Merge of changes from develop for 1.10.5.

Added RELEASE.txt entries for new features.

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*/