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-rw-r--r--Carpet/CarpetIOHDF5/src/CarpetIOHDF5.cc28
-rw-r--r--Carpet/CarpetIOHDF5/src/CarpetIOHDF5.hh3
-rw-r--r--Carpet/CarpetIOHDF5/src/Output.cc41
3 files changed, 66 insertions, 6 deletions
diff --git a/Carpet/CarpetIOHDF5/src/CarpetIOHDF5.cc b/Carpet/CarpetIOHDF5/src/CarpetIOHDF5.cc
index 452323ba2..cee765395 100644
--- a/Carpet/CarpetIOHDF5/src/CarpetIOHDF5.cc
+++ b/Carpet/CarpetIOHDF5/src/CarpetIOHDF5.cc
@@ -371,6 +371,12 @@ static void* SetupGH (tFleshConfig* const fleshconfig,
"'proc'. Ignoring setting for IO::out_unchunked...");
}
+ if (output_index && CCTK_EQUALS (out_mode, "onefile"))
+ CCTK_VWarn (CCTK_WARN_COMPLAIN, __LINE__, __FILE__, CCTK_THORNSTRING,
+ "CarpetIOHDF5::output_index with IO::out_mode = '%s' is not implemented in %s. "
+ "Index will not be output",
+ out_mode, CCTK_THORNSTRING);
+
// Now set hdf5 complex datatypes
HDF5_ERROR (myGH->HDF5_COMPLEX =
H5Tcreate (H5T_COMPOUND, sizeof (CCTK_COMPLEX)));
@@ -694,7 +700,12 @@ static int OutputVarAs (const cGH* const cctkGH, const char* const fullname,
snprintf (buffer, sizeof (buffer), ".file_%d", ioproc);
filename.append (buffer);
}
+
+ string base_filename(filename);
filename.append (out_extension);
+
+ string index_filename(base_filename + ".idx" + out_extension);
+
const char* const c_filename = filename.c_str();
// check if the file has been created already
@@ -751,6 +762,7 @@ static int OutputVarAs (const cGH* const cctkGH, const char* const fullname,
// Open the output file if this is a designated I/O processor
hid_t file = -1;
+ hid_t index_file = -1;
CCTK_REAL io_files = 0;
CCTK_REAL io_bytes = 0;
BeginTimingIO (cctkGH);
@@ -765,11 +777,23 @@ static int OutputVarAs (const cGH* const cctkGH, const char* const fullname,
if (is_new_file) {
HDF5_ERROR (file = H5Fcreate (c_filename, H5F_ACC_TRUNC, H5P_DEFAULT,
H5P_DEFAULT));
+ if (output_index) {
+ HDF5_ERROR (index_file = H5Fcreate (index_filename.c_str(),
+ H5F_ACC_TRUNC, H5P_DEFAULT,
+ H5P_DEFAULT));
+ }
// write metadata information
error_count +=
WriteMetadata (cctkGH, nioprocs, firstvar, numvars, false, file);
+
+ if (output_index) {
+ error_count +=
+ WriteMetadata (cctkGH, nioprocs, firstvar, numvars, false, index_file);
+ }
} else {
HDF5_ERROR (file = H5Fopen (c_filename, H5F_ACC_RDWR, H5P_DEFAULT));
+ if (output_index)
+ HDF5_ERROR (index_file = H5Fopen (index_filename.c_str(), H5F_ACC_RDWR, H5P_DEFAULT));
}
io_files += 1;
}
@@ -795,7 +819,7 @@ static int OutputVarAs (const cGH* const cctkGH, const char* const fullname,
} else if (CCTK_EQUALS (out_mode, "onefile")) {
error_count += WriteVarChunkedSequential (cctkGH, file, io_bytes, r, false);
} else {
- error_count += WriteVarChunkedParallel (cctkGH, file, io_bytes, r, false);
+ error_count += WriteVarChunkedParallel (cctkGH, file, io_bytes, r, false, index_file);
}
if (r != myGH->requests[var]) IOUtil_FreeIORequest (&r);
@@ -811,6 +835,8 @@ static int OutputVarAs (const cGH* const cctkGH, const char* const fullname,
// Close the file
if (file >= 0) {
HDF5_ERROR (H5Fclose (file));
+ if (output_index)
+ HDF5_ERROR (H5Fclose (index_file));
}
{
CCTK_REAL local[2], global[2];
diff --git a/Carpet/CarpetIOHDF5/src/CarpetIOHDF5.hh b/Carpet/CarpetIOHDF5/src/CarpetIOHDF5.hh
index 3a30ba48f..dfe3e01cc 100644
--- a/Carpet/CarpetIOHDF5/src/CarpetIOHDF5.hh
+++ b/Carpet/CarpetIOHDF5/src/CarpetIOHDF5.hh
@@ -124,7 +124,8 @@ namespace CarpetIOHDF5
hid_t file,
CCTK_REAL & io_bytes,
const ioRequest* const request,
- bool called_from_checkpoint);
+ bool called_from_checkpoint,
+ hid_t index = -1);
int WriteMetadata (const cGH * const cctkGH, int const nioprocs,
int const firstvar, int const numvars,
diff --git a/Carpet/CarpetIOHDF5/src/Output.cc b/Carpet/CarpetIOHDF5/src/Output.cc
index 1a77b2a39..4967785d6 100644
--- a/Carpet/CarpetIOHDF5/src/Output.cc
+++ b/Carpet/CarpetIOHDF5/src/Output.cc
@@ -25,7 +25,7 @@ using namespace Carpet;
static int AddAttributes (const cGH *const cctkGH, const char *fullname,
int vdim, int refinementlevel,
const ioRequest* const request,
- const ibbox& bbox, hid_t dataset);
+ const ibbox& bbox, hid_t dataset, bool is_index = false);
int WriteVarUnchunked (const cGH* const cctkGH,
@@ -486,7 +486,8 @@ int WriteVarChunkedParallel (const cGH* const cctkGH,
hid_t outfile,
CCTK_REAL & io_bytes,
const ioRequest* const request,
- bool called_from_checkpoint)
+ bool called_from_checkpoint,
+ hid_t indexfile)
{
DECLARE_CCTK_PARAMETERS;
@@ -586,20 +587,24 @@ int WriteVarChunkedParallel (const cGH* const cctkGH,
if (request->check_exist) {
H5E_BEGIN_TRY {
H5Gunlink (outfile, datasetname.str().c_str());
+ if (indexfile != -1)
+ H5Gunlink (indexfile, datasetname.str().c_str());
} H5E_END_TRY;
}
// Get the shape of the HDF5 dataset (in Fortran index order)
hsize_t shape[dim];
+ hsize_t index_shape[dim];
hssize_t origin[dim];
for (int d = 0; d < group.dim; ++d) {
assert (group.dim-1-d>=0 and group.dim-1-d<dim);
origin[group.dim-1-d] = (bbox.lower() / bbox.stride())[d];
shape[group.dim-1-d] = (bbox.shape() / bbox.stride())[d];
+ index_shape[group.dim-1-d] = 1;
}
// Write the component as an individual dataset
- hid_t plist, dataspace, dataset;
+ hid_t plist, dataspace, dataset, index_dataspace, index_dataset;
HDF5_ERROR (plist = H5Pcreate (H5P_DATASET_CREATE));
// enable compression if requested
const int compression_lvl = request->compression_level >= 0 ?
@@ -617,6 +622,14 @@ int WriteVarChunkedParallel (const cGH* const cctkGH,
HDF5_ERROR (dataspace = H5Screate_simple (group.dim, shape, NULL));
HDF5_ERROR (dataset = H5Dcreate (outfile, datasetname.str().c_str(),
filedatatype, dataspace, plist));
+
+ if (indexfile != -1) {
+ HDF5_ERROR (index_dataspace = H5Screate_simple (group.dim,
+ index_shape, NULL));
+ HDF5_ERROR (index_dataset = H5Dcreate (indexfile, datasetname.str().c_str(),
+ filedatatype, index_dataspace, H5P_DEFAULT));
+ }
+
io_bytes +=
H5Sget_simple_extent_npoints (dataspace) * H5Tget_size (filedatatype);
HDF5_ERROR (H5Pclose (plist));
@@ -627,6 +640,13 @@ int WriteVarChunkedParallel (const cGH* const cctkGH,
request, bbox, dataset);
HDF5_ERROR (H5Dclose (dataset));
+ if (indexfile != -1) {
+ HDF5_ERROR (H5Sclose (index_dataspace));
+ error_count += AddAttributes (cctkGH, fullname, group.dim,refinementlevel,
+ request, bbox, index_dataset, true);
+ HDF5_ERROR (H5Dclose (index_dataset));
+ }
+
if (data != mydata) free (data);
} END_LOCAL_COMPONENT_LOOP;
@@ -643,7 +663,7 @@ int WriteVarChunkedParallel (const cGH* const cctkGH,
static int AddAttributes (const cGH *const cctkGH, const char *fullname,
int vdim, int refinementlevel,
const ioRequest* request,
- const ibbox& bbox, hid_t dataset)
+ const ibbox& bbox, hid_t dataset, bool is_index)
{
assert (vdim>=0 and vdim<=dim);
int error_count = 0;
@@ -790,6 +810,19 @@ static int AddAttributes (const cGH *const cctkGH, const char *fullname,
HDF5_ERROR (H5Awrite (attr, H5T_NATIVE_INT, &iorigin[0]));
HDF5_ERROR (H5Aclose (attr));
+ hsize_t shape[vdim];
+ for (int d = 0; d < vdim; ++d) {
+ assert (vdim-1-d>=0 and vdim-1-d<vdim);
+ shape[vdim-1-d] = (bbox.shape() / bbox.stride())[d];
+ }
+
+ if (is_index) {
+ HDF5_ERROR (attr = H5Acreate (dataset, "h5shape", H5T_NATIVE_HSIZE,
+ dataspace, H5P_DEFAULT));
+ HDF5_ERROR (H5Awrite (attr, H5T_NATIVE_HSIZE, &shape[0]));
+ HDF5_ERROR (H5Aclose (attr));
+ }
+
HDF5_ERROR (H5Sclose (dataspace));
// return the number of errors that occured during this output
generated by cgit v1.2.3 (git 2.39.1) at 2024-07-14 14:15:04 +0000