From 5560adcf27410fa1946b390c97e542a3428dfbf7 Mon Sep 17 00:00:00 2001
From: Lucian Smith <lpsmith@uw.edu>
Date: Fri, 19 Apr 2024 09:44:19 -0700
Subject: [PATCH 1/9] Fix for issue #1210

(I hope.)

Also, re-enable test, and add new one for loading from scratch.

The savedState files are different on different OSes because the size of things is different (notably 'unsigned long').
---
 source/llvm/LLJit.cpp                         |   4 +-
 source/llvm/MCJit.cpp                         |  66 ++++++++++--------
 .../StateSavingTests/savedState_linux.rr      | Bin 0 -> 13262 bytes
 .../StateSavingTests/savedState_windows.rr    | Bin 0 -> 12286 bytes
 test/serialization/state_saving.cpp           |  19 +++--
 5 files changed, 51 insertions(+), 38 deletions(-)
 create mode 100644 test/models/StateSavingTests/savedState_linux.rr
 create mode 100644 test/models/StateSavingTests/savedState_windows.rr

diff --git a/source/llvm/LLJit.cpp b/source/llvm/LLJit.cpp
index ab07765f0b..5ff3b1e2d9 100644
--- a/source/llvm/LLJit.cpp
+++ b/source/llvm/LLJit.cpp
@@ -73,7 +73,9 @@ namespace rrllvm {
     }
 
     LLJit::LLJit(std::uint32_t options)
-            : Jit(options) {
+        : Jit(options)
+        , llJit()
+    {
 
         // todo, can we cross compile providing a different host arch?
 
diff --git a/source/llvm/MCJit.cpp b/source/llvm/MCJit.cpp
index f96aa2ac42..1913789c59 100644
--- a/source/llvm/MCJit.cpp
+++ b/source/llvm/MCJit.cpp
@@ -44,7 +44,7 @@ namespace rrllvm {
      * file type.
      */
 #if LLVM_VERSION_MAJOR == 6
-    llvm::LLVMTargetMachine::CodeGenFileType getCodeGenFileType(){
+    llvm::LLVMTargetMachine::CodeGenFileType getCodeGenFileType() {
         return llvm::TargetMachine::CGFT_ObjectFile;
     }
 #elif LLVM_VERSION_MAJOR >= 12
@@ -57,25 +57,29 @@ namespace rrllvm {
 
 
     MCJit::MCJit(std::uint32_t opt)
-            : Jit(opt),
-              engineBuilder(EngineBuilder(std::move(module))) {
+        : Jit(opt)
+        , engineBuilder(EngineBuilder(std::move(module)))
+        , executionEngine()
+        , functionPassManager()
+        , errString()
+    {
 
         compiledModuleBinaryStream = std::make_unique<llvm::raw_svector_ostream>(moduleBuffer);
 
         engineBuilder
-                .setErrorStr(errString.get())
-                .setMCJITMemoryManager(std::make_unique<SectionMemoryManager>());
-        executionEngine = std::unique_ptr<ExecutionEngine>(engineBuilder.create());
+            .setErrorStr(errString.get())
+            .setMCJITMemoryManager(std::make_unique<SectionMemoryManager>());
+        executionEngine.reset(engineBuilder.create());
 
         MCJit::mapFunctionsToJitSymbols();
         MCJit::initFunctionPassManager();
     }
 
 
-    ExecutionEngine *MCJit::getExecutionEngineNonOwning() const {
+    ExecutionEngine* MCJit::getExecutionEngineNonOwning() const {
         return executionEngine.get();
     }
-    std::string MCJit::mangleName(const std::string &unmangledName) const {
+    std::string MCJit::mangleName(const std::string& unmangledName) const {
         std::string mangledName;
         llvm::raw_string_ostream mangledNameStream(mangledName);
         llvm::Mangler::getNameWithPrefix(mangledNameStream, unmangledName, getDataLayout());
@@ -86,9 +90,9 @@ namespace rrllvm {
         llvm::sys::DynamicLibrary::LoadLibraryPermanently(nullptr); // for symbols in current process
 
 
-        for (auto [fnName, fnTy_addr_pair] : externalFunctionSignatures()){
+        for (auto [fnName, fnTy_addr_pair] : externalFunctionSignatures()) {
             auto [fnTy, addr] = fnTy_addr_pair;
-            rrLogDebug << "Creating function \"" << fnName << "\"; fn type: " << toStringRef(fnTy).str() << "; at addr: " <<addr;
+            rrLogDebug << "Creating function \"" << fnName << "\"; fn type: " << toStringRef(fnTy).str() << "; at addr: " << addr;
             Function::Create(fnTy, Function::ExternalLinkage, fnName, getModuleNonOwning());
             llvm::sys::DynamicLibrary::AddSymbol(fnName, addr);
         }
@@ -98,8 +102,8 @@ namespace rrllvm {
         ModelDataIRBuilder::getCSRMatrixSetNZDecl(getModuleNonOwning());
         ModelDataIRBuilder::getCSRMatrixGetNZDecl(getModuleNonOwning());
         // Add the symbol to the library
-        llvm::sys::DynamicLibrary::AddSymbol(ModelDataIRBuilder::csr_matrix_set_nzName, (void*) rr::csr_matrix_set_nz);
-        llvm::sys::DynamicLibrary::AddSymbol(ModelDataIRBuilder::csr_matrix_get_nzName, (void*) rr::csr_matrix_get_nz);
+        llvm::sys::DynamicLibrary::AddSymbol(ModelDataIRBuilder::csr_matrix_set_nzName, (void*)rr::csr_matrix_set_nz);
+        llvm::sys::DynamicLibrary::AddSymbol(ModelDataIRBuilder::csr_matrix_get_nzName, (void*)rr::csr_matrix_get_nz);
     }
 
     void MCJit::transferObjectsToResources(std::shared_ptr<rrllvm::ModelResources> modelResources) {
@@ -112,12 +116,12 @@ namespace rrllvm {
 
     }
 
-    std::uint64_t MCJit::lookupFunctionAddress(const std::string &name) {
-        void *v = executionEngine->getPointerToNamedFunction(mangleName(name));
-        return (std::uint64_t) v;
+    std::uint64_t MCJit::lookupFunctionAddress(const std::string& name) {
+        void* v = executionEngine->getPointerToNamedFunction(mangleName(name));
+        return (std::uint64_t)v;
     }
 
-    llvm::TargetMachine *MCJit::getTargetMachine() {
+    llvm::TargetMachine* MCJit::getTargetMachine() {
         return executionEngine->getTargetMachine();
     }
 
@@ -138,7 +142,7 @@ namespace rrllvm {
 
 
         llvm::Expected<std::unique_ptr<llvm::object::ObjectFile> > objectFileExpected =
-                llvm::object::ObjectFile::createObjectFile(obj->getMemBufferRef());
+            llvm::object::ObjectFile::createObjectFile(obj->getMemBufferRef());
         if (!objectFileExpected) {
             throw std::invalid_argument("Failed to load object data");
         }
@@ -147,11 +151,11 @@ namespace rrllvm {
     }
 
 
-    const llvm::DataLayout &MCJit::getDataLayout() const {
+    const llvm::DataLayout& MCJit::getDataLayout() const {
         return getExecutionEngineNonOwning()->getDataLayout();
     }
 
-    void MCJit::addModule(llvm::Module *M) {
+    void MCJit::addModule(llvm::Module* M) {
 
     }
 
@@ -169,7 +173,7 @@ namespace rrllvm {
 
         if (compiledModuleBinaryStream->str().empty()) {
             std::string err = "Attempt to add module before its been written to binary. Make a call to "
-                              "MCJit::writeObjectToBinaryStream() before addModule()";
+                "MCJit::writeObjectToBinaryStream() before addModule()";
             rrLogErr << err;
             throw_llvm_exception(err);
         }
@@ -177,8 +181,8 @@ namespace rrllvm {
         auto memBuffer(llvm::MemoryBuffer::getMemBuffer(compiledModuleBinaryStream->str().str()));
 
         llvm::Expected<std::unique_ptr<llvm::object::ObjectFile> > objectFileExpected =
-                llvm::object::ObjectFile::createObjectFile(
-                        llvm::MemoryBufferRef(compiledModuleBinaryStream->str(), "id"));
+            llvm::object::ObjectFile::createObjectFile(
+                llvm::MemoryBufferRef(compiledModuleBinaryStream->str(), "id"));
 
         if (!objectFileExpected) {
             //LS DEBUG:  find a way to get the text out of the error.
@@ -196,7 +200,7 @@ namespace rrllvm {
         getExecutionEngineNonOwning()->finalizeObject();
     }
 
-    std::unique_ptr<llvm::MemoryBuffer> MCJit::getCompiledModelFromCache(const std::string &sbmlMD5) {
+    std::unique_ptr<llvm::MemoryBuffer> MCJit::getCompiledModelFromCache(const std::string& sbmlMD5) {
         return nullptr;
     }
 
@@ -213,8 +217,8 @@ namespace rrllvm {
 
         //Write the object file to modBufferOut
         std::error_code EC;
-//        llvm::SmallVector<char, 10> modBufferOut;
-//        postOptimizedModuleStream(modBufferOut);
+        // llvm::SmallVector<char, 10> modBufferOut;
+        // postOptimizedModuleStream(modBufferOut);
 
         llvm::legacy::PassManager pass;
         auto FileType = getCodeGenFileType();
@@ -244,10 +248,10 @@ namespace rrllvm {
              * Note to developers - passes are stored in llvm/Transforms/Scalar.h.
              */
 
-            // we only support LLVM >= 3.1
+             // we only support LLVM >= 3.1
 #if (LLVM_VERSION_MAJOR == 3) && (LLVM_VERSION_MINOR == 1)
             //#if (LLVM_VERSION_MAJOR == 6)
-                functionPassManager->add(new TargetData(*executionEngine->getTargetData()));
+            functionPassManager->add(new TargetData(*executionEngine->getTargetData()));
 #elif (LLVM_VERSION_MAJOR == 3) && (LLVM_VERSION_MINOR <= 4)
             functionPassManager->add(new DataLayout(*executionEngine->getDataLayout()));
 #elif (LLVM_VERSION_MINOR > 4)
@@ -271,7 +275,7 @@ namespace rrllvm {
                 functionPassManager->add(createInstSimplifyLegacyPass());
 #else
                 rrLogWarn << "Not using llvm optimization \"OPTIMIZE_INSTRUCTION_SIMPLIFIER\" "
-                             "because llvm version is " << LLVM_VERSION_MAJOR;
+                    "because llvm version is " << LLVM_VERSION_MAJOR;
 #endif
             }
 
@@ -300,7 +304,7 @@ namespace rrllvm {
                 // or replaced with createDeadCodeEliminationPass, which we add below anyway
 #else
                 rrLogWarn << "Not using OPTIMIZE_DEAD_INST_ELIMINATION because you are using"
-                             "LLVM version " << LLVM_VERSION_MAJOR;
+                    "LLVM version " << LLVM_VERSION_MAJOR;
 #endif
             }
 
@@ -313,11 +317,11 @@ namespace rrllvm {
         }
     }
 
-    llvm::legacy::FunctionPassManager *MCJit::getFunctionPassManager() const {
+    llvm::legacy::FunctionPassManager* MCJit::getFunctionPassManager() const {
         return functionPassManager.get();
     }
 
-    llvm::raw_svector_ostream &MCJit::getCompiledModuleStream() {
+    llvm::raw_svector_ostream& MCJit::getCompiledModuleStream() {
         return *compiledModuleBinaryStream;
     }
 
diff --git a/test/models/StateSavingTests/savedState_linux.rr b/test/models/StateSavingTests/savedState_linux.rr
new file mode 100644
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GIT binary patch
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diff --git a/test/models/StateSavingTests/savedState_windows.rr b/test/models/StateSavingTests/savedState_windows.rr
new file mode 100644
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GIT binary patch
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z2t}`~H;UK}(0y1x>>D4J8+>=zIoY(Zgzbr0vkohwwvA@`P&vaj^Mm@B=M)6+rF1l8
z&ly|HcAV6*Wxa{DU|}C?2icZFKJ(F+H&?`<7<K`%9Yqilq}RjrB^u55C1g4!U!O#X
z{37@dnqO8kY%L#kf<x?l$O@yYKh71#p{q0@3#95!XKP1ob_&hfq1ez3L}#rsoC=}!
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T&_G>>PN4J4iaCAk^t0l>h{wXj

literal 0
HcmV?d00001

diff --git a/test/serialization/state_saving.cpp b/test/serialization/state_saving.cpp
index 696e0c31a5..92a9a002a0 100644
--- a/test/serialization/state_saving.cpp
+++ b/test/serialization/state_saving.cpp
@@ -46,7 +46,7 @@ static std::mutex SerializationMutex;
  */
 class StateSavingTests : public RoadRunnerTest {
 public:
-    path stateSavingModelsDir = rrTestModelsDir_ / "StateSaving";
+    path stateSavingModelsDir = rrTestModelsDir_ / "StateSavingTests";
     path stateSavingOutputDir = rrTestDir_ / "StateSavingOutput";
     path fname_ = stateSavingOutputDir / "state-saving-test.rr";
     std::string fname;
@@ -430,13 +430,20 @@ bool StateSavingTests::StateRunTestModelFromScratch(void(*generate)(RoadRunner *
 //  accordingly.  The reverse can't be tested, since it'll either
 //  exit or throw, depending.
 TEST_F(StateSavingTests, LOAD_INVALID_FILE) {
-// on mac systems this test causes abort signal. We disable on mac.
-#if (!defined(__APPLE__))
-#  if LLVM_VERSION_PATCH > 1
     RoadRunner rri;
-    EXPECT_THROW(rri.loadState((rrTestModelsDir_ / "wrong-save-state.rr").string()), std::exception);
-#  endif
+    EXPECT_THROW(rri.loadState((stateSavingModelsDir / "wrong-save-state.rr").string()), std::exception);
+}
+
+TEST_F(StateSavingTests, LOAD_VALID_FILE) {
+    RoadRunner rri;
+#if defined(_WIN32)
+    rri.loadState((stateSavingModelsDir / "savedState_windows.rr").string());
+    //#elif defined(__unix__)
+    //#if (defined(__APPLE__))
+#else
+    rri.loadState((stateSavingModelsDir / "savedState_linux.rr").string());
 #endif
+    EXPECT_EQ(rri.getNumberOfFloatingSpecies(), 2);
 }
 
 TEST_F(StateSavingTests, LOAD_NONEXISTENT_FILE) {

From 55e90da4e2cf5f337bf6d6a41faebf7d53a950c1 Mon Sep 17 00:00:00 2001
From: Lucian Smith <lpsmith@uw.edu>
Date: Fri, 19 Apr 2024 10:57:09 -0700
Subject: [PATCH 2/9] Update version number; declare enum type.

---
 CMakeLists.txt             | 2 +-
 source/rrSelectionRecord.h | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/CMakeLists.txt b/CMakeLists.txt
index 107bb71708..fcf6e56f10 100644
--- a/CMakeLists.txt
+++ b/CMakeLists.txt
@@ -9,7 +9,7 @@ cmake_minimum_required(VERSION 3.16)
 
 set(ROADRUNNER_VERSION_MAJOR 2)
 set(ROADRUNNER_VERSION_MINOR 6)
-set(ROADRUNNER_VERSION_PATCH 0)
+set(ROADRUNNER_VERSION_PATCH 1)
 
 set(ROADRUNNER_VERSION "${ROADRUNNER_VERSION_MAJOR}.${ROADRUNNER_VERSION_MINOR}.${ROADRUNNER_VERSION_PATCH}")
 
diff --git a/source/rrSelectionRecord.h b/source/rrSelectionRecord.h
index 01da75910f..ed3f1d2927 100644
--- a/source/rrSelectionRecord.h
+++ b/source/rrSelectionRecord.h
@@ -17,7 +17,7 @@ using std::ostream;
 class RR_DECLSPEC SelectionRecord
 {
 public:
-    enum SelectionType
+    enum SelectionType : unsigned long
     {
         /**
         * SelectionType for time.

From 2e794414c14415562a25cc07580559d84a62f0c0 Mon Sep 17 00:00:00 2001
From: Lucian Smith <lpsmith@uw.edu>
Date: Fri, 19 Apr 2024 16:24:45 -0700
Subject: [PATCH 3/9] Comment out read-file test.

The test seems to work in some contexts but not others.  Committing this version so we can test it on python on other platforms.
---
 source/llvm/Jit.cpp                 | 2 +-
 source/llvm/LLJit.cpp               | 5 +++++
 source/llvm/LLJit.h                 | 2 +-
 source/llvm/MCJit.cpp               | 6 +++++-
 source/llvm/MCJit.h                 | 8 ++++++++
 test/serialization/state_saving.cpp | 6 ++++--
 6 files changed, 24 insertions(+), 5 deletions(-)

diff --git a/source/llvm/Jit.cpp b/source/llvm/Jit.cpp
index 72aab7b5e6..d358c03969 100644
--- a/source/llvm/Jit.cpp
+++ b/source/llvm/Jit.cpp
@@ -67,7 +67,7 @@ namespace rrllvm {
     }
 
     Jit::Jit()
-            : Jit(LoadSBMLOptions().modelGeneratorOpt) {}
+        : Jit(LoadSBMLOptions().modelGeneratorOpt) {}
 
     llvm::Module *Jit::getModuleNonOwning() {
         return moduleNonOwning;
diff --git a/source/llvm/LLJit.cpp b/source/llvm/LLJit.cpp
index 5ff3b1e2d9..b59e938e0e 100644
--- a/source/llvm/LLJit.cpp
+++ b/source/llvm/LLJit.cpp
@@ -72,6 +72,11 @@ namespace rrllvm {
         return mangledNameStream.str();
     }
 
+    LLJit::LLJit()
+        : LLJit(LoadSBMLOptions().modelGeneratorOpt)
+    {
+    }
+
     LLJit::LLJit(std::uint32_t options)
         : Jit(options)
         , llJit()
diff --git a/source/llvm/LLJit.h b/source/llvm/LLJit.h
index 90aba4ed9a..feec0e569c 100644
--- a/source/llvm/LLJit.h
+++ b/source/llvm/LLJit.h
@@ -42,7 +42,7 @@ namespace rrllvm {
     class LLJit : public Jit {
     public:
 
-        LLJit() = default;
+        LLJit();
 
         ~LLJit() override = default;
 
diff --git a/source/llvm/MCJit.cpp b/source/llvm/MCJit.cpp
index 1913789c59..baf46628f6 100644
--- a/source/llvm/MCJit.cpp
+++ b/source/llvm/MCJit.cpp
@@ -63,7 +63,6 @@ namespace rrllvm {
         , functionPassManager()
         , errString()
     {
-
         compiledModuleBinaryStream = std::make_unique<llvm::raw_svector_ostream>(moduleBuffer);
 
         engineBuilder
@@ -75,10 +74,15 @@ namespace rrllvm {
         MCJit::initFunctionPassManager();
     }
 
+    MCJit::MCJit()
+        : MCJit(LoadSBMLOptions().modelGeneratorOpt)
+    {
+    }
 
     ExecutionEngine* MCJit::getExecutionEngineNonOwning() const {
         return executionEngine.get();
     }
+
     std::string MCJit::mangleName(const std::string& unmangledName) const {
         std::string mangledName;
         llvm::raw_string_ostream mangledNameStream(mangledName);
diff --git a/source/llvm/MCJit.h b/source/llvm/MCJit.h
index e194d1de40..9094d554a0 100644
--- a/source/llvm/MCJit.h
+++ b/source/llvm/MCJit.h
@@ -37,6 +37,14 @@ namespace rrllvm {
 
         explicit MCJit(std::uint32_t options);
 
+        /**
+         * @brief default constructor.
+         * @details delegates to MCJit(std::uint32_t options). The options
+         * argument is the default constructed from LoadSBMLOptions.modelGeneratorOpt.
+         * Note, that LoadSBMLOptions is influenced by the global Config.
+         */
+        MCJit();
+
         ~MCJit() override = default;
 
 
diff --git a/test/serialization/state_saving.cpp b/test/serialization/state_saving.cpp
index 92a9a002a0..d86bc7ea50 100644
--- a/test/serialization/state_saving.cpp
+++ b/test/serialization/state_saving.cpp
@@ -437,13 +437,15 @@ TEST_F(StateSavingTests, LOAD_INVALID_FILE) {
 TEST_F(StateSavingTests, LOAD_VALID_FILE) {
     RoadRunner rri;
 #if defined(_WIN32)
+    // This only works on Windows, and lord only knows why.
     rri.loadState((stateSavingModelsDir / "savedState_windows.rr").string());
+    EXPECT_EQ(rri.getNumberOfFloatingSpecies(), 2);
     //#elif defined(__unix__)
     //#if (defined(__APPLE__))
 #else
-    rri.loadState((stateSavingModelsDir / "savedState_linux.rr").string());
+    //rri.loadState((stateSavingModelsDir / "savedState_linux.rr").string());
+    //EXPECT_EQ(rri.getNumberOfFloatingSpecies(), 2);
 #endif
-    EXPECT_EQ(rri.getNumberOfFloatingSpecies(), 2);
 }
 
 TEST_F(StateSavingTests, LOAD_NONEXISTENT_FILE) {

From e8c75549d5f9143a7644249b54f7be6b9197f66e Mon Sep 17 00:00:00 2001
From: Lucian Smith <lpsmith@uw.edu>
Date: Tue, 23 Apr 2024 14:11:40 -0700
Subject: [PATCH 4/9] Fix!

The trick turned out to be that on linux, loading loadBinary into jit->compiledModuleBinaryStream corrupted the compiledModuleBinaryStream.  Instead, we now convert to and from a string, and that seems to work.

At the same time, I changed the factory to return Jit* objects instead of unique_ptr objects, which also seems to work, though that might be a purely cosmetic change.
---
 source/llvm/Jit.cpp                   | 15 +++++++++------
 source/llvm/JitFactory.cpp            | 22 ++++++++++++++--------
 source/llvm/JitFactory.h              |  4 ++--
 source/llvm/LLVMExecutableModel.cpp   |  2 ++
 source/llvm/MCJit.cpp                 |  3 ++-
 source/llvm/ModelGeneratorContext.cpp |  5 +++--
 source/llvm/ModelGeneratorContext.h   |  2 +-
 source/llvm/ModelResources.cpp        | 24 +++++++++++++++++-------
 source/rrRoadRunner.cpp               | 13 ++++++++++---
 9 files changed, 60 insertions(+), 30 deletions(-)

diff --git a/source/llvm/Jit.cpp b/source/llvm/Jit.cpp
index d358c03969..75bd6ddff6 100644
--- a/source/llvm/Jit.cpp
+++ b/source/llvm/Jit.cpp
@@ -34,13 +34,16 @@ using namespace rr;
 namespace rrllvm {
 
     Jit::Jit(std::uint32_t options)
-            : options(options),
-              context(std::make_unique<llvm::LLVMContext>()),
-            // todo the module name should be the sbmlMD5. Might be cleaner to
+        : options(options)
+        , context(std::make_unique<llvm::LLVMContext>())
+                   // todo the module name should be the sbmlMD5. Might be cleaner to
             //  add this as a parameter to Jit constructor.
-              module(std::make_unique<llvm::Module>("LLVM Module", *context)),
-              moduleNonOwning(module.get()), /*Maintain a weak ref so we don't lose our handle to the module*/
-              builder(std::make_unique<llvm::IRBuilder<>>(*context)) {
+        , module(std::make_unique<llvm::Module>("LLVM Module", *context))
+        , moduleNonOwning(module.get()) /*Maintain a weak ref so we don't lose our handle to the module*/
+        , builder(std::make_unique<llvm::IRBuilder<>>(*context))
+        , compiledModuleBinaryStream(nullptr)
+        , moduleBuffer() 
+    {
 
 
         // IR module is initialized with just a ModuleID and a source filename
diff --git a/source/llvm/JitFactory.cpp b/source/llvm/JitFactory.cpp
index 139fdd11ae..6d7d16cf8e 100644
--- a/source/llvm/JitFactory.cpp
+++ b/source/llvm/JitFactory.cpp
@@ -6,22 +6,28 @@
 
 namespace rrllvm {
 
-    std::unique_ptr<Jit> JitFactory::makeJitEngine(std::uint32_t opt) {
-        std::unique_ptr<Jit> jit;
+    Jit* JitFactory::makeJitEngine(std::uint32_t opt) {
+        rrLog(Logger::LOG_DEBUG) << __FUNC__;
+        Jit* jit = NULL;
         if (opt & LoadSBMLOptions::MCJIT) {
-            jit = std::move(std::make_unique<MCJit>(opt));
+            rrLog(Logger::LOG_DEBUG) << "Creating an MCJit object.";
+            jit = new rrllvm::MCJit(opt);
         }
 
         else if (opt & LoadSBMLOptions::LLJIT) {
-            jit = std::move(std::make_unique<LLJit>(opt));
+            jit = new rrllvm::LLJit(opt);
+        }
+        
+        else {
+            throw std::invalid_argument("Cannot create JIT object; need to say whether it's MCJit or LLJit in the options.");
         }
 
-        return std::move(jit);
+        rrLog(Logger::LOG_DEBUG) << "Done creating a Jit object.";
+        return jit;
     }
 
-    std::unique_ptr<Jit> JitFactory::makeJitEngine() {
+    Jit* JitFactory::makeJitEngine() {
         LoadSBMLOptions opt;
-        std::unique_ptr<Jit> j = JitFactory::makeJitEngine(opt.modelGeneratorOpt);
-        return std::move(j);
+        return JitFactory::makeJitEngine(opt.modelGeneratorOpt);
     }
 }
diff --git a/source/llvm/JitFactory.h b/source/llvm/JitFactory.h
index a61fdb9b00..4ba533ea64 100644
--- a/source/llvm/JitFactory.h
+++ b/source/llvm/JitFactory.h
@@ -37,7 +37,7 @@ namespace rrllvm {
         /**
          * @brief Create a Jit engine using local options provided by the user
          */
-        static std::unique_ptr<Jit> makeJitEngine(std::uint32_t opt);
+        static Jit* makeJitEngine(std::uint32_t opt);
 
         /**
          * @brief Create a Jit engine using the global options in Config.
@@ -45,7 +45,7 @@ namespace rrllvm {
          * This function instantiates the LoadSBMLOptions and provides the default
          * modelGeneratorOpt to JitFactory::makeJitEngine(opt);
          */
-        static std::unique_ptr<Jit> makeJitEngine();
+        static Jit* makeJitEngine();
 
     };
 
diff --git a/source/llvm/LLVMExecutableModel.cpp b/source/llvm/LLVMExecutableModel.cpp
index 229d97d9a5..1b767e1613 100644
--- a/source/llvm/LLVMExecutableModel.cpp
+++ b/source/llvm/LLVMExecutableModel.cpp
@@ -274,6 +274,8 @@ LLVMExecutableModel::LLVMExecutableModel(std::istream& in, uint modelGeneratorOp
     conversionFactor(1.0),
     flags(defaultFlags())
 {
+
+    rrLog(Logger::LOG_DEBUG) << __FUNC__ << std::endl;
     modelData = LLVMModelData_from_save(in);
     resources->loadState(in, modelGeneratorOpt);
 
diff --git a/source/llvm/MCJit.cpp b/source/llvm/MCJit.cpp
index baf46628f6..29b95e3abe 100644
--- a/source/llvm/MCJit.cpp
+++ b/source/llvm/MCJit.cpp
@@ -44,7 +44,8 @@ namespace rrllvm {
      * file type.
      */
 #if LLVM_VERSION_MAJOR == 6
-    llvm::LLVMTargetMachine::CodeGenFileType getCodeGenFileType() {
+    llvm::LLVMTargetMachine::CodeGenFileType getCodeGenFileType()
+    {
         return llvm::TargetMachine::CGFT_ObjectFile;
     }
 #elif LLVM_VERSION_MAJOR >= 12
diff --git a/source/llvm/ModelGeneratorContext.cpp b/source/llvm/ModelGeneratorContext.cpp
index f16edaf5bc..2c87b73f8d 100644
--- a/source/llvm/ModelGeneratorContext.cpp
+++ b/source/llvm/ModelGeneratorContext.cpp
@@ -106,7 +106,7 @@ namespace rrllvm {
 #endif
 
     ModelGeneratorContext::ModelGeneratorContext(const libsbml::SBMLDocument* doc_, unsigned options,
-                                                 std::unique_ptr<Jit> jitEngine)
+                                                 Jit* jitEngine)
             :
             ownedDoc(nullptr),
             doc(nullptr),
@@ -114,7 +114,8 @@ namespace rrllvm {
             symbols(nullptr),
             options(options),
             random(nullptr),
-            jit(std::move(jitEngine)) {
+            jit(jitEngine) 
+    {
         if (useSymbolCache()) {
             rrLog(Logger::LOG_INFORMATION) << "Using LLVM symbol/value cache";
         } else {
diff --git a/source/llvm/ModelGeneratorContext.h b/source/llvm/ModelGeneratorContext.h
index 7e26483351..6c09a01a24 100644
--- a/source/llvm/ModelGeneratorContext.h
+++ b/source/llvm/ModelGeneratorContext.h
@@ -101,7 +101,7 @@ namespace rrllvm {
         ModelGeneratorContext(
                 const libsbml::SBMLDocument *_doc,
                 unsigned options,
-                std::unique_ptr<Jit> jitEngine);
+                Jit* jitEngine);
 
         /**
          * does not attach to any sbml doc,
diff --git a/source/llvm/ModelResources.cpp b/source/llvm/ModelResources.cpp
index fb6c0984f2..4b640e8432 100644
--- a/source/llvm/ModelResources.cpp
+++ b/source/llvm/ModelResources.cpp
@@ -55,8 +55,14 @@ using rr::LoadSBMLOptions;
 namespace rrllvm {
     /** @cond PRIVATE */
 
-    ModelResources::ModelResources() :
-            symbols(nullptr), executionEngine(nullptr), context(nullptr), random(nullptr), errStr(nullptr) {
+    ModelResources::ModelResources() 
+        : symbols(nullptr)
+        , executionEngine(nullptr)
+        , context(nullptr)
+        , random(nullptr)
+        , errStr(nullptr)
+        , jit(nullptr)
+    {
         // the reset of the ivars are assigned by the generator,
         // and in an exception they are not, does not matter as
         // we don't have to delete them.
@@ -128,14 +134,13 @@ namespace rrllvm {
         rr::saveBinary(out, usingCompiledModuleBinaryStream);
 
         if (usingCompiledModuleBinaryStream) {
-            rr::saveBinary(out, jit->compiledModuleBinaryStream.get());
+            rr::saveBinary(out, jit->compiledModuleBinaryStream.get()->str().str());
         }
 
     }
 
     void ModelResources::loadState(std::istream &in, uint modelGeneratorOpt) {
-
-        jit = std::move(JitFactory::makeJitEngine(modelGeneratorOpt));
+        jit.reset(JitFactory::makeJitEngine(modelGeneratorOpt));
 
         // get rid of sumbols, if not nullptr.
         // todo make symbols a unique_ptr
@@ -164,8 +169,13 @@ namespace rrllvm {
          * a roadrunner instance cannot saveState.
          */
         if (usingCompiledModuleBinaryStream) {
-            //Get the object file binary string from the input stream
-            rr::loadBinary(in, jit->compiledModuleBinaryStream.get());
+            //We saved this as a string; convert it back to a 'raw_svector_ostream'
+            string stream_str;
+            rr::loadBinary(in, stream_str);
+            llvm::raw_svector_ostream* binarystream = new llvm::raw_svector_ostream(jit->moduleBuffer);
+            *binarystream << stream_str;
+
+            jit->compiledModuleBinaryStream.reset(binarystream);
         }
 
         //Set up a buffer to read the object code from
diff --git a/source/rrRoadRunner.cpp b/source/rrRoadRunner.cpp
index faf290dd15..6b095b2f98 100644
--- a/source/rrRoadRunner.cpp
+++ b/source/rrRoadRunner.cpp
@@ -259,7 +259,10 @@ namespace rr {
                 simulateOpt(),
                 mInstanceID(0),
                 loadOpt(dict),
-                compiler(Compiler::New()) {
+                compiler(Compiler::New()),
+                model(nullptr),
+                document(nullptr)
+        {
             // have to init integrators the hard way in c++98
             //memset((void*)integrators, 0, sizeof(integrators)/sizeof(char));
         }
@@ -276,7 +279,10 @@ namespace rr {
                 mLS(0),
                 simulateOpt(),
                 mInstanceID(0),
-                compiler(Compiler::New()) {
+                compiler(Compiler::New()),
+                model(nullptr),
+                document(nullptr)
+        {
             loadOpt.setItem("compiler", Setting(_compiler));
             loadOpt.setItem("tempDir", Setting(_tempDir));
             loadOpt.setItem("supportCodeDir", Setting(_supportCodeDir));
@@ -295,13 +301,13 @@ namespace rr {
                 mSelectionList(rri.mSelectionList),
                 loadOpt(rri.loadOpt),
                 mSteadyStateSelection(rri.mSteadyStateSelection),
-                //model(NULL), //Create below instead.  Constructing with 'NULL' doesn't work.
                 compiler(Compiler::New()),
                 mLS(NULL), //Create only if asked.
                 simulateOpt(rri.simulateOpt),
                 roadRunnerOptions(rri.roadRunnerOptions),
                 configurationXML(rri.configurationXML),
                 simulatedSinceReset(false),
+                model(nullptr),
                 document(rri.document->clone()) {
             //There may be an easier way to save and load the model state, but this
             // is at least straightforward.  We call 'saveState', convert it to an
@@ -5578,6 +5584,7 @@ namespace rr {
     }
 
     void RoadRunner::loadStateS(std::stringstream *in) {
+        rrLog(Logger::LOG_DEBUG) << __FUNC__;
         int inMagicNumber;
         rr::loadBinary(*in, inMagicNumber);
         std::string x = in->str();

From 4f129ef4954d527d5dd4be8664ca7968164c7200 Mon Sep 17 00:00:00 2001
From: Lucian Smith <lpsmith@uw.edu>
Date: Tue, 23 Apr 2024 14:17:55 -0700
Subject: [PATCH 5/9] Update linux test.

Also, bugs appeared only after loading twice, so check that.
---
 .../StateSavingTests/savedState_linux.rr      | Bin 13262 -> 21030 bytes
 test/serialization/state_saving.cpp           |  17 ++++++++++++-----
 2 files changed, 12 insertions(+), 5 deletions(-)

diff --git a/test/models/StateSavingTests/savedState_linux.rr b/test/models/StateSavingTests/savedState_linux.rr
index da296743b950825f610daa069dcb8fd50832e251..8a405aa0e3387248a89725bf12d030e025510512 100644
GIT binary patch
delta 22
ecmX??zHABOhH#b5+gKOKO}@dTuz9}<KR*C<%n2C)

delta 35
rcmZ3sgz;SZhHw?O1WAW!j1`kFGFh=r@Ka3Qn=-kOQE9WdGe187>|G1>

diff --git a/test/serialization/state_saving.cpp b/test/serialization/state_saving.cpp
index d86bc7ea50..6489721e90 100644
--- a/test/serialization/state_saving.cpp
+++ b/test/serialization/state_saving.cpp
@@ -437,14 +437,21 @@ TEST_F(StateSavingTests, LOAD_INVALID_FILE) {
 TEST_F(StateSavingTests, LOAD_VALID_FILE) {
     RoadRunner rri;
 #if defined(_WIN32)
-    // This only works on Windows, and lord only knows why.
     rri.loadState((stateSavingModelsDir / "savedState_windows.rr").string());
     EXPECT_EQ(rri.getNumberOfFloatingSpecies(), 2);
-    //#elif defined(__unix__)
-    //#if (defined(__APPLE__))
+    rri.loadState((stateSavingModelsDir / "savedState_windows.rr").string());
+    EXPECT_EQ(rri.getNumberOfFloatingSpecies(), 2);
+#elif (defined(__APPLE__))
+    //Try the linux one?
+    rri.loadState((stateSavingModelsDir / "savedState_linux.rr").string());
+    EXPECT_EQ(rri.getNumberOfFloatingSpecies(), 2);
+    rri.loadState((stateSavingModelsDir / "savedState_linux.rr").string());
+    EXPECT_EQ(rri.getNumberOfFloatingSpecies(), 2);
 #else
-    //rri.loadState((stateSavingModelsDir / "savedState_linux.rr").string());
-    //EXPECT_EQ(rri.getNumberOfFloatingSpecies(), 2);
+    rri.loadState((stateSavingModelsDir / "savedState_linux.rr").string());
+    EXPECT_EQ(rri.getNumberOfFloatingSpecies(), 2);
+    rri.loadState((stateSavingModelsDir / "savedState_linux.rr").string());
+    EXPECT_EQ(rri.getNumberOfFloatingSpecies(), 2);
 #endif
 }
 

From 8cd0c042e02a39fb3a99ae0c5989bca2a6756fef Mon Sep 17 00:00:00 2001
From: Lucian Smith <lpsmith@uw.edu>
Date: Tue, 23 Apr 2024 14:29:54 -0700
Subject: [PATCH 6/9] Update minor version number.

Because this changes the save file format slightly.
---
 CMakeLists.txt | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/CMakeLists.txt b/CMakeLists.txt
index fcf6e56f10..9b56e13368 100644
--- a/CMakeLists.txt
+++ b/CMakeLists.txt
@@ -8,8 +8,8 @@ cmake_minimum_required(VERSION 3.16)
 # Version information and include modules
 
 set(ROADRUNNER_VERSION_MAJOR 2)
-set(ROADRUNNER_VERSION_MINOR 6)
-set(ROADRUNNER_VERSION_PATCH 1)
+set(ROADRUNNER_VERSION_MINOR 7)
+set(ROADRUNNER_VERSION_PATCH 0)
 
 set(ROADRUNNER_VERSION "${ROADRUNNER_VERSION_MAJOR}.${ROADRUNNER_VERSION_MINOR}.${ROADRUNNER_VERSION_PATCH}")
 

From 686888cf5fe34a9f4ee2754662f48f258fe7e94b Mon Sep 17 00:00:00 2001
From: Lucian Smith <lpsmith@uw.edu>
Date: Tue, 23 Apr 2024 14:52:55 -0700
Subject: [PATCH 7/9] Fix Jit factory tests.

---
 test/llvm_tests/JitFactoryTests.cpp            | 8 ++++----
 test/llvm_tests/LLVMGeneratedFunctionTests.cpp | 4 ++--
 2 files changed, 6 insertions(+), 6 deletions(-)

diff --git a/test/llvm_tests/JitFactoryTests.cpp b/test/llvm_tests/JitFactoryTests.cpp
index 928604a82e..7a44cf18c9 100644
--- a/test/llvm_tests/JitFactoryTests.cpp
+++ b/test/llvm_tests/JitFactoryTests.cpp
@@ -21,26 +21,26 @@ class JitFactoryTests : public ::testing::Test {
 
 TEST_F(JitFactoryTests, MCJitFromConfig){
     Config::setValue(Config::LLVM_BACKEND, Config::LLVM_BACKEND_VALUES::MCJIT);
-    std::unique_ptr<Jit> j = JitFactory::makeJitEngine();
+    Jit* j = JitFactory::makeJitEngine();
     ASSERT_TRUE(typeid((*j)) == typeid(MCJit));
 }
 
 TEST_F(JitFactoryTests, LLJitFromConfig){
     Config::setValue(Config::LLVM_BACKEND, Config::LLVM_BACKEND_VALUES::LLJIT);
-    std::unique_ptr<Jit> j = JitFactory::makeJitEngine();
+    Jit* j = JitFactory::makeJitEngine();
     ASSERT_TRUE(typeid((*j)) == typeid(LLJit));
 }
 
 TEST_F(JitFactoryTests, MCJitFromOpt){
     LoadSBMLOptions opt;
     opt.setLLVMBackend(LoadSBMLOptions::MCJIT);
-    std::unique_ptr<Jit> j = JitFactory::makeJitEngine(opt.modelGeneratorOpt);
+    Jit* j = JitFactory::makeJitEngine(opt.modelGeneratorOpt);
     ASSERT_TRUE(typeid((*j)) == typeid(MCJit));
 }
 
 TEST_F(JitFactoryTests, LLJitFromOpt){
     LoadSBMLOptions opt;
     opt.setLLVMBackend(LoadSBMLOptions::LLJIT);
-    std::unique_ptr<Jit> j = JitFactory::makeJitEngine(opt.modelGeneratorOpt);
+    Jit* j = JitFactory::makeJitEngine(opt.modelGeneratorOpt);
     ASSERT_TRUE(typeid((*j)) == typeid(LLJit));
 }
diff --git a/test/llvm_tests/LLVMGeneratedFunctionTests.cpp b/test/llvm_tests/LLVMGeneratedFunctionTests.cpp
index 66ad2df745..4264ca464a 100644
--- a/test/llvm_tests/LLVMGeneratedFunctionTests.cpp
+++ b/test/llvm_tests/LLVMGeneratedFunctionTests.cpp
@@ -22,8 +22,8 @@ void LLVMGeneratedFunctionTests::checkInitialEvaluationSpecies(int options, int
         s->setInitialAmount(speciesAmt); // so 4.5 after initial eval?
 
         // create the Jit engine and give to ModelGeneratorContext.
-        std::unique_ptr<Jit> j = JitFactory::makeJitEngine(options);
-        ModelGeneratorContext mgc(doc.get() /*borrowed*/, options, std::move(j));
+        Jit* j = JitFactory::makeJitEngine(options);
+        ModelGeneratorContext mgc(doc.get() /*borrowed*/, options, j);
 
         // code gen (limited scope, this test only needs a few functions)
         EvalInitialConditionsCodeGen(mgc).createFunction();

From 63e79035b22b05e7f0c370994ab2191ce60c5da2 Mon Sep 17 00:00:00 2001
From: Lucian Smith <lpsmith@uw.edu>
Date: Tue, 23 Apr 2024 16:24:40 -0700
Subject: [PATCH 8/9] Updated savedState files for all platforms.

---
 .../StateSavingTests/savedState_linux.rr      | Bin 21030 -> 15374 bytes
 .../models/StateSavingTests/savedState_mac.rr | Bin 0 -> 11430 bytes
 .../StateSavingTests/savedState_windows.rr    | Bin 12286 -> 12286 bytes
 test/serialization/state_saving.cpp           |   4 ++--
 4 files changed, 2 insertions(+), 2 deletions(-)
 create mode 100644 test/models/StateSavingTests/savedState_mac.rr

diff --git a/test/models/StateSavingTests/savedState_linux.rr b/test/models/StateSavingTests/savedState_linux.rr
index 8a405aa0e3387248a89725bf12d030e025510512..83e9e184b67db3898c6f5080270b4c438dc59d41 100644
GIT binary patch
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diff --git a/test/models/StateSavingTests/savedState_mac.rr b/test/models/StateSavingTests/savedState_mac.rr
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ze)<&vwYXWe*ug56AfgIV&cmqHTxU#7AR{bjnq;NdXOJbKhL@Erx4=Q>68U`xnNoI8
zB|!!ds#?4Bji5?gNhuHF8z*t1Q#H~&f<@*+LqXT@LL*npuKVseKi>2FHEL~#TxYyw
zR&|_=!%m3|P*eAA+p3zVBY&I#diZ^=l^u7~a7)UO3MoDC|L@?&vq0tll<#0ws#T{d
zS5L=riFYDhr_>gznxno`Rg31CRS##)2$q@4fMnHP5L?+ds-{!-R9OssDI%x}m~IxP
zYnIwsD(?+d?Ce;@u6ljBVc)M^-Pt)hI@&?(4#(ZnNrO%s?=O3KC%?42JByBM=CXp@
zms_68GSHXn&aFHvo6T47-mtT%R>Law<;HSZ*%1cRwmg4LIdVbpBmgM#<Akg?<g7Q{
zN?&g9x;0mKp?$8qOIk|#DMK#n)o_#<_5gM(GKHIyh>VU@3M*R#2MO}~a=u$PbDbPZ
z=X}9%lzhDm0`%k+RZM75m<@hS(U(h&i(e733qfBFGZ{9#HC20jus%eA70oZ>U4o#?
zhV3D_LwqNOp1dyxNH`NI%2Pr1V!`#$oIfnV<vGu>baIM=D_>X!_<@SN1&Tc5XD28z
zx(YQ}NlZVXRSuN8I_52aMm4-|BZ?x6X_eEcI22Lqn%AMqL~_=g40Y`ebK&wuT%-cO
zMagAd>_*(4acu}{qHK7mY*`PgRuQ2r?zOH{su%shq}YU9E9=ZMjssL5_K*1Rh3$se
zJ#j6y9Bg5CylK|qh1a&xO&%*}`c`qZF&YL11$;ytPC0W%mx~jp`>LyYJ8yxA`0tk0
z;z*&GWy=?>m01{uUyQ_w!ayh44LSMFM)&znl};s>R}9WCCjVaZE7lB0%Lkp{6hH5C
zg;CWX<`u@p%N|z?6s$YlvAy813)rF@$_>>(xG0su?i4KF+2A98O3DYB{lLrTeXd?w
z`84hjk+=VCgEpjA*le<VgFPur#LGuNGE6~F(E_ToOXP+w4ODfg1iHVhJS#75KP&$O
DS?*Xf

literal 0
HcmV?d00001

diff --git a/test/models/StateSavingTests/savedState_windows.rr b/test/models/StateSavingTests/savedState_windows.rr
index 8cb255f58d4ff95c5bfc74e9c4f28f7b3e0dd57f..5fb71d7f3ff33616f711e4035575ba91c6cff060 100644
GIT binary patch
delta 14
Vcmewt|1X|3D1R-3^hVa7`T#S81}6Xj

delta 14
Vcmewt|1X|3D1R-3)JE2y`T#S31||Ri

diff --git a/test/serialization/state_saving.cpp b/test/serialization/state_saving.cpp
index 6489721e90..b7af244a3f 100644
--- a/test/serialization/state_saving.cpp
+++ b/test/serialization/state_saving.cpp
@@ -443,9 +443,9 @@ TEST_F(StateSavingTests, LOAD_VALID_FILE) {
     EXPECT_EQ(rri.getNumberOfFloatingSpecies(), 2);
 #elif (defined(__APPLE__))
     //Try the linux one?
-    rri.loadState((stateSavingModelsDir / "savedState_linux.rr").string());
+    rri.loadState((stateSavingModelsDir / "savedState_mac.rr").string());
     EXPECT_EQ(rri.getNumberOfFloatingSpecies(), 2);
-    rri.loadState((stateSavingModelsDir / "savedState_linux.rr").string());
+    rri.loadState((stateSavingModelsDir / "savedState_mac.rr").string());
     EXPECT_EQ(rri.getNumberOfFloatingSpecies(), 2);
 #else
     rri.loadState((stateSavingModelsDir / "savedState_linux.rr").string());

From 92b3d025c3c23f39db8fb5ba0cff4d40315c3e35 Mon Sep 17 00:00:00 2001
From: Lucian Smith <lpsmith@uw.edu>
Date: Wed, 24 Apr 2024 12:19:21 -0700
Subject: [PATCH 9/9] Updates from Adel's code review.

* Move string conversion of compiledModuleBinaryStream to Jit class itself.
* Remove spurious endl.
* Initialize all object children in ModelGeneratorContext's default constructor.
* Clean up Jit objects in factory test.
* Describe new state_saving test and how to fix it when it inevitably breaks.
---
 source/llvm/Jit.cpp                           | 15 ++++++-
 source/llvm/Jit.h                             | 17 +++++++-
 source/llvm/LLVMExecutableModel.cpp           |  2 +-
 source/llvm/MCJit.cpp                         |  2 +-
 source/llvm/ModelGeneratorContext.cpp         | 18 ++++----
 source/llvm/ModelResources.cpp                |  7 +---
 test/llvm_tests/JitFactoryTests.cpp           |  4 ++
 .../llvm_tests/LLVMGeneratedFunctionTests.cpp |  3 +-
 test/serialization/state_saving.cpp           | 42 ++++++++++++-------
 9 files changed, 78 insertions(+), 32 deletions(-)

diff --git a/source/llvm/Jit.cpp b/source/llvm/Jit.cpp
index 75bd6ddff6..8f77cb9d57 100644
--- a/source/llvm/Jit.cpp
+++ b/source/llvm/Jit.cpp
@@ -36,7 +36,7 @@ namespace rrllvm {
     Jit::Jit(std::uint32_t options)
         : options(options)
         , context(std::make_unique<llvm::LLVMContext>())
-                   // todo the module name should be the sbmlMD5. Might be cleaner to
+            // todo the module name should be the sbmlMD5. Might be cleaner to
             //  add this as a parameter to Jit constructor.
         , module(std::make_unique<llvm::Module>("LLVM Module", *context))
         , moduleNonOwning(module.get()) /*Maintain a weak ref so we don't lose our handle to the module*/
@@ -310,6 +310,19 @@ namespace rrllvm {
                                FunctionType::get(double_type, args_d2, false));
     }
 
+    std::string Jit::getModuleBinaryStreamAsString()
+    {
+        return compiledModuleBinaryStream->str().str();
+    }
+
+    void Jit::resetModuleBinaryStream(std::string cmbs)
+    {
+        //There might be a way to do this directly, but this is at least clean.
+        llvm::raw_svector_ostream* binarystream = new llvm::raw_svector_ostream(moduleBuffer);
+        *binarystream << cmbs;
+        compiledModuleBinaryStream.reset(binarystream);
+    }
+
     /**
     * getProcessTriple() - Return an appropriate target triple for generating
     * code to be loaded into the current process, e.g. when using the JIT.
diff --git a/source/llvm/Jit.h b/source/llvm/Jit.h
index 40837297d2..f41e421435 100644
--- a/source/llvm/Jit.h
+++ b/source/llvm/Jit.h
@@ -328,11 +328,26 @@ namespace rrllvm {
          */
         virtual std::string getModuleAsString(std::string sbmlMD5) = 0;
 
+        /**
+         * @brief Return MCJit's compiled binary stream as a string.
+         * @details Converts the binary stream to a string.  Useful for saving and
+         * loading state for MCJit objects (LLJit doesn't use it).
+         */
+        virtual std::string getModuleBinaryStreamAsString();
+
+        /**
+         * @brief Reset MCJit's compiled binary stream with the given string.
+         * @details MCJit is the only Jit that uses this. (It's bad interface design
+         * but works at least.). LLJit uses a caching mechanism which allows us
+         * to retrieve object files directly, foregoing the need for this function.
+         */
+        virtual void resetModuleBinaryStream(std::string cmbs);
+
         /**
          * @brief MCJit compiles the generated LLVM IR to this binary stream
          * which is then used both for adding to the Jit as a module and for
          * saveState.
-         * @details MCJit is the only Jit that uses this. (Its bad interface design
+         * @details MCJit is the only Jit that uses this. (It's bad interface design
          * but works at least.). LLJit uses a caching mechanism which allows us
          * to retrieve object files directly, foregoing the need for this variable.
          */
diff --git a/source/llvm/LLVMExecutableModel.cpp b/source/llvm/LLVMExecutableModel.cpp
index 1b767e1613..7f81e4e2a8 100644
--- a/source/llvm/LLVMExecutableModel.cpp
+++ b/source/llvm/LLVMExecutableModel.cpp
@@ -275,7 +275,7 @@ LLVMExecutableModel::LLVMExecutableModel(std::istream& in, uint modelGeneratorOp
     flags(defaultFlags())
 {
 
-    rrLog(Logger::LOG_DEBUG) << __FUNC__ << std::endl;
+    rrLog(Logger::LOG_DEBUG) << __FUNC__;
     modelData = LLVMModelData_from_save(in);
     resources->loadState(in, modelGeneratorOpt);
 
diff --git a/source/llvm/MCJit.cpp b/source/llvm/MCJit.cpp
index 29b95e3abe..1ff03d8b6f 100644
--- a/source/llvm/MCJit.cpp
+++ b/source/llvm/MCJit.cpp
@@ -183,7 +183,7 @@ namespace rrllvm {
             throw_llvm_exception(err);
         }
 
-        auto memBuffer(llvm::MemoryBuffer::getMemBuffer(compiledModuleBinaryStream->str().str()));
+        auto memBuffer(llvm::MemoryBuffer::getMemBuffer(getModuleBinaryStreamAsString()));
 
         llvm::Expected<std::unique_ptr<llvm::object::ObjectFile> > objectFileExpected =
             llvm::object::ObjectFile::createObjectFile(
diff --git a/source/llvm/ModelGeneratorContext.cpp b/source/llvm/ModelGeneratorContext.cpp
index 2c87b73f8d..c4115a67f1 100644
--- a/source/llvm/ModelGeneratorContext.cpp
+++ b/source/llvm/ModelGeneratorContext.cpp
@@ -210,13 +210,17 @@ namespace rrllvm {
         return doc;
     }
 
-    ModelGeneratorContext::ModelGeneratorContext() :
-            ownedDoc(createEmptyDocument()),
-            doc(ownedDoc),
-            mPiecewiseTriggers(),
-            symbols(new LLVMModelDataSymbols(doc->getModel(), 0)),
-            modelSymbols(new LLVMModelSymbols(getModel(), *symbols)),
-            options(0)
+    ModelGeneratorContext::ModelGeneratorContext() 
+        : ownedDoc(createEmptyDocument())
+        , doc(ownedDoc)
+        , mPiecewiseTriggers()
+        , symbols(new LLVMModelDataSymbols(doc->getModel(), 0))
+        , modelSymbols(new LLVMModelSymbols(doc->getModel(), *symbols))
+        , model(doc->getModel())
+        , random(NULL)
+        , options(0)
+        , jit(nullptr)
+        , moietyConverter(nullptr)
     {
         // initialize LLVM
         // TODO check result
diff --git a/source/llvm/ModelResources.cpp b/source/llvm/ModelResources.cpp
index 4b640e8432..b8f6a93464 100644
--- a/source/llvm/ModelResources.cpp
+++ b/source/llvm/ModelResources.cpp
@@ -134,7 +134,7 @@ namespace rrllvm {
         rr::saveBinary(out, usingCompiledModuleBinaryStream);
 
         if (usingCompiledModuleBinaryStream) {
-            rr::saveBinary(out, jit->compiledModuleBinaryStream.get()->str().str());
+            rr::saveBinary(out, jit->getModuleBinaryStreamAsString());
         }
 
     }
@@ -172,10 +172,7 @@ namespace rrllvm {
             //We saved this as a string; convert it back to a 'raw_svector_ostream'
             string stream_str;
             rr::loadBinary(in, stream_str);
-            llvm::raw_svector_ostream* binarystream = new llvm::raw_svector_ostream(jit->moduleBuffer);
-            *binarystream << stream_str;
-
-            jit->compiledModuleBinaryStream.reset(binarystream);
+            jit->resetModuleBinaryStream(stream_str);
         }
 
         //Set up a buffer to read the object code from
diff --git a/test/llvm_tests/JitFactoryTests.cpp b/test/llvm_tests/JitFactoryTests.cpp
index 7a44cf18c9..be7f5ef3da 100644
--- a/test/llvm_tests/JitFactoryTests.cpp
+++ b/test/llvm_tests/JitFactoryTests.cpp
@@ -23,12 +23,14 @@ TEST_F(JitFactoryTests, MCJitFromConfig){
     Config::setValue(Config::LLVM_BACKEND, Config::LLVM_BACKEND_VALUES::MCJIT);
     Jit* j = JitFactory::makeJitEngine();
     ASSERT_TRUE(typeid((*j)) == typeid(MCJit));
+    delete j;
 }
 
 TEST_F(JitFactoryTests, LLJitFromConfig){
     Config::setValue(Config::LLVM_BACKEND, Config::LLVM_BACKEND_VALUES::LLJIT);
     Jit* j = JitFactory::makeJitEngine();
     ASSERT_TRUE(typeid((*j)) == typeid(LLJit));
+    delete j;
 }
 
 TEST_F(JitFactoryTests, MCJitFromOpt){
@@ -36,6 +38,7 @@ TEST_F(JitFactoryTests, MCJitFromOpt){
     opt.setLLVMBackend(LoadSBMLOptions::MCJIT);
     Jit* j = JitFactory::makeJitEngine(opt.modelGeneratorOpt);
     ASSERT_TRUE(typeid((*j)) == typeid(MCJit));
+    delete j;
 }
 
 TEST_F(JitFactoryTests, LLJitFromOpt){
@@ -43,4 +46,5 @@ TEST_F(JitFactoryTests, LLJitFromOpt){
     opt.setLLVMBackend(LoadSBMLOptions::LLJIT);
     Jit* j = JitFactory::makeJitEngine(opt.modelGeneratorOpt);
     ASSERT_TRUE(typeid((*j)) == typeid(LLJit));
+    delete j;
 }
diff --git a/test/llvm_tests/LLVMGeneratedFunctionTests.cpp b/test/llvm_tests/LLVMGeneratedFunctionTests.cpp
index 4264ca464a..c6d5e6a9fe 100644
--- a/test/llvm_tests/LLVMGeneratedFunctionTests.cpp
+++ b/test/llvm_tests/LLVMGeneratedFunctionTests.cpp
@@ -22,8 +22,7 @@ void LLVMGeneratedFunctionTests::checkInitialEvaluationSpecies(int options, int
         s->setInitialAmount(speciesAmt); // so 4.5 after initial eval?
 
         // create the Jit engine and give to ModelGeneratorContext.
-        Jit* j = JitFactory::makeJitEngine(options);
-        ModelGeneratorContext mgc(doc.get() /*borrowed*/, options, j);
+        ModelGeneratorContext mgc(doc.get() /*borrowed*/, options, JitFactory::makeJitEngine(options));
 
         // code gen (limited scope, this test only needs a few functions)
         EvalInitialConditionsCodeGen(mgc).createFunction();
diff --git a/test/serialization/state_saving.cpp b/test/serialization/state_saving.cpp
index b7af244a3f..f949da60d0 100644
--- a/test/serialization/state_saving.cpp
+++ b/test/serialization/state_saving.cpp
@@ -435,6 +435,20 @@ TEST_F(StateSavingTests, LOAD_INVALID_FILE) {
 }
 
 TEST_F(StateSavingTests, LOAD_VALID_FILE) {
+    //NOTE:  This test will fail every time roadrunner comes out with a new minor
+    // version, and/or the save state format changes.  In fact, if the save state
+    // format changes, the minor version *must* change, so that existing roadrunner
+    // instances don't try to load new save files and visa versa.  These files
+    // are copied versions of the file generated by the 'FromFile' test, below, so
+    // when the format changes, run that test on the three platforms, and replace
+    // the three files with the 'savedState.rr' file for each.
+    //
+    // The format is different per platform because things like 'what is the size
+    // of an unsigned long' can be different per compiler.
+    //
+    // At some point, it might be good to auto-generate these files from a different
+    // run, but issue #1210 was discovered only when loading state from a different
+    // instance than the one that had saved it, so we need this sort of test.
     RoadRunner rri;
 #if defined(_WIN32)
     rri.loadState((stateSavingModelsDir / "savedState_windows.rr").string());
@@ -455,6 +469,20 @@ TEST_F(StateSavingTests, LOAD_VALID_FILE) {
 #endif
 }
 
+TEST_F(StateSavingTests, FromFile) {
+    std::filesystem::path p = std::filesystem::current_path() / "savedState.rr";
+    //std::cout << "saved to " << p << std::endl;
+    RoadRunner rr(OpenLinearFlux().str());
+    rr.saveState(p.string());
+    RoadRunner rr2;
+    rr2.loadState(p.string());
+    auto actualDataLsMatrix = *rr2.simulate(0, 10, 11);
+    auto actualData = rr::Matrix<double>(actualDataLsMatrix); // for almostEquals
+    auto expectedData = OpenLinearFlux().timeSeriesResult();
+    ASSERT_TRUE(expectedData.almostEquals(actualData, 1e-4));
+}
+
+
 TEST_F(StateSavingTests, LOAD_NONEXISTENT_FILE) {
     RoadRunner rri;
     EXPECT_THROW(rri.loadState((rrTestModelsDir_ / "nonexistent-save-state.rr").string()), std::invalid_argument);
@@ -853,20 +881,6 @@ TEST_F(StateSavingTests, FromString) {
     ASSERT_TRUE(expectedData.almostEquals(actualData, 1e-4));
 }
 
-TEST_F(StateSavingTests, FromFile) {
-    std::filesystem::path p = std::filesystem::current_path() / "savedState.rr";
-    //std::cout << "saved to " << p << std::endl;
-    RoadRunner rr(OpenLinearFlux().str());
-    rr.saveState(p.string());
-    RoadRunner rr2;
-    rr2.loadState(p.string());
-    auto actualDataLsMatrix = *rr2.simulate(0, 10, 11);
-    auto actualData = rr::Matrix<double>(actualDataLsMatrix); // for almostEquals
-    auto expectedData = OpenLinearFlux().timeSeriesResult();
-    ASSERT_TRUE(expectedData.almostEquals(actualData, 1e-4));
-}
-
-
 class StateSavingTestsModelData : public RoadRunnerTest {
 public:
     StateSavingTestsModelData() {