diff options
| -rw-r--r-- | src/H5Epublic.h | 1 | ||||
| -rw-r--r-- | src/H5F.c | 7 | ||||
| -rw-r--r-- | src/H5FD.c | 3 | ||||
| -rw-r--r-- | src/H5FDgass.c | 648 | ||||
| -rw-r--r-- | src/H5FDgass.h | 48 | ||||
| -rw-r--r-- | src/H5public.h | 6 | ||||
| -rw-r--r-- | src/Makefile.in | 2 | ||||
| -rw-r--r-- | src/hdf5.h | 1 | ||||
| -rw-r--r-- | test/Makefile.in | 16 | ||||
| -rw-r--r-- | test/gass_append.c | 148 | ||||
| -rw-r--r-- | test/gass_read.c | 200 | ||||
| -rw-r--r-- | test/gass_write.c | 157 |
12 files changed, 1233 insertions, 4 deletions
diff --git a/src/H5Epublic.h b/src/H5Epublic.h index 7d835d2..07ba0f1 100644 --- a/src/H5Epublic.h +++ b/src/H5Epublic.h @@ -100,6 +100,7 @@ typedef enum H5E_minor_t { H5E_FILEOPEN, /*file already open */ H5E_CANTCREATE, /*Can't create file */ H5E_CANTOPENFILE, /*Can't open file */ + H5E_CANTCLOSEFILE, /*Can't close file */ H5E_NOTHDF5, /*not an HDF5 format file */ H5E_BADFILE, /*bad file ID accessed */ H5E_TRUNCATED, /*file has been truncated */ @@ -11,7 +11,7 @@ * MODIFICATIONS * Robb Matzke, 30 Aug 1997 * Added `ERRORS' fields to function prologues. -* * +* ****************************************************************************/ #ifdef RCSID @@ -24,6 +24,7 @@ static char RcsId[] = "@(#)$Revision$"; #include <H5FDcore.h> /*temporary in-memory files */ #include <H5FDfamily.h> /*family of files */ #include <H5FDmpio.h> /*MPI-2 I/O */ +#include <H5FDgass.h> /*GASS I/O */ #include <H5FDmulti.h> /*multiple files partitioned by mem usage */ #include <H5FDsec2.h> /*Posix unbuffered I/O */ @@ -202,6 +203,9 @@ H5F_init_interface(void) H5E_BEGIN_TRY { if ((status=H5FD_SEC2)<0) goto end_registration; if ((status=H5FD_FAMILY)<0) goto end_registration; +#ifdef HAVE_GASS + if ((status=H5FD_GASS)<0) goto end_registration; +#endif if ((status=H5FD_CORE)<0) goto end_registration; if ((status=H5FD_MULTI)<0) goto end_registration; #ifdef HAVE_PARALLEL @@ -209,6 +213,7 @@ H5F_init_interface(void) #endif end_registration: ; } H5E_END_TRY; + if (status<0) { HRETURN_ERROR(H5E_FILE, H5E_CANTINIT, FAIL, "file driver registration failed"); @@ -163,14 +163,17 @@ H5FDregister(const H5FD_class_t *cls) HRETURN_ERROR(H5E_ARGS, H5E_UNINITIALIZED, FAIL, "null class pointer is disallowed"); } + if (!cls->open || !cls->close) { HRETURN_ERROR(H5E_ARGS, H5E_UNINITIALIZED, FAIL, "`open' and/or `close' methods are not defined"); } + if (!cls->get_eoa || !cls->set_eoa) { HRETURN_ERROR(H5E_ARGS, H5E_UNINITIALIZED, FAIL, "`get_eoa' and/or `set_eoa' methods are not defined"); } + if (!cls->get_eof) { HRETURN_ERROR(H5E_ARGS, H5E_UNINITIALIZED, FAIL, "`get_eof' method is not defined"); diff --git a/src/H5FDgass.c b/src/H5FDgass.c new file mode 100644 index 0000000..055e12f --- /dev/null +++ b/src/H5FDgass.c @@ -0,0 +1,648 @@ +/* + * Copyright © 1999 NCSA + * All rights reserved. + * + * Programmer: Saurabh Bagchi (bagchi@uiuc.edu) + * Thursday, August 12 -Tuesday, August 17, 1999 + * + * Purpose: This is the GASS I/O driver. + * + */ +#include <assert.h> +#include <errno.h> +#include <fcntl.h> +#include <hdf5.h> +#include <stdlib.h> +#include <sys/stat.h> +#include <unistd.h> + +/* Packages needed by this file.*/ +#include <H5Eprivate.h> + +#undef MAX +#define MAX(X,Y) ((X)>(Y)?(X):(Y)) + +/* The driver identification number, initialized at runtime */ +static hid_t H5FD_GASS_g = 0; + +#ifdef HAVE_GASS + +/* File operations */ +#define OP_UNKNOWN 0 +#define OP_READ 1 +#define OP_WRITE 2 + +/* + * The description of a file belonging to this driver. The `eoa' and `eof' + * determine the amount of hdf5 address space in use and the high-water mark + * of the file (the current size of the underlying Unix file). The `pos' + * value is used to eliminate file position updates when they would be a + * no-op. Unfortunately we've found systems that use separate file position + * indicators for reading and writing so the lseek can only be eliminated if + * the current operation is the same as the previous operation. When opening + * a file the `eof' will be set to the current file size, `eoa' will be set + * to zero, `pos' will be set to H5F_ADDR_UNDEF (as it is when an error + * occurs), and `op' will be set to H5F_OP_UNKNOWN. + */ +typedef struct H5FD_gass_t { + H5FD_t pub; /*public stuff, must be first */ + int fd; /*the unix file */ + GASS_Info info; /*file information */ + haddr_t eoa; /*end of allocated region */ + haddr_t eof; /*end of file; current file size*/ + haddr_t pos; /*current file I/O position */ + int op; /*last operation */ + + +} H5FD_gass_t; + +/* + * This driver supports systems that have the lseek64() function by defining + * some macros here so we don't have to have conditional compilations later + * throughout the code. + * + * file_offset_t: The datatype for file offsets, the second argument of + * the lseek() or lseek64() call. + * + * file_seek: The function which adjusts the current file position, + * either lseek() or lseek64(). + */ +#ifdef HAVE_LSEEK64 +# define file_offset_t off64_t +# define file_seek lseek64 +#else +# define file_offset_t off_t +# define file_seek lseek +#endif + +/* + * These macros check for overflow of various quantities. These macros + * assume that file_offset_t is signed and haddr_t and size_t are unsigned. + * + * ADDR_OVERFLOW: Checks whether a file address of type `haddr_t' + * is too large to be represented by the second argument + * of the file seek function. + * + * SIZE_OVERFLOW: Checks whether a buffer size of type `hsize_t' is too + * large to be represented by the `size_t' type. + * + * REGION_OVERFLOW: Checks whether an address and size pair describe data + * which can be addressed entirely by the second + * argument of the file seek function. + */ +#define MAXADDR (((haddr_t)1<<(8*sizeof(file_offset_t)-1))-1) +#define ADDR_OVERFLOW(A) (HADDR_UNDEF==(A) || \ + ((A) & ~(haddr_t)MAXADDR)) +#define SIZE_OVERFLOW(Z) ((Z) & ~(hsize_t)MAXADDR) +#define REGION_OVERFLOW(A,Z) (ADDR_OVERFLOW(A) || SIZE_OVERFLOW(Z) || \ + sizeof(file_offset_t)<sizeof(size_t) || \ + HADDR_UNDEF==(A)+(Z) || \ + (file_offset_t)((A)+(Z))<(file_offset_t)(A)) + +/* Prototypes */ +static H5FD_t *H5FD_gass_open(const char *name, unsigned flags, hid_t fapl_id, + haddr_t maxaddr); +static herr_t H5FD_gass_close(H5FD_t *_file); +static haddr_t H5FD_gass_get_eoa(H5FD_t *_file); +static herr_t H5FD_gass_set_eoa(H5FD_t *_file, haddr_t addr); +static haddr_t H5FD_gass_get_eof(H5FD_t *_file); +static herr_t H5FD_gass_read(H5FD_t *_file, hid_t fapl_id, haddr_t addr, + hsize_t size, void *buf); +static herr_t H5FD_gass_write(H5FD_t *_file, hid_t fapl_id, haddr_t addr, + hsize_t size, const void *buf); + +/* GASS I/O-specific file access properties */ +typedef struct H5FD_gass_fapl_t { + GASS_Info info; /* access property parameters */ +} H5FD_gass_fapl_t; + +/* The GASS IO driver information */ +static const H5FD_class_t H5FD_gass_g = { + "gass", /*name */ + MAXADDR, /*maxaddr */ + NULL, /*sb_size */ + NULL, /*sb_encode */ + NULL, /*sb_decode */ + sizeof(H5FD_gass_fapl_t), /*fapl_size */ + NULL, /*fapl_get */ + NULL, /*fapl_copy */ + NULL, /*fapl_free */ + 0, /*dxpl_size */ + NULL, /*dxpl_copy */ + NULL, /*dxpl_free */ + H5FD_gass_open, /*open */ + H5FD_gass_close, /*close */ + NULL, /*cmp */ + NULL, /*alloc */ + NULL, /*free */ + H5FD_gass_get_eoa, /*get_eoa */ + H5FD_gass_set_eoa, /*set_eoa */ + H5FD_gass_get_eof, /*get_eof */ + H5FD_gass_read, /*read */ + H5FD_gass_write, /*write */ + NULL, /*flush */ + H5FD_FLMAP_SINGLE, /*fl_map */ +}; + + +/*------------------------------------------------------------------------- + * Function: H5FD_gass_init + * + * Purpose: Initialize this driver by registering the driver with the + * library. + * + * Return: Success: The driver ID for the gass driver. + * + * Failure: Negative. + * + * Programmer: Saurabh Bagchi + * Friday, August 13, 1999 + * + * Modifications: + * + *------------------------------------------------------------------------- + */ +hid_t +H5FD_gass_init(void) +{ + if (!H5FD_GASS_g) { + H5FD_GASS_g = H5FDregister(&H5FD_gass_g); + } + globus_module_activate (GLOBUS_COMMON_MODULE); + globus_module_activate (GLOBUS_GASS_FILE_MODULE); + + return H5FD_GASS_g; +} + + +/*------------------------------------------------------------------------- + * Function: H5Pset_fapl_gass + * + * Purpose: Store the user supplied GASS INFO in + * the file access property list FAPL_ID which can then be used + * to create and/or open the file. + * + * GASS info object to be used for file open using GASS. + * Any modification to info after + * this function call returns may have undetermined effect + * to the access property list. Users should call this + * function again to setup the property list. + * + * + * Return: Success: Non-negative + * + * Failure: Negative + * + * Programmer: Saurabh Bagchi + * Friday, August 13, 1999 + * + * Modifications: + * + *------------------------------------------------------------------------- + */ +herr_t +H5Pset_fapl_gass(hid_t fapl_id, GASS_Info info) +{ + H5FD_gass_fapl_t fa; + + /*NO TRACE*/ + + /* Check arguments */ + if (H5P_FILE_ACCESS!=H5Pget_class(fapl_id)) return -1; +#ifdef LATER +#warning "We need to verify that INFO contain sensible information." +#endif + + /* Initialize driver specific properties */ + fa.info = info; + return H5Pset_driver(fapl_id, H5FD_GASS, &fa); +} + + +/*------------------------------------------------------------------------- + * Function: H5Pget_fapl_gass + * + * Purpose: If the file access property list is set to the H5FD_GASS + * driver then this function returns the GASS info object + * through the INFO pointer. + * + * Return: Success: Non-negative with the info object returned + * through the INFO arguments if non-null. + * The information is copied and it is therefore + * valid only until the file access property + * list is modified or closed. + * + * Failure: Negative + * + * Programmer: Saurabh Bagchi + * Friday, August 13, 1999 + * + * Modifications: + * + *------------------------------------------------------------------------- + */ +herr_t +H5Pget_fapl_gass(hid_t fapl_id, GASS_Info *info/*out*/) +{ + H5FD_gass_fapl_t *fa; + + /*NO TRACE*/ + + if (H5P_FILE_ACCESS!=H5Pget_class(fapl_id)) return -1; + if (H5FD_GASS!=H5Pget_driver(fapl_id)) return -1; + if (NULL==(fa=H5Pget_driver_info(fapl_id))) return -1; + + if (info) *info = fa->info; + return 0; +} + + +/*------------------------------------------------------------------------- + * Function: H5FD_gass_open + * + * Purpose: Opens a file with name NAME. The FLAGS are a bit field with + * purpose similar to the second argument of open(2) and which + * are defined in H5Fpublic.h. The file access property list + * FAPL_ID contains the driver properties and MAXADDR + * is the largest address which this file will be expected to + * access. + * + * Return: Success: A pointer to a new file data structure. The + * public fields will be initialized by the + * caller, which is always H5FD_open(). + * + * Failure: NULL + * + * Programmer: Saurabh Bagchi + * Friday, August 13, 1999 + * + * Modifications: + * + *------------------------------------------------------------------------- + */ +static H5FD_t * +H5FD_gass_open(const char *name, unsigned flags, hid_t fapl_id, + haddr_t maxaddr) +{ + int fd; + struct stat sb; + H5FD_gass_t *file=NULL; + const H5FD_gass_fapl_t *fa=NULL; + H5FD_gass_fapl_t _fa; + char *filename = (char *) malloc(80 * sizeof(char)); + + /* fprintf(stdout, "Entering H5FD_gass_open name=%s flags=0x%x\n", name, flags); */ + + strcpy (filename, name); + + /* Obtain a pointer to gass-specific file access properties */ + if (H5P_DEFAULT==fapl_id || H5FD_GASS!=H5Pget_driver(fapl_id)) { + GASS_INFO_NULL (_fa.info); + /* _fa.info = GASS_INFO_NULL; */ + /* _fa.info = {0,0}; */ /*default*/ + fa = &_fa; + } else { + fa = H5Pget_driver_info(fapl_id); + assert(fa); + } + + /* Check arguments */ + if (!name || !*name) return NULL; + if (0==maxaddr || HADDR_UNDEF==maxaddr) return NULL; + if (ADDR_OVERFLOW(maxaddr)) return NULL; + + /* When I come down here, the possible flag values and the correct + responses are given here :- + + 1. H5F_ACC_CREAT | H5F_ACC_RDWR | H5F_ACC_EXCL : The file is + a new one. Go ahead and open it in O_RDWR. + + 2. H5F_ACC_CREAT | H5F_ACC_RDWR | H5F_ACC_TRUNC : Use + O_RDWR | O_TRUNC with gass_open. + + 3. H5F_ACC_RDWR | H5F_ACC_TRUNC : File already exists. Truncate it. + + 4. H5F_ACC_RDWR : Use O_RDWR with gass_open + + 5. H5F_ACC_RDWR is not set : Use O_RDONLY with gass_open + + One reason why we cannot simply pass on the flags to gass_open + is that gass_open does not support many of them (e.g., O_CREAT) + */ + + /* fprintf (stderr, "flags=0x%x\n", flags); */ + + if ((flags & H5F_ACC_CREAT) && (flags & H5F_ACC_RDWR) && (flags & H5F_ACC_EXCL)) { + if ((fd = globus_gass_open (filename, O_RDWR|O_TRUNC)) < 0) { + /* HRETURN_ERROR(H5E_IO, H5E_CANTOPENFILE, FAIL, "open failed"); */ + fprintf (stderr, "Can't open file. \n"); + return NULL; + } + + } + else if ((flags & H5F_ACC_CREAT) && (flags & H5F_ACC_RDWR) && (flags & H5F_ACC_TRUNC)) { + if ((fd = globus_gass_open (filename, O_RDWR|O_TRUNC)) < 0) { + /* HRETURN_ERROR(H5E_IO, H5E_CANTOPENFILE, NULL, "open failed"); */ + fprintf (stderr, "Can't open file. \n"); + return NULL; + } + + } + else if ((flags & H5F_ACC_RDWR) && (flags & H5F_ACC_TRUNC)) { + if ((fd = globus_gass_open (filename, O_RDWR|O_TRUNC)) < 0) { + /* HRETURN_ERROR(H5E_IO, H5E_CANTOPENFILE, NULL, "open failed"); */ + fprintf (stderr, "Can't open file. \n"); + return NULL; + } + + } + else if (flags & H5F_ACC_RDWR) { + printf ("I'm here in H5FDgass_open going to call globus_gass_open with O_RDWR. \n"); + printf ("Name of URL =%s \n", filename); + if ((fd = globus_gass_open (filename, O_RDWR)) < 0) { + /* HRETURN_ERROR(H5E_IO, H5E_CANTOPENFILE, NULL, "open failed"); */ + fprintf (stderr, "Can't open file. \n"); + return NULL; + } + + } + else { /* This is case where H5F_ACC_RDWR is not set */ + if ((fd = globus_gass_open (filename, O_RDONLY)) < 0) { + /* HRETURN_ERROR(H5E_IO, H5E_CANTOPENFILE, NULL, "open failed");*/ + fprintf (stderr, "Can't open file. \n"); + return NULL; + } + + } + + if (fstat(fd, &sb)<0) { + close(fd); + return NULL; + } + + /* Create the new file struct */ + file = calloc(1, sizeof(H5FD_gass_t)); + file->fd = fd; + file->eof = sb.st_size; + file->pos = HADDR_UNDEF; + file->op = OP_UNKNOWN; + file->info = fa->info; + + return (H5FD_t*)file; +} + +/*------------------------------------------------------------------------- + * Function: H5FD_gass_close + * + * Purpose: Closes a GASS file. + * + * Return: Success: 0 + * + * Failure: -1, file not closed. + * + * Programmer: Saurabh Bagchi + * Monday, August 16, 1999 + * + * Modifications: + * + *------------------------------------------------------------------------- + */ +static herr_t +H5FD_gass_close (H5FD_t *_file) +{ + int gasserr; + H5FD_gass_t *file = (H5FD_gass_t *)_file; + + if (file == NULL) { + /* HRETURN_ERROR(H5E_IO, H5E_CANTCLOSEFILE, NULL, "close failed"); */ + fprintf (stderr, "Can't close file. \n"); + return -1; + } + + gasserr = globus_gass_close (file->fd); + if (gasserr == -1) + fprintf (stderr, "GASS close failed. \n"); + + return gasserr; +} + + +/*------------------------------------------------------------------------- + * Function: H5FD_gass_get_eoa + * + * Purpose: Gets the end-of-address marker for the file. The EOA marker + * is the first address past the last byte allocated in the + * format address space. + * + * Return: Success: The end-of-address marker. + * + * Failure: HADDR_UNDEF + * + * Programmer: Saurabh Bagchi + * Monday, August 16, 1999 + * + * Modifications: + * + *------------------------------------------------------------------------- + */ +static haddr_t +H5FD_gass_get_eoa(H5FD_t *_file) +{ + H5FD_gass_t *file = (H5FD_gass_t *)_file; + return file->eoa; +} + + +/*------------------------------------------------------------------------- + * Function: H5FD_gass_set_eoa + * + * Purpose: Set the end-of-address marker for the file. This function is + * called shortly after an existing HDF5 file is opened in order + * to tell the driver where the end of the HDF5 data is located. + * + * Return: Success: 0 + * + * Programmer: Saurabh Bagchi + * Monday, August 16, 1999 + * + * Modifications: + * + *------------------------------------------------------------------------- + */ +static herr_t +H5FD_gass_set_eoa(H5FD_t *_file, haddr_t addr) +{ + H5FD_gass_t *file = (H5FD_gass_t *)_file; + file->eoa = addr; + return 0; +} + + +/*------------------------------------------------------------------------- + * Function: H5FD_gass_get_eof + * + * Purpose: Returns the end-of-file marker, which is the greater of + * either the Unix end-of-file or the HDF5 end-of-address + * markers. + * + * Return: Success: End of file address, the first address past + * the end of the "file", either the Unix file + * or the HDF5 file. + * + * Failure: HADDR_UNDEF + * + * Programmer: Saurabh Bagchi + * Monday, August 16, 1999 + * + * Modifications: + * + *------------------------------------------------------------------------- + */ +static haddr_t +H5FD_gass_get_eof(H5FD_t *_file) +{ + H5FD_gass_t *file = (H5FD_gass_t*)_file; + return MAX(file->eof, file->eoa); +} + +/*------------------------------------------------------------------------- + * Function: H5FD_gass_read + * + * Purpose: Reads SIZE bytes of data from FILE beginning at address ADDR + * into buffer BUF. + * + * Return: Success: Zero. Result is stored in caller-supplied + * buffer BUF. + * + * Failure: -1, Contents of buffer BUF are undefined. + * + * Programmer: Saurabh Bagchi + * Monday, August 16, 1999 + * + * Modifications: + * + *------------------------------------------------------------------------- + */ +static herr_t +H5FD_gass_read(H5FD_t *_file, hid_t dxpl_id/*unused*/, haddr_t addr, + hsize_t size, void *buf/*out*/) +{ + H5FD_gass_t *file = (H5FD_gass_t*)_file; + ssize_t nbytes; + + assert(file && file->pub.cls); + assert(buf); + + /* Check for overflow conditions */ + if (HADDR_UNDEF==addr) return -1; + if (REGION_OVERFLOW(addr, size)) return -1; + if (addr+size>file->eoa) return -1; + + /* Seek to the correct location */ + if ((addr!=file->pos || OP_READ!=file->op) && + file_seek(file->fd, (file_offset_t)addr, SEEK_SET)<0) { + file->pos = HADDR_UNDEF; + file->op = OP_UNKNOWN; + return -1; + } + + /* + * Read data, being careful of interrupted system calls, partial results, + * and the end of the file. + */ + while (size>0) { +do nbytes = read(file->fd, buf, size); + while (-1==nbytes && EINTR==errno); + if (-1==nbytes) { + /* error */ + file->pos = HADDR_UNDEF; + file->op = OP_UNKNOWN; + return -1; + } + if (0==nbytes) { + /* end of file but not end of format address space */ + memset(buf, 0, size); + size = 0; + } + assert(nbytes>=0); + assert((hsize_t)nbytes<=size); + size -= (hsize_t)nbytes; + addr += (haddr_t)nbytes; + buf = (char*)buf + nbytes; + } + + /* Update current position */ + file->pos = addr; + file->op = OP_READ; + return 0; +} + +/*------------------------------------------------------------------------- + * Function: H5FD_gass_write + * + * Purpose: Writes SIZE bytes of data to FILE beginning at address ADDR + * from buffer BUF. + * + * Return: Success: Zero + * + * Failure: -1 + * + * Programmer: Saurabh Bagchi + * Tuesday, August 17, 1999 + * + * Modifications: + * + *------------------------------------------------------------------------- + */ +static herr_t +H5FD_gass_write(H5FD_t *_file, hid_t dxpl_id/*unused*/, haddr_t addr, + hsize_t size, const void *buf) +{ + H5FD_gass_t *file = (H5FD_gass_t*)_file; + ssize_t nbytes; + + assert(file && file->pub.cls); + assert(buf); + + /* Check for overflow conditions */ + if (HADDR_UNDEF==addr) return -1; + if (REGION_OVERFLOW(addr, size)) return -1; + if (addr+size>file->eoa) return -1; + + /* Seek to the correct location */ + if ((addr!=file->pos || OP_WRITE!=file->op) && + file_seek(file->fd, (file_offset_t)addr, SEEK_SET)<0) { + file->pos = HADDR_UNDEF; + file->op = OP_UNKNOWN; + return -1; + } + + /* + * Write the data, being careful of interrupted system calls and partial + * results + */ + while (size>0) { + do nbytes = write(file->fd, buf, size); + while (-1==nbytes && EINTR==errno); +if (-1==nbytes) { + /* error */ + file->pos = HADDR_UNDEF; + file->op = OP_UNKNOWN; + return -1; + } + assert(nbytes>0); + assert((hsize_t)nbytes<=size); + size -= (hsize_t)nbytes; + addr += (haddr_t)nbytes; + buf = (const char*)buf + nbytes; + } + + /* Update current position and eof */ + file->pos = addr; + file->op = OP_WRITE; + if (file->pos>file->eof) file->eof = file->pos; + + return 0; +} + +#endif diff --git a/src/H5FDgass.h b/src/H5FDgass.h new file mode 100644 index 0000000..94cabbd --- /dev/null +++ b/src/H5FDgass.h @@ -0,0 +1,48 @@ +/* + * Copyright © 1999 NCSA + * All rights reserved. + * + * Programmer: Saurabh Bagchi <bagchi@uiuc.edu> + * Tuesday, August 17, 1999 + * + * Purpose: The public header file for the gass driver. + */ +#ifndef H5FDgass_H +#define H5FDgass_H + +#include <H5FDpublic.h> +#include <H5Ipublic.h> +#include <H5Eprivate.h> + +#include <string.h> + +#ifdef HAVE_GASS +#define H5FD_GASS (H5FD_gass_init()) +#else +#define H5FD_GASS (-1) +#endif + +#ifdef HAVE_GASS +/* Define the GASS info object. (Will be added to later as more GASS + functionality is sought to be exposed. */ +typedef struct GASS_Info { + unsigned long block_size; + unsigned long max_length; +} GASS_Info; + +#define GASS_INFO_NULL(v) memset((void *)&v, 0, sizeof(GASS_Info)); +/* + GASS_Info zzGassInfo = {0L,0L}; + #define GASS_INFO_NULL zzGassInfo +*/ +#endif + +/* Function prototypes */ +#ifdef HAVE_GASS +hid_t H5FD_gass_init(void); +herr_t H5Pset_fapl_gass(hid_t fapl_id, GASS_Info info); +herr_t H5Pget_fapl_gass(hid_t fapl_id, GASS_Info *info/*out*/); + +#endif + +#endif // H5FDgass_H diff --git a/src/H5public.h b/src/H5public.h index d2ef7ec..0a0321b 100644 --- a/src/H5public.h +++ b/src/H5public.h @@ -38,6 +38,12 @@ static char RcsId[] = "@(#)$Revision$"; # include <mpio.h> #endif #endif + +#ifdef HAVE_GASS +#include "globus_common.h" +#include "globus_gass_file.h" +#endif + #include <H5api_adpt.h> /* Version numbers */ diff --git a/src/Makefile.in b/src/Makefile.in index 2c3be81..5368802 100644 --- a/src/Makefile.in +++ b/src/Makefile.in @@ -22,7 +22,7 @@ CLEAN=libhdf5.settings ## Source and object files for the library (lexicographically)... LIB_SRC=H5.c H5A.c H5AC.c H5B.c H5D.c H5E.c H5F.c H5Farray.c H5Fistore.c \ - H5FD.c H5FDsec2.c H5FDfamily.c H5FDmpio.c H5FDcore.c H5FDmulti.c H5G.c \ + H5FD.c H5FDsec2.c H5FDfamily.c H5FDmpio.c H5FDcore.c H5FDmulti.c H5FDgass.c H5G.c \ H5Gent.c H5Gnode.c H5Gstab.c H5HG.c H5HL.c H5I.c H5MF.c H5MM.c H5O.c \ H5Oattr.c H5Ocomp.c H5Ocont.c H5Odtype.c H5Oefl.c H5Ofill.c H5Olayout.c \ H5Omtime.c H5Oname.c H5Onull.c H5Osdspace.c H5Oshared.c H5Ostab.c H5P.c \ @@ -44,6 +44,7 @@ #include <H5FDfamily.h> /* File families */ #include <H5FDmpio.h> /* Parallel files using MPI-2 I/O */ #include <H5FDsec2.h> /* POSIX unbuffered file I/O */ +#include <H5FDgass.h> /* Remote files using GASS I/O */ #include <H5FDmulti.h> /* Usage-partitioned file family */ #endif diff --git a/test/Makefile.in b/test/Makefile.in index 2e602a4..f438e6a 100644 --- a/test/Makefile.in +++ b/test/Makefile.in @@ -20,7 +20,7 @@ CPPFLAGS=-I. -I$(srcdir) -I../src -I$(top_srcdir)/src @CPPFLAGS@ RUNTEST=$(LT_RUN) TEST_PROGS=testhdf5 lheap ohdr stab gheap hyperslab istore bittests dtypes \ dsets cmpd_dset extend external links unlink big mtime fillval mount \ - flush1 flush2 enum + flush1 flush2 enum gass_write gass_read gass_append TIMINGS=iopipe chunk ragged overhead ## The libh5test.a library provides common support code for the tests. We link @@ -58,7 +58,9 @@ TEST_SRC=big.c bittests.c chunk.c cmpd_dset.c dsets.c dtypes.c extend.c \ external.c fillval.c flush1.c flush2.c gheap.c h5test.c hyperslab.c \ iopipe.c istore.c lheap.c links.c mount.c mtime.c ohdr.c overhead.c \ ragged.c stab.c tattr.c testhdf5.c tfile.c th5s.c tmeta.c trefer.c \ - tselect.c tvltypes.c unlink.c enum.c + tselect.c tvltypes.c unlink.c enum.c gass_write.c gass_read.c \ + gass_append.c + TEST_OBJ=$(TEST_SRC:.c=.lo) ## Private header files (not to be installed)... @@ -155,4 +157,14 @@ flush2: flush2.lo enum: enum.lo @$(LT_LINK_EXE) $(CFLAGS) -o $@ enum.lo $(LIB) $(LIBHDF5) $(LDFLAGS) $(LIBS) +gass_write: gass_write.lo + @$(LT_LINK_EXE) $(CFLAGS) -o $@ gass_write.lo $(LIB) $(LIBHDF5) $(LDFLAGS) $(LIBS) + +gass_read: gass_read.lo + @$(LT_LINK_EXE) $(CFLAGS) -o $@ gass_read.lo $(LIB) $(LIBHDF5) $(LDFLAGS) $(LIBS) + +gass_append: gass_append.lo + @$(LT_LINK_EXE) $(CFLAGS) -o $@ gass_append.lo $(LIB) $(LIBHDF5) $(LDFLAGS) $(LIBS) + @CONCLUDE@ + diff --git a/test/gass_append.c b/test/gass_append.c new file mode 100644 index 0000000..0764a39 --- /dev/null +++ b/test/gass_append.c @@ -0,0 +1,148 @@ +/* + * Copyright © 1998 NCSA + * All rights reserved. + * + * Programmer: Saurabh Bagchi (bagchi@uiuc.edu) + * Wednesday, August 11, 1999. + * + * Modifications: Saurabh Bagchi (Aug 17, 1999) + * Modified to work with VFL (HDF51.3). + */ + +/* Test the following functionality of the GASS driver. + 1. Open a remote file for append. + 2. Create a new dataset within the file. + 3. Create a local memory buffer to hold the data. + 4. Write the local data to the remote dataset. +*/ +#include <h5test.h> + +#ifndef HAVE_GASS +int main(void) +{ + printf("Test skipped because GASS driver not available\n"); + return 0; +} +#else + +#define URL "ftp://bagchi:bagchi12@hdfspare1/scratch-fuga/home/bagchi/junk.w" +#define DATASETNAME "Int1Array" +#define NX 5 /* dataset dimensions */ +#define NY 6 +#define RANK 2 + +int main (void) +{ + + hid_t fapl =-1, file; + hid_t dataspace, datatype, dataset; + hsize_t dimsf[2]; + + herr_t status = 0; + int data[NX][NY]; /* data to write */ + int i, j; + GASS_Info ginf; + + /* + * Data and output buffer initialization. + */ + for (j = 0; j < NX; j++) { + for (i = 0; i < NY; i++) + data[j][i] = i*i + j*j; + } + /* + * 0 1 4 9 16 25 + * 1 2 5 10 17 26 + * 4 5 8 13 20 29 + * 9 10 13 18 25 34 + * 16 17 20 25 32 41 + */ + + /* Create access property list and set the driver to GASS */ + fapl = H5Pcreate (H5P_FILE_ACCESS); + if (fapl < 0) { + printf (" H5Pcreate failed. \n"); + return -1; + } + + ginf.block_size = 0; + ginf.max_length =0; + /* ginf = GASS_INFO_NULL; */ + + status = H5Pset_fapl_gass (fapl, ginf); + if (status < 0) { + printf ("H5Pset_fapl_gass failed. \n"); + return -1; + } + + /* + * Open an existing file using H5F_ACC_RDWR access, + * and gass file access properties. + */ + file = H5Fopen(URL, H5F_ACC_RDWR, fapl); + if (file < 0) { + printf ("H5Fopen failed. \n"); + return -1; + } + + /* + * Describe the size of the array and create the data space for fixed + * size dataset. + */ + dimsf[0] = NX; + dimsf[1] = NY; + dataspace = H5Screate_simple(RANK, dimsf, NULL); + if (dataspace < 0) { + printf ("H5Screate failed. \n"); + return -1; + } + + /* + * Define datatype for the data in the file. + * We will store little endian INT numbers. + */ + datatype = H5Tcopy(H5T_NATIVE_INT); + if (datatype < 0) { + printf ("H5Tcopy failed. \n"); + return -1; + } + + status = H5Tset_order(datatype, H5T_ORDER_LE); + if (status < 0) { + printf ("H5Tset_order failed. \n"); + return -1; + } + + /* + * Create a new dataset within the file using defined dataspace and + * datatype and default dataset creation properties. + */ + dataset = H5Dcreate(file, DATASETNAME, datatype, dataspace, + H5P_DEFAULT); + if (dataset < 0) { + printf ("H5Dcreate failed. \n"); + return -1; + } + + /* + * Write the data to the dataset using default transfer properties. + */ + status = H5Dwrite(dataset, H5T_NATIVE_INT, H5S_ALL, H5S_ALL, + H5P_DEFAULT, data); + if (status < 0) { + printf ("H5Dwrite failed. \n"); + return -1; + } + + /* + * Close/release resources. + */ + H5Sclose(dataspace); + H5Tclose(datatype); + H5Dclose(dataset); + H5Fclose(file); + H5Pclose(fapl); + + return 0; +} +#endif diff --git a/test/gass_read.c b/test/gass_read.c new file mode 100644 index 0000000..f43cd02 --- /dev/null +++ b/test/gass_read.c @@ -0,0 +1,200 @@ +/* + * Copyright © 1998 NCSA + * All rights reserved. + * + * Programmer: Saurabh Bagchi (bagchi@uiuc.edu) + * Wednesday, August 11, 1999. + * + * Modifications: Saurabh Bagchi (Aug 17, 1999) + * Modified to work with VFL (HDF51.3). + */ + +/* Test the following functionality of the GASS driver. + 1. Open a remote file for read (the dataset was written using gass_write.c). + 2. Create a memory buffer to hold the dataset. + 3. Read the dataset into the memory buffer. + 4. Get some information about the dataset from the file. +*/ +#include <h5test.h> +#include <strings.h> + +#ifndef HAVE_GASS +int main(void) +{ + printf("Test skipped because GASS driver not available\n"); + return 0; +} +#else + +#define URL "ftp://bagchi:bagchi12@hdfspare1/scratch-fuga/home/bagchi/junk.w" + +/* #define DATASETNAME "Int1Array" */ +#define NX_SUB 3 /* hyperslab dimensions */ +#define NY_SUB 4 +#define NX 7 /* output buffer dimensions */ +#define NY 7 +#define NZ 3 +#define RANK 2 +#define RANK_OUT 3 + +int +main (int argc, char **argv) +{ + hid_t fapl = -1, file, dataset; /* handles */ + char DATASETNAME[32]; + hid_t datatype, dataspace; + hid_t memspace; + H5T_class_t class; /* data type class */ + H5T_order_t order; /* data order */ + size_t size; /* + * size of the data element + * stored in file + */ + hsize_t dimsm[3]; /* memory space dimensions */ + hsize_t dims_out[2]; /* dataset dimensions */ + herr_t status; + + int data_out[NX][NY][NZ ]; /* output buffer */ + + hsize_t count[2]; /* size of the hyperslab in the file */ + hssize_t offset[2]; /* hyperslab offset in the file */ + hsize_t count_out[3]; /* size of the hyperslab in memory */ + hssize_t offset_out[3]; /* hyperslab offset in memory */ + int i, j, k, status_n, rank; + GASS_Info ginf; + + if (argc > 2) { + printf ("Incorrect command line. \n"); + printf ("Correct command line: %s [DATASET NAME] \n", argv[0]); + printf ("The two datasets present in the file are: \"IntArray\" and " + "\"Int1Array\"\n"); + exit(1); + } + + printf ("Correct command line: %s [DATASET NAME] \n", argv[0]); + printf ("The two datasets present in the file are: \"IntArray\" and " + "\"Int1Array\"\n"); + printf ("Default dataset is IntArray. \n"); + + if (argc == 1) + strcpy (DATASETNAME, "IntArray"); + else if (!strcmp(argv[1],"IntArray") || !strcmp(argv[1],"Int1Array")) + strcpy (DATASETNAME, argv[1]); + else + strcpy (DATASETNAME, "IntArray"); + printf ("\n Reading dataset %s \n\n", DATASETNAME); + + for (j = 0; j < NX; j++) { + for (i = 0; i < NY; i++) { + for (k = 0; k < NZ ; k++) + data_out[j][i][k] = 0; + } + } + + /* Create access property list and set the driver to GASS */ + fapl = H5Pcreate (H5P_FILE_ACCESS); + if (fapl < 0) { + printf (" H5Pcreate failed. \n"); + return -1; + } + + + ginf.block_size = 0; + ginf.max_length =0; + + /* ginf = GASS_INFO_NULL; */ + + status = H5Pset_fapl_gass (fapl, ginf); + if (status < 0) { + printf ("H5Pset_fapl_gass failed. \n"); + return -1; + } + + /* + * Open the file and the dataset. + */ + file = H5Fopen(URL, H5F_ACC_RDONLY, fapl); + dataset = H5Dopen(file, DATASETNAME); + + /* + * Get datatype and dataspace handles and then query + * dataset class, order, size, rank and dimensions. + */ + datatype = H5Dget_type(dataset); /* datatype handle */ + class = H5Tget_class(datatype); + if (class == H5T_INTEGER) printf("Data set has INTEGER type \n"); + order = H5Tget_order(datatype); + if (order == H5T_ORDER_LE) printf("Little endian order \n"); + + size = H5Tget_size(datatype); + printf(" Data size is %d \n", size); + + dataspace = H5Dget_space(dataset); /* dataspace handle */ + rank = H5Sget_simple_extent_ndims(dataspace); + status_n = H5Sget_simple_extent_dims(dataspace, dims_out, NULL); + printf("rank %d, dimensions %lu x %lu \n", rank, + (unsigned long)(dims_out[0]), (unsigned long)(dims_out[1])); + + /* + * Define hyperslab in the dataset. + */ + offset[0] = 1; + offset[1] = 2; + count[0] = NX_SUB; + count[1] = NY_SUB; + status = H5Sselect_hyperslab(dataspace, H5S_SELECT_SET, offset, NULL, + count, NULL); + + /* + * Define the memory dataspace. + */ + dimsm[0] = NX; + dimsm[1] = NY; + dimsm[2] = NZ ; + memspace = H5Screate_simple(RANK_OUT,dimsm,NULL); + + /* + * Define memory hyperslab. + */ + offset_out[0] = 3; + offset_out[1] = 0; + offset_out[2] = 0; + count_out[0] = NX_SUB; + count_out[1] = NY_SUB; + count_out[2] = 1; + status = H5Sselect_hyperslab(memspace, H5S_SELECT_SET, offset_out, NULL, + count_out, NULL); + + /* + * Read data from hyperslab in the file into the hyperslab in + * memory and display. + */ + status = H5Dread(dataset, H5T_NATIVE_INT, memspace, dataspace, + H5P_DEFAULT, data_out); + for (j = 0; j < NX; j++) { + for (i = 0; i < NY; i++) printf("%d ", data_out[j][i][0]); + printf("\n"); + } + /* + * 0 0 0 0 0 0 0 + * 0 0 0 0 0 0 0 + * 0 0 0 0 0 0 0 + * 3 4 5 6 0 0 0 + * 4 5 6 7 0 0 0 + * 5 6 7 8 0 0 0 + * 0 0 0 0 0 0 0 + */ + + /* + * Close/release resources. + */ + H5Tclose(datatype); + H5Dclose(dataset); + H5Sclose(dataspace); + H5Sclose(memspace); + H5Fclose(file); + H5Pclose(fapl); + + return 0; +} +#endif diff --git a/test/gass_write.c b/test/gass_write.c new file mode 100644 index 0000000..a6000ed --- /dev/null +++ b/test/gass_write.c @@ -0,0 +1,157 @@ +/* + * Copyright © 1998 NCSA + * All rights reserved. + * + * Programmer: Saurabh Bagchi (bagchi@uiuc.edu) + * Friday, August 6, 1999. + * + * Modifications: Saurabh Bagchi (Aug 17, 1999) + * Modified to work with VFL (HDF51.3). + */ + +/* Test the following functionality of the GASS driver. + 1. Open a remote file for write. + 2. Create a new dataset within the file. + 3. Create a local memory buffer to hold the data. + 4. Write the local data to the remote dataset. +*/ +#include <h5test.h> + +#ifndef HAVE_GASS +int main(void) +{ + printf("Test skipped because GASS driver not available\n"); + return 0; +} +#else + +#define URL "ftp://bagchi:bagchi12@hdfspare1/scratch-fuga/home/bagchi/junk.w" + +#define DATASETNAME "IntArray" +#define NX 5 /* dataset dimensions */ +#define NY 6 +#define RANK 2 + +int main (void) +{ + + hid_t fapl =-1, file; + hid_t dataspace, datatype, dataset; + hsize_t dimsf[2]; + + herr_t status = 0; + int data[NX][NY]; /* data to write */ + int i, j; + GASS_Info ginf; + + /* + * Data and output buffer initialization. + */ + for (j = 0; j < NX; j++) { + for (i = 0; i < NY; i++) + data[j][i] = i + j; + } + /* + * 0 1 2 3 4 5 + * 1 2 3 4 5 6 + * 2 3 4 5 6 7 + * 3 4 5 6 7 8 + * 4 5 6 7 8 9 + */ + + /* Create access property list and set the driver to GASS */ + fapl = H5Pcreate (H5P_FILE_ACCESS); + if (fapl < 0) { + printf (" H5Pcreate failed. \n"); + return -1; + } + + ginf.block_size = 0; + ginf.max_length =0; + /* ginf = GASS_INFO_NULL;*/ + + status = H5Pset_fapl_gass (fapl, ginf); + if (status < 0) { + printf ("H5Pset_fapl_gass failed. \n"); + return -1; + } + + /* + * Create a new file using H5F_ACC_TRUNC access, + * default file creation properties, and gass file + * access properties. + */ + // file = H5Fcreate(URL, H5F_ACC_TRUNC, H5P_DEFAULT, fapl); + // Works. Truncates existing files. + // file = H5Fcreate(URL, H5F_ACC_EXCL, H5P_DEFAULT, fapl); + // Works. Croaks if existing file, else creates. + // Any other flag has no effect as long as one and exactly one of TRUNC/ + // EXCL is there + /* printf ("I'm here just before H5Fcreate. \n");*/ + file = H5Fcreate(URL, H5F_ACC_TRUNC, H5P_DEFAULT, fapl); + if (file < 0) { + printf ("H5Fcreate failed. \n"); + return -1; + } + + /* + * Describe the size of the array and create the data space for fixed + * size dataset. + */ + dimsf[0] = NX; + dimsf[1] = NY; + dataspace = H5Screate_simple(RANK, dimsf, NULL); + if (dataspace < 0) { + printf ("H5Screate failed. \n"); + return -1; + } + + /* + * Define datatype for the data in the file. + * We will store little endian INT numbers. + */ + datatype = H5Tcopy(H5T_NATIVE_INT); + if (datatype < 0) { + printf ("H5Tcopy failed. \n"); + return -1; + } + + status = H5Tset_order(datatype, H5T_ORDER_LE); + if (status < 0) { + printf ("H5Tset_order failed. \n"); + return -1; + } + + /* + * Create a new dataset within the file using defined dataspace and + * datatype and default dataset creation properties. + */ + dataset = H5Dcreate(file, DATASETNAME, datatype, dataspace, + H5P_DEFAULT); + if (dataset < 0) { + printf ("H5Dcreate failed. \n"); + return -1; + } + + /* + * Write the data to the dataset using default transfer properties. + */ + status = H5Dwrite(dataset, H5T_NATIVE_INT, H5S_ALL, H5S_ALL, + H5P_DEFAULT, data); + if (status < 0) { + printf ("H5Dwrite failed. \n"); + return -1; + } + + /* + * Close/release resources. + */ + H5Sclose(dataspace); + H5Tclose(datatype); + H5Dclose(dataset); + H5Fclose(file); + H5Pclose(fapl); + + return 0; +} +#endif |