darshan-posix.c 61.5 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 _XOPEN_SOURCE 500
#define _GNU_SOURCE

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#include "darshan-runtime-config.h"
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#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>
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#include <libgen.h>
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#include <aio.h>
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#include <pthread.h>
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#include "uthash.h"
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#include "utlist.h"

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#include "darshan.h"
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#include "darshan-dynamic.h"
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#ifndef HAVE_OFF64_T
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typedef int64_t off64_t;
#endif
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#ifndef HAVE_AIOCB64
#define aiocb64 aiocb
#endif
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DARSHAN_FORWARD_DECL(open, int, (const char *path, int flags, ...));
DARSHAN_FORWARD_DECL(open64, int, (const char *path, int flags, ...));
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DARSHAN_FORWARD_DECL(creat, int, (const char* path, mode_t mode));
DARSHAN_FORWARD_DECL(creat64, int, (const char* path, mode_t mode));
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DARSHAN_FORWARD_DECL(mkstemp, int, (char *template));
DARSHAN_FORWARD_DECL(mkostemp, int, (char *template, int flags));
DARSHAN_FORWARD_DECL(mkstemps, int, (char *template, int suffixlen));
DARSHAN_FORWARD_DECL(mkostemps, int, (char *template, int suffixlen, int flags));
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DARSHAN_FORWARD_DECL(read, ssize_t, (int fd, void *buf, size_t count));
DARSHAN_FORWARD_DECL(write, ssize_t, (int fd, const void *buf, size_t count));
DARSHAN_FORWARD_DECL(pread, ssize_t, (int fd, void *buf, size_t count, off_t offset));
DARSHAN_FORWARD_DECL(pwrite, ssize_t, (int fd, const void *buf, size_t count, off_t offset));
DARSHAN_FORWARD_DECL(pread64, ssize_t, (int fd, void *buf, size_t count, off64_t offset));
DARSHAN_FORWARD_DECL(pwrite64, ssize_t, (int fd, const void *buf, size_t count, off64_t offset));
DARSHAN_FORWARD_DECL(readv, ssize_t, (int fd, const struct iovec *iov, int iovcnt));
DARSHAN_FORWARD_DECL(writev, ssize_t, (int fd, const struct iovec *iov, int iovcnt));
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DARSHAN_FORWARD_DECL(lseek, off_t, (int fd, off_t offset, int whence));
DARSHAN_FORWARD_DECL(lseek64, off64_t, (int fd, off64_t offset, int whence));
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DARSHAN_FORWARD_DECL(__xstat, int, (int vers, const char* path, struct stat *buf));
DARSHAN_FORWARD_DECL(__xstat64, int, (int vers, const char* path, struct stat64 *buf));
DARSHAN_FORWARD_DECL(__lxstat, int, (int vers, const char* path, struct stat *buf));
DARSHAN_FORWARD_DECL(__lxstat64, int, (int vers, const char* path, struct stat64 *buf));
DARSHAN_FORWARD_DECL(__fxstat, int, (int vers, int fd, struct stat *buf));
DARSHAN_FORWARD_DECL(__fxstat64, int, (int vers, int fd, struct stat64 *buf));
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DARSHAN_FORWARD_DECL(mmap, void*, (void *addr, size_t length, int prot, int flags, int fd, off_t offset));
DARSHAN_FORWARD_DECL(mmap64, void*, (void *addr, size_t length, int prot, int flags, int fd, off64_t offset));
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DARSHAN_FORWARD_DECL(fsync, int, (int fd));
DARSHAN_FORWARD_DECL(fdatasync, int, (int fd));
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DARSHAN_FORWARD_DECL(close, int, (int fd));
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DARSHAN_FORWARD_DECL(aio_read, int, (struct aiocb *aiocbp));
DARSHAN_FORWARD_DECL(aio_write, int, (struct aiocb *aiocbp));
DARSHAN_FORWARD_DECL(aio_read64, int, (struct aiocb64 *aiocbp));
DARSHAN_FORWARD_DECL(aio_write64, int, (struct aiocb64 *aiocbp));
DARSHAN_FORWARD_DECL(aio_return, ssize_t, (struct aiocb *aiocbp));
DARSHAN_FORWARD_DECL(aio_return64, ssize_t, (struct aiocb64 *aiocbp));
DARSHAN_FORWARD_DECL(lio_listio, int, (int mode, struct aiocb *const aiocb_list[], int nitems, struct sigevent *sevp));
DARSHAN_FORWARD_DECL(lio_listio64, int, (int mode, struct aiocb64 *const aiocb_list[], int nitems, struct sigevent *sevp));
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/* struct to track information about aio operations in flight */
struct posix_aio_tracker
{
    double tm1;
    void *aiocbp;
    struct posix_aio_tracker* next;
};

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/* The posix_file_runtime structure maintains necessary runtime metadata
 * for the POSIX file record (darshan_posix_file structure, defined in
 * darshan-posix-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 POSIX file records for this process. 
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 *
 * RATIONALE: the POSIX 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
 * stored in the darshan_posix_file struct because we don't want it to appear in
 * the final darshan log file.  We therefore associate a posix_file_runtime
 * struct with each darshan_posix_file struct in order to track this information.
  *
 * NOTE: There is a one-to-one mapping of posix_file_runtime structs to
 * darshan_posix_file structs.
 *
 * NOTE: The posix_file_runtime struct contains a pointer to a darshan_posix_file
 * struct (see the *file_record member) rather than simply embedding an entire
 * darshan_posix_file struct.  This is done so that all of the darshan_posix_file
 * structs can be kept contiguous in memory as a single array to simplify
 * reduction, compression, and storage.
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 */
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struct posix_file_runtime
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{
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    struct darshan_posix_file* file_record;
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    int64_t offset;
    int64_t last_byte_read;
    int64_t last_byte_written;
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    enum darshan_io_type last_io_type;
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    double last_meta_end;
    double last_read_end;
    double last_write_end;
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    void* access_root;
    int access_count;
    void* stride_root;
    int stride_count;
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    struct posix_aio_tracker* aio_list;
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    UT_hash_handle hlink;
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};
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/* The posix_file_runtime_ref structure is used to associate a POSIX
 * file descriptor with an already existing POSIX file record. This is
 * necessary as many POSIX I/O functions take only an input file descriptor,
 * but POSIX file records are indexed by their full file paths (i.e., darshan
 * record identifiers for POSIX 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 (posix_file_runtime) or by POSIX file
 * descriptor (posix_file_runtime_ref), depending on which parameters are
 * available. This structure includes another hash table link, since separate
 * hashes are maintained for posix_file_runtime structures and posix_file_runtime_ref
 * structures.
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 *
 * RATIONALE: In theory the fd information could be included in the
 * posix_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 file descriptors and thus
 * simulataneously referenced using different file descriptors.  This practice is
 * not common, but we must support it.
 *
 * NOTE: there are potentially multiple posix_file_runtime_ref structures
 * referring to a single posix_file_runtime structure.  Most of the time there is
 * only one, however.
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 */
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struct posix_file_runtime_ref
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{
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    struct posix_file_runtime* file;
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    int fd;
    UT_hash_handle hlink;
};

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/* The posix_runtime structure maintains necessary state for storing
 * POSIX file records and for coordinating with darshan-core at 
 * shutdown time.
 */
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struct posix_runtime
{
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    struct posix_file_runtime* file_runtime_array;
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    struct darshan_posix_file* file_record_array;
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    int file_array_size;
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    int file_array_ndx;
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    struct posix_file_runtime* file_hash;
    struct posix_file_runtime_ref* fd_hash;
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};

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static struct posix_runtime *posix_runtime = NULL;
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static pthread_mutex_t posix_runtime_mutex = PTHREAD_RECURSIVE_MUTEX_INITIALIZER_NP;
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static int instrumentation_disabled = 0;
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static int my_rank = -1;
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static int darshan_mem_alignment = 1;
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static void posix_runtime_initialize(void);
static struct posix_file_runtime* posix_file_by_name(const char *name);
static struct posix_file_runtime* posix_file_by_name_setfd(const char* name, int fd);
static struct posix_file_runtime* posix_file_by_fd(int fd);
static void posix_file_close_fd(int fd);
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static void posix_aio_tracker_add(int fd, void *aiocbp);
static struct posix_aio_tracker* posix_aio_tracker_del(int fd, void *aiocbp);
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static int posix_record_compare(const void* a, const void* b);
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static void posix_record_reduction_op(void* infile_v, void* inoutfile_v,
    int *len, MPI_Datatype *datatype);
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static void posix_shared_record_variance(MPI_Comm mod_comm,
    struct darshan_posix_file *inrec_array, struct darshan_posix_file *outrec_array,
    int shared_rec_count);
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static void posix_begin_shutdown(void);
static void posix_get_output_data(MPI_Comm mod_comm, darshan_record_id *shared_recs,
    int shared_rec_count, void **posix_buf, int *posix_buf_sz);
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static void posix_shutdown(void);

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#define POSIX_LOCK() pthread_mutex_lock(&posix_runtime_mutex)
#define POSIX_UNLOCK() pthread_mutex_unlock(&posix_runtime_mutex)
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#define POSIX_RECORD_OPEN(__ret, __path, __mode, __tm1, __tm2) do { \
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    struct posix_file_runtime* file; \
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    char* exclude; \
    int tmp_index = 0; \
    if(__ret < 0) break; \
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    while((exclude = darshan_path_exclusions[tmp_index])) { \
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        if(!(strncmp(exclude, __path, strlen(exclude)))) \
            break; \
        tmp_index++; \
    } \
    if(exclude) break; \
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    file = posix_file_by_name_setfd(__path, __ret); \
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    if(!file) break; \
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    if(__mode) \
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        file->file_record->counters[POSIX_MODE] = __mode; \
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    file->offset = 0; \
    file->last_byte_written = 0; \
    file->last_byte_read = 0; \
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    file->file_record->counters[POSIX_OPENS] += 1; \
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    if(file->file_record->fcounters[POSIX_F_OPEN_TIMESTAMP] == 0 || \
     file->file_record->fcounters[POSIX_F_OPEN_TIMESTAMP] > __tm1) \
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        file->file_record->fcounters[POSIX_F_OPEN_TIMESTAMP] = __tm1; \
    DARSHAN_TIMER_INC_NO_OVERLAP(file->file_record->fcounters[POSIX_F_META_TIME], __tm1, __tm2, file->last_meta_end); \
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} while(0)

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#define POSIX_RECORD_READ(__ret, __fd, __pread_flag, __pread_offset, __aligned, __tm1, __tm2) do{ \
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    size_t stride; \
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    int64_t this_offset; \
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    struct posix_file_runtime* file; \
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    int64_t file_alignment; \
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    double __elapsed = __tm2-__tm1; \
    if(__ret < 0) break; \
    file = posix_file_by_fd(__fd); \
    if(!file) break; \
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    if(__pread_flag) \
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        this_offset = __pread_offset; \
    else \
        this_offset = file->offset; \
    if(this_offset > file->last_byte_read) \
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        file->file_record->counters[POSIX_SEQ_READS] += 1;  \
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    if(this_offset == (file->last_byte_read + 1)) \
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        file->file_record->counters[POSIX_CONSEC_READS] += 1;  \
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    if(this_offset > 0 && this_offset > file->last_byte_read \
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        && file->last_byte_read != 0) \
        stride = this_offset - file->last_byte_read - 1; \
    else \
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        stride = 0; \
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    file->last_byte_read = this_offset + __ret - 1; \
    file->offset = this_offset + __ret; \
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    if(file->file_record->counters[POSIX_MAX_BYTE_READ] < (this_offset + __ret - 1)) \
        file->file_record->counters[POSIX_MAX_BYTE_READ] = (this_offset + __ret - 1); \
    file->file_record->counters[POSIX_BYTES_READ] += __ret; \
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    file->file_record->counters[POSIX_READS] += 1; \
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    DARSHAN_BUCKET_INC(&(file->file_record->counters[POSIX_SIZE_READ_0_100]), __ret); \
    darshan_common_val_counter(&file->access_root, &file->access_count, __ret); \
    darshan_common_val_counter(&file->stride_root, &file->stride_count, stride); \
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    if(!__aligned) \
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        file->file_record->counters[POSIX_MEM_NOT_ALIGNED] += 1; \
    file_alignment = file->file_record->counters[POSIX_FILE_ALIGNMENT]; \
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    if(file_alignment > 0 && (this_offset % file_alignment) != 0) \
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        file->file_record->counters[POSIX_FILE_NOT_ALIGNED] += 1; \
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    if(file->last_io_type == DARSHAN_IO_WRITE) \
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        file->file_record->counters[POSIX_RW_SWITCHES] += 1; \
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    file->last_io_type = DARSHAN_IO_READ; \
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    if(file->file_record->fcounters[POSIX_F_READ_START_TIMESTAMP] == 0 || \
     file->file_record->fcounters[POSIX_F_READ_START_TIMESTAMP] > __tm1) \
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        file->file_record->fcounters[POSIX_F_READ_START_TIMESTAMP] = __tm1; \
    file->file_record->fcounters[POSIX_F_READ_END_TIMESTAMP] = __tm2; \
    if(file->file_record->fcounters[POSIX_F_MAX_READ_TIME] < __elapsed) { \
        file->file_record->fcounters[POSIX_F_MAX_READ_TIME] = __elapsed; \
        file->file_record->counters[POSIX_MAX_READ_TIME_SIZE] = __ret; } \
    DARSHAN_TIMER_INC_NO_OVERLAP(file->file_record->fcounters[POSIX_F_READ_TIME], __tm1, __tm2, file->last_read_end); \
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} while(0)

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#define POSIX_RECORD_WRITE(__ret, __fd, __pwrite_flag, __pwrite_offset, __aligned, __tm1, __tm2) do{ \
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    size_t stride; \
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    int64_t this_offset; \
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    struct posix_file_runtime* file; \
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    int64_t file_alignment; \
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    double __elapsed = __tm2-__tm1; \
    if(__ret < 0) break; \
    file = posix_file_by_fd(__fd); \
    if(!file) break; \
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    if(__pwrite_flag) \
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        this_offset = __pwrite_offset; \
    else \
        this_offset = file->offset; \
    if(this_offset > file->last_byte_written) \
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        file->file_record->counters[POSIX_SEQ_WRITES] += 1; \
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    if(this_offset == (file->last_byte_written + 1)) \
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        file->file_record->counters[POSIX_CONSEC_WRITES] += 1; \
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    if(this_offset > 0 && this_offset > file->last_byte_written \
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        && file->last_byte_written != 0) \
        stride = this_offset - file->last_byte_written - 1; \
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    else \
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        stride = 0; \
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    file->last_byte_written = this_offset + __ret - 1; \
    file->offset = this_offset + __ret; \
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    if(file->file_record->counters[POSIX_MAX_BYTE_WRITTEN] < (this_offset + __ret - 1)) \
        file->file_record->counters[POSIX_MAX_BYTE_WRITTEN] = (this_offset + __ret - 1); \
    file->file_record->counters[POSIX_BYTES_WRITTEN] += __ret; \
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    file->file_record->counters[POSIX_WRITES] += 1; \
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    DARSHAN_BUCKET_INC(&(file->file_record->counters[POSIX_SIZE_WRITE_0_100]), __ret); \
    darshan_common_val_counter(&file->access_root, &file->access_count, __ret); \
    darshan_common_val_counter(&file->stride_root, &file->stride_count, stride); \
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    if(!__aligned) \
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        file->file_record->counters[POSIX_MEM_NOT_ALIGNED] += 1; \
    file_alignment = file->file_record->counters[POSIX_FILE_ALIGNMENT]; \
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    if(file_alignment > 0 && (this_offset % file_alignment) != 0) \
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        file->file_record->counters[POSIX_FILE_NOT_ALIGNED] += 1; \
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    if(file->last_io_type == DARSHAN_IO_READ) \
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        file->file_record->counters[POSIX_RW_SWITCHES] += 1; \
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    file->last_io_type = DARSHAN_IO_WRITE; \
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    if(file->file_record->fcounters[POSIX_F_WRITE_START_TIMESTAMP] == 0 || \
     file->file_record->fcounters[POSIX_F_WRITE_START_TIMESTAMP] > __tm1) \
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        file->file_record->fcounters[POSIX_F_WRITE_START_TIMESTAMP] = __tm1; \
    file->file_record->fcounters[POSIX_F_WRITE_END_TIMESTAMP] = __tm2; \
    if(file->file_record->fcounters[POSIX_F_MAX_WRITE_TIME] < __elapsed) { \
        file->file_record->fcounters[POSIX_F_MAX_WRITE_TIME] = __elapsed; \
        file->file_record->counters[POSIX_MAX_WRITE_TIME_SIZE] = __ret; } \
    DARSHAN_TIMER_INC_NO_OVERLAP(file->file_record->fcounters[POSIX_F_WRITE_TIME], __tm1, __tm2, file->last_write_end); \
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} while(0)
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#define POSIX_LOOKUP_RECORD_STAT(__path, __statbuf, __tm1, __tm2) do { \
    char* exclude; \
    int tmp_index = 0; \
    struct posix_file_runtime* file; \
    while((exclude = darshan_path_exclusions[tmp_index])) { \
        if(!(strncmp(exclude, __path, strlen(exclude)))) \
            break; \
        tmp_index++; \
    } \
    if(exclude) break; \
    file = posix_file_by_name(__path); \
    if(file) \
    { \
        POSIX_RECORD_STAT(file, __statbuf, __tm1, __tm2); \
    } \
} while(0)

#define POSIX_RECORD_STAT(__file, __statbuf, __tm1, __tm2) do { \
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    DARSHAN_TIMER_INC_NO_OVERLAP((__file)->file_record->fcounters[POSIX_F_META_TIME], __tm1, __tm2, (__file)->last_meta_end); \
    (__file)->file_record->counters[POSIX_STATS] += 1; \
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} while(0)

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/**********************************************************
 *      Wrappers for POSIX I/O functions of interest      * 
 **********************************************************/

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int DARSHAN_DECL(open)(const char *path, int flags, ...)
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{
    int mode = 0;
    int ret;
    double tm1, tm2;

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    MAP_OR_FAIL(open);

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    if(flags & O_CREAT) 
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    {
        va_list arg;
        va_start(arg, flags);
        mode = va_arg(arg, int);
        va_end(arg);

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        tm1 = darshan_core_wtime();
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        ret = __real_open(path, flags, mode);
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        tm2 = darshan_core_wtime();
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    }
    else
    {
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        tm1 = darshan_core_wtime();
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        ret = __real_open(path, flags);
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        tm2 = darshan_core_wtime();
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    }

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    POSIX_LOCK();
    posix_runtime_initialize();
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    POSIX_RECORD_OPEN(ret, path, mode, tm1, tm2);
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    POSIX_UNLOCK();
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    return(ret);
}

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int DARSHAN_DECL(open64)(const char *path, int flags, ...)
{
    int mode = 0;
    int ret;
    double tm1, tm2;

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    MAP_OR_FAIL(open64);
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    if(flags & O_CREAT)
    {
        va_list arg;
        va_start(arg, flags);
        mode = va_arg(arg, int);
        va_end(arg);

        tm1 = darshan_core_wtime();
        ret = __real_open64(path, flags, mode);
        tm2 = darshan_core_wtime();
    }
    else
    {
        tm1 = darshan_core_wtime();
        ret = __real_open64(path, flags);
        tm2 = darshan_core_wtime();
    }

    POSIX_LOCK();
    posix_runtime_initialize();
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    POSIX_RECORD_OPEN(ret, path, mode, tm1, tm2);
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    POSIX_UNLOCK();

    return(ret);
}

int DARSHAN_DECL(creat)(const char* path, mode_t mode)
{
    int ret;
    double tm1, tm2;

    MAP_OR_FAIL(creat);

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

    POSIX_LOCK();
    posix_runtime_initialize();
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    POSIX_RECORD_OPEN(ret, path, mode, tm1, tm2);
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    POSIX_UNLOCK();

    return(ret);
}

int DARSHAN_DECL(creat64)(const char* path, mode_t mode)
{
    int ret;
    double tm1, tm2;

    MAP_OR_FAIL(creat64);
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    tm1 = darshan_core_wtime();
    ret = __real_creat64(path, mode);
    tm2 = darshan_core_wtime();

    POSIX_LOCK();
    posix_runtime_initialize();
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    POSIX_RECORD_OPEN(ret, path, mode, tm1, tm2);
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    POSIX_UNLOCK();

    return(ret);
}

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int DARSHAN_DECL(mkstemp)(char* template)
{
    int ret;
    double tm1, tm2;

    MAP_OR_FAIL(mkstemp);

    tm1 = darshan_core_wtime();
    ret = __real_mkstemp(template);
    tm2 = darshan_core_wtime();

    POSIX_LOCK();
    posix_runtime_initialize();
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    POSIX_RECORD_OPEN(ret, template, 0, tm1, tm2);
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    POSIX_UNLOCK();

    return(ret);
}

int DARSHAN_DECL(mkostemp)(char* template, int flags)
{
    int ret;
    double tm1, tm2;

    MAP_OR_FAIL(mkostemp);

    tm1 = darshan_core_wtime();
    ret = __real_mkostemp(template, flags);
    tm2 = darshan_core_wtime();

    POSIX_LOCK();
    posix_runtime_initialize();
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    POSIX_RECORD_OPEN(ret, template, 0, tm1, tm2);
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    POSIX_UNLOCK();

    return(ret);
}

int DARSHAN_DECL(mkstemps)(char* template, int suffixlen)
{
    int ret;
    double tm1, tm2;

    MAP_OR_FAIL(mkstemps);

    tm1 = darshan_core_wtime();
    ret = __real_mkstemps(template, suffixlen);
    tm2 = darshan_core_wtime();

    POSIX_LOCK();
    posix_runtime_initialize();
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    POSIX_RECORD_OPEN(ret, template, 0, tm1, tm2);
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    POSIX_UNLOCK();

    return(ret);
}

int DARSHAN_DECL(mkostemps)(char* template, int suffixlen, int flags)
{
    int ret;
    double tm1, tm2;

    MAP_OR_FAIL(mkostemps);

    tm1 = darshan_core_wtime();
    ret = __real_mkostemps(template, suffixlen, flags);
    tm2 = darshan_core_wtime();

    POSIX_LOCK();
    posix_runtime_initialize();
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    POSIX_RECORD_OPEN(ret, template, 0, tm1, tm2);
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    POSIX_UNLOCK();

    return(ret);
}

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ssize_t DARSHAN_DECL(read)(int fd, void *buf, size_t count)
{
    ssize_t ret;
    int aligned_flag = 0;
    double tm1, tm2;

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    MAP_OR_FAIL(read);
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    if((unsigned long)buf % darshan_mem_alignment == 0) aligned_flag = 1;
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    tm1 = darshan_core_wtime();
    ret = __real_read(fd, buf, count);
    tm2 = darshan_core_wtime();

    POSIX_LOCK();
    posix_runtime_initialize();
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    POSIX_RECORD_READ(ret, fd, 0, 0, aligned_flag, tm1, tm2);
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    POSIX_UNLOCK();

    return(ret);
}

ssize_t DARSHAN_DECL(write)(int fd, const void *buf, size_t count)
{
    ssize_t ret;
    int aligned_flag = 0;
    double tm1, tm2;

    MAP_OR_FAIL(write);

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    if((unsigned long)buf % darshan_mem_alignment == 0) aligned_flag = 1;
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    tm1 = darshan_core_wtime();
    ret = __real_write(fd, buf, count);
    tm2 = darshan_core_wtime();

    POSIX_LOCK();
    posix_runtime_initialize();
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    POSIX_RECORD_WRITE(ret, fd, 0, 0, aligned_flag, tm1, tm2);
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    POSIX_UNLOCK();

    return(ret);
}

ssize_t DARSHAN_DECL(pread)(int fd, void *buf, size_t count, off_t offset)
{
    ssize_t ret;
    int aligned_flag = 0;
    double tm1, tm2;

    MAP_OR_FAIL(pread);

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    if((unsigned long)buf % darshan_mem_alignment == 0) aligned_flag = 1;
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    tm1 = darshan_core_wtime();
    ret = __real_pread(fd, buf, count, offset);
    tm2 = darshan_core_wtime();

    POSIX_LOCK();
    posix_runtime_initialize();
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    POSIX_RECORD_READ(ret, fd, 1, offset, aligned_flag, tm1, tm2);
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    POSIX_UNLOCK();

    return(ret);
}

ssize_t DARSHAN_DECL(pwrite)(int fd, const void *buf, size_t count, off_t offset)
{
    ssize_t ret;
    int aligned_flag = 0;
    double tm1, tm2;

    MAP_OR_FAIL(pwrite);

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    if((unsigned long)buf % darshan_mem_alignment == 0) aligned_flag = 1;
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    tm1 = darshan_core_wtime();
    ret = __real_pwrite(fd, buf, count, offset);
    tm2 = darshan_core_wtime();

    POSIX_LOCK();
    posix_runtime_initialize();
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    POSIX_RECORD_WRITE(ret, fd, 1, offset, aligned_flag, tm1, tm2);
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    POSIX_UNLOCK();

    return(ret);
}

ssize_t DARSHAN_DECL(pread64)(int fd, void *buf, size_t count, off64_t offset)
{
    ssize_t ret;
    int aligned_flag = 0;
    double tm1, tm2;

    MAP_OR_FAIL(pread64);

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    if((unsigned long)buf % darshan_mem_alignment == 0) aligned_flag = 1;
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    tm1 = darshan_core_wtime();
    ret = __real_pread64(fd, buf, count, offset);
    tm2 = darshan_core_wtime();

    POSIX_LOCK();
    posix_runtime_initialize();
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    POSIX_RECORD_READ(ret, fd, 1, offset, aligned_flag, tm1, tm2);
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    POSIX_UNLOCK();

    return(ret);
}

ssize_t DARSHAN_DECL(pwrite64)(int fd, const void *buf, size_t count, off64_t offset)
{
    ssize_t ret;
    int aligned_flag = 0;
    double tm1, tm2;

    MAP_OR_FAIL(pwrite64);

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    if((unsigned long)buf % darshan_mem_alignment == 0) aligned_flag = 1;
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    tm1 = darshan_core_wtime();
    ret = __real_pwrite64(fd, buf, count, offset);
    tm2 = darshan_core_wtime();

    POSIX_LOCK();
    posix_runtime_initialize();
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    POSIX_RECORD_WRITE(ret, fd, 1, offset, aligned_flag, tm1, tm2);
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    POSIX_UNLOCK();

    return(ret);
}

ssize_t DARSHAN_DECL(readv)(int fd, const struct iovec *iov, int iovcnt)
{
    ssize_t ret;
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    int aligned_flag = 1;
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    int i;
    double tm1, tm2;

    MAP_OR_FAIL(readv);
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    for(i=0; i<iovcnt; i++)
    {
        if(((unsigned long)iov[i].iov_base % darshan_mem_alignment) != 0)
            aligned_flag = 0;
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    }
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    tm1 = darshan_core_wtime();
    ret = __real_readv(fd, iov, iovcnt);
    tm2 = darshan_core_wtime();

    POSIX_LOCK();
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    posix_runtime_initialize();
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    POSIX_RECORD_READ(ret, fd, 0, 0, aligned_flag, tm1, tm2);
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    POSIX_UNLOCK();

    return(ret);
}

ssize_t DARSHAN_DECL(writev)(int fd, const struct iovec *iov, int iovcnt)
{
    ssize_t ret;
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    int i;
    double tm1, tm2;

    MAP_OR_FAIL(writev);
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    for(i=0; i<iovcnt; i++)
    {
        if(((unsigned long)iov[i].iov_base % darshan_mem_alignment) != 0)
            aligned_flag = 0;
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    }
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    tm1 = darshan_core_wtime();
    ret = __real_writev(fd, iov, iovcnt);
    tm2 = darshan_core_wtime();

    POSIX_LOCK();
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    posix_runtime_initialize();
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    POSIX_RECORD_WRITE(ret, fd, 0, 0, aligned_flag, tm1, tm2);
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    POSIX_UNLOCK();

    return(ret);
}

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off_t DARSHAN_DECL(lseek)(int fd, off_t offset, int whence)
{
    off_t ret;
    struct posix_file_runtime* file;
    double tm1, tm2;

    MAP_OR_FAIL(lseek);

    tm1 = darshan_core_wtime();
    ret = __real_lseek(fd, offset, whence);
    tm2 = darshan_core_wtime();

    if(ret >= 0)
    {
        POSIX_LOCK();
        posix_runtime_initialize();
        file = posix_file_by_fd(fd);
        if(file)
        {
            file->offset = ret;
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            DARSHAN_TIMER_INC_NO_OVERLAP(
                file->file_record->fcounters[POSIX_F_META_TIME],
                tm1, tm2, file->last_meta_end);
            file->file_record->counters[POSIX_SEEKS] += 1;
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        }
        POSIX_UNLOCK();
    }

    return(ret);
}

off_t DARSHAN_DECL(lseek64)(int fd, off_t offset, int whence)
{
    off_t ret;
    struct posix_file_runtime* file;
    double tm1, tm2;

    MAP_OR_FAIL(lseek64);

    tm1 = darshan_core_wtime();
    ret = __real_lseek64(fd, offset, whence);
    tm2 = darshan_core_wtime();

    if(ret >= 0)
    {
        POSIX_LOCK();
        posix_runtime_initialize();
        file = posix_file_by_fd(fd);
        if(file)
        {
            file->offset = ret;
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            DARSHAN_TIMER_INC_NO_OVERLAP(
                file->file_record->fcounters[POSIX_F_META_TIME],
                tm1, tm2, file->last_meta_end);
            file->file_record->counters[POSIX_SEEKS] += 1;
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        }
        POSIX_UNLOCK();
    }

    return(ret);
}

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int DARSHAN_DECL(__xstat)(int vers, const char *path, struct stat *buf)
{
    int ret;
    double tm1, tm2;

    MAP_OR_FAIL(__xstat);

    tm1 = darshan_core_wtime();
    ret = __real___xstat(vers, path, buf);
    tm2 = darshan_core_wtime();

    if(ret < 0 || !S_ISREG(buf->st_mode))
        return(ret);

    POSIX_LOCK();
    posix_runtime_initialize();
    POSIX_LOOKUP_RECORD_STAT(path, buf, tm1, tm2);
    POSIX_UNLOCK();

    return(ret);
}

int DARSHAN_DECL(__xstat64)(int vers, const char *path, struct stat64 *buf)
{
    int ret;
    double tm1, tm2;

    MAP_OR_FAIL(__xstat64);

    tm1 = darshan_core_wtime();
    ret = __real___xstat64(vers, path, buf);
    tm2 = darshan_core_wtime();

    if(ret < 0 || !S_ISREG(buf->st_mode))
        return(ret);

    POSIX_LOCK();
    posix_runtime_initialize();
    POSIX_LOOKUP_RECORD_STAT(path, buf, tm1, tm2);
    POSIX_UNLOCK();

    return(ret);
}

int DARSHAN_DECL(__lxstat)(int vers, const char *path, struct stat *buf)
{
    int ret;
    double tm1, tm2;

    MAP_OR_FAIL(__lxstat);

    tm1 = darshan_core_wtime();
    ret = __real___lxstat(vers, path, buf);
    tm2 = darshan_core_wtime();

    if(ret < 0 || !S_ISREG(buf->st_mode))
        return(ret);

    POSIX_LOCK();
    posix_runtime_initialize();
    POSIX_LOOKUP_RECORD_STAT(path, buf, tm1, tm2);
    POSIX_UNLOCK();

    return(ret);
}

int DARSHAN_DECL(__lxstat64)(int vers, const char *path, struct stat64 *buf)
{
    int ret;
    double tm1, tm2;

    MAP_OR_FAIL(__lxstat64);

    tm1 = darshan_core_wtime();
    ret = __real___lxstat64(vers, path, buf);
    tm2 = darshan_core_wtime();

    if(ret < 0 || !S_ISREG(buf->st_mode))
        return(ret);

    POSIX_LOCK();
    posix_runtime_initialize();
    POSIX_LOOKUP_RECORD_STAT(path, buf, tm1, tm2);
    POSIX_UNLOCK();

    return(ret);
}

int DARSHAN_DECL(__fxstat)(int vers, int fd, struct stat *buf)
{
    int ret;
    struct posix_file_runtime* file;
    double tm1, tm2;

    MAP_OR_FAIL(__fxstat);

    tm1 = darshan_core_wtime();
    ret = __real___fxstat(vers, fd, buf);
    tm2 = darshan_core_wtime();

    if(ret < 0 || !S_ISREG(buf->st_mode))
        return(ret);

    POSIX_LOCK();
    posix_runtime_initialize();
    file = posix_file_by_fd(fd);
    if(file)
    {
        POSIX_RECORD_STAT(file, buf, tm1, tm2);
    }
    POSIX_UNLOCK();

    return(ret);
}

int DARSHAN_DECL(__fxstat64)(int vers, int fd, struct stat64 *buf)
{
    int ret;
    struct posix_file_runtime* file;
    double tm1, tm2;

    MAP_OR_FAIL(__fxstat64);

    tm1 = darshan_core_wtime();
    ret = __real___fxstat64(vers, fd, buf);
    tm2 = darshan_core_wtime();

    if(ret < 0 || !S_ISREG(buf->st_mode))
        return(ret);

    POSIX_LOCK();
    posix_runtime_initialize();
    file = posix_file_by_fd(fd);
    if(file)
    {
        POSIX_RECORD_STAT(file, buf, tm1, tm2);
    }
    POSIX_UNLOCK();

    return(ret);
}

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void* DARSHAN_DECL(mmap)(void *addr, size_t length, int prot, int flags,
    int fd, off_t offset)
{
    void* ret;
    struct posix_file_runtime* file;

    MAP_OR_FAIL(mmap);

    ret = __real_mmap(addr, length, prot, flags, fd, offset);
    if(ret == MAP_FAILED)
        return(ret);

    POSIX_LOCK();
    posix_runtime_initialize();
    file = posix_file_by_fd(fd);
    if(file)
    {
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        file->file_record->counters[POSIX_MMAPS] += 1;
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    }
    POSIX_UNLOCK();

    return(ret);
}

void* DARSHAN_DECL(mmap64)(void *addr, size_t length, int prot, int flags,
    int fd, off64_t offset)
{
    void* ret;
    struct posix_file_runtime* file;

    MAP_OR_FAIL(mmap64);

    ret = __real_mmap64(addr, length, prot, flags, fd, offset);
    if(ret == MAP_FAILED)
        return(ret);

    POSIX_LOCK();
    posix_runtime_initialize();
    file = posix_file_by_fd(fd);
    if(file)
    {
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        file->file_record->counters[POSIX_MMAPS] += 1;
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    }
    POSIX_UNLOCK();

    return(ret);
}

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int DARSHAN_DECL(fsync)(int fd)
{
    int ret;
    struct posix_file_runtime* file;
    double tm1, tm2;

    MAP_OR_FAIL(fsync);

    tm1 = darshan_core_wtime();
    ret = __real_fsync(fd);
    tm2 = darshan_core_wtime();

    if(ret < 0)
        return(ret);

    POSIX_LOCK();
    posix_runtime_initialize();
    file = posix_file_by_fd(fd);
    if(file)
    {
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        DARSHAN_TIMER_INC_NO_OVERLAP(
            file->file_record->fcounters[POSIX_F_WRITE_TIME],
            tm1, tm2, file->last_write_end);
        file->file_record->counters[POSIX_FSYNCS] += 1;
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    }
    POSIX_UNLOCK();

    return(ret);
}

int DARSHAN_DECL(fdatasync)(int fd)
{
    int ret;
    struct posix_file_runtime* file;
    double tm1, tm2;

    MAP_OR_FAIL(fdatasync);

    tm1 = darshan_core_wtime();
    ret = __real_fdatasync(fd);
    tm2 = darshan_core_wtime();

    if(ret < 0)
        return(ret);

    POSIX_LOCK();
    posix_runtime_initialize();
    file = posix_file_by_fd(fd);
    if(file)
    {
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            file->file_record->fcounters[POSIX_F_WRITE_TIME],
            tm1, tm2, file->last_write_end);
        file->file_record->counters[POSIX_FDSYNCS] += 1;
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    }
    POSIX_UNLOCK();

    return(ret);
}

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int DARSHAN_DECL(close)(int fd)
{
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    int ret;

    MAP_OR_FAIL(close);

    tm1 = darshan_core_wtime();
    ret = __real_close(fd);
    tm2 = darshan_core_wtime();

    POSIX_LOCK();
    posix_runtime_initialize();
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    file = posix_file_by_fd(fd);
    if(file)
    {
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        file->last_byte_written = 0;
        file->last_byte_read = 0;
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        file->file_record->fcounters[POSIX_F_CLOSE_TIMESTAMP] =
            darshan_core_wtime();
        DARSHAN_TIMER_INC_NO_OVERLAP(
            file->file_record->fcounters[POSIX_F_META_TIME],
            tm1, tm2, file->last_meta_end);
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        posix_file_close_fd(fd);
    }
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    POSIX_UNLOCK();    

    return(ret);
}

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int DARSHAN_DECL(aio_read)(struct aiocb *aiocbp)
{
    int ret;

    MAP_OR_FAIL(aio_read);

    ret = __real_aio_read(aiocbp);
    if(ret == 0)
    {
        POSIX_LOCK();
        posix_runtime_initialize();
        posix_aio_tracker_add(aiocbp->aio_fildes, aiocbp);
        POSIX_UNLOCK();
    }

    return(ret);
}

int DARSHAN_DECL(aio_write)(struct aiocb *aiocbp)
{
    int ret;

    MAP_OR_FAIL(aio_write);

    ret = __real_aio_write(aiocbp);
    if(ret == 0)
    {
        POSIX_LOCK();
        posix_runtime_initialize();
        posix_aio_tracker_add(aiocbp->aio_fildes, aiocbp);
        POSIX_UNLOCK();
    }

    return(ret);
}

int DARSHAN_DECL(aio_read64)(struct aiocb64 *aiocbp)
{
    int ret;

    MAP_OR_FAIL(aio_read64);

    ret = __real_aio_read64(aiocbp);
    if(ret == 0)
    {
        POSIX_LOCK();
        posix_runtime_initialize();
        posix_aio_tracker_add(aiocbp->aio_fildes, aiocbp);
        POSIX_UNLOCK();
    }

    return(ret);
}

int DARSHAN_DECL(aio_write64)(struct aiocb64 *aiocbp)
{
    int ret;

    MAP_OR_FAIL(aio_write64);

    ret = __real_aio_write64(aiocbp);
    if(ret == 0)
    {
        POSIX_LOCK();
        posix_runtime_initialize();
        posix_aio_tracker_add(aiocbp->aio_fildes, aiocbp);
        POSIX_UNLOCK();
    }

    return(ret);
}

ssize_t DARSHAN_DECL(aio_return)(struct aiocb *aiocbp)
{
    int ret;
    double tm2;
    struct posix_aio_tracker *tmp;
    int aligned_flag = 0;

    MAP_OR_FAIL(aio_return);

    ret = __real_aio_return(aiocbp);
    tm2 = darshan_core_wtime();

    POSIX_LOCK();
    posix_runtime_initialize();
    tmp = posix_aio_tracker_del(aiocbp->aio_fildes, aiocbp);
    if (tmp)
    {
        if((unsigned long)aiocbp->aio_buf % darshan_mem_alignment == 0)
            aligned_flag = 1;
        if(aiocbp->aio_lio_opcode == LIO_WRITE)
        {
            POSIX_RECORD_WRITE(ret, aiocbp->aio_fildes,
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                1, aiocbp->aio_offset, aligned_flag,
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                tmp->tm1, tm2);
        }
        else if(aiocbp->aio_lio_opcode == LIO_READ)
        {
            POSIX_RECORD_READ(ret, aiocbp->aio_fildes,
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                1, aiocbp->aio_offset, aligned_flag,
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                tmp->tm1, tm2);
        }
        free(tmp);
    }
    POSIX_UNLOCK();

    return(ret);
}

ssize_t DARSHAN_DECL(aio_return64)(struct aiocb64 *aiocbp)
{
    int ret;
    double tm2;
    struct posix_aio_tracker *tmp;
    int aligned_flag = 0;

    MAP_OR_FAIL(aio_return64);

    ret = __real_aio_return64(aiocbp);
    tm2 = darshan_core_wtime();

    POSIX_LOCK();
    posix_runtime_initialize();
    tmp = posix_aio_tracker_del(aiocbp->aio_fildes, aiocbp);
    if (tmp)
    {
        if((unsigned long)aiocbp->aio_buf % darshan_mem_alignment == 0)
            aligned_flag = 1;
        if(aiocbp->aio_lio_opcode == LIO_WRITE)
        {
            POSIX_RECORD_WRITE(ret, aiocbp->aio_fildes,
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                1, aiocbp->aio_offset, aligned_flag,
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                tmp->tm1, tm2);
        }
        else if(aiocbp->aio_lio_opcode == LIO_READ)
        {
            POSIX_RECORD_READ(ret, aiocbp->aio_fildes,
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                1, aiocbp->aio_offset, aligned_flag,
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                tmp->tm1, tm2);
        }
        free(tmp);
    }
    POSIX_UNLOCK();

    return(ret);
}

int DARSHAN_DECL(lio_listio)(int mode, struct aiocb *const aiocb_list[],
    int nitems, struct sigevent *sevp)
{
    int ret;
    int i;

    MAP_OR_FAIL(lio_listio);

    ret = __real_lio_listio(mode, aiocb_list, nitems, sevp);
    if(ret == 0)
    {
        POSIX_LOCK();
        posix_runtime_initialize();
        for(i = 0; i < nitems; i++)
        {
            posix_aio_tracker_add(aiocb_list[i]->aio_fildes, aiocb_list[i]);
        }
        POSIX_UNLOCK();
    }

    return(ret);
}

int DARSHAN_DECL(lio_listio64)(int mode, struct aiocb64 *const aiocb_list[],
    int nitems, struct sigevent *sevp)
{
    int ret;
    int i;

    MAP_OR_FAIL(lio_listio64);

    ret = __real_lio_listio64(mode, aiocb_list, nitems, sevp);
    if(ret == 0)
    {
        POSIX_LOCK();
        posix_runtime_initialize();
        for(i = 0; i < nitems; i++)
        {
            posix_aio_tracker_add(aiocb_list[i]->aio_fildes, aiocb_list[i]);
        }
        POSIX_UNLOCK();
    }

    return(ret);
}

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/**********************************************************
 * Internal functions for manipulating POSIX module state *
 **********************************************************/
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/* initialize internal POSIX module data structures and register with darshan-core */
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static void posix_runtime_initialize()
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{
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    int mem_limit;
    struct darshan_module_funcs posix_mod_fns =
    {
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        .begin_shutdown = &posix_begin_shutdown,
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        .get_output_data = &posix_get_output_data,
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        .shutdown = &posix_shutdown
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    };
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    /* don't do anything if already initialized or instrumenation is disabled */
    if(posix_runtime || instrumentation_disabled)
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        return;
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    /* register the posix module with darshan core */
    darshan_core_register_module(
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        &posix_mod_fns,
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        &my_rank,
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        &mem_limit,
        &darshan_mem_alignment);
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    /* return if no memory assigned by darshan core */
    if(mem_limit == 0)
        return;

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

    /* set maximum number of file records according to max memory limit */
    /* NOTE: maximum number of records is based on the size of a posix file record */
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    /* TODO: should we base memory usage off file record or total runtime structure sizes? */
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    posix_runtime->file_array_size = mem_limit / sizeof(struct darshan_posix_file);
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    posix_runtime->file_array_ndx = 0;
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    /* allocate array of runtime file records */
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    posix_runtime->file_runtime_array = malloc(posix_runtime->file_array_size *
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                                               sizeof(struct posix_file_runtime));
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    posix_runtime->file_record_array = malloc(posix_runtime->file_array_size *
                                              sizeof(struct darshan_posix_file));
    if(!posix_runtime->file_runtime_array || !posix_runtime->file_record_array)
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    {
        posix_runtime->file_array_size = 0;
        return;
    }
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    memset(posix_runtime->file_runtime_array, 0, posix_runtime->file_array_size *
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    memset(posix_runtime->file_record_array, 0, posix_runtime->file_array_size *
           sizeof(struct darshan_posix_file));
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    return;
}
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/* get a POSIX file record for the given file path */
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static struct posix_file_runtime* posix_file_by_name(const char *name)
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{
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    char *newname = NULL;
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    darshan_record_id file_id;
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    int file_alignment;
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    int limit_flag;
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    if(!posix_runtime || instrumentation_disabled)
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        return(NULL);
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    newname = darshan_clean_file_path(name);
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    if(!newname)
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        newname = (char*)name;
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    limit_flag = (posix_runtime->file_array_ndx >= posix_runtime->file_array_size);

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    /* get a unique id for this file from darshan core */
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    darshan_core_register_record(
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        (void*)newname,
        strlen(newname),
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        DARSHAN_POSIX_MOD,
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        limit_flag,
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        &file_id,
        &file_alignment);
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     * new records -- just fall through and ignore this record
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     */
    if(file_id == 0)
    {
        if(newname != name)
            free(newname);
        return(NULL);
    }

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

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

    /* add new record to file hash table */
    HASH_ADD(hlink, posix_runtime->file_hash, file_record->f_id, sizeof(darshan_record_id), file);
    posix_runtime->file_array_ndx++;
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    if(newname != name)
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        free(newname);
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    return(file);
}

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/* get a POSIX file record for the given file path, and also create a
 * reference structure using the returned file descriptor
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{
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    struct posix_file_runtime_ref* ref;
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    if(!posix_runtime || instrumentation_disabled)
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        return(NULL);

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

    if(!file)
        return(NULL);

    /* search hash table for existing file ref for this fd */
    HASH_FIND(hlink, posix_runtime->fd_hash, &fd, sizeof(int), 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 fd
     * in the table yet.  Add it.
     */
    ref = malloc(sizeof(*ref));
    if(!ref)
        return(NULL);
    memset(ref, 0, sizeof(*ref));
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    ref->file = file;
    ref->fd = fd;    
    HASH_ADD(hlink, posix_runtime->fd_hash, fd, sizeof(int), ref);

    return(file);
}

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static struct posix_file_runtime* posix_file_by_fd(int fd)
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{
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    struct posix_file_runtime_ref* ref;
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    if(!posix_runtime || instrumentation_disabled)
        return(NULL);

    /* search hash table for existing file ref for this fd */
    HASH_FIND(hlink, posix_runtime->fd_hash, &fd, sizeof(int), ref);
    if(ref)
        return(ref->file);

    return(NULL);
}

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/* free up reference data structures for the given file descriptor */
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static void posix_file_close_fd(int fd)
{
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    struct posix_file_runtime_ref* ref;
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    if(!posix_runtime || instrumentation_disabled)
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        return;

    /* search hash table for this fd */
    HASH_FIND(hlink, posix_runtime->fd_hash, &fd, sizeof(int), ref);
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