From 1c50d7a7947164b7209b4f8f790ff8c151ae99de Mon Sep 17 00:00:00 2001
From: Cristian C Lalescu <Cristian.Lalescu@ds.mpg.de>
Date: Wed, 24 May 2017 11:07:20 +0200
Subject: [PATCH] merge io_tools with hdf5_tools
---
bfps/_base.py | 2 +-
bfps/cpp/base.hpp | 2 +-
bfps/cpp/full_code/hdf5_tools.cpp | 52 ---------
bfps/cpp/hdf5_tools.cpp | 142 ++++++++++++++++++++++++
bfps/cpp/{full_code => }/hdf5_tools.hpp | 15 +++
bfps/cpp/io_tools.cpp | 62 -----------
bfps/cpp/io_tools.hpp | 41 -------
setup.py | 3 +-
8 files changed, 160 insertions(+), 159 deletions(-)
delete mode 100644 bfps/cpp/full_code/hdf5_tools.cpp
create mode 100644 bfps/cpp/hdf5_tools.cpp
rename bfps/cpp/{full_code => }/hdf5_tools.hpp (83%)
delete mode 100644 bfps/cpp/io_tools.cpp
delete mode 100644 bfps/cpp/io_tools.hpp
diff --git a/bfps/_base.py b/bfps/_base.py
index 72f833da..03604896 100644
--- a/bfps/_base.py
+++ b/bfps/_base.py
@@ -123,7 +123,7 @@ class _base(object):
template_par = 'int'
elif parameters[key[i]].dtype == np.float64:
template_par = 'double'
- src_txt += '{0} = read_vector<{1}>(parameter_file, "/{2}/{0}");\n'.format(
+ src_txt += '{0} = hdf5_tools::read_vector<{1}>(parameter_file, "/{2}/{0}");\n'.format(
key_prefix + key[i], template_par, file_group)
else:
src_txt += 'H5Dread(dset, H5T_NATIVE_DOUBLE, H5S_ALL, H5S_ALL, H5P_DEFAULT, &{0});\n'.format(key_prefix + key[i])
diff --git a/bfps/cpp/base.hpp b/bfps/cpp/base.hpp
index 8fc5942f..61029c26 100644
--- a/bfps/cpp/base.hpp
+++ b/bfps/cpp/base.hpp
@@ -29,7 +29,7 @@
#include <stdarg.h>
#include <iostream>
#include <typeinfo>
-#include "io_tools.hpp"
+#include "hdf5_tools.hpp"
#ifndef BASE
diff --git a/bfps/cpp/full_code/hdf5_tools.cpp b/bfps/cpp/full_code/hdf5_tools.cpp
deleted file mode 100644
index 2262db98..00000000
--- a/bfps/cpp/full_code/hdf5_tools.cpp
+++ /dev/null
@@ -1,52 +0,0 @@
-#include "hdf5_tools.hpp"
-
-int hdf5_tools::grow_single_dataset(hid_t dset, int tincrement)
-{
- 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);
- dims[0] += tincrement;
- H5Dset_extent(dset, dims);
- H5Sclose(space);
- delete[] dims;
- return EXIT_SUCCESS;
-}
-
-herr_t hdf5_tools::grow_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);
- grow_single_dataset(dset, *((int*)(op_data)));
- H5Dclose(dset);
- }
- return EXIT_SUCCESS;
-}
-
-
-int hdf5_tools::grow_file_datasets(
- const hid_t stat_file,
- const std::string group_name,
- int tincrement)
-{
- 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,
- grow_dataset_visitor,
- &tincrement);
- H5Gclose(group);
- return file_problems;
-}
-
diff --git a/bfps/cpp/hdf5_tools.cpp b/bfps/cpp/hdf5_tools.cpp
new file mode 100644
index 00000000..6158607d
--- /dev/null
+++ b/bfps/cpp/hdf5_tools.cpp
@@ -0,0 +1,142 @@
+#include "hdf5_tools.hpp"
+
+int hdf5_tools::grow_single_dataset(hid_t dset, int tincrement)
+{
+ 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);
+ dims[0] += tincrement;
+ H5Dset_extent(dset, dims);
+ H5Sclose(space);
+ delete[] dims;
+ return EXIT_SUCCESS;
+}
+
+herr_t hdf5_tools::grow_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);
+ grow_single_dataset(dset, *((int*)(op_data)));
+ H5Dclose(dset);
+ }
+ return EXIT_SUCCESS;
+}
+
+
+int hdf5_tools::grow_file_datasets(
+ const hid_t stat_file,
+ const std::string group_name,
+ int tincrement)
+{
+ 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,
+ grow_dataset_visitor,
+ &tincrement);
+ H5Gclose(group);
+ return file_problems;
+}
+
+template <typename number>
+std::vector<number> hdf5_tools::read_vector(
+ const hid_t group,
+ const std::string dset_name)
+{
+ std::vector<number> result;
+ hsize_t vector_length;
+ // first, read size of array
+ hid_t dset, dspace;
+ hid_t mem_dtype;
+ if (typeid(number) == typeid(int))
+ mem_dtype = H5Tcopy(H5T_NATIVE_INT);
+ else if (typeid(number) == typeid(double))
+ mem_dtype = H5Tcopy(H5T_NATIVE_DOUBLE);
+ dset = H5Dopen(group, dset_name.c_str(), H5P_DEFAULT);
+ dspace = H5Dget_space(dset);
+ assert(H5Sget_simple_extent_ndims(dspace) == 1);
+ H5Sget_simple_extent_dims(dspace, &vector_length, NULL);
+ result.resize(vector_length);
+ H5Dread(dset, mem_dtype, H5S_ALL, H5S_ALL, H5P_DEFAULT, &result.front());
+ H5Sclose(dspace);
+ H5Dclose(dset);
+ H5Tclose(mem_dtype);
+ return result;
+}
+
+template <typename dtype>
+std::vector<dtype> hdf5_tools::read_vector_with_single_rank(
+ const int myrank,
+ const int rank_to_use,
+ const MPI_Comm COMM,
+ const hid_t file_id,
+ const std::string dset_name)
+{
+ std::vector<dtype> data;
+ int vector_size;
+ if (myrank == rank_to_use)
+ {
+ data = hdf5_tools::read_vector<dtype>(
+ file_id,
+ dset_name);
+ vector_size = data.size();
+ }
+ MPI_Bcast(
+ &vector_size,
+ 1,
+ MPI_INT,
+ rank_to_use,
+ COMM);
+
+ if (myrank != rank_to_use)
+ data.resize(vector_size);
+ MPI_Bcast(
+ &data.front(),
+ vector_size,
+ (typeid(dtype) == typeid(int)) ? MPI_INT : MPI_DOUBLE,
+ rank_to_use,
+ COMM);
+ return data;
+}
+
+namespace hdf5_tools
+{
+template <>
+std::vector<int> read_vector(
+ const hid_t,
+ const std::string);
+
+template <>
+std::vector<double> read_vector(
+ const hid_t,
+ const std::string);
+
+template <>
+std::vector<int> read_vector_with_single_rank(
+ const int myrank,
+ const int rank_to_use,
+ const MPI_Comm COMM,
+ const hid_t file_id,
+ const std::string dset_name);
+
+template <>
+std::vector<double> read_vector_with_single_rank(
+ const int myrank,
+ const int rank_to_use,
+ const MPI_Comm COMM,
+ const hid_t file_id,
+ const std::string dset_name);
+}
+
diff --git a/bfps/cpp/full_code/hdf5_tools.hpp b/bfps/cpp/hdf5_tools.hpp
similarity index 83%
rename from bfps/cpp/full_code/hdf5_tools.hpp
rename to bfps/cpp/hdf5_tools.hpp
index aaa98b5d..0e3b38fe 100644
--- a/bfps/cpp/full_code/hdf5_tools.hpp
+++ b/bfps/cpp/hdf5_tools.hpp
@@ -27,6 +27,8 @@
#ifndef HDF5_TOOLS_HPP
#define HDF5_TOOLS_HPP
+#include <vector>
+#include <hdf5.h>
#include "base.hpp"
namespace hdf5_tools
@@ -45,6 +47,19 @@ namespace hdf5_tools
const hid_t stat_file,
const std::string group_name,
int tincrement);
+
+ template <typename number>
+ std::vector<number> read_vector(
+ const hid_t group,
+ const std::string dset_name);
+
+ template <typename number>
+ std::vector<number> read_vector_with_single_rank(
+ const int myrank,
+ const int rank_to_use,
+ const MPI_Comm COMM,
+ const hid_t group,
+ const std::string dset_name);
}
#endif//HDF5_TOOLS_HPP
diff --git a/bfps/cpp/io_tools.cpp b/bfps/cpp/io_tools.cpp
deleted file mode 100644
index 224803dc..00000000
--- a/bfps/cpp/io_tools.cpp
+++ /dev/null
@@ -1,62 +0,0 @@
-/**********************************************************************
-* *
-* Copyright 2015 Max Planck Institute *
-* for Dynamics and Self-Organization *
-* *
-* This file is part of bfps. *
-* *
-* bfps is free software: you can redistribute it and/or modify *
-* it under the terms of the GNU General Public License as published *
-* by the Free Software Foundation, either version 3 of the License, *
-* or (at your option) any later version. *
-* *
-* bfps is distributed in the hope that it will be useful, *
-* but WITHOUT ANY WARRANTY; without even the implied warranty of *
-* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the *
-* GNU General Public License for more details. *
-* *
-* You should have received a copy of the GNU General Public License *
-* along with bfps. If not, see <http://www.gnu.org/licenses/> *
-* *
-* Contact: Cristian.Lalescu@ds.mpg.de *
-* *
-**********************************************************************/
-
-
-
-#include <typeinfo>
-#include <cassert>
-#include "io_tools.hpp"
-
-
-template <typename number>
-std::vector<number> read_vector(
- hid_t group,
- std::string dset_name)
-{
- std::vector<number> result;
- hsize_t vector_length;
- // first, read size of array
- hid_t dset, dspace;
- hid_t mem_dtype;
- if (typeid(number) == typeid(int))
- mem_dtype = H5Tcopy(H5T_NATIVE_INT);
- else if (typeid(number) == typeid(double))
- mem_dtype = H5Tcopy(H5T_NATIVE_DOUBLE);
- dset = H5Dopen(group, dset_name.c_str(), H5P_DEFAULT);
- dspace = H5Dget_space(dset);
- assert(H5Sget_simple_extent_ndims(dspace) == 1);
- H5Sget_simple_extent_dims(dspace, &vector_length, NULL);
- result.resize(vector_length);
- H5Dread(dset, mem_dtype, H5S_ALL, H5S_ALL, H5P_DEFAULT, &result.front());
- H5Sclose(dspace);
- H5Dclose(dset);
- H5Tclose(mem_dtype);
- return result;
-}
-
-template std::vector<int> read_vector(
- hid_t, std::string);
-template std::vector<double> read_vector(
- hid_t, std::string);
-
diff --git a/bfps/cpp/io_tools.hpp b/bfps/cpp/io_tools.hpp
deleted file mode 100644
index 69c0e8bb..00000000
--- a/bfps/cpp/io_tools.hpp
+++ /dev/null
@@ -1,41 +0,0 @@
-/**********************************************************************
-* *
-* Copyright 2015 Max Planck Institute *
-* for Dynamics and Self-Organization *
-* *
-* This file is part of bfps. *
-* *
-* bfps is free software: you can redistribute it and/or modify *
-* it under the terms of the GNU General Public License as published *
-* by the Free Software Foundation, either version 3 of the License, *
-* or (at your option) any later version. *
-* *
-* bfps is distributed in the hope that it will be useful, *
-* but WITHOUT ANY WARRANTY; without even the implied warranty of *
-* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the *
-* GNU General Public License for more details. *
-* *
-* You should have received a copy of the GNU General Public License *
-* along with bfps. If not, see <http://www.gnu.org/licenses/> *
-* *
-* Contact: Cristian.Lalescu@ds.mpg.de *
-* *
-**********************************************************************/
-
-
-
-#include <hdf5.h>
-#include <vector>
-#include <string>
-
-#ifndef IO_TOOLS
-
-#define IO_TOOLS
-
-template <typename number>
-std::vector<number> read_vector(
- hid_t group,
- std::string dset_name);
-
-#endif//IO_TOOLS
-
diff --git a/setup.py b/setup.py
index 63941c1d..f9574c84 100644
--- a/setup.py
+++ b/setup.py
@@ -88,7 +88,7 @@ print('This is bfps version ' + VERSION)
### lists of files and MANIFEST.in
-src_file_list = ['full_code/hdf5_tools',
+src_file_list = ['hdf5_tools',
'full_code/code_base',
'full_code/direct_numerical_simulation',
'full_code/NSVE',
@@ -108,7 +108,6 @@ src_file_list = ['full_code/hdf5_tools',
'interpolator_base',
'fluid_solver',
'fluid_solver_base',
- 'io_tools',
'fftw_tools',
'spline_n1',
'spline_n2',
--
GitLab