support for specifying a restart directory

src/io.cpp

@@ -35,6 +35,8 @@
 #include "io.hpp"
 
 #include <hdf5.h>
+#include <sys/stat.h>
+#include <sys/types.h>
 
 #include "M2ulPhyS.hpp"
 #include "utils.hpp"
@@ -268,7 +270,8 @@ void M2ulPhyS::restart_files_hdf5(string mode, string inputFileName) {
   return;
 }
 
-void partitioning_file_hdf5(std::string mode, MPI_Groups *groupsMPI, int nelemGlobal, Array<int> &partitioning) {
+void partitioning_file_hdf5(std::string mode, MPI_Groups *groupsMPI, int nelemGlobal, Array<int> &partitioning,
+                            std::string pathName) {
   MPI_Comm TPSCommWorld = groupsMPI->getTPSCommWorld();
   const bool rank0 = groupsMPI->isWorldRoot();
   const int nprocs = groupsMPI->getTPSWorldSize();
@@ -281,8 +284,10 @@ void partitioning_file_hdf5(std::string mode, MPI_Groups *groupsMPI, int nelemGl
   // hid_t file, dataspace, data_soln;
   hid_t file = -1, dataspace;
   herr_t status;
-  std::string fileName("partition");
-  fileName += "." + std::to_string(nprocs) + "p.h5";
+  std::string fileNameEnd("partition");
+  fileNameEnd += "." + std::to_string(nprocs) + "p.h5";
+  std::string fileName;
+  fileName = pathName + fileNameEnd;
 
   assert((mode == "read") || (mode == "write"));
 
@@ -402,7 +407,7 @@ void read_variable_data_hdf5(hid_t file, string varName, size_t index, double *d
   H5Dclose(data_soln);
 }
 
-IOOptions::IOOptions() : output_dir_("output"), restart_mode_("standard") {}
+IOOptions::IOOptions() : output_dir_("output"), restart_dir_("./"), restart_mode_("standard") {}
 
 void IOOptions::read(TPS::Tps *tps, std::string prefix) {
   std::string basename;
@@ -417,8 +422,12 @@ void IOOptions::read(TPS::Tps *tps, std::string prefix) {
   tps->getInput((basename + "/exitCheckFreq").c_str(), exit_check_frequency_, 500);
   assert(exit_check_frequency_ > 0);
 
+  tps->getInput((basename + "/restartBase").c_str(), restart_dir_, std::string("./"));
   tps->getInput((basename + "/restartMode").c_str(), restart_mode_, std::string("standard"));
   setRestartFlags();
+
+  int status = mkdir(restart_dir_.c_str(), S_IRWXU | S_IRWXG | S_IROTH | S_IXOTH);
+  if (status == 0) std::cout << "created restartBase directory: " << restart_dir_ << endl;
 }
 
 void IOOptions::setRestartFlags() {

src/io.hpp

@@ -66,8 +66,8 @@ class IOOptions {
 
   int exit_check_frequency_ = 500;
 
+  std::string restart_dir_;
   std::string restart_mode_;
-
   bool restart_variable_order_ = false;
   bool restart_serial_read_ = false;
   bool restart_serial_write_ = false;
@@ -362,5 +362,6 @@ void write_variable_data_hdf5(hid_t group, std::string varName, hid_t dataspace,
  * @todo Refactor this function to make it more generic and fit better
  * into the IODataOrganizer paradigm.
  */
-void partitioning_file_hdf5(std::string mode, MPI_Groups *groupsMPI, int nelemGlobal, mfem::Array<int> &partitioning);
+void partitioning_file_hdf5(std::string mode, MPI_Groups *groupsMPI, int nelemGlobal, mfem::Array<int> &partitioning,
+                            std::string fileName = "./");
 #endif  // IO_HPP_

src/loMachIO.cpp

@@ -181,7 +181,8 @@ void LoMachSolver::restart_files_hdf5(string mode, string inputFileName) {
     }
     serialName = inputFileName;
   } else {
-    serialName = "restart_";
+    serialName = loMach_opts_.io_opts_.restart_dir_;
+    serialName.append("/restart_");
     serialName.append(loMach_opts_.io_opts_.output_dir_);
     serialName.append(".sol.h5");
   }

src/mesh_base.cpp

@@ -174,13 +174,17 @@ void MeshBase::initializeMesh() {
     // nelemGlobal_ = mesh->GetNE();
     if (rank0_) grvy_printf(ginfo, "Total # of mesh elements = %i\n", nelemGlobal_);
 
+    string restartDir;
+    restartDir = loMach_opts_->io_opts_.restart_dir_;
+    restartDir += "/";
+
     if (nprocs_ > 1) {
       if (loMach_opts_->io_opts_.restart_serial_read_) {
         assert(serial_mesh_->Conforming());
         partitioning_ = Array<int>(serial_mesh_->GeneratePartitioning(nprocs_, defaultPartMethod), nelemGlobal_);
-        partitioning_file_hdf5("write", groupsMPI, nelemGlobal_, partitioning_);
+        partitioning_file_hdf5("write", groupsMPI, nelemGlobal_, partitioning_, restartDir);
       } else {
-        partitioning_file_hdf5("read", groupsMPI, nelemGlobal_, partitioning_);
+        partitioning_file_hdf5("read", groupsMPI, nelemGlobal_, partitioning_, restartDir);
       }
     }
 
@@ -203,12 +207,16 @@ void MeshBase::initializeMesh() {
       serial_mesh_->UniformRefinement();
     }
 
+    string restartDir;
+    restartDir = loMach_opts_->io_opts_.restart_dir_;
+    restartDir += "/";
+
     // generate partitioning file (we assume conforming meshes)
     nelemGlobal_ = serial_mesh_->GetNE();
     if (nprocs_ > 1) {
       assert(serial_mesh_->Conforming());
       partitioning_ = Array<int>(serial_mesh_->GeneratePartitioning(nprocs_, defaultPartMethod), nelemGlobal_);
-      if (rank0_) partitioning_file_hdf5("write", groupsMPI, nelemGlobal_, partitioning_);
+      if (rank0_) partitioning_file_hdf5("write", groupsMPI, nelemGlobal_, partitioning_, restartDir);
     }
   }
 

src/utils.cpp

@@ -1156,6 +1156,13 @@ void Orthogonalize(Vector &v, MPI_Comm comm) {
   v -= global_sum / static_cast<double>(global_size);
 }
 
+bool copyFile(const char *SRC, const char *DEST) {
+  std::ifstream src(SRC, std::ios::binary);
+  std::ofstream dest(DEST, std::ios::binary);
+  dest << src.rdbuf();
+  return src && dest;
+}
+
 namespace mfem {
 GradientVectorGridFunctionCoefficient::GradientVectorGridFunctionCoefficient(const GridFunction *gf)
     : MatrixCoefficient((gf) ? gf->VectorDim() : 0) {

src/utils.hpp

@@ -174,6 +174,8 @@ void scalarGrad3D(ParGridFunction &u, ParGridFunction &gu);
 void vectorGrad3DV(FiniteElementSpace *fes, Vector u, Vector *gu, Vector *gv, Vector *gw);
 void scalarGrad3DV(FiniteElementSpace *fes, FiniteElementSpace *vfes, Vector u, Vector *gu);
 
+bool copyFile(const char *SRC, const char *DEST);
+
 /// Eliminate essential BCs in an Operator and apply to RHS.
 /// rename this to something sensible "ApplyEssentialBC" or something
 void EliminateRHS(Operator &A, ConstrainedOperator &constrainedA, const Array<int> &ess_tdof_list, Vector &x, Vector &b,