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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 2021-03-29 13:27:54 +02:00 committed by GitHub
parent e39a0b1ef4
commit 18c6fb845f
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GPG Key ID: 4AEE18F83AFDEB23
3 changed files with 43 additions and 54 deletions

View File

@ -6,7 +6,7 @@ ifeq ($(COMPILER),GNU)
CC=gcc -g
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
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
endif
RM=rm -f
OBJECT_FILES= trexio.o trexio_text.o trexio_hdf5.o
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

View File

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

View File

@ -73,7 +73,7 @@
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
@ -88,7 +88,7 @@ typedef struct $group$_s {
#+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
@ -110,7 +110,7 @@ typedef struct trexio_text_s {
#+end_src
*** Init/deinit functions (constant part)
** Init/deinit functions (constant part)
#+begin_src c :tangle basic_text.h
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
*** Init/deinit functions (templated part)
** Init/deinit functions (templated part)
#+begin_src c :tangle basic_text_group.c
trexio_exit_code trexio_text_finalize(trexio_t* const file) {
if (file == NULL) return TREXIO_INVALID_ARG_1;
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);
@ -236,7 +234,7 @@ trexio_exit_code trexio_text_finalize(trexio_t* const file) {
}
#+end_src
*** Template for text read struct
** Template for text read struct
#+begin_src c :tangle read_group_text.h
$group$_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 */
int rc;
// START REPEAT GROUP_DSET
rc = fscanf(f, "%1023s", buffer);
if ((rc != 1) || (strcmp(buffer, "rank_$group_dset$") != 0)) {
FREE(buffer);
@ -325,7 +321,7 @@ $group$_t* trexio_text_read_$group$(trexio_text_t* const file) {
FREE(file_name);
fclose(f);
FREE($group$);
return NULL;
return NULL;
}
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];
}
// END REPEAT GROUP_DSET
// START REPEAT GROUP_NUM
/* Read data */
rc = fscanf(f, "%1023s", buffer);
assert(!((rc != 1) || (strcmp(buffer, "$group_num$") != 0)));
@ -365,11 +359,9 @@ $group$_t* trexio_text_read_$group$(trexio_text_t* const file) {
FREE($group$);
return NULL;
}
// END REPEAT GROUP_NUM
// START REPEAT GROUP_DSET
/* Allocate arrays */
$group$->$group_dset$ = CALLOC(size_$group_dset$, $group_dset_dtype$);
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);
assert(!((rc != 1) || (strcmp(buffer, "$group_dset$") != 0)));
if ((rc != 1) || (strcmp(buffer, "$group_dset$") != 0)) {
FREE(buffer);
FREE(file_name);
fclose(f);
// TODO: free all dsets
FREE($group$->$group_dset$);
FREE($group$);
return NULL;
FREE(buffer);
FREE(file_name);
fclose(f);
FREE($group$->$group_dset$);
FREE($group$);
return NULL;
}
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(file_name);
fclose(f);
// TODO: free all dsets
FREE($group$->$group_dset$);
FREE($group$);
return NULL;
}
}
// END REPEAT GROUP_DSET
FREE(buffer);
@ -422,7 +411,6 @@ $group$_t* trexio_text_read_$group$(trexio_text_t* const file) {
FREE(file_name);
assert (!($group$->file == NULL));
if ($group$->file == NULL) {
// TODO: free all dsets
FREE($group$->$group_dset$);
FREE($group$);
return NULL;
@ -434,7 +422,7 @@ $group$_t* trexio_text_read_$group$(trexio_text_t* const file) {
}
#+end_src
*** Template for text flush struct
** Template for text flush struct
#+begin_src c :tangle flush_group_text.h
trexio_exit_code trexio_text_flush_$group$(trexio_text_t* const file);
@ -457,11 +445,8 @@ trexio_exit_code trexio_text_flush_$group$(trexio_text_t* const file) {
fseek(f, 0L, SEEK_SET);
/* Write the dimensioning variables */
// START REPEAT GROUP_DSET
fprintf(f, "rank_$group_dset$ %u\n", $group$->rank_$group_dset$);
// workaround for the case of missing blocks in the file
uint64_t size_$group_dset$ = 0;
if ($group$->rank_$group_dset$ != 0) size_$group_dset$ = 1;
@ -474,20 +459,16 @@ trexio_exit_code trexio_text_flush_$group$(trexio_text_t* const file) {
// END REPEAT GROUP_DSET
// START REPEAT GROUP_NUM
fprintf(f, "$group_num$ %lu\n", $group$->$group_num$);
// END REPEAT GROUP_NUM
// START REPEAT GROUP_DSET
/* Write arrays */
// START REPEAT GROUP_DSET
fprintf(f, "$group_dset$\n");
for (uint64_t i=0 ; i<size_$group_dset$ ; ++i) {
fprintf(f, "%$group_dset_std_dtype$\n", $group$->$group_dset$[i]);
}
// END REPEAT GROUP_DSET
fflush(f);
@ -496,7 +477,7 @@ trexio_exit_code trexio_text_flush_$group$(trexio_text_t* const file) {
}
#+end_src
*** Template for text free memory
** Template for text free memory
Memory is allocated when reading. The following function frees memory.
@ -522,11 +503,9 @@ trexio_exit_code trexio_text_free_$group$(trexio_text_t* const file) {
}
// START REPEAT GROUP_DSET
if ($group$->$group_dset$ != NULL) {
FREE ($group$->$group_dset$);
}
// END REPEAT GROUP_DSET
FREE ($group$);
@ -534,7 +513,7 @@ trexio_exit_code trexio_text_free_$group$(trexio_text_t* const file) {
}
#+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
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
*** 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.
@ -642,8 +621,8 @@ trexio_exit_code trexio_text_write_$group_dset$(trexio_t* const file, const $gro
#+end_src
*** RDM struct
**** Read the complete struct
** RDM struct
*** Read the complete struct
#+begin_src c :tangle rdm_text.h
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
**** Flush the complete struct
*** Flush the complete struct
#+begin_src c :tangle rdm_text.h
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
**** Free memory
*** Free 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
**** Read/Write the one_e attribute
*** Read/Write the one_e attribute
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
**** 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
in memory. So we provide functions to read and write it by