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[svn-r8121] Purpose:

Browse Source 
bug fix

Description:
avoid reading and writing data when one of the dimensions is 0 (attributes case )

Solution:
linux
solaris
AIX

Platforms tested:

Misc. update:
This commit is contained in:
Pedro Vicente Nunes 2004-01-28 14:07:21 -05:00
parent 500292582f
commit 48c7a5e35e
3 changed files with 124 additions and 138 deletions
Show Stats Download Patch File Download Diff File Expand all files Collapse all files

2
tools/h5repack/h5repack.h
View File

@ -166,8 +166,6 @@ int do_copy_refobjs(hid_t fidin,
void read_info(const char *filename,pack_opt_t *options);
void close_obj(H5G_obj_t obj_type, hid_t obj_id);
void init_packobject(pack_info_t *obj);
int print_filters(hid_t dcpl_id);

6
tools/h5repack/h5repack_main.c
View File

@ -50,7 +50,7 @@ int main(int argc, char **argv)
}
else if (strcmp(argv[i], "-f") == 0) {
/* add the -t option */
/* add the -f filter option */
h5repack_addfilter(argv[i+1],&options);
/* jump to next */
@ -58,7 +58,7 @@ int main(int argc, char **argv)
}
else if (strcmp(argv[i], "-l") == 0) {
/* parse the -c option */
/* parse the -l layout option */
h5repack_addlayout(argv[i+1],&options);
/* jump to next */
@ -75,7 +75,7 @@ int main(int argc, char **argv)
++i;
}
else if (strcmp(argv[i], "-f") == 0) {
else if (strcmp(argv[i], "-e") == 0) {
read_info(argv[++i],&options);
}

254
tools/h5repack/h5repack_refs.c
View File

@ -22,6 +22,9 @@
static const char* MapIdToName(hid_t refobj_id,
trav_table_t *travt);
static void close_obj(H5G_obj_t obj_type, hid_t obj_id);
static int copy_refs_attr(hid_t loc_in,
hid_t loc_out,
pack_opt_t *options,
@ -64,8 +67,6 @@ int do_copy_refobjs(hid_t fidin,
hsize_t dims[H5S_MAX_RANK];/* dimensions of dataset */
int i, j;
/* initialize to test for non reference cases */
/*-------------------------------------------------------------------------
* browse
*-------------------------------------------------------------------------
@ -73,7 +74,6 @@ int do_copy_refobjs(hid_t fidin,
for ( i = 0; i < travt->nobjs; i++)
{
switch ( travt->objs[i].type )
{
/*-------------------------------------------------------------------------
@ -181,13 +181,12 @@ int do_copy_refobjs(hid_t fidin,
/* create the reference, -1 parameter for objects */
if (H5Rcreate(&refbuf[u],fidout,refname,H5R_OBJECT,-1)<0)
goto error;
if (options->verbose)
printf("object <%s> object reference created to <%s>\n",
travt->objs[i].name,
refname);
close_obj(obj_type,refobj_id);
}/*refname*/
close_obj(obj_type,refobj_id);
}/* u */
}/*nelmts*/
@ -260,23 +259,19 @@ int do_copy_refobjs(hid_t fidin,
if ((refname=MapIdToName(refobj_id,travt))!=NULL)
{
hid_t region_id; /* region id of the referenced dataset */
if ((region_id = H5Rget_region(dset_in,H5R_DATASET_REGION,&buf[u]))<0)
goto error;
/* create the reference, we need the space_id */
if (H5Rcreate(&refbuf[u],fidout,refname,H5R_DATASET_REGION,region_id)<0)
goto error;
if (H5Sclose(region_id)<0)
goto error;
if (options->verbose)
printf("object <%s> region reference created to <%s>\n",
travt->objs[i].name,
refname);
close_obj(obj_type,refobj_id);
}/*refname*/
close_obj(obj_type,refobj_id);
}/* u */
}/*nelmts*/
@ -518,50 +513,52 @@ static int copy_refs_attr(hid_t loc_in,
{
H5G_obj_t obj_type;
hid_t refobj_id;
hobj_ref_t *refbuf;
hobj_ref_t *refbuf=NULL;
unsigned k;
const char* refname;
hobj_ref_t *buf;
hobj_ref_t *buf=NULL;
/*-------------------------------------------------------------------------
* read input to memory
*-------------------------------------------------------------------------
*/
buf=(void *) HDmalloc((unsigned)(nelmts*msize));
if ( buf==NULL){
printf( "cannot read into memory\n" );
goto error;
}
if (H5Aread(attr_id,mtype_id,buf)<0)
goto error;
if ((obj_type = H5Rget_obj_type(attr_id,H5R_OBJECT,buf))<0)
goto error;
refbuf=HDmalloc((unsigned)nelmts*msize);
if ( refbuf==NULL){
printf( "cannot allocate memory\n" );
goto error;
}
for ( k=0; k<nelmts; k++)
if (nelmts)
{
if ((refobj_id = H5Rdereference(attr_id,H5R_OBJECT,&buf[k]))<0)
buf=(void *) HDmalloc((unsigned)(nelmts*msize));
if ( buf==NULL){
printf( "cannot read into memory\n" );
goto error;
}
if (H5Aread(attr_id,mtype_id,buf)<0)
goto error;
/* get the name. a valid name could only occur in the
second traversal of the file */
if ((refname=MapIdToName(refobj_id,travt))!=NULL)
{
/* create the reference */
if (H5Rcreate(&refbuf[k],fidout,refname,H5R_OBJECT,-1)<0)
goto error;
if (options->verbose)
printf("object <%s> reference created to <%s>\n",name,refname);
if ((obj_type = H5Rget_obj_type(attr_id,H5R_OBJECT,buf))<0)
goto error;
refbuf=HDmalloc((unsigned)nelmts*msize);
if ( refbuf==NULL){
printf( "cannot allocate memory\n" );
goto error;
}
close_obj(obj_type,refobj_id);
}/* i */
for ( k=0; k<nelmts; k++)
{
H5E_BEGIN_TRY {
if ((refobj_id = H5Rdereference(attr_id,H5R_OBJECT,&buf[k]))<0)
goto error;
} H5E_END_TRY;
/* get the name. a valid name could only occur in the
second traversal of the file */
if ((refname=MapIdToName(refobj_id,travt))!=NULL)
{
/* create the reference */
if (H5Rcreate(&refbuf[k],fidout,refname,H5R_OBJECT,-1)<0)
goto error;
if (options->verbose)
printf("object <%s> reference created to <%s>\n",name,refname);
}
close_obj(obj_type,refobj_id);
}/* k */
}/*nelmts*/
/*-------------------------------------------------------------------------
* copy
@ -570,14 +567,18 @@ static int copy_refs_attr(hid_t loc_in,
if ((attr_out=H5Acreate(loc_out,name,ftype_id,space_id,H5P_DEFAULT))<0)
goto error;
if(H5Awrite(attr_out,mtype_id,refbuf)<0)
goto error;
if (nelmts) {
if(H5Awrite(attr_out,mtype_id,refbuf)<0)
goto error;
}
if (H5Aclose(attr_out)<0)
goto error;
free(refbuf);
free(buf);
if (refbuf)
free(refbuf);
if (buf)
free(buf);
}/*H5T_STD_REF_OBJ*/
@ -589,65 +590,62 @@ static int copy_refs_attr(hid_t loc_in,
{
H5G_obj_t obj_type;
hid_t refobj_id;
hdset_reg_ref_t *refbuf; /* input buffer for region references */
hdset_reg_ref_t *buf; /* output buffer */
hdset_reg_ref_t *refbuf=NULL; /* input buffer for region references */
hdset_reg_ref_t *buf=NULL; /* output buffer */
const char* refname;
unsigned u;
unsigned k;
/*-------------------------------------------------------------------------
* read input to memory
*-------------------------------------------------------------------------
*/
buf=(void *) HDmalloc((unsigned)(nelmts*msize));
if ( buf==NULL){
printf( "cannot read into memory\n" );
goto error;
}
if (H5Aread(attr_id,mtype_id,buf)<0)
goto error;
if ((obj_type = H5Rget_obj_type(attr_id,H5R_DATASET_REGION,buf))<0)
goto error;
/*-------------------------------------------------------------------------
* create output
*-------------------------------------------------------------------------
*/
refbuf=HDcalloc(sizeof(hdset_reg_ref_t),(size_t)nelmts); /*init to zero */
if ( refbuf==NULL){
printf( "cannot allocate memory\n" );
goto error;
}
for ( u=0; u<nelmts; u++)
if (nelmts)
{
H5E_BEGIN_TRY {
if ((refobj_id = H5Rdereference(attr_id,H5R_DATASET_REGION,&buf[u]))<0)
continue;
} H5E_END_TRY;
/* get the name. a valid name could only occur in the
second traversal of the file */
if ((refname=MapIdToName(refobj_id,travt))!=NULL)
{
hid_t region_id; /* region id of the referenced dataset */
if ((region_id = H5Rget_region(attr_id,H5R_DATASET_REGION,&buf[u]))<0)
goto error;
/* create the reference, we need the space_id */
if (H5Rcreate(&refbuf[u],fidout,refname,H5R_DATASET_REGION,region_id)<0)
goto error;
if (H5Sclose(region_id)<0)
goto error;
if (options->verbose)
printf("object <%s> region reference created to <%s>\n",name,refname);
buf=(void *) HDmalloc((unsigned)(nelmts*msize));
if ( buf==NULL){
printf( "cannot read into memory\n" );
goto error;
}
close_obj(obj_type,refobj_id);
}/* u */
if (H5Aread(attr_id,mtype_id,buf)<0)
goto error;
if ((obj_type = H5Rget_obj_type(attr_id,H5R_DATASET_REGION,buf))<0)
goto error;
/*-------------------------------------------------------------------------
* create output
*-------------------------------------------------------------------------
*/
refbuf=HDcalloc(sizeof(hdset_reg_ref_t),(size_t)nelmts); /*init to zero */
if ( refbuf==NULL){
printf( "cannot allocate memory\n" );
goto error;
}
for ( k=0; k<nelmts; k++)
{
H5E_BEGIN_TRY {
if ((refobj_id = H5Rdereference(attr_id,H5R_DATASET_REGION,&buf[k]))<0)
continue;
} H5E_END_TRY;
/* get the name. a valid name could only occur in the
second traversal of the file */
if ((refname=MapIdToName(refobj_id,travt))!=NULL)
{
hid_t region_id; /* region id of the referenced dataset */
if ((region_id = H5Rget_region(attr_id,H5R_DATASET_REGION,&buf[k]))<0)
goto error;
/* create the reference, we need the space_id */
if (H5Rcreate(&refbuf[k],fidout,refname,H5R_DATASET_REGION,region_id)<0)
goto error;
if (H5Sclose(region_id)<0)
goto error;
if (options->verbose)
printf("object <%s> region reference created to <%s>\n",name,refname);
}
close_obj(obj_type,refobj_id);
}/* k */
}/*nelmts */
/*-------------------------------------------------------------------------
* copy
@ -656,18 +654,18 @@ static int copy_refs_attr(hid_t loc_in,
if ((attr_out=H5Acreate(loc_out,name,ftype_id,space_id,H5P_DEFAULT))<0)
goto error;
if(H5Awrite(attr_out,mtype_id,refbuf)<0)
goto error;
if (nelmts) {
if(H5Awrite(attr_out,mtype_id,refbuf)<0)
goto error;
}
if (H5Aclose(attr_out)<0)
goto error;
free(refbuf);
free(buf);
if (refbuf)
free(refbuf);
if (buf)
free(buf);
} /* H5T_STD_REF_DSETREG */
/*-------------------------------------------------------------------------
* close
*-------------------------------------------------------------------------
@ -700,23 +698,25 @@ error:
*-------------------------------------------------------------------------
*/
void close_obj(H5G_obj_t obj_type, hid_t obj_id)
static void close_obj(H5G_obj_t obj_type, hid_t obj_id)
{
switch (obj_type) {
case H5G_GROUP:
H5Gclose(obj_id);
break;
case H5G_DATASET:
H5Dclose(obj_id);
break;
case H5G_TYPE:
H5Tclose(obj_id);
break;
default:
assert(0);
break;
}
H5E_BEGIN_TRY
{
switch (obj_type)
{
case H5G_GROUP:
H5Gclose(obj_id);
break;
case H5G_DATASET:
H5Dclose(obj_id);
break;
case H5G_TYPE:
H5Tclose(obj_id);
break;
default:
break;
}
} H5E_END_TRY;
}
/*-------------------------------------------------------------------------
@ -737,7 +737,6 @@ static const char* MapIdToName(hid_t refobj_id,
/* obtains the file ID given an object ID. This ID must be closed */
if ((fid = H5Iget_file_id(refobj_id))<0)
{
assert(0);
return NULL;
}
@ -747,13 +746,8 @@ static const char* MapIdToName(hid_t refobj_id,
switch ( travt->objs[i].type )
{
default:
assert(0);
break;
case H5G_GROUP:
case H5G_TYPE:
case H5G_LINK:
break;
/*-------------------------------------------------------------------------
* H5G_DATASET
*-------------------------------------------------------------------------
@ -762,15 +756,9 @@ static const char* MapIdToName(hid_t refobj_id,
case H5G_DATASET:
if ((id = H5Dopen(fid,travt->objs[i].name))<0)
{
assert(0);
return NULL;
}
if (H5Dclose(id)<0)
{
assert(0);
return NULL;
}
if (id==refobj_id)
{
H5Fclose(fid);