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src/H5Part.c

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- use "-1" to indicate an uninitialized "timegroup" in "H5PartFile"
	  a valid "timegroup" is greater or equal zeros
	- _set_step()
		* added, derived from "H5PartSetStep()"
	- H5PartSetStep()
		* call "_set_step()" to do the real work
	- _H5Part_get_num_particles()
		* added, derived from "H5PartGetNumParticles()"
	- H5PartGetNumParticles()
		* call "_H5Part_get_num_particles()" to do the real work
	- H5PartSetNumParticles()
		* use new function "_set_step()" instead of "H5PartSetStep()"
		* print no extra error message if "_set_step()" returns
		  with an errror
	- _reset_view()
		* added, derived from "H5PartSetView()"
	- H5PartResetView()
		* added, was a macro before
	- H5PartHasView()
		* added, was a macro before
	- _set_view()
		* added, derived from "H5PartSetView()"
		* "#ifdef HDF5V160" block removed
	-  H5PartSetView()
		* call "_set_view()" to do the real work
	- H5PartGetView()
		* use vars "viewend" and "viewstart" to instead "range[0]"
		  and range[1]
		* call "_set_step()" if timegroup not initialized
	- H5PartSetCanonicalView()
		* check whether we are in read-only mode replaced with macro
		* "_reset_view()" used instead of "H5PartSetView(f,-1,-1)
This commit is contained in:
gsell
2006-09-25 20:05:47 +00:00
parent 1d011f5482
commit 6e32226992
1 changed files with 251 additions and 201 deletions
Download Patch File Download Diff File Expand all files Collapse all files
src/H5Part.c
+251 -201
View File
@@ -2,14 +2,6 @@
H5Part C API
*/
/*
H5PartSetStep()
H5PartGetNumParticles()
H5PartSetView()
H5PartHasView()
*/
#include <stdio.h>
#include <stdlib.h>
#include <stdarg.h> /* va_arg - System dependent ?! */
@@ -180,7 +172,7 @@ H5PartOpenFileParallel (
goto error_cleanup;
}
f->mode = flags;
f->timegroup = 0;
f->timegroup = -1;
f->shape = 0;
f->diskshape = H5S_ALL;
f->memshape = H5S_ALL;
@@ -290,7 +282,7 @@ H5PartOpenFile (
}
f->mode = flags;
f->timegroup = 0;
f->timegroup = -1;
f->shape = 0;
f->diskshape = H5S_ALL;
f->memshape = H5S_ALL;
@@ -359,10 +351,10 @@ H5PartCloseFile (
if ( r < 0 ) HANDLE_H5S_CLOSE_ERR;
f->shape = 0;
}
if( f->timegroup > 0 ) {
if( f->timegroup >= 0 ) {
r = H5Gclose( f->timegroup );
if ( r < 0 ) HANDLE_H5G_CLOSE_ERR;
f->timegroup = 0;
f->timegroup = -1;
}
if( f->diskshape != H5S_ALL ) {
r = H5Sclose( f->diskshape );
@@ -535,8 +527,8 @@ H5PartSetNumParticles (
if ( r < 0 ) return HANDLE_H5S_SELECT_HYPERSLAB_ERR;
if ( f->timegroup < 0 ) {
r = H5PartSetStep ( f, 0 );
if ( r < 0 ) return HANDLE_H5PART_SETSTEP_ERR( r, 0 );
r = _set_step ( f, 0 );
if ( r < 0 ) return r;
}
#endif
@@ -1218,6 +1210,52 @@ H5PartReadFileAttrib (
(they require explicit advancing by selecting a particular timestep).
*/
static h5part_int64_t
_set_step (
H5PartFile *f, /*!< [in] Handle to open file */
const h5part_int64_t step /*!< [in] Time-step to set. */
) {
char name[128];
sprintf ( name, "%s#%lld", H5PART_PARTICLES_GROUP, (long long) step );
herr_t herr = H5Gget_objinfo( f->file, name, 1, NULL );
if ( (f->mode != H5PART_READ) && ( herr >= 0 ) ) {
return HANDLE_H5PART_STEP_EXISTS_ERR ( step );
}
if ( f->timegroup >= 0 ) {
herr = H5Gclose ( f->timegroup );
if ( herr < 0 ) return HANDLE_H5G_CLOSE_ERR;
}
f->timegroup = -1;
f->timestep = step;
if( f->mode == H5PART_READ ) {
_H5Part_print_info (
"Proc[%d]: Set step to #%lld for file %lld",
f->myproc,
(long long)step,
(long long)(size_t) f );
f->timegroup = H5Gopen ( f->file, name );
if ( f->timegroup < 0 ) return HANDLE_H5G_OPEN_ERR( name );
}
else {
_H5Part_print_debug (
"Proc[%d]: Create step #%lld for file %lld",
f->myproc,
(long long)step,
(long long)(size_t) f );
f->timegroup = H5Gcreate ( f->file, name, 0 );
if ( f->timegroup < 0 ) return HANDLE_H5G_CREATE_ERR ( name );
}
return H5PART_SUCCESS;
}
/*!
Set the current time-step.
@@ -1236,44 +1274,14 @@ H5PartReadFileAttrib (
h5part_int64_t
H5PartSetStep (
H5PartFile *f, /*!< [in] Handle to open file */
h5part_int64_t step /*!< [in] Time-step to set. */
const h5part_int64_t step /*!< [in] Time-step to set. */
) {
SET_FNAME ( "H5PartSetStep" );
herr_t r;
char name[128];
CHECK_FILEHANDLE ( f );
_H5Part_print_info ( "Proc[%d]: Set step to #%lld for file %lld",
f->myproc, (long long)step, (long long) f );
sprintf ( name, "%s#%lld", H5PART_PARTICLES_GROUP, (long long) step );
r = H5Gget_objinfo( f->file, name, 1, NULL );
if ( ( (f->mode == H5PART_APPEND) || (f->mode == H5PART_WRITE) )
&& ( r >= 0 ) ) {
return HANDLE_H5PART_STEP_EXISTS_ERR ( step );
}
if(f->timegroup>0) {
r = H5Gclose(f->timegroup); if ( r < 0 ) HANDLE_H5G_CLOSE_ERR;
}
f->timegroup = -1;
f->timestep = step;
if(f->mode==H5PART_READ) {
f->timegroup = H5Gopen(f->file,name);
if ( f->timegroup < 0 ) return HANDLE_H5G_OPEN_ERR( name );
}
else {
_H5Part_print_debug ( "Proc[%d]: create step #%lld",
f->myproc, (long long)step );
f->timegroup = H5Gcreate(f->file,name,0);
if ( f->timegroup < 0 ) return HANDLE_H5G_CREATE_ERR ( name );
}
return H5PART_SUCCESS;
return _set_step ( f, step );
}
/********************** query file structure *********************************/
@@ -1505,7 +1513,7 @@ H5PartGetDatasetInfo (
len_dataset_name );
if ( herr < 0 ) return herr;
*nelem = H5PartGetNumParticles(f);
*nelem = _H5Part_get_num_particles ( f );
if ( *nelem < 0 ) return *nelem;
dataset_id = H5Dopen ( f->timegroup, dataset_name );
@@ -1612,13 +1620,12 @@ _get_memshape_for_reading (
\return number of particles in current timestep or an error
code.
*/
h5part_int64_t
H5PartGetNumParticles (
_H5Part_get_num_particles (
H5PartFile *f /*!< [in] Handle to open file */
) {
SET_FNAME ( "H5PartGetNumParticles" );
h5part_int64_t herr;
hid_t space_id;
hid_t dataset_id;
@@ -1626,24 +1633,20 @@ H5PartGetNumParticles (
char step_name[128];
hsize_t nparticles;
CHECK_FILEHANDLE( f );
if(f->timegroup<0) {
h5part_int64_t step = (f->timestep<0 ? 0 : f->timestep );
herr = H5PartSetStep ( f, step );
if ( herr < 0 )
return HANDLE_H5PART_SETSTEP_ERR ( herr, step );
}
/* Get first dataset in current time-step */
sprintf ( step_name, "%s#%lld",
H5PART_PARTICLES_GROUP, (long long) f->timestep );
herr = _H5Part_get_object_name ( f->file, step_name, H5G_DATASET, 0,
dataset_name, sizeof (dataset_name) );
sprintf (
step_name, "%s#%lld",
H5PART_PARTICLES_GROUP, (long long) f->timestep );
herr = _H5Part_get_object_name (
f->file,
step_name,
H5G_DATASET,
0,
dataset_name, sizeof (dataset_name) );
if ( herr < 0 ) return herr;
dataset_id = H5Dopen ( f->timegroup, dataset_name );
if ( dataset_id < 0 )
if ( dataset_id < 0 )
return HANDLE_H5D_OPEN_ERR ( dataset_name );
space_id = _get_diskshape_for_reading ( f, dataset_id );
@@ -1668,53 +1671,30 @@ H5PartGetNumParticles (
return (h5part_int64_t) nparticles;
}
/*!
For parallel I/O or for subsetting operations on the datafile, the
\c H5PartSetView() function allows you to define a subset of the total
particle dataset to read. The concept of "view" works for both serial
and for parallel I/O. The "view" will remain in effect until a new view
is set, or the number of particles in a dataset changes, or the view is
"unset" by calling \c H5PartSetView(file,-1,-1);
Before you set a view, the \c H5PartGetNumParticles() will return the
total number of particles in the current time-step (even for the parallel
reads). However, after you set a view, it will return the number of
particles contained in the view.
The range is inclusive (the start and the end index).
\return \c H5PART_SUCCESS or error code
*/
h5part_int64_t
H5PartSetView (
H5PartFile *f, /*!< [in] Handle to open file */
h5part_int64_t start, /*!< [in] Start particle */
h5part_int64_t end /*!< [in] End particle */
H5PartGetNumParticles (
H5PartFile *f /*!< [in] Handle to open file */
) {
SET_FNAME ( "H5PartSetView" );
h5part_int64_t herr = 0;
hsize_t total;
hsize_t stride;
hsize_t dmax=H5S_UNLIMITED;
#ifdef HDF5V160
hssize_t range[2];
#else
hsize_t range[2];
#endif
SET_FNAME ( "H5PartGetNumParticles" );
CHECK_FILEHANDLE( f );
if(f->mode==H5PART_WRITE || f->mode==H5PART_APPEND)
return HANDLE_H5PART_FILE_ACCESS_TYPE_ERR ( f->mode );
if ( f->timegroup < 0 ) {
h5part_int64_t herr = _set_step ( f, 0 );
if ( herr < 0 ) return herr;
}
_H5Part_print_debug ( "Set view (%lld,%lld).",
(long long)start,(long long)end);
return _H5Part_get_num_particles ( f );
}
static h5part_int64_t
_reset_view (
H5PartFile *f /*!< [in] Handle to open file */
) {
herr_t herr = 0;
/* if there is already a view selected, lets destroy it */
f->viewstart = -1;
f->viewend = -1;
if ( f->shape != 0 ){
@@ -1733,41 +1713,99 @@ H5PartSetView (
if ( herr < 0 ) return HANDLE_H5S_CLOSE_ERR;
f->memshape=H5S_ALL;
}
if(start==-1 && end==-1) {
_H5Part_print_debug( "Early Termination: Unsetting View" );
return H5PART_SUCCESS; /* all done */
}
/* for now, we interpret start=-1 to mean 0 and
end==-1 to mean end of file */
total = (hsize_t) H5PartGetNumParticles(f);
return H5PART_SUCCESS;
}
h5part_int64_t
H5PartResetView (
H5PartFile *f /*!< [in] Handle to open file */
) {
SET_FNAME ( "H5PartResetView" );
CHECK_FILEHANDLE( f );
CHECK_READONLY_MODE ( f );
return _reset_view ( f );
}
h5part_int64_t
H5PartHasView (
H5PartFile *f /*!< [in] Handle to open file */
) {
SET_FNAME ( "H5PartResetView" );
CHECK_FILEHANDLE( f );
CHECK_READONLY_MODE ( f );
return ( f->viewstart >= 0 ) && ( f->viewend >= 0 );
}
/*!
For parallel I/O or for subsetting operations on the datafile, the
\c H5PartSetView() function allows you to define a subset of the total
particle dataset to read. The concept of "view" works for both serial
and for parallel I/O. The "view" will remain in effect until a new view
is set, or the number of particles in a dataset changes, or the view is
"unset" by calling \c H5PartSetView(file,-1,-1);
Before you set a view, the \c H5PartGetNumParticles() will return the
total number of particles in the current time-step (even for the parallel
reads). However, after you set a view, it will return the number of
particles contained in the view.
The range is inclusive (the start and the end index).
\return \c H5PART_SUCCESS or error code
*/
static h5part_int64_t
_set_view (
H5PartFile *f, /*!< [in] Handle to open file */
h5part_int64_t start, /*!< [in] Start particle */
h5part_int64_t end /*!< [in] End particle */
) {
h5part_int64_t herr = 0;
hsize_t total;
hsize_t stride = 1;
hsize_t dmax = H5S_UNLIMITED;
_H5Part_print_debug (
"Set view (%lld,%lld).",
(long long)start,(long long)end);
herr = _reset_view ( f );
if ( herr < 0 ) return herr;
if ( start == -1 && end == -1 ) return H5PART_SUCCESS;
/*
View has been reset so H5PartGetNumParticles will tell
us the total number of particles.
For now, we interpret start=-1 to mean 0 and
end==-1 to mean end of file
*/
total = (hsize_t) _H5Part_get_num_particles ( f );
if ( total < 0 ) return HANDLE_H5PART_GET_NUM_PARTICLES_ERR ( total );
if ( start == -1 ) start = 0;
if ( end == -1 ) end = total;
_H5Part_print_debug ( "Total nparticles=%lld", (long long)total );
if(start==-1) start=0;
if(end==-1) end=total; /* can we trust nparticles (no)?
fortunately, view has been reset
so H5PartGetNumParticles will tell
us the total number of particles. */
/* so, is this selection inclusive or exclusive?
it appears to be inclusive for both ends of the range.
*/
if(end<start) {
if ( end < start ) {
_H5Part_print_warn (
"Nonfatal error. "
"End of view (%lld) is less than start (%lld).",
(long long)end, (long long)start );
end = start; /* ensure that we don't have a range error */
}
range[0]=start;
range[1]=end;
/* setting up the new view */
f->viewstart=range[0]; /* inclusive start */
f->viewend=range[1]; /* inclusive end */
f->nparticles=range[1]-range[0];
_H5Part_print_debug ( "Range is now %lld:%lld",
(long long)range[0], (long long)range[1]);
/* OK, now we must create a selection from this */
f->viewstart = start;
f->viewend = end;
f->nparticles = end - start;
/* declare overall datasize */
f->shape = H5Screate_simple ( 1, &total, &total );
@@ -1782,22 +1820,40 @@ H5PartSetView (
/* declare local memory datasize */
f->memshape = H5Screate_simple(1,&(f->nparticles),&dmax);
if ( f->memshape < 0 )
return HANDLE_H5S_CREATE_SIMPLE_ERR ( f->nparticles );;
return HANDLE_H5S_CREATE_SIMPLE_ERR ( f->nparticles );
stride=1;
herr = H5Sselect_hyperslab (
f->diskshape,
H5S_SELECT_SET,
range,
(hsize_t*)&start,
&stride,
&total,
NULL );
if ( herr < 0 ) return HANDLE_H5S_SELECT_HYPERSLAB_ERR;
return H5PART_SUCCESS;
}
h5part_int64_t
H5PartSetView (
H5PartFile *f, /*!< [in] Handle to open file */
const h5part_int64_t start, /*!< [in] Start particle */
const h5part_int64_t end /*!< [in] End particle */
) {
SET_FNAME ( "H5PartSetView" );
CHECK_FILEHANDLE( f );
CHECK_READONLY_MODE ( f );
if ( f->timegroup < 0 ) {
h5part_int64_t herr = _set_step ( f, 0 );
if ( herr < 0 ) return herr;
}
return _set_view ( f, start, end );
}
/*!
Allows you to query the current view. Start and End
will be \c -1 if there is no current view established.
@@ -1815,31 +1871,32 @@ H5PartGetView (
SET_FNAME ( "H5PartGetView" );
h5part_int64_t range[2];
h5part_int64_t viewend;
CHECK_FILEHANDLE( f );
range[0] = (f->viewstart>=0) ? f->viewstart : 0;
if ( f->timegroup < 0 ) {
h5part_int64_t herr = _set_step ( f, 0 );
if ( herr < 0 ) return herr;
}
h5part_int64_t viewstart = 0;
h5part_int64_t viewend = 0;
if ( f->viewstart >= 0 )
viewstart = f->viewstart;
if ( f->viewend >= 0 ) {
viewend = f->viewend;
}
else {
viewend = H5PartGetNumParticles(f);
viewend = _H5Part_get_num_particles ( f );
if ( viewend < 0 )
return HANDLE_H5PART_GET_NUM_PARTICLES_ERR ( viewend );
}
range[1] = viewend;
if(start) {
*start=range[0];
}
if(end) {
*end=range[1];
}
if ( start ) *start = viewstart;
if ( end ) *end = viewend;
return range[1]-range[0];
return viewend - viewstart;
}
/*!
@@ -1850,6 +1907,13 @@ H5PartGetView (
\return H5PART_SUCCESS or error code
*/
/*
\note
There is a bug in this function:
If (NumParticles % f->nprocs) != 0 then
the last (NumParticles % f->nprocs) particles are not handled!
*/
h5part_int64_t
H5PartSetCanonicalView (
H5PartFile *f /*!< [in] Handle to open file */
@@ -1857,66 +1921,53 @@ H5PartSetCanonicalView (
SET_FNAME ( "H5PartSetCanonicalView" );
h5part_int64_t r;
h5part_int64_t herr;
CHECK_FILEHANDLE( f );
CHECK_READONLY_MODE ( f )
if(f->mode==H5PART_WRITE || f->mode==H5PART_APPEND)
return HANDLE_H5PART_FILE_ACCESS_TYPE_ERR ( f->mode );
herr = _reset_view ( f );
if ( herr < 0 ) return HANDLE_H5PART_SET_VIEW_ERR( herr, -1, -1 );
/* if a read_only file, search for on-disk canonical view */
/* if this view does not exist, then if MPI, subdivide by numprocs */
/* else, "unset" any existing View */
/* unset the view */
r = H5PartSetView(f,-1,-1);
if ( r < 0 ) return HANDLE_H5PART_SET_VIEW_ERR( r, -1, -1 );
#ifdef PARALLEL_IO
{
h5part_int64_t start = 0;
h5part_int64_t end = 0;
h5part_int64_t n = 0;
int i = 0;
if ( f->timegroup < 0 ) {
/* set to first step in file */
r = H5PartSetStep(f,0);
if ( r < 0 ) return HANDLE_H5PART_SETSTEP_ERR ( r, 0 );
}
n = H5PartGetNumParticles(f);
if ( n < 0 ) return HANDLE_H5PART_GET_NUM_PARTICLES_ERR ( n );
/*
now lets query the attributes for this group to see if there
is a 'pnparticles' group that contains the offsets for the
processors.
*/
/* try to read pnparticles right off of the disk */
if ( _H5Part_read_attrib (
f->timegroup,
"pnparticles", f->pnparticles ) < 0) {
/*
automatically subdivide the view into NP mostly
equal pieces
*/
n /= f->nprocs;
for ( i=0; i<f->nprocs; i++ ) {
f->pnparticles[i] = n;
}
}
/* now we set the view for this processor */
for ( i = 0; i < f->myproc; i++ ){
start += f->pnparticles[i];
}
end = start + f->pnparticles[f->myproc] - 1;
r = H5PartSetView ( f, start, end );
if ( r < 0 )
return HANDLE_H5PART_SET_VIEW_ERR ( r, start, end );
h5part_int64_t start = 0;
h5part_int64_t end = 0;
h5part_int64_t n = 0;
int i = 0;
if ( f->timegroup < 0 ) {
herr = _set_step ( f, 0 );
if ( herr < 0 ) return herr;
}
n = _H5Part_get_num_particles ( f );
if ( n < 0 ) return HANDLE_H5PART_GET_NUM_PARTICLES_ERR ( n );
/*
now lets query the attributes for this group to see if there
is a 'pnparticles' group that contains the offsets for the
processors.
*/
if ( _H5Part_read_attrib (
f->timegroup,
"pnparticles", f->pnparticles ) < 0) {
/*
Attribute "pnparticles" is not available. So
subdivide the view into NP mostly equal pieces
*/
n /= f->nprocs;
for ( i=0; i<f->nprocs; i++ ) {
f->pnparticles[i] = n;
}
}
for ( i = 0; i < f->myproc; i++ ){
start += f->pnparticles[i];
}
end = start + f->pnparticles[f->myproc] - 1;
r = _set_view ( f, start, end );
if ( r < 0 ) return HANDLE_H5PART_SET_VIEW_ERR ( r, start, end );
#endif
/* the canonical view is to see everything if this is serial
so there is nothing left to do */
return H5PART_SUCCESS;
}
@@ -1933,10 +1984,9 @@ _read_data (
hid_t space_id;
hid_t memspace_id;
if ( ! f->timegroup ) {
herr = H5PartSetStep ( f, f->timestep );
if ( herr < 0 )
return HANDLE_H5PART_SETSTEP_ERR ( herr, f->timestep );
if ( f->timegroup < 0 ) {
herr = _set_step ( f, f->timestep );
if ( herr < 0 ) return herr;
}
dataset_id = H5Dopen ( f->timegroup, name );
if ( dataset_id < 0 ) return HANDLE_H5D_OPEN_ERR ( name );
@@ -2015,7 +2065,7 @@ H5PartReadDataFloat64 (
h5part_int64_t
H5PartReadDataInt64 (
H5PartFile *f, /*!< [in] Handle to open file */
char *name, /*!< [in] Name to associate dataset with */
const char *name, /*!< [in] Name to associate dataset with */
h5part_int64_t *array /*!< [out] Array of data */
) {
@@ -2061,8 +2111,8 @@ H5PartReadParticleStep (
CHECK_FILEHANDLE( f );
herr = H5PartSetStep(f,step);
if ( herr < 0 ) return HANDLE_H5PART_SETSTEP_ERR ( herr, step );
herr = _set_step ( f, step );
if ( herr < 0 ) return herr;
herr = _read_data ( f, "x", (void*)x, H5T_NATIVE_DOUBLE );
if ( herr < 0 ) return herr;