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-rw-r--r--src/DumpVar.c365
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diff --git a/src/DumpVar.c b/src/DumpVar.c
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--- a/src/DumpVar.c
+++ /dev/null
@@ -1,365 +0,0 @@
-/*@@
- @file DumpVar.c
- @date Fri May 21 1999
- @author Thomas Radke / Gerd Lanfermann
- @desc
- Do the actual writing of a variable.
- @enddesc
- @history
- @hauthor Thomas Radke @hdate May 21 1999
- @hdesc Just copied from thorn FlexIO.
- @hendhistory
- @@*/
-
-
-#include <stdio.h>
-#include <stdlib.h>
-
-#include "cctk.h"
-#include "cctk_Parameters.h"
-#include "CactusBase/IOUtil/src/ioGH.h"
-#include "CactusPUGH/PUGHSlab/src/PUGHSlab.h"
-#include "StreamedHDF5GH.h"
-
-
-/*#define StreamedHDF5_DEBUG 1 */
-
-/* local function prototypes */
-static void StreamedHDF5_Dump (cGH *GH, int index, int timelevel, void *outme,
- int hdim, int *hsizes, int hdf5_type, hid_t fid);
-static void StreamedHDF5_AddCommonAttributes (cGH *GH, int hdim, hid_t dataset);
-static int GetHDF5type (StreamedHDF5GH *myGH, int vtype, hid_t *hdf5_type);
-
-/*@@
- @routine StreamedHDF5_DumpVar
- @date 16 Apr 1999
- @author Thomas Radke
- @desc
- Generic dump routine, just calls the appropriate dump routine
- Extracts the data with Hyperslab.
- @enddesc
- @calledby StreamedHDF5_DumpGH IOHDF5_Write3D
- @history
- @endhistory
- @var GH
- @vdesc Pointer to CCTK grid hierarchy
- @vtype cGH
- @vio in
- @endvar
- @var index
- @vdesc global index of the variable to be dumped
- @vtype int
- @vio in
- @endvar
- @var timelevel
- @vdesc the timelevel to store
- @vtype int
- @vio in
- @endvar
- @var fid
- @vdesc the HDF5 file handle
- @vtype hid_t
- @vio in
- @endvar
-@@*/
-int StreamedHDF5_DumpVar (cGH *GH, int index, int timelevel, hid_t fid)
-{
- DECLARE_CCTK_PARAMETERS
- void *data;
- int *hsizes;
- hid_t hdf5_type;
- StreamedHDF5GH *myGH;
- StreamGeo_t geo;
- int vtype;
-
- int sdir[3] = {0,0,0};
-
-
- /* Get the handle for StreamedHDF5 extensions */
- myGH = (StreamedHDF5GH *) GH->extensions [CCTK_GHExtensionHandle ("StreamedHDF5")];
-
- vtype = CCTK_VarTypeI (index);
- if (GetHDF5type (myGH, vtype, &hdf5_type) < 0)
- {
- CCTK_VWarn (1, __LINE__, __FILE__, CCTK_THORNSTRING,
- "Unsupported variable type %d", vtype);
- return (-1);
- }
- /* shortcut to the slab geometry */
- geo = myGH->geo_output[index];
-
- /* get the dimension of the variable */
-
- hsizes = (int*)malloc(geo.sdim*sizeof(int));
-
- data = NULL;
-
- /* TEMPORARY FIX DUE TO INCONSISTENT DIR SPECIFICATION */
- /* direction vector of 1d line in 3d volume */
- if (geo.sdim==1) {
- sdir[0] = (geo.direction[0]==0) ? 1:0;
- sdir[1] = (geo.direction[0]==1) ? 1:0;
- sdir[2] = (geo.direction[0]==2) ? 1:0;
- }
- /* norm vector of 2d surface in 3d volume */
- else if (geo.sdim==2)
- {
- sdir[0] = ((geo.direction[0]==1)&&(geo.direction[1]==2)) ? 1:0;
- sdir[1] = ((geo.direction[0]==0)&&(geo.direction[1]==2)) ? 1:0;
- sdir[2] = ((geo.direction[0]==0)&&(geo.direction[1]==1)) ? 1:0;
- }
- /* spanning directions for 3d */
- else if (geo.sdim==3)
- {
- sdir[0] = geo.direction[0];
- sdir[1] = geo.direction[1];
- sdir[2] = geo.direction[2];
- }
- else
- {
- char *fullname = CCTK_FullName (index);
- CCTK_VWarn (1, __LINE__, __FILE__, CCTK_THORNSTRING,
- "No 0-dim extraction possible: '%s'", fullname);
- free (fullname);
- return (-1);
- }
-
- if (Hyperslab_GetHyperslab (GH, 0, index, timelevel, geo.sdim, geo.origin,
- sdir, geo.length, geo.downs,
- &data, hsizes) < 0)
- {
- char *fullname = CCTK_FullName (index);
-
-
- CCTK_VWarn (1, __LINE__, __FILE__, CCTK_THORNSTRING,
- "Failed to extract hyperslab for variable '%s'", fullname);
- free (fullname);
- return (-1);
- }
-
- if (fid >= 0)
- {
- StreamedHDF5_Dump (GH, index, timelevel, data, geo.sdim, hsizes, hdf5_type, fid);
- }
-
- if (data)
- {
- free (data);
- }
- if (hsizes)
- {
- free (hsizes);
- }
-
- return (0);
-}
-
-
-/***************************** local functions ****************************/
-
-static int GetHDF5type (StreamedHDF5GH *myGH, int vtype, hid_t *hdf5_type)
-{
- int retval = 0;
-
-
- switch (vtype)
- {
- case CCTK_VARIABLE_CHAR:
- *hdf5_type = IOHDF5_CHAR;
- break;
- case CCTK_VARIABLE_INT:
- *hdf5_type = IOHDF5_INT;
- break;
- case CCTK_VARIABLE_REAL:
- *hdf5_type = IOHDF5_REAL;
- break;
- case CCTK_VARIABLE_COMPLEX:
- *hdf5_type = myGH->IOHDF5_COMPLEX;
- break;
- default:
- retval = -1;
- break;
- }
-
- return (retval);
-}
-
-
-/*@@
- @routine StreamedHDF5_AddCommonAttributes
- @date May 21 1999
- @author Thomas Radke
- @desc
- Add "Common" attributes, these are:
- <ul>
- <li> the variable's groupname
- <li> the grouptype
- <li> number of timelevels
- <li> the current date
- Note that the datestamp should be turned of if you are byte
- comparing two output files.
- <li> simulation time
- <li> origin
- <li> bounding box
- <li> gridspacings (both downsampled and evolution)
- <li> global grid size
- </ul>
- @enddesc
- @calledby StreamedHDF5_DumpGS, IOHDF5_collectiveDump, IOHDF5_procDump
- @history
- @endhistory
- @var GH
- @vdesc Pointer to CCTK grid hierarchy
- @vtype cGH
- @vio in
- @endvar
- @var index
- @vdesc global index of the variable to be dumped
- @vtype int
- @vio in
- @endvar
- @var timelevel
- @vdesc the timelevel to store
- @vtype int
- @vio in
- @endvar
- @var dataset
- @vdesc the dataset handle where the attributes should be attached to
- @vtype hid_t
- @vio in
- @endvar
-@@*/
-static void StreamedHDF5_AddCommonAttributes (cGH *GH, int hdim, hid_t dataset)
-{
- DECLARE_CCTK_PARAMETERS
- CCTK_REAL realAttr [6];
- StreamedHDF5GH *myGH;
- CCTK_REAL dummy;
-
- /* Get the handles for IOUtil and StreamedHDF5 extensions */
- myGH = (StreamedHDF5GH *) GH->extensions [CCTK_GHExtensionHandle ("StreamedHDF5")];
-
- WRITE_ATTRIBUTE ("time", &GH->cctk_time, dataset, myGH->scalarDataspace, 0,
- IOHDF5_REAL);
-
- /* NOTE: the attributes "origin", "min_ext", "max_ext", and "delta"
- are always stored as 3-dimensional points */
- CCTK_CoordRange (GH, &realAttr [0], &dummy, -1, "x", "cart3d");
- CCTK_CoordRange (GH, &realAttr [1], &dummy, -1, "y", "cart3d");
- CCTK_CoordRange (GH, &realAttr [2], &dummy, -1, "z", "cart3d");
-
- WRITE_ATTRIBUTE ("origin", realAttr, dataset, myGH->arrayDataspace, hdim,
- IOHDF5_REAL);
-
- CCTK_CoordRange (GH, &realAttr [0], &realAttr [3], -1, "x","cart3d");
- CCTK_CoordRange (GH, &realAttr [1], &realAttr [4], -1, "y","cart3d");
- CCTK_CoordRange (GH, &realAttr [2], &realAttr [5], -1, "z","cart3d");
- WRITE_ATTRIBUTE ("min_ext", realAttr, dataset, myGH->arrayDataspace, hdim,
- IOHDF5_REAL);
- WRITE_ATTRIBUTE ("max_ext", realAttr + 3, dataset, myGH->arrayDataspace, hdim,
- IOHDF5_REAL);
-
- WRITE_ATTRIBUTE ("delta", GH->cctk_delta_space, dataset, myGH->arrayDataspace,
- hdim, IOHDF5_REAL);
-}
-
-
-/*@@
- @routine StreamedHDF5_procDump
- @author Thomas Radke
- @date May 21 1999
- @desc All IO processors dump the data of their group into the file,
- either as one chunk per processor or unchunked
- (depending on parameter "unchunked").
- @enddesc
- @calledby StreamedHDF5_DumpGA
- @history
- @endhistory
- @var GH
- @vdesc Pointer to CCTK grid hierarchy
- @vtype cGH
- @vio in
- @endvar
- @var index
- @vdesc global index of the variable to be dumped
- @vtype int
- @vio in
- @endvar
- @var timelevel
- @vdesc the timelevel to store
- @vtype int
- @vio in
- @endvar
- @var outme
- @vdesc pointer to the chunk to dump
- @vtype void *
- @vio in
- @endvar
- @var geom
- @vdesc bounds and sizes of the output
- @vtype CCTK_INT [3*dim]
- @vio in
- @vcomment geom [0*dim..1*dim-1]: lower bounds
- geom [1*dim..2*dim-1]: (local) data sizes
- geom [2*dim..3*dim-1]: global space
- @endvar
- @var proc
- @vdesc the processor which's chunk is to be dumped
- @vtype int
- @vio in
- @endvar
- @var hdf5io_type
- @vdesc the HDF5 datatype identifier
- @vtype int
- @vio in
- @endvar
- @var fid
- @vdesc the HDF5 file handle
- @vtype hid_t
- @vio in
- @endvar
-@@*/
-static void StreamedHDF5_Dump (cGH *GH, int index, int timelevel, void *outme,
- int hdim, int *hsizes, int hdf5_type, hid_t fid)
-{
- DECLARE_CCTK_PARAMETERS
- int i;
- hid_t dataset, memspace;
- char *name, *datasetname;
- hsize_t *dims;
-
-
- dims = (hsize_t *) malloc (hdim * sizeof (hsize_t));
-
- /* HDF5 needs it in reverse order */
- for (i = 0; i < hdim; i++)
- {
- dims [i] = hsizes [hdim - 1 - i];
- }
-
- /* build the unique dataset name */
- name = CCTK_FullName (index);
- datasetname = (char *) malloc (strlen (name) + 30); /* 30 chars should be
- enough for 2 ints */
- sprintf (datasetname, "%s@%d@%d", name, GH->cctk_iteration, timelevel);
- free (name);
-
- /* create the memspace according to chunk dims */
- CACTUS_IOHDF5_ERROR (memspace = H5Screate_simple (hdim, dims, NULL));
-
- /* create the dataset */
- CACTUS_IOHDF5_ERROR (dataset = H5Dcreate (fid, datasetname, hdf5_type,
- memspace, H5P_DEFAULT));
- /* write the data */
- CACTUS_IOHDF5_ERROR (H5Dwrite (dataset, hdf5_type, H5S_ALL, H5S_ALL,
- H5P_DEFAULT, outme));
-
- StreamedHDF5_AddCommonAttributes (GH, hdim, dataset);
-
- /* close the dataset and the memspace */
- CACTUS_IOHDF5_ERROR (H5Dclose (dataset));
- CACTUS_IOHDF5_ERROR (H5Sclose (memspace));
-
- free (datasetname);
- free (dims);
-}
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