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Remove HD from C std lib file ops #3206

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merged 6 commits into from
Jun 29, 2023
Merged

Remove HD from C std lib file ops #3206

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4154aed
Remove HD from C std lib file ops
Jun 29, 2023
ec459e6
Forgot header file fixup
Jun 29, 2023
42eb68b
Committing clang-format changes
github-actions[bot] Jun 29, 2023
d1ec68b
Missed C++
Jun 29, 2023
0b32caf
Merge branch 'yank_HD_file_ops' of https://github.com/derobins/hdf5 i…
Jun 29, 2023
f4718c8
Merge branch 'develop' into yank_HD_file_ops
derobins Jun 29, 2023
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16 changes: 8 additions & 8 deletions hl/c++/test/ptableTest.cpp
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Original file line number Diff line number Diff line change
Expand Up @@ -81,7 +81,7 @@ BasicTest()
int error;

printf("Testing %-62s", "basic functionality");
HDfflush(stdout);
fflush(stdout);

FL_PacketTable wrapper(fileID, H5P_DEFAULT, BASICTEST_PT, H5T_NATIVE_INT, 1);
if (!wrapper.IsValid())
Expand Down Expand Up @@ -139,7 +139,7 @@ TestCompoundDatatype()
int error;

printf("Testing %-62s", "compound datatypes");
HDfflush(stdout);
fflush(stdout);

/* Create compound datatype */
typedef struct {
Expand Down Expand Up @@ -210,7 +210,7 @@ TestGetNext()
int i;

printf("Testing %-62s", "GetNextPacket");
HDfflush(stdout);
fflush(stdout);

/* Create a dataset */
FL_PacketTable wrapper(fileID, H5P_DEFAULT, GETNEXT_PT, H5T_NATIVE_INT, 500);
Expand Down Expand Up @@ -277,7 +277,7 @@ TestCompress()
size_t cd_nelemts = 0;

printf("Testing %-62s", "compression");
HDfflush(stdout);
fflush(stdout);
try {
/* Prepare property list to set compression, randomly use deflate */
DSetCreatPropList dscreatplist;
Expand Down Expand Up @@ -326,7 +326,7 @@ TestGetPacket()
int theRecs[3];
int i;
printf("Testing %-62s", "GetPacket");
HDfflush(stdout);
fflush(stdout);

/* Create a dataset. Does not need to specify property list because
there is no compression. */
Expand Down Expand Up @@ -365,7 +365,7 @@ int
TestErrors()
{
printf("Testing %-62s", "error conditions");
HDfflush(stdout);
fflush(stdout);

/* Create a dataset */
FL_PacketTable wrapper(fileID, PT_TESTERROR, H5T_NATIVE_INT, 1);
Expand Down Expand Up @@ -484,7 +484,7 @@ int
SystemTest()
{
printf("Testing %-62s", "multiple datatypes");
HDfflush(stdout);
fflush(stdout);

hid_t dtypeID1, dtypeID2;
hsize_t count;
Expand Down Expand Up @@ -626,7 +626,7 @@ TestHDFFV_9758()
}

printf("Testing %-62s", "data corruption in packed structs (HDFFV-9758)");
HDfflush(stdout);
fflush(stdout);

// Build a compound datatype
compound_type = H5Tcreate(H5T_COMPOUND, sizeof(s1_t));
Expand Down
4 changes: 2 additions & 2 deletions src/H5.c
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Original file line number Diff line number Diff line change
Expand Up @@ -488,7 +488,7 @@ H5_term_library(void)
H5_debug_open_stream_t *tmp_open_stream;

tmp_open_stream = H5_debug_g.open_stream;
(void)HDfclose(H5_debug_g.open_stream->stream);
(void)fclose(H5_debug_g.open_stream->stream);
H5_debug_g.open_stream = H5_debug_g.open_stream->next;
(void)H5MM_free(tmp_open_stream);
} /* end while */
Expand Down Expand Up @@ -753,7 +753,7 @@ H5__debug_mask(const char *s)

if (NULL ==
(open_stream = (H5_debug_open_stream_t *)H5MM_malloc(sizeof(H5_debug_open_stream_t)))) {
(void)HDfclose(stream);
(void)fclose(stream);
return;
} /* end if */

Expand Down
4 changes: 2 additions & 2 deletions src/H5Clog_json.c
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Original file line number Diff line number Diff line change
Expand Up @@ -249,7 +249,7 @@ H5C__log_json_set_up(H5C_log_info_t *log_info, const char log_location[], int mp
HDsnprintf(file_name, n_chars, "RANK_%d.%s", mpi_rank, log_location);

/* Open log file and set it to be unbuffered */
if (NULL == (json_udata->outfile = HDfopen(file_name, "w")))
if (NULL == (json_udata->outfile = fopen(file_name, "w")))
HGOTO_ERROR(H5E_CACHE, H5E_LOGGING, FAIL, "can't create mdc log file")
HDsetbuf(json_udata->outfile, NULL);

Expand Down Expand Up @@ -303,7 +303,7 @@ H5C__json_tear_down_logging(H5C_log_info_t *log_info)
H5MM_xfree(json_udata->message);

/* Close log file */
if (EOF == HDfclose(json_udata->outfile))
if (EOF == fclose(json_udata->outfile))
HGOTO_ERROR(H5E_CACHE, H5E_LOGGING, FAIL, "problem closing mdc log file")
json_udata->outfile = NULL;

Expand Down
4 changes: 2 additions & 2 deletions src/H5Clog_trace.c
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Original file line number Diff line number Diff line change
Expand Up @@ -244,7 +244,7 @@ H5C__log_trace_set_up(H5C_log_info_t *log_info, const char log_location[], int m
HDsnprintf(file_name, n_chars, "%s.%d", log_location, mpi_rank);

/* Open log file and set it to be unbuffered */
if (NULL == (trace_udata->outfile = HDfopen(file_name, "w")))
if (NULL == (trace_udata->outfile = fopen(file_name, "w")))
HGOTO_ERROR(H5E_CACHE, H5E_LOGGING, FAIL, "can't create mdc log file")
HDsetbuf(trace_udata->outfile, NULL);

Expand Down Expand Up @@ -301,7 +301,7 @@ H5C__trace_tear_down_logging(H5C_log_info_t *log_info)
H5MM_xfree(trace_udata->message);

/* Close log file */
if (EOF == HDfclose(trace_udata->outfile))
if (EOF == fclose(trace_udata->outfile))
HGOTO_ERROR(H5E_CACHE, H5E_LOGGING, FAIL, "problem closing mdc log file")
trace_udata->outfile = NULL;

Expand Down
8 changes: 4 additions & 4 deletions src/H5Dmpio.c
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Original file line number Diff line number Diff line change
Expand Up @@ -433,7 +433,7 @@ static FILE *debug_stream = NULL;
do { \
if (debug_stream && H5D_MPIO_DEBUG_THIS_RANK(rank)) { \
fprintf(debug_stream, "%*s(Rank %d) " string "\n", debug_indent, "", rank); \
HDfflush(debug_stream); \
fflush(debug_stream); \
} \
} while (0)

Expand All @@ -442,7 +442,7 @@ static FILE *debug_stream = NULL;
do { \
if (debug_stream && H5D_MPIO_DEBUG_THIS_RANK(rank)) { \
fprintf(debug_stream, "%*s(Rank %d) " string "\n", debug_indent, "", rank, __VA_ARGS__); \
HDfflush(debug_stream); \
fflush(debug_stream); \
} \
} while (0)

Expand Down Expand Up @@ -1145,7 +1145,7 @@ H5D__piece_io(H5D_io_info_t *io_info)

HDsnprintf(debug_log_filename, 1024, "H5Dmpio_debug.rank%d", mpi_rank);

if (NULL == (debug_log_file = HDfopen(debug_log_filename, "a")))
if (NULL == (debug_log_file = fopen(debug_log_filename, "a")))
HGOTO_ERROR(H5E_IO, H5E_OPENERROR, FAIL, "couldn't open debugging log file")

/* Print a short header for this I/O operation */
Expand Down Expand Up @@ -1357,7 +1357,7 @@ H5D__piece_io(H5D_io_info_t *io_info)
/* Close debugging log file */
if (debug_log_file) {
fprintf(debug_log_file, "##############\n\n");
if (EOF == HDfclose(debug_log_file))
if (EOF == fclose(debug_log_file))
HDONE_ERROR(H5E_IO, H5E_CLOSEERROR, FAIL, "couldn't close debugging log file")
debug_stream = H5DEBUG(D);
}
Expand Down
2 changes: 1 addition & 1 deletion src/H5FDhdfs.c
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Original file line number Diff line number Diff line change
Expand Up @@ -1158,7 +1158,7 @@ hdfs__fprint_stats(FILE *stream, const H5FD_hdfs_t *file)
br_val, br_suffix, /* raw data bytes */
am_val, am_suffix, /* metadata average */
ar_val, ar_suffix); /* raw data average */
HDfflush(stream);
fflush(stream);
}

done:
Expand Down
4 changes: 2 additions & 2 deletions src/H5FDlog.c
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Original file line number Diff line number Diff line change
Expand Up @@ -599,7 +599,7 @@ H5FD__log_open(const char *name, unsigned flags, hid_t fapl_id, haddr_t maxaddr)

/* Set the log file pointer */
if (fa->logfile)
file->logfp = HDfopen(fa->logfile, "w");
file->logfp = fopen(fa->logfile, "w");
else
file->logfp = stderr;

Expand Down Expand Up @@ -797,7 +797,7 @@ H5FD__log_close(H5FD_t *_file)
if (file->fa.flags & H5FD_LOG_FLAVOR)
file->flavor = (unsigned char *)H5MM_xfree(file->flavor);
if (file->logfp != stderr)
HDfclose(file->logfp);
fclose(file->logfp);
} /* end if */

if (file->fa.logfile)
Expand Down
4 changes: 2 additions & 2 deletions src/H5FDmirror.c
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Original file line number Diff line number Diff line change
Expand Up @@ -122,7 +122,7 @@ typedef struct H5FD_mirror_t {
/* end partial line */ \
fprintf(stdout, "\n"); \
fprintf(stdout, "```\n"); \
HDfflush(stdout); \
fflush(stdout); \
} while (0)
#else
#define LOG_XMIT_BYTES(label, buf, len) /* no-op */
Expand All @@ -132,7 +132,7 @@ typedef struct H5FD_mirror_t {
#define LOG_OP_CALL(name) \
do { \
printf("called %s()\n", (name)); \
HDfflush(stdout); \
fflush(stdout); \
} while (0)
#else
#define LOG_OP_CALL(name) /* no-op */
Expand Down
2 changes: 1 addition & 1 deletion src/H5FDros3.c
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Original file line number Diff line number Diff line change
Expand Up @@ -1048,7 +1048,7 @@ ros3_fprint_stats(FILE *stream, const H5FD_ros3_t *file)
am_val, am_suffix, /* metadata average */
ar_val, ar_suffix); /* raw data average */

HDfflush(stream);
fflush(stream);
}

done:
Expand Down
42 changes: 21 additions & 21 deletions src/H5FDs3comms.c
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Original file line number Diff line number Diff line change
Expand Up @@ -229,7 +229,7 @@ H5FD_s3comms_hrb_node_set(hrb_node_t **L, const char *name, const char *value)
for (node_ptr = (*L); node_ptr != NULL; node_ptr = node_ptr->next)
fprintf(stdout, "{%s}\n->", node_ptr->cat);
printf("(null)\n");
HDfflush(stdout);
fflush(stdout);
node_ptr = NULL;
#endif

Expand Down Expand Up @@ -302,7 +302,7 @@ H5FD_s3comms_hrb_node_set(hrb_node_t **L, const char *name, const char *value)
else {
#if S3COMMS_DEBUG
printf("CREATE NEW\n");
HDfflush(stdout);
fflush(stdout);
#endif
/*******************
* CREATE NEW LIST *
Expand Down Expand Up @@ -333,7 +333,7 @@ H5FD_s3comms_hrb_node_set(hrb_node_t **L, const char *name, const char *value)
if (value == NULL) {
#if S3COMMS_DEBUG
printf("REMOVE HEAD\n");
HDfflush(stdout);
fflush(stdout);
#endif
/***************
* REMOVE HEAD *
Expand All @@ -343,47 +343,47 @@ H5FD_s3comms_hrb_node_set(hrb_node_t **L, const char *name, const char *value)

#if S3COMMS_DEBUG
printf("FREEING CAT (node)\n");
HDfflush(stdout);
fflush(stdout);
#endif
H5MM_xfree(node_ptr->cat);
#if S3COMMS_DEBUG
printf("FREEING LOWERNAME (node)\n");
HDfflush(stdout);
fflush(stdout);
#endif
H5MM_xfree(node_ptr->lowername);
#if S3COMMS_DEBUG
printf("FREEING NAME (node)\n");
HDfflush(stdout);
fflush(stdout);
#endif
H5MM_xfree(node_ptr->name);
#if S3COMMS_DEBUG
printf("FREEING VALUE (node)\n");
HDfflush(stdout);
fflush(stdout);
#endif
H5MM_xfree(node_ptr->value);
#if S3COMMS_DEBUG
printf("MAGIC OK? %s\n", (node_ptr->magic == S3COMMS_HRB_NODE_MAGIC) ? "YES" : "NO");
HDfflush(stdout);
fflush(stdout);
#endif
assert(node_ptr->magic == S3COMMS_HRB_NODE_MAGIC);
node_ptr->magic += 1ul;
#if S3COMMS_DEBUG
printf("FREEING POINTER\n");
HDfflush(stdout);
fflush(stdout);
#endif
H5MM_xfree(node_ptr);

#if S3COMMS_DEBUG
printf("FREEING WORKING LOWERNAME\n");
HDfflush(stdout);
fflush(stdout);
#endif
H5MM_xfree(lowername);
lowername = NULL;
}
else {
#if S3COMMS_DEBUG
printf("MODIFY HEAD\n");
HDfflush(stdout);
fflush(stdout);
#endif
/***************
* MODIFY HEAD *
Expand Down Expand Up @@ -413,7 +413,7 @@ H5FD_s3comms_hrb_node_set(hrb_node_t **L, const char *name, const char *value)
else {
#if S3COMMS_DEBUG
printf("PREPEND NEW HEAD\n");
HDfflush(stdout);
fflush(stdout);
#endif
/*******************
* INSERT NEW HEAD *
Expand Down Expand Up @@ -442,7 +442,7 @@ H5FD_s3comms_hrb_node_set(hrb_node_t **L, const char *name, const char *value)
else {
#if S3COMMS_DEBUG
printf("APPEND A NODE\n");
HDfflush(stdout);
fflush(stdout);
#endif
/*******************
* APPEND NEW NODE *
Expand All @@ -465,7 +465,7 @@ H5FD_s3comms_hrb_node_set(hrb_node_t **L, const char *name, const char *value)
else {
#if S3COMMS_DEBUG
printf("INSERT A NODE\n");
HDfflush(stdout);
fflush(stdout);
#endif
/*******************
* INSERT NEW NODE *
Expand Down Expand Up @@ -494,7 +494,7 @@ H5FD_s3comms_hrb_node_set(hrb_node_t **L, const char *name, const char *value)

#if S3COMMS_DEBUG
printf("REMOVE A NODE\n");
HDfflush(stdout);
fflush(stdout);
#endif
H5MM_xfree(tmp->cat);
H5MM_xfree(tmp->lowername);
Expand All @@ -511,7 +511,7 @@ H5FD_s3comms_hrb_node_set(hrb_node_t **L, const char *name, const char *value)
else {
#if S3COMMS_DEBUG
printf("MODIFY A NODE\n");
HDfflush(stdout);
fflush(stdout);
#endif
/*****************
* MODIFY A NODE *
Expand Down Expand Up @@ -2077,27 +2077,27 @@ H5FD_s3comms_load_aws_profile(const char *profile_name, char *key_id_out, char *
if (ret < 0 || (size_t)ret >= 128)
HGOTO_ERROR(H5E_ARGS, H5E_CANTCOPY, FAIL, "unable to format credentials path")

credfile = HDfopen(filepath, "r");
credfile = fopen(filepath, "r");
if (credfile != NULL) {
if (H5FD__s3comms_load_aws_creds_from_file(credfile, profile_name, key_id_out, secret_access_key_out,
aws_region_out) == FAIL)
HGOTO_ERROR(H5E_ARGS, H5E_BADVALUE, FAIL, "unable to load from aws credentials")
if (HDfclose(credfile) == EOF)
if (fclose(credfile) == EOF)
HGOTO_ERROR(H5E_FILE, H5E_CANTCLOSEFILE, FAIL, "unable to close credentials file")
credfile = NULL;
} /* end if credential file opened */

ret = HDsnprintf(filepath, 128, "%s%s", awspath, "config");
if (ret < 0 || (size_t)ret >= 128)
HGOTO_ERROR(H5E_ARGS, H5E_CANTCOPY, FAIL, "unable to format config path")
credfile = HDfopen(filepath, "r");
credfile = fopen(filepath, "r");
if (credfile != NULL) {
if (H5FD__s3comms_load_aws_creds_from_file(
credfile, profile_name, (*key_id_out == 0) ? key_id_out : NULL,
(*secret_access_key_out == 0) ? secret_access_key_out : NULL,
(*aws_region_out == 0) ? aws_region_out : NULL) == FAIL)
HGOTO_ERROR(H5E_ARGS, H5E_BADVALUE, FAIL, "unable to load from aws config")
if (HDfclose(credfile) == EOF)
if (fclose(credfile) == EOF)
HGOTO_ERROR(H5E_FILE, H5E_CANTCLOSEFILE, FAIL, "unable to close config file")
credfile = NULL;
} /* end if credential file opened */
Expand All @@ -2108,7 +2108,7 @@ H5FD_s3comms_load_aws_profile(const char *profile_name, char *key_id_out, char *

done:
if (credfile != NULL)
if (HDfclose(credfile) == EOF)
if (fclose(credfile) == EOF)
HDONE_ERROR(H5E_ARGS, H5E_ARGS, FAIL, "problem error-closing aws configuration file")

FUNC_LEAVE_NOAPI(ret_value)
Expand Down
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