darshan-logutils.c 41.9 KB
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/*
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Shane Snyder committed
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 * Copyright (C) 2015 University of Chicago.
 * See COPYRIGHT notice in top-level directory.
 *
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 */

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#define _GNU_SOURCE
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#include "darshan-util-config.h"
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#include <stdio.h>
#include <string.h>
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#include <assert.h>
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#include <stdlib.h>
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#include <unistd.h>
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#include <inttypes.h>
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#include <sys/types.h>
#include <sys/stat.h>
#include <fcntl.h>
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#include <errno.h>
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#include "darshan-logutils.h"

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/* default input buffer size for decompression algorithm */
#define DARSHAN_DEF_COMP_BUF_SZ (1024*1024) /* 1 MiB */

/* special identifers for referring to header, job,  and
 * record map regions of the darshan log file
 */
#define DARSHAN_HEADER_REGION_ID    (-3)
#define DARSHAN_JOB_REGION_ID       (-2)
#define DARSHAN_REC_MAP_REGION_ID   (-1)

static int darshan_log_getheader(darshan_fd fd);
static int darshan_log_putheader(darshan_fd fd);
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static int darshan_log_seek(darshan_fd fd, off_t offset);
static int darshan_log_read(darshan_fd fd, void *buf, int len);
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static int darshan_log_write(darshan_fd fd, void *buf, int len);
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static int darshan_log_dzinit(darshan_fd fd);
static void darshan_log_dzdestroy(darshan_fd fd);
static int darshan_log_dzread(darshan_fd fd, int region_id, void *buf, int len);
static int darshan_log_dzwrite(darshan_fd fd, int region_id, void *buf, int len);
static int darshan_log_libz_read(darshan_fd fd, int region_id, void *buf, int len);
static int darshan_log_libz_write(darshan_fd fd, int region_id, void *buf, int len);
static int darshan_log_libz_flush(darshan_fd fd, int region_id);
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#ifdef HAVE_LIBBZ2
static int darshan_log_bzip2_read(darshan_fd fd, int region_id, void *buf, int len);
static int darshan_log_bzip2_write(darshan_fd fd, int region_id, void *buf, int len);
static int darshan_log_bzip2_flush(darshan_fd fd, int region_id);
#endif
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static int darshan_log_dzload(darshan_fd fd, struct darshan_log_map map);
static int darshan_log_dzunload(darshan_fd fd, struct darshan_log_map *map_p);

/* TODO: check comments on functions to make sure they are right /cleanup */
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/* TODO: can we make this s.t. we don't care about ordering (i.e., X macro it ) */
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/* see gzip interface for ideas */
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struct darshan_mod_logutil_funcs *mod_logutils[DARSHAN_MAX_MODS] =
{
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    NULL,               /* NULL */
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    &posix_logutils,    /* POSIX */
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    &mpiio_logutils,    /* MPI-IO */
    &hdf5_logutils,     /* HDF5 */
    &pnetcdf_logutils,  /* PNETCDF */
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    &bgq_logutils,      /* BG/Q */
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    NULL,
    NULL,
    NULL,
    NULL,
    NULL,
    NULL,
    NULL,
    NULL,
    NULL,
    NULL
};
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/* darshan_log_open()
 *
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 * open an existing darshan log file for reading only
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 *
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 * returns file descriptor on success, NULL on failure
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 */
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darshan_fd darshan_log_open(const char *name)
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{
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    darshan_fd tmp_fd;
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    int o_flags = O_RDONLY;
    int ret;
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    tmp_fd = malloc(sizeof(*tmp_fd));
    if(!tmp_fd)
        return(NULL);
    memset(tmp_fd, 0, sizeof(*tmp_fd));

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    /* open the log file in read mode */
    tmp_fd->fildes = open(name, o_flags);
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    if(tmp_fd->fildes < 0)
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    {
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        fprintf(stderr, "Error: failed to open darshan log file %s.\n", name);
        free(tmp_fd);
        return(NULL);
    }
    tmp_fd->o_flags = o_flags;
    strncpy(tmp_fd->logfile_path, name, PATH_MAX);

    /* read the header from the log file to init fd data structures */
    ret = darshan_log_getheader(tmp_fd);
    if(ret < 0)
    {
        close(tmp_fd->fildes);
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        free(tmp_fd);
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        return(NULL);
    }

    /* initialize compression data structures */
    ret = darshan_log_dzinit(tmp_fd);
    if(ret < 0)
    {
        fprintf(stderr, "Error: failed to initialize decompression data structures.\n");
        close(tmp_fd->fildes);
        free(tmp_fd);
        return(NULL);
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    }

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    return(tmp_fd);
}

/* darshan_log_create()
 *
 * create a darshan log file for writing with the given compression method
 *
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 * returns file descriptor on success, NULL on failure
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 */
darshan_fd darshan_log_create(const char *name, enum darshan_comp_type comp_type)
{
    darshan_fd tmp_fd;
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    int o_flags = O_WRONLY | O_CREAT | O_EXCL;
    int ret;
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    tmp_fd = malloc(sizeof(*tmp_fd));
    if(!tmp_fd)
        return(NULL);
    memset(tmp_fd, 0, sizeof(*tmp_fd));

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    /* open the log for writing, making sure to not overwrite existing log */
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    /* TODO: permissions when creating?  umask */
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    tmp_fd->fildes = open(name, o_flags, 0400);
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    if(tmp_fd->fildes < 0)
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    {
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        fprintf(stderr, "Error: failed to open darshan log file %s.\n", name);
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        free(tmp_fd);
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        return(NULL);
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    }
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    tmp_fd->o_flags = o_flags;
    tmp_fd->comp_type = comp_type;
    strncpy(tmp_fd->logfile_path, name, PATH_MAX);
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    /* position file pointer to prealloc space for the log file header
     * NOTE: the header is written at close time, after all internal data
     * structures have been properly set
     */
    ret = darshan_log_seek(tmp_fd, sizeof(struct darshan_header));
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    if(ret < 0)
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    {
        fprintf(stderr, "Error: unable to seek in darshan log file.\n");
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        close(tmp_fd->fildes);
        free(tmp_fd);
        unlink(name);
        return(NULL);
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    }

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    /* initialize compression data structures */
    ret = darshan_log_dzinit(tmp_fd);
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    if(ret < 0)
    {
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        fprintf(stderr, "Error: failed to initialize compression data structures.\n");
        close(tmp_fd->fildes);
        free(tmp_fd);
        unlink(name);
        return(NULL);
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    }

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    return(tmp_fd);
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}

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/* darshan_log_getjob()
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 *
 * read job level metadata from the darshan log file
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 *
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 * returns 0 on success, -1 on failure
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 */
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int darshan_log_getjob(darshan_fd fd, struct darshan_job *job)
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{
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    char job_buf[DARSHAN_JOB_RECORD_SIZE] = {0};
    int job_buf_sz = DARSHAN_JOB_RECORD_SIZE;
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    int ret;
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    assert(fd->job_map.len > 0 && fd->job_map.off > 0);

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    /* read the compressed job data from the log file */
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    ret = darshan_log_dzread(fd, DARSHAN_JOB_REGION_ID, job_buf, job_buf_sz);
    if(ret <= sizeof(*job))
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    {
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        fprintf(stderr, "Error: failed to read darshan log file job data.\n");
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        return(-1);
    }
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    memcpy(job, job_buf, sizeof(*job));
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    if(fd->swap_flag)
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    {
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        /* swap bytes if necessary */
        DARSHAN_BSWAP64(&job->uid);
        DARSHAN_BSWAP64(&job->start_time);
        DARSHAN_BSWAP64(&job->end_time);
        DARSHAN_BSWAP64(&job->nprocs);
        DARSHAN_BSWAP64(&job->jobid);
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    }

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    /* save trailing exe & mount information, so it can be retrieved later */
    if(!fd->exe_mnt_data)
        fd->exe_mnt_data = malloc(DARSHAN_EXE_LEN+1);
    if(!fd->exe_mnt_data)
        return(-1);
    memcpy(fd->exe_mnt_data, &job_buf[sizeof(*job)], DARSHAN_EXE_LEN+1);

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    return(0);
}

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/* darshan_log_putjob()
 *
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 * write job level metadata to darshan log file
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 *
 * returns 0 on success, -1 on failure
 */
int darshan_log_putjob(darshan_fd fd, struct darshan_job *job)
{
    struct darshan_job job_copy;
    int len;
    int ret;

    memset(&job_copy, 0, sizeof(*job));
    memcpy(&job_copy, job, sizeof(*job));

    /* check for newline in existing metadata, add if needed */
    len = strlen(job_copy.metadata);
    if(len > 0 && len < DARSHAN_JOB_METADATA_LEN)
    {
        if(job_copy.metadata[len-1] != '\n')
        {
            job_copy.metadata[len] = '\n';
            job_copy.metadata[len+1] = '\0';
        }
    }

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    /* write the compressed job data to log file */
    ret = darshan_log_dzwrite(fd, DARSHAN_JOB_REGION_ID, &job_copy, sizeof(*job));
    if(ret != sizeof(*job))
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    {
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        fd->err = -1;
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        fprintf(stderr, "Error: failed to write darshan log file job data.\n");
        return(-1);
    }

    return(0);
}

/* darshan_log_getexe()
 *
 * reads the application exe name from darshan log file
 * 
 * returns 0 on success, -1 on failure 
 */
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int darshan_log_getexe(darshan_fd fd, char *buf)
{
    char *newline;
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    int ret;
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    /* if the exe/mount data has not been saved yet, read in the job info */
    if(!fd->exe_mnt_data)
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    {
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        struct darshan_job job;
        ret = darshan_log_getjob(fd, &job);
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        if(ret < 0 || !fd->exe_mnt_data)
            return(-1);
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    }
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    /* exe string is located before the first line break */
    newline = strchr(fd->exe_mnt_data, '\n');

    /* copy over the exe string */
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    if(newline)
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        memcpy(buf, fd->exe_mnt_data, (newline - fd->exe_mnt_data));
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    return (0);
}

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/* darshan_log_putexe()
 *
 * wrties the application exe name to darshan log file
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 * NOTE: this needs to be called immediately following put_job as it
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 * expects the file pointer to be positioned immediately following
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 * the darshan job information
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 *
 * returns 0 on success, -1 on failure 
 */
int darshan_log_putexe(darshan_fd fd, char *buf)
{
    int len;
    int ret;
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    len = strlen(buf);
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    ret = darshan_log_dzwrite(fd, DARSHAN_JOB_REGION_ID, buf, len);
    if(ret != len)
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    {
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        fd->err = -1;
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        fprintf(stderr, "Error: failed to write exe string to darshan log file.\n");
        return(-1);
    }

    return(0);
}

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/* darshan_log_getmounts()
 * 
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 * retrieves mount table information from the log. Note that mnt_pts and
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 * fs_types are arrays that will be allocated by the function and must be
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 * freed by the caller. count will indicate the size of the arrays
 *
 * returns 0 on success, -1 on failure
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 */
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int darshan_log_getmounts(darshan_fd fd, char*** mnt_pts,
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    char*** fs_types, int* count)
{
    char *pos;
    int array_index = 0;
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    int ret;
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    /* if the exe/mount data has not been saved yet, read in the job info */
    if(!fd->exe_mnt_data)
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    {
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        struct darshan_job job;
        ret = darshan_log_getjob(fd, &job);
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        if(ret < 0 || !fd->exe_mnt_data)
            return(-1);
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    }
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    /* count entries */
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    *count = 0;
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    pos = fd->exe_mnt_data;
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    while((pos = strchr(pos, '\n')) != NULL)
    {
        pos++;
        (*count)++;
    }

    if(*count == 0)
    {
        /* no mount entries present */
        return(0);
    }

    /* allocate output arrays */
    *mnt_pts = malloc((*count)*sizeof(char*));
    assert(*mnt_pts);
    *fs_types = malloc((*count)*sizeof(char*));
    assert(*fs_types);

    /* work backwards through the table and parse each line (except for
     * first, which holds command line information)
     */
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    while((pos = strrchr(fd->exe_mnt_data, '\n')) != NULL)
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    {
        /* overestimate string lengths */
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        (*mnt_pts)[array_index] = malloc(DARSHAN_EXE_LEN);
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        assert((*mnt_pts)[array_index]);
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        (*fs_types)[array_index] = malloc(DARSHAN_EXE_LEN);
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        assert((*fs_types)[array_index]);

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        ret = sscanf(++pos, "%s\t%s", (*fs_types)[array_index],
            (*mnt_pts)[array_index]);
        if(ret != 2)
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        {
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            fprintf(stderr, "Error: poorly formatted mount table in darshan log file.\n");
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            return(-1);
        }
        pos--;
        *pos = '\0';
        array_index++;
    }

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    return(0);
}

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/* darshan_log_putmounts()
 *
 * writes mount information to the darshan log file
 * NOTE: this function call should follow immediately after the call
 * to darshan_log_putexe(), as it assumes the darshan log file pointer
 * is pointing to the offset immediately following the exe string
 *
 * returns 0 on success, -1 on failure
 */
int darshan_log_putmounts(darshan_fd fd, char** mnt_pts, char** fs_types, int count)
{
    int i;
    char line[1024];
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    char mnt_dat[DARSHAN_EXE_LEN] = {0};
    int mnt_dat_sz = 0;
    char *tmp;
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    int ret;

    /* write each mount entry to file */
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    tmp = mnt_dat;
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    for(i=count-1; i>=0; i--)
    {
        sprintf(line, "\n%s\t%s", fs_types[i], mnt_pts[i]);
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        memcpy(tmp, line, strlen(line));
        tmp += strlen(line);
        mnt_dat_sz += strlen(line);
    }

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    ret = darshan_log_dzwrite(fd, DARSHAN_JOB_REGION_ID, mnt_dat, mnt_dat_sz);
    if (ret != mnt_dat_sz)
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    {
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        fd->err = -1;
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        fprintf(stderr, "Error: failed to write darshan log mount data.\n");
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        return(-1);
    }

    return(0);
}

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/* darshan_log_gethash()
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 *
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 * read the hash of records from the darshan log file
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 *
 * returns 0 on success, -1 on failure
 */
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int darshan_log_gethash(darshan_fd fd, struct darshan_record_ref **hash)
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{
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    char *hash_buf;
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    int hash_buf_sz;
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    char *buf_ptr;
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    darshan_record_id *rec_id_ptr;
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    uint32_t *path_len_ptr, tmp_path_len;
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    char *path_ptr;
    struct darshan_record_ref *ref;
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    int read;
    int read_req_sz;
    int buf_remaining = 0;
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    /* default to hash buffer twice as big as default compression buf */
    hash_buf = malloc(DARSHAN_DEF_COMP_BUF_SZ * 2);
    if(!hash_buf)
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        return(-1);
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    memset(hash_buf, 0, DARSHAN_DEF_COMP_BUF_SZ * 2);
    hash_buf_sz = DARSHAN_DEF_COMP_BUF_SZ * 2;
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    do
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    {
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        /* read chunks of the darshan record id -> file name mapping from log file,
         * constructing a hash table in the process
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         */
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        read_req_sz = hash_buf_sz - buf_remaining;
        read = darshan_log_dzread(fd, DARSHAN_REC_MAP_REGION_ID,
            hash_buf + buf_remaining, read_req_sz);
        if(read < 0)
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        {
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            fprintf(stderr, "Error: failed to read record hash from darshan log file.\n");
            free(hash_buf);
            return(-1);
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        }

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        /* work through the hash buffer -- deserialize the mapping data and
         * add to the output hash table
         * NOTE: these mapping pairs are variable in length, so we have to be able
         * to handle incomplete mappings temporarily here
         */
        buf_ptr = hash_buf;
        buf_remaining += read;
        while(buf_remaining > (sizeof(darshan_record_id) + sizeof(uint32_t)))
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        {
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            /* see if we have enough buf space to read in the next full record */
            tmp_path_len = *(uint32_t *)(buf_ptr + sizeof(darshan_record_id));
            if(fd->swap_flag)
                DARSHAN_BSWAP32(&tmp_path_len);

            /* we need to read more before we continue deserializing */
            if(buf_remaining <
                (sizeof(darshan_record_id) + sizeof(uint32_t) + tmp_path_len))
                break;

            /* get pointers for each field of this darshan record */
            /* NOTE: darshan record hash serialization method: 
             *          ... darshan_record_id | (uint32_t) path_len | path ...
             */
            rec_id_ptr = (darshan_record_id *)buf_ptr;
            buf_ptr += sizeof(darshan_record_id);
            path_len_ptr = (uint32_t *)buf_ptr;
            buf_ptr += sizeof(uint32_t);
            path_ptr = (char *)buf_ptr;

            if(fd->swap_flag)
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            {
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                /* we need to sort out endianness issues before deserializing */
                DARSHAN_BSWAP64(rec_id_ptr);
                DARSHAN_BSWAP32(path_len_ptr);
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            }
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            HASH_FIND(hlink, *hash, rec_id_ptr, sizeof(darshan_record_id), ref);
            if(!ref)
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            {
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                ref = malloc(sizeof(*ref));
                if(!ref)
                {
                    free(hash_buf);
                    return(-1);
                }
                ref->rec.name = malloc(*path_len_ptr + 1);
                if(!ref->rec.name)
                {
                    free(ref);
                    free(hash_buf);
                    return(-1);
                }

                /* set the fields for this record */
                ref->rec.id = *rec_id_ptr;
                memcpy(ref->rec.name, path_ptr, *path_len_ptr);
                ref->rec.name[*path_len_ptr] = '\0';

                /* add this record to the hash */
                HASH_ADD(hlink, *hash, rec.id, sizeof(darshan_record_id), ref);
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            }

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            buf_ptr += *path_len_ptr;
            buf_remaining -=
                (sizeof(darshan_record_id) + sizeof(uint32_t) + *path_len_ptr);
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        }
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        /* copy any leftover data to beginning of buffer to parse next */
        memcpy(hash_buf, buf_ptr, buf_remaining);

        /* we keep reading until we get a short read informing us we have
         * read all of the record hash
         */
    } while(read == read_req_sz);
    assert(buf_remaining == 0);
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    free(hash_buf);
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    return(0);
}

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/* darshan_log_puthash()
 *
 * writes the hash table of records to the darshan log file
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 * NOTE: this function call should follow immediately after the call
 * to darshan_log_putmounts(), as it assumes the darshan log file pointer
 * is pointing to the offset immediately following the mount information
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 *
 * returns 0 on success, -1 on failure
 */
int darshan_log_puthash(darshan_fd fd, struct darshan_record_ref *hash)
{
    char *hash_buf;
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    int hash_buf_sz;
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    struct darshan_record_ref *ref, *tmp;
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    char *buf_ptr;
    int path_len;
    int wrote;
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    /* allocate memory for largest possible hash record */
    hash_buf_sz = sizeof(darshan_record_id) + sizeof(uint32_t) + PATH_MAX;
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    hash_buf = malloc(hash_buf_sz);
    if(!hash_buf)
        return(-1);
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    memset(hash_buf, 0, hash_buf_sz);
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    /* individually serialize each hash record and write to log file */
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    HASH_ITER(hlink, hash, ref, tmp)
    {
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        buf_ptr = hash_buf;
        path_len = strlen(ref->rec.name);
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        /* the hash buffer has space to serialize this record
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         * NOTE: darshan record hash serialization method: 
         *          ... darshan_record_id | (uint32_t) path_len | path ...
         */
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        *((darshan_record_id *)buf_ptr) = ref->rec.id;
        buf_ptr += sizeof(darshan_record_id);
        *((uint32_t *)buf_ptr) = path_len;
        buf_ptr += sizeof(uint32_t);
        memcpy(buf_ptr, ref->rec.name, path_len);
        buf_ptr += path_len;
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        /* write this hash entry to log file */
        wrote = darshan_log_dzwrite(fd, DARSHAN_REC_MAP_REGION_ID,
            hash_buf, (buf_ptr - hash_buf));
        if(wrote != (buf_ptr - hash_buf))
        {
            fd->err = -1;
            fprintf(stderr, "Error: failed to write record hash to darshan log file.\n");
            free(hash_buf);
            return(-1);
        }
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    }

    free(hash_buf);
    return(0);
}

/* darshan_log_getmod()
 *
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 * get a chunk of module data from the darshan log file
 *
 * returns 0 on success, -1 on failure
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 */
int darshan_log_getmod(darshan_fd fd, darshan_module_id mod_id,
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    void *buf, int len)
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{
    int ret;
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    if(mod_id < 0 || mod_id >= DARSHAN_MAX_MODS)
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    {
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        fprintf(stderr, "Error: invalid Darshan module id.\n");
        return(-1);
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    }

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    if(fd->mod_map[mod_id].len == 0)
        return(0); /* no data corresponding to this mod_id */

    /* read this module's data from the log file */
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    ret = darshan_log_dzread(fd, mod_id, buf, len);
    if(ret < 0)
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    {
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        fprintf(stderr,
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            "Error: failed to read module %s data from darshan log file.\n",
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            darshan_module_names[mod_id]);
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        return(-1);
    }

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    return(ret);
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}

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/* darshan_log_putmod()
 *
 * write a chunk of module data to the darshan log file
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 * NOTE: this function call should be called directly after the
 * put_hash() function, as it expects the file pointer to be
 * positioned directly past the record hash location. Also,
 * for a set of modules with data to write to file, this function
 * should be called in order of increasing module identifiers,
 * as the darshan log file format expects this ordering.
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 *
 * returns 0 on success, -1 on failure
 */
int darshan_log_putmod(darshan_fd fd, darshan_module_id mod_id,
    void *mod_buf, int mod_buf_sz)
{
    int ret;

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    if(mod_id < 0 || mod_id >= DARSHAN_MAX_MODS)
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    {
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        fd->err = -1;
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        fprintf(stderr, "Error: invalid Darshan module id.\n");
        return(-1);
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    }

    /* write the module chunk to the log file */
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    ret = darshan_log_dzwrite(fd, mod_id, mod_buf, mod_buf_sz);
    if(ret != mod_buf_sz)
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    {
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        fd->err = -1;
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        fprintf(stderr,
            "Error: failed to write module %s data to darshan log file.\n",
            darshan_module_names[mod_id]);
        return(-1);
    }

    return(0);
}

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/* darshan_log_close()
 *
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 * close an open darshan file descriptor, freeing any resources
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 *
 * returns 0 on success, -1 on failure
 */
void darshan_log_close(darshan_fd fd)
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{
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    int ret;

    if(fd->o_flags & O_WRONLY)
    {
        /* flush the last region of the log to file */
        switch(fd->comp_type)
        {
            case DARSHAN_ZLIB_COMP:
                ret = darshan_log_libz_flush(fd, fd->dz_prev_reg_id);
                if(ret == 0)
                    break;
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#ifdef HAVE_LIBBZ2
            case DARSHAN_BZIP2_COMP:
                ret = darshan_log_bzip2_flush(fd, fd->dz_prev_reg_id);
                if(ret == 0)
                    break;
#endif 
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            default:
                /* if flush fails, remove the output log file */
                fd->err = -1;
                fprintf(stderr, "Error: final flush to log file failed.\n");
                break;
        }

        /* if no errors flushing, write the log header before closing */
        if(fd->err != -1)
        {
            ret = darshan_log_putheader(fd);
            if(ret < 0)
                fd->err = -1;
        }
    }

    close(fd->fildes);

    /* remove output log file if error writing to it */
    if((fd->o_flags & O_WRONLY ) && (fd->err == -1))
    {
        fprintf(stderr, "Unlinking darshan log file %s ...\n",
            fd->logfile_path);
        unlink(fd->logfile_path);
    }
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    darshan_log_dzdestroy(fd);
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    if(fd->exe_mnt_data)
        free(fd->exe_mnt_data);
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    free(fd);
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    return;
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}

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/* **************************************************** */
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/* read the header of the darshan log and set internal fd data structures
 * NOTE: this is the only portion of the darshan log that is uncompressed
 *
 * returns 0 on success, -1 on failure
 */
static int darshan_log_getheader(darshan_fd fd)
{
    struct darshan_header header;
    int i;
    int ret;

    ret = darshan_log_seek(fd, 0);
    if(ret < 0)
    {
        fprintf(stderr, "Error: unable to seek in darshan log file.\n");
        return(-1);
    }

    /* read uncompressed header from log file */
    ret = darshan_log_read(fd, &header, sizeof(header));
    if(ret != sizeof(header))
    {
        fprintf(stderr, "Error: failed to read darshan log file header.\n");
        return(-1);
    }

    /* save the version string */
    strncpy(fd->version, header.version_string, 8);

    if(header.magic_nr == DARSHAN_MAGIC_NR)
    {
        /* no byte swapping needed, this file is in host format already */
        fd->swap_flag = 0;
    }
    else
    {
        /* try byte swapping */
        DARSHAN_BSWAP64(&(header.magic_nr));
        if(header.magic_nr == DARSHAN_MAGIC_NR)
        {
            fd->swap_flag = 1;

            /* swap the log map variables in the header */
            DARSHAN_BSWAP64(&(header.rec_map.off));
            DARSHAN_BSWAP64(&(header.rec_map.len));
            for(i = 0; i < DARSHAN_MAX_MODS; i++)
            {
                DARSHAN_BSWAP64(&(header.mod_map[i].off));
                DARSHAN_BSWAP64(&(header.mod_map[i].len));
            }
        }
        else
        {
            /* otherwise this file is just broken */
            fprintf(stderr, "Error: bad magic number in darshan log file.\n");
            return(-1);
        }
    }

    fd->comp_type = header.comp_type;

    /* save the mapping of data within log file to this file descriptor */
    fd->job_map.off = sizeof(struct darshan_header);
    fd->job_map.len = header.rec_map.off - fd->job_map.off;
    memcpy(&fd->rec_map, &(header.rec_map), sizeof(struct darshan_log_map));
    memcpy(&fd->mod_map, &(header.mod_map), DARSHAN_MAX_MODS * sizeof(struct darshan_log_map));

    return(0);
}

/* write a darshan header to log file
 *
 * returns 0 on success, -1 on failure
 */
static int darshan_log_putheader(darshan_fd fd)
{
    struct darshan_header header;
    int ret;

    ret = darshan_log_seek(fd, 0);
    if(ret < 0)
    {
        fprintf(stderr, "Error: unable to seek in darshan log file.\n");
        return(-1);
    }

    memset(&header, 0, sizeof(header));
    strcpy(header.version_string, DARSHAN_LOG_VERSION);
    header.magic_nr = DARSHAN_MAGIC_NR;
    header.comp_type = fd->comp_type;

    /* copy the mapping information to the header */
    memcpy(&header.rec_map, &fd->rec_map, sizeof(struct darshan_log_map));
    memcpy(&header.mod_map, &fd->mod_map, DARSHAN_MAX_MODS * sizeof(struct darshan_log_map));

    /* write header to file */
    ret = darshan_log_write(fd, &header, sizeof(header));
    if(ret != sizeof(header))
    {
        fprintf(stderr, "Error: failed to write Darshan log file header.\n");
        return(-1);
    }

    return(0);
}

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/* return 0 on successful seek to offset, -1 on failure.
 */
static int darshan_log_seek(darshan_fd fd, off_t offset)
{
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    off_t ret_off;
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    if(fd->pos == offset)
        return(0);

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    ret_off = lseek(fd->fildes, offset, SEEK_SET);
    if(ret_off == offset)
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    {
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        fd->pos = offset;
        return(0);
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    }

    return(-1);
}

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/* return amount read on success, 0 on EOF, -1 on failure.
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 */
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static int darshan_log_read(darshan_fd fd, void* buf, int len)
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{
    int ret;

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    /* read data from the log file using the given map */
    ret = read(fd->fildes, buf, len);
    if(ret > 0)
        fd->pos += ret;
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    return(ret);
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}

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/* return amount written on success, -1 on failure.
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 */
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static int darshan_log_write(darshan_fd fd, void* buf, int len)
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{
    int ret;

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    ret = write(fd->fildes, buf, len);
    if(ret > 0)
        fd->pos += ret;

    return(ret);
}

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static int darshan_log_dzinit(darshan_fd fd)
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{
    int ret;

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    /* initialize buffers for staging compressed data to/from log file */
    fd->dz_buf = malloc(DARSHAN_DEF_COMP_BUF_SZ);
    if(fd->dz_buf == NULL)
        return(-1);

    fd->dz_prev_reg_id = DARSHAN_HEADER_REGION_ID;

    switch(fd->comp_type)
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    {
        case DARSHAN_ZLIB_COMP:
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        {
            z_stream *tmp_zstrm = malloc(sizeof(*tmp_zstrm));
            if(!tmp_zstrm)
            {
                free(fd->dz_buf);
                return(-1);
            }
            tmp_zstrm->zalloc = Z_NULL;
            tmp_zstrm->zfree = Z_NULL;
            tmp_zstrm->opaque = Z_NULL;
            tmp_zstrm->avail_in = 0;
            tmp_zstrm->next_in = Z_NULL;

            /* TODO: worth using {inflate/deflate}Init2 ?? */
            if(fd->o_flags == O_RDONLY)
            {
                /* read only file, init inflate algorithm */
                ret = inflateInit(tmp_zstrm);
            }
            else
            {
                /* write only file, init deflate algorithm */
                ret = deflateInit(tmp_zstrm, Z_DEFAULT_COMPRESSION);
                tmp_zstrm->avail_out = DARSHAN_DEF_COMP_BUF_SZ;
                tmp_zstrm->next_out = fd->dz_buf;
            }
            if(ret != Z_OK)
            {
                free(tmp_zstrm);
                free(fd->dz_buf);
                return(-1);
            }
            fd->dz_strm = tmp_zstrm;
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            break;
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        }
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#ifdef HAVE_LIBBZ2
        case DARSHAN_BZIP2_COMP:
        {
            bz_stream *tmp_bzstrm = malloc(sizeof(*tmp_bzstrm));
            if(!tmp_bzstrm)
            {
                free(fd->dz_buf);
                return(-1);
            }
            tmp_bzstrm->bzalloc = NULL;
            tmp_bzstrm->bzfree = NULL;
            tmp_bzstrm->opaque = NULL;
            tmp_bzstrm->avail_in = 0;
            tmp_bzstrm->next_in = Z_NULL;

            if(fd->o_flags == O_RDONLY)
            {
                /* read only file, init decompress algorithm */
                ret = BZ2_bzDecompressInit(tmp_bzstrm, 1, 0);
            }
            else
            {
                /* write only file, init compress algorithm */
                ret = BZ2_bzCompressInit(tmp_bzstrm, 9, 1, 30);
                tmp_bzstrm->avail_out = DARSHAN_DEF_COMP_BUF_SZ;
                tmp_bzstrm->next_out = (char *)fd->dz_buf;
            }
            if(ret != BZ_OK)
            {
                free(tmp_bzstrm);
                free(fd->dz_buf);
                return(-1);
            }
            fd->dz_strm = tmp_bzstrm;
            break;
        }
#endif
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        default:
            fprintf(stderr, "Error: invalid compression type.\n");
            return(-1);
    }

    return(0);
}

static void darshan_log_dzdestroy(darshan_fd fd)
{
    switch(fd->comp_type)
    {
        case DARSHAN_ZLIB_COMP:
            if(fd->o_flags == O_RDONLY)
                inflateEnd(fd->dz_strm);
            else
                deflateEnd(fd->dz_strm);
            free(fd->dz_strm);
            break;
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#ifdef HAVE_LIBBZ2
        case DARSHAN_BZIP2_COMP:
            if(fd->o_flags == O_RDONLY)
                BZ2_bzDecompressEnd(fd->dz_strm);
            else
                BZ2_bzCompressEnd(fd->dz_strm);
            free(fd->dz_strm);
            break;
#endif
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        default:
            fprintf(stderr, "Error: invalid compression type.\n");
    }

    free(fd->dz_buf);
    return;
}

static int darshan_log_dzread(darshan_fd fd, int region_id, void *buf, int len)
{
    int ret;

    switch(fd->comp_type)
    {
        case DARSHAN_ZLIB_COMP:
            ret = darshan_log_libz_read(fd, region_id, buf, len);
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            break;
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#ifdef HAVE_LIBBZ2
        case DARSHAN_BZIP2_COMP:
            ret = darshan_log_bzip2_read(fd, region_id, buf, len);
            break;
#endif
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        default:
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            fprintf(stderr, "Error: invalid compression type.\n");
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            return(-1);
    }

    return(ret);
}

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static int darshan_log_dzwrite(darshan_fd fd, int region_id, void *buf, int len)
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{
    int ret;

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    switch(fd->comp_type)
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    {
        case DARSHAN_ZLIB_COMP:
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            ret = darshan_log_libz_write(fd, region_id, buf, len);
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            break;
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#ifdef HAVE_LIBBZ2
        case DARSHAN_BZIP2_COMP:
            ret = darshan_log_bzip2_write(fd, region_id, buf, len);
            break;
#endif
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        default:
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            fprintf(stderr, "Error: invalid compression type.\n");
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            return(-1);
    }

    return(ret);
}

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static int darshan_log_libz_read(darshan_fd fd, int region_id, void *buf, int len)
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{
    int ret;
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    int total_bytes = 0;
    int tmp_out_bytes;
    struct darshan_log_map map;
    z_stream *z_strmp = (z_stream *)fd->dz_strm;
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    assert(z_strmp);
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    /* if new log region, we reload buffers and clear eor flag */
    if(region_id != fd->dz_prev_reg_id)
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    {
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        z_strmp->avail_in = 0;
        fd->dz_eor = 0;
        fd->dz_prev_reg_id = region_id;
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    }

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    if(region_id == DARSHAN_JOB_REGION_ID)
        map = fd->job_map;
    else if(region_id == DARSHAN_REC_MAP_REGION_ID)
        map = fd->rec_map;
    else
        map = fd->mod_map[region_id];

    z_strmp->avail_out = len;
    z_strmp->next_out = buf;

    /* we just decompress until the output buffer is full, assuming there
     * is enough compressed data in file to satisfy the request size.
     */
    while(z_strmp->avail_out)
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    {
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        /* check if we need more compressed data */
        if(z_strmp->avail_in == 0)
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        {
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            /* if the eor flag is set, clear it and return -- future
             * reads of this log region will restart at the beginning
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             */
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            if(fd->dz_eor)
            {
                fd->dz_eor = 0;
                break;
            }

            /* read more data from input file */
            ret = darshan_log_dzload(fd, map);
            if(ret < 0)
                return(-1);
            assert(fd->dz_size > 0);

            z_strmp->avail_in = fd->dz_size;
            z_strmp->next_in = fd->dz_buf;
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        }

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        tmp_out_bytes = z_strmp->total_out;
        ret = inflate(z_strmp, Z_NO_FLUSH);
        if(ret != Z_OK && ret != Z_STREAM_END)
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        {
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            fprintf(stderr, "Error: unable to inflate darshan log data.\n");
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            return(-1);
        }
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        total_bytes += (z_strmp->total_out - tmp_out_bytes);
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        /* reset the decompression if we encountered end of stream */
        if(ret == Z_STREAM_END)
            inflateReset(z_strmp);
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    }

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    return(total_bytes);
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}

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static int darshan_log_libz_write(darshan_fd fd, int region_id, void *buf, int len)
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{
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    int ret;
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    int total_bytes = 0;
    int tmp_in_bytes;
    int tmp_out_bytes;
    struct darshan_log_map *map_p;
    z_stream *z_strmp = (z_stream *)fd->dz_strm;
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    assert(z_strmp);
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    /* if new log region, finish prev region's zstream and flush to log file */
    if(region_id != fd->dz_prev_reg_id)
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    {
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        /* error out if the region we are writing to precedes the previous
         * region we wrote -- we shouldn't be moving backwards in the log
         */
        if(region_id < fd->dz_prev_reg_id)
            return(-1);

        if(fd->dz_prev_reg_id != DARSHAN_HEADER_REGION_ID)
        {
            ret = darshan_log_libz_flush(fd, fd->dz_prev_reg_id);
            if(ret < 0)
                return(-1);
        }

        fd->dz_prev_reg_id = region_id;
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    }

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    if(region_id == DARSHAN_JOB_REGION_ID)
        map_p = &(fd->job_map);
    else if(region_id == DARSHAN_REC_MAP_REGION_ID)
        map_p = &(fd->rec_map);
    else
        map_p = &(fd->mod_map[region_id]);

    z_strmp->avail_in = len;
    z_strmp->next_in = buf;

    /* compress input data until none left */
    while(z_strmp->avail_in)
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    {
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        /* if we are out of output, flush to log file */
        if(z_strmp->avail_out == 0)
        {
            assert(fd->dz_size == DARSHAN_DEF_COMP_BUF_SZ);

            ret = darshan_log_dzunload(fd, map_p);
            if(ret < 0)
                return(-1);

            z_strmp->avail_out = DARSHAN_DEF_COMP_BUF_SZ;
            z_strmp->next_out = fd->dz_buf;
        }

        tmp_in_bytes = z_strmp->total_in;
        tmp_out_bytes = z_strmp->total_out;
        ret = deflate(z_strmp, Z_NO_FLUSH);
        if(ret != Z_OK)
        {
            fprintf(stderr, "Error: unable to deflate darshan log data.\n");
            return(-1);
        }
        total_bytes += (z_strmp->total_in - tmp_in_bytes);
        fd->dz_size += (z_strmp->total_out - tmp_out_bytes);
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    }

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    return(total_bytes);
}

static int darshan_log_libz_flush(darshan_fd fd, int region_id)
{
    int ret;
    int tmp_out_bytes;
    struct darshan_log_map *map_p;
    z_stream *z_strmp = (z_stream *)fd->dz_strm;

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    assert(z_strmp);

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    if(region_id == DARSHAN_JOB_REGION_ID)
        map_p = &(fd->job_map);
    else if(region_id == DARSHAN_REC_MAP_REGION_ID)
        map_p = &(fd->rec_map);
    else
        map_p = &(fd->mod_map[region_id]);

    /* make sure deflate finishes this stream */
    z_strmp->avail_in = 0;
    z_strmp->next_in = NULL;
    do
    {
        tmp_out_bytes = z_strmp->total_out;
        ret = deflate(z_strmp, Z_FINISH);
        if(ret < 0)
        {
            fprintf(stderr, "Error: unable to deflate darshan log data.\n");
            return(-1);
        }
        fd->dz_size += (z_strmp->total_out - tmp_out_bytes);

        if(fd->dz_size)
        {
            /* flush to file */
            if(darshan_log_dzunload(fd, map_p) < 0)
                return(-1);

            z_strmp->avail_out = DARSHAN_DEF_COMP_BUF_SZ;
            z_strmp->next_out = fd->dz_buf;
        }
    } while (ret != Z_STREAM_END);

    deflateReset(z_strmp);
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    return(0);
}

#ifdef HAVE_LIBBZ2
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static int darshan_log_bzip2_read(darshan_fd fd, int region_id, void *buf, int len)
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{
    int ret;
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    int total_bytes = 0;
    int tmp_out_bytes;
    struct darshan_log_map map;
    bz_stream *bz_strmp = (bz_stream *)fd->dz_strm;

    assert(bz_strmp);

    /* if new log region, we reload buffers and clear eor flag */
    if(region_id != fd->dz_prev_reg_id)
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    {
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        bz_strmp->avail_in = 0;
        fd->dz_eor = 0;
        fd->dz_prev_reg_id = region_id;
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    }

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    if(region_id == DARSHAN_JOB_REGION_ID)
        map = fd->job_map;
    else if(region_id == DARSHAN_REC_MAP_REGION_ID)
        map = fd->rec_map;
    else
        map = fd->mod_map[region_id];

    bz_strmp->avail_out = len;
    bz_strmp->next_out = buf;

    /* we just decompress until the output buffer is full, assuming there
     * is enough compressed data in file to satisfy the request size.
     */
    while(bz_strmp->avail_out)
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    {
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        /* check if we need more compressed data */
        if(bz_strmp->avail_in == 0)
1290
        {
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            /* if the eor flag is set, clear it and return -- future
             * reads of this log region will restart at the beginning
1293
             */
1294 1295 1296 1297 1298 1299 1300 1301 1302 1303 1304 1305 1306 1307
            if(fd->dz_eor)
            {
                fd->dz_eor = 0;
                break;
            }

            /* read more data from input file */
            ret = darshan_log_dzload(fd, map);
            if(ret < 0)
                return(-1);
            assert(fd->dz_size > 0);

            bz_strmp->avail_in = fd->dz_size;
            bz_strmp->next_in = (char *)fd->dz_buf;
1308 1309
        }

1310 1311 1312
        tmp_out_bytes = bz_strmp->total_out_lo32;
        ret = BZ2_bzDecompress(bz_strmp);
        if(ret != BZ_OK && ret != BZ_STREAM_END)
1313
        {
1314
            fprintf(stderr, "Error: unable to decompress darshan log data.\n");
1315 1316
            return(-1);
        }
1317
        total_bytes += (bz_strmp->total_out_lo32 - tmp_out_bytes);
1318

1319 1320
        /* reset the decompression if we encountered end of stream */
        if(ret == BZ_STREAM_END)
1321
        {
1322 1323
            BZ2_bzDecompressEnd(bz_strmp);
            BZ2_bzDecompressInit(bz_strmp, 1, 0);
1324
        }
1325
    }
1326

1327
    return(total_bytes);
1328
}
1329

1330
static int darshan_log_bzip2_write(darshan_fd fd, int region_id, void *buf, int len)
1331
{
1332
    int ret;
1333 1334 1335 1336 1337 1338 1339 1340 1341 1342
    int total_bytes = 0;
    int tmp_in_bytes;
    int tmp_out_bytes;
    struct darshan_log_map *map_p;
    bz_stream *bz_strmp = (bz_stream *)fd->dz_strm;

    assert(bz_strmp);

    /* if new log region, finish prev region's zstream and flush to log file */
    if(region_id != fd->dz_prev_reg_id)
1343
    {
1344 1345 1346 1347 1348 1349 1350 1351 1352 1353 1354 1355 1356 1357
        /* error out if the region we are writing to precedes the previous
         * region we wrote -- we shouldn't be moving backwards in the log
         */
        if(region_id < fd->dz_prev_reg_id)
            return(-1);

        if(fd->dz_prev_reg_id != DARSHAN_HEADER_REGION_ID)
        {
            ret = darshan_log_bzip2_flush(fd, fd->dz_prev_reg_id);
            if(ret < 0)
                return(-1);
        }

        fd->dz_prev_reg_id = region_id;
1358 1359
    }

1360 1361 1362 1363 1364 1365 1366 1367 1368 1369 1370 1371 1372 1373 1374 1375 1376 1377 1378 1379 1380 1381 1382 1383 1384 1385 1386 1387 1388 1389 1390 1391 1392 1393 1394 1395 1396 1397 1398 1399 1400 1401 1402 1403 1404 1405 1406 1407 1408 1409 1410 1411 1412 1413 1414 1415 1416 1417 1418 1419
    if(region_id == DARSHAN_JOB_REGION_ID)
        map_p = &(fd->job_map);
    else if(region_id == DARSHAN_REC_MAP_REGION_ID)
        map_p = &(fd->rec_map);
    else
        map_p = &(fd->mod_map[region_id]);

    bz_strmp->avail_in