initial templator

src/templates_hdf5/templator_hdf5.org

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+
+#+Title: Templator for HDF5 backend
+
+** Constant file prefixes (not used by generator) for HDF5          :noxport:  
+
+  #+NAME:header
+  #+begin_src c 
+/* This file was generated from the org-mode file.
+   To generate it, open templator_hdf5.org file in Emacs and execute
+   M-x org-babel-tangle
+*/
+
+  #+end_src
+
+  #+begin_src c :tangle prefix_hdf5.h :noweb yes
+<<header>>
+#ifndef _TREXIO_HDF5_H
+#define _TREXIO_HDF5_H
+
+#include "trexio.h"
+#include "trexio_s.h"
+#include <stdint.h>
+#include <stdio.h>
+#include <stdlib.h>
+#include <string.h>
+#include <assert.h>
+#include <sys/stat.h>
+
+#include "hdf5.h"
+#include "hdf5_hl.h" // needed for high-level APIs like H5LT, requires additional linking in Makefile
+
+  #+end_src
+  
+  #+begin_src c :tangle prefix_hdf5.c :noweb yes
+<<header>>
+#include "trexio_hdf5.h"
+
+  #+end_src
+
+  
+** Template for HDF5 definitions 
+
+#+begin_src c :tangle def_hdf5.c
+  #define $GROUP$_GROUP_NAME          "$group$"
+  #define $GROUP_NUM$_NAME            "$group_num$"
+  #define $GROUP$_$GROUP_DSET$_NAME   "$group_dset$"
+  
+#+end_src
+
+
+** Template for HDF5 structures
+
+  #+begin_src c :tangle struct_hdf5.h
+
+typedef struct trexio_hdf5_s {
+  trexio_t     parent ;
+  hid_t      file_id;
+  hid_t      $group$_group;
+  const char* file_name;
+} trexio_hdf5_t;
+
+  #+end_src
+  
+
+** Template for HDF5 init/deinit  
+
+  #+begin_src c :tangle basic_hdf5.c
+
+trexio_exit_code trexio_hdf5_init(trexio_t* file) {
+
+  trexio_hdf5_t* f = (trexio_hdf5_t*) file;
+
+ /* If file doesn't exist, create it */
+  int f_exists = 0;
+  struct stat st;
+  
+  if (stat(file->file_name, &st) == 0) f_exists = 1;
+  
+  if (f_exists == 1) {
+
+    switch (file->mode) {
+    case 'r': 
+      // reading the existing file -> open as RDONLY
+      f->file_id = H5Fopen(file->file_name, H5F_ACC_RDONLY, H5P_DEFAULT);
+      break;
+    case 'a': 
+      // appending the existing file -> open as RDWR
+      f->file_id = H5Fopen(file->file_name, H5F_ACC_RDWR, H5P_DEFAULT);
+      break;
+    case 'w': 
+      // writing the existing file -> overwrite it (_TRUNC) [_EXCL | H5F_ACC_DEBUG as an alternative]
+      f->file_id = H5Fcreate(file->file_name, H5F_ACC_TRUNC, H5P_DEFAULT, H5P_DEFAULT);
+      break;
+    }  
+
+  } else {
+
+    switch (file->mode) {
+    case 'r': 
+    case 'a': 
+      // reading or appending non-existing file -> error
+      return TREXIO_FAILURE;
+    case 'w': 
+      // writing non-existing file -> create it
+      f->file_id = H5Fcreate(file->file_name, H5F_ACC_EXCL, H5P_DEFAULT, H5P_DEFAULT);
+      break;
+    }  
+
+  }  
+
+ /* Create or open groups in the hdf5 file assuming that they exist if file exists */    
+  switch (file->mode) {
+    // the switch for 'r'/'a' is reached only if file exists
+    case 'r':
+    case 'a': 
+      f->$group$_group = H5Gopen(f->file_id, $GROUP$_GROUP_NAME, H5P_DEFAULT);
+      //f->electron_group = H5Gopen(f->file_id, ELECTRON_GROUP_NAME, H5P_DEFAULT); 
+      break;
+    case 'w':
+      f->$group$_group = H5Gcreate(f->file_id, $GROUP$_GROUP_NAME, H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT);
+      //f->electron_group = H5Gcreate(f->file_id, ELECTRON_GROUP_NAME, H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT);
+      break;
+  }
+  assert (f->$group$_group > 0L);
+  //assert (f->electron_group > 0L);
+
+  return TREXIO_SUCCESS;
+}
+
+trexio_exit_code trexio_hdf5_finalize(trexio_t* file) {
+
+  trexio_hdf5_t* f = (trexio_hdf5_t*) file;
+
+  H5Gclose(f->$group$_group);
+  f->$group$_group = 0;
+
+/*
+  H5Gclose(f->electron_group);
+  f->electron_group = 0; 
+*/
+
+  H5Fclose(f->file_id);
+  f->file_id = 0;
+
+  return TREXIO_SUCCESS;
+}
+
+  #+end_src
+
+
+
+** Template for HDF5 read/write a number
+
+  #+begin_src c :tangle rw_num_hdf5.h
+trexio_exit_code trexio_hdf5_read_$group_num$(const trexio_t* file, uint64_t* num);
+trexio_exit_code trexio_hdf5_write_$group_num$(const trexio_t* file, const uint64_t num);
+  #+end_src
+
+   
+  #+begin_src c :tangle rw_num_hdf5.c
+trexio_exit_code trexio_hdf5_read_$group_num$const trexio_t* file, uint64_t* num) {
+
+  assert (file != NULL);
+  assert (num  != NULL);
+  
+  trexio_hdf5_t* f = (trexio_hdf5_t*) file;
+ /* Quit if the dimensioning attribute is missing in the file */
+  if (H5Aexists(f->$group$_group, $GROUP_NUM$_NAME) == 0) return TREXIO_FAILURE;
+
+ /* Read the nucleus_num attribute of nucleus group */
+  hid_t num_id = H5Aopen(f->$group$_group, $GROUP_NUM$_NAME, H5P_DEFAULT);
+  if (num_id <= 0) return TREXIO_INVALID_ID;
+
+  herr_t status = H5Aread(num_id, H5T_NATIVE_ULLONG, num);
+  if (status < 0) return TREXIO_FAILURE;
+
+  return TREXIO_SUCCESS;
+}
+
+ 
+trexio_exit_code trexio_hdf5_write_$group_num$(const trexio_t* file, const uint64_t num) {
+
+  assert (file != NULL);
+  assert (num > 0L);
+ 
+  trexio_hdf5_t* f = (trexio_hdf5_t*) file;
+  hid_t num_id;
+  herr_t status;
+ /* Write the dimensioning variables */
+  hid_t dtype = H5Tcopy(H5T_NATIVE_ULLONG);
+
+  if (H5Aexists(f->$group$_group, $GROUP_NUM$_NAME) == 0) {
+   
+    hid_t dspace = H5Screate(H5S_SCALAR);
+
+    num_id = H5Acreate(f->$group$_group, $GROUP_NUM$_NAME, dtype, dspace,
+                     H5P_DEFAULT, H5P_DEFAULT);
+    if (num_id <= 0) return TREXIO_INVALID_ID;
+  
+    status = H5Awrite(num_id, dtype, &(num));
+    if (status < 0) return TREXIO_FAILURE;
+
+    H5Sclose(dspace);
+    
+  } else {
+
+    uint64_t infile_num;
+    trexio_exit_code rc = trexio_hdf5_read_$group_num$(file, &(infile_num));
+    if (rc != TREXIO_SUCCESS) return rc;
+
+    if (infile_num != num) {
+
+      if (infile_num != 0) {
+	printf("%ld -> %ld %s \n", num, infile_num, 
+	       "This variable already exists. Overwriting it is not supported");
+        H5Tclose(dtype);
+    	return TREXIO_FAILURE;
+
+      } else {
+    
+        num_id = H5Aopen(f->$group$_group, $GROUP_NUM$_NAME, H5P_DEFAULT);
+        if (num_id <= 0) return TREXIO_INVALID_ID;
+       
+        status = H5Awrite(num_id, dtype, &(num));
+        if (status < 0) return TREXIO_FAILURE;
+
+      }
+    }
+  }
+
+  H5Aclose(num_id);
+  H5Tclose(dtype);
+  return TREXIO_SUCCESS;
+  
+}
+    #+end_src
+
+
+** Template for HDF5 read/write a dataset
+
+    
+   #+begin_src c :tangle rw_dset_hdf5.h
+trexio_exit_code trexio_hdf5_read_$group$_$group_dset$(const trexio_t* file, double* $group_dset$, const uint32_t rank, const uint64_t* dims);
+trexio_exit_code trexio_hdf5_write_$group$_$group_dset$(const trexio_t* file, const double* $group_dset$, const uint32_t rank, const uint64_t* dims);
+  #+end_src
+
+   #+begin_src c :tangle rw_dset_hdf5.c
+trexio_exit_code trexio_hdf5_read_$group$_$group_dset$(const trexio_t* file, $group_dset_dtype$* $group_dset$, const uint32_t rank, const uint64_t* dims) {
+
+  assert (file != NULL);
+  assert ($group_dset$ != NULL);
+  
+  trexio_hdf5_t* f = (trexio_hdf5_t*) file;
+  
+  herr_t status;
+  int rrank;
+  // get the rank of the dataset in a file
+  status = H5LTget_dataset_ndims (f->$group$_group, $GROUP$_$GROUP_DSET$_NAME, 
+                                  &rrank);
+
+  if (status < 0) return TREXIO_FAILURE;
+
+  if (rrank != (int) rank) return TREXIO_INVALID_ARG_3;
+
+  // open the dataset to get its dimensions  
+  hid_t dset_id = H5Dopen(f->$group$_group, $GROUP$_$GROUP_DSET$_NAME,  H5P_DEFAULT);
+  if (dset_id <= 0) return TREXIO_INVALID_ID; 
+
+  // allocate space for the dimensions to be read
+  hsize_t* ddims = (hsize_t*) calloc( (int) rank, sizeof(hsize_t));
+  if (ddims == NULL) return TREXIO_FAILURE;
+
+  // read dimensions from the existing dataset
+  status = H5LDget_dset_dims(dset_id, ddims);
+
+  H5Dclose(dset_id);
+  if (status < 0) {
+    free(ddims);
+    return TREXIO_FAILURE;
+  }
+
+  for (uint32_t i=0; i<rank; i++){
+     if (ddims[i] != dims[i]) {
+       free(ddims);
+       return TREXIO_INVALID_ARG_4;
+     }
+  }
+  free(ddims);
+
+ /* High-level H5LT API. No need to deal with dataspaces and datatypes */
+  status = H5LTread_dataset_double(f->$group$_group,
+                                    $GROUP$_$GROUP_DSET$_NAME,
+                                    $group_dset$);				   
+  if (status < 0) return TREXIO_FAILURE;
+
+  return TREXIO_SUCCESS;
+}
+
+
+trexio_exit_code trexio_hdf5_write_$group$_$group_dset$(const trexio_t* file, const $group_dset_dtype$* $group_dset$, const uint32_t rank, const uint64_t* dims) {
+
+  assert (file != NULL);
+  assert ($group_dset$ != NULL);
+    
+  uint64_t $group_dset_dim$;
+  trexio_exit_code rc = trexio_hdf5_read_$group_dset_dim$(file, &($group_dset_dim$));
+  if (rc != TREXIO_SUCCESS) return rc;
+  if ($group_dset_dim$ <= 0L) return TREXIO_INVALID_NUM;
+
+  trexio_hdf5_t* f = (trexio_hdf5_t*) file; 
+
+  herr_t status;
+  if ( H5LTfind_dataset(f->$group$_group, $GROUP$_$GROUP_DSET$_NAME) != 1) { 
+    
+    status = H5LTmake_dataset_$group_dset_dtype$ (f->$group$_group, $GROUP$_$GROUP_DSET$_NAME, 
+                                      (int) rank, (hsize_t*) dims, $group_dset$);
+    if (status < 0) return TREXIO_FAILURE;
+
+  } else {   
+
+    hid_t dset_id = H5Dopen(f->$group$_group, $GROUP$_$GROUP_DSET$_NAME, H5P_DEFAULT);
+    if (dset_id <= 0) return TREXIO_INVALID_ID;
+    
+    status = H5Dwrite(dset_id, H5T_NATIVE_DOUBLE, H5S_ALL, H5S_ALL, H5P_DEFAULT, $group_dset$);
+    
+    H5Dclose(dset_id);
+    if (status < 0) return TREXIO_FAILURE;
+
+  }
+  
+  return TREXIO_SUCCESS;
+}
+
+    #+end_src
+  #+end_src
+
+
+** Constant file suffixes (not used by generator) for HDF5          :noxport:  
+
+  #+begin_src c :tangle suffix_hdf5.h
+
+#endif
+  #+end_src