darshan-mpi-io.c 78.9 KB
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/*
 *  (C) 2009 by Argonne National Laboratory.
 *      See COPYRIGHT in top-level directory.
 */

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#define _XOPEN_SOURCE 500
#define _GNU_SOURCE /* for tdestroy() */

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#include "darshan-runtime-config.h"
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#include <stdio.h>
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#ifdef HAVE_MNTENT_H
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#include <mntent.h>
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#endif
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#include <stdlib.h>
#include <string.h>
#include <time.h>
#include <limits.h>
#include <unistd.h>
#include <pthread.h>
#include <sys/types.h>
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#include <sys/stat.h>
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#include <sys/vfs.h>
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#include <zlib.h>
#include <assert.h>
#include <search.h>

#include "mpi.h"
#include "darshan.h"
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#include "darshan-dynamic.h"
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extern char* __progname;

/* maximum number of memory segments each process will write to the log */
#define CP_MAX_MEM_SEGMENTS 8

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/* Some old versions of MPI don't provide all of these COMBINER definitions.  
 * If any are missing then we define them to an arbitrary value just to 
 * prevent compile errors in DATATYPE_INC().
 */
#ifndef MPI_COMBINER_NAMED
    #define MPI_COMBINER_NAMED CP_COMBINER_NAMED
#endif
#ifndef MPI_COMBINER_DUP
    #define MPI_COMBINER_DUP CP_COMBINER_DUP
#endif
#ifndef MPI_COMBINER_CONTIGUOUS
    #define MPI_COMBINER_CONTIGUOUS CP_COMBINER_CONTIGUOUS
#endif
#ifndef MPI_COMBINER_VECTOR
    #define MPI_COMBINER_VECTOR CP_COMBINER_VECTOR
#endif
#ifndef MPI_COMBINER_HVECTOR_INTEGER
    #define MPI_COMBINER_HVECTOR_INTEGER CP_COMBINER_HVECTOR_INTEGER
#endif
#ifndef MPI_COMBINER_HVECTOR
    #define MPI_COMBINER_HVECTOR CP_COMBINER_HVECTOR
#endif
#ifndef MPI_COMBINER_INDEXED
    #define MPI_COMBINER_INDEXED CP_COMBINER_INDEXED
#endif
#ifndef MPI_COMBINER_HINDEXED_INTEGER
    #define MPI_COMBINER_HINDEXED_INTEGER CP_COMBINER_HINDEXED_INTEGER
#endif
#ifndef MPI_COMBINER_HINDEXED
    #define MPI_COMBINER_HINDEXED CP_COMBINER_HINDEXED
#endif
#ifndef MPI_COMBINER_INDEXED_BLOCK
    #define MPI_COMBINER_INDEXED_BLOCK CP_COMBINER_INDEXED_BLOCK
#endif
#ifndef MPI_COMBINER_STRUCT_INTEGER
    #define MPI_COMBINER_STRUCT_INTEGER CP_COMBINER_STRUCT_INTEGER
#endif
#ifndef MPI_COMBINER_STRUCT
    #define MPI_COMBINER_STRUCT CP_COMBINER_STRUCT
#endif
#ifndef MPI_COMBINER_SUBARRAY
    #define MPI_COMBINER_SUBARRAY CP_COMBINER_SUBARRAY
#endif
#ifndef MPI_COMBINER_DARRAY
    #define MPI_COMBINER_DARRAY CP_COMBINER_DARRAY
#endif
#ifndef MPI_COMBINER_F90_REAL
    #define MPI_COMBINER_F90_REAL CP_COMBINER_F90_REAL
#endif
#ifndef MPI_COMBINER_F90_COMPLEX
    #define MPI_COMBINER_F90_COMPLEX CP_COMBINER_F90_COMPLEX
#endif
#ifndef MPI_COMBINER_F90_INTEGER
    #define MPI_COMBINER_F90_INTEGER CP_COMBINER_F90_INTEGER
#endif
#ifndef MPI_COMBINER_RESIZED
    #define MPI_COMBINER_RESIZED CP_COMBINER_RESIZED
#endif

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#define CP_DATATYPE_INC(__file, __datatype) do {\
    int num_integers, num_addresses, num_datatypes, combiner, ret; \
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    ret = DARSHAN_MPI_CALL(PMPI_Type_get_envelope)(__datatype, &num_integers, \
        &num_addresses, &num_datatypes, &combiner); \
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    if(ret == MPI_SUCCESS) { \
        switch(combiner) { \
            case MPI_COMBINER_NAMED:\
                CP_INC(__file,CP_COMBINER_NAMED,1); break; \
            case MPI_COMBINER_DUP:\
                CP_INC(__file,CP_COMBINER_DUP,1); break; \
            case MPI_COMBINER_CONTIGUOUS:\
                CP_INC(__file,CP_COMBINER_CONTIGUOUS,1); break; \
            case MPI_COMBINER_VECTOR:\
                CP_INC(__file,CP_COMBINER_VECTOR,1); break; \
            case MPI_COMBINER_HVECTOR_INTEGER:\
                CP_INC(__file,CP_COMBINER_HVECTOR_INTEGER,1); break; \
            case MPI_COMBINER_HVECTOR:\
                CP_INC(__file,CP_COMBINER_HVECTOR,1); break; \
            case MPI_COMBINER_INDEXED:\
                CP_INC(__file,CP_COMBINER_INDEXED,1); break; \
            case MPI_COMBINER_HINDEXED_INTEGER:\
                CP_INC(__file,CP_COMBINER_HINDEXED_INTEGER,1); break; \
            case MPI_COMBINER_HINDEXED:\
                CP_INC(__file,CP_COMBINER_HINDEXED,1); break; \
            case MPI_COMBINER_INDEXED_BLOCK:\
                CP_INC(__file,CP_COMBINER_INDEXED_BLOCK,1); break; \
            case MPI_COMBINER_STRUCT_INTEGER:\
                CP_INC(__file,CP_COMBINER_STRUCT_INTEGER,1); break; \
            case MPI_COMBINER_STRUCT:\
                CP_INC(__file,CP_COMBINER_STRUCT,1); break; \
            case MPI_COMBINER_SUBARRAY:\
                CP_INC(__file,CP_COMBINER_SUBARRAY,1); break; \
            case MPI_COMBINER_DARRAY:\
                CP_INC(__file,CP_COMBINER_DARRAY,1); break; \
            case MPI_COMBINER_F90_REAL:\
                CP_INC(__file,CP_COMBINER_F90_REAL,1); break; \
            case MPI_COMBINER_F90_COMPLEX:\
                CP_INC(__file,CP_COMBINER_F90_COMPLEX,1); break; \
            case MPI_COMBINER_F90_INTEGER:\
                CP_INC(__file,CP_COMBINER_F90_INTEGER,1); break; \
            case MPI_COMBINER_RESIZED:\
                CP_INC(__file,CP_COMBINER_RESIZED,1); break; \
        } \
    } \
} while(0)

#define CP_RECORD_MPI_WRITE(__ret, __fh, __count, __datatype, __counter, __tm1, __tm2) do { \
    struct darshan_file_runtime* file; \
    int size = 0; \
    MPI_Aint extent = 0; \
    if(__ret != MPI_SUCCESS) break; \
    file = darshan_file_by_fh(__fh); \
    if(!file) break; \
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    DARSHAN_MPI_CALL(PMPI_Type_size)(__datatype, &size);  \
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    size = size * __count; \
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    DARSHAN_MPI_CALL(PMPI_Type_extent)(__datatype, &extent); \
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    CP_BUCKET_INC(file, CP_SIZE_WRITE_AGG_0_100, size); \
    CP_BUCKET_INC(file, CP_EXTENT_WRITE_0_100, extent); \
    CP_INC(file, __counter, 1); \
    CP_DATATYPE_INC(file, __datatype); \
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    CP_F_INC_NO_OVERLAP(file, __tm1, __tm2, file->last_mpi_write_end, CP_F_MPI_WRITE_TIME); \
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    if(CP_F_VALUE(file, CP_F_WRITE_START_TIMESTAMP) == 0) \
        CP_F_SET(file, CP_F_WRITE_START_TIMESTAMP, __tm1); \
    CP_F_SET(file, CP_F_WRITE_END_TIMESTAMP, __tm2); \
} while(0)

#define CP_RECORD_MPI_READ(__ret, __fh, __count, __datatype, __counter, __tm1, __tm2) do { \
    struct darshan_file_runtime* file; \
    int size = 0; \
    MPI_Aint extent = 0; \
    if(__ret != MPI_SUCCESS) break; \
    file = darshan_file_by_fh(__fh); \
    if(!file) break; \
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    DARSHAN_MPI_CALL(PMPI_Type_size)(__datatype, &size);  \
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    size = size * __count; \
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    DARSHAN_MPI_CALL(PMPI_Type_extent)(__datatype, &extent); \
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    CP_BUCKET_INC(file, CP_SIZE_READ_AGG_0_100, size); \
    CP_BUCKET_INC(file, CP_EXTENT_READ_0_100, extent); \
    CP_INC(file, __counter, 1); \
    CP_DATATYPE_INC(file, __datatype); \
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    CP_F_INC_NO_OVERLAP(file, __tm1, __tm2, file->last_mpi_read_end, CP_F_MPI_READ_TIME); \
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    if(CP_F_VALUE(file, CP_F_READ_START_TIMESTAMP) == 0) \
        CP_F_SET(file, CP_F_READ_START_TIMESTAMP, __tm1); \
    CP_F_SET(file, CP_F_READ_END_TIMESTAMP, __tm2); \
} while(0)

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static void cp_normalize_timestamps(struct darshan_job_runtime* final_job);
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static void cp_log_construct_indices(struct darshan_job_runtime* final_job,
    int rank, int* inout_count, int* lengths, void** pointers, char*
    trailing_data);
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static int cp_log_write(struct darshan_job_runtime* final_job, int rank, 
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    char* logfile_name, int count, int* lengths, void** pointers, double start_log_time);
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static void cp_log_record_hints_and_ver(struct darshan_job_runtime* final_job, int rank);
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static int cp_log_reduction(struct darshan_job_runtime* final_job, int rank, 
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    char* logfile_name, MPI_Offset* next_offset);
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static void darshan_file_reduce(void* infile_v, 
    void* inoutfile_v, int *len, 
    MPI_Datatype *datatype);
static int cp_log_compress(struct darshan_job_runtime* final_job,
    int rank, int* inout_count, int* lengths, void** pointers);
static int file_compare(const void* a, const void* b);
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static int darshan_file_variance(
    struct darshan_file *infile_array,
    struct darshan_file *outfile_array,
    int count, int rank);
static void pairwise_variance_reduce (
    void *invec, void *inoutvec, int *len, MPI_Datatype *dt);
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#if 0
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static void debug_mounts(const char* mtab_file, const char* out_file);
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#endif
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static struct darshan_file_runtime* darshan_file_by_fh(MPI_File fh);
static void darshan_file_close_fh(MPI_File fh);
static struct darshan_file_runtime* darshan_file_by_name_setfh(const char* name, MPI_File fh);
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#define CP_MAX_MNTS 64
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#define CP_MAX_MNT_PATH 256
#define CP_MAX_MNT_TYPE 32
struct mnt_data
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{
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    int64_t hash;
    int64_t block_size;
    char path[CP_MAX_MNT_PATH];
    char type[CP_MAX_MNT_TYPE];
};
static struct mnt_data mnt_data_array[CP_MAX_MNTS];
static int mnt_data_count = 0;
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struct variance_dt
{
    double n;
    double T;
    double S;
};

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void darshan_mpi_initialize(int *argc, char ***argv)
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{
    int nprocs;
    int rank;
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    int timing_flag = 0;
    double init_start, init_time, init_max;
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    DARSHAN_MPI_CALL(PMPI_Comm_size)(MPI_COMM_WORLD, &nprocs);
    DARSHAN_MPI_CALL(PMPI_Comm_rank)(MPI_COMM_WORLD, &rank);
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    if(getenv("DARSHAN_INTERNAL_TIMING"))
        timing_flag = 1;

    if(timing_flag)
        init_start = DARSHAN_MPI_CALL(PMPI_Wtime)();
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    if(argc && argv)
    {
        darshan_initialize(*argc, *argv, nprocs, rank);
    }
    else
    {
        /* we don't see argc and argv here in fortran */
        darshan_initialize(0, NULL, nprocs, rank);
    }
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    if(timing_flag)
    {
        init_time = DARSHAN_MPI_CALL(PMPI_Wtime)() - init_start;
        DARSHAN_MPI_CALL(PMPI_Reduce)(&init_time, &init_max, 1,
            MPI_DOUBLE, MPI_MAX, 0, MPI_COMM_WORLD);
        if(rank == 0)
        {
            printf("#darshan:<op>\t<nprocs>\t<time>\n");
            printf("darshan:init\t%d\t%f\n", nprocs, init_max);
        }
    }
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    return;
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}

void darshan_shutdown(int timing_flag)
{
    int rank;
    char* logfile_name;
    struct darshan_job_runtime* final_job;
    double start_log_time = 0;
    int all_ret = 0;
    int local_ret = 0;
    MPI_Offset next_offset = 0;
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    char* user_logfile_name;
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    char* jobid_str;
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    char* envjobid;
    char* logpath;
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    int jobid;
    int index_count = 0;
    int lengths[CP_MAX_MEM_SEGMENTS];
    void* pointers[CP_MAX_MEM_SEGMENTS];
    int ret;
    double red1=0, red2=0, gz1=0, gz2=0, write1=0, write2=0, tm_end=0;
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    double bcst=0;
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    int nprocs;
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    time_t start_time_tmp = 0;
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    uint64_t logmod;
    char hname[HOST_NAME_MAX];
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    char* logpath_override = NULL;
#ifdef __CP_LOG_ENV
    char env_check[256];
    char* env_tok;
#endif
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    uint64_t hlevel;
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    int64_t first_start_time;
    int64_t last_end_time;
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    CP_LOCK();
    if(!darshan_global_job)
    {
        CP_UNLOCK();
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        return;
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    }
    /* disable further tracing while hanging onto the data so that we can
     * write it out
     */
    final_job = darshan_global_job;
    darshan_global_job = NULL;
    CP_UNLOCK();

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    start_log_time = DARSHAN_MPI_CALL(PMPI_Wtime)();
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    /* figure out which access sizes to log */
    darshan_walk_file_accesses(final_job);

    /* if the records have been condensed, then zero out fields that are no
     * longer valid for safety 
     */
    if(final_job->flags & CP_FLAG_CONDENSED && final_job->file_count)
    {
        CP_SET(&final_job->file_runtime_array[0], CP_MODE, 0);
        CP_SET(&final_job->file_runtime_array[0], CP_CONSEC_READS, 0);
        CP_SET(&final_job->file_runtime_array[0], CP_CONSEC_WRITES, 0);
        CP_SET(&final_job->file_runtime_array[0], CP_SEQ_READS, 0);
        CP_SET(&final_job->file_runtime_array[0], CP_SEQ_WRITES, 0);
        CP_SET(&final_job->file_runtime_array[0], CP_STRIDE1_STRIDE, 0);
        CP_SET(&final_job->file_runtime_array[0], CP_STRIDE2_STRIDE, 0);
        CP_SET(&final_job->file_runtime_array[0], CP_STRIDE3_STRIDE, 0);
        CP_SET(&final_job->file_runtime_array[0], CP_STRIDE4_STRIDE, 0);
        CP_SET(&final_job->file_runtime_array[0], CP_STRIDE1_COUNT, 0);
        CP_SET(&final_job->file_runtime_array[0], CP_STRIDE2_COUNT, 0);
        CP_SET(&final_job->file_runtime_array[0], CP_STRIDE3_COUNT, 0);
        CP_SET(&final_job->file_runtime_array[0], CP_STRIDE4_COUNT, 0);
        CP_SET(&final_job->file_runtime_array[0], CP_ACCESS1_ACCESS, 0);
        CP_SET(&final_job->file_runtime_array[0], CP_ACCESS2_ACCESS, 0);
        CP_SET(&final_job->file_runtime_array[0], CP_ACCESS3_ACCESS, 0);
        CP_SET(&final_job->file_runtime_array[0], CP_ACCESS4_ACCESS, 0);
        CP_SET(&final_job->file_runtime_array[0], CP_ACCESS1_COUNT, 0);
        CP_SET(&final_job->file_runtime_array[0], CP_ACCESS2_COUNT, 0);
        CP_SET(&final_job->file_runtime_array[0], CP_ACCESS3_COUNT, 0);
        CP_SET(&final_job->file_runtime_array[0], CP_ACCESS4_COUNT, 0);
        
        CP_F_SET(&final_job->file_runtime_array[0], CP_F_OPEN_TIMESTAMP, 0);
        CP_F_SET(&final_job->file_runtime_array[0], CP_F_CLOSE_TIMESTAMP, 0);
        CP_F_SET(&final_job->file_runtime_array[0], CP_F_READ_START_TIMESTAMP, 0);
        CP_F_SET(&final_job->file_runtime_array[0], CP_F_READ_END_TIMESTAMP, 0);
        CP_F_SET(&final_job->file_runtime_array[0], CP_F_WRITE_START_TIMESTAMP, 0);
        CP_F_SET(&final_job->file_runtime_array[0], CP_F_WRITE_END_TIMESTAMP, 0);
    }

    logfile_name = malloc(PATH_MAX);
    if(!logfile_name)
    {
        darshan_finalize(final_job);
        return;
    }

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    DARSHAN_MPI_CALL(PMPI_Comm_rank)(MPI_COMM_WORLD, &rank);
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    /* construct log file name */
    if(rank == 0)
    {
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        /* Use CP_JOBID_OVERRIDE for the env var or CP_JOBID */
        envjobid = getenv(CP_JOBID_OVERRIDE);
        if (!envjobid)
        {
            envjobid = CP_JOBID;
        }

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        /* find a job id */
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        jobid_str = getenv(envjobid);
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        if(jobid_str)
        {
            /* in cobalt we can find it in env var */
            ret = sscanf(jobid_str, "%d", &jobid);
        }
        if(!jobid_str || ret != 1)
        {
            /* use pid as fall back */
            jobid = getpid();
        }

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        /* add jobid to darshan runtime info */
        final_job->log_job.jobid = (int64_t)jobid;

        /* if user specifies a logfile name (and path), use that. otherwise automatically generate */
        user_logfile_name = getenv("DARSHAN_LOGFILE");
        if(user_logfile_name)
        {
            if(strlen(user_logfile_name) >= PATH_MAX)
            {
                logfile_name[0] = '\0';
                fprintf(stderr, "darshan library warning: user given log file path too long\n");
            }
            else
            {
                strncpy(logfile_name, user_logfile_name, PATH_MAX);
            }
        }
        else
        {
            char cuser[L_cuserid] = {0};
            struct tm* my_tm;

            /* Use CP_LOG_PATH_OVERRIDE for the value or __CP_LOG_PATH */
            logpath = getenv(CP_LOG_PATH_OVERRIDE);
            if (!logpath)
            {
#ifdef __CP_LOG_PATH
                logpath = __CP_LOG_PATH;
#endif
            }

            /* break out time into something human readable */
            start_time_tmp += final_job->log_job.start_time;
            my_tm = localtime(&start_time_tmp);

            /* get the username for this job.  In order we will try each of the
             * following until one of them succeeds:
             *
             * - cuserid()
             * - getenv("LOGNAME")
             * - snprintf(..., geteuid());
             *
             * Note that we do not use getpwuid() because it generally will not
             * work in statically compiled binaries.
             */
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#ifndef DARSHAN_DISABLE_CUSERID
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            cuserid(cuser);
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#endif
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            /* if cuserid() didn't work, then check the environment */
            if (strcmp(cuser, "") == 0)
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            {
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                char* logname_string;
                logname_string = getenv("LOGNAME");
                if(logname_string)
                {
                    strncpy(cuser, logname_string, (L_cuserid-1));
                }
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            }
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            /* if cuserid() and environment both fail, then fall back to uid */
            if (strcmp(cuser, "") == 0)
            {
                uid_t uid = geteuid();
                snprintf(cuser, sizeof(cuser), "%u", uid);
            }
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            /* generate a random number to help differentiate the log */
            hlevel=DARSHAN_MPI_CALL(PMPI_Wtime)() * 1000000;
            (void) gethostname(hname, sizeof(hname));
            logmod = darshan_hash((void*)hname,strlen(hname),hlevel);
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            /* see if darshan was configured using the --with-logpath-by-env
             * argument, which allows the user to specify an absolute path to
             * place logs via an env variable.
             */
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#ifdef __CP_LOG_ENV
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            /* just silently skip if the environment variable list is too big */
            if(strlen(__CP_LOG_ENV) < 256)
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            {
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                /* copy env variable list to a temporary buffer */
                strcpy(env_check, __CP_LOG_ENV);
                /* tokenize the comma-separated list */
                env_tok = strtok(env_check, ",");
                if(env_tok)
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                {
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                    do
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                    {
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                        /* check each env variable in order */
                        logpath_override = getenv(env_tok); 
                        if(logpath_override)
                        {
                            /* stop as soon as we find a match */
                            break;
                        }
                    }while((env_tok = strtok(NULL, ",")));
                }
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            }
#endif
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            if(logpath_override)
            {
                ret = snprintf(logfile_name, PATH_MAX, 
                    "%s/%s_%s_id%d_%d-%d-%d-%" PRIu64 ".darshan_partial",
                    logpath_override, 
                    cuser, __progname, jobid,
                    (my_tm->tm_mon+1), 
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                my_tm->tm_mday, 
                (my_tm->tm_hour*60*60 + my_tm->tm_min*60 + my_tm->tm_sec),
                logmod);
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                if(ret == (PATH_MAX-1))
                {
                    /* file name was too big; squish it down */
                    snprintf(logfile_name, PATH_MAX,
                        "%s/id%d.darshan_partial",
                        logpath_override, jobid);
                }
            }
            else if(logpath)
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            {
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                ret = snprintf(logfile_name, PATH_MAX, 
                    "%s/%d/%d/%d/%s_%s_id%d_%d-%d-%d-%" PRIu64 ".darshan_partial",
                    logpath, (my_tm->tm_year+1900), 
                    (my_tm->tm_mon+1), my_tm->tm_mday, 
                    cuser, __progname, jobid,
                    (my_tm->tm_mon+1), 
                    my_tm->tm_mday, 
                    (my_tm->tm_hour*60*60 + my_tm->tm_min*60 + my_tm->tm_sec),
                    logmod);
                if(ret == (PATH_MAX-1))
                {
                    /* file name was too big; squish it down */
                    snprintf(logfile_name, PATH_MAX,
                        "%s/id%d.darshan_partial",
                        logpath, jobid);
                }
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            }
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            else
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            {
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                logfile_name[0] = '\0';
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            }
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        }
    }

    /* broadcast log file name */
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    bcst=DARSHAN_MPI_CALL(PMPI_Wtime)();
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    DARSHAN_MPI_CALL(PMPI_Bcast)(logfile_name, PATH_MAX, MPI_CHAR, 0,
        MPI_COMM_WORLD);
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    if(strlen(logfile_name) == 0)
    {
        /* failed to generate log file name */
        darshan_finalize(final_job);
545
        return;
546 547
    }

548 549
    final_job->log_job.end_time = time(NULL);

550 551 552 553 554 555 556 557 558 559 560
    /* reduce to report first start time and last end time across all ranks
     * at rank 0
     */
    DARSHAN_MPI_CALL(PMPI_Reduce)(&final_job->log_job.start_time, &first_start_time, 1, MPI_LONG_LONG, MPI_MIN, 0, MPI_COMM_WORLD); 
    DARSHAN_MPI_CALL(PMPI_Reduce)(&final_job->log_job.end_time, &last_end_time, 1, MPI_LONG_LONG, MPI_MAX, 0, MPI_COMM_WORLD); 
    if(rank == 0)
    {
        final_job->log_job.start_time = first_start_time;
        final_job->log_job.end_time = last_end_time;
    }

561 562
    /* reduce records for shared files */
    if(timing_flag)
563
        red1 = DARSHAN_MPI_CALL(PMPI_Wtime)();
564 565 566 567 568 569 570 571 572
    if(getenv("DARSHAN_DISABLE_SHARED_REDUCTION"))
    {
        local_ret = 0;
    }
    else
    {
        local_ret = cp_log_reduction(final_job, rank, logfile_name, 
            &next_offset);
    }
573
    if(timing_flag)
574 575
        red2 = DARSHAN_MPI_CALL(PMPI_Wtime)();
    DARSHAN_MPI_CALL(PMPI_Allreduce)(&local_ret, &all_ret, 1, MPI_INT, MPI_LOR, 
576 577
        MPI_COMM_WORLD);

578 579 580
    /* adjust timestamps in any remaining records */
    cp_normalize_timestamps(final_job);

581 582 583
    /* if we are using any hints to write the log file, then record those
     * hints in the log file header
     */
584
    cp_log_record_hints_and_ver(final_job, rank);
585

586 587 588 589
    if(all_ret == 0)
    {
        /* collect data to write from local process */
        cp_log_construct_indices(final_job, rank, &index_count, lengths, 
590
            pointers, final_job->trailing_data);
591 592 593 594 595 596
    }

    if(all_ret == 0)
    {
        /* compress data */
        if(timing_flag)
597
            gz1 = DARSHAN_MPI_CALL(PMPI_Wtime)();
598 599 600
        local_ret = cp_log_compress(final_job, rank, &index_count, 
            lengths, pointers);
        if(timing_flag)
601 602 603
            gz2 = DARSHAN_MPI_CALL(PMPI_Wtime)();
        DARSHAN_MPI_CALL(PMPI_Allreduce)(&local_ret, &all_ret, 1,
            MPI_INT, MPI_LOR, MPI_COMM_WORLD);
604 605 606 607 608 609
    }

    if(all_ret == 0)
    {
        /* actually write out log file */
        if(timing_flag)
610
            write1 = DARSHAN_MPI_CALL(PMPI_Wtime)();
611
        local_ret = cp_log_write(final_job, rank, logfile_name, 
612 613
            index_count, lengths, pointers, start_log_time);
        if(timing_flag)
614 615 616
            write2 = DARSHAN_MPI_CALL(PMPI_Wtime)();
        DARSHAN_MPI_CALL(PMPI_Allreduce)(&local_ret, &all_ret, 1,
            MPI_INT, MPI_LOR, MPI_COMM_WORLD);
617 618
    }

619
    if(rank == 0)
620
    {
621 622 623 624 625 626 627 628
        if(all_ret != 0)
        {
            fprintf(stderr, "darshan library warning: unable to write log file %s\n", logfile_name);
            /* if any process failed to write log, then delete the whole 
             * file so we don't leave corrupted results
             */
            unlink(logfile_name);
        }
629 630 631 632 633 634 635 636 637
        else if (user_logfile_name)
        {
            /* we do not need to rename file, just change the permissions */
#ifdef __CP_GROUP_READABLE_LOGS
            chmod(user_logfile_name, (S_IRUSR|S_IRGRP));
#else
            chmod(user_logfile_name, (S_IRUSR));
#endif
        }
638 639 640 641 642 643 644 645 646 647 648 649 650 651 652 653 654 655 656 657
        else
        {
            /* rename from *.darshan_partial to *-<logwritetime>.darshan.gz,
             * which indicates that this log file is complete and ready for
             * analysis
             */ 
            char* mod_index;
            double end_log_time;
            char* new_logfile_name;

            new_logfile_name = malloc(PATH_MAX);
            if(new_logfile_name)
            {
                new_logfile_name[0] = '\0';
                end_log_time = DARSHAN_MPI_CALL(PMPI_Wtime)();
                strcat(new_logfile_name, logfile_name);
                mod_index = strstr(new_logfile_name, ".darshan_partial");
                sprintf(mod_index, "_%d.darshan.gz", (int)(end_log_time-start_log_time+1));
                rename(logfile_name, new_logfile_name);
                /* set permissions on log file */
658 659 660
#ifdef __CP_GROUP_READABLE_LOGS
                chmod(new_logfile_name, (S_IRUSR|S_IRGRP)); 
#else
661
                chmod(new_logfile_name, (S_IRUSR)); 
662
#endif
663 664 665
                free(new_logfile_name);
            }
        }
666 667
    }

668 669
    if(final_job->trailing_data)
        free(final_job->trailing_data);
670
    mnt_data_count = 0;
671 672 673 674 675 676 677 678 679
    free(logfile_name);
    darshan_finalize(final_job);
    
    if(timing_flag)
    {
        double red_tm, red_slowest;
        double gz_tm, gz_slowest;
        double write_tm, write_slowest;
        double all_tm, all_slowest;
680
        double bcst_tm, bcst_slowest;
681
        
682
        tm_end = DARSHAN_MPI_CALL(PMPI_Wtime)();
683

684
        bcst_tm= red1-bcst;
685 686 687 688 689
        red_tm = red2-red1;
        gz_tm = gz2-gz1;
        write_tm = write2-write1;
        all_tm = tm_end-start_log_time;

690 691 692 693 694 695 696 697 698 699
        DARSHAN_MPI_CALL(PMPI_Reduce)(&red_tm, &red_slowest, 1,
            MPI_DOUBLE, MPI_MAX, 0, MPI_COMM_WORLD);
        DARSHAN_MPI_CALL(PMPI_Reduce)(&gz_tm, &gz_slowest, 1,
            MPI_DOUBLE, MPI_MAX, 0, MPI_COMM_WORLD);
        DARSHAN_MPI_CALL(PMPI_Reduce)(&write_tm, &write_slowest, 1,
            MPI_DOUBLE, MPI_MAX, 0, MPI_COMM_WORLD);
        DARSHAN_MPI_CALL(PMPI_Reduce)(&all_tm, &all_slowest, 1,
            MPI_DOUBLE, MPI_MAX, 0, MPI_COMM_WORLD);
        DARSHAN_MPI_CALL(PMPI_Reduce)(&bcst_tm, &bcst_slowest, 1,
            MPI_DOUBLE, MPI_MAX, 0, MPI_COMM_WORLD);
700 701 702

        if(rank == 0)
        {
703
            DARSHAN_MPI_CALL(PMPI_Comm_size)(MPI_COMM_WORLD, &nprocs);
704 705 706 707 708
            printf("#darshan:<op>\t<nprocs>\t<time>\n");
            printf("darshan:bcst\t%d\t%f\n", nprocs, bcst_slowest);
            printf("darshan:reduce\t%d\t%f\n", nprocs, red_slowest);
            printf("darshan:gzip\t%d\t%f\n", nprocs, gz_slowest);
            printf("darshan:write\t%d\t%f\n", nprocs, write_slowest);
709
            printf("darshan:bcast+reduce+gzip+write\t%d\t%f\n", nprocs, all_slowest);
710 711 712 713 714 715
        }
    }

    return;
}

716 717 718
#ifdef HAVE_MPIIO_CONST
int MPI_File_open(MPI_Comm comm, const char *filename, int amode, MPI_Info info, MPI_File *fh) 
#else
719
int MPI_File_open(MPI_Comm comm, char *filename, int amode, MPI_Info info, MPI_File *fh) 
720
#endif
721 722 723 724 725 726 727 728
{
    int ret;
    struct darshan_file_runtime* file;
    char* tmp;
    int comm_size;
    double tm1, tm2;

    tm1 = darshan_wtime();
729
    ret = DARSHAN_MPI_CALL(PMPI_File_open)(comm, filename, amode, info, fh);
730 731 732 733 734 735 736 737 738 739 740 741 742 743 744 745
    tm2 = darshan_wtime();

    if(ret == MPI_SUCCESS)
    {
        CP_LOCK();

        /* use ROMIO approach to strip prefix if present */
        /* strip off prefix if there is one, but only skip prefixes
         * if they are greater than length one to allow for windows
         * drive specifications (e.g. c:\...) 
         */
        tmp = strchr(filename, ':');
        if (tmp > filename + 1) {
            filename = tmp + 1;
        }

746 747
        file = darshan_file_by_name_setfh(filename, (*fh));
        if(file)
748 749
        {
            CP_SET(file, CP_MODE, amode);
750
            CP_F_INC_NO_OVERLAP(file, tm1, tm2, file->last_mpi_meta_end, CP_F_MPI_META_TIME);
751
            if(CP_F_VALUE(file, CP_F_OPEN_TIMESTAMP) == 0)
752
                CP_F_SET(file, CP_F_OPEN_TIMESTAMP,
753
                tm1);
754
            DARSHAN_MPI_CALL(PMPI_Comm_size)(comm, &comm_size);
755 756 757 758 759 760 761 762 763 764 765 766 767
            if(comm_size == 1)
            {
                CP_INC(file, CP_INDEP_OPENS, 1);
            }
            else
            {
                CP_INC(file, CP_COLL_OPENS, 1);
            }
            if(info != MPI_INFO_NULL)
            {
                CP_INC(file, CP_HINTS, 1);
            }
        }
768

769 770 771 772 773 774 775 776 777 778 779 780 781 782
        CP_UNLOCK();
    }

    return(ret);
}

int MPI_File_close(MPI_File *fh) 
{
    struct darshan_file_runtime* file;
    MPI_File tmp_fh = *fh;
    double tm1, tm2;
    int ret;
    
    tm1 = darshan_wtime();
783
    ret = DARSHAN_MPI_CALL(PMPI_File_close)(fh);
784 785 786 787 788 789
    tm2 = darshan_wtime();

    CP_LOCK();
    file = darshan_file_by_fh(tmp_fh);
    if(file)
    {
790
        CP_F_SET(file, CP_F_CLOSE_TIMESTAMP, DARSHAN_MPI_CALL(PMPI_Wtime)());
791
        CP_F_INC_NO_OVERLAP(file, tm1, tm2, file->last_mpi_meta_end, CP_F_MPI_META_TIME);
792
        darshan_file_close_fh(tmp_fh);
793 794 795 796 797 798 799 800 801 802 803 804 805
    }
    CP_UNLOCK();

    return(ret);
}

int MPI_File_sync(MPI_File fh)
{
    int ret;
    struct darshan_file_runtime* file;
    double tm1, tm2;

    tm1 = darshan_wtime();
806
    ret = DARSHAN_MPI_CALL(PMPI_File_sync)(fh);
807 808 809 810 811 812 813
    tm2 = darshan_wtime();
    if(ret == MPI_SUCCESS)
    {
        CP_LOCK();
        file = darshan_file_by_fh(fh);
        if(file)
        {
814
            CP_F_INC_NO_OVERLAP(file, tm1, tm2, file->last_mpi_write_end, CP_F_MPI_WRITE_TIME);
815 816 817 818 819 820 821 822 823
            CP_INC(file, CP_SYNCS, 1);
        }
        CP_UNLOCK();
    }

    return(ret);
}


824 825 826 827
#ifdef HAVE_MPIIO_CONST
int MPI_File_set_view(MPI_File fh, MPI_Offset disp, MPI_Datatype etype, 
    MPI_Datatype filetype, const char *datarep, MPI_Info info)
#else
828 829
int MPI_File_set_view(MPI_File fh, MPI_Offset disp, MPI_Datatype etype, 
    MPI_Datatype filetype, char *datarep, MPI_Info info)
830
#endif
831 832 833 834 835 836
{
    int ret;
    struct darshan_file_runtime* file;
    double tm1, tm2;

    tm1 = darshan_wtime();
837 838
    ret = DARSHAN_MPI_CALL(PMPI_File_set_view)(fh, disp, etype,
        filetype, datarep, info);
839 840 841 842 843 844 845 846 847 848
    tm2 = darshan_wtime();
    if(ret == MPI_SUCCESS)
    {
        CP_LOCK();
        file = darshan_file_by_fh(fh);
        if(file)
        {
            CP_INC(file, CP_VIEWS, 1);
            if(info != MPI_INFO_NULL)
            {
849
                CP_F_INC_NO_OVERLAP(file, tm1, tm2, file->last_mpi_meta_end, CP_F_MPI_META_TIME);
850 851 852 853 854 855 856 857 858 859 860 861 862 863 864 865 866
                CP_INC(file, CP_HINTS, 1);
            }
            CP_DATATYPE_INC(file, filetype);
        }
        CP_UNLOCK();
    }

    return(ret);
}

int MPI_File_read(MPI_File fh, void *buf, int count, 
    MPI_Datatype datatype, MPI_Status *status)
{
    int ret;
    double tm1, tm2;

    tm1 = darshan_wtime();
867
    ret = DARSHAN_MPI_CALL(PMPI_File_read)(fh, buf, count, datatype, status);
868 869 870 871 872 873 874 875 876 877 878 879 880 881
    tm2 = darshan_wtime();
    CP_LOCK();
    CP_RECORD_MPI_READ(ret, fh, count, datatype, CP_INDEP_READS, tm1, tm2);
    CP_UNLOCK();
    return(ret);
}

int MPI_File_read_at(MPI_File fh, MPI_Offset offset, void *buf,
    int count, MPI_Datatype datatype, MPI_Status *status)
{
    int ret;
    double tm1, tm2;

    tm1 = darshan_wtime();
882 883
    ret = DARSHAN_MPI_CALL(PMPI_File_read_at)(fh, offset, buf,
        count, datatype, status);
884 885 886 887 888 889 890 891 892 893 894 895 896 897
    tm2 = darshan_wtime();
    CP_LOCK();
    CP_RECORD_MPI_READ(ret, fh, count, datatype, CP_INDEP_READS, tm1, tm2);
    CP_UNLOCK();
    return(ret);
}

int MPI_File_read_at_all(MPI_File fh, MPI_Offset offset, void * buf,
    int count, MPI_Datatype datatype, MPI_Status * status)
{
    int ret;
    double tm1, tm2;

    tm1 = darshan_wtime();
898 899
    ret = DARSHAN_MPI_CALL(PMPI_File_read_at_all)(fh, offset, buf,
        count, datatype, status);
900 901 902 903 904 905 906 907 908 909 910 911 912
    tm2 = darshan_wtime();
    CP_LOCK();
    CP_RECORD_MPI_READ(ret, fh, count, datatype, CP_COLL_READS, tm1, tm2);
    CP_UNLOCK();
    return(ret);
}

int MPI_File_read_all(MPI_File fh, void * buf, int count, MPI_Datatype datatype, MPI_Status *status)
{
    int ret;
    double tm1, tm2;

    tm1 = darshan_wtime();
913 914
    ret = DARSHAN_MPI_CALL(PMPI_File_read_all)(fh, buf, count,
        datatype, status);
915 916 917 918 919 920 921 922 923 924 925 926 927
    tm2 = darshan_wtime();
    CP_LOCK();
    CP_RECORD_MPI_READ(ret, fh, count, datatype, CP_COLL_READS, tm1, tm2);
    CP_UNLOCK();
    return(ret);
}

int MPI_File_read_shared(MPI_File fh, void * buf, int count, MPI_Datatype datatype, MPI_Status *status)
{
    int ret;
    double tm1, tm2;

    tm1 = darshan_wtime();
928 929
    ret = DARSHAN_MPI_CALL(PMPI_File_read_shared)(fh, buf, count,
        datatype, status);
930 931 932 933 934 935 936 937 938 939 940 941 942 943
    tm2 = darshan_wtime();
    CP_LOCK();
    CP_RECORD_MPI_READ(ret, fh, count, datatype, CP_INDEP_READS, tm1, tm2);
    CP_UNLOCK();
    return(ret);
}

int MPI_File_read_ordered(MPI_File fh, void * buf, int count, 
    MPI_Datatype datatype, MPI_Status * status)
{
    int ret;
    double tm1, tm2;

    tm1 = darshan_wtime();
944 945
    ret = DARSHAN_MPI_CALL(PMPI_File_read_ordered)(fh, buf, count,
        datatype, status);
946 947 948 949 950 951 952 953 954 955 956 957 958 959
    tm2 = darshan_wtime();
    CP_LOCK();
    CP_RECORD_MPI_READ(ret, fh, count, datatype, CP_COLL_READS, tm1, tm2);
    CP_UNLOCK();
    return(ret);
}

int MPI_File_read_at_all_begin(MPI_File fh, MPI_Offset offset, void * buf,
    int count, MPI_Datatype datatype)
{
    int ret;
    double tm1, tm2;

    tm1 = darshan_wtime();
960 961
    ret = DARSHAN_MPI_CALL(PMPI_File_read_at_all_begin)(fh, offset, buf,
        count, datatype);
962 963 964 965 966 967 968 969 970 971 972 973 974
    tm2 = darshan_wtime();
    CP_LOCK();
    CP_RECORD_MPI_READ(ret, fh, count, datatype, CP_SPLIT_READS, tm1, tm2);
    CP_UNLOCK();
    return(ret);
}

int MPI_File_read_all_begin(MPI_File fh, void * buf, int count, MPI_Datatype datatype)
{
    int ret;
    double tm1, tm2;

    tm1 = darshan_wtime();
975
    ret = DARSHAN_MPI_CALL(PMPI_File_read_all_begin)(fh, buf, count, datatype);
976 977 978 979 980 981 982 983 984 985 986 987 988
    tm2 = darshan_wtime();
    CP_LOCK();
    CP_RECORD_MPI_READ(ret, fh, count, datatype, CP_SPLIT_READS, tm1, tm2);
    CP_UNLOCK();
    return(ret);
}

int MPI_File_read_ordered_begin(MPI_File fh, void * buf, int count, MPI_Datatype datatype)
{
    int ret;
    double tm1, tm2;

    tm1 = darshan_wtime();
989 990
    ret = DARSHAN_MPI_CALL(PMPI_File_read_ordered_begin)(fh, buf, count,
        datatype);
991 992 993 994 995 996 997 998
    tm2 = darshan_wtime();
    CP_LOCK();
    CP_RECORD_MPI_READ(ret, fh, count, datatype, CP_SPLIT_READS, tm1, tm2);
    CP_UNLOCK();
    return(ret);
}

int MPI_File_iread_at(MPI_File fh, MPI_Offset offset, void * buf,
999
    int count, MPI_Datatype datatype, __D_MPI_REQUEST *request)
1000 1001 1002 1003 1004
{
    int ret;
    double tm1, tm2;

    tm1 = darshan_wtime();
1005 1006
    ret = DARSHAN_MPI_CALL(PMPI_File_iread_at)(fh, offset, buf, count,
        datatype, request);
1007 1008 1009 1010 1011 1012 1013
    tm2 = darshan_wtime();
    CP_LOCK();
    CP_RECORD_MPI_READ(ret, fh, count, datatype, CP_NB_READS, tm1, tm2);
    CP_UNLOCK();
    return(ret);
}

1014
int MPI_File_iread(MPI_File fh, void * buf, int count, MPI_Datatype datatype, __D_MPI_REQUEST * request)
1015 1016 1017 1018 1019
{
    int ret;
    double tm1, tm2;

    tm1 = darshan_wtime();
1020
    ret = DARSHAN_MPI_CALL(PMPI_File_iread)(fh, buf, count, datatype, request);
1021 1022 1023 1024 1025 1026 1027 1028
    tm2 = darshan_wtime();
    CP_LOCK();
    CP_RECORD_MPI_READ(ret, fh, count, datatype, CP_NB_READS, tm1, tm2);
    CP_UNLOCK();
    return(ret);
}

int MPI_File_iread_shared(MPI_File fh, void * buf, int count,
1029
    MPI_Datatype datatype, __D_MPI_REQUEST * request)
1030 1031 1032 1033 1034
{
    int ret;
    double tm1, tm2;

    tm1 = darshan_wtime();
1035 1036
    ret = DARSHAN_MPI_CALL(PMPI_File_iread_shared)(fh, buf, count,
        datatype, request);
1037 1038 1039 1040 1041 1042 1043 1044
    tm2 = darshan_wtime();
    CP_LOCK();
    CP_RECORD_MPI_READ(ret, fh, count, datatype, CP_NB_READS, tm1, tm2);
    CP_UNLOCK();
    return(ret);
}


1045 1046 1047 1048
#ifdef HAVE_MPIIO_CONST
int MPI_File_write(MPI_File fh, const void *buf, int count, 
    MPI_Datatype datatype, MPI_Status *status)
#else
1049 1050
int MPI_File_write(MPI_File fh, void *buf, int count, 
    MPI_Datatype datatype, MPI_Status *status)
1051
#endif
1052 1053 1054 1055 1056
{
    int ret;
    double tm1, tm2;

    tm1 = darshan_wtime();
1057
    ret = DARSHAN_MPI_CALL(PMPI_File_write)(fh, buf, count, datatype, status);
1058 1059 1060 1061 1062 1063 1064
    tm2 = darshan_wtime();
    CP_LOCK();
    CP_RECORD_MPI_WRITE(ret, fh, count, datatype, CP_INDEP_WRITES, tm1, tm2);
    CP_UNLOCK();
    return(ret);
}

1065 1066 1067 1068
#ifdef HAVE_MPIIO_CONST
int MPI_File_write_at(MPI_File fh, MPI_Offset offset, const void *buf,
    int count, MPI_Datatype datatype, MPI_Status *status)
#else
1069 1070
int MPI_File_write_at(MPI_File fh, MPI_Offset offset, void *buf,
    int count, MPI_Datatype datatype, MPI_Status *status)
1071
#endif
1072 1073 1074 1075 1076
{
    int ret;
    double tm1, tm2;

    tm1 = darshan_wtime();
1077 1078
    ret = DARSHAN_MPI_CALL(PMPI_File_write_at)(fh, offset, buf,
        count, datatype, status);
1079 1080 1081 1082 1083 1084 1085
    tm2 = darshan_wtime();
    CP_LOCK();
    CP_RECORD_MPI_WRITE(ret, fh, count, datatype, CP_INDEP_WRITES, tm1, tm2);
    CP_UNLOCK();
    return(ret);
}

1086 1087 1088 1089
#ifdef HAVE_MPIIO_CONST
int MPI_File_write_at_all(MPI_File fh, MPI_Offset offset, const void * buf,
    int count, MPI_Datatype datatype, MPI_Status * status)
#else
1090 1091
int MPI_File_write_at_all(MPI_File fh, MPI_Offset offset, void * buf,
    int count, MPI_Datatype datatype, MPI_Status * status)
1092
#endif
1093 1094 1095 1096 1097
{
    int ret;
    double tm1, tm2;

    tm1 = darshan_wtime();
1098 1099
    ret = DARSHAN_MPI_CALL(PMPI_File_write_at_all)(fh, offset, buf,
        count, datatype, status);
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    tm2 = darshan_wtime();
    CP_LOCK();
    CP_RECORD_MPI_WRITE(ret, fh, count, datatype, CP_COLL_WRITES, tm1, tm2);
    CP_UNLOCK();
    return(ret);
}

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#ifdef HAVE_MPIIO_CONST
int MPI_File_write_all(MPI_File fh, const void * buf, int count, MPI_Datatype datatype, MPI_Status *status)
#else
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int MPI_File_write_all(MPI_File fh, void * buf, int count, MPI_Datatype datatype, MPI_Status *status)
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#endif
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{
    int ret;
    double tm1, tm2;

    tm1 = darshan_wtime();
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    ret = DARSHAN_MPI_CALL(PMPI_File_write_all)(fh, buf, count,
        datatype, status);
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    tm2 = darshan_wtime();
    CP_LOCK();
    CP_RECORD_MPI_WRITE(ret, fh, count, datatype, CP_COLL_WRITES, tm1, tm2);
    CP_UNLOCK();
    return(ret);
}

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#ifdef HAVE_MPIIO_CONST
int MPI_File_write_shared(MPI_File fh, const void * buf, int count, MPI_Datatype datatype, MPI_Status *status)
#else
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int MPI_File_write_shared(MPI_File fh, void * buf, int count, MPI_Datatype datatype, MPI_Status *status)
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#endif
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{
    int ret;
    double tm1, tm2;

    tm1 = darshan_wtime();
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    ret = DARSHAN_MPI_CALL(PMPI_File_write_shared)(fh, buf, count,
        datatype, status);
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    tm2 = darshan_wtime();
    CP_LOCK();
    CP_RECORD_MPI_WRITE(ret, fh, count, datatype, CP_INDEP_WRITES, tm1, tm2);
    CP_UNLOCK();
    return(ret);
}

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#ifdef HAVE_MPIIO_CONST
int MPI_File_write_ordered(MPI_File fh, const void * buf, int count, 
    MPI_Datatype datatype, MPI_Status * status)
#else
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int MPI_File_write_ordered(MPI_File fh, void * buf, int count, 
    MPI_Datatype datatype, MPI_Status * status)
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#endif
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{
    int ret;
    double tm1, tm2;

    tm1 = darshan_wtime();
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    ret = DARSHAN_MPI_CALL(PMPI_File_write_ordered)(fh, buf, count,
         datatype, status);
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    tm2 = darshan_wtime();
    CP_LOCK();
    CP_RECORD_MPI_WRITE(ret, fh, count, datatype, CP_COLL_WRITES, tm1, tm2);
    CP_UNLOCK();
    return(ret);
}

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#ifdef HAVE_MPIIO_CONST
int MPI_File_write_at_all_begin(MPI_File fh, MPI_Offset offset, const void * buf,
    int count, MPI_Datatype datatype)
#else
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int MPI_File_write_at_all_begin(MPI_File fh, MPI_Offset offset, void * buf,
    int count, MPI_Datatype datatype)
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#endif
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{
    int ret;
    double tm1, tm2;

    tm1 = darshan_wtime();
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    ret = DARSHAN_MPI_CALL(PMPI_File_write_at_all_begin)(fh, offset,
        buf, count, datatype);
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    tm2 = darshan_wtime();
    CP_LOCK();
    CP_RECORD_MPI_WRITE(ret, fh, count, datatype, CP_SPLIT_WRITES, tm1, tm2);
    CP_UNLOCK();
    return(ret);
}

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#ifdef HAVE_MPIIO_CONST
int MPI_File_write_all_begin(MPI_File fh, const void * buf, int count, MPI_Datatype datatype)
#else
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int MPI_File_write_all_begin(MPI_File fh, void * buf, int count, MPI_Datatype datatype)
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#endif
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{
    int ret;
    double tm1, tm2;

    tm1 = darshan_wtime();
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    ret = DARSHAN_MPI_CALL(PMPI_File_write_all_begin)(fh, buf, count, datatype);
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    tm2 = darshan_wtime();
    CP_LOCK();
    CP_RECORD_MPI_WRITE(ret, fh, count, datatype, CP_SPLIT_WRITES, tm1, tm2);
    CP_UNLOCK();
    return(ret);
}

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#ifdef HAVE_MPIIO_CONST
int MPI_File_write_ordered_begin(MPI_File fh, const void * buf, int count, MPI_Datatype datatype)
#else
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int MPI_File_write_ordered_begin(MPI_File fh, void * buf, int count, MPI_Datatype datatype)
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#endif
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{
    int ret;
    double tm1, tm2;

    tm1 = darshan_wtime();
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    ret = DARSHAN_MPI_CALL(PMPI_File_write_ordered_begin)(fh, buf, count,
        datatype);
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    tm2 = darshan_wtime();
    CP_LOCK();
    CP_RECORD_MPI_WRITE(ret, fh, count, datatype, CP_SPLIT_WRITES, tm1, tm2);
    CP_UNLOCK();
    return(ret);
}

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#ifdef HAVE_MPIIO_CONST
int MPI_File_iwrite_at(MPI_File fh, MPI_Offset offset, const void * buf,
    int count, MPI_Datatype datatype, __D_MPI_REQUEST *request)
#else
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int MPI_File_iwrite_at(MPI_File fh, MPI_Offset offset, void * buf,
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    int count, MPI_Datatype datatype, __D_MPI_REQUEST *request)
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#endif
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{
    int ret;
    double tm1, tm2;

    tm1 = darshan_wtime();
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    ret = DARSHAN_MPI_CALL(PMPI_File_iwrite_at)(fh, offset, buf,
        count, datatype, request);
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    tm2 = darshan_wtime();
    CP_LOCK();
    CP_RECORD_MPI_WRITE(ret, fh, count, datatype, CP_NB_WRITES, tm1, tm2);
    CP_UNLOCK();
    return(ret);
}

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#ifdef HAVE_MPIIO_CONST
int MPI_File_iwrite(MPI_File fh, const void * buf, int count, MPI_Datatype datatype, __D_MPI_REQUEST * request)
#else
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int MPI_File_iwrite(MPI_File fh, void * buf, int count, MPI_Datatype datatype, __D_MPI_REQUEST * request)
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#endif
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{
    int ret;
    double tm1, tm2;

    tm1 = darshan_wtime();
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    ret = DARSHAN_MPI_CALL(PMPI_File_iwrite)(fh, buf, count, datatype, request);
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    tm2 = darshan_wtime();
    CP_LOCK();
    CP_RECORD_MPI_WRITE(ret, fh, count, datatype, CP_NB_WRITES, tm1, tm2);
    CP_UNLOCK();
    return(ret);
}

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#ifdef HAVE_MPIIO_CONST
int MPI_File_iwrite_shared(MPI_File fh, const void * buf, int count,
    MPI_Datatype datatype, __D_MPI_REQUEST * request)
#else
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int MPI_File_iwrite_shared(MPI_File fh, void * buf, int count,
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    MPI_Datatype datatype, __D_MPI_REQUEST * request)
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#endif
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{
    int ret;
    double tm1, tm2;

    tm1 = darshan_wtime();
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    ret = DARSHAN_MPI_CALL(PMPI_File_iwrite_shared)(fh, buf, count,
        datatype, request);
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    tm2 = darshan_wtime();
    CP_LOCK();
    CP_RECORD_MPI_WRITE(ret, fh, count, datatype, CP_NB_WRITES, tm1, tm2);
    CP_UNLOCK();
    return(ret);
}

/* cp_log_reduction()
 *
 * Identify shared files and reduce them to one log entry
 *
 * returns 0 on success, -1 on failure
 */
static int cp_log_reduction(struct darshan_job_runtime* final_job, int rank, 
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    char* logfile_name, MPI_Offset* next_offset)
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{
    /* TODO: these need to be allocated differently now, too big */
    uint64_t hash_array[CP_MAX_FILES] = {0};
    int mask_array[CP_MAX_FILES] = {0};
    int all_mask_array[CP_MAX_FILES] = {0};
    int ret;
    int i;
    int j;
    MPI_Op reduce_op;
    MPI_Datatype rtype;
    struct darshan_file* tmp_array = NULL;
    int shared_count = 0;
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    double mpi_time, posix_time;
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    /* register a reduction operation */
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    ret = DARSHAN_MPI_CALL(PMPI_Op_create)(darshan_file_reduce, 1, &reduce_op); 
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    if(ret != 0)
    {
        return(-1);
    }

    /* construct a datatype for a file record.  This is serving no purpose
     * except to make sure we can do a reduction on proper boundaries
     */
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    DARSHAN_MPI_CALL(PMPI_Type_contiguous)(sizeof(struct darshan_file),
        MPI_BYTE, &rtype); 
    DARSHAN_MPI_CALL(PMPI_Type_commit)(&rtype); 
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    /* gather list of files that root process has opened */
    if(rank == 0)
    {
        for(i=0; i<final_job->file_count; i++)
        {
            hash_array[i] = final_job->file_array[i].hash;
        }
    }

    /* broadcast list of files to all other processes */
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    ret = DARSHAN_MPI_CALL(PMPI_Bcast)(hash_array,
        (CP_MAX_FILES * sizeof(uint64_t)), 
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        MPI_BYTE, 0, MPI_COMM_WORLD);
    if(ret != 0)
    {
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        DARSHAN_MPI_CALL(PMPI_Op_free)(&reduce_op);
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        DARSHAN_MPI_CALL(PMPI_Type_free)(&rtype);
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        return(-1);
    }

    /* everyone looks to see if they have also opened that same file */
    for(i=0; (i<CP_MAX_FILES && hash_array[i] != 0); i++)
    {
        for(j=0; j<final_job->file_count; j++)
        {
            if(hash_array[i] && final_job->file_array[j].hash == hash_array[i])
            {
                /* we opened that file too */
                mask_array[i] = 1;
                break;
            }
        }
    }

    /* now allreduce so that everyone agrees on which files are shared */
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    ret = DARSHAN_MPI_CALL(PMPI_Allreduce)(mask_array, all_mask_array,
        CP_MAX_FILES, MPI_INT, MPI_LAND, MPI_COMM_WORLD);
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    if(ret != 0)
    {
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        DARSHAN_MPI_CALL(PMPI_Op_free)(&reduce_op);
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        DARSHAN_MPI_CALL(PMPI_Type_free)(&rtype);
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        return(-1);
    }

    /* walk through mask array counting entries and marking corresponding
     * files with a rank of -1
     */
    for(i=0; i<CP_MAX_FILES; i++)
    {
        if(all_mask_array[i])
        {
            shared_count++;
            for(j=0; j<final_job->file_count; j++)
            {
                if(final_job->file_array[j].hash == hash_array[i])
                {
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                    posix_time = 
                      final_job->file_array[j].fcounters[CP_F_POSIX_META_TIME] +
                      final_job->file_array[j].fcounters[CP_F_POSIX_READ_TIME] +
                      final_job->file_array[j].fcounters[CP_F_POSIX_WRITE_TIME];
                    mpi_time = 
                      final_job->file_array[j].fcounters[CP_F_MPI_META_TIME] +
                      final_job->file_array[j].fcounters[CP_F_MPI_READ_TIME] +
                      final_job->file_array[j].fcounters[CP_F_MPI_WRITE_TIME];
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                    /*
                     * Initialize fastest/slowest info prior
                     * to the reduction.
                     */
                    final_job->file_array[j].counters[CP_FASTEST_RANK] =
                      final_job->file_array[j].rank;
                    final_job->file_array[j].counters[CP_FASTEST_RANK_BYTES] =
                      final_job->file_array[j].counters[CP_BYTES_READ] +
                      final_job->file_array[j].counters[CP_BYTES_WRITTEN];
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                    /* use MPI timing if this file was accessed with MPI */
                    if(mpi_time > 0)
                    {
                        final_job->file_array[j].fcounters[CP_F_FASTEST_RANK_TIME] =
                        mpi_time;
                    }
                    else
                    {
                        final_job->file_array[j].fcounters[CP_F_FASTEST_RANK_TIME] =
                        posix_time;
                    }
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                    /* Until reduction occurs, we assume that this rank is
                     * both the fastest and slowest.  It is up to the
                     * reduction operator to find the true min and max if it
                     * is a shared file.
                     */
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                    final_job->file_array[j].counters[CP_SLOWEST_RANK] =
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                        final_job->file_array[j].counters[CP_FASTEST_RANK];
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                    final_job->file_array[j].counters[CP_SLOWEST_RANK_BYTES] =
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                        final_job->file_array[j].counters[CP_FASTEST_RANK_BYTES];
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                    final_job->file_array[j].fcounters[CP_F_SLOWEST_RANK_TIME] =
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                        final_job->file_array[j].fcounters[CP_F_FASTEST_RANK_TIME];
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                    final_job->file_array[j].rank = -1;
                    break;
                }
            }
        }
    }

    if(shared_count)
    {
        if(rank == 0)
        {
            /* root proc needs to allocate memory to store reduction */
            tmp_array = malloc(shared_count*sizeof(struct darshan_file));
            if(!tmp_array)
            {
                /* TODO: think more about how to handle errors like this */
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                DARSHAN_MPI_CALL(PMPI_Op_free)(&reduce_op);
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                DARSHAN_MPI_CALL(PMPI_Type_free)(&rtype);
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                return(-1);
            }
        }

        /* sort the array of files descending by rank so that we get all of the 
         * shared files (marked by rank -1) in a contiguous portion at end 
         * of the array
         */
        qsort(final_job->file_array, final_job->file_count, 
            sizeof(struct darshan_file), file_compare);

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        ret = DARSHAN_MPI_CALL(PMPI_Reduce)(
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            &final_job->file_array[final_job->file_count-shared_count], 
            tmp_array, shared_count, rtype, reduce_op, 0, MPI_COMM_WORLD);
        if(ret != 0)
        {
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            DARSHAN_MPI_CALL(PMPI_Op_free)(&reduce_op);
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            DARSHAN_MPI_CALL(PMPI_Type_free)(&rtype);
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            return(-1);
        }

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        ret = darshan_file_variance(
            &final_job->file_array[final_job->file_count-shared_count],
            tmp_array, shared_count, rank);
        if (ret)
        {
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            DARSHAN_MPI_CALL(PMPI_Op_free)(&reduce_op);
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            DARSHAN_MPI_CALL(PMPI_Type_free)(&rtype);
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            return(-1);
        }

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        if(rank == 0)
        {
            /* root replaces local files with shared ones */
            memcpy(&final_job->file_array[final_job->file_count-shared_count],
                tmp_array, shared_count*sizeof(struct darshan_file));
            free(tmp_array);
            tmp_array = NULL;
        }
        else
        {
            /* everyone else simply discards those file records */
            final_job->file_count -= shared_count;
        }
    }
    
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    DARSHAN_MPI_CALL(PMPI_Op_free)(&reduce_op);
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    DARSHAN_MPI_CALL(PMPI_Type_free)(&rtype);
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    return(0);
}

/* TODO: should we use more of the CP macros here? */
static void darshan_file_reduce(void* infile_v, 
    void* inoutfile_v, int *len, 
    MPI_Datatype *datatype)
{
    struct darshan_file tmp_file;
    struct darshan_file* infile = infile_v;
    struct darshan_file* inoutfile = inoutfile_v;
    struct darshan_file_runtime tmp_runtime;
    int i;
    int j;
    int k;

    for(i=0; i<*len; i++)
    {
        memset(&tmp_file, 0, sizeof(tmp_file));

        tmp_file.hash = infile->hash;
        tmp_file.rank = -1; /* indicates shared across all procs */

        /* sum */
        for(j=CP_INDEP_OPENS; j<=CP_VIEWS; j++)
        {
            tmp_file.counters[j] = infile->counters[j] + 
                inoutfile->counters[j];
        }

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        /* pick one, favoring complete records if available */
        if(CP_FILE_PARTIAL(infile))
            tmp_file.counters[CP_MODE] = inoutfile->counters[CP_MODE];
        else
            tmp_file.counters[CP_MODE] = infile->counters[CP_MODE];
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        /* sum */
        for(j=CP_BYTES_READ; j<=CP_BYTES_WRITTEN; j++)
        {
            tmp_file.counters[j] = infile->counters[j] + 
                inoutfile->counters[j];
        }

        /* max */
        for(j=CP_MAX_BYTE_READ; j<=CP_MAX_BYTE_WRITTEN; j++)
        {
            tmp_file.counters[j] = (
                (infile->counters[j] > inoutfile->counters[j]) ? 
                infile->counters[j] :
                inoutfile->counters[j]);
        }

        /* sum */
        for(j=CP_CONSEC_READS; j<=CP_MEM_NOT_ALIGNED; j++)
        {
            tmp_file.counters[j] = infile->counters[j] + 
                inoutfile->counters[j];
        }

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        /* pick one, favoring complete records if available */
        if(CP_FILE_PARTIAL(infile))
            tmp_file.counters[CP_MEM_ALIGNMENT] = inoutfile->counters[CP_MEM_ALIGNMENT];
        else
            tmp_file.counters[CP_MEM_ALIGNMENT] = infile->counters[CP_MEM_ALIGNMENT];

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        /* sum */
        for(j=CP_FILE_NOT_ALIGNED; j<=CP_FILE_NOT_ALIGNED; j++)
        {
            tmp_file.counters[j] = infile->counters[j] + 
                inoutfile->counters[j];
        }

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        /* pick one, favoring complete records if available */
        if(CP_FILE_PARTIAL(infile))
            tmp_file.counters[CP_FILE_ALIGNMENT] = inoutfile->counters[CP_FILE_ALIGNMENT];
        else
            tmp_file.counters[CP_FILE_ALIGNMENT] = infile->counters[CP_FILE_ALIGNMENT];
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        /* skip CP_MAX_*_TIME_SIZE; handled in floating point section */

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        /* sum */
        for(j=CP_SIZE_READ_0_100; j<=CP_EXTENT_WRITE_1G_PLUS; j++)
        {
            tmp_file.counters[j] = infile->counters[j] + 
                inoutfile->counters[j];
        }

        /* pick the 4 most common strides out of the 8 we have to chose from */

        /* first collapse any duplicates */
        for(j=CP_STRIDE1_STRIDE; j<=CP_STRIDE4_STRIDE; j++)
        {
            for(k=CP_STRIDE1_STRIDE; k<=CP_STRIDE4_STRIDE; k++)
            {
                if(infile->counters[j] == inoutfile->counters[k])
                {
                    infile->counters[j+4] += inoutfile->counters[k+4];
                    inoutfile->counters[k] = 0;
                    inoutfile->counters[k+4] = 0;
                }
            }
        }

        /* placeholder so we can re-use macros */
        tmp_runtime.log_file = &tmp_file;
        /* first set */
        for(j=CP_STRIDE1_STRIDE; j<=CP_STRIDE4_STRIDE; j++)
        {
            CP_COUNTER_INC(&tmp_runtime, infile->counters[j],
                infile->counters[j+4], 1, CP_STRIDE1_STRIDE, CP_STRIDE1_COUNT);
        }
        /* second set */
        for(j=CP_STRIDE1_STRIDE; j<=CP_STRIDE4_STRIDE; j++)
        {
            CP_COUNTER_INC(&tmp_runtime, inoutfile->counters[j],
                inoutfile->counters[j+4], 1, CP_STRIDE1_STRIDE, CP_STRIDE1_COUNT);
        }

        /* TODO: subroutine so we don't duplicate so much */
        /* same for access counts */

        /* first collapse any duplicates */
        for(j=CP_ACCESS1_ACCESS; j<=CP_ACCESS4_ACCESS; j++)
        {
            for(k=CP_ACCESS1_ACCESS; k<=CP_ACCESS4_ACCESS; k++)
            {
                if(infile->counters[j] == inoutfile->counters[k])
                {
                    infile->counters[j+4] += inoutfile->counters[k+4];
                    inoutfile->counters[k] = 0;
                    inoutfile->counters[k+4] = 0;
                }
            }
        }

        /* placeholder so we can re-use macros */
        tmp_runtime.log_file = &tmp_file;
        /* first set */
        for(j=CP_ACCESS1_ACCESS; j<=CP_ACCESS4_ACCESS; j++)
        {
            CP_COUNTER_INC(&tmp_runtime, infile->counters[j],
                infile->counters[j+4], 1, CP_ACCESS1_ACCESS, CP_ACCESS1_COUNT);
        }
        /* second set */
        for(j=CP_ACCESS1_ACCESS; j<=CP_ACCESS4_ACCESS; j++)
        {
            CP_COUNTER_INC(&tmp_runtime, inoutfile->counters[j],
                inoutfile->counters[j+4], 1, CP_ACCESS1_ACCESS, CP_ACCESS1_COUNT);
        }

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        /* min non-zero (if available) value */
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        for(j=CP_F_OPEN_TIMESTAMP; j<=CP_F_WRITE_START_TIMESTAMP; j++)
        {
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            if(infile->fcounters[j] > inoutfile->fcounters[j] && inoutfile->fcounters[j] > 0)
1640 1641 1642 1643 1644 1645 1646 1647 1648 1649 1650 1651 1652 1653 1654 1655 1656 1657 1658 1659 1660
                tmp_file.fcounters[j] = inoutfile->fcounters[j];
            else
                tmp_file.fcounters[j] = infile->fcounters[j];
        }

        /* max */
        for(j=CP_F_CLOSE_TIMESTAMP; j<=CP_F_WRITE_END_TIMESTAMP; j++)
        {
            if(infile->fcounters[j] > inoutfile->fcounters[j])
                tmp_file.fcounters[j] = infile->fcounters[j];
            else
                tmp_file.fcounters[j] = inoutfile->fcounters[j];
        }

        /* sum */
        for(j=CP_F_POSIX_READ_TIME; j<=CP_F_MPI_WRITE_TIME; j++)
        {
            tmp_file.fcounters[j] = infile->fcounters[j] + 
                inoutfile->fcounters[j];
        }

1661 1662 1663 1664 1665 1666 1667 1668 1669 1670 1671 1672 1673 1674 1675 1676 1677 1678 1679 1680 1681 1682 1683 1684 1685 1686 1687 1688 1689 1690 1691 1692 1693
        /* max (special case) */
        if(infile->fcounters[CP_F_MAX_WRITE_TIME] > 
            inoutfile->fcounters[CP_F_MAX_WRITE_TIME])
        {
            tmp_file.fcounters[CP_F_MAX_WRITE_TIME] = 
                infile->fcounters[CP_F_MAX_WRITE_TIME];
            tmp_file.counters[CP_MAX_WRITE_TIME_SIZE] = 
                infile->counters[CP_MAX_WRITE_TIME_SIZE];
        }
        else
        {
            tmp_file.fcounters[CP_F_MAX_WRITE_TIME] = 
                inoutfile->fcounters[CP_F_MAX_WRITE_TIME];
            tmp_file.counters[CP_MAX_WRITE_TIME_SIZE] = 
                inoutfile->counters[CP_MAX_WRITE_TIME_SIZE];
        }

        if(infile->fcounters[CP_F_MAX_READ_TIME] > 
            inoutfile->fcounters[CP_F_MAX_READ_TIME])
        {
            tmp_file.fcounters[CP_F_MAX_READ_TIME] = 
                infile->fcounters[CP_F_MAX_READ_TIME];
            tmp_file.counters[CP_MAX_READ_TIME_SIZE] = 
                infile->counters[CP_MAX_READ_TIME_SIZE];
        }
        else
        {
            tmp_file.fcounters[CP_F_MAX_READ_TIME] = 
                inoutfile->fcounters[CP_F_MAX_READ_TIME];
            tmp_file.counters[CP_MAX_READ_TIME_SIZE] = 
                inoutfile->counters[CP_MAX_READ_TIME_SIZE];
        }

1694
        /* min (zeroes are ok here; some procs don't do I/O) */
1695 1696
        if(infile->fcounters[CP_F_FASTEST_RANK_TIME] <
           inoutfile->fcounters[CP_F_FASTEST_RANK_TIME])
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        {
            tmp_file.counters[CP_FASTEST_RANK] =
                infile->counters[CP_FASTEST_RANK];
            tmp_file.counters[CP_FASTEST_RANK_BYTES] = 
                infile->counters[CP_FASTEST_RANK_BYTES];
            tmp_file.fcounters[CP_F_FASTEST_RANK_TIME] =
                infile->fcounters[CP_F_FASTEST_RANK_TIME];
        }
        else
        {
            tmp_file.counters[CP_FASTEST_RANK] =
                inoutfile->counters[CP_FASTEST_RANK];
            tmp_file.counters[CP_FASTEST_RANK_BYTES] =
                inoutfile->counters[CP_FASTEST_RANK_BYTES];
            tmp_file.fcounters[CP_F_FASTEST_RANK_TIME] = 
                inoutfile->fcounters[CP_F_FASTEST_RANK_TIME];
        }

        /* max */
        if(infile->fcounters[CP_F_SLOWEST_RANK_TIME] >
           inoutfile->fcounters[CP_F_SLOWEST_RANK_TIME])
        {
            tmp_file.counters[CP_SLOWEST_RANK] =
                infile->counters[CP_SLOWEST_RANK];
            tmp_file.counters[CP_SLOWEST_RANK_BYTES] =
                infile->counters[CP_SLOWEST_RANK_BYTES];
            tmp_file.fcounters[CP_F_SLOWEST_RANK_TIME] = 
                infile->fcounters[CP_F_SLOWEST_RANK_TIME];
        }
        else
        {
            tmp_file.counters[CP_SLOWEST_RANK] = 
                inoutfile->counters[CP_SLOWEST_RANK];
            tmp_file.counters[CP_SLOWEST_RANK_BYTES] = 
                inoutfile->counters[CP_SLOWEST_RANK_BYTES];
            tmp_file.fcounters[CP_F_SLOWEST_RANK_TIME] = 
                inoutfile->fcounters[CP_F_SLOWEST_RANK_TIME];
        }

1736 1737 1738 1739 1740 1741 1742 1743 1744 1745 1746 1747 1748
        /* pick one device id and file size, favoring complete records if
         * available
         */
        if(CP_FILE_PARTIAL(infile))
        {
            tmp_file.counters[CP_DEVICE] = inoutfile->counters[CP_DEVICE];
            tmp_file.counters[CP_SIZE_AT_OPEN] = inoutfile->counters[CP_SIZE_AT_OPEN];
        }
        else
        {
            tmp_file.counters[CP_DEVICE] = infile->counters[CP_DEVICE];
            tmp_file.counters[CP_SIZE_AT_OPEN] = infile->counters[CP_SIZE_AT_OPEN];
        }
1749

1750 1751 1752
        /* pick one name suffix (every file record should have this, whether
         * it is a partial record or not
         */
1753 1754 1755 1756 1757 1758 1759 1760 1761 1762 1763 1764 1765 1766
        strcpy(tmp_file.name_suffix, infile->name_suffix);

        *inoutfile = tmp_file;
        inoutfile++;
        infile++;
    }
    
    return;
}
/* cp_log_construct_indices()
 *
 * create memory datatypes to describe the log data to write out
 */
static void cp_log_construct_indices(struct darshan_job_runtime* final_job, 
1767 1768
    int rank, int* inout_count, int* lengths, void** pointers, char*
    trailing_data)
1769 1770 1771 1772 1773 1774 1775 1776 1777 1778 1779 1780
{
    *inout_count = 0;

    if(rank == 0)
    {
        /* root process is responsible for writing header */
        lengths[*inout_count] = sizeof(final_job->log_job);
        pointers[*inout_count] = &final_job->log_job;
        (*inout_count)++;

        /* also string containing exe command line */
        lengths[*inout_count] = CP_EXE_LEN + 1;