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
|
/*********************************************************************
*
* Copyright (C) 2015, Northwestern University and Argonne National Laboratory
* See COPYRIGHT notice in top-level directory.
*
*********************************************************************/
/* $Id$ */
/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *
* This example shows how to use
* 1. NcmpiVar::setFill() to define the variable's fill value
* 2. NcmpiVar::getFillModeParameters() to inquire the variable's fill mode
* information
* 3. NcmpiVar::fillVar() to write two 2D 4-byte integer array in parallel.
* It first defines a netCDF record variable of size NC_UNLIMITED * global_ny
* where
* global_nx == (NX * number of MPI processes).
* It then defines a netCDF fixed-size variable of size global_nx * global_ny
* where
* global_ny == NY and
* global_nx == (NX * number of MPI processes).
*
* To compile:
* mpicxx -O2 fill_mode.cpp -o fill_mode -lpnetcdf
*
* Example commands for MPI run and outputs from running ncmpidump on the
* NC file produced by this example program:
*
* % mpiexec -n 4 ./fill_mode /pvfs2/wkliao/testfile.nc
*
* % ncmpidump /pvfs2/wkliao/testfile.nc
* netcdf testfile {
* // file format: CDF-5 (big variables)
* dimensions:
* REC_DIM = UNLIMITED ; // (2 currently)
* X = 16 ;
* Y = 3 ;
* variables:
* int rec_var(REC_DIM, X) ;
* rec_var:_FillValue = -1 ;
* int fix_var(Y, X) ;
*
* // global attributes:
* :history = "Mon Aug 13 21:27:48 2018" ;
* "" ;
* data:
*
* rec_var =
* 0, 0, 0, _, 1, 1, 1, _, 2, 2, 2, _, 3, 3, 3, _,
* 0, 0, 0, _, 1, 1, 1, _, 2, 2, 2, _, 3, 3, 3, _ ;
*
* fix_var =
* 0, 0, 0, _, 1, 1, 1, _, 2, 2, 2, _, 3, 3, 3, _,
* 0, 0, 0, _, 1, 1, 1, _, 2, 2, 2, _, 3, 3, 3, _,
* 0, 0, 0, _, 1, 1, 1, _, 2, 2, 2, _, 3, 3, 3, _ ;
* }
*
* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */
#include <stdio.h>
#include <stdlib.h>
#include <iostream>
using namespace std;
#include <string.h> /* strcpy(), strncpy() */
#include <unistd.h> /* getopt() */
#include <time.h> /* time() localtime(), asctime() */
#include <pnetcdf>
using namespace PnetCDF;
using namespace PnetCDF::exceptions;
#define NY 3
#define NX 4
static void
usage(char *argv0)
{
cerr <<
"Usage: %s [-h] | [-q] [file_name]\n"
" [-h] Print help\n"
" [-q] Quiet mode (reports when fail)\n"
" [filename] output netCDF file name\n"
<< argv0;
}
int main(int argc, char** argv)
{
extern int optind;
char filename[256], str_att[256];
int i, j, verbose=1, rank, nprocs, buf[NY][NX];
MPI_Offset global_ny, global_nx;
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, "hq")) != EOF)
switch(i) {
case 'q': verbose = 0;
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]);
try {
/* create a new file for writing ------------------------------------*/
NcmpiFile ncFile(MPI_COMM_WORLD, filename, NcmpiFile::replace,
NcmpiFile::classic5);
/* the global array is NY * (NX * nprocs) */
global_ny = NY;
global_nx = NX * nprocs;
for (i=0; i<NY; i++)
for (j=0; j<NX; j++)
buf[i][j] = rank;
/* add a global attribute: a time stamp at rank 0 */
time_t ltime = time(NULL); /* get the current calendar time */
asctime_r(localtime(<ime), str_att);
strcpy(str_att, "Mon Aug 13 21:27:48 2018");
/* make sure the time string are consistent among all processes */
MPI_Bcast(str_att, 256, MPI_CHAR, 0, MPI_COMM_WORLD);
ncFile.putAtt(string("history"), string(str_att));
/* define dimensions Y and X */
vector<NcmpiDim> dimid(2);
dimid[0] = ncFile.addDim("REC_DIM", NC_UNLIMITED);
dimid[1] = ncFile.addDim("X", global_nx);
/* define a 2D record variable of integer type */
NcmpiVar rec_var = ncFile.addVar("rec_var", ncmpiInt, dimid);
dimid[0] = ncFile.addDim("Y", global_ny);
/* define a 2D fixed-size variable of integer type */
NcmpiVar fix_var = ncFile.addVar("fix_var", ncmpiInt, dimid);
/* set the variable's fill mode to NC_FILL with default fill value */
fix_var.setFill(true);
/* set a customized fill value -1 */
int fill_value = -1;
rec_var.setFill(true, &fill_value);
/* now we are in data mode */
vector<MPI_Offset> start(2), count(2);
start[0] = 0;
start[1] = NX * rank;
count[0] = NY;
count[1] = NX;
if (verbose)
printf("%d: start=%lld %lld count=%lld %lld\n",rank,
start[0],start[1],count[0],count[1]);
/* do not write the variable in full */
count[1]--;
fix_var.putVar_all(start, count, &buf[0][0]);
bool fillMode=true;
fix_var.getFillModeParameters(fillMode, &fill_value);
if (!fillMode)
printf("Error: expecting fillMode to be false\n");
if (fill_value != NC_FILL_INT)
printf("Error: expecting fillMode to be %d but got %d\n",NC_FILL_INT,fill_value);
/* fill the 1st record of the record variable */
start[0] = 0;
rec_var.fillRec(start[0]);
/* write to the 1st record */
count[0] = 1;
rec_var.putVar_all(start, count, &buf[0][0]);
/* fill the 2nd record of the record variable */
start[0] = 1;
rec_var.fillRec(start[0]);
/* write to the 2nd record */
rec_var.putVar_all(start, count, &buf[0][0]);
/* file is close implicitly */
}
catch(NcmpiException& e) {
cout << e.what() << " error code=" << e.errorCode() << " Error!\n";
return 1;
}
/* check if there is any PnetCDF internal malloc residue */
MPI_Offset malloc_size, sum_size;
int err = ncmpi_inq_malloc_size(&malloc_size);
if (err == NC_NOERR) {
MPI_Reduce(&malloc_size, &sum_size, 1, MPI_OFFSET, MPI_SUM, 0, MPI_COMM_WORLD);
if (rank == 0 && sum_size > 0)
printf("heap memory allocated by PnetCDF internally has %lld bytes yet to be freed\n",
sum_size);
}
MPI_Finalize();
return 0;
}
|
