[svn-r14826] Files for the serial benchmarking tool, h5perf_serial.

Tested on kagiso, smirom, and linew.

1 files changed, 1747 insertions, 0 deletions

diff --git a/perform/sio_engine.c b/perform/sio_engine.c
new file mode 100644
index 0000000..3519f9b
--- /dev/null
+++ b/perform/sio_engine.c
@@ -0,0 +1,1747 @@
+/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *
+ * Copyright by the Board of Trustees of the University of Illinois.         *
+ * All rights reserved.                                                      *
+ *                                                                           *
+ * This file is part of HDF5.  The full HDF5 copyright notice, including     *
+ * terms governing use, modification, and redistribution, is contained in    *
+ * the files COPYING and Copyright.html.  COPYING can be found at the root   *
+ * of the source code distribution tree; Copyright.html can be found at the  *
+ * root level of an installed copy of the electronic HDF5 document set and   *
+ * is linked from the top-level documents page.  It can also be found at     *
+ * http://hdf.ncsa.uiuc.edu/HDF5/doc/Copyright.html.  If you do not have     *
+ * access to either file, you may request a copy from hdfhelp@ncsa.uiuc.edu. *
+ * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */
+
+/*
+ * Author: Christian Chilan, April 2008 
+ */
+
+#include <sys/types.h>
+#include <sys/stat.h>
+#include <stdio.h>
+#include <stdlib.h>
+#include <fcntl.h>
+#include <unistd.h>
+#include <errno.h>
+
+#include "hdf5.h"
+
+#ifdef H5_HAVE_GPFS
+#   include <gpfs_fcntl.h>
+#endif  /* H5_HAVE_GPFS */
+
+#include "sio_perf.h"
+#include "sio_timer.h"
+
+/* Macro definitions */
+
+/* sizes of various items. these sizes won't change during program execution */
+/* The following three must have the same type */
+#define ELMT_SIZE           (sizeof(unsigned char))     /* we're doing bytes */
+#define ELMT_H5_TYPE        H5T_NATIVE_UCHAR
+
+#define GOTOERROR(errcode)  { ret_code = errcode; goto done; }
+#define GOTODONE        { goto done; }
+#define ERRMSG(mesg) {                                                  \
+    fprintf(stderr, "*** Assertion failed (%s) at line %4d in %s\n",    \
+        mesg, (int)__LINE__, __FILE__);                             \
+}
+
+#define MSG(mesg) {                                     \
+    fprintf(stderr, "(%s) at line %4d in %s\n",         \
+        mesg, (int)__LINE__, __FILE__);             \
+}
+
+/* verify: if val is false (0), print mesg. */
+#define VRFY(val, mesg) do {                            \
+    if (!val) {                                         \
+    ERRMSG(mesg);                                   \
+    GOTOERROR(FAIL);                                \
+    }                                                   \
+} while(0)
+
+/* POSIX I/O macros */
+#define POSIXCREATE(fn)           HDopen(fn, O_CREAT|O_TRUNC|O_RDWR, 0600)
+#define POSIXOPEN(fn, F)          HDopen(fn, F, 0600)
+#define POSIXCLOSE(F)             HDclose(F)
+#define POSIXSEEK(F,L)            HDlseek(F, L, SEEK_SET)
+#define POSIXWRITE(F,B,S)         HDwrite(F,B,S)
+#define POSIXREAD(F,B,S)          HDread(F,B,S)
+
+enum {
+    SIO_CREATE = 1,
+    SIO_WRITE = 2,
+    SIO_READ = 4
+};
+
+/* Global variables */
+static int  clean_file_g = -1;  /*whether to cleanup temporary test     */
+/*files. -1 is not defined;             */
+/*0 is no cleanup; 1 is do cleanup      */
+
+/*
+ * In a parallel machine, the filesystem suitable for compiling is
+ * unlikely a parallel file system that is suitable for parallel I/O.
+ * There is no standard pathname for the parallel file system.  /tmp
+ * is about the best guess.
+ */
+#ifndef HDF5_PARAPREFIX
+#  ifdef __PUMAGON__
+/* For the PFS of TFLOPS */
+#    define HDF5_PARAPREFIX     "pfs:/pfs_grande/multi/tmp_1"
+#  else
+#    define HDF5_PARAPREFIX     ""
+#  endif    /* __PUMAGON__ */
+#endif  /* !HDF5_PARAPREFIX */
+
+#ifndef MIN
+#   define MIN(a,b) ((a) < (b) ? (a) : (b))
+#endif  /* !MIN */
+
+/* the different types of file descriptors we can expect */
+typedef union _file_descr {
+    int         posixfd;    /* POSIX file handle*/
+    hid_t       h5fd;       /* HDF5 file        */
+} file_descr;
+
+/* local functions */
+static char  *sio_create_filename(iotype iot, const char *base_name,
+    char *fullname, size_t size, parameters *param);
+static herr_t do_write(results *res, file_descr *fd, parameters *parms, void *buffer);
+static herr_t do_read(results *res, file_descr *fd, parameters *parms, void *buffer);
+static herr_t dset_write(int local_dim, file_descr *fd, parameters *parms, void *buffer);
+static herr_t posix_buffer_write(int local_dim, file_descr *fd, parameters *parms, void *buffer);
+static herr_t dset_read(int localrank, file_descr *fd, parameters *parms, void *buffer);
+static herr_t posix_buffer_read(int local_dim, file_descr *fd, parameters *parms, void *buffer);
+static herr_t do_fopen(parameters *param, char *fname, file_descr *fd /*out*/,
+    int flags);
+hid_t set_vfd(parameters *param);
+static herr_t do_fclose(iotype iot, file_descr *fd);
+static void do_cleanupfile(iotype iot, char *fname);
+
+/* GPFS-specific functions */
+#ifdef H5_HAVE_GPFS
+static void gpfs_access_range(int handle, off_t start, off_t length, int is_write);
+static void gpfs_free_range(int handle, off_t start, off_t length);
+static void gpfs_clear_file_cache(int handle);
+static void gpfs_cancel_hints(int handle);
+static void gpfs_start_data_shipping(int handle, int num_insts);
+static void gpfs_start_data_ship_map(int handle, int partition_size,
+    int agent_count, int *agent_node_num);
+static void gpfs_stop_data_shipping(int handle);
+static void gpfs_invalidate_file_cache(const char *filename);
+#endif /* H5_HAVE_GPFS */
+
+/* global variables */
+static off_t offset[MAX_DIMS];       /* dataset size in bytes     */
+static size_t buf_offset[MAX_DIMS];   /* dataset size in bytes     */
+static int order[MAX_DIMS];        /* dimension access order */
+static size_t      linear_buf_size;        /* linear buffer size     */
+static int         cont_dim;       /* lowest dimension for contiguous POSIX  
+                                      access */
+static size_t      cont_size;      /* size of contiguous POSIX access */
+static hid_t       fapl;           /* file access list */
+static unsigned char *buf_p;       /* buffer pointer */
+static unsigned char *buf2_p;      /* buffer pointer */
+static const char *multi_letters = "msbrglo"; /* string for multi driver */
+static char *buffer2=NULL;         /* buffer for data verification */
+
+/* HDF5 global variables */
+static hsize_t     h5count[MAX_DIMS];      /*selection count               */
+static hssize_t    h5offset[MAX_DIMS];     /* Selection offset within dataspace */
+static hid_t       h5dset_space_id = -1;   /*dataset space ID              */
+static hid_t       h5mem_space_id = -1;    /*memory dataspace ID           */
+static hid_t       h5ds_id = -1;           /*dataset handle                */
+static hid_t       h5dcpl = -1;            /* Dataset creation property list */
+static hid_t       h5dxpl = -1;            /* Dataset transfer property list */
+
+/*
+ * Function:        do_sio
+ * Purpose:         SIO Engine where IO are executed.
+ * Return:          results
+ * Programmer:      Christian Chilan, April, 2008 
+ * Modifications:
+ */
+    results
+do_sio(parameters param)
+{
+    char       *buffer = NULL; /*data buffer pointer           */
+    off_t       nbytes;                 /* dataset raw size */
+    off_t       dset_size[MAX_DIMS];    /* dataset size in bytes     */
+    size_t      buf_size[MAX_DIMS];     /* general buffer size in bytes     */
+    size_t      chk_size[MAX_DIMS];     /* chunk size in bytes     */
+    file_descr  fd;                     /* file handles */
+    iotype      iot;                    /* API type */
+    char base_name[256];                /* test file base name */
+    /* return codes */
+    herr_t      ret_code = 0;   /*return code                           */
+    results     res;
+
+    char        fname[FILENAME_MAX];    /* test file name */
+    int     i;
+    /* HDF5 variables */
+    herr_t          hrc;        /*HDF5 return code              */
+
+    /* Sanity check parameters */
+
+    /* IO type */
+    iot = param.io_type;
+
+    switch (iot) {
+    case POSIXIO:
+        fd.posixfd = -1;
+        res.timers = sio_time_new();
+        break;
+    case HDF5:
+        fd.h5fd = -1;
+        res.timers = sio_time_new();
+        break;
+    default:
+        /* unknown request */
+        fprintf(stderr, "Unknown IO type request (%d)\n", iot);
+        GOTOERROR(FAIL);
+    }
+
+    nbytes = param.num_bytes;     
+    linear_buf_size = 1;
+
+    for (i=0; i<param.rank; i++){
+        dset_size[i] = param.dset_size[i];
+        buf_size[i] = param.buf_size[i];
+        chk_size[i] = param.chk_size[i];
+        order[i] = param.order[i];
+        linear_buf_size *= buf_size[i];
+        buf_offset[i] = 0;
+        offset[i] = 0;
+
+        /* Validate transfer buffer size */
+        if (param.buf_size[i]<=0) {
+            HDfprintf(stderr,
+            "Transfer buffer size[%d] (%Hd) must be > 0\n", i,(long_long)buf_size[i]);
+            GOTOERROR(FAIL);
+        }
+
+        if ((param.dset_size[i]%param.buf_size[i])!=0) {
+            HDfprintf(stderr,
+            "Dataset size[%d] (%Hd) must be a multiple of the "
+            "trasfer buffer size[%d] (%Hd)\n",param.rank,
+            (long_long)param.dset_size[i], param.rank, (long_long)param.buf_size[i]);
+            GOTOERROR(FAIL);
+        }
+
+    }
+
+    /* Allocate transfer buffer */
+    buffer2 = malloc(linear_buf_size); 
+    if ((buffer = malloc(linear_buf_size)) == NULL){
+        HDfprintf(stderr, "malloc for transfer buffer size (%Hd) failed\n",
+        (long_long)(linear_buf_size));
+        GOTOERROR(FAIL);
+    }
+
+    if (sio_debug_level >= 4) 
+
+    /* output all of the times for all iterations */
+        fprintf(output, "Timer details:\n");
+
+    /*
+     * Write performance measurement
+     */
+    /* Open file for write */
+
+    strcpy(base_name, "#sio_tmp");
+    sio_create_filename(iot, base_name, fname, sizeof(fname), &param);
+
+    if (sio_debug_level > 0)
+        HDfprintf(output, "data filename=%s\n",
+             fname);
+
+    set_time(res.timers, HDF5_GROSS_WRITE_FIXED_DIMS, START);
+    hrc = do_fopen(&param, fname, &fd, SIO_CREATE | SIO_WRITE);
+    VRFY((hrc == SUCCESS), "do_fopen failed");
+
+    set_time(res.timers, HDF5_FINE_WRITE_FIXED_DIMS, START);
+    hrc = do_write(&res, &fd, &param, buffer);
+    set_time(res.timers, HDF5_FINE_WRITE_FIXED_DIMS, STOP);
+    VRFY((hrc == SUCCESS), "do_write failed");
+
+    /* Close file for write */
+    hrc = do_fclose(iot, &fd);
+    set_time(res.timers, HDF5_GROSS_WRITE_FIXED_DIMS, STOP);
+    VRFY((hrc == SUCCESS), "do_fclose failed");
+
+    if (!param.h5_write_only) {
+        /*
+         * Read performance measurement
+         */
+
+        /* Open file for read */
+        set_time(res.timers, HDF5_GROSS_READ_FIXED_DIMS, START);
+        hrc = do_fopen(&param, fname, &fd, SIO_READ);
+        VRFY((hrc == SUCCESS), "do_fopen failed");
+
+        set_time(res.timers, HDF5_FINE_READ_FIXED_DIMS, START);
+        hrc = do_read(&res, &fd, &param, buffer);
+        set_time(res.timers, HDF5_FINE_READ_FIXED_DIMS, STOP);
+        VRFY((hrc == SUCCESS), "do_read failed");
+
+        /* Close file for read */
+        hrc = do_fclose(iot, &fd);
+
+        set_time(res.timers, HDF5_GROSS_READ_FIXED_DIMS, STOP);
+        VRFY((hrc == SUCCESS), "do_fclose failed");
+    }
+    
+    do_cleanupfile(iot, fname);
+
+done:
+    /* clean up */
+    /* release HDF5 objects */
+
+    /* close any opened files */
+    /* no remove(fname) because that should have happened normally. */
+    switch (iot) {
+        case POSIXIO:
+            if (fd.posixfd != -1)
+                hrc = do_fclose(iot, &fd);
+            break;
+        case HDF5:
+            if (fd.h5fd != -1)
+                hrc = do_fclose(iot, &fd);
+            break;
+    }
+
+    /* release generic resources */
+    if (buffer)
+        free(buffer);
+
+    res.ret_code = ret_code;
+    return res;
+}
+
+/*
+ * Function:    sio_create_filename
+ * Purpose:     Create a new filename to write to. Determine the correct
+ *              suffix to append to the filename by the type of I/O we're
+ *              doing. Also, place in the /tmp/{$USER,$LOGIN} directory if
+ *              USER or LOGIN are specified in the environment.
+ * Return:      Pointer to filename or NULL
+ * Programmer:  Bill Wendling, 21. November 2001
+ * Modifications: Support for file drivers. Christian Chilan, April, 2008
+ */
+    static char *
+sio_create_filename(iotype iot, const char *base_name, char *fullname, size_t size, parameters *param)
+{
+    const char *prefix, *suffix="";
+    char *ptr, last = '\0';
+    size_t i, j;
+    vfdtype vfd; 
+    vfd = param->vfd; 
+
+    if (!base_name || !fullname || size < 1)
+    return NULL;
+
+    memset(fullname, 0, size);
+
+    switch (iot) {
+    case POSIXIO:
+        suffix = ".posix";
+        break;
+    case HDF5:
+        suffix = ".h5";
+        if (vfd == family)
+            suffix = "%05d.h5";
+        else if (vfd == multi)
+            suffix = NULL;
+        break;
+    }
+
+    /* First use the environment variable and then try the constant */
+    prefix = getenv("HDF5_PARAPREFIX");
+
+#ifdef HDF5_PARAPREFIX
+    if (!prefix)
+    prefix = HDF5_PARAPREFIX;
+#endif  /* HDF5_PARAPREFIX */
+
+    /* Prepend the prefix value to the base name */
+    if (prefix && *prefix) {
+    /* If the prefix specifies the HDF5_PARAPREFIX directory, then
+     * default to using the "/tmp/$USER" or "/tmp/$LOGIN"
+     * directory instead. */
+    register char *user, *login, *subdir;
+
+    user = getenv("USER");
+    login = getenv("LOGIN");
+    subdir = (user ? user : login);
+
+    if (subdir) {
+        for (i = 0; i < size && prefix[i]; i++)
+        fullname[i] = prefix[i];
+
+        fullname[i++] = '/';
+
+        for (j = 0; i < size && subdir[j]; i++, j++)
+        fullname[i] = subdir[j];
+    } else {
+        /* We didn't append the prefix yet */
+        strncpy(fullname, prefix, MIN(strlen(prefix), size));
+    }
+
+    if ((strlen(fullname) + strlen(base_name) + 1) < size) {
+        /* Append the base_name with a slash first. Multiple slashes are
+         * handled below. */
+        h5_stat_t buf;
+
+        if (HDstat(fullname, &buf) < 0)
+        /* The directory doesn't exist just yet */
+        if (mkdir(fullname, (mode_t)0755) < 0 && errno != EEXIST) {
+            /* We couldn't make the "/tmp/${USER,LOGIN}" subdirectory.
+             * Default to PREFIX's original prefix value. */
+            strcpy(fullname, prefix);
+        }
+
+        strcat(fullname, "/");
+        strcat(fullname, base_name);
+    } else {
+        /* Buffer is too small */
+        return NULL;
+    }
+    } else if (strlen(base_name) >= size) {
+    /* Buffer is too small */
+        return NULL;
+    } else {
+        strcpy(fullname, base_name);
+    }
+
+    /* Append a suffix */
+    if (suffix) {
+        if (strlen(fullname) + strlen(suffix) >= size)
+            return NULL;
+
+        strcat(fullname, suffix);
+    }
+
+    /* Remove any double slashes in the filename */
+    for (ptr = fullname, i = j = 0; ptr && i < size; i++, ptr++) {
+    if (*ptr != '/' || last != '/')
+        fullname[j++] = *ptr;
+
+    last = *ptr;
+    }
+
+    return fullname;
+}
+
+/*
+ * Function:        do_write
+ * Purpose:         Write the required amount of data to the file.
+ * Return:          SUCCESS or FAIL
+ * Programmer:      Christian Chilan, April, 2008 
+ * Modifications:
+ */
+static herr_t
+do_write(results *res, file_descr *fd, parameters *parms, void *buffer)
+{
+    int         ret_code = SUCCESS;
+    char        dname[64];
+    long        i;
+    /* HDF5 variables */
+    herr_t      hrc;                    /*HDF5 return code              */
+    hsize_t     h5dims[MAX_DIMS];       /*dataset dim sizes             */
+    hsize_t     h5chunk[MAX_DIMS];      /*dataset dim sizes             */
+    hsize_t     h5block[MAX_DIMS];      /*dataspace selection           */
+    hsize_t     h5stride[MAX_DIMS];     /*selection stride              */
+    hsize_t     h5start[MAX_DIMS];      /*selection start               */
+    hsize_t     h5maxdims[MAX_DIMS];
+    int         rank;                   /*rank of dataset */
+        /* Prepare buffer for verifying data */
+//    if (parms->verify)
+         //   memset(buffer,1,linear_buf_size);
+
+    buf_p=(unsigned char *)buffer;
+
+    for (i=0; i < linear_buf_size; i++)
+        buf_p[i]=i%128;
+
+    rank = parms->rank;
+
+    for (i=0; i<rank; i++) {
+        h5offset[i] = offset[i] = 0;
+    }
+
+    /* I/O Access specific setup */
+    switch (parms->io_type) {
+    case POSIXIO:
+
+            /* determine lowest dimension for contiguous POSIX access */
+            cont_dim = rank;
+            
+            for (i=rank-1; i>=0; i--) {
+                if (parms->buf_size[i]==parms->dset_size[i])
+                    cont_dim = i;
+                else
+                    break;
+            }
+
+            /* determine size of the contiguous POSIX access */ 
+            cont_size = (!cont_dim)? 1 : parms->buf_size[cont_dim-1];
+            for (i=cont_dim; i<rank; i++)
+                cont_size *= parms->buf_size[i];
+
+        break;
+
+    case HDF5: /* HDF5 setup */
+
+        for (i=0; i < rank; i++){
+            h5dims[i] = parms->dset_size[i];
+            h5start[i] = 0;
+            h5stride[i] = 1;
+            h5block[i] = 1;
+            h5count[i] = parms->buf_size[i];
+            h5chunk[i] = parms->chk_size[i];
+            h5maxdims[i] = H5S_UNLIMITED;
+            
+        }
+
+        if (parms->h5_use_chunks && parms->h5_extendable) {
+            h5dset_space_id = H5Screate_simple(rank, h5count, h5maxdims);
+            VRFY((h5dset_space_id >= 0), "H5Screate_simple");
+        }
+        else {
+            h5dset_space_id = H5Screate_simple(rank, h5dims, NULL);
+            VRFY((h5dset_space_id >= 0), "H5Screate_simple");
+        }
+
+        hrc = H5Sselect_hyperslab(h5dset_space_id, H5S_SELECT_SET,
+                    h5start, h5stride, h5count, h5block); 
+        VRFY((hrc >= 0), "H5Sselect_hyperslab");
+
+        /* Create the memory dataspace that corresponds to the xfer buffer */
+        h5mem_space_id = H5Screate_simple(rank, h5count, NULL);
+        VRFY((h5mem_space_id >= 0), "H5Screate_simple");
+
+        /* Create the dataset transfer property list */
+        h5dxpl = H5Pcreate(H5P_DATASET_XFER);
+        if (h5dxpl < 0) {
+            fprintf(stderr, "HDF5 Property List Create failed\n");
+            GOTOERROR(FAIL);
+        }
+
+        break;        
+    } /* end switch */
+
+
+    /* create dataset */
+    switch (parms->io_type) {
+        case POSIXIO:
+        break;
+
+        case HDF5:
+            h5dcpl = H5Pcreate(H5P_DATASET_CREATE);
+
+        if (h5dcpl < 0) {
+            fprintf(stderr, "HDF5 Property List Create failed\n");
+            GOTOERROR(FAIL);
+        }
+
+        if(parms->h5_use_chunks) {
+        /* Set the chunk size to be the same as the buffer size */
+            hrc = H5Pset_chunk(h5dcpl, rank, h5chunk);
+            if (hrc < 0) {
+                fprintf(stderr, "HDF5 Property List Set failed\n");
+                GOTOERROR(FAIL);
+            } /* end if */
+        } /* end if */
+
+        sprintf(dname, "Dataset_%ld", (unsigned long)parms->num_bytes);
+        h5ds_id = H5Dcreate1(fd->h5fd, dname, ELMT_H5_TYPE,
+            h5dset_space_id, h5dcpl);
+
+        if (h5ds_id < 0) {
+            fprintf(stderr, "HDF5 Dataset Create failed\n");
+            GOTOERROR(FAIL);
+        }
+
+        hrc = H5Pclose(h5dcpl);
+        /* verifying the close of the dcpl */
+        if (hrc < 0) {
+            fprintf(stderr, "HDF5 Property List Close failed\n");
+            GOTOERROR(FAIL);
+        }
+
+        break;
+    }
+
+    /* Start "raw data" write timer */
+    set_time(res->timers, HDF5_RAW_WRITE_FIXED_DIMS, START);
+
+    /* Perform write */
+    hrc = dset_write(rank-1, fd, parms, buffer);
+    
+    if (hrc < 0) {
+        fprintf(stderr, "Error in dataset write\n");
+        GOTOERROR(FAIL);
+    }
+
+
+    /* Stop "raw data" write timer */
+    set_time(res->timers, HDF5_RAW_WRITE_FIXED_DIMS, STOP);
+
+    /* Calculate write time */
+
+    /* Close dataset. Only HDF5 needs to do an explicit close. */
+    if (parms->io_type == HDF5) {
+        hrc = H5Dclose(h5ds_id);
+
+        if (hrc < 0) {
+            fprintf(stderr, "HDF5 Dataset Close failed\n");
+            GOTOERROR(FAIL);
+        }
+
+        h5ds_id = -1;
+    } /* end if */
+
+done:
+
+    /* release HDF5 objects */
+    if (h5dset_space_id != -1) {
+        hrc = H5Sclose(h5dset_space_id);
+        if (hrc < 0){
+            fprintf(stderr, "HDF5 Dataset Space Close failed\n");
+            ret_code = FAIL;
+        } else {
+            h5dset_space_id = -1;
+        }
+    }
+
+    if (h5mem_space_id != -1) {
+        hrc = H5Sclose(h5mem_space_id);
+        if (hrc < 0) {
+            fprintf(stderr, "HDF5 Memory Space Close failed\n");
+            ret_code = FAIL;
+        } else {
+            h5mem_space_id = -1;
+        }
+    }
+
+    if (h5dxpl != -1) {
+        hrc = H5Pclose(h5dxpl);
+        if (hrc < 0) {
+            fprintf(stderr, "HDF5 Dataset Transfer Property List Close failed\n");
+            ret_code = FAIL;
+        } else {
+            h5dxpl = -1;
+        }
+    }
+
+    return ret_code;
+}
+
+/*
+ * Function:        dset_write
+ * Purpose:         Write buffer into the dataset. 
+ * Return:          SUCCESS or FAIL
+ * Programmer:      Christian Chilan, April, 2008
+ * Modifications:
+ */
+
+static herr_t dset_write(int local_dim, file_descr *fd, parameters *parms, void *buffer)
+{
+    int cur_dim = order[local_dim]-1;
+    int         ret_code = SUCCESS;
+    int         k;
+    hsize_t	dims[MAX_DIMS], maxdims[MAX_DIMS];
+    long i,j;
+    herr_t hrc;
+
+    /* iterates according to the dimensions in order array */ 
+    for (i=0; i < parms->dset_size[cur_dim]; i += parms->buf_size[cur_dim]){
+
+        h5offset[cur_dim] = offset[cur_dim] = i;
+            
+        if (local_dim > 0){
+
+            dset_write(local_dim-1, fd, parms, buffer);
+
+        }else{
+
+            switch (parms->io_type) {
+
+            case POSIXIO:
+                /* initialize POSIX offset in the buffer */
+                for (j=0; j < parms->rank; j++) {
+                    buf_offset[j]=0;
+                }
+                buf_p = (unsigned char *)buffer;
+                /* write POSIX buffer */
+                posix_buffer_write(0, fd, parms, buffer);
+                break;
+
+            case HDF5:
+                /* if dimensions are extendable, extend them as needed during
+                access */
+                if (parms->h5_use_chunks && parms->h5_extendable) {
+
+                    hrc=H5Sget_simple_extent_dims(h5dset_space_id,dims,maxdims);
+                    VRFY((hrc >= 0), "H5Sget_simple_extent_dims");
+
+                    for (k=0; k < parms->rank; k++){
+
+                        if (dims[k] <= h5offset[k]) {
+                            dims[k] = dims[k]+h5count[k];
+                            hrc=H5Sset_extent_simple(h5dset_space_id,parms->rank,dims,maxdims);
+                            VRFY((hrc >= 0), "H5Sset_extent_simple");
+                            hrc=H5Dextend(h5ds_id,dims);
+                            VRFY((hrc >= 0), "H5Dextend");
+                        }
+                    }
+                }
+                /* applies offset */               
+                hrc = H5Soffset_simple(h5dset_space_id, h5offset);
+                VRFY((hrc >= 0), "H5Soffset_simple");
+
+                /* Write the buffer out */
+                hrc=H5Sget_simple_extent_dims(h5dset_space_id,dims,maxdims);
+                hrc = H5Dwrite(h5ds_id, ELMT_H5_TYPE, h5mem_space_id,
+                    h5dset_space_id, h5dxpl, buffer);
+                VRFY((hrc >= 0), "H5Dwrite");
+
+                break;
+            } /* switch (parms->io_type) */
+        }
+    }
+done:
+    return ret_code;
+}
+
+/*
+ * Function:        posix_buffer_write 
+ * Purpose:         Write buffer into the POSIX file considering contiguity.
+ * Return:          SUCCESS or FAIL
+ * Programmer:      Christian Chilan, April, 2008
+ * Modifications:
+ */
+
+static herr_t posix_buffer_write(int local_dim, file_descr *fd, parameters *parms, void *buffer)
+{
+    int dtype_size = 1;
+    int         ret_code = SUCCESS;
+    long i;
+
+    /* if dimension is not contiguous, call recursively */
+    if (local_dim < parms->rank-1 && local_dim != cont_dim) {
+
+        for (i=0; i < parms->buf_size[local_dim]; i += dtype_size) {
+            buf_offset[local_dim] = i;
+            posix_buffer_write(local_dim+1, fd, parms, buffer);
+
+            /* if next dimension is cont_dim, it will fill out the buffer
+               traversing the entire dimension local_dim without the need
+               of performing iteration */
+            if (local_dim+1==cont_dim)
+                break;
+        }
+    /* otherwise, perform contiguous POSIX access */
+    } else {
+
+        buf_offset[local_dim] = 0;
+        size_t linear_dset_offset = 0, d_offset;
+        int j, rc;
+
+        /* determine offset in the buffer */
+        for (i=0; i < parms->rank; i++){
+            d_offset=1;
+
+            for (j=i+1; j < parms->rank; j++)
+                d_offset *= parms->dset_size[j];
+
+            linear_dset_offset += (offset[i]+buf_offset[i])*d_offset;
+        }
+
+        /* only care if seek returns error */
+        rc = POSIXSEEK(fd->posixfd, linear_dset_offset) < 0 ? -1 : 0;
+        VRFY((rc==0), "POSIXSEEK");
+        /* check if all bytes are written */
+        rc = ((ssize_t)cont_size ==
+             POSIXWRITE(fd->posixfd, buf_p, cont_size));
+        VRFY((rc != 0), "POSIXWRITE");
+
+        /* Advance location in buffer */
+        buf_p += cont_size;
+
+    }
+done:
+    return ret_code;
+}
+
+/*
+ * Function:        do_read
+ * Purpose:         Read the required amount of data to the file.
+ * Return:          SUCCESS or FAIL
+ * Programmer:      Christian Chilan, April, 2008 
+ * Modifications:
+ */
+static herr_t
+do_read(results *res, file_descr *fd, parameters *parms, void *buffer)
+{
+    int         ret_code = SUCCESS;
+    char        dname[64];
+    long        i;
+    /* HDF5 variables */
+    herr_t      hrc;                    /*HDF5 return code              */
+    hsize_t     h5dims[MAX_DIMS];       /*dataset dim sizes             */
+    hsize_t     h5chunk[MAX_DIMS];      /*dataset dim sizes             */
+    hsize_t     h5block[MAX_DIMS];      /*dataspace selection           */
+    hsize_t     h5stride[MAX_DIMS];     /*selection stride              */
+    hsize_t     h5start[MAX_DIMS];      /*selection start               */
+    int         rank;
+
+        /* Prepare buffer for verifying data */
+       // if (parms->verify)
+         //   memset(buffer,1,linear_buf_size);
+//    if (parms->verify)
+        for (i=0; i < linear_buf_size; i++)
+            buffer2[i]=i%128;
+
+    rank = parms->rank;
+    for (i=0; i<rank; i++) {
+        h5offset[i] = offset[i] = 0;
+    }
+
+    /* I/O Access specific setup */
+    switch (parms->io_type) {
+    case POSIXIO:
+            cont_dim = rank;
+            
+            for (i=rank-1; i>=0; i--) {
+                if (parms->buf_size[i]==parms->dset_size[i])
+                    cont_dim = i;
+                else
+                    break;
+            }
+            cont_size = (!cont_dim)? 1 : parms->buf_size[cont_dim-1];
+            for (i=cont_dim; i<rank; i++)
+                cont_size *= parms->buf_size[i];
+
+        break;
+
+    case HDF5: /* HDF5 setup */
+        for (i=0; i < rank; i++){
+            h5dims[i] = parms->dset_size[i];
+            h5start[i] = 0;
+            h5stride[i] = 1;
+            h5block[i] = 1;
+            h5count[i] = parms->buf_size[i];
+            h5chunk[i] = parms->chk_size[i];
+        }
+
+        h5dset_space_id = H5Screate_simple(rank, h5dims, NULL);
+        VRFY((h5dset_space_id >= 0), "H5Screate_simple");
+
+        hrc = H5Sselect_hyperslab(h5dset_space_id, H5S_SELECT_SET,
+                    h5start, h5stride, h5count, h5block); 
+        VRFY((hrc >= 0), "H5Sselect_hyperslab");
+
+        /* Create the memory dataspace that corresponds to the xfer buffer */
+        h5mem_space_id = H5Screate_simple(rank, h5count, NULL);
+        VRFY((h5mem_space_id >= 0), "H5Screate_simple");
+
+        /* Create the dataset transfer property list */
+        h5dxpl = H5Pcreate(H5P_DATASET_XFER);
+        if (h5dxpl < 0) {
+            fprintf(stderr, "HDF5 Property List Create failed\n");
+            GOTOERROR(FAIL);
+        }
+
+        break;        
+    } /* end switch */
+
+
+    /* create dataset */
+    switch (parms->io_type) {
+        case POSIXIO:
+        break;
+
+        case HDF5:
+        sprintf(dname, "Dataset_%ld", parms->num_bytes);
+        h5ds_id = H5Dopen1(fd->h5fd, dname);
+        if (h5ds_id < 0) {
+            fprintf(stderr, "HDF5 Dataset open failed\n");
+            GOTOERROR(FAIL);
+        }
+
+        break;
+
+    } /* end switch */
+
+    /* Start "raw data" read timer */
+    set_time(res->timers, HDF5_RAW_READ_FIXED_DIMS, START);
+    hrc = dset_read(rank-1, fd, parms, buffer);
+
+    if (hrc < 0) {
+        fprintf(stderr, "Error in dataset read\n");
+        GOTOERROR(FAIL);
+    }
+
+    /* Stop "raw data" read timer */
+    set_time(res->timers, HDF5_RAW_READ_FIXED_DIMS, STOP);
+
+    /* Calculate read time */
+
+    /* Close dataset. Only HDF5 needs to do an explicit close. */
+    if (parms->io_type == HDF5) {
+        hrc = H5Dclose(h5ds_id);
+
+        if (hrc < 0) {
+        fprintf(stderr, "HDF5 Dataset Close failed\n");
+        GOTOERROR(FAIL);
+        }
+
+        h5ds_id = -1;
+    } /* end if */
+
+done:
+
+    /* release HDF5 objects */
+    if (h5dset_space_id != -1) {
+    hrc = H5Sclose(h5dset_space_id);
+    if (hrc < 0){
+        fprintf(stderr, "HDF5 Dataset Space Close failed\n");
+        ret_code = FAIL;
+    } else {
+        h5dset_space_id = -1;
+    }
+    }
+
+    if (h5mem_space_id != -1) {
+    hrc = H5Sclose(h5mem_space_id);
+    if (hrc < 0) {
+        fprintf(stderr, "HDF5 Memory Space Close failed\n");
+        ret_code = FAIL;
+    } else {
+        h5mem_space_id = -1;
+    }
+    }
+
+    if (h5dxpl != -1) {
+    hrc = H5Pclose(h5dxpl);
+    if (hrc < 0) {
+        fprintf(stderr, "HDF5 Dataset Transfer Property List Close failed\n");
+        ret_code = FAIL;
+    } else {
+        h5dxpl = -1;
+    }
+    }
+
+    return ret_code;
+}
+
+/*
+ * Function:        dset_read
+ * Purpose:         Read buffer into the dataset.
+ * Return:          SUCCESS or FAIL
+ * Programmer:      Christian Chilan, April, 2008
+ * Modifications:
+ */
+
+static herr_t dset_read(int local_dim, file_descr *fd, parameters *parms, void *buffer)
+{
+    int cur_dim = order[local_dim]-1;
+    int         ret_code = SUCCESS;
+    long i,j;
+    herr_t hrc;
+
+    /* iterate on the current dimension */ 
+    for (i=0; i < parms->dset_size[cur_dim]; i += parms->buf_size[cur_dim]){
+
+        h5offset[cur_dim] = offset[cur_dim] = i;
+        
+        /* if traverse in order array is incomplete, recurse */     
+        if (local_dim > 0){
+
+            ret_code = dset_read(local_dim-1, fd, parms, buffer);
+
+        /* otherwise, write buffer into dataset */
+        }else{
+
+            switch (parms->io_type) {
+
+            case POSIXIO:
+                for (j=0; j<parms->rank; j++) {
+                   buf_offset[j] = 0;
+                }
+                buf_p = (unsigned char*)buffer;
+                buf2_p = (unsigned char*)buffer2;
+                posix_buffer_read(0, fd, parms, buffer);
+                break;
+
+            case HDF5:
+                hrc = H5Soffset_simple(h5dset_space_id, h5offset);
+                VRFY((hrc >= 0), "H5Soffset_simple");
+                /* Read the buffer out */
+                hrc = H5Dread(h5ds_id, ELMT_H5_TYPE, h5mem_space_id,
+                    h5dset_space_id, h5dxpl, buffer);
+                VRFY((hrc >= 0), "H5Dread");
+#if 0 
+                for (j=0; j<linear_buf_size; j++) {
+                     buf_p = (unsigned char*)buffer;
+                     if (buf_p[j]!=buffer2[j])
+                        printf("Inconsistent data in %d\n", j);
+                }
+#endif
+                break;
+            } /* switch (parms->io_type) */
+        }
+    }
+done:
+    return ret_code;
+}
+
+/*
+ * Function:        posix_buffer_read
+ * Purpose:         Read buffer into the POSIX file considering contiguity.
+ * Return:          SUCCESS or FAIL
+ * Programmer:      Christian Chilan, April, 2008
+ * Modifications:
+ */
+
+static herr_t posix_buffer_read(int local_dim, file_descr *fd, parameters *parms, void *buffer)
+{
+    int dtype_size = 1;
+    int         ret_code = SUCCESS;
+    long i;
+
+    /* if local dimension is not contiguous, recurse */
+    if (local_dim < parms->rank-1 && local_dim != cont_dim) {
+
+        for (i=0; i < parms->buf_size[local_dim]; i += dtype_size) {
+            buf_offset[local_dim] = i;
+            ret_code = posix_buffer_read(local_dim+1, fd, parms, buffer);
+            if (local_dim+1==cont_dim)
+                break;
+        }
+    /* otherwise, perform contiguous POSIX access */
+    } else {
+
+        buf_offset[local_dim] = 0;
+        size_t linear_dset_offset = 0, d_offset;
+        int j, rc;
+        /* determine offset in buffer */
+        for (i=0; i<parms->rank; i++){
+            d_offset=1;
+
+            for (j=i+1; j<parms->rank; j++)
+                d_offset *= parms->dset_size[j];
+
+            linear_dset_offset += (offset[i]+buf_offset[i])*d_offset;
+        }
+
+        /* only care if seek returns error */
+        rc = POSIXSEEK(fd->posixfd, linear_dset_offset) < 0 ? -1 : 0;
+        VRFY((rc==0), "POSIXSEEK");
+        /* check if all bytes are read */
+        rc = ((ssize_t)cont_size ==
+             POSIXREAD(fd->posixfd, buf_p, cont_size));
+        VRFY((rc != 0), "POSIXREAD");
+#if 0 
+        for (j=0; j<cont_size; j++) {
+            if (buf_p[j]!=buf2_p[j])
+                printf("Inconsistent data in %d\n", j);
+        }
+        buf2_p += cont_size;
+#endif
+
+        /* Advance location in buffer */
+        buf_p += cont_size;
+
+    }
+done:
+    return ret_code;
+}
+
+
+/*
+ * Function:    do_fopen
+ * Purpose:     Open the specified file.
+ * Return:      SUCCESS or FAIL
+ * Programmer:  Albert Cheng, Bill Wendling, 2001/12/13
+ * Modifications: Support for file drivers, Christian Chilan, April, 2008
+ */
+    static herr_t
+do_fopen(parameters *param, char *fname, file_descr *fd /*out*/, int flags)
+{
+    int ret_code = SUCCESS;
+
+    switch (param->io_type) {
+    case POSIXIO:
+        if (flags & (SIO_CREATE | SIO_WRITE))
+            fd->posixfd = POSIXCREATE(fname);
+        else
+            fd->posixfd = POSIXOPEN(fname, O_RDONLY);
+
+        if (fd->posixfd < 0 ) {
+            fprintf(stderr, "POSIX File Open failed(%s)\n", fname);
+            GOTOERROR(FAIL);
+        }
+
+        break;
+
+    case HDF5:
+
+        fapl = set_vfd(param);
+
+        if (fapl < 0) {
+            fprintf(stderr, "HDF5 Property List Create failed\n");
+            GOTOERROR(FAIL);
+        }
+
+        /* create the parallel file */
+        if (flags & (SIO_CREATE | SIO_WRITE)) {
+            fd->h5fd = H5Fcreate(fname, H5F_ACC_TRUNC, H5P_DEFAULT, fapl);
+        } else {
+            fd->h5fd = H5Fopen(fname, H5F_ACC_RDONLY, fapl);
+        }
+
+
+        if (fd->h5fd < 0) {
+            fprintf(stderr, "HDF5 File Create failed(%s)\n", fname);
+            GOTOERROR(FAIL);
+        }
+        break;
+    } 
+
+done:
+    return ret_code;
+}
+
+/*
+ * Function:    set_vfd 
+ * Purpose:     Sets file driver. 
+ * Return:      SUCCESS or FAIL
+ * Programmer:  Christian Chilan, April, 2008 
+ * Modifications: 
+ */
+
+hid_t
+set_vfd(parameters *param)
+{
+    hid_t fapl = -1;
+    vfdtype  vfd;
+
+    vfd = param->vfd;
+
+    if ((fapl=H5Pcreate(H5P_FILE_ACCESS))<0) return -1;
+
+    if (vfd == sec2) {
+        /* Unix read() and write() system calls */
+        if (H5Pset_fapl_sec2(fapl)<0) return -1;
+    } else if (vfd == stdio) {
+        /* Standard C fread() and fwrite() system calls */
+        if (H5Pset_fapl_stdio(fapl)<0) return -1;
+    } else if (vfd == core) {
+        /* In-core temporary file with 1MB increment */
+        if (H5Pset_fapl_core(fapl, (size_t)1024*1024, TRUE)<0) return -1;
+    } else if (vfd == split) {
+        /* Split meta data and raw data each using default driver */
+        if (H5Pset_fapl_split(fapl,
+                              "-m.h5", H5P_DEFAULT,
+                              "-r.h5", H5P_DEFAULT)<0)
+            return -1;
+    } else if (vfd == multi) {
+        /* Multi-file driver, general case of the split driver */
+        H5FD_mem_t memb_map[H5FD_MEM_NTYPES];
+        hid_t memb_fapl[H5FD_MEM_NTYPES];
+        const char *memb_name[H5FD_MEM_NTYPES];
+        char sv[H5FD_MEM_NTYPES][1024];
+        haddr_t memb_addr[H5FD_MEM_NTYPES];
+        H5FD_mem_t      mt;
+
+        HDmemset(memb_map, 0, sizeof memb_map);
+        HDmemset(memb_fapl, 0, sizeof memb_fapl);
+        HDmemset(memb_name, 0, sizeof memb_name);
+        HDmemset(memb_addr, 0, sizeof memb_addr);
+
+        assert(HDstrlen(multi_letters)==H5FD_MEM_NTYPES);
+        for (mt=H5FD_MEM_DEFAULT; mt<H5FD_MEM_NTYPES; H5_INC_ENUM(H5FD_mem_t,mt)) {
+            memb_fapl[mt] = H5P_DEFAULT;
+            sprintf(sv[mt], "%%s-%c.h5", multi_letters[mt]);
+            memb_name[mt] = sv[mt];
+            memb_addr[mt] = MAX(mt-1,0)*(HADDR_MAX/10);
+        }
+
+        if (H5Pset_fapl_multi(fapl, memb_map, memb_fapl, memb_name,
+                              memb_addr, FALSE)<0) {
+            return -1;
+        }
+    } else if (vfd == family) {
+        hsize_t fam_size = 1*1024*1024; /*100 MB*/
+
+        /* Family of files, each 1MB and using the default driver */
+        /* if ((val=HDstrtok(NULL, " \t\n\r")))
+            fam_size = (hsize_t)(HDstrtod(val, NULL) * 1024*1024); */
+        if (H5Pset_fapl_family(fapl, fam_size, H5P_DEFAULT)<0)
+            return -1;
+    } else if (vfd == direct) {
+#ifdef H5_HAVE_DIRECT
+        /* Linux direct read() and write() system calls.  Set memory boundary, file block size,
+         * and copy buffer size to the default values. */
+        if (H5Pset_fapl_direct(fapl, 1024, 4096, 8*4096)<0) return -1;
+#endif
+    } else {
+        /* Unknown driver */
+        return -1;
+    }
+
+    return fapl;
+}
+
+/*
+ * Function:    do_fclose
+ * Purpose:     Close the specified file descriptor.
+ * Return:      SUCCESS or FAIL
+ * Programmer:  Albert Cheng, Bill Wendling, 2001/12/13
+ * Modifications:
+ */
+    static herr_t
+do_fclose(iotype iot, file_descr *fd /*out*/)
+{
+    herr_t ret_code = SUCCESS, hrc;
+    int  rc = 0;
+
+    switch (iot) {
+    case POSIXIO:
+        rc = POSIXCLOSE(fd->posixfd);
+
+        if (rc != 0){
+        fprintf(stderr, "POSIX File Close failed\n");
+        GOTOERROR(FAIL);
+        }
+
+        fd->posixfd = -1;
+        break;
+
+    case HDF5:
+        hrc = H5Fclose(fd->h5fd);
+
+        if (hrc < 0) {
+        fprintf(stderr, "HDF5 File Close failed\n");
+        GOTOERROR(FAIL);
+        }
+
+        fd->h5fd = -1;
+        break;
+    }
+
+done:
+    return ret_code;
+}
+
+
+/*
+ * Function:    do_cleanupfile
+ * Purpose:     Cleanup temporary file unless HDF5_NOCLEANUP is set.
+ * Return:      void
+ * Programmer:  Albert Cheng 2001/12/12
+ * Modifications: Support for file drivers. Christian Chilan, April, 2008
+ */
+    static void
+do_cleanupfile(iotype iot, char *filename)
+{
+    char        temp[2048];
+    int         j;
+    hid_t       driver;
+
+    if (clean_file_g == -1)
+    clean_file_g = (getenv("HDF5_NOCLEANUP")==NULL) ? 1 : 0;
+
+    if (clean_file_g){
+
+     switch (iot) {
+    case POSIXIO:
+          HDremove(filename);
+        break;
+
+    case HDF5:
+           driver = H5Pget_driver(fapl);
+
+            if (driver == H5FD_FAMILY) {
+                for (j = 0; /*void*/; j++) {
+                    HDsnprintf(temp, sizeof temp, filename, j);
+
+                    if (HDaccess(temp, F_OK) < 0)
+                        break;
+
+                    HDremove(temp);
+                }
+            } else if (driver == H5FD_CORE) {
+                hbool_t backing;        /* Whether the core file has backing store */
+
+                H5Pget_fapl_core(fapl,NULL,&backing);
+
+                /* If the file was stored to disk with bacing store, remove it */
+                if(backing)
+                    HDremove(filename);
+
+            } else if (driver == H5FD_MULTI) {
+                H5FD_mem_t mt;
+                assert(HDstrlen(multi_letters)==H5FD_MEM_NTYPES);
+
+                for (mt = H5FD_MEM_DEFAULT; mt < H5FD_MEM_NTYPES; H5_INC_ENUM(H5FD_mem_t,mt)) {
+                    HDsnprintf(temp, sizeof temp, "%s-%c.h5",
+                               filename, multi_letters[mt]);
+                    HDremove(temp); /*don't care if it fails*/
+                }
+            } else {
+                HDremove(filename);
+            }
+            H5Pclose(fapl);
+            break;
+      }   
+}
+}
+
+#ifdef H5_HAVE_GPFS
+
+/* Descriptions here come from the IBM GPFS Manual */
+
+/*
+ * Function:    gpfs_access_range
+ * Purpose:     Declares an access range within a file for an
+ *              application.
+ *
+ *              The application will access file offsets within the given
+ *              range, and will not access offsets outside the range.
+ *              Violating this hint may produce worse performance than if
+ *              no hint was specified.
+ *
+ *              This hint is useful in situations where a file is
+ *              partitioned coarsely among several nodes. If the ranges
+ *              do not overlap, each node can specify which range of the
+ *              file it will access, with a performance improvement in
+ *              some cases, such as for sequential writing within a
+ *              range.
+ *
+ *              Subsequent GPFS_ACCESS_RANGE hints will replace a hint
+ *              passed earlier.
+ *
+ *                  START    - The start of the access range offset, in
+ *                             bytes, from the beginning of the file
+ *                  LENGTH   - Length of the access range. 0 indicates to
+ *                             the end of the file
+ *                  IS_WRITE - 0 indicates READ access, 1 indicates WRITE access
+ * Return:      Nothing
+ * Programmer:  Bill Wendling, 03. June 2002
+ * Modifications:
+ */
+    static void
+gpfs_access_range(int handle, off_t start, off_t length, int is_write)
+{
+    struct {
+    gpfsFcntlHeader_t hdr;
+    gpfsAccessRange_t access;
+    } access_range;
+
+    access_range.hdr.totalLength = sizeof(access_range);
+    access_range.hdr.fcntlVersion = GPFS_FCNTL_CURRENT_VERSION;
+    access_range.hdr.fcntlReserved = 0;
+    access_range.access.structLen = sizeof(gpfsAccessRange_t);
+    access_range.access.structType = GPFS_ACCESS_RANGE;
+    access_range.access.start = start;
+    access_range.access.length = length;
+    access_range.access.isWrite = is_write;
+
+    if (gpfs_fcntl(handle, &access_range) != 0) {
+    fprintf(stderr,
+        "gpfs_fcntl DS start directive failed. errno=%d errorOffset=%d\n",
+        errno, access_range.hdr.errorOffset);
+    exit(EXIT_FAILURE);
+    }
+}
+
+/*
+ * Function:    gpfs_free_range
+ * Purpose:     Undeclares an access range within a file for an
+ *              application.
+ *
+ *              The application will no longer access file offsets within
+ *              the given range. GPFS flushes the data at the file
+ *              offsets and removes it from the cache.
+ *
+ *              Multi-node applications that have finished one phase of
+ *              their computation may wish to use this hint before the
+ *              file is accessed in a conflicting mode from another node
+ *              in a later phase. The potential performance benefit is
+ *              that GPFS can avoid later synchronous cache consistency
+ *              operations.
+ *
+ *                  START  - The start of the access range offset, in
+ *                           bytes from the beginning of the file.
+ *                  LENGTH - Length of the access range. 0 indicates to
+ *                           the end of the file.
+ * Return:      Nothing
+ * Programmer:  Bill Wendling, 03. June 2002
+ * Modifications:
+ */
+    static void
+gpfs_free_range(int handle, off_t start, off_t length)
+{
+    struct {
+    gpfsFcntlHeader_t hdr;
+    gpfsFreeRange_t range;
+    } free_range;
+
+    /* Issue the invalidate hint */
+    free_range.hdr.totalLength = sizeof(free_range);
+    free_range.hdr.fcntlVersion = GPFS_FCNTL_CURRENT_VERSION;
+    free_range.hdr.fcntlReserved = 0;
+    free_range.range.structLen = sizeof(gpfsFreeRange_t);
+    free_range.range.structType = GPFS_FREE_RANGE;
+    free_range.range.start = start;
+    free_range.range.length = length;
+
+    if (gpfs_fcntl(handle, &free_range) != 0) {
+    fprintf(stderr,
+        "gpfs_fcntl free range failed for range %d:%d. errno=%d errorOffset=%d\n",
+        start, length, errno, free_range.hdr.errorOffset);
+    exit(EXIT_FAILURE);
+    }
+}
+
+/*
+ * Function:    gpfs_clear_file_cache
+ * Purpose:     Indicates file access in the near future is not expected.
+ *
+ *              The application does not expect to make any further
+ *              accesses to the file in the near future, so GPFS removes
+ *              any data or metadata pertaining to the file from its
+ *              cache.
+ *
+ *              Multi-node applications that have finished one phase of
+ *              their computation may wish to use this hint before the
+ *              file is accessed in a conflicting mode from another node
+ *              in a later phase. The potential performance benefit is
+ *              that GPFS can avoid later synchronous cache consistency
+ *              operations.
+ * Return:      Nothing
+ * Programmer:  Bill Wendling, 03. June 2002
+ * Modifications:
+ */
+    static void
+gpfs_clear_file_cache(int handle)
+{
+    struct {
+    gpfsFcntlHeader_t hdr;
+    gpfsClearFileCache_t clear;
+    } clear_cache;
+
+    clear_cache.hdr.totalLength = sizeof(clear_cache);
+    clear_cache.hdr.fcntlVersion = GPFS_FCNTL_CURRENT_VERSION;
+    clear_cache.hdr.fcntlReserved = 0;
+    clear_cache.clear.structLen = sizeof(gpfsClearFileCache_t);
+    clear_cache.clear.structType = GPFS_CLEAR_FILE_CACHE;
+
+    if (gpfs_fcntl(handle, &clear_cache) != 0) {
+    fprintf(stderr,
+        "gpfs_fcntl clear file cache directive failed. errno=%d errorOffset=%d\n",
+        errno, clear_cache.hdr.errorOffset);
+    exit(EXIT_FAILURE);
+    }
+}
+
+/*
+ * Function:    gpfs_cancel_hints
+ * Purpose:     Indicates to remove any hints against the open file
+ *              handle.
+ *
+ *              GPFS removes any hints that may have been issued against
+ *              this open file handle:
+ *
+ *                  - The hint status of the file is restored ot what it
+ *                    would have been immediately after being opened, but
+ *                    does not affect the contents of the GPFS file
+ *                    cache. Cancelling an earlier hint that resulted in
+ *                    data being removed from the GPFS file cache does
+ *                    not bring that data back int othe cache; data
+ *                    re-enters the cache only pon access by the
+ *                    application or by user-driven or automatic
+ *                    prefetching.
+ *                  - Only the GPFS_MULTIPLE_ACCESS_RANGE hint has a
+ *                    state that might be removed by the
+ *                    GPFS_CANCEL_HINTS directive.
+ * Return:      Nothing
+ * Programmer:  Bill Wendling, 03. June 2002
+ * Modifications:
+ */
+    static void
+gpfs_cancel_hints(int handle)
+{
+    struct {
+    gpfsFcntlHeader_t hdr;
+    gpfsCancelHints_t cancel;
+    } cancel_hints;
+
+    cancel_hints.hdr.totalLength = sizeof(cancel_hints);
+    cancel_hints.hdr.fcntlVersion = GPFS_FCNTL_CURRENT_VERSION;
+    cancel_hints.hdr.fcntlReserved = 0;
+    cancel_hints.cancel.structLen = sizeof(gpfsCancelHints_t);
+    cancel_hints.cancel.structType = GPFS_CANCEL_HINTS;
+
+    if (gpfs_fcntl(handle, &cancel_hints) != 0) {
+    fprintf(stderr,
+        "gpfs_fcntl cancel hints directive failed. errno=%d errorOffset=%d\n",
+        errno, cancel_hints.hdr.errorOffset);
+    exit(EXIT_FAILURE);
+    }
+}
+
+/*
+ * Function:    gpfs_start_data_shipping
+ * Purpose:     Initiates data shipping mode.
+ *
+ *              Once all participating threads have issued this directive
+ *              for a file, GPFS enters a mode where it logically
+ *              partitions the blocks of the file among a group of agent
+ *              nodes. The agents are those nodes on which one or more
+ *              threads have issued the GPFS_DATA_SHIP_START directive.
+ *              Each thread that has issued a GPFS_DATA_SHIP_START
+ *              directive and the associated agent nodes are referred to
+ *              as the data shipping collective.
+ *
+ *              The second parameter is the total number of open
+ *              instances on all nodes that will be operating on the
+ *              file. Must be called for every such instance with the
+ *              same value of NUM_INSTS.
+ *
+ *                  NUM_INSTS - The number of open file instances, on all
+ *                              nodes, collaborating to operate on the file
+ * Return:      Nothing
+ * Programmer:  Bill Wendling, 28. May 2002
+ * Modifications:
+ */
+    static void
+gpfs_start_data_shipping(int handle, int num_insts)
+{
+    struct {
+    gpfsFcntlHeader_t hdr;
+    gpfsDataShipStart_t start;
+    } ds_start;
+
+    ds_start.hdr.totalLength = sizeof(ds_start);
+    ds_start.hdr.fcntlVersion = GPFS_FCNTL_CURRENT_VERSION;
+    ds_start.hdr.fcntlReserved = 0;
+    ds_start.start.structLen = sizeof(gpfsDataShipStart_t);
+    ds_start.start.structType = GPFS_DATA_SHIP_START;
+    ds_start.start.numInstances = num_insts;
+    ds_start.start.reserved = 0;
+
+    if (gpfs_fcntl(handle, &ds_start) != 0) {
+    fprintf(stderr,
+        "gpfs_fcntl DS start directive failed. errno=%d errorOffset=%d\n",
+        errno, ds_start.hdr.errorOffset);
+    exit(EXIT_FAILURE);
+    }
+}
+
+/*
+ * Function:    gpfs_start_data_ship_map
+ * Purpose:     Indicates which agent nodes are to be used for data
+ *              shipping. GPFS recognizes which agent nodes to use for
+ *              data shipping.
+ *
+ *                  PARTITION_SIZE - The number of contiguous bytes per
+ *                                   server. This value must be a
+ *                                   multiple of the number of bytes in a
+ *                                   single file system block
+ *                  AGENT_COUNT    - The number of entries in the
+ *                                   agentNodeNumber array
+ *                  AGENT_NODE_NUM - The data ship agent node numbers as
+ *                                   listed in the SDT or the global ODM
+ *
+ * Return:      Nothing
+ * Programmer:  Bill Wendling, 10. Jul 2002
+ * Modifications:
+ */
+    static void
+gpfs_start_data_ship_map(int handle, int partition_size, int agent_count,
+    int *agent_node_num)
+{
+    int i;
+    struct {
+    gpfsFcntlHeader_t hdr;
+    gpfsDataShipMap_t map;
+    } ds_map;
+
+    ds_map.hdr.totalLength = sizeof(ds_map);
+    ds_map.hdr.fcntlVersion = GPFS_FCNTL_CURRENT_VERSION;
+    ds_map.hdr.fcntlReserved = 0;
+    ds_map.map.structLen = sizeof(gpfsDataShipMap_t);
+    ds_map.map.structType = GPFS_DATA_SHIP_MAP;
+    ds_map.map.partitionSize = partition_size;
+    ds_map.map.agentCount = agent_count;
+
+    for (i = 0; i < agent_count; ++i)
+    ds_map.map.agentNodeNumber[i] = agent_node_num[i];
+
+    if (gpfs_fcntl(handle, &ds_map) != 0) {
+    fprintf(stderr,
+        "gpfs_fcntl DS map directive failed. errno=%d errorOffset=%d\n",
+        errno, ds_map.hdr.errorOffset);
+    exit(EXIT_FAILURE);
+    }
+}
+
+/*
+ * Function:    gpfs_stop_data_shipping
+ * Purpose:     Takes a file out of the data shipping mode.
+ *
+ *              - GPFS waits for all threads that issued the
+ *                GPFS_DATA_SHIP_START directive to issue this directive,
+ *                then flushes the dirty file data to disk.
+ *
+ *              - While a gpfs_cntl() call is blocked for other threads,
+ *                the call can be interrupted by any signal. If a signal
+ *                is delivered to any of the waiting calls, all waiting
+ *                calls on every node will be interrupted and will return
+ *                EINTR. GPFS will not cancel data shipping mode if such
+ *                a signal occurs. It is the responsibility of the
+ *                application to mask off any signals that might normally
+ *                occur while waiting for another node in the data
+ *                shipping collective. Several libraries use SIGALRM; the
+ *                thread that makes the gpfs_fcntl() call should use
+ *                sigthreadmask to mask off delivery of this signal while
+ *                inside the call.
+ * Return:      Nothing
+ * Programmer:  Bill Wendling, 28. May 2002
+ * Modifications:
+ */
+    static void
+gpfs_stop_data_shipping(int handle)
+{
+    struct {
+    gpfsFcntlHeader_t hdr;
+    gpfsDataShipStop_t stop;
+    } ds_stop;
+
+    ds_stop.hdr.totalLength = sizeof(ds_stop);
+    ds_stop.hdr.fcntlVersion = GPFS_FCNTL_CURRENT_VERSION;
+    ds_stop.hdr.fcntlReserved = 0;
+    ds_stop.stop.structLen = sizeof(ds_stop.stop);
+    ds_stop.stop.structType = GPFS_DATA_SHIP_STOP;
+
+    if (gpfs_fcntl(handle, &ds_stop) != 0)
+    fprintf(stderr,
+        "gpfs_fcntl DS stop directive failed. errno=%d errorOffset=%d\n",
+        errno, ds_stop.hdr.errorOffset);
+}
+
+/*
+ * Function:    gpfs_invalidate_file_cache
+ * Purpose:     Invalidate all cached data held on behalf of a file on
+ *              this node.
+ * Return:      Nothing
+ * Programmer:  Bill Wendling, 03. June 2002
+ * Modifications:
+ */
+    static void
+gpfs_invalidate_file_cache(const char *filename)
+{
+    int handle;
+    struct {
+    gpfsFcntlHeader_t hdr;
+    gpfsClearFileCache_t inv;
+    } inv_cache_hint;
+
+    /* Open the file.  If the open fails, the file cannot be cached. */
+    handle = open(filename, O_RDONLY, 0);
+
+    if (handle == -1)
+    return;
+
+    /* Issue the invalidate hint */
+    inv_cache_hint.hdr.totalLength = sizeof(inv_cache_hint);
+    inv_cache_hint.hdr.fcntlVersion = GPFS_FCNTL_CURRENT_VERSION;
+    inv_cache_hint.hdr.fcntlReserved = 0;
+    inv_cache_hint.inv.structLen = sizeof(gpfsClearFileCache_t);
+    inv_cache_hint.inv.structType = GPFS_CLEAR_FILE_CACHE;
+
+    if (gpfs_fcntl(handle, &inv_cache_hint) != 0) {
+    fprintf(stderr,
+        "gpfs_fcntl clear cache hint failed for file '%s'.",
+        filename);
+    fprintf(stderr, " errno=%d errorOffset=%d\n",
+        errno, inv_cache_hint.hdr.errorOffset);
+    exit(1);
+    }
+
+    /* Close the file */
+    if (close(handle) == -1) {
+    fprintf(stderr,
+        "could not close file '%s' after flushing file cache, ",
+        filename);
+    fprintf(stderr, "errno=%d\n", errno);
+    exit(1);
+    }
+}
+
+#else
+
+/* turn the stubs off since some compilers are warning they are not used */
+#if 0
+/* H5_HAVE_GPFS isn't defined...stub functions */
+
+    static void
+gpfs_access_range(int UNUSED handle, off_t UNUSED start, off_t UNUSED length,
+    int UNUSED is_write)
+{
+    return;
+}
+
+    static void
+gpfs_free_range(int UNUSED handle, off_t UNUSED start, off_t UNUSED length)
+{
+    return;
+}
+
+    static void
+gpfs_clear_file_cache(int UNUSED handle)
+{
+    return;
+}
+
+    static void
+gpfs_cancel_hints(int UNUSED handle)
+{
+    return;
+}
+
+    static void
+gpfs_start_data_shipping(int UNUSED handle, int UNUSED num_insts)
+{
+    return;
+}
+
+    static void
+gpfs_stop_data_shipping(int UNUSED handle)
+{
+    return;
+}
+
+    static void
+gpfs_start_data_ship_map(int UNUSED handle, int UNUSED partition_size,
+    int UNUSED agent_count, int UNUSED *agent_node_num)
+{
+    return;
+}
+
+    static void
+gpfs_invalidate_file_cache(const char UNUSED *filename)
+{
+    return;
+}
+
+#endif  /* 0 */
+
+#endif  /* H5_HAVE_GPFS */
+
+