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[svn-r12841] Bug fix. The mechanism to handle interupted system call or partial I/O for reading data

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may not work well for Direct I/O because of the requirement for data alignment.  Took it out.
This commit is contained in:
Raymond Lu 2006-11-01 16:01:14 -05:00
parent 712e344e99
commit 0f84d2fb15
2 changed files with 51 additions and 89 deletions
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139
src/H5FDdirect.c
View File

@ -861,8 +861,8 @@ H5FD_direct_read(H5FD_t *_file, H5FD_mem_t UNUSED type, hid_t UNUSED dxpl_id, ha
{ {
H5FD_direct_t *file = (H5FD_direct_t*)_file; H5FD_direct_t *file = (H5FD_direct_t*)_file;
ssize_t nbytes; ssize_t nbytes;
size_t alloc_size, dup_size; size_t alloc_size;
void *copy_buf, *p1, *p2, *p3; void *copy_buf, *p2, *p3;
size_t _boundary; size_t _boundary;
size_t _fbsize; size_t _fbsize;
size_t _cbsize; size_t _cbsize;
@ -898,7 +898,8 @@ H5FD_direct_read(H5FD_t *_file, H5FD_mem_t UNUSED type, hid_t UNUSED dxpl_id, ha
if ((addr!=file->pos || OP_READ!=file->op) && if ((addr!=file->pos || OP_READ!=file->op) &&
file_seek(file->fd, (file_offset_t)addr, SEEK_SET)<0) file_seek(file->fd, (file_offset_t)addr, SEEK_SET)<0)
HSYS_GOTO_ERROR(H5E_IO, H5E_SEEKERROR, FAIL, "unable to seek to proper position") HSYS_GOTO_ERROR(H5E_IO, H5E_SEEKERROR, FAIL, "unable to seek to proper position")
/* Read the aligned data in file first, being careful of interrupted
* system calls and partial results. */
while (size>0) { while (size>0) {
do { do {
nbytes = HDread(file->fd, buf, size); nbytes = HDread(file->fd, buf, size);
@ -926,7 +927,7 @@ H5FD_direct_read(H5FD_t *_file, H5FD_mem_t UNUSED type, hid_t UNUSED dxpl_id, ha
alloc_size = (size / _fbsize + 1) * _fbsize + _fbsize; alloc_size = (size / _fbsize + 1) * _fbsize + _fbsize;
else else
alloc_size = _cbsize; alloc_size = _cbsize;
if (posix_memalign(&copy_buf, _boundary, alloc_size) != 0) if (HDposix_memalign(&copy_buf, _boundary, alloc_size) != 0)
HGOTO_ERROR(H5E_RESOURCE, H5E_CANTALLOC, FAIL, "posix_memalign failed") HGOTO_ERROR(H5E_RESOURCE, H5E_CANTALLOC, FAIL, "posix_memalign failed")
/* look for the aligned position for reading the data */ /* look for the aligned position for reading the data */
@ -941,30 +942,18 @@ H5FD_direct_read(H5FD_t *_file, H5FD_mem_t UNUSED type, hid_t UNUSED dxpl_id, ha
*/ */
p3 = buf; p3 = buf;
do { do {
/* Read the aligned data in file first, being careful of interrupted system calls, /* Read the aligned data in file first. Not able to handle interrupted
* partial results, and the end of the file. */ * system calls and partial results like sec2 driver does because the
memset(copy_buf, 0, alloc_size); * data may no longer be aligned. It's expecially true when the data in
p1 = copy_buf; * file is smaller than ALLOC_SIZE. */
dup_size = alloc_size; HDmemset(copy_buf, 0, alloc_size);
while(dup_size > 0) {
do {
nbytes = HDread(file->fd, p1, dup_size);
} while(-1==nbytes && EINTR==errno);
if (-1==nbytes) /* error */ do {
HSYS_GOTO_ERROR(H5E_IO, H5E_READERROR, FAIL, "file read failed") nbytes = HDread(file->fd, copy_buf, alloc_size);
if (0==nbytes) { } while(-1==nbytes && EINTR==errno);
/* end of file but not end of format address space */
break; if (-1==nbytes) /* error */
} else { HSYS_GOTO_ERROR(H5E_IO, H5E_READERROR, FAIL, "file read failed")
assert(nbytes>0);
assert((size_t)nbytes<=dup_size);
H5_CHECK_OVERFLOW(nbytes,ssize_t,size_t);
H5_CHECK_OVERFLOW(nbytes,ssize_t,haddr_t);
dup_size -= (size_t)nbytes;
p1 = (unsigned char*)p1 + nbytes;
}
}
/* look for the right position and copy the data to the original buffer. /* look for the right position and copy the data to the original buffer.
* Consider all possible situations here: file address is not aligned on * Consider all possible situations here: file address is not aligned on
@ -972,11 +961,11 @@ H5FD_direct_read(H5FD_t *_file, H5FD_mem_t UNUSED type, hid_t UNUSED dxpl_id, ha
* address is aligned; data size is smaller or bigger than maximal copy size.*/ * address is aligned; data size is smaller or bigger than maximal copy size.*/
p2 = (unsigned char*)copy_buf + (size_t)(copy_addr % _fbsize); p2 = (unsigned char*)copy_buf + (size_t)(copy_addr % _fbsize);
if(size < _cbsize) if(size < _cbsize)
memcpy(p3, p2, size); HDmemcpy(p3, p2, size);
else if(size >= _cbsize && copy_size <= (alloc_size-(size_t)(copy_addr%_fbsize))) else if(size >= _cbsize && copy_size <= (alloc_size-(size_t)(copy_addr%_fbsize)))
memcpy(p3, p2, copy_size); HDmemcpy(p3, p2, copy_size);
else if(size >= _cbsize && copy_size > (alloc_size-(size_t)(copy_addr%_fbsize))) { else if(size >= _cbsize && copy_size > (alloc_size-(size_t)(copy_addr%_fbsize))) {
memcpy(p3, p2, (alloc_size - (size_t)(copy_addr % _fbsize))); HDmemcpy(p3, p2, (alloc_size - (size_t)(copy_addr % _fbsize)));
p3 = (unsigned char*)p3 + (alloc_size - (size_t)(copy_addr % _fbsize)); p3 = (unsigned char*)p3 + (alloc_size - (size_t)(copy_addr % _fbsize));
} }
@ -1035,8 +1024,8 @@ H5FD_direct_write(H5FD_t *_file, H5FD_mem_t UNUSED type, hid_t UNUSED dxpl_id, h
{ {
H5FD_direct_t *file = (H5FD_direct_t*)_file; H5FD_direct_t *file = (H5FD_direct_t*)_file;
ssize_t nbytes; ssize_t nbytes;
size_t alloc_size, dup_size; size_t alloc_size;
void *copy_buf, *p1, *p2, *p3; void *copy_buf, *p1, *p3;
size_t _boundary; size_t _boundary;
size_t _fbsize; size_t _fbsize;
size_t _cbsize; size_t _cbsize;
@ -1098,7 +1087,7 @@ H5FD_direct_write(H5FD_t *_file, H5FD_mem_t UNUSED type, hid_t UNUSED dxpl_id, h
else else
alloc_size = _cbsize; alloc_size = _cbsize;
if (posix_memalign(&copy_buf, _boundary, alloc_size) != 0) if (HDposix_memalign(&copy_buf, _boundary, alloc_size) != 0)
HGOTO_ERROR(H5E_RESOURCE, H5E_CANTALLOC, FAIL, "posix_memalign failed") HGOTO_ERROR(H5E_RESOURCE, H5E_CANTALLOC, FAIL, "posix_memalign failed")
/* look for the right position for reading the data */ /* look for the right position for reading the data */
@ -1108,32 +1097,21 @@ H5FD_direct_write(H5FD_t *_file, H5FD_mem_t UNUSED type, hid_t UNUSED dxpl_id, h
p3 = buf; p3 = buf;
do { do {
/* /*
* Read the aligned data first if the aligned region doesn't fall entirely in * Read the aligned data first if the aligned region doesn't fall
* the range to be writen. Be careful of interrupted system calls, partial * entirely in the range to be writen. Not able to handle interrupted
* results, and the end of the file. * system calls and partial results like sec2 driver does because the
* data may no longer be aligned. It's expecially true when the data in
* file is smaller than ALLOC_SIZE.
*/ */
memset(copy_buf, 0, alloc_size); HDmemset(copy_buf, 0, alloc_size);
p2 = copy_buf;
dup_size = alloc_size;
if(copy_addr <= addr || (copy_addr + alloc_size) >= (addr + size)) { if(copy_addr <= addr || (copy_addr + alloc_size) >= (addr + size)) {
while(dup_size > 0) { do {
do { nbytes = read(file->fd, copy_buf, alloc_size);
nbytes = read(file->fd, p2, dup_size); } while (-1==nbytes && EINTR==errno);
} while (-1==nbytes && EINTR==errno);
if (-1==nbytes) /* error */ if (-1==nbytes) /* error */
HSYS_GOTO_ERROR(H5E_IO, H5E_READERROR, FAIL, "file read failed") HSYS_GOTO_ERROR(H5E_IO, H5E_READERROR, FAIL, "file read failed")
if (0==nbytes) {
/* end of file but not end of format address space */
break;
} else {
assert(nbytes>0);
assert((size_t)nbytes<=dup_size);
H5_CHECK_OVERFLOW(nbytes,ssize_t,size_t);
H5_CHECK_OVERFLOW(nbytes,ssize_t,haddr_t);
dup_size -= (size_t)nbytes;
p2 = (unsigned char*)p2 + nbytes;
}
}
} }
/* look for the right position and append or copy the data to be written to /* look for the right position and append or copy the data to be written to
@ -1144,11 +1122,11 @@ H5FD_direct_write(H5FD_t *_file, H5FD_mem_t UNUSED type, hid_t UNUSED dxpl_id, h
*/ */
p1 = (unsigned char*)copy_buf + (size_t)(copy_addr % _fbsize); p1 = (unsigned char*)copy_buf + (size_t)(copy_addr % _fbsize);
if(size < _cbsize) if(size < _cbsize)
memcpy(p1, p3, size); HDmemcpy(p1, p3, size);
else if(size >= _cbsize && copy_size <= (alloc_size-(size_t)(copy_addr%_fbsize))) { else if(size >= _cbsize && copy_size <= (alloc_size-(size_t)(copy_addr%_fbsize))) {
memcpy(p1, p3, copy_size); HDmemcpy(p1, p3, copy_size);
}else if(size >= _cbsize && copy_size > (alloc_size-(size_t)(copy_addr%_fbsize))) { }else if(size >= _cbsize && copy_size > (alloc_size-(size_t)(copy_addr%_fbsize))) {
memcpy(p1, p3, (alloc_size - (size_t)(copy_addr % _fbsize))); HDmemcpy(p1, p3, (alloc_size - (size_t)(copy_addr % _fbsize)));
p3 = (unsigned char*)p3 + (alloc_size - (size_t)(copy_addr % _fbsize)); p3 = (unsigned char*)p3 + (alloc_size - (size_t)(copy_addr % _fbsize));
} }
@ -1157,32 +1135,15 @@ H5FD_direct_write(H5FD_t *_file, H5FD_mem_t UNUSED type, hid_t UNUSED dxpl_id, h
HSYS_GOTO_ERROR(H5E_IO, H5E_SEEKERROR, FAIL, "unable to seek to proper position") HSYS_GOTO_ERROR(H5E_IO, H5E_SEEKERROR, FAIL, "unable to seek to proper position")
/* /*
* Write the data, being careful of interrupted system calls and partial write. * Write the data. It doesn't truncate the extra data introduced by
* It doesn't truncate the extra data introduced by alignment because that step * alignment because that step is done in H5FD_direct_flush.
* is done in H5FD_direct_flush.
*/ */
p2 = copy_buf; do {
dup_size = alloc_size; nbytes = HDwrite(file->fd, copy_buf, alloc_size);
while (dup_size>0) { } while (-1==nbytes && EINTR==errno);
do {
nbytes = HDwrite(file->fd, p2, dup_size);
} while (-1==nbytes && EINTR==errno);
if (-1==nbytes) { /* error */ if (-1==nbytes) /* error */
HSYS_GOTO_ERROR(H5E_IO, H5E_WRITEERROR, FAIL, "file write failed") HSYS_GOTO_ERROR(H5E_IO, H5E_WRITEERROR, FAIL, "file write failed")
}
if (0==nbytes) {
/* end of file but not end of format address space */
break;
} else {
assert(nbytes>0);
assert((size_t)nbytes<=dup_size);
H5_CHECK_OVERFLOW(nbytes,ssize_t,size_t);
H5_CHECK_OVERFLOW(nbytes,ssize_t,haddr_t);
dup_size -= (size_t)nbytes;
p2 = (unsigned char*)p2 + nbytes;
}
}
/* update the size and address of data being read. */ /* update the size and address of data being read. */
if(copy_size > (alloc_size - (size_t)(copy_addr % _fbsize))) if(copy_size > (alloc_size - (size_t)(copy_addr % _fbsize)))
@ -1193,12 +1154,12 @@ H5FD_direct_write(H5FD_t *_file, H5FD_mem_t UNUSED type, hid_t UNUSED dxpl_id, h
copy_addr += (alloc_size - (size_t)(copy_addr % _fbsize)); copy_addr += (alloc_size - (size_t)(copy_addr % _fbsize));
} while (copy_size > 0); } while (copy_size > 0);
/*Update the address and size*/ /*Update the address and size*/
addr += (haddr_t)size; addr += (haddr_t)size;
buf = (const char*)buf + size; buf = (const char*)buf + size;
if(copy_buf) if(copy_buf)
HDfree(copy_buf); HDfree(copy_buf);
} }
/* Update current position and eof */ /* Update current position and eof */

1
src/H5private.h
View File

@ -726,6 +726,7 @@ H5_DLL int HDfprintf (FILE *stream, const char *fmt, ...);
#define HDlseek(F,O,W) lseek(F,O,W) #define HDlseek(F,O,W) lseek(F,O,W)
#endif #endif
#define HDmalloc(Z) malloc(Z) #define HDmalloc(Z) malloc(Z)
#define HDposix_memalign(P,A,Z) posix_memalign(P,A,Z)
#define HDmblen(S,N) mblen(S,N) #define HDmblen(S,N) mblen(S,N)
#define HDmbstowcs(P,S,Z) mbstowcs(P,S,Z) #define HDmbstowcs(P,S,Z) mbstowcs(P,S,Z)
#define HDmbtowc(P,S,Z) mbtowc(P,S,Z) #define HDmbtowc(P,S,Z) mbtowc(P,S,Z)