darshan-posix.c 58.4 KB
Newer Older
1
/*
Shane Snyder's avatar
Shane Snyder committed
2
3
4
 * Copyright (C) 2015 University of Chicago.
 * See COPYRIGHT notice in top-level directory.
 *
5
6
 */

7
8
9
#define _XOPEN_SOURCE 500
#define _GNU_SOURCE

10
#include "darshan-runtime-config.h"
11
12
13
14
15
16
17
18
19
20
21
22
23
24
#include <stdio.h>
#include <unistd.h>
#include <sys/types.h>
#include <sys/stat.h>
#include <fcntl.h>
#include <stdarg.h>
#include <string.h>
#include <time.h>
#include <stdlib.h>
#include <errno.h>
#include <sys/uio.h>
#include <sys/mman.h>
#include <search.h>
#include <assert.h>
25
#include <libgen.h>
Philip Carns's avatar
Philip Carns committed
26
#include <aio.h>
27
#include <pthread.h>
28

29
#include "uthash.h"
30
#include "darshan.h"
31
#include "darshan-posix-log-format.h"
32

33
#ifndef HAVE_OFF64_T
34
35
typedef int64_t off64_t;
#endif
36
37
38
#ifndef HAVE_AIOCB64
#define aiocb64 aiocb
#endif
39

40
/* TODO: this probably shouldn't be here long term -- MPI symbols mess up LD_PRELOAD */
Shane Snyder's avatar
Shane Snyder committed
41
42
43
44
#ifdef DARSHAN_PRELOAD
extern double (*__real_PMPI_Comm_rank)(MPI_Comm comm, int *rank);
#endif

45
46
/* TODO: more libc, fgetc, etc etc etc. */

47
48
DARSHAN_FORWARD_DECL(open, int, (const char *path, int flags, ...));
DARSHAN_FORWARD_DECL(open64, int, (const char *path, int flags, ...));
49
50
DARSHAN_FORWARD_DECL(creat, int, (const char* path, mode_t mode));
DARSHAN_FORWARD_DECL(creat64, int, (const char* path, mode_t mode));
51
52
DARSHAN_FORWARD_DECL(fopen, FILE*, (const char *path, const char *mode));
DARSHAN_FORWARD_DECL(fopen64, FILE*, (const char *path, const char *mode));
53
54
55
56
DARSHAN_FORWARD_DECL(mkstemp, int, (char *template));
DARSHAN_FORWARD_DECL(mkostemp, int, (char *template, int flags));
DARSHAN_FORWARD_DECL(mkstemps, int, (char *template, int suffixlen));
DARSHAN_FORWARD_DECL(mkostemps, int, (char *template, int suffixlen, int flags));
57
58
59
60
61
62
63
64
DARSHAN_FORWARD_DECL(read, ssize_t, (int fd, void *buf, size_t count));
DARSHAN_FORWARD_DECL(write, ssize_t, (int fd, const void *buf, size_t count));
DARSHAN_FORWARD_DECL(pread, ssize_t, (int fd, void *buf, size_t count, off_t offset));
DARSHAN_FORWARD_DECL(pwrite, ssize_t, (int fd, const void *buf, size_t count, off_t offset));
DARSHAN_FORWARD_DECL(pread64, ssize_t, (int fd, void *buf, size_t count, off64_t offset));
DARSHAN_FORWARD_DECL(pwrite64, ssize_t, (int fd, const void *buf, size_t count, off64_t offset));
DARSHAN_FORWARD_DECL(readv, ssize_t, (int fd, const struct iovec *iov, int iovcnt));
DARSHAN_FORWARD_DECL(writev, ssize_t, (int fd, const struct iovec *iov, int iovcnt));
65
66
67
68
69
DARSHAN_FORWARD_DECL(fread, size_t, (void *ptr, size_t size, size_t nmemb, FILE *stream));
DARSHAN_FORWARD_DECL(fwrite, size_t, (const void *ptr, size_t size, size_t nmemb, FILE *stream));
DARSHAN_FORWARD_DECL(lseek, off_t, (int fd, off_t offset, int whence));
DARSHAN_FORWARD_DECL(lseek64, off64_t, (int fd, off64_t offset, int whence));
DARSHAN_FORWARD_DECL(fseek, int, (FILE *stream, long offset, int whence));
70
71
72
73
74
75
DARSHAN_FORWARD_DECL(__xstat, int, (int vers, const char* path, struct stat *buf));
DARSHAN_FORWARD_DECL(__xstat64, int, (int vers, const char* path, struct stat64 *buf));
DARSHAN_FORWARD_DECL(__lxstat, int, (int vers, const char* path, struct stat *buf));
DARSHAN_FORWARD_DECL(__lxstat64, int, (int vers, const char* path, struct stat64 *buf));
DARSHAN_FORWARD_DECL(__fxstat, int, (int vers, int fd, struct stat *buf));
DARSHAN_FORWARD_DECL(__fxstat64, int, (int vers, int fd, struct stat64 *buf));
Shane Snyder's avatar
Shane Snyder committed
76
77
DARSHAN_FORWARD_DECL(mmap, void*, (void *addr, size_t length, int prot, int flags, int fd, off_t offset));
DARSHAN_FORWARD_DECL(mmap64, void*, (void *addr, size_t length, int prot, int flags, int fd, off64_t offset));
78
79
DARSHAN_FORWARD_DECL(fsync, int, (int fd));
DARSHAN_FORWARD_DECL(fdatasync, int, (int fd));
80
DARSHAN_FORWARD_DECL(close, int, (int fd));
81
DARSHAN_FORWARD_DECL(fclose, int, (FILE *fp));
82
83
/* TODO aio */
/* TODO listio */
84

85
86
87
88
89
/* maximum number of access sizes and stride sizes that darshan will track
 * per file at runtime; at log time they will be reduced into the 4 most
 * frequently occurring ones 
 */
#define POSIX_MAX_ACCESS_COUNT_RUNTIME 32
90

91
92
93
94
95
96
enum posix_io_type
{
    POSIX_READ = 1,
    POSIX_WRITE = 2,
};

97
98
99
100
101
102
103
104
105
106
107
108
enum posix_counter_type
{
    POSIX_COUNTER_ACCESS,
    POSIX_COUNTER_STRIDE
};

struct posix_access_counter
{
    int64_t size;
    int freq;
};

109
110
111
112
113
114
/* The posix_file_runtime structure maintains necessary runtime metadata
 * for the POSIX file record (darshan_posix_file structure, defined in
 * darshan-posix-log-format.h) pointed to by 'file_record'. This metadata
 * assists with the instrumenting of specific statistics in the file record.
 * 'hlink' is a hash table link structure used to add/remove this record
 * from the hash table of POSIX file records for this process. 
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
 *
 * RATIONALE: the POSIX module needs to track some stateful, volatile 
 * information about each open file (like the current file offset, most recent 
 * access time, etc.) to aid in instrumentation, but this information can't be
 * stored in the darshan_posix_file struct because we don't want it to appear in
 * the final darshan log file.  We therefore associate a posix_file_runtime
 * struct with each darshan_posix_file struct in order to track this information.
  *
 * NOTE: There is a one-to-one mapping of posix_file_runtime structs to
 * darshan_posix_file structs.
 *
 * NOTE: The posix_file_runtime struct contains a pointer to a darshan_posix_file
 * struct (see the *file_record member) rather than simply embedding an entire
 * darshan_posix_file struct.  This is done so that all of the darshan_posix_file
 * structs can be kept contiguous in memory as a single array to simplify
 * reduction, compression, and storage.
131
 */
132
struct posix_file_runtime
133
{
134
    struct darshan_posix_file* file_record;
135
136
137
138
    int64_t offset;
    int64_t last_byte_read;
    int64_t last_byte_written;
    enum posix_io_type last_io_type;
139
140
141
    double last_meta_end;
    double last_read_end;
    double last_write_end;
142
143
144
145
    void* access_root;
    int access_count;
    void* stride_root;
    int stride_count;
146
    UT_hash_handle hlink;
147
};
148

149
150
151
152
153
154
155
156
157
158
159
/* The posix_file_runtime_ref structure is used to associate a POSIX
 * file descriptor with an already existing POSIX file record. This is
 * necessary as many POSIX I/O functions take only an input file descriptor,
 * but POSIX file records are indexed by their full file paths (i.e., darshan
 * record identifiers for POSIX files are created by hashing the file path).
 * In other words, this structure is necessary as it allows us to look up a
 * file record either by a pathname (posix_file_runtime) or by POSIX file
 * descriptor (posix_file_runtime_ref), depending on which parameters are
 * available. This structure includes another hash table link, since separate
 * hashes are maintained for posix_file_runtime structures and posix_file_runtime_ref
 * structures.
160
161
162
163
164
165
166
167
168
169
170
 *
 * RATIONALE: In theory the fd information could be included in the
 * posix_file_runtime struct rather than in a separate structure here.  The
 * reason we don't do that is because the same file could be opened multiple
 * times by a given process with different file descriptors and thus
 * simulataneously referenced using different file descriptors.  This practice is
 * not common, but we must support it.
 *
 * NOTE: there are potentially multiple posix_file_runtime_ref structures
 * referring to a single posix_file_runtime structure.  Most of the time there is
 * only one, however.
171
 */
172
struct posix_file_runtime_ref
173
{
174
    struct posix_file_runtime* file;
175
176
177
178
    int fd;
    UT_hash_handle hlink;
};

179
180
181
182
/* The posix_runtime structure maintains necessary state for storing
 * POSIX file records and for coordinating with darshan-core at 
 * shutdown time.
 */
183
184
struct posix_runtime
{
185
    struct posix_file_runtime* file_runtime_array;
186
    struct darshan_posix_file* file_record_array;
187
    int file_array_size;
188
    int file_array_ndx;
189
190
    struct posix_file_runtime* file_hash;
    struct posix_file_runtime_ref* fd_hash;
191
192
    void *red_buf;
    int shared_rec_count;
193
194
};

195
static struct posix_runtime *posix_runtime = NULL;
196
static pthread_mutex_t posix_runtime_mutex = PTHREAD_RECURSIVE_MUTEX_INITIALIZER_NP;
Shane Snyder's avatar
Shane Snyder committed
197
static int instrumentation_disabled = 0;
198
static int my_rank = -1;
199
static int darshan_mem_alignment = 1;
200

201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
/* global variables for determining 4 most common accesses/strides */
static struct posix_file_runtime* walker_file = NULL;
static int walker_validx;
static int walker_cntidx;

static void posix_runtime_initialize(void);
static struct posix_file_runtime* posix_file_by_name(const char *name);
static struct posix_file_runtime* posix_file_by_name_setfd(const char* name, int fd);
static struct posix_file_runtime* posix_file_by_fd(int fd);
static void posix_file_close_fd(int fd);
static void posix_access_counter(struct posix_file_runtime* file, ssize_t size,
    enum posix_counter_type type);
static void posix_access_walker(const void* nodep, const VISIT which, const int depth);
static void posix_walk_file_accesses(void);
static int posix_access_compare(const void* a_p, const void* b_p);
static int posix_file_compare(const void* a, const void* b);

218
219
220
static void posix_begin_shutdown(void);
static void posix_setup_reduction(darshan_record_id *shared_recs, int *shared_rec_count,
    void **send_buf, void **recv_buf, int *rec_size);
221
222
223
224
225
static void posix_record_reduction_op(void* infile_v, void* inoutfile_v,
    int *len, MPI_Datatype *datatype);
static void posix_get_output_data(void **buffer, int *size);
static void posix_shutdown(void);

226
227
#define POSIX_LOCK() pthread_mutex_lock(&posix_runtime_mutex)
#define POSIX_UNLOCK() pthread_mutex_unlock(&posix_runtime_mutex)
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
#define POSIX_COMMON_COUNTER_INC(__rec_p, __value, __count, __validx, __cntidx) do {\
    int i; \
    int set = 0; \
    int64_t min = DARSHAN_COUNTER_VALUE(__rec_p, __cntidx); \
    int min_index = 0; \
    if(__value == 0) break; \
    for(i=0; i<4; i++) { \
        /* increment bucket if already exists */ \
        if(DARSHAN_COUNTER_VALUE(__rec_p, __validx + i) == __value) { \
            DARSHAN_COUNTER_INC(__rec_p, __cntidx + i, __count); \
            set = 1; \
            break; \
        } \
        /* otherwise find the least frequently used bucket */ \
        else if(DARSHAN_COUNTER_VALUE(__rec_p, __cntidx + i) < min) { \
            min = DARSHAN_COUNTER_VALUE(__rec_p, __cntidx + i); \
            min_index = i; \
        } \
    } \
    if(!set && (__count > min)) { \
        DARSHAN_COUNTER_SET(__rec_p, __cntidx+min_index, __count); \
        DARSHAN_COUNTER_SET(__rec_p, __validx+min_index, __value); \
    } \
} while(0)

254
#define POSIX_RECORD_OPEN(__ret, __path, __mode, __stream_flag, __tm1, __tm2) do { \
255
    struct posix_file_runtime* file; \
256
257
258
    char* exclude; \
    int tmp_index = 0; \
    if(__ret < 0) break; \
259
    while((exclude = darshan_path_exclusions[tmp_index])) { \
260
261
262
263
264
        if(!(strncmp(exclude, __path, strlen(exclude)))) \
            break; \
        tmp_index++; \
    } \
    if(exclude) break; \
265
    file = posix_file_by_name_setfd(__path, __ret); \
266
    if(!file) break; \
267
    file->file_record->rank = my_rank; \
268
    if(__mode) \
269
270
271
272
        DARSHAN_COUNTER_SET(file->file_record, POSIX_MODE, __mode); \
    file->offset = 0; \
    file->last_byte_written = 0; \
    file->last_byte_read = 0; \
273
    if(__stream_flag)\
274
        DARSHAN_COUNTER_INC(file->file_record, POSIX_FOPENS, 1); \
275
    else \
276
277
278
279
        DARSHAN_COUNTER_INC(file->file_record, POSIX_OPENS, 1); \
    if(DARSHAN_COUNTER_F_VALUE(file->file_record, POSIX_F_OPEN_TIMESTAMP) == 0) \
        DARSHAN_COUNTER_F_SET(file->file_record, POSIX_F_OPEN_TIMESTAMP, __tm1); \
    DARSHAN_COUNTER_F_INC_NO_OVERLAP(file->file_record, __tm1, __tm2, file->last_meta_end, POSIX_F_META_TIME); \
280
281
282
} while(0)

#define POSIX_RECORD_READ(__ret, __fd, __pread_flag, __pread_offset, __aligned, __stream_flag, __tm1, __tm2) do{ \
283
    size_t stride; \
284
    int64_t this_offset; \
285
    struct posix_file_runtime* file; \
286
    int64_t file_alignment; \
287
288
289
290
    double __elapsed = __tm2-__tm1; \
    if(__ret < 0) break; \
    file = posix_file_by_fd(__fd); \
    if(!file) break; \
291
    if(__pread_flag) \
292
293
294
295
        this_offset = __pread_offset; \
    else \
        this_offset = file->offset; \
    if(this_offset > file->last_byte_read) \
296
        DARSHAN_COUNTER_INC(file->file_record, POSIX_SEQ_READS, 1); \
297
    if(this_offset == (file->last_byte_read + 1)) \
298
        DARSHAN_COUNTER_INC(file->file_record, POSIX_CONSEC_READS, 1); \
299
    if(this_offset > 0 && this_offset > file->last_byte_read \
300
301
302
        && file->last_byte_read != 0) \
        stride = this_offset - file->last_byte_read - 1; \
    else \
303
        stride = 0; \
304
305
    file->last_byte_read = this_offset + __ret - 1; \
    file->offset = this_offset + __ret; \
306
307
    DARSHAN_COUNTER_MAX(file->file_record, POSIX_MAX_BYTE_READ, (this_offset + __ret - 1)); \
    DARSHAN_COUNTER_INC(file->file_record, POSIX_BYTES_READ, __ret); \
308
    if(__stream_flag)\
309
        DARSHAN_COUNTER_INC(file->file_record, POSIX_FREADS, 1); \
310
    else\
311
        DARSHAN_COUNTER_INC(file->file_record, POSIX_READS, 1); \
312
313
314
    DARSHAN_BUCKET_INC(file->file_record, POSIX_SIZE_READ_0_100, __ret); \
    posix_access_counter(file, __ret, POSIX_COUNTER_ACCESS); \
    posix_access_counter(file, stride, POSIX_COUNTER_STRIDE); \
315
    if(!__aligned) \
316
317
        DARSHAN_COUNTER_INC(file->file_record, POSIX_MEM_NOT_ALIGNED, 1); \
    file_alignment = DARSHAN_COUNTER_VALUE(file->file_record, POSIX_FILE_ALIGNMENT); \
318
    if(file_alignment > 0 && (this_offset % file_alignment) != 0) \
319
        DARSHAN_COUNTER_INC(file->file_record, POSIX_FILE_NOT_ALIGNED, 1); \
320
321
322
323
324
325
326
327
328
329
    if(file->last_io_type == POSIX_WRITE) \
        DARSHAN_COUNTER_INC(file->file_record, POSIX_RW_SWITCHES, 1); \
    file->last_io_type = POSIX_READ; \
    DARSHAN_COUNTER_F_INC_NO_OVERLAP(file->file_record, __tm1, __tm2, file->last_read_end, POSIX_F_READ_TIME); \
    if(DARSHAN_COUNTER_F_VALUE(file->file_record, POSIX_F_READ_START_TIMESTAMP) == 0) \
        DARSHAN_COUNTER_F_SET(file->file_record, POSIX_F_READ_START_TIMESTAMP, __tm1); \
    DARSHAN_COUNTER_F_SET(file->file_record, POSIX_F_READ_END_TIMESTAMP, __tm2); \
    if(DARSHAN_COUNTER_F_VALUE(file->file_record, POSIX_F_MAX_READ_TIME) < __elapsed){ \
        DARSHAN_COUNTER_F_SET(file->file_record, POSIX_F_MAX_READ_TIME, __elapsed); \
        DARSHAN_COUNTER_SET(file->file_record, POSIX_MAX_READ_TIME_SIZE, __ret); } \
330
331
332
} while(0)

#define POSIX_RECORD_WRITE(__ret, __fd, __pwrite_flag, __pwrite_offset, __aligned, __stream_flag, __tm1, __tm2) do{ \
333
    size_t stride; \
334
    int64_t this_offset; \
335
    struct posix_file_runtime* file; \
336
    int64_t file_alignment; \
337
338
339
340
    double __elapsed = __tm2-__tm1; \
    if(__ret < 0) break; \
    file = posix_file_by_fd(__fd); \
    if(!file) break; \
341
    if(__pwrite_flag) \
342
343
344
345
        this_offset = __pwrite_offset; \
    else \
        this_offset = file->offset; \
    if(this_offset > file->last_byte_written) \
346
        DARSHAN_COUNTER_INC(file->file_record, POSIX_SEQ_WRITES, 1); \
347
    if(this_offset == (file->last_byte_written + 1)) \
348
        DARSHAN_COUNTER_INC(file->file_record, POSIX_CONSEC_WRITES, 1); \
349
    if(this_offset > 0 && this_offset > file->last_byte_written \
350
351
        && file->last_byte_written != 0) \
        stride = this_offset - file->last_byte_written - 1; \
352
    else \
353
        stride = 0; \
354
355
    file->last_byte_written = this_offset + __ret - 1; \
    file->offset = this_offset + __ret; \
356
357
    DARSHAN_COUNTER_MAX(file->file_record, POSIX_MAX_BYTE_WRITTEN, (this_offset + __ret - 1)); \
    DARSHAN_COUNTER_INC(file->file_record, POSIX_BYTES_WRITTEN, __ret); \
358
    if(__stream_flag) \
359
        DARSHAN_COUNTER_INC(file->file_record, POSIX_FWRITES, 1); \
360
    else \
361
        DARSHAN_COUNTER_INC(file->file_record, POSIX_WRITES, 1); \
362
363
364
    DARSHAN_BUCKET_INC(file->file_record, POSIX_SIZE_WRITE_0_100, __ret); \
    posix_access_counter(file, __ret, POSIX_COUNTER_ACCESS); \
    posix_access_counter(file, stride, POSIX_COUNTER_STRIDE);  \
365
    if(!__aligned) \
366
367
        DARSHAN_COUNTER_INC(file->file_record, POSIX_MEM_NOT_ALIGNED, 1); \
    file_alignment = DARSHAN_COUNTER_VALUE(file->file_record, POSIX_FILE_ALIGNMENT); \
368
    if(file_alignment > 0 && (this_offset % file_alignment) != 0) \
369
        DARSHAN_COUNTER_INC(file->file_record, POSIX_FILE_NOT_ALIGNED, 1); \
370
371
372
373
374
375
376
377
378
379
    if(file->last_io_type == POSIX_READ) \
        DARSHAN_COUNTER_INC(file->file_record, POSIX_RW_SWITCHES, 1); \
    file->last_io_type = POSIX_WRITE; \
    DARSHAN_COUNTER_F_INC_NO_OVERLAP(file->file_record, __tm1, __tm2, file->last_write_end, POSIX_F_WRITE_TIME); \
    if(DARSHAN_COUNTER_F_VALUE(file->file_record, POSIX_F_WRITE_START_TIMESTAMP) == 0) \
        DARSHAN_COUNTER_F_SET(file->file_record, POSIX_F_WRITE_START_TIMESTAMP, __tm1); \
    DARSHAN_COUNTER_F_SET(file->file_record, POSIX_F_WRITE_END_TIMESTAMP, __tm2); \
    if(DARSHAN_COUNTER_F_VALUE(file->file_record, POSIX_F_MAX_WRITE_TIME) < __elapsed){ \
        DARSHAN_COUNTER_F_SET(file->file_record, POSIX_F_MAX_WRITE_TIME, __elapsed); \
        DARSHAN_COUNTER_SET(file->file_record, POSIX_MAX_WRITE_TIME_SIZE, __ret); } \
380
} while(0)
381

382
383
384
385
386
387
388
389
390
391
392
393
394
395
396
397
398
399
400
401
402
403
404
#define POSIX_LOOKUP_RECORD_STAT(__path, __statbuf, __tm1, __tm2) do { \
    char* exclude; \
    int tmp_index = 0; \
    struct posix_file_runtime* file; \
    while((exclude = darshan_path_exclusions[tmp_index])) { \
        if(!(strncmp(exclude, __path, strlen(exclude)))) \
            break; \
        tmp_index++; \
    } \
    if(exclude) break; \
    file = posix_file_by_name(__path); \
    if(file) \
    { \
        POSIX_RECORD_STAT(file, __statbuf, __tm1, __tm2); \
    } \
} while(0)

#define POSIX_RECORD_STAT(__file, __statbuf, __tm1, __tm2) do { \
    (__file)->file_record->rank = my_rank; \
    DARSHAN_COUNTER_F_INC_NO_OVERLAP((__file)->file_record, __tm1, __tm2, (__file)->last_meta_end, POSIX_F_META_TIME); \
    DARSHAN_COUNTER_INC((__file)->file_record, POSIX_STATS, 1); \
} while(0)

405
406
407
408
/**********************************************************
 *      Wrappers for POSIX I/O functions of interest      * 
 **********************************************************/

409
int DARSHAN_DECL(open)(const char *path, int flags, ...)
410
411
412
413
414
{
    int mode = 0;
    int ret;
    double tm1, tm2;

415
416
    MAP_OR_FAIL(open);

417
    if(flags & O_CREAT) 
418
419
420
421
422
423
    {
        va_list arg;
        va_start(arg, flags);
        mode = va_arg(arg, int);
        va_end(arg);

424
        tm1 = darshan_core_wtime();
425
        ret = __real_open(path, flags, mode);
426
        tm2 = darshan_core_wtime();
427
428
429
    }
    else
    {
430
        tm1 = darshan_core_wtime();
431
        ret = __real_open(path, flags);
432
        tm2 = darshan_core_wtime();
433
434
    }

435
436
    POSIX_LOCK();
    posix_runtime_initialize();
437
    POSIX_RECORD_OPEN(ret, path, mode, 0, tm1, tm2);
438
    POSIX_UNLOCK();
439
440
441
442

    return(ret);
}

Shane Snyder's avatar
Shane Snyder committed
443
444
445
446
447
448
int DARSHAN_DECL(open64)(const char *path, int flags, ...)
{
    int mode = 0;
    int ret;
    double tm1, tm2;

449
    MAP_OR_FAIL(open64);
Shane Snyder's avatar
Shane Snyder committed
450
451
452
453
454
455
456
457
458
459
460
461
462
463
464
465
466
467
468
469
470

    if(flags & O_CREAT)
    {
        va_list arg;
        va_start(arg, flags);
        mode = va_arg(arg, int);
        va_end(arg);

        tm1 = darshan_core_wtime();
        ret = __real_open64(path, flags, mode);
        tm2 = darshan_core_wtime();
    }
    else
    {
        tm1 = darshan_core_wtime();
        ret = __real_open64(path, flags);
        tm2 = darshan_core_wtime();
    }

    POSIX_LOCK();
    posix_runtime_initialize();
471
472
473
474
475
476
477
478
479
480
481
482
483
484
485
486
487
488
489
490
491
492
493
494
495
496
497
498
499
500
501
    POSIX_RECORD_OPEN(ret, path, mode, 0, tm1, tm2);
    POSIX_UNLOCK();

    return(ret);
}

int DARSHAN_DECL(creat)(const char* path, mode_t mode)
{
    int ret;
    double tm1, tm2;

    MAP_OR_FAIL(creat);

    tm1 = darshan_core_wtime();
    ret = __real_creat(path, mode);
    tm2 = darshan_core_wtime();

    POSIX_LOCK();
    posix_runtime_initialize();
    POSIX_RECORD_OPEN(ret, path, mode, 0, tm1, tm2);
    POSIX_UNLOCK();

    return(ret);
}

int DARSHAN_DECL(creat64)(const char* path, mode_t mode)
{
    int ret;
    double tm1, tm2;

    MAP_OR_FAIL(creat64);
Shane Snyder's avatar
Shane Snyder committed
502

503
504
505
506
507
508
    tm1 = darshan_core_wtime();
    ret = __real_creat64(path, mode);
    tm2 = darshan_core_wtime();

    POSIX_LOCK();
    posix_runtime_initialize();
Shane Snyder's avatar
Shane Snyder committed
509
510
511
512
513
514
    POSIX_RECORD_OPEN(ret, path, mode, 0, tm1, tm2);
    POSIX_UNLOCK();

    return(ret);
}

515
516
517
518
519
520
521
522
523
524
525
526
527
528
529
530
531
532
533
534
535
536
537
538
539
540
541
542
543
544
545
546
547
548
549
550
551
552
553
554
555
556
557
558
559
560
561
562
563
564
FILE* DARSHAN_DECL(fopen)(const char *path, const char *mode)
{
    FILE* ret;
    int fd;
    double tm1, tm2;

    MAP_OR_FAIL(fopen);

    tm1 = darshan_core_wtime();
    ret = __real_fopen(path, mode);
    tm2 = darshan_core_wtime();

    if(ret == NULL)
        fd = -1;
    else
        fd = fileno(ret);

    POSIX_LOCK();
    posix_runtime_initialize();
    POSIX_RECORD_OPEN(fd, path, 0, 1, tm1, tm2);
    POSIX_UNLOCK();

    return(ret);
}

FILE* DARSHAN_DECL(fopen64)(const char *path, const char *mode)
{
    FILE* ret;
    int fd;
    double tm1, tm2;

    MAP_OR_FAIL(fopen64);

    tm1 = darshan_core_wtime();
    ret = __real_fopen64(path, mode);
    tm2 = darshan_core_wtime();

    if(ret == NULL)
        fd = -1;
    else
        fd = fileno(ret);

    POSIX_LOCK();
    posix_runtime_initialize();
    POSIX_RECORD_OPEN(fd, path, 0, 1, tm1, tm2);
    POSIX_UNLOCK();

    return(ret);
}

565
566
567
568
569
570
571
572
573
574
575
576
577
578
579
580
581
582
583
584
585
586
587
588
589
590
591
592
593
594
595
596
597
598
599
600
601
602
603
604
605
606
607
608
609
610
611
612
613
614
615
616
617
618
619
620
621
622
623
624
625
626
627
628
629
630
631
632
633
634
635
636
637
638
639
640
int DARSHAN_DECL(mkstemp)(char* template)
{
    int ret;
    double tm1, tm2;

    MAP_OR_FAIL(mkstemp);

    tm1 = darshan_core_wtime();
    ret = __real_mkstemp(template);
    tm2 = darshan_core_wtime();

    POSIX_LOCK();
    posix_runtime_initialize();
    POSIX_RECORD_OPEN(ret, template, 0, 0, tm1, tm2);
    POSIX_UNLOCK();

    return(ret);
}

int DARSHAN_DECL(mkostemp)(char* template, int flags)
{
    int ret;
    double tm1, tm2;

    MAP_OR_FAIL(mkostemp);

    tm1 = darshan_core_wtime();
    ret = __real_mkostemp(template, flags);
    tm2 = darshan_core_wtime();

    POSIX_LOCK();
    posix_runtime_initialize();
    POSIX_RECORD_OPEN(ret, template, 0, 0, tm1, tm2);
    POSIX_UNLOCK();

    return(ret);
}

int DARSHAN_DECL(mkstemps)(char* template, int suffixlen)
{
    int ret;
    double tm1, tm2;

    MAP_OR_FAIL(mkstemps);

    tm1 = darshan_core_wtime();
    ret = __real_mkstemps(template, suffixlen);
    tm2 = darshan_core_wtime();

    POSIX_LOCK();
    posix_runtime_initialize();
    POSIX_RECORD_OPEN(ret, template, 0, 0, tm1, tm2);
    POSIX_UNLOCK();

    return(ret);
}

int DARSHAN_DECL(mkostemps)(char* template, int suffixlen, int flags)
{
    int ret;
    double tm1, tm2;

    MAP_OR_FAIL(mkostemps);

    tm1 = darshan_core_wtime();
    ret = __real_mkostemps(template, suffixlen, flags);
    tm2 = darshan_core_wtime();

    POSIX_LOCK();
    posix_runtime_initialize();
    POSIX_RECORD_OPEN(ret, template, 0, 0, tm1, tm2);
    POSIX_UNLOCK();

    return(ret);
}

641
642
643
644
645
646
ssize_t DARSHAN_DECL(read)(int fd, void *buf, size_t count)
{
    ssize_t ret;
    int aligned_flag = 0;
    double tm1, tm2;

Shane Snyder's avatar
Shane Snyder committed
647
    MAP_OR_FAIL(read);
648

649
    if((unsigned long)buf % darshan_mem_alignment == 0) aligned_flag = 1;
650
651
652
653
654
655
656
657
658
659
660
661
662
663
664
665
666
667
668
669
670

    tm1 = darshan_core_wtime();
    ret = __real_read(fd, buf, count);
    tm2 = darshan_core_wtime();

    POSIX_LOCK();
    posix_runtime_initialize();
    POSIX_RECORD_READ(ret, fd, 0, 0, aligned_flag, 0, tm1, tm2);
    POSIX_UNLOCK();

    return(ret);
}

ssize_t DARSHAN_DECL(write)(int fd, const void *buf, size_t count)
{
    ssize_t ret;
    int aligned_flag = 0;
    double tm1, tm2;

    MAP_OR_FAIL(write);

671
    if((unsigned long)buf % darshan_mem_alignment == 0) aligned_flag = 1;
672
673
674
675
676
677
678
679
680
681
682
683
684
685
686
687
688
689
690
691
692

    tm1 = darshan_core_wtime();
    ret = __real_write(fd, buf, count);
    tm2 = darshan_core_wtime();

    POSIX_LOCK();
    posix_runtime_initialize();
    POSIX_RECORD_WRITE(ret, fd, 0, 0, aligned_flag, 0, tm1, tm2);
    POSIX_UNLOCK();

    return(ret);
}

ssize_t DARSHAN_DECL(pread)(int fd, void *buf, size_t count, off_t offset)
{
    ssize_t ret;
    int aligned_flag = 0;
    double tm1, tm2;

    MAP_OR_FAIL(pread);

693
    if((unsigned long)buf % darshan_mem_alignment == 0) aligned_flag = 1;
694
695
696
697
698
699
700
701
702
703
704
705
706
707
708
709
710
711
712
713
714

    tm1 = darshan_core_wtime();
    ret = __real_pread(fd, buf, count, offset);
    tm2 = darshan_core_wtime();

    POSIX_LOCK();
    posix_runtime_initialize();
    POSIX_RECORD_READ(ret, fd, 1, offset, aligned_flag, 0, tm1, tm2);
    POSIX_UNLOCK();

    return(ret);
}

ssize_t DARSHAN_DECL(pwrite)(int fd, const void *buf, size_t count, off_t offset)
{
    ssize_t ret;
    int aligned_flag = 0;
    double tm1, tm2;

    MAP_OR_FAIL(pwrite);

715
    if((unsigned long)buf % darshan_mem_alignment == 0) aligned_flag = 1;
716
717
718
719
720
721
722
723
724
725
726
727
728
729
730
731
732
733
734
735
736

    tm1 = darshan_core_wtime();
    ret = __real_pwrite(fd, buf, count, offset);
    tm2 = darshan_core_wtime();

    POSIX_LOCK();
    posix_runtime_initialize();
    POSIX_RECORD_WRITE(ret, fd, 1, offset, aligned_flag, 0, tm1, tm2);
    POSIX_UNLOCK();

    return(ret);
}

ssize_t DARSHAN_DECL(pread64)(int fd, void *buf, size_t count, off64_t offset)
{
    ssize_t ret;
    int aligned_flag = 0;
    double tm1, tm2;

    MAP_OR_FAIL(pread64);

737
    if((unsigned long)buf % darshan_mem_alignment == 0) aligned_flag = 1;
738
739
740
741
742
743
744
745
746
747
748
749
750
751
752
753
754
755
756
757
758

    tm1 = darshan_core_wtime();
    ret = __real_pread64(fd, buf, count, offset);
    tm2 = darshan_core_wtime();

    POSIX_LOCK();
    posix_runtime_initialize();
    POSIX_RECORD_READ(ret, fd, 1, offset, aligned_flag, 0, tm1, tm2);
    POSIX_UNLOCK();

    return(ret);
}

ssize_t DARSHAN_DECL(pwrite64)(int fd, const void *buf, size_t count, off64_t offset)
{
    ssize_t ret;
    int aligned_flag = 0;
    double tm1, tm2;

    MAP_OR_FAIL(pwrite64);

759
    if((unsigned long)buf % darshan_mem_alignment == 0) aligned_flag = 1;
760
761
762
763
764
765
766
767
768
769
770
771
772
773
774
775

    tm1 = darshan_core_wtime();
    ret = __real_pwrite64(fd, buf, count, offset);
    tm2 = darshan_core_wtime();

    POSIX_LOCK();
    posix_runtime_initialize();
    POSIX_RECORD_WRITE(ret, fd, 1, offset, aligned_flag, 0, tm1, tm2);
    POSIX_UNLOCK();

    return(ret);
}

ssize_t DARSHAN_DECL(readv)(int fd, const struct iovec *iov, int iovcnt)
{
    ssize_t ret;
776
    int aligned_flag = 1;
777
778
779
780
    int i;
    double tm1, tm2;

    MAP_OR_FAIL(readv);
781

782
783
784
785
    for(i=0; i<iovcnt; i++)
    {
        if(((unsigned long)iov[i].iov_base % darshan_mem_alignment) != 0)
            aligned_flag = 0;
786
    }
787
788
789
790
791
792

    tm1 = darshan_core_wtime();
    ret = __real_readv(fd, iov, iovcnt);
    tm2 = darshan_core_wtime();

    POSIX_LOCK();
793
    posix_runtime_initialize();
794
795
796
797
798
799
800
801
802
    POSIX_RECORD_READ(ret, fd, 0, 0, aligned_flag, 0, tm1, tm2);
    POSIX_UNLOCK();

    return(ret);
}

ssize_t DARSHAN_DECL(writev)(int fd, const struct iovec *iov, int iovcnt)
{
    ssize_t ret;
803
    int aligned_flag = 1;
804
805
806
807
    int i;
    double tm1, tm2;

    MAP_OR_FAIL(writev);
808

809
810
811
812
    for(i=0; i<iovcnt; i++)
    {
        if(((unsigned long)iov[i].iov_base % darshan_mem_alignment) != 0)
            aligned_flag = 0;
813
    }
814
815
816
817
818
819

    tm1 = darshan_core_wtime();
    ret = __real_writev(fd, iov, iovcnt);
    tm2 = darshan_core_wtime();

    POSIX_LOCK();
820
    posix_runtime_initialize();
821
822
823
824
825
826
    POSIX_RECORD_WRITE(ret, fd, 0, 0, aligned_flag, 0, tm1, tm2);
    POSIX_UNLOCK();

    return(ret);
}

827
828
829
830
831
832
833
834
size_t DARSHAN_DECL(fread)(void *ptr, size_t size, size_t nmemb, FILE *stream)
{
    size_t ret;
    int aligned_flag = 0;
    double tm1, tm2;

    MAP_OR_FAIL(fread);

835
    if((unsigned long)ptr % darshan_mem_alignment == 0) aligned_flag = 1;
836
837
838
839
840
841
842
843
844
845
846
847
848
849
850
851
852
853
854
855
856
857
858
859
860
861
862
863
864
865

    tm1 = darshan_core_wtime();
    ret = __real_fread(ptr, size, nmemb, stream);
    tm2 = darshan_core_wtime();

    POSIX_LOCK();
    posix_runtime_initialize();
    if(ret > 0)
    {
        POSIX_RECORD_READ(size*ret, fileno(stream), 0, 0,
            aligned_flag, 1, tm1, tm2);
    }
    else
    {
        POSIX_RECORD_READ(ret, fileno(stream), 0, 0,
            aligned_flag, 1, tm1, tm2);
    }
    POSIX_UNLOCK();

    return(ret);
}

size_t DARSHAN_DECL(fwrite)(const void *ptr, size_t size, size_t nmemb, FILE *stream)
{
    size_t ret;
    int aligned_flag = 0;
    double tm1, tm2;

    MAP_OR_FAIL(fwrite);

866
    if((unsigned long)ptr % darshan_mem_alignment == 0) aligned_flag = 1;
867
868
869
870
871
872
873
874
875
876
877
878
879
880
881
882
883
884
885
886
887
888
889
890
891
892
893
894
895
896
897
898
899
900
901
902
903
904
905
906
907
908
909
910
911
912
913
914
915
916
917
918
919
920
921
922
923
924
925
926
927
928
929
930
931
932
933
934
935
936
937
938
939
940
941
942
943
944
945
946
947
948
949
950
951
952
953
954
955
956
957
958
959
960
961
962
963
964
965
966
967

    tm1 = darshan_core_wtime();
    ret = __real_fwrite(ptr, size, nmemb, stream);
    tm2 = darshan_core_wtime();

    POSIX_LOCK();
    posix_runtime_initialize();
    if(ret > 0)
    {
        POSIX_RECORD_WRITE(size*ret, fileno(stream), 0, 0,
            aligned_flag, 1, tm1, tm2);
    }
    else
    {
        POSIX_RECORD_WRITE(ret, fileno(stream), 0, 0,
            aligned_flag, 1, tm1, tm2);
    }
    POSIX_UNLOCK();

    return(ret);
}

off_t DARSHAN_DECL(lseek)(int fd, off_t offset, int whence)
{
    off_t ret;
    struct posix_file_runtime* file;
    double tm1, tm2;

    MAP_OR_FAIL(lseek);

    tm1 = darshan_core_wtime();
    ret = __real_lseek(fd, offset, whence);
    tm2 = darshan_core_wtime();

    if(ret >= 0)
    {
        POSIX_LOCK();
        posix_runtime_initialize();
        file = posix_file_by_fd(fd);
        if(file)
        {
            file->offset = ret;
            DARSHAN_COUNTER_F_INC_NO_OVERLAP(file->file_record,
                tm1, tm2, file->last_meta_end, POSIX_F_META_TIME);
            DARSHAN_COUNTER_INC(file->file_record, POSIX_SEEKS, 1);
        }
        POSIX_UNLOCK();
    }

    return(ret);
}

off_t DARSHAN_DECL(lseek64)(int fd, off_t offset, int whence)
{
    off_t ret;
    struct posix_file_runtime* file;
    double tm1, tm2;

    MAP_OR_FAIL(lseek64);

    tm1 = darshan_core_wtime();
    ret = __real_lseek64(fd, offset, whence);
    tm2 = darshan_core_wtime();

    if(ret >= 0)
    {
        POSIX_LOCK();
        posix_runtime_initialize();
        file = posix_file_by_fd(fd);
        if(file)
        {
            file->offset = ret;
            DARSHAN_COUNTER_F_INC_NO_OVERLAP(file->file_record,
                tm1, tm2, file->last_meta_end, POSIX_F_META_TIME);
            DARSHAN_COUNTER_INC(file->file_record, POSIX_SEEKS, 1);
        }
        POSIX_UNLOCK();
    }

    return(ret);
}

int DARSHAN_DECL(fseek)(FILE *stream, long offset, int whence)
{
    int ret;
    struct posix_file_runtime* file;
    double tm1, tm2;

    MAP_OR_FAIL(fseek);

    tm1 = darshan_core_wtime();
    ret = __real_fseek(stream, offset, whence);
    tm2 = darshan_core_wtime();

    if(ret >= 0)
    {
        POSIX_LOCK();
        posix_runtime_initialize();
        file = posix_file_by_fd(fileno(stream));
        if(file)
        {
968
            file->offset = ftell(stream);
969
970
971
972
973
974
975
976
977
978
            DARSHAN_COUNTER_F_INC_NO_OVERLAP(file->file_record,
                tm1, tm2, file->last_meta_end, POSIX_F_META_TIME);
            DARSHAN_COUNTER_INC(file->file_record, POSIX_FSEEKS, 1);
        }
        POSIX_UNLOCK();
    }

    return(ret);
}

979
980
981
982
983
984
985
986
987
988
989
990
991
992
993
994
995
996
997
998
999
1000
1001
1002
1003
1004
1005
1006
1007
1008
1009
1010
1011
1012
1013
1014
1015
1016
1017
1018
1019
1020
1021
1022
1023
1024
1025
1026
1027
1028
1029
1030
1031
1032
1033
1034
1035
1036
1037
1038
1039
1040
1041
1042
1043
1044
1045
1046
1047
1048
1049
1050
1051
1052
1053
1054
1055
1056
1057
1058
1059
1060
1061
1062
1063
1064
1065
1066
1067
1068
1069
1070
1071
1072
1073
1074
1075
1076
1077
1078
1079
1080
1081
1082
1083
1084
1085
1086
1087
1088
1089
1090
1091
1092
1093
1094
1095
1096
1097
1098
1099
1100
1101
1102
1103
1104
1105
1106
1107
1108
1109
1110
1111
1112
1113
1114
1115
1116
1117
1118
1119
1120
int DARSHAN_DECL(__xstat)(int vers, const char *path, struct stat *buf)
{
    int ret;
    double tm1, tm2;

    MAP_OR_FAIL(__xstat);

    tm1 = darshan_core_wtime();
    ret = __real___xstat(vers, path, buf);
    tm2 = darshan_core_wtime();

    if(ret < 0 || !S_ISREG(buf->st_mode))
        return(ret);

    POSIX_LOCK();
    posix_runtime_initialize();
    POSIX_LOOKUP_RECORD_STAT(path, buf, tm1, tm2);
    POSIX_UNLOCK();

    return(ret);
}

int DARSHAN_DECL(__xstat64)(int vers, const char *path, struct stat64 *buf)
{
    int ret;
    double tm1, tm2;

    MAP_OR_FAIL(__xstat64);

    tm1 = darshan_core_wtime();
    ret = __real___xstat64(vers, path, buf);
    tm2 = darshan_core_wtime();

    if(ret < 0 || !S_ISREG(buf->st_mode))
        return(ret);

    POSIX_LOCK();
    posix_runtime_initialize();
    POSIX_LOOKUP_RECORD_STAT(path, buf, tm1, tm2);
    POSIX_UNLOCK();

    return(ret);
}

int DARSHAN_DECL(__lxstat)(int vers, const char *path, struct stat *buf)
{
    int ret;
    double tm1, tm2;

    MAP_OR_FAIL(__lxstat);

    tm1 = darshan_core_wtime();
    ret = __real___lxstat(vers, path, buf);
    tm2 = darshan_core_wtime();

    if(ret < 0 || !S_ISREG(buf->st_mode))
        return(ret);

    POSIX_LOCK();
    posix_runtime_initialize();
    POSIX_LOOKUP_RECORD_STAT(path, buf, tm1, tm2);
    POSIX_UNLOCK();

    return(ret);
}

int DARSHAN_DECL(__lxstat64)(int vers, const char *path, struct stat64 *buf)
{
    int ret;
    double tm1, tm2;

    MAP_OR_FAIL(__lxstat64);

    tm1 = darshan_core_wtime();
    ret = __real___lxstat64(vers, path, buf);
    tm2 = darshan_core_wtime();

    if(ret < 0 || !S_ISREG(buf->st_mode))
        return(ret);

    POSIX_LOCK();
    posix_runtime_initialize();
    POSIX_LOOKUP_RECORD_STAT(path, buf, tm1, tm2);
    POSIX_UNLOCK();

    return(ret);
}

int DARSHAN_DECL(__fxstat)(int vers, int fd, struct stat *buf)
{
    int ret;
    struct posix_file_runtime* file;
    double tm1, tm2;

    MAP_OR_FAIL(__fxstat);

    tm1 = darshan_core_wtime();
    ret = __real___fxstat(vers, fd, buf);
    tm2 = darshan_core_wtime();

    if(ret < 0 || !S_ISREG(buf->st_mode))
        return(ret);

    POSIX_LOCK();
    posix_runtime_initialize();
    file = posix_file_by_fd(fd);
    if(file)
    {
        POSIX_RECORD_STAT(file, buf, tm1, tm2);
    }
    POSIX_UNLOCK();

    return(ret);
}

int DARSHAN_DECL(__fxstat64)(int vers, int fd, struct stat64 *buf)
{
    int ret;
    struct posix_file_runtime* file;
    double tm1, tm2;

    MAP_OR_FAIL(__fxstat64);

    tm1 = darshan_core_wtime();
    ret = __real___fxstat64(vers, fd, buf);
    tm2 = darshan_core_wtime();

    if(ret < 0 || !S_ISREG(buf->st_mode))
        return(ret);

    POSIX_LOCK();
    posix_runtime_initialize();
    file = posix_file_by_fd(fd);
    if(file)
    {
        POSIX_RECORD_STAT(file, buf, tm1, tm2);
    }
    POSIX_UNLOCK();

    return(ret);
}

Shane Snyder's avatar
Shane Snyder committed
1121
1122
1123
1124
1125
1126
1127
1128
1129
1130
1131
1132
1133
1134
1135
1136
1137
1138
1139
1140
1141
1142
1143
1144
1145
1146
1147
1148
1149
1150
1151
1152
1153
1154
1155
1156
1157
1158
1159
1160
1161
1162
1163
1164
1165
1166
1167
1168
void* DARSHAN_DECL(mmap)(void *addr, size_t length, int prot, int flags,
    int fd, off_t offset)
{
    void* ret;
    struct posix_file_runtime* file;

    MAP_OR_FAIL(mmap);

    ret = __real_mmap(addr, length, prot, flags, fd, offset);
    if(ret == MAP_FAILED)
        return(ret);

    POSIX_LOCK();
    posix_runtime_initialize();
    file = posix_file_by_fd(fd);
    if(file)
    {
        DARSHAN_COUNTER_INC(file->file_record, POSIX_MMAPS, 1);
    }
    POSIX_UNLOCK();

    return(ret);
}

void* DARSHAN_DECL(mmap64)(void *addr, size_t length, int prot, int flags,
    int fd, off64_t offset)
{
    void* ret;
    struct posix_file_runtime* file;

    MAP_OR_FAIL(mmap64);

    ret = __real_mmap64(addr, length, prot, flags, fd, offset);
    if(ret == MAP_FAILED)
        return(ret);

    POSIX_LOCK();
    posix_runtime_initialize();
    file = posix_file_by_fd(fd);
    if(file)
    {
        DARSHAN_COUNTER_INC(file->file_record, POSIX_MMAPS, 1);
    }
    POSIX_UNLOCK();

    return(ret);
}

1169
1170
1171
1172
1173
1174
1175
1176
1177
1178
1179
1180
1181
1182
1183
1184
1185
1186
1187
1188
1189
1190
1191
1192
1193
1194
1195
1196
1197
1198
1199
1200
1201
1202
1203
1204
1205
1206
1207
1208
1209
1210
1211
1212
1213
1214
1215
1216
1217
1218
1219
1220
1221
1222
1223
1224
1225
1226
int DARSHAN_DECL(fsync)(int fd)
{
    int ret;
    struct posix_file_runtime* file;
    double tm1, tm2;

    MAP_OR_FAIL(fsync);

    tm1 = darshan_core_wtime();
    ret = __real_fsync(fd);
    tm2 = darshan_core_wtime();

    if(ret < 0)
        return(ret);

    POSIX_LOCK();
    posix_runtime_initialize();
    file = posix_file_by_fd(fd);
    if(file)
    {
        DARSHAN_COUNTER_F_INC_NO_OVERLAP(file->file_record,
            tm1, tm2, file->last_write_end, POSIX_F_WRITE_TIME);
        DARSHAN_COUNTER_INC(file->file_record, POSIX_FSYNCS, 1);
    }
    POSIX_UNLOCK();

    return(ret);
}

int DARSHAN_DECL(fdatasync)(int fd)
{
    int ret;
    struct posix_file_runtime* file;
    double tm1, tm2;

    MAP_OR_FAIL(fdatasync);

    tm1 = darshan_core_wtime();
    ret = __real_fdatasync(fd);
    tm2 = darshan_core_wtime();

    if(ret < 0)
        return(ret);

    POSIX_LOCK();
    posix_runtime_initialize();
    file = posix_file_by_fd(fd);
    if(file)
    {
        DARSHAN_COUNTER_F_INC_NO_OVERLAP(file->file_record,
            tm1, tm2, file->last_write_end, POSIX_F_WRITE_TIME); 
        DARSHAN_COUNTER_INC(file->file_record, POSIX_FDSYNCS, 1);
    }
    POSIX_UNLOCK();

    return(ret);
}

1227
1228
int DARSHAN_DECL(close)(int fd)
{
1229
    struct posix_file_runtime* file;
1230
1231
1232
1233
1234
1235
1236
1237
1238
1239
1240
    double tm1, tm2;
    int ret;

    MAP_OR_FAIL(close);

    tm1 = darshan_core_wtime();
    ret = __real_close(fd);
    tm2 = darshan_core_wtime();

    POSIX_LOCK();
    posix_runtime_initialize();
Shane Snyder's avatar
Shane Snyder committed
1241
1242
1243
    file = posix_file_by_fd(fd);
    if(file)
    {
1244
1245
1246
1247
1248
1249
        file->last_byte_written = 0;
        file->last_byte_read = 0;
        DARSHAN_COUNTER_F_SET(file->file_record,
            POSIX_F_CLOSE_TIMESTAMP, darshan_core_wtime());
        DARSHAN_COUNTER_F_INC_NO_OVERLAP(file->file_record,
             tm1, tm2, file->last_meta_end, POSIX_F_META_TIME);
Shane Snyder's avatar
Shane Snyder committed
1250
1251
        posix_file_close_fd(fd);
    }
1252
1253
1254
1255
1256
    POSIX_UNLOCK();    

    return(ret);
}

1257
1258
1259
1260
1261
1262
1263
1264
1265
1266
1267
1268
1269
1270
1271
1272
1273
1274
1275
1276
1277
1278
1279
1280
1281
1282
1283
1284
1285
1286
1287
int DARSHAN_DECL(fclose)(FILE *fp)
{
    struct posix_file_runtime* file;
    int fd = fileno(fp);
    double tm1, tm2;
    int ret;

    MAP_OR_FAIL(fclose);

    tm1 = darshan_core_wtime();
    ret = __real_fclose(fp);
    tm2 = darshan_core_wtime();

    POSIX_LOCK();
    posix_runtime_initialize();
    file = posix_file_by_fd(fd);
    if(file)
    {
        file->last_byte_written = 0;
        file->last_byte_read = 0;
        DARSHAN_COUNTER_F_SET(file->file_record,
            POSIX_F_CLOSE_TIMESTAMP, darshan_core_wtime());
        DARSHAN_COUNTER_F_INC_NO_OVERLAP(file->file_record,
            tm1, tm2, file->last_meta_end, POSIX_F_META_TIME);
        posix_file_close_fd(fd);
    }
    POSIX_UNLOCK();

    return(ret);
}

1288
1289
1290
/**********************************************************
 * Internal functions for manipulating POSIX module state *
 **********************************************************/
1291

1292
/* initialize internal POSIX module data structures and register with darshan-core */
1293
static void posix_runtime_initialize()
1294
{
1295
1296
1297
    int mem_limit;
    struct darshan_module_funcs posix_mod_fns =
    {
1298
1299
        .begin_shutdown = &posix_begin_shutdown,
        .setup_reduction = &posix_setup_reduction,
1300
        .record_reduction_op = &posix_record_reduction_op,
1301
        .get_output_data = &posix_get_output_data,
1302
        .shutdown = &posix_shutdown
1303
    };
1304

Shane Snyder's avatar
Shane Snyder committed
1305
1306
    /* don't do anything if already initialized or instrumenation is disabled */
    if(posix_runtime || instrumentation_disabled)
1307
        return;
1308

1309
1310
    /* register the posix module with darshan core */
    darshan_core_register_module(
1311
        DARSHAN_POSIX_MOD,
1312
        &posix_mod_fns,
1313
1314
        &mem_limit,
        &darshan_mem_alignment);
1315
1316
1317
1318
1319
1320
1321
1322
1323
1324
1325
1326

    /* return if no memory assigned by darshan core */
    if(mem_limit == 0)
        return;

    posix_runtime = malloc(sizeof(*posix_runtime));
    if(!posix_runtime)
        return;
    memset(posix_runtime, 0, sizeof(*posix_runtime));

    /* set maximum number of file records according to max memory limit */
    /* NOTE: maximum number of records is based on the size of a posix file record */
1327
    /* TODO: should we base memory usage off file record or total runtime structure sizes? */
1328
    posix_runtime->file_array_size = mem_limit / sizeof(struct darshan_posix_file);
1329
    posix_runtime->file_array_ndx = 0;
1330
1331

    /* allocate array of runtime file records */
1332
    posix_runtime->file_runtime_array = malloc(posix_runtime->file_array_size *
1333
                                               sizeof(struct posix_file_runtime));
1334
1335
1336
    posix_runtime->file_record_array = malloc(posix_runtime->file_array_size *
                                              sizeof(struct darshan_posix_file));
    if(!posix_runtime->file_runtime_array || !posix_runtime->file_record_array)
1337
1338
1339
1340
    {
        posix_runtime->file_array_size = 0;
        return;
    }
1341
    memset(posix_runtime->file_runtime_array, 0, posix_runtime->file_array_size *
1342
           sizeof(struct posix_file_runtime));
1343
1344
    memset(posix_runtime->file_record_array, 0, posix_runtime->file_array_size *
           sizeof(struct darshan_posix_file));
1345

Shane Snyder's avatar
Shane Snyder committed
1346
1347
    /* TODO: can we move this out of here? perhaps register_module returns rank? */
    DARSHAN_MPI_CALL(PMPI_Comm_rank)(MPI_COMM_WORLD, &my_rank);
1348

1349
1350
    return;
}
1351

1352
/* get a POSIX file record for the given file path */
1353
static struct posix_file_runtime* posix_file_by_name(const char *name)
1354
{
1355
    struct posix_file_runtime *file = NULL;
1356
    char *newname = NULL;
1357
    darshan_record_id file_id;
1358
    int file_alignment;
1359

Shane Snyder's avatar
Shane Snyder committed
1360
    if(!posix_runtime || instrumentation_disabled)
1361
        return(NULL);
1362

1363
    newname = darshan_clean_file_path(name);
1364
    if(!newname)
1365
        newname = (char*)name;
1366

1367
    /* get a unique id for this file from darshan core */
Shane Snyder's avatar
Shane Snyder committed
1368
    darshan_core_register_record(
1369
1370
1371
        (void*)newname,
        strlen(newname),
        1,
1372
        DARSHAN_POSIX_MOD,
1373
1374
        &file_id,
        &file_alignment);
1375

1376
    /* search the hash table for this file record, and return if found */
1377
    HASH_FIND(hlink, posix_runtime->file_hash, &file_id, sizeof(darshan_record_id), file);
1378
    if(file)
1379
    {
1380
        if(newname != name)
1381
            free(newname);
1382
        return(file);
1383
1384
    }

1385
1386
1387
1388
1389
1390
    if(posix_runtime->file_array_ndx < posix_runtime->file_array_size);
    {
        /* no existing record, assign a new file record from the global array */
        file = &(posix_runtime->file_runtime_array[posix_runtime->file_array_ndx]);
        file->file_record = &(posix_runtime->file_record_array[posix_runtime->file_array_ndx]);
        file->file_record->f_id = file_id;
1391
1392
        DARSHAN_COUNTER_SET(file->file_record, POSIX_MEM_ALIGNMENT, darshan_mem_alignment);
        DARSHAN_COUNTER_SET(file->file_record, POSIX_FILE_ALIGNMENT, file_alignment);
1393

1394
        /* add new record to file hash table */
1395
        HASH_ADD(hlink, posix_runtime->file_hash, file_record->f_id, sizeof(darshan_record_id), file);
1396

1397
1398
        posix_runtime->file_array_ndx++;
    }
1399
1400

    if(newname != name)
1401
        free(newname);
1402
1403
1404
    return(file);
}

1405
1406
1407
/* get a POSIX file record for the given file path, and also create a
 * reference structure using the returned file descriptor
 */
1408
static struct posix_file_runtime* posix_file_by_name_setfd(const char* name, int fd)
1409
{
1410
1411
    struct posix_file_runtime* file;
    struct posix_file_runtime_ref* ref;
1412

Shane Snyder's avatar
Shane Snyder committed
1413
    if(!posix_runtime || instrumentation_disabled)
1414
1415
1416
1417
1418
1419
1420
1421
1422
1423
1424
1425
1426
1427
1428
1429
1430
1431
1432
1433
1434
1435
1436
1437
1438
1439
        return(NULL);

    /* find file record by name first */
    file = posix_file_by_name(name);

    if(!file)
        return(NULL);

    /* search hash table for existing file ref for this fd */
    HASH_FIND(hlink, posix_runtime->fd_hash, &fd, sizeof(int), ref);
    if(ref)
    {
        /* we have a reference.  Make sure it points to the correct file
         * and return it
         */
        ref->file = file;
        return(file);
    }

    /* if we hit this point, then we don't have a reference for this fd
     * in the table yet.  Add it.
     */
    ref = malloc(sizeof(*ref));
    if(!ref)
        return(NULL);
    memset(ref, 0, sizeof(*ref));
Shane Snyder's avatar
Shane Snyder committed
1440

1441
1442
1443
1444
1445
1446
1447
    ref->file = file;
    ref->fd = fd;    
    HASH_ADD(hlink, posix_runtime->fd_hash, fd, sizeof(int), ref);

    return(file);
}

1448
/* get a POSIX file record for the given file descriptor */
1449
static struct posix_file_runtime* posix_file_by_fd(int fd)
Shane Snyder's avatar
Shane Snyder committed
1450
{
1451
    struct posix_file_runtime_ref* ref;
Shane Snyder's avatar
Shane Snyder committed
1452
1453
1454
1455
1456
1457
1458
1459
1460
1461
1462
1463

    if(!posix_runtime || instrumentation_disabled)
        return(NULL);

    /* search hash table for existing file ref for this fd */
    HASH_FIND(hlink, posix_runtime->fd_hash, &fd, sizeof(int), ref);
    if(ref)
        return(ref->file);

    return(NULL);
}

1464
/* free up reference data structures for the given file descriptor */
1465
1466
static void posix_file_close_fd(int fd)
{
1467
    struct posix_file_runtime_ref* ref;
1468

Shane Snyder's avatar
Shane Snyder committed
1469
    if(!posix_runtime || instrumentation_disabled)
1470
1471
1472
1473
        return;

    /* search hash table for this fd */
    HASH_FIND(hlink, posix_runtime->fd_hash, &fd, sizeof(int), ref);
1474
    if(ref)
1475
1476
1477
1478
1479
1480
1481
    {
        /* we have a reference, delete it */
        HASH_DELETE(hlink, posix_runtime->fd_hash, ref);
        free(ref);
    }

    return;
1482
1483
}

1484
1485
1486
1487
1488
1489
1490
1491
1492
1493
1494
1495
1496
1497
1498
1499
1500
1501
1502
1503
1504
1505
1506
1507
1508
1509
1510
1511
1512
1513
1514
1515
1516
1517
1518
1519
1520
1521
1522
1523
1524
1525
1526
1527
1528
1529
1530
1531
1532
1533
1534
1535
1536
1537
1538
1539
1540
1541
1542
1543
1544
1545
1546
1547
1548
1549
1550
1551
1552
1553
1554
1555
1556
1557
1558
1559
1560
1561
1562
1563
1564
1565
1566
1567
1568
1569
1570
1571
1572
1573
1574
1575
1576
1577
1578
1579
1580
1581
1582
1583
1584
1585
1586
1587
1588
1589
1590
1591
1592
1593
1594
1595
1596
1597
1598
1599
1600
1601
1602
1603
1604
1605
1606
1607
1608
1609
1610
1611
static void posix_access_counter(struct posix_file_runtime* file, ssize_t size,
    enum posix_counter_type type)
{
    struct posix_access_counter* counter;
    struct posix_access_counter* found;
    void* tmp;
    void** root;
    int* count;
    struct posix_access_counter tmp_counter;

    /* don't count sizes or strides of 0 */
    if(size == 0)
        return;

    switch(type)
    {
        case POSIX_COUNTER_ACCESS:
            root = &file->access_root;
            count = &file->access_count;
            break;
        case POSIX_COUNTER_STRIDE:
            root = &file->stride_root;
            count = &file->stride_count;
            break;
        default:
            return;
    }

    /* check to see if this size is already recorded */
    tmp_counter.size = size;
    tmp_counter.freq = 1;
    tmp = tfind(&tmp_counter, root, posix_access_compare);
    if(tmp)
    {
        found = *(struct posix_access_counter**)tmp;
        found->freq++;
        return;
    }

    /* we can add a new one as long as we haven't hit the limit */
    if(*count < POSIX_MAX_ACCESS_COUNT_RUNTIME)
    {
        counter = malloc(sizeof(*counter));
        if(!counter)
        {
            return;
        }

        counter->size = size;
        counter->freq = 1;

        tmp = tsearch(counter, root, posix_access_compare);
        found = *(struct posix_access_counter**)tmp;
        /* if we get a new answer out here we are in trouble; this was
         * already checked with the tfind()
         */
        assert(found == counter);

        (*count)++;
    }

    return;
}

static void posix_access_walker(const void* nodep, const VISIT which, const int depth)
{
    struct posix_access_counter* counter;

    switch (which)
    {
        case postorder:
        case leaf:
            counter = *(struct posix_access_counter**)nodep;
            POSIX_COMMON_COUNTER_INC(walker_file->file_record, counter->size, counter->freq,
                walker_validx, walker_cntidx);
        default:
            break;
    }

    return;
};

/* posix_walk_file_accesses()
 *
 * goes through runtime collections of accesses sizes and chooses the 4 most
 * common for logging
 */
static void posix_walk_file_accesses()
{
    int i;

    for(i=0; i<posix_runtime->file_array_ndx; i++)
    {
        /* walk trees for both access sizes and stride sizes to pick 4 most
         * common of each
         */

        /* NOTE: setting global variables here for cp_access_walker() */
        walker_file = &posix_runtime->file_runtime_array[i];
        walker_validx = POSIX_ACCESS1_ACCESS;
        walker_cntidx = POSIX_ACCESS1_COUNT;
        twalk(walker_file->access_root,
            posix_access_walker);
        tdestroy(walker_file->access_root, free);

        walker_validx = POSIX_STRIDE1_STRIDE;
        walker_cntidx = POSIX_STRIDE1_COUNT;
        twalk(walker_file->stride_root,
            posix_access_walker);
        tdestroy(walker_file->stride_root