Error and logging files¶

When you run a simulation, EMOD will output basic error and logging information to help track the progress and help debug any issues that may occur. If you run the simulation on an HPC cluster, the cluster will generate additional logging and error files. See Troubleshooting EMOD simulations if you need help resolving an error.

Status¶

A status.txt file will be saved to the working directory that provides one output line per time step and includes the total run time of the simulation. A simulation with 50 time steps will look something like this:

Beginning Simulation...
of 50 steps complete.
of 50 steps complete.
of 50 steps complete.
of 50 steps complete.
of 50 steps complete.
of 50 steps complete.
of 50 steps complete.
of 50 steps complete.
of 50 steps complete.
of 50 steps complete.
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Done - 0:00:02

Standard output¶

When you run a simulation on an HPC cluster, it will generate a standard output logging file (StdOut.txt) in the working directory that captures all standard output messages. When you run a simulation locally, the Command Prompt window will display the same information. If you want to save this information to a text file instead, you can append > stdout.txt to the command used to run the local EMOD simulation to redirect the console output to the file specified.

The file contains information about a particular simulation, such as the EMOD version used and the files in use, as well as other initialization information, including the default logging level and the logging levels set for particular modules. The file follows that information with log output using the following format: <timestep><HPC rank><log level><module><message>.

By default, the logging level is set to “INFO”. If you want to change the logging level, see Set log levels.

For example:

..\..\..\Eradication.exe --config config.json --input-path ..\..\..\Demographics_Files
Intellectual Ventures(R)/EMOD Disease Transmission Kernel 2.18.16.0
Built on Jul  5 2018 15:32:59 by SYSTEM from master (e98fbf4) checked in on 2018-06-12 11:32:40 -0700
Supports sim_types: GENERIC, VECTOR, MALARIA, AIRBORNE, TBHIV, STI, HIV, PY.
Using config file: config.json
Using input path: ..\..\..\Demographics_Files
Using output path: output
Using dll path:
Python not initialized because --python-script-path (-P) not set.
Initializing environment...
Log-levels:
        Default -> INFO
        Eradication -> INFO
00:00 [0] [I] [Eradication] Loaded Configuration...
00:00 [0] [I] [Eradication] 56 parameters found.
00:00 [0] [I] [Eradication] Initializing Controller...
00:00 [0] [I] [Controller] DefaultController::execute_internal()...
00:00 [0] [I] [Simulation] Using PSEUDO_DES random number generator.
00:00 [0] [I] [DllLoader] ReadEmodulesJson: no file, returning.
00:00 [0] [I] [DllLoader] dllPath not passed in, getting from EnvPtr
00:00 [0] [I] [DllLoader] Trying to copy from string to wstring.
00:00 [0] [I] [DllLoader] DLL ws root path:
00:00 [0] [W] [Simulation] 00:00:00 [0] [W] [Simulation] Failed to load reporter emodules for SimType: GENERIC_SIM from path: reporter_plugins
Failed to load reporter emodules for SimType: GENERIC_SIM from path: reporter_plugins
00:00 [0] [I] [Simulation] Found 0 Custom Report DLL's to consider loading, load_all_reports=1
00:00 [0] [I] [Controller] DefaultController::execute_internal() populate simulation...
00:00 [0] [I] [Simulation] Campaign file name identified as: campaign.json
00:00 [0] [I] [Climate] Initialize
00:00 [0] [I] [LoadBalanceScheme] Using Checkerboard Load Balance Scheme.
00:00 [0] [I] [Simulation] Looking for campaign file campaign.json
00:00 [0] [I] [Simulation] Found campaign file successfully.
00:00 [0] [I] [DllLoader] ReadEmodulesJson: no file, returning.
00:00 [0] [I] [DllLoader] dllPath not passed in, getting from EnvPtr
00:00 [0] [I] [DllLoader] Trying to copy from string to wstring.
00:00 [0] [I] [DllLoader] DLL ws root path:
00:00 [0] [W] [Simulation] 00:00:00 [0] [W] [Simulation] Failed to load intervention emodules for SimType: GENERIC_SIM from path: interventions
Failed to load intervention emodules for SimType: GENERIC_SIM from path: interventions
00:01 [0] [I] [JsonConfigurable] Using the default value ( "Number_Repetitions" : 1 ) for unspecified parameter.
00:01 [0] [I] [JsonConfigurable] Using the default value ( "Timesteps_Between_Repetitions" : -1 ) for unspecified parameter.
00:01 [0] [I] [JsonConfigurable] Using the default value ( "Incubation_Period_Override" : -1 ) for unspecified parameter.
00:01 [0] [I] [Simulation] populateFromDemographics() created 1 nodes
00:01 [0] [I] [Simulation] populateFromDemographics() generated 1 nodes.
00:01 [0] [I] [Simulation] Rank 0 contributes 1 nodes...
00:01 [0] [I] [Simulation] Merging node rank maps...
00:01 [0] [I] [Simulation] Merged rank 0 map now has 1 nodes.
00:01 [0] [I] [Simulation] Rank map contents not displayed until NodeRankMap::ToString() (re)implemented.
00:01 [0] [I] [Simulation] Initialized 'InsetChart.json' reporter
00:01 [0] [I] [Simulation] Initialized 'BinnedReport.json' reporter
00:01 [0] [I] [Simulation] Initialized 'DemographicsSummary.json' reporter
00:01 [0] [I] [Simulation] Update(): Time: 1.0 Rank: 0 StatPop: 10000 Infected: 0
00:01 [0] [I] [SimulationEventContext] Time for campaign event. Calling Dispatch...
00:01 [0] [I] [SimulationEventContext] 1 node(s) visited.
00:01 [0] [I] [JsonConfigurable] Using the default value ( "Incubation_Period_Override" : -1 ) for unspecified parameter.
00:01 [0] [I] [StandardEventCoordinator] UpdateNodes() gave out 4 'OutbreakIndividual' interventions at node 1
00:01 [0] [I] [Simulation] Update(): Time: 2.0 Rank: 0 StatPop: 10000 Infected: 4
00:01 [0] [I] [Simulation] Update(): Time: 3.0 Rank: 0 StatPop: 10000 Infected: 13
00:01 [0] [I] [Simulation] Update(): Time: 4.0 Rank: 0 StatPop: 10000 Infected: 65
00:01 [0] [I] [Simulation] Update(): Time: 5.0 Rank: 0 StatPop: 10000 Infected: 283
00:01 [0] [I] [Simulation] Update(): Time: 6.0 Rank: 0 StatPop: 10000 Infected: 1149
00:01 [0] [I] [Simulation] Update(): Time: 7.0 Rank: 0 StatPop: 10000 Infected: 3777
00:01 [0] [I] [Simulation] Update(): Time: 8.0 Rank: 0 StatPop: 10000 Infected: 7268
00:01 [0] [I] [Simulation] Update(): Time: 9.0 Rank: 0 StatPop: 10000 Infected: 7065
00:01 [0] [I] [Simulation] Update(): Time: 10.0 Rank: 0 StatPop: 10000 Infected: 5578
00:01 [0] [I] [Simulation] Update(): Time: 11.0 Rank: 0 StatPop: 10000 Infected: 4377
00:01 [0] [I] [Simulation] Update(): Time: 12.0 Rank: 0 StatPop: 10000 Infected: 3392
00:01 [0] [I] [Simulation] Update(): Time: 13.0 Rank: 0 StatPop: 10000 Infected: 2640
00:01 [0] [I] [Simulation] Update(): Time: 14.0 Rank: 0 StatPop: 10000 Infected: 2054
00:01 [0] [I] [Simulation] Update(): Time: 15.0 Rank: 0 StatPop: 10000 Infected: 1624
00:01 [0] [I] [Simulation] Update(): Time: 16.0 Rank: 0 StatPop: 10000 Infected: 1247
00:01 [0] [I] [Simulation] Update(): Time: 17.0 Rank: 0 StatPop: 10000 Infected: 975
00:01 [0] [I] [Simulation] Update(): Time: 18.0 Rank: 0 StatPop: 10000 Infected: 742
00:01 [0] [I] [Simulation] Update(): Time: 19.0 Rank: 0 StatPop: 10000 Infected: 605
00:01 [0] [I] [Simulation] Update(): Time: 20.0 Rank: 0 StatPop: 10000 Infected: 469
00:01 [0] [I] [Simulation] Update(): Time: 21.0 Rank: 0 StatPop: 10000 Infected: 355
00:01 [0] [I] [Simulation] Update(): Time: 22.0 Rank: 0 StatPop: 10000 Infected: 267
00:01 [0] [I] [Simulation] Update(): Time: 23.0 Rank: 0 StatPop: 10000 Infected: 206
00:01 [0] [I] [Simulation] Update(): Time: 24.0 Rank: 0 StatPop: 10000 Infected: 164
00:01 [0] [I] [Simulation] Update(): Time: 25.0 Rank: 0 StatPop: 10000 Infected: 122
00:01 [0] [I] [Simulation] Update(): Time: 26.0 Rank: 0 StatPop: 10000 Infected: 89
00:01 [0] [I] [Simulation] Update(): Time: 27.0 Rank: 0 StatPop: 10000 Infected: 73
00:01 [0] [I] [Simulation] Update(): Time: 28.0 Rank: 0 StatPop: 10000 Infected: 57
00:01 [0] [I] [Simulation] Update(): Time: 29.0 Rank: 0 StatPop: 10000 Infected: 46
00:01 [0] [I] [Simulation] Update(): Time: 30.0 Rank: 0 StatPop: 10000 Infected: 32
00:01 [0] [I] [Simulation] Update(): Time: 31.0 Rank: 0 StatPop: 10000 Infected: 22
00:01 [0] [I] [Simulation] Update(): Time: 32.0 Rank: 0 StatPop: 10000 Infected: 17
00:01 [0] [I] [Simulation] Update(): Time: 33.0 Rank: 0 StatPop: 10000 Infected: 16
00:01 [0] [I] [Simulation] Update(): Time: 34.0 Rank: 0 StatPop: 10000 Infected: 15
00:01 [0] [I] [Simulation] Update(): Time: 35.0 Rank: 0 StatPop: 10000 Infected: 10
00:01 [0] [I] [Simulation] Update(): Time: 36.0 Rank: 0 StatPop: 10000 Infected: 6
00:01 [0] [I] [Simulation] Update(): Time: 37.0 Rank: 0 StatPop: 10000 Infected: 4
00:01 [0] [I] [Simulation] Update(): Time: 38.0 Rank: 0 StatPop: 10000 Infected: 3
00:01 [0] [I] [Simulation] Update(): Time: 39.0 Rank: 0 StatPop: 10000 Infected: 3
00:01 [0] [I] [Simulation] Update(): Time: 40.0 Rank: 0 StatPop: 10000 Infected: 2
00:01 [0] [I] [Simulation] Update(): Time: 41.0 Rank: 0 StatPop: 10000 Infected: 1
00:01 [0] [I] [Simulation] Update(): Time: 42.0 Rank: 0 StatPop: 10000 Infected: 1
00:01 [0] [I] [Simulation] Update(): Time: 43.0 Rank: 0 StatPop: 10000 Infected: 1
00:01 [0] [I] [Simulation] Update(): Time: 44.0 Rank: 0 StatPop: 10000 Infected: 1
00:01 [0] [I] [Simulation] Update(): Time: 45.0 Rank: 0 StatPop: 10000 Infected: 1
00:01 [0] [I] [Simulation] Update(): Time: 46.0 Rank: 0 StatPop: 10000 Infected: 0
00:01 [0] [I] [Simulation] Update(): Time: 47.0 Rank: 0 StatPop: 10000 Infected: 0
00:01 [0] [I] [Simulation] Update(): Time: 48.0 Rank: 0 StatPop: 10000 Infected: 0
00:01 [0] [I] [Simulation] Update(): Time: 49.0 Rank: 0 StatPop: 10000 Infected: 0
00:01 [0] [I] [Simulation] Update(): Time: 50.0 Rank: 0 StatPop: 10000 Infected: 0
00:01 [0] [I] [Simulation] Update(): Time: 51.0 Rank: 0 StatPop: 10000 Infected: 0
00:01 [0] [I] [Simulation] Update(): Time: 52.0 Rank: 0 StatPop: 10000 Infected: 0
00:01 [0] [I] [Simulation] Update(): Time: 53.0 Rank: 0 StatPop: 10000 Infected: 0
00:02 [0] [I] [Simulation] Update(): Time: 54.0 Rank: 0 StatPop: 10000 Infected: 0
00:02 [0] [I] [Simulation] Update(): Time: 55.0 Rank: 0 StatPop: 10000 Infected: 0
00:02 [0] [I] [Simulation] Update(): Time: 56.0 Rank: 0 StatPop: 10000 Infected: 0
00:02 [0] [I] [Simulation] Update(): Time: 57.0 Rank: 0 StatPop: 10000 Infected: 0
00:02 [0] [I] [Simulation] Update(): Time: 58.0 Rank: 0 StatPop: 10000 Infected: 0
00:02 [0] [I] [Simulation] Update(): Time: 59.0 Rank: 0 StatPop: 10000 Infected: 0
00:02 [0] [I] [Simulation] Update(): Time: 60.0 Rank: 0 StatPop: 10000 Infected: 0
00:02 [0] [I] [Simulation] Update(): Time: 61.0 Rank: 0 StatPop: 10000 Infected: 0
00:02 [0] [I] [Simulation] Update(): Time: 62.0 Rank: 0 StatPop: 10000 Infected: 0
00:02 [0] [I] [Simulation] Update(): Time: 63.0 Rank: 0 StatPop: 10000 Infected: 0
00:02 [0] [I] [Simulation] Update(): Time: 64.0 Rank: 0 StatPop: 10000 Infected: 0
00:02 [0] [I] [Simulation] Update(): Time: 65.0 Rank: 0 StatPop: 10000 Infected: 0
00:02 [0] [I] [Simulation] Update(): Time: 66.0 Rank: 0 StatPop: 10000 Infected: 0
00:02 [0] [I] [Simulation] Update(): Time: 67.0 Rank: 0 StatPop: 10000 Infected: 0
00:02 [0] [I] [Simulation] Update(): Time: 68.0 Rank: 0 StatPop: 10000 Infected: 0
00:02 [0] [I] [Simulation] Update(): Time: 69.0 Rank: 0 StatPop: 10000 Infected: 0
00:02 [0] [I] [Simulation] Update(): Time: 70.0 Rank: 0 StatPop: 10000 Infected: 0
00:02 [0] [I] [Simulation] Update(): Time: 71.0 Rank: 0 StatPop: 10000 Infected: 0
00:02 [0] [I] [Simulation] Update(): Time: 72.0 Rank: 0 StatPop: 10000 Infected: 0
00:02 [0] [I] [Simulation] Update(): Time: 73.0 Rank: 0 StatPop: 10000 Infected: 0
00:02 [0] [I] [Simulation] Update(): Time: 74.0 Rank: 0 StatPop: 10000 Infected: 0
00:02 [0] [I] [Simulation] Update(): Time: 75.0 Rank: 0 StatPop: 10000 Infected: 0
00:02 [0] [I] [Simulation] Update(): Time: 76.0 Rank: 0 StatPop: 10000 Infected: 0
00:02 [0] [I] [Simulation] Update(): Time: 77.0 Rank: 0 StatPop: 10000 Infected: 0
00:02 [0] [I] [Simulation] Update(): Time: 78.0 Rank: 0 StatPop: 10000 Infected: 0
00:02 [0] [I] [Simulation] Update(): Time: 79.0 Rank: 0 StatPop: 10000 Infected: 0
00:02 [0] [I] [Simulation] Update(): Time: 80.0 Rank: 0 StatPop: 10000 Infected: 0
00:02 [0] [I] [Simulation] Update(): Time: 81.0 Rank: 0 StatPop: 10000 Infected: 0
00:02 [0] [I] [Simulation] Update(): Time: 82.0 Rank: 0 StatPop: 10000 Infected: 0
00:02 [0] [I] [Simulation] Update(): Time: 83.0 Rank: 0 StatPop: 10000 Infected: 0
00:02 [0] [I] [Simulation] Update(): Time: 84.0 Rank: 0 StatPop: 10000 Infected: 0
00:02 [0] [I] [Simulation] Update(): Time: 85.0 Rank: 0 StatPop: 10000 Infected: 0
00:02 [0] [I] [Simulation] Update(): Time: 86.0 Rank: 0 StatPop: 10000 Infected: 0
00:02 [0] [I] [Simulation] Update(): Time: 87.0 Rank: 0 StatPop: 10000 Infected: 0
00:02 [0] [I] [Simulation] Update(): Time: 88.0 Rank: 0 StatPop: 10000 Infected: 0
00:02 [0] [I] [Simulation] Update(): Time: 89.0 Rank: 0 StatPop: 10000 Infected: 0
00:02 [0] [I] [Simulation] Update(): Time: 90.0 Rank: 0 StatPop: 10000 Infected: 0
00:02 [0] [I] [Simulation] Finalizing 'InsetChart.json' reporter.
00:02 [0] [I] [Simulation] Finalized  'InsetChart.json' reporter.
00:02 [0] [I] [Simulation] Finalizing 'BinnedReport.json' reporter.
00:02 [0] [I] [Simulation] Finalized  'BinnedReport.json' reporter.
00:02 [0] [I] [Simulation] Finalizing 'DemographicsSummary.json' reporter.
00:02 [0] [I] [Simulation] Finalized  'DemographicsSummary.json' reporter.
00:02 [0] [I] [Controller] Exiting DefaultController::execute_internal
00:02 [0] [I] [Eradication] Controller executed successfully.

Standard error¶

When you run a simulation on an HPC cluster, it will also generate a standard error logging file (StdErr.txt) in the working directory that captures all standard error messages.