Tutorial materials as referenced in IDM's documentation for EMOD, an agent-based disease dynamics model.
Home Page: http://idmod.org/docs/general/tutorials.html
License: Other
Integrate Bobby's code (Rwrappers) into a separate scripts folder
Need to update the README.md with more comprehensive instructions on setup and requirements.
A couple of the TB scenarios fail when attempting to write output. The output is attached. I installed rapidjson and that didn’t solve the issue, so I suspect it’s because they run out of memory. They are TB/HIVCoinfection and TB/PopulationBurnin.
Error log:
00:00:49 [0] [I] [SerializedPopulation] Writing state to 'output/state-00974.dtk'
Eradication: rapidjson/include/rapidjson/writer.h:233: void rapidjson::Writer<Stream, Encoding, Allocator>::Prefix(rapidjson::Type) [with Stream = rapidjson::GenericStringBuffer<rapidjson::UTF8<> >; Encoding = rapidjson::UTF8<>; Allocator = rapidjson::MemoryPoolAllocator<>]: Assertion `type == kStringType' failed.
[idmod:05892] *** Process received signal ***
[idmod:05892] Signal: Aborted (6)
[idmod:05892] Signal code: (-6)
[idmod:05892] [ 0] /lib/x86_64-linux-gnu/libpthread.so.0(+0x12890)[0x7f0b69780890]
[idmod:05892] [ 1] /lib/x86_64-linux-gnu/libc.so.6(gsignal+0xc7)[0x7f0b67cc1e97]
[idmod:05892] [ 2] /lib/x86_64-linux-gnu/libc.so.6(abort+0x141)[0x7f0b67cc3801]
[idmod:05892] [ 3] /lib/x86_64-linux-gnu/libc.so.6(+0x3039a)[0x7f0b67cb339a]
[idmod:05892] [ 4] /lib/x86_64-linux-gnu/libc.so.6(+0x30412)[0x7f0b67cb3412]
[idmod:05892] [ 5] ./../../../../../Eradication(_ZN6Kernel14JsonFullWriteranERb+0x2d7)[0x562258a71a87]
[idmod:05892] [ 6] ./../../../../../Eradication(_ZN6Kernel13ISerializable9serializeERNS_8IArchiveERPS0_+0x2f3)[0x562258a68113]
[idmod:05892] [ 7] ./../../../../../Eradication(_ZN6Kernel8IArchiveanERPNS_13ISerializableE+0x9)[0x562258a5f4b9]
[idmod:05892] [ 8] ./../../../../../Eradication(_ZN6Kernel22InterventionsContainer9serializeERNS_8IArchiveEPS0_+0xf4)[0x562258752fe4]
[idmod:05892] [ 9] ./../../../../../Eradication(_ZZN6Kernel31SerializationRegistrationCallerINS_24TBInterventionsContainerEE26in_class_registration_hookEvENUlRNS_8IArchiveEPNS_13ISerializableEE_4_FUNES4_S6_+0x36)[0x56225878e256]
[idmod:05892] [10] ./../../../../../Eradication(_ZN6Kernel13ISerializable9serializeERNS_8IArchiveERPS0_+0x2f3)[0x562258a68113]
[idmod:05892] [11] ./../../../../../Eradication(_ZN6Kernel8IArchiveanERPNS_13ISerializableE+0x9)[0x562258a5f4b9]
[idmod:05892] [12] ./../../../../../Eradication(_ZZN6Kernel31SerializationRegistrationCallerINS_28MasterInterventionsContainerEE26in_class_registration_hookEvENUlRNS_8IArchiveEPNS_13ISerializableEE_4_FUNES4_S6_+0xc4)[0x5622587a1fe4]
[idmod:05892] [13] ./../../../../../Eradication(_ZN6Kernel13ISerializable9serializeERNS_8IArchiveERPS0_+0x2f3)[0x562258a68113]
[idmod:05892] [14] ./../../../../../Eradication(_ZN6Kernel8IArchiveanERPNS_13ISerializableE+0x9)[0x562258a5f4b9]
[idmod:05892] [15] ./../../../../../Eradication(_ZN6Kernel15IndividualHuman9serializeERNS_8IArchiveEPS0_+0x694)[0x56225863c824]
[idmod:05892] [16] ./../../../../../Eradication(_ZN6Kernel26IndividualHumanCoInfection9serializeERNS_8IArchiveEPS0_+0x3b)[0x562258554a4b]
[idmod:05892] [17] ./../../../../../Eradication(_ZN6Kernel13ISerializable9serializeERNS_8IArchiveERPS0_+0x2f3)[0x562258a68113]
[idmod:05892] [18] ./../../../../../Eradication(_ZN6Kernel8IArchiveanERPNS_13ISerializableE+0x9)[0x562258a5f4b9]
[idmod:05892] [19] ./../../../../../Eradication(_ZN6Kernel4Node9serializeERNS_8IArchiveEPS0_+0xdb8)[0x562258846ce8]
[idmod:05892] [20] ./../../../../../Eradication(_ZN6Kernel6NodeTB9serializeERNS_8IArchiveEPS0_+0x11)[0x562258633c21]
[idmod:05892] [21] ./../../../../../Eradication(_ZN6Kernel13ISerializable9serializeERNS_8IArchiveERPS0_+0x2f3)[0x562258a68113]
[idmod:05892] [22] ./../../../../../Eradication(_ZN6Kernel8IArchiveanERPNS_13ISerializableE+0x9)[0x562258a5f4b9]
[idmod:05892] [23] ./../../../../../Eradication(_ZN15SerializedState15PrepareNodeDataERSt3mapIN6Kernel5suids4suidEPNS1_12INodeContextESt4lessIS3_ESaISt4pairIKS3_S5_EEERSt6vectorIPNS1_8IArchiveESaISG_EERSE_IPKcSaISL_EERSE_ImSaImEE+0x159)[0x5622587eccd9]
[idmod:05892] [24] ./../../../../../Eradication(_ZN15SerializedState24SaveSerializedSimulationEPN6Kernel10SimulationEjb+0x128)[0x5622587ed1e8]
[idmod:05892] [25] ./../../../../../Eradication(_Z13RunSimulationIN6Kernel11ISimulationEEvRT_if+0x164)[0x5622587fcb44]
[idmod:05892] [26] ./../../../../../Eradication(_ZN17DefaultController16execute_internalEv+0x947)[0x5622587fb6b7]
[idmod:05892] [27] ./../../../../../Eradication(_Z21ControllerInitWrapperiPPcPN6IdmMpi16MessageInterfaceE+0x399a)[0x5622589d5eaa]
[idmod:05892] [28] ./../../../../../Eradication(_Z14MPIInitWrapperiPPc+0x24)[0x5622589d7fb4]
[idmod:05892] [29] ./../../../../../Eradication(main+0xd7e)[0x562258516dbe]
[idmod:05892] *** End of error message ***
Aborted (core dumped)
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