aboutsummaryrefslogtreecommitdiff
diff options
context:
space:
mode:
Diffstat
-rw-r--r--Carpet/CarpetIOHDF5/src/Input.cc100
1 files changed, 85 insertions, 15 deletions
diff --git a/Carpet/CarpetIOHDF5/src/Input.cc b/Carpet/CarpetIOHDF5/src/Input.cc
index 0c16ca264..5b947aa8b 100644
--- a/Carpet/CarpetIOHDF5/src/Input.cc
+++ b/Carpet/CarpetIOHDF5/src/Input.cc
@@ -42,8 +42,8 @@ typedef struct {
// structure describing the contents of an HDF5 file to read from
typedef struct {
- char *filename;
- hid_t file;
+ char *filename, *indexfilename;
+ hid_t file, indexfile;
list<patch_t> patches;
} file_t;
@@ -52,6 +52,7 @@ typedef struct {
string setname;
string basefilename;
int first_ioproc;
+ bool has_index;
vector<file_t> files; // [nioprocs]
int nioprocs;
@@ -309,18 +310,25 @@ void CarpetIOHDF5_CloseFiles (CCTK_ARGUMENTS)
for (list<fileset_t>::const_iterator set = filesets.begin();
set != filesets.end(); set++) {
for (unsigned int i = 0; i < set->files.size(); i++) {
- if (set->files[i].file >= 0) {
-
+ if (set->files[i].file >= 0 or set->files[i].indexfile >= 0) {
if (CCTK_Equals (verbose, "full")) {
CCTK_VInfo (CCTK_THORNSTRING, "closing file '%s' after recovery",
set->files[i].filename);
}
- HDF5_ERROR (H5Fclose (set->files[i].file));
+ if (set->files[i].file >= 0) {
+ HDF5_ERROR (H5Fclose (set->files[i].file));
+ }
+ if (set->files[i].indexfile >= 0) {
+ HDF5_ERROR (H5Fclose (set->files[i].indexfile));
+ }
}
if (set->files[i].filename != NULL) {
free (set->files[i].filename);
}
+ if (set->files[i].indexfilename) {
+ free (set->files[i].indexfilename);
+ }
}
}
@@ -540,23 +548,41 @@ int Recover (cGH* cctkGH, const char *basefilename, int called_from)
// open the file (if it hasn't been already) and read its metadata
// if we already browsed this file once we defer opening it again until we have to
if (not file.filename) {
+ assert(not file.indexfilename);
+ file.indexfilename =
+ IOUtil_AssembleFilename (NULL, fileset->basefilename.c_str(),
+ "", ".idx.h5", called_from, file_idx, 0);
+ assert (file.indexfilename);
+
file.filename =
IOUtil_AssembleFilename (NULL, fileset->basefilename.c_str(),
"", ".h5", called_from, file_idx, 0);
assert (file.filename);
}
if (file.patches.size() == 0) {
- HDF5_ERROR (file.file = H5Fopen (file.filename, H5F_ACC_RDONLY,
- H5P_DEFAULT));
-
+ // we defer opening the actual data file until we have to
+ // and open only the index file if it exists
+
io_files += 1;
-
- if (CCTK_Equals (verbose, "full")) {
- CCTK_VInfo (CCTK_THORNSTRING, "opening %s file '%s'",
- in_recovery ? "checkpoint" : "input", file.filename);
+ if (file.indexfile < 0 and fileset->has_index) {
+ HDF5_ERROR (file.indexfile = H5Fopen (file.indexfilename, H5F_ACC_RDONLY,
+ H5P_DEFAULT));
+ if (CCTK_Equals (verbose, "full")) {
+ CCTK_VInfo (CCTK_THORNSTRING, "opening index file '%s'",
+ file.indexfilename);
+ }
+ } else {
+ HDF5_ERROR (file.file = H5Fopen (file.filename, H5F_ACC_RDONLY,
+ H5P_DEFAULT));
+ if (CCTK_Equals (verbose, "full")) {
+ CCTK_VInfo (CCTK_THORNSTRING, "opening %s file '%s'",
+ in_recovery ? "checkpoint" : "input", file.filename);
+ }
}
- HDF5_ERROR (H5Giterate (file.file, "/", NULL, BrowseDatasets, &file));
+ // browse through all datasets contained in this file
+ HDF5_ERROR (H5Giterate (file.indexfile >= 0 ? file.indexfile : file.file,
+ "/", NULL, BrowseDatasets, &file));
}
assert (file.patches.size() > 0);
if (myGH->recovery_filename_list and not myGH->recovery_filename_list[i]) {
@@ -670,6 +696,14 @@ int Recover (cGH* cctkGH, const char *basefilename, int called_from)
free(file.filename);
file.filename = NULL;
}
+ if (file.indexfile >= 0) {
+ HDF5_ERROR (H5Fclose (file.indexfile));
+ file.indexfile = -1;
+ }
+ if (file.indexfilename) {
+ free(file.indexfilename);
+ file.indexfilename = NULL;
+ }
}
}
@@ -822,6 +856,10 @@ static list<fileset_t>::iterator OpenFileSet (const cGH* const cctkGH,
file.filename = IOUtil_AssembleFilename (NULL, basefilename, "", ".h5",
called_from, fileset.first_ioproc, 0);
assert (file.filename);
+ file.indexfilename = IOUtil_AssembleFilename (NULL, basefilename, "",
+ ".idx.h5", called_from,
+ fileset.first_ioproc, 0);
+ assert (file.indexfilename);
// try to open the file (prevent HDF5 error messages if it fails)
H5E_BEGIN_TRY {
@@ -832,11 +870,16 @@ static list<fileset_t>::iterator OpenFileSet (const cGH* const cctkGH,
// if that failed, try a chunked file written on processor 0
// (which always is an I/O proc)
if (file.file < 0) {
+ free (file.indexfilename);
free (file.filename);
fileset.first_ioproc = 0;
file.filename = IOUtil_AssembleFilename (NULL, basefilename, "", ".h5",
called_from, fileset.first_ioproc, 0);
assert (file.filename);
+ file.indexfilename = IOUtil_AssembleFilename (NULL, basefilename, "",
+ ".idx.h5", called_from,
+ fileset.first_ioproc, 0);
+ assert (file.indexfilename);
H5E_BEGIN_TRY {
filenames.push_back (string (file.filename));
file.file = H5Fopen (file.filename, H5F_ACC_RDONLY, H5P_DEFAULT);
@@ -846,10 +889,15 @@ static list<fileset_t>::iterator OpenFileSet (const cGH* const cctkGH,
// if that still failed, try an unchunked file
// (which is always written on processor 0)
if (file.file < 0) {
+ free (file.indexfilename);
free (file.filename);
file.filename = IOUtil_AssembleFilename (NULL, basefilename, "", ".h5",
called_from, fileset.first_ioproc, 1);
assert (file.filename);
+ file.indexfilename = IOUtil_AssembleFilename (NULL, basefilename, "",
+ ".idx.h5", called_from,
+ fileset.first_ioproc, 1);
+ assert (file.indexfilename);
H5E_BEGIN_TRY {
filenames.push_back (string (file.filename));
file.file = H5Fopen (file.filename, H5F_ACC_RDONLY, H5P_DEFAULT);
@@ -861,8 +909,12 @@ static list<fileset_t>::iterator OpenFileSet (const cGH* const cctkGH,
CCTK_VWarn (1, __LINE__, __FILE__, CCTK_THORNSTRING,
"No valid HDF5 file with basename \"%s\" found", basefilename);
free (file.filename);
+ free (file.indexfilename);
file.filename = NULL;
+ file.indexfilename = NULL;
file.file = -1;
+ file.indexfile = -1; // to avoid trying to close it later
+
for (list<string>::const_iterator
lsi = filenames.begin(); lsi != filenames.end(); ++ lsi)
{
@@ -871,6 +923,13 @@ static list<fileset_t>::iterator OpenFileSet (const cGH* const cctkGH,
}
return (filesets.end());
}
+
+ // open index file if it exists
+ H5E_BEGIN_TRY {
+ file.indexfile = H5Fopen (file.indexfilename, H5F_ACC_RDONLY,
+ H5P_DEFAULT);
+ } H5E_END_TRY;
+ fileset.has_index = file.indexfile >= 0;
if (CCTK_Equals (verbose, "full")) {
CCTK_VInfo (CCTK_THORNSTRING, "opening %s file '%s'",
@@ -885,7 +944,10 @@ static list<fileset_t>::iterator OpenFileSet (const cGH* const cctkGH,
// first try to open a chunked file written on this processor
// browse through all datasets contained in this file
- HDF5_ERROR (H5Giterate (file.file, "/", NULL, BrowseDatasets, &file));
+ // TODO: measure if it is actually beneficial to open the index file for this
+ // file where we always read the metadata group
+ HDF5_ERROR (H5Giterate (file.indexfile >= 0 ? file.indexfile : file.file,
+ "/", NULL, BrowseDatasets, &file));
assert (file.patches.size() > 0);
// recover parameters
@@ -913,7 +975,9 @@ static list<fileset_t>::iterator OpenFileSet (const cGH* const cctkGH,
fileset.files.resize (fileset.nioprocs);
for (int i = 0; i < fileset.nioprocs; i++) {
fileset.files[i].file = -1;
+ fileset.files[i].indexfile = -1;
fileset.files[i].filename = NULL;
+ fileset.files[i].indexfilename = NULL;
}
fileset.files[fileset.first_ioproc] = file;
fileset.setname = setname;
@@ -1094,7 +1158,13 @@ static herr_t BrowseDatasets (hid_t group, const char *objectname, void *arg)
patch.rank = H5Sget_simple_extent_ndims (dataspace);
assert (patch.rank > 0 and patch.rank <= ::dim);
patch.shape.resize (patch.rank);
- HDF5_ERROR (H5Sget_simple_extent_dims (dataspace, &patch.shape[0], NULL));
+ if (file->indexfile >= 0) { // index files store shape of master file in attr
+ HDF5_ERROR (attr = H5Aopen_name (dataset, "h5shape"));
+ HDF5_ERROR (H5Aread (attr, H5T_NATIVE_HSIZE, &patch.shape[0]));
+ HDF5_ERROR (H5Aclose (attr));
+ } else {
+ HDF5_ERROR (H5Sget_simple_extent_dims (dataspace, &patch.shape[0], NULL));
+ }
HDF5_ERROR (H5Sclose (dataspace));
HDF5_ERROR (attr = H5Aopen_name (dataset, "name"));
HDF5_ERROR (attrtype = H5Aget_type (attr));
generated by cgit v1.2.3 (git 2.39.1) at 2024-05-19 12:33:00 +0000