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authorRaymond Lu <songyulu@hdfgroup.org>2006-11-01 21:01:14 (GMT)
committerRaymond Lu <songyulu@hdfgroup.org>2006-11-01 21:01:14 (GMT)
commit0f84d2fb15813c10fca48f95772626c34039619d (patch)
treec01c3e75bc4de391f9117ed2fbabc8e39c4013e3 /src
parent712e344e999a6d757f80ea8ab33a3e63f4fa96df (diff)
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[svn-r12841] Bug fix. The mechanism to handle interupted system call or partial I/O for reading data
may not work well for Direct I/O because of the requirement for data alignment. Took it out.
Diffstat (limited to 'src')
-rw-r--r--src/H5FDdirect.c139
-rw-r--r--src/H5private.h1
2 files changed, 51 insertions, 89 deletions
diff --git a/src/H5FDdirect.c b/src/H5FDdirect.c
index 431bcc7..4a830cd 100644
--- a/src/H5FDdirect.c
+++ b/src/H5FDdirect.c
@@ -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;
ssize_t nbytes;
- size_t alloc_size, dup_size;
- void *copy_buf, *p1, *p2, *p3;
+ size_t alloc_size;
+ void *copy_buf, *p2, *p3;
size_t _boundary;
size_t _fbsize;
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) &&
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")
-
+ /* Read the aligned data in file first, being careful of interrupted
+ * system calls and partial results. */
while (size>0) {
do {
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;
else
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")
/* 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;
do {
- /* Read the aligned data in file first, being careful of interrupted system calls,
- * partial results, and the end of the file. */
- memset(copy_buf, 0, alloc_size);
- p1 = copy_buf;
- dup_size = alloc_size;
- while(dup_size > 0) {
- do {
- nbytes = HDread(file->fd, p1, dup_size);
- } while(-1==nbytes && EINTR==errno);
+ /* Read the aligned data in file first. Not able to handle interrupted
+ * 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. */
+ HDmemset(copy_buf, 0, alloc_size);
- if (-1==nbytes) /* error */
- 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;
- p1 = (unsigned char*)p1 + nbytes;
- }
- }
+ do {
+ nbytes = HDread(file->fd, copy_buf, alloc_size);
+ } while(-1==nbytes && EINTR==errno);
+
+ if (-1==nbytes) /* error */
+ HSYS_GOTO_ERROR(H5E_IO, H5E_READERROR, FAIL, "file read failed")
/* look for the right position and copy the data to the original buffer.
* 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.*/
p2 = (unsigned char*)copy_buf + (size_t)(copy_addr % _fbsize);
if(size < _cbsize)
- memcpy(p3, p2, size);
+ HDmemcpy(p3, p2, size);
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))) {
- 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));
}
@@ -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;
ssize_t nbytes;
- size_t alloc_size, dup_size;
- void *copy_buf, *p1, *p2, *p3;
+ size_t alloc_size;
+ void *copy_buf, *p1, *p3;
size_t _boundary;
size_t _fbsize;
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
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")
/* 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;
do {
/*
- * Read the aligned data first if the aligned region doesn't fall entirely in
- * the range to be writen. Be careful of interrupted system calls, partial
- * results, and the end of the file.
+ * Read the aligned data first if the aligned region doesn't fall
+ * entirely in the range to be writen. Not able to handle interrupted
+ * 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);
- p2 = copy_buf;
- dup_size = alloc_size;
+ HDmemset(copy_buf, 0, alloc_size);
+
if(copy_addr <= addr || (copy_addr + alloc_size) >= (addr + size)) {
- while(dup_size > 0) {
- do {
- nbytes = read(file->fd, p2, dup_size);
- } while (-1==nbytes && EINTR==errno);
- if (-1==nbytes) /* error */
- 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;
- }
- }
+ do {
+ nbytes = read(file->fd, copy_buf, alloc_size);
+ } while (-1==nbytes && EINTR==errno);
+
+ if (-1==nbytes) /* error */
+ HSYS_GOTO_ERROR(H5E_IO, H5E_READERROR, FAIL, "file read failed")
}
/* 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);
if(size < _cbsize)
- memcpy(p1, p3, size);
+ HDmemcpy(p1, p3, size);
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))) {
- 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));
}
@@ -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")
/*
- * Write the data, being careful of interrupted system calls and partial write.
- * It doesn't truncate the extra data introduced by alignment because that step
- * is done in H5FD_direct_flush.
+ * Write the data. It doesn't truncate the extra data introduced by
+ * alignment because that step is done in H5FD_direct_flush.
*/
- p2 = copy_buf;
- dup_size = alloc_size;
- while (dup_size>0) {
- do {
- nbytes = HDwrite(file->fd, p2, dup_size);
- } while (-1==nbytes && EINTR==errno);
+ do {
+ nbytes = HDwrite(file->fd, copy_buf, alloc_size);
+ } while (-1==nbytes && EINTR==errno);
- if (-1==nbytes) { /* error */
- 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;
- }
- }
+ if (-1==nbytes) /* error */
+ HSYS_GOTO_ERROR(H5E_IO, H5E_WRITEERROR, FAIL, "file write failed")
/* update the size and address of data being read. */
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));
} while (copy_size > 0);
- /*Update the address and size*/
- addr += (haddr_t)size;
- buf = (const char*)buf + size;
+ /*Update the address and size*/
+ addr += (haddr_t)size;
+ buf = (const char*)buf + size;
- if(copy_buf)
- HDfree(copy_buf);
+ if(copy_buf)
+ HDfree(copy_buf);
}
/* Update current position and eof */
diff --git a/src/H5private.h b/src/H5private.h
index a43661b..b0f1292 100644
--- a/src/H5private.h
+++ b/src/H5private.h
@@ -726,6 +726,7 @@ H5_DLL int HDfprintf (FILE *stream, const char *fmt, ...);
#define HDlseek(F,O,W) lseek(F,O,W)
#endif
#define HDmalloc(Z) malloc(Z)
+#define HDposix_memalign(P,A,Z) posix_memalign(P,A,Z)
#define HDmblen(S,N) mblen(S,N)
#define HDmbstowcs(P,S,Z) mbstowcs(P,S,Z)
#define HDmbtowc(P,S,Z) mbtowc(P,S,Z)