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
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
222
223
224
225
226
227
228
229
230
231
232
233
234
|
/*********************************************************************
*
* Copyright (C) 2014, Northwestern University and Argonne National Laboratory
* See COPYRIGHT notice in top-level directory.
*
*********************************************************************/
/* $Id$ */
/*
* This example shows how to use varm API to write six 3D integer array
* variables into a file. Each variable in the file is a dimensional
* transposed array from the one stored in memory. In memory, a 3D array is
* partitioned among all processes in a block-block-block fashion and in
* ZYX (i.e. C) order. The dimension structures of the transposed six
* arrays are
* int ZYX_var(Z, Y, X) ; ZYX -> ZYX
* int ZXY_var(Z, X, Y) ; ZYX -> ZXY
* int YZX_var(Y, Z, X) ; ZYX -> YZX
* int YXZ_var(Y, X, Z) ; ZYX -> YXZ
* int XZY_var(X, Z, Y) ; ZYX -> XZY
* int XYZ_var(X, Y, Z) ; ZYX -> XYZ
*
* To compile:
* mpicxx -O2 transpose.cpp -o transpose -lpnetcdf
* To run:
* mpiexec -n num_processes ./transpose [filename] [len]
* where len decides the size of local array, which is len x len+1 x len+2.
* So, each variable is of size len*(len+1)*(len+2) * nprocs * sizeof(int)
*
*/
#include <stdio.h>
#include <stdlib.h>
#include <iostream>
#include <sstream> // for ostringstream
using namespace std;
#include <string.h> /* strlen(), strcpy(), strncpy() */
#include <unistd.h> /* getopt() */
#include <pnetcdf>
using namespace PnetCDF;
using namespace PnetCDF::exceptions;
#define NDIMS 3
#define HANDLE_ERROR { \
if (err != NC_NOERR) \
printf("Error at line %d (%s)\n", __LINE__, \
ncmpi_strerror(err)); \
}
static void
usage(char *argv0)
{
cerr <<
"Usage: %s [-h] | [-q] [-l len] [file_name]\n"
" [-h] Print help\n"
" [-q] Quiet mode (reports when fail)\n"
" [-l len] size of each dimension of the local array\n"
" [filename] output netCDF file name\n"
<< argv0;
}
/*----< main() >------------------------------------------------------------*/
int main(int argc, char **argv)
{
extern int optind;
extern char *optarg;
char filename[256];
int i, j, k, rank, nprocs, len=0, bufsize, verbose=1;
int *buf, psizes[NDIMS];
vector<MPI_Offset> gsizes(NDIMS), starts(NDIMS), counts(NDIMS), imap(NDIMS);
vector<MPI_Offset> startsT(NDIMS), countsT(NDIMS), strides(NDIMS);
MPI_Init(&argc,&argv);
MPI_Comm_rank(MPI_COMM_WORLD, &rank);
MPI_Comm_size(MPI_COMM_WORLD, &nprocs);
/* get command-line arguments */
while ((i = getopt(argc, argv, "hql:")) != EOF)
switch(i) {
case 'q': verbose = 0;
break;
case 'l': len = atoi(optarg);
break;
case 'h':
default: if (rank==0) usage(argv[0]);
MPI_Finalize();
return 1;
}
if (argv[optind] == NULL) strcpy(filename, "testfile.nc");
else snprintf(filename, 256, "%s", argv[optind]);
len = (len <= 0) ? 10 : len;
for (i=0; i<NDIMS; i++)
psizes[i] = 0;
/* calculate number of processes along each dimension */
MPI_Dims_create(nprocs, NDIMS, psizes);
if (verbose && rank == 0) {
std::ostringstream name;
name << "psizes=";
for (i=0; i<NDIMS; i++) name << " " << psizes[i];
std::cout << name.str() << "\n";
}
/* for each MPI rank, find its local rank IDs along each dimension in
* starts[] */
int lower_dims=1;
for (i=NDIMS-1; i>=0; i--) {
starts[i] = rank / lower_dims % psizes[i];
lower_dims *= psizes[i];
}
if (verbose) {
std::ostringstream name;
name << "proc " << rank << " dim rank=";
for (i=0; i<NDIMS; i++) name << " " << starts[i];
std::cout << name.str() << "\n";
}
bufsize = 1;
for (i=0; i<NDIMS; i++) {
gsizes[i] = (len + i) * psizes[i]; /* global array size */
starts[i] *= (len + i); /* start indices */
counts[i] = (len + i); /* array elements */
bufsize *= (len + i);
}
/* allocate buffer and initialize with contiguous numbers */
buf = (int *) malloc(sizeof(int) * bufsize);
for (k=0; k<counts[0]; k++)
for (j=0; j<counts[1]; j++)
for (i=0; i<counts[2]; i++)
buf[k*counts[1]*counts[2] +
j*counts[2] + i] = (int)
((starts[0]+k)*gsizes[1]*gsizes[2]
+ (starts[1]+j)*gsizes[2]
+ (starts[2]+i));
try {
/* create the file */
NcmpiFile nc(MPI_COMM_WORLD, filename, NcmpiFile::replace,
NcmpiFile::classic5);
/* define dimensions */
vector<NcmpiDim> dimids(NDIMS);
for (i=0; i<NDIMS; i++) {
char name[2];
name[0] = 'Z'-i;
name[1] = '\0';
dimids[i] = nc.addDim(name, gsizes[i]);
}
/* define variable with no transposed file layout: ZYX */
NcmpiVar ZYX_id = nc.addVar("ZYX_var", ncmpiInt, dimids);
/* define variable with transposed file layout: ZYX -> ZXY */
vector<NcmpiDim> dimidsT(NDIMS);
dimidsT[0] = dimids[0]; dimidsT[1] = dimids[2]; dimidsT[2] = dimids[1];
NcmpiVar ZXY_id = nc.addVar("ZXY_var", ncmpiInt, dimidsT);
/* define variable with transposed file layout: ZYX -> YZX */
dimidsT[0] = dimids[1]; dimidsT[1] = dimids[0]; dimidsT[2] = dimids[2];
NcmpiVar YZX_id = nc.addVar("YZX_var", ncmpiInt, dimidsT);
/* define variable with transposed file layout: ZYX -> YXZ */
dimidsT[0] = dimids[1]; dimidsT[1] = dimids[2]; dimidsT[2] = dimids[0];
NcmpiVar YXZ_id = nc.addVar("YXZ_var", ncmpiInt, dimidsT);
/* define variable with transposed file layout: ZYX -> XZY */
dimidsT[0] = dimids[2]; dimidsT[1] = dimids[0]; dimidsT[2] = dimids[1];
NcmpiVar XZY_id = nc.addVar("XZY_var", ncmpiInt, dimidsT);
/* define variable with transposed file layout: ZYX -> XYZ */
dimidsT[0] = dimids[2]; dimidsT[1] = dimids[1]; dimidsT[2] = dimids[0];
NcmpiVar XYZ_id = nc.addVar("XYZ_var", ncmpiInt, dimidsT);
/* write the whole variable in file: ZYX */
ZYX_id.putVar_all(starts, counts, &buf[0]);
strides[0] = strides[1] = strides[2] = 1;
/* ZYX -> ZXY: */
imap[1] = 1; imap[2] = counts[2]; imap[0] = counts[1]*counts[2];
startsT[0] = starts[0]; startsT[1] = starts[2]; startsT[2] = starts[1];
countsT[0] = counts[0]; countsT[1] = counts[2]; countsT[2] = counts[1];
/* write the transposed variable */
ZXY_id.putVar_all(startsT, countsT, strides, imap, &buf[0]);
/* ZYX -> YZX: */
imap[2] = 1; imap[0] = counts[2]; imap[1] = counts[1]*counts[2];
startsT[0] = starts[1]; startsT[1] = starts[0]; startsT[2] = starts[2];
countsT[0] = counts[1]; countsT[1] = counts[0]; countsT[2] = counts[2];
/* write the transposed variable */
YZX_id.putVar_all(startsT, countsT, strides, imap, &buf[0]);
/* ZYX -> YXZ: */
imap[1] = 1; imap[0] = counts[2]; imap[2] = counts[1]*counts[2];
startsT[0] = starts[1]; startsT[1] = starts[2]; startsT[2] = starts[0];
countsT[0] = counts[1]; countsT[1] = counts[2]; countsT[2] = counts[0];
/* write the transposed variable */
YXZ_id.putVar_all(startsT, countsT, strides, imap, &buf[0]);
/* ZYX -> XZY: */
imap[0] = 1; imap[2] = counts[2]; imap[1] = counts[1]*counts[2];
startsT[0] = starts[2]; startsT[1] = starts[0]; startsT[2] = starts[1];
countsT[0] = counts[2]; countsT[1] = counts[0]; countsT[2] = counts[1];
/* write the transposed variable */
XZY_id.putVar_all(startsT, countsT, strides, imap, &buf[0]);
/* ZYX -> XYZ: */
imap[0] = 1; imap[1] = counts[2]; imap[2] = counts[1]*counts[2];
startsT[0] = starts[2]; startsT[1] = starts[1]; startsT[2] = starts[0];
countsT[0] = counts[2]; countsT[1] = counts[1]; countsT[2] = counts[0];
/* write the transposed variable */
XYZ_id.putVar_all(startsT, countsT, strides, imap, &buf[0]);
/* file is close implicitly */
}
catch(NcmpiException& e) {
cout << e.what() << " error code=" << e.errorCode() << " Error!\n";
return 1;
}
free(buf);
MPI_Finalize();
return 0;
}
|
