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[svn-r29182] Re-commit of HDFFV-8740 fix, which adds the ability to configure

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external dataset storage path behavior.

This check-in fixes a bug in the original check-in where the
external path stored in the file struct was not copied on reopen
causing subsequent dataset operations to fail.

Tested on: 64-bit Ubuntu 15.10 (Linux 4.2.0 x86_64) gcc 5.2.1
           autotools serial w/ fortran and C++
           autotools parallel (MPICH 3.1.4) w/ fortran
This commit is contained in:
Dana Robinson 2016-02-22 16:40:03 -05:00
parent 7511d8b469
commit 19a8216bd5
18 changed files with 1554 additions and 317 deletions
Show Stats Download Patch File Download Diff File Expand all files Collapse all files

7
fortran/test/tH5F.F90
View File

@ -356,13 +356,6 @@ CONTAINS
end do
end do
!
!Initialize FORTRAN predifined datatypes
!
! CALL h5init_types_f(error)
! CALL check("h5init_types_f",error,total_error)
!
!Create file "reopen.h5" using default properties.
!

3
src/H5.c
View File

@ -193,7 +193,8 @@ H5_init_library(void)
/* Normal library termination code */
(void)HDatexit(H5_term_library);
H5_dont_atexit_g = TRUE;
H5_dont_atexit_g = TRUE;
} /* end if */
/*

172
src/H5Defl.c
View File

@ -28,12 +28,13 @@
/***********/
/* Headers */
/***********/
#include "H5private.h" /* Generic Functions */
#include "H5Dpkg.h" /* Datasets */
#include "H5Eprivate.h" /* Error handling */
#include "H5Fprivate.h" /* Files */
#include "H5HLprivate.h" /* Local Heaps */
#include "H5VMprivate.h" /* Vector and array functions */
#include "H5private.h" /* Generic Functions */
#include "H5Dpkg.h" /* Datasets */
#include "H5Eprivate.h" /* Error handling */
#include "H5Fprivate.h" /* Files */
#include "H5HLprivate.h" /* Local Heaps */
#include "H5MMprivate.h" /* Memory management */
#include "H5VMprivate.h" /* Vector and array functions */
/****************/
@ -48,12 +49,14 @@
/* Callback info for readvv operation */
typedef struct H5D_efl_readvv_ud_t {
const H5O_efl_t *efl; /* Pointer to efl info */
const H5D_t *dset; /* The dataset */
unsigned char *rbuf; /* Read buffer */
} H5D_efl_readvv_ud_t;
/* Callback info for writevv operation */
typedef struct H5D_efl_writevv_ud_t {
const H5O_efl_t *efl; /* Pointer to efl info */
const H5D_t *dset; /* The dataset */
const unsigned char *wbuf; /* Write buffer */
} H5D_efl_writevv_ud_t;
@ -75,9 +78,9 @@ static ssize_t H5D__efl_writevv(const H5D_io_info_t *io_info,
size_t mem_max_nseq, size_t *mem_curr_seq, size_t mem_len_arr[], hsize_t mem_offset_arr[]);
/* Helper routines */
static herr_t H5D__efl_read(const H5O_efl_t *efl, haddr_t addr, size_t size,
static herr_t H5D__efl_read(const H5O_efl_t *efl, const H5D_t *dset, haddr_t addr, size_t size,
uint8_t *buf);
static herr_t H5D__efl_write(const H5O_efl_t *efl, haddr_t addr, size_t size,
static herr_t H5D__efl_write(const H5O_efl_t *efl, const H5D_t *dset, haddr_t addr, size_t size,
const uint8_t *buf);
@ -232,25 +235,22 @@ H5D__efl_io_init(const H5D_io_info_t *io_info, const H5D_type_info_t H5_ATTR_UNU
/*-------------------------------------------------------------------------
* Function: H5D__efl_read
* Function: H5D__efl_read
*
* Purpose: Reads data from an external file list. It is an error to
* read past the logical end of file, but reading past the end
* of any particular member of the external file list results in
* zeros.
* Purpose: Reads data from an external file list. It is an error to
* read past the logical end of file, but reading past the end
* of any particular member of the external file list results in
* zeros.
*
* Return: Non-negative on success/Negative on failure
* Return: SUCCEED/FAIL
*
* Programmer: Robb Matzke
* Programmer: Robb Matzke
* Wednesday, March 4, 1998
*
* Modifications:
* Robb Matzke, 1999-07-28
* The ADDR argument is passed by value.
*-------------------------------------------------------------------------
*/
static herr_t
H5D__efl_read(const H5O_efl_t *efl, haddr_t addr, size_t size, uint8_t *buf)
H5D__efl_read(const H5O_efl_t *efl, const H5D_t *dset, haddr_t addr, size_t size, uint8_t *buf)
{
int fd = -1;
size_t to_read;
@ -261,6 +261,7 @@ H5D__efl_read(const H5O_efl_t *efl, haddr_t addr, size_t size, uint8_t *buf)
haddr_t cur;
ssize_t n;
size_t u; /* Local index variable */
char *full_name = NULL; /* File name with prefix */
herr_t ret_value = SUCCEED; /* Return value */
FUNC_ENTER_STATIC
@ -273,44 +274,49 @@ H5D__efl_read(const H5O_efl_t *efl, haddr_t addr, size_t size, uint8_t *buf)
/* Find the first efl member from which to read */
for (u=0, cur=0; u<efl->nused; u++) {
if(H5O_EFL_UNLIMITED == efl->slot[u].size || addr < cur + efl->slot[u].size) {
skip = addr - cur;
break;
} /* end if */
cur += efl->slot[u].size;
if(H5O_EFL_UNLIMITED == efl->slot[u].size || addr < cur + efl->slot[u].size) {
skip = addr - cur;
break;
} /* end if */
cur += efl->slot[u].size;
} /* end for */
/* Read the data */
while(size) {
HDassert(buf);
if(u >= efl->nused)
HGOTO_ERROR(H5E_EFL, H5E_OVERFLOW, FAIL, "read past logical end of file")
if(H5F_OVERFLOW_HSIZET2OFFT(efl->slot[u].offset + skip))
HGOTO_ERROR(H5E_EFL, H5E_OVERFLOW, FAIL, "external file address overflowed")
if((fd = HDopen(efl->slot[u].name, O_RDONLY, 0)) < 0)
HGOTO_ERROR(H5E_EFL, H5E_CANTOPENFILE, FAIL, "unable to open external raw data file")
if(HDlseek(fd, (HDoff_t)(efl->slot[u].offset + skip), SEEK_SET) < 0)
HGOTO_ERROR(H5E_EFL, H5E_SEEKERROR, FAIL, "unable to seek in external raw data file")
if(u >= efl->nused)
HGOTO_ERROR(H5E_EFL, H5E_OVERFLOW, FAIL, "read past logical end of file")
if(H5F_OVERFLOW_HSIZET2OFFT(efl->slot[u].offset + skip))
HGOTO_ERROR(H5E_EFL, H5E_OVERFLOW, FAIL, "external file address overflowed")
if(H5_combine_path(dset->shared->extfile_prefix, efl->slot[u].name, &full_name) < 0)
HGOTO_ERROR(H5E_EFL, H5E_NOSPACE, FAIL, "can't build external file name")
if((fd = HDopen(full_name, O_RDONLY, 0)) < 0)
HGOTO_ERROR(H5E_EFL, H5E_CANTOPENFILE, FAIL, "unable to open external raw data file")
if(HDlseek(fd, (HDoff_t)(efl->slot[u].offset + skip), SEEK_SET) < 0)
HGOTO_ERROR(H5E_EFL, H5E_SEEKERROR, FAIL, "unable to seek in external raw data file")
#ifndef NDEBUG
tempto_read = MIN(efl->slot[u].size-skip, (hsize_t)size);
tempto_read = MIN((size_t)(efl->slot[u].size-skip), (hsize_t)size);
H5_CHECK_OVERFLOW(tempto_read, hsize_t, size_t);
to_read = (size_t)tempto_read;
to_read = (size_t)tempto_read;
#else /* NDEBUG */
to_read = MIN((size_t)(efl->slot[u].size - skip), size);
to_read = MIN((size_t)(efl->slot[u].size - skip), (hsize_t)size);
#endif /* NDEBUG */
if((n = HDread(fd, buf, to_read)) < 0)
HGOTO_ERROR(H5E_EFL, H5E_READERROR, FAIL, "read error in external raw data file")
else if((size_t)n < to_read)
HDmemset(buf + n, 0, to_read - (size_t)n);
HDclose(fd);
fd = -1;
size -= to_read;
buf += to_read;
skip = 0;
u++;
if((n = HDread(fd, buf, to_read)) < 0)
HGOTO_ERROR(H5E_EFL, H5E_READERROR, FAIL, "read error in external raw data file")
else if((size_t)n < to_read)
HDmemset(buf + n, 0, to_read - (size_t)n);
full_name = (char *)H5MM_xfree(full_name);
HDclose(fd);
fd = -1;
size -= to_read;
buf += to_read;
skip = 0;
u++;
} /* end while */
done:
if(full_name)
full_name = (char *)H5MM_xfree(full_name);
if(fd >= 0)
HDclose(fd);
@ -337,7 +343,7 @@ done:
*-------------------------------------------------------------------------
*/
static herr_t
H5D__efl_write(const H5O_efl_t *efl, haddr_t addr, size_t size, const uint8_t *buf)
H5D__efl_write(const H5O_efl_t *efl, const H5D_t *dset, haddr_t addr, size_t size, const uint8_t *buf)
{
int fd = -1;
size_t to_write;
@ -346,7 +352,8 @@ H5D__efl_write(const H5O_efl_t *efl, haddr_t addr, size_t size, const uint8_t *b
#endif /* NDEBUG */
haddr_t cur;
hsize_t skip = 0;
size_t u; /* Local index variable */
size_t u; /* Local index variable */
char *full_name = NULL; /* File name with prefix */
herr_t ret_value = SUCCEED; /* Return value */
FUNC_ENTER_STATIC
@ -359,46 +366,51 @@ H5D__efl_write(const H5O_efl_t *efl, haddr_t addr, size_t size, const uint8_t *b
/* Find the first efl member in which to write */
for(u = 0, cur = 0; u < efl->nused; u++) {
if(H5O_EFL_UNLIMITED == efl->slot[u].size || addr < cur + efl->slot[u].size) {
skip = addr - cur;
break;
} /* end if */
cur += efl->slot[u].size;
if(H5O_EFL_UNLIMITED == efl->slot[u].size || addr < cur + efl->slot[u].size) {
skip = addr - cur;
break;
} /* end if */
cur += efl->slot[u].size;
} /* end for */
/* Write the data */
while(size) {
HDassert(buf);
if(u >= efl->nused)
HGOTO_ERROR(H5E_EFL, H5E_OVERFLOW, FAIL, "write past logical end of file")
if(H5F_OVERFLOW_HSIZET2OFFT(efl->slot[u].offset + skip))
HGOTO_ERROR(H5E_EFL, H5E_OVERFLOW, FAIL, "external file address overflowed")
if((fd = HDopen(efl->slot[u].name, O_CREAT | O_RDWR, 0666)) < 0) {
if(HDaccess(efl->slot[u].name, F_OK) < 0)
HGOTO_ERROR(H5E_EFL, H5E_CANTOPENFILE, FAIL, "external raw data file does not exist")
else
HGOTO_ERROR(H5E_EFL, H5E_CANTOPENFILE, FAIL, "unable to open external raw data file")
} /* end if */
if(HDlseek(fd, (HDoff_t)(efl->slot[u].offset + skip), SEEK_SET) < 0)
HGOTO_ERROR(H5E_EFL, H5E_SEEKERROR, FAIL, "unable to seek in external raw data file")
if(u >= efl->nused)
HGOTO_ERROR(H5E_EFL, H5E_OVERFLOW, FAIL, "write past logical end of file")
if(H5F_OVERFLOW_HSIZET2OFFT(efl->slot[u].offset + skip))
HGOTO_ERROR(H5E_EFL, H5E_OVERFLOW, FAIL, "external file address overflowed")
if(H5_combine_path(dset->shared->extfile_prefix, efl->slot[u].name, &full_name) < 0)
HGOTO_ERROR(H5E_EFL, H5E_NOSPACE, FAIL, "can't build external file name")
if((fd = HDopen(full_name, O_CREAT | O_RDWR, 0666)) < 0) {
if(HDaccess(full_name, F_OK) < 0)
HGOTO_ERROR(H5E_EFL, H5E_CANTOPENFILE, FAIL, "external raw data file does not exist")
else
HGOTO_ERROR(H5E_EFL, H5E_CANTOPENFILE, FAIL, "unable to open external raw data file")
} /* end if */
if(HDlseek(fd, (HDoff_t)(efl->slot[u].offset + skip), SEEK_SET) < 0)
HGOTO_ERROR(H5E_EFL, H5E_SEEKERROR, FAIL, "unable to seek in external raw data file")
#ifndef NDEBUG
tempto_write = MIN(efl->slot[u].size - skip, (hsize_t)size);
tempto_write = MIN(efl->slot[u].size - skip, (hsize_t)size);
H5_CHECK_OVERFLOW(tempto_write, hsize_t, size_t);
to_write = (size_t)tempto_write;
#else /* NDEBUG */
to_write = MIN((size_t)(efl->slot[u].size - skip), size);
to_write = MIN((size_t)(efl->slot[u].size - skip), size);
#endif /* NDEBUG */
if((size_t)HDwrite(fd, buf, to_write) != to_write)
HGOTO_ERROR(H5E_EFL, H5E_READERROR, FAIL, "write error in external raw data file")
HDclose (fd);
fd = -1;
size -= to_write;
buf += to_write;
skip = 0;
u++;
if((size_t)HDwrite(fd, buf, to_write) != to_write)
HGOTO_ERROR(H5E_EFL, H5E_READERROR, FAIL, "write error in external raw data file")
full_name = (char *)H5MM_xfree(full_name);
HDclose (fd);
fd = -1;
size -= to_write;
buf += to_write;
skip = 0;
u++;
} /* end while */
done:
if(full_name)
full_name = (char *)H5MM_xfree(full_name);
if(fd >= 0)
HDclose(fd);
@ -427,7 +439,7 @@ H5D__efl_readvv_cb(hsize_t dst_off, hsize_t src_off, size_t len, void *_udata)
FUNC_ENTER_STATIC
/* Read data */
if(H5D__efl_read(udata->efl, dst_off, len, (udata->rbuf + src_off)) < 0)
if(H5D__efl_read(udata->efl, udata->dset, dst_off, len, (udata->rbuf + src_off)) < 0)
HGOTO_ERROR(H5E_DATASET, H5E_READERROR, FAIL, "EFL read failed")
done:
@ -464,6 +476,9 @@ H5D__efl_readvv(const H5D_io_info_t *io_info,
HDassert(io_info);
HDassert(io_info->store->efl.nused > 0);
HDassert(io_info->u.rbuf);
HDassert(io_info->dset);
HDassert(io_info->dset->shared);
HDassert(io_info->dset->shared->extfile_prefix);
HDassert(dset_curr_seq);
HDassert(dset_len_arr);
HDassert(dset_off_arr);
@ -473,6 +488,7 @@ H5D__efl_readvv(const H5D_io_info_t *io_info,
/* Set up user data for H5VM_opvv() */
udata.efl = &(io_info->store->efl);
udata.dset = io_info->dset;
udata.rbuf = (unsigned char *)io_info->u.rbuf;
/* Call generic sequence operation routine */
@ -507,7 +523,7 @@ H5D__efl_writevv_cb(hsize_t dst_off, hsize_t src_off, size_t len, void *_udata)
FUNC_ENTER_STATIC
/* Write data */
if(H5D__efl_write(udata->efl, dst_off, len, (udata->wbuf + src_off)) < 0)
if(H5D__efl_write(udata->efl, udata->dset, dst_off, len, (udata->wbuf + src_off)) < 0)
HGOTO_ERROR(H5E_DATASET, H5E_WRITEERROR, FAIL, "EFL write failed")
done:
@ -544,6 +560,9 @@ H5D__efl_writevv(const H5D_io_info_t *io_info,
HDassert(io_info);
HDassert(io_info->store->efl.nused > 0);
HDassert(io_info->u.wbuf);
HDassert(io_info->dset);
HDassert(io_info->dset->shared);
HDassert(io_info->dset->shared->extfile_prefix);
HDassert(dset_curr_seq);
HDassert(dset_len_arr);
HDassert(dset_off_arr);
@ -553,6 +572,7 @@ H5D__efl_writevv(const H5D_io_info_t *io_info,
/* Set up user data for H5VM_opvv() */
udata.efl = &(io_info->store->efl);
udata.dset = io_info->dset;
udata.wbuf = (const unsigned char *)io_info->u.wbuf;
/* Call generic sequence operation routine */

113
src/H5Dint.c
View File

@ -63,6 +63,8 @@ static herr_t H5D__cache_dataspace_info(const H5D_t *dset);
static herr_t H5D__init_space(H5F_t *file, const H5D_t *dset, const H5S_t *space);
static herr_t H5D__update_oh_info(H5F_t *file, hid_t dxpl_id, H5D_t *dset,
hid_t dapl_id);
static herr_t H5D_build_extfile_prefix(const H5D_t *dset, hid_t dapl_id,
char **extfile_prefix);
static herr_t H5D__open_oid(H5D_t *dataset, hid_t dapl_id, hid_t dxpl_id);
static herr_t H5D__init_storage(const H5D_io_info_t *io_info, hbool_t full_overwrite,
hsize_t old_dim[]);
@ -981,6 +983,84 @@ done:
FUNC_LEAVE_NOAPI(ret_value)
} /* end H5D__update_oh_info() */
/*--------------------------------------------------------------------------
* Function: H5D_build_extfile_prefix
*
* Purpose: Determine the external file prefix to be used and store
* it in extfile_prefix. Stores an empty string if no prefix
* should be used.
*
* Return: SUCCEED/FAIL
*
* Programmer: Steffen Kiess
* October 16, 2015
*--------------------------------------------------------------------------
*/
static herr_t
H5D_build_extfile_prefix(const H5D_t *dset, hid_t dapl_id, char **extfile_prefix /*out*/)
{
char *prefix = NULL; /* prefix used to look for the file */
char *extpath = NULL; /* absolute path of directory the HDF5 file is in */
size_t extpath_len; /* length of extpath */
size_t prefix_len; /* length of prefix */
size_t extfile_prefix_len; /* length of expanded prefix */
H5P_genplist_t *plist = NULL; /* Property list pointer */
herr_t ret_value = SUCCEED; /* Return value */
FUNC_ENTER_NOAPI_NOINIT
HDassert(dset);
HDassert(dset->oloc.file);
extpath = H5F_EXTPATH(dset->oloc.file);
HDassert(extpath);
/* XXX: Future thread-safety note - getenv is not required
* to be reentrant.
*/
prefix = HDgetenv("HDF5_EXTFILE_PREFIX");
if(prefix == NULL || *prefix == '\0') {
/* Set prefix to value of H5D_ACS_EFILE_PREFIX_NAME property */
if(NULL == (plist = H5P_object_verify(dapl_id, H5P_DATASET_ACCESS)))
HGOTO_ERROR(H5E_ATOM, H5E_BADATOM, FAIL, "can't find object for ID")
if(H5P_peek(plist, H5D_ACS_EFILE_PREFIX_NAME, &prefix) < 0)
HGOTO_ERROR(H5E_PLIST, H5E_CANTGET, FAIL, "can't get external file prefix")
} /* end if */
/* Prefix has to be checked for NULL / empty string again because the
* code above might have updated it.
*/
if(prefix == NULL || *prefix == '\0' || HDstrcmp(prefix, ".") == 0) {
/* filename is interpreted as relative to the current directory,
* does not need to be expanded
*/
if(NULL == (*extfile_prefix = (char *)H5MM_strdup("")))
HGOTO_ERROR(H5E_RESOURCE, H5E_NOSPACE, FAIL, "memory allocation failed")
} /* end if */
else {
if (HDstrncmp(prefix, "${ORIGIN}", HDstrlen("${ORIGIN}")) == 0) {
/* Replace ${ORIGIN} at beginning of prefix by directory of HDF5 file */
extpath_len = HDstrlen(extpath);
prefix_len = HDstrlen(prefix);
extfile_prefix_len = extpath_len + prefix_len - HDstrlen("${ORIGIN}") + 1;
if(NULL == (*extfile_prefix = (char *)H5MM_malloc(extfile_prefix_len)))
HGOTO_ERROR(H5E_RESOURCE, H5E_NOSPACE, FAIL, "unable to allocate buffer")
HDsnprintf(*extfile_prefix, extfile_prefix_len, "%s%s", extpath, prefix + HDstrlen("${ORIGIN}"));
} /* end if */
else {
if(NULL == (*extfile_prefix = (char *)H5MM_strdup(prefix)))
HGOTO_ERROR(H5E_RESOURCE, H5E_NOSPACE, FAIL, "memory allocation failed")
} /* end else */
} /* end else */
done:
FUNC_LEAVE_NOAPI(ret_value)
} /* H5D_build_extfile_prefix() */
/*-------------------------------------------------------------------------
* Function: H5D__create
@ -1151,6 +1231,10 @@ H5D__create(H5F_t *file, hid_t type_id, const H5S_t *space, hid_t dcpl_id,
/* Indicate that the layout information was initialized */
layout_init = TRUE;
/* Set the external file prefix */
if(H5D_build_extfile_prefix(new_dset, dapl_id, &new_dset->shared->extfile_prefix) < 0)
HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, NULL, "unable to initialize external file prefix")
/* Add the dataset to the list of opened objects in the file */
if(H5FO_top_incr(new_dset->oloc.file, new_dset->oloc.addr) < 0)
HGOTO_ERROR(H5E_DATASET, H5E_CANTINC, NULL, "can't incr object ref. count")
@ -1195,6 +1279,7 @@ done:
} /* end if */
if(new_dset->shared->dcpl_id != 0 && H5I_dec_ref(new_dset->shared->dcpl_id) < 0)
HDONE_ERROR(H5E_DATASET, H5E_CANTDEC, NULL, "unable to decrement ref count on property list")
new_dset->shared->extfile_prefix = (char *)H5MM_xfree(new_dset->shared->extfile_prefix);
new_dset->shared = H5FL_FREE(H5D_shared_t, new_dset->shared);
} /* end if */
new_dset->oloc.file = NULL;
@ -1288,7 +1373,8 @@ H5D_open(const H5G_loc_t *loc, hid_t dapl_id, hid_t dxpl_id)
{
H5D_shared_t *shared_fo = NULL;
H5D_t *dataset = NULL;
H5D_t *ret_value = NULL; /* Return value */
char *extfile_prefix = NULL; /* Expanded external file prefix */
H5D_t *ret_value = NULL; /* Return value */
FUNC_ENTER_NOAPI(NULL)
@ -1307,6 +1393,10 @@ H5D_open(const H5G_loc_t *loc, hid_t dapl_id, hid_t dxpl_id)
if(H5G_name_copy(&(dataset->path), loc->path, H5_COPY_SHALLOW) < 0)
HGOTO_ERROR(H5E_DATASET, H5E_CANTCOPY, NULL, "can't copy path")
/* Get the external file prefix */
if(H5D_build_extfile_prefix(dataset, dapl_id, &extfile_prefix) < 0)
HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, NULL, "unable to initialize external file prefix")
/* Check if dataset was already open */
if(NULL == (shared_fo = (H5D_shared_t *)H5FO_opened(dataset->oloc.file, dataset->oloc.addr))) {
/* Clear any errors from H5FO_opened() */
@ -1326,6 +1416,12 @@ H5D_open(const H5G_loc_t *loc, hid_t dapl_id, hid_t dxpl_id)
/* We're the first dataset to use the the shared info */
dataset->shared->fo_count = 1;
/* Set the external file prefix */
dataset->shared->extfile_prefix = extfile_prefix;
/* Prevent string from being freed during done: */
extfile_prefix = NULL;
} /* end if */
else {
/* Point to shared info */
@ -1334,6 +1430,12 @@ H5D_open(const H5G_loc_t *loc, hid_t dapl_id, hid_t dxpl_id)
/* Increment # of datasets using shared information */
shared_fo->fo_count++;
/* Check whether the external file prefix of the already open dataset
* matches the new external file prefix
*/
if(HDstrcmp(extfile_prefix, dataset->shared->extfile_prefix) != 0)
HGOTO_ERROR(H5E_DATASET, H5E_CANTOPENOBJ, NULL, "new external file prefix does not match external file prefix of already open dataset")
/* Check if the object has been opened through the top file yet */
if(H5FO_top_count(dataset->oloc.file, dataset->oloc.addr) == 0) {
/* Open the object through this top file */
@ -1350,11 +1452,15 @@ H5D_open(const H5G_loc_t *loc, hid_t dapl_id, hid_t dxpl_id)
ret_value = dataset;
done:
extfile_prefix = (char *)H5MM_xfree(extfile_prefix);
if(ret_value == NULL) {
/* Free the location--casting away const*/
if(dataset) {
if(shared_fo == NULL) /* Need to free shared fo */
if(shared_fo == NULL && dataset->shared) { /* Need to free shared fo */
dataset->shared->extfile_prefix = (char *)H5MM_xfree(dataset->shared->extfile_prefix);
dataset->shared = H5FL_FREE(H5D_shared_t, dataset->shared);
}
H5O_loc_free(&(dataset->oloc));
H5G_name_free(&(dataset->path));
@ -1658,6 +1764,9 @@ H5D_close(H5D_t *dataset)
if(dataset->shared->layout.ops->dest && (dataset->shared->layout.ops->dest)(dataset, H5AC_ind_read_dxpl_id) < 0)
HDONE_ERROR(H5E_DATASET, H5E_CANTRELEASE, FAIL, "unable to destroy layout info")
/* Free the external file prefix */
dataset->shared->extfile_prefix = (char *)H5MM_xfree(dataset->shared->extfile_prefix);
/* Release layout, fill-value, efl & pipeline messages */
if(dataset->shared->dcpl_id != H5P_DATASET_CREATE_DEFAULT)
free_failed |= (H5O_msg_reset(H5O_PLINE_ID, &dataset->shared->dcpl_cache.pline) < 0) ||

2
src/H5Dpkg.h
View File

@ -441,6 +441,8 @@ typedef struct H5D_shared_t {
*/
H5D_rdcc_t chunk; /* Information about chunked data */
} cache;
char *extfile_prefix; /* expanded external file prefix */
} H5D_shared_t;
struct H5D_t {

1
src/H5Dprivate.h
View File

@ -54,6 +54,7 @@
#define H5D_ACS_PREEMPT_READ_CHUNKS_NAME "rdcc_w0" /* Preemption read chunks first */
#define H5D_ACS_VDS_VIEW_NAME "vds_view" /* VDS view option */
#define H5D_ACS_VDS_PRINTF_GAP_NAME "vds_printf_gap" /* VDS printf gap size */
#define H5D_ACS_EFILE_PREFIX_NAME "external file prefix" /* External file prefix */
/* ======== Data transfer properties ======== */
#define H5D_XFER_MAX_TEMP_BUF_NAME "max_temp_buf" /* Maximum temp buffer size */

15
src/H5F.c
View File

@ -785,10 +785,6 @@ done:
* Programmer: Robb Matzke
* Friday, October 16, 1998
*
* Modifications:
* Quincey Koziol, May 14, 2002
* Keep old file's read/write intent in reopened file.
*
*-------------------------------------------------------------------------
*/
hid_t
@ -803,26 +799,27 @@ H5Freopen(hid_t file_id)
/* Check arguments */
if(NULL == (old_file = (H5F_t *)H5I_object_verify(file_id, H5I_FILE)))
HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "not a file")
HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "not a file")
/* Get a new "top level" file struct, sharing the same "low level" file struct */
if(NULL == (new_file = H5F_new(old_file->shared, 0, H5P_FILE_CREATE_DEFAULT, H5P_FILE_ACCESS_DEFAULT, NULL)))
HGOTO_ERROR(H5E_FILE, H5E_CANTINIT, FAIL, "unable to reopen file")
HGOTO_ERROR(H5E_FILE, H5E_CANTINIT, FAIL, "unable to reopen file")
/* Duplicate old file's names */
new_file->open_name = H5MM_xstrdup(old_file->open_name);
new_file->actual_name = H5MM_xstrdup(old_file->actual_name);
new_file->extpath = H5MM_xstrdup(old_file->extpath);
if((ret_value = H5I_register(H5I_FILE, new_file, TRUE)) < 0)
HGOTO_ERROR(H5E_ATOM, H5E_CANTREGISTER, FAIL, "unable to atomize file handle")
HGOTO_ERROR(H5E_ATOM, H5E_CANTREGISTER, FAIL, "unable to atomize file handle")
/* Keep this ID in file object structure */
new_file->file_id = ret_value;
done:
if(ret_value < 0 && new_file)
if(H5F_dest(new_file, H5AC_ind_read_dxpl_id, FALSE) < 0)
HDONE_ERROR(H5E_FILE, H5E_CANTCLOSEFILE, FAIL, "can't close file")
if(H5F_dest(new_file, H5AC_ind_read_dxpl_id, FALSE) < 0)
HDONE_ERROR(H5E_FILE, H5E_CANTCLOSEFILE, FAIL, "can't close file")
FUNC_LEAVE_API(ret_value)
} /* end H5Freopen() */

2
src/H5Fquery.c
View File

@ -158,7 +158,7 @@ H5F_get_actual_name(const H5F_t *f)
* Function: H5F_get_extpath
*
* Purpose: Retrieve the file's 'extpath' flags
* This is used by H5L_extern_traverse() to retrieve the main file's location
* This is used by H5L_extern_traverse() and H5D_build_extfile_prefix() to retrieve the main file's location
* when searching the target file.
*
* Return: 'extpath' on success/abort on failure (shouldn't fail)

44
src/H5MM.c
View File

@ -125,10 +125,10 @@ static size_t H5MM_peak_alloc_blocks_count_s = 0;
* Function: H5MM__is_our_block
*
* Purpose: Try to determine if a memory buffer has been allocated through
* the H5MM* interface, instead of the system's malloc() routines.
* the H5MM* interface, instead of the system's malloc() routines.
*
* Return: Success: TRUE/FALSE
* Failure: (Can't fail)
* Return: Success: TRUE/FALSE
* Failure: (Can't fail)
*
* Programmer: Quincey Koziol
* Dec 30 2015
@ -149,7 +149,7 @@ H5MM__is_our_block(void *mem)
*
* Purpose: Check a block wrapper around a buffer to validate it.
*
* Return: N/A (void)
* Return: N/A (void)
*
* Programmer: Quincey Koziol
* Dec 30 2015
@ -173,9 +173,9 @@ H5MM__sanity_check_block(const H5MM_block_t *block)
* Function: H5MM__sanity_check
*
* Purpose: Check a buffer to validate it (just calls
* H5MM__sanity_check_block after finding block for buffer)
* H5MM__sanity_check_block after finding block for buffer)
*
* Return: N/A (void)
* Return: N/A (void)
*
* Programmer: Quincey Koziol
* Dec 30 2015
@ -196,7 +196,7 @@ H5MM__sanity_check(void *mem)
*
* Purpose: Sanity check all current memory allocations.
*
* Return: N/A (void)
* Return: N/A (void)
*
* Programmer: Quincey Koziol
* Jan 5 2016
@ -206,7 +206,7 @@ H5MM__sanity_check(void *mem)
void
H5MM_sanity_check_all(void)
{
H5MM_block_t *curr;
H5MM_block_t *curr = NULL;
curr = H5MM_block_head_s.next;
while(curr != &H5MM_block_head_s) {
@ -221,7 +221,7 @@ H5MM_sanity_check_all(void)
*
* Purpose: Final sanity checks on memory allocation.
*
* Return: N/A (void)
* Return: N/A (void)
*
* Programmer: Quincey Koziol
* Jan 1 2016
@ -257,8 +257,8 @@ H5MM_final_sanity_check(void)
* considered an error condition since allocations of zero
* bytes usually indicate problems.
*
* Return: Success: Pointer new memory
* Failure: NULL
* Return: Success: Pointer to new memory
* Failure: NULL
*
* Programmer: Quincey Koziol
* Nov 8 2003
@ -268,7 +268,7 @@ H5MM_final_sanity_check(void)
void *
H5MM_malloc(size_t size)
{
void *ret_value;
void *ret_value = NULL;
HDassert(size);
@ -346,8 +346,8 @@ H5MM_malloc(size_t size)
* bytes usually indicate problems.
*
*
* Return: Success: Pointer new memory
* Failure: NULL
* Return: Success: Pointer to new memory
* Failure: NULL
*
* Programmer: Quincey Koziol
* Nov 8 2003
@ -357,7 +357,7 @@ H5MM_malloc(size_t size)
void *
H5MM_calloc(size_t size)
{
void *ret_value;
void *ret_value = NULL;
HDassert(size);
@ -392,8 +392,9 @@ H5MM_calloc(size_t size)
* Note that the (NULL, 0) combination is undefined behavior
* in the C standard.
*
* Return: Success: Ptr to new memory if size > 0, NULL if size is zero
* Failure: NULL (input buffer is unchanged on failure)
* Return: Success: Ptr to new memory if size > 0
* NULL if size is zero
* Failure: NULL (input buffer is unchanged on failure)
*
* Programmer: Robb Matzke
* Jul 10 1997
@ -403,7 +404,7 @@ H5MM_calloc(size_t size)
void *
H5MM_realloc(void *mem, size_t size)
{
void *ret_value;
void *ret_value = NULL;
/* Use FUNC_ENTER_NOAPI_NOINIT_NOERR here to avoid performance issues */
FUNC_ENTER_NOAPI_NOINIT_NOERR
@ -458,7 +459,6 @@ H5MM_realloc(void *mem, size_t size)
* Failure: abort()
*
* Programmer: Robb Matzke
* matzke@llnl.gov
* Jul 10 1997
*-------------------------------------------------------------------------
*/
@ -490,17 +490,16 @@ done:
* an error will be raised.
*
* Return: Success: Pointer to a new string
* Failure: abort()
* Failure: NULL
*
* Programmer: Robb Matzke
* matzke@llnl.gov
* Jul 10 1997
*-------------------------------------------------------------------------
*/
char *
H5MM_strdup(const char *s)
{
char *ret_value;
char *ret_value = NULL;
FUNC_ENTER_NOAPI(NULL)
@ -528,7 +527,6 @@ done:
* Failure: never fails
*
* Programmer: Robb Matzke
* matzke@llnl.gov
* Jul 10 1997
*
*-------------------------------------------------------------------------

384
src/H5Pdapl.c
View File

@ -16,8 +16,8 @@
/*-------------------------------------------------------------------------
*
* Created: H5Pdapl.c
* October 27, 2008
* Neil Fortner <nfortne2@hdfgroup.org>
* October 27, 2008
* Neil Fortner <nfortne2@hdfgroup.org>
*
* Purpose: Dataset access property list class routines
*
@ -39,7 +39,8 @@
#include "H5Eprivate.h" /* Error handling */
#include "H5Fprivate.h" /* Files */
#include "H5Iprivate.h" /* IDs */
#include "H5Ppkg.h" /* Property lists */
#include "H5Ppkg.h" /* Property lists */
#include "H5MMprivate.h" /* Memory management */
/****************/
@ -72,6 +73,17 @@
#define H5D_ACS_VDS_PRINTF_GAP_DEF (hsize_t)0
#define H5D_ACS_VDS_PRINTF_GAP_ENC H5P__encode_hsize_t
#define H5D_ACS_VDS_PRINTF_GAP_DEC H5P__decode_hsize_t
/* Definitions for external file prefix */
#define H5D_ACS_EFILE_PREFIX_SIZE sizeof(char *)
#define H5D_ACS_EFILE_PREFIX_DEF NULL /*default is no prefix */
#define H5D_ACS_EFILE_PREFIX_SET H5P__dapl_efile_pref_set
#define H5D_ACS_EFILE_PREFIX_GET H5P__dapl_efile_pref_get
#define H5D_ACS_EFILE_PREFIX_ENC H5P__dapl_efile_pref_enc
#define H5D_ACS_EFILE_PREFIX_DEC H5P__dapl_efile_pref_dec
#define H5D_ACS_EFILE_PREFIX_DEL H5P__dapl_efile_pref_del
#define H5D_ACS_EFILE_PREFIX_COPY H5P__dapl_efile_pref_copy
#define H5D_ACS_EFILE_PREFIX_CMP H5P__dapl_efile_pref_cmp
#define H5D_ACS_EFILE_PREFIX_CLOSE H5P__dapl_efile_pref_close
/******************/
/* Local Typedefs */
@ -100,6 +112,16 @@ static herr_t H5P__decode_chunk_cache_nbytes(const void **_pp, void *_value);
static herr_t H5P__dacc_vds_view_enc(const void *value, void **pp, size_t *size);
static herr_t H5P__dacc_vds_view_dec(const void **pp, void *value);
/* Property list callbacks */
static herr_t H5P__dapl_efile_pref_set(hid_t prop_id, const char* name, size_t size, void* value);
static herr_t H5P__dapl_efile_pref_get(hid_t prop_id, const char* name, size_t size, void* value);
static herr_t H5P__dapl_efile_pref_enc(const void *value, void **_pp, size_t *size);
static herr_t H5P__dapl_efile_pref_dec(const void **_pp, void *value);
static herr_t H5P__dapl_efile_pref_del(hid_t prop_id, const char* name, size_t size, void* value);
static herr_t H5P__dapl_efile_pref_copy(const char* name, size_t size, void* value);
static int H5P__dapl_efile_pref_cmp(const void *value1, const void *value2, size_t size);
static herr_t H5P__dapl_efile_pref_close(const char* name, size_t size, void* value);
/*********************/
/* Package Variables */
@ -134,6 +156,9 @@ const H5P_libclass_t H5P_CLS_DACC[1] = {{
/* Local Variables */
/*******************/
/* Property value defaults */
static const char *H5D_def_efile_prefix_g = H5D_ACS_EFILE_PREFIX_DEF; /* Default external file prefix string */
/*-------------------------------------------------------------------------
@ -187,10 +212,272 @@ H5P__dacc_reg_prop(H5P_genclass_t *pclass)
NULL, NULL, NULL, NULL) < 0)
HGOTO_ERROR(H5E_PLIST, H5E_CANTINSERT, FAIL, "can't insert property into class")
/* Register property for external file prefix */
if(H5P_register_real(pclass, H5D_ACS_EFILE_PREFIX_NAME, H5D_ACS_EFILE_PREFIX_SIZE, &H5D_def_efile_prefix_g,
NULL, H5D_ACS_EFILE_PREFIX_SET, H5D_ACS_EFILE_PREFIX_GET, H5D_ACS_EFILE_PREFIX_ENC, H5D_ACS_EFILE_PREFIX_DEC,
H5D_ACS_EFILE_PREFIX_DEL, H5D_ACS_EFILE_PREFIX_COPY, H5D_ACS_EFILE_PREFIX_CMP, H5D_ACS_EFILE_PREFIX_CLOSE) < 0)
HGOTO_ERROR(H5E_PLIST, H5E_CANTINSERT, FAIL, "can't insert property into class")
done:
FUNC_LEAVE_NOAPI(ret_value)
} /* end H5P__dacc_reg_prop() */
/*-------------------------------------------------------------------------
* Function: H5P__dapl_efile_pref_set
*
* Purpose: Copies an external file prefix property when it's set
* for a property list
*
* Return: SUCCEED/FAIL
*
*-------------------------------------------------------------------------
*/
static herr_t
H5P__dapl_efile_pref_set(hid_t H5_ATTR_UNUSED prop_id, const char H5_ATTR_UNUSED *name,
size_t H5_ATTR_UNUSED size, void *value)
{
FUNC_ENTER_STATIC_NOERR
/* Sanity check */
HDassert(value);
/* Copy the prefix */
*(char **)value = H5MM_xstrdup(*(const char **)value);
FUNC_LEAVE_NOAPI(SUCCEED)
} /* end H5P__dapl_efile_pref_set() */
/*-------------------------------------------------------------------------
* Function: H5P__dapl_efile_pref_get
*
* Purpose: Copies an external file prefix property when it's retrieved
* from a property list
*
* Return: SUCCEED/FAIL
*
*-------------------------------------------------------------------------
*/
static herr_t
H5P__dapl_efile_pref_get(hid_t H5_ATTR_UNUSED prop_id, const char H5_ATTR_UNUSED *name,
size_t H5_ATTR_UNUSED size, void *value)
{
FUNC_ENTER_STATIC_NOERR
/* Sanity check */
HDassert(value);
/* Copy the prefix */
*(char **)value = H5MM_xstrdup(*(const char **)value);
FUNC_LEAVE_NOAPI(SUCCEED)
} /* end H5P__dapl_efile_pref_get() */
/*-------------------------------------------------------------------------
* Function: H5P__dapl_efile_pref_enc
*
* Purpose: Callback routine which is called whenever the efile flags
* property in the dataset access property list is
* encoded.
*
* Return: SUCCEED/FAIL
*
*-------------------------------------------------------------------------
*/
static herr_t
H5P__dapl_efile_pref_enc(const void *value, void **_pp, size_t *size)
{
const char *efile_pref = *(const char * const *)value;
uint8_t **pp = (uint8_t **)_pp;
size_t len = 0;
uint64_t enc_value;
unsigned enc_size;
FUNC_ENTER_NOAPI_NOINIT_NOERR
HDcompile_assert(sizeof(size_t) <= sizeof(uint64_t));
/* calculate prefix length */
if(NULL != efile_pref)
len = HDstrlen(efile_pref);
enc_value = (uint64_t)len;
enc_size = H5VM_limit_enc_size(enc_value);
HDassert(enc_size < 256);
if(NULL != *pp) {
/* encode the length of the prefix */
*(*pp)++ = (uint8_t)enc_size;
UINT64ENCODE_VAR(*pp, enc_value, enc_size);
/* encode the prefix */
if(NULL != efile_pref) {
HDmemcpy(*(char **)pp, efile_pref, len);
*pp += len;
} /* end if */
} /* end if */
*size += (1 + enc_size);
if(NULL != efile_pref)
*size += len;
FUNC_LEAVE_NOAPI(SUCCEED)
} /* end H5P__dapl_efile_pref_enc() */
/*-------------------------------------------------------------------------
* Function: H5P__dapl_efile_pref_dec
*
* Purpose: Callback routine which is called whenever the efile prefix
* property in the dataset access property list is
* decoded.
*
* Return: SUCCEED/FAIL
*
*-------------------------------------------------------------------------
*/
static herr_t
H5P__dapl_efile_pref_dec(const void **_pp, void *_value)
{
char **efile_pref = (char **)_value;
const uint8_t **pp = (const uint8_t **)_pp;
size_t len;
uint64_t enc_value; /* Decoded property value */
unsigned enc_size; /* Size of encoded property */
herr_t ret_value = SUCCEED;
FUNC_ENTER_NOAPI_NOINIT
HDassert(pp);
HDassert(*pp);
HDassert(efile_pref);
HDcompile_assert(sizeof(size_t) <= sizeof(uint64_t));
/* Decode the size */
enc_size = *(*pp)++;
HDassert(enc_size < 256);
/* Decode the value */
UINT64DECODE_VAR(*pp, enc_value, enc_size);
len = (size_t)enc_value;
if(0 != len) {
/* Make a copy of the user's prefix string */
if(NULL == (*efile_pref = (char *)H5MM_malloc(len + 1)))
HGOTO_ERROR(H5E_RESOURCE, H5E_CANTINIT, FAIL, "memory allocation failed for prefix")
HDstrncpy(*efile_pref, *(const char **)pp, len);
(*efile_pref)[len] = '\0';
*pp += len;
} /* end if */
else
*efile_pref = NULL;
done:
FUNC_LEAVE_NOAPI(ret_value)
} /* end H5P__dapl_efile_pref_dec() */
/*-------------------------------------------------------------------------
* Function: H5P__dapl_efile_pref_del
*
* Purpose: Frees memory used to store the external file prefix string
*
* Return: SUCCEED (Can't fail)
*
*-------------------------------------------------------------------------
*/
static herr_t
H5P__dapl_efile_pref_del(hid_t H5_ATTR_UNUSED prop_id, const char H5_ATTR_UNUSED *name,
size_t H5_ATTR_UNUSED size, void *value)
{
FUNC_ENTER_NOAPI_NOINIT_NOERR
HDassert(value);
H5MM_xfree(*(void **)value);
FUNC_LEAVE_NOAPI(SUCCEED)
} /* end H5P__dapl_efile_pref_del() */
/*-------------------------------------------------------------------------
* Function: H5P__dapl_efile_pref_copy
*
* Purpose: Creates a copy of the external file prefix string
*
* Return: SUCCEED/FAIL
*
*-------------------------------------------------------------------------
*/
static herr_t
H5P__dapl_efile_pref_copy(const char H5_ATTR_UNUSED *name, size_t H5_ATTR_UNUSED size, void *value)
{
FUNC_ENTER_NOAPI_NOINIT_NOERR
HDassert(value);
*(char **)value = H5MM_xstrdup(*(const char **)value);
FUNC_LEAVE_NOAPI(SUCCEED)
} /* end H5P__dapl_efile_pref_copy() */
/*-------------------------------------------------------------------------
* Function: H5P__dapl_efile_pref_cmp
*
* Purpose: Callback routine which is called whenever the efile prefix
* property in the dataset creation property list is
* compared.
*
* Return: zero if VALUE1 and VALUE2 are equal, non zero otherwise.
*
*-------------------------------------------------------------------------
*/
static int
H5P__dapl_efile_pref_cmp(const void *value1, const void *value2, size_t H5_ATTR_UNUSED size)
{
const char *pref1 = *(const char * const *)value1;
const char *pref2 = *(const char * const *)value2;
int ret_value = 0;
FUNC_ENTER_NOAPI_NOINIT_NOERR
if(NULL == pref1 && NULL != pref2)
HGOTO_DONE(1);
if(NULL != pref1 && NULL == pref2)
HGOTO_DONE(-1);
if(NULL != pref1 && NULL != pref2)
ret_value = HDstrcmp(pref1, pref2);
done:
FUNC_LEAVE_NOAPI(ret_value)
} /* end H5P__dapl_efile_pref_cmp() */
/*-------------------------------------------------------------------------
* Function: H5P__dapl_efile_pref_close
*
* Purpose: Frees memory used to store the external file prefix string
*
* Return: SUCCEED/FAIL
*
*-------------------------------------------------------------------------
*/
static herr_t
H5P__dapl_efile_pref_close(const char H5_ATTR_UNUSED *name, size_t H5_ATTR_UNUSED size, void *value)
{
FUNC_ENTER_NOAPI_NOINIT_NOERR
HDassert(value);
H5MM_xfree(*(void **)value);
FUNC_LEAVE_NOAPI(SUCCEED)
} /* end H5P__dapl_efile_pref_close() */
/*-------------------------------------------------------------------------
* Function: H5Pset_chunk_cache
@ -787,3 +1074,94 @@ done:
FUNC_LEAVE_API(ret_value)
} /* end H5Pget_virtual_printf_gap() */
/*-------------------------------------------------------------------------
* Function: H5Pset_efile_prefix
*
* Purpose: Set a prefix to be used for any external files.
*
* If the prefix starts with ${ORIGIN}, this will be replaced by
* the absolute path of the directory of the HDF5 file containing
* the dataset.
*
* If the prefix is ".", no prefix will be applied.
*
* This property can be overwritten by the environment variable
* HDF5_EXTFILE_PREFIX.
*
* Return: Non-negative on success/Negative on failure
*
*-------------------------------------------------------------------------
*/
herr_t
H5Pset_efile_prefix(hid_t plist_id, const char *prefix)
{
H5P_genplist_t *plist; /* Property list pointer */
herr_t ret_value = SUCCEED; /* Return value */
FUNC_ENTER_API(FAIL)
H5TRACE2("e", "i*s", plist_id, prefix);
/* Get the plist structure */
if(NULL == (plist = H5P_object_verify(plist_id, H5P_DATASET_ACCESS)))
HGOTO_ERROR(H5E_ATOM, H5E_BADATOM, FAIL, "can't find object for ID")
/* Set prefix */
if(H5P_set(plist, H5D_ACS_EFILE_PREFIX_NAME, &prefix) < 0)
HGOTO_ERROR(H5E_PLIST, H5E_CANTSET, FAIL, "can't set prefix info")
done:
FUNC_LEAVE_API(ret_value)
} /* end H5Pset_efile_prefix() */
/*-------------------------------------------------------------------------
* Function: H5Pget_efile_prefix
*
* Purpose: Gets the prefix to be used for any external files.
*
* If the pointer is not NULL, it points to a user-allocated
* buffer.
*
* Return: Non-negative on success/Negative on failure
*
*-------------------------------------------------------------------------
*/
ssize_t
H5Pget_efile_prefix(hid_t plist_id, char *prefix, size_t size)
{
H5P_genplist_t *plist; /* Property list pointer */
char *my_prefix; /* Library's copy of the prefix */
size_t len; /* Length of prefix string */
ssize_t ret_value; /* Return value */
FUNC_ENTER_API(FAIL)
H5TRACE3("Zs", "i*sz", plist_id, prefix, size);
/* Get the plist structure */
if(NULL == (plist = H5P_object_verify(plist_id, H5P_DATASET_ACCESS)))
HGOTO_ERROR(H5E_ATOM, H5E_BADATOM, FAIL, "can't find object for ID")
/* Get the current prefix */
if(H5P_peek(plist, H5D_ACS_EFILE_PREFIX_NAME, &my_prefix) < 0)
HGOTO_ERROR(H5E_PLIST, H5E_CANTGET, FAIL, "can't get external file prefix")
/* Check for prefix being set */
if(my_prefix) {
/* Copy to user's buffer, if given */
len = HDstrlen(my_prefix);
if(prefix) {
HDstrncpy(prefix, my_prefix, MIN(len + 1, size));
if(len >= size)
prefix[size - 1] = '\0';
} /* end if */
} /* end if */
else
len = 0;
/* Set return value */
ret_value = (ssize_t)len;
done:
FUNC_LEAVE_API(ret_value)
} /* end H5Pget_efile_prefix() */

3
src/H5Plapl.c
View File

@ -800,7 +800,8 @@ done:
*-------------------------------------------------------------------------
*/
static herr_t
H5P__lacc_elink_pref_del(hid_t H5_ATTR_UNUSED prop_id, const char H5_ATTR_UNUSED *name, size_t H5_ATTR_UNUSED size, void *value)
H5P__lacc_elink_pref_del(hid_t H5_ATTR_UNUSED prop_id, const char H5_ATTR_UNUSED *name,
size_t H5_ATTR_UNUSED size, void *value)
{
FUNC_ENTER_STATIC_NOERR

2
src/H5Ppublic.h
View File

@ -406,6 +406,8 @@ H5_DLL herr_t H5Pset_virtual_view(hid_t plist_id, H5D_vds_view_t view);
H5_DLL herr_t H5Pget_virtual_view(hid_t plist_id, H5D_vds_view_t *view);
H5_DLL herr_t H5Pset_virtual_printf_gap(hid_t plist_id, hsize_t gap_size);
H5_DLL herr_t H5Pget_virtual_printf_gap(hid_t plist_id, hsize_t *gap_size);
H5_DLL herr_t H5Pset_efile_prefix(hid_t dapl_id, const char* prefix);
H5_DLL ssize_t H5Pget_efile_prefix(hid_t dapl_id, char* prefix /*out*/, size_t size);
/* Dataset xfer property list (DXPL) routines */
H5_DLL herr_t H5Pset_data_transform(hid_t plist_id, const char* expression);

6
src/H5private.h
View File

@ -1189,6 +1189,9 @@ typedef off_t h5_stat_size_t;
#ifndef HDsetbuf
#define HDsetbuf(F,S) setbuf(F,S)
#endif /* HDsetbuf */
#ifndef HDsetenv
#define HDsetenv(N,V,O) setenv(N,V,O)
#endif /* HDsetenv */
#ifndef HDsetgid
#define HDsetgid(G) setgid(G)
#endif /* HDsetgid */
@ -2560,7 +2563,8 @@ H5_DLL uint32_t H5_hash_string(const char *str);
H5_DLL time_t H5_make_time(struct tm *tm);
/* Functions for building paths, etc. */
H5_DLL herr_t H5_build_extpath(const char *, char ** /*out*/ );
H5_DLL herr_t H5_build_extpath(const char *name, char **extpath /*out*/);
H5_DLL herr_t H5_combine_path(const char *path1, const char *path2, char **full_name /*out*/);
/* Functions for debugging */
H5_DLL herr_t H5_buffer_dump(FILE *stream, int indent, const uint8_t *buf,

129
src/H5system.c
View File

@ -757,7 +757,7 @@ done:
*/
int
Wgettimeofday(struct timeval *tv, struct timezone *tz)
{
{
union {
unsigned long long ns100; /*time since 1 Jan 1601 in 100ns units */
FILETIME ft;
@ -783,7 +783,42 @@ Wgettimeofday(struct timeval *tv, struct timezone *tz)
/* Always return 0 as per Open Group Base Specifications Issue 6.
Do not set errno on error. */
return 0;
}
} /* end Wgettimeofday() */
/*-------------------------------------------------------------------------
* Function: Wsetenv
*
* Purpose: Wrapper function for setenv on Windows systems.
* Interestingly, getenv *is* available in the Windows
* POSIX layer, just not setenv.
*
* Return: Success: 0
* Failure: non-zero error code
*
* Programmer: Dana Robinson
* February 2016
*
*-------------------------------------------------------------------------
*/
int
Wsetenv(const char *name, const char *value, int overwrite)
{
size_t bufsize;
errno_t err;
/* If we're not overwriting, check if the environment variable exists.
* If it does (i.e.: the required buffer size to store the variable's
* value is non-zero), then return an error code.
*/
if(!overwrite) {
err = getenv_s(&bufsize, NULL, 0, name);
if (err || bufsize)
return (int)err;
} /* end if */
return (int)_putenv_s(name, value);
} /* end Wsetenv() */
#ifdef H5_HAVE_WINSOCK2_H
#pragma comment(lib, "advapi32.lib")
@ -881,26 +916,25 @@ Wflock(int fd, int operation) {
/*-------------------------------------------------------------------------
* Function: H5_build_extpath
* Function: H5_build_extpath
*
* Purpose: To build the path for later searching of target file for external
* link. This path can be either:
* Purpose: To build the path for later searching of target file for external
* links and external files. This path can be either:
* 1. The absolute path of NAME
* or
* 2. The current working directory + relative path of NAME
*
* Return: Success: 0
* Failure: -1
* Return: SUCCEED/FAIL
*
* Programmer: Vailin Choi
* April 2, 2008
* April 2, 2008
*
*-------------------------------------------------------------------------
*/
#define MAX_PATH_LEN 1024
herr_t
H5_build_extpath(const char *name, char **extpath/*out*/)
H5_build_extpath(const char *name, char **extpath /*out*/)
{
char *full_path = NULL; /* Pointer to the full path, as built or passed in */
char *cwdpath = NULL; /* Pointer to the current working directory path */
@ -998,5 +1032,80 @@ done:
H5MM_xfree(new_name);
FUNC_LEAVE_NOAPI(ret_value)
} /* H5_build_extpath() */
} /* end H5_build_extpath() */
/*--------------------------------------------------------------------------
* Function: H5_combine_path
*
* Purpose: If path2 is relative, interpret path2 as relative to path1
* and store the result in full_name. Otherwise store path2
* in full_name.
*
* Return: SUCCEED/FAIL
*
* Programmer: Steffen Kiess
* June 22, 2015
*--------------------------------------------------------------------------
*/
herr_t
H5_combine_path(const char* path1, const char* path2, char **full_name /*out*/)
{
size_t path1_len; /* length of path1 */
size_t path2_len; /* length of path2 */
herr_t ret_value = SUCCEED; /* Return value */
FUNC_ENTER_NOAPI_NOINIT
HDassert(path1);
HDassert(path2);
path1_len = HDstrlen(path1);
path2_len = HDstrlen(path2);
if(*path1 == '\0' || H5_CHECK_ABSOLUTE(path2)) {
/* If path1 is empty or path2 is absolute, simply use path2 */
if(NULL == (*full_name = (char *)H5MM_strdup(path2)))
HGOTO_ERROR(H5E_RESOURCE, H5E_NOSPACE, FAIL, "memory allocation failed")
} /* end if */
else if(H5_CHECK_ABS_PATH(path2)) {
/* On windows path2 is a path absolute name */
if (H5_CHECK_ABSOLUTE(path1) || H5_CHECK_ABS_DRIVE(path1)) {
/* path1 is absolute or drive absolute and path2 is path absolute.
* Use the drive letter of path1 + path2
*/
if(NULL == (*full_name = (char *)H5MM_malloc(path2_len + 3)))
HGOTO_ERROR(H5E_RESOURCE, H5E_NOSPACE, FAIL, "unable to allocate path2 buffer")
HDsnprintf(*full_name, (path2_len + 3), "%c:%s", path1[0], path2);
} /* end if */
else {
/* On windows path2 is path absolute name ("\foo\bar"),
* path1 does not have a drive letter (i.e. is "a\b" or "\a\b").
* Use path2.
*/
if(NULL == (*full_name = (char *)H5MM_strdup(path2)))
HGOTO_ERROR(H5E_RESOURCE, H5E_NOSPACE, FAIL, "memory allocation failed")
} /* end else */
} /* end else if */
else {
/* Relative path2:
* Allocate a buffer to hold path1 + path2 + possibly the delimiter
* + terminating null byte
*/
if(NULL == (*full_name = (char *)H5MM_malloc(path1_len + path2_len + 2)))
HGOTO_ERROR(H5E_RESOURCE, H5E_NOSPACE, FAIL, "unable to allocate filename buffer")
/* Compose the full file name */
HDsnprintf(*full_name, (path1_len + path2_len + 2), "%s%s%s", path1,
(H5_CHECK_DELIMITER(path1[path1_len - 1]) ? "" : H5_DIR_SEPS), path2);
} /* end else */
done:
FUNC_LEAVE_NOAPI(ret_value)
} /* end H5_combine_name() */

23
src/H5win32defs.h
View File

@ -71,21 +71,24 @@ struct timezone {
};
#ifdef __cplusplus
extern "C" {
extern "C" {
#endif /* __cplusplus */
H5_DLL int Wgettimeofday(struct timeval *tv, struct timezone *tz);
H5_DLL int Wflock(int fd, int operation);
H5_DLL char* Wgetlogin(void);
H5_DLL int c99_snprintf(char* str, size_t size, const char* format, ...);
H5_DLL int c99_vsnprintf(char* str, size_t size, const char* format, va_list ap);
H5_DLL int Wgettimeofday(struct timeval *tv, struct timezone *tz);
H5_DLL int Wsetenv(const char *name, const char *value, int overwrite);
H5_DLL int Wflock(int fd, int operation);
H5_DLL char* Wgetlogin(void);
H5_DLL int c99_snprintf(char* str, size_t size, const char* format, ...);
H5_DLL int c99_vsnprintf(char* str, size_t size, const char* format, va_list ap);
#ifdef __cplusplus
}
}
#endif /* __cplusplus */
#define HDgettimeofday(V,Z) Wgettimeofday(V,Z)
#define HDsetenv(N,V,O) Wsetenv(N,V,O)
#define HDflock(F,L) Wflock(F,L)
#define HDgetlogin() Wgetlogin()
#define HDsnprintf c99_snprintf /*varargs*/
#define HDvsnprintf c99_vsnprintf
#define HDvsnprintf c99_vsnprintf /*varargs*/
#endif /* H5_HAVE_VISUAL_STUDIO */
@ -98,5 +101,7 @@ struct timezone {
#ifndef H5_HAVE_MINGW
#define HDftruncate(F,L) _chsize_s(F,L)
#define HDfseek(F,O,W) _fseeki64(F,O,W)
#endif
#endif /* H5_HAVE_MINGW */
#endif /* H5_HAVE_WIN32_API */

2
test/Makefile.am
View File

@ -129,7 +129,7 @@ CHECK_CLEANFILES+=accum.h5 cmpd_dset.h5 compact_dataset.h5 dataset.h5 dset_offse
huge_chunks.h5 chunk_cache.h5 big_chunk.h5 chunk_expand.h5 \
copy_dcpl_newfile.h5 extend.h5 istore.h5 extlinks*.h5 frspace.h5 links*.h5 \
sys_file1 tfile[1-7].h5 th5s[1-4].h5 lheap.h5 fheap.h5 ohdr.h5 \
stab.h5 extern_[1-3].h5 extern_[1-4][ab].raw gheap[0-4].h5 \
stab.h5 extern_[1-4].h5 extern_[1-4][rw].raw gheap[0-4].h5 \
dt_arith[1-2] links.h5 links[0-6]*.h5 extlinks[0-15].h5 tmp \
big.data big[0-9][0-9][0-9][0-9][0-9].h5 \
stdio.h5 sec2.h5 dtypes[0-9].h5 dtypes1[0].h5 dt_arith[1-2].h5 tattr.h5 \

903
test/external.c
View File

File diff suppressed because it is too large Load Diff

60
test/tfile.c
View File

@ -52,6 +52,9 @@
#define FILE1 "tfile1.h5"
#define SFILE1 "sys_file1"
#define REOPEN_FILE "tfile_reopen.h5"
#define REOPEN_DSET "dset"
#define F2_USERBLOCK_SIZE (hsize_t)512
#define F2_OFFSET_SIZE 8
#define F2_LENGTH_SIZE 8
@ -530,6 +533,59 @@ test_file_open(void)
CHECK(ret, FAIL, "H5Pclose");
} /* test_file_open() */
/****************************************************************
**
** test_file_reopen(): File reopen test routine.
**
****************************************************************/
static void
test_file_reopen(void)
{
hid_t fid = -1; /* file ID from initial open */
hid_t rfid = -1; /* file ID from reopen */
hid_t did = -1; /* dataset ID (both opens) */
hid_t sid = -1; /* dataspace ID for dataset creation */
hsize_t dims = 6; /* dataspace size */
herr_t ret; /* Generic return value */
/* Output message about test being performed */
MESSAGE(5, ("Testing File Re-opening\n"));
/* Create file via first ID */
fid = H5Fcreate(REOPEN_FILE, H5F_ACC_TRUNC, H5P_DEFAULT, H5P_DEFAULT);
CHECK_I(fid, "H5Fcreate");
/* Create a dataset in the file */
sid = H5Screate_simple(1, &dims, &dims);
CHECK_I(sid, "H5Screate_simple")
did = H5Dcreate2(fid, REOPEN_DSET, H5T_NATIVE_INT, sid, H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT);
CHECK_I(did, "H5Dcreate2");
/* Close dataset and dataspace */
ret = H5Sclose(sid);
CHECK(ret, FAIL, "H5Sclose");
ret = H5Dclose(did);
CHECK(ret, FAIL, "H5Dclose");
/* Reopen the file with a different file ID */
rfid = H5Freopen(fid);
CHECK_I(rfid, "H5Freopen");
/* Reopen the dataset through the reopen file ID */
did = H5Dopen2(rfid, REOPEN_DSET, H5P_DEFAULT);
CHECK_I(did, "H5Dopen2");
/* Close and clean up */
ret = H5Dclose(did);
CHECK(ret, FAIL, "H5Dclose");
ret = H5Fclose(fid);
CHECK(ret, FAIL, "H5Fclose");
ret = H5Fclose(rfid);
CHECK(ret, FAIL, "H5Fclose");
HDremove(REOPEN_FILE);
} /* test_file_reopen() */
/****************************************************************
**
** test_file_close(): low-level file close test routine.
@ -3660,8 +3716,8 @@ test_file(void)
/* Output message about test being performed */
MESSAGE(5, ("Testing Low-Level File I/O\n"));
test_file_create(); /* Test file creation(also creation templates)*/
test_file_open(); /* Test file opening */
test_file_create(); /* Test file creation(also creation templates)*/
test_file_open(); /* Test file opening */
test_file_close(); /* Test file close behavior */
test_get_file_id(); /* Test H5Iget_file_id */
test_get_obj_ids(); /* Test H5Fget_obj_ids for Jira Issue 8528 */