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Smart deallocation of dsets upon failure in read_group [text] (#35)

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* fix FC variable
* smart deallocation of dsets + some cleaning in templator [text]
This commit is contained in:
Evgeny Posenitskiy 2021-03-29 13:27:54 +02:00 committed by GitHub
parent e39a0b1ef4
commit 18c6fb845f
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3 changed files with 43 additions and 54 deletions
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4
src/Makefile
View File

@ -6,7 +6,7 @@ ifeq ($(COMPILER),GNU)
CC=gcc -g CC=gcc -g
CFLAGS=-fPIC -fexceptions -Wall -Werror -Wpedantic -Wextra CFLAGS=-fPIC -fexceptions -Wall -Werror -Wpedantic -Wextra
FS=gfortran -g FC=gfortran -g
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 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
LIBS= -L/usr/lib/x86_64-linux-gnu/hdf5/serial/ -lz -lm -lhdf5 -lhdf5_hl -lgfortran LIBS= -L/usr/lib/x86_64-linux-gnu/hdf5/serial/ -lz -lm -lhdf5 -lhdf5_hl -lgfortran
@ -34,8 +34,6 @@ FFLAGS=fPIC -g -O2
LIBS=-lm LIBS=-lm
endif endif
RM=rm -f
OBJECT_FILES= trexio.o trexio_text.o trexio_hdf5.o OBJECT_FILES= trexio.o trexio_text.o trexio_hdf5.o
SOURCE_FILES= test.c trexio.c trexio_hdf5.c trexio_text.c SOURCE_FILES= test.c trexio.c trexio_hdf5.c trexio_text.c
HEADER_FILES= trexio.h trexio_text.h trexio_hdf5.h trexio_s.h HEADER_FILES= trexio.h trexio_text.h trexio_hdf5.h trexio_s.h

18
src/generator.py
View File

@ -121,6 +121,7 @@ for fname in files_funcs_groups:
do_dset = False do_dset = False
do_num = False do_num = False
loop_body = '' loop_body = ''
dset_allocated = []
with open(join(templ_path,fname), 'r') as f_in : with open(join(templ_path,fname), 'r') as f_in :
with open(join(templ_path,fname_new), 'a') as f_out : with open(join(templ_path,fname_new), 'a') as f_out :
for line in f_in : for line in f_in :
@ -133,12 +134,22 @@ for fname in files_funcs_groups:
if dset_grname != grname: if dset_grname != grname:
continue continue
templine1 = loop_body.replace('$group_dset$', dset) dset_allocated.append(dset)
templine2 = templine1.replace('$group$', grname)
templine1 = templine2.replace('$group_dset_dtype$', params['dtype']) templine1 = loop_body.replace('$group_dset_dtype$', params['dtype'])
templine2 = templine1 templine2 = templine1
if 'FREE($group$->$group_dset$)' in loop_body:
tmp_string = ''
for dset_alloc in dset_allocated:
tmp_string += f'FREE({grname}->{dset_alloc});\n '
templine1 = templine2.replace('FREE($group$->$group_dset$);',tmp_string)
templine2 = templine1
templine1 = templine2.replace('$group_dset$', dset)
templine2 = templine1.replace('$group$', grname)
if params['dtype'] == 'double': if params['dtype'] == 'double':
std_dtype = 'lf' std_dtype = 'lf'
elif params['dtype'] == 'int64_t': elif params['dtype'] == 'int64_t':
@ -163,6 +174,7 @@ for fname in files_funcs_groups:
print('fishy') print('fishy')
loop_body = '' loop_body = ''
dset_allocated = []
subloop = False subloop = False
do_dset = False do_dset = False
do_num = False do_num = False

75
src/templates_text/templator_text.org
View File

@ -73,7 +73,7 @@
The file is written when closed, or when the flush function is called. The file is written when closed, or when the flush function is called.
*** Template for group-related structures in text back end ** Template for group-related structures in text back end
#+begin_src c :tangle struct_text_group_dset.h #+begin_src c :tangle struct_text_group_dset.h
@ -88,7 +88,7 @@ typedef struct $group$_s {
#+end_src #+end_src
*** Template for general structure in text back end ** Template for general structure in text back end
#+begin_src c :tangle struct_text_group.h #+begin_src c :tangle struct_text_group.h
@ -110,7 +110,7 @@ typedef struct trexio_text_s {
#+end_src #+end_src
*** Init/deinit functions (constant part) ** Init/deinit functions (constant part)
#+begin_src c :tangle basic_text.h #+begin_src c :tangle basic_text.h
trexio_exit_code trexio_text_init(trexio_t* const file); trexio_exit_code trexio_text_init(trexio_t* const file);
@ -217,15 +217,13 @@ trexio_exit_code trexio_text_unlock(trexio_t* const file) {
#+end_src #+end_src
*** Init/deinit functions (templated part) ** Init/deinit functions (templated part)
#+begin_src c :tangle basic_text_group.c #+begin_src c :tangle basic_text_group.c
trexio_exit_code trexio_text_finalize(trexio_t* const file) { trexio_exit_code trexio_text_finalize(trexio_t* const file) {
if (file == NULL) return TREXIO_INVALID_ARG_1; if (file == NULL) return TREXIO_INVALID_ARG_1;
trexio_exit_code rc; trexio_exit_code rc;
//rc = trexio_text_free_$group$( (trexio_text_t*) file);
//assert (rc == TREXIO_SUCCESS);
assert (trexio_text_free_$group$( (trexio_text_t*) file) == TREXIO_SUCCESS); assert (trexio_text_free_$group$( (trexio_text_t*) file) == TREXIO_SUCCESS);
@ -236,7 +234,7 @@ trexio_exit_code trexio_text_finalize(trexio_t* const file) {
} }
#+end_src #+end_src
*** Template for text read struct ** Template for text read struct
#+begin_src c :tangle read_group_text.h #+begin_src c :tangle read_group_text.h
$group$_t* trexio_text_read_$group$(trexio_text_t* const file); $group$_t* trexio_text_read_$group$(trexio_text_t* const file);
@ -290,9 +288,7 @@ $group$_t* trexio_text_read_$group$(trexio_text_t* const file) {
/* Read the dimensioning variables */ /* Read the dimensioning variables */
int rc; int rc;
// START REPEAT GROUP_DSET // START REPEAT GROUP_DSET
rc = fscanf(f, "%1023s", buffer); rc = fscanf(f, "%1023s", buffer);
if ((rc != 1) || (strcmp(buffer, "rank_$group_dset$") != 0)) { if ((rc != 1) || (strcmp(buffer, "rank_$group_dset$") != 0)) {
FREE(buffer); FREE(buffer);
@ -325,7 +321,7 @@ $group$_t* trexio_text_read_$group$(trexio_text_t* const file) {
FREE(file_name); FREE(file_name);
fclose(f); fclose(f);
FREE($group$); FREE($group$);
return NULL; return NULL;
} }
rc = fscanf(f, "%lu\n", &($group$->dims_$group_dset$[i])); rc = fscanf(f, "%lu\n", &($group$->dims_$group_dset$[i]));
@ -340,11 +336,9 @@ $group$_t* trexio_text_read_$group$(trexio_text_t* const file) {
size_$group_dset$ *= $group$->dims_$group_dset$[i]; size_$group_dset$ *= $group$->dims_$group_dset$[i];
} }
// END REPEAT GROUP_DSET // END REPEAT GROUP_DSET
// START REPEAT GROUP_NUM // START REPEAT GROUP_NUM
/* Read data */ /* Read data */
rc = fscanf(f, "%1023s", buffer); rc = fscanf(f, "%1023s", buffer);
assert(!((rc != 1) || (strcmp(buffer, "$group_num$") != 0))); assert(!((rc != 1) || (strcmp(buffer, "$group_num$") != 0)));
@ -365,11 +359,9 @@ $group$_t* trexio_text_read_$group$(trexio_text_t* const file) {
FREE($group$); FREE($group$);
return NULL; return NULL;
} }
// END REPEAT GROUP_NUM // END REPEAT GROUP_NUM
// START REPEAT GROUP_DSET // START REPEAT GROUP_DSET
/* Allocate arrays */ /* Allocate arrays */
$group$->$group_dset$ = CALLOC(size_$group_dset$, $group_dset_dtype$); $group$->$group_dset$ = CALLOC(size_$group_dset$, $group_dset_dtype$);
assert (!($group$->$group_dset$ == NULL)); assert (!($group$->$group_dset$ == NULL));
@ -384,13 +376,12 @@ $group$_t* trexio_text_read_$group$(trexio_text_t* const file) {
rc = fscanf(f, "%1023s", buffer); rc = fscanf(f, "%1023s", buffer);
assert(!((rc != 1) || (strcmp(buffer, "$group_dset$") != 0))); assert(!((rc != 1) || (strcmp(buffer, "$group_dset$") != 0)));
if ((rc != 1) || (strcmp(buffer, "$group_dset$") != 0)) { if ((rc != 1) || (strcmp(buffer, "$group_dset$") != 0)) {
FREE(buffer); FREE(buffer);
FREE(file_name); FREE(file_name);
fclose(f); fclose(f);
// TODO: free all dsets FREE($group$->$group_dset$);
FREE($group$->$group_dset$); FREE($group$);
FREE($group$); return NULL;
return NULL;
} }
for (uint64_t i=0 ; i<size_$group_dset$ ; ++i) { for (uint64_t i=0 ; i<size_$group_dset$ ; ++i) {
@ -400,13 +391,11 @@ $group$_t* trexio_text_read_$group$(trexio_text_t* const file) {
FREE(buffer); FREE(buffer);
FREE(file_name); FREE(file_name);
fclose(f); fclose(f);
// TODO: free all dsets
FREE($group$->$group_dset$); FREE($group$->$group_dset$);
FREE($group$); FREE($group$);
return NULL; return NULL;
} }
} }
// END REPEAT GROUP_DSET // END REPEAT GROUP_DSET
FREE(buffer); FREE(buffer);
@ -422,7 +411,6 @@ $group$_t* trexio_text_read_$group$(trexio_text_t* const file) {
FREE(file_name); FREE(file_name);
assert (!($group$->file == NULL)); assert (!($group$->file == NULL));
if ($group$->file == NULL) { if ($group$->file == NULL) {
// TODO: free all dsets
FREE($group$->$group_dset$); FREE($group$->$group_dset$);
FREE($group$); FREE($group$);
return NULL; return NULL;
@ -434,7 +422,7 @@ $group$_t* trexio_text_read_$group$(trexio_text_t* const file) {
} }
#+end_src #+end_src
*** Template for text flush struct ** Template for text flush struct
#+begin_src c :tangle flush_group_text.h #+begin_src c :tangle flush_group_text.h
trexio_exit_code trexio_text_flush_$group$(trexio_text_t* const file); trexio_exit_code trexio_text_flush_$group$(trexio_text_t* const file);
@ -456,12 +444,9 @@ trexio_exit_code trexio_text_flush_$group$(trexio_text_t* const file) {
assert (f != NULL); assert (f != NULL);
fseek(f, 0L, SEEK_SET); fseek(f, 0L, SEEK_SET);
/* Write the dimensioning variables */ /* Write the dimensioning variables */
// START REPEAT GROUP_DSET // START REPEAT GROUP_DSET
fprintf(f, "rank_$group_dset$ %u\n", $group$->rank_$group_dset$); fprintf(f, "rank_$group_dset$ %u\n", $group$->rank_$group_dset$);
// workaround for the case of missing blocks in the file // workaround for the case of missing blocks in the file
uint64_t size_$group_dset$ = 0; uint64_t size_$group_dset$ = 0;
if ($group$->rank_$group_dset$ != 0) size_$group_dset$ = 1; if ($group$->rank_$group_dset$ != 0) size_$group_dset$ = 1;
@ -469,25 +454,21 @@ trexio_exit_code trexio_text_flush_$group$(trexio_text_t* const file) {
for (unsigned int i=0; i<$group$->rank_$group_dset$; ++i){ for (unsigned int i=0; i<$group$->rank_$group_dset$; ++i){
fprintf(f, "dims_$group_dset$ %u %lu\n", i, $group$->dims_$group_dset$[i]); fprintf(f, "dims_$group_dset$ %u %lu\n", i, $group$->dims_$group_dset$[i]);
size_$group_dset$ *= $group$->dims_$group_dset$[i]; size_$group_dset$ *= $group$->dims_$group_dset$[i];
} }
// END REPEAT GROUP_DSET // END REPEAT GROUP_DSET
// START REPEAT GROUP_NUM // START REPEAT GROUP_NUM
fprintf(f, "$group_num$ %lu\n", $group$->$group_num$); fprintf(f, "$group_num$ %lu\n", $group$->$group_num$);
// END REPEAT GROUP_NUM // END REPEAT GROUP_NUM
// START REPEAT GROUP_DSET
/* Write arrays */ /* Write arrays */
// START REPEAT GROUP_DSET
fprintf(f, "$group_dset$\n"); fprintf(f, "$group_dset$\n");
for (uint64_t i=0 ; i<size_$group_dset$ ; ++i) { for (uint64_t i=0 ; i<size_$group_dset$ ; ++i) {
fprintf(f, "%$group_dset_std_dtype$\n", $group$->$group_dset$[i]); fprintf(f, "%$group_dset_std_dtype$\n", $group$->$group_dset$[i]);
} }
// END REPEAT GROUP_DSET // END REPEAT GROUP_DSET
fflush(f); fflush(f);
@ -496,7 +477,7 @@ trexio_exit_code trexio_text_flush_$group$(trexio_text_t* const file) {
} }
#+end_src #+end_src
*** Template for text free memory ** Template for text free memory
Memory is allocated when reading. The following function frees memory. Memory is allocated when reading. The following function frees memory.
@ -522,19 +503,17 @@ trexio_exit_code trexio_text_free_$group$(trexio_text_t* const file) {
} }
// START REPEAT GROUP_DSET // START REPEAT GROUP_DSET
if ($group$->$group_dset$ != NULL) { if ($group$->$group_dset$ != NULL) {
FREE ($group$->$group_dset$); FREE ($group$->$group_dset$);
} }
// END REPEAT GROUP_DSET // END REPEAT GROUP_DSET
FREE ($group$); FREE ($group$);
return TREXIO_SUCCESS; return TREXIO_SUCCESS;
} }
#+end_src #+end_src
*** Template for read/write the $group_num$ attribute ** Template for read/write the $group_num$ attribute
#+begin_src c :tangle rw_num_text.h #+begin_src c :tangle rw_num_text.h
trexio_exit_code trexio_text_read_$group_num$ (trexio_t* const file, uint64_t* const num); trexio_exit_code trexio_text_read_$group_num$ (trexio_t* const file, uint64_t* const num);
@ -574,7 +553,7 @@ trexio_exit_code trexio_text_write_$group_num$(trexio_t* const file, const uint6
} }
#+end_src #+end_src
*** Template for read/write the $group_dset$ dataset ** Template for read/write the $group_dset$ dataset
The ~dset~ array is assumed allocated with the appropriate size. The ~dset~ array is assumed allocated with the appropriate size.
@ -642,8 +621,8 @@ trexio_exit_code trexio_text_write_$group_dset$(trexio_t* const file, const $gro
#+end_src #+end_src
*** RDM struct ** RDM struct
**** Read the complete struct *** Read the complete struct
#+begin_src c :tangle rdm_text.h #+begin_src c :tangle rdm_text.h
rdm_t* trexio_text_read_rdm(trexio_text_t* const file); rdm_t* trexio_text_read_rdm(trexio_text_t* const file);
@ -733,7 +712,7 @@ rdm_t* trexio_text_read_rdm(trexio_text_t* const file) {
} }
#+end_src #+end_src
**** Flush the complete struct *** Flush the complete struct
#+begin_src c :tangle rdm_text.h #+begin_src c :tangle rdm_text.h
trexio_exit_code trexio_text_flush_rdm(trexio_text_t* const file); trexio_exit_code trexio_text_flush_rdm(trexio_text_t* const file);
@ -772,7 +751,7 @@ trexio_exit_code trexio_text_flush_rdm(trexio_text_t* const file) {
} }
#+end_src #+end_src
**** Free memory *** Free memory
Memory is allocated when reading. The followig function frees memory. Memory is allocated when reading. The followig function frees memory.
@ -811,7 +790,7 @@ trexio_exit_code trexio_text_free_rdm(trexio_text_t* const file) {
} }
#+end_src #+end_src
**** Read/Write the one_e attribute *** Read/Write the one_e attribute
The ~one_e~ array is assumed allocated with the appropriate size. The ~one_e~ array is assumed allocated with the appropriate size.
@ -871,7 +850,7 @@ trexio_text_write_rdm_one_e(trexio_t* const file,
} }
#+end_src #+end_src
**** Read/Write the two_e attribute *** Read/Write the two_e attribute
~two_e~ is a sparse data structure, which can be too large to fit ~two_e~ is a sparse data structure, which can be too large to fit
in memory. So we provide functions to read and write it by in memory. So we provide functions to read and write it by