darshan-core.c 40.2 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
#define _XOPEN_SOURCE 500
8
#define _GNU_SOURCE
9

10 11 12 13 14 15
#include "darshan-runtime-config.h"

#include <stdio.h>
#ifdef HAVE_MNTENT_H
#include <mntent.h>
#endif
16 17 18 19 20
#include <stdlib.h>
#include <string.h>
#include <time.h>
#include <limits.h>
#include <pthread.h>
21
#include <fcntl.h>
22 23
#include <sys/types.h>
#include <sys/stat.h>
24
#include <sys/mman.h>
25
#include <sys/vfs.h>
26
#include <zlib.h>
27
#include <mpi.h>
28
#include <assert.h>
29

30
#include "uthash.h"
Shane Snyder's avatar
Shane Snyder committed
31
#include "darshan.h"
32
#include "darshan-core.h"
Shane Snyder's avatar
Shane Snyder committed
33
#include "darshan-dynamic.h"
34

35
extern char* __progname;
36
extern char* __progname_full;
37

38
/* internal variable delcarations */
39
static struct darshan_core_runtime *darshan_core = NULL;
40
static pthread_mutex_t darshan_core_mutex = PTHREAD_RECURSIVE_MUTEX_INITIALIZER_NP;
41
static int my_rank = -1;
42
static int nprocs = -1;
43
static int darshan_mem_alignment = 1;
44

45 46 47 48 49 50 51 52 53 54 55 56 57 58 59
/* paths prefixed with the following directories are not traced by darshan */
char* darshan_path_exclusions[] = {
"/etc/",
"/dev/",
"/usr/",
"/bin/",
"/boot/",
"/lib/",
"/opt/",
"/sbin/",
"/sys/",
"/proc/",
NULL
};

60 61 62 63 64 65 66 67 68 69 70 71 72 73 74
#ifdef DARSHAN_BGQ
extern void bgq_runtime_initialize();
#endif

/* array of init functions for modules which need to be statically
 * initialized by darshan at startup time
 */
void (*mod_static_init_fns[])(void) =
{
#ifdef DARSHAN_BGQ
    &bgq_runtime_initialize,
#endif
    NULL
};

Shane Snyder's avatar
Shane Snyder committed
75 76 77
#define DARSHAN_CORE_LOCK() pthread_mutex_lock(&darshan_core_mutex)
#define DARSHAN_CORE_UNLOCK() pthread_mutex_unlock(&darshan_core_mutex)

78 79 80 81 82 83
/* FS mount information */
#define DARSHAN_MAX_MNTS 64
#define DARSHAN_MAX_MNT_PATH 256
#define DARSHAN_MAX_MNT_TYPE 32
struct mnt_data
{
84
    int block_size;
85 86 87 88 89 90
    char path[DARSHAN_MAX_MNT_PATH];
    char type[DARSHAN_MAX_MNT_TYPE];
};
static struct mnt_data mnt_data_array[DARSHAN_MAX_MNTS];
static int mnt_data_count = 0;

91 92 93 94
/* prototypes for internal helper functions */
static void darshan_get_logfile_name(
    char* logfile_name, int jobid, struct tm* start_tm);
static void darshan_log_record_hints_and_ver(
95 96
    struct darshan_core_runtime* core);
static void darshan_get_exe_and_mounts_root(
97 98 99
    struct darshan_core_runtime *core, int argc, char **argv);
static void darshan_get_exe_and_mounts(
    struct darshan_core_runtime *core, int argc, char **argv);
100 101
static void darshan_block_size_from_path(
    const char *path, int *block_size);
102
static void darshan_get_shared_records(
103 104
    struct darshan_core_runtime *core, darshan_record_id **shared_recs,
    int *shared_rec_cnt);
105
static int darshan_log_open_all(
106
    char *logfile_name, MPI_File *log_fh);
107
static int darshan_deflate_buffer(
Shane Snyder's avatar
Shane Snyder committed
108 109
    void **pointers, int *lengths, int count, char *comp_buf,
    int *comp_buf_length);
110
static int darshan_log_write_record_hash(
111
    MPI_File log_fh, struct darshan_core_runtime *core,
112 113 114
    uint64_t *inout_off);
static int darshan_log_append_all(
    MPI_File log_fh, struct darshan_core_runtime *core, void *buf,
Shane Snyder's avatar
Shane Snyder committed
115
    int count, uint64_t *inout_off);
Shane Snyder's avatar
Shane Snyder committed
116 117
static void darshan_core_cleanup(
    struct darshan_core_runtime* core);
118

119 120
/* *********************************** */

Shane Snyder's avatar
Shane Snyder committed
121
void darshan_core_initialize(int argc, char **argv)
122
{
123
    struct darshan_core_runtime *init_core = NULL;
124 125
    int internal_timing_flag = 0;
    double init_start, init_time, init_max;
126
    char mmap_log_name[PATH_MAX];
127 128 129
    int mmap_fd;
    int mmap_size;
    int sys_page_size;
130
    char *envstr;
131 132
    char *jobid_str;
    int jobid;
133 134
    int ret;
    int tmpval;
135
    int i;
136 137

    DARSHAN_MPI_CALL(PMPI_Comm_size)(MPI_COMM_WORLD, &nprocs);
138
    DARSHAN_MPI_CALL(PMPI_Comm_rank)(MPI_COMM_WORLD, &my_rank);
139 140 141 142

    if(getenv("DARSHAN_INTERNAL_TIMING"))
        internal_timing_flag = 1;

143
    if(internal_timing_flag)
144 145 146
        init_start = DARSHAN_MPI_CALL(PMPI_Wtime)();

    /* setup darshan runtime if darshan is enabled and hasn't been initialized already */
147
    if(!getenv("DARSHAN_DISABLE") && !darshan_core)
148
    {
149
        #if (__DARSHAN_MEM_ALIGNMENT < 1)
150 151
            #error Darshan must be configured with a positive value for --with-mem-align
        #endif
152
        envstr = getenv(DARSHAN_MEM_ALIGNMENT_OVERRIDE);
153 154 155 156 157 158 159 160 161 162 163
        if(envstr)
        {
            ret = sscanf(envstr, "%d", &tmpval);
            /* silently ignore if the env variable is set poorly */
            if(ret == 1 && tmpval > 0)
            {
                darshan_mem_alignment = tmpval;
            }
        }
        else
        {
164
            darshan_mem_alignment = __DARSHAN_MEM_ALIGNMENT;
165 166 167 168 169 170 171
        }

        /* avoid floating point errors on faulty input */
        if (darshan_mem_alignment < 1)
        {
            darshan_mem_alignment = 1;
        }
172

173 174 175
        /* allocate structure to track darshan core runtime information */
        init_core = malloc(sizeof(*init_core));
        if(init_core)
176
        {
177 178 179
            memset(init_core, 0, sizeof(*init_core));
            init_core->wtime_offset = DARSHAN_MPI_CALL(PMPI_Wtime)();

180 181 182 183 184 185 186 187 188 189 190 191 192 193 194 195 196 197 198 199
            /* Use DARSHAN_JOBID_OVERRIDE for the env var for __DARSHAN_JOBID */
            envstr = getenv(DARSHAN_JOBID_OVERRIDE);
            if(!envstr)
            {
                envstr = __DARSHAN_JOBID;
            }

            /* find a job id */
            jobid_str = getenv(envstr);
            if(jobid_str)
            {
                /* in cobalt we can find it in env var */
                ret = sscanf(jobid_str, "%d", &jobid);
            }
            if(!jobid_str || ret != 1)
            {
                /* use pid as fall back */
                jobid = getpid();
            }

200 201
            sys_page_size = sysconf(_SC_PAGESIZE);
            assert(sys_page_size > 0);
202

203 204 205 206 207 208 209
            /* set the size of the mmap, making sure to round up to the
             * nearest page size. One mmap chunk is used for the job-level
             * metadata, and the rest are statically assigned to modules
             */
            mmap_size = (1 + DARSHAN_MAX_MODS) * DARSHAN_MMAP_CHUNK_SIZE;
            if(mmap_size % sys_page_size)
                mmap_size = ((mmap_size / sys_page_size) + 1) * sys_page_size;
210

211 212 213 214 215 216 217
            /* construct a unique temporary log file name for this process
             * to write mmap log data to
             */
            snprintf(mmap_log_name, PATH_MAX, "/tmp/darshan_job%d.%d",
                jobid, my_rank);

            /* create the temporary mmapped darshan log */
218 219
            mmap_fd = open(mmap_log_name, O_CREAT|O_RDWR|O_EXCL , 0644);
            if(mmap_fd < 0)
220
            {
221 222 223 224
                fprintf(stderr, "darshan library warning: "
                    "unable to create darshan log file %s\n", mmap_log_name);
                free(init_core);
                return;
225 226
            }

227 228 229 230 231 232 233 234 235 236 237 238 239 240
            /* allocate the necessary space in the log file */
            ret = ftruncate(mmap_fd, mmap_size);
            if(ret < 0)
            {
                fprintf(stderr, "darshan library warning: "
                    "unable to allocate darshan log file %s\n", mmap_log_name);
                free(init_core);
                close(mmap_fd);
                unlink(mmap_log_name);
                return;
            }

            /* memory map buffers for getting at least some summary i/o data
             * into a log file if darshan does not shut down properly
241
             */
242 243 244
            init_core->mmap_p = mmap(NULL, mmap_size, PROT_WRITE, MAP_SHARED,
                mmap_fd, 0);
            if(init_core->mmap_p == MAP_FAILED)
245
            {
246 247 248 249 250 251
                fprintf(stderr, "darshan library warning: "
                    "unable to mmap darshan log file %s\n", mmap_log_name);
                free(init_core);
                close(mmap_fd);
                unlink(mmap_log_name);
                return;
252 253
            }

254 255 256 257 258 259 260 261 262 263 264 265 266 267 268 269 270 271 272 273 274
            /* close darshan log file (this does *not* unmap the log file) */
            close(mmap_fd);

            /* set the pointers for each log file region */
            init_core->mmap_job_p = (struct darshan_job *)(init_core->mmap_p);
            init_core->mmap_exe_mnt_p =
                (char *)(((char *)init_core->mmap_p) + sizeof(struct darshan_job));
            init_core->mmap_mod_p =
                (void *)(((char *)init_core->mmap_p) + DARSHAN_MMAP_CHUNK_SIZE);

            /* set known job-level metadata files for the log file */
            init_core->mmap_job_p->uid = getuid();
            init_core->mmap_job_p->start_time = time(NULL);
            init_core->mmap_job_p->nprocs = nprocs;
            init_core->mmap_job_p->jobid = (int64_t)jobid;

            /* if we are using any hints to write the log file, then record those
             * hints with the darshan job information
             */
            darshan_log_record_hints_and_ver(init_core);

275
            /* collect information about command line and mounted file systems */
276
            darshan_get_exe_and_mounts(init_core, argc, argv);
277

Shane Snyder's avatar
Shane Snyder committed
278
            /* bootstrap any modules with static initialization routines */
279 280 281 282 283 284 285 286
            i = 0;
            while(mod_static_init_fns[i])
            {
                (*mod_static_init_fns[i])();
                i++;
            }

            darshan_core = init_core;
287
        }
288 289
    }

290 291 292 293 294
    if(internal_timing_flag)
    {
        init_time = DARSHAN_MPI_CALL(PMPI_Wtime)() - init_start;
        DARSHAN_MPI_CALL(PMPI_Reduce)(&init_time, &init_max, 1,
            MPI_DOUBLE, MPI_MAX, 0, MPI_COMM_WORLD);
295
        if(my_rank == 0)
296
        {
297 298
            fprintf(stderr, "#darshan:<op>\t<nprocs>\t<time>\n");
            fprintf(stderr, "darshan:init\t%d\t%f\n", nprocs, init_max);
299 300 301 302 303 304
        }
    }

    return;
}

Shane Snyder's avatar
Shane Snyder committed
305
void darshan_core_shutdown()
306
{
307
    int i;
308
    struct darshan_core_runtime *final_core;
309
    int internal_timing_flag = 0;
310
    double start_log_time;
311
    double tm_end;
312 313 314 315

    if(getenv("DARSHAN_INTERNAL_TIMING"))
        internal_timing_flag = 1;

316 317
    if(internal_timing_flag)
        start_log_time = DARSHAN_MPI_CALL(PMPI_Wtime)();
318

Shane Snyder's avatar
Shane Snyder committed
319
    /* disable darhan-core while we shutdown */
320
    DARSHAN_CORE_LOCK();
321
    if(!darshan_core)
322
    {
323
        DARSHAN_CORE_UNLOCK();
324 325
        return;
    }
326 327
    final_core = darshan_core;
    darshan_core = NULL;
Shane Snyder's avatar
Shane Snyder committed
328 329 330 331 332

    for(i = 0; i < DARSHAN_MAX_MODS; i++)
    {
        if(final_core->mod_array[i])
        {
333
            final_core->mod_array[i]->mod_funcs.begin_shutdown();
Shane Snyder's avatar
Shane Snyder committed
334 335
        }
    }
336
    DARSHAN_CORE_UNLOCK();
337

338
    final_core->mmap_job_p->end_time = time(NULL);
339

340
    darshan_core_cleanup(final_core);
341

342
    if(internal_timing_flag)
343
    {
344 345 346 347 348 349 350 351 352 353 354
        double all_tm, all_slowest;

        tm_end = DARSHAN_MPI_CALL(PMPI_Wtime)();

        all_tm = tm_end - start_log_time;

        DARSHAN_MPI_CALL(PMPI_Reduce)(&all_tm, &all_slowest, 1,
            MPI_DOUBLE, MPI_MAX, 0, MPI_COMM_WORLD);

        if(my_rank == 0)
        {
355 356
            fprintf(stderr, "#darshan:<op>\t<nprocs>\t<time>\n");
            fprintf(stderr, "darshan:core_shutdown\t%d\t%f\n", nprocs, all_slowest);
357
        }
358
    }
359

360 361
    return;
}
362

Shane Snyder's avatar
Shane Snyder committed
363
/* *********************************** */
364

365
/* construct the darshan log file name */
366
static void darshan_get_logfile_name(char* logfile_name, int jobid, struct tm* start_tm)
367
{
Shane Snyder's avatar
Shane Snyder committed
368
    char* user_logfile_name;
369 370 371
    char* logpath;
    char* logname_string;
    char* logpath_override = NULL;
372
#ifdef __DARSHAN_LOG_ENV
373 374 375 376 377 378 379 380 381
    char env_check[256];
    char* env_tok;
#endif
    uint64_t hlevel;
    char hname[HOST_NAME_MAX];
    uint64_t logmod;
    char cuser[L_cuserid] = {0};
    int ret;

Shane Snyder's avatar
Shane Snyder committed
382 383 384 385 386 387 388 389 390 391 392 393 394 395 396
    /* first, check if user specifies a complete logpath to use */
    user_logfile_name = getenv("DARSHAN_LOGFILE");
    if(user_logfile_name)
    {
        if(strlen(user_logfile_name) >= (PATH_MAX-1))
        {
            fprintf(stderr, "darshan library warning: user log file name too long.\n");
            logfile_name[0] = '\0';
        }
        else
        {
            strcpy(logfile_name, user_logfile_name);
        }
    }
    else
397
    {
Shane Snyder's avatar
Shane Snyder committed
398 399
        /* otherwise, generate the log path automatically */

400 401
        /* Use DARSHAN_LOG_PATH_OVERRIDE for the value or __DARSHAN_LOG_PATH */
        logpath = getenv(DARSHAN_LOG_PATH_OVERRIDE);
Shane Snyder's avatar
Shane Snyder committed
402 403
        if(!logpath)
        {
404 405
#ifdef __DARSHAN_LOG_PATH
            logpath = __DARSHAN_LOG_PATH;
406
#endif
Shane Snyder's avatar
Shane Snyder committed
407
        }
408

Shane Snyder's avatar
Shane Snyder committed
409 410 411 412 413 414 415 416 417 418
        /* get the username for this job.  In order we will try each of the
         * following until one of them succeeds:
         *
         * - cuserid()
         * - getenv("LOGNAME")
         * - snprintf(..., geteuid());
         *
         * Note that we do not use getpwuid() because it generally will not
         * work in statically compiled binaries.
         */
419 420

#ifndef DARSHAN_DISABLE_CUSERID
Shane Snyder's avatar
Shane Snyder committed
421
        cuserid(cuser);
422 423
#endif

Shane Snyder's avatar
Shane Snyder committed
424 425
        /* if cuserid() didn't work, then check the environment */
        if(strcmp(cuser, "") == 0)
426
        {
Shane Snyder's avatar
Shane Snyder committed
427 428 429 430 431
            logname_string = getenv("LOGNAME");
            if(logname_string)
            {
                strncpy(cuser, logname_string, (L_cuserid-1));
            }
432 433
        }

Shane Snyder's avatar
Shane Snyder committed
434 435 436 437 438 439
        /* if cuserid() and environment both fail, then fall back to uid */
        if(strcmp(cuser, "") == 0)
        {
            uid_t uid = geteuid();
            snprintf(cuser, sizeof(cuser), "%u", uid);
        }
440

Shane Snyder's avatar
Shane Snyder committed
441 442 443 444
        /* generate a random number to help differentiate the log */
        hlevel=DARSHAN_MPI_CALL(PMPI_Wtime)() * 1000000;
        (void)gethostname(hname, sizeof(hname));
        logmod = darshan_hash((void*)hname,strlen(hname),hlevel);
445

Shane Snyder's avatar
Shane Snyder committed
446 447 448 449
        /* see if darshan was configured using the --with-logpath-by-env
         * argument, which allows the user to specify an absolute path to
         * place logs via an env variable.
         */
450
#ifdef __DARSHAN_LOG_ENV
Shane Snyder's avatar
Shane Snyder committed
451
        /* just silently skip if the environment variable list is too big */
452
        if(strlen(__DARSHAN_LOG_ENV) < 256)
453
        {
Shane Snyder's avatar
Shane Snyder committed
454
            /* copy env variable list to a temporary buffer */
455
            strcpy(env_check, __DARSHAN_LOG_ENV);
Shane Snyder's avatar
Shane Snyder committed
456 457 458
            /* tokenize the comma-separated list */
            env_tok = strtok(env_check, ",");
            if(env_tok)
459
            {
Shane Snyder's avatar
Shane Snyder committed
460
                do
461
                {
Shane Snyder's avatar
Shane Snyder committed
462 463 464 465 466 467 468 469 470
                    /* check each env variable in order */
                    logpath_override = getenv(env_tok);
                    if(logpath_override)
                    {
                        /* stop as soon as we find a match */
                        break;
                    }
                }while((env_tok = strtok(NULL, ",")));
            }
471 472 473
        }
#endif

Shane Snyder's avatar
Shane Snyder committed
474
        if(logpath_override)
475
        {
Shane Snyder's avatar
Shane Snyder committed
476 477 478 479 480 481 482 483 484 485 486 487 488 489 490
            ret = snprintf(logfile_name, PATH_MAX,
                "%s/%s_%s_id%d_%d-%d-%d-%" PRIu64 ".darshan_partial",
                logpath_override,
                cuser, __progname, jobid,
                (start_tm->tm_mon+1),
                start_tm->tm_mday,
                (start_tm->tm_hour*60*60 + start_tm->tm_min*60 + start_tm->tm_sec),
                logmod);
            if(ret == (PATH_MAX-1))
            {
                /* file name was too big; squish it down */
                snprintf(logfile_name, PATH_MAX,
                    "%s/id%d.darshan_partial",
                    logpath_override, jobid);
            }
491
        }
Shane Snyder's avatar
Shane Snyder committed
492
        else if(logpath)
493
        {
Shane Snyder's avatar
Shane Snyder committed
494 495 496 497 498 499 500 501 502 503 504 505 506 507 508 509 510 511 512 513
            ret = snprintf(logfile_name, PATH_MAX,
                "%s/%d/%d/%d/%s_%s_id%d_%d-%d-%d-%" PRIu64 ".darshan_partial",
                logpath, (start_tm->tm_year+1900),
                (start_tm->tm_mon+1), start_tm->tm_mday,
                cuser, __progname, jobid,
                (start_tm->tm_mon+1),
                start_tm->tm_mday,
                (start_tm->tm_hour*60*60 + start_tm->tm_min*60 + start_tm->tm_sec),
                logmod);
            if(ret == (PATH_MAX-1))
            {
                /* file name was too big; squish it down */
                snprintf(logfile_name, PATH_MAX,
                    "%s/id%d.darshan_partial",
                    logpath, jobid);
            }
        }
        else
        {
            logfile_name[0] = '\0';
514 515 516 517
        }
    }

    return;
518 519
}

520
/* record any hints used to write the darshan log in the log header */
521
static void darshan_log_record_hints_and_ver(struct darshan_core_runtime* core)
522 523 524 525 526 527 528 529 530
{
    char* hints;
    char* header_hints;
    int meta_remain = 0;
    char* m;

    /* check environment variable to see if the default MPI file hints have
     * been overridden
     */
531
    hints = getenv(DARSHAN_LOG_HINTS_OVERRIDE);
532 533
    if(!hints)
    {
534
        hints = __DARSHAN_LOG_HINTS;
535 536 537 538 539 540 541 542 543 544
    }

    if(!hints || strlen(hints) < 1)
        return;

    header_hints = strdup(hints);
    if(!header_hints)
        return;

    meta_remain = DARSHAN_JOB_METADATA_LEN -
545
        strlen(core->mmap_job_p->metadata) - 1;
546 547
    if(meta_remain >= (strlen(PACKAGE_VERSION) + 9))
    {
548
        sprintf(core->mmap_job_p->metadata, "lib_ver=%s\n", PACKAGE_VERSION);
549 550 551 552
        meta_remain -= (strlen(PACKAGE_VERSION) + 9);
    }
    if(meta_remain >= (3 + strlen(header_hints)))
    {
553
        m = core->mmap_job_p->metadata + strlen(core->mmap_job_p->metadata);
554 555 556 557 558 559 560 561 562 563 564 565
        /* We have room to store the hints in the metadata portion of
         * the job header.  We just prepend an h= to the hints list.  The
         * metadata parser will ignore = characters that appear in the value
         * portion of the metadata key/value pair.
         */
        sprintf(m, "h=%s\n", header_hints);
    }
    free(header_hints);

    return;
}

566 567 568 569 570 571 572 573 574 575 576 577 578 579
static int mnt_data_cmp(const void* a, const void* b)
{
    const struct mnt_data *d_a = (const struct mnt_data*)a;
    const struct mnt_data *d_b = (const struct mnt_data*)b;

    if(strlen(d_a->path) > strlen(d_b->path))
        return(-1);
    else if(strlen(d_a->path) < strlen(d_b->path))
        return(1);
    else
        return(0);
}

/* adds an entry to table of mounted file systems */
580
static void add_entry(char* buf, int* space_left, struct mntent *entry)
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
{
    int ret;
    char tmp_mnt[256];
    struct statfs statfsbuf;

    strncpy(mnt_data_array[mnt_data_count].path, entry->mnt_dir,
        DARSHAN_MAX_MNT_PATH-1);
    strncpy(mnt_data_array[mnt_data_count].type, entry->mnt_type,
        DARSHAN_MAX_MNT_TYPE-1);
    /* NOTE: we now try to detect the preferred block size for each file 
     * system using fstatfs().  On Lustre we assume a size of 1 MiB 
     * because fstatfs() reports 4 KiB. 
     */
#ifndef LL_SUPER_MAGIC
#define LL_SUPER_MAGIC 0x0BD00BD0
#endif
    ret = statfs(entry->mnt_dir, &statfsbuf);
    if(ret == 0 && statfsbuf.f_type != LL_SUPER_MAGIC)
        mnt_data_array[mnt_data_count].block_size = statfsbuf.f_bsize;
    else if(ret == 0 && statfsbuf.f_type == LL_SUPER_MAGIC)
        mnt_data_array[mnt_data_count].block_size = 1024*1024;
    else
        mnt_data_array[mnt_data_count].block_size = 4096;

    /* store mount information for use in header of darshan log */
606
    ret = snprintf(tmp_mnt, 256, "\n%s\t%s",
607 608 609
        entry->mnt_type, entry->mnt_dir);
    if(ret < 256 && strlen(tmp_mnt) <= (*space_left))
    {
610
        strcat(buf, tmp_mnt);
611 612 613 614 615 616 617 618 619 620 621 622 623
        (*space_left) -= strlen(tmp_mnt);
    }

    mnt_data_count++;
    return;
}

/* darshan_get_exe_and_mounts_root()
 *
 * collects command line and list of mounted file systems into a string that
 * will be stored with the job header
 */
static void darshan_get_exe_and_mounts_root(struct darshan_core_runtime *core,
624
    int argc, char **argv)
625 626 627 628
{
    FILE* tab;
    struct mntent *entry;
    char* exclude;
629 630 631 632
    char* truncate_string = "<TRUNCATED>";
    int truncate_offset;
    int space_left = DARSHAN_EXE_LEN;
    int i;
633 634 635 636 637 638 639 640 641 642 643 644 645 646 647 648 649 650 651 652 653
    int tmp_index = 0;
    int skip = 0;

    /* skip these fs types */
    static char* fs_exclusions[] = {
        "tmpfs",
        "proc",
        "sysfs",
        "devpts",
        "binfmt_misc",
        "fusectl",
        "debugfs",
        "securityfs",
        "nfsd",
        "none",
        "rpc_pipefs",
        "hugetlbfs",
        "cgroup",
        NULL
    };

654 655 656 657 658 659 660 661 662 663 664 665 666 667 668 669 670 671 672 673 674 675 676 677 678 679 680 681 682 683 684
    /* record exe and arguments */
    for(i=0; i<argc; i++)
    {
        strncat(core->mmap_exe_mnt_p, argv[i], space_left);
        space_left = DARSHAN_EXE_LEN-strlen(core->mmap_exe_mnt_p);
        if(i < (argc-1))
        {
            strncat(core->mmap_exe_mnt_p, " ", space_left);
            space_left = DARSHAN_EXE_LEN-strlen(core->mmap_exe_mnt_p);
        }
    }

    /* if we don't see any arguments, then use glibc symbol to get
     * program name at least (this happens in fortran)
     */
    if(argc == 0)
    {
        strncat(core->mmap_exe_mnt_p, __progname_full, space_left);
        space_left = DARSHAN_EXE_LEN-strlen(core->mmap_exe_mnt_p);
        strncat(core->mmap_exe_mnt_p, " <unknown args>", space_left);
        space_left = DARSHAN_EXE_LEN-strlen(core->mmap_exe_mnt_p);
    }

    if(space_left == 0)
    {
        /* we ran out of room; mark that string was truncated */
        truncate_offset = DARSHAN_EXE_LEN - strlen(truncate_string);
        sprintf(&core->mmap_exe_mnt_p[truncate_offset], "%s",
            truncate_string);
    }

685 686 687 688 689 690 691 692 693 694 695 696 697 698 699 700 701 702 703 704 705 706 707 708 709 710 711
    /* we make two passes through mounted file systems; in the first pass we
     * grab any non-nfs mount points, then on the second pass we grab nfs
     * mount points
     */

    tab = setmntent("/etc/mtab", "r");
    if(!tab)
        return;
    /* loop through list of mounted file systems */
    while(mnt_data_count<DARSHAN_MAX_MNTS && (entry = getmntent(tab)) != NULL)
    {
        /* filter out excluded fs types */
        tmp_index = 0;
        skip = 0;
        while((exclude = fs_exclusions[tmp_index]))
        {
            if(!(strcmp(exclude, entry->mnt_type)))
            {
                skip =1;
                break;
            }
            tmp_index++;
        }

        if(skip || (strcmp(entry->mnt_type, "nfs") == 0))
            continue;

712
        add_entry(core->mmap_exe_mnt_p, &space_left, entry);
713 714 715 716 717 718 719 720 721 722 723 724
    }
    endmntent(tab);

    tab = setmntent("/etc/mtab", "r");
    if(!tab)
        return;
    /* loop through list of mounted file systems */
    while(mnt_data_count<DARSHAN_MAX_MNTS && (entry = getmntent(tab)) != NULL)
    {
        if(strcmp(entry->mnt_type, "nfs") != 0)
            continue;

725
        add_entry(core->mmap_exe_mnt_p, &space_left, entry);
726 727 728 729 730 731 732 733 734 735 736 737 738 739 740 741
    }
    endmntent(tab);

    /* Sort mount points in order of longest path to shortest path.  This is
     * necessary so that if we try to match file paths to mount points later
     * we don't match on "/" every time.
     */
    qsort(mnt_data_array, mnt_data_count, sizeof(mnt_data_array[0]), mnt_data_cmp);
    return;
}

/* darshan_get_exe_and_mounts()
 *
 * collects command line and list of mounted file systems into a string that
 * will be stored with the job header
 */
742 743
static void darshan_get_exe_and_mounts(struct darshan_core_runtime *core,
    int argc, char **argv)
744 745 746
{
    if(my_rank == 0)
    {
747
        darshan_get_exe_and_mounts_root(core, argc, argv);
748 749 750 751 752 753 754 755 756
    }

    /* broadcast mount count to all nodes */
    DARSHAN_MPI_CALL(PMPI_Bcast)(&mnt_data_count, 1, MPI_INT, 0,
        MPI_COMM_WORLD);
    /* broadcast mount data to all nodes */
    DARSHAN_MPI_CALL(PMPI_Bcast)(mnt_data_array,
        mnt_data_count*sizeof(mnt_data_array[0]), MPI_BYTE, 0, MPI_COMM_WORLD);

757
    return;
758 759
}

760 761 762 763 764 765 766 767 768 769 770 771 772 773 774 775 776
static void darshan_block_size_from_path(const char *path, int *block_size)
{
    int i;
    *block_size = -1;

    for(i=0; i<mnt_data_count; i++)
    {
        if(!(strncmp(mnt_data_array[i].path, path, strlen(mnt_data_array[i].path))))
        {
            *block_size = mnt_data_array[i].block_size;
            return;
        }
    }

    return;
}

777
static void darshan_get_shared_records(struct darshan_core_runtime *core,
778
    darshan_record_id **shared_recs, int *shared_rec_cnt)
779
{
780 781
    int i, j;
    int tmp_cnt = core->rec_count;
782
    struct darshan_core_record_ref *tmp, *ref;
783 784 785 786 787 788 789 790 791 792 793 794 795 796 797 798 799
    darshan_record_id *id_array;
    uint64_t *mod_flags;
    uint64_t *global_mod_flags;

    /* broadcast root's number of records to all other processes */
    DARSHAN_MPI_CALL(PMPI_Bcast)(&tmp_cnt, 1, MPI_INT, 0, MPI_COMM_WORLD);

    /* use root record count to allocate data structures */
    id_array = malloc(tmp_cnt * sizeof(darshan_record_id));
    mod_flags = malloc(tmp_cnt * sizeof(uint64_t));
    global_mod_flags = malloc(tmp_cnt * sizeof(uint64_t));
    *shared_recs = malloc(tmp_cnt * sizeof(darshan_record_id));
    assert(id_array && mod_flags && global_mod_flags && *shared_recs);

    memset(mod_flags, 0, tmp_cnt * sizeof(uint64_t));
    memset(global_mod_flags, 0, tmp_cnt * sizeof(uint64_t));
    memset(*shared_recs, 0, tmp_cnt * sizeof(darshan_record_id));
800 801 802 803

    /* first, determine list of records root process has opened */
    if(my_rank == 0)
    {
804
        i = 0;
805
        HASH_ITER(hlink, core->rec_hash, ref, tmp)
806
        {
807
            id_array[i++] = ref->rec.id;           
808 809 810 811
        }
    }

    /* broadcast root's list of records to all other processes */
812
    DARSHAN_MPI_CALL(PMPI_Bcast)(id_array, (tmp_cnt * sizeof(darshan_record_id)),
813 814 815
        MPI_BYTE, 0, MPI_COMM_WORLD);

    /* everyone looks to see if they opened the same records as root */
816
    for(i=0; i<tmp_cnt; i++)
817
    {
818 819
        HASH_FIND(hlink, core->rec_hash, &id_array[i], sizeof(darshan_record_id), ref);
        if(ref)
820
        {
821 822
            /* we opened that record too, save the mod_flags */
            mod_flags[i] = ref->mod_flags;
823 824 825
        }
    }

826 827 828
    /* now allreduce so everyone agrees which files are shared and
     * which modules accessed them collectively
     */
829 830
    DARSHAN_MPI_CALL(PMPI_Allreduce)(mod_flags, global_mod_flags, tmp_cnt,
        MPI_UINT64_T, MPI_BAND, MPI_COMM_WORLD);
831

832 833
    j = 0;
    for(i=0; i<tmp_cnt; i++)
834
    {
835
        if(global_mod_flags[i] != 0)
836
        {
837
            (*shared_recs)[j++] = id_array[i];
838 839 840 841 842 843 844 845

            /* set global_mod_flags so we know which modules collectively
             * accessed this module. we need this info to support shared
             * file reductions
             */
            HASH_FIND(hlink, core->rec_hash, &id_array[i], sizeof(darshan_record_id), ref);
            assert(ref);
            ref->global_mod_flags = global_mod_flags[i];
846 847
        }
    }
848
    *shared_rec_cnt = j;
849

850 851 852
    return;
}

853
static int darshan_log_open_all(char *logfile_name, MPI_File *log_fh)
854 855 856 857 858 859 860 861 862 863 864 865 866 867 868
{
    char *hints;
    char *tok_str;
    char *orig_tok_str;
    char *key;
    char *value;
    char *saveptr = NULL;
    int ret;
    MPI_Info info;

    /* check environment variable to see if the default MPI file hints have
     * been overridden
     */
    MPI_Info_create(&info);

869
    hints = getenv(DARSHAN_LOG_HINTS_OVERRIDE);
870 871
    if(!hints)
    {
872
        hints = __DARSHAN_LOG_HINTS;
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
    }

    if(hints && strlen(hints) > 0)
    {
        tok_str = strdup(hints);
        if(tok_str)
        {
            orig_tok_str = tok_str;
            do
            {
                /* split string on semicolon */
                key = strtok_r(tok_str, ";", &saveptr);
                if(key)
                {
                    tok_str = NULL;
                    /* look for = sign splitting key/value pairs */
                    value = index(key, '=');
                    if(value)
                    {
                        /* break key and value into separate null terminated strings */
                        value[0] = '\0';
                        value++;
                        if(strlen(key) > 0)
                            MPI_Info_set(info, key, value);
                    }
                }
            }while(key != NULL);
            free(orig_tok_str);
        }
    }

    /* open the darshan log file for writing */
    ret = DARSHAN_MPI_CALL(PMPI_File_open)(MPI_COMM_WORLD, logfile_name,
        MPI_MODE_CREATE | MPI_MODE_WRONLY | MPI_MODE_EXCL, info, log_fh);
Shane Snyder's avatar
Shane Snyder committed
907
    if(ret != MPI_SUCCESS)
908 909 910
        return(-1);

    MPI_Info_free(&info);
Shane Snyder's avatar
Shane Snyder committed
911 912 913
    return(0);
}

914
static int darshan_deflate_buffer(void **pointers, int *lengths, int count,
Shane Snyder's avatar
Shane Snyder committed
915
    char *comp_buf, int *comp_buf_length)
916 917 918 919 920 921
{
    int ret = 0;
    int i;
    int total_target = 0;
    z_stream tmp_stream;

922 923 924 925 926 927 928 929 930 931 932
    /* just return if there is no data */
    for(i = 0; i < count; i++)
    {
        total_target += lengths[i];
    }
    if(total_target)
    {
        total_target = 0;
    }
    else
    {
Shane Snyder's avatar
Shane Snyder committed
933
        *comp_buf_length = 0;
934 935 936
        return(0);
    }

937 938 939 940 941 942 943
    memset(&tmp_stream, 0, sizeof(tmp_stream));
    tmp_stream.zalloc = Z_NULL;
    tmp_stream.zfree = Z_NULL;
    tmp_stream.opaque = Z_NULL;

    /* initialize the zlib compression parameters */
    /* TODO: check these parameters? */
Shane Snyder's avatar
Shane Snyder committed
944 945 946
//    ret = deflateInit2(&tmp_stream, Z_DEFAULT_COMPRESSION, Z_DEFLATED,
//        15 + 16, 8, Z_DEFAULT_STRATEGY);
    ret = deflateInit(&tmp_stream, Z_DEFAULT_COMPRESSION);
947 948 949 950 951
    if(ret != Z_OK)
    {
        return(-1);
    }

Shane Snyder's avatar
Shane Snyder committed
952
    tmp_stream.next_out = (unsigned char *)comp_buf;
953
    tmp_stream.avail_out = DARSHAN_COMP_BUF_SIZE;
954 955 956 957 958 959 960 961 962 963 964 965 966 967 968 969 970 971 972 973 974 975 976 977 978 979 980 981 982 983 984 985 986 987 988 989 990 991 992 993 994 995

    /* loop over the input pointers */
    for(i = 0; i < count; i++)
    {
        total_target += lengths[i];
        tmp_stream.next_in = pointers[i];
        tmp_stream.avail_in = lengths[i];
        /* while we have not finished consuming all of the data available to
         * this point in the loop
         */
        while(tmp_stream.total_in < total_target)
        {
            if(tmp_stream.avail_out == 0)
            {
                /* We ran out of buffer space for compression.  In theory,
                 * we could start using some of the file_array buffer space
                 * without having to malloc again.  In practice, this case 
                 * is going to be practically impossible to hit.
                 */
                deflateEnd(&tmp_stream);
                return(-1);
            }

            /* compress data */
            ret = deflate(&tmp_stream, Z_NO_FLUSH);
            if(ret != Z_OK)
            {
                deflateEnd(&tmp_stream);
                return(-1);
            }
        }
    }

    /* flush compression and end */
    ret = deflate(&tmp_stream, Z_FINISH);
    if(ret != Z_STREAM_END)
    {
        deflateEnd(&tmp_stream);
        return(-1);
    }
    deflateEnd(&tmp_stream);

Shane Snyder's avatar
Shane Snyder committed
996
    *comp_buf_length = tmp_stream.total_out;
997 998 999
    return(0);
}

1000 1001 1002
/* NOTE: the map written to file may contain duplicate id->name entries if a
 *       record is opened by multiple ranks, but not all ranks
 */
1003
static int darshan_log_write_record_hash(MPI_File log_fh, struct darshan_core_runtime *core,
1004
    uint64_t *inout_off)
1005
{
1006 1007 1008 1009
    int ret;
    struct darshan_core_record_ref *ref, *tmp;
    uint32_t name_len;
    size_t record_sz;
1010
    size_t hash_buf_sz = 0;
1011 1012
    char *hash_buf;
    char *hash_buf_off;
1013

1014
    /* allocate a buffer to store at most 64 bytes for each registered record */
1015
    /* NOTE: this buffer may be reallocated if estimate is too small */
1016
    hash_buf_sz = core->rec_count * 64;
1017 1018
    hash_buf = malloc(hash_buf_sz);
    if(!hash_buf)
1019
    {
Shane Snyder's avatar
Shane Snyder committed
1020
        return(-1);
1021 1022
    }

1023
    /* serialize the record hash into a buffer for writing */
1024
    hash_buf_off = hash_buf;
1025
    HASH_ITER(hlink, core->rec_hash, ref, tmp)
1026
    {
1027 1028 1029 1030
        /* to avoid duplicate records, only rank 0 will write shared records */
        if(my_rank > 0 && ref->global_mod_flags)
            continue;

1031
        name_len = strlen(ref->rec.name);
1032
        record_sz = sizeof(darshan_record_id) + sizeof(uint32_t) + name_len;
1033
        /* make sure there is room in the buffer for this record */
1034
        if((hash_buf_off + record_sz) > (hash_buf + hash_buf_sz))
1035
        {
1036
            char *tmp_buf;
1037 1038
            size_t old_buf_sz;

1039
            /* if no room, reallocate the hash buffer at twice the current size */
1040 1041 1042
            old_buf_sz = hash_buf_off - hash_buf;
            hash_buf_sz *= 2;
            tmp_buf = malloc(hash_buf_sz);
1043 1044
            if(!tmp_buf)
            {
1045
                free(hash_buf);
Shane Snyder's avatar
Shane Snyder committed
1046
                return(-1);
1047 1048
            }

1049 1050 1051 1052
            memcpy(tmp_buf, hash_buf, old_buf_sz);
            free(hash_buf);
            hash_buf = tmp_buf;
            hash_buf_off = hash_buf + old_buf_sz;
1053 1054
        }

1055 1056
        /* now serialize the record into the hash buffer.
         * NOTE: darshan record hash serialization method: 
1057 1058
         *          ... darshan_record_id | (uint32_t) path_len | path ...
         */
1059 1060 1061 1062 1063 1064
        *((darshan_record_id *)hash_buf_off) = ref->rec.id;
        hash_buf_off += sizeof(darshan_record_id);
        *((uint32_t *)hash_buf_off) = name_len;
        hash_buf_off += sizeof(uint32_t);
        memcpy(hash_buf_off, ref->rec.name, name_len);
        hash_buf_off += name_len;
1065
    }
Shane Snyder's avatar
Shane Snyder committed
1066
    hash_buf_sz = hash_buf_off - hash_buf;
1067

1068
    /* collectively write out the record hash to the darshan log */
Shane Snyder's avatar
Shane Snyder committed
1069
    ret = darshan_log_append_all(log_fh, core, hash_buf, hash_buf_sz, inout_off);
1070

1071
    free(hash_buf);
1072

1073
    return(ret);
Shane Snyder's avatar
Shane Snyder committed
1074 1075
}

1076 1077
/* NOTE: inout_off contains the starting offset of this append at the beginning
 *       of the call, and contains the ending offset at the end of the call.
Shane Snyder's avatar
Shane Snyder committed
1078
 *       This variable is only valid on the root rank (rank 0).
Shane Snyder's avatar
Shane Snyder committed
1079
 */