output_xmf.h

XMDF
- Light Data
  - Typical example
- Heavy Data

XMDF

Light data is stored using eXtensible Markup Language (XML) to describe the data model and the data format. We’re going to output two main types of files. Heavy files are set to H5FILE_NAME for 3D fields and H5FILE_NAME2 for extracting slices.

#ifndef H5FILE_NAME
#define H5FILE_NAME "output_fields.h5"
#endif

#ifndef H5FILE_NAME2
#define H5FILE_NAME2 "output_slices.h5"
#endif

Light Data

Light files are created by the auxiliar functions write_xml_h5_head, write_xml_h5_body and write_xml_h5_tail.

void write_xml_h5_head(char * subname){
	if (pid() == 0){
		char name[111];
		sprintf(name, "%s.xmf", subname);
		FILE *fp = fopen(name, "w");

#if defined(_OPENMP)
		int num_omp = omp_get_max_threads();
		omp_set_num_threads(1);
#endif

		/* Write the xmf file. */
		fputs("<?xml version=\"1.0\"?>\n", fp);
		fputs("<!DOCTYPE Xdmf SYSTEM \"Xdmf.dtd\" []>\n", fp);
		fputs("<Xdmf xmlns:xi=\"http://www.w3.org/2003/XInclude\" Version=\"2.2\">\n",
					fp);
		fputs("\t <Domain>\n", fp);
		fputs("\t\t <Grid GridType=\"Collection\" CollectionType=\"Temporal\" >\n", fp);
		fputs("\n", fp);

#if defined(_OPENMP)
		omp_set_num_threads(num_omp);
#endif
		fflush(fp);
		fclose(fp);
	}
}

void write_xml_h5_body(scalar *list, vector *vlist, char * filename, char * subname, char *stamp, int no_cells, int no_point, int dim){
	char name[111];
	sprintf(name, "%s.xmf", subname);
  FILE * fp = fopen(name, "a");

#if defined(_OPENMP)
  int num_omp = omp_get_max_threads();
  omp_set_num_threads(1);
#endif

	/* Write the xmf file. */
	fputs("\t\t\t <Grid GridType=\"Uniform\">\n", fp);
	fprintf(fp, "\t\t\t\t <Time Type=\"Single\" Value=\"%g\" />\n", t);

	if (dim == 2)
	{
		fprintf(fp, "\t\t\t\t <Topology TopologyType=\"Quadrilateral\" Dimensions=\"%d\">\n", no_cells);
		fprintf(fp, "\t\t\t\t\t <DataItem Dimensions=\"%d 4\" NumberType=\"Int\" Precision=\"8\" Format=\"HDF\">\n", no_cells);
	}

	if (dim == 3)
	{
		fprintf(fp, "\t\t\t\t <Topology TopologyType=\"Hexahedron\" Dimensions=\"%d\">\n", no_cells);
		fprintf(fp, "\t\t\t\t\t <DataItem Dimensions=\"%d 8\" NumberType=\"Int\" Precision=\"8\" Format=\"HDF\">\n", no_cells);
	}

	fprintf(fp, "\t\t\t\t\t\t %s:/%s/Topology\n", filename, stamp);
	fputs("\t\t\t\t\t </DataItem>\n", fp);
	fputs("\t\t\t\t </Topology>\n", fp);
	fputs("\t\t\t\t <Geometry GeometryType=\"XYZ\">\n", fp);
	fprintf(fp, "\t\t\t\t\t <DataItem Dimensions=\"%d 3\" NumberType=\"Float\" Precision=\"8\" Format=\"HDF\">\n", no_point);
	fprintf(fp, "\t\t\t\t\t\t %s:/%s/Geometry/Points\n", filename, stamp);
	fputs("\t\t\t\t\t </DataItem>\n", fp);
	fputs("\t\t\t\t </Geometry>\n", fp);
	for (scalar s in list)
	{
		fprintf(fp, "\t\t\t\t <Attribute Name=\"%s\" Active=\"1\" AttributeType=\"Scalar\" Center=\"Cell\">\n", s.name);
		fprintf(fp, "\t\t\t\t\t <DataItem Dimensions=\"%d\" NumberType=\"Float\" Precision=\"8\" Format=\"HDF\">\n", no_cells);
		fprintf(fp, "\t\t\t\t\t\t %s:/%s/Cell/%s\n", filename, stamp, s.name);
		fputs("\t\t\t\t\t </DataItem>\n", fp);
		fputs("\t\t\t\t </Attribute>\n", fp);
	}
	for (vector v in vlist)
	{
		fprintf(fp, "\t\t\t\t <Attribute Name=\"%s\" Active=\"1\" AttributeType=\"Vector\" Center=\"Cell\">\n", v.x.name);
		fprintf(fp, "\t\t\t\t\t <DataItem Dimensions=\"%d 3\" NumberType=\"Float\" Precision=\"8\" Format=\"HDF\">\n", no_cells);
		fprintf(fp, "\t\t\t\t\t\t %s:/%s/Cell/%s\n", filename, stamp, v.x.name);
		fputs("\t\t\t\t\t </DataItem>\n", fp);
		fputs("\t\t\t\t </Attribute>\n", fp);
	}
	fputs("\t\t\t </Grid>\n", fp);
	fputs("\n", fp);
#if defined(_OPENMP)
  omp_set_num_threads(num_omp);
#endif
	fflush(fp);
	fclose (fp);
}

void write_xml_h5_tail(char *subname)
{
	if (pid() == 0){
		char name[111];
		sprintf(name, "%s.xmf", subname);
		FILE *fp = fopen(name, "a");

#if defined(_OPENMP)
		int num_omp = omp_get_max_threads();
		omp_set_num_threads(1);
#endif

		/* Write the xmf file. */
		fputs("\t\t </Grid>\n", fp);
		fputs("\t </Domain>\n", fp);
		fputs("</Xdmf>\n", fp);

#if defined(_OPENMP)
		omp_set_num_threads(num_omp);
#endif
		fflush(fp);
		fclose(fp);
	}
}

Typical example

A typical example would look like this

  create_output_h5(H5FILE_NAME);
  write_xml_h5_head("test");
  output_xmf (slist, vlist, "test", "3D000");
  write_xml_h5_tail("test");

This creates a file “output_fields.h5” which contains

>> h5ls -r output_fields.h5
/                        Group
/3D000                   Group
/3D000/Cell              Group
/3D000/Cell/s            Dataset {3050496, 1}
/3D000/Cell/u.x          Dataset {3050496, 3}
...

and a file test.xmf explaining how to read the data

<?xml version="1.0"?>
<!DOCTYPE Xdmf SYSTEM "Xdmf.dtd" []>
<Xdmf xmlns:xi="http://www.w3.org/2003/XInclude" Version="2.2">
         <Domain>
                 <Grid GridType="Collection" CollectionType="Temporal" >

                         ...

                 </Grid>
         </Domain>
</Xdmf>

Heavy Data

Heavy data is composed of large datasets stored using the Hierarchical Data Format HDF5. Additional features include support for a large number of objects, file compression, a parallel I/O implementation through the MPI-IO or MPI POSIX drivers.

To use HDF5 we need to “declare” the library in the qcc system

 echo "@include <hdf5.h>" > $BASILISK/ast/std/hdf5.h
 echo "@include <hdf5_hl.h>" > $BASILISK/ast/std/hdf5_hl.h

and declade the datatypes at the end of $BASILISK/ast/defaults.h

 echo "typedef hid_t, hsize_t, herr_t, H5L_info_t;" >> $BASILISK/ast/defaults.h

see more about declaractions with qcc in the forum.

#include "output_hdf5.h"