1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
|
/*
* Distributed under the OSI-approved Apache License, Version 2.0. See
* accompanying file Copyright.txt for details.
*
* hdf5Reader.cpp
*
* Created on: Jan 24, 2018
* Author: Junmin Gu
*/
#include <ios> //std::ios_base::failure
#include <iostream> //std::cout
#include <mpi.h>
#include <stdexcept> //std::invalid_argument std::exception
#include <vector>
#include <adios2.h>
template <class T>
void ReadData(adios2::IO h5IO, adios2::Engine &h5Reader, const std::string &name)
{
adios2::Variable<T> var = h5IO.InquireVariable<T>(name);
if (var)
{
size_t nDims = var.Shape().size();
size_t totalSize = 1;
for (size_t i = 0; i < nDims; i++)
{
totalSize *= var.Shape()[i];
}
std::vector<T> myValues(totalSize);
// myFloats.data is pre-allocated
h5Reader.Get<T>(var, myValues.data(), adios2::Mode::Sync);
// std::cout << "\tValues of "<<name<<": ";
std::cout << "\tPeek Values: ";
if (totalSize < 20)
{ // print all
for (const auto number : myValues)
{
std::cout << number << " ";
}
}
else
{
size_t counter = 0;
for (const auto number : myValues)
{
if ((counter < 5) || (counter > totalSize - 5))
{
std::cout << number << " ";
}
else if (counter == 5)
{
std::cout << " ...... ";
}
counter++;
}
}
std::cout << "\n";
}
}
int main(int argc, char *argv[])
{
int provided;
// MPI_THREAD_MULTIPLE is only required if you enable the SST MPI_DP
MPI_Init_thread(&argc, &argv, MPI_THREAD_MULTIPLE, &provided);
int rank, size;
MPI_Comm_rank(MPI_COMM_WORLD, &rank);
MPI_Comm_size(MPI_COMM_WORLD, &size);
/** Application variable */
const std::size_t Nx = 10;
std::vector<float> myFloats(Nx);
std::vector<int> myInts(Nx);
const char *filename = "myVector.h5";
if (argc > 1)
{
filename = argv[1];
}
std::cout << " Using file: " << filename << std::endl;
try
{
/** ADIOS class factory of IO class objects */
adios2::ADIOS adios(MPI_COMM_WORLD);
/*** IO class object: settings and factory of Settings: Variables,
* Parameters, Transports, and Execution: Engines */
adios2::IO h5IO = adios.DeclareIO("ReadHDF5");
h5IO.SetEngine("HDF5");
/** Engine derived class, spawned to start IO operations */
adios2::Engine h5Reader = h5IO.Open(filename, adios2::Mode::Read);
h5Reader.BeginStep();
const std::map<std::string, adios2::Params> variables = h5IO.AvailableVariables();
for (const auto &variablePair : variables)
{
std::cout << "Name: " << variablePair.first;
std::cout << std::endl;
for (const auto ¶meter : variablePair.second)
{
std::cout << "\t" << parameter.first << ": " << parameter.second << "\n";
if (parameter.second == "double")
{
ReadData<double>(h5IO, h5Reader, variablePair.first);
}
else if (parameter.second == "float")
{
ReadData<float>(h5IO, h5Reader, variablePair.first);
}
else if (parameter.second == "unsigned int")
{
ReadData<unsigned int>(h5IO, h5Reader, variablePair.first);
}
else if (parameter.second == "int")
{
ReadData<int>(h5IO, h5Reader, variablePair.first);
}
//... add more types if needed
}
}
const std::map<std::string, adios2::Params> attributes = h5IO.AvailableAttributes();
for (const auto &attrPair : attributes)
{
std::cout << "AttrName: " << attrPair.first;
std::cout << std::endl;
for (const auto ¶meter : attrPair.second)
{
std::cout << "\t" << parameter.first << ": " << parameter.second << "\n";
if (parameter.second == "double")
{
// ReadData<double>(h5IO, h5Reader, variablePair.first);
}
else if (parameter.second == "float")
{
// ReadData<float>(h5IO, h5Reader, variablePair.first);
}
else if (parameter.second == "unsigned int")
{
// ReadData<unsigned int>(h5IO, h5Reader,
// variablePair.first);
}
else if (parameter.second == "int")
{
// ReadData<int>(h5IO, h5Reader, variablePair.first);
}
//... add more types if needed
}
}
h5Reader.EndStep();
h5Reader.Close();
}
catch (std::invalid_argument &e)
{
std::cout << "Invalid argument exception, STOPPING PROGRAM from rank " << rank << "\n";
std::cout << e.what() << "\n";
}
catch (std::ios_base::failure &e)
{
std::cout << "IO System base failure exception, STOPPING PROGRAM "
"from rank "
<< rank << "\n";
std::cout << e.what() << "\n";
}
catch (std::exception &e)
{
std::cout << "Exception, STOPPING PROGRAM from rank " << rank << "\n";
std::cout << e.what() << "\n";
}
MPI_Finalize();
return 0;
}
|
