Troubleshooting EMOD simulations¶
If you encounter any of the following problems when attempting to run EMOD simulations, see the information below to resolve the issue.
If you need assistance, you can contact support for help with solving issues. You can contact Institute for Disease Modeling (IDM) support at email@example.com. When submitting the issue, please include any error information. See Debugging and testing for troubleshooting issues when attempting to build Eradication.exe or Eradication binary.
- CentOS on Azure environment
Whenever EMOD encounters an error condition while running a simulation, it should throw an exception. These exceptions are designed to help you diagnose any problems so that you can quickly resolve the issue. You can find the exceptions code in the utils directory of the EMOD source code within the files Exceptions.h and Exceptions.cpp.
Each exception will return, at a minimum, the following information:
- Exception type caught
- The filename where the exception occurred
- The line number in the file where the exception was thrown (which may not be exactly where the error actually occurred in the code)
- The function name where the exception was thrown
Specific exceptions may also return additional information in a message format. This message (msg) may contain variable names or the values of those variables, the name of a file that wasn’t found, and other informational text regarding the nature of the problem. For example, a file not found exception (FileNotFoundException) might look similar to the following:
00:00:00  [E] [Eradication] FileNotFoundException caught: msg = Could not find file ./Namawala_single_node_demographics.compiled.json, filename = NodeDemographics.cpp, lineNumber = 227
This exception is thrown when an enumeration value is not handled in the switch statement. In other words, this exception signals that there is a problem with an enumeration value, typically stemming from one of the configuration files, though this is not always the case.
It is possible the enumeration value is not a valid value (out of range of the numeric range of the enumeration), or perhaps the string value is currently not implemented in the code (and should not be used in configuration settings yet).
This exception is thrown when there is a standard template library (STL) mapping error. Usually, this occurs where spatial output channel names are specified in the configuration file if an unrecognized channel name is used.
If you have not modified the EMOD source code or used an unrecognized channel name, this error could signal an internal problem with the code. Contact firstname.lastname@example.org.
EMOD performs a large number of mathematical operations on parameter values. Therefore, it is possible that, despite original parameter values being with range, the values resulting from these multiple calculations may end up outside its valid range. For example, a probability value (range: 0 to 1.0) that after multiple calculations during a simulation now exceeds 1.0.
This exception is thrown when such a situation is detected. This exception only applies to numeric or Boolean values, not enumeration values.
This exception is thrown if a parameter value read from a configuration file is detected to be outside its valid range. This exception is similar to the more general case OutOfRangeException. However, this exception is only thrown if the out of range exception comes from a numeric or Boolean value, not enumeration value, read from a configuration file.
The EMOD architecture is modularized and can be built as a core Eradication.exe along with a series of custom reporter EMODules, as opposed to a single monolithic Eradication.exe. This exception indicates that EMOD couldn’t load on of the EMODule DLLs.
This situation could occur for several reasons:
- EMOD couldn’t find the EMODule
- Unresolved symbols were found (Windows)
- EMOD could not find the necessary symbol during the GetProcAddress call
- The custom reporter EMODules were built using a version of Visual Studio that is no longer supported. Rebuild the EMODules using Visual Studio 2015 (Professional, Premium, or Ultimate).
EMOD implements class factories that instantiate objects at run time and use information from JSON- based configuration information in the creation of these objects. The exception indicates something is incorrect with the JSON information.
In particular, in some cases, the JSON information is nested into a hierarchy of information. Therefore, as the factories are called to create the objects described by the outer layers of one of these nested hierarchies, the factories do not have any knowledge yet of the inner layers of the hierarchies. This inner information contains information the factory needs to complete the object instantiation, but this information might not be correct. If that happens, then the factory will throw this exception.
Campaign files often have this kind of nested hierarchical structure, so it’s important to t verify that the hierarchy is set up correctly. For example, if the class name were mistyped and EMOD had no implementation of that class, this exception will be thrown.
This exception is generated if there is an unrecoverable problem loading data from a file. The data might be corrupted or there may be a mismatch. For example, if the file format or configuration information indicates that there should be ten values of some array and there are only nine included in the file, then this exception would be thrown.
This exception is not the same as the exception thrown for a file that is not found. In this case, the file is found and loaded, but there is a problem with the data in the file.
This exception is thrown if a file cannot be found. Possible causes might include a incorrectly typed filename in the configuration file, a wrong path to the file, or even the path not being set in the system environment leading to the system not finding a relative path to the file. One of the most likely causes is that quotes are missing around the file name.
This exception is only thrown if a more specific exception cannot be used for the configuration problem detected. This exception is likely thrown when there is very little information available about the root problem.
For example, this exception might be thrown if a parameter name is invalid, such as using an older, deprecated version of a parameter name.
This exception is thrown if an illegal operation was detected. In most cases, a more specific exception will be thrown rather than this more general one. This exception is likely thrown when there is very little information available about the root problem. For example, when a utility function error is detected, there is very sparse information available as to what may have led to the error. As a result, calling a more specific exception with more context is not an option.
This exception is thrown if mutually contradictory or incompatible configuration settings have been detected. For example, if mutually exclusive parameters are set, the minimum parameter value is greater than the maximum value, or two distribution axes are specified in a demographics file but there is a mismatch with the number of axes scale factors included. The exception can also occur if there isn’t a corresponding mapping between an reference ID in the metadata of a demographics file and its corresponding data file.
This exception is thrown if a problem with initialization was detected. In most cases, a more specific exception will be thrown rather than this more general one. This exception is likely thrown when there is very little information available about the root problem.
For example, if the very first part of a JSON file has corrupted or badly formatted data, this exception may be thrown instead of the more expected file input/output exception, FileIOException.
This exception is thrown when a problem with an input data file is detected. For example, if the wrong data type was detected, such as a float being detected when a string is expected you would see this exception thrown, or even, if a parameter has an invalid value even if the value is of the correct type. As the input data file most likely to have significant modifications, verify that the demographics file is set up correctly.
This exception occurs when required parameters are missing. Verify that you are not using deprecated parameters and that all required parameters are specified (or set Use_Defaults to 1).
This exception is thrown if there is an MPI error. As such, these types of issues are related to interfacing with MPI (and/or networking issues) and do not necessary imply something wrong with the EMOD code or JSON files.
This exception is thrown if an attempt is made to execute code that is not yet implemented. For example, there are areas of EMOD where placeholder enumeration values are defined but not yet implemented. If you specify a value like this, it is considered within a valid range, but this exception will be thrown in response. Verify that any enumeration values use one of the available values as described in the documentation and do not contain any typos.
This exception is thrown when a NULL pointer is detected in the code, or rather when a NULL pointer - that should NOT be NULL - is used. When thrown at the application level, a NULL pointer exception is usually caused by some sort of initialization error, for example, a file not being found.
As a result, in most cases, a more specific exception will be thrown before the code execution reaches a point where this exception would occur. Therefore, this exception is uncommon and likely thrown only when there is very little information available about the root problem.
This exception is thrown when a numeric or Boolean value is out of range. For example, if you index an array outside of its valid range, this exception will be thrown. There are other situations where more specific exceptions are thrown instead of this more general one. For example, when the numeric or Boolean values are from a configuration file, but are detected to be out of range, the ConfigurationRangeException is thrown. Likewise, if the value goes out of range as the result of a calculation, the CalculatedValueOutOfRangeException is thrown instead.
The EMOD architecture is modularized and many components now implement QueryInterface. This exception is thrown when a required interface is queried on an object and the object that returns that the interface is not supported.
If you have not modified the EMOD source code and receive this error, it could signal an internal problem with the code. Contact email@example.com.
The following problems are specific to running simulations using the Eradication binary on CentOS 7.1 on Azure.
After you run regression simulations on CentOS on Azure using runemod.sh in the Scripts directory, it plots graphs from the simulation output data with a red line for the reference output and a blue line for the new output. The reference output was created by running the simulation on Windows, which in some cases may be slightly different than the output from CentOS on Azure.
For simulations that plot a baseline, you can override the Windows reference output by modifying runemod.sh to use output/InsetChart.linux.json as the output location. In that case, the red reference plots should always be completely covered by the blue plots.
If you chose not to have the PrepareLinuxEnvironment.sh script download the EMOD source code and input data files, you need to set up the environment variable, path and symlink that are needed to run simulations on CentOS on Azure. See Install EMOD on CentOS on Azure.