| #Flow-Control | |
| #Remote Login (client-server) | |
| Client-Side | |
| -cbit.vcell.client.VCellClientMain | |
| --cbit.vcell.client.VCellClient | |
| ---org.vcell.api.server.ClientServerManager | |
| ----org.vcell.api.messaging.RemoteProxyVCellConnectionFactory | |
| -----cbit.vcell.server.VCellConnection (Connection to outside for all of VCell) | |
| ------org.vcell.api.messaging.LocalVCellConnectionMessaging (Presents restful VCellApiClient services) | |
| -------org.vcell.api.messaging.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 | |
| ... | |
| -org.vcell.api.messaging.LocalVCellConnectionMessaging.getUserMetaDbServer() | |
| --org.vcell.api.messaging.LocalUserMetaDbServerMessaging.getVCInfoContainer() | |
| ---cbit.vcell.message.server.bootstrap.client.RpcDbServerProxy.getVCInfoContainer() | |
| ----org.vcell.api.messaging.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-oracle.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() | |
| ----org.vcell.api.messaging.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 | |