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https://github.com/TREX-CoE/trexio.git
synced 2024-08-25 06:31:43 +02:00
add functions to read the number of stored sparse elements
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@ -188,10 +188,16 @@ __trexio_path__ = None
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| ~TREXIO_DSET_MISSING~ | 25 | 'Dataset does not exist in the file' |
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| ~TREXIO_BACK_END_MISSING~ | 26 | 'Requested back end is disabled' |
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| ~TREXIO_INVALID_STR_LEN~ | 30 | 'Invalid max_str_len' |
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| ~TREXIO_INT_SIZE_OVERFLOW~ | 31 | 'Possible integer overflow' |
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# We need to force Emacs not to indent the Python code:
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# -*- org-src-preserve-indentation: t
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*IMPORTANT!*
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The code below has to be executed within Emacs each time
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a new error code is added to the table above. Otherwise, the codes
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and the corresponding message are not propagated to the source code.
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#+begin_src python :var table=table-exit-codes :results drawer
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""" This script generates the C and Fortran constants for the error
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codes from the org-mode table.
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@ -257,6 +263,7 @@ return '\n'.join(result)
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#define TREXIO_DSET_MISSING ((trexio_exit_code) 25)
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#define TREXIO_BACK_END_MISSING ((trexio_exit_code) 26)
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#define TREXIO_INVALID_STR_LEN ((trexio_exit_code) 30)
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#define TREXIO_INT_SIZE_OVERFLOW ((trexio_exit_code) 31)
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#+end_src
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#+begin_src f90 :tangle prefix_fortran.f90 :exports none
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@ -289,6 +296,7 @@ return '\n'.join(result)
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integer(trexio_exit_code), parameter :: TREXIO_DSET_MISSING = 25
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integer(trexio_exit_code), parameter :: TREXIO_BACK_END_MISSING = 26
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integer(trexio_exit_code), parameter :: TREXIO_INVALID_STR_LEN = 30
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integer(trexio_exit_code), parameter :: TREXIO_INT_SIZE_OVERFLOW = 31
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#+end_src
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#+begin_src python :tangle prefix_python.py :exports none
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@ -322,6 +330,7 @@ return '\n'.join(result)
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TREXIO_DSET_MISSING = 25
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TREXIO_BACK_END_MISSING = 26
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TREXIO_INVALID_STR_LEN = 30
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TREXIO_INT_SIZE_OVERFLOW = 31
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#+end_src
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:END:
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@ -342,7 +351,10 @@ const char* trexio_string_of_error(const trexio_exit_code error);
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void trexio_string_of_error_f(const trexio_exit_code error, char result[<<MAX_STRING_LENGTH()>>]);
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#+end_src
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The text strings are extracted from the previous table.
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*IMPORTANT!*
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The code below has to be executed within Emacs each time
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a new error code is added to the table above. Otherwise, the codes
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and the corresponding message are not propagated to the source code.
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#+NAME:cases
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#+begin_src python :var table=table-exit-codes :exports none :noweb yes
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@ -442,9 +454,15 @@ return '\n'.join(result)
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case TREXIO_DSET_MISSING:
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return "Dataset does not exist in the file";
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break;
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case TREXIO_BACK_END_MISSING:
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return "Requested back end is disabled";
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break;
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case TREXIO_INVALID_STR_LEN:
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return "Invalid max_str_len";
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break;
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case TREXIO_INT_SIZE_OVERFLOW:
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return "Possible integer overflow";
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break;
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#+end_example
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**** C source code
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@ -2397,6 +2415,7 @@ def has_$group_dset$(trexio_file) -> bool:
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#+begin_src c :tangle hrw_dset_sparse_front.h :exports none
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trexio_exit_code trexio_has_$group_sparse_dset$(trexio_t* const file);
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trexio_exit_code trexio_read_$group_sparse_dset$(trexio_t* const file, const int64_t offset_file, const int64_t buffer_size, int32_t* const index_sparse, double* const value_sparse);
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trexio_exit_code trexio_read_$group_sparse_dset$_size(trexio_t* const file, int64_t* const size_max);
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trexio_exit_code trexio_write_$group_sparse_dset$(trexio_t* const file, const int64_t offset_file, const int64_t buffer_size, const int32_t* index_sparse, const double* value_sparse);
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#+end_src
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@ -2416,18 +2435,16 @@ trexio_read_$group_sparse_dset$(trexio_t* const file,
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if (buffer_size <= 0L) return TREXIO_INVALID_ARG_3;
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if (index_sparse == NULL) return TREXIO_INVALID_ARG_4;
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if (value_sparse == NULL) return TREXIO_INVALID_ARG_5;
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if (trexio_has_$group_sparse_dset$(file) != TREXIO_SUCCESS) return TREXIO_DSET_MISSING;
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const uint32_t rank = $group_dset_rank$; // To be set by generator : number of indices
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int64_t size_max; // Max number of integrals (already in the file)
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trexio_exit_code rc;
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// temporary
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size_max = buffer_size;
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/* TODO
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rc = trexio_read_$group_sparse_dset$_num(file, &size_max);
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/* Read the max number of integrals stored in the file */
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rc = trexio_read_$group_sparse_dset$_size(file, &size_max);
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if (rc != TREXIO_SUCCESS) return rc;
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*/
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switch (file->back_end) {
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@ -2446,13 +2463,46 @@ trexio_read_$group_sparse_dset$(trexio_t* const file,
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case TREXIO_JSON:
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return trexio_json_read_$group_sparse_dset$(...);
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break;
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*/
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,*/
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default:
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return TREXIO_FAILURE; /* Impossible case */
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}
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}
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#+end_src
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#+begin_src c :tangle read_dset_sparse_size_front.c
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trexio_exit_code
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trexio_read_$group_sparse_dset$_size(trexio_t* const file, int64_t* const size_max)
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{
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if (file == NULL) return TREXIO_INVALID_ARG_1;
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if (trexio_has_$group_sparse_dset$(file) != TREXIO_SUCCESS) return TREXIO_DSET_MISSING;
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switch (file->back_end) {
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case TREXIO_TEXT:
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return trexio_text_read_$group_sparse_dset$_size(file, size_max);
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break;
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case TREXIO_HDF5:
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#ifdef HAVE_HDF5
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return trexio_hdf5_read_$group_sparse_dset$_size(file, size_max);
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break;
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#else
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return TREXIO_BACK_END_MISSING;
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#endif
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/*
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case TREXIO_JSON:
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return trexio_json_read_$group_sparse_dset$_size(...);
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break;
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,*/
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default:
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return TREXIO_FAILURE; /* Impossible case */
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}
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}
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#+end_src
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#+begin_src c :tangle write_dset_sparse_front.c
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trexio_exit_code
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trexio_write_$group_sparse_dset$(trexio_t* const file,
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@ -2470,15 +2520,17 @@ trexio_write_$group_sparse_dset$(trexio_t* const file,
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const uint32_t rank = $group_dset_rank$; // To be set by generator : number of indices
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int64_t size_max; // Max number of integrals (already in the file)
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int64_t size_max=0L; // Max number of integrals (already in the file)
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trexio_exit_code rc;
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// temporary
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size_max = buffer_size;
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/* TODO
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rc = trexio_read_$group_sparse_dset$_num(file, &size_max);
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if (rc != TREXIO_SUCCESS) return rc;
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*/
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/* Read the max number of integrals stored in the file */
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rc = trexio_has_$group_sparse_dset$(file);
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if (rc == TREXIO_SUCCESS) {
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rc = trexio_read_$group_sparse_dset$_size(file, &size_max);
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if (rc != TREXIO_SUCCESS) return rc;
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} else {
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size_max = 0L;
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}
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switch (file->back_end) {
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@ -2573,6 +2625,17 @@ interface
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end interface
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#+end_src
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#+begin_src f90 :tangle read_dset_sparse_size_front_fortran.f90
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interface
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integer function trexio_read_$group_sparse_dset$_size (trex_file, &
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size_max) bind(C)
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use, intrinsic :: iso_c_binding
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integer(8), intent(in), value :: trex_file
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integer(8), intent(out) :: size_max
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end function trexio_read_$group_sparse_dset$_size
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end interface
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#+end_src
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#+begin_src f90 :tangle has_dset_sparse_front_fortran.f90
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interface
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integer function trexio_has_$group_sparse_dset$ (trex_file) bind(C)
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@ -1006,9 +1006,11 @@ trexio_text_has_$group_str$ (trexio_t* const file)
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#+begin_src c :tangle hrw_dset_sparse_text.h :exports none
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trexio_exit_code trexio_text_has_$group_sparse_dset$(trexio_t* const file);
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trexio_exit_code trexio_text_read_$group_sparse_dset$(trexio_t* const file, const int64_t offset_file, const int64_t size, const int64_t size_max, int32_t* const index_sparse, double* const value_sparse);
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trexio_exit_code trexio_text_read_$group_sparse_dset$_size(trexio_t* const file, int64_t* const size_max);
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trexio_exit_code trexio_text_write_$group_sparse_dset$(trexio_t* const file, const int64_t offset_file, const int64_t size, const int64_t size_max, const int32_t* index_sparse, const double* value_sparse);
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#+end_src
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#+begin_src c :tangle write_dset_sparse_text.c
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trexio_exit_code trexio_text_write_$group_sparse_dset$(trexio_t* const file,
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const int64_t offset_file,
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@ -1035,10 +1037,13 @@ trexio_exit_code trexio_text_write_$group_sparse_dset$(trexio_t* const file,
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FILE* f = fopen(file_full_path, "a");
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if(f == NULL) return TREXIO_FILE_ERROR;
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/* Get the starting position of the IO stream to be written in the .size file */
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int64_t io_start_pos = (int64_t) ftell(f);
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/* Specify the line length in order to offset properly. For example, for 4-index quantities
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the line_length is 69 because 10 per index + 4 spaces + 24 for floating point value + 1 for the new line char.
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CURRENTLY NO OFFSET IS USED WHEN WRITING !
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*/
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,*/
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const uint64_t line_length = $group_sparse_dset_line_length$L;
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//fseek(f, (long) offset_file * line_length, SEEK_SET);
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@ -1061,6 +1066,27 @@ trexio_exit_code trexio_text_write_$group_sparse_dset$(trexio_t* const file,
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rc = fclose(f);
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if(rc != 0) return TREXIO_FILE_ERROR;
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/* Append .size to the file_full_path in order to write additional info about the written buffer of data */
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strncat(file_full_path, ".size", 6);
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/* Open the new file in "a" (append) mode to append info about the buffer that has been just written */
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FILE *f_wSize = fopen(file_full_path, "a");
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if (f_wSize == NULL) return TREXIO_FILE_ERROR;
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/* Write the buffer_size */
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rc = fprintf(f_wSize, "%ld %ld\n", size, io_start_pos);
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if (rc <= 0) {
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fclose(f_wSize);
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return TREXIO_FAILURE;
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}
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/* Close the TXT file */
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rc = fclose(f_wSize);
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if(rc != 0) return TREXIO_FILE_ERROR;
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/* Exit upon success */
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return TREXIO_SUCCESS;
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}
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#+end_src
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@ -1078,7 +1104,7 @@ trexio_exit_code trexio_text_read_$group_sparse_dset$(trexio_t* const file,
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/* Build the name of the file with sparse data.
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The $group_sparse_dset$.txt is limited to 256 symbols for the moment. What are the chances that it will exceed?
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,*/
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*/
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const char $group_sparse_dset$_file_name[256] = "/$group_sparse_dset$.txt";
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/* The full path to the destination TXT file with sparse data. This will include TREXIO directory name. */
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char file_full_path[TREXIO_MAX_FILENAME_LENGTH];
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@ -1130,6 +1156,57 @@ trexio_exit_code trexio_text_read_$group_sparse_dset$(trexio_t* const file,
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return TREXIO_SUCCESS;
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}
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#+end_src
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#+begin_src c :tangle read_dset_sparse_text.c
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trexio_exit_code trexio_text_read_$group_sparse_dset$_size(trexio_t* const file, int64_t* const size_max)
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{
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if (file == NULL) return TREXIO_INVALID_ARG_1;
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/* Build the name of the file with sparse data.
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The $group_sparse_dset$.txt is limited to 256 symbols for the moment. What are the chances that it will exceed?
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,*/
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const char $group_sparse_dset$_file_name[256] = "/$group_sparse_dset$.txt.size";
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/* The full path to the destination TXT file with sparse data. This will include TREXIO directory name. */
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char file_full_path[TREXIO_MAX_FILENAME_LENGTH];
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/* Copy directory name in file_full_path */
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strncpy (file_full_path, file->file_name, TREXIO_MAX_FILENAME_LENGTH);
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/* Append name of the file with sparse data */
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strncat (file_full_path, $group_sparse_dset$_file_name,
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TREXIO_MAX_FILENAME_LENGTH-strlen($group_sparse_dset$_file_name));
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/* Open the file in "r" (read) mode to guarantee that no truncation happens upon consecutive reads */
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FILE* f = fopen(file_full_path, "r");
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if(f == NULL) return TREXIO_FILE_ERROR;
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/* Read the data from the file and check the return code of fprintf to verify that > 0 bytes have been read or reached EOF */
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int rc;
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int64_t size_item, offset_item, size_accum=0L;
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/* Read the values from the file. BEWARE OF POSSIBLE MAX_INT64 OVERFLOW ! */
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while(fscanf(f, "%ld %ld", &size_item, &offset_item) != EOF) {
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/* Check that summation will not overflow the int64_t value */
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if (INT64_MAX - size_accum > size_item) {
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size_accum += size_item;
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} else {
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fclose(f);
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*size_max = -1L;
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return TREXIO_INT_SIZE_OVERFLOW;
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}
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}
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/* Close the TXT file */
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rc = fclose(f);
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if(rc != 0) return TREXIO_FILE_ERROR;
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/* Overwrite the value at the input address and return TREXIO_SUCCESS */
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*size_max = size_accum;
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return TREXIO_SUCCESS;
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}
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#+end_src
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