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https://github.com/TREX-CoE/trexio.git
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Smart deallocation of dsets upon failure in read_group [text] (#35)
* fix FC variable * smart deallocation of dsets + some cleaning in templator [text]
This commit is contained in:
Evgeny Posenitskiy
GitHub
parent
e39a0b1ef4
commit
18c6fb845f
@ -6,7 +6,7 @@ ifeq ($(COMPILER),GNU)
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CC=gcc -g
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CFLAGS=-fPIC -fexceptions -Wall -Werror -Wpedantic -Wextra
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FS=gfortran -g
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FC=gfortran -g
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FFLAGS=-fPIC -fcheck=all -Waliasing -Wampersand -Wconversion -Wsurprising -Wintrinsics-std -Wno-tabs -Wintrinsic-shadow -Wline-truncation -Wreal-q-constant -Wuninitialized -fbacktrace -ffpe-trap=zero,overflow,underflow -finit-real=nan
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LIBS= -L/usr/lib/x86_64-linux-gnu/hdf5/serial/ -lz -lm -lhdf5 -lhdf5_hl -lgfortran
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@ -34,8 +34,6 @@ FFLAGS=fPIC -g -O2
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LIBS=-lm
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endif
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RM=rm -f
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OBJECT_FILES= trexio.o trexio_text.o trexio_hdf5.o
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SOURCE_FILES= test.c trexio.c trexio_hdf5.c trexio_text.c
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HEADER_FILES= trexio.h trexio_text.h trexio_hdf5.h trexio_s.h
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@ -121,6 +121,7 @@ for fname in files_funcs_groups:
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do_dset = False
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do_num = False
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loop_body = ''
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dset_allocated = []
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with open(join(templ_path,fname), 'r') as f_in :
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with open(join(templ_path,fname_new), 'a') as f_out :
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for line in f_in :
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@ -133,12 +134,22 @@ for fname in files_funcs_groups:
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if dset_grname != grname:
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continue
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templine1 = loop_body.replace('$group_dset$', dset)
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templine2 = templine1.replace('$group$', grname)
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dset_allocated.append(dset)
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templine1 = templine2.replace('$group_dset_dtype$', params['dtype'])
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templine1 = loop_body.replace('$group_dset_dtype$', params['dtype'])
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templine2 = templine1
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if 'FREE($group$->$group_dset$)' in loop_body:
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tmp_string = ''
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for dset_alloc in dset_allocated:
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tmp_string += f'FREE({grname}->{dset_alloc});\n '
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templine1 = templine2.replace('FREE($group$->$group_dset$);',tmp_string)
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templine2 = templine1
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templine1 = templine2.replace('$group_dset$', dset)
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templine2 = templine1.replace('$group$', grname)
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if params['dtype'] == 'double':
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std_dtype = 'lf'
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elif params['dtype'] == 'int64_t':
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@ -163,6 +174,7 @@ for fname in files_funcs_groups:
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print('fishy')
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loop_body = ''
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dset_allocated = []
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subloop = False
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do_dset = False
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do_num = False
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@ -73,7 +73,7 @@
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The file is written when closed, or when the flush function is called.
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*** Template for group-related structures in text back end
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** Template for group-related structures in text back end
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#+begin_src c :tangle struct_text_group_dset.h
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@ -88,7 +88,7 @@ typedef struct $group$_s {
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#+end_src
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*** Template for general structure in text back end
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** Template for general structure in text back end
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#+begin_src c :tangle struct_text_group.h
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@ -110,7 +110,7 @@ typedef struct trexio_text_s {
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#+end_src
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*** Init/deinit functions (constant part)
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** Init/deinit functions (constant part)
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#+begin_src c :tangle basic_text.h
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trexio_exit_code trexio_text_init(trexio_t* const file);
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@ -217,15 +217,13 @@ trexio_exit_code trexio_text_unlock(trexio_t* const file) {
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#+end_src
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*** Init/deinit functions (templated part)
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** Init/deinit functions (templated part)
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#+begin_src c :tangle basic_text_group.c
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trexio_exit_code trexio_text_finalize(trexio_t* const file) {
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if (file == NULL) return TREXIO_INVALID_ARG_1;
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trexio_exit_code rc;
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//rc = trexio_text_free_$group$( (trexio_text_t*) file);
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//assert (rc == TREXIO_SUCCESS);
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assert (trexio_text_free_$group$( (trexio_text_t*) file) == TREXIO_SUCCESS);
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@ -236,7 +234,7 @@ trexio_exit_code trexio_text_finalize(trexio_t* const file) {
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}
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#+end_src
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*** Template for text read struct
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** Template for text read struct
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#+begin_src c :tangle read_group_text.h
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$group$_t* trexio_text_read_$group$(trexio_text_t* const file);
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@ -290,9 +288,7 @@ $group$_t* trexio_text_read_$group$(trexio_text_t* const file) {
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/* Read the dimensioning variables */
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int rc;
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// START REPEAT GROUP_DSET
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rc = fscanf(f, "%1023s", buffer);
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if ((rc != 1) || (strcmp(buffer, "rank_$group_dset$") != 0)) {
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FREE(buffer);
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@ -325,7 +321,7 @@ $group$_t* trexio_text_read_$group$(trexio_text_t* const file) {
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FREE(file_name);
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fclose(f);
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FREE($group$);
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return NULL;
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return NULL;
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}
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rc = fscanf(f, "%lu\n", &($group$->dims_$group_dset$[i]));
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@ -340,11 +336,9 @@ $group$_t* trexio_text_read_$group$(trexio_text_t* const file) {
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size_$group_dset$ *= $group$->dims_$group_dset$[i];
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}
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// END REPEAT GROUP_DSET
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// START REPEAT GROUP_NUM
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/* Read data */
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rc = fscanf(f, "%1023s", buffer);
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assert(!((rc != 1) || (strcmp(buffer, "$group_num$") != 0)));
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@ -365,11 +359,9 @@ $group$_t* trexio_text_read_$group$(trexio_text_t* const file) {
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FREE($group$);
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return NULL;
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}
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// END REPEAT GROUP_NUM
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// START REPEAT GROUP_DSET
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/* Allocate arrays */
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$group$->$group_dset$ = CALLOC(size_$group_dset$, $group_dset_dtype$);
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assert (!($group$->$group_dset$ == NULL));
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@ -384,13 +376,12 @@ $group$_t* trexio_text_read_$group$(trexio_text_t* const file) {
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rc = fscanf(f, "%1023s", buffer);
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assert(!((rc != 1) || (strcmp(buffer, "$group_dset$") != 0)));
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if ((rc != 1) || (strcmp(buffer, "$group_dset$") != 0)) {
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FREE(buffer);
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FREE(file_name);
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fclose(f);
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// TODO: free all dsets
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FREE($group$->$group_dset$);
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FREE($group$);
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return NULL;
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FREE(buffer);
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FREE(file_name);
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fclose(f);
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FREE($group$->$group_dset$);
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FREE($group$);
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return NULL;
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}
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for (uint64_t i=0 ; i<size_$group_dset$ ; ++i) {
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@ -400,13 +391,11 @@ $group$_t* trexio_text_read_$group$(trexio_text_t* const file) {
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FREE(buffer);
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FREE(file_name);
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fclose(f);
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// TODO: free all dsets
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FREE($group$->$group_dset$);
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FREE($group$);
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return NULL;
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}
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}
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// END REPEAT GROUP_DSET
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FREE(buffer);
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@ -422,7 +411,6 @@ $group$_t* trexio_text_read_$group$(trexio_text_t* const file) {
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FREE(file_name);
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assert (!($group$->file == NULL));
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if ($group$->file == NULL) {
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// TODO: free all dsets
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FREE($group$->$group_dset$);
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FREE($group$);
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return NULL;
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@ -434,7 +422,7 @@ $group$_t* trexio_text_read_$group$(trexio_text_t* const file) {
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}
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#+end_src
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*** Template for text flush struct
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** Template for text flush struct
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#+begin_src c :tangle flush_group_text.h
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trexio_exit_code trexio_text_flush_$group$(trexio_text_t* const file);
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@ -456,12 +444,9 @@ trexio_exit_code trexio_text_flush_$group$(trexio_text_t* const file) {
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assert (f != NULL);
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fseek(f, 0L, SEEK_SET);
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/* Write the dimensioning variables */
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/* Write the dimensioning variables */
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// START REPEAT GROUP_DSET
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fprintf(f, "rank_$group_dset$ %u\n", $group$->rank_$group_dset$);
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// workaround for the case of missing blocks in the file
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uint64_t size_$group_dset$ = 0;
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if ($group$->rank_$group_dset$ != 0) size_$group_dset$ = 1;
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@ -469,25 +454,21 @@ trexio_exit_code trexio_text_flush_$group$(trexio_text_t* const file) {
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for (unsigned int i=0; i<$group$->rank_$group_dset$; ++i){
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fprintf(f, "dims_$group_dset$ %u %lu\n", i, $group$->dims_$group_dset$[i]);
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size_$group_dset$ *= $group$->dims_$group_dset$[i];
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}
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}
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// END REPEAT GROUP_DSET
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// START REPEAT GROUP_NUM
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fprintf(f, "$group_num$ %lu\n", $group$->$group_num$);
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// END REPEAT GROUP_NUM
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// START REPEAT GROUP_DSET
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/* Write arrays */
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// START REPEAT GROUP_DSET
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fprintf(f, "$group_dset$\n");
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for (uint64_t i=0 ; i<size_$group_dset$ ; ++i) {
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fprintf(f, "%$group_dset_std_dtype$\n", $group$->$group_dset$[i]);
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}
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// END REPEAT GROUP_DSET
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fflush(f);
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@ -496,7 +477,7 @@ trexio_exit_code trexio_text_flush_$group$(trexio_text_t* const file) {
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}
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#+end_src
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*** Template for text free memory
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** Template for text free memory
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Memory is allocated when reading. The following function frees memory.
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@ -522,19 +503,17 @@ trexio_exit_code trexio_text_free_$group$(trexio_text_t* const file) {
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}
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// START REPEAT GROUP_DSET
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if ($group$->$group_dset$ != NULL) {
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FREE ($group$->$group_dset$);
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}
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// END REPEAT GROUP_DSET
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FREE ($group$);
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return TREXIO_SUCCESS;
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}
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#+end_src
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*** Template for read/write the $group_num$ attribute
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** Template for read/write the $group_num$ attribute
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#+begin_src c :tangle rw_num_text.h
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trexio_exit_code trexio_text_read_$group_num$ (trexio_t* const file, uint64_t* const num);
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@ -574,7 +553,7 @@ trexio_exit_code trexio_text_write_$group_num$(trexio_t* const file, const uint6
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}
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#+end_src
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*** Template for read/write the $group_dset$ dataset
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** Template for read/write the $group_dset$ dataset
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The ~dset~ array is assumed allocated with the appropriate size.
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@ -642,8 +621,8 @@ trexio_exit_code trexio_text_write_$group_dset$(trexio_t* const file, const $gro
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#+end_src
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*** RDM struct
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**** Read the complete struct
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** RDM struct
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*** Read the complete struct
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#+begin_src c :tangle rdm_text.h
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rdm_t* trexio_text_read_rdm(trexio_text_t* const file);
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@ -733,7 +712,7 @@ rdm_t* trexio_text_read_rdm(trexio_text_t* const file) {
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}
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#+end_src
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**** Flush the complete struct
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*** Flush the complete struct
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#+begin_src c :tangle rdm_text.h
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trexio_exit_code trexio_text_flush_rdm(trexio_text_t* const file);
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@ -772,7 +751,7 @@ trexio_exit_code trexio_text_flush_rdm(trexio_text_t* const file) {
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}
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#+end_src
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**** Free memory
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*** Free memory
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Memory is allocated when reading. The followig function frees memory.
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@ -811,7 +790,7 @@ trexio_exit_code trexio_text_free_rdm(trexio_text_t* const file) {
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}
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#+end_src
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**** Read/Write the one_e attribute
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*** Read/Write the one_e attribute
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The ~one_e~ array is assumed allocated with the appropriate size.
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@ -871,7 +850,7 @@ trexio_text_write_rdm_one_e(trexio_t* const file,
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}
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#+end_src
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**** Read/Write the two_e attribute
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*** Read/Write the two_e attribute
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~two_e~ is a sparse data structure, which can be too large to fit
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in memory. So we provide functions to read and write it by
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