Add slow verification for debugging

include/mull/Config/Configuration.h

@@ -12,6 +12,7 @@ extern int MullDefaultTimeoutMilliseconds;
 class Diagnostics;
 
 struct Configuration {
+  std::string pathOnDisk;
   bool debugEnabled;
   bool quiet;
   bool silent;

include/mull/Config/ConfigurationOptions.h

@@ -22,6 +22,7 @@ struct DebugConfig {
   bool coverage = false;
   bool gitDiff = false;
   bool filters = false;
+  bool slowIRVerification = false;
 };
 
 } // namespace mull

include/mull/Parallelization/Tasks/ApplyMutationTask.h

@@ -7,16 +7,21 @@
 namespace mull {
 class progress_counter;
 class MutationPoint;
+struct Configuration;
+class Diagnostics;
 
 class ApplyMutationTask {
 public:
+  explicit ApplyMutationTask(const Configuration &config, Diagnostics &diagnostics);
   using In = const std::vector<MutationPoint *>;
   using Out = std::vector<int>;
   using iterator = In::const_iterator;
 
-  ApplyMutationTask() = default;
-
   void operator()(iterator begin, iterator end, Out &storage,
                   progress_counter &counter);
+
+private:
+  const Configuration &config;
+  Diagnostics &diagnostics;
 };
 } // namespace mull

lib/Config/Configuration.cpp

@@ -5,7 +5,7 @@ namespace mull {
 int MullDefaultTimeoutMilliseconds = 3000;
 
 Configuration::Configuration()
-    : debugEnabled(false), quiet(true), silent(false), dryRunEnabled(false),
+    : pathOnDisk(), debugEnabled(false), quiet(true), silent(false), dryRunEnabled(false),
       captureTestOutput(true), captureMutantOutput(true), includeNotCovered(false),
       junkDetectionDisabled(false), timeout(MullDefaultTimeoutMilliseconds),
       diagnostics(IDEDiagnosticsKind::None),

lib/Config/ConfigurationParser.cpp

@@ -34,6 +34,7 @@ template <> struct llvm::yaml::MappingTraits<DebugConfig> {
     io.mapOptional("coverage", config.coverage);
     io.mapOptional("gitDiff", config.gitDiff);
     io.mapOptional("filters", config.filters);
+    io.mapOptional("slowIRVerification", config.slowIRVerification);
   }
 };
 
@@ -94,5 +95,6 @@ Configuration Configuration::loadFromDisk(Diagnostics &diagnostics, const std::s
   llvm::yaml::Input input(bufferOrError.get()->getMemBufferRef());
   Configuration configuration;
   input >> configuration;
+  configuration.pathOnDisk = path;
   return configuration;
 }

lib/Driver.cpp

@@ -210,8 +210,11 @@ void mull::mutateBitcode(llvm::Module &module) {
     InsertMutationTrampolinesTask::insertTrampolines(bitcode, configuration);
   });
 
-  TaskExecutor<ApplyMutationTask> applyMutations(
-      diagnostics, "Applying mutations", mutations, Nothing, { ApplyMutationTask() });
+  TaskExecutor<ApplyMutationTask> applyMutations(diagnostics,
+                                                 "Applying mutations",
+                                                 mutations,
+                                                 Nothing,
+                                                 { ApplyMutationTask(configuration, diagnostics) });
   applyMutations.execute();
 
   if (configuration.debug.printIR || configuration.debug.printIRAfter) {
@@ -224,7 +227,15 @@ void mull::mutateBitcode(llvm::Module &module) {
     if (llvm::verifyModule(module, &errorStream)) {
       std::stringstream message;
       message << "Uh oh! Mull corrupted LLVM module.\n"
-              << "Please, report the following error message here "
+              << "Please, add the following lines:\n"
+              << "debug:\n"
+              << " slowIRVerification: true\n"
+              << "to the config file ";
+      if (!configuration.pathOnDisk.empty()) {
+        message << "(" << configuration.pathOnDisk << ") ";
+      }
+      message << "and re-run the failing command.\n\n";
+      message << "Otherwise, report the following error message here "
                  "https://github.com/mull-project/mull/issues\n"
               << "Underlying error message:\n"
               << errorStream.str();

lib/Parallelization/Tasks/ApplyMutationTask.cpp

@@ -1,15 +1,46 @@
 #include "mull/Parallelization/Tasks/ApplyMutationTask.h"
 
+#include "mull/Config/Configuration.h"
+#include "mull/Diagnostics/Diagnostics.h"
 #include "mull/MutationPoint.h"
 #include "mull/Parallelization/Progress.h"
+#include <llvm/IR/Verifier.h>
+#include <sstream>
 
 using namespace mull;
 
+ApplyMutationTask::ApplyMutationTask(const Configuration &config, Diagnostics &diagnostics)
+    : config(config), diagnostics(diagnostics) {}
+
 void ApplyMutationTask::operator()(iterator begin, iterator end, Out &storage,
                                    progress_counter &counter) {
   for (auto it = begin; it != end; ++it, counter.increment()) {
     auto point = *it;
     point->recordMutation();
     point->applyMutation();
+    if (config.debug.slowIRVerification) {
+      auto module = point->getBitcode()->getModule();
+      std::string error;
+      llvm::raw_string_ostream errorStream(error);
+      if (llvm::verifyModule(*module, &errorStream)) {
+        std::stringstream message;
+        std::string mutator = point->getMutatorIdentifier();
+        message << "Uh oh! Mull corrupted LLVM module.\n"
+                << "Please, report the following error message here "
+                   "https://github.com/mull-project/mull/issues\n"
+                << "Underlying error message:\n"
+                << errorStream.str() << "\n"
+                << "The module was corrupted by '" << mutator << "' mutator.\n"
+                << "To disable it, add the following:\n"
+                   "ignoreMutators:\n"
+                << "  - " << mutator << "\n"
+                << "to the config file";
+        if (!config.pathOnDisk.empty()) {
+          message << " (" << config.pathOnDisk << ")";
+        }
+        message << "\n";
+        diagnostics.error(message.str());
+      }
+    }
   }
 }

tests-lit/tests/command_line_input_validation/valid_input/01_executable_is_dot_slash_relative_path_binary/main.c

@@ -8,6 +8,6 @@ int main(int argc, char **argv) {
 
 // clang-format off
 
-// RUN: %clang_cc %pass_mull_ir_frontend  %s -g -o %s.exe
+// RUN: %clang_cc %sysroot %pass_mull_ir_frontend  %s -g -o %s.exe
 // RUN: %mull_runner main.c.exe -ide-reporter-show-killed | %filecheck %s --dump-input=fail --match-full-lines
 // CHECK: [info] Killed mutants (1/1):

tests-lit/tests/debug/printIRAfter/main.c

@@ -8,6 +8,6 @@ int main() {
   return sum(0, 0);
 }
 
-// RUN: %clang_cc %pass_mull_ir_frontend -g %s -o %s.exe 2>&1 | %filecheck %s --dump-input=fail --strict-whitespace --match-full-lines
+// RUN: %clang_cc %sysroot %pass_mull_ir_frontend -g %s -o %s.exe 2>&1 | %filecheck %s --dump-input=fail --strict-whitespace --match-full-lines
 // CHECK:define{{.*}}@sum{{.*}}
 // CHECK:define{{.*}}cxx_add_to_sub{{.*}}

tests-lit/tests/debug/printIRBefore/main.c

@@ -8,6 +8,6 @@ int main() {
   return sum(0, 0);
 }
 
-// RUN: %clang_cc %pass_mull_ir_frontend -g %s -o %s.exe 2>&1 | %filecheck %s --dump-input=fail --strict-whitespace --match-full-lines
+// RUN: %clang_cc %sysroot %pass_mull_ir_frontend -g %s -o %s.exe 2>&1 | %filecheck %s --dump-input=fail --strict-whitespace --match-full-lines
 // CHECK:define{{.*}}@sum{{.*}}
 // CHECK-NOT:define{{.*}}cxx_add_to_sub{{.*}}

tests-lit/tests/debug/traceMutants/main.c

@@ -8,7 +8,7 @@ int main() {
   return sum(0, 0);
 }
 
-// RUN: %clang_cc %pass_mull_ir_frontend -g %s -o %s.exe
+// RUN: %clang_cc %sysroot %pass_mull_ir_frontend -g %s -o %s.exe
 // RUN: %s.exe | %filecheck %s --dump-input=fail --strict-whitespace --match-full-lines --check-prefix=CHECK
 // RUN: env "cxx_add_to_sub:%s:4:12=1" %s.exe | %filecheck %s --dump-input=fail --strict-whitespace --match-full-lines --check-prefix=CHECK-MUTANT
 

tests-lit/tests/filters/blockaddress/main.c

@@ -14,7 +14,7 @@ int main(int argc, char **argv) {
   return 0;
 }
 
-// RUN: %clang_cc %pass_mull_ir_frontend -g %s -o %s.exe
+// RUN: %clang_cc %sysroot %pass_mull_ir_frontend -g %s -o %s.exe
 // RUN: %s.exe | %filecheck %s --dump-input=fail --strict-whitespace --match-full-lines --check-prefix=CHECK1
 // CHECK1:label1
 // RUN: %s.exe x | %filecheck %s --dump-input=fail --strict-whitespace --match-full-lines --check-prefix=CHECK2

tests-lit/tests/filters/variadic-functions/main.c

@@ -43,7 +43,7 @@ int main() {
   return 0;
 }
 
-// RUN: %clang_cc %pass_mull_ir_frontend -g %s -o %s.exe
+// RUN: %clang_cc %sysroot %pass_mull_ir_frontend -g %s -o %s.exe
 // RUN: %s.exe | %filecheck %s --dump-input=fail --strict-whitespace --match-full-lines
 // CHECK:_est
 // CHECK-NEXT:t_st