darshan-logutils.c 45.8 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
{
    /* (libz/bzip2) stream data structure for managing
     * compression and decompression state */
    void *strm;
    /* buffer for staging compressed data to/from log file */
    unsigned char *buf;
    /* size of staging buffer */
    int size;
    /* for reading logs, flag indicating end of log file region */
    int eor;
    /* the region we last tried reading/writing */
    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;
    /* compression type used on log file (libz or bzip2) */
    enum darshan_comp_type comp_type;
    /* 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;

    /* compression/decompression state */
    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(struct darshan_fd_int_state *state);
static void darshan_log_dzdestroy(struct darshan_fd_int_state *state);
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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);
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);

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/* each module's implementation of the darshan logutil functions */
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#define X(a, b, c, d) d,
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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->state);
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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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    /* 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;
    tmp_fd->state->comp_type = comp_type;
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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->state);
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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);
    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 */
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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));
    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;
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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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    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_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)
{
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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 path_len;
    int wrote;
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    assert(state);

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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);
656

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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))
        {
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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,
691
    void *mod_buf, int mod_buf_sz)
692
{
693
    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)
699
    {
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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)
710
    {
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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);
    }

717
    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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Shane Snyder committed
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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,
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    void *mod_buf, int mod_buf_sz, int ver)
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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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        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);
    }

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    /* set the version number for this module's data */
    fd->mod_ver[mod_id] = ver;

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    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)
770
{
771
    struct darshan_fd_int_state *state = fd->state;
772 773
    int ret;

774 775 776 777
    assert(state);

    /* if the file was created for writing */
    if(state->creat_flag)
778 779
    {
        /* flush the last region of the log to file */
780
        switch(state->comp_type)
781 782
        {
            case DARSHAN_ZLIB_COMP:
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                ret = darshan_log_libz_flush(fd, state->dz.prev_reg_id);
784 785
                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 */
800
        if(state->err != -1)
801 802 803
        {
            ret = darshan_log_putheader(fd);
            if(ret < 0)
804
                state->err = -1;
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        }
    }

808
    close(state->fildes);
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    /* remove output log file if error writing to it */
811
    if((state->creat_flag) && (state->err == -1))
812 813
    {
        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(state);
    if(state->exe_mnt_data)
        free(state->exe_mnt_data);
    free(state);
822
    free(fd);
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    return;
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}

827
/* **************************************************** */
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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)
{
836
    struct darshan_fd_int_state *state = fd->state;
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    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);
        }
    }

889
    /* set some fd fields based on what's stored in the header */
890
    state->comp_type = header.comp_type;
891
    fd->partial_flag = header.partial_flag;
892
    memcpy(fd->mod_ver, header.mod_ver, DARSHAN_MAX_MODS * sizeof(uint32_t));
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    /* 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)
{
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    struct darshan_fd_int_state *state = fd->state;
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    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 = state->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));
    if(ret != sizeof(header))
    {
        fprintf(stderr, "Error: failed to write Darshan log file header.\n");
        return(-1);
    }

    return(0);
}

941 942 943 944
/* return 0 on successful seek to offset, -1 on failure.
 */
static int darshan_log_seek(darshan_fd fd, off_t offset)
{
945
    struct darshan_fd_int_state *state = fd->state;
946
    off_t ret_off;
947

948
    if(state->pos == offset)
949 950
        return(0);

951
    ret_off = lseek(state->fildes, offset, SEEK_SET);
952
    if(ret_off == offset)
953
    {
954
        state->pos = offset;
955
        return(0);
956 957 958 959 960
    }

    return(-1);
}

961
/* return amount read on success, 0 on EOF, -1 on failure.
962
 */
963
static int darshan_log_read(darshan_fd fd, void* buf, int len)
964
{
965
    struct darshan_fd_int_state *state = fd->state;
966 967
    int ret;

968
    /* read data from the log file using the given map */
969
    ret = read(state->fildes, buf, len);
970
    if(ret > 0)
971
        state->pos += ret;
972

973
    return(ret);
974 975
}

976
/* return amount written on success, -1 on failure.
977
 */
978
static int darshan_log_write(darshan_fd fd, void* buf, int len)
979
{
980
    struct darshan_fd_int_state *state = fd->state;
981 982
    int ret;

983
    ret = write(state->fildes, buf, len);
984
    if(ret > 0)
985
        state->pos += ret;
986 987 988 989

    return(ret);
}

990
static int darshan_log_dzinit(struct darshan_fd_int_state *state)
991 992 993
{
    int ret;

994
    /* initialize buffers for staging compressed data to/from log file */
995 996
    state->dz.buf = malloc(DARSHAN_DEF_COMP_BUF_SZ);
    if(state->dz.buf == NULL)
997 998
        return(-1);

999
    state->dz.prev_reg_id = DARSHAN_HEADER_REGION_ID;
1000

1001
    switch(state->comp_type)
1002 1003
    {
        case DARSHAN_ZLIB_COMP:
1004 1005 1006 1007
        {
            z_stream *tmp_zstrm = malloc(sizeof(*tmp_zstrm));
            if(!tmp_zstrm)
            {
1008
                free(state->dz.buf);
1009 1010 1011 1012 1013 1014 1015 1016 1017
                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 ?? */
1018
            if(!(state->creat_flag))
1019 1020 1021 1022 1023 1024 1025 1026 1027
            {
                /* 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;
1028
                tmp_zstrm->next_out = state->dz.buf;
1029 1030 1031 1032
            }
            if(ret != Z_OK)
            {
                free(tmp_zstrm);
1033
                free(state->dz.buf);
1034 1035
                return(-1);
            }
1036
            state->dz.strm = tmp_zstrm;
1037
            break;
1038
        }
1039 1040 1041 1042 1043 1044
#ifdef HAVE_LIBBZ2
        case DARSHAN_BZIP2_COMP:
        {
            bz_stream *tmp_bzstrm = malloc(sizeof(*tmp_bzstrm));
            if(!tmp_bzstrm)
            {
1045
                free(state->dz.buf);
1046 1047 1048 1049 1050 1051 1052 1053
                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;

1054
            if(state->creat_flag)
1055 1056 1057 1058 1059 1060 1061 1062 1063
            {
                /* 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;
1064
                tmp_bzstrm->next_out = (char *)state->dz.buf;
1065 1066 1067 1068
            }
            if(ret != BZ_OK)
            {
                free(tmp_bzstrm);
1069
                free(state->dz.buf);
1070 1071
                return(-1);
            }
1072
            state->dz.strm = tmp_bzstrm;
1073 1074 1075
            break;
        }
#endif
1076 1077 1078 1079 1080 1081 1082 1083
        default:
            fprintf(stderr, "Error: invalid compression type.\n");
            return(-1);
    }

    return(0);
}

1084
static void darshan_log_dzdestroy(struct darshan_fd_int_state *state)
1085
{
1086
    switch(state->comp_type)
1087 1088
    {
        case DARSHAN_ZLIB_COMP:
1089 1090
            if(!(state->creat_flag))
                inflateEnd(state->dz.strm);
1091
            else
1092 1093
                deflateEnd(state->dz.strm);
            free(state->dz.strm);
1094
            break;
1095 1096
#ifdef HAVE_LIBBZ2
        case DARSHAN_BZIP2_COMP:
1097 1098
            if(!(state->creat_flag))
                BZ2_bzDecompressEnd(state->dz.strm);
1099
            else
1100 1101
                BZ2_bzCompressEnd(state->dz.strm);
            free(state->dz.strm);
1102 1103
            break;
#endif
1104 1105 1106 1107
        default:
            fprintf(stderr, "Error: invalid compression type.\n");
    }

1108
    free(state->dz.buf);
1109 1110 1111 1112 1113
    return;
}

static int darshan_log_dzread(darshan_fd fd, int region_id, void *buf, int len)
{
1114
    struct darshan_fd_int_state *state = fd->state;
1115 1116
    int ret;

1117
    switch(state->comp_type)
1118 1119 1120
    {
        case DARSHAN_ZLIB_COMP:
            ret = darshan_log_libz_read(fd, region_id, buf, len);
1121
            break;
1122 1123 1124 1125 1126
#ifdef HAVE_LIBBZ2
        case DARSHAN_BZIP2_COMP:
            ret = darshan_log_bzip2_read(fd, region_id, buf, len);
            break;
#endif
1127
        default:
1128
            fprintf(stderr, "Error: invalid compression type.\n");
1129 1130 1131 1132 1133 1134
            return(-1);
    }

    return(ret);
}

1135
static int darshan_log_dzwrite(darshan_fd fd, int region_id, void *buf, int len)
1136
{
1137
    struct darshan_fd_int_state *state = fd->state;
1138 1139
    int ret;

1140
    switch(state->comp_type)
1141 1142
    {
        case DARSHAN_ZLIB_COMP:
1143
            ret = darshan_log_libz_write(fd, region_id, buf, len);
1144
            break;
1145 1146 1147 1148 1149
#ifdef HAVE_LIBBZ2
        case DARSHAN_BZIP2_COMP:
            ret = darshan_log_bzip2_write(fd, region_id, buf, len);
            break;
#endif
1150
        default:
1151
            fprintf(stderr, "Error: invalid compression type.\n");
1152 1153 1154 1155 1156 1157
            return(-1);
    }

    return(ret);
}

1158
static int darshan_log_libz_read(darshan_fd fd, int region_id, void *buf, int len)
1159
{
1160
    struct darshan_fd_int_state *state = fd->state;
1161
    int ret;
1162 1163 1164
    int total_bytes = 0;
    int tmp_out_bytes;
    struct darshan_log_map map;
1165
    z_stream *z_strmp = (z_stream *)state->dz.strm;
1166

1167
    assert(z_strmp);
1168

1169
    /* if new log region, we reload buffers and clear eor flag */
1170
    if(region_id != state->dz.prev_reg_id)
1171
    {
1172
        z_strmp->avail_in = 0;
1173 1174
        state->dz.eor = 0;
        state->dz.prev_reg_id = region_id;
1175 1176
    }

1177 1178 1179 1180 1181 1182 1183 1184 1185 1186 1187 1188 1189 1190
    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)
1191
    {
1192 1193
        /* check if we need more compressed data */
        if(z_strmp->avail_in == 0)
1194
        {
1195 1196
            /* if the eor flag is set, clear it and return -- future
             * reads of this log region will restart at the beginning
1197
             */
1198
            if(state->dz.eor)
1199
            {
1200
                state->dz.eor = 0;
1201 1202 1203 1204 1205 1206 1207
                break;
            }

            /* read more data from input file */
            ret = darshan_log_dzload(fd, map);
            if(ret < 0)
                return(-1);
1208
            assert(state->dz.size > 0);
1209

1210 1211
            z_strmp->avail_in = state->dz.size;
            z_strmp->next_in = state->dz.buf;
1212 1213
        }

1214 1215 1216
        tmp_out_bytes = z_strmp->total_out;
        ret = inflate(z_strmp, Z_NO_FLUSH);
        if(ret != Z_OK && ret != Z_STREAM_END)
1217
        {
1218
            fprintf(stderr, "Error: unable to inflate darshan log data.\n");
1219 1220
            return(-1);
        }
1221
        total_bytes += (z_strmp->total_out - tmp_out_bytes);
1222

1223 1224 1225
        /* reset the decompression if we encountered end of stream */
        if(ret == Z_STREAM_END)
            inflateReset(z_strmp);
1226 1227
    }

1228
    return(total_bytes);
1229 1230
}

1231
static int darshan_log_libz_write(darshan_fd fd, int region_id, void *buf, int len)
1232
{
1233
    struct darshan_fd_int_state *state = fd->state;
1234
    int ret;
1235 1236 1237 1238
    int total_bytes = 0;
    int tmp_in_bytes;
    int tmp_out_bytes;
    struct darshan_log_map *map_p;
1239
    z_stream *z_strmp = (z_stream *)state->dz.strm;
1240

1241
    assert(z_strmp);
1242

1243
    /* if new log region, finish prev region's zstream and flush to log file */
1244
    if(region_id != state->dz.prev_reg_id)
1245
    {
1246 1247 1248
        /* error out if the region we are writing to precedes the previous
         * region we wrote -- we shouldn't be moving backwards in the log
         */
1249
        if(region_id < state->dz.prev_reg_id)
1250 1251
            return(-1);

1252
        if(state->dz.prev_reg_id != DARSHAN_HEADER_REGION_ID)
1253
        {
1254
            ret = darshan_log_libz_flush(fd, state->dz.prev_reg_id);
1255 1256 1257 1258
            if(ret < 0)
                return(-1);
        }

1259
        state->dz.prev_reg_id = region_id;
1260 1261
    }

1262 1263 1264 1265 1266 1267 1268 1269 1270 1271 1272 1273
    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)
1274
    {
1275 1276 1277
        /* if we are out of output, flush to log file */
        if(z_strmp->avail_out == 0)
        {
1278
            assert(state->dz.size == DARSHAN_DEF_COMP_BUF_SZ);
1279 1280 1281 1282 1283 1284 </