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
235
236
237
238
239
240
241
242
243
244
245
246
247
248
249
250
251
252
253
254
255
256
257
258
259
260
261
262
263
264
265
266
267
268
269
270
271
272
273
274
275
276
277
278
279
280
281
282
283
284
285
286
287
288
289
290
291
292
293
294
295
296
297
298
299
300
301
302
303
304
305
306
307
308
309
310
311
312
313
314
315
316
317
318
319
320
321
322
323
324
325
326
327
328
329
330
331
332
333
334
335
336
337
338
339
340
341
342
343
344
345
346
347
348
349
350
351
352
353
354
355
356
357
358
359
360
361
362
363
364
365
366
367
368
369
370
371
372
373
374
375
376
377
378
379
380
381
382
383
384
385
386
387
388
389
390
391
392
393
394
395
396
397
398
399
400
401
402
403
404
405
406
407
408
409
410
411
412
413
414
415
416
417
418
|
/*
* test_client.c: Client side of Milestone 4.2 Asynchronous I/O and initial
* IOD VOL plugin demonstration. This is, in effect, the application program that
* would run on one or more compute nodes and make calls to the HDF5 API.
*/
#include <stdio.h>
#include <stdlib.h>
#include <assert.h>
#include <string.h>
#include "mpi.h"
#include "hdf5.h"
int main(int argc, char **argv) {
const char file_name1[]="eff_file_1";
const char file_name2[]="eff_file_2";
hid_t fid1, fid2;
hid_t gid1, gid2;
hid_t did1, did2;
hid_t dtid1, dtid2;
hid_t sid;
hid_t tid1, tid2, rid1, rid2, rid3, rid4;
hid_t fapl_id, trspl_id;
hid_t e_stack;
void *token1, *token2, *token3, *token4, *token5, *token6;
size_t token_size1, token_size2, token_size3, token_size4, token_size5, token_size6;
uint64_t version;
uint64_t trans_num;
const unsigned int nelem=60;
int *wdata1 = NULL, *wdata2 = NULL;
int *rdata1 = NULL, *rdata2 = NULL;
unsigned int i = 0;
hsize_t dims[1];
int my_rank, my_size;
int provided;
MPI_Request mpi_req, mpi_reqs[12];
H5ES_status_t status;
size_t num_events = 0;
herr_t ret;
MPI_Init_thread(&argc, &argv, MPI_THREAD_MULTIPLE, &provided);
if(MPI_THREAD_MULTIPLE != provided) {
fprintf(stderr, "MPI does not have MPI_THREAD_MULTIPLE support\n");
exit(1);
}
/* Call EFF_init to initialize the EFF stack.
As a result of this call, the Function Shipper client is started,
and HDF5 VOL calls are registered with the function shipper.
An "IOD init" call is forwarded from the FS client to the FS server
which should already be running. */
EFF_init(MPI_COMM_WORLD, MPI_INFO_NULL);
MPI_Comm_rank(MPI_COMM_WORLD, &my_rank);
MPI_Comm_size(MPI_COMM_WORLD, &my_size);
fprintf(stderr, "APP processes = %d, my rank is %d\n", my_size, my_rank);
fprintf(stderr, "Create the FAPL to set the IOD VOL plugin and create the file\n");
/* Choose the IOD VOL plugin to use with this file.
First we create a file access property list. Then we call a new routine to set
the IOD plugin to use with this fapl */
fapl_id = H5Pcreate (H5P_FILE_ACCESS);
H5Pset_fapl_iod(fapl_id, MPI_COMM_WORLD, MPI_INFO_NULL);
/* allocate and initialize arrays for dataset & attribute writes and reads.
The write arrays are intialized to contain 60 integers (0-59).
The read arrays are intialized to contain 60 integers all 0s. */
wdata1 = malloc (sizeof(int)*nelem);
wdata2 = malloc (sizeof(int)*nelem);
rdata1 = malloc (sizeof(int)*nelem);
rdata2 = malloc (sizeof(int)*nelem);
for(i=0;i<nelem;++i) {
rdata1[i] = 0;
wdata1[i]=my_rank+1;
rdata2[i] = 0;
wdata2[i]=my_rank+1;
}
/* create a 32 bit integer LE datatype. This is a local operation
that does not touch the file */
dtid1 = H5Tcopy(H5T_NATIVE_INT);
dtid2 = H5Tcopy(H5T_NATIVE_INT);
/* create a dataspace. This is a local Bookeeping operation that
does not touch the file */
dims [0] = 60;
sid = H5Screate_simple(1, dims, NULL);
/* create an event Queue for managing asynchronous requests.
Event Queues will releive the use from managing and completing
individual requests for every operation. Instead of passing a
request for every operation, the event queue is passed and
internally the HDF5 library creates a request and adds it to
the event queue.
Multiple Event queue can be created used by the application. */
e_stack = H5EScreate();
assert(e_stack);
/* create the file. */
fid1 = H5Fcreate(file_name1, H5F_ACC_TRUNC, H5P_DEFAULT, fapl_id);
assert(fid1);
/* create second file */
fid2 = H5Fcreate(file_name2, H5F_ACC_TRUNC, H5P_DEFAULT, fapl_id);
assert(fid2);
/* acquire container version 0 on both containers - EXACT
This can be asynchronous, but here we need the acquired ID
right after the call to start the transaction so we make synchronous. */
version = 0;
rid1 = H5RCacquire(fid1, &version, H5P_DEFAULT, H5_EVENT_STACK_NULL);
assert(0 == version);
rid2 = H5RCacquire(fid2, &version, H5P_DEFAULT, H5_EVENT_STACK_NULL);
assert(0 == version);
/* create transaction objects */
tid1 = H5TRcreate(fid1, rid1, (uint64_t)1);
assert(tid1);
tid2 = H5TRcreate(fid2, rid2, (uint64_t)1);
assert(tid2);
/* start transaction 1 with default Leader/Delegate model. Leader
which is rank 0 here starts the transaction. It can be
asynchronous, but we make it synchronous here so that the
Leader can tell its delegates that the transaction is
started. */
if(0 == my_rank) {
ret = H5TRstart(tid1, H5P_DEFAULT, e_stack);
assert(0 == ret);
ret = H5TRstart(tid2, H5P_DEFAULT, e_stack);
assert(0 == ret);
/* create groups */
gid1 = H5Gcreate_ff(fid1, "G1", H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT, tid1, e_stack);
gid2 = H5Gcreate_ff(fid2, "G1", H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT, tid2, e_stack);
/* Commit datatypes to the files */
H5Tcommit_ff(fid1, "int", dtid1, H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT,
tid1, e_stack);
H5Tcommit_ff(fid2, "int", dtid2, H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT,
tid2, e_stack);
/* create Datasets */
did1 = H5Dcreate_ff(gid1, "D1", dtid1, sid,
H5P_DEFAULT,H5P_DEFAULT,H5P_DEFAULT, tid1, e_stack);
did2 = H5Dcreate_ff(gid2, "D1", dtid2, sid,
H5P_DEFAULT,H5P_DEFAULT,H5P_DEFAULT, tid2, e_stack);
/* Raw data write on D1. */
H5Dwrite_ff(did1, dtid1, sid, sid, H5P_DEFAULT, wdata1, tid1, e_stack);
H5Dwrite_ff(did2, dtid2, sid, sid, H5P_DEFAULT, wdata2, tid2, e_stack);
trans_num = 1;
}
/* Tell other procs that transaction 1 is started */
MPI_Ibcast(&trans_num, 1, MPI_UINT64_T, 0, MPI_COMM_WORLD, &mpi_req);
/* Do the local-to-global, global-to-local, so all delegates can
write the gids created in transaction 1 */
if(0 == my_rank) {
/* get the token size of each map */
ret = H5Oget_token(gid1, NULL, &token_size1);
assert(0 == ret);
ret = H5Oget_token(gid2, NULL, &token_size2);
assert(0 == ret);
ret = H5Oget_token(dtid1, NULL, &token_size3);
assert(0 == ret);
ret = H5Oget_token(dtid2, NULL, &token_size4);
assert(0 == ret);
ret = H5Oget_token(did1, NULL, &token_size5);
assert(0 == ret);
ret = H5Oget_token(did2, NULL, &token_size6);
assert(0 == ret);
/* allocate buffers for each token */
token1 = malloc(token_size1);
token2 = malloc(token_size2);
token3 = malloc(token_size3);
token4 = malloc(token_size4);
token5 = malloc(token_size5);
token6 = malloc(token_size6);
/* get the token buffer */
ret = H5Oget_token(gid1, token1, &token_size1);
assert(0 == ret);
ret = H5Oget_token(gid2, token2, &token_size2);
assert(0 == ret);
ret = H5Oget_token(dtid1, token3, &token_size3);
assert(0 == ret);
ret = H5Oget_token(dtid2, token4, &token_size4);
assert(0 == ret);
ret = H5Oget_token(did1, token5, &token_size5);
assert(0 == ret);
ret = H5Oget_token(did2, token6, &token_size6);
assert(0 == ret);
/* make sure the create operations have completed before
telling the delegates to open them */
H5ESget_count(e_stack, &num_events);
H5ESwait_all(e_stack, &status);
H5ESclear(e_stack);
printf("%d events in event stack. Completion status = %d\n", num_events, status);
/* bcast the token sizes and the tokens */
MPI_Ibcast(&token_size1, sizeof(size_t), MPI_BYTE, 0, MPI_COMM_WORLD, &mpi_reqs[0]);
MPI_Ibcast(&token_size2, sizeof(size_t), MPI_BYTE, 0, MPI_COMM_WORLD, &mpi_reqs[1]);
MPI_Ibcast(&token_size3, sizeof(size_t), MPI_BYTE, 0, MPI_COMM_WORLD, &mpi_reqs[2]);
MPI_Ibcast(&token_size4, sizeof(size_t), MPI_BYTE, 0, MPI_COMM_WORLD, &mpi_reqs[3]);
MPI_Ibcast(&token_size5, sizeof(size_t), MPI_BYTE, 0, MPI_COMM_WORLD, &mpi_reqs[4]);
MPI_Ibcast(&token_size6, sizeof(size_t), MPI_BYTE, 0, MPI_COMM_WORLD, &mpi_reqs[5]);
MPI_Ibcast(token1, token_size1, MPI_BYTE, 0, MPI_COMM_WORLD, &mpi_reqs[6]);
MPI_Ibcast(token2, token_size2, MPI_BYTE, 0, MPI_COMM_WORLD, &mpi_reqs[7]);
MPI_Ibcast(token3, token_size3, MPI_BYTE, 0, MPI_COMM_WORLD, &mpi_reqs[8]);
MPI_Ibcast(token4, token_size4, MPI_BYTE, 0, MPI_COMM_WORLD, &mpi_reqs[9]);
MPI_Ibcast(token5, token_size5, MPI_BYTE, 0, MPI_COMM_WORLD, &mpi_reqs[10]);
MPI_Ibcast(token6, token_size6, MPI_BYTE, 0, MPI_COMM_WORLD, &mpi_reqs[11]);
}
/* Leader can continue writing to transaction 1,
while others wait for the ibcast to complete */
if(0 != my_rank) {
/* this wait if for the transaction start */
MPI_Wait(&mpi_req, MPI_STATUS_IGNORE);
assert(1 == trans_num);
/* recieve the token sizes */
MPI_Ibcast(&token_size1, sizeof(size_t), MPI_BYTE, 0, MPI_COMM_WORLD, &mpi_reqs[0]);
MPI_Ibcast(&token_size2, sizeof(size_t), MPI_BYTE, 0, MPI_COMM_WORLD, &mpi_reqs[1]);
MPI_Ibcast(&token_size3, sizeof(size_t), MPI_BYTE, 0, MPI_COMM_WORLD, &mpi_reqs[2]);
MPI_Ibcast(&token_size4, sizeof(size_t), MPI_BYTE, 0, MPI_COMM_WORLD, &mpi_reqs[3]);
MPI_Ibcast(&token_size5, sizeof(size_t), MPI_BYTE, 0, MPI_COMM_WORLD, &mpi_reqs[4]);
MPI_Ibcast(&token_size6, sizeof(size_t), MPI_BYTE, 0, MPI_COMM_WORLD, &mpi_reqs[5]);
MPI_Waitall(6, mpi_reqs, MPI_STATUS_IGNORE);
/* allocate buffers for each token */
token1 = malloc(token_size1);
token2 = malloc(token_size2);
token3 = malloc(token_size3);
token4 = malloc(token_size4);
token5 = malloc(token_size5);
token6 = malloc(token_size6);
/* recieve the tokens */
MPI_Ibcast(token1, token_size1, MPI_BYTE, 0, MPI_COMM_WORLD, &mpi_reqs[0]);
MPI_Ibcast(token2, token_size2, MPI_BYTE, 0, MPI_COMM_WORLD, &mpi_reqs[1]);
MPI_Ibcast(token3, token_size3, MPI_BYTE, 0, MPI_COMM_WORLD, &mpi_reqs[2]);
MPI_Ibcast(token4, token_size4, MPI_BYTE, 0, MPI_COMM_WORLD, &mpi_reqs[3]);
MPI_Ibcast(token5, token_size5, MPI_BYTE, 0, MPI_COMM_WORLD, &mpi_reqs[4]);
MPI_Ibcast(token6, token_size6, MPI_BYTE, 0, MPI_COMM_WORLD, &mpi_reqs[5]);
MPI_Waitall(6, mpi_reqs, MPI_STATUS_IGNORE);
gid1 = H5Oopen_by_token(token1, tid1, e_stack);
gid2 = H5Oopen_by_token(token2, tid2, e_stack);
dtid1 = H5Oopen_by_token(token3, tid1, e_stack);
dtid2 = H5Oopen_by_token(token4, tid2, e_stack);
did1 = H5Oopen_by_token(token5, tid1, e_stack);
did2 = H5Oopen_by_token(token6, tid2, e_stack);
/* Raw data write on D1. */
H5Dwrite_ff(did1, dtid1, sid, sid, H5P_DEFAULT, wdata1, tid1, e_stack);
H5Dwrite_ff(did2, dtid2, sid, sid, H5P_DEFAULT, wdata2, tid2, e_stack);
/* none leader procs have to complete operations before notifying the leader */
H5ESget_count(e_stack, &num_events);
H5ESwait_all(e_stack, &status);
H5ESclear(e_stack);
printf("%d events in event stack. Completion status = %d\n", num_events, status);
}
/* Barrier to make sure all processes are done writing so Process
0 can finish transaction 1 and acquire a read context on it. */
MPI_Barrier(MPI_COMM_WORLD);
/* Leader process finishes/commits the transaction */
if(0 == my_rank) {
MPI_Wait(&mpi_req, MPI_STATUS_IGNORE);
MPI_Waitall(12, mpi_reqs, MPI_STATUS_IGNORE);
ret = H5TRfinish(tid1, H5P_DEFAULT, NULL, H5_EVENT_STACK_NULL);
assert(0 == ret);
ret = H5TRfinish(tid2, H5P_DEFAULT, NULL, H5_EVENT_STACK_NULL);
assert(0 == ret);
}
MPI_Barrier(MPI_COMM_WORLD);
/* Close the first transaction object. Local op */
ret = H5TRclose(tid1);
assert(0 == ret);
ret = H5TRclose(tid2);
assert(0 == ret);
/* release container version 0. This is async. */
ret = H5RCrelease(rid1, H5_EVENT_STACK_NULL);
assert(0 == ret);
ret = H5RCrelease(rid2, H5_EVENT_STACK_NULL);
assert(0 == ret);
ret = H5RCclose(rid1);
assert(0 == ret);
ret = H5RCclose(rid2);
assert(0 == ret);
version = 1;
rid1 = H5RCacquire(fid1, &version, H5P_DEFAULT, e_stack);
assert(1 == version);
rid2 = H5RCacquire(fid2, &version, H5P_DEFAULT, e_stack);
assert(1 == version);
{
hid_t dxpl_id;
uint64_t cs_scope;
dxpl_id = H5Pcreate (H5P_DATASET_XFER);
/* tell HDF5 to disable all data integrity checks for this write */
cs_scope = 0;
ret = H5Pset_rawdata_integrity_scope(dxpl_id, cs_scope);
assert(ret == 0);
ret = H5Dread_ff(did1, dtid1, sid, sid, dxpl_id, rdata1, rid1, e_stack);
assert(ret == 0);
ret = H5Dread_ff(did2, dtid2, sid, sid, dxpl_id, rdata2, rid2, e_stack);
assert(ret == 0);
H5Pclose(dxpl_id);
H5ESget_count(e_stack, &num_events);
H5ESwait_all(e_stack, &status);
H5ESclear(e_stack);
printf("%d events in event stack. Completion status = %d\n", num_events, status);
fprintf(stderr, "Read Data from container 1: ");
for(i=0;i<nelem;++i)
fprintf(stderr, "%d ",rdata1[i]);
fprintf(stderr, "\n");
fprintf(stderr, "Read Data from container 2: ");
for(i=0;i<nelem;++i)
fprintf(stderr, "%d ",rdata2[i]);
fprintf(stderr, "\n");
}
MPI_Barrier(MPI_COMM_WORLD);
/* release container version 1. This is async. */
ret = H5RCrelease(rid1, e_stack);
assert(0 == ret);
ret = H5RCrelease(rid2, e_stack);
assert(0 == ret);
H5ESget_count(e_stack, &num_events);
H5ESwait_all(e_stack, &status);
H5ESclear(e_stack);
printf("%d events in event stack. Completion status = %d\n", num_events, status);
fprintf(stderr, "\n*****************************************************************************************************************\n");
fprintf(stderr, "Close Objects\n");
fprintf(stderr, "*****************************************************************************************************************\n");
assert(H5Dclose_ff(did1, e_stack) == 0);
assert(H5Dclose_ff(did2, e_stack) == 0);
assert(H5Tclose_ff(dtid1, e_stack) == 0);
assert(H5Tclose_ff(dtid2, e_stack) == 0);
assert(H5Gclose_ff(gid1, e_stack) == 0);
assert(H5Gclose_ff(gid2, e_stack) == 0);
ret = H5RCclose(rid1);
assert(0 == ret);
ret = H5RCclose(rid2);
assert(0 == ret);
assert(H5Fclose_ff(fid1, H5_EVENT_STACK_NULL) == 0);
assert(H5Fclose_ff(fid2, H5_EVENT_STACK_NULL) == 0);
/* wait on all requests and print completion status */
H5ESget_count(e_stack, &num_events);
H5ESwait_all(e_stack, &status);
H5ESclear(e_stack);
printf("%d events in event stack. Completion status = %d\n", num_events, status);
H5ESclose(e_stack);
H5Sclose(sid);
H5Pclose(fapl_id);
free(token1);
free(token2);
free(token3);
free(token4);
free(token5);
free(token6);
free(wdata1);
free(rdata1);
free(wdata2);
free(rdata2);
fprintf(stderr, "\n*****************************************************************************************************************\n");
fprintf(stderr, "Finalize EFF stack\n");
fprintf(stderr, "*****************************************************************************************************************\n");
MPI_Barrier(MPI_COMM_WORLD);
/* This finalizes the EFF stack. ships a terminate and IOD finalize to the server
and shutsdown the FS server (when all clients send the terminate request)
and client */
EFF_finalize();
MPI_Finalize();
return 0;
}
|