite of automated docking tools',
> applicationInterfaceId='AutoDock_730469ef-3ddd-4753-86c4-f9472b805ab5',
> applicationInputs=[InputDataObjectType(userFriendlyDescription='Heating up
> the system equilibration stage', name='Heat_Restart_File', value=None,
> applicationArgument=None, standardInput=False, type=3, metaData=None),
> InputDataObjectType(userFriendlyDescription='Constant pressure and
> temperature for production stage', name='Production_Control_File',
> value=None, applicationArgument=None, standardInput=False, type=3,
> metaData=None), InputDataObjectType(userFriendlyDescription='Parameter and
> Topology coordinates', name='Parameter_Topology_File', value=None,
> applicationArgument=None, standardInput=False, type=3, metaData=None)],
> applicationOutputs=[OutputDataObjectType(type=0, name='Echoed_Output',
> value='')],
> applicationModules=['AutoDock_61929da5-81c2-4568-b9d5-b3b64a0447bb']),
> ApplicationInterfaceDescription(applicationName='ESPRESSO',
> applicationDesription='Nanoscale electronic-structure calculations and
> materials modeling',
> applicationInterfaceId='ESPRESSO_7b4e5bce-b878-4556-9f74-0e2609fa9d37',
> applicationInputs=[InputDataObjectType(userFriendlyDescription='AI_Metal_Input_File
> - Al.sample.in', name='AI_Primitive_Cell', value=None,
> applicationArgument=None, standardInput=False, type=3, metaData=None),
> InputDataObjectType(userFriendlyDescription='Constant pressure and
> temperature for production stage - Al.pz-vbc.UPF',
> name='AI_Pseudopotential_File', value=None, applicationArgument=None,
> standardInput=False, type=3, metaData=None)],
> applicationOutputs=[OutputDataObjectType(type=3,
> name='ESPRESSO_Execution_Log', value=None), OutputDataObjectType(type=3,
> name='ESPRESSO_WFC_Binary_file', value=None)],
> applicationModules=['ESPRESSO_abb99ab0-a8c6-404f-a7bb-baf39aaaadbd']),
> ApplicationInterfaceDescription(applicationName='GROMACS',
> applicationDesription='GROMACS Molecular Dynamics Package',
> applicationInterfaceId='GROMACS_44c214db-83cb-4993-8cf9-e4cfeb57ae47',
> applicationInputs=[InputDataObjectType(userFriendlyDescription='Coordinates
> velocities, molecular topology and simulation parameters -
> pdb1y6l-EM-vacuum.tpr', name='Portable_Input_Binary_File', value=None,
> applicationArgument=None, standardInput=False, type=3, metaData=None),
> InputDataObjectType(userFriendlyDescription='Trajectory Coordinates Molecular
> Structure in Gromos87 format - pdb1y6l-EM-vacuum.gro',
> name='GROMOS_Coordinate_File', value=None, applicationArgument=None,
> standardInput=False, type=3, metaData=None)],
> applicationOutputs=[OutputDataObjectType(type=3,
> name='GROMACS_Execution_Log', value=None), OutputDataObjectType(type=3,
> name='Full_Precision_Trajectory_file', value=None),
> OutputDataObjectType(type=3, name='Portable_Energy_file', value=None)],
> applicationModules=['GROMACS_d9e4c1a9-7850-4a2d-982d-7fbb451a95de']),
> ApplicationInterfaceDescription(applicationName='LAMMPS',
> applicationDesription='Large-scale Atomic/Molecular Massively Parallel
> Simulator',
> applicationInterfaceId='LAMMPS_a5e8cb34-6a6c-4821-bc2f-00f434218355',
> applicationInputs=[InputDataObjectType(userFriendlyDescription='Friction
> Simulation Input - in.friction', name='Friction_Simulation_Input',
> value=None, applicationArgument=None, standardInput=False, type=3,
> metaData=None)], applicationOutputs=[OutputDataObjectType(type=3,
> name='LAMMPS_Simulation_Log', value=None)],
> applicationModules=['LAMMPS_ae75b917-e483-4ccd-99b4-d69a274056e8']),
> ApplicationInterfaceDescription(applicationName='NWChem',
> applicationDesription='Ab initio computational chemistry software package',
> applicationInterfaceId='NWChem_c901c844-42e6-4fee-9e70-c597260b34e7',
> applicationInputs=[InputDataObjectType(userFriendlyDescription='Water
> Molecule Input File - water.nw', name='Water_Molecule_Input', value=None,
> applicationArgument=None, standardInput=False, type=3, metaData=None)],
> applicationOutputs=[OutputDataObjectType(type=3, name='NWChem_Execution_Log',
> value=None)],
> applicationModules=['NWChem_5f331911-8626-4785-a643-80a49c700eb6']),
> ApplicationInterfaceDescription(applicationName='Trinity',
> applicationDesription='de novo reconstruction of transcriptomes from RNA-seq
> data', applicationInterfaceId='Trinity_4aff86b1-fa7d-4e96-b176-392821719f45',
> applicationInputs=[InputDataObjectType(userFriendlyDescription='RNA-Seq Left
> Library - reads.left.fq', name='RNA_Seq_Left_Input', value=None,
> applicationArgument=None, standardInput=False, type=3, metaData=None),
> InputDataObjectType(userFriendlyDescription='RNA-Seq Right Library -
> reads.right.fq', name='RNA_Seq_Right_Input', value=None,
> applicationArgument=None, standardInput=False, type=3, metaData=None)],
> applicationOutputs=[OutputDataObjectType(type=3,
> name='Trinity_Execution_Log', value=None), OutputDataObjectType(type=3,
> name='Trinity_FASTA_File', value=None)],
> applicationModules=['Trinity_a1a7301f-db64-4925-bf3d-8f4153b02823']),
> ApplicationInterfaceDescription(applicationName='WRF',
> applicationDesription='Weather Research and Forecasting',
> applicationInterfaceId='WRF_adf13b52-53c1-4fa8-80fe-cdd76c757b86',
> applicationInputs=[InputDataObjectType(userFriendlyDescription='Namelist
> Configuration File - namelist.input', name='Config_Namelist_File',
> value=None, applicationArgument=None, standardInput=False, type=3,
> metaData=None), InputDataObjectType(userFriendlyDescription='Initial
> Conditions File - wrfinput_d01', name='WRF_Initial_Conditions', value=None,
> applicationArgument=None, standardInput=False, type=3, metaData=None),
> InputDataObjectType(userFriendlyDescription='Boundary Conditions File -
> wrfbdy_d01', name='WRF_Boundary_File', value=None, applicationArgument=None,
> standardInput=False, type=3, metaData=None)],
> applicationOutputs=[OutputDataObjectType(type=3, name='WRF_Output',
> value=''), OutputDataObjectType(type=3, name='WRF_Execution_Log', value='')],
> applicationModules=['WRF_c1f0435d-ebc1-49ed-953a-01c301ad68eb']),
> ApplicationInterfaceDescription(applicationName='Echo',
> applicationDesription='A Simple Echo Application',
> applicationInterfaceId='Echo_7c58876f-dda8-4ed8-8807-d93f626388a3',
> applicationInputs=[InputDataObjectType(userFriendlyDescription='A test string
> to Echo', name='Input_to_Echo', value='Hello World',
> applicationArgument=None, standardInput=False, type=0, metaData=None)],
> applicationOutputs=[OutputDataObjectType(type=0, name='Echoed_Output',
> value='')], applicationModules=['Echo_8d6ea68b-57f4-4920-bb13-f4f8db99a04e']),
> ApplicationInterfaceDescription(applicationName='Amber',
> applicationDesription='Assisted Model Building with Energy Refinement MD
> Package',
> applicationInterfaceId='Amber_ecd8e7b4-ce44-47ab-a2f7-c3acb11b8e36',
> applicationInputs=[InputDataObjectType(userFriendlyDescription='Heating up
> the system equilibration stage - 02_Heat.rst', name='Heat_Restart_File',
> value=None, applicationArgument=None, standardInput=False, type=3,
> metaData=None), InputDataObjectType(userFriendlyDescription='Constant
> pressure and temperature for production stage - 03_Prod.in',
> name='Production_Control_File', value=None, applicationArgument=None,
> standardInput=False, type=3, metaData=None),
> InputDataObjectType(userFriendlyDescription='Parameter and Topology
> coordinates - prmtop', name='Parameter_Topology_File', value=None,
> applicationArgument=None, standardInput=False, type=3, metaData=None)],
> applicationOutputs=[OutputDataObjectType(type=3,
> name='AMBER_Execution_Summary', value=None), OutputDataObjectType(type=3,
> name='AMBER_Execution_log', value=None), OutputDataObjectType(type=3,
> name='AMBER_Trajectory_file', value=None), OutputDataObjectType(type=3,
> name='AMBER_Restart_file', value=None)],
> applicationModules=['Amber_506b76fc-5780-4873-92aa-2db52ef85fd4']),
> ApplicationInterfaceDescription(applicationName='AutoDock',
> applicationDesription='AutoDock suite of automated docking tools',
> applicationInterfaceId='AutoDock_d3089626-a36f-4ed2-9290-6c7687fa5fb0',
> applicationInputs=[InputDataObjectType(userFriendlyDescription='Heating up
> the system equilibration stage', name='Heat_Restart_File', value=None,
> applicationArgument=None, standardInput=False, type=3, metaData=None),
> InputDataObjectType(userFriendlyDescription='Constant pressure and
> temperature for production stage', name='Production_Control_File',
> value=None, applicationArgument=None, standardInput=False, type=3,
> metaData=None), InputDataObjectType(userFriendlyDescription='Parameter and
> Topology coordinates', name='Parameter_Topology_File', value=None,
> applicationArgument=None, standardInput=False, type=3, metaData=None)],
> applicationOutputs=[OutputDataObjectType(type=0, name='Echoed_Output',
> value='')],
> applicationModules=['AutoDock_b2265253-7966-4d90-a799-79cb22cd5b28']),
> ApplicationInterfaceDescription(applicationName='ESPRESSO',
> applicationDesription='Nanoscale electronic-structure calculations and
> materials modeling',
> applicationInterfaceId='ESPRESSO_fa045f70-3ac2-4126-b4a8-2dab1ddd8aee',
> applicationInputs=[InputDataObjectType(userFriendlyDescription='AI_Metal_Input_File
> - Al.sample.in', name='AI_Primitive_Cell', value=None,
> applicationArgument=None, standardInput=False, type=3, metaData=None),
> InputDataObjectType(userFriendlyDescription='Constant pressure and
> temperature for production stage - Al.pz-vbc.UPF',
> name='AI_Pseudopotential_File', value=None, applicationArgument=None,
> standardInput=False, type=3, metaData=None)],
> applicationOutputs=[OutputDataObjectType(type=3,
> name='ESPRESSO_Execution_Log', value=None), OutputDataObjectType(type=3,
> name='ESPRESSO_WFC_Binary_file', value=None)],
> applicationModules=['ESPRESSO_805611c5-893c-4a29-9891-791492a3aa47']),
> ApplicationInterfaceDescription(applicationName='GROMACS',
> applicationDesription='GROMACS Molecular Dynamics Package',
> applicationInterfaceId='GROMACS_08035974-82fc-4b98-82b8-45790bd3a31b',
> applicationInputs=[InputDataObjectType(userFriendlyDescription='Coordinates
> velocities, molecular topology and simulation parameters -
> pdb1y6l-EM-vacuum.tpr', name='Portable_Input_Binary_File', value=None,
> applicationArgument=None, standardInput=False, type=3, metaData=None),
> InputDataObjectType(userFriendlyDescription='Trajectory Coordinates Molecular
> Structure in Gromos87 format - pdb1y6l-EM-vacuum.gro',
> name='GROMOS_Coordinate_File', value=None, applicationArgument=None,
> standardInput=False, type=3, metaData=None)],
> applicationOutputs=[OutputDataObjectType(type=3,
> name='GROMACS_Execution_Log', value=None), OutputDataObjectType(type=3,
> name='Full_Precision_Trajectory_file', value=None),
> OutputDataObjectType(type=3, name='Portable_Energy_file', value=None)],
> applicationModules=['GROMACS_9f322fba-0600-4728-8929-4f258cecdfbb']),
> ApplicationInterfaceDescription(applicationName='LAMMPS',
> applicationDesription='Large-scale Atomic/Molecular Massively Parallel
> Simulator',
> applicationInterfaceId='LAMMPS_cf77273d-d947-4985-9f5f-3c5285ae63e1',
> applicationInputs=[InputDataObjectType(userFriendlyDescription='Friction
> Simulation Input - in.friction', name='Friction_Simulation_Input',
> value=None, applicationArgument=None, standardInput=False, type=3,
> metaData=None)], applicationOutputs=[OutputDataObjectType(type=3,
> name='LAMMPS_Simulation_Log', value=None)],
> applicationModules=['LAMMPS_94bdcda9-690c-42b1-bf79-498da52f84a6']),
> ApplicationInterfaceDescription(applicationName='NWChem',
> applicationDesription='Ab initio computational chemistry software package',
> applicationInterfaceId='NWChem_82dfa63e-ea05-4247-b3f0-17b327b953d0',
> applicationInputs=[InputDataObjectType(userFriendlyDescription='Water
> Molecule Input File - water.nw', name='Water_Molecule_Input', value=None,
> applicationArgument=None, standardInput=False, type=3, metaData=None)],
> applicationOutputs=[OutputDataObjectType(type=3, name='NWChem_Execution_Log',
> value=None)],
> applicationModules=['NWChem_8986dc65-85d3-445f-ae3b-25b3624212b3']),
> ApplicationInterfaceDescription(applicationName='Trinity',
> applicationDesription='de novo reconstruction of transcriptomes from RNA-seq
> data', applicationInterfaceId='Trinity_7e8f7763-e9b3-437c-9b54-2f0c9b567137',
> applicationInputs=[InputDataObjectType(userFriendlyDescription='RNA-Seq Left
> Library - reads.left.fq', name='RNA_Seq_Left_Input', value=None,
> applicationArgument=None, standardInput=False, type=3, metaData=None),
> InputDataObjectType(userFriendlyDescription='RNA-Seq Right Library -
> reads.right.fq', name='RNA_Seq_Right_Input', value=None,
> applicationArgument=None, standardInput=False, type=3, metaData=None)],
> applicationOutputs=[OutputDataObjectType(type=3,
> name='Trinity_Execution_Log', value=None), OutputDataObjectType(type=3,
> name='Trinity_FASTA_File', value=None)],
> applicationModules=['Trinity_12cb9f4c-d866-421d-a66c-8c1d900238f4']),
> ApplicationInterfaceDescription(applicationName='WRF',
> applicationDesription='Weather Research and Forecasting',
> applicationInterfaceId='WRF_2aa3f5a2-81fe-4240-802c-3be124dff371',
> applicationInputs=[InputDataObjectType(userFriendlyDescription='Namelist
> Configuration File - namelist.input', name='Config_Namelist_File',
> value=None, applicationArgument=None, standardInput=False, type=3,
> metaData=None), InputDataObjectType(userFriendlyDescription='Initial
> Conditions File - wrfinput_d01', name='WRF_Initial_Conditions', value=None,
> applicationArgument=None, standardInput=False, type=3, metaData=None),
> InputDataObjectType(userFriendlyDescription='Boundary Conditions File -
> wrfbdy_d01', name='WRF_Boundary_File', value=None, applicationArgument=None,
> standardInput=False, type=3, metaData=None)],
> applicationOutputs=[OutputDataObjectType(type=3, name='WRF_Output',
> value=''), OutputDataObjectType(type=3, name='WRF_Execution_Log', value='')],
> applicationModules=['WRF_7d342236-134e-477c-9c78-56b5907a1596']),
> ApplicationInterfaceDescription(applicationName='testecho',
> applicationDesription=None,
> applicationInterfaceId='testecho_72968890-bf93-4e93-b7a1-b336b813baec',
> applicationInputs=None, applicationOutputs=None,
> applicationModules=['test1moduleid_a3eaf9f9-8b55-44d4-a188-e788fb02c100'])]
> john@anya:/media/scigap/scigap/javaclient/airavata/airavata-api/thrift-interface-descriptions/gen-py/apache/airavata/api$
>
> >
>
> Here is an attempt at experiment launch:
>
>
> john@anya:/media/scigap/scigap/javaclient/airavata/airavata-api/thrift-interface-descriptions/gen-py/apache/airavata/api$
> ./Airavata-remote2 -h localhost:8930 getAllUserExperiments kenneth1
> [ Experiment(userName='kenneth1', experimentOutputs=[], errors=None,
> applicationVersion=None, name='echoexperiment', workflowTemplateId=None,
> projectID='echoproject_e422632d-f873-4a1e-9290-0c7dc355d3d0',
> stateChangeList=[WorkflowNodeStatus(timeOfStateChange=1415834224364,
> workflowNodeState=7)], creationTime=1415835163643,
> workflowNodeDetailsList=[WorkflowNodeDetails(nodeInstanceId='IDontNeedaNode_c4407bd7-6654-49f1-87b3-5595c1565cb0',
> errors=[], nodeName='IDontNeedaNode', nodeOutputs=[],
> executionUnitData=None,
> workflowNodeStatus=WorkflowNodeStatus(timeOfStateChange=1415834224364,
> workflowNodeState=7), creationTime=1415834224252, executionUnit=1,
> taskDetailsList=[TaskDetails(applicationInputs=[], errors=[],
> applicationVersion=None, applicationOutputs=[], applicationDeploymentId=None,
> advancedOutputDataHandling=None, creationTime=None,
> dataTransferDetailsList=[],
> taskStatus=TaskStatus(timeOfStateChange=1415834224512, executionState=12),
> advancedInputDataHandling=None,
> taskID='IDontNeedaNode_713ea733-0784-44e1-a54e-542a042614e7',
> jobDetailsList=[], taskScheduling=None,
> applicationId='testecho_72968890-bf93-4e93-b7a1-b336b813baec')],
> nodeInputs=[])],
> experimentID='echoexperiment_4cbf1edf-5769-4129-88eb-3bd42914674b',
> workflowTemplateVersion=None, workflowExecutionInstanceId=None,
> userConfigurationData=None, experimentInputs=[],
> experimentStatus=ExperimentStatus(timeOfStateChange=1415828345114,
> experimentState=0),
> applicationId='localhost_849317db-7963-4c41-8bf6-b9124232edd9_test1moduleid',
> description=None)]
>
> john@anya:/media/scigap/scigap/javaclient/airavata/airavata-api/thrift-interface-descriptions/gen-py/apache/airavata/api$
> ./Airavata-remote2 -h localhost:8930 launchExperiment
> echoexperiment_4cbf1edf-5769-4129-88eb-3bd42914674b runme
> Traceback (most recent call last):
> File "./Airavata-remote2", line 291, in <module>
> pp.pprint(client.launchExperiment(args[0],args[1],))
> File
> "/media/scigap/scigap/javaclient/airavata/airavata-api/thrift-interface-descriptions/gen-py/apache/airavata/api/Airavata.py",
> line 2474, in launchExperiment
> self.recv_launchExperiment()
> File
> "/media/scigap/scigap/javaclient/airavata/airavata-api/thrift-interface-descriptions/gen-py/apache/airavata/api/Airavata.py",
> line 2496, in recv_launchExperiment
> raise result.ire
> airavata.api.error.ttypes.InvalidRequestException:
> InvalidRequestException(_message="Experiment
> 'echoexperiment_4cbf1edf-5769-4129-88eb-3bd42914674b' launch failed. Unable
> to figureout execution type for application
> localhost_849317db-7963-4c41-8bf6-b9124232edd9_test1moduleid")
> john@anya:/media/scigap/scigap/javaclient/airavata/airavata-api/thrift-interface-descriptions/gen-py/apache/airavata/api$
>
> >
> > Lahiru
> >
> > On Wed, Nov 12, 2014 at 6:36 PM, K Yoshimoto <[email protected]> wrote:
> >
> > >
> > > I've been playing with the Python API. I can
> > > registerApplicationDeployment
> > > registerApplicationInterface, registerApplicationModule. I am
> > > trying to createExperiment, but when I launch, I either get an
> > > internal error on the server side, or it complains that it can't
> > > figure out application type, Unable to figureout execution type for
> > > application
> > >
> > > Do I need to specify an applicationId for createExperiment?
> > > How do I generate an applicationId? Or is execution type set
> > > somewhere else?
> > >
> > > Thanks,
> > > Kenneth
> > >
> >
> >
> >
> > --
> > Research Assistant
> > Science Gateways Group
> > Indiana University
