Merge remote-tracking branch 'origin/main' into feature_joss_submission

examples/combi_example/TaskExample.hpp

@@ -20,7 +20,7 @@ class TaskExample : public Task {
    */
   TaskExample(const LevelVector& l, const std::vector<BoundaryType>& boundary, real coeff,
               LoadModel* loadModel, real dt, size_t nsteps,
-              std::vector<int> p = std::vector<int>(0),
+              const std::vector<int>& p = std::vector<int>(0),
               FaultCriterion* faultCrit = (new StaticFaults({0, IndexVector(0), IndexVector(0)})))
       : Task(l, boundary, coeff, loadModel, faultCrit),
         dt_(dt),
@@ -31,7 +31,7 @@ class TaskExample : public Task {
         dfg_(NULL) {}
 
   void init(CommunicatorType lcomm,
-            std::vector<IndexVector> decomposition = std::vector<IndexVector>()) {
+            const std::vector<IndexVector>& decomposition = std::vector<IndexVector>()) {
     assert(!initialized_);
     assert(dfg_ == NULL);
 
@@ -108,8 +108,6 @@ class TaskExample : public Task {
   void run(CommunicatorType lcomm) {
     assert(initialized_);
 
-    int lrank = theMPISystem()->getLocalRank();
-
     auto elements = dfg_->getData();
     // TODO if your Example uses another data structure, you need to copy
     // the data from elements to that data structure
@@ -152,9 +150,9 @@ class TaskExample : public Task {
     dfg_->gatherFullGrid(fg, r);
   }
 
-  DistributedFullGrid<CombiDataType>& getDistributedFullGrid(int n = 0) override { return *dfg_; }
+  DistributedFullGrid<CombiDataType>& getDistributedFullGrid(size_t n = 0) override { return *dfg_; }
 
-  const DistributedFullGrid<CombiDataType>& getDistributedFullGrid(int n = 0) const override { return *dfg_; }
+  const DistributedFullGrid<CombiDataType>& getDistributedFullGrid(size_t n = 0) const override { return *dfg_; }
 
   static real myfunction(std::vector<real>& coords, real t) {
     real u = std::cos(M_PI * t);
@@ -183,7 +181,7 @@ class TaskExample : public Task {
 
   // new variables that are set by manager. need to be added to serialize
   real dt_;
-  size_t nsteps_;
+  size_t nsteps_ = 0;
   std::vector<int> p_;
 
   // pure local variables that exist only on the worker processes

examples/combi_example_faults/TaskExample.hpp

@@ -22,7 +22,7 @@ class TaskExample: public Task {
    */
   TaskExample(DimType dim, const LevelVector& l, const std::vector<BoundaryType>& boundary,
               real coeff, LoadModel* loadModel, real dt, size_t nsteps,
-              std::vector<int> p = std::vector<int>(0),
+              const std::vector<int>& p = std::vector<int>(0),
               FaultCriterion* faultCrit = (new StaticFaults({0, IndexVector(0), IndexVector(0)})))
       : Task(l, boundary, coeff, loadModel, faultCrit),
         dt_(dt),
@@ -33,7 +33,7 @@ class TaskExample: public Task {
         combiStep_(0),
         dfg_(NULL) {}
 
-  void init(CommunicatorType lcomm, std::vector<IndexVector> decomposition = std::vector<IndexVector>()) {
+  void init(CommunicatorType lcomm, const std::vector<IndexVector>& decomposition = std::vector<IndexVector>()) {
     assert(!initialized_);
     assert(dfg_ == NULL);
 
@@ -110,9 +110,6 @@ class TaskExample: public Task {
   void run(CommunicatorType lcomm) {
     assert(initialized_);
 
-    int globalRank = theMPISystem()->getGlobalRank();
-    int lrank = theMPISystem()->getLocalRank();
-
     /* pseudo timestepping to demonstrate the behaviour of your typical
      * time-dependent simulation problem. */
     auto elements = dfg_->getData();
@@ -147,11 +144,12 @@ class TaskExample: public Task {
     dfg_->gatherFullGrid(fg, r);
   }
 
-  DistributedFullGrid<CombiDataType>& getDistributedFullGrid(int n) override {
+  DistributedFullGrid<CombiDataType>& getDistributedFullGrid(size_t n) override {
     return *dfg_;
   }
 
-  const DistributedFullGrid<CombiDataType>& getDistributedFullGrid(int n) const override{
+  const DistributedFullGrid<CombiDataType>& getDistributedFullGrid(size_t n) const override{
+    assert(n == 0);
     return *dfg_;
   }
 
@@ -200,7 +198,7 @@ class TaskExample: public Task {
 
   // new variables that are set by manager. need to be added to serialize
   real dt_;
-  size_t nsteps_;
+  size_t nsteps_ = 0;
   size_t stepsTotal_;
   std::vector<int> p_;
 

examples/combi_workers_only/combi_example_worker_only.cpp

@@ -152,7 +152,7 @@ int main(int argc, char** argv) {
       interpolationCoords = broadcastParameters::getCoordinatesFromRankZero(
           interpolationCoordsFile, theMPISystem()->getWorldComm());
 
-      if (interpolationCoords.size() != 1e5) {
+      if (interpolationCoords.size() != static_cast<size_t>(1e5)) {
         sleep(1);
         throw std::runtime_error("not enough interpolation coordinates");
       }

examples/distributed_advection/TaskAdvection.hpp

@@ -33,7 +33,7 @@ class TaskAdvection : public Task {
    */
   TaskAdvection(const LevelVector& l, const std::vector<BoundaryType>& boundary, real coeff,
                 LoadModel* loadModel, real dt, size_t nsteps,
-                std::vector<int> p = std::vector<int>(0),
+                const std::vector<int>& p = std::vector<int>(0),
                 FaultCriterion* faultCrit = (new StaticFaults({0, IndexVector(0), IndexVector(0)})))
       : Task(l, boundary, coeff, loadModel, faultCrit),
         dt_(dt),
@@ -42,17 +42,16 @@ class TaskAdvection : public Task {
         initialized_(false),
         stepsTotal_(0),
         dfg_(nullptr) {
-    for (const auto& b : boundary) {
+    for ([[maybe_unused]] const auto& b : boundary) {
       assert(b == 1);
     }
   }
 
   void init(CommunicatorType lcomm,
-            std::vector<IndexVector> decomposition = std::vector<IndexVector>()) override {
+            const std::vector<IndexVector>& decomposition = std::vector<IndexVector>()) override {
     assert(!initialized_);
     assert(dfg_ == NULL);
 
-    auto lrank = theMPISystem()->getLocalRank();
     DimType dim = this->getDim();
     const LevelVector& l = this->getLevelVector();
 
@@ -105,7 +104,7 @@ class TaskAdvection : public Task {
       // swap at the end of each time step
       auto& u_dot_dphi = *phi_;
       auto const ElementVector = dfg_->getData();
-      for (unsigned int d = 0; d < this->getDim(); ++d) {
+      for (DimType d = 0; d < this->getDim(); ++d) {
         static std::vector<int> subarrayExtents;
         std::vector<CombiDataType> phi_ghost{};
         dfg_->exchangeGhostLayerUpward(d, subarrayExtents, phi_ghost);
@@ -183,7 +182,7 @@ class TaskAdvection : public Task {
     dfg_->gatherFullGrid(fg, r);
   }
 
-  DistributedFullGrid<CombiDataType>& getDistributedFullGrid(int n = 0) override { return *dfg_; }
+  DistributedFullGrid<CombiDataType>& getDistributedFullGrid(size_t n = 0) override { return *dfg_; }
 
   void setZero() override {
     dfg_->setZero();

examples/distributed_third_level/TaskAdvection.hpp

@@ -33,7 +33,7 @@ class TaskAdvection : public Task {
    */
   TaskAdvection(const LevelVector& l, const std::vector<BoundaryType>& boundary, real coeff,
                 LoadModel* loadModel, real dt, size_t nsteps,
-                std::vector<int> p = std::vector<int>(0),
+                const std::vector<int>& p = std::vector<int>(0),
                 FaultCriterion* faultCrit = (new StaticFaults({0, IndexVector(0), IndexVector(0)})))
       : Task(l, boundary, coeff, loadModel, faultCrit),
         dt_(dt),
@@ -42,13 +42,13 @@ class TaskAdvection : public Task {
         initialized_(false),
         stepsTotal_(0),
         dfg_(nullptr) {
-    for (const auto& b : boundary) {
+    for ([[maybe_unused]] const auto& b : boundary) {
       assert(b == 1);
     }
   }
 
   void init(CommunicatorType lcomm,
-            std::vector<IndexVector> decomposition = std::vector<IndexVector>()) override {
+            const std::vector<IndexVector>& decomposition = std::vector<IndexVector>()) override {
     assert(!initialized_);
     assert(dfg_ == NULL);
 
@@ -157,7 +157,7 @@ class TaskAdvection : public Task {
         }
         // iterate the lowest layer and update the values, compensating for the wrong update
         // before
-        assert(numLocalElements / dfg_->getLocalSizes()[d] == phi_ghost.size());
+        assert(static_cast<size_t>(numLocalElements) / dfg_->getLocalSizes()[d] == phi_ghost.size());
         const auto& stride = fullOffsetsInThisDimension;
         const IndexType jump = stride * dfg_->getLocalSizes()[d];
         const IndexType numberOfPolesHigherDimensions = numLocalElements / jump;
@@ -235,7 +235,7 @@ class TaskAdvection : public Task {
     dfg_->gatherFullGrid(fg, r);
   }
 
-  DistributedFullGrid<CombiDataType>& getDistributedFullGrid(int n = 0) override { return *dfg_; }
+  DistributedFullGrid<CombiDataType>& getDistributedFullGrid(size_t n = 0) override { return *dfg_; }
 
   void setZero() override {
     dfg_->setZero();

examples/distributed_third_level/combi_example_worker_only.cpp

@@ -70,7 +70,7 @@ int main(int argc, char** argv) {
     bool evalMCError = cfg.get<bool>("application.mcerror", false);
     uint16_t numberOfFileParts = cfg.get<uint16_t>("io.numberParts", 1);
 
-    theMPISystem()->initOuputGroupComm(numberOfFileParts);
+    theMPISystem()->initOutputGroupComm(numberOfFileParts);
 
     // read in third level parameters if available
     std::string thirdLevelHost, thirdLevelSSHCommand = "";
@@ -166,7 +166,7 @@ int main(int argc, char** argv) {
     interpolationCoords = broadcastParameters::getCoordinatesFromRankZero(
         interpolationCoordsFile, theMPISystem()->getWorldComm());
 
-    if (interpolationCoords.size() != 1e5) {
+    if (interpolationCoords.size() != static_cast<size_t>(1e5)) {
       sleep(1);
       throw std::runtime_error("not enough interpolation coordinates");
     }

examples/distributed_third_level/tools/worker_only_io_test.cpp

@@ -69,7 +69,7 @@ int main(int argc, char** argv) {
     nsteps = cfg.get<size_t>("application.nsteps");
     bool evalMCError = cfg.get<bool>("application.mcerror", false);
     uint16_t numberOfFileParts = cfg.get<uint16_t>("io.numberParts", 1);
-    theMPISystem()->initOuputGroupComm(numberOfFileParts);
+    theMPISystem()->initOutputGroupComm(numberOfFileParts);
 
     // read in third level parameters if available
     std::string thirdLevelHost, thirdLevelSSHCommand = "";
@@ -86,8 +86,7 @@ int main(int argc, char** argv) {
       MIDDLE_PROCESS_EXCLUSIVE_SECTION std::cout << "running in file-based third level mode"
                                                  << std::endl;
     } else {
-      MIDDLE_PROCESS_EXCLUSIVE_SECTION std::cout << "running in file-based local mode"
-                                                 << std::endl;
+      MIDDLE_PROCESS_EXCLUSIVE_SECTION std::cout << "running in file-based local mode" << std::endl;
     }
 
     // periodic boundary conditions
@@ -239,13 +238,12 @@ int main(int argc, char** argv) {
         readSparseGridFile =
             "dsg_" + std::to_string((systemNumber + 1) % 2) + "_step" + std::to_string(i);
         std::string readSparseGridFileToken = readSparseGridFile + "_token.txt";
-        OUTPUT_GROUP_EXCLUSIVE_SECTION {
-        }
+        OUTPUT_GROUP_EXCLUSIVE_SECTION {}
 
       } else {
         readSparseGridFile = writeSparseGridFile;
-	OUTPUT_GROUP_EXCLUSIVE_SECTION {
-	  worker.waitForTokenFile(writeSparseGridFileToken);
+        OUTPUT_GROUP_EXCLUSIVE_SECTION {
+          worker.waitForTokenFile(writeSparseGridFileToken);
           Stats::startEvent("read SG");
           int numRead = worker.readReduce(readSparseGridFile, true);
           Stats::stopEvent("read SG");

examples/gene_distributed/src/GeneTask.cpp

@@ -163,7 +163,7 @@ void GeneTask::decideToKill(){ //toDo check if combiStep should be included in t
 /**
  * This routine initializes GeneTask; currently it only sets a bool value.
  */
-void GeneTask::init(CommunicatorType lcomm, std::vector<IndexVector> decomposition){
+void GeneTask::init(CommunicatorType lcomm, const std::vector<IndexVector>& decomposition){
 //  if( dfg_ == NULL ){
 //      dfg_ = new OwningDistributedFullGrid<CombiDataType>( dim_, l_, lcomm,
 //          this->getBoundary(), p_, false);
@@ -247,7 +247,7 @@ void GeneTask::getFullGrid( FullGrid<CombiDataType>& fg, RankType lroot,
 /**
  * This routine returns the local part of the fullgrid
  */
-DistributedFullGrid<complex>& GeneTask::getDistributedFullGrid(int specie){
+DistributedFullGrid<complex>& GeneTask::getDistributedFullGrid(size_t specie) override {
   return *dfgVector_[specie];
 }
 

examples/gene_distributed/src/GeneTask.hpp

@@ -31,7 +31,7 @@ class GeneTask : public combigrid::Task {
  public:
   GeneTask(DimType dim, const LevelVector& l, const std::vector<BoundaryType>& boundary, real coeff,
            LoadModel* loadModel, std::string& path, real dt, real combitime, size_t nsteps,
-           real shat, real lx, int ky0_ind, std::vector<int> p = std::vector<int>(0),
+           real shat, real lx, int ky0_ind, const std::vector<int>& p = std::vector<int>(0),
            FaultCriterion* faultCrit = (new StaticFaults({0, IndexVector(0), IndexVector(0)})),
            IndexType numSpecies = 1, bool GENE_Global = false, bool GENE_Linear = true,
            size_t checkpointFrequency = 1, size_t offsetForDiagnostics = 0);
@@ -57,20 +57,21 @@ class GeneTask : public combigrid::Task {
    */
   void changeDir(CommunicatorType lcomm);
 
-  //void init(CommunicatorType lcomm);
+  // void init(CommunicatorType lcomm);
 
   /**
    * This method initializes the task
    * lcomm is the local communicator of the process group.
    * decomposition is the spatial decomposition of the component grid
    */
-  void init(CommunicatorType lcomm, std::vector<IndexVector> decomposition = std::vector<IndexVector>());
+  void init(CommunicatorType lcomm,
+            const std::vector<IndexVector>& decomposition = std::vector<IndexVector>());
 
   /**
    * This method returns the decomposition of the grid of the specified species
    */
-  std::vector<IndexVector> getDecomposition(int species){
-      return dfgVector_[species]->getDecomposition();
+  std::vector<IndexVector> getDecomposition(int species) {
+    return dfgVector_[species]->getDecomposition();
   }
 
   /**
@@ -108,7 +109,7 @@ class GeneTask : public combigrid::Task {
   /**
    * Returns the distributed full grid of the specified specie
    */
-  DistributedFullGrid<CombiDataType>& getDistributedFullGrid(int specie);
+  DistributedFullGrid<CombiDataType>& getDistributedFullGrid(size_t specie);
 
   /*
    * Convert fg to GeneGrid and scatter over processes of pgroup. The fullgrid

examples/gene_distributed/tools/testBoundaryZ.cpp

@@ -19,7 +19,7 @@
 using namespace combigrid;
 
 
-void testBoundaryZ(FullGrid<CombiDataType>& fg, std::string filePrefix ){
+void testBoundaryZ(FullGrid<CombiDataType>& fg, const std::string& filePrefix ){
   const double tol = 1e-15;
 
   MultiArrayRef6 fgData = createMultiArrayRef<CombiDataType,6>( fg );

examples/gene_distributed_linear/src/GeneTask.cpp

@@ -184,7 +184,7 @@ void GeneTask::decideToKill(){ //toDo check if combiStep should be included in t
 /**
  * This routine initializes GeneTask; currently it only sets a bool value.
  */
-void GeneTask::init(CommunicatorType lcomm, std::vector<IndexVector> decomposition){
+void GeneTask::init(CommunicatorType lcomm, const std::vector<IndexVector>& decomposition){
 //  if( dfg_ == NULL ){
 //      dfg_ = new DistributedFullGrid<CombiDataType>( dim_, l_, lcomm,
 //          this->getBoundary(), p_, false);
@@ -279,7 +279,7 @@ void GeneTask::getFullGrid( FullGrid<CombiDataType>& fg, RankType lroot,
 /**
  * This routine returns the local part of the fullgrid
  */
-DistributedFullGrid<complex>& GeneTask::getDistributedFullGrid(int specie){
+DistributedFullGrid<complex>& GeneTask::getDistributedFullGrid(size_t specie) override {
   return *dfgVector_[specie];
 }
 

examples/gene_distributed_linear/src/GeneTask.hpp

@@ -32,7 +32,7 @@ class GeneTask : public combigrid::Task {
  public:
   GeneTask(DimType dim, const LevelVector& l, const std::vector<BoundaryType>& boundary, real coeff,
            LoadModel* loadModel, std::string& path, real dt, real combitime, size_t nsteps,
-           real shat, real lx, int ky0_ind, std::vector<int> p = std::vector<int>(0),
+           real shat, real lx, int ky0_ind, const std::vector<int>& p = std::vector<int>(0),
            FaultCriterion* faultCrit = (new StaticFaults({0, IndexVector(0), IndexVector(0)})),
            IndexType numSpecies = 1, bool GENE_Global = false, bool GENE_Linear = true);
 
@@ -51,20 +51,21 @@ class GeneTask : public combigrid::Task {
    */
   void changeDir(CommunicatorType lcomm);
 
-  //void init(CommunicatorType lcomm);
+  // void init(CommunicatorType lcomm);
 
   /**
    * This method initializes the task
    * lcomm is the local communicator of the process group.
    * decomposition is the spatial decomposition of the component grid
    */
-  void init(CommunicatorType lcomm, std::vector<IndexVector> decomposition = std::vector<IndexVector>());
+  void init(CommunicatorType lcomm,
+            const std::vector<IndexVector>& decomposition = std::vector<IndexVector>());
 
   /**
    * This method returns the decomposition of the grid of the specified species
    */
-  std::vector<IndexVector> getDecomposition(int species){
-      return dfgVector_[species]->getDecomposition();
+  std::vector<IndexVector> getDecomposition(int species) {
+    return dfgVector_[species]->getDecomposition();
   }
 
   /**
@@ -102,7 +103,7 @@ class GeneTask : public combigrid::Task {
   /**
    * Returns the distributed full grid of the specified specie
    */
-  DistributedFullGrid<CombiDataType>& getDistributedFullGrid(int specie);
+  DistributedFullGrid<CombiDataType>& getDistributedFullGrid(size_t specie);
 
   /*
    * Convert fg to GeneGrid and scatter over processes of pgroup. The fullgrid