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HDF5 is generating unnecessary error messages when netcdf4 logging is enabled

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re: github netcdf-c issue #271

This occurs for several reasons, including:
1. using H5Aopen_name instead of H5Aexists to test if attribute exists.
2. using H5Eset_auto instead of H5Eset_auto2.
There are probably others that will have to be extinguished as encountered.
p.s Hope I did not overdo this and kill too much.
This commit is contained in:
Dennis Heimbigner 2016-05-27 10:08:01 -06:00
parent 7764a03f04
commit 835511eaeb
10 changed files with 59 additions and 21 deletions
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2
cf
View File

@ -1,6 +1,6 @@
#!/bin/bash
#NB=1
#DB=1
DB=1
#X=-x
#FAST=1

3
libdap2/ncd2dispatch.c
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@ -2420,7 +2420,7 @@ NCD2_var_par_access(int ncid, int p2, int p3)
#ifdef USE_NETCDF4
EXTERNL int
int
NCD2_inq_ncid(int ncid, const char* name, int* grp_ncid)
{
NC* drno;
@ -2430,6 +2430,7 @@ NCD2_inq_ncid(int ncid, const char* name, int* grp_ncid)
return THROW(ret);
}
int
NCD2_show_metadata(int ncid)
{
NC* drno;

11
libsrc4/nc4attr.c
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@ -73,10 +73,15 @@ nc4_get_att(int ncid, NC *nc, int varid, const char *name,
}
#endif
/* Find the attribute, if it exists. If we don't find it, we are
major failures. */
if ((retval = nc4_find_grp_att(grp, varid, norm_name, my_attnum, &att)))
/* Find the attribute, if it exists.
<strike>If we don't find it, we are major failures.</strike>
*/
if ((retval = nc4_find_grp_att(grp, varid, norm_name, my_attnum, &att))) {
if(retval == NC_ENOTATT)
return retval;
else
BAIL(retval);
}
/* If mem_type is NC_NAT, it means we want to use the attribute's
* file type as the mem type as well. */

3
libsrc4/nc4file.c
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@ -602,8 +602,7 @@ read_scale(NC_GRP_INFO_T *grp, hid_t datasetid, const char *obj_name,
BAIL(NC_EHDFERR);
if (attr_exists)
{
if ((attid = H5Aopen_by_name(datasetid, ".", NC_DIMID_ATT_NAME,
H5P_DEFAULT, H5P_DEFAULT)) < 0)
if ((attid = H5Aopen_name(datasetid, NC_DIMID_ATT_NAME)) < 0)
BAIL(NC_EHDFERR);
if (H5Aread(attid, H5T_NATIVE_INT, &new_dim->dimid) < 0)

8
libsrc4/nc4info.c
View File

@ -127,8 +127,8 @@ NC4_get_propattr(NC_HDF5_FILE_INFO_T* h5)
/* Get root group */
grp = h5->root_grp->hdf_grpid; /* get root group */
/* Try to extract the NCPROPS attribute */
attid = H5Aopen_name(grp, NCPROPS);
if(attid >= 0) {
if(H5Aexists(grp,NCPROPS) > 0) { /* Does exist */
attid = H5Aopen_name(grp, NCPROPS);
herr = -1;
aspace = H5Aget_space(attid); /* dimensions of attribute data */
atype = H5Aget_type(attid);
@ -170,8 +170,7 @@ NC4_put_propattr(NC_HDF5_FILE_INFO_T* h5)
/* Get root group */
grp = h5->root_grp->hdf_grpid; /* get root group */
/* See if the NCPROPS attribute exists */
exists = H5Aopen_name(grp, NCPROPS);
if(exists < 0) {/* Does not exist */
if(H5Aexists(grp,NCPROPS) == 0) { /* Does not exist */
herr = -1;
/* Create a datatype to refer to. */
HCHECK((atype = H5Tcopy(H5T_C_S1)));
@ -183,7 +182,6 @@ NC4_put_propattr(NC_HDF5_FILE_INFO_T* h5)
herr = 0;
}
done:
if(exists >= 0) HCHECK((H5Aclose(exists)));
if(attid >= 0) HCHECK((H5Aclose(attid)));
if(aspace >= 0) HCHECK((H5Sclose(aspace)));
if(atype >= 0) HCHECK((H5Tclose(atype)));

31
libsrc4/nc4internal.c
View File

@ -21,6 +21,19 @@ conditions.
#define MEGABYTE 1048576
#undef DEBUGH5
#ifdef DEBUGH5
/* Provide a catchable error reporting function */
static herr_t
h5catch(void* ignored)
{
H5Eprint(NULL);
return 0;
}
#endif
/* These are the default chunk cache sizes for HDF5 files created or
* opened with netCDF-4. */
extern size_t nc4_chunk_cache_size;
@ -43,14 +56,26 @@ int nc_log_level = -1;
int nc4_hdf5_initialized = 0;
/* Provide a wrapper for H5Eset_auto */
static herr_t
set_auto(void* func, void *client_data)
{
#ifdef DEBUGH5
return H5Eset_auto2(H5E_DEFAULT,(H5E_auto2_t)h5catch,client_data);
#else
return H5Eset_auto2(H5E_DEFAULT,(H5E_auto2_t)func,client_data);
#endif
}
/*
Provide a function to do any necessary initialization
of the HDF5 library.
*/
void
nc4_hdf5_initialize(void)
{
if (H5Eset_auto(NULL, NULL) < 0)
if (set_auto(NULL, NULL) < 0)
LOG((0, "Couldn't turn off HDF5 error messages!"));
LOG((1, "HDF5 error messages have been turned off."));
nc4_hdf5_initialized = 1;
@ -1401,7 +1426,7 @@ nc_set_log_level(int new_level)
fails, so just ignore the return code. */
if (new_level == NC_TURN_OFF_LOGGING)
{
H5Eset_auto(NULL, NULL);
set_auto(NULL,NULL);
LOG((1, "HDF5 error messages turned off!"));
}
@ -1409,7 +1434,7 @@ nc_set_log_level(int new_level)
if (new_level > NC_TURN_OFF_LOGGING &&
nc_log_level <= NC_TURN_OFF_LOGGING)
{
if (H5Eset_auto((H5E_auto_t)&H5Eprint, stderr) < 0)
if (set_auto((H5E_auto_t)&H5Eprint, stderr) < 0)
LOG((0, "H5Eset_auto failed!"));
LOG((1, "HDF5 error messages turned on."));
}

2
nc_test4/Make0
View File

@ -1,5 +1,5 @@
# Test c output
T=tst_chunk_hdf4
T=tst_misc
#CMD=valgrind --leak-check=full
CMD=gdb --args

4
nc_test4/tst_empty_vlen_unlim.c
View File

@ -120,7 +120,7 @@ int main() {
/* Close File. */
printf("\t* Closing file:\tnc_close().\n");
if (stat = nc_close(ncid)) ERR;
if ((stat = nc_close(ncid))) ERR;
}
@ -212,7 +212,7 @@ int main() {
/* Close File. */
printf("\t* Closing file:\tnc_close().\n");
if (stat = nc_close(ncid)) ERR;
if ((stat = nc_close(ncid))) ERR;
}

2
nc_test4/tst_misc.sh
View File

@ -11,7 +11,7 @@ set -e
echo "*** Testing phony dimension creation on pure h5 file"
rm -f ./tmp
if ../ncdump/ncdump -K ${srcdir}/tdset.h5 >./tmp ; then
if ../ncdump/ncdump -L0 -K ${srcdir}/tdset.h5 >./tmp ; then
echo "*** Pass: phony dimension creation"
ECODE=0
else

14
ncdump/ncdump.c
View File

@ -118,10 +118,11 @@ usage(void)
[-w] With client-side caching of variables for DAP URLs\n\
[-x] Output XML (NcML) instead of CDL\n\
[-Xp] Unconditionally suppress output of the properties attribute\n\
[-Ln] Set log level to n (>= 0); ignore if logging not enabled.\n\
file Name of netCDF file (or URL if DAP access enabled)\n"
(void) fprintf(stderr,
"%s [-c|-h] [-v ...] [[-b|-f] [c|f]] [-l len] [-n name] [-p n[,n]] [-k] [-x] [-s] [-t|-i] [-g ...] [-w] file\n%s",
"%s [-c|-h] [-v ...] [[-b|-f] [c|f]] [-l len] [-n name] [-p n[,n]] [-k] [-x] [-s] [-t|-i] [-g ...] [-w] [-Ln] file\n%s",
progname,
USAGE);
@ -2112,7 +2113,7 @@ main(int argc, char *argv[])
exit(EXIT_SUCCESS);
}
while ((c = getopt(argc, argv, "b:cd:f:g:hikl:n:p:stv:xwKX:")) != EOF)
while ((c = getopt(argc, argv, "b:cd:f:g:hikl:n:p:stv:xwKL:X:")) != EOF)
switch(c) {
case 'h': /* dump header only, no data */
formatting_specs.header_only = true;
@ -2213,6 +2214,15 @@ main(int argc, char *argv[])
break;
}
break;
case 'L':
#ifdef LOGGING
{
int level = atoi(optarg);
if(level >= 0)
nc_set_log_level(level);
}
#endif
break;
case '?':
usage();
exit(EXIT_FAILURE);