darshan-logutils.c 47.3 KB
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/*
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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 */

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/* special identifers for referring to header, job, and
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 * 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)

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struct darshan_dz_state
{
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    /* pointer to arbitrary data structure used for managing
     * compression/decompression state (e.g., z_stream
     * structure needed for libz)
     */
    void *comp_dat;
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    /* buffer for staging compressed data to/from log file */
    unsigned char *buf;
    /* size of staging buffer */
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    unsigned int size;
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    /* for reading logs, flag indicating end of log file region */
    int eor;
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    /* the region id we last tried reading/writing */
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    int prev_reg_id;
};

/* internal fd data structure */
struct darshan_fd_int_state
{
    /* posix file descriptor for the log file */
    int fildes;
    /* file pointer position */
    int64_t pos;
    /* flag indicating whether log file was created (and written) */
    int creat_flag;
    /* log file path name */
    char logfile_path[PATH_MAX];
    /* pointer to exe & mount data in darshan job data structure */
    char *exe_mnt_data;
    /* whether previous file operations have failed */
    int err;

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    /* compression/decompression stream read/write state */
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    struct darshan_dz_state dz;
};

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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);
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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);
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static int darshan_log_libz_read(darshan_fd fd, struct darshan_log_map map, 
    void *buf, int len, int reset_strm_flag);
static int darshan_log_libz_write(darshan_fd fd, struct darshan_log_map *map_p,
    void *buf, int len, int flush_strm_flag);
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static int darshan_log_libz_flush(darshan_fd fd, int region_id);
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#ifdef HAVE_LIBBZ2
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static int darshan_log_bzip2_read(darshan_fd fd, struct darshan_log_map map, 
    void *buf, int len, int reset_strm_flag);
static int darshan_log_bzip2_write(darshan_fd fd, struct darshan_log_map *map_p,
    void *buf, int len, int flush_strm_flag);
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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);
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static int darshan_log_noz_read(darshan_fd fd, struct darshan_log_map map,
    void *buf, int len, int reset_strm_flag);
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/* each module's implementation of the darshan logutil functions */
#define X(a, b, c) c,
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struct darshan_mod_logutil_funcs *mod_logutils[DARSHAN_MAX_MODS] =
{
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    DARSHAN_MODULE_IDS
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};
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#undef X
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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 ret;
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    /* allocate a darshan file descriptor */
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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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    tmp_fd->state = malloc(sizeof(struct darshan_fd_int_state));
    if(!tmp_fd->state)
    {
        free(tmp_fd->state);
        return(NULL);
    }
    memset(tmp_fd->state, 0, sizeof(struct darshan_fd_int_state));
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    /* open the log file in read mode */
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    tmp_fd->state->fildes = open(name, O_RDONLY);
    if(tmp_fd->state->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->state);
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        free(tmp_fd);
        return(NULL);
    }
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    strncpy(tmp_fd->state->logfile_path, name, PATH_MAX);
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    /* read the header from the log file to init fd data structures */
    ret = darshan_log_getheader(tmp_fd);
    if(ret < 0)
    {
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        close(tmp_fd->state->fildes);
        free(tmp_fd->state);
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        free(tmp_fd);
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        return(NULL);
    }

    /* initialize compression data structures */
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    ret = darshan_log_dzinit(tmp_fd);
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    if(ret < 0)
    {
        fprintf(stderr, "Error: failed to initialize decompression data structures.\n");
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        close(tmp_fd->state->fildes);
        free(tmp_fd->state);
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        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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 */
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darshan_fd darshan_log_create(const char *name, enum darshan_comp_type comp_type,
    int partial_flag)
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{
    darshan_fd tmp_fd;
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    int ret;
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    /* allocate a darshan file descriptor */
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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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    tmp_fd->state = malloc(sizeof(struct darshan_fd_int_state));
    if(!tmp_fd->state)
    {
        free(tmp_fd);
        return(NULL);
    }
    memset(tmp_fd->state, 0, sizeof(struct darshan_fd_int_state));
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    tmp_fd->comp_type = comp_type;
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    /* create the log for writing, making sure to not overwrite existing log */
    tmp_fd->state->fildes = creat(name, 0400);
    if(tmp_fd->state->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->state);
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        free(tmp_fd);
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        return(NULL);
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    }
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    tmp_fd->state->creat_flag = 1;
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    tmp_fd->partial_flag = partial_flag;
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    strncpy(tmp_fd->state->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->state->fildes);
        free(tmp_fd->state);
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        free(tmp_fd);
        unlink(name);
        return(NULL);
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    }

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    /* initialize compression data structures */
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    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");
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        close(tmp_fd->state->fildes);
        free(tmp_fd->state);
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        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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    struct darshan_fd_int_state *state = fd->state;
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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(state);
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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);
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    if(ret <= (int)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 */
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    if(!(state->exe_mnt_data))
        state->exe_mnt_data = malloc(DARSHAN_EXE_LEN+1);
    if(!(state->exe_mnt_data))
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        return(-1);
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    memcpy(state->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)
{
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    struct darshan_fd_int_state *state = fd->state;
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    struct darshan_job job_copy;
    int len;
    int ret;

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    assert(state);

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    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));
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    if(ret != sizeof(*job))
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    {
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        state->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)
{
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    struct darshan_fd_int_state *state = fd->state;
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    char *newline;
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    int ret;
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    assert(state);

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    /* if the exe/mount data has not been saved yet, read in the job info */
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    if(!(state->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 || !(state->exe_mnt_data))
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            return(-1);
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    }
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    /* exe string is located before the first line break */
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    newline = strchr(state->exe_mnt_data, '\n');
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    /* copy over the exe string */
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    if(newline)
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        memcpy(buf, state->exe_mnt_data, (newline - state->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)
{
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    struct darshan_fd_int_state *state = fd->state;
    int len = strlen(buf);
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    int ret;
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    assert(fd->state);
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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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        state->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)
{
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    struct darshan_fd_int_state *state = fd->state;
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    char *pos;
    int array_index = 0;
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    int ret;
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    assert(state);

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    /* if the exe/mount data has not been saved yet, read in the job info */
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    if(!(state->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 || !(state->exe_mnt_data))
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            return(-1);
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    }
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    /* count entries */
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    *count = 0;
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    pos = state->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(state->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)
{
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    struct darshan_fd_int_state *state = fd->state;
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    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;

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    assert(state);

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    /* 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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        state->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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    struct darshan_fd_int_state *state = fd->state;
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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;
    char *path_ptr;
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    char *tmp_p;
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    struct darshan_record_ref *ref;
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    int read;
    int read_req_sz;
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    int buf_rem = 0;
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    assert(state);

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    /* just return if there is no record mapping data */
    if(fd->rec_map.len == 0)
    {
        *hash = NULL;
        return(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_rem;
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        read = darshan_log_dzread(fd, DARSHAN_REC_MAP_REGION_ID,
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            hash_buf + buf_rem, read_req_sz);
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        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;
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        buf_rem += read;
        while(buf_rem > (sizeof(darshan_record_id) + 1))
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        {
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            tmp_p = buf_ptr + sizeof(darshan_record_id);
            while(tmp_p < (buf_ptr + buf_rem))
            {
                /* look for terminating null character for record name */
                if(*tmp_p == '\0')
                    break;
                tmp_p++;
            }
            if(*tmp_p != '\0')
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                break;

            /* get pointers for each field of this darshan record */
            /* NOTE: darshan record hash serialization method: 
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             *          ... darshan_record_id | path '\0' ...
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             */
            rec_id_ptr = (darshan_record_id *)buf_ptr;
            buf_ptr += sizeof(darshan_record_id);
            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);
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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);
                }
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                ref->rec.name = malloc(strlen(path_ptr) + 1);
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                if(!ref->rec.name)
                {
                    free(ref);
                    free(hash_buf);
                    return(-1);
                }

                /* set the fields for this record */
                ref->rec.id = *rec_id_ptr;
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                strcpy(ref->rec.name, path_ptr);
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                /* 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 += strlen(path_ptr) + 1;
            buf_rem -= (sizeof(darshan_record_id) + strlen(path_ptr) + 1);
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        }
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        /* copy any leftover data to beginning of buffer to parse next */
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        memcpy(hash_buf, buf_ptr, buf_rem);
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        /* we keep reading until we get a short read informing us we have
         * read all of the record hash
         */
    } while(read == read_req_sz);
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    assert(buf_rem == 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)
{
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    struct darshan_fd_int_state *state = fd->state;
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    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 wrote;
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    assert(state);

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    /* allocate memory for largest possible hash record */
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    hash_buf_sz = sizeof(darshan_record_id) + PATH_MAX + 1;
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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;
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        /* the hash buffer has space to serialize this record
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         * NOTE: darshan record hash serialization method: 
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         *          ... darshan_record_id | path '\0' ...
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         */
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        *((darshan_record_id *)buf_ptr) = ref->rec.id;
        buf_ptr += sizeof(darshan_record_id);
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        strcpy(buf_ptr, ref->rec.name);
        buf_ptr += strlen(ref->rec.name) + 1;
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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))
        {
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            state->err = -1;
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            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
 *
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 * returns number of bytes read 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 *mod_buf, int mod_buf_sz)
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{
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    struct darshan_fd_int_state *state = fd->state;
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    int ret;
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    assert(state);

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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, mod_buf, mod_buf_sz);
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    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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 *
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 * returns number of bytes written on success, -1 on failure
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 */
int darshan_log_putmod(darshan_fd fd, darshan_module_id mod_id,
    void *mod_buf, int mod_buf_sz)
{
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    struct darshan_fd_int_state *state = fd->state;
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    int ret;

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    assert(state);

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    if(mod_id < 0 || mod_id >= DARSHAN_MAX_MODS)
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    {
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        state->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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        state->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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 *
 */
void darshan_log_close(darshan_fd fd)
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{
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    struct darshan_fd_int_state *state = fd->state;
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    int ret;

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    assert(state);

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

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

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    close(state->fildes);
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    /* remove output log file if error writing to it */
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    if((state->creat_flag) && (state->err == -1))
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    {
        fprintf(stderr, "Unlinking darshan log file %s ...\n",
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            state->logfile_path);
        unlink(state->logfile_path);
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    }
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    darshan_log_dzdestroy(fd);
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    if(state->exe_mnt_data)
        free(state->exe_mnt_data);
    free(state);
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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));
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    if(ret != (int)sizeof(header))
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    {
        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);
        }
    }

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    fd->comp_type = header.comp_type;
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    fd->partial_flag = header.partial_flag;
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    /* save the mapping of data within log file to this file descriptor */
    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));

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    /* there may be nothing following the job data, so safety check map */
    fd->job_map.off = sizeof(struct darshan_header);
    if(fd->rec_map.off == 0)
    {
        for(i = 0; i < DARSHAN_MAX_MODS; i++)
        {
            if(fd->mod_map[i].off != 0)
            {
                fd->job_map.len = fd->mod_map[i].off - fd->job_map.off;
                break;
            }
        }

        if(fd->job_map.len == 0)
        {
            struct stat sbuf;
            if(fstat(fd->state->fildes, &sbuf) != 0)
            {
                fprintf(stderr, "Error: unable to stat darshan log file.\n");
                return(-1);
            }
            fd->job_map.len = sbuf.st_size - fd->job_map.off;
        }
    }
    else
    {
        fd->job_map.len = fd->rec_map.off - fd->job_map.off;
    }

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    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;
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    header.comp_type = fd->comp_type;
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    header.partial_flag = fd->partial_flag;
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    /* 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));
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    if(ret != (int)sizeof(header))
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    {
        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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    struct darshan_fd_int_state *state = fd->state;
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    off_t ret_off;
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    if(state->pos == offset)
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        return(0);

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    ret_off = lseek(state->fildes, offset, SEEK_SET);
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    if(ret_off == offset)
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    {
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        state->pos = offset;
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        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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{
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    struct darshan_fd_int_state *state = fd->state;
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    int ret;
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    unsigned int read_so_far = 0;
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    do
    {
        ret = read(state->fildes, buf + read_so_far, len - read_so_far);
        if(ret <= 0)
            break;
        read_so_far += ret;
    } while(read_so_far < len);
    if(ret < 0)
        return(-1);
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    state->pos += read_so_far;
    return(read_so_far);
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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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{
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    struct darshan_fd_int_state *state = fd->state;
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    int ret;
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    unsigned int wrote_so_far = 0;
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    do
    {
        ret = write(state->fildes, buf + wrote_so_far, len - wrote_so_far);
        if(ret <= 0)
            break;
        wrote_so_far += ret;
    } while(wrote_so_far < len);
    if(ret < 0)
        return(-1);
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    state->pos += wrote_so_far;
    return(wrote_so_far);
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}

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static int darshan_log_dzinit(darshan_fd fd)
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{
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    struct darshan_fd_int_state *state = fd->state;
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    int ret;

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    /* initialize buffers for staging compressed data
     * to/from log file
     */
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    state->dz.buf = malloc(DARSHAN_DEF_COMP_BUF_SZ);
    if(state->dz.buf == NULL)
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        return(-1);
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    state->dz.size = 0;
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    state->dz.prev_reg_id = DARSHAN_HEADER_REGION_ID;
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    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)
            {
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                free(state->dz.buf);
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                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 ?? */
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            if(!(state->creat_flag))
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            {
                /* 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;
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                tmp_zstrm->next_out = state->dz.buf;
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            }
            if(ret != Z_OK)
            {
                free(tmp_zstrm);
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                free(state->dz.buf);
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                return(-1);
            }
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            state->dz.comp_dat = tmp_zstrm;
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            break;