darshan-stdio.c 20.9 KB
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/*
 * Copyright (C) 2015 University of Chicago.
 * See COPYRIGHT notice in top-level directory.
 *
 */

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/* TODO list (general) for this module:
 * - finish remaining function wrappers, see log format header
 * - implement reduction operator
 * - add stdio page to darshan-job-summary
 * - figure out what to do about posix module compatibility
 *   - remove stdio counters in POSIX or keep and set to -1?
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 *   - affected counters in posix module:
 *     - POSIX_FOPENS
 *     - POSIX_FREADS
 *     - POSIX_FWRITES
 *     - POSIX_FSEEKS
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 */

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/* catalog of stdio functions instrumented by this module
 *
 * functions for opening streams
 * --------------
 * FILE    *fdopen(int, const char *);                      DONE
 * FILE    *fopen(const char *, const char *);
 * FILE    *freopen(const char *, const char *, FILE *);
 *
 * functions for closing streams
 * --------------
 * int      fclose(FILE *);                                 DONE
 *
 * functions for flushing streams
 * --------------
 * int      fflush(FILE *);
 *
 * functions for reading data
 * --------------
 * int      fgetc(FILE *);
 * char    *fgets(char *, int, FILE *);
 * size_t   fread(void *, size_t, size_t, FILE *);          DONE
 * int      fscanf(FILE *, const char *, ...);
 * int      getc(FILE *);
 * int      getc_unlocked(FILE *);
 * int      getw(FILE *);
 *
 * functions for writing data
 * --------------
 * int      fprintf(FILE *, const char *, ...);
 * int      fputc(int, FILE *);
 * int      fputs(const char *, FILE *);
 * size_t   fwrite(const void *, size_t, size_t, FILE *);   DONE
 * int      putc(int, FILE *);
 * int      putc_unlocked(int, FILE *);
 * int      putw(int, FILE *);
 * int      vfprintf(FILE *, const char *, va_list);
 *
 * functions for changing file position
 * --------------
 * int      fseek(FILE *, long int, int);                   DONE
 * int      fseeko(FILE *, off_t, int);
 * int      fsetpos(FILE *, const fpos_t *);
 * void     rewind(FILE *);
 * int      ungetc(int, FILE *);
 */

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#define _XOPEN_SOURCE 500
#define _GNU_SOURCE

#include "darshan-runtime-config.h"
#include <stdio.h>
#include <unistd.h>
#include <sys/types.h>
#include <sys/stat.h>
#include <fcntl.h>
#include <stdarg.h>
#include <string.h>
#include <time.h>
#include <stdlib.h>
#include <errno.h>
#include <sys/uio.h>
#include <sys/mman.h>
#include <search.h>
#include <assert.h>
#include <libgen.h>
#include <pthread.h>

#include "uthash.h"
#include "utlist.h"

#include "darshan.h"
#include "darshan-dynamic.h"

DARSHAN_FORWARD_DECL(fopen, FILE*, (const char *path, const char *mode));
DARSHAN_FORWARD_DECL(fopen64, FILE*, (const char *path, const char *mode));
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DARSHAN_FORWARD_DECL(fclose, int, (FILE *fp));
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DARSHAN_FORWARD_DECL(fwrite, size_t, (const void *ptr, size_t size, size_t nmemb, FILE *stream));
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DARSHAN_FORWARD_DECL(fread, size_t, (void *ptr, size_t size, size_t nmemb, FILE *stream));
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DARSHAN_FORWARD_DECL(fseek, int, (FILE *stream, long offset, int whence));
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/* The stdio_file_runtime structure maintains necessary runtime metadata
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 * for the STDIO file record (darshan_stdio_record structure, defined in
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 * darshan-stdio-log-format.h) pointed to by 'file_record'. This metadata
 * assists with the instrumenting of specific statistics in the file record.
 * 'hlink' is a hash table link structure used to add/remove this record
 * from the hash table of STDIO file records for this process. 
 *
 * RATIONALE: the STDIO module needs to track some stateful, volatile 
 * information about each open file (like the current file offset, most recent 
 * access time, etc.) to aid in instrumentation, but this information can't be
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 * stored in the darshan_stdio_record struct because we don't want it to appear in
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 * the final darshan log file.  We therefore associate a stdio_file_runtime
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 * struct with each darshan_stdio_record struct in order to track this information.
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  *
 * NOTE: There is a one-to-one mapping of stdio_file_runtime structs to
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 * darshan_stdio_record structs.
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 *
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 * NOTE: The stdio_file_runtime struct contains a pointer to a darshan_stdio_record
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 * struct (see the *file_record member) rather than simply embedding an entire
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 * darshan_stdio_record struct.  This is done so that all of the darshan_stdio_record
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 * structs can be kept contiguous in memory as a single array to simplify
 * reduction, compression, and storage.
 */
struct stdio_file_runtime
{
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    struct darshan_stdio_record* file_record;
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    int64_t offset;
    double last_meta_end;
    double last_read_end;
    double last_write_end;
    UT_hash_handle hlink;
};

/* The stdio_file_runtime_ref structure is used to associate a STDIO
 * stream with an already existing STDIO file record. This is
 * necessary as many STDIO I/O functions take only an input stream,
 * but STDIO file records are indexed by their full file paths (i.e., darshan
 * record identifiers for STDIO files are created by hashing the file path).
 * In other words, this structure is necessary as it allows us to look up a
 * file record either by a pathname (stdio_file_runtime) or by STDIO stream 
 * (stdio_file_runtime_ref), depending on which parameters are
 * available. This structure includes another hash table link, since separate
 * hashes are maintained for stdio_file_runtime structures and stdio_file_runtime_ref
 * structures.
 *
 * RATIONALE: In theory the FILE* information could be included in the
 * stdio_file_runtime struct rather than in a separate structure here.  The
 * reason we don't do that is because the same file could be opened multiple
 * times by a given process with different stream pointers and thus
 * simulataneously referenced using different stream pointers.  This practice is
 * not common, but we must support it.
 *
 * NOTE: there are potentially multiple stdio_file_runtime_ref structures
 * referring to a single stdio_file_runtime structure.  Most of the time there is
 * only one, however.
 */
struct stdio_file_runtime_ref
{
    struct stdio_file_runtime* file;
    FILE* stream;
    UT_hash_handle hlink;
};

/* The stdio_runtime structure maintains necessary state for storing
 * STDIO file records and for coordinating with darshan-core at 
 * shutdown time.
 */
struct stdio_runtime
{
    struct stdio_file_runtime* file_runtime_array;
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    struct darshan_stdio_record* file_record_array;
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    int file_array_size;
    int file_array_ndx;
    struct stdio_file_runtime* file_hash;
    struct stdio_file_runtime_ref* stream_hash;
};

static struct stdio_runtime *stdio_runtime = NULL;
static pthread_mutex_t stdio_runtime_mutex = PTHREAD_RECURSIVE_MUTEX_INITIALIZER_NP;
static int instrumentation_disabled = 0;
static int darshan_mem_alignment = 1;
static int my_rank = -1;

static void stdio_runtime_initialize(void);
static struct stdio_file_runtime* stdio_file_by_name(const char *name);
static struct stdio_file_runtime* stdio_file_by_name_setstream(const char* name, FILE *stream);
static struct stdio_file_runtime* stdio_file_by_stream(FILE* stream);
static void stdio_file_close_stream(FILE *stream);

static void stdio_begin_shutdown(void);
static void stdio_get_output_data(MPI_Comm mod_comm, darshan_record_id *shared_recs,
    int shared_rec_count, void **stdio_buf, int *stdio_buf_sz);
static void stdio_shutdown(void);

#define STDIO_LOCK() pthread_mutex_lock(&stdio_runtime_mutex)
#define STDIO_UNLOCK() pthread_mutex_unlock(&stdio_runtime_mutex)

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#define STDIO_RECORD_OPEN(__ret, __path, __tm1, __tm2) do { \
    struct stdio_file_runtime* file; \
    char* exclude; \
    int tmp_index = 0; \
    if(__ret == NULL) break; \
    while((exclude = darshan_path_exclusions[tmp_index])) { \
        if(!(strncmp(exclude, __path, strlen(exclude)))) \
            break; \
        tmp_index++; \
    } \
    if(exclude) break; \
    file = stdio_file_by_name_setstream(__path, __ret); \
    if(!file) break; \
    file->offset = 0; \
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    file->file_record->counters[STDIO_OPENS] += 1; \
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    if(file->file_record->fcounters[STDIO_F_OPEN_START_TIMESTAMP] == 0 || \
     file->file_record->fcounters[STDIO_F_OPEN_START_TIMESTAMP] > __tm1) \
        file->file_record->fcounters[STDIO_F_OPEN_START_TIMESTAMP] = __tm1; \
    file->file_record->fcounters[STDIO_F_OPEN_END_TIMESTAMP] = __tm2; \
    DARSHAN_TIMER_INC_NO_OVERLAP(file->file_record->fcounters[STDIO_F_META_TIME], __tm1, __tm2, file->last_meta_end); \
} while(0)


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#define STDIO_RECORD_READ(__fp, __bytes,  __tm1, __tm2) do{ \
    int64_t this_offset; \
    struct stdio_file_runtime* file; \
    file = stdio_file_by_stream(__fp); \
    if(!file) break; \
    this_offset = file->offset; \
    file->offset = this_offset + __bytes; \
    if(file->file_record->counters[STDIO_MAX_BYTE_READ] < (this_offset + __bytes - 1)) \
        file->file_record->counters[STDIO_MAX_BYTE_READ] = (this_offset + __bytes - 1); \
    file->file_record->counters[STDIO_BYTES_READ] += __bytes; \
    file->file_record->counters[STDIO_READS] += 1; \
    if(file->file_record->fcounters[STDIO_F_READ_START_TIMESTAMP] == 0 || \
     file->file_record->fcounters[STDIO_F_READ_START_TIMESTAMP] > __tm1) \
        file->file_record->fcounters[STDIO_F_READ_START_TIMESTAMP] = __tm1; \
    file->file_record->fcounters[STDIO_F_READ_END_TIMESTAMP] = __tm2; \
    DARSHAN_TIMER_INC_NO_OVERLAP(file->file_record->fcounters[STDIO_F_READ_TIME], __tm1, __tm2, file->last_write_end); \
} while(0)

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#define STDIO_RECORD_WRITE(__fp, __bytes,  __tm1, __tm2) do{ \
    int64_t this_offset; \
    struct stdio_file_runtime* file; \
    file = stdio_file_by_stream(__fp); \
    if(!file) break; \
    this_offset = file->offset; \
    file->offset = this_offset + __bytes; \
    if(file->file_record->counters[STDIO_MAX_BYTE_WRITTEN] < (this_offset + __bytes - 1)) \
        file->file_record->counters[STDIO_MAX_BYTE_WRITTEN] = (this_offset + __bytes - 1); \
    file->file_record->counters[STDIO_BYTES_WRITTEN] += __bytes; \
    file->file_record->counters[STDIO_WRITES] += 1; \
    if(file->file_record->fcounters[STDIO_F_WRITE_START_TIMESTAMP] == 0 || \
     file->file_record->fcounters[STDIO_F_WRITE_START_TIMESTAMP] > __tm1) \
        file->file_record->fcounters[STDIO_F_WRITE_START_TIMESTAMP] = __tm1; \
    file->file_record->fcounters[STDIO_F_WRITE_END_TIMESTAMP] = __tm2; \
    DARSHAN_TIMER_INC_NO_OVERLAP(file->file_record->fcounters[STDIO_F_WRITE_TIME], __tm1, __tm2, file->last_write_end); \
} while(0)
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FILE* DARSHAN_DECL(fopen)(const char *path, const char *mode)
{
    FILE* ret;
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    double tm1, tm2;
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    MAP_OR_FAIL(fopen);

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

    STDIO_LOCK();
    stdio_runtime_initialize();
    STDIO_RECORD_OPEN(ret, path, tm1, tm2);
    STDIO_UNLOCK();
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    return(ret);
}

FILE* DARSHAN_DECL(fopen64)(const char *path, const char *mode)
{
    FILE* ret;
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    double tm1, tm2;
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    MAP_OR_FAIL(fopen);
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    tm1 = darshan_core_wtime();
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    ret = __real_fopen64(path, mode);
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    tm2 = darshan_core_wtime();

    STDIO_LOCK();
    stdio_runtime_initialize();
    STDIO_RECORD_OPEN(ret, path, tm1, tm2);
    STDIO_UNLOCK();
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    return(ret);
}

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int DARSHAN_DECL(fclose)(FILE *fp)
{
    struct stdio_file_runtime* file;
    double tm1, tm2;
    int ret;

    MAP_OR_FAIL(fclose);

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

    STDIO_LOCK();
    stdio_runtime_initialize();
    file = stdio_file_by_stream(fp);
    if(file)
    {
        if(file->file_record->fcounters[STDIO_F_CLOSE_START_TIMESTAMP] == 0 ||
         file->file_record->fcounters[STDIO_F_CLOSE_START_TIMESTAMP] > tm1)
           file->file_record->fcounters[STDIO_F_CLOSE_START_TIMESTAMP] = tm1;
        file->file_record->fcounters[STDIO_F_CLOSE_END_TIMESTAMP] = tm2;
        DARSHAN_TIMER_INC_NO_OVERLAP(
            file->file_record->fcounters[STDIO_F_META_TIME],
            tm1, tm2, file->last_meta_end);
        stdio_file_close_stream(fp);
    }
    STDIO_UNLOCK();

    return(ret);
}

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

    MAP_OR_FAIL(fwrite);

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

    STDIO_LOCK();
    stdio_runtime_initialize();
    if(ret > 0)
        STDIO_RECORD_WRITE(stream, size*ret, tm1, tm2);
    STDIO_UNLOCK();

    return(ret);
}

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size_t DARSHAN_DECL(fread)(void *ptr, size_t size, size_t nmemb, FILE *stream)
{
    size_t ret;
    double tm1, tm2;

    MAP_OR_FAIL(fread);

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

    STDIO_LOCK();
    stdio_runtime_initialize();
    if(ret > 0)
        STDIO_RECORD_READ(stream, size*ret, tm1, tm2);
    STDIO_UNLOCK();

    return(ret);
}

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

    MAP_OR_FAIL(fseek);

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

    if(ret >= 0)
    {
        STDIO_LOCK();
        stdio_runtime_initialize();
        file = stdio_file_by_stream(stream);
        if(file)
        {
            file->offset = ftell(stream);
            DARSHAN_TIMER_INC_NO_OVERLAP(
                file->file_record->fcounters[STDIO_F_META_TIME],
                tm1, tm2, file->last_meta_end);
            file->file_record->counters[STDIO_SEEKS] += 1;
        }
        STDIO_UNLOCK();
    }

    return(ret);
}

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/**********************************************************
 * Internal functions for manipulating STDIO module state *
 **********************************************************/

/* initialize internal STDIO module data structures and register with darshan-core */
static void stdio_runtime_initialize()
{
    int mem_limit;
    struct darshan_module_funcs stdio_mod_fns =
    {
        .begin_shutdown = &stdio_begin_shutdown,
        .get_output_data = &stdio_get_output_data,
        .shutdown = &stdio_shutdown
    };

    /* don't do anything if already initialized or instrumenation is disabled */
    if(stdio_runtime || instrumentation_disabled)
        return;

    /* register the stdio module with darshan core */
    darshan_core_register_module(
        DARSHAN_STDIO_MOD,
        &stdio_mod_fns,
        &my_rank,
        &mem_limit,
        &darshan_mem_alignment);

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

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

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

    /* allocate array of runtime file records */
    stdio_runtime->file_runtime_array = malloc(stdio_runtime->file_array_size *
                                               sizeof(struct stdio_file_runtime));
    stdio_runtime->file_record_array = malloc(stdio_runtime->file_array_size *
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                                              sizeof(struct darshan_stdio_record));
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    if(!stdio_runtime->file_runtime_array || !stdio_runtime->file_record_array)
    {
        stdio_runtime->file_array_size = 0;
        return;
    }
    memset(stdio_runtime->file_runtime_array, 0, stdio_runtime->file_array_size *
           sizeof(struct stdio_file_runtime));
    memset(stdio_runtime->file_record_array, 0, stdio_runtime->file_array_size *
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           sizeof(struct darshan_stdio_record));
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    return;
}

/* get a STDIO file record for the given file path */
static struct stdio_file_runtime* stdio_file_by_name(const char *name)
{
    struct stdio_file_runtime *file = NULL;
    char *newname = NULL;
    darshan_record_id file_id;
    int file_alignment;
    int limit_flag;

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

    newname = darshan_clean_file_path(name);
    if(!newname)
        newname = (char*)name;

    limit_flag = (stdio_runtime->file_array_ndx >= stdio_runtime->file_array_size);

    /* get a unique id for this file from darshan core */
    darshan_core_register_record(
        (void*)newname,
        strlen(newname),
        DARSHAN_STDIO_MOD,
        1,
        limit_flag,
        &file_id,
        &file_alignment);

    /* the file record id is set to 0 if no memory is available for tracking
     * new records -- just fall through and ignore this record
     */
    if(file_id == 0)
    {
        if(newname != name)
            free(newname);
        return(NULL);
    }

    /* search the hash table for this file record, and return if found */
    HASH_FIND(hlink, stdio_runtime->file_hash, &file_id, sizeof(darshan_record_id), file);
    if(file)
    {
        if(newname != name)
            free(newname);
        return(file);
    }

    /* no existing record, assign a new file record from the global array */
    file = &(stdio_runtime->file_runtime_array[stdio_runtime->file_array_ndx]);
    file->file_record = &(stdio_runtime->file_record_array[stdio_runtime->file_array_ndx]);
    file->file_record->f_id = file_id;
    file->file_record->rank = my_rank;

    /* add new record to file hash table */
    HASH_ADD(hlink, stdio_runtime->file_hash, file_record->f_id, sizeof(darshan_record_id), file);
    stdio_runtime->file_array_ndx++;

    if(newname != name)
        free(newname);
    return(file);
}

/* get a STDIO file record for the given file path, and also create a
 * reference structure using the returned stream
 */
static struct stdio_file_runtime* stdio_file_by_name_setstream(const char* name, FILE *stream)
{
    struct stdio_file_runtime* file;
    struct stdio_file_runtime_ref* ref;

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

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

    if(!file)
        return(NULL);

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

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

    ref->file = file;
    ref->stream = stream;    
    HASH_ADD(hlink, stdio_runtime->stream_hash, stream, sizeof(FILE*), ref);

    return(file);
}

/* get a STDIO file record for the given stream */
static struct stdio_file_runtime* stdio_file_by_stream(FILE *stream)
{
    struct stdio_file_runtime_ref* ref;

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

    /* search hash table for existing file ref for this stream */
    HASH_FIND(hlink, stdio_runtime->stream_hash, &stream, sizeof(FILE*), ref);
    if(ref)
        return(ref->file);

    return(NULL);
}

/* free up reference data structures for the given stream */
static void stdio_file_close_stream(FILE *stream)
{
    struct stdio_file_runtime_ref* ref;

    if(!stdio_runtime || instrumentation_disabled)
        return;

    /* search hash table for this stream */
    HASH_FIND(hlink, stdio_runtime->stream_hash, &stream, sizeof(FILE*), ref);
    if(ref)
    {
        /* we have a reference, delete it */
        HASH_DELETE(hlink, stdio_runtime->stream_hash, ref);
        free(ref);
    }

    return;
}

/************************************************************************
 * Functions exported by this module for coordinating with darshan-core *
 ************************************************************************/

static void stdio_begin_shutdown()
{
    assert(stdio_runtime);

    STDIO_LOCK();
    /* disable further instrumentation while Darshan shuts down */
    instrumentation_disabled = 1;
    STDIO_UNLOCK();

    return;
}

static void stdio_get_output_data(
    MPI_Comm mod_comm,
    darshan_record_id *shared_recs,
    int shared_rec_count,
    void **stdio_buf,
    int *stdio_buf_sz)
{
    assert(stdio_runtime);

    *stdio_buf = (void *)(stdio_runtime->file_record_array);
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    *stdio_buf_sz = stdio_runtime->file_array_ndx * sizeof(struct darshan_stdio_record);
624 625 626 627 628 629 630 631 632 633 634 635 636 637 638 639 640 641 642 643 644 645 646 647 648 649 650 651 652 653 654 655 656 657 658

    return;
}

static void stdio_shutdown()
{
    struct stdio_file_runtime_ref *ref, *tmp;

    assert(stdio_runtime);

    HASH_ITER(hlink, stdio_runtime->stream_hash, ref, tmp)
    {
        HASH_DELETE(hlink, stdio_runtime->stream_hash, ref);
        free(ref);
    }

    HASH_CLEAR(hlink, stdio_runtime->file_hash); /* these entries are freed all at once below */

    free(stdio_runtime->file_runtime_array);
    free(stdio_runtime->file_record_array);
    free(stdio_runtime);
    stdio_runtime = NULL;
    instrumentation_disabled = 0;
    
    return;
}

/*
 * Local variables:
 *  c-indent-level: 4
 *  c-basic-offset: 4
 * End:
 *
 * vim: ts=8 sts=4 sw=4 expandtab
 */