Start writing more HDF5 interface functions in C++

src/hdf5_interface.h

@@ -1,44 +1,153 @@
 #ifndef HDF5_INTERFACE_H
 #define HDF5_INTERFACE_H
 
-#include <array>
-#include <string.h>
+#include "error.h"
 
 #include "hdf5.h"
+#include "hdf5_hl.h"
 
-#include "error.h"
+#include <array>
+#include <string>
+#include <sstream>
 
 
 namespace openmc {
 
+bool
+using_mpio_device(hid_t obj_id) {
+  // Determine file that this object is part of
+  hid_t file_id = H5Iget_file_id(obj_id);
+
+  // Get file access property list
+  hid_t fapl_id = H5Fget_access_plist(file_id);
+
+  // Get low-level driver identifier
+  hid_t driver = H5Pget_driver(fapl_id);
+
+  // Free resources
+  H5Pclose(fapl_id);
+  H5Fclose(file_id);
+
+  return driver == H5FD_MPIO;
+}
+
 
 hid_t
 create_group(hid_t parent_id, char const *name)
 {
   hid_t out = H5Gcreate(parent_id, name, H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT);
   if (out < 0) {
-    std::string err_msg{"Failed to create HDF5 group \""};
-    err_msg += name;
-    err_msg += "\"";
+    std::stringstream err_msg;
+    err_msg << "Failed to create HDF5 group \"" << name << "\"";
     fatal_error(err_msg);
   }
   return out;
 }
 
-
 hid_t
 create_group(hid_t parent_id, const std::string &name)
 {
   return create_group(parent_id, name.c_str());
 }
 
+void
+close_dataset(hid_t dataset_id)
+{
+  if (H5Dclose(dataset_id) < 0) fatal_error("Failed to close dataset");
+}
+
 
 void
 close_group(hid_t group_id)
 {
-  herr_t err = H5Gclose(group_id);
-  if (err < 0) {
-    fatal_error("Failed to close HDF5 group");
+  if (H5Gclose(group_id) < 0) fatal_error("Failed to close group");
+}
+
+
+hid_t
+file_open(const char* filename, char mode, bool parallel=false)
+{
+  bool create;
+  unsigned int flags;
+  switch (mode) {
+  case 'r':
+  case 'a':
+    create = false;
+    flags = (mode == 'r' ? H5F_ACC_RDONLY : H5F_ACC_RDWR);
+    break;
+  case 'w':
+  case 'x':
+    create = true;
+    flags = (mode == 'x' ? H5F_ACC_EXCL : H5F_ACC_TRUNC);
+    break;
+  }
+
+  hid_t plist;
+  if (parallel) {
+    // Setup file access property list with parallel I/O access
+    plist = H5Pcreate(H5P_FILE_ACCESS);
+#ifdef PHDF5
+    H5Pset_fapl_mpio(plist, mpi_intracomm, MPI_INFO_NULL);
+#endif
+  } else {
+    plist = H5P_DEFAULT;
+  }
+
+  // Open the file collectively
+  hid_t file_id;
+  if (create) {
+    file_id = H5Fopen(filename, flags, plist);
+  } else {
+    file_id = H5Fcreate(filename, flags, H5P_DEFAULT, plist);
+  }
+
+  // Close the property list
+  if (parallel) H5Pclose(plist);
+
+  return file_id;
+}
+
+hid_t
+file_open(const std::string& filename, char mode, bool parallel=false) {
+  file_open(filename.c_str(), mode, parallel);
+}
+
+void file_close(hid_t file_id) {
+  H5Fclose(file_id);
+}
+
+bool
+object_exists(hid_t object_id, const char* name) {
+  htri_t out = H5LTpath_valid(object_id, name, true);
+  if (out < 0) {
+    std::stringstream err_msg;
+    err_msg << "Failed to check if object \"" << name << "\" exists.";
+    fatal_error(err_msg);
+  }
+  return (out > 0);
+}
+
+
+hid_t
+open_dataset(hid_t group_id, const char* name){
+  if (object_exists(group_id, name)) {
+    return H5Dopen(group_id, name, H5P_DEFAULT);
+  } else {
+    std::stringstream err_msg;
+    err_msg << "Group \"" << name << "\" does not exist";
+    fatal_error(err_msg);
+  }
+}
+
+
+hid_t
+open_group(hid_t group_id, const char* name){
+  if (object_exists(group_id, name)) {
+    return H5Gopen(group_id, name, H5P_DEFAULT);
+  } else {
+    std::stringstream err_msg;
+    err_msg << "Group \"" << name << "\" does not exist";
+    fatal_error(err_msg);
   }
 }
 
@@ -60,6 +169,35 @@ write_double_1D(hid_t group_id, char const *name,
   H5Dclose(dataset);
 }
 
+void
+write_double(hid_t group_id, int ndim, const hsize_t* dims, const char* name,
+             double* buffer, bool indep) {
+  hid_t dspace = H5Screate_simple(ndim, dims, nullptr);
+  hid_t dset = H5Dcreate(group_id, name, H5T_NATIVE_DOUBLE, dspace,
+                         H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT);
+
+  if (using_mpio_device(group_id)) {
+#ifdef PHDF5
+    // Set up collective vs independent I/O
+    auto data_xfer_mode {indep ? H5FD_MPIO_INDEPENDENT : H5FD_MPIO_COLLECTIVE};
+
+    // Create dataset transfer property list
+    hid_t plist = H5Pcreate(H5P_DATASET_XFER);
+    H5Pset_dxpl_mpio(plist, data_xfer_mode);
+
+    // Write data
+    H5Dwrite(dset, H5T_NATIVE_DOUBLE, H5S_ALL, H5S_ALL, plist, buffer);
+    H5Pclose(plist);
+#endif
+  } else {
+    H5Dwrite(dset, H5T_NATIVE_DOUBLE, H5S_ALL, H5S_ALL, H5P_DEFAULT, buffer);
+  }
+
+  // Free resources
+  H5Dclose(dset);
+  H5Sclose(dspace);
+}
+
 
 void
 write_string(hid_t group_id, char const *name, char const *buffer)