summaryrefslogtreecommitdiffstats
diff options
context:
space:
mode:
Diffstat
-rw-r--r--release_docs/RELEASE.txt15
-rw-r--r--src/H5FDcore.c12
-rw-r--r--src/H5FDlog.c10
-rw-r--r--src/H5FDsec2.c14
4 files changed, 36 insertions, 15 deletions
diff --git a/release_docs/RELEASE.txt b/release_docs/RELEASE.txt
index f668207..3ddb9c7 100644
--- a/release_docs/RELEASE.txt
+++ b/release_docs/RELEASE.txt
@@ -609,6 +609,21 @@ Bug Fixes since HDF5-1.10.3 release
(DER - 2019/08/27, HDFFV-10892)
+ - Torn pread/pwrite I/O would result in read and write corruption.
+
+ In the sec2, log, and core (with backing store) virtual file drivers
+ (VFDs), the read and write calls incorrectly reset the offset parameter
+ on torn pread and pwrite operations (i.e., I/O operations which fail to
+ be written atomically by the OS). For this bug to occur, pread/pwrite
+ have to be configured (this is the default if they are present on the
+ system) and the pread/pwrite operation has to fail to transfer all
+ the bytes, resulting in a multiple pread/pwrite calls.
+
+ This feature was initially enabled in HDF5 1.10.5 so the bug is
+ limited to that version.
+
+ (DER - 2019/12/09, HDFFV-10945)
+
Java Library:
----------------
diff --git a/src/H5FDcore.c b/src/H5FDcore.c
index 6db8af6..552b7ca 100644
--- a/src/H5FDcore.c
+++ b/src/H5FDcore.c
@@ -342,6 +342,7 @@ H5FD__core_write_to_bstore(H5FD_core_t *file, haddr_t addr, size_t size)
unsigned char *ptr = file->mem + addr; /* mutable pointer into the
* buffer (can't change mem)
*/
+ HDoff_t offset = (HDoff_t)addr; /* Offset to write at */
herr_t ret_value = SUCCEED; /* Return value */
FUNC_ENTER_NOAPI_NOINIT
@@ -358,7 +359,6 @@ H5FD__core_write_to_bstore(H5FD_core_t *file, haddr_t addr, size_t size)
h5_posix_io_t bytes_in = 0; /* # of bytes to write */
h5_posix_io_ret_t bytes_wrote = -1; /* # of bytes written */
- HDoff_t offset = (HDoff_t)addr;
/* Trying to write more bytes than the return type can handle is
* undefined behavior in POSIX.
@@ -371,7 +371,8 @@ H5FD__core_write_to_bstore(H5FD_core_t *file, haddr_t addr, size_t size)
do {
#ifdef H5_HAVE_PREADWRITE
bytes_wrote = HDpwrite(file->fd, ptr, bytes_in, offset);
- offset += bytes_wrote;
+ if(bytes_wrote > 0)
+ offset += bytes_wrote;
#else
bytes_wrote = HDwrite(file->fd, ptr, bytes_in);
#endif /* H5_HAVE_PREADWRITE */
@@ -856,12 +857,12 @@ H5FD__core_open(const char *name, unsigned flags, hid_t fapl_id, haddr_t maxaddr
* partial results, and the end of the file.
*/
- uint8_t *mem = file->mem; /* memory pointer for writes */
+ uint8_t *mem = file->mem; /* memory pointer for writes */
+ HDoff_t offset = (HDoff_t)0; /* offset for reading */
while(size > 0) {
h5_posix_io_t bytes_in = 0; /* # of bytes to read */
h5_posix_io_ret_t bytes_read = -1; /* # of bytes actually read */
- HDoff_t offset = (HDoff_t)0;
/* Trying to read more bytes than the return type can handle is
* undefined behavior in POSIX.
@@ -874,7 +875,8 @@ H5FD__core_open(const char *name, unsigned flags, hid_t fapl_id, haddr_t maxaddr
do {
#ifdef H5_HAVE_PREADWRITE
bytes_read = HDpread(file->fd, mem, bytes_in, offset);
- offset += bytes_read;
+ if(bytes_read > 0)
+ offset += bytes_read;
#else
bytes_read = HDread(file->fd, mem, bytes_in);
#endif /* H5_HAVE_PREADWRITE */
diff --git a/src/H5FDlog.c b/src/H5FDlog.c
index ac5667f..60255e5 100644
--- a/src/H5FDlog.c
+++ b/src/H5FDlog.c
@@ -1171,6 +1171,7 @@ H5FD_log_read(H5FD_t *_file, H5FD_mem_t type, hid_t H5_ATTR_UNUSED dxpl_id, hadd
#ifdef H5_HAVE_GETTIMEOFDAY
struct timeval timeval_start, timeval_stop;
#endif /* H5_HAVE_GETTIMEOFDAY */
+ HDoff_t offset = (HDoff_t)addr;
herr_t ret_value = SUCCEED; /* Return value */
FUNC_ENTER_NOAPI_NOINIT
@@ -1255,7 +1256,6 @@ H5FD_log_read(H5FD_t *_file, H5FD_mem_t type, hid_t H5_ATTR_UNUSED dxpl_id, hadd
h5_posix_io_t bytes_in = 0; /* # of bytes to read */
h5_posix_io_ret_t bytes_read = -1; /* # of bytes actually read */
- HDoff_t offset = (HDoff_t)addr;
/* Trying to read more bytes than the return type can handle is
* undefined behavior in POSIX.
@@ -1268,7 +1268,8 @@ H5FD_log_read(H5FD_t *_file, H5FD_mem_t type, hid_t H5_ATTR_UNUSED dxpl_id, hadd
do {
#ifdef H5_HAVE_PREADWRITE
bytes_read = HDpread(file->fd, buf, bytes_in, offset);
- offset += bytes_read;
+ if(bytes_read > 0)
+ offset += bytes_read;
#else
bytes_read = HDread(file->fd, buf, bytes_in);
#endif /* H5_HAVE_PREADWRITE */
@@ -1382,6 +1383,7 @@ H5FD_log_write(H5FD_t *_file, H5FD_mem_t type, hid_t H5_ATTR_UNUSED dxpl_id, had
#ifdef H5_HAVE_GETTIMEOFDAY
struct timeval timeval_start, timeval_stop;
#endif /* H5_HAVE_GETTIMEOFDAY */
+ HDoff_t offset = (HDoff_t)addr;
herr_t ret_value = SUCCEED; /* Return value */
FUNC_ENTER_NOAPI_NOINIT
@@ -1471,7 +1473,6 @@ H5FD_log_write(H5FD_t *_file, H5FD_mem_t type, hid_t H5_ATTR_UNUSED dxpl_id, had
h5_posix_io_t bytes_in = 0; /* # of bytes to write */
h5_posix_io_ret_t bytes_wrote = -1; /* # of bytes written */
- HDoff_t offset = (HDoff_t)addr;
/* Trying to write more bytes than the return type can handle is
* undefined behavior in POSIX.
@@ -1484,7 +1485,8 @@ H5FD_log_write(H5FD_t *_file, H5FD_mem_t type, hid_t H5_ATTR_UNUSED dxpl_id, had
do {
#ifdef H5_HAVE_PREADWRITE
bytes_wrote = HDpwrite(file->fd, buf, bytes_in, offset);
- offset += bytes_wrote;
+ if(bytes_wrote > 0)
+ offset += bytes_wrote;
#else
bytes_wrote = HDwrite(file->fd, buf, bytes_in);
#endif /* H5_HAVE_PREADWRITE */
diff --git a/src/H5FDsec2.c b/src/H5FDsec2.c
index 0054a86..a393490 100644
--- a/src/H5FDsec2.c
+++ b/src/H5FDsec2.c
@@ -669,6 +669,7 @@ H5FD_sec2_read(H5FD_t *_file, H5FD_mem_t H5_ATTR_UNUSED type, hid_t H5_ATTR_UNUS
haddr_t addr, size_t size, void *buf /*out*/)
{
H5FD_sec2_t *file = (H5FD_sec2_t *)_file;
+ HDoff_t offset = (HDoff_t)addr;
herr_t ret_value = SUCCEED; /* Return value */
FUNC_ENTER_NOAPI_NOINIT
@@ -687,7 +688,7 @@ H5FD_sec2_read(H5FD_t *_file, H5FD_mem_t H5_ATTR_UNUSED type, hid_t H5_ATTR_UNUS
if(addr != file->pos || OP_READ != file->op) {
if(HDlseek(file->fd, (HDoff_t)addr, SEEK_SET) < 0)
HSYS_GOTO_ERROR(H5E_IO, H5E_SEEKERROR, FAIL, "unable to seek to proper position")
- } /* end if */
+ }
#endif /* H5_HAVE_PREADWRITE */
/* Read data, being careful of interrupted system calls, partial results,
@@ -697,7 +698,6 @@ H5FD_sec2_read(H5FD_t *_file, H5FD_mem_t H5_ATTR_UNUSED type, hid_t H5_ATTR_UNUS
h5_posix_io_t bytes_in = 0; /* # of bytes to read */
h5_posix_io_ret_t bytes_read = -1; /* # of bytes actually read */
- HDoff_t offset = (HDoff_t)addr;
/* Trying to read more bytes than the return type can handle is
* undefined behavior in POSIX.
@@ -710,7 +710,8 @@ H5FD_sec2_read(H5FD_t *_file, H5FD_mem_t H5_ATTR_UNUSED type, hid_t H5_ATTR_UNUS
do {
#ifdef H5_HAVE_PREADWRITE
bytes_read = HDpread(file->fd, buf, bytes_in, offset);
- offset += bytes_read;
+ if(bytes_read > 0)
+ offset += bytes_read;
#else
bytes_read = HDread(file->fd, buf, bytes_in);
#endif /* H5_HAVE_PREADWRITE */
@@ -773,6 +774,7 @@ H5FD_sec2_write(H5FD_t *_file, H5FD_mem_t H5_ATTR_UNUSED type, hid_t H5_ATTR_UNU
haddr_t addr, size_t size, const void *buf)
{
H5FD_sec2_t *file = (H5FD_sec2_t *)_file;
+ HDoff_t offset = (HDoff_t)addr;
herr_t ret_value = SUCCEED; /* Return value */
FUNC_ENTER_NOAPI_NOINIT
@@ -791,7 +793,7 @@ H5FD_sec2_write(H5FD_t *_file, H5FD_mem_t H5_ATTR_UNUSED type, hid_t H5_ATTR_UNU
if(addr != file->pos || OP_WRITE != file->op) {
if(HDlseek(file->fd, (HDoff_t)addr, SEEK_SET) < 0)
HSYS_GOTO_ERROR(H5E_IO, H5E_SEEKERROR, FAIL, "unable to seek to proper position")
- } /* end if */
+ }
#endif /* H5_HAVE_PREADWRITE */
/* Write the data, being careful of interrupted system calls and partial
@@ -801,7 +803,6 @@ H5FD_sec2_write(H5FD_t *_file, H5FD_mem_t H5_ATTR_UNUSED type, hid_t H5_ATTR_UNU
h5_posix_io_t bytes_in = 0; /* # of bytes to write */
h5_posix_io_ret_t bytes_wrote = -1; /* # of bytes written */
- HDoff_t offset = (HDoff_t)addr;
/* Trying to write more bytes than the return type can handle is
* undefined behavior in POSIX.
@@ -814,7 +815,8 @@ H5FD_sec2_write(H5FD_t *_file, H5FD_mem_t H5_ATTR_UNUSED type, hid_t H5_ATTR_UNU
do {
#ifdef H5_HAVE_PREADWRITE
bytes_wrote = HDpwrite(file->fd, buf, bytes_in, offset);
- offset += bytes_wrote;
+ if(bytes_wrote > 0)
+ offset += bytes_wrote;
#else
bytes_wrote = HDwrite(file->fd, buf, bytes_in);
#endif /* H5_HAVE_PREADWRITE */
generated by cgit v0.12 at 2024-10-30 04:45:29 (GMT)