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-rw-r--r--Carpet/CarpetIOHDF5/src/iohdf5utils.cc521
1 files changed, 521 insertions, 0 deletions
diff --git a/Carpet/CarpetIOHDF5/src/iohdf5utils.cc b/Carpet/CarpetIOHDF5/src/iohdf5utils.cc
new file mode 100644
index 000000000..5545a3563
--- /dev/null
+++ b/Carpet/CarpetIOHDF5/src/iohdf5utils.cc
@@ -0,0 +1,521 @@
+#include <assert.h>
+#include <limits.h>
+#include <stdio.h>
+#include <stdlib.h>
+#include <string.h>
+#include <sys/stat.h>
+#include <sys/types.h>
+
+#include <algorithm>
+#include <fstream>
+#include <sstream>
+#include <vector>
+
+#include <hdf5.h>
+
+#include "cctk.h"
+#include "cctk_Parameters.h"
+
+extern "C" {
+ static const char* rcsid = "$Header: /home/eschnett/C/carpet/Carpet/Carpet/CarpetIOHDF5/src/iohdf5utils.cc,v 1.8 2004/07/07 17:09:17 tradke Exp $";
+ CCTK_FILEVERSION(Carpet_CarpetIOHDF5_iohdf5utils_cc);
+}
+
+#include "CactusBase/IOUtil/src/ioGH.h"
+#include "CactusBase/IOUtil/src/ioutil_CheckpointRecovery.h"
+
+#include "bbox.hh"
+#include "data.hh"
+#include "gdata.hh"
+#include "ggf.hh"
+#include "vect.hh"
+
+#include "carpet.hh"
+
+#include "iohdf5.hh"
+#include "iohdf5GH.h"
+
+
+
+namespace CarpetIOHDF5 {
+
+ using namespace std;
+ using namespace Carpet;
+
+
+
+ bool CheckForVariable (const char* const varlist, const int vindex)
+ {
+ const int numvars = CCTK_NumVars();
+ assert (vindex>=0 && vindex<numvars);
+
+ vector<bool> flags(numvars);
+
+ CCTK_TraverseString (varlist, SetFlag, &flags, CCTK_GROUP_OR_VAR);
+
+ return flags.at(vindex);
+ }
+
+ void SetFlag (int vindex, const char* optstring, void* arg)
+ {
+ if (optstring)
+ {
+ char *fullname = CCTK_FullName (vindex);
+ CCTK_VWarn (2, __LINE__, __FILE__, CCTK_THORNSTRING,
+ "Option string '%s' will be ignored for HDF5 output of "
+ "variable '%s'", optstring, fullname);
+ free (fullname);
+ }
+ vector<bool>& flags = *(vector<bool>*)arg;
+ flags.at(vindex) = true;
+ }
+
+
+
+ void WriteAttribute (const hid_t dataset, const char* const name, const int value)
+ {
+ WriteAttribute (dataset, name, &value, 1);
+ }
+
+ void WriteAttribute (const hid_t dataset, const char* const name, const int* const values, const int nvalues)
+ {
+ assert (dataset>=0);
+ assert (name);
+ assert (values);
+ assert (nvalues>=0);
+
+ herr_t herr;
+
+ hsize_t shape[1];
+ shape[0] = nvalues;
+ const hid_t dataspace = nvalues==1 ? H5Screate (H5S_SCALAR) : H5Screate_simple (1, shape, NULL);
+ assert (dataspace>=0);
+
+ const hid_t datatype = H5T_NATIVE_INT;
+
+ const hid_t attribute = H5Acreate (dataset, name, datatype, dataspace, H5P_DEFAULT);
+ assert (attribute>=0);
+ herr = H5Awrite (attribute, datatype, values);
+ assert (!herr);
+ herr = H5Aclose (attribute);
+ assert (!herr);
+
+ herr = H5Sclose (dataspace);
+ assert (!herr);
+ }
+
+
+
+ void WriteAttribute (const hid_t dataset, const char* const name, const double value)
+ {
+ WriteAttribute (dataset, name, &value, 1);
+ }
+
+ void WriteAttribute (const hid_t dataset, const char* const name, const double* const values, const int nvalues)
+ {
+ assert (dataset>=0);
+ assert (name);
+ assert (values);
+ assert (nvalues>=0);
+
+ herr_t herr;
+
+ hsize_t shape[1];
+ shape[0] = nvalues;
+ const hid_t dataspace = nvalues==1 ? H5Screate (H5S_SCALAR) : H5Screate_simple (1, shape, NULL);
+ assert (dataspace>=0);
+
+ const hid_t datatype = H5T_NATIVE_DOUBLE;
+
+ const hid_t attribute = H5Acreate (dataset, name, datatype, dataspace, H5P_DEFAULT);
+ assert (attribute>=0);
+ herr = H5Awrite (attribute, datatype, values);
+ assert (!herr);
+ herr = H5Aclose (attribute);
+ assert (!herr);
+
+ herr = H5Sclose (dataspace);
+ assert (!herr);
+ }
+
+
+
+ void WriteAttribute (const hid_t dataset, const char* const name, const char value)
+ {
+ WriteAttribute (dataset, name, &value, 1);
+ }
+
+ void WriteAttribute (const hid_t dataset, const char* const name, const char* const values)
+ {
+ WriteAttribute (dataset, name, values, strlen(values));
+ }
+
+ void WriteAttribute (const hid_t dataset, const char* const name, const char* const values, const int nvalues)
+ {
+ assert (dataset>=0);
+ assert (name);
+ assert (values);
+ assert (nvalues>=0);
+
+ herr_t herr;
+
+ const hid_t dataspace = H5Screate (H5S_SCALAR);
+ assert (dataspace>=0);
+
+ const hid_t datatype = H5Tcopy (H5T_C_S1);
+ assert (datatype>=0);
+ herr = H5Tset_size (datatype, nvalues);
+ assert (!herr);
+
+ const hid_t attribute = H5Acreate (dataset, name, datatype, dataspace, H5P_DEFAULT);
+ assert (attribute>=0);
+ herr = H5Awrite (attribute, datatype, values);
+ assert (!herr);
+ herr = H5Aclose (attribute);
+ assert (!herr);
+
+ herr = H5Tclose (datatype);
+ assert (!herr);
+
+ herr = H5Sclose (dataspace);
+ assert (!herr);
+ }
+
+
+
+ int ReadAttribute (const hid_t dataset, const char* const name, int& value)
+ {
+ return ReadAttribute (dataset, name, &value, 1);
+ }
+
+ int ReadAttribute (const hid_t dataset, const char* name, int* const values, const int nvalues)
+ {
+ assert (dataset>=0);
+ assert (name);
+ assert (values);
+ assert (nvalues>=0);
+
+ herr_t herr;
+
+ const hid_t attribute = H5Aopen_name (dataset, name);
+ if (attribute<0) return attribute;
+
+ const hid_t dataspace = H5Aget_space (attribute);
+ assert (dataspace>=0);
+
+ // cout << "reading int attribute " << name << endl;
+
+ hsize_t rank = H5Sget_simple_extent_ndims (dataspace);
+ hsize_t shape[1];
+ if (rank==0) {
+ shape[0] = 1;
+ } else if (rank==1) {
+ herr = H5Sget_simple_extent_dims (dataspace, shape, NULL);
+ assert (herr >= 0);
+ } else {
+ assert (0);
+ }
+ const int length = shape[0];
+
+ const hid_t datatype = H5Aget_type (attribute);
+ assert (datatype>=0);
+
+ assert(H5Tequal(datatype, H5T_NATIVE_INT));
+
+ vector<int> values1(length);
+
+ herr = H5Aread (attribute, datatype, &values1.at(0));
+ assert (!herr);
+
+ for (int i=0; i<min(length, nvalues); ++i) {
+ values[i] = values1[i];
+ }
+
+ herr = H5Tclose (datatype);
+ assert (!herr);
+
+ herr = H5Sclose (dataspace);
+ assert (!herr);
+
+ herr = H5Aclose (attribute);
+ assert (!herr);
+
+ return length;
+ }
+
+
+
+ int ReadAttribute (const hid_t dataset, const char* const name, double& value)
+ {
+ return ReadAttribute (dataset, name, &value, 1);
+ }
+
+ int ReadAttribute (const hid_t dataset, const char* const name, double* const values, const int nvalues)
+ {
+ assert (dataset>=0);
+ assert (name);
+ assert (values);
+ assert (nvalues>=0);
+
+ herr_t herr;
+
+ const hid_t attribute = H5Aopen_name (dataset, name);
+ if (attribute<0) return attribute;
+
+ const hid_t dataspace = H5Aget_space (attribute);
+ assert (dataspace>=0);
+
+ hsize_t rank = H5Sget_simple_extent_ndims (dataspace);
+ hsize_t shape[1];
+ if (rank==0) {
+ shape[0] = 1;
+ } else if (rank==1) {
+ rank = H5Sget_simple_extent_dims (dataspace, shape, NULL);
+ assert (rank == 1);
+ } else {
+ assert (0);
+ }
+ const int length = shape[0];
+
+ const hid_t datatype = H5Aget_type (attribute);
+ assert (datatype>=0);
+ assert(H5Tequal(datatype, H5T_NATIVE_DOUBLE));
+
+ vector<double> values1(length);
+
+ herr = H5Aread (attribute, datatype, &values1.at(0));
+ assert (!herr);
+
+ for (int i=0; i<min(length, nvalues); ++i) {
+ values[i] = values1[i];
+ }
+
+ herr = H5Tclose (datatype);
+ assert (!herr);
+
+ herr = H5Sclose (dataspace);
+ assert (!herr);
+
+ herr = H5Aclose (attribute);
+ assert (!herr);
+
+ return length;
+ }
+
+
+
+ int ReadAttribute (const hid_t dataset, const char* const name, char& value)
+ {
+ return ReadAttribute (dataset, name, &value, 1);
+ }
+
+ int ReadAttribute (const hid_t dataset, const char* const name, char*& values)
+ {
+ assert (dataset>=0);
+ assert (name);
+
+ herr_t herr;
+
+ const hid_t attribute = H5Aopen_name (dataset, name);
+ if (attribute<0) return attribute;
+
+ const hid_t dataspace = H5Aget_space (attribute);
+ assert (dataspace>=0);
+
+ hsize_t rank = H5Sget_simple_extent_ndims (dataspace);
+ assert (rank==0);
+
+ const hid_t datatype = H5Aget_type (attribute);
+ assert (datatype>=0);
+ assert (H5Tget_class (datatype) == H5T_STRING);
+ const int length = H5Tget_size (datatype);
+ assert (length>=0);
+
+ values = (char*) malloc (length+1);
+ assert (values);
+
+ herr = H5Aread (attribute, datatype, values);
+ assert (!herr);
+ values[length] = '\0';
+
+ herr = H5Tclose (datatype);
+ assert (!herr);
+
+ herr = H5Sclose (dataspace);
+ assert (!herr);
+
+ herr = H5Aclose (attribute);
+ assert (!herr);
+
+ return length;
+ }
+
+ int ReadAttribute (const hid_t dataset, const char* const name, char* const values, const int nvalues)
+ {
+ assert (dataset>=0);
+ assert (name);
+ assert (values);
+ assert (nvalues>=0);
+
+ herr_t herr;
+
+ const hid_t attribute = H5Aopen_name (dataset, name);
+ if (attribute<0) return attribute;
+
+ const hid_t dataspace = H5Aget_space (attribute);
+ assert (dataspace>=0);
+
+ hsize_t rank = H5Sget_simple_extent_ndims (dataspace);
+ assert (rank==0);
+
+ const hid_t datatype = H5Aget_type (attribute);
+ assert (datatype>=0);
+ assert(H5Tget_class (datatype) == H5T_STRING);
+ const int length = H5Tget_size (datatype);
+ assert (length>=0);
+
+ vector<char> values1(length);
+
+ herr = H5Aread (attribute, datatype, &values1.at(0));
+ assert (!herr);
+
+ for (int i=0; i<min(length, nvalues); ++i) {
+ values[i] = values1[i];
+ }
+
+ herr = H5Tclose (datatype);
+ assert (!herr);
+
+ herr = H5Sclose (dataspace);
+ assert (!herr);
+
+ herr = H5Aclose (attribute);
+ assert (!herr);
+
+ return length;
+ }
+
+ herr_t DatasetCounter(hid_t group_id, const char *member_name, void *operator_data)
+ /* Counts datasets. Used by GetnDatasets; straight from John Shalf's FlexIO library */
+ {
+ int *count = (int*)operator_data;
+ H5G_stat_t objinfo;
+ // request info about the type of objects in root group
+ if(H5Gget_objinfo(group_id,member_name,1 /* follow links */,&objinfo)<0) {
+ return 0;
+ }
+ // only count objects that are datasets (not subgroups)
+ if(objinfo.type==H5G_DATASET) {
+ (*count)++;
+ }
+ return 0;
+ }
+
+
+ int GetnDatasets(const hid_t reader)
+ {
+ //this is straight from John Shalf's FlexIO library
+
+ int count=0;
+ int idx=0;
+ while(H5Giterate(reader, /* hid_t loc_id, */
+ "/", /*const char *name, */
+ &idx, /* int *idx, */
+ DatasetCounter,
+ &count)<0){}
+ return count;
+ }
+
+ struct H5IO_getname_t {
+ //this is straight from John Shalf's FlexIO library
+ int index,count;
+ char *name;
+ };
+
+
+ herr_t GetName(hid_t group_id, const char *member_name, void *operator_data)
+ {
+ //this is straight from John Shalf's FlexIO library
+ H5IO_getname_t *getn = (H5IO_getname_t*)operator_data;
+ // check type first (only respond if it is a dataset)
+ H5G_stat_t objinfo;
+ // request info about the type of objects in root group
+ if(H5Gget_objinfo(group_id,
+ member_name,
+ 1 /* follow links */,
+ &objinfo)<0) return 0; // error (probably bad symlink)
+ // only count objects that are datasets (not subgroups)
+ if(objinfo.type!=H5G_DATASET)
+ return 0; // do not increment count if it isn't a dataset.
+ if(getn->index==getn->count){
+ strcpy(getn->name,member_name);
+ return 1; // success
+ }
+ getn->count++;
+ return 0;
+ }
+
+
+ void GetDatasetName(const hid_t reader, const int _index, char *name) {
+ //this is straight from John Shalf's FlexIO library
+ H5IO_getname_t getn;
+ int idx=_index;
+ getn.index=_index; getn.name=name; getn.count=_index;
+ while(H5Giterate(reader, /* hid_t loc_id, */
+ "/", /*const char *name, */
+ &idx, /* int *idx, */
+ GetName,
+ &getn)<0){}
+ }
+
+ hid_t h5DataType (const cGH* const cctkGH, int cctk_type) {
+
+ hid_t retval;
+
+ CarpetIOHDF5GH *myGH;
+ myGH = (CarpetIOHDF5GH *) CCTK_GHExtension (cctkGH, "CarpetIOHDF5");
+
+ // this is adapted from Thomas Radke's IOHDF5Util. Thanks, Thomas!
+
+ switch (cctk_type)
+ {
+ case CCTK_VARIABLE_CHAR: retval = HDF5_CHAR; break;
+ case CCTK_VARIABLE_INT: retval = HDF5_INT; break;
+ case CCTK_VARIABLE_REAL: retval = HDF5_REAL; break;
+ case CCTK_VARIABLE_COMPLEX: retval = myGH->HDF5_COMPLEX; break;
+#ifdef CCTK_INT1
+ case CCTK_VARIABLE_INT1: retval = HDF5_INT1; break;
+#endif
+#ifdef CCTK_INT2
+ case CCTK_VARIABLE_INT2: retval = HDF5_INT2; break;
+#endif
+#ifdef CCTK_INT4
+ case CCTK_VARIABLE_INT4: retval = HDF5_INT4; break;
+#endif
+#ifdef CCTK_INT8
+ case CCTK_VARIABLE_INT8: retval = HDF5_INT8; break;
+#endif
+#ifdef CCTK_REAL4
+ case CCTK_VARIABLE_REAL4: retval = HDF5_REAL4; break;
+ case CCTK_VARIABLE_COMPLEX8: retval = myGH->HDF5_COMPLEX8; break;
+#endif
+#ifdef CCTK_REAL8
+ case CCTK_VARIABLE_REAL8: retval = HDF5_REAL8; break;
+ case CCTK_VARIABLE_COMPLEX16: retval = myGH->HDF5_COMPLEX16; break;
+#endif
+#ifdef CCTK_REAL16
+ case CCTK_VARIABLE_REAL16: retval = HDF5_REAL16; break;
+ case CCTK_VARIABLE_COMPLEX32: retval = myGH->HDF5_COMPLEX32; break;
+#endif
+
+ default: CCTK_VWarn (1, __LINE__, __FILE__, CCTK_THORNSTRING,
+ "Unsupported CCTK variable datatype %d", cctk_type);
+ retval = -1;
+ }
+
+ return (retval);
+ }
+
+
+
+} // namespace CarpetIOHDF5
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