EMOD Release 2.6

EMOD-Hub · May 18, 2016 · 6fed29f · 6fed29f
1 parent 683157e
commit 6fed29f
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Showing 424 changed files with 125,584 additions and 10,471,973 deletions.
diff --git a/Eradication/Eradication.cpp b/Eradication/Eradication.cpp
@@ -130,7 +130,10 @@ int main(int argc, char* argv[])
     auto sims = getSimTypeList();
     std::stringstream output;
     output << "Intellectual Ventures(R)/EMOD Disease Transmission Kernel " << pv->getVersion() << std::endl
-           << "Built on " << pv->getBuildDate() << " from " << pv->getSccsBranch() << " checked in on " << pv->getSccsDate() << std::endl;
+           << "Built on " << pv->getBuildDate() <<
+           " by " << pv->getBuilderName() <<
+           " from " << pv->getSccsBranch() <<
+           " checked in on " << pv->getSccsDate() << std::endl;
 
     std::string sim_types_str = "Supports sim_types: ";
     for( auto sim_type: sims  )

diff --git a/Eradication/Eradication.vcxproj.filters b/Eradication/Eradication.vcxproj.filters
@@ -2070,18 +2070,42 @@
     <ClInclude Include="IVectorMigrationReporting.h">
       <Filter>Header Files</Filter>
     </ClInclude>
-    <ClInclude Include="..\utils\BinaryArchiveReader.h" />
-    <ClInclude Include="..\utils\BinaryArchiveWriter.h" />
-    <ClInclude Include="..\utils\DurationDistribution.h" />
-    <ClInclude Include="..\utils\FileSystem.h" />
-    <ClInclude Include="..\utils\IArchive.h" />
-    <ClInclude Include="..\utils\ISerializable.h" />
-    <ClInclude Include="..\utils\JsonFullReader.h" />
-    <ClInclude Include="..\utils\JsonFullWriter.h" />
-    <ClInclude Include="..\utils\JsonRawReader.h" />
-    <ClInclude Include="..\utils\JsonRawWriter.h" />
-    <ClInclude Include="..\rapidjson\include\rapidjson\rapidjson.h" />
-    <ClInclude Include="..\utils\Serialization.h" />
+    <ClInclude Include="..\utils\BinaryArchiveReader.h">
+      <Filter>Header Files</Filter>
+    </ClInclude>
+    <ClInclude Include="..\utils\BinaryArchiveWriter.h">
+      <Filter>Header Files</Filter>
+    </ClInclude>
+    <ClInclude Include="..\utils\DurationDistribution.h">
+      <Filter>Header Files</Filter>
+    </ClInclude>
+    <ClInclude Include="..\utils\FileSystem.h">
+      <Filter>Header Files</Filter>
+    </ClInclude>
+    <ClInclude Include="..\utils\IArchive.h">
+      <Filter>Header Files</Filter>
+    </ClInclude>
+    <ClInclude Include="..\utils\ISerializable.h">
+      <Filter>Header Files</Filter>
+    </ClInclude>
+    <ClInclude Include="..\utils\JsonFullReader.h">
+      <Filter>Header Files</Filter>
+    </ClInclude>
+    <ClInclude Include="..\utils\JsonFullWriter.h">
+      <Filter>Header Files</Filter>
+    </ClInclude>
+    <ClInclude Include="..\utils\JsonRawReader.h">
+      <Filter>Header Files</Filter>
+    </ClInclude>
+    <ClInclude Include="..\utils\JsonRawWriter.h">
+      <Filter>Header Files</Filter>
+    </ClInclude>
+    <ClInclude Include="..\rapidjson\include\rapidjson\rapidjson.h">
+      <Filter>Header Files</Filter>
+    </ClInclude>
+    <ClInclude Include="..\utils\Serialization.h">
+      <Filter>Header Files</Filter>
+    </ClInclude>
   </ItemGroup>
   <ItemGroup>
     <ResourceCompile Include="Eradication.rc" />

diff --git a/Eradication/MpiDataExchanger.cpp b/Eradication/MpiDataExchanger.cpp
@@ -66,6 +66,7 @@ namespace Kernel
                 uint32_t buffer_size = message_size_by_rank[destination_rank] = writer->GetBufferSize();
                 IdmMpi::Request size_request;
                 EnvPtr->MPI.p_idm_mpi->SendIntegers( &message_size_by_rank[destination_rank], 1, destination_rank, &size_request );
+                outbound_requests.Add( size_request );
 
                 if (buffer_size > 0)
                 {

diff --git a/EradicationKernel.sln b/EradicationKernel.sln
@@ -18,28 +18,6 @@ Project("{8BC9CEB8-8B4A-11D0-8D11-00A0C91BC942}") = "utils", "utils\utils.vcxpro
 EndProject
 Project("{8BC9CEB8-8B4A-11D0-8D11-00A0C91BC942}") = "campaign", "campaign\campaign.vcxproj", "{FAB434AD-C0FC-490D-8F18-E05C99B2FD52}"
 EndProject
-Project("{2150E333-8FDC-42A3-9474-1A3956D46DE8}") = "intervention emodules", "intervention emodules", "{24F5E1B1-F61A-4DA4-995B-421A9E18F995}"
-EndProject
-Project("{2150E333-8FDC-42A3-9474-1A3956D46DE8}") = "disease emodules", "disease emodules", "{0F1B34B4-6AD2-49A8-9759-200427297588}"
-EndProject
-Project("{2150E333-8FDC-42A3-9474-1A3956D46DE8}") = "rapidjson", "rapidjson", "{3CA6C23F-2BEE-4E03-AD7A-AD12E90C6043}"
-	ProjectSection(SolutionItems) = preProject
-		rapidjson\include\rapidjson\document.h = rapidjson\include\rapidjson\document.h
-		rapidjson\include\rapidjson\filestream.h = rapidjson\include\rapidjson\filestream.h
-		rapidjson\include\rapidjson\prettywriter.h = rapidjson\include\rapidjson\prettywriter.h
-		rapidjson\include\rapidjson\rapidjson.h = rapidjson\include\rapidjson\rapidjson.h
-		rapidjson\include\rapidjson\reader.h = rapidjson\include\rapidjson\reader.h
-		rapidjson\include\rapidjson\stringbuffer.h = rapidjson\include\rapidjson\stringbuffer.h
-		rapidjson\include\rapidjson\writer.h = rapidjson\include\rapidjson\writer.h
-	EndProjectSection
-EndProject
-Project("{2150E333-8FDC-42A3-9474-1A3956D46DE8}") = "internal", "internal", "{640883B0-F6A0-433B-8255-9E307509D5C8}"
-	ProjectSection(SolutionItems) = preProject
-		rapidjson\include\rapidjson\internal\pow10.h = rapidjson\include\rapidjson\internal\pow10.h
-		rapidjson\include\rapidjson\internal\stack.h = rapidjson\include\rapidjson\internal\stack.h
-		rapidjson\include\rapidjson\internal\strfunc.h = rapidjson\include\rapidjson\internal\strfunc.h
-	EndProjectSection
-EndProject
 Project("{8BC9CEB8-8B4A-11D0-8D11-00A0C91BC942}") = "snappy", "snappy\snappy.vcxproj", "{E672EB5A-934B-4B47-834B-ABDD133D6B63}"
 EndProject
 Project("{8BC9CEB8-8B4A-11D0-8D11-00A0C91BC942}") = "UnitTestLib", "UnitTest++\UnitTestLib.vcxproj", "{64A4FEFE-0461-4E95-8CC1-91EF5F57DBC6}"
@@ -111,6 +89,5 @@ Global
 		HideSolutionNode = FALSE
 	EndGlobalSection
 	GlobalSection(NestedProjects) = preSolution
-		{640883B0-F6A0-433B-8255-9E307509D5C8} = {3CA6C23F-2BEE-4E03-AD7A-AD12E90C6043}
 	EndGlobalSection
 EndGlobal
diff --git a/Regression/00_Households/Scripts/convert_demog_to_migration_txt.py b/Regression/00_Households/Scripts/convert_demog_to_migration_txt.py
diff --git a/Regression/00_Households/Scripts/home_node_tracking.py b/Regression/00_Households/Scripts/home_node_tracking.py
diff --git a/Regression/00_Households/Scripts/human_tracking_common.py b/Regression/00_Households/Scripts/human_tracking_common.py
diff --git a/Regression/00_Households/Scripts/infected_village.py b/Regression/00_Households/Scripts/infected_village.py
diff --git a/Regression/00_Households/Scripts/malaria_counter.py b/Regression/00_Households/Scripts/malaria_counter.py
diff --git a/Regression/00_Households/Scripts/population_common.py b/Regression/00_Households/Scripts/population_common.py
diff --git a/Regression/00_Households/Scripts/population_map.py b/Regression/00_Households/Scripts/population_map.py
diff --git a/Regression/00_Households/Scripts/population_map_animation.py b/Regression/00_Households/Scripts/population_map_animation.py
diff --git a/Regression/00_Households/Scripts/reduce.py b/Regression/00_Households/Scripts/reduce.py
diff --git a/Regression/00_Households/Scripts/tracking.py b/Regression/00_Households/Scripts/tracking.py
diff --git a/Regression/00_Households/Scripts/vector_tracking.py b/Regression/00_Households/Scripts/vector_tracking.py
diff --git a/Regression/149_PyDemo/dtk_pydemo_individual.py b/Regression/149_PyDemo/dtk_pydemo_individual.py
diff --git a/Regression/68_Malaria_Barcode_Genetics/output/createimmunelayer.py b/Regression/68_Malaria_Barcode_Genetics/output/createimmunelayer.py
diff --git a/Regression/68_Malaria_Barcode_Genetics/output/patient_analysis.py b/Regression/68_Malaria_Barcode_Genetics/output/patient_analysis.py
diff --git a/Regression/68_Malaria_Barcode_Genetics/output/plot_barcodes.py b/Regression/68_Malaria_Barcode_Genetics/output/plot_barcodes.py
diff --git a/Regression/68_Malaria_Barcode_Genetics/output/plot_habitat.py b/Regression/68_Malaria_Barcode_Genetics/output/plot_habitat.py
diff --git a/Regression/68_Malaria_Barcode_Genetics/output/plot_inset_chart.py b/Regression/68_Malaria_Barcode_Genetics/output/plot_inset_chart.py
diff --git a/Regression/68_Malaria_Barcode_Genetics/output/plot_summary.py b/Regression/68_Malaria_Barcode_Genetics/output/plot_summary.py
diff --git a/Regression/68_Malaria_Barcode_Genetics/output/plot_vector_report.py b/Regression/68_Malaria_Barcode_Genetics/output/plot_vector_report.py
diff --git a/Regression/GitHub-434/README.txt b/Regression/GitHub-434/README.txt
@@ -0,0 +1,52 @@
+May 2, 2016
+GitHub-434
+https://github.com/InstituteforDiseaseModeling/DtkTrunk/issues/434
+
+It turns out this is due to a problem in MpiDataExchanger. 
+We need to add the sending of the size_request to the outbound_requests 
+so that we wait for the receiving cores to get the size value.
+
+===============================
+Example Error Message Below
+===============================
+
+
+00:07:15 [0] [I] [Simulation] Update(): Time: 2846.0 Rank: 0 StatPop: 327 Infected: 124
+
+job aborted:
+[ranks] message
+
+[0-2] fatal error
+Fatal error in MPI_Recv: Other MPI error, error stack:
+MPI_Recv(buf=0x000000000603EE40, count=1, MPI_UNSIGNED, src=3, tag=0, MPI_COMM_WORLD, status=0x000000000603EDB8) failed
+Out of memory
+
+[3] terminated
+
+[4] fatal error
+Fatal error in MPI_Recv: Other MPI error, error stack:
+MPI_Recv(buf=0x000000000603EE40, count=1, MPI_UNSIGNED, src=3, tag=0, MPI_COMM_WORLD, status=0x000000000603EDB8) failed
+Out of memory
+
+[5] terminated
+
+[6] fatal error
+Fatal error in MPI_Recv: Other MPI error, error stack:
+MPI_Recv(buf=0x000000000603EE40, count=1, MPI_UNSIGNED, src=3, tag=0, MPI_COMM_WORLD, status=0x000000000603EDB8) failed
+Out of memory
+
+[7-12] terminated
+
+[13] fatal error
+Fatal error in MPI_Recv: Other MPI error, error stack:
+MPI_Recv(buf=0x000000000603EE40, count=1, MPI_UNSIGNED, src=3, tag=0, MPI_COMM_WORLD, status=0x000000000603EDB8) failed
+Out of memory
+
+[14-23] terminated
+
+---- error analysis -----
+
+[0-2,4,6,13] on IDMPPHPC01-0016
+mpi has detected a fatal error and aborted \\idmppfil01\IDM\home\jgerardin\bin\4ef6c5c0f0615f3e3e145ab935d4e7ac\Eradication.exe
+
+---- error analysis -----