[Avida-SVN] r1524 - in branches/collect: . Avida.xcodeproj source source/actions source/analyze source/classification source/cpu source/drivers source/main source/platform source/platform/tcmalloc source/targets source/targets/avida source/targets/avida-viewer source/testsuites source/tools source/utils/task_events support support/config tests tests/_testrunner tests/demes_clique_repl/expected/data tests/demes_germline/expected/data tests/demes_grid_repl/expected/data tests/demes_torus_repl/expected/data
blwalker at myxo.css.msu.edu
blwalker at myxo.css.msu.edu
Thu May 3 10:36:50 PDT 2007
Author: blwalker
Date: 2007-05-03 13:36:49 -0400 (Thu, 03 May 2007)
New Revision: 1524
Added:
branches/collect/tests/_analyze_fulllandscape_2step/
branches/collect/tests/demes_hex_repl/
Removed:
branches/collect/source/CMakeLists.txt
branches/collect/source/actions/CMakeLists.txt
branches/collect/source/analyze/CMakeLists.txt
branches/collect/source/classification/CMakeLists.txt
branches/collect/source/cpu/CMakeLists.txt
branches/collect/source/drivers/CMakeLists.txt
branches/collect/source/main/CMakeLists.txt
branches/collect/source/platform/CMakeLists.txt
branches/collect/source/platform/tcmalloc/CMakeLists.txt
branches/collect/source/targets/CMakeLists.txt
branches/collect/source/targets/avida-viewer/CMakeLists.txt
branches/collect/source/targets/avida/CMakeLists.txt
branches/collect/source/tools/CMakeLists.txt
branches/collect/source/tools/tests/
branches/collect/source/utils/task_events/CMakeLists.txt
branches/collect/support/CMakeLists.txt
branches/collect/support/config/CMakeLists.txt
branches/collect/tests/analyze_fulllandscape_2step/
Modified:
branches/collect/Avida.xcodeproj/project.pbxproj
branches/collect/CMakeLists.txt
branches/collect/source/actions/PrintActions.cc
branches/collect/source/main/cPopulation.cc
branches/collect/source/main/cStats.cc
branches/collect/source/main/nGeometry.h
branches/collect/source/testsuites/CMakeLists.txt
branches/collect/source/tools/cTopology.h
branches/collect/source/utils/task_events/task_event_gen.cc
branches/collect/tests/_testrunner/testrunner.py
branches/collect/tests/demes_clique_repl/expected/data/stats.dat
branches/collect/tests/demes_germline/expected/data/stats.dat
branches/collect/tests/demes_grid_repl/expected/data/stats.dat
branches/collect/tests/demes_torus_repl/expected/data/stats.dat
Log:
Ported r1508:1523 from development.
Modified: branches/collect/Avida.xcodeproj/project.pbxproj
===================================================================
--- branches/collect/Avida.xcodeproj/project.pbxproj 2007-05-03 17:00:16 UTC (rev 1523)
+++ branches/collect/Avida.xcodeproj/project.pbxproj 2007-05-03 17:36:49 UTC (rev 1524)
@@ -10,10 +10,7 @@
1097463F0AE9606E00929ED6 /* cDeme.cc in Sources */ = {isa = PBXBuildFile; fileRef = 1097463D0AE9606E00929ED6 /* cDeme.cc */; };
109746410AE9606E00929ED6 /* cDeme.cc in Sources */ = {isa = PBXBuildFile; fileRef = 1097463D0AE9606E00929ED6 /* cDeme.cc */; };
109746430AE9606E00929ED6 /* cDeme.cc in Sources */ = {isa = PBXBuildFile; fileRef = 1097463D0AE9606E00929ED6 /* cDeme.cc */; };
- 4201F39B0BE187F6006279B9 /* cTopology.h in CopyFiles */ = {isa = PBXBuildFile; fileRef = 4201F39A0BE187F6006279B9 /* cTopology.h */; };
4233358A0BC067E3000DF681 /* cHardwareGX.cc in Sources */ = {isa = PBXBuildFile; fileRef = 423335880BC067E3000DF681 /* cHardwareGX.cc */; };
- 4233358B0BC067E3000DF681 /* cHardwareGX.h in CopyFiles */ = {isa = PBXBuildFile; fileRef = 423335890BC067E3000DF681 /* cHardwareGX.h */; };
- 42490F000BE2472800318058 /* cGermline.h in CopyFiles */ = {isa = PBXBuildFile; fileRef = 42490EFE0BE2472800318058 /* cGermline.h */; };
7005A70409BA0FA90007E16E /* cTestCPUInterface.cc in Sources */ = {isa = PBXBuildFile; fileRef = 7005A70209BA0FA90007E16E /* cTestCPUInterface.cc */; };
7005A70609BA0FA90007E16E /* cTestCPUInterface.cc in Sources */ = {isa = PBXBuildFile; fileRef = 7005A70209BA0FA90007E16E /* cTestCPUInterface.cc */; };
7005A70809BA0FA90007E16E /* cTestCPUInterface.cc in Sources */ = {isa = PBXBuildFile; fileRef = 7005A70209BA0FA90007E16E /* cTestCPUInterface.cc */; };
@@ -427,9 +424,6 @@
7049F3730A66AD7E00640512 /* default-transsmt.org in CopyFiles */,
70B1A7430B7E3FFD00067486 /* instset-experimental.cfg in CopyFiles */,
70B1A75A0B7E431F00067486 /* experimental.org in CopyFiles */,
- 4233358B0BC067E3000DF681 /* cHardwareGX.h in CopyFiles */,
- 4201F39B0BE187F6006279B9 /* cTopology.h in CopyFiles */,
- 42490F000BE2472800318058 /* cGermline.h in CopyFiles */,
);
runOnlyForDeploymentPostprocessing = 0;
};
@@ -461,8 +455,6 @@
7009E0C50B9A2FAC00070F8F /* cRWLock.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = cRWLock.h; sourceTree = "<group>"; };
700AE91B09DB65F200A073FD /* cTaskContext.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = cTaskContext.h; sourceTree = "<group>"; };
700E11BC0A0815B600B604CD /* cDataEntry.cc */ = {isa = PBXFileReference; fileEncoding = 30; lastKnownFileType = sourcecode.cpp.cpp; path = cDataEntry.cc; sourceTree = "<group>"; };
- 700E12610A097A0800B604CD /* CMakeLists.txt */ = {isa = PBXFileReference; fileEncoding = 30; lastKnownFileType = text; path = CMakeLists.txt; sourceTree = "<group>"; };
- 700E12630A097A1700B604CD /* CMakeLists.txt */ = {isa = PBXFileReference; fileEncoding = 30; lastKnownFileType = text; path = CMakeLists.txt; sourceTree = "<group>"; };
700E28CF0859FFD700CF158A /* tObjectFactory.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = tObjectFactory.h; sourceTree = "<group>"; };
700E2B83085DE50C00CF158A /* avida-viewer */ = {isa = PBXFileReference; explicitFileType = "compiled.mach-o.executable"; includeInIndex = 0; path = "avida-viewer"; sourceTree = BUILT_PRODUCTS_DIR; };
7013845F09028B3E0087ED2E /* cAvidaConfig.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = cAvidaConfig.h; sourceTree = "<group>"; };
@@ -480,7 +472,6 @@
701D9382094CBA69008B845F /* cDriverManager.cc */ = {isa = PBXFileReference; fileEncoding = 30; lastKnownFileType = sourcecode.cpp.cpp; path = cDriverManager.cc; sourceTree = "<group>"; };
701D93E6094CBF71008B845F /* cDefaultAnalyzeDriver.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = cDefaultAnalyzeDriver.h; sourceTree = "<group>"; };
701D93E7094CBF71008B845F /* cDefaultAnalyzeDriver.cc */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = cDefaultAnalyzeDriver.cc; sourceTree = "<group>"; };
- 701D941C094CC5F1008B845F /* CMakeLists.txt */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = text; path = CMakeLists.txt; sourceTree = "<group>"; };
7027621909D73E5900741717 /* cOrgSourceMessage.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = cOrgSourceMessage.h; sourceTree = "<group>"; };
7027621A09D73E7700741717 /* cOrgSinkMessage.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = cOrgSinkMessage.h; sourceTree = "<group>"; };
702D4EF508DA5328007BA469 /* cEnvironment.h */ = {isa = PBXFileReference; fileEncoding = 30; lastKnownFileType = sourcecode.c.h; path = cEnvironment.h; sourceTree = "<group>"; };
@@ -499,7 +490,6 @@
703CA3710A50734500AB4DB4 /* SConscript */ = {isa = PBXFileReference; fileEncoding = 30; lastKnownFileType = text; path = SConscript; sourceTree = "<group>"; };
703CA3720A50735B00AB4DB4 /* SConscript */ = {isa = PBXFileReference; fileEncoding = 30; lastKnownFileType = text; path = SConscript; sourceTree = "<group>"; };
703CA3730A50737700AB4DB4 /* SConscript */ = {isa = PBXFileReference; fileEncoding = 30; lastKnownFileType = text; path = SConscript; sourceTree = "<group>"; };
- 703CA3740A50739600AB4DB4 /* SConscript */ = {isa = PBXFileReference; fileEncoding = 30; lastKnownFileType = text; path = SConscript; sourceTree = "<group>"; };
703CA3760A5073CD00AB4DB4 /* SConscript */ = {isa = PBXFileReference; fileEncoding = 30; lastKnownFileType = text; path = SConscript; sourceTree = "<group>"; };
703CA3770A50740300AB4DB4 /* SConscript */ = {isa = PBXFileReference; fileEncoding = 30; lastKnownFileType = text; path = SConscript; sourceTree = "<group>"; };
703CA3780A50749F00AB4DB4 /* SConstruct */ = {isa = PBXFileReference; fileEncoding = 30; lastKnownFileType = text; path = SConstruct; sourceTree = "<group>"; };
@@ -514,7 +504,6 @@
70422A23091B141000A5E67F /* cAnalyzeFunction.h */ = {isa = PBXFileReference; fileEncoding = 30; lastKnownFileType = sourcecode.c.h; path = cAnalyzeFunction.h; sourceTree = "<group>"; };
70422A24091B141000A5E67F /* cAnalyzeGenotype.cc */ = {isa = PBXFileReference; fileEncoding = 30; lastKnownFileType = sourcecode.cpp.cpp; path = cAnalyzeGenotype.cc; sourceTree = "<group>"; };
70422A25091B141000A5E67F /* cAnalyzeGenotype.h */ = {isa = PBXFileReference; fileEncoding = 30; lastKnownFileType = sourcecode.c.h; path = cAnalyzeGenotype.h; sourceTree = "<group>"; };
- 70422A44091B1B8500A5E67F /* CMakeLists.txt */ = {isa = PBXFileReference; fileEncoding = 30; lastKnownFileType = text; path = CMakeLists.txt; sourceTree = "<group>"; };
7049F2D70A66859300640512 /* cHardwareTransSMT.cc */ = {isa = PBXFileReference; fileEncoding = 30; lastKnownFileType = sourcecode.cpp.cpp; path = cHardwareTransSMT.cc; sourceTree = "<group>"; };
7049F2D80A66859300640512 /* cHardwareTransSMT.h */ = {isa = PBXFileReference; fileEncoding = 30; lastKnownFileType = sourcecode.c.h; path = cHardwareTransSMT.h; sourceTree = "<group>"; };
7049F3520A66A8F500640512 /* instset-classic.cfg */ = {isa = PBXFileReference; fileEncoding = 30; lastKnownFileType = text; path = "instset-classic.cfg"; sourceTree = "<group>"; };
@@ -547,7 +536,6 @@
7053336C092A3DF4006BD186 /* nInjectGenotype.h */ = {isa = PBXFileReference; fileEncoding = 30; lastKnownFileType = sourcecode.c.h; path = nInjectGenotype.h; sourceTree = "<group>"; };
705333E5092A4B7C006BD186 /* cLineage.cc */ = {isa = PBXFileReference; fileEncoding = 30; lastKnownFileType = sourcecode.cpp.cpp; path = cLineage.cc; sourceTree = "<group>"; };
705333E6092A4B7C006BD186 /* cLineage.h */ = {isa = PBXFileReference; fileEncoding = 30; lastKnownFileType = sourcecode.c.h; path = cLineage.h; sourceTree = "<group>"; };
- 7053345E092A4D88006BD186 /* CMakeLists.txt */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = text; path = CMakeLists.txt; sourceTree = "<group>"; };
7054A11E09A7BEFC00038658 /* cThread.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = cThread.h; sourceTree = "<group>"; };
7054A11F09A7BEFC00038658 /* cThread.cc */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = cThread.cc; sourceTree = "<group>"; };
7054A16E09A8014600038658 /* cAnalyzeJobQueue.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = cAnalyzeJobQueue.h; sourceTree = "<group>"; };
@@ -580,10 +568,8 @@
707AEF8C09EA8B2D001AEA89 /* cAnalyzeCommandAction.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = cAnalyzeCommandAction.h; sourceTree = "<group>"; };
707AF04409EAB529001AEA89 /* LandscapeActions.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = LandscapeActions.h; sourceTree = "<group>"; };
707AF04509EAB529001AEA89 /* LandscapeActions.cc */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = LandscapeActions.cc; sourceTree = "<group>"; };
- 707AF0F809EACC5E001AEA89 /* CMakeLists.txt */ = {isa = PBXFileReference; fileEncoding = 30; lastKnownFileType = text; path = CMakeLists.txt; sourceTree = "<group>"; };
707AF2D309EE8501001AEA89 /* analyze.cfg */ = {isa = PBXFileReference; fileEncoding = 30; lastKnownFileType = text; path = analyze.cfg; sourceTree = "<group>"; };
707AF2D509EE8501001AEA89 /* avida.cfg */ = {isa = PBXFileReference; fileEncoding = 30; lastKnownFileType = text; path = avida.cfg; sourceTree = "<group>"; };
- 707AF2D609EE8501001AEA89 /* CMakeLists.txt */ = {isa = PBXFileReference; fileEncoding = 30; lastKnownFileType = text; path = CMakeLists.txt; sourceTree = "<group>"; };
707AF2D709EE8501001AEA89 /* environment.cfg */ = {isa = PBXFileReference; fileEncoding = 30; lastKnownFileType = text; path = environment.cfg; sourceTree = "<group>"; };
707AF2D809EE8501001AEA89 /* events.cfg */ = {isa = PBXFileReference; fileEncoding = 30; lastKnownFileType = text; path = events.cfg; sourceTree = "<group>"; };
707AF2DE09EE8501001AEA89 /* environment.2paths */ = {isa = PBXFileReference; fileEncoding = 30; lastKnownFileType = text; path = environment.2paths; sourceTree = "<group>"; };
@@ -854,7 +840,6 @@
70DCAC5D097AF730002F8733 /* cEnvironmentScreen.h */ = {isa = PBXFileReference; fileEncoding = 30; lastKnownFileType = sourcecode.c.h; path = cEnvironmentScreen.h; sourceTree = "<group>"; };
70DCAC5E097AF730002F8733 /* cHistScreen.cc */ = {isa = PBXFileReference; fileEncoding = 30; lastKnownFileType = sourcecode.cpp.cpp; path = cHistScreen.cc; sourceTree = "<group>"; };
70DCAC5F097AF730002F8733 /* cHistScreen.h */ = {isa = PBXFileReference; fileEncoding = 30; lastKnownFileType = sourcecode.c.h; path = cHistScreen.h; sourceTree = "<group>"; };
- 70DCAC60097AF730002F8733 /* CMakeLists.txt */ = {isa = PBXFileReference; fileEncoding = 30; lastKnownFileType = text; path = CMakeLists.txt; sourceTree = "<group>"; };
70DCAC61097AF730002F8733 /* cMapScreen.cc */ = {isa = PBXFileReference; fileEncoding = 30; lastKnownFileType = sourcecode.cpp.cpp; path = cMapScreen.cc; sourceTree = "<group>"; };
70DCAC62097AF730002F8733 /* cMapScreen.h */ = {isa = PBXFileReference; fileEncoding = 30; lastKnownFileType = sourcecode.c.h; path = cMapScreen.h; sourceTree = "<group>"; };
70DCAC63097AF730002F8733 /* cMenuWindow.cc */ = {isa = PBXFileReference; fileEncoding = 30; lastKnownFileType = sourcecode.cpp.cpp; path = cMenuWindow.cc; sourceTree = "<group>"; };
@@ -885,8 +870,6 @@
70DCAD20097AF81A002F8733 /* cLexer.h */ = {isa = PBXFileReference; fileEncoding = 30; lastKnownFileType = sourcecode.c.h; path = cLexer.h; sourceTree = "<group>"; };
70DCAD21097AF81A002F8733 /* cLexer.l */ = {isa = PBXFileReference; fileEncoding = 30; lastKnownFileType = sourcecode.lex; path = cLexer.l; sourceTree = "<group>"; };
70DCAD22097AF81A002F8733 /* FlexLexer.h */ = {isa = PBXFileReference; fileEncoding = 30; lastKnownFileType = sourcecode.c.h; path = FlexLexer.h; sourceTree = "<group>"; };
- 70DCAD37097AF972002F8733 /* CMakeLists.txt */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = text; path = CMakeLists.txt; sourceTree = "<group>"; };
- 70DCAD39097AF985002F8733 /* CMakeLists.txt */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = text; path = CMakeLists.txt; sourceTree = "<group>"; };
70DCF50109CFB0B400924128 /* system-alloc.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = "system-alloc.h"; sourceTree = "<group>"; };
70DCF50209CFB0B400924128 /* system-alloc.cc */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = "system-alloc.cc"; sourceTree = "<group>"; };
70DCF52809CFB93200924128 /* spinlock.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = spinlock.h; sourceTree = "<group>"; };
@@ -909,19 +892,12 @@
70F7DE730929678E009E311D /* cGenotype_TestData.h */ = {isa = PBXFileReference; fileEncoding = 30; lastKnownFileType = sourcecode.c.h; path = cGenotype_TestData.h; sourceTree = "<group>"; };
70F7DE76092967A8009E311D /* cGenotypeBatch.h */ = {isa = PBXFileReference; fileEncoding = 30; lastKnownFileType = sourcecode.c.h; path = cGenotypeBatch.h; sourceTree = "<group>"; };
70FB86A908BFAFEC00BDF589 /* CMakeLists.txt */ = {isa = PBXFileReference; fileEncoding = 30; lastKnownFileType = text; path = CMakeLists.txt; sourceTree = "<group>"; };
- DCC30F7B0762539D008F7A48 /* CMakeLists.txt */ = {isa = PBXFileReference; fileEncoding = 30; lastKnownFileType = text; path = CMakeLists.txt; sourceTree = "<group>"; };
- DCC30FA90762539D008F7A48 /* CMakeLists.txt */ = {isa = PBXFileReference; fileEncoding = 30; lastKnownFileType = text; path = CMakeLists.txt; sourceTree = "<group>"; };
DCC30FCF0762539D008F7A48 /* Doxyfile */ = {isa = PBXFileReference; fileEncoding = 30; lastKnownFileType = text; path = Doxyfile; sourceTree = "<group>"; };
DCC3109C0762539E008F7A48 /* avida.cc */ = {isa = PBXFileReference; fileEncoding = 30; lastKnownFileType = sourcecode.cpp.cpp; path = avida.cc; sourceTree = "<group>"; };
- DCC310A90762539E008F7A48 /* CMakeLists.txt */ = {isa = PBXFileReference; fileEncoding = 30; lastKnownFileType = text; path = CMakeLists.txt; sourceTree = "<group>"; };
- DCC31345076253A0008F7A48 /* CMakeLists.txt */ = {isa = PBXFileReference; fileEncoding = 30; lastKnownFileType = text; path = CMakeLists.txt; sourceTree = "<group>"; };
DCC31547076253A4008F7A48 /* cCycleCheck.cc */ = {isa = PBXFileReference; fileEncoding = 30; lastKnownFileType = sourcecode.cpp.cpp; path = cCycleCheck.cc; sourceTree = "<group>"; };
- DCC3154A076253A4008F7A48 /* CMakeLists.txt */ = {isa = PBXFileReference; fileEncoding = 30; lastKnownFileType = text; path = CMakeLists.txt; sourceTree = "<group>"; };
DCC31585076253A4008F7A48 /* recursive_tests_decl_hdrs.hh */ = {isa = PBXFileReference; fileEncoding = 30; lastKnownFileType = sourcecode.cpp.h; path = recursive_tests_decl_hdrs.hh; sourceTree = "<group>"; };
DCC31586076253A4008F7A48 /* recursive_tests_defn_hdrs.hh */ = {isa = PBXFileReference; fileEncoding = 30; lastKnownFileType = sourcecode.cpp.h; path = recursive_tests_defn_hdrs.hh; sourceTree = "<group>"; };
DCC31587076253A4008F7A48 /* recursive_tests_macros.hh */ = {isa = PBXFileReference; fileEncoding = 30; lastKnownFileType = sourcecode.cpp.h; path = recursive_tests_macros.hh; sourceTree = "<group>"; };
- DCC315A5076253A4008F7A48 /* CMakeLists.txt */ = {isa = PBXFileReference; fileEncoding = 30; lastKnownFileType = text; path = CMakeLists.txt; sourceTree = "<group>"; };
- DCC315A6076253A4008F7A48 /* UnitTest_recursive_tests.cc */ = {isa = PBXFileReference; fileEncoding = 30; lastKnownFileType = sourcecode.cpp.cpp; path = UnitTest_recursive_tests.cc; sourceTree = "<group>"; };
DCC315AD076253A5008F7A48 /* tUnitTestSuite.hh */ = {isa = PBXFileReference; fileEncoding = 30; lastKnownFileType = sourcecode.cpp.h; path = tUnitTestSuite.hh; sourceTree = "<group>"; };
DCC315AE076253A5008F7A48 /* tUnitTestSuiteRecurser.hh */ = {isa = PBXFileReference; fileEncoding = 30; lastKnownFileType = sourcecode.cpp.h; path = tUnitTestSuiteRecurser.hh; sourceTree = "<group>"; };
DCC315B0076253A5008F7A48 /* tVerifierSuite.hh */ = {isa = PBXFileReference; fileEncoding = 30; lastKnownFileType = sourcecode.cpp.h; path = tVerifierSuite.hh; sourceTree = "<group>"; };
@@ -932,7 +908,6 @@
DCC315C4076253A5008F7A48 /* matlabify.cc */ = {isa = PBXFileReference; fileEncoding = 30; lastKnownFileType = sourcecode.cpp.cpp; path = matlabify.cc; sourceTree = "<group>"; };
DCC315CD076253A5008F7A48 /* CMakeLists.txt */ = {isa = PBXFileReference; fileEncoding = 30; lastKnownFileType = text; path = CMakeLists.txt; sourceTree = "<group>"; };
DCC315CE076253A5008F7A48 /* environment.rotate */ = {isa = PBXFileReference; fileEncoding = 30; lastKnownFileType = text; path = environment.rotate; sourceTree = "<group>"; };
- DCC315CF076253A5008F7A48 /* Makefile */ = {isa = PBXFileReference; fileEncoding = 30; lastKnownFileType = sourcecode.make; path = Makefile; sourceTree = "<group>"; };
DCC315D0076253A5008F7A48 /* task_event_gen.cc */ = {isa = PBXFileReference; fileEncoding = 30; lastKnownFileType = sourcecode.cpp.cpp; path = task_event_gen.cc; sourceTree = "<group>"; };
DCC315D1076253A5008F7A48 /* task_event_gen.old.cc */ = {isa = PBXFileReference; fileEncoding = 30; lastKnownFileType = sourcecode.cpp.cpp; path = task_event_gen.old.cc; sourceTree = "<group>"; };
DCC3164D07626CF3008F7A48 /* avida */ = {isa = PBXFileReference; includeInIndex = 0; lastKnownFileType = "compiled.mach-o.executable"; path = avida; sourceTree = BUILT_PRODUCTS_DIR; };
@@ -986,7 +961,6 @@
701D930C094CAD6B008B845F /* cDefaultRunDriver.cc */,
701D93E6094CBF71008B845F /* cDefaultAnalyzeDriver.h */,
701D93E7094CBF71008B845F /* cDefaultAnalyzeDriver.cc */,
- 701D941C094CC5F1008B845F /* CMakeLists.txt */,
);
path = drivers;
sourceTree = "<group>";
@@ -999,7 +973,6 @@
709D924A0A5D94FD00D6A163 /* cMutationalNeighborhoodResults.h */,
70C054F50A4F701B002703C1 /* SConscript */,
70F7DE76092967A8009E311D /* cGenotypeBatch.h */,
- 70422A44091B1B8500A5E67F /* CMakeLists.txt */,
70422A1C091B141000A5E67F /* cAnalyze.cc */,
70422A1D091B141000A5E67F /* cAnalyze.h */,
70422A1E091B141000A5E67F /* cAnalyzeCommand.h */,
@@ -1025,7 +998,6 @@
isa = PBXGroup;
children = (
70C054F10A4F6FF1002703C1 /* SConscript */,
- 707AF0F809EACC5E001AEA89 /* CMakeLists.txt */,
707AEEEF09E80725001AEA89 /* cAction.h */,
707AEEFE09E83381001AEA89 /* cActionLibrary.h */,
707AF04409EAB529001AEA89 /* LandscapeActions.h */,
@@ -1056,7 +1028,6 @@
7049F36F0A66AD7E00640512 /* default-transsmt.org */,
707AF2D309EE8501001AEA89 /* analyze.cfg */,
707AF2D509EE8501001AEA89 /* avida.cfg */,
- 707AF2D609EE8501001AEA89 /* CMakeLists.txt */,
707AF2D709EE8501001AEA89 /* environment.cfg */,
707AF2D809EE8501001AEA89 /* events.cfg */,
7049F3520A66A8F500640512 /* instset-classic.cfg */,
@@ -1160,7 +1131,6 @@
70DCAC55097AF730002F8733 /* avida */,
70DCAC56097AF730002F8733 /* avida-s */,
70DCAC58097AF730002F8733 /* avida-viewer */,
- 70DCAD37097AF972002F8733 /* CMakeLists.txt */,
703CA3710A50734500AB4DB4 /* SConscript */,
);
path = targets;
@@ -1171,7 +1141,6 @@
children = (
703CA3720A50735B00AB4DB4 /* SConscript */,
70DCAC9B097AF7C0002F8733 /* primitive.cc */,
- 70DCAD39097AF985002F8733 /* CMakeLists.txt */,
);
path = avida;
sourceTree = "<group>";
@@ -1205,7 +1174,6 @@
70DCAC5D097AF730002F8733 /* cEnvironmentScreen.h */,
70DCAC5E097AF730002F8733 /* cHistScreen.cc */,
70DCAC5F097AF730002F8733 /* cHistScreen.h */,
- 70DCAC60097AF730002F8733 /* CMakeLists.txt */,
70DCAC61097AF730002F8733 /* cMapScreen.cc */,
70DCAC62097AF730002F8733 /* cMapScreen.h */,
70DCAC63097AF730002F8733 /* cMenuWindow.cc */,
@@ -1259,7 +1227,6 @@
isa = PBXGroup;
children = (
703CA3700A5072E600AB4DB4 /* SConscript */,
- 700E12610A097A0800B604CD /* CMakeLists.txt */,
70DCF50009CF823500924128 /* tcmalloc */,
);
path = platform;
@@ -1268,7 +1235,6 @@
70DCF50009CF823500924128 /* tcmalloc */ = {
isa = PBXGroup;
children = (
- 700E12630A097A1700B604CD /* CMakeLists.txt */,
70DCF57F09CFBD3D00924128 /* tcmalloc-logging.cc */,
70DCF58009CFBD3D00924128 /* tcmalloc-logging.h */,
70DCF50109CFB0B400924128 /* system-alloc.h */,
@@ -1314,7 +1280,6 @@
70F7DC9F09293E6F009E311D /* cGenotype.h */,
70F7DAEF09290468009E311D /* cClassificationManager.h */,
70F7DAF009290468009E311D /* cClassificationManager.cc */,
- 7053345E092A4D88006BD186 /* CMakeLists.txt */,
);
path = classification;
sourceTree = "<group>";
@@ -1345,9 +1310,7 @@
70DCF4FF09CF81E400924128 /* platform */,
70DCAD1E097AF81A002F8733 /* script */,
70DCAC54097AF730002F8733 /* targets */,
- DCC31340076253A0008F7A48 /* third-party */,
DCC314D8076253A2008F7A48 /* tools */,
- DCC30F7B0762539D008F7A48 /* CMakeLists.txt */,
701384A10902A16F0087ED2E /* defs.h */,
DCC30FCF0762539D008F7A48 /* Doxyfile */,
703CA3770A50740300AB4DB4 /* SConscript */,
@@ -1396,7 +1359,6 @@
70C1F0A808C3FF1800F50912 /* nHardware.h */,
70C1EF6708C395D300F50912 /* sCPUStats.h */,
706D30CC0852328F00D7DC8F /* tInstLib.h */,
- DCC30FA90762539D008F7A48 /* CMakeLists.txt */,
7005A70109BA0FA90007E16E /* cTestCPUInterface.h */,
7005A70209BA0FA90007E16E /* cTestCPUInterface.cc */,
705260BB0B87A7DB0007426F /* cInstLibEntry.h */,
@@ -1480,7 +1442,6 @@
70B0875A08F5EC8900FC65FE /* nGeometry.h */,
70B0867208F499C100FC65FE /* nMutation.h */,
70B0875C08F5ECBC00FC65FE /* nReaction.h */,
- DCC310A90762539E008F7A48 /* CMakeLists.txt */,
7005A70909BA0FBE0007E16E /* cOrgInterface.h */,
701D51CB09C645F50009B4F8 /* cAvidaContext.h */,
7027621909D73E5900741717 /* cOrgSourceMessage.h */,
@@ -1493,15 +1454,6 @@
path = main;
sourceTree = "<group>";
};
- DCC31340076253A0008F7A48 /* third-party */ = {
- isa = PBXGroup;
- children = (
- DCC31345076253A0008F7A48 /* CMakeLists.txt */,
- 703CA3740A50739600AB4DB4 /* SConscript */,
- );
- path = "third-party";
- sourceTree = "<group>";
- };
DCC314D8076253A2008F7A48 /* tools */ = {
isa = PBXGroup;
children = (
@@ -1601,11 +1553,9 @@
70B087DD08F5F4A900FC65FE /* cID.h */,
70B087DE08F5F4A900FC65FE /* cVerifierSuiteRecurser.h */,
DCC31547076253A4008F7A48 /* cCycleCheck.cc */,
- DCC3154A076253A4008F7A48 /* CMakeLists.txt */,
DCC31585076253A4008F7A48 /* recursive_tests_decl_hdrs.hh */,
DCC31586076253A4008F7A48 /* recursive_tests_defn_hdrs.hh */,
DCC31587076253A4008F7A48 /* recursive_tests_macros.hh */,
- DCC315A0076253A4008F7A48 /* tests */,
DCC315AD076253A5008F7A48 /* tUnitTestSuite.hh */,
DCC315AE076253A5008F7A48 /* tUnitTestSuiteRecurser.hh */,
DCC315B0076253A5008F7A48 /* tVerifierSuite.hh */,
@@ -1627,15 +1577,6 @@
path = tools;
sourceTree = "<group>";
};
- DCC315A0076253A4008F7A48 /* tests */ = {
- isa = PBXGroup;
- children = (
- DCC315A5076253A4008F7A48 /* CMakeLists.txt */,
- DCC315A6076253A4008F7A48 /* UnitTest_recursive_tests.cc */,
- );
- path = tests;
- sourceTree = "<group>";
- };
DCC315B6076253A5008F7A48 /* Utilities */ = {
isa = PBXGroup;
children = (
@@ -1662,7 +1603,6 @@
children = (
DCC315CD076253A5008F7A48 /* CMakeLists.txt */,
DCC315CE076253A5008F7A48 /* environment.rotate */,
- DCC315CF076253A5008F7A48 /* Makefile */,
DCC315D0076253A5008F7A48 /* task_event_gen.cc */,
DCC315D1076253A5008F7A48 /* task_event_gen.old.cc */,
);
@@ -2241,6 +2181,7 @@
isa = XCBuildConfiguration;
buildSettings = {
GCC_MODEL_CPU = G4;
+ HEADER_SEARCH_PATHS = /usr/local/boost;
OTHER_LDFLAGS = (
"-multiply_defined",
suppress,
Modified: branches/collect/CMakeLists.txt
===================================================================
--- branches/collect/CMakeLists.txt 2007-05-03 17:00:16 UTC (rev 1523)
+++ branches/collect/CMakeLists.txt 2007-05-03 17:36:49 UTC (rev 1524)
@@ -1,17 +1,10 @@
-
-# This section introduces the Avida project to CMake. In this file, it
-# must be between the configuration options above (otherwise it
-# overrides their defaults) and the configuration options, cmake module
-# includes, and convenience variables below (otherwise some variables
-# can't be properly defined because PROJECT_SOURCE_DIR and
-# PROJECT_BUILD_DIR aren't yet defined).
-
PROJECT(AVIDA)
-# The following three variables must be after the PROJECT statement, otherwise newer versions of cmake
-# will (correctly) use an empty value of PROJECT_BINARY_DIR, since the project didn't exist yet.
+# The following three variables must be after the PROJECT statement, otherwise
+# newer versions of cmake will (correctly) use an empty value of
+# PROJECT_BINARY_DIR, since the project didn't exist yet.
-# Default location for installed software / configs / docs is the build directory.
+# Default location for installed software/configs/ docs is the build directory.
SET(CMAKE_INSTALL_PREFIX
"${PROJECT_BINARY_DIR}"
CACHE PATH
@@ -34,16 +27,12 @@
-# This section defines default builtin configure options.
-
+# This section defines default builtin compiler options
+# ------------------------------------------------------------------------------
IF(UNIX)
+ SET(COMPILER_WARNING_FLAGS "-Wextra -Wno-unknown-pragmas -Wconversion -Wno-trigraphs")
+ SET(COMPILER_OPTIMIZATION_FLAGS "-ffast-math -fno-rtti -funroll-loops -fstrict-aliasing -ftree-vectorize -fvisibility-inlines-hidden")
- IF(APPLE)
- SET(COMPILER_WARNING_FLAGS "-Wall -Wno-long-double -Wno-long-long")
- ELSE(APPLE)
- SET(COMPILER_WARNING_FLAGS "-Wall -Wno-long-long")
- ENDIF(APPLE)
-
# Four types of c++ compilations:
# - debug (Debug)
# - minimum-size release (MinSizeRel)
@@ -53,39 +42,16 @@
"-g ${COMPILER_WARNING_FLAGS} -DDEBUG"
CACHE STRING "Flags used by the compiler during debug builds." FORCE)
SET(CMAKE_CXX_FLAGS_MINSIZEREL
- "-Os -DNDEBUG"
+ "-Os ${COMPILER_WARNING_FLAGS} -DNDEBUG"
CACHE STRING "Flags used by the compiler during release minsize builds." FORCE)
SET(CMAKE_CXX_FLAGS_RELWITHDEBINFO
- "-O2 -ffast-math -g ${COMPILER_WARNING_FLAGS} -DDEBUG"
+ "-O2 -g ${COMPILER_OPTIMIZATION_FLAGS} ${COMPILER_WARNING_FLAGS} -DDEBUG"
CACHE STRING "Flags used by the compiler during release builds." FORCE)
SET(CMAKE_CXX_FLAGS_RELEASE
- "-O3 -ffast-math -DNDEBUG"
+ "-O3 ${COMPILER_OPTIMIZATION_FLAGS} ${COMPILER_WARNING_FLAGS} -DNDEBUG"
CACHE STRING "Flags used by the compiler during release builds." FORCE)
-
- # Four types of c compilations:
- # - debug (Debug)
- # - minimum-size release (MinSizeRel)
- # - release (Release)
- # - release with debug info (RelWithDebInfo)
- SET(CMAKE_C_FLAGS_DEBUG
- "-g ${COMPILER_WARNING_FLAGS} -DDEBUG"
- CACHE STRING "Flags used by the compiler during debug builds." FORCE)
- SET(CMAKE_C_FLAGS_MINSIZEREL
- "-Os -DNDEBUG"
- CACHE STRING "Flags used by the compiler during release minsize builds." FORCE)
- SET(CMAKE_C_FLAGS_RELEASE
- "-O3 -ffast-math -DNDEBUG"
- CACHE STRING "Flags used by the compiler during release builds." FORCE)
- SET(CMAKE_C_FLAGS_RELWITHDEBINFO
- "-O2 -ffast-math -g ${COMPILER_WARNING_FLAGS} -DDEBUG"
- CACHE STRING "Flags used by the compiler during release builds." FORCE)
-
- # By default, show all build commands.
- SET(CMAKE_VERBOSE_MAKEFILE TRUE CACHE BOOL
- "If this value is on, makefiles will be generated without the .SILENT directive, and all commands will be echoed to the console during the make. This is useful for debugging only.")
ENDIF(UNIX)
-SET(CMAKE_SKIP_RPATH TRUE CACHE INTERNAL "Fix Library Path Issues?")
# Default build mode compiles c++ and c code with debug info and no
# optimizations.
@@ -93,32 +59,362 @@
SET(CMAKE_BUILD_TYPE
Release
CACHE STRING
- "Choose the type of build, options are: None(CMAKE_CXX_FLAGS or CMAKE_C_FLAGS used) Debug Release RelWithDebInfo MinSizeRel."
+ "Choose the type of build, options are: Debug Release RelWithDebInfo MinSizeRel."
FORCE
)
ENDIF(NOT CMAKE_BUILD_TYPE)
+
+# Build Instructions for the Avida Core functionality
+# - Below are groups of sources, based on directory. Each appends the source
+# - files to the master AVIDA_CORE_SOURCES list that is used to build a
+# - static library that is linked into relevant targets.
+# ------------------------------------------------------------------------------
+SET(AVIDA_CORE_SOURCES)
+SET(ALL_INC_DIRS
+ ${PROJECT_SOURCE_DIR}/source
+)
+
+
+# The actions directory
+SET(ACTIONS_DIR ${PROJECT_SOURCE_DIR}/source/actions)
+SET(ACTIONS_SOURCES
+ ${ACTIONS_DIR}/cActionLibrary.cc
+ ${ACTIONS_DIR}/DriverActions.cc
+ ${ACTIONS_DIR}/EnvironmentActions.cc
+ ${ACTIONS_DIR}/LandscapeActions.cc
+ ${ACTIONS_DIR}/PopulationActions.cc
+ ${ACTIONS_DIR}/PrintActions.cc
+ ${ACTIONS_DIR}/SaveLoadActions.cc
+)
+SOURCE_GROUP(actions FILES ${ACTIONS_SOURCES})
+LIST(APPEND AVIDA_CORE_SOURCES ${ACTIONS_SOURCES})
+LIST(APPEND ALL_INC_DIRS ${ACTIONS_DIR})
+
+
+# The analyze directory
+SET(ANALYZE_DIR ${PROJECT_SOURCE_DIR}/source/analyze)
+SET(ANALYZE_SOURCES
+ ${ANALYZE_DIR}/cAnalyze.cc
+ ${ANALYZE_DIR}/cAnalyzeGenotype.cc
+ ${ANALYZE_DIR}/cAnalyzeJobQueue.cc
+ ${ANALYZE_DIR}/cAnalyzeJobWorker.cc
+ ${ANALYZE_DIR}/cMutationalNeighborhood.cc
+)
+SOURCE_GROUP(analyze FILES ${ANALYZE_SOURCES})
+LIST(APPEND AVIDA_CORE_SOURCES ${ANALYZE_SOURCES})
+LIST(APPEND ALL_INC_DIRS ${ANALYZE_DIR})
+
+
+# The classification directory
+SET(CLASSIFICATION_DIR ${PROJECT_SOURCE_DIR}/source/classification)
+SET(CLASSIFICATION_SOURCES
+ ${CLASSIFICATION_DIR}/cClassificationManager.cc
+ ${CLASSIFICATION_DIR}/cGenotype.cc
+ ${CLASSIFICATION_DIR}/cGenotype_BirthData.cc
+ ${CLASSIFICATION_DIR}/cGenotypeControl.cc
+ ${CLASSIFICATION_DIR}/cInjectGenotype.cc
+ ${CLASSIFICATION_DIR}/cInjectGenotypeControl.cc
+ ${CLASSIFICATION_DIR}/cInjectGenotypeQueue.cc
+ ${CLASSIFICATION_DIR}/cLineage.cc
+ ${CLASSIFICATION_DIR}/cSpecies.cc
+ ${CLASSIFICATION_DIR}/cSpeciesControl.cc
+ ${CLASSIFICATION_DIR}/cSpeciesQueue.cc
+)
+SOURCE_GROUP(classification FILES ${CLASSIFICATION_SOURCES})
+LIST(APPEND AVIDA_CORE_SOURCES ${CLASSIFICATION_SOURCES})
+LIST(APPEND ALL_INC_DIRS ${CLASSIFICATION_DIR})
+
+
+# The cpu directory
+SET(CPU_DIR ${PROJECT_SOURCE_DIR}/source/cpu)
+SET(CPU_SOURCES
+ ${CPU_DIR}/cCodeLabel.cc
+ ${CPU_DIR}/cCPUMemory.cc
+ ${CPU_DIR}/cCPUStack.cc
+ ${CPU_DIR}/cCPUTestInfo.cc
+ ${CPU_DIR}/cHardwareBase.cc
+ ${CPU_DIR}/cHardwareCPU.cc
+ ${CPU_DIR}/cHardwareExperimental.cc
+ ${CPU_DIR}/cHardwareGX.cc
+ ${CPU_DIR}/cHardwareManager.cc
+ ${CPU_DIR}/cHardwareSMT.cc
+ ${CPU_DIR}/cHardwareStatusPrinter.cc
+ ${CPU_DIR}/cHardwareTransSMT.cc
+ ${CPU_DIR}/cHeadCPU.cc
+ ${CPU_DIR}/cInstSet.cc
+ ${CPU_DIR}/cTestCPU.cc
+ ${CPU_DIR}/cTestCPUInterface.cc
+)
+SOURCE_GROUP(cpu FILES ${CPU_SOURCES})
+LIST(APPEND AVIDA_CORE_SOURCES ${CPU_SOURCES})
+LIST(APPEND ALL_INC_DIRS ${CPU_DIR})
+
+
+# The drivers directory
+SET(DRIVERS_DIR ${PROJECT_SOURCE_DIR}/source/drivers)
+SET(DRIVERS_SOURCES
+ ${DRIVERS_DIR}/cDefaultAnalyzeDriver.cc
+ ${DRIVERS_DIR}/cDefaultRunDriver.cc
+ ${DRIVERS_DIR}/cDriverManager.cc
+ ${DRIVERS_DIR}/cFallbackWorldDriver.cc
+)
+SOURCE_GROUP(drivers FILES ${DRIVERS_SOURCES})
+LIST(APPEND AVIDA_CORE_SOURCES ${DRIVERS_SOURCES})
+LIST(APPEND ALL_INC_DIRS ${DRIVERS_DIR})
+
+
+# The main directory
+SET(MAIN_DIR ${PROJECT_SOURCE_DIR}/source/main)
+SET(MAIN_SOURCES
+ ${MAIN_DIR}/avida.cc
+ ${MAIN_DIR}/cAvidaConfig.cc
+ ${MAIN_DIR}/cBirthChamber.cc
+ ${MAIN_DIR}/cDeme.cc
+ ${MAIN_DIR}/cEnvironment.cc
+ ${MAIN_DIR}/cEventList.cc
+ ${MAIN_DIR}/cFitnessMatrix.cc
+ ${MAIN_DIR}/cGenome.cc
+ ${MAIN_DIR}/cGenomeUtil.cc
+ ${MAIN_DIR}/cInstruction.cc
+ ${MAIN_DIR}/cLandscape.cc
+ ${MAIN_DIR}/cLocalMutations.cc
+ ${MAIN_DIR}/cMutationLib.cc
+ ${MAIN_DIR}/cMutationRates.cc
+ ${MAIN_DIR}/cMxCodeArray.cc
+ ${MAIN_DIR}/cOrganism.cc
+ ${MAIN_DIR}/cPhenotype.cc
+ ${MAIN_DIR}/cPopulation.cc
+ ${MAIN_DIR}/cPopulationCell.cc
+ ${MAIN_DIR}/cPopulationInterface.cc
+ ${MAIN_DIR}/cReaction.cc
+ ${MAIN_DIR}/cReactionLib.cc
+ ${MAIN_DIR}/cReactionResult.cc
+ ${MAIN_DIR}/cResource.cc
+ ${MAIN_DIR}/cResourceCount.cc
+ ${MAIN_DIR}/cResourceLib.cc
+ ${MAIN_DIR}/cSpatialCountElem.cc
+ ${MAIN_DIR}/cSpatialResCount.cc
+ ${MAIN_DIR}/cStats.cc
+ ${MAIN_DIR}/cTaskLib.cc
+ ${MAIN_DIR}/cWorld.cc
+)
+SOURCE_GROUP(main FILES ${MAIN_SOURCES})
+LIST(APPEND AVIDA_CORE_SOURCES ${MAIN_SOURCES})
+LIST(APPEND ALL_INC_DIRS ${MAIN_DIR})
+
+
+# The tools directory
+SET(TOOLS_DIR ${PROJECT_SOURCE_DIR}/source/tools)
+SET(TOOLS_SOURCES
+ ${TOOLS_DIR}/cArgContainer.cc
+ ${TOOLS_DIR}/cArgSchema.cc
+ ${TOOLS_DIR}/cChangeList.cc
+ ${TOOLS_DIR}/cConstSchedule.cc
+ ${TOOLS_DIR}/cDataEntry.cc
+ ${TOOLS_DIR}/cDataFile.cc
+ ${TOOLS_DIR}/cDataFileManager.cc
+ ${TOOLS_DIR}/cDataManager_Base.cc
+ ${TOOLS_DIR}/cDefaultMessageDisplay.cc
+ ${TOOLS_DIR}/cDoubleSum.cc
+ ${TOOLS_DIR}/cFile.cc
+ ${TOOLS_DIR}/cHelpAlias.cc
+ ${TOOLS_DIR}/cHelpManager.cc
+ ${TOOLS_DIR}/cHelpType.cc
+ ${TOOLS_DIR}/cHistogram.cc
+ ${TOOLS_DIR}/cInitFile.cc
+ ${TOOLS_DIR}/cIntSum.cc
+ ${TOOLS_DIR}/cIntegratedSchedule.cc
+ ${TOOLS_DIR}/cIntegratedScheduleNode.cc
+ ${TOOLS_DIR}/cMerit.cc
+ ${TOOLS_DIR}/cProbSchedule.cc
+ ${TOOLS_DIR}/cRandom.cc
+ ${TOOLS_DIR}/cRunningAverage.cc
+ ${TOOLS_DIR}/cSchedule.cc
+ ${TOOLS_DIR}/cString.cc
+ ${TOOLS_DIR}/cStringIterator.cc
+ ${TOOLS_DIR}/cStringList.cc
+ ${TOOLS_DIR}/cStringUtil.cc
+ ${TOOLS_DIR}/cThread.cc
+ ${TOOLS_DIR}/cTools.cc
+ ${TOOLS_DIR}/cWeightedIndex.cc
+)
+SOURCE_GROUP(tools FILES ${TOOLS_SOURCES})
+LIST(APPEND AVIDA_CORE_SOURCES ${TOOLS_SOURCES})
+LIST(APPEND ALL_INC_DIRS ${TOOLS_DIR})
+
+
+# Create the static library from the master source list
+INCLUDE_DIRECTORIES(${ALL_INC_DIRS})
+ADD_LIBRARY(avidacore ${AVIDA_CORE_SOURCES})
+
+
+
+# Build Instructions for the TCMalloc library
+# ------------------------------------------------------------------------------
IF(UNIX)
SET(AVD_ENABLE_TCMALLOC TRUE)
ELSE(UNIX)
SET(AVD_ENABLE_TCMALLOC FALSE)
ENDIF(UNIX)
+IF(AVD_ENABLE_TCMALLOC)
+ SET(TCMALLOC_DIR source/platform/tcmalloc)
+ SET(TCMALLOC_SOURCES
+ ${TCMALLOC_DIR}/system-alloc.cc
+ ${TCMALLOC_DIR}/tcmalloc-logging.cc
+ ${TCMALLOC_DIR}/tcmalloc.cc
+ )
+ ADD_LIBRARY(tcmalloc ${TCMALLOC_SOURCES})
+ENDIF(AVD_ENABLE_TCMALLOC)
-IF(EXISTS ${PROJECT_SOURCE_DIR}/source/archive)
- OPTION(AVD_SERIALIZATION
- "Enable boost serialization support"
- OFF
+
+
+# Target Processing
+# - For each enabled target, process its build instructions. Must occur after
+# - avidacore has been defined.
+# ------------------------------------------------------------------------------
+OPTION(AVD_CMDLINE
+ "Enable building standard command line Avida (fastest version)."
+ ON
+)
+IF(AVD_CMDLINE)
+ SET(AVIDA_CMDLINE_DIR source/targets/avida)
+ SET(AVIDA_CMDLINE_SOURCES ${AVIDA_CMDLINE_DIR}/primitive.cc)
+ SOURCE_GROUP(target\\avida FILES ${AVIDA_CMDLINE_SOURCES})
+ ADD_EXECUTABLE(avida ${AVIDA_CMDLINE_SOURCES})
+
+ SET(AVIDA_CMDLINE_LIBS avidacore)
+ IF(NOT MSVC)
+ LIST(APPEND AVIDA_CMDLINE_LIBS pthread)
+ ENDIF(NOT MSVC)
+ IF(AVD_ENABLE_TCMALLOC)
+ LIST(APPEND AVIDA_CMDLINE_LIBS tcmalloc)
+ ENDIF(AVD_ENABLE_TCMALLOC)
+ TARGET_LINK_LIBRARIES(avida ${AVIDA_CMDLINE_LIBS})
+
+ INSTALL_TARGETS(/work avida)
+ENDIF(AVD_CMDLINE)
+
+
+# By default, build the console interface to Avida.
+OPTION(AVD_GUI_NCURSES
+ "Enable building Avida console interface."
+ OFF
+)
+# Make sure requisites are present for build of console interface. Give
+# user feedback if they're missing.
+IF(AVD_GUI_NCURSES)
+ # Locate the ncurses screen handling package (for Avida's console
+ # interface) and the Qt graphics API (for Avida's graphic interface).
+ INCLUDE(${PROJECT_SOURCE_DIR}/CMakeModules/FindNcurses.cmake)
+ IF(NOT NCURSES_INCLUDE_PATH)
+ MESSAGE("Unable to locate header files for the ncurses CRT screen handling package. Please set the advanced variable NCURSES_INCLUDE_PATH to their location.")
+ ENDIF(NOT NCURSES_INCLUDE_PATH)
+ IF(NOT NCURSES_LIBRARY)
+ MESSAGE("Unable to locate 'libncurses'. Please set the advanced variable NCURSES_LIBRARY to its location.")
+ ENDIF(NOT NCURSES_LIBRARY)
+
+ IF(NCURSES_LIBRARY AND NCURSES_INCLUDE_PATH)
+
+ INCLUDE_DIRECTORIES(${NCURSES_INCLUDE_PATH})
+
+ SET(AVIDA_VIEWER_DIR source/targets/avida-viewer)
+ SET(AVIDA_VIEWER_SOURCES
+ ${AVIDA_VIEWER_DIR}/cAnalyzeScreen.cc
+ ${AVIDA_VIEWER_DIR}/cAnalyzeView.cc
+ ${AVIDA_VIEWER_DIR}/cBarScreen.cc
+ ${AVIDA_VIEWER_DIR}/cEnvironmentScreen.cc
+ ${AVIDA_VIEWER_DIR}/cHistScreen.cc
+ ${AVIDA_VIEWER_DIR}/cMapScreen.cc
+ ${AVIDA_VIEWER_DIR}/cMenuWindow.cc
+ ${AVIDA_VIEWER_DIR}/cOptionsScreen.cc
+ ${AVIDA_VIEWER_DIR}/cScreen.cc
+ ${AVIDA_VIEWER_DIR}/cStatsScreen.cc
+ ${AVIDA_VIEWER_DIR}/cSymbolUtil.cc
+ ${AVIDA_VIEWER_DIR}/cTextViewerAnalyzeDriver.cc
+ ${AVIDA_VIEWER_DIR}/cTextViewerDriver.cc
+ ${AVIDA_VIEWER_DIR}/cTextViewerDriver_Base.cc
+ ${AVIDA_VIEWER_DIR}/cTextWindow.cc
+ ${AVIDA_VIEWER_DIR}/cView.cc
+ ${AVIDA_VIEWER_DIR}/cViewInfo.cc
+ ${AVIDA_VIEWER_DIR}/cZoomScreen.cc
+ ${AVIDA_VIEWER_DIR}/viewer.cc
+ )
+ SOURCE_GROUP(targets\\avida-viewer FILES ${AVIDA_VIEWER_SOURCES})
+ ADD_EXECUTABLE(avida-viewer ${AVIDA_VIEWER_SOURCES})
+
+ SET(AVIDA_VIEWER_LIBS avidacore ${NCURSES_LIBRARY})
+ IF(NOT MSVC)
+ LIST(APPEND AVIDA_VIEWER_LIBS pthread)
+ ENDIF(NOT MSVC)
+ IF(AVD_ENABLE_TCMALLOC)
+ LIST(APPEND AVIDA_VIEWER_LIBS tcmalloc)
+ ENDIF(AVD_ENABLE_TCMALLOC)
+ TARGET_LINK_LIBRARIES(avida-viewer ${AVIDA_VIEWER_LIBS})
+
+ INSTALL_TARGETS(/work avida-viewer)
+
+ ENDIF(NCURSES_LIBRARY AND NCURSES_INCLUDE_PATH)
+ENDIF(AVD_GUI_NCURSES)
+
+
+OPTION(AVD_TASK_EVENT_GEN
+ "Enable building the task_event_gen utility"
+ OFF
+)
+IF(AVD_TASK_EVENT_GEN)
+ SET(UTILS_DIR source/utils)
+ SET(TASK_EVENT_GEN_SOURCES
+ ${TOOLS_DIR}/cFile.cc
+ ${TOOLS_DIR}/cRandom.cc
+ ${TOOLS_DIR}/cString.cc
+ ${TOOLS_DIR}/cInitFIle.cc
+ ${TOOLS_DIR}/cStringIterator.cc
+ ${TOOLS_DIR}/cStringList.cc
+ ${UTILS_DIR}/task_events/task_event_gen.cc
)
-ELSE(EXISTS ${PROJECT_SOURCE_DIR}/source/archive)
- SET(AVD_SERIALIZATION FALSE)
-ENDIF(EXISTS ${PROJECT_SOURCE_DIR}/source/archive)
-IF(AVD_SERIALIZATION)
- ADD_DEFINITIONS(-DENABLE_SERIALIZATION=1)
-ELSE(AVD_SERIALIZATION)
- REMOVE_DEFINITIONS(-DENABLE_SERIALIZATION=1)
-ENDIF(AVD_SERIALIZATION)
+ ADD_EXECUTABLE(task_event_gen ${TASK_EVENT_GEN_SOURCES})
+ INSTALL_TARGETS(/work task_event_gen)
+ENDIF(AVD_TASK_EVENT_GEN)
+
+
+# Default Configuration Files
+# - Installed into the work directory alongside selected targets
+# ------------------------------------------------------------------------------
+SET(CFG_FILES_DIR support/config)
+SET(CFG_FILES
+ ${CFG_FILES_DIR}/analyze.cfg
+ ${CFG_FILES_DIR}/avida.cfg
+ ${CFG_FILES_DIR}/environment.cfg
+ ${CFG_FILES_DIR}/events.cfg
+ ${CFG_FILES_DIR}/instset-classic.cfg
+ ${CFG_FILES_DIR}/instset-sex-classic.cfg
+ ${CFG_FILES_DIR}/instset-smt.cfg
+ ${CFG_FILES_DIR}/instset-transsmt.cfg
+ ${CFG_FILES_DIR}/default-classic.org
+ ${CFG_FILES_DIR}/default-sex-classic.org
+ ${CFG_FILES_DIR}/default-smt.org
+ ${CFG_FILES_DIR}/default-transsmt.org
+)
+INSTALL_FILES(/work FILES ${CFG_FILES})
+
+
+
+# Avida-ED Related
+# ------------------------------------------------------------------------------
+
+OPTION(AVD_GUI_PYQT
+ "Enable the PyQt GUI interface. (EXPERIMENTAL)"
+ OFF
+)
+IF(AVD_GUI_PYQT)
+ SET(AVD_PY_BINDINGS ON CACHE BOOL "Avida Python Bindings MUST be built for the PyQt GUI." FORCE)
+ FIND_PROGRAM(PYUIC pyuic DOC "Path to pyuic. Used to compile python files from .ui files.")
+ENDIF(AVD_GUI_PYQT)
+
+
# Experimental Boost.Python interface to avida is disabled by default.
OPTION(AVD_PY_BINDINGS
"Enable Python interface to Avida. (EXPERIMENTAL)"
@@ -151,53 +447,12 @@
DOC "gccxml must be in the search path specified by your PATH environment variable in order for pyste to operate"
)
SET(UNIT_TESTS TRUE)
+
+ ADD_SUBDIRECTORY(source/bindings)
+ ADD_SUBDIRECTORY(source/python)
ENDIF(AVD_PY_BINDINGS)
-# By default, build the console interface to Avida.
-OPTION(AVD_GUI_NCURSES
- "Enable building Avida console interface."
- OFF
-)
-# Make sure requisites are present for build of console interface. Give
-# user feedback if they're missing.
-IF(AVD_GUI_NCURSES)
- # Locate the ncurses screen handling package (for Avida's console
- # interface) and the Qt graphics API (for Avida's graphic interface).
- INCLUDE(${PROJECT_SOURCE_DIR}/CMakeModules/FindNcurses.cmake)
- IF(NOT NCURSES_INCLUDE_PATH)
- MESSAGE(
- "Building Avida's console interface requires header files for the ncurses CRT screen handling package. I can't find those header files. If you know that the headers are installed, set the advanced variable NCURSES_INCLUDE_PATH to their include directory."
- )
- ENDIF(NOT NCURSES_INCLUDE_PATH)
- IF(NOT NCURSES_LIBRARY)
- MESSAGE(
- "Building Avida's console interface requires the ncurses library 'libncurses', which I can't find. If you know that the library is installed, set the advanced variable NCURSES_LIBRARY to its location."
- )
- ENDIF(NOT NCURSES_LIBRARY)
-ENDIF(AVD_GUI_NCURSES)
-
-# By default, build the primitive version of Avida.
-OPTION(AVD_PRIMITIVE
- "Enable building interfaceless Avida (fastest version)."
- ON
-)
-
-OPTION(AVD_GUI_PYQT
- "Enable the PyQt GUI interface. (EXPERIMENTAL)"
- OFF
-)
-IF(AVD_GUI_PYQT)
- SET(AVD_PY_BINDINGS ON CACHE BOOL "Avida Python Bindings MUST be built for the PyQt GUI." FORCE)
- FIND_PROGRAM(PYUIC pyuic DOC "Path to pyuic. Used to compile python files from .ui files.")
-ENDIF(AVD_GUI_PYQT)
-
-OPTION(AVD_TASK_EVENT_GEN
- "Enable building the task_event_gen utility"
- OFF
-)
-
-
# By default, compile all unit tests of primitive Avida classes. Tests
# are run via 'make test' under unix.
OPTION(AVD_UNIT_TESTS
@@ -215,71 +470,9 @@
REMOVE_DEFINITIONS(-DUSE_tMemTrack=1)
ENDIF(AVD_UNIT_TESTS)
-IF(MSVC)
- INCLUDE_DIRECTORIES(${PROJECT_SOURCE_DIR}/source/platform/win32-pthread)
-ENDIF(MSVC)
-# This section defines convenience variables. They're available to
-# CMakeList.txt files in all subdirectories beneath the directory
-# containing this file..
-
-# Shortcuts to the source subdirectories.
-SET(THIRDPARTY_SRC_DIR ${PROJECT_SOURCE_DIR}/source/third-party)
-SET(TOOLS_SRC_DIR ${PROJECT_SOURCE_DIR}/source/tools)
-SET(ACTIONS_SRC_DIR ${PROJECT_SOURCE_DIR}/source/actions)
-SET(ANALYZE_SRC_DIR ${PROJECT_SOURCE_DIR}/source/analyze)
-SET(ARCHIVE_SRC_DIR ${PROJECT_SOURCE_DIR}/source/archive)
-SET(BOOST_SRC_DIR ${PROJECT_SOURCE_DIR}/source/third-party/boost)
-SET(CLASSIFICATION_SRC_DIR ${PROJECT_SOURCE_DIR}/source/classification)
-SET(CPU_SRC_DIR ${PROJECT_SOURCE_DIR}/source/cpu)
-SET(DRIVERS_SRC_DIR ${PROJECT_SOURCE_DIR}/source/drivers)
-SET(EVENT_SRC_DIR ${PROJECT_SOURCE_DIR}/source/event)
-SET(MAIN_SRC_DIR ${PROJECT_SOURCE_DIR}/source/main)
-
-# Shortcuts to the build subdirectories.
-SET(THIRDPARTY_BLD_DIR ${PROJECT_BINARY_DIR}/source/third-party)
-SET(TOOLS_BLD_DIR ${PROJECT_BINARY_DIR}/source/tools)
-SET(ACTIONS_BLD_DIR ${PROJECT_BINARY_DIR}/source/actions)
-SET(ANALYZE_BLD_DIR ${PROJECT_BINARY_DIR}/source/analyze)
-SET(ARCHIVE_BLD_DIR ${PROJECT_BINARY_DIR}/source/archive)
-SET(BOOST_SERIALIZATION_BLD_DIR ${PROJECT_BINARY_DIR}/source/third-party/boost/serialization)
-SET(CLASSSIFICATION_BLD_DIR ${PROJECT_BINARY_DIR}/source/classification)
-SET(CPU_BLD_DIR ${PROJECT_BINARY_DIR}/source/cpu)
-SET(DRIVERS_BLD_DIR ${PROJECT_BINARY_DIR}/source/drivers)
-SET(EVENT_BLD_DIR ${PROJECT_BINARY_DIR}/source/event)
-SET(MAIN_BLD_DIR ${PROJECT_BINARY_DIR}/source/main)
-
-# A list of all source subdirectories (convenient for naming
-# include-directories).
-SET(ALL_INC_DIRS
- ${TOOLS_SRC_DIR}
- ${ACTIONS_SRC_DIR}
- ${ANALYZE_SRC_DIR}
- ${ARCHIVE_SRC_DIR}
- ${BOOST_SRC_DIR}
- ${CLASSIFICATION_SRC_DIR}
- ${CPU_SRC_DIR}
- ${DRIVERS_SRC_DIR}
- ${EVENT_SRC_DIR}
- ${EVENT_BLD_DIR}
- ${MAIN_SRC_DIR}
- ${PROJECT_SOURCE_DIR}/source
-)
-
-# A list of all build subdirectories (convenient for naming
-# link-subdirecties).
-SET(ALL_LIB_DIRS
- ${TOOLS_BLD_DIR}
- ${ACTIONS_BLD_DIR}
- ${ANALYZE_BLD_DIR}
- ${ARCHIVE_BLD_DIR}
- ${BOOST_SERIALIZATION_BLD_DIR}
- ${CLASSIFICATION_BLD_DIR}
- ${CPU_BLD_DIR}
- ${DRIVERS_BLD_DIR}
- ${EVENT_BLD_DIR}
- ${MAIN_BLD_DIR}
- ${LIBRARY_OUTPUT_PATH}
-)
-
-SUBDIRS(source support)
+IF(BUILD_AvidaSupportLibs)
+ IF(EXISTS source/third-party/AvidaSupportLibs/CMakeLists.txt)
+ ADD_SUBDIRECTORY(source/third-party/AvidaSupportLibs)
+ ENDIF(EXISTS source/third-party/AvidaSupportLibs/CMakeLists.txt)
+ENDIF(BUILD_AvidaSupportLibs)
Deleted: branches/collect/source/CMakeLists.txt
===================================================================
--- branches/collect/source/CMakeLists.txt 2007-05-03 17:00:16 UTC (rev 1523)
+++ branches/collect/source/CMakeLists.txt 2007-05-03 17:36:49 UTC (rev 1524)
@@ -1,11 +0,0 @@
-
-SUBDIRS(actions analyze classification cpu drivers main platform targets third-party tools utils/task_events)
-IF(AVD_SERIALIZATION)
- SUBDIRS(archive)
-ENDIF(AVD_SERIALIZATION)
-IF(AVD_PY_BINDINGS)
- SUBDIRS(bindings python)
-ENDIF(AVD_PY_BINDINGS)
-#IF(AVD_UNIT_TESTS)
-# SUBDIRS(testsuites)
-#ENDIF(AVD_UNIT_TESTS)
Deleted: branches/collect/source/actions/CMakeLists.txt
===================================================================
--- branches/collect/source/actions/CMakeLists.txt 2007-05-03 17:00:16 UTC (rev 1523)
+++ branches/collect/source/actions/CMakeLists.txt 2007-05-03 17:36:49 UTC (rev 1524)
@@ -1,14 +0,0 @@
-INCLUDE_DIRECTORIES(${ALL_INC_DIRS})
-
-SET(libactions_a_SOURCES
- cActionLibrary.cc
- DriverActions.cc
- EnvironmentActions.cc
- LandscapeActions.cc
- PopulationActions.cc
- PrintActions.cc
- SaveLoadActions.cc
-)
-
-ADD_LIBRARY(actions ${libactions_a_SOURCES})
-
Modified: branches/collect/source/actions/PrintActions.cc
===================================================================
--- branches/collect/source/actions/PrintActions.cc 2007-05-03 17:00:16 UTC (rev 1523)
+++ branches/collect/source/actions/PrintActions.cc 2007-05-03 17:36:49 UTC (rev 1524)
@@ -903,7 +903,7 @@
for (int c = 0; c < inst_count.GetSize(); c++)
{
double p = (inst_count[c] > 0) ? inst_count[c] / static_cast<double>(total_count) : 0.0;
- site_entropy[pos] += (p > 0.0) ? - p * log(p) / log(inst_count.GetSize()) : 0.0;
+ site_entropy[pos] += (p > 0.0) ? - p * log(p) / log(static_cast<double>(inst_count.GetSize())) : 0.0;
}
}
}
Deleted: branches/collect/source/analyze/CMakeLists.txt
===================================================================
--- branches/collect/source/analyze/CMakeLists.txt 2007-05-03 17:00:16 UTC (rev 1523)
+++ branches/collect/source/analyze/CMakeLists.txt 2007-05-03 17:36:49 UTC (rev 1524)
@@ -1,12 +0,0 @@
-INCLUDE_DIRECTORIES(${ALL_INC_DIRS})
-
-SET(libanalyze_a_SOURCES
- cAnalyze.cc
- cAnalyzeGenotype.cc
- cAnalyzeJobQueue.cc
- cAnalyzeJobWorker.cc
- cMutationalNeighborhood.cc
-)
-
-ADD_LIBRARY(analyze ${libanalyze_a_SOURCES})
-
Deleted: branches/collect/source/classification/CMakeLists.txt
===================================================================
--- branches/collect/source/classification/CMakeLists.txt 2007-05-03 17:00:16 UTC (rev 1523)
+++ branches/collect/source/classification/CMakeLists.txt 2007-05-03 17:36:49 UTC (rev 1524)
@@ -1,18 +0,0 @@
-INCLUDE_DIRECTORIES(${ALL_INC_DIRS})
-
-SET(libclassification_a_SOURCES
- cClassificationManager.cc
- cGenotype.cc
- cGenotype_BirthData.cc
- cGenotypeControl.cc
- cInjectGenotype.cc
- cInjectGenotypeControl.cc
- cInjectGenotypeQueue.cc
- cLineage.cc
- cSpecies.cc
- cSpeciesControl.cc
- cSpeciesQueue.cc
-)
-
-ADD_LIBRARY(classification ${libclassification_a_SOURCES})
-
Deleted: branches/collect/source/cpu/CMakeLists.txt
===================================================================
--- branches/collect/source/cpu/CMakeLists.txt 2007-05-03 17:00:16 UTC (rev 1523)
+++ branches/collect/source/cpu/CMakeLists.txt 2007-05-03 17:36:49 UTC (rev 1524)
@@ -1,23 +0,0 @@
-SET(libcpu_a_SOURCES
- cCodeLabel.cc
- cCPUMemory.cc
- cCPUStack.cc
- cCPUTestInfo.cc
- cHardwareBase.cc
- cHardwareCPU.cc
- cHardwareExperimental.cc
- cHardwareGX.cc
- cHardwareManager.cc
- cHardwareSMT.cc
- cHardwareStatusPrinter.cc
- cHardwareTransSMT.cc
- cHeadCPU.cc
- cInstSet.cc
- cTestCPU.cc
- cTestCPUInterface.cc
-)
-
-INCLUDE_DIRECTORIES(${ALL_INC_DIRS})
-
-ADD_LIBRARY(cpu ${libcpu_a_SOURCES})
-
Deleted: branches/collect/source/drivers/CMakeLists.txt
===================================================================
--- branches/collect/source/drivers/CMakeLists.txt 2007-05-03 17:00:16 UTC (rev 1523)
+++ branches/collect/source/drivers/CMakeLists.txt 2007-05-03 17:36:49 UTC (rev 1524)
@@ -1,11 +0,0 @@
-INCLUDE_DIRECTORIES(${ALL_INC_DIRS})
-
-SET(libdrivers_a_SOURCES
- cDefaultAnalyzeDriver.cc
- cDefaultRunDriver.cc
- cDriverManager.cc
- cFallbackWorldDriver.cc
-)
-
-ADD_LIBRARY(drivers ${libdrivers_a_SOURCES})
-
Deleted: branches/collect/source/main/CMakeLists.txt
===================================================================
--- branches/collect/source/main/CMakeLists.txt 2007-05-03 17:00:16 UTC (rev 1523)
+++ branches/collect/source/main/CMakeLists.txt 2007-05-03 17:36:49 UTC (rev 1524)
@@ -1,37 +0,0 @@
-INCLUDE_DIRECTORIES(${ALL_INC_DIRS})
-
-SET(libmain_a_SOURCES
- avida.cc
- cAvidaConfig.cc
- cBirthChamber.cc
- cDeme.cc
- cEnvironment.cc
- cEventList.cc
- cFitnessMatrix.cc
- cGenome.cc
- cGenomeUtil.cc
- cInstruction.cc
- cLandscape.cc
- cLocalMutations.cc
- cMutationLib.cc
- cMutationRates.cc
- cMxCodeArray.cc
- cOrganism.cc
- cPhenotype.cc
- cPopulation.cc
- cPopulationCell.cc
- cPopulationInterface.cc
- cReaction.cc
- cReactionLib.cc
- cReactionResult.cc
- cResource.cc
- cResourceCount.cc
- cResourceLib.cc
- cSpatialCountElem.cc
- cSpatialResCount.cc
- cStats.cc
- cTaskLib.cc
- cWorld.cc
-)
-
-ADD_LIBRARY(main ${libmain_a_SOURCES})
Modified: branches/collect/source/main/cPopulation.cc
===================================================================
--- branches/collect/source/main/cPopulation.cc 2007-05-03 17:00:16 UTC (rev 1523)
+++ branches/collect/source/main/cPopulation.cc 2007-05-03 17:36:49 UTC (rev 1524)
@@ -91,6 +91,7 @@
case nGeometry::GRID: { cout << "Geometry: Bounded grid" << endl; break; }
case nGeometry::TORUS: { cout << "Geometry: Torus" << endl; break; }
case nGeometry::CLIQUE: { cout << "Geometry: Clique" << endl; break; }
+ case nGeometry::HEX: { cout << "Geometry: Hex" << endl; break; }
default: {
cout << "Unknown geometry!" << endl;
assert(false);
@@ -111,7 +112,7 @@
cell_array.Resize(num_cells);
resource_count.ResizeSpatialGrids(world_x, world_y);
market.Resize(MARKET_SIZE);
-
+
// Setup the cells. Do things that are not dependent upon topology here.
for(int i=0; i<num_cells; ++i) {
cell_array[i].Setup(world, i, environment.GetMutRates());
@@ -161,6 +162,11 @@
deme_size_x, deme_size_y);
break;
}
+ case nGeometry::HEX: {
+ build_hex(&cell_array.begin()[i], &cell_array.begin()[i+deme_size],
+ deme_size_x, deme_size_y);
+ break;
+ }
default: {
assert(false);
}
@@ -1650,7 +1656,7 @@
// to the output stage, but behavior is dependent on compiler used and optimization
// level. For consistent output, ensures that 0.0 is returned.
const double p = ((double) abundance) / (double) num_organisms;
- const double partial_ent = (p == 1.0) ? 0.0 : -(p * Log(p));
+ const double partial_ent = (abundance == num_organisms) ? 0.0 : -(p * Log(p));
entropy += partial_ent;
// Do any special calculations for threshold genotypes.
@@ -1705,7 +1711,7 @@
// level. For consistent output, ensures that 0.0 is returned.
if (abundance > 0) {
double p = ((double) abundance) / (double) num_organisms;
- double partial_ent = (p == 1.0) ? 0.0 : -(p * Log(p));
+ double partial_ent = (abundance == num_organisms) ? 0.0 : -(p * Log(p));
species_entropy += partial_ent;
}
Modified: branches/collect/source/main/cStats.cc
===================================================================
--- branches/collect/source/main/cStats.cc 2007-05-03 17:00:16 UTC (rev 1523)
+++ branches/collect/source/main/cStats.cc 2007-05-03 17:36:49 UTC (rev 1524)
@@ -350,10 +350,16 @@
assert(sum_fitness.Average() >= 0.0);
assert(dom_fitness >= 0);
- if (sum_fitness.Average() == 0.0 || dom_fitness == 0.0) {
+
+ // Note: When average fitness and dominant fitness are close in value (i.e. should be identical)
+ // floating point rounding error can cause output variances. To mitigate this, threshold
+ // caps off values that differ by less than it, flushing the effective output value to zero.
+ const double ave_fitness = sum_fitness.Average();
+ const double threshold = 1.0e-14;
+ if (ave_fitness == 0.0 || dom_fitness == 0.0 || fabs(ave_fitness - dom_fitness) < threshold) {
energy = 0.0;
} else {
- energy = Log(dom_fitness / sum_fitness.Average());
+ energy = Log(dom_fitness / ave_fitness);
}
}
Modified: branches/collect/source/main/nGeometry.h
===================================================================
--- branches/collect/source/main/nGeometry.h 2007-05-03 17:00:16 UTC (rev 1523)
+++ branches/collect/source/main/nGeometry.h 2007-05-03 17:36:49 UTC (rev 1524)
@@ -30,7 +30,8 @@
GLOBAL = 0,
GRID,
TORUS,
- CLIQUE
+ CLIQUE,
+ HEX
};
}
Deleted: branches/collect/source/platform/CMakeLists.txt
===================================================================
--- branches/collect/source/platform/CMakeLists.txt 2007-05-03 17:00:16 UTC (rev 1523)
+++ branches/collect/source/platform/CMakeLists.txt 2007-05-03 17:36:49 UTC (rev 1524)
@@ -1,3 +0,0 @@
-IF(AVD_ENABLE_TCMALLOC)
- SUBDIRS(tcmalloc)
-ENDIF(AVD_ENABLE_TCMALLOC)
Deleted: branches/collect/source/platform/tcmalloc/CMakeLists.txt
===================================================================
--- branches/collect/source/platform/tcmalloc/CMakeLists.txt 2007-05-03 17:00:16 UTC (rev 1523)
+++ branches/collect/source/platform/tcmalloc/CMakeLists.txt 2007-05-03 17:36:49 UTC (rev 1524)
@@ -1,8 +0,0 @@
-
-SET(tcmalloc_SOURCES
- system-alloc.cc
- tcmalloc-logging.cc
- tcmalloc.cc
-)
-
-ADD_LIBRARY(tcmalloc ${tcmalloc_SOURCES})
Deleted: branches/collect/source/targets/CMakeLists.txt
===================================================================
--- branches/collect/source/targets/CMakeLists.txt 2007-05-03 17:00:16 UTC (rev 1523)
+++ branches/collect/source/targets/CMakeLists.txt 2007-05-03 17:36:49 UTC (rev 1524)
@@ -1,6 +0,0 @@
-IF(AVD_PRIMITIVE)
- SUBDIRS(avida)
-ENDIF(AVD_PRIMITIVE)
-IF(AVD_GUI_NCURSES)
- SUBDIRS(avida-viewer)
-ENDIF(AVD_GUI_NCURSES)
Deleted: branches/collect/source/targets/avida/CMakeLists.txt
===================================================================
--- branches/collect/source/targets/avida/CMakeLists.txt 2007-05-03 17:00:16 UTC (rev 1523)
+++ branches/collect/source/targets/avida/CMakeLists.txt 2007-05-03 17:36:49 UTC (rev 1524)
@@ -1,33 +0,0 @@
-INCLUDE_DIRECTORIES(${ALL_INC_DIRS})
-
-ADD_EXECUTABLE(avida primitive.cc)
-
-SET(avida_target_link_libs
- main classification cpu analyze drivers cpu tools actions analyze
-)
-
-IF(NOT MSVC)
- SET(avida_target_link_libs
- ${avida_target_link_libs} pthread
- )
-ENDIF(NOT MSVC)
-
-IF(AVD_ENABLE_TCMALLOC)
- SET(avida_target_link_libs
- ${avida_target_link_libs} tcmalloc
- )
-ENDIF(AVD_ENABLE_TCMALLOC)
-
-IF(AVD_SERIALIZATION)
- SET(avida_target_link_libs
- ${avida_target_link_libs} archive boost_serialization
- )
-ENDIF(AVD_SERIALIZATION)
-
-SET(avida_target_link_libs
- ${avida_target_link_libs} main
-)
-
-TARGET_LINK_LIBRARIES(avida ${avida_target_link_libs})
-LINK_DIRECTORIES(${ALL_LIB_DIRS})
-INSTALL_TARGETS(/work avida)
Deleted: branches/collect/source/targets/avida-viewer/CMakeLists.txt
===================================================================
--- branches/collect/source/targets/avida-viewer/CMakeLists.txt 2007-05-03 17:00:16 UTC (rev 1523)
+++ branches/collect/source/targets/avida-viewer/CMakeLists.txt 2007-05-03 17:36:49 UTC (rev 1524)
@@ -1,61 +0,0 @@
-INCLUDE(${PROJECT_SOURCE_DIR}/CMakeModules/FindNcurses.cmake)
-
-INCLUDE_DIRECTORIES(
- ${ALL_INC_DIRS}
- ${NCURSES_INCLUDE_PATH}
-)
-
-SET(libviewer_SOURCES
- cAnalyzeScreen.cc
- cAnalyzeView.cc
- cBarScreen.cc
- cEnvironmentScreen.cc
- cHistScreen.cc
- cMapScreen.cc
- cMenuWindow.cc
- cOptionsScreen.cc
- cScreen.cc
- cStatsScreen.cc
- cSymbolUtil.cc
- cTextViewerAnalyzeDriver.cc
- cTextViewerDriver.cc
- cTextViewerDriver_Base.cc
- cTextWindow.cc
- cView.cc
- cViewInfo.cc
- cZoomScreen.cc
-)
-ADD_LIBRARY(cursesviewer ${libviewer_SOURCES})
-
-ADD_EXECUTABLE(avida-viewer viewer.cc)
-
-SET(avida_viewer_target_link_libs
- cursesviewer main classification cpu analyze drivers cpu tools trio actions analyze ${NCURSES_LIBRARY}
-)
-
-
-IF(NOT MSVC)
- SET(avida_viewer_target_link_libs
- ${avida_viewer_target_link_libs} pthread
- )
-ENDIF(NOT MSVC)
-
-IF(AVD_ENABLE_TCMALLOC)
- SET(avida_viewer_target_link_libs
- ${avida_viewer_target_link_libs} tcmalloc
- )
-ENDIF(AVD_ENABLE_TCMALLOC)
-
-IF(AVD_SERIALIZATION)
- SET(avida_viewer_target_link_libs
- ${avida_viewer_target_link_libs} archive boost_serialization
- )
-ENDIF(AVD_SERIALIZATION)
-
-SET(avida_viewer_target_link_libs
- ${avida_viewer_target_link_libs} main
-)
-
-TARGET_LINK_LIBRARIES(avida-viewer ${avida_viewer_target_link_libs})
-LINK_DIRECTORIES(${ALL_LIB_DIRS} ${THIRDPARTY_BLD_DIR}/trio)
-INSTALL_TARGETS(/work avida-viewer)
Modified: branches/collect/source/testsuites/CMakeLists.txt
===================================================================
--- branches/collect/source/testsuites/CMakeLists.txt 2007-05-03 17:00:16 UTC (rev 1523)
+++ branches/collect/source/testsuites/CMakeLists.txt 2007-05-03 17:36:49 UTC (rev 1524)
@@ -1,6 +1,5 @@
INCLUDE_DIRECTORIES(${ALL_INC_DIRS})
-LINK_DIRECTORIES(${ALL_LIB_DIRS})
#
# This setup assumes that unit test suite source code has the same name as the
@@ -15,9 +14,9 @@
FOREACH(TEST_SUITE ${UNITTEST_SUITES})
ADD_EXECUTABLE(${TEST_SUITE} ${TEST_SUITE}.cc)
IF(MSVC)
- TARGET_LINK_LIBRARIES(${TEST_SUITE} main classification cpu analyze drivers analyze cpu tools actions main archive boost_serialization)
+ TARGET_LINK_LIBRARIES(${TEST_SUITE} avidacore)
ELSE(MSVC)
- TARGET_LINK_LIBRARIES(${TEST_SUITE} main classification cpu analyze drivers analyze cpu tools actions pthread main archive boost_serialization)
+ TARGET_LINK_LIBRARIES(${TEST_SUITE} avidacore pthread)
ENDIF(MSVC)
INSTALL_TARGETS(/work ${TEST_SUITE})
Deleted: branches/collect/source/tools/CMakeLists.txt
===================================================================
--- branches/collect/source/tools/CMakeLists.txt 2007-05-03 17:00:16 UTC (rev 1523)
+++ branches/collect/source/tools/CMakeLists.txt 2007-05-03 17:36:49 UTC (rev 1524)
@@ -1,45 +0,0 @@
-SET(libtools_a_SOURCES
- cArgContainer.cc
- cArgSchema.cc
- cChangeList.cc
- cConstSchedule.cc
- cDataEntry.cc
- cDataFile.cc
- cDataFileManager.cc
- cDataManager_Base.cc
- cDefaultMessageDisplay.cc
- cDoubleSum.cc
- cFile.cc
- cFixedCoords.cc
- cHelpAlias.cc
- cHelpManager.cc
- cHelpType.cc
- cHistogram.cc
- cIndexedBlockStruct.cc
- cInitFile.cc
- cIntSum.cc
- cIntegratedSchedule.cc
- cIntegratedScheduleNode.cc
- cMessageDisplay.cc
- cMerit.cc
- cProbSchedule.cc
- cRandom.cc
- cRunningAverage.cc
- cSchedule.cc
- cString.cc
- cStringIterator.cc
- cStringList.cc
- cStringUtil.cc
- cThread.cc
- cTools.cc
- cWeightedIndex.cc
- cCycleCheck.cc
-)
-
-IF(AVD_SERIALIZATION)
- SET(libtools_a_SOURCES ${libtools_a_SOURCES} nTemplateTests.cc)
-ENDIF(AVD_SERIALIZATION)
-
-INCLUDE_DIRECTORIES(${ALL_INC_DIRS})
-
-ADD_LIBRARY(tools ${libtools_a_SOURCES})
Modified: branches/collect/source/tools/cTopology.h
===================================================================
--- branches/collect/source/tools/cTopology.h 2007-05-03 17:00:16 UTC (rev 1523)
+++ branches/collect/source/tools/cTopology.h 2007-05-03 17:36:49 UTC (rev 1524)
@@ -10,6 +10,8 @@
#ifndef _C_TOPOLOGY_H_
#define _C_TOPOLOGY_H_
+#include "functions.h"
+
/*! Builds a torus topology out of the cells betwen the iterators.
In a torus, each cell is connected to up to 8 neighbors (including diagonals),
and connections DO wrap around the logical edges of the torus.
@@ -88,4 +90,21 @@
}
}
+
+/*! Builds a hexagonal grid topology out of the cells between the iterators. In
+a hex grid, each cell has at most 6 neighbors, and connections do not wrap around
+edges.
+*/
+template< typename InputIterator >
+void build_hex(InputIterator begin, InputIterator end, unsigned int rowSize, unsigned int colSize) {
+ // Start with a grid:
+ build_grid(begin, end, rowSize, colSize);
+ int offset = begin->GetID();
+ // ... and remove connections to the NE,SW:
+ for(InputIterator i=begin; i!=end; ++i) {
+ i->ConnectionList().Remove(&begin[GridNeighbor(i->GetID()-offset, colSize, rowSize, 1, -1)]);
+ i->ConnectionList().Remove(&begin[GridNeighbor(i->GetID()-offset, colSize, rowSize, -1, 1)]);
+ }
+}
+
#endif
Deleted: branches/collect/source/utils/task_events/CMakeLists.txt
===================================================================
--- branches/collect/source/utils/task_events/CMakeLists.txt 2007-05-03 17:00:16 UTC (rev 1523)
+++ branches/collect/source/utils/task_events/CMakeLists.txt 2007-05-03 17:36:49 UTC (rev 1524)
@@ -1,12 +0,0 @@
-INCLUDE_DIRECTORIES(${ALL_INC_DIRS})
-
-IF(AVD_TASK_EVENT_GEN)
- ADD_EXECUTABLE(task_event_gen task_event_gen.cc)
- SET(task_event_gen_link_libraries tools)
- IF(AVD_SERIALIZATION)
- SET(task_event_gen_link_libraries ${task_event_gen_link_libraries} archive boost_serialization)
- ENDIF(AVD_SERIALIZATION)
- TARGET_LINK_LIBRARIES(task_event_gen ${task_event_gen_link_libraries})
- LINK_DIRECTORIES(${ALL_LIB_DIRS})
- INSTALL_TARGETS(/work task_event_gen)
-ENDIF(AVD_TASK_EVENT_GEN)
Modified: branches/collect/source/utils/task_events/task_event_gen.cc
===================================================================
--- branches/collect/source/utils/task_events/task_event_gen.cc 2007-05-03 17:00:16 UTC (rev 1523)
+++ branches/collect/source/utils/task_events/task_event_gen.cc 2007-05-03 17:36:49 UTC (rev 1524)
@@ -1,11 +1,11 @@
#include <iostream>
-#include "../../tools/tArray.h"
-#include "../../tools/cFile.h"
-#include "../../tools/cRandom.h"
-#include "../../tools/cString.h"
-#include "../../tools/cInitFile.h"
-#include "../../tools/cStringList.h"
+#include "tArray.h"
+#include "cFile.h"
+#include "cRandom.h"
+#include "cString.h"
+#include "cInitFile.h"
+#include "cStringList.h"
using namespace std;
Deleted: branches/collect/support/CMakeLists.txt
===================================================================
--- branches/collect/support/CMakeLists.txt 2007-05-03 17:00:16 UTC (rev 1523)
+++ branches/collect/support/CMakeLists.txt 2007-05-03 17:36:49 UTC (rev 1524)
@@ -1,2 +0,0 @@
-SUBDIRS(config)
-
Deleted: branches/collect/support/config/CMakeLists.txt
===================================================================
--- branches/collect/support/config/CMakeLists.txt 2007-05-03 17:00:16 UTC (rev 1523)
+++ branches/collect/support/config/CMakeLists.txt 2007-05-03 17:36:49 UTC (rev 1524)
@@ -1,14 +0,0 @@
-INSTALL_FILES(/work FILES
- analyze.cfg
- avida.cfg
- environment.cfg
- events.cfg
- instset-classic.cfg
- instset-sex-classic.cfg
- instset-smt.cfg
- instset-transsmt.cfg
- default-classic.org
- default-sex-classic.org
- default-smt.org
- default-transsmt.org
-)
Copied: branches/collect/tests/_analyze_fulllandscape_2step (from rev 1523, development/tests/_analyze_fulllandscape_2step)
Modified: branches/collect/tests/_testrunner/testrunner.py
===================================================================
--- branches/collect/tests/_testrunner/testrunner.py 2007-05-03 17:00:16 UTC (rev 1523)
+++ branches/collect/tests/_testrunner/testrunner.py 2007-05-03 17:36:49 UTC (rev 1524)
@@ -52,7 +52,7 @@
# Global Constants
# ---------------------------------------------------------------------------------------------------------------------------
-TESTRUNNER_VERSION = "1.2"
+TESTRUNNER_VERSION = "1.3b"
TESTRUNNER_COPYRIGHT = "2007"
TRUE_STRINGS = ("y","Y","yes","Yes","true","True","1")
@@ -521,31 +521,8 @@
except (IOError, OSError): pass
- # Run warm up
- p = popen2.Popen4("cd %s; %s %s" % (rundir, self.app, self.args))
-
- # Process output from app
- # Note: must at least swallow app output so that the process output buffer does not fill and block execution
- if settings.has_key("_verbose"): print
- for line in p.fromchild:
- if settings.has_key("_verbose"):
- sys.stdout.write("%s output: %s" % (self.name, line))
- sys.stdout.flush()
-
- exitcode = p.wait()
-
- # Check exit code
- nz = self.getConfig("main", "nonzeroexit", "disallow")
- if (nz == "disallow" and exitcode != 0) or (nz == "require" and exitcode == 0):
- try:
- shutil.rmtree(rundir, True) # Clean up test directory
- except (IOError, OSError): pass
- self.psuccess = False
- self.presult = "test app returned non-zero exit code"
- return
-
-
# Run test X times, take min value
+ nz = self.getConfig("main", "nonzeroexit", "disallow")
r_times = []
t_times = []
for i in range(settings["perf_repeat"]):
@@ -633,16 +610,17 @@
r_margin = settings["perf_user_margin"] * r_base
r_umargin = r_base + r_margin
r_lmargin = r_base - r_margin
+ r_ratio = r_min / r_base
+
t_margin = settings["perf_wall_margin"] * t_base
t_umargin = t_base + t_margin
t_lmargin = t_base - t_margin
+ t_ratio = t_min / t_base
if r_min > r_umargin or t_min > t_umargin:
self.psuccess = False
self.presult = "failed"
- if t_min > t_umargin: self.presult += " - wall = b: %3.4f t: %3.4f" % (t_base, t_min)
- if r_min > r_umargin: self.presult += " - user = b: %3.4f t: %3.4f" % (r_base, r_min)
elif r_min < r_lmargin or t_min < t_lmargin:
# new baseline, move old baseline and write out new results
try:
@@ -662,15 +640,12 @@
fp.flush()
fp.close()
except (IOError, OSError, shutil.Error):
- try:
- shutil.rmtree(rundir, True) # Clean up test directory
- except (IOError, OSError): pass
print "Warning: error updating '%s' performance baseline" % self.name
- return
-
self.presult = "exceeded"
- if t_min < t_lmargin: self.presult += " - wall = b: %3.4f t: %3.4f" % (t_base, t_min)
- if r_min < r_lmargin: self.presult += " - user = b: %3.4f t: %3.4f" % (r_base, r_min)
+
+ # Print output on all tests
+ self.presult += "\n - wall: %2.2f base = %3.4f test = %3.4f" % (t_ratio, t_base, t_min)
+ self.presult += "\n - user: %2.2f base = %3.4f test = %3.4f" % (r_ratio, r_base, r_min)
# Clean up test directory
try:
Modified: branches/collect/tests/demes_clique_repl/expected/data/stats.dat
===================================================================
--- branches/collect/tests/demes_clique_repl/expected/data/stats.dat 2007-05-03 17:00:16 UTC (rev 1523)
+++ branches/collect/tests/demes_clique_repl/expected/data/stats.dat 2007-05-03 17:36:49 UTC (rev 1524)
@@ -15,7 +15,7 @@
0 0.000000 0.097500 0.562358 0.102587 0.826353 1 0.000000 0.000000 0 0 0
10 0 0.562358 0.562358 0.826353 0.826353 0 0 0 0 0 0
-20 2.44249e-15 0.56231 0.562358 0.826245 0.826353 0 1.66246 0 0 0 0
+20 0 0.56231 0.562358 0.826245 0.826353 0 1.66246 0 0 0 0
30 0.0112117 0.562277 0.562358 0.826168 0.826353 0 3.04105 0 0 0 0
40 0.00834928 0.562358 0.562358 0.826353 0.826353 -190 2.83844 0 0 0 0
50 0.0243085 0.562358 0.562358 0.826353 0.826353 1 2.87929 0 0 0 0
Modified: branches/collect/tests/demes_germline/expected/data/stats.dat
===================================================================
--- branches/collect/tests/demes_germline/expected/data/stats.dat 2007-05-03 17:00:16 UTC (rev 1523)
+++ branches/collect/tests/demes_germline/expected/data/stats.dat 2007-05-03 17:36:49 UTC (rev 1524)
@@ -15,7 +15,7 @@
0 0.000000 0.097500 0.562358 0.102587 0.826353 1 0.000000 0.000000 0 0 0
10 0 0.562358 0.562358 0.826353 0.826353 0 0 0 0 0 0
-20 2.44249e-15 0.562405 0.562358 0.826462 0.826353 0 1.7334 0 0 0 0
+20 0 0.562405 0.562358 0.826462 0.826353 0 1.7334 0 0 0 0
30 0.0093872 0.562374 0.562358 0.82639 0.826353 0 3.29336 0 0 0 0
40 0 0.562358 0.562358 0.826353 0.826353 -217 1.68364 0 0 0 0
50 0 0.562358 0.562358 0.826353 0.826353 0 1.68364 0 0 0 0
Modified: branches/collect/tests/demes_grid_repl/expected/data/stats.dat
===================================================================
--- branches/collect/tests/demes_grid_repl/expected/data/stats.dat 2007-05-03 17:00:16 UTC (rev 1523)
+++ branches/collect/tests/demes_grid_repl/expected/data/stats.dat 2007-05-03 17:36:49 UTC (rev 1524)
@@ -15,7 +15,7 @@
0 0.000000 0.097500 0.562358 0.102587 0.826353 1 0.000000 0.000000 0 0 0
10 0 0.562358 0.562358 0.826353 0.826353 0 0 0 0 0 0
-20 2.44249e-15 0.562405 0.562358 0.826462 0.826353 0 1.7334 0 0 0 0
+20 0 0.562405 0.562358 0.826462 0.826353 0 1.7334 0 0 0 0
30 0.0093872 0.562374 0.562358 0.82639 0.826353 0 3.29336 0 0 0 0
40 0.0176158 0.562548 0.562358 0.826788 0.826353 -215 2.62128 0 0 0 0
50 0.034041 0.562544 0.562358 0.826779 0.826353 1 2.67998 0 0 0 0
Copied: branches/collect/tests/demes_hex_repl (from rev 1523, development/tests/demes_hex_repl)
Modified: branches/collect/tests/demes_torus_repl/expected/data/stats.dat
===================================================================
--- branches/collect/tests/demes_torus_repl/expected/data/stats.dat 2007-05-03 17:00:16 UTC (rev 1523)
+++ branches/collect/tests/demes_torus_repl/expected/data/stats.dat 2007-05-03 17:36:49 UTC (rev 1524)
@@ -15,7 +15,7 @@
0 0.000000 0.097500 0.562358 0.102587 0.826353 1 0.000000 0.000000 0 0 0
10 0 0.562358 0.562358 0.826353 0.826353 0 0 0 0 0 0
-20 2.44249e-15 0.562294 0.562358 0.826209 0.826353 0 1.66677 0 0 0 0
+20 0 0.562294 0.562358 0.826209 0.826353 0 1.66677 0 0 0 0
30 0.0142025 0.562309 0.562358 0.826243 0.826353 0 3.07983 0 0 0 0
40 0.0188194 0.562421 0.562358 0.826498 0.826353 -204 3.07702 0 0 0 0
50 0.0309456 0.562513 0.562358 0.826708 0.826353 0 3.12679 0 0 0 0
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