From 12fc6bf95507244b2f18a56f8ff76cc0ea922fea Mon Sep 17 00:00:00 2001 From: Dana Robinson Date: Sun, 3 Feb 2019 23:47:51 -0800 Subject: Merge of changes from develop for 1.10.5. Added RELEASE.txt entries for new features. --- CMakeLists.txt | 9 ++++++ config/cmake/H5pubconf.h.in | 3 ++ config/cmake_ext_mod/ConfigureChecks.cmake | 8 ++++-- configure.ac | 46 ++++++++++++++++++++++++++++-- release_docs/RELEASE.txt | 39 +++++++++++++++++++++++++ src/H5AC.c | 2 +- src/H5Clog.c | 5 ++-- src/H5Clog.h | 4 +-- src/H5Clog_json.c | 9 +++--- src/H5Clog_trace.c | 7 ++--- src/H5Dio.c | 9 ++---- src/H5FDcore.c | 28 ++++++++++++++---- src/H5FDlog.c | 30 +++++++++++++++---- src/H5FDsec2.c | 32 ++++++++++++++++----- src/H5private.h | 6 ++++ 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 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*/ -- cgit v0.12