H5File::H5File(const std::string & _filename, const std::string & _path, const std::string & access, const std::string & driver) : H5Object(H5Object::getRoot()), filename(_filename), path(_path), flags(getFlags(access))
{
hid_t fapl = H5Pcreate(H5P_FILE_ACCESS);
H5Pset_fclose_degree(fapl, H5F_CLOSE_STRONG);
if (driver == "stdio")
{
H5Pset_fapl_stdio(fapl);
}
else if (driver == "sec2")
{
H5Pset_fapl_sec2(fapl);
}
try
{
init(fapl);
H5Pclose(fapl);
}
catch (const H5Exception & /*e*/)
{
H5Pclose(fapl);
throw;
}
}
//--------------------------------------------------------------------------
// Function: FileAccPropList::setSec2
///\brief Modifies this file access property list to use the sec2
/// driver.
///
///\exception H5::PropListIException
// Programmer: Binh-Minh Ribler - April, 2004
//--------------------------------------------------------------------------
void FileAccPropList::setSec2() const
{
herr_t ret_value = H5Pset_fapl_sec2(id);
if( ret_value < 0 )
{
throw PropListIException("FileAccPropList::setSec2", "H5Pset_fapl_sec2 failed");
}
}
/*-------------------------------------------------------------------------
* Function: test_sec2
*
* Purpose: Tests the file handle interface for SEC2 driver
*
* Return: Success: 0
* Failure: -1
*
* Programmer: Raymond Lu
* Tuesday, Sept 24, 2002
*
* Modifications:
*
* Raymond Lu
* Wednesday, June 23, 2004
* Added test for H5Fget_filesize.
*
*-------------------------------------------------------------------------
*/
static herr_t
test_sec2(void)
{
hid_t file=(-1), fapl, access_fapl = -1;
char filename[1024];
int *fhandle=NULL;
hsize_t file_size;
TESTING("SEC2 file driver");
/* Set property list and file name for SEC2 driver. */
fapl = h5_fileaccess();
if(H5Pset_fapl_sec2(fapl) < 0)
TEST_ERROR;
h5_fixname(FILENAME[0], fapl, filename, sizeof filename);
if((file=H5Fcreate(filename, H5F_ACC_TRUNC, H5P_DEFAULT, fapl)) < 0)
TEST_ERROR;
/* Retrieve the access property list... */
if ((access_fapl = H5Fget_access_plist(file)) < 0)
TEST_ERROR;
/* ...and close the property list */
if (H5Pclose(access_fapl) < 0)
TEST_ERROR;
/* Check file handle API */
if(H5Fget_vfd_handle(file, H5P_DEFAULT, (void **)&fhandle) < 0)
TEST_ERROR;
if(*fhandle<0)
TEST_ERROR;
/* Check file size API */
if(H5Fget_filesize(file, &file_size) < 0)
TEST_ERROR;
/* There is no garantee the size of metadata in file is constant.
* Just try to check if it's reasonable. It's 2KB right now.
*/
if(file_size<1*KB || file_size>4*KB)
TEST_ERROR;
if(H5Fclose(file) < 0)
TEST_ERROR;
h5_cleanup(FILENAME, fapl);
PASSED();
return 0;
error:
H5E_BEGIN_TRY {
H5Pclose (fapl);
H5Fclose(file);
} H5E_END_TRY;
return -1;
}
/*-------------------------------------------------------------------------
* Function: h5_fileaccess
*
* Purpose: Returns a file access template which is the default template
* but with a file driver set according to the constant or
* environment variable HDF5_DRIVER
*
* Return: Success: A file access property list
*
* Failure: -1
*
* Programmer: Robb Matzke
* Thursday, November 19, 1998
*
* Modifications:
*
*-------------------------------------------------------------------------
*/
hid_t
h5_fileaccess(void)
{
const char *val = NULL;
const char *name;
char s[1024];
hid_t fapl = -1;
/* First use the environment variable, then the constant */
val = HDgetenv("HDF5_DRIVER");
#ifdef HDF5_DRIVER
if (!val)
val = HDF5_DRIVER;
#endif
if ((fapl=H5Pcreate(H5P_FILE_ACCESS))<0)
return -1;
if (!val || !*val)
return fapl; /*use default*/
HDstrncpy(s, val, sizeof s);
s[sizeof(s)-1] = '\0';
if (NULL==(name=HDstrtok(s, " \t\n\r"))) return fapl;
if (!HDstrcmp(name, "sec2")) {
/* Unix read() and write() system calls */
if (H5Pset_fapl_sec2(fapl)<0) return -1;
} else if (!HDstrcmp(name, "stdio")) {
/* Standard C fread() and fwrite() system calls */
if (H5Pset_fapl_stdio(fapl)<0) return -1;
} else if (!HDstrcmp(name, "core")) {
/* In-memory driver settings (backing store on, 1 MB increment) */
if (H5Pset_fapl_core(fapl, (size_t)1, TRUE)<0) return -1;
} else if (!HDstrcmp(name, "core_paged")) {
/* In-memory driver with write tracking and paging on */
if (H5Pset_fapl_core(fapl, (size_t)1, TRUE)<0) return -1;
if (H5Pset_core_write_tracking(fapl, TRUE, (size_t)4096)<0) return -1;
} else if (!HDstrcmp(name, "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 (!HDstrcmp(name, "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);
HDassert(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] = (haddr_t)MAX(mt - 1, 0) * (HADDR_MAX / 10);
} /* end for */
if (H5Pset_fapl_multi(fapl, memb_map, memb_fapl, memb_name,
memb_addr, FALSE)<0) {
return -1;
}
} else if (!HDstrcmp(name, "family")) {
hsize_t fam_size = 100*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 (!HDstrcmp(name, "log")) {
unsigned log_flags = H5FD_LOG_LOC_IO | H5FD_LOG_ALLOC;
/* Log file access */
if ((val = HDstrtok(NULL, " \t\n\r")))
log_flags = (unsigned)HDstrtol(val, NULL, 0);
if (H5Pset_fapl_log(fapl, NULL, log_flags, (size_t)0) < 0)
return -1;
} else if (!HDstrcmp(name, "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 if(!HDstrcmp(name, "latest")) {
/* use the latest format */
if(H5Pset_libver_bounds(fapl, H5F_LIBVER_LATEST, H5F_LIBVER_LATEST) < 0)
return -1;
} else {
/* Unknown driver */
return -1;
}
return fapl;
}
hid_t
set_vfd(parameters *param)
{
hid_t my_fapl = -1;
vfdtype vfd;
vfd = param->vfd;
if ((my_fapl=H5Pcreate(H5P_FILE_ACCESS))<0) return -1;
if (vfd == sec2) {
/* Unix read() and write() system calls */
if (H5Pset_fapl_sec2(my_fapl)<0) return -1;
} else if (vfd == stdio) {
/* Standard C fread() and fwrite() system calls */
if (H5Pset_fapl_stdio(my_fapl)<0) return -1;
} else if (vfd == core) {
/* In-core temporary file with 1MB increment */
if (H5Pset_fapl_core(my_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(my_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);
HDassert(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] = (haddr_t)MAX(mt - 1,0) * (HADDR_MAX / 10);
}
if (H5Pset_fapl_multi(my_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(my_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(my_fapl, 1024, 4096, 8*4096)<0) return -1;
#endif
} else {
/* Unknown driver */
return -1;
}
return my_fapl;
}
/*-------------------------------------------------------------------------
* Function: test_4
*
* Purpose: Tests opening an external link twice. It exposed a bug
* in the library. This function tests the fix. This test
* doesn't work with MULTI driver.
*
* Return: Success: 0
*
* Failure: number of errors
*
* Programmer: Raymond Lu
* 5 November 2007
*
* Modifications:
*
*-------------------------------------------------------------------------
*/
static int
test_4 (hid_t fapl)
{
hid_t fid = -1;
hid_t gid = -1;
hid_t xid = -1;
hid_t xid2 = -1;
char filename[1024]; /*file name */
char pathname[1024];
char *srcdir = getenv("srcdir"); /*where the src code is located*/
TESTING("opening external link twice");
/* Make a copy of the FAPL, in order to switch to the sec2 driver */
/* (useful when running test with another VFD) */
if((fapl = H5Pcopy(fapl)) < 0) FAIL_STACK_ERROR;
/* Switch local copy of the fapl to the sec2 driver */
if(H5Pset_fapl_sec2(fapl) < 0) FAIL_STACK_ERROR;
h5_fixname(FILENAME[3], fapl, filename, sizeof filename);
if((fid = H5Fcreate(filename, H5F_ACC_TRUNC, H5P_DEFAULT, fapl)) < 0)
goto error;
if((gid = H5Gopen2(fid, "/", H5P_DEFAULT)) < 0)
goto error;
pathname[0] = '\0';
/* Generate correct name for test file by prepending the source path */
if(srcdir && ((HDstrlen(srcdir) + HDstrlen(LINKED_FILE) + 1) < sizeof(pathname))) {
HDstrcpy(pathname, srcdir);
HDstrcat(pathname, "/");
}
HDstrcat(pathname, LINKED_FILE);
/* Create an external link to an existing file*/
if(H5Lcreate_external(pathname, "/group", gid, " link", H5P_DEFAULT, H5P_DEFAULT) < 0)
goto error;
if(H5Gclose(gid) < 0)
goto error;
if(H5Fclose(fid) < 0)
goto error;
/* Reopen the file */
if((fid = H5Fopen(filename, H5F_ACC_RDONLY, fapl)) < 0)
goto error;
/* Open the external link which is "/ link" as created previously via H5Lcreate_external() */
if((xid = H5Gopen2(fid, "/ link", H5P_DEFAULT)) < 0)
goto error;
/* Open the external link twice */
if((xid2 = H5Gopen2(xid, ".", H5P_DEFAULT)) < 0)
goto error;
if(H5Gclose(xid2) < 0)
goto error;
if(H5Gclose(xid) < 0)
goto error;
if(H5Fclose(fid) < 0)
goto error;
if(H5Pclose(fapl) < 0)
TEST_ERROR
PASSED();
return 0;
error:
H5E_BEGIN_TRY {
H5Gclose(gid);
H5Gclose(xid);
H5Gclose(xid2);
H5Fclose(fid);
} H5E_END_TRY;
return 1;
}
/*-------------------------------------------------------------------------
* Function: main
*
* Purpose:
*
* Return: Success:
*
* Failure:
*
* Programmer: Robb Matzke
* Friday, April 10, 1998
*
* Modifications:
* Albert Cheng, 2002/03/28
* Added command option -fsize.
* Albert Cheng, 2002/04/19
* Added command option -c.
*
*-------------------------------------------------------------------------
*/
int
main (int ac, char **av)
{
hid_t fapl=-1;
hsize_t family_size;
hsize_t family_size_def; /* default family file size */
double family_size_def_dbl; /* default family file size */
int cflag=1; /* check file system before test */
char filename[1024];
/* parameters setup */
family_size_def = FAMILY_SIZE;
while (--ac > 0){
av++;
if (strcmp("-fsize", *av)==0){
/* specify a different family file size */
ac--; av++;
if (ac > 0){
family_size_def_dbl = atof(*av);
H5_ASSIGN_OVERFLOW(family_size_def,family_size_def_dbl,double,hsize_t);
if (family_size_def <= 0)
family_size_def = (hsize_t)FAMILY_SIZE;
}
else{
printf("***Missing fsize value***\n");
usage();
return 1;
}
}
else if (strcmp("-c", *av)==0){
/* turn off file system check before test */
cflag=0;
}
else if (strcmp("-h", *av)==0){
usage();
return 0;
}else{
usage();
return 1;
}
}
/* Reset library */
h5_reset();
fapl = h5_fileaccess();
/* Test big file with the family driver */
puts("Testing big file with the Family Driver ");
if (H5FD_FAMILY!=H5Pget_driver(fapl)) {
HDfprintf(stdout,
"Changing file drivers to the family driver, %Hu bytes each\n",
family_size_def);
if (H5Pset_fapl_family(fapl, family_size_def, H5P_DEFAULT)<0) goto error;
} else if (H5Pget_fapl_family(fapl, &family_size, NULL)<0) {
goto error;
} else if (family_size!=family_size_def) {
HDfprintf(stdout, "Changing family member size from %Hu to %Hu\n",
family_size, family_size_def);
if (H5Pset_fapl_family(fapl, family_size_def, H5P_DEFAULT)<0)
goto error;
}
if (cflag){
/*
* We shouldn't run this test if the file system doesn't support holes
* because we would generate multi-gigabyte files.
*/
puts("Checking if file system is adequate for this test...");
if (sizeof(long_long)<8 || 0==GB8LL) {
puts("Test skipped because sizeof(long_long) is too small. This");
puts("hardware apparently doesn't support 64-bit integer types.");
usage();
goto quit;
}
if (!is_sparse()) {
puts("Test skipped because file system does not support holes.");
usage();
goto quit;
}
if (!enough_room(fapl)) {
puts("Test skipped because of quota (file size or num open files).");
usage();
goto quit;
}
if (sizeof(hsize_t)<=4) {
puts("Test skipped because the hdf5 library was configured with the");
puts("--disable-hsizet flag in order to work around a compiler bug.");
usage();
goto quit;
}
}
/* Do the test with the Family Driver */
h5_fixname(FILENAME[0], fapl, filename, sizeof filename);
if (writer(filename, fapl, WRT_N)) goto error;
if (reader(filename, fapl)) goto error;
puts("Test passed with the Family Driver.");
/*
* We shouldn't run this test if the file system doesn't support big files
* because we would generate multi-gigabyte files.
*/
puts("\nChecking if file system supports big files...");
if (!supports_big()) {
puts("Tests for sec2 and stdio are skipped because file system does not support big files.");
usage();
goto quit;
}
/* Clean up the test file */
if (h5_cleanup(FILENAME, fapl)) remove(DNAME);
/* Test big file with the SEC2 driver */
puts("Testing big file with the SEC2 Driver ");
fapl = h5_fileaccess();
if(H5Pset_fapl_sec2(fapl)<0)
HDmemset(filename, 0, sizeof(filename));
h5_fixname(FILENAME[2], fapl, filename, sizeof filename);
if (writer(filename, fapl, WRT_N)) goto error;
if (reader(filename, fapl)) goto error;
puts("Test passed with the SEC2 Driver.");
#ifdef H5_HAVE_FSEEKO
/* Clean up the test file */
if (h5_cleanup(FILENAME, fapl)) remove(DNAME);
/* Test big file with the STDIO driver only if fseeko is supported,
* because the OFFSET parameter of fseek has the type LONG, not big
* enough to support big files. */
puts("\nTesting big file with the STDIO Driver ");
fapl = h5_fileaccess();
if(H5Pset_fapl_stdio(fapl)<0)
HDmemset(filename, 0, sizeof(filename));
h5_fixname(FILENAME[1], fapl, filename, sizeof filename);
if (writer(filename, fapl, WRT_N)) goto error;
if (reader(filename, fapl)) goto error;
puts("Test passed with the STDIO Driver.");
#endif
quit:
/* End with normal exit code */
if (h5_cleanup(FILENAME, fapl)) remove(DNAME);
return 0;
error:
if (fapl>=0) H5Pclose(fapl);
puts("*** TEST FAILED ***");
return 1;
}
/*-------------------------------------------------------------------------
* Function: H5tools_get_symlink_info
*
* Purpose: Get symbolic link (soft, external) info and its target object type
(dataset, group, named datatype) and path, if exist
*
* Patameters:
* - [IN] fileid : link file id
* - [IN] linkpath : link path
* - [OUT] link_info: returning target object info (h5tool_link_info_t)
*
* Return:
* 2 : given pathname is object
* 1 : Succed to get link info.
* 0 : Detected as a dangling link
* -1 : H5 API failed.
*
* NOTE:
* link_info->trg_path must be freed out of this function
*
* Programmer: Jonathan Kim
*
* Date: Feb 8, 2010
*-------------------------------------------------------------------------*/
int
H5tools_get_symlink_info(hid_t file_id, const char * linkpath, h5tool_link_info_t *link_info,
hbool_t get_obj_type)
{
htri_t l_ret;
H5O_info_t trg_oinfo;
hid_t fapl = H5P_DEFAULT;
hid_t lapl = H5P_DEFAULT;
int ret = -1; /* init to fail */
/* init */
link_info->trg_type = H5O_TYPE_UNKNOWN;
/* if path is root, return group type */
if(!HDstrcmp(linkpath,"/"))
{
link_info->trg_type = H5O_TYPE_GROUP;
ret = 2;
goto out;
}
/* check if link itself exist */
if(H5Lexists(file_id, linkpath, H5P_DEFAULT) <= 0) {
if(link_info->opt.msg_mode == 1)
parallel_print("Warning: link <%s> doesn't exist \n",linkpath);
goto out;
} /* end if */
/* get info from link */
if(H5Lget_info(file_id, linkpath, &(link_info->linfo), H5P_DEFAULT) < 0) {
if(link_info->opt.msg_mode == 1)
parallel_print("Warning: unable to get link info from <%s>\n",linkpath);
goto out;
} /* end if */
/* given path is hard link (object) */
if(link_info->linfo.type == H5L_TYPE_HARD) {
ret = 2;
goto out;
} /* end if */
/* trg_path must be freed out of this function when finished using */
link_info->trg_path = (char*)HDcalloc(link_info->linfo.u.val_size, sizeof(char));
HDassert(link_info->trg_path);
/* get link value */
if(H5Lget_val(file_id, linkpath, (void *)link_info->trg_path, link_info->linfo.u.val_size, H5P_DEFAULT) < 0) {
if(link_info->opt.msg_mode == 1)
parallel_print("Warning: unable to get link value from <%s>\n",linkpath);
goto out;
} /* end if */
/*-----------------------------------------------------
* if link type is external link use different lapl to
* follow object in other file
*/
if(link_info->linfo.type == H5L_TYPE_EXTERNAL) {
if((fapl = H5Pcreate(H5P_FILE_ACCESS)) < 0)
goto out;
if(H5Pset_fapl_sec2(fapl) < 0)
goto out;
if((lapl = H5Pcreate(H5P_LINK_ACCESS)) < 0)
goto out;
if(H5Pset_elink_fapl(lapl, fapl) < 0)
goto out;
} /* end if */
/* Check for retrieving object info */
if(get_obj_type) {
/*--------------------------------------------------------------
* if link's target object exist, get type
*/
/* check if target object exist */
l_ret = H5Oexists_by_name(file_id, linkpath, lapl);
/* detect dangling link */
if(l_ret == FALSE) {
ret = 0;
goto out;
} /* end if */
/* function failed */
else if(l_ret < 0)
goto out;
/* get target object info */
if(H5Oget_info_by_name(file_id, linkpath, &trg_oinfo, lapl) < 0) {
if(link_info->opt.msg_mode == 1)
parallel_print("Warning: unable to get object information for <%s>\n", linkpath);
goto out;
} /* end if */
/* check unknown type */
if(trg_oinfo.type < H5O_TYPE_GROUP || trg_oinfo.type >=H5O_TYPE_NTYPES) {
if(link_info->opt.msg_mode == 1)
parallel_print("Warning: target object of <%s> is unknown type\n", linkpath);
goto out;
} /* end if */
/* set target obj type to return */
link_info->trg_type = trg_oinfo.type;
link_info->objno = trg_oinfo.addr;
link_info->fileno = trg_oinfo.fileno;
} /* end if */
else
link_info->trg_type = H5O_TYPE_UNKNOWN;
/* succeed */
ret = 1;
out:
if(fapl != H5P_DEFAULT)
H5Pclose(fapl);
if(lapl != H5P_DEFAULT)
H5Pclose(lapl);
return ret;
} /* end H5tools_get_symlink_info() */
