Hotfixes | diffLength and max compartments, rdesigneur+py3 etc, build system (#368)

* Don't run streamer multitab tests on OSX/Travis.

* Disable all socket streamer tests.

* IMplemented std::async to launch the thread with given policy. Needs
profiling.  minor refactoring.
Since we can not order order in launching thread, setting moose.seed
would not result in deterministic number #365

* temp commit.

* removed npy support. On large files, it was not working properly. Only
csv format is supported in Streamer.

* Fixes to CylMesh x0/x1 and diffLength bug.

* Added ASN support.
Address leak in symbol table.
No move in copy contructor.

* Invalid chunk size again.
minor cleanup.
A bit of refactoring. Need to fix the RNG in Gsolve.cpp

* Build is passing.

* Fixes to travis file.

* Fixes to tests.

* Fixed test_gsolve_parallel.

* NSDF related fixes.

* Fixed boost compile flags.

Author: dilawar

.travis.yml

@@ -3,14 +3,10 @@ sudo: required
 
 matrix:
     include:
-        - os : linux
-          dist: xenial
-        - os : osx
-            - osx_image: xcode9.4
-            - osx_image: xcode10.2
-    allow_failures:
-        - os: osx
-          - osx_image: xcode10.2
+    - os: linux
+      dist: xenial
+    - os: osx
+      osx_image: xcode10.2
 
 notifications:
   email:
@@ -30,12 +26,6 @@ before_script:
 - if [[ "$TRAVIS_OS_NAME" == "osx" ]]; then ./.travis/travis_prepare_osx.sh; fi
 - if [[ "$TRAVIS_OS_NAME" == "linux" ]]; then sudo ./.travis/travis_prepare_linux.sh; fi
 
-
-before_script:
-- if [[ "$TRAVIS_OS_NAME" == "osx" ]]; then nvm get head || true; fi
-- if [[ "$TRAVIS_OS_NAME" == "osx" ]]; then ./.travis/travis_prepare_osx.sh; fi
-- if [[ "$TRAVIS_OS_NAME" == "linux" ]]; then sudo ./.travis/travis_prepare_linux.sh; fi
-
 script:
 - if [[ "$TRAVIS_OS_NAME" == "osx" ]]; then ./.travis/travis_build_osx.sh; fi
 - if [[ "$TRAVIS_OS_NAME" == "linux" ]]; then ./.travis/travis_build_linux.sh; fi

CMakeLists.txt

@@ -4,7 +4,6 @@ project(pymoose)
 set(CMAKE_MODULE_PATH "${CMAKE_SOURCE_DIR}/cmake_modules")
 include(CheckCXXCompiler.cmake)
 include(CheckIncludeFileCXX)
-include(FindPkgConfig)
 
 # getgit revision number
 find_program( GIT_EXEC git )
@@ -78,6 +77,7 @@ option(WITH_BOOST_ODE       "Use boost library ode2 library instead of GSL" OFF)
 option(WITH_GSL             "Use gsl-library. Alternative is WITH_BOOST" ON)
 option(PARALLELIZED_CLOCK   "High level parallelization of moose::Clock (alpha)" OFF )
 option(USE_PRIVATE_RNG      "Stochastic Objects use their private RNG" ON)
+option(WITH_ASAN            "Use AddressSanitizer in DEBUG mode." OFF)
 
 
 ############################ BUILD CONFIGURATION #################################
@@ -87,7 +87,7 @@ add_definitions(-DUSE_GENESIS_PARSER)
 
 if(DEBUG OR "${CMAKE_BUILD_TYPE}" STREQUAL "Debug")
     message(STATUS "Building for Debug/Unit testing")
-    add_definitions(-DDO_UNIT_TESTS)
+    add_definitions(-DDO_UNIT_TESTS -O)
     set(CMAKE_BUILD_TYPE Debug)
 elseif(ENABLE_UNIT_TESTS)
     MESSAGE(STATUS "Enabled Unit tests")
@@ -109,8 +109,14 @@ if(GPROF AND "${CMAKE_BUILD_TYPE}" STREQUAL "Debug")
     set(CMAKE_EXE_LINKER_FLAGS_DEBUG "-pg")
 endif()
 
-find_package(Threads)
-
+if(WITH_ASAN AND "${CMAKE_BUILD_TYPE}" STREQUAL "Debug")
+    message(STATUS "Compiling with ASAN")
+    set(CMAKE_CXX_FLAGS_DEBUG "${CMAKE_CXX_FLAGS_DEBUG} \
+        -fno-omit-frame-pointer -fsanitize=leak -fsanitize=address")
+    set(CMAKE_LINKER_FLAGS_DEBUG "${CMAKE_LINKER_FLAGS_DEBUG} \
+        -fno-omit-frame-pointer -fsanitize=leak -fsanitize=address")
+    set(CMAKE_MODULE_LINKER_FLAGS "${CMAKE_MODULE_LINKER_FLAGS} -fsanitize=address")
+endif()
 
 ################################### TARGETS ####################################
 
@@ -132,8 +138,6 @@ if(WITH_BOOST_ODE)
     set(WITH_GSL OFF)
 endif(WITH_BOOST_ODE)
 
-include_directories(msg basecode)
-
 set_target_properties(libmoose PROPERTIES COMPILE_DEFINITIONS  "MOOSE_LIB")
 set_target_properties(libmoose PROPERTIES PREFIX "")
 
@@ -202,6 +206,7 @@ if(WITH_BOOST_ODE)
     list(APPEND SYSTEM_SHARED_LIBS ${Boost_LIBRARIES})
 endif(WITH_BOOST_ODE)
 
+find_package( Threads )
 list(APPEND SYSTEM_SHARED_LIBS ${CMAKE_THREAD_LIBS_INIT})
 
 # These libraries could be static of dynamic. We need to discrimate between
@@ -265,6 +270,7 @@ list(APPEND MOOSE_LIBRARIES
     msg
     benchmarks
     shell
+    randnum
     scheduling
     moose_mpi
     biophysics

basecode/FuncOrder.h

@@ -13,28 +13,31 @@
 
 class FuncOrder
 {
-    public:
-            FuncOrder()
-                : func_( 0 ), index_( 0 )
-            {;}
+public:
+    FuncOrder()
+        : func_( 0 ), index_( 0 )
+    {;}
 
-            const OpFunc* func() const {
-                    return func_;
-            }
-            unsigned int index() const {
-                    return index_;
-            }
+    const OpFunc* func() const
+    {
+        return func_;
+    }
+    unsigned int index() const
+    {
+        return index_;
+    }
 
-            void set( const OpFunc* func, unsigned int index ) {
-                func_ = func;
-                   index_ = index;
-            }
+    void set( const OpFunc* func, unsigned int index )
+    {
+        func_ = func;
+        index_ = index;
+    }
 
-            bool operator<( const FuncOrder& other ) const
-            {
-                return func_ < other.func_;
-            }
-    private:
-        const OpFunc* func_;
-        unsigned int index_;
+    bool operator<( const FuncOrder& other ) const
+    {
+        return func_ < other.func_;
+    }
+private:
+    const OpFunc* func_;
+    unsigned int index_;
 };

basecode/global.cpp

@@ -49,7 +49,7 @@ namespace moose {
         { "HSolve", {0.0, 0} }
     };
 
-    moose::RNG<double> rng;
+    moose::RNG rng;
 
     /* Check if path is OK */
     int checkPath( const string& path  )
@@ -104,6 +104,11 @@ namespace moose {
         return moose::rng.uniform( );
     }
 
+    double mtrand( double a, double b )
+    {
+        return (b-a) * mtrand() + a; 
+    }
+
     // MOOSE suffixes [0] to all elements to path. Remove [0] with null
     // character whenever possible. For n > 0, [n] should not be touched. Its
     // the user job to take the pain and write the correct path.

basecode/global.h

@@ -56,7 +56,7 @@ extern unsigned int totalTests;
 namespace moose
 {
 
-    extern moose::RNG<double> rng;
+    extern moose::RNG rng;
 
     extern map<string, valarray<double>> solverProfMap;
 
@@ -114,6 +114,18 @@ namespace moose
      */
     double mtrand( void );
 
+    /* --------------------------------------------------------------------------*/
+    /**
+     * @Synopsis  Overloaded function. Random number between a and b
+     *
+     * @Param a lower limit.
+     * @Param b Upper limit.
+     *
+     * @Returns   
+     */
+    /* ----------------------------------------------------------------------------*/
+    double mtrand( double a, double b );
+
     /**
      * @brief Create a POSIX compatible path from a given string.
      * Remove/replace bad characters.

biophysics/Compartment.cpp

@@ -268,7 +268,7 @@ void Compartment::vRandInject( const Eref& e, double prob, double current)
 
 #ifdef DO_UNIT_TESTS
 
-#include "header.h"
+#include "../basecode/header.h"
 #include "../shell/Shell.h"
 //#include "../randnum/randnum.h"
 

biophysics/ReadCell.cpp

@@ -11,7 +11,6 @@
 #include "../shell/Shell.h"
 #include "ReadCell.h"
 #include "../utility/utility.h"
-#include "../utility/numutil.h"
 #include "CompartmentBase.h"
 #include "Compartment.h"
 #include "SymCompartment.h"

builtins/Function.cpp

@@ -48,14 +48,12 @@
 #include "../basecode/header.h"
 #include "../utility/utility.h"
 #include "../utility/numutil.h"
+#include "../utility/print_function.hpp"
 #include "Variable.h"
 
 #include "Function.h"
 #include "../basecode/ElementValueFinfo.h"
 
-#define PARSER_MAXVARS 100
-
-
 static const double TriggerThreshold = 0.0;
 
 static SrcFinfo1<double> *valueOut()
@@ -345,12 +343,14 @@ Function::Function(): _t(0.0), _valid(false), _numVar(0), _lastValue(0.0),
     _valid = true;
 }
 
-Function::Function(const Function& rhs): _numVar(rhs._numVar),
+Function::Function(const Function& rhs):
+    _numVar(rhs._numVar),
     _lastValue(rhs._lastValue),
     _value(rhs._value), _rate(rhs._rate),
     _mode(rhs._mode),
     _useTrigger( rhs._useTrigger),
-    _stoich(0)
+    _stoich(0),
+    map_(rhs.map_)
 {
     static Eref er;
     _independent = rhs._independent;
@@ -440,7 +440,7 @@ void Function::_clearBuffer()
 
 void Function::_showError(mu::Parser::exception_type &e) const
 {
-    cout << "Error occurred in parser.\n"
+    cerr << "Error occurred in parser.\n"
          << "Message:  " << e.GetMsg() << "\n"
          << "Formula:  " << e.GetExpr() << "\n"
          << "Token:    " << e.GetToken() << "\n"
@@ -474,7 +474,7 @@ double * _functionAddVar(const char *name, void *data)
     string strname(name);
 
     // Names starting with x are variables, everything else is constant.
-    if (strname[0] == 'x')
+    if (name[0] == 'x')
     {
         int index = atoi(strname.substr(1).c_str());
         if ((unsigned)index >= function->_varbuf.size()){
@@ -488,7 +488,7 @@ double * _functionAddVar(const char *name, void *data)
         }
         ret = &(function->_varbuf[index]->value);
     } 
-    else if (strname[0] == 'y')
+    else if (name[0] == 'y')
     {
         int index = atoi(strname.substr(1).c_str());
         if ((unsigned)index >= function->_pullbuf.size()){
@@ -507,11 +507,11 @@ double * _functionAddVar(const char *name, void *data)
     }
     else 
     {
-        cerr << "Got an undefined symbol: " << name << endl
-             << "Variables must be named xi, yi, where i is integer index."
-	     << " You must define the constants beforehand using LookupField c: c[name]"
+        MOOSE_WARN( "Got an undefined symbol: " << strname << ".\n"
+                << "Variables must be named xi, yi, where i is integer index."
+                << " You must define the constants beforehand using LookupField c: c[name]"
                 " = value"
-             << endl;
+                );
         throw mu::ParserError("Undefined constant.");
     }
 
@@ -741,21 +741,21 @@ void Function::process(const Eref &e, ProcPtr p)
     switch (_mode){
         case 1: {
             valueOut()->send(e, _value);
-            break;
+            return;
         }
         case 2: {
             derivativeOut()->send(e, getDerivative());
-            break;
+            return;
         }
         case 3: {
             rateOut()->send(e, _rate);
-            break;
+            return;
         }
         default: {
             valueOut()->send(e, _value);
             derivativeOut()->send(e, getDerivative());
             rateOut()->send(e, _rate);
-            break;
+            return;
         }
     }
     _lastValue = _value;
@@ -801,13 +801,4 @@ void Function::reinit(const Eref &e, ProcPtr p)
     }
 }
 
-#if 0
-mu::value_type Function::muCallbackFMod( mu::value_type a, mu::value_type b)
-{
-    cerr << "Callback: " << a << " " << b << endl;
-    return fmod(a, b);
-}
-#endif
-
-//
 // Function.cpp ends here

builtins/Function.h

@@ -68,7 +68,6 @@ class Function
     void setExpr( const Eref& e, string expr);
     string getExpr( const Eref& e ) const;
 
-
     // get a list of variable identifiers.
     // this is created by the parser
     vector<string> getVars() const;
@@ -166,6 +165,10 @@ class Function
 
     // Used by kinetic solvers when this is zombified.
     char* _stoich;
+
+    // These variables may be redundant but used for interfacing with
+    // MooseParser.
+    map<string, double*> map_;
 };
 
 

builtins/HDF5DataWriter.cpp

@@ -12,7 +12,7 @@
 
 #include "hdf5.h"
 
-#include "header.h"
+#include "../basecode/header.h"
 #include "../utility/utility.h"
 
 #include "HDF5DataWriter.h"