Merge pull request #663 from sys-bio/develop

Merge fixes for mac to 2.0.1

CMakeLists.txt

@@ -6,7 +6,7 @@ project(rr)
 
 set(ROADRUNNER_VERSION_MAJOR 2)
 set(ROADRUNNER_VERSION_MINOR 0)
-set(ROADRUNNER_VERSION_PATCH 0)
+set(ROADRUNNER_VERSION_PATCH 1)
 
 set(ROADRUNNER_VERSION "${ROADRUNNER_VERSION_MAJOR}.${ROADRUNNER_VERSION_MINOR}.${ROADRUNNER_VERSION_PATCH}")
 
@@ -143,7 +143,6 @@ set(BUILD_SHARED_LIBS            ON)
 
 set(RR_ROOT                      ${CMAKE_CURRENT_SOURCE_DIR})
 set(RR_SOURCE_ROOT               ${CMAKE_CURRENT_SOURCE_DIR}/source)
-set(THIRD_PARTY_FOLDER           ${CMAKE_CURRENT_SOURCE_DIR}/third_party)
 
 set(exe_path                     ${PROJECT_BINARY_DIR}/bin)
 set(lib_path                     ${PROJECT_BINARY_DIR}/lib)
@@ -191,7 +190,7 @@ endif()
 
 include_directories(
     ${RR_ROOT}
-    ${THIRD_PARTY_FOLDER}
+    ${THIRD_PARTY_INSTALL_FOLDER}
 )
 
 # TODO libxml2 handling is excedingly hackish, it is all homegrown
@@ -239,15 +238,13 @@ endif()
 if (${BUILD_LLVM})
     link_directories(
         ${LIBRARY_OUTPUT_PATH}
-        ${THIRD_PARTY_FOLDER}/dependencies/libsbml/lib
         ${THIRD_PARTY_INSTALL_FOLDER}/lib
         ${THIRD_PARTY_INSTALL_FOLDER}/lib64
         ${LLVM_LIBRARY_DIRS}
     )
 else()
     link_directories(
         ${LIBRARY_OUTPUT_PATH}
-        ${THIRD_PARTY_FOLDER}/dependencies/libsbml/lib
         ${THIRD_PARTY_INSTALL_FOLDER}/lib
         ${THIRD_PARTY_INSTALL_FOLDER}/lib64
     )
@@ -281,7 +278,7 @@ if(${MINGW})
 endif()
 
 if(${BORLAND})
-    link_directories(${THIRD_PARTY_FOLDER}/dependencies/libsbml/lib)
+    link_directories(${THIRD_PARTY_INSTALL_FOLDER}/lib)
 add_definitions(
     -DUSE_PCH                   #Enable pre-compiled headers
     -H=${PROJECT_BINARY_DIR}/rr_pch.csm
@@ -442,7 +439,7 @@ if(${BORLAND})
     set(CG_RUNTIMES        cc32110MT.dll)
     foreach(runtime ${CG_RUNTIMES})
         install (FILES
-            ${THIRD_PARTY_FOLDER}/dependencies/cg/xe/${runtime}
+            ${THIRD_PARTY_INSTALL_FOLDER}/cg/xe/${runtime}
             DESTINATION bin
             COMPONENT rr_core)
     endforeach()

cmake/FindLLVM.cmake

@@ -102,6 +102,22 @@ if (LLVM_CONFIG_EXECUTABLE)
         )
     message(STATUS "LLVM_LIBRARY_DIRS:  ${LLVM_LIBRARY_DIRS}")
 
+    # System libs
+    execute_process(
+        COMMAND ${LLVM_CONFIG_EXECUTABLE} --system-libs
+        OUTPUT_VARIABLE LLVM_SYSTEM_LIBS
+        OUTPUT_STRIP_TRAILING_WHITESPACE
+        )
+    message(STATUS "LLVM_SYSTEM_LIBS:  ${LLVM_SYSTEM_LIBS}")
+    # For some reason, the return value for system-libs for macos is of the
+    # form '-llib1 -llib2 ...", but the return value for system-libs for windows
+    # is of the form "lib1.lib lib2.lib ..." which doesn't work the same way.
+    # The only system it was failing for was macos, so we'll just set it for that.
+    if(APPLE)
+        set(LLVM_SYSTEM_LIBS_THISOS ${LLVM_SYSTEM_LIBS})
+    endif()
+    message(STATUS "LLVM_SYSTEM_LIBS_THISOS:  ${LLVM_SYSTEM_LIBS_THISOS}")
+
     # C++ Flags, strip out stuff that CMake build adds
     execute_process(
         COMMAND ${LLVM_CONFIG_EXECUTABLE} --cxxflags

source/CMakeLists.txt

@@ -397,6 +397,7 @@ if(RR_BUILD_SHARED_CORE)
     if(BUILD_LLVM)
         target_link_libraries(${target}
             ${LLVM_LIBRARIES}
+            ${LLVM_SYSTEM_LIBS_THISOS}
             )
     endif(BUILD_LLVM)
 
@@ -428,6 +429,7 @@ set_property(TARGET ${target}-static
 if(BUILD_LLVM)
     target_link_libraries(${target}-static
         ${LLVM_LIBRARIES}
+        ${LLVM_SYSTEM_LIBS_THISOS}
         )
 endif(BUILD_LLVM)
 

source/CVODEIntegrator.cpp

@@ -1176,8 +1176,9 @@ namespace rr
 				Log(Logger::LOG_INFORMATION) << "Set tolerance to abs: " << setprecision(16) << "[";
 				vector<double> v = getValueAsDoubleVector("absolute_tolerance");
 				for (int i = 0; i < v.size(); i++) {
-					if (i != 0)
+					if (i != 0) {
 						Log(Logger::LOG_INFORMATION) << ", ";
+					}
 					Log(Logger::LOG_INFORMATION) << v[i];
 				}
 				Log(Logger::LOG_INFORMATION) << "], rel: " << getValueAsDouble("relative_tolerance") << endl;

source/llvm/CodeGenBase.cpp

@@ -80,7 +80,7 @@ class LLVMCodeGenTest
         BasicBlock *basicBlock = BasicBlock::Create(context, "entry", func);
         builder.SetInsertPoint(basicBlock);
 
-        assert(func->getArgumentList().size() == N);
+        assert(func->arg_size() == N);
 
         int i = 0;
 

source/llvm/LLVMModelDataSymbols.cpp

@@ -467,7 +467,19 @@ std::string LLVMModelDataSymbols::getFloatingSpeciesId(size_t indx) const
         }
     }
 
-    throw std::out_of_range("attempted to access floating species id at index " + rr::toStringSize(indx));
+    std::stringstream errSS;
+    errSS << "attempted to access floating species id at index " << indx << ", but ";
+    auto size = floatingSpeciesMap.size();
+    if (size == 0) {
+        errSS << "there are no floating species in the model.";
+    }
+    else if (size == 1) {
+        errSS << "there is only a single floating species in the model with index '0'.";
+    }
+    else {
+        errSS << "there are only " << size << "floating species in the model with indexes '0'-'" << (size - 1) << "'.";
+    }
+    throw std::out_of_range(errSS.str());
 }
 
 
@@ -567,8 +579,19 @@ std::string rrllvm::LLVMModelDataSymbols::getRateRuleId(size_t indx) const
         }
     }
 
-    throw std::out_of_range("attempted to access rate rule id at index " +
-            rr::toStringSize(indx));
+    std::stringstream errSS;
+    errSS << "attempted to access global parameter at index " << indx << ", but ";
+    auto size = rateRules.size();
+    if (size == 0) {
+        errSS << "there are no rate rules in the model.";
+    }
+    else if (size == 1) {
+        errSS << "there is only a single rate rule in the model with index '0'.";
+    }
+    else {
+        errSS << "there are only " << size << "rate rules in the model with indexes '0'-'" << (size - 1) << "'.";
+    }
+    throw std::out_of_range(errSS.str());
 }
 
 bool LLVMModelDataSymbols::isIndependentElement(const std::string& id) const
@@ -1017,7 +1040,19 @@ std::string LLVMModelDataSymbols::getGlobalParameterId(size_t indx) const
         }
     }
 
-    throw std::out_of_range("attempted to access global parameter id at index " + rr::toStringSize(indx));
+    std::stringstream errSS;
+    errSS << "attempted to access global parameter at index " << indx << ", but ";
+    auto size = globalParametersMap.size();
+    if (size == 0) {
+        errSS << "there are no global parameters in the model.";
+    }
+    else if (size == 1) {
+        errSS << "there is only a single global parameter in the model with index '0'.";
+    }
+    else {
+        errSS << "there are only " << size << "global parameters in the model with indexes '0'-'" << (size - 1) << "'.";
+    }
+    throw std::out_of_range(errSS.str());
 }
 
 int LLVMModelDataSymbols::getCompartmentIndexForFloatingSpecies(
@@ -1169,9 +1204,6 @@ void LLVMModelDataSymbols::initReactions(const libsbml::Model* model)
             if (isValidFloatingSpeciesReference(p, "product"))
             {
                 uint speciesIdx = getFloatingSpeciesIndex(p->getSpecies());
-                if (speciesIdx < 0) {
-                    continue;
-                }
 
                 UIntUMap::const_iterator si = speciesMap.find(speciesIdx);
 
@@ -1494,7 +1526,19 @@ std::string LLVMModelDataSymbols::getEventId(size_t indx) const
         }
     }
 
-    throw std::out_of_range("attempted to access event id at index " + rr::toStringSize(indx));
+    std::stringstream errSS;
+    errSS << "attempted to access event id at index " << indx << ", but ";
+    auto size = eventIds.size();
+    if (size == 0) {
+        errSS << "there are no events in the model.";
+    }
+    else if (size == 1) {
+        errSS << "there is only a single event in the model with index '0'.";
+    }
+    else {
+        errSS << "there are only " << size << "events in the model with indexes '0'-'" << (size - 1) << "'.";
+    }
+    throw std::out_of_range(errSS.str());
 }
 
 int LLVMModelDataSymbols::getEventIndex(const std::string& id) const

source/llvm/LLVMModelSymbols.cpp

@@ -67,12 +67,6 @@ LLVMModelSymbols::LLVMModelSymbols(const libsbml::Model *m, LLVMModelDataSymbols
             if (model->getInitialAssignment(id) == NULL &&
                     model->getAssignmentRule(id) == NULL)
             {
-                Log(Logger::LOG_WARNING) << "Global parameter, \'"
-                        << param->getId() << "\' missing value and missing init "
-                        "assignment and assignment rule!, defaulting value to 0.0.";
-                Log(Logger::LOG_WARNING) << "This probably is NOT what you want "
-                        "with global parameter \'" << param->getId() << "\'.";
-                value->setValue(0.0);
                 std::stringstream ss;
                 ss << "Global parameter '" << param->getId() << "' missing value and missing init assignment and assignment rule!";
                 rr::UninitializedValue(ss.str());

source/rrRoadRunner.cpp

@@ -1089,14 +1089,18 @@ void RoadRunner::load(const string& uriOrSbml, const Dictionary *dict)
 		}
 	}
     try {
-
-    // the following lines load and compile the model. If anything fails here,
-    // we validate the model to provide explicit details about where it
-    // failed. Its *VERY* expensive to pre-validate the model.
-		libsbml::SBMLReader reader;
-		impl->document = std::unique_ptr<libsbml::SBMLDocument>(reader.readSBMLFromString(mCurrentSBML));
-		impl->model = std::unique_ptr<ExecutableModel>(ExecutableModelFactory::createModel(mCurrentSBML, &impl->loadOpt));
-    } catch (std::exception& e) {
+
+        // the following lines load and compile the model. If anything fails here,
+        // we validate the model to provide explicit details about where it
+        // failed. Its *VERY* expensive to pre-validate the model.
+        libsbml::SBMLReader reader;
+        impl->document = std::unique_ptr<libsbml::SBMLDocument>(reader.readSBMLFromString(mCurrentSBML));
+        impl->model = std::unique_ptr<ExecutableModel>(ExecutableModelFactory::createModel(mCurrentSBML, &impl->loadOpt));
+    } catch (const rr::UninitializedValueException& e) {
+        // catch specifically for UninitializedValueException, otherwise for some
+        // reason the message is erased, and an 'unknown error' is displayed to the user.
+        throw e;
+    } catch (const std::exception& e) {
         string errors = validateSBML(mCurrentSBML);
 
         if(!errors.empty()) {
@@ -2324,43 +2328,53 @@ DoubleMatrix RoadRunner::getFullJacobian()
 
     get_self();
 
+    // function pointers to the model get values and get init values based on
+    // if we are doing amounts or concentrations.
+    typedef int (ExecutableModel::*GetValueFuncPtr)(size_t len, int const *indx,
+        double *values);
+    typedef int (ExecutableModel::*SetValueFuncPtr)(size_t len, int const *indx,
+        double const *values);
+    typedef int (ExecutableModel::* SetValueFuncPtrSize)(size_t len, int const* indx,
+        double const* values);
+
+    GetValueFuncPtr getValuePtr = 0;
+    GetValueFuncPtr getInitValuePtr = 0;
+    SetValueFuncPtr setValuePtr = 0;
+    SetValueFuncPtrSize setInitValuePtr = 0;
+
+    if (Config::getValue(Config::ROADRUNNER_JACOBIAN_MODE).convert<unsigned>()
+        == Config::ROADRUNNER_JACOBIAN_MODE_AMOUNTS)
+    {
+        getValuePtr = &ExecutableModel::getFloatingSpeciesAmounts;
+        getInitValuePtr = &ExecutableModel::getFloatingSpeciesInitAmounts;
+        setValuePtr = &ExecutableModel::setFloatingSpeciesAmounts;
+        setInitValuePtr = &ExecutableModel::setFloatingSpeciesInitAmounts;
+    }
+    else
+    {
+        getValuePtr = &ExecutableModel::getFloatingSpeciesConcentrations;
+        getInitValuePtr = &ExecutableModel::getFloatingSpeciesInitConcentrations;
+        setValuePtr = &ExecutableModel::setFloatingSpeciesConcentrations;
+        setInitValuePtr = &ExecutableModel::setFloatingSpeciesInitConcentrations;
+    }
+
+
     if (self.model->getNumReactions() == 0 && self.model->getNumRateRules() > 0)
     {
+        if (self.model->getNumFloatingSpecies() < self.model->getNumRateRules()) {
+            std::stringstream errSS;
+            errSS << "cannot compute full Jacobian because there are fewer floating species (" <<
+                self.model->getNumFloatingSpecies() << ")" << " than rate rules (" << self.model->getNumRateRules() << ").";
+            errSS << " You may need to declare one or more of your variables as a species. See " <<
+                "https://tellurium.readthedocs.io/en/latest/antimony.html#rate-rules if you are using Antimony.";
+            throw std::out_of_range(errSS.str());
+        }
         DoubleMatrix jac(self.model->getNumRateRules(), self.model->getNumRateRules());
 
         for (int i = 0; i < self.model->getNumRateRules(); i++)
         {
             for (int j = 0; j < self.model->getNumRateRules(); j++)
             {
-                // function pointers to the model get values and get init values based on
-                // if we are doing amounts or concentrations.
-                typedef int (ExecutableModel::*GetValueFuncPtr)(size_t len, int const *indx,
-                    double *values);
-                typedef int (ExecutableModel::*SetValueFuncPtr)(size_t len, int const *indx,
-                    double const *values);
-                typedef int (ExecutableModel::* SetValueFuncPtrSize)(size_t len, int const* indx,
-                    double const* values);
-
-                GetValueFuncPtr getValuePtr = 0;
-                GetValueFuncPtr getInitValuePtr = 0;
-                SetValueFuncPtr setValuePtr = 0;
-                SetValueFuncPtrSize setInitValuePtr = 0;
-
-                if (Config::getValue(Config::ROADRUNNER_JACOBIAN_MODE).convert<unsigned>()
-                    == Config::ROADRUNNER_JACOBIAN_MODE_AMOUNTS)
-                {
-                    getValuePtr = &ExecutableModel::getFloatingSpeciesAmounts;
-                    getInitValuePtr = &ExecutableModel::getFloatingSpeciesInitAmounts;
-                    setValuePtr = &ExecutableModel::setFloatingSpeciesAmounts;
-                    setInitValuePtr = &ExecutableModel::setFloatingSpeciesInitAmounts;
-                }
-                else
-                {
-                    getValuePtr = &ExecutableModel::getFloatingSpeciesConcentrations;
-                    getInitValuePtr = &ExecutableModel::getFloatingSpeciesInitConcentrations;
-                    setValuePtr = &ExecutableModel::setFloatingSpeciesConcentrations;
-                    setInitValuePtr = &ExecutableModel::setFloatingSpeciesInitConcentrations;
-                }
 
                 double value;
                 double originalConc = 0;

source/rrStringUtils.cpp

@@ -504,7 +504,7 @@ vector<string> splitString(const string &text, const string &separators)
     size_t n = text.length();
     size_t start = text.find_first_not_of(separators);
 
-    while( (start >= 0) && (start < n) )
+    while( (start < n) )
     {
         size_t stop = text.find_first_of(separators, start);
         if( (stop == string::npos) || (stop > n) )

source/rrUtils.cpp

@@ -472,6 +472,20 @@ bool hasUnimplementedTags(const string& descriptionFileName)
     return false;
 }
 
+bool isSemiStochasticTest(const string& descriptionFileName)
+{
+    ifstream descfile(descriptionFileName);
+    if (descfile.good()) {
+        string line;
+        while (getline(descfile, line)) {
+            if (line.find("synopsis") != string::npos && line.find("STOCHASTIC") != string::npos) {
+                return true;
+            }
+        }
+    }
+    return false;
+}
+
 bool isFBCTest(const string& descriptionFileName)
 {
     ifstream descfile(descriptionFileName);

source/rrUtils.h

@@ -109,6 +109,8 @@ RR_DECLSPEC string          getTestSuiteSubFolderName(int caseNr);
 
 RR_DECLSPEC bool            hasUnimplementedTags(const string& descriptionFileName);
 
+RR_DECLSPEC bool            isSemiStochasticTest(const string& descriptionFileName);
+
 RR_DECLSPEC bool            isFBCTest(const string& descriptionFileName);
 
 //CArray utilities

source/testing/CMakeLists.txt

@@ -37,7 +37,7 @@ ${THIRD_PARTY_INSTALL_FOLDER}/lib
 include_directories(
 src
 ${RR_ROOT}
-${THIRD_PARTY_FOLDER}/unit_test/src
+${THIRD_PARTY_INSTALL_FOLDER}/include/
 )
 
 if(UNIX)

source/testing/tests/sbml_test_suite.cpp

@@ -1926,6 +1926,11 @@ bool RunTest(int caseNumber)
     else {
         if (!first.empty()) {
             ret = RunTest(first, caseNumber);
+            if (!ret && isSemiStochasticTest(modelFilePath + "/" + descriptionFileName)) {
+                //semistochastic tests fail once in a great while, but very very rarely twice in a row.
+                Log(Logger::LOG_WARNING) << "Test " << caseNumber << " failed, but we expect it to fail every so often.  Trying again...";
+                ret = RunTest(first, caseNumber);
+            }
         }
         else {
             Log(Logger::LOG_ERROR) << "No models found for test case" << caseNumber << endl;