1/*
2 * HDF5_loader_vector_dist.hpp
3 *
4 * Created on: May 1, 2017
5 * Author: i-bird
6 */
7
8#ifndef OPENFPM_IO_SRC_HDF5_WR_HDF5_WRITER_VD_HPP_
9#define OPENFPM_IO_SRC_HDF5_WR_HDF5_WRITER_VD_HPP_
10
11#include "Packer_Unpacker/Pack_selector.hpp"
12#include "Packer_Unpacker/Packer.hpp"
13#include "Packer_Unpacker/Unpacker.hpp"
14
15template <>
16class HDF5_writer<VECTOR_DIST>
17{
18public:
19
20 template<typename vector_pos_type, typename vector_prp_type>
21 inline void save(const std::string & filename,
22 const vector_pos_type & v_pos,
23 const vector_prp_type & v_prp) const
24 {
25 Vcluster<> & v_cl = create_vcluster();
26
27 //Pack_request vector
28 size_t req = 0;
29
30 //std::cout << "V_pos.size() before save: " << v_pos.size() << std::endl;
31
32 //Pack request
33 Packer<typename std::remove_reference<decltype(v_pos)>::type,HeapMemory>::packRequest(v_pos,req);
34 Packer<typename std::remove_reference<decltype(v_prp)>::type,HeapMemory>::packRequest(v_prp,req);
35
36 // allocate the memory
37 HeapMemory pmem;
38 //pmem.allocate(req);
39 ExtPreAlloc<HeapMemory> & mem = *(new ExtPreAlloc<HeapMemory>(req,pmem));
40 mem.incRef();
41
42 //Packing
43
44 Pack_stat sts;
45
46 Packer<typename std::remove_reference<decltype(v_pos)>::type,HeapMemory>::pack(mem,v_pos,sts);
47 Packer<typename std::remove_reference<decltype(v_prp)>::type,HeapMemory>::pack(mem,v_prp,sts);
48
49 /*****************************************************************
50 * Create a new file with default creation and access properties.*
51 * Then create a dataset and write data to it and close the file *
52 * and dataset. *
53 *****************************************************************/
54
55 int mpi_rank = v_cl.getProcessUnitID();
56 int mpi_size = v_cl.getProcessingUnits();
57
58 MPI_Comm comm = v_cl.getMPIComm();
59 MPI_Info info = MPI_INFO_NULL;
60
61 // Set up file access property list with parallel I/O access
62
63 hid_t plist_id = H5Pcreate(H5P_FILE_ACCESS);
64 H5Pset_fapl_mpio(plist_id, comm, info);
65
66 // Create a new file collectively and release property list identifier.
67 hid_t file = H5Fcreate (filename.c_str(), H5F_ACC_TRUNC, H5P_DEFAULT, plist_id);
68 H5Pclose(plist_id);
69
70 size_t sz = pmem.size();
71 //std::cout << "Pmem.size: " << pmem.size() << std::endl;
72 openfpm::vector<size_t> sz_others;
73 v_cl.allGather(sz,sz_others);
74 v_cl.execute();
75
76 size_t sum = 0;
77
78 for (size_t i = 0; i < sz_others.size(); i++)
79 sum += sz_others.get(i);
80
81 //Size for data space in file
82 hsize_t fdim[1] = {sum};
83
84 //Size for data space in file
85 hsize_t fdim2[1] = {(size_t)mpi_size};
86
87 //Create data space in file
88 hid_t file_dataspace_id = H5Screate_simple(1, fdim, NULL);
89
90 //Create data space in file
91 hid_t file_dataspace_id_2 = H5Screate_simple(1, fdim2, NULL);
92
93 //Size for data space in memory
94 hsize_t mdim[1] = {pmem.size()};
95
96 //Create data space in memory
97 hid_t mem_dataspace_id = H5Screate_simple(1, mdim, NULL);
98
99 //Create data set in file
100 hid_t file_dataset = H5Dcreate (file, "vector_dist", H5T_NATIVE_CHAR, file_dataspace_id, H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT);
101
102 //Create data set 2 in file
103 hid_t file_dataset_2 = H5Dcreate (file, "metadata", H5T_NATIVE_INT, file_dataspace_id_2, H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT);
104
105 //H5Pclose(plist_id);
106 H5Sclose(file_dataspace_id);
107 H5Sclose(file_dataspace_id_2);
108
109 hsize_t block[1] = {pmem.size()};
110
111 //hsize_t stride[1] = {1};
112
113 hsize_t count[1] = {1};
114
115 hsize_t offset[1] = {0};
116
117 for (int i = 0; i < mpi_rank; i++)
118 {
119 if (mpi_rank == 0)
120 {
121 /* coverity[dead_error_line] */
122 offset[0] = 0;
123 }
124 else
125 {offset[0] += sz_others.get(i);}
126 }
127
128 int metadata[mpi_size];
129
130 for (int i = 0; i < mpi_size; i++)
131 metadata[i] = sz_others.get(i);
132
133 //Select hyperslab in the file.
134 file_dataspace_id = H5Dget_space(file_dataset);
135 H5Sselect_hyperslab(file_dataspace_id, H5S_SELECT_SET, offset, NULL, count, block);
136
137 file_dataspace_id_2 = H5Dget_space(file_dataset_2);
138
139
140 //Create property list for collective dataset write.
141 plist_id = H5Pcreate(H5P_DATASET_XFER);
142 H5Pset_dxpl_mpio(plist_id, H5FD_MPIO_COLLECTIVE);
143
144 //Write a data set to a file
145 H5Dwrite(file_dataset, H5T_NATIVE_CHAR, mem_dataspace_id, file_dataspace_id, plist_id, (const char *)pmem.getPointer());
146
147 //Write a data set 2 to a file
148 H5Dwrite(file_dataset_2, H5T_NATIVE_INT, H5S_ALL, file_dataspace_id_2, plist_id, metadata);
149
150
151 //Close/release resources.
152 H5Dclose(file_dataset);
153 H5Sclose(file_dataspace_id);
154 H5Dclose(file_dataset_2);
155 H5Sclose(file_dataspace_id_2);
156 H5Sclose(mem_dataspace_id);
157 H5Pclose(plist_id);
158 H5Fclose(file);
159 mem.decRef();
160 delete &mem;
161 }
162
163 /*! \brief Return the equivalent HDF5 type for T
164 *
165 * \return The HDF5 type equivalent to T
166 *
167 */
168 template<typename T>
169 hid_t getType()
170 {
171 if (std::is_same<T,float>::value)
172 {return H5T_IEEE_F32LE;}
173 else if (std::is_same<T,double>::value)
174 {return H5T_IEEE_F64LE;}
175 else if (std::is_same<T,char>::value || std::is_same<T,unsigned char>::value)
176 {return H5T_STD_I8LE;}
177 else if (std::is_same<T,short>::value || std::is_same<T,unsigned short>::value)
178 {return H5T_STD_I16LE;}
179 else if (std::is_same<T,int>::value || std::is_same<T,unsigned int>::value)
180 {return H5T_STD_I32LE;}
181 else if (std::is_same<T,long int>::value || std::is_same<T,unsigned long int>::value)
182 {return H5T_STD_I64LE;}
183 }
184
185 /*! \brief It add an attribute to an already opened file
186 *
187 * \param dataset_id dataset_id
188 * \param name_ name of the attribute
189 * \param att_ attribute value
190 */
191 template<typename value_type>
192 void addAttributeHDF5(hid_t dataset_id, std::string name_, value_type att_)
193 {
194 //create the data space for the scalar attibute
195 hid_t dataspace_id = H5Screate(H5S_SCALAR);
196
197 //create the dataset attribute (H5T_IEEE_F64BE: 64-bit float little endian)
198 hid_t attribute_id = H5Acreate2(dataset_id, name_.c_str(), H5T_IEEE_F32LE, dataspace_id, H5P_DEFAULT, H5P_DEFAULT);
199 //write the attibute data
200 herr_t status = H5Awrite(attribute_id,H5T_NATIVE_DOUBLE, &att_);
201 //close the attribute
202 status = H5Aclose(attribute_id);
203 //close the dataspace
204 status = H5Sclose(dataspace_id);
205 }
206
207 /*! \brief It add an attribute to an already opened file
208 *
209 * \param dataset_id dataset_id
210 * \param name_ name of the attribute
211 * \param att_ attribute value
212 */
213 template<typename value_type>
214 void addAttributeHDF5(std::string filename, std::string name_, value_type att_)
215 {
216 Vcluster<> & v_cl = create_vcluster();
217 MPI_Comm comm = v_cl.getMPIComm();
218 MPI_Info info = MPI_INFO_NULL;
219 // Set up file access property list with parallel I/O access
220 hid_t plist_id = H5Pcreate(H5P_FILE_ACCESS);
221
222 hid_t file_id = H5Fopen(filename.c_str(),H5F_ACC_RDWR, plist_id);
223 hid_t dataset_id = H5Dopen2(file_id,"/vector_dist", H5P_DEFAULT);
224
225 addAttributeHDF5(dataset_id,name_.c_str(),att_);
226
227 //close the dataset
228 herr_t status = H5Dclose(dataset_id);
229 //close the file
230 status = H5Fclose(file_id);
231 }
232
233};
234
235
236#endif /* OPENFPM_IO_SRC_HDF5_WR_HDF5_WRITER_VD_HPP_ */
237