#Flow-Control
#Remote Login (client-server)
Client-Side
-cbit.vcell.client.test.VCellClientTest
--cbit.vcell.client.VCellClient
---cbit.vcell.client.server.ClientServerManager
----cbit.vcell.message.server.bootstrap.client.RemoteProxyVCellConnectionFactory
-----cbit.vcell.server.VCellConnection (Connection to outside for all of VCell)
------cbit.vcell.message.server.bootstrap.client.LocalVCellConnectionMessaging (Presents restful VCellApiClient services)
-------cbit.vcell.message.server.bootstrap.client.RemoteProxyVCellConnectionFactory.RemoteProxyRpcSender (manages VCellApiClient)
--------org.vcell.api.client.VCellApiClient (.authenticate(...), and all VCell client calls (with AccessTokenRepresentation) leave host from here)
Server-side
vcell-api container
--------org.vcell.rest.VCellApiMain (entrypoint, Starts http restlet server)
-------org.vcell.rest.VCellApiApplication (Registers handlers with the restlet server)
------org.vcell.rest.auth.AuthenticationTokenRestlet (login authentication, return AccessTokenRepresentation)
#Populate Client Database metadata
Client-Side
...
-cbit.vcell.message.server.bootstrap.client.LocalVCellConnectionMessaging.getUserMetaDbServer()
--cbit.vcell.message.server.bootstrap.client.LocalUserMetaDbServerMessaging.getVCInfoContainer()
---cbit.vcell.message.server.bootstrap.client.RpcDbServerProxy.getVCInfoContainer()
----cbit.vcell.message.server.bootstrap.client.RemoteProxyVCellConnectionFactory.RemoteProxyRpcSender.sendRpcMessage(...)
-----org.vcell.api.client.VCellApiClient.sendRpcMessage(...) (blocking call, waits for http response)
Server-Side
vcell-api container
------org.vcell.rest.rpc.RpcRestlet.handle(...) (blocking call)
-------org.vcell.rest.rpc.RpcService (sends request to AMQint) (blocking call, waits for message response on temporary queue)
activemqint container
-------recieves rpc request 'dbReq' queue
-------notifies vcell-db container that a rpc request is ready (traditional point to point message queue rather than publish/subscribe)
vcell-db container
--------cbit.vcell.message.VCRpcMessageHandler.onQueueMessage(...)
---------cbit.vcell.message.VCRpcRequest.rpc(...)
----------cbit.vcell.modeldb.DatabaseServerImpl.getVCInfoContainer() (sends data response to AMQint on temp queue)
activemqint container
-----------receives rpcresponse
-----------notifies vcell-api (point to point queue)
vcell-api container
-----org.vcell.api.client.VCellApiClient.sendRpcMessage(...) (return from blicking call started above)
#Server solver send status to Server database
SOLVER executables, c++ code
each solver calls vcell-solver/VCellMessaging/src/SimulationMessaging.cpp.start(...) once at startup (sets AMQ host and port)
all solvers call vcell-solver/VCellMessaging/src/SimulationMessaging.cpp.setWorkerEvent(...) to put messages in queue
-SimulationMessaging.sendStatus(...) (polling thread to get status from queue, sends http POST using curl to AMQsim)
activemqsim container (runs ActiveMQ)
-recieves sim status messages on 'workerEvent queue'
--notifies sched container that a workerEvent is ready (traditional point to point message queue rather than publish/subscribe)
sched container (AMQsim java, contains entire database driver code, does not use vcell-db container)
-SimulationDispatcher.onWorkerEventMessage(..)
--SimulationDispatcherEngine.onworkerEvent(...)
---SimulationStateMachine.onWorkerEvent(...)
----SimulationDatabaseDirect.updateSimulationJobStatus(...)
-----AdminDBToplevel.updateSimulationJobStatus(...) (updates Oracle real database host vcell-db.cam.uchc.edu, NOT vcell-db container)
----StatusMessage.sendToClient(...) (sends to AMQint container clientStatus topic)
activemqint container
-recieves sim status message on the 'clientStatus' topic
--notifies all vcell-api container subscribers
VCell-Api container
-RestEventService.newEventMessage(...) (add to local cache called 'events' simulationJobStatus,ExportEvent,DataJobEvent)
#Client asks for server side events includes (Solver status,Export, DataJob)
Client-side
-AsynchMessageManager.poll() (feeds a single AnychMessageManager, client code add listeners to get events)
--ClientServerManager.getmessageEvents()
---LocalVCellConnectionMessaging.getMessageEvents()
----cbit.vcell.message.server.bootstrap.client.RemoteProxyVCellConnectionFactory.RemoteProxyRpcSender (manages VCellApiClient)
-----org.vcell.api.client.VCellApiClient.getEvents() (uses https://host:port/events?beginTimestamp=xxx)
Server-side
vcell-api container
-EventsRestlet.handle(...) (handles any uri of type '/events', defined in VCellApiApplication)
--RestEventService.query(userid,lastTimestamp) (return json encoded events/timestamp since last timestamp)
#Client to Server starting a simulation
Client-side
-Green button -> SimulationListPanel.runSimulations(...)
--Simulationworkspce.runSimulation(...)
---ClientRequestManager.runSimulations(...)
----RunSims.run()
----ClientJobManager.startSimulation(...)
-----LocalSimulationControllerMessaging.startSimulation(...)
-----RpcSimServerProxy.startsimulation(...)
------RemoteProxyRpcSender.sendRpcMessage(...)
------VCellApiClient.sendRpcMessage(...)
Server-side
vcell-api container
------org.vcell.rest.rpc.RpcRestlet.handle(...) (blocking call)
-------org.vcell.rest.rpc.RpcService (sends request to AMQint) (blocking call, waits for message response on temporary queue)
activemqint container
-------recieves rpc request 'simReq' queue
-------notifies vcell-sched container that a rpc request is ready (traditional point to point message queue rather than publish/subscribe)
vcell-sched container
--------cbit.vcell.message.VCRpcMessageHandler.onQueueMessage(...)
---------cbit.vcell.message.VCRpcRequest.rpc(...)
----------SimulationDispatcher.SimulationServiceImpl.startSimulation(...)
-----------SimulationDispatcherEngine.onStartRequest(...)
------------SimulationStateMachine.onStartRequest(...)
-------------SimulationDatabseDirect.insertSimulationJobStatus(...) (save SimJobStatus to DB with status 'waiting'
-------------StatusMessage.sendToClient(...) (send message to AMQint topic:clientStatus, then returns to client)
=====Now Sim request waits to be processed in different separate thread according to scheduler=====
vcell-sched container
-SimulationDispatcher.DispatchThread.run(...) (run continuously, polls db)
--SimulationDatabaseDirect.getActiveJobs(...)
--BatchScheduler.schedule(...) (return list of jobs that should be done after deciding)
--SimulationDispatcherEngine.onDispatch(...) {done for each job to be run, get simulation from db)
---SimulationStateMachine.onDispatch(...) (create simulation task)
----SimulationDatabseDirect.updateSimulationJobStatus(...) (SimJobStatus to DB with status 'dispatched')
----SimulationTaskMessage.sendSimulationTask(...) (send message to AMQint queue 'simJob')
----StatusMessage.sendToClient(...) (send message AMQint topic:clientStatus, return from processing)
=====Now scheduled sim task is waiting in queue to be read by vcell-submit
vcell-submit container/service
-HtcSimulationWorker.initQueueConsumer().QueueListener.onQueueMessage(...) (receives sim task message)
--HtcSimulationWorker.submit2PBS(...) (writes simtask.xml to the user directory)
---SlurmProxy.submitJb(...) (generates .slurm.sub script, writes to htclogs dir (/htclogs inside container) (/share/apps/vcell/htclogs outside container))
----SlurmProxy.submitJobFile(...) (ssh vcell-service (because this is a slurm submit node), executes sbatch xxx.slurm.sub, parses stdout from sbatch to get slurm jobid)
-----WorkerEventMessage.sendAccepted(...) (sends message to AMQsim queue 'workerEvent' type jobAccepted)
=====Now submitted sim task waits to be processed by SLURM
-SLURM read xxx.slurm.sub, parses #SBATCH directives, chooses a hpc node and executes bash script xxx.slurm.sub
-Solvers running on hpc hosts inside singularity images named as vcell-docker.cam.uchc.edu_5000_schaff_vcell-batch_xxx.img
-solvers write data to /share/apps/vcell3/users mapped to /simdata
-Uses "Server solver send status to Server database" as described above
#Client get simulation Data
Client-side
-ClientServerManager.getVCDataManager().getDatasetController().xxx
--LocalDatasetControllerMessaging.xxx
---RpcDataServerProxy.xxx
----RemoteProxyRpcSender.sendRpcMessage(...)
-----VCellApiClient.sendRpcMessage(...) (blocking call, waits for http response)
Server-side
vcell-api container
------org.vcell.rest.rpc.RpcRestlet.handle(...) (blocking call)
-------org.vcell.rest.rpc.RpcService (sends request to AMQint) (blocking call, waits for message response on temporary queue)
activemqint container
-------recieves rpc request 'dataReq' queue
-------notifies vcell-data container that a rpc request is ready (traditional point to point message queue rather than publish/subscribe)
vcell-data container
--------cbit.vcell.message.VCRpcMessageHandler.onQueueMessage(...)
---------cbit.vcell.message.VCRpcRequest.rpc(...)
----------DataserverImpl.xxx
----------cbit.vcell.modeldb.DatasetControllerImpl.xxx (sends data response to AMQint on temp queue)
activemqint container
-----------receives rpcresponse
-----------notifies vcell-api (point to point queue)
vcell-api container
-----org.vcell.api.client.VCellApiClient.sendRpcMessage(...) (return from blocking call started above)
#Client get Bio/Math Model client-side