From fe341a249822f3c08da9cad198159b984e81510b Mon Sep 17 00:00:00 2001
From: Cristian C Lalescu <Cristian.Lalescu@ds.mpg.de>
Date: Thu, 1 Jun 2017 23:08:43 +0200
Subject: [PATCH] add "require_size" hdf5 functionality
---
bfps/_base.py | 7 ++++--
bfps/cpp/hdf5_tools.cpp | 53 +++++++++++++++++++++++++++++++++++++++++
bfps/cpp/hdf5_tools.hpp | 15 ++++++++++++
3 files changed, 73 insertions(+), 2 deletions(-)
diff --git a/bfps/_base.py b/bfps/_base.py
index 03604896..77040a01 100644
--- a/bfps/_base.py
+++ b/bfps/_base.py
@@ -175,9 +175,12 @@ class _base(object):
def rewrite_par(
self,
group = None,
- parameters = None):
+ parameters = None,
+ file_name = None):
assert(group != 'parameters')
- ofile = h5py.File(os.path.join(self.work_dir, self.simname + '.h5'), 'r+')
+ if type(file_name) == None:
+ file_name = os.path.join(self.work_dir, self.simname + '.h5')
+ ofile = h5py.File(file_name, 'a')
for k in parameters.keys():
if group not in ofile.keys():
ofile.create_group(group)
diff --git a/bfps/cpp/hdf5_tools.cpp b/bfps/cpp/hdf5_tools.cpp
index abd894aa..1383b28b 100644
--- a/bfps/cpp/hdf5_tools.cpp
+++ b/bfps/cpp/hdf5_tools.cpp
@@ -1,5 +1,23 @@
#include "hdf5_tools.hpp"
+int hdf5_tools::require_size_single_dataset(hid_t dset, int tsize)
+{
+ int ndims;
+ hsize_t space;
+ space = H5Dget_space(dset);
+ ndims = H5Sget_simple_extent_ndims(space);
+ hsize_t *dims = new hsize_t[ndims];
+ H5Sget_simple_extent_dims(space, dims, NULL);
+ if (dims[0] < tsize)
+ {
+ dims[0] = tsize;
+ H5Dset_extent(dset, dims);
+ }
+ H5Sclose(space);
+ delete[] dims;
+ return EXIT_SUCCESS;
+}
+
int hdf5_tools::grow_single_dataset(hid_t dset, int tincrement)
{
int ndims;
@@ -15,6 +33,21 @@ int hdf5_tools::grow_single_dataset(hid_t dset, int tincrement)
return EXIT_SUCCESS;
}
+herr_t hdf5_tools::require_size_dataset_visitor(
+ hid_t o_id,
+ const char *name,
+ const H5O_info_t *info,
+ void *op_data)
+{
+ if (info->type == H5O_TYPE_DATASET)
+ {
+ hsize_t dset = H5Dopen(o_id, name, H5P_DEFAULT);
+ require_size_single_dataset(dset, *((int*)(op_data)));
+ H5Dclose(dset);
+ }
+ return EXIT_SUCCESS;
+}
+
herr_t hdf5_tools::grow_dataset_visitor(
hid_t o_id,
const char *name,
@@ -50,6 +83,26 @@ int hdf5_tools::grow_file_datasets(
return file_problems;
}
+
+int hdf5_tools::require_size_file_datasets(
+ const hid_t stat_file,
+ const std::string group_name,
+ int tsize)
+{
+ int file_problems = 0;
+
+ hid_t group;
+ group = H5Gopen(stat_file, group_name.c_str(), H5P_DEFAULT);
+ H5Ovisit(
+ group,
+ H5_INDEX_NAME,
+ H5_ITER_NATIVE,
+ require_size_dataset_visitor,
+ &tsize);
+ H5Gclose(group);
+ return file_problems;
+}
+
template <typename number>
std::vector<number> hdf5_tools::read_vector(
const hid_t group,
diff --git a/bfps/cpp/hdf5_tools.hpp b/bfps/cpp/hdf5_tools.hpp
index 0e3b38fe..0eebd84b 100644
--- a/bfps/cpp/hdf5_tools.hpp
+++ b/bfps/cpp/hdf5_tools.hpp
@@ -48,6 +48,21 @@ namespace hdf5_tools
const std::string group_name,
int tincrement);
+ int require_size_single_dataset(
+ hid_t dset,
+ int tincrement);
+
+ herr_t require_size_dataset_visitor(
+ hid_t o_id,
+ const char *name,
+ const H5O_info_t *info,
+ void *op_data);
+
+ int require_size_file_datasets(
+ const hid_t stat_file,
+ const std::string group_name,
+ int tincrement);
+
template <typename number>
std::vector<number> read_vector(
const hid_t group,
--
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