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-rw-r--r--CMakeLists.txt9
-rw-r--r--config/cmake/H5pubconf.h.in3
-rw-r--r--config/cmake_ext_mod/ConfigureChecks.cmake8
-rw-r--r--configure.ac46
-rw-r--r--release_docs/RELEASE.txt39
-rw-r--r--src/H5AC.c2
-rw-r--r--src/H5Clog.c5
-rw-r--r--src/H5Clog.h4
-rw-r--r--src/H5Clog_json.c9
-rw-r--r--src/H5Clog_trace.c7
-rw-r--r--src/H5Dio.c9
-rw-r--r--src/H5FDcore.c28
-rw-r--r--src/H5FDlog.c30
-rw-r--r--src/H5FDsec2.c32
-rw-r--r--src/H5private.h6
15 files changed, 193 insertions, 44 deletions
diff --git a/CMakeLists.txt b/CMakeLists.txt
index f1603f0..7b1a3ba 100644
--- a/CMakeLists.txt
+++ b/CMakeLists.txt
@@ -482,6 +482,15 @@ if (HDF5_MEMORY_ALLOC_SANITY_CHECK)
endif ()
#-----------------------------------------------------------------------------
+# Option to enable/disable using pread/pwrite for VFDs
+#-----------------------------------------------------------------------------
+option (HDF5_ENABLE_PREADWRITE "Use pread/pwrite in sec2/log/core VFDs in place of read/write (when available)" ON)
+mark_as_advanced (HDF5_ENABLE_PREADWRITE)
+if (HDF5_ENABLE_PREADWRITE AND H5_HAVE_PREAD AND H5_HAVE_PWRITE)
+ set (H5_HAVE_PREADWRITE 1)
+endif ()
+
+#-----------------------------------------------------------------------------
# Option to use deprecated public API symbols
#-----------------------------------------------------------------------------
option (HDF5_ENABLE_DEPRECATED_SYMBOLS "Enable deprecated public API symbols" ON)
diff --git a/config/cmake/H5pubconf.h.in b/config/cmake/H5pubconf.h.in
index 871a78d..05b0fff 100644
--- a/config/cmake/H5pubconf.h.in
+++ b/config/cmake/H5pubconf.h.in
@@ -267,6 +267,9 @@
/* Define if we have parallel support */
#cmakedefine H5_HAVE_PARALLEL @H5_HAVE_PARALLEL@
+/* Define if both pread and pwrite exist. */
+#cmakedefine H5_HAVE_PREADWRITE @H5_HAVE_PREADWRITE@
+
/* Define to 1 if you have the <pthread.h> header file. */
#cmakedefine H5_HAVE_PTHREAD_H @H5_HAVE_PTHREAD_H@
diff --git a/config/cmake_ext_mod/ConfigureChecks.cmake b/config/cmake_ext_mod/ConfigureChecks.cmake
index c24c1f8..986280f 100644
--- a/config/cmake_ext_mod/ConfigureChecks.cmake
+++ b/config/cmake_ext_mod/ConfigureChecks.cmake
@@ -274,10 +274,12 @@ if (NOT WINDOWS)
# functionality so clock_gettime and CLOCK_MONOTONIC are defined
# correctly. This was later updated to 200112L so that
# posix_memalign() is visible for the direct VFD code on Linux
- # systems.
+ # systems. Even later, this was changed to 200809L to support
+ # pread/pwrite in VFDs.
+ #
# POSIX feature information can be found in the gcc manual at:
# http://www.gnu.org/s/libc/manual/html_node/Feature-Test-Macros.html
- set (HDF_EXTRA_C_FLAGS -D_POSIX_C_SOURCE=200112L)
+ set (HDF_EXTRA_C_FLAGS -D_POSIX_C_SOURCE=200809L)
# Need to add this so that O_DIRECT is visible for the direct
# VFD on Linux systems.
@@ -506,6 +508,8 @@ CHECK_FUNCTION_EXISTS (lround ${HDF_PREFIX}_HAVE_LROUND)
CHECK_FUNCTION_EXISTS (lroundf ${HDF_PREFIX}_HAVE_LROUNDF)
CHECK_FUNCTION_EXISTS (lstat ${HDF_PREFIX}_HAVE_LSTAT)
+CHECK_FUNCTION_EXISTS (pread ${HDF_PREFIX}_HAVE_PREAD)
+CHECK_FUNCTION_EXISTS (pwrite ${HDF_PREFIX}_HAVE_PWRITE)
CHECK_FUNCTION_EXISTS (rand_r ${HDF_PREFIX}_HAVE_RAND_R)
CHECK_FUNCTION_EXISTS (random ${HDF_PREFIX}_HAVE_RANDOM)
CHECK_FUNCTION_EXISTS (round ${HDF_PREFIX}_HAVE_ROUND)
diff --git a/configure.ac b/configure.ac
index 4f37bd4..5d997b0 100644
--- a/configure.ac
+++ b/configure.ac
@@ -1131,11 +1131,12 @@ case "$host_cpu-$host_vendor-$host_os" in
## functionality so clock_gettime and CLOCK_MONOTONIC are defined
## correctly. This was later updated to 200112L so that
## posix_memalign() is visible for the direct VFD code on Linux
- ## systems.
+ ## systems. Even later, this was changed to 200809L to support
+ ## pread/pwrite in VFDs.
##
## POSIX feature information can be found in the gcc manual at:
## http://www.gnu.org/s/libc/manual/html_node/Feature-Test-Macros.html
- H5_CPPFLAGS="-D_POSIX_C_SOURCE=200112L $H5_CPPFLAGS"
+ H5_CPPFLAGS="-D_POSIX_C_SOURCE=200809L $H5_CPPFLAGS"
## Need to add this so that O_DIRECT is visible for the direct
## VFD on Linux systems.
@@ -3262,6 +3263,47 @@ esac
## ----------------------------------------------------------------------
+## Enable use of pread/pwrite instead of read/write in certain VFDs.
+##
+AC_SUBST([PREADWRITE])
+
+## Check these first to avoid interspersed output in the AC_ARG_ENABLE line
+## below. (Probably overkill to check for both, but we'll be extra careful)
+PREADWRITE_HAVE_BOTH=yes
+AC_CHECK_FUNC([pread], [], [PREADWRITE_HAVE_BOTH=no])
+AC_CHECK_FUNC([pwrite], [], [PREADWRITE_HAVE_BOTH=no])
+
+AC_MSG_CHECKING([whether to use pread/pwrite instead of read/write in certain VFDs])
+AC_ARG_ENABLE([preadwrite],
+ [AS_HELP_STRING([--enable-preadwrite],
+ [Enable using pread/pwrite instead of read/write in sec2/log/core VFDs.
+ [default=yes if pread/pwrite are present]])],
+ [PREADWRITE=$enableval])
+
+## Set the default level.
+if test "X-$PREADWRITE" = X- ; then
+ PREADWRITE=yes
+fi
+
+case "X-$PREADWRITE" in
+ X-yes)
+ if test "X-$PREADWRITE_HAVE_BOTH" = "X-yes"; then
+ AC_DEFINE([HAVE_PREADWRITE], [1], [Define if both pread and pwrite exist.])
+ AC_MSG_RESULT([yes])
+ else
+ AC_MSG_RESULT([no])
+ fi
+ ;;
+ X-no)
+ AC_MSG_RESULT([no])
+ ;;
+ *)
+ AC_MSG_ERROR([Unrecognized value: $PREADWRITE])
+ ;;
+esac
+
+
+## ----------------------------------------------------------------------
## Enable embedded library information
##
AC_MSG_CHECKING([whether to have library information embedded in the executables])
diff --git a/release_docs/RELEASE.txt b/release_docs/RELEASE.txt
index ffb3092..fd8de96 100644
--- a/release_docs/RELEASE.txt
+++ b/release_docs/RELEASE.txt
@@ -135,6 +135,16 @@ New Features
(DER - 2018/10/26, HDFFV-10614)
+ - Added a new option to enable/disable using pread/pwrite instead of
+ read/write in the sec2, log, and core VFDs.
+
+ This option is enabled by default when pread/pwrite are detected.
+
+ Autotools: --enable-preadwrite
+ CMake: HDF5_ENABLE_PREADWRITE
+
+ (DER - 2019/02/03, HDFFV-10696)
+
Library:
--------
@@ -197,6 +207,16 @@ New Features
(JOS - 2019/01/04, TRILAB-45)
+ - The sec2, log, and core VFDs can now use pread/pwrite instead of
+ read/write.
+
+ pread and pwrite do not change the file offset, a feature that was
+ requested by a user working with a multi-threaded application.
+
+ The option to configure this feature is described above.
+
+ (DER - 2019/02/03, HDFFV-10696)
+
Parallel Library:
-----------------
@@ -433,6 +453,25 @@ Bug Fixes since HDF5-1.10.3 release
(BMR - 2019/01/29, HDFFV-10684)
+ - Uninitialized bytes from a type conversion buffer could be written
+ to disk in H5Dwrite calls where type conversion takes place
+ and the type conversion buffer was created by the HDF5 library.
+
+ When H5Dwrite is called and datatype conversion must be performed,
+ the library will create a temporary buffer for type conversion if
+ one is not provided by the user via H5Pset_buffer. This internal
+ buffer is allocated via malloc and contains uninitialized data. In
+ some datatype conversions (float to long double, possibly others),
+ some of this uninitialized data could be written to disk.
+
+ This was flagged by valgrind in the dtransform test and does not
+ appear to be a common occurrence (it is flagged in one test out
+ of the entire HDF5 test suite).
+
+ Switching to calloc fixed the problem.
+
+ (DER - 2019/02/03, HDFFV-10694)
+
Java Library:
----------------
diff --git a/src/H5AC.c b/src/H5AC.c
index a14852e..7315030 100644
--- a/src/H5AC.c
+++ b/src/H5AC.c
@@ -1612,7 +1612,7 @@ H5AC_unprotect(H5F_t *f, const H5AC_class_t *type, haddr_t addr, void *thing,
done:
/* If currently logging, generate a message */
if(f->shared->cache->log_info->logging)
- if(H5C_log_write_unprotect_entry_msg(f->shared->cache, (H5AC_info_t *)thing, type->id, flags, ret_value) < 0)
+ if(H5C_log_write_unprotect_entry_msg(f->shared->cache, addr, type->id, flags, ret_value) < 0)
HDONE_ERROR(H5E_CACHE, H5E_LOGGING, FAIL, "unable to emit log message")
FUNC_LEAVE_NOAPI(ret_value)
diff --git a/src/H5Clog.c b/src/H5Clog.c
index 0ae7f13..cf9b7e8 100644
--- a/src/H5Clog.c
+++ b/src/H5Clog.c
@@ -887,7 +887,7 @@ done:
*-------------------------------------------------------------------------
*/
herr_t
-H5C_log_write_unprotect_entry_msg(H5C_t *cache, const H5C_cache_entry_t *entry,
+H5C_log_write_unprotect_entry_msg(H5C_t *cache, haddr_t address,
int type_id, unsigned flags, herr_t fxn_ret_value)
{
herr_t ret_value = SUCCEED;
@@ -898,9 +898,8 @@ H5C_log_write_unprotect_entry_msg(H5C_t *cache, const H5C_cache_entry_t *entry,
HDassert(cache);
/* Write a log message */
- HDassert(entry);
if(cache->log_info->cls->write_unprotect_entry_log_msg)
- if(cache->log_info->cls->write_unprotect_entry_log_msg(cache->log_info->udata, entry, type_id, flags, fxn_ret_value) < 0)
+ if(cache->log_info->cls->write_unprotect_entry_log_msg(cache->log_info->udata, address, type_id, flags, fxn_ret_value) < 0)
HGOTO_ERROR(H5E_CACHE, H5E_LOGGING, FAIL, "log-specific unprotect entry call failed")
done:
diff --git a/src/H5Clog.h b/src/H5Clog.h
index 9ba6786..0235c4a 100644
--- a/src/H5Clog.h
+++ b/src/H5Clog.h
@@ -59,7 +59,7 @@ typedef struct H5C_log_class_t {
herr_t (*write_resize_entry_log_msg)(void *udata, const H5C_cache_entry_t *entry, size_t new_size, herr_t fxn_ret_value);
herr_t (*write_unpin_entry_log_msg)(void *udata, const H5C_cache_entry_t *entry, herr_t fxn_ret_value);
herr_t (*write_destroy_fd_log_msg)(void *udata, const H5C_cache_entry_t *parent, const H5C_cache_entry_t *child, herr_t fxn_ret_value);
- herr_t (*write_unprotect_entry_log_msg)(void *udata, const H5C_cache_entry_t *entry, int type_id, unsigned flags, herr_t fxn_ret_value);
+ herr_t (*write_unprotect_entry_log_msg)(void *udata, haddr_t address, int type_id, unsigned flags, herr_t fxn_ret_value);
herr_t (*write_set_cache_config_log_msg)(void *udata, const H5AC_cache_config_t *config, herr_t fxn_ret_value);
herr_t (*write_remove_entry_log_msg)(void *udata, const H5C_cache_entry_t *entry, herr_t fxn_ret_value);
@@ -102,7 +102,7 @@ H5_DLL herr_t H5C_log_write_protect_entry_msg(H5C_t *cache, const H5C_cache_entr
H5_DLL herr_t H5C_log_write_resize_entry_msg(H5C_t *cache, const H5C_cache_entry_t *entry, size_t new_size, herr_t fxn_ret_value);
H5_DLL herr_t H5C_log_write_unpin_entry_msg(H5C_t *cache, const H5C_cache_entry_t *entry, herr_t fxn_ret_value);
H5_DLL herr_t H5C_log_write_destroy_fd_msg(H5C_t *cache, const H5C_cache_entry_t *parent, const H5C_cache_entry_t *child, herr_t fxn_ret_value);
-H5_DLL herr_t H5C_log_write_unprotect_entry_msg(H5C_t *cache, const H5C_cache_entry_t *entry, int type_id, unsigned flags, herr_t fxn_ret_value);
+H5_DLL herr_t H5C_log_write_unprotect_entry_msg(H5C_t *cache, haddr_t address, int type_id, unsigned flags, herr_t fxn_ret_value);
H5_DLL herr_t H5C_log_write_set_cache_config_msg(H5C_t *cache, const H5AC_cache_config_t *config, herr_t fxn_ret_value);
H5_DLL herr_t H5C_log_write_remove_entry_msg(H5C_t *cache, const H5C_cache_entry_t *entry, herr_t fxn_ret_value);
diff --git a/src/H5Clog_json.c b/src/H5Clog_json.c
index ccfa222..dd9e9b2 100644
--- a/src/H5Clog_json.c
+++ b/src/H5Clog_json.c
@@ -41,7 +41,7 @@
/****************/
/* Max log message size */
-#define H5C_MAX_JSON_LOG_MSG_SIZE 128
+#define H5C_MAX_JSON_LOG_MSG_SIZE 1024
/******************/
@@ -87,7 +87,7 @@ static herr_t H5C__json_write_protect_entry_log_msg(void *udata, const H5C_cache
static herr_t H5C__json_write_resize_entry_log_msg(void *udata, const H5C_cache_entry_t *entry, size_t new_size, herr_t fxn_ret_value);
static herr_t H5C__json_write_unpin_entry_log_msg(void *udata, const H5C_cache_entry_t *entry, herr_t fxn_ret_value);
static herr_t H5C__json_write_destroy_fd_log_msg(void *udata, const H5C_cache_entry_t *parent, const H5C_cache_entry_t *child, herr_t fxn_ret_value);
-static herr_t H5C__json_write_unprotect_entry_log_msg(void *udata, const H5C_cache_entry_t *entry, int type_id, unsigned flags, herr_t fxn_ret_value);
+static herr_t H5C__json_write_unprotect_entry_log_msg(void *udata, haddr_t address, int type_id, unsigned flags, herr_t fxn_ret_value);
static herr_t H5C__json_write_set_cache_config_log_msg(void *udata, const H5AC_cache_config_t *config, herr_t fxn_ret_value);
static herr_t H5C__json_write_remove_entry_log_msg(void *udata, const H5C_cache_entry_t *entry, herr_t fxn_ret_value);
@@ -1232,7 +1232,7 @@ done:
*-------------------------------------------------------------------------
*/
static herr_t
-H5C__json_write_unprotect_entry_log_msg(void *udata, const H5C_cache_entry_t *entry,
+H5C__json_write_unprotect_entry_log_msg(void *udata, haddr_t address,
int type_id, unsigned flags, herr_t fxn_ret_value)
{
H5C_log_json_udata_t *json_udata = (H5C_log_json_udata_t *)(udata);
@@ -1243,7 +1243,6 @@ H5C__json_write_unprotect_entry_log_msg(void *udata, const H5C_cache_entry_t *en
/* Sanity checks */
HDassert(json_udata);
HDassert(json_udata->message);
- HDassert(entry);
/* Create the log message string */
HDsnprintf(json_udata->message, H5C_MAX_JSON_LOG_MSG_SIZE,
@@ -1257,7 +1256,7 @@ H5C__json_write_unprotect_entry_log_msg(void *udata, const H5C_cache_entry_t *en
\"returned\":%d\
},\n\
"
- , (long long)HDtime(NULL), (unsigned long)entry->addr,
+ , (long long)HDtime(NULL), (unsigned long)address,
type_id, flags, (int)fxn_ret_value);
/* Write the log message to the file */
diff --git a/src/H5Clog_trace.c b/src/H5Clog_trace.c
index f7d6889..7c1305c 100644
--- a/src/H5Clog_trace.c
+++ b/src/H5Clog_trace.c
@@ -82,7 +82,7 @@ static herr_t H5C__trace_write_protect_entry_log_msg(void *udata, const H5C_cach
static herr_t H5C__trace_write_resize_entry_log_msg(void *udata, const H5C_cache_entry_t *entry, size_t new_size, herr_t fxn_ret_value);
static herr_t H5C__trace_write_unpin_entry_log_msg(void *udata, const H5C_cache_entry_t *entry, herr_t fxn_ret_value);
static herr_t H5C__trace_write_destroy_fd_log_msg(void *udata, const H5C_cache_entry_t *parent, const H5C_cache_entry_t *child, herr_t fxn_ret_value);
-static herr_t H5C__trace_write_unprotect_entry_log_msg(void *udata, const H5C_cache_entry_t *entry, int type_id, unsigned flags, herr_t fxn_ret_value);
+static herr_t H5C__trace_write_unprotect_entry_log_msg(void *udata, haddr_t address, int type_id, unsigned flags, herr_t fxn_ret_value);
static herr_t H5C__trace_write_set_cache_config_log_msg(void *udata, const H5AC_cache_config_t *config, herr_t fxn_ret_value);
static herr_t H5C__trace_write_remove_entry_log_msg(void *udata, const H5C_cache_entry_t *entry, herr_t fxn_ret_value);
@@ -872,7 +872,7 @@ done:
*-------------------------------------------------------------------------
*/
static herr_t
-H5C__trace_write_unprotect_entry_log_msg(void *udata, const H5C_cache_entry_t *entry,
+H5C__trace_write_unprotect_entry_log_msg(void *udata, haddr_t address,
int type_id, unsigned flags, herr_t fxn_ret_value)
{
H5C_log_trace_udata_t *trace_udata = (H5C_log_trace_udata_t *)(udata);
@@ -883,11 +883,10 @@ H5C__trace_write_unprotect_entry_log_msg(void *udata, const H5C_cache_entry_t *e
/* Sanity checks */
HDassert(trace_udata);
HDassert(trace_udata->message);
- HDassert(entry);
/* Create the log message string */
HDsnprintf(trace_udata->message, H5C_MAX_TRACE_LOG_MSG_SIZE, "H5AC_unprotect 0x%lx %d 0x%x %d\n",
- (unsigned long)(entry->addr), type_id, flags, (int)fxn_ret_value);
+ (unsigned long)(address), type_id, flags, (int)fxn_ret_value);
/* Write the log message to the file */
if(H5C__trace_write_log_message(trace_udata) < 0)
diff --git a/src/H5Dio.c b/src/H5Dio.c
index 2ce47f9..8abcd81 100644
--- a/src/H5Dio.c
+++ b/src/H5Dio.c
@@ -1060,16 +1060,13 @@ H5D__typeinfo_init(const H5D_t *dset, hid_t mem_type_id, hbool_t do_write,
if(type_info->request_nelmts == 0)
HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "temporary buffer max size is too small")
- /*
- * Get a temporary buffer for type conversion unless the app has already
+ /* Get a temporary buffer for type conversion unless the app has already
* supplied one through the xfer properties. Instead of allocating a
- * buffer which is the exact size, we allocate the target size. The
- * malloc() is usually less resource-intensive if we allocate/free the
- * same size over and over.
+ * buffer which is the exact size, we allocate the target size.
*/
if(NULL == (type_info->tconv_buf = (uint8_t *)tconv_buf)) {
/* Allocate temporary buffer */
- if(NULL == (type_info->tconv_buf = H5FL_BLK_MALLOC(type_conv, target_size)))
+ if(NULL == (type_info->tconv_buf = H5FL_BLK_CALLOC(type_conv, target_size)))
HGOTO_ERROR(H5E_RESOURCE, H5E_NOSPACE, FAIL, "memory allocation failed for type conversion")
type_info->tconv_buf_allocated = TRUE;
} /* end if */
diff --git a/src/H5FDcore.c b/src/H5FDcore.c
index 2ab04dc..395107e 100644
--- a/src/H5FDcore.c
+++ b/src/H5FDcore.c
@@ -343,14 +343,17 @@ H5FD__core_write_to_bstore(H5FD_core_t *file, haddr_t addr, size_t size)
HDassert(file);
- /* Write to backing store */
- if((off_t)addr != HDlseek(file->fd, (off_t)addr, SEEK_SET))
+#ifndef H5_HAVE_PREADWRITE
+ /* Seek to the correct location (if we don't have pwrite) */
+ if((HDoff_t)addr != HDlseek(file->fd, (off_t)addr, SEEK_SET))
HGOTO_ERROR(H5E_IO, H5E_SEEKERROR, FAIL, "error seeking in backing store")
+#endif /* H5_HAVE_PREADWRITE */
while (size > 0) {
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.
@@ -361,15 +364,21 @@ H5FD__core_write_to_bstore(H5FD_core_t *file, haddr_t addr, size_t size)
bytes_in = (h5_posix_io_t)size;
do {
+#ifdef H5_HAVE_PREADWRITE
+ bytes_wrote = HDpwrite(file->fd, ptr, bytes_in, offset);
+ offset += bytes_wrote;
+#else
bytes_wrote = HDwrite(file->fd, ptr, bytes_in);
+#endif /* H5_HAVE_PREADWRITE */
} while(-1 == bytes_wrote && EINTR == errno);
if(-1 == bytes_wrote) { /* error */
int myerrno = errno;
time_t mytime = HDtime(NULL);
- HDoff_t myoffset = HDlseek(file->fd, (HDoff_t)0, SEEK_CUR);
- HGOTO_ERROR(H5E_IO, H5E_WRITEERROR, FAIL, "write to backing store failed: time = %s, filename = '%s', file descriptor = %d, errno = %d, error message = '%s', ptr = %p, total write size = %llu, bytes this sub-write = %llu, bytes actually written = %llu, offset = %llu", HDctime(&mytime), file->name, file->fd, myerrno, HDstrerror(myerrno), ptr, (unsigned long long)size, (unsigned long long)bytes_in, (unsigned long long)bytes_wrote, (unsigned long long)myoffset);
+ offset = HDlseek(file->fd, (HDoff_t)0, SEEK_CUR);
+
+ HGOTO_ERROR(H5E_IO, H5E_WRITEERROR, FAIL, "write to backing store failed: time = %s, filename = '%s', file descriptor = %d, errno = %d, error message = '%s', ptr = %p, total write size = %llu, bytes this sub-write = %llu, bytes actually written = %llu, offset = %llu", HDctime(&mytime), file->name, file->fd, myerrno, HDstrerror(myerrno), ptr, (unsigned long long)size, (unsigned long long)bytes_in, (unsigned long long)bytes_wrote, (unsigned long long)offset);
} /* end if */
HDassert(bytes_wrote > 0);
@@ -745,6 +754,7 @@ H5FD__core_open(const char *name, unsigned flags, hid_t fapl_id, haddr_t maxaddr
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.
@@ -755,15 +765,21 @@ H5FD__core_open(const char *name, unsigned flags, hid_t fapl_id, haddr_t maxaddr
bytes_in = (h5_posix_io_t)size;
do {
+#ifdef H5_HAVE_PREADWRITE
+ bytes_read = HDpread(file->fd, mem, bytes_in, offset);
+ offset += bytes_read;
+#else
bytes_read = HDread(file->fd, mem, bytes_in);
+#endif /* H5_HAVE_PREADWRITE */
} while(-1 == bytes_read && EINTR == errno);
if(-1 == bytes_read) { /* error */
int myerrno = errno;
time_t mytime = HDtime(NULL);
- HDoff_t myoffset = HDlseek(file->fd, (HDoff_t)0, SEEK_CUR);
- HGOTO_ERROR(H5E_IO, H5E_READERROR, NULL, "file read failed: time = %s, filename = '%s', file descriptor = %d, errno = %d, error message = '%s', file->mem = %p, total read size = %llu, bytes this sub-read = %llu, bytes actually read = %llu, offset = %llu", HDctime(&mytime), file->name, file->fd, myerrno, HDstrerror(myerrno), file->mem, (unsigned long long)size, (unsigned long long)bytes_in, (unsigned long long)bytes_read, (unsigned long long)myoffset);
+ offset = HDlseek(file->fd, (HDoff_t)0, SEEK_CUR);
+
+ HGOTO_ERROR(H5E_IO, H5E_READERROR, NULL, "file read failed: time = %s, filename = '%s', file descriptor = %d, errno = %d, error message = '%s', file->mem = %p, total read size = %llu, bytes this sub-read = %llu, bytes actually read = %llu, offset = %llu", HDctime(&mytime), file->name, file->fd, myerrno, HDstrerror(myerrno), file->mem, (unsigned long long)size, (unsigned long long)bytes_in, (unsigned long long)bytes_read, (unsigned long long)offset);
} /* end if */
HDassert(bytes_read >= 0);
diff --git a/src/H5FDlog.c b/src/H5FDlog.c
index 3dcd7f5..74df95c 100644
--- a/src/H5FDlog.c
+++ b/src/H5FDlog.c
@@ -1189,7 +1189,8 @@ H5FD_log_read(H5FD_t *_file, H5FD_mem_t type, hid_t H5_ATTR_UNUSED dxpl_id, hadd
} /* end if */
} /* end if */
- /* Seek to the correct location */
+#ifndef H5_HAVE_PREADWRITE
+ /* Seek to the correct location (if we don't have pread) */
if(addr != file->pos || OP_READ != file->op) {
#ifdef H5_HAVE_GETTIMEOFDAY
if(file->fa.flags & H5FD_LOG_TIME_SEEK)
@@ -1232,6 +1233,7 @@ H5FD_log_read(H5FD_t *_file, H5FD_mem_t type, hid_t H5_ATTR_UNUSED dxpl_id, hadd
#endif /* H5_HAVE_GETTIMEOFDAY */
} /* end if */
} /* end if */
+#endif /* H5_HAVE_PREADWRITE */
/*
* Read data, being careful of interrupted system calls, partial results,
@@ -1245,6 +1247,7 @@ 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.
@@ -1255,18 +1258,24 @@ H5FD_log_read(H5FD_t *_file, H5FD_mem_t type, hid_t H5_ATTR_UNUSED dxpl_id, hadd
bytes_in = (h5_posix_io_t)size;
do {
+#ifdef H5_HAVE_PREADWRITE
+ bytes_read = HDpread(file->fd, buf, bytes_in, offset);
+ offset += bytes_read;
+#else
bytes_read = HDread(file->fd, buf, bytes_in);
+#endif /* H5_HAVE_PREADWRITE */
} while(-1 == bytes_read && EINTR == errno);
if(-1 == bytes_read) { /* error */
int myerrno = errno;
time_t mytime = HDtime(NULL);
- HDoff_t myoffset = HDlseek(file->fd, (HDoff_t)0, SEEK_CUR);
+
+ offset = HDlseek(file->fd, (HDoff_t)0, SEEK_CUR);
if(file->fa.flags & H5FD_LOG_LOC_READ)
HDfprintf(file->logfp, "Error! Reading: %10a-%10a (%10Zu bytes)\n", orig_addr, (orig_addr + orig_size) - 1, orig_size);
- HGOTO_ERROR(H5E_IO, H5E_READERROR, FAIL, "file read failed: time = %s, filename = '%s', file descriptor = %d, errno = %d, error message = '%s', buf = %p, total read size = %llu, bytes this sub-read = %llu, bytes actually read = %llu, offset = %llu", HDctime(&mytime), file->filename, file->fd, myerrno, HDstrerror(myerrno), buf, (unsigned long long)size, (unsigned long long)bytes_in, (unsigned long long)bytes_read, (unsigned long long)myoffset);
+ HGOTO_ERROR(H5E_IO, H5E_READERROR, FAIL, "file read failed: time = %s, filename = '%s', file descriptor = %d, errno = %d, error message = '%s', buf = %p, total read size = %llu, bytes this sub-read = %llu, bytes actually read = %llu, offset = %llu", HDctime(&mytime), file->filename, file->fd, myerrno, HDstrerror(myerrno), buf, (unsigned long long)size, (unsigned long long)bytes_in, (unsigned long long)bytes_read, (unsigned long long)offset);
} /* end if */
if(0 == bytes_read) {
@@ -1396,7 +1405,8 @@ H5FD_log_write(H5FD_t *_file, H5FD_mem_t type, hid_t H5_ATTR_UNUSED dxpl_id, had
file->nwrite[tmp_addr++]++;
} /* end if */
- /* Seek to the correct location */
+#ifndef H5_HAVE_PREADWRITE
+ /* Seek to the correct location (if we don't have pwrite) */
if(addr != file->pos || OP_WRITE != file->op) {
#ifdef H5_HAVE_GETTIMEOFDAY
if(file->fa.flags & H5FD_LOG_TIME_SEEK)
@@ -1439,6 +1449,7 @@ H5FD_log_write(H5FD_t *_file, H5FD_mem_t type, hid_t H5_ATTR_UNUSED dxpl_id, had
#endif /* H5_HAVE_GETTIMEOFDAY */
} /* end if */
} /* end if */
+#endif /* H5_HAVE_PREADWRITE */
/*
* Write the data, being careful of interrupted system calls and partial
@@ -1452,6 +1463,7 @@ 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.
@@ -1462,18 +1474,24 @@ H5FD_log_write(H5FD_t *_file, H5FD_mem_t type, hid_t H5_ATTR_UNUSED dxpl_id, had
bytes_in = (h5_posix_io_t)size;
do {
+#ifdef H5_HAVE_PREADWRITE
+ bytes_wrote = HDpwrite(file->fd, buf, bytes_in, offset);
+ offset += bytes_wrote;
+#else
bytes_wrote = HDwrite(file->fd, buf, bytes_in);
+#endif /* H5_HAVE_PREADWRITE */
} while(-1 == bytes_wrote && EINTR == errno);
if(-1 == bytes_wrote) { /* error */
int myerrno = errno;
time_t mytime = HDtime(NULL);
- HDoff_t myoffset = HDlseek(file->fd, (HDoff_t)0, SEEK_CUR);
+
+ offset = HDlseek(file->fd, (HDoff_t)0, SEEK_CUR);
if(file->fa.flags & H5FD_LOG_LOC_WRITE)
HDfprintf(file->logfp, "Error! Writing: %10a-%10a (%10Zu bytes)\n", orig_addr, (orig_addr + orig_size) - 1, orig_size);
- HGOTO_ERROR(H5E_IO, H5E_WRITEERROR, FAIL, "file write failed: time = %s, filename = '%s', file descriptor = %d, errno = %d, error message = '%s', buf = %p, total write size = %llu, bytes this sub-write = %llu, bytes actually written = %llu, offset = %llu", HDctime(&mytime), file->filename, file->fd, myerrno, HDstrerror(myerrno), buf, (unsigned long long)size, (unsigned long long)bytes_in, (unsigned long long)bytes_wrote, (unsigned long long)myoffset);
+ HGOTO_ERROR(H5E_IO, H5E_WRITEERROR, FAIL, "file write failed: time = %s, filename = '%s', file descriptor = %d, errno = %d, error message = '%s', buf = %p, total write size = %llu, bytes this sub-write = %llu, bytes actually written = %llu, offset = %llu", HDctime(&mytime), file->filename, file->fd, myerrno, HDstrerror(myerrno), buf, (unsigned long long)size, (unsigned long long)bytes_in, (unsigned long long)bytes_wrote, (unsigned long long)offset);
} /* end if */
HDassert(bytes_wrote > 0);
diff --git a/src/H5FDsec2.c b/src/H5FDsec2.c
index 06c008d..54f5a95 100644
--- a/src/H5FDsec2.c
+++ b/src/H5FDsec2.c
@@ -682,11 +682,13 @@ H5FD_sec2_read(H5FD_t *_file, H5FD_mem_t H5_ATTR_UNUSED type, hid_t H5_ATTR_UNUS
if(REGION_OVERFLOW(addr, size))
HGOTO_ERROR(H5E_ARGS, H5E_OVERFLOW, FAIL, "addr overflow, addr = %llu", (unsigned long long)addr)
- /* Seek to the correct location */
+#ifndef H5_HAVE_PREADWRITE
+ /* Seek to the correct location (if we don't have pread) */
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,
* and the end of the file.
@@ -694,7 +696,8 @@ H5FD_sec2_read(H5FD_t *_file, H5FD_mem_t H5_ATTR_UNUSED type, hid_t H5_ATTR_UNUS
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 */
+ 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.
@@ -705,15 +708,21 @@ H5FD_sec2_read(H5FD_t *_file, H5FD_mem_t H5_ATTR_UNUSED type, hid_t H5_ATTR_UNUS
bytes_in = (h5_posix_io_t)size;
do {
+#ifdef H5_HAVE_PREADWRITE
+ bytes_read = HDpread(file->fd, buf, bytes_in, offset);
+ offset += bytes_read;
+#else
bytes_read = HDread(file->fd, buf, bytes_in);
+#endif /* H5_HAVE_PREADWRITE */
} while(-1 == bytes_read && EINTR == errno);
if(-1 == bytes_read) { /* error */
int myerrno = errno;
time_t mytime = HDtime(NULL);
- HDoff_t myoffset = HDlseek(file->fd, (HDoff_t)0, SEEK_CUR);
- HGOTO_ERROR(H5E_IO, H5E_READERROR, FAIL, "file read failed: time = %s, filename = '%s', file descriptor = %d, errno = %d, error message = '%s', buf = %p, total read size = %llu, bytes this sub-read = %llu, bytes actually read = %llu, offset = %llu", HDctime(&mytime), file->filename, file->fd, myerrno, HDstrerror(myerrno), buf, (unsigned long long)size, (unsigned long long)bytes_in, (unsigned long long)bytes_read, (unsigned long long)myoffset);
+ offset = HDlseek(file->fd, (HDoff_t)0, SEEK_CUR);
+
+ HGOTO_ERROR(H5E_IO, H5E_READERROR, FAIL, "file read failed: time = %s, filename = '%s', file descriptor = %d, errno = %d, error message = '%s', buf = %p, total read size = %llu, bytes this sub-read = %llu, bytes actually read = %llu, offset = %llu", HDctime(&mytime), file->filename, file->fd, myerrno, HDstrerror(myerrno), buf, (unsigned long long)size, (unsigned long long)bytes_in, (unsigned long long)bytes_read, (unsigned long long)offset);
} /* end if */
if(0 == bytes_read) {
@@ -777,11 +786,13 @@ H5FD_sec2_write(H5FD_t *_file, H5FD_mem_t H5_ATTR_UNUSED type, hid_t H5_ATTR_UNU
if(REGION_OVERFLOW(addr, size))
HGOTO_ERROR(H5E_ARGS, H5E_OVERFLOW, FAIL, "addr overflow, addr = %llu, size = %llu", (unsigned long long)addr, (unsigned long long)size)
- /* Seek to the correct location */
+#ifndef H5_HAVE_PREADWRITE
+ /* Seek to the correct location (if we don't have pwrite) */
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
* results
@@ -790,6 +801,7 @@ 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.
@@ -800,15 +812,21 @@ H5FD_sec2_write(H5FD_t *_file, H5FD_mem_t H5_ATTR_UNUSED type, hid_t H5_ATTR_UNU
bytes_in = (h5_posix_io_t)size;
do {
+#ifdef H5_HAVE_PREADWRITE
+ bytes_wrote = HDpwrite(file->fd, buf, bytes_in, offset);
+ offset += bytes_wrote;
+#else
bytes_wrote = HDwrite(file->fd, buf, bytes_in);
+#endif /* H5_HAVE_PREADWRITE */
} while(-1 == bytes_wrote && EINTR == errno);
if(-1 == bytes_wrote) { /* error */
int myerrno = errno;
time_t mytime = HDtime(NULL);
- HDoff_t myoffset = HDlseek(file->fd, (HDoff_t)0, SEEK_CUR);
- HGOTO_ERROR(H5E_IO, H5E_WRITEERROR, FAIL, "file write failed: time = %s, filename = '%s', file descriptor = %d, errno = %d, error message = '%s', buf = %p, total write size = %llu, bytes this sub-write = %llu, bytes actually written = %llu, offset = %llu", HDctime(&mytime), file->filename, file->fd, myerrno, HDstrerror(myerrno), buf, (unsigned long long)size, (unsigned long long)bytes_in, (unsigned long long)bytes_wrote, (unsigned long long)myoffset);
+ offset = HDlseek(file->fd, (HDoff_t)0, SEEK_CUR);
+
+ HGOTO_ERROR(H5E_IO, H5E_WRITEERROR, FAIL, "file write failed: time = %s, filename = '%s', file descriptor = %d, errno = %d, error message = '%s', buf = %p, total write size = %llu, bytes this sub-write = %llu, bytes actually written = %llu, offset = %llu", HDctime(&mytime), file->filename, file->fd, myerrno, HDstrerror(myerrno), buf, (unsigned long long)size, (unsigned long long)bytes_in, (unsigned long long)bytes_wrote, (unsigned long long)offset);
} /* end if */
HDassert(bytes_wrote > 0);
diff --git a/src/H5private.h b/src/H5private.h
index 196d001..4f5323a 100644
--- a/src/H5private.h
+++ b/src/H5private.h
@@ -1148,6 +1148,9 @@ typedef off_t h5_stat_size_t;
#ifndef HDpowf
#define HDpowf(X,Y) powf(X,Y)
#endif /* HDpowf */
+#ifndef HDpread
+ #define HDpread(F,B,C,O) pread(F,B,C,O)
+#endif /* HDpread */
#ifndef HDprintf
#define HDprintf(...) HDfprintf(stdout, __VA_ARGS__)
#endif /* HDprintf */
@@ -1160,6 +1163,9 @@ typedef off_t h5_stat_size_t;
#ifndef HDputs
#define HDputs(S) puts(S)
#endif /* HDputs */
+#ifndef HDpwrite
+ #define HDpwrite(F,B,C,O) pwrite(F,B,C,O)
+#endif /* HDpwrite */
#ifndef HDqsort
#define HDqsort(M,N,Z,F) qsort(M,N,Z,F)
#endif /* HDqsort*/
generated by cgit v0.12 at 2024-12-27 16:01:01 (GMT)