Combined 391+386+337+281 (#392)

* Hotfix | some old scripts in moose-examples failed because of regression caused by #390.

* Added graph utility.
Renamed to network_utils. Imported by default when moose.utils is imported. Renamed functions.

* Added Boost ODE based solvers of MarkovChannel. Now GSL is optional.
Renamed MarkovGslSolver class to MarkovOdeSolver. It compiles with both boost and gsl.

* This is squashed version of #281

- Added new solver based on 'LSODA' method.

This is a CPP version of the LSODA library for integration into MOOSE simulator. These source code are released under MIT license which is compatible with MOOSE. See Credit below.
Adds three tests (1 python). Results are equivalent to scipy's lsoda solver.
Following changes are made to this version:

Used <array> and <vector> instead of raw array where-ever possible.
Craeted a class LSODA and added a function to integrate it smoothly with moose.
Various tweaks in various functions especially initialization.
Core computing functions starts with index 1 rather than 0; this is hidden away from MOOSE api.
The performance of this solver is really good. In debug mode, on a small model, I got 6.7x speedup without any multi-threading. The solver is not recommended for stiff systems. Once it is integrated we do more profiling vis-a-vis standard RK5 solver.

- Licensing

Work by Heng Li was released under MIT Incense which is less restrictive than GNU-GPLv3. See here. The LSODA class is released under the same license.

- Logs

https://docs.google.com/document/d/e/2PACX-1vQ3wU9xiMSMVcluDrNSzuSGHsttOqAqc8xN4a9qo7wFfYjwl-0KhKyY1LlM5XkQ_5CqJd3eFnUCYiAb/pub

- Credit

The original was aquired from http://www.ccl.net/cca/software/SOURCES/C/kinetics2/index.shtml and modified by Heng Li lh3lh3@gmail.com. Heng merged several C files into one and added a simpler interface. His version can be found http://lh3lh3.users.sourceforge.net/download/lsoda.c .

Author: upibhalla

.travis.yml

@@ -32,8 +32,3 @@ before_script:
 script:
   - if [[ "$TRAVIS_OS_NAME" == "osx" ]]; then ./.ci/travis_build_osx.sh; fi
   - if [[ "$TRAVIS_OS_NAME" == "linux" ]]; then ./.ci/travis_build_linux.sh; fi
-
-after_success:
-  - if [[ "$TRAVIS_OS_NAME" == "linux" ]]; then\
-      mkdir _sdist && cd _sdist && cmake .. && make sdist && make upload_test;\
-    fi

CMakeLists.txt

@@ -102,6 +102,14 @@ if(WITH_ASAN AND "${CMAKE_BUILD_TYPE}" STREQUAL "Debug")
     set(CMAKE_MODULE_LINKER_FLAGS "${CMAKE_MODULE_LINKER_FLAGS} -fsanitize=address")
 endif()
 
+if(WITH_GSL)
+    set(WITH_BOOST OFF)
+    set(WITH_BOOST_ODE OFF)
+elseif(WITH_BOOST)
+    set(WITH_BOOST_ODE ON)
+    set(WITH_GSL OFF)
+endif()
+
 ################################### TARGETS ####################################
 
 link_directories(${CMAKE_BINARY_DIR})
@@ -112,17 +120,6 @@ add_executable(moose.bin basecode/main.cpp)
 ################################### SETUP BUILD ################################
 # default include paths.
 include_directories( ${CMAKE_CURRENT_SOURCE_DIR} )
-
-if(WITH_BOOST)
-    set(WITH_BOOST_ODE ON)
-    set(WITH_GSL       OFF)
-endif(WITH_BOOST)
-
-# If using BOOST ODE2 library to solve ODE system, then don't use GSL.
-if(WITH_BOOST_ODE)
-    set(WITH_GSL OFF)
-endif(WITH_BOOST_ODE)
-
 set_target_properties(libmoose PROPERTIES COMPILE_DEFINITIONS  "MOOSE_LIB")
 set_target_properties(libmoose PROPERTIES PREFIX "")
 
@@ -235,6 +232,7 @@ add_subdirectory(benchmarks)
 add_subdirectory(kinetics)
 add_subdirectory(synapse)
 add_subdirectory(intfire)
+add_subdirectory(external/libsoda)
 
 ###################################### LINKING #################################
 list(APPEND MOOSE_LIBRARIES
@@ -255,6 +253,7 @@ list(APPEND MOOSE_LIBRARIES
     signeur
     diffusion
     ksolve
+    lsoda
     device
     basecode
     )

basecode/global.cpp

@@ -144,6 +144,22 @@ namespace moose {
         if( p.size() == 0 )
             return true;
 
+#ifdef  USE_BOOST_FILESYSTEM
+        try
+        {
+            boost::filesystem::path pdirs( p );
+            boost::filesystem::create_directories( pdirs );
+            LOG( moose::info, "Created directory " << p );
+            return true;
+        }
+        catch(const boost::filesystem::filesystem_error& e)
+        {
+            LOG( moose::warning, "create_directories(" << p << ") failed with "
+                    << e.code().message()
+               );
+            return false;
+        }
+#else      /* -----  not USE_BOOST_FILESYSTEM  ----- */
         string command( "mkdir -p ");
         command += p;
         int ret = system( command.c_str() );
@@ -163,6 +179,7 @@ namespace moose {
             LOG( moose::warning, p << " is no directory" );
             return false;
         }
+#endif     /* -----  not USE_BOOST_FILESYSTEM  ----- */
         return true;
     }
 

basecode/global.h

@@ -17,7 +17,12 @@
 #include <sstream>
 #include <valarray>
 
-#include "../randnum/RNG.h"                        /* Use inbuilt rng */
+
+#ifdef  USE_BOOST_FILESYSTEM
+#include <boost/filesystem.hpp>
+#endif
+
+#include "randnum/RNG.h"                        /* Use inbuilt rng */
 #include "../utility/print_function.hpp"
 
 using namespace std;

basecode/main.cpp

@@ -35,7 +35,6 @@ int testIndex = 0;
     f; \
     cout << std::right << "  [DONE]" << endl; \
 
-extern void testSync();
 extern void testAsync();
 extern void testSyncArray( unsigned int size, unsigned int method );
 extern void testShell();
@@ -67,9 +66,9 @@ extern void testSigNeurProcess();
 extern unsigned int initMsgManagers();
 extern void destroyMsgManagers();
 // void regressionTests();
-#endif
-extern void speedTestMultiNodeIntFireNetwork(
-    unsigned int size, unsigned int runsteps );
+#endif   // DO_UNIT_TESTS
+
+extern void speedTestMultiNodeIntFireNetwork(unsigned int size, unsigned int runsteps);
 
 #ifdef USE_SMOLDYN
 extern void testSmoldyn();

biophysics/CMakeLists.txt

@@ -2,7 +2,11 @@ cmake_minimum_required(VERSION 2.8)
 include(${CMAKE_CURRENT_SOURCE_DIR}/../CheckCXXCompiler.cmake)
 
 if(WITH_GSL)
+    find_package(GSL 1.16)
     include_directories(${GSL_INCLUDE_DIRS})
+elseif(WITH_BOOST_ODE)
+    find_package(Boost)
+    include_directories(${Boost_INCLUDE_DIRS})
 endif(WITH_GSL)
 
 set(BIOPHYSICS_SRCS
@@ -32,7 +36,6 @@ set(BIOPHYSICS_SRCS
     ReadSwc.cpp
     SynChan.cpp
     NMDAChan.cpp
-    testBiophysics.cpp
     IzhikevichNrn.cpp
     DifShellBase.cpp
     DifShell.cpp
@@ -48,10 +51,9 @@ set(BIOPHYSICS_SRCS
     MarkovSolver.cpp
     VClamp.cpp
     Spine.cpp
+    MarkovOdeSolver.cpp
+    testBiophysics.cpp
     )
 
-if(WITH_GSL)
-    list(APPEND BIOPHYSICS_SRCS MarkovGslSolver.cpp)
-endif(WITH_GSL)
+add_library(biophysics ${BIOPHYSICS_SRCS})
 
-add_library( biophysics ${BIOPHYSICS_SRCS} )