diff options
| author | Mohamad Chaarawi <chaarawi@hdfgroup.org> | 2014-04-01 15:42:43 (GMT) |
|---|---|---|
| committer | Mohamad Chaarawi <chaarawi@hdfgroup.org> | 2014-04-01 15:42:43 (GMT) |
| commit | 72e8017eadf211257caceb43095b2aed76e81632 (patch) | |
| tree | 0fae8d91bc2587a7b3b44129c5afaf37d4842098 /src | |
| parent | d4c2e51d1e255fde2c0b2e359078cfd0de82720a (diff) | |
| parent | c86aedeba1f683daaf0289435450fd4e518fecc4 (diff) | |
| download | hdf5-72e8017eadf211257caceb43095b2aed76e81632.zip hdf5-72e8017eadf211257caceb43095b2aed76e81632.tar.gz hdf5-72e8017eadf211257caceb43095b2aed76e81632.tar.bz2 | |
[svn-r24940] merge from trunk.
Diffstat (limited to 'src')
45 files changed, 1550 insertions, 2225 deletions
diff --git a/src/CMakeLists.txt b/src/CMakeLists.txt index eb43b3d..565e030 100644 --- a/src/CMakeLists.txt +++ b/src/CMakeLists.txt @@ -1,15 +1,15 @@ -cmake_minimum_required (VERSION 2.8.10) +cmake_minimum_required (VERSION 2.8.11) PROJECT (HDF5_SRC C CXX) #----------------------------------------------------------------------------- # Apply Definitions to compiler in this directory and below #----------------------------------------------------------------------------- -ADD_DEFINITIONS (${HDF5_EXTRA_C_FLAGS}) +add_definitions (${HDF5_EXTRA_C_FLAGS}) #----------------------------------------------------------------------------- # List Source Files #----------------------------------------------------------------------------- -SET (H5_SRCS +set (H5_SRCS ${HDF5_SRC_DIR}/H5.c ${HDF5_SRC_DIR}/H5checksum.c ${HDF5_SRC_DIR}/H5dbg.c @@ -18,7 +18,7 @@ SET (H5_SRCS ${HDF5_SRC_DIR}/H5trace.c ) -SET (H5_HDRS +set (H5_HDRS ${HDF5_SRC_DIR}/hdf5.h ${HDF5_SRC_DIR}/H5api_adpt.h ${HDF5_SRC_DIR}/H5public.h @@ -27,7 +27,7 @@ SET (H5_HDRS ) IDE_GENERATED_PROPERTIES ("H5" "${H5_HDRS}" "${H5_SRCS}" ) -SET (H5A_SRCS +set (H5A_SRCS ${HDF5_SRC_DIR}/H5A.c ${HDF5_SRC_DIR}/H5Abtree2.c ${HDF5_SRC_DIR}/H5Adense.c @@ -36,35 +36,35 @@ SET (H5A_SRCS ${HDF5_SRC_DIR}/H5Atest.c ) -SET (H5A_HDRS +set (H5A_HDRS ${HDF5_SRC_DIR}/H5Apkg.h ${HDF5_SRC_DIR}/H5Apublic.h ) IDE_GENERATED_PROPERTIES ("H5A" "${H5A_HDRS}" "${H5A_SRCS}" ) -SET (H5AC_SRCS +set (H5AC_SRCS ${HDF5_SRC_DIR}/H5AC.c ) -SET (H5AC_HDRS +set (H5AC_HDRS ${HDF5_SRC_DIR}/H5ACpkg.h ${HDF5_SRC_DIR}/H5ACpublic.h ) IDE_GENERATED_PROPERTIES ("H5AC" "${H5AC_HDRS}" "${H5AC_SRCS}" ) -SET (H5B_SRCS +set (H5B_SRCS ${HDF5_SRC_DIR}/H5B.c ${HDF5_SRC_DIR}/H5Bcache.c ${HDF5_SRC_DIR}/H5Bdbg.c ) -SET (H5B_HDRS +set (H5B_HDRS ${HDF5_SRC_DIR}/H5Bpkg.h ${HDF5_SRC_DIR}/H5Bpublic.h ) IDE_GENERATED_PROPERTIES ("H5B" "${H5B_HDRS}" "${H5B_SRCS}" ) -SET (H5B2_SRCS +set (H5B2_SRCS ${HDF5_SRC_DIR}/H5B2.c ${HDF5_SRC_DIR}/H5B2cache.c ${HDF5_SRC_DIR}/H5B2dbg.c @@ -73,32 +73,32 @@ SET (H5B2_SRCS ${HDF5_SRC_DIR}/H5B2stat.c ${HDF5_SRC_DIR}/H5B2test.c ) -SET (H5B2_HDRS +set (H5B2_HDRS ${HDF5_SRC_DIR}/H5B2pkg.h ${HDF5_SRC_DIR}/H5B2public.h ) IDE_GENERATED_PROPERTIES ("H5B2" "${H5B2_HDRS}" "${H5B2_SRCS}" ) -SET (H5C_SRCS +set (H5C_SRCS ${HDF5_SRC_DIR}/H5C.c ) -SET (H5C_HDRS +set (H5C_HDRS ${HDF5_SRC_DIR}/H5Cpkg.h ${HDF5_SRC_DIR}/H5Cpublic.h ) IDE_GENERATED_PROPERTIES ("H5C" "${H5C_HDRS}" "${H5C_SRCS}" ) -SET (H5CS_SRCS +set (H5CS_SRCS ${HDF5_SRC_DIR}/H5CS.c ) -SET (H5CS_HDRS +set (H5CS_HDRS ) IDE_GENERATED_PROPERTIES ("H5CS" "${H5CS_HDRS}" "${H5CS_SRCS}" ) -SET (H5D_SRCS +set (H5D_SRCS ${HDF5_SRC_DIR}/H5D.c ${HDF5_SRC_DIR}/H5Dbtree.c ${HDF5_SRC_DIR}/H5Dchunk.c @@ -118,19 +118,19 @@ SET (H5D_SRCS ${HDF5_SRC_DIR}/H5Dtest.c ) -SET (H5D_HDRS +set (H5D_HDRS ${HDF5_SRC_DIR}/H5Dpkg.h ${HDF5_SRC_DIR}/H5Dpublic.h ) IDE_GENERATED_PROPERTIES ("H5D" "${H5D_HDRS}" "${H5D_SRCS}" ) -SET (H5E_SRCS +set (H5E_SRCS ${HDF5_SRC_DIR}/H5E.c ${HDF5_SRC_DIR}/H5Edeprec.c ${HDF5_SRC_DIR}/H5Eint.c ) -SET (H5E_HDRS +set (H5E_HDRS ${HDF5_SRC_DIR}/H5Edefin.h ${HDF5_SRC_DIR}/H5Einit.h ${HDF5_SRC_DIR}/H5Epkg.h @@ -141,7 +141,7 @@ SET (H5E_HDRS IDE_GENERATED_PROPERTIES ("H5E" "${H5E_HDRS}" "${H5E_SRCS}" ) -SET (H5EA_SRCS +set (H5EA_SRCS ${HDF5_SRC_DIR}/H5EA.c ${HDF5_SRC_DIR}/H5EAcache.c ${HDF5_SRC_DIR}/H5EAdbg.c @@ -154,13 +154,13 @@ SET (H5EA_SRCS ${HDF5_SRC_DIR}/H5EAstat.c ${HDF5_SRC_DIR}/H5EAtest.c ) -SET (H5EA_HDRS +set (H5EA_HDRS ${HDF5_SRC_DIR}/H5EApkg.h ) IDE_GENERATED_PROPERTIES ("H5EA" "${H5EA_HDRS}" "${H5EA_SRCS}" ) -SET (H5F_SRCS +set (H5F_SRCS ${HDF5_SRC_DIR}/H5F.c ${HDF5_SRC_DIR}/H5Fint.c ${HDF5_SRC_DIR}/H5Faccum.c @@ -179,14 +179,14 @@ SET (H5F_SRCS ${HDF5_SRC_DIR}/H5Ftest.c ) -SET (H5F_HDRS +set (H5F_HDRS ${HDF5_SRC_DIR}/H5Fpkg.h ${HDF5_SRC_DIR}/H5Fpublic.h ) IDE_GENERATED_PROPERTIES ("H5F" "${H5F_HDRS}" "${H5F_SRCS}" ) -SET (H5FA_SRCS +set (H5FA_SRCS ${HDF5_SRC_DIR}/H5FA.c ${HDF5_SRC_DIR}/H5FAcache.c ${HDF5_SRC_DIR}/H5FAdbg.c @@ -196,13 +196,13 @@ SET (H5FA_SRCS ${HDF5_SRC_DIR}/H5FAstat.c ${HDF5_SRC_DIR}/H5FAtest.c ) -SET (H5FA_HDRS +set (H5FA_HDRS ${HDF5_SRC_DIR}/H5FApkg.h ) IDE_GENERATED_PROPERTIES ("H5FA" "${H5FA_HDRS}" "${H5FA_SRCS}" ) -SET (H5FD_SRCS +set (H5FD_SRCS ${HDF5_SRC_DIR}/H5FD.c ${HDF5_SRC_DIR}/H5FDcore.c ${HDF5_SRC_DIR}/H5FDdirect.c @@ -211,7 +211,6 @@ SET (H5FD_SRCS ${HDF5_SRC_DIR}/H5FDlog.c ${HDF5_SRC_DIR}/H5FDmpi.c ${HDF5_SRC_DIR}/H5FDmpio.c - ${HDF5_SRC_DIR}/H5FDmpiposix.c ${HDF5_SRC_DIR}/H5FDmulti.c ${HDF5_SRC_DIR}/H5FDsec2.c ${HDF5_SRC_DIR}/H5FDspace.c @@ -219,14 +218,13 @@ SET (H5FD_SRCS ${HDF5_SRC_DIR}/H5FDwindows.c ) -SET (H5FD_HDRS +set (H5FD_HDRS ${HDF5_SRC_DIR}/H5FDcore.h ${HDF5_SRC_DIR}/H5FDdirect.h ${HDF5_SRC_DIR}/H5FDfamily.h ${HDF5_SRC_DIR}/H5FDlog.h ${HDF5_SRC_DIR}/H5FDmpi.h ${HDF5_SRC_DIR}/H5FDmpio.h - ${HDF5_SRC_DIR}/H5FDmpiposix.h ${HDF5_SRC_DIR}/H5FDmulti.h ${HDF5_SRC_DIR}/H5FDpkg.h ${HDF5_SRC_DIR}/H5FDpublic.h @@ -237,23 +235,23 @@ SET (H5FD_HDRS IDE_GENERATED_PROPERTIES ("H5FD" "${H5FD_HDRS}" "${H5FD_SRCS}" ) -SET (H5FL_SRCS +set (H5FL_SRCS ${HDF5_SRC_DIR}/H5FL.c ) -SET (H5FL_HDRS +set (H5FL_HDRS ) IDE_GENERATED_PROPERTIES ("H5FL" "${H5FL_HDRS}" "${H5FL_SRCS}" ) -SET (H5FO_SRCS +set (H5FO_SRCS ${HDF5_SRC_DIR}/H5FO.c ) -SET (H5FO_HDRS +set (H5FO_HDRS ) IDE_GENERATED_PROPERTIES ("H5FO" "${H5FO_HDRS}" "${H5FO_SRCS}" ) -SET (H5FS_SRCS +set (H5FS_SRCS ${HDF5_SRC_DIR}/H5FS.c ${HDF5_SRC_DIR}/H5FScache.c ${HDF5_SRC_DIR}/H5FSdbg.c @@ -262,13 +260,13 @@ SET (H5FS_SRCS ${HDF5_SRC_DIR}/H5FStest.c ) -SET (H5FS_HDRS +set (H5FS_HDRS ${HDF5_SRC_DIR}/H5FSpkg.h ${HDF5_SRC_DIR}/H5FSpublic.h ) IDE_GENERATED_PROPERTIES ("H5FS" "${H5FS_HDRS}" "${H5FS_SRCS}" ) -SET (H5G_SRCS +set (H5G_SRCS ${HDF5_SRC_DIR}/H5G.c ${HDF5_SRC_DIR}/H5Gbtree2.c ${HDF5_SRC_DIR}/H5Gcache.c @@ -289,13 +287,13 @@ SET (H5G_SRCS ${HDF5_SRC_DIR}/H5Gtraverse.c ) -SET (H5G_HDRS +set (H5G_HDRS ${HDF5_SRC_DIR}/H5Gpkg.h ${HDF5_SRC_DIR}/H5Gpublic.h ) IDE_GENERATED_PROPERTIES ("H5G" "${H5G_HDRS}" "${H5G_SRCS}" ) -SET (H5HF_SRCS +set (H5HF_SRCS ${HDF5_SRC_DIR}/H5HF.c ${HDF5_SRC_DIR}/H5HFbtree2.c ${HDF5_SRC_DIR}/H5HFcache.c @@ -314,101 +312,101 @@ SET (H5HF_SRCS ${HDF5_SRC_DIR}/H5HFtiny.c ) -SET (H5HF_HDRS +set (H5HF_HDRS ${HDF5_SRC_DIR}/H5HFpkg.h ${HDF5_SRC_DIR}/H5HFpublic.h ) IDE_GENERATED_PROPERTIES ("H5HF" "${H5HF_HDRS}" "${H5HF_SRCS}" ) -SET (H5HG_SRCS +set (H5HG_SRCS ${HDF5_SRC_DIR}/H5HG.c ${HDF5_SRC_DIR}/H5HGcache.c ${HDF5_SRC_DIR}/H5HGdbg.c ${HDF5_SRC_DIR}/H5HGquery.c ) -SET (H5HG_HDRS +set (H5HG_HDRS ${HDF5_SRC_DIR}/H5HGpkg.h ${HDF5_SRC_DIR}/H5HGpublic.h ) IDE_GENERATED_PROPERTIES ("H5HG" "${H5HG_HDRS}" "${H5HG_SRCS}" ) -SET (H5HL_SRCS +set (H5HL_SRCS ${HDF5_SRC_DIR}/H5HL.c ${HDF5_SRC_DIR}/H5HLcache.c ${HDF5_SRC_DIR}/H5HLdbg.c ${HDF5_SRC_DIR}/H5HLint.c ) -SET (H5HL_HDRS +set (H5HL_HDRS ${HDF5_SRC_DIR}/H5HLpkg.h ${HDF5_SRC_DIR}/H5HLpublic.h ) IDE_GENERATED_PROPERTIES ("H5HL" "${H5HL_HDRS}" "${H5HL_SRCS}" ) -SET (H5HP_SRCS +set (H5HP_SRCS ${HDF5_SRC_DIR}/H5HP.c ) -SET (H5HP_HDRS +set (H5HP_HDRS ) IDE_GENERATED_PROPERTIES ("H5HP" "${H5HP_HDRS}" "${H5HP_SRCS}" ) -SET (H5I_SRCS +set (H5I_SRCS ${HDF5_SRC_DIR}/H5I.c ${HDF5_SRC_DIR}/H5Itest.c ) -SET (H5I_HDRS +set (H5I_HDRS ${HDF5_SRC_DIR}/H5Ipkg.h ${HDF5_SRC_DIR}/H5Ipublic.h ) IDE_GENERATED_PROPERTIES ("H5I" "${H5I_HDRS}" "${H5I_SRCS}" ) -SET (H5L_SRCS +set (H5L_SRCS ${HDF5_SRC_DIR}/H5L.c ${HDF5_SRC_DIR}/H5Lexternal.c ) -SET (H5L_HDRS +set (H5L_HDRS ${HDF5_SRC_DIR}/H5Lpkg.h ${HDF5_SRC_DIR}/H5Lpublic.h ) IDE_GENERATED_PROPERTIES ("H5L" "${H5L_HDRS}" "${H5L_SRCS}" ) -SET (H5MF_SRCS +set (H5MF_SRCS ${HDF5_SRC_DIR}/H5MF.c ${HDF5_SRC_DIR}/H5MFaggr.c ${HDF5_SRC_DIR}/H5MFdbg.c ${HDF5_SRC_DIR}/H5MFsection.c ) -SET (H5MF_HDRS +set (H5MF_HDRS ) IDE_GENERATED_PROPERTIES ("H5MF" "${H5MF_HDRS}" "${H5MF_SRCS}" ) -SET (H5MM_SRCS +set (H5MM_SRCS ${HDF5_SRC_DIR}/H5MM.c ) -SET (H5MM_HDRS +set (H5MM_HDRS ${HDF5_SRC_DIR}/H5MMpublic.h ) IDE_GENERATED_PROPERTIES ("H5MM" "${H5MM_HDRS}" "${H5MM_SRCS}" ) -SET (H5MP_SRCS +set (H5MP_SRCS ${HDF5_SRC_DIR}/H5MP.c ${HDF5_SRC_DIR}/H5MPtest.c ) -SET (H5MP_HDRS +set (H5MP_HDRS ${HDF5_SRC_DIR}/H5MPpkg.h ) IDE_GENERATED_PROPERTIES ("H5MP" "${H5MP_HDRS}" "${H5MP_SRCS}" ) -SET (H5O_SRCS +set (H5O_SRCS ${HDF5_SRC_DIR}/H5O.c ${HDF5_SRC_DIR}/H5Oainfo.c ${HDF5_SRC_DIR}/H5Oalloc.c @@ -444,14 +442,14 @@ SET (H5O_SRCS ${HDF5_SRC_DIR}/H5Ounknown.c ) -SET (H5O_HDRS +set (H5O_HDRS ${HDF5_SRC_DIR}/H5Opkg.h ${HDF5_SRC_DIR}/H5Opublic.h ${HDF5_SRC_DIR}/H5Oshared.h ) IDE_GENERATED_PROPERTIES ("H5O" "${H5O_HDRS}" "${H5O_SRCS}" ) -SET (H5P_SRCS +set (H5P_SRCS ${HDF5_SRC_DIR}/H5P.c ${HDF5_SRC_DIR}/H5Pacpl.c ${HDF5_SRC_DIR}/H5Pdapl.c @@ -472,50 +470,50 @@ SET (H5P_SRCS ${HDF5_SRC_DIR}/H5Ptest.c ) -SET (H5P_HDRS +set (H5P_HDRS ${HDF5_SRC_DIR}/H5Ppkg.h ${HDF5_SRC_DIR}/H5Ppublic.h ) IDE_GENERATED_PROPERTIES ("H5P" "${H5P_HDRS}" "${H5P_SRCS}" ) -SET (H5PL_SRCS +set (H5PL_SRCS ${HDF5_SRC_DIR}/H5PL.c ) -SET (H5PL_HDRS +set (H5PL_HDRS ${HDF5_SRC_DIR}/H5PLextern.h ) IDE_GENERATED_PROPERTIES ("H5PL" "${H5PL_HDRS}" "${H5PL_SRCS}" ) -SET (H5R_SRCS +set (H5R_SRCS ${HDF5_SRC_DIR}/H5R.c ${HDF5_SRC_DIR}/H5Rdeprec.c ) -SET (H5R_HDRS +set (H5R_HDRS ${HDF5_SRC_DIR}/H5Rpkg.h ${HDF5_SRC_DIR}/H5Rpublic.h ) IDE_GENERATED_PROPERTIES ("H5R" "${H5R_HDRS}" "${H5R_SRCS}" ) -SET (H5UC_SRCS +set (H5UC_SRCS ${HDF5_SRC_DIR}/H5UC.c ) -SET (H5UC_HDRS +set (H5UC_HDRS ) IDE_GENERATED_PROPERTIES ("H5UC" "${H5UC_HDRS}" "${H5UC_SRCS}" ) -SET (H5RS_SRCS +set (H5RS_SRCS ${HDF5_SRC_DIR}/H5RS.c ) -SET (H5RS_HDRS +set (H5RS_HDRS ) IDE_GENERATED_PROPERTIES ("H5RS" "${H5RS_HDRS}" "${H5RS_SRCS}" ) -SET (H5S_SRCS +set (H5S_SRCS ${HDF5_SRC_DIR}/H5S.c ${HDF5_SRC_DIR}/H5Sall.c ${HDF5_SRC_DIR}/H5Sdbg.c @@ -527,22 +525,22 @@ SET (H5S_SRCS ${HDF5_SRC_DIR}/H5Stest.c ) -SET (H5S_HDRS +set (H5S_HDRS ${HDF5_SRC_DIR}/H5Spkg.h ${HDF5_SRC_DIR}/H5Spublic.h ) IDE_GENERATED_PROPERTIES ("H5S" "${H5S_HDRS}" "${H5S_SRCS}" ) -SET (H5SL_SRCS +set (H5SL_SRCS ${HDF5_SRC_DIR}/H5SL.c ) -SET (H5SL_HDRS +set (H5SL_HDRS ) IDE_GENERATED_PROPERTIES ("H5SL" "${H5SL_HDRS}" "${H5SL_SRCS}" ) -SET (H5SM_SRCS +set (H5SM_SRCS ${HDF5_SRC_DIR}/H5SM.c ${HDF5_SRC_DIR}/H5SMbtree2.c ${HDF5_SRC_DIR}/H5SMcache.c @@ -550,21 +548,21 @@ SET (H5SM_SRCS ${HDF5_SRC_DIR}/H5SMtest.c ) -SET (H5SM_HDRS +set (H5SM_HDRS ${HDF5_SRC_DIR}/H5SMpkg.h ) IDE_GENERATED_PROPERTIES ("H5SM" "${H5SM_HDRS}" "${H5SM_SRCS}" ) -SET (H5ST_SRCS +set (H5ST_SRCS ${HDF5_SRC_DIR}/H5ST.c ) -SET (H5ST_HDRS +set (H5ST_HDRS ) IDE_GENERATED_PROPERTIES ("H5ST" "${H5ST_HDRS}" "${H5ST_SRCS}" ) -SET (H5T_SRCS +set (H5T_SRCS ${HDF5_SRC_DIR}/H5T.c ${HDF5_SRC_DIR}/H5Tarray.c ${HDF5_SRC_DIR}/H5Tbit.c @@ -590,25 +588,25 @@ SET (H5T_SRCS ${HDF5_SRC_DIR}/H5Tvlen.c ) -SET (H5T_HDRS +set (H5T_HDRS ${HDF5_SRC_DIR}/H5Tpkg.h ${HDF5_SRC_DIR}/H5Tpublic.h ) IDE_GENERATED_PROPERTIES ("H5T" "${H5T_HDRS}" "${H5T_SRCS}" ) -SET (H5TS_SRCS +set (H5TS_SRCS ${HDF5_SRC_DIR}/H5TS.c ) -SET (H5TS_HDRS +set (H5TS_HDRS ) IDE_GENERATED_PROPERTIES ("H5TS" "${H5TS_HDRS}" "${H5TS_SRCS}" ) -SET (H5VM_SRCS +set (H5VM_SRCS ${HDF5_SRC_DIR}/H5VM.c ) -SET (H5VM_HDRS +set (H5VM_HDRS ) IDE_GENERATED_PROPERTIES ("H5VM" "${H5VM_HDRS}" "${H5VM_SRCS}" ) @@ -624,15 +622,15 @@ SET (H5VL_HDRS ) IDE_GENERATED_PROPERTIES ("H5VL" "${H5VL_HDRS}" "${H5VL_SRCS}" ) -SET (H5WB_SRCS +set (H5WB_SRCS ${HDF5_SRC_DIR}/H5WB.c ) -SET (H5WB_HDRS +set (H5WB_HDRS ) IDE_GENERATED_PROPERTIES ("H5WB" "${H5WB_HDRS}" "${H5WB_SRCS}" ) -SET (H5Z_SRCS +set (H5Z_SRCS ${HDF5_SRC_DIR}/H5Z.c ${HDF5_SRC_DIR}/H5Zdeflate.c ${HDF5_SRC_DIR}/H5Zfletcher32.c @@ -642,19 +640,19 @@ SET (H5Z_SRCS ${HDF5_SRC_DIR}/H5Zszip.c ${HDF5_SRC_DIR}/H5Ztrans.c ) -IF (H5_ZLIB_HEADER) +if (H5_ZLIB_HEADER) SET_PROPERTY(SOURCE ${HDF5_SRC_DIR}/H5Zdeflate.c PROPERTY COMPILE_DEFINITIONS H5_ZLIB_HEADER="${H5_ZLIB_HEADER}") -ENDIF (H5_ZLIB_HEADER) +endif (H5_ZLIB_HEADER) -SET (H5Z_HDRS +set (H5Z_HDRS ${HDF5_SRC_DIR}/H5Zpkg.h ${HDF5_SRC_DIR}/H5Zpublic.h ) IDE_GENERATED_PROPERTIES ("H5Z" "${H5Z_HDRS}" "${H5Z_SRCS}" ) -SET (common_SRCS +set (common_SRCS ${H5_SRCS} ${H5A_SRCS} ${H5AC_SRCS} @@ -699,7 +697,7 @@ SET (common_SRCS ${H5Z_SRCS} ) -SET (H5_PUBLIC_HEADERS +set (H5_PUBLIC_HEADERS ${H5_HDRS} ${H5A_HDRS} ${H5AC_HDRS} @@ -734,7 +732,7 @@ SET (H5_PUBLIC_HEADERS ) -SET (H5_PRIVATE_HEADERS +set (H5_PRIVATE_HEADERS ${HDF5_SRC_DIR}/H5private.h ${HDF5_SRC_DIR}/H5Aprivate.h ${HDF5_SRC_DIR}/H5ACprivate.h @@ -781,35 +779,32 @@ SET (H5_PRIVATE_HEADERS ${HDF5_SRC_DIR}/H5win32defs.h ) -INCLUDE_DIRECTORIES (${HDF5_SOURCE_DIR}) -INCLUDE_DIRECTORIES (${CMAKE_BINARY_DIR}) - #----------------------------------------------------------------------------- # Setup the H5Detect utility which generates H5Tinit with platform # specific type checks inside #----------------------------------------------------------------------------- -ADD_EXECUTABLE (H5detect ${HDF5_SRC_DIR}/H5detect.c) +add_executable (H5detect ${HDF5_SRC_DIR}/H5detect.c) TARGET_C_PROPERTIES (H5detect " " " ") -IF (MSVC) - TARGET_LINK_LIBRARIES (H5detect "ws2_32.lib") -ENDIF (MSVC) +if (MSVC OR MINGW) + target_link_libraries (H5detect "ws2_32.lib") +endif (MSVC OR MINGW) -SET (CMD $<TARGET_FILE:H5detect>) -ADD_CUSTOM_COMMAND ( +set (CMD $<TARGET_FILE:H5detect>) +add_custom_command ( OUTPUT ${HDF5_BINARY_DIR}/H5Tinit.c COMMAND ${CMD} ARGS > ${HDF5_BINARY_DIR}/H5Tinit.c DEPENDS H5detect ) -ADD_EXECUTABLE (H5make_libsettings ${HDF5_SRC_DIR}/H5make_libsettings.c) +add_executable (H5make_libsettings ${HDF5_SRC_DIR}/H5make_libsettings.c) TARGET_C_PROPERTIES (H5make_libsettings " " " ") -IF (MSVC) - TARGET_LINK_LIBRARIES (H5make_libsettings "ws2_32.lib") -ENDIF (MSVC) +if (MSVC OR MINGW) + target_link_libraries (H5make_libsettings "ws2_32.lib") +endif (MSVC OR MINGW) -SET (CMD $<TARGET_FILE:H5make_libsettings>) -ADD_CUSTOM_COMMAND ( +set (CMD $<TARGET_FILE:H5make_libsettings>) +add_custom_command ( OUTPUT ${HDF5_BINARY_DIR}/H5lib_settings.c COMMAND ${CMD} ARGS > ${HDF5_BINARY_DIR}/H5lib_settings.c @@ -817,21 +812,21 @@ ADD_CUSTOM_COMMAND ( WORKING_DIRECTORY ${HDF5_BINARY_DIR} ) -ADD_CUSTOM_COMMAND ( +add_custom_command ( TARGET ${HDF5_BINARY_DIR}/H5Edefin.h PRE_BUILD COMMAND ${CMAKE_COMMAND} -E perl ${HDF5_SOURCE_DIR}/bin/make_err ${HDF5_SOURCE_DIR}/src/H5err.txt COMMENT " Creating err headers" ) -ADD_CUSTOM_COMMAND ( +add_custom_command ( TARGET ${HDF5_BINARY_DIR}/H5version.h PRE_BUILD COMMAND ${CMAKE_COMMAND} -E perl ${HDF5_SOURCE_DIR}/bin/make_vers ${HDF5_SOURCE_DIR}/src/H5vers.txt COMMENT " Creating API version macro" ) -ADD_CUSTOM_COMMAND ( +add_custom_command ( TARGET ${HDF5_BINARY_DIR}/H5overflow.h PRE_BUILD COMMAND ${CMAKE_COMMAND} -E perl ${HDF5_SOURCE_DIR}/bin/make_overflow ${HDF5_SOURCE_DIR}/src/H5overflow.txt @@ -841,51 +836,67 @@ ADD_CUSTOM_COMMAND ( #----------------------------------------------------------------------------- # Add H5Tinit source to build - generated by H5Detect/CMake at configure time #----------------------------------------------------------------------------- -SET (common_SRCS ${common_SRCS} ${HDF5_BINARY_DIR}/H5Tinit.c) -SET_SOURCE_FILES_PROPERTIES (${HDF5_BINARY_DIR}/H5Tinit.c GENERATED) -SET (common_SRCS ${common_SRCS} ${HDF5_BINARY_DIR}/H5lib_settings.c) -SET_SOURCE_FILES_PROPERTIES (${HDF5_BINARY_DIR}/H5lib_settings.c GENERATED) -SET (common_SRCS ${common_SRCS} ${HDF5_BINARY_DIR}/H5Edefin.h) -SET_SOURCE_FILES_PROPERTIES (${HDF5_BINARY_DIR}/H5Edefin.h GENERATED) -SET (common_SRCS ${common_SRCS} ${HDF5_BINARY_DIR}/H5version.h) -SET_SOURCE_FILES_PROPERTIES (${HDF5_BINARY_DIR}/H5version.h GENERATED) -SET (common_SRCS ${common_SRCS} ${HDF5_BINARY_DIR}/H5overflow.h) -SET_SOURCE_FILES_PROPERTIES (${HDF5_BINARY_DIR}/H5overflow.h GENERATED) - -ADD_LIBRARY (${HDF5_LIB_TARGET} ${LIB_TYPE} ${common_SRCS} ${H5_PUBLIC_HEADERS} ${H5_PRIVATE_HEADERS}) +set (common_SRCS ${common_SRCS} ${HDF5_BINARY_DIR}/H5Tinit.c) +set_source_files_properties (${HDF5_BINARY_DIR}/H5Tinit.c GENERATED) +set (common_SRCS ${common_SRCS} ${HDF5_BINARY_DIR}/H5lib_settings.c) +set_source_files_properties (${HDF5_BINARY_DIR}/H5lib_settings.c GENERATED) +set (common_SRCS ${common_SRCS} ${HDF5_BINARY_DIR}/H5Edefin.h) +set_source_files_properties (${HDF5_BINARY_DIR}/H5Edefin.h GENERATED) +set (common_SRCS ${common_SRCS} ${HDF5_BINARY_DIR}/H5version.h) +set_source_files_properties (${HDF5_BINARY_DIR}/H5version.h GENERATED) +set (common_SRCS ${common_SRCS} ${HDF5_BINARY_DIR}/H5overflow.h) +set_source_files_properties (${HDF5_BINARY_DIR}/H5overflow.h GENERATED) + +add_library (${HDF5_LIB_TARGET} ${LIB_TYPE} ${common_SRCS} ${H5_PUBLIC_HEADERS} ${H5_PRIVATE_HEADERS}) TARGET_C_PROPERTIES (${HDF5_LIB_TARGET} " " " ") -TARGET_LINK_LIBRARIES (${HDF5_LIB_TARGET} ${LINK_LIBS}) -IF (NOT WIN32) - TARGET_LINK_LIBRARIES (${HDF5_LIB_TARGET} dl) -ENDIF (NOT WIN32) -SET_GLOBAL_VARIABLE (HDF5_LIBRARIES_TO_EXPORT ${HDF5_LIB_TARGET}) +target_link_libraries (${HDF5_LIB_TARGET} ${LINK_LIBS}) +if (NOT WIN32) + target_link_libraries (${HDF5_LIB_TARGET} dl) +endif (NOT WIN32) +if (H5_HAVE_PARALLEL AND MPI_C_FOUND) + target_link_libraries (${HDF5_LIB_TARGET} ${MPI_C_LIBRARIES}) +endif (H5_HAVE_PARALLEL AND MPI_C_FOUND) +set_global_variable (HDF5_LIBRARIES_TO_EXPORT ${HDF5_LIB_TARGET}) H5_SET_LIB_OPTIONS (${HDF5_LIB_TARGET} ${HDF5_LIB_NAME} ${LIB_TYPE}) -SET_TARGET_PROPERTIES (${HDF5_LIB_TARGET} PROPERTIES FOLDER libraries) +set_target_properties (${HDF5_LIB_TARGET} PROPERTIES + FOLDER libraries + INTERFACE_INCLUDE_DIRECTORIES "$<INSTALL_INTERFACE:$<INSTALL_PREFIX>/include>" +) + +option (HDF5_ENABLE_DEBUG_APIS "Turn on debugging in all packages" OFF) +if (HDF5_ENABLE_DEBUG_APIS) + set_target_properties (${HDF5_LIB_TARGET} PROPERTIES + COMPILE_DEFINITIONS + "-DH5Z_DEBUG -DH5VM_DEBUG -DH5T_DEBUG + -DH5S_DEBUG -DH5P_DEBUG -DH5O_DEBUG -DH5MM_DEBUG -DH5MF_DEBUG + -DH5I_DEBUG -DH5HL_DEBUG -DH5HG_DEBUG -DH5G_DEBUG -DH5F_DEBUG + -DH5E_DEBUG -DH5D_DEBUG -DH5B_DEBUG -DH5AC_DEBUG -UNDEBUG" + ) +endif (HDF5_ENABLE_DEBUG_APIS) #----------------------------------------------------------------------------- # Add file(s) to CMake Install #----------------------------------------------------------------------------- -IF (NOT HDF5_INSTALL_NO_DEVELOPMENT) - INSTALL ( +if (NOT HDF5_INSTALL_NO_DEVELOPMENT) + install ( FILES ${H5_PUBLIC_HEADERS} - ${H5_PRIVATE_HEADERS} DESTINATION ${HDF5_INSTALL_INCLUDE_DIR} COMPONENT headers ) -ENDIF (NOT HDF5_INSTALL_NO_DEVELOPMENT) +endif (NOT HDF5_INSTALL_NO_DEVELOPMENT) #----------------------------------------------------------------------------- # Add Target(s) to CMake Install for import into other projects #----------------------------------------------------------------------------- -IF (HDF5_EXPORTED_TARGETS) - IF (BUILD_SHARED_LIBS) +if (HDF5_EXPORTED_TARGETS) + if (BUILD_SHARED_LIBS) INSTALL_TARGET_PDB (${HDF5_LIB_TARGET} ${HDF5_INSTALL_LIB_DIR} libraries) - ENDIF (BUILD_SHARED_LIBS) + endif (BUILD_SHARED_LIBS) - INSTALL ( + install ( TARGETS ${HDF5_LIB_TARGET} EXPORT @@ -894,4 +905,4 @@ IF (HDF5_EXPORTED_TARGETS) ARCHIVE DESTINATION ${HDF5_INSTALL_LIB_DIR} COMPONENT libraries RUNTIME DESTINATION ${HDF5_INSTALL_BIN_DIR} COMPONENT libraries ) -ENDIF (HDF5_EXPORTED_TARGETS) +endif (HDF5_EXPORTED_TARGETS) @@ -809,3 +809,28 @@ H5close(void) FUNC_LEAVE_API_NOFS(SUCCEED) } /* end H5close() */ + +/*------------------------------------------------------------------------- + * Function: H5free_memory + * + * Purpose: Frees memory allocated by the library that it is the user's + * responsibility to free. Ensures that the same library + * that was used to allocate the memory frees it. Passing + * NULL pointers is allowed. + * + * Return: SUCCEED/FAIL + * + *------------------------------------------------------------------------- + */ +herr_t +H5free_memory(void *mem) +{ + FUNC_ENTER_API_NOINIT + H5TRACE1("e", "*x", mem); + + /* At this time, it is impossible for this to fail. */ + HDfree(mem); + + FUNC_LEAVE_API(SUCCEED) +} /* end H5free_memory() */ + diff --git a/src/H5Dchunk.c b/src/H5Dchunk.c index e834aa3..92db446 100644 --- a/src/H5Dchunk.c +++ b/src/H5Dchunk.c @@ -164,10 +164,18 @@ typedef struct H5D_chunk_it_ud4_t { /* Callback info for nonexistent readvv operation */ typedef struct H5D_chunk_readvv_ud_t { unsigned char *rbuf; /* Read buffer to initialize */ - H5D_t *dset; /* Dataset to operate on */ + const H5D_t *dset; /* Dataset to operate on */ hid_t dxpl_id; /* DXPL for operation */ } H5D_chunk_readvv_ud_t; +/* Callback info for file selection iteration */ +typedef struct H5D_chunk_file_iter_ud_t { + H5D_chunk_map_t *fm; /* File->memory chunk mapping info */ +#ifdef H5_HAVE_PARALLEL + const H5D_io_info_t *io_info; /* I/O info for operation */ +#endif /* H5_HAVE_PARALLEL */ +} H5D_chunk_file_iter_ud_t; + /********************/ /* Local Prototypes */ @@ -297,7 +305,7 @@ H5FL_BLK_DEFINE_STATIC(chunk); */ herr_t H5D__chunk_direct_write(const H5D_t *dset, hid_t dxpl_id, uint32_t filters, hsize_t *offset, - size_t data_size, const void *buf) + uint32_t data_size, const void *buf) { const H5O_layout_t *layout = &(dset->shared->layout); /* Dataset layout */ H5D_chunk_ud_t udata; /* User data for querying chunk info */ @@ -329,8 +337,7 @@ H5D__chunk_direct_write(const H5D_t *dset, hid_t dxpl_id, uint32_t filters, hsiz HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "can't get chunk index") /* Find out the file address of the chunk */ - if(H5D__chunk_lookup(dset, dxpl_id, offset, chunk_idx, - &udata) < 0) + if(H5D__chunk_lookup(dset, dxpl_id, offset, chunk_idx, &udata) < 0) HGOTO_ERROR(H5E_DATASET, H5E_CANTGET, FAIL, "error looking up chunk address") udata.filter_mask = filters; @@ -685,7 +692,7 @@ H5D__chunk_io_init(const H5D_io_info_t *io_info, const H5D_type_info_t *type_inf hsize_t nelmts, const H5S_t *file_space, const H5S_t *mem_space, H5D_chunk_map_t *fm) { - H5D_t *dataset = io_info->dset; /* Local pointer to dataset info */ + const H5D_t *dataset = io_info->dset; /* Local pointer to dataset info */ const H5T_t *mem_type = type_info->mem_type; /* Local pointer to memory datatype */ H5S_t *tmp_mspace = NULL; /* Temporary memory dataspace */ hssize_t old_offset[H5O_LAYOUT_NDIMS]; /* Old selection offset */ @@ -698,7 +705,6 @@ H5D__chunk_io_init(const H5D_io_info_t *io_info, const H5D_type_info_t *type_inf H5S_sel_type fsel_type; /* Selection type on disk */ char bogus; /* "bogus" buffer to pass to selection iterator */ unsigned u; /* Local index variable */ - hbool_t sel_hyper_flag; herr_t ret_value = SUCCEED; /* Return value */ FUNC_ENTER_STATIC @@ -796,6 +802,8 @@ H5D__chunk_io_init(const H5D_io_info_t *io_info, const H5D_type_info_t *type_inf HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "unable to create chunk selections for single element") } /* end if */ else { + hbool_t sel_hyper_flag; /* Whether file selection is a hyperslab */ + /* Initialize skip list for chunk selections */ if(NULL == dataset->shared->cache.chunk.sel_chunks) { if(NULL == (dataset->shared->cache.chunk.sel_chunks = H5SL_create(H5SL_TYPE_HSIZE, NULL))) @@ -843,12 +851,20 @@ H5D__chunk_io_init(const H5D_io_info_t *io_info, const H5D_type_info_t *type_inf } /* end while */ } /* end if */ else { + H5D_chunk_file_iter_ud_t udata; /* User data for iteration */ + /* Create temporary datatypes for selection iteration */ if((f_tid = H5I_register(H5I_DATATYPE, H5T_copy(dataset->shared->type, H5T_COPY_ALL), FALSE)) < 0) HGOTO_ERROR(H5E_DATATYPE, H5E_CANTREGISTER, FAIL, "unable to register file datatype") + /* Initialize the user data */ + udata.fm = fm; +#ifdef H5_HAVE_PARALLEL + udata.io_info = io_info; +#endif /* H5_HAVE_PARALLEL */ + /* Spaces might not be the same shape, iterate over the file selection directly */ - if(H5S_select_iterate(&bogus, f_tid, file_space, H5D__chunk_file_cb, fm) < 0) + if(H5S_select_iterate(&bogus, f_tid, file_space, H5D__chunk_file_cb, &udata) < 0) HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "unable to create file chunk selections") /* Reset "last chunk" info */ @@ -1265,7 +1281,7 @@ H5D__create_chunk_file_map_hyper(H5D_chunk_map_t *fm, const H5D_io_info_t /* Add temporary chunk to the list of chunks */ /* Allocate the file & memory chunk information */ - if (NULL==(new_chunk_info = H5FL_MALLOC (H5D_chunk_info_t))) { + if (NULL==(new_chunk_info = H5FL_MALLOC(H5D_chunk_info_t))) { (void)H5S_close(tmp_fchunk); HGOTO_ERROR(H5E_RESOURCE, H5E_NOSPACE, FAIL, "can't allocate chunk info") } /* end if */ @@ -1276,7 +1292,7 @@ H5D__create_chunk_file_map_hyper(H5D_chunk_map_t *fm, const H5D_io_info_t new_chunk_info->index=chunk_index; #ifdef H5_HAVE_PARALLEL - /* store chunk selection information */ + /* Store chunk selection information, for multi-chunk I/O */ if(io_info->using_mpi_vfd) fm->select_chunk[chunk_index] = new_chunk_info; #endif /* H5_HAVE_PARALLEL */ @@ -1476,9 +1492,10 @@ done: *------------------------------------------------------------------------- */ static herr_t -H5D__chunk_file_cb(void UNUSED *elem, hid_t UNUSED type_id, unsigned ndims, const hsize_t *coords, void *_fm) +H5D__chunk_file_cb(void UNUSED *elem, hid_t UNUSED type_id, unsigned ndims, const hsize_t *coords, void *_udata) { - H5D_chunk_map_t *fm = (H5D_chunk_map_t *)_fm; /* File<->memory chunk mapping info */ + H5D_chunk_file_iter_ud_t *udata = (H5D_chunk_file_iter_ud_t *)_udata; /* User data for operation */ + H5D_chunk_map_t *fm = udata->fm; /* File<->memory chunk mapping info */ H5D_chunk_info_t *chunk_info; /* Chunk information for current chunk */ hsize_t coords_in_chunk[H5O_LAYOUT_NDIMS]; /* Coordinates of element in chunk */ hsize_t chunk_index; /* Chunk index */ @@ -1496,7 +1513,7 @@ H5D__chunk_file_cb(void UNUSED *elem, hid_t UNUSED type_id, unsigned ndims, cons /* If the chunk index is the same as the last chunk index we used, * get the cached info to operate on. */ - chunk_info=fm->last_chunk_info; + chunk_info = fm->last_chunk_info; } /* end if */ else { /* If the chunk index is not the same as the last chunk index we used, @@ -1553,14 +1570,20 @@ H5D__chunk_file_cb(void UNUSED *elem, hid_t UNUSED type_id, unsigned ndims, cons } /* end if */ } /* end if */ +#ifdef H5_HAVE_PARALLEL + /* Store chunk selection information, for collective multi-chunk I/O */ + if(udata->io_info->using_mpi_vfd) + fm->select_chunk[chunk_index] = chunk_info; +#endif /* H5_HAVE_PARALLEL */ + /* Update the "last chunk seen" information */ - fm->last_index=chunk_index; - fm->last_chunk_info=chunk_info; + fm->last_index = chunk_index; + fm->last_chunk_info = chunk_info; } /* end else */ - /* Get the coordinates of the element in the chunk */ + /* Get the offset of the element within the chunk */ for(u = 0; u < fm->f_ndims; u++) - coords_in_chunk[u] = coords[u] % fm->layout->u.chunk.dim[u]; + coords_in_chunk[u] = coords[u] - chunk_info->coords[u]; /* Add point to file selection for chunk */ if(H5S_select_elements(chunk_info->fspace, H5S_SELECT_APPEND, (size_t)1, coords_in_chunk) < 0) @@ -1669,8 +1692,8 @@ done: htri_t H5D__chunk_cacheable(const H5D_io_info_t *io_info, haddr_t caddr, hbool_t write_op) { - const H5D_t *dataset = io_info->dset; - htri_t ret_value = FAIL; + const H5D_t *dataset = io_info->dset; /* Local pointer to dataset info */ + htri_t ret_value = FAIL; /* Return value */ FUNC_ENTER_PACKAGE @@ -1815,8 +1838,7 @@ H5D__chunk_read(H5D_io_info_t *io_info, const H5D_type_info_t *type_info, chunk_info = H5D_CHUNK_GET_NODE_INFO(fm, chunk_node); /* Get the info for the chunk in the file */ - if(H5D__chunk_lookup(io_info->dset, io_info->dxpl_id, - chunk_info->coords, chunk_info->index, &udata) < 0) + if(H5D__chunk_lookup(io_info->dset, io_info->dxpl_id, chunk_info->coords, chunk_info->index, &udata) < 0) HGOTO_ERROR(H5E_DATASET, H5E_CANTGET, FAIL, "error looking up chunk address") /* Check for non-existant chunk & skip it if appropriate */ @@ -1945,8 +1967,7 @@ H5D__chunk_write(H5D_io_info_t *io_info, const H5D_type_info_t *type_info, /* Load the chunk into cache. But if the whole chunk is written, * simply allocate space instead of load the chunk. */ - if(H5D__chunk_lookup(io_info->dset, io_info->dxpl_id, chunk_info->coords, - chunk_info->index, &udata) < 0) + if(H5D__chunk_lookup(io_info->dset, io_info->dxpl_id, chunk_info->coords, chunk_info->index, &udata) < 0) HGOTO_ERROR(H5E_DATASET, H5E_CANTGET, FAIL, "error looking up chunk address") if((cacheable = H5D__chunk_cacheable(io_info, udata.addr, TRUE)) < 0) HGOTO_ERROR(H5E_DATASET, H5E_CANTGET, FAIL, "can't tell if chunk is cacheable") @@ -2296,7 +2317,7 @@ done: *------------------------------------------------------------------------- */ herr_t -H5D__chunk_create(H5D_t *dset /*in,out*/, hid_t dxpl_id) +H5D__chunk_create(const H5D_t *dset /*in,out*/, hid_t dxpl_id) { H5D_chk_idx_info_t idx_info; /* Chunked index info */ herr_t ret_value = SUCCEED; /* Return value */ @@ -2777,7 +2798,7 @@ void * H5D__chunk_lock(const H5D_io_info_t *io_info, H5D_chunk_ud_t *udata, hbool_t relax) { - H5D_t *dset = io_info->dset; /* Local pointer to the dataset info */ + const H5D_t *dset = io_info->dset; /* Local pointer to the dataset info */ const H5O_pline_t *pline = &(dset->shared->dcpl_cache.pline); /* I/O pipeline info - always equal to the pline passed to H5D__chunk_alloc */ const H5O_layout_t *layout = &(dset->shared->layout); /* Dataset layout */ const H5O_fill_t *fill = &(dset->shared->dcpl_cache.fill); /* Fill value info */ @@ -3216,7 +3237,7 @@ done: *------------------------------------------------------------------------- */ herr_t -H5D__chunk_allocate(H5D_t *dset, hid_t dxpl_id, hbool_t full_overwrite, +H5D__chunk_allocate(const H5D_t *dset, hid_t dxpl_id, hbool_t full_overwrite, hsize_t old_dim[]) { H5D_chk_idx_info_t idx_info; /* Chunked index info */ @@ -3417,8 +3438,7 @@ H5D__chunk_allocate(H5D_t *dset, hid_t dxpl_id, hbool_t full_overwrite, &chunk_idx) < 0) HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "can't get chunk index") - if(H5D__chunk_lookup(dset, dxpl_id, chunk_offset, chunk_idx, - &udata) < 0) + if(H5D__chunk_lookup(dset, dxpl_id, chunk_offset, chunk_idx, &udata) < 0) HGOTO_ERROR(H5E_DATASET, H5E_CANTGET, FAIL, "error looking up chunk address") HDassert(!H5F_addr_defined(udata.addr)); @@ -3583,7 +3603,7 @@ static herr_t H5D__chunk_prune_fill(H5D_chunk_it_ud1_t *udata) { const H5D_io_info_t *io_info = udata->io_info; /* Local pointer to I/O info */ - H5D_t *dset = io_info->dset; /* Local pointer to the dataset info */ + const H5D_t *dset = io_info->dset; /* Local pointer to the dataset info */ const H5O_layout_t *layout = &(dset->shared->layout); /* Dataset's layout */ unsigned rank = udata->common.layout->ndims - 1; /* Dataset rank */ const hsize_t *chunk_offset = io_info->store->chunk.offset; /* Chunk offset */ @@ -3605,8 +3625,7 @@ H5D__chunk_prune_fill(H5D_chunk_it_ud1_t *udata) H5_ASSIGN_OVERFLOW(chunk_size, layout->u.chunk.size, uint32_t, size_t); /* Get the info for the chunk in the file */ - if(H5D__chunk_lookup(dset, io_info->dxpl_id, chunk_offset, - io_info->store->chunk.index, &chk_udata) < 0) + if(H5D__chunk_lookup(dset, io_info->dxpl_id, chunk_offset, io_info->store->chunk.index, &chk_udata) < 0) HGOTO_ERROR(H5E_DATASET, H5E_CANTGET, FAIL, "error looking up chunk address") /* If this chunk does not exist in cache or on disk, no need to do anything @@ -4015,8 +4034,7 @@ H5D__chunk_prune_by_extent(H5D_t *dset, hid_t dxpl_id, const hsize_t *old_dim) #endif /* NDEBUG */ /* Check if the chunk exists in cache or on disk */ - if(H5D__chunk_lookup(dset, dxpl_id, chunk_offset, - chk_io_info.store->chunk.index, &chk_udata) < 0) + if(H5D__chunk_lookup(dset, dxpl_id, chunk_offset, chk_io_info.store->chunk.index, &chk_udata) < 0) HGOTO_ERROR(H5E_DATASET, H5E_CANTGET, FAIL, "error looking up chunk") /* Evict the entry from the cache if present, but do not flush @@ -4155,7 +4173,7 @@ herr_t H5D__chunk_addrmap(const H5D_io_info_t *io_info, haddr_t chunk_addr[]) { H5D_chk_idx_info_t idx_info; /* Chunked index info */ - H5D_t *dset = io_info->dset; /* Local pointer to dataset info */ + const H5D_t *dset = io_info->dset; /* Local pointer to dataset info */ H5D_chunk_it_ud2_t udata; /* User data for iteration callback */ herr_t ret_value = SUCCEED; /* Return value */ diff --git a/src/H5Dcompact.c b/src/H5Dcompact.c index 0b34c07..789beab 100644 --- a/src/H5Dcompact.c +++ b/src/H5Dcompact.c @@ -117,7 +117,7 @@ H5FL_BLK_EXTERN(type_conv); *------------------------------------------------------------------------- */ herr_t -H5D__compact_fill(H5D_t *dset, hid_t dxpl_id) +H5D__compact_fill(const H5D_t *dset, hid_t dxpl_id) { H5D_fill_buf_info_t fb_info; /* Dataset's fill buffer info */ hbool_t fb_info_init = FALSE; /* Whether the fill value buffer has been initialized */ diff --git a/src/H5Dcontig.c b/src/H5Dcontig.c index 69db7d4..8d4cd02 100644 --- a/src/H5Dcontig.c +++ b/src/H5Dcontig.c @@ -192,7 +192,7 @@ done: *------------------------------------------------------------------------- */ herr_t -H5D__contig_fill(H5D_t *dset, hid_t dxpl_id) +H5D__contig_fill(const H5D_t *dset, hid_t dxpl_id) { H5D_io_info_t ioinfo; /* Dataset I/O info */ H5D_storage_t store; /* Union of storage info for dataset */ diff --git a/src/H5Dint.c b/src/H5Dint.c index af81244..c55609a 100644 --- a/src/H5Dint.c +++ b/src/H5Dint.c @@ -67,7 +67,7 @@ static herr_t H5D__init_space(H5F_t *file, const H5D_t *dset, const H5S_t *space static herr_t H5D__update_oh_info(H5F_t *file, hid_t dxpl_id, H5D_t *dset, hid_t dapl_id); static herr_t H5D__open_oid(H5D_t *dataset, hid_t dapl_id, hid_t dxpl_id); -static herr_t H5D__init_storage(H5D_t *dataset, hbool_t full_overwrite, +static herr_t H5D__init_storage(const H5D_t *dataset, hbool_t full_overwrite, hsize_t old_dim[], hid_t dxpl_id); @@ -1587,7 +1587,7 @@ H5D_typeof(const H5D_t *dset) *------------------------------------------------------------------------- */ herr_t -H5D__alloc_storage(H5D_t *dset/*in,out*/, hid_t dxpl_id, H5D_time_alloc_t time_alloc, +H5D__alloc_storage(const H5D_t *dset, hid_t dxpl_id, H5D_time_alloc_t time_alloc, hbool_t full_overwrite, hsize_t old_dim[]) { H5F_t *f = dset->oloc.file; /* The dataset's file pointer */ @@ -1750,7 +1750,7 @@ done: *------------------------------------------------------------------------- */ static herr_t -H5D__init_storage(H5D_t *dset, hbool_t full_overwrite, hsize_t old_dim[], +H5D__init_storage(const H5D_t *dset, hbool_t full_overwrite, hsize_t old_dim[], hid_t dxpl_id) { herr_t ret_value = SUCCEED; /* Return value */ @@ -2372,7 +2372,7 @@ done: *------------------------------------------------------------------------- */ herr_t -H5D__mark(H5D_t *dataset, hid_t UNUSED dxpl_id, unsigned flags) +H5D__mark(const H5D_t *dataset, hid_t UNUSED dxpl_id, unsigned flags) { herr_t ret_value = SUCCEED; /* Return value */ diff --git a/src/H5Dio.c b/src/H5Dio.c index e4ea7af..b717ee0 100644 --- a/src/H5Dio.c +++ b/src/H5Dio.c @@ -53,7 +53,11 @@ /********************/ /* Setup/teardown routines */ -static herr_t H5D__ioinfo_init(H5D_t *dset, const H5D_dxpl_cache_t *dxpl_cache, +static herr_t H5D__ioinfo_init(H5D_t *dset, +#ifndef H5_HAVE_PARALLEL +const +#endif /* H5_HAVE_PARALLEL */ + H5D_dxpl_cache_t *dxpl_cache, hid_t dxpl_id, const H5D_type_info_t *type_info, H5D_storage_t *store, H5D_io_info_t *io_info); static herr_t H5D__typeinfo_init(const H5D_t *dset, const H5D_dxpl_cache_t *dxpl_cache, @@ -255,14 +259,15 @@ H5D__pre_write(H5D_t *dset, hid_t mem_type_id, const H5S_t *mem_space, /* Get the dataset transfer property list */ if(NULL == (plist = (H5P_genplist_t *)H5I_object(dxpl_id))) HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "not a dataset transfer property list") + /* Retrieve the 'direct write' flag */ if(H5P_get(plist, H5D_XFER_DIRECT_CHUNK_WRITE_FLAG_NAME, &direct_write) < 0) HGOTO_ERROR(H5E_PLIST, H5E_CANTGET, FAIL, "error getting flag for direct chunk write") /* Direct chunk write */ if(direct_write) { - uint32_t direct_filters = 0; + uint32_t direct_filters; hsize_t *direct_offset; - size_t direct_datasize = 0; + uint32_t direct_datasize; int ndims = 0; hsize_t dims[H5O_LAYOUT_NDIMS]; hsize_t internal_offset[H5O_LAYOUT_NDIMS]; @@ -271,12 +276,11 @@ H5D__pre_write(H5D_t *dset, hid_t mem_type_id, const H5S_t *mem_space, if(H5D_CHUNKED != dset->shared->layout.type) HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "not a chunked dataset") + /* Retrieve parameters for direct chunk write */ if(H5P_get(plist, H5D_XFER_DIRECT_CHUNK_WRITE_FILTERS_NAME, &direct_filters) < 0) HGOTO_ERROR(H5E_PLIST, H5E_CANTGET, FAIL, "error getting filter info for direct chunk write") - if(H5P_get(plist, H5D_XFER_DIRECT_CHUNK_WRITE_OFFSET_NAME, &direct_offset) < 0) HGOTO_ERROR(H5E_PLIST, H5E_CANTGET, FAIL, "error getting offset info for direct chunk write") - if(H5P_get(plist, H5D_XFER_DIRECT_CHUNK_WRITE_DATASIZE_NAME, &direct_datasize) < 0) HGOTO_ERROR(H5E_PLIST, H5E_CANTGET, FAIL, "error getting data size for direct chunk write") @@ -285,7 +289,7 @@ H5D__pre_write(H5D_t *dset, hid_t mem_type_id, const H5S_t *mem_space, if((ndims = H5S_get_simple_extent_dims(dset->shared->space, dims, NULL)) < 0) HGOTO_ERROR(H5E_DATASPACE, H5E_CANTGET, FAIL, "can't retrieve dataspace extent dims") - for(i=0; i<ndims; i++) { + for(i = 0; i < ndims; i++) { /* Make sure the offset doesn't exceed the dataset's dimensions */ if(direct_offset[i] > dims[i]) HGOTO_ERROR(H5E_DATASPACE, H5E_BADTYPE, FAIL, "offset exceeds dimensions of dataset") @@ -295,7 +299,7 @@ H5D__pre_write(H5D_t *dset, hid_t mem_type_id, const H5S_t *mem_space, HGOTO_ERROR(H5E_DATASPACE, H5E_BADTYPE, FAIL, "offset doesn't fall on chunks's boundary") internal_offset[i] = direct_offset[i]; - } + } /* end for */ /* Terminate the offset with a zero */ internal_offset[ndims] = 0; @@ -303,7 +307,8 @@ H5D__pre_write(H5D_t *dset, hid_t mem_type_id, const H5S_t *mem_space, /* write raw data */ if(H5D__chunk_direct_write(dset, dxpl_id, direct_filters, internal_offset, direct_datasize, buf) < 0) HGOTO_ERROR(H5E_DATASET, H5E_WRITEERROR, FAIL, "can't write chunk directly") - } else { /* Normal write */ + } /* end if */ + else { /* Normal write */ /* write raw data */ if(H5D__write(dset, mem_type_id, mem_space, file_space, dxpl_id, buf) < 0) HGOTO_ERROR(H5E_DATASET, H5E_WRITEERROR, FAIL, "can't write data") @@ -418,7 +423,7 @@ H5D__read(H5D_t *dataset, hid_t mem_type_id, const H5S_t *mem_space, /* Attempt to construct projected dataspace for memory dataspace */ if(H5S_select_construct_projection(mem_space, &projected_mem_space, - (unsigned)H5S_GET_EXTENT_NDIMS(file_space), buf, &adj_buf, type_info.dst_type_size) < 0) + (unsigned)H5S_GET_EXTENT_NDIMS(file_space), buf, (const void **)&adj_buf, type_info.dst_type_size) < 0) HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "unable to construct projected memory dataspace") HDassert(projected_mem_space); HDassert(adj_buf); @@ -644,7 +649,7 @@ H5D__write(H5D_t *dataset, hid_t mem_type_id, const H5S_t *mem_space, /* Attempt to construct projected dataspace for memory dataspace */ if(H5S_select_construct_projection(mem_space, &projected_mem_space, - (unsigned)H5S_GET_EXTENT_NDIMS(file_space), buf, &adj_buf, type_info.src_type_size) < 0) + (unsigned)H5S_GET_EXTENT_NDIMS(file_space), buf, (const void **)&adj_buf, type_info.src_type_size) < 0) HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "unable to construct projected memory dataspace") HDassert(projected_mem_space); HDassert(adj_buf); @@ -771,7 +776,11 @@ done: *------------------------------------------------------------------------- */ static herr_t -H5D__ioinfo_init(H5D_t *dset, const H5D_dxpl_cache_t *dxpl_cache, hid_t dxpl_id, +H5D__ioinfo_init(H5D_t *dset, +#ifndef H5_HAVE_PARALLEL +const +#endif /* H5_HAVE_PARALLEL */ + H5D_dxpl_cache_t *dxpl_cache, hid_t dxpl_id, const H5D_type_info_t *type_info, H5D_storage_t *store, H5D_io_info_t *io_info) { FUNC_ENTER_STATIC_NOERR diff --git a/src/H5Dmpio.c b/src/H5Dmpio.c index 3b5bb30..c294e42 100644 --- a/src/H5Dmpio.c +++ b/src/H5Dmpio.c @@ -157,12 +157,9 @@ H5D__mpio_opt_possible(const H5D_io_info_t *io_info, const H5S_t *file_space, const H5S_t *mem_space, const H5D_type_info_t *type_info, const H5D_chunk_map_t *fm, H5P_genplist_t *dx_plist) { - /* variables to set cause of broken collective I/O */ - int local_cause = 0; - int global_cause = 0; - - int mpi_code; /* MPI error code */ - htri_t ret_value = TRUE; + int local_cause = 0; /* Local reason(s) for breaking collective mode */ + int global_cause = 0; /* Global reason(s) for breaking collective mode */ + htri_t ret_value; /* Return value */ FUNC_ENTER_PACKAGE @@ -174,51 +171,35 @@ H5D__mpio_opt_possible(const H5D_io_info_t *io_info, const H5S_t *file_space, /* For independent I/O, get out quickly and don't try to form consensus */ - if(io_info->dxpl_cache->xfer_mode == H5FD_MPIO_INDEPENDENT) { - local_cause = H5D_MPIO_SET_INDEPENDENT; - global_cause = H5D_MPIO_SET_INDEPENDENT; - HGOTO_DONE(FALSE); - } - - /* Optimized MPI types flag must be set and it must be collective IO */ - /* (Don't allow parallel I/O for the MPI-posix driver, since it doesn't do real collective I/O) */ - if(!(H5S_mpi_opt_types_g && io_info->dxpl_cache->xfer_mode == H5FD_MPIO_COLLECTIVE - && !IS_H5FD_MPIPOSIX(io_info->dset->oloc.file))) { - local_cause |= H5D_MPIO_SET_MPIPOSIX; - } /* end if */ + if(io_info->dxpl_cache->xfer_mode == H5FD_MPIO_INDEPENDENT) + local_cause |= H5D_MPIO_SET_INDEPENDENT; + + /* Optimized MPI types flag must be set */ + /* (based on 'HDF5_MPI_OPT_TYPES' environment variable) */ + if(!H5FD_mpi_opt_types_g) + local_cause |= H5D_MPIO_MPI_OPT_TYPES_ENV_VAR_DISABLED; /* Don't allow collective operations if datatype conversions need to happen */ - if(!type_info->is_conv_noop) { + if(!type_info->is_conv_noop) local_cause |= H5D_MPIO_DATATYPE_CONVERSION; - } /* end if */ /* Don't allow collective operations if data transform operations should occur */ - if(!type_info->is_xform_noop) { + if(!type_info->is_xform_noop) local_cause |= H5D_MPIO_DATA_TRANSFORMS; - } /* end if */ /* Check whether these are both simple or scalar dataspaces */ if(!((H5S_SIMPLE == H5S_GET_EXTENT_TYPE(mem_space) || H5S_SCALAR == H5S_GET_EXTENT_TYPE(mem_space)) - && (H5S_SIMPLE == H5S_GET_EXTENT_TYPE(file_space) || H5S_SCALAR == H5S_GET_EXTENT_TYPE(file_space)))) { + && (H5S_SIMPLE == H5S_GET_EXTENT_TYPE(file_space) || H5S_SCALAR == H5S_GET_EXTENT_TYPE(file_space)))) local_cause |= H5D_MPIO_NOT_SIMPLE_OR_SCALAR_DATASPACES; - } /* end if */ - - /* Can't currently handle point selections */ - if(H5S_SEL_POINTS == H5S_GET_SELECT_TYPE(mem_space) - || H5S_SEL_POINTS == H5S_GET_SELECT_TYPE(file_space)) { - local_cause |= H5D_MPIO_POINT_SELECTIONS; - } /* end if */ /* Dataset storage must be contiguous or chunked */ if(!(io_info->dset->shared->layout.type == H5D_CONTIGUOUS || - io_info->dset->shared->layout.type == H5D_CHUNKED)) { + io_info->dset->shared->layout.type == H5D_CHUNKED)) local_cause |= H5D_MPIO_NOT_CONTIGUOUS_OR_CHUNKED_DATASET; - } /* end if */ /* check if external-file storage is used */ - if (io_info->dset->shared->dcpl_cache.efl.nused > 0) { + if(io_info->dset->shared->dcpl_cache.efl.nused > 0) local_cause |= H5D_MPIO_NOT_CONTIGUOUS_OR_CHUNKED_DATASET; - } /* The handling of memory space is different for chunking and contiguous * storage. For contiguous storage, mem_space and file_space won't change @@ -228,22 +209,23 @@ H5D__mpio_opt_possible(const H5D_io_info_t *io_info, const H5S_t *file_space, */ /* Don't allow collective operations if filters need to be applied */ - if(io_info->dset->shared->layout.type == H5D_CHUNKED) { - if(io_info->dset->shared->dcpl_cache.pline.nused > 0) { - local_cause |= H5D_MPIO_FILTERS; - } /* end if */ - } /* end if */ + if(io_info->dset->shared->layout.type == H5D_CHUNKED && + io_info->dset->shared->dcpl_cache.pline.nused > 0) + local_cause |= H5D_MPIO_FILTERS; - /* Form consensus opinion among all processes about whether to perform - * collective I/O - */ - if(MPI_SUCCESS != (mpi_code = MPI_Allreduce(&local_cause, &global_cause, 1, MPI_INT, MPI_BOR, io_info->comm))) - HMPI_GOTO_ERROR(FAIL, "MPI_Allreduce failed", mpi_code) - - ret_value = global_cause > 0 ? FALSE : TRUE; + /* Check for independent I/O */ + if(local_cause & H5D_MPIO_SET_INDEPENDENT) + global_cause = local_cause; + else { + int mpi_code; /* MPI error code */ + /* Form consensus opinion among all processes about whether to perform + * collective I/O + */ + if(MPI_SUCCESS != (mpi_code = MPI_Allreduce(&local_cause, &global_cause, 1, MPI_INT, MPI_BOR, io_info->comm))) + HMPI_GOTO_ERROR(FAIL, "MPI_Allreduce failed", mpi_code) + } /* end else */ -done: /* Write the local value of no-collective-cause to the DXPL. */ if(H5P_set(dx_plist, H5D_MPIO_LOCAL_NO_COLLECTIVE_CAUSE_NAME, &local_cause) < 0) HGOTO_ERROR(H5E_PLIST, H5E_CANTSET, FAIL, "couldn't set local no collective cause property") @@ -252,6 +234,10 @@ done: if(H5P_set(dx_plist, H5D_MPIO_GLOBAL_NO_COLLECTIVE_CAUSE_NAME, &global_cause) < 0) HGOTO_ERROR(H5E_PLIST, H5E_CANTSET, FAIL, "couldn't set global no collective cause property") + /* Set the return value, based on the global cause */ + ret_value = global_cause > 0 ? FALSE : TRUE; + +done: FUNC_LEAVE_NOAPI(ret_value) } /* H5D__mpio_opt_possible() */ @@ -946,15 +932,58 @@ if(H5DEBUG(D)) /* Obtain MPI derived datatype from all individual chunks */ for(u = 0; u < num_chunk; u++) { - /* Disk MPI derived datatype */ + hsize_t *permute_map = NULL; /* array that holds the mapping from the old, + out-of-order displacements to the in-order + displacements of the MPI datatypes of the + point selection of the file space */ + hbool_t is_permuted = FALSE; + + /* Obtain disk and memory MPI derived datatype */ + /* NOTE: The permute_map array can be allocated within H5S_mpio_space_type + * and will be fed into the next call to H5S_mpio_space_type + * where it will be freed. + */ if(H5S_mpio_space_type(chunk_addr_info_array[u].chunk_info.fspace, - type_info->src_type_size, &chunk_ftype[u], &chunk_mpi_file_counts[u], &(chunk_mft_is_derived_array[u])) < 0) + type_info->src_type_size, + &chunk_ftype[u], /* OUT: datatype created */ + &chunk_mpi_file_counts[u], /* OUT */ + &(chunk_mft_is_derived_array[u]), /* OUT */ + TRUE, /* this is a file space, + so permute the + datatype if the point + selections are out of + order */ + &permute_map,/* OUT: a map to indicate the + permutation of points + selected in case they + are out of order */ + &is_permuted /* OUT */) < 0) HGOTO_ERROR(H5E_DATASPACE, H5E_BADTYPE, FAIL, "couldn't create MPI file type") - - /* Buffer MPI derived datatype */ + /* Sanity check */ + if(is_permuted) + HDassert(permute_map); if(H5S_mpio_space_type(chunk_addr_info_array[u].chunk_info.mspace, - type_info->dst_type_size, &chunk_mtype[u], &chunk_mpi_mem_counts[u], &(chunk_mbt_is_derived_array[u])) < 0) + type_info->dst_type_size, &chunk_mtype[u], + &chunk_mpi_mem_counts[u], + &(chunk_mbt_is_derived_array[u]), + FALSE, /* this is a memory + space, so if the file + space is not + permuted, there is no + need to permute the + datatype if the point + selections are out of + order*/ + &permute_map, /* IN: the permutation map + generated by the + file_space selection + and applied to the + memory selection */ + &is_permuted /* IN */) < 0) HGOTO_ERROR(H5E_DATASPACE, H5E_BADTYPE, FAIL, "couldn't create MPI buf type") + /* Sanity check */ + if(is_permuted) + HDassert(!permute_map); /* Chunk address relative to the first chunk */ chunk_addr_info_array[u].chunk_addr -= ctg_store.contig.dset_addr; @@ -1309,12 +1338,51 @@ H5D__inter_collective_io(H5D_io_info_t *io_info, const H5D_type_info_t *type_inf if((file_space != NULL) && (mem_space != NULL)) { int mpi_file_count; /* Number of file "objects" to transfer */ + hsize_t *permute_map = NULL; /* array that holds the mapping from the old, + out-of-order displacements to the in-order + displacements of the MPI datatypes of the + point selection of the file space */ + hbool_t is_permuted = FALSE; /* Obtain disk and memory MPI derived datatype */ - if(H5S_mpio_space_type(file_space, type_info->src_type_size, &mpi_file_type, &mpi_file_count, &mft_is_derived) < 0) + /* NOTE: The permute_map array can be allocated within H5S_mpio_space_type + * and will be fed into the next call to H5S_mpio_space_type + * where it will be freed. + */ + if(H5S_mpio_space_type(file_space, type_info->src_type_size, + &mpi_file_type, &mpi_file_count, &mft_is_derived, /* OUT: datatype created */ + TRUE, /* this is a file space, so + permute the datatype if the + point selection is out of + order */ + &permute_map, /* OUT: a map to indicate + the permutation of + points selected in + case they are out of + order */ + &is_permuted /* OUT */) < 0) HGOTO_ERROR(H5E_DATASPACE, H5E_BADTYPE, FAIL, "couldn't create MPI file type") - if(H5S_mpio_space_type(mem_space, type_info->src_type_size, &mpi_buf_type, &mpi_buf_count, &mbt_is_derived) < 0) + /* Sanity check */ + if(is_permuted) + HDassert(permute_map); + if(H5S_mpio_space_type(mem_space, type_info->src_type_size, + &mpi_buf_type, &mpi_buf_count, &mbt_is_derived, /* OUT: datatype created */ + FALSE, /* this is a memory space, so if + the file space is not + permuted, there is no need to + permute the datatype if the + point selections are out of + order*/ + &permute_map /* IN: the permutation map + generated by the + file_space selection + and applied to the + memory selection */, + &is_permuted /* IN */) < 0) HGOTO_ERROR(H5E_DATASPACE, H5E_BADTYPE, FAIL, "couldn't create MPI buffer type") + /* Sanity check */ + if(is_permuted) + HDassert(!permute_map); } /* end if */ else { /* For non-selection, participate with a none MPI derived datatype, the count is 0. */ diff --git a/src/H5Dpkg.h b/src/H5Dpkg.h index bc862dd..6e8ca09 100644 --- a/src/H5Dpkg.h +++ b/src/H5Dpkg.h @@ -187,7 +187,7 @@ typedef enum H5D_io_op_type_t { } H5D_io_op_type_t; typedef struct H5D_io_info_t { - H5D_t *dset; /* Pointer to dataset being operated on */ + const H5D_t *dset; /* Pointer to dataset being operated on */ #ifndef H5_HAVE_PARALLEL const #endif /* H5_HAVE_PARALLEL */ @@ -532,7 +532,7 @@ H5_DLL H5D_t *H5D__create_named(const H5G_loc_t *loc, const char *name, hid_t dapl_id, hid_t dxpl_id); H5_DLL herr_t H5D__get_space_status(H5D_t *dset, H5D_space_status_t *allocation, hid_t dxpl_id); -H5_DLL herr_t H5D__alloc_storage(H5D_t *dset, hid_t dxpl_id, H5D_time_alloc_t time_alloc, +H5_DLL herr_t H5D__alloc_storage(const H5D_t *dset, hid_t dxpl_id, H5D_time_alloc_t time_alloc, hbool_t full_overwrite, hsize_t old_dim[]); H5_DLL herr_t H5D__get_storage_size(H5D_t *dset, hid_t dxpl_id, hsize_t *storage_size); H5_DLL haddr_t H5D__get_offset(const H5D_t *dset); @@ -545,7 +545,7 @@ H5_DLL herr_t H5D__check_filters(H5D_t *dataset); H5_DLL herr_t H5D__set_extent(H5D_t *dataset, const hsize_t *size, hid_t dxpl_id); H5_DLL herr_t H5D__get_dxpl_cache(hid_t dxpl_id, H5D_dxpl_cache_t **cache); H5_DLL herr_t H5D__flush_sieve_buf(H5D_t *dataset, hid_t dxpl_id); -H5_DLL herr_t H5D__mark(H5D_t *dataset, hid_t dxpl_id, unsigned flags); +H5_DLL herr_t H5D__mark(const H5D_t *dataset, hid_t dxpl_id, unsigned flags); H5_DLL herr_t H5D__flush_real(H5D_t *dataset, hid_t dxpl_id); /* Functions that perform direct serial I/O operations */ @@ -582,7 +582,7 @@ H5_DLL herr_t H5D__layout_oh_write(H5D_t *dataset, hid_t dxpl_id, H5O_t *oh, H5_DLL herr_t H5D__contig_alloc(H5F_t *f, hid_t dxpl_id, H5O_storage_contig_t *storage); H5_DLL hbool_t H5D__contig_is_space_alloc(const H5O_storage_t *storage); -H5_DLL herr_t H5D__contig_fill(H5D_t *dset, hid_t dxpl_id); +H5_DLL herr_t H5D__contig_fill(const H5D_t *dset, hid_t dxpl_id); H5_DLL herr_t H5D__contig_read(H5D_io_info_t *io_info, const H5D_type_info_t *type_info, hsize_t nelmts, const H5S_t *file_space, const H5S_t *mem_space, H5D_chunk_map_t *fm); @@ -599,7 +599,7 @@ H5_DLL herr_t H5D__contig_delete(H5F_t *f, hid_t dxpl_id, /* Functions that operate on chunked dataset storage */ H5_DLL htri_t H5D__chunk_cacheable(const H5D_io_info_t *io_info, haddr_t caddr, hbool_t write_op); -H5_DLL herr_t H5D__chunk_create(H5D_t *dset /*in,out*/, hid_t dxpl_id); +H5_DLL herr_t H5D__chunk_create(const H5D_t *dset /*in,out*/, hid_t dxpl_id); H5_DLL herr_t H5D__chunk_set_info(const H5D_t *dset); H5_DLL herr_t H5D__chunk_init(H5F_t *f, hid_t dxpl_id, const H5D_t *dset, hid_t dapl_id); @@ -612,7 +612,7 @@ H5_DLL herr_t H5D__chunk_unlock(const H5D_io_info_t *io_info, const H5D_chunk_ud_t *udata, hbool_t dirty, void *chunk, uint32_t naccessed); H5_DLL herr_t H5D__chunk_allocated(H5D_t *dset, hid_t dxpl_id, hsize_t *nbytes); -H5_DLL herr_t H5D__chunk_allocate(H5D_t *dset, hid_t dxpl_id, +H5_DLL herr_t H5D__chunk_allocate(const H5D_t *dset, hid_t dxpl_id, hbool_t full_overwrite, hsize_t old_dim[]); H5_DLL herr_t H5D__chunk_prune_by_extent(H5D_t *dset, hid_t dxpl_id, const hsize_t *old_dim); @@ -630,12 +630,14 @@ H5_DLL herr_t H5D__chunk_dump_index(H5D_t *dset, hid_t dxpl_id, FILE *stream); H5_DLL herr_t H5D__chunk_dest(H5F_t *f, hid_t dxpl_id, H5D_t *dset); H5_DLL herr_t H5D__chunk_delete(H5F_t *f, hid_t dxpl_id, H5O_t *oh, H5O_storage_t *store); +H5_DLL herr_t H5D__chunk_direct_write(const H5D_t *dset, hid_t dxpl_id, uint32_t filters, + hsize_t *offset, uint32_t data_size, const void *buf); #ifdef H5D_CHUNK_DEBUG H5_DLL herr_t H5D__chunk_stats(const H5D_t *dset, hbool_t headers); #endif /* H5D_CHUNK_DEBUG */ /* Functions that operate on compact dataset storage */ -H5_DLL herr_t H5D__compact_fill(H5D_t *dset, hid_t dxpl_id); +H5_DLL herr_t H5D__compact_fill(const H5D_t *dset, hid_t dxpl_id); H5_DLL herr_t H5D__compact_copy(H5F_t *f_src, H5O_storage_compact_t *storage_src, H5F_t *f_dst, H5O_storage_compact_t *storage_dst, H5T_t *src_dtype, H5O_copy_t *cpy_info, hid_t dxpl_id); diff --git a/src/H5Dprivate.h b/src/H5Dprivate.h index fe26137..faa10c2 100644 --- a/src/H5Dprivate.h +++ b/src/H5Dprivate.h @@ -187,8 +187,5 @@ H5_DLL herr_t H5D_chunk_idx_reset(H5O_storage_chunk_t *storage, hbool_t reset_ad H5_DLL herr_t H5D_btree_debug(H5F_t *f, hid_t dxpl_id, haddr_t addr, FILE * stream, int indent, int fwidth, unsigned ndims); -H5_DLL herr_t H5D__chunk_direct_write(const H5D_t *dset, hid_t dxpl_id, uint32_t filters, - hsize_t *offset, size_t data_size, const void *buf); - #endif /* _H5Dprivate_H */ diff --git a/src/H5FDmpi.h b/src/H5FDmpi.h index dcb8df9..784fe70 100644 --- a/src/H5FDmpi.h +++ b/src/H5FDmpi.h @@ -57,7 +57,6 @@ typedef enum H5FD_mpio_collective_opt_t { /* Include all the MPI VFL headers */ #include "H5FDmpio.h" /* MPI I/O file driver */ -#include "H5FDmpiposix.h" /* MPI/posix I/O file driver */ #endif /* H5FDmpi_H */ diff --git a/src/H5FDmpio.c b/src/H5FDmpio.c index f23a3b5..d4b8fdc 100644 --- a/src/H5FDmpio.c +++ b/src/H5FDmpio.c @@ -44,6 +44,10 @@ */ static hid_t H5FD_MPIO_g = 0; +/* Whether to allow collective I/O operations */ +/* (Value can be set from environment variable also) */ +hbool_t H5FD_mpi_opt_types_g = TRUE; + /* * The view is set to this value */ @@ -189,51 +193,54 @@ H5FD_mpio_init_interface(void) * library. * * Return: Success: The driver ID for the mpio driver. - * * Failure: Negative. * * Programmer: Robb Matzke * Thursday, August 5, 1999 * - * Modifications: - * *------------------------------------------------------------------------- */ hid_t H5FD_mpio_init(void) { #ifdef H5FDmpio_DEBUG - static int H5FD_mpio_Debug_inited=0; + static int H5FD_mpio_Debug_inited = 0; #endif /* H5FDmpio_DEBUG */ + const char *s; /* String for environment variables */ hid_t ret_value; /* Return value */ FUNC_ENTER_NOAPI(FAIL) - if (H5I_VFL!=H5I_get_type(H5FD_MPIO_g)) - H5FD_MPIO_g = H5FD_register((const H5FD_class_t *)&H5FD_mpio_g,sizeof(H5FD_class_mpi_t),FALSE); + /* Register the MPI-IO VFD, if it isn't already */ + if(H5I_VFL != H5I_get_type(H5FD_MPIO_g)) + H5FD_MPIO_g = H5FD_register((const H5FD_class_t *)&H5FD_mpio_g, sizeof(H5FD_class_mpi_t), FALSE); + + /* Allow MPI buf-and-file-type optimizations? */ + s = HDgetenv("HDF5_MPI_OPT_TYPES"); + if(s && HDisdigit(*s)) + H5FD_mpi_opt_types_g = (hbool_t)HDstrtol(s, NULL, 0); #ifdef H5FDmpio_DEBUG - if (!H5FD_mpio_Debug_inited) - { - /* set debug mask */ - /* Should this be done in H5F global initialization instead of here? */ - const char *s = HDgetenv ("H5FD_mpio_Debug"); - if (s) { - while (*s){ + if(!H5FD_mpio_Debug_inited) { + /* Retrieve MPI-IO debugging environment variable */ + s = HDgetenv("H5FD_mpio_Debug"); + if(s) { + /* Set debug mask */ + while(*s) { H5FD_mpio_Debug[(int)*s]++; s++; - } - } + } /* end while */ + } /* end if */ H5FD_mpio_Debug_inited++; - } + } /* end if */ #endif /* H5FDmpio_DEBUG */ /* Set return value */ - ret_value=H5FD_MPIO_g; + ret_value = H5FD_MPIO_g; done: FUNC_LEAVE_NOAPI(ret_value) -} +} /* end H5FD_mpio_init() */ /*--------------------------------------------------------------------------- diff --git a/src/H5FDmpio.h b/src/H5FDmpio.h index d836086..858e8ba 100644 --- a/src/H5FDmpio.h +++ b/src/H5FDmpio.h @@ -22,14 +22,14 @@ #ifndef H5FDmpio_H #define H5FDmpio_H +/* Macros */ + #ifdef H5_HAVE_PARALLEL # define H5FD_MPIO (H5FD_mpio_init()) #else # define H5FD_MPIO (-1) #endif /* H5_HAVE_PARALLEL */ -/* Macros */ - #ifdef H5_HAVE_PARALLEL /*Turn on H5FDmpio_debug if H5F_DEBUG is on */ #ifdef H5F_DEBUG @@ -38,6 +38,10 @@ #endif #endif +/* Global var whose value comes from environment variable */ +/* (Defined in H5FDmpio.c) */ +H5_DLLVAR hbool_t H5FD_mpi_opt_types_g; + /* Function prototypes */ #ifdef __cplusplus extern "C" { diff --git a/src/H5FDmpiposix.c b/src/H5FDmpiposix.c deleted file mode 100644 index 7248dff..0000000 --- a/src/H5FDmpiposix.c +++ /dev/null @@ -1,1488 +0,0 @@ -/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * - * Copyright by The HDF Group. * - * Copyright by the Board of Trustees of the University of Illinois. * - * All rights reserved. * - * * - * This file is part of HDF5. The full HDF5 copyright notice, including * - * terms governing use, modification, and redistribution, is contained in * - * the files COPYING and Copyright.html. COPYING can be found at the root * - * of the source code distribution tree; Copyright.html can be found at the * - * root level of an installed copy of the electronic HDF5 document set and * - * is linked from the top-level documents page. It can also be found at * - * http://hdfgroup.org/HDF5/doc/Copyright.html. If you do not have * - * access to either file, you may request a copy from help@hdfgroup.org. * - * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */ - -/* - * Programmer: Quincey Koziol <koziol@hdfgroup.org> - * Thursday, July 11, 2002 - * - * Purpose: This is a "combination" MPI-2 and posix I/O driver. - * It uses MPI for coordinating the actions of several processes - * and posix I/O calls to do the actual I/O to the disk. - * - * This driver was derived from the H5FDmpio.c driver and may - * share bugs/quirks/etc. - * - * Limitations: - * There is no "collective" I/O mode with this driver. - * - * This will almost certainly _not_ work correctly for files - * accessed on distributed parallel systems with the file located - * on a non-parallel filesystem. - * - */ - -/* Interface initialization */ -#define H5_INTERFACE_INIT_FUNC H5FD_mpiposix_init_interface - - -#include "H5private.h" /* Generic Functions */ -#include "H5ACprivate.h" /* Metadata cache */ -#include "H5Eprivate.h" /* Error handling */ -#include "H5Fprivate.h" /* File access */ -#include "H5FDprivate.h" /* File drivers */ -#include "H5FDmpi.h" /* MPI-based file drivers */ -#include "H5Iprivate.h" /* IDs */ -#include "H5MMprivate.h" /* Memory management */ -#include "H5Pprivate.h" /* Property lists */ - -/* Features: - * H5_HAVE_GPFS -- issue gpfs_fcntl() calls to hopefully improve - * performance when accessing files on a GPFS - * file system. - * - * REPORT_IO -- if set then report all POSIX file calls to stderr. - * - */ -/* #define REPORT_IO */ - -#ifdef H5_HAVE_GPFS -# include <gpfs_fcntl.h> -#endif - -#ifdef H5_HAVE_PARALLEL - -/* - * The driver identification number, initialized at runtime if H5_HAVE_PARALLEL - * is defined. This allows applications to still have the H5FD_MPIPOSIX - * "constants" in their source code (it also makes this file strictly ANSI - * compliant when H5_HAVE_PARALLEL isn't defined) - */ -static hid_t H5FD_MPIPOSIX_g = 0; - -/* - * The description of a file belonging to this driver. - * The EOF value is only used just after the file is opened in order for the - * library to determine whether the file is empty, truncated, or okay. The - * MPIPOSIX driver doesn't bother to keep it updated since it's an expensive - * operation. - */ -typedef struct H5FD_mpiposix_t { - H5FD_t pub; /* public stuff, must be first */ - int fd; /* the unix file handle */ - MPI_Comm comm; /* communicator */ - int mpi_rank; /* This process's rank */ - int mpi_size; /* Total number of processes */ - haddr_t eof; /* end-of-file marker */ - haddr_t eoa; /* end-of-address marker */ - haddr_t last_eoa; /* Last known end-of-address marker */ - haddr_t pos; /* Current file I/O position */ - H5FD_file_op_t op; /* Last file I/O operation */ - hsize_t naccess; /* Number of (write) accesses to file */ -#ifdef H5_HAVE_GPFS - size_t blksize; /* Block size of file system */ -#endif - hbool_t use_gpfs; /* Use GPFS to write things */ -#ifndef H5_HAVE_WIN32_API - /* On most systems the combination of device and i-node number uniquely - * identify a file. Note that Cygwin, MinGW and other Windows POSIX - * environments have the stat function (which fakes inodes) - * and will use the 'device + inodes' scheme as opposed to the - * Windows code further below. - */ - dev_t device; /* file device number */ -#ifdef H5_VMS - ino_t inode[3]; /* file i-node number */ -#else - ino_t inode; /* file i-node number */ -#endif /* H5_VMS */ -#else - /* Files in windows are uniquely identified by the volume serial - * number and the file index (both low and high parts). - * - * There are caveats where these numbers can change, especially - * on FAT file systems. On NTFS, however, a file should keep - * those numbers the same until renamed or deleted (though you - * can use ReplaceFile() on NTFS to keep the numbers the same - * while renaming). - * - * See the MSDN "BY_HANDLE_FILE_INFORMATION Structure" entry for - * more information. - * - * http://msdn.microsoft.com/en-us/library/aa363788(v=VS.85).aspx - */ - DWORD nFileIndexLow; - DWORD nFileIndexHigh; - DWORD dwVolumeSerialNumber; - - HANDLE hFile; /* Native windows file handle */ -#endif /* H5_HAVE_WIN32_API */ -} H5FD_mpiposix_t; - -/* - * These macros check for overflow of various quantities. These macros - * assume that HDoff_t is signed and haddr_t and size_t are unsigned. - * - * ADDR_OVERFLOW: Checks whether a file address of type `haddr_t' - * is too large to be represented by the second argument - * of the file seek function. - * - * SIZE_OVERFLOW: Checks whether a buffer size of type `hsize_t' is too - * large to be represented by the `size_t' type. - * - * REGION_OVERFLOW: Checks whether an address and size pair describe data - * which can be addressed entirely by the second - * argument of the file seek function. - */ -#define MAXADDR (((haddr_t)1 << (8*sizeof(HDoff_t) - 1)) - 1) -#define ADDR_OVERFLOW(A) (HADDR_UNDEF == (A) || ((A) & ~(haddr_t)MAXADDR)) -#define SIZE_OVERFLOW(Z) ((Z) & ~(hsize_t)MAXADDR) -#define REGION_OVERFLOW(A,Z) (ADDR_OVERFLOW(A) || SIZE_OVERFLOW(Z) || \ - HADDR_UNDEF == (A) + (Z) || \ - (HDoff_t)((A) + (Z)) < (HDoff_t)(A)) - -/* Callbacks */ -static herr_t H5FD_mpiposix_term(void); -static void *H5FD_mpiposix_fapl_get(H5FD_t *_file); -static void *H5FD_mpiposix_fapl_copy(const void *_old_fa); -static herr_t H5FD_mpiposix_fapl_free(void *_fa); -static H5FD_t *H5FD_mpiposix_open(const char *name, unsigned flags, hid_t fapl_id, - haddr_t maxaddr); -static herr_t H5FD_mpiposix_close(H5FD_t *_file); -static int H5FD_mpiposix_cmp(const H5FD_t *_f1, const H5FD_t *_f2); -static herr_t H5FD_mpiposix_query(const H5FD_t *_f1, unsigned long *flags); -static haddr_t H5FD_mpiposix_get_eoa(const H5FD_t *_file, H5FD_mem_t UNUSED type); -static herr_t H5FD_mpiposix_set_eoa(H5FD_t *_file, H5FD_mem_t type, haddr_t addr); -static haddr_t H5FD_mpiposix_get_eof(const H5FD_t *_file); -static herr_t H5FD_mpiposix_get_handle(H5FD_t *_file, hid_t fapl, void** file_handle); -static herr_t H5FD_mpiposix_read(H5FD_t *_file, H5FD_mem_t type, hid_t fapl_id, haddr_t addr, - size_t size, void *buf); -static herr_t H5FD_mpiposix_write(H5FD_t *_file, H5FD_mem_t type, hid_t fapl_id, haddr_t addr, - size_t size, const void *buf); -static herr_t H5FD_mpiposix_truncate(H5FD_t *_file, hid_t dxpl_id, hbool_t closing); -static int H5FD_mpiposix_mpi_rank(const H5FD_t *_file); -static int H5FD_mpiposix_mpi_size(const H5FD_t *_file); -static MPI_Comm H5FD_mpiposix_communicator(const H5FD_t *_file); - -/* MPIPOSIX-specific file access properties */ -typedef struct H5FD_mpiposix_fapl_t { - hbool_t use_gpfs; /* use GPFS hints */ - MPI_Comm comm; /* communicator */ -} H5FD_mpiposix_fapl_t; - -/* The MPIPOSIX file driver information */ -static const H5FD_class_mpi_t H5FD_mpiposix_g = { - { /* Start of superclass information */ - "mpiposix", /* name */ - MAXADDR, /* maxaddr */ - H5F_CLOSE_SEMI, /* fc_degree */ - H5FD_mpiposix_term, /* terminate */ - NULL, /* sb_size */ - NULL, /* sb_encode */ - NULL, /* sb_decode */ - sizeof(H5FD_mpiposix_fapl_t), /* fapl_size */ - H5FD_mpiposix_fapl_get, /* fapl_get */ - H5FD_mpiposix_fapl_copy, /* fapl_copy */ - H5FD_mpiposix_fapl_free, /* fapl_free */ - 0, /* dxpl_size */ - NULL, /* dxpl_copy */ - NULL, /* dxpl_free */ - H5FD_mpiposix_open, /* open */ - H5FD_mpiposix_close, /* close */ - H5FD_mpiposix_cmp, /* cmp */ - H5FD_mpiposix_query, /* query */ - NULL, /* get_type_map */ - NULL, /* alloc */ - NULL, /* free */ - H5FD_mpiposix_get_eoa, /* get_eoa */ - H5FD_mpiposix_set_eoa, /* set_eoa */ - H5FD_mpiposix_get_eof, /* get_eof */ - H5FD_mpiposix_get_handle, /* get_handle */ - H5FD_mpiposix_read, /* read */ - H5FD_mpiposix_write, /* write */ - NULL, /* flush */ - H5FD_mpiposix_truncate, /* truncate */ - NULL, /* lock */ - NULL, /* unlock */ - H5FD_FLMAP_DICHOTOMY /* fl_map */ - }, /* End of superclass information */ - H5FD_mpiposix_mpi_rank, /* get_rank */ - H5FD_mpiposix_mpi_size, /* get_size */ - H5FD_mpiposix_communicator /* get_comm */ -}; - - -/*------------------------------------------------------------------------- - * Function: H5FD_mpiposix_init_interface - * - * Purpose: Initializes any interface-specific data or routines. - * - * Return: Success: The driver ID for the mpiposix driver. - * Failure: Negative. - * - *------------------------------------------------------------------------- - */ -static herr_t -H5FD_mpiposix_init_interface(void) -{ - FUNC_ENTER_NOAPI_NOINIT_NOERR - - FUNC_LEAVE_NOAPI(H5FD_mpiposix_init()) -} /* H5FD_mpiposix_init_interface() */ - - -/*------------------------------------------------------------------------- - * Function: H5FD_mpiposix_init - * - * Purpose: Initialize this driver by registering the driver with the - * library. - * - * Return: Success: The driver ID for the mpiposix driver. - * Failure: Negative. - * - * Programmer: Quincey Koziol - * Thursday, July 11, 2002 - * - *------------------------------------------------------------------------- - */ -hid_t -H5FD_mpiposix_init(void) -{ - hid_t ret_value = H5FD_MPIPOSIX_g; /* Return value */ - - FUNC_ENTER_NOAPI(FAIL) - - if(H5I_VFL != H5I_get_type(H5FD_MPIPOSIX_g)) - H5FD_MPIPOSIX_g = H5FD_register((const H5FD_class_t *)&H5FD_mpiposix_g, sizeof(H5FD_class_mpi_t), FALSE); - - /* Set return value */ - ret_value = H5FD_MPIPOSIX_g; - -done: - FUNC_LEAVE_NOAPI(ret_value) -} /* end H5FD_mpiposix_init() */ - - -/*--------------------------------------------------------------------------- - * Function: H5FD_mpiposix_term - * - * Purpose: Shut down the VFD - * - * Returns: SUCCEED (can't fail) - * - * Programmer: Quincey Koziol - * Friday, Jan 30, 2004 - * - *--------------------------------------------------------------------------- - */ -static herr_t -H5FD_mpiposix_term(void) -{ - FUNC_ENTER_NOAPI_NOINIT_NOERR - - /* Reset VFL ID */ - H5FD_MPIPOSIX_g = 0; - - FUNC_LEAVE_NOAPI(SUCCEED) -} /* end H5FD_mpiposix_term() */ - - -/*------------------------------------------------------------------------- - * Function: H5Pset_fapl_mpiposix - * - * Purpose: Store the user supplied MPI communicator COMM in - * the file access property list FAPL_ID which can then be used - * to create and/or open the file. This function is available - * only in the parallel HDF5 library and is not collective. - * - * comm is the MPI communicator to be used for file open as - * defined in MPI_FILE_OPEN of MPI-2. This function makes a - * duplicate of comm. Any modification to comm after this function - * call returns has no effect on the access property list. - * - * If fapl_id has previously set comm value, it will be replaced - * and the old communicator is freed. - * - * Return: SUCCEED/FAIL - * - * Programmer: Quincey Koziol - * Thursday, July 11, 2002 - * - *------------------------------------------------------------------------- - */ -herr_t -H5Pset_fapl_mpiposix(hid_t fapl_id, MPI_Comm comm, hbool_t use_gpfs) -{ - H5FD_mpiposix_fapl_t fa; - H5P_genplist_t *plist; /* Property list pointer */ - herr_t ret_value; - - FUNC_ENTER_API(FAIL) - H5TRACE3("e", "iMcb", fapl_id, comm, use_gpfs); - - /* Check arguments */ - if(NULL == (plist = H5P_object_verify(fapl_id,H5P_FILE_ACCESS))) - HGOTO_ERROR(H5E_PLIST, H5E_BADTYPE, FAIL, "not a file access list") - if (MPI_COMM_NULL == comm) - HGOTO_ERROR(H5E_PLIST, H5E_BADTYPE, FAIL, "not a valid communicator") - - /* Initialize driver specific properties */ - fa.comm = comm; - fa.use_gpfs = use_gpfs; - - /* duplication is done during driver setting. */ - ret_value = H5P_set_driver(plist, H5FD_MPIPOSIX, &fa); - -done: - FUNC_LEAVE_API(ret_value) -} /* end H5Pset_fapl_mpiposix() */ - - -/*------------------------------------------------------------------------- - * Function: H5Pget_fapl_mpiposix - * - * Purpose: If the file access property list is set to the H5FD_MPIPOSIX - * driver then this function returns a duplicate of the MPI - * communicator through the comm pointer. It is the responsibility - * of the application to free the returned communicator. - * - * Return: Success: Non-negative with the communicator and - * information returned through the COMM - * argument if non-null. Since it is a duplicate - * of the stored object, future modifications to - * the access property list do not affect it and - * it is the responsibility of the application to - * free it. - * Failure: Negative - * - * Programmer: Quincey Koziol - * Thursday, July 11, 2002 - * - *------------------------------------------------------------------------- - */ -herr_t -H5Pget_fapl_mpiposix(hid_t fapl_id, MPI_Comm *comm/*out*/, hbool_t *use_gpfs/*out*/) -{ - H5FD_mpiposix_fapl_t *fa; - H5P_genplist_t *plist; /* Property list pointer */ - int mpi_code; /* mpi return code */ - herr_t ret_value = SUCCEED; /* Return value */ - - FUNC_ENTER_API(FAIL) - H5TRACE3("e", "ixx", fapl_id, comm, use_gpfs); - - if(NULL == (plist = H5P_object_verify(fapl_id,H5P_FILE_ACCESS))) - HGOTO_ERROR(H5E_PLIST, H5E_BADTYPE, FAIL, "not a file access list") - if (H5FD_MPIPOSIX != H5P_get_driver(plist)) - HGOTO_ERROR(H5E_PLIST, H5E_BADVALUE, FAIL, "incorrect VFL driver") - if (NULL == (fa = H5P_get_driver_info(plist))) - HGOTO_ERROR(H5E_PLIST, H5E_BADVALUE, FAIL, "bad VFL driver info") - - /* Get MPI Communicator */ - if (comm){ - if (MPI_SUCCESS != (mpi_code = MPI_Comm_dup(fa->comm, comm))) - HMPI_GOTO_ERROR(FAIL, "MPI_Comm_dup failed", mpi_code) - } - - if (use_gpfs) - *use_gpfs = fa->use_gpfs; - -done: - FUNC_LEAVE_API(ret_value) -} /* end H5Pget_fapl_mpiposix() */ - - -/*------------------------------------------------------------------------- - * Function: H5FD_mpiposix_fapl_get - * - * Purpose: Returns a file access property list which could be used to - * create another file the same as this one. - * - * Return: Success: Ptr to new file access property list with all - * fields copied from the file pointer. - * Failure: NULL - * - * Programmer: Quincey Koziol - * Thursday, July 11, 2002 - * - *------------------------------------------------------------------------- - */ -static void * -H5FD_mpiposix_fapl_get(H5FD_t *_file) -{ - H5FD_mpiposix_t *file = (H5FD_mpiposix_t*)_file; - H5FD_mpiposix_fapl_t *fa = NULL; - int mpi_code; /* MPI return code */ - void *ret_value; /* Return value */ - - FUNC_ENTER_NOAPI_NOINIT - - HDassert(file); - HDassert(H5FD_MPIPOSIX == file->pub.driver_id); - - if (NULL == (fa = H5MM_calloc(sizeof(H5FD_mpiposix_fapl_t)))) - HGOTO_ERROR(H5E_RESOURCE, H5E_NOSPACE, NULL, "memory allocation failed") - - /* Duplicate the communicator. */ - if (MPI_SUCCESS != (mpi_code=MPI_Comm_dup(file->comm, &fa->comm))) - HMPI_GOTO_ERROR(NULL, "MPI_Comm_dup failed", mpi_code) - - fa->use_gpfs = file->use_gpfs; - - /* Set return value */ - ret_value=fa; - -done: - FUNC_LEAVE_NOAPI(ret_value) -} /* end H5FD_mpiposix_fapl_get() */ - - -/*------------------------------------------------------------------------- - * Function: H5FD_mpiposix_fapl_copy - * - * Purpose: Copies the mpiposix-specific file access properties. - * - * Return: Success: Ptr to a new property list - * Failure: NULL - * - * Programmer: Albert Cheng - * Apr 24, 2003 - * - *------------------------------------------------------------------------- - */ -static void * -H5FD_mpiposix_fapl_copy(const void *_old_fa) -{ - void *ret_value = NULL; - const H5FD_mpiposix_fapl_t *old_fa = (const H5FD_mpiposix_fapl_t*)_old_fa; - H5FD_mpiposix_fapl_t *new_fa = NULL; - int mpi_code; /* MPI return code */ - - FUNC_ENTER_NOAPI_NOINIT - - if (NULL == (new_fa = H5MM_malloc(sizeof(H5FD_mpiposix_fapl_t)))) - HGOTO_ERROR(H5E_RESOURCE, H5E_NOSPACE, NULL, "memory allocation failed") - - /* Copy the general information */ - HDmemcpy(new_fa, old_fa, sizeof(H5FD_mpiposix_fapl_t)); - - /* Duplicate communicator. */ - if (MPI_SUCCESS != (mpi_code = MPI_Comm_dup(old_fa->comm, &new_fa->comm))) - HMPI_GOTO_ERROR(NULL, "MPI_Comm_dup failed", mpi_code) - - new_fa->use_gpfs = old_fa->use_gpfs; - ret_value = new_fa; - -done: - if (NULL == ret_value){ - /* cleanup */ - if (new_fa) - H5MM_xfree(new_fa); - } - - FUNC_LEAVE_NOAPI(ret_value) -} /* end H5FD_mpiposix_fapl_copy() */ - - -/*------------------------------------------------------------------------- - * Function: H5FD_mpiposix_fapl_free - * - * Purpose: Frees the mpiposix-specific file access properties. - * - * Return: SUCCEED (can't fail) - * - * Programmer: Albert Cheng - * Apr 24, 2003 - * - *------------------------------------------------------------------------- - */ -static herr_t -H5FD_mpiposix_fapl_free(void *_fa) -{ - H5FD_mpiposix_fapl_t *fa = (H5FD_mpiposix_fapl_t*)_fa; - - FUNC_ENTER_NOAPI_NOINIT_NOERR - - HDassert(fa); - - /* Free the internal communicator */ - HDassert(MPI_COMM_NULL != fa->comm); - MPI_Comm_free(&fa->comm); - H5MM_xfree(fa); - - FUNC_LEAVE_NOAPI(SUCCEED) -} /* end H5FD_mpiposix_fapl_free() */ - - -/*------------------------------------------------------------------------- - * Function: H5FD_mpiposix_open - * - * Purpose: Opens a file with name NAME. The FLAGS are a bit field with - * purpose similar to the second argument of open(2) and which - * are defined in H5Fpublic.h. The file access property list - * FAPL_ID contains the properties driver properties and MAXADDR - * is the largest address which this file will be expected to - * access. This is collective. - * - * Return: Success: A new file pointer. - * Failure: NULL - * - * Programmer: Quincey Koziol - * Thursday, July 11, 2002 - * - *------------------------------------------------------------------------- - */ -static H5FD_t * -H5FD_mpiposix_open(const char *name, unsigned flags, hid_t fapl_id, - haddr_t maxaddr) -{ - H5FD_mpiposix_t *file = NULL; /* New MPIPOSIX file struct */ - int o_flags; /* Flags for file open call */ - int fd = -1; /* File handle for file opened */ - int mpi_rank; /* MPI rank of this process */ - int mpi_size; /* Total number of MPI processes */ - int mpi_code; /* mpi return code */ - const H5FD_mpiposix_fapl_t *fa = NULL; /* MPIPOSIX file access property list information */ - H5FD_mpiposix_fapl_t _fa; /* Private copy of default file access property list information */ - H5P_genplist_t *plist; /* Property list pointer */ - h5_stat_t sb; /* Portable 'stat' struct */ -#ifdef H5_HAVE_WIN32_API - struct _BY_HANDLE_FILE_INFORMATION fileinfo; -#endif - H5FD_t *ret_value = NULL; /* Return value */ - MPI_Comm comm_dup = MPI_COMM_NULL; - - FUNC_ENTER_NOAPI_NOINIT - - /* Check arguments */ - if (!name || !*name) - HGOTO_ERROR(H5E_ARGS, H5E_BADVALUE, NULL, "invalid file name") - if (0 == maxaddr || HADDR_UNDEF == maxaddr) - HGOTO_ERROR(H5E_ARGS, H5E_BADRANGE, NULL, "bogus maxaddr") - if (ADDR_OVERFLOW(maxaddr)) - HGOTO_ERROR(H5E_ARGS, H5E_OVERFLOW, NULL, "bogus maxaddr") - - /* Obtain a pointer to mpiposix-specific file access properties */ - if(NULL == (plist = H5P_object_verify(fapl_id,H5P_FILE_ACCESS))) - HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, NULL, "not a file access property list") - if (H5P_FILE_ACCESS_DEFAULT == fapl_id || H5FD_MPIPOSIX != H5P_get_driver(plist)) { - _fa.comm = MPI_COMM_SELF; /*default*/ - _fa.use_gpfs = FALSE; - fa = &_fa; - } /* end if */ - else { - if(NULL == (fa = (const H5FD_mpiposix_fapl_t *)H5P_get_driver_info(plist))) - HGOTO_ERROR(H5E_PLIST, H5E_BADVALUE, NULL, "bad VFL driver info") - } /* end else */ - - /* Duplicate the communicator for use by this file. */ - if (MPI_SUCCESS != (mpi_code = MPI_Comm_dup(fa->comm, &comm_dup))) - HMPI_GOTO_ERROR(NULL, "MPI_Comm_dup failed", mpi_code) - - /* Get the MPI rank of this process and the total number of processes */ - if (MPI_SUCCESS != (mpi_code = MPI_Comm_rank (comm_dup, &mpi_rank))) - HMPI_GOTO_ERROR(NULL, "MPI_Comm_rank failed", mpi_code) - if (MPI_SUCCESS != (mpi_code = MPI_Comm_size (comm_dup, &mpi_size))) - HMPI_GOTO_ERROR(NULL, "MPI_Comm_size failed", mpi_code) - - /* Build the open flags */ - o_flags = (H5F_ACC_RDWR & flags) ? O_RDWR : O_RDONLY; - - /* Only set the creation flag(s) for process 0 */ - if(0 == mpi_rank) { - if (H5F_ACC_TRUNC & flags) - o_flags |= O_TRUNC; - if (H5F_ACC_CREAT & flags) - o_flags |= O_CREAT; - if (H5F_ACC_EXCL & flags) - o_flags |= O_EXCL; - } /* end if */ - - /* Process 0 opens (or creates) the file while the rest of the - * processes wait. Then process 0 signals the other processes and they - * open (never create) the file and all processes proceed. - */ - /* Process 0 opens (or creates) file and broadcasts result to other processes */ - if(0 == mpi_rank) { - /* Open the file */ - fd = HDopen(name, o_flags, 0666); - } /* end if */ - - /* Broadcast the results of the open() from process 0 - * - * This is necessary because of the "tentative open" code in H5F_open() - * where the file is attempted to be opened with different flags from the - * user's, in order to check for the file's existence, etc. Here, process 0 - * gets different flags from the other processes (since it is in charge of - * creating the file, if necessary) and can fail in situations where the - * other process's file opens would succeed, so allow the other processes - * to check for that situation and bail out now also. - QAK - */ - if (MPI_SUCCESS != (mpi_code= MPI_Bcast(&fd, sizeof(int), MPI_BYTE, 0, comm_dup))) - HMPI_GOTO_ERROR(NULL, "MPI_Bcast failed", mpi_code) - - /* If the file open on process 0 failed, bail out on all processes now */ - if(fd < 0) - HGOTO_ERROR(H5E_FILE, H5E_CANTOPENFILE, NULL, "unable to open file") - - /* Other processes (non 0) wait for broadcast result from process 0 and then open file */ - if(mpi_rank != 0) { - /* Open the file */ - if ((fd = HDopen(name, o_flags, 0666)) < 0) - HGOTO_ERROR(H5E_FILE, H5E_CANTOPENFILE, NULL, "unable to open file") - } /* end if */ - - /* Process 0 fstat()s the file and broadcasts the results to the other processes */ - if(0 == mpi_rank) { - /* Get the stat information */ - if (HDfstat(fd, &sb) < 0) - HGOTO_ERROR(H5E_FILE, H5E_BADFILE, NULL, "unable to fstat file") - } /* end if */ - - /* Broadcast the results of the fstat() from process 0 */ - if (MPI_SUCCESS != (mpi_code = MPI_Bcast(&sb, sizeof(h5_stat_t), MPI_BYTE, 0, comm_dup))) - HMPI_GOTO_ERROR(NULL, "MPI_Bcast failed", mpi_code) - -#ifdef H5_HAVE_GPFS - if (fa->use_gpfs) { - /* - * Free all byte range tokens. This is a good thing to do if raw data - * is aligned on 256kB boundaries (a GPFS page is 256kB). Care should - * be taken that there aren't too many sub-page writes, or the mmfsd - * may become overwhelmed. This should probably eventually be passed - * down here as a property. The gpfs_fcntl() will most likely fail if - * 'fd' isn't on a GPFS file system. */ - struct { - gpfsFcntlHeader_t hdr; - gpfsFreeRange_t fr; - } hint; - HDmemset(&hint, 0, sizeof hint); - hint.hdr.totalLength = sizeof hint; - hint.hdr.fcntlVersion = GPFS_FCNTL_CURRENT_VERSION; - hint.fr.structLen = sizeof hint.fr; - hint.fr.structType = GPFS_FREE_RANGE; - hint.fr.start = 0; - hint.fr.length = 0; - - if (gpfs_fcntl(fd, &hint) < 0) - HGOTO_ERROR(H5E_FILE, H5E_FCNTL, NULL, "failed to send hints to GPFS") - } -#endif /* H5_HAVE_GPFS */ - - /* Build the file struct and initialize it */ - if (NULL == (file=H5MM_calloc(sizeof(H5FD_mpiposix_t)))) - HGOTO_ERROR(H5E_RESOURCE, H5E_NOSPACE, NULL, "memory allocation failed") - -#ifdef REPORT_IO - HDfprintf(stderr, "open: rank=%d name=%s file=0x%08lx\n", mpi_rank, name, (unsigned long)file); -#endif - - /* Set the general file information */ - file->fd = fd; - file->eof = sb.st_size; - - /* for H5_HAVE_WIN32_API support. H5_HAVE_WIN32_API 'stat' does not have - * st_blksize and st_blksize is only used for the H5_HAVE_GPFS case. - */ -#ifdef H5_HAVE_GPFS - file->blksize = sb.st_blksize; -#endif - - /* Set this field in the H5FD_mpiposix_t struct for later use */ - file->use_gpfs = fa->use_gpfs; - - /* Set the MPI information */ - file->comm = comm_dup; - file->mpi_rank = mpi_rank; - file->mpi_size = mpi_size; - - /* Reset the last file I/O operation */ - file->pos = HADDR_UNDEF; - file->op = OP_UNKNOWN; - - /* Set the information for the file's device and inode */ -#ifdef H5_HAVE_WIN32_API - file->hFile = (HANDLE)_get_osfhandle(fd); - if(INVALID_HANDLE_VALUE == file->hFile) - HGOTO_ERROR(H5E_FILE, H5E_CANTOPENFILE, NULL, "unable to get Windows file handle") - - if(!GetFileInformationByHandle((HANDLE)file->hFile, &fileinfo)) - HGOTO_ERROR(H5E_FILE, H5E_CANTOPENFILE, NULL, "unable to get Windows file information") - - file->nFileIndexHigh = fileinfo.nFileIndexHigh; - file->nFileIndexLow = fileinfo.nFileIndexLow; - file->dwVolumeSerialNumber = fileinfo.dwVolumeSerialNumber; -#else /* H5_HAVE_WIN32_API */ - file->device = sb.st_dev; -#ifdef H5_VMS - file->inode[0] = sb.st_ino[0]; - file->inode[1] = sb.st_ino[1]; - file->inode[2] = sb.st_ino[2]; -#else /* H5_VMS */ - file->inode = sb.st_ino; -#endif /* H5_VMS */ -#endif /* H5_HAVE_WIN32_API */ - - /* Indicate success */ - ret_value = (H5FD_t *)file; - -done: - /* Error cleanup */ - if(NULL == ret_value) { - /* Close the file if it was left open */ - if(fd != -1) - HDclose(fd); - if (MPI_COMM_NULL != comm_dup) - MPI_Comm_free(&comm_dup); - } /* end if */ - - FUNC_LEAVE_NOAPI(ret_value) -} /* end H5FD_mpiposix_open() */ - - -/*------------------------------------------------------------------------- - * Function: H5FD_mpiposix_close - * - * Purpose: Closes a file. - * - * Return: SUCCEED/FAIL - * - * Programmer: Quincey Koziol - * Thursday, July 11, 2002 - * - *------------------------------------------------------------------------- - */ -static herr_t -H5FD_mpiposix_close(H5FD_t *_file) -{ - H5FD_mpiposix_t *file = (H5FD_mpiposix_t*)_file; - herr_t ret_value = SUCCEED; /* Return value */ - - FUNC_ENTER_NOAPI_NOINIT - - HDassert(file); - HDassert(H5FD_MPIPOSIX == file->pub.driver_id); - - /* Close the unix file */ - if(HDclose(file->fd) < 0) - HGOTO_ERROR(H5E_IO, H5E_CANTCLOSEFILE, FAIL, "unable to close file") - - /* make sure all processes have closed the file before returning. */ - MPI_Barrier(file->comm); - /* Clean up other stuff */ - MPI_Comm_free(&file->comm); - H5MM_xfree(file); - -done: - FUNC_LEAVE_NOAPI(ret_value) -} /* end H5FD_mpiposix_close() */ - - -/*------------------------------------------------------------------------- - * Function: H5FD_mpiposix_cmp - * - * Purpose: Compares two files belonging to this driver using an - * arbitrary (but consistent) ordering. - * - * Return: Success: A value like strcmp() - * Failure: never fails (arguments were checked by the caller). - * - * Programmer: Quincey Koziol - * Thursday, July 11, 2002 - * - *------------------------------------------------------------------------- - */ -static int -H5FD_mpiposix_cmp(const H5FD_t *_f1, const H5FD_t *_f2) -{ - const H5FD_mpiposix_t *f1 = (const H5FD_mpiposix_t*)_f1; - const H5FD_mpiposix_t *f2 = (const H5FD_mpiposix_t*)_f2; - int ret_value = 0; - - FUNC_ENTER_NOAPI_NOINIT_NOERR - -#ifdef H5_HAVE_WIN32_API - if(f1->dwVolumeSerialNumber < f2->dwVolumeSerialNumber) HGOTO_DONE(-1) - if(f1->dwVolumeSerialNumber > f2->dwVolumeSerialNumber) HGOTO_DONE(1) - - if(f1->nFileIndexHigh < f2->nFileIndexHigh) HGOTO_DONE(-1) - if(f1->nFileIndexHigh > f2->nFileIndexHigh) HGOTO_DONE(1) - - if(f1->nFileIndexLow < f2->nFileIndexLow) HGOTO_DONE(-1) - if(f1->nFileIndexLow > f2->nFileIndexLow) HGOTO_DONE(1) -#else /* H5_HAVE_WIN32_API */ -#ifdef H5_DEV_T_IS_SCALAR - if(f1->device < f2->device) HGOTO_DONE(-1) - if(f1->device > f2->device) HGOTO_DONE(1) -#else /* H5_DEV_T_IS_SCALAR */ - /* If dev_t isn't a scalar value on this system, just use memcmp to - * determine if the values are the same or not. The actual return value - * shouldn't really matter... - */ - if(HDmemcmp(&(f1->device),&(f2->device),sizeof(dev_t)) < 0) HGOTO_DONE(-1) - if(HDmemcmp(&(f1->device),&(f2->device),sizeof(dev_t)) > 0) HGOTO_DONE(1) -#endif /* H5_DEV_T_IS_SCALAR */ -#ifdef H5_VMS - if(HDmemcmp(&(f1->inode), &(f2->inode), 3 * sizeof(ino_t)) < 0) HGOTO_DONE(-1) - if(HDmemcmp(&(f1->inode), &(f2->inode), 3 * sizeof(ino_t)) > 0) HGOTO_DONE(1) -#else /* H5_VMS */ - if(f1->inode < f2->inode) HGOTO_DONE(-1) - if(f1->inode > f2->inode) HGOTO_DONE(1) -#endif /* H5_VMS */ -#endif /* H5_HAVE_WIN32_API */ - -done: - FUNC_LEAVE_NOAPI(ret_value) -} /* end H5FD_mpiposix_cmp() */ - - -/*------------------------------------------------------------------------- - * Function: H5FD_mpiposix_query - * - * Purpose: Set the flags that this VFL driver is capable of supporting. - * (listed in H5FDpublic.h) - * - * Return: SUCCEED (can't fail) - * - * Programmer: Quincey Koziol - * Thursday, July 11, 2002 - * - *------------------------------------------------------------------------- - */ -static herr_t -H5FD_mpiposix_query(const H5FD_t UNUSED *_file, unsigned long *flags /* out */) -{ - FUNC_ENTER_NOAPI_NOINIT_NOERR - - /* Set the VFL feature flags that this driver supports */ - if(flags) { - *flags=0; - *flags |= H5FD_FEAT_AGGREGATE_METADATA; /* OK to aggregate metadata allocations */ - *flags |= H5FD_FEAT_AGGREGATE_SMALLDATA; /* OK to aggregate "small" raw data allocations */ - *flags |= H5FD_FEAT_HAS_MPI; /* This driver uses MPI */ - *flags |= H5FD_FEAT_ALLOCATE_EARLY; /* Allocate space early instead of late */ - } /* end if */ - - FUNC_LEAVE_NOAPI(SUCCEED) -} /* end H5FD_mpiposix_query() */ - - -/*------------------------------------------------------------------------- - * Function: H5FD_mpiposix_get_eoa - * - * Purpose: Gets the end-of-address marker for the file. The EOA marker - * is the first address past the last byte allocated in the - * format address space. - * - * Return: Success: The end-of-address marker. - * Failure: HADDR_UNDEF - * - * Programmer: Quincey Koziol - * Thursday, July 11, 2002 - * - *------------------------------------------------------------------------- - */ -static haddr_t -H5FD_mpiposix_get_eoa(const H5FD_t *_file, H5FD_mem_t UNUSED type) -{ - const H5FD_mpiposix_t *file = (const H5FD_mpiposix_t*)_file; - - FUNC_ENTER_NOAPI_NOINIT_NOERR - - HDassert(file); - HDassert(H5FD_MPIPOSIX == file->pub.driver_id); - - FUNC_LEAVE_NOAPI(file->eoa) -} /* end H5FD_mpiposix_get_eoa() */ - - -/*------------------------------------------------------------------------- - * Function: H5FD_mpiposix_set_eoa - * - * Purpose: Set the end-of-address marker for the file. This function is - * called shortly after an existing HDF5 file is opened in order - * to tell the driver where the end of the HDF5 data is located. - * - * Return: SUCCEED (can't fail) - * - * Programmer: Quincey Koziol - * Thursday, July 11, 2002 - * - *------------------------------------------------------------------------- - */ -static herr_t -H5FD_mpiposix_set_eoa(H5FD_t *_file, H5FD_mem_t UNUSED type, haddr_t addr) -{ - H5FD_mpiposix_t *file = (H5FD_mpiposix_t*)_file; - - FUNC_ENTER_NOAPI_NOINIT_NOERR - - HDassert(file); - HDassert(H5FD_MPIPOSIX == file->pub.driver_id); - - file->eoa = addr; - - FUNC_LEAVE_NOAPI(SUCCEED) -} /* end H5FD_mpi_posix_set_eoa() */ - - -/*------------------------------------------------------------------------- - * Function: H5FD_mpiposix_get_eof - * - * Purpose: Gets the end-of-file marker for the file. The EOF marker - * is the real size of the file. - * - * The MPIPOSIX driver doesn't bother keeping this field updated - * since that's a relatively expensive operation. Fortunately - * the library only needs the EOF just after the file is opened - * in order to determine whether the file is empty, truncated, - * or okay. - * - * Return: Success: The end-of-address marker. - * Failure: HADDR_UNDEF - * - * Programmer: Quincey Koziol - * Thursday, July 11, 2002 - * - *------------------------------------------------------------------------- - */ -static haddr_t -H5FD_mpiposix_get_eof(const H5FD_t *_file) -{ - const H5FD_mpiposix_t *file = (const H5FD_mpiposix_t*)_file; - - FUNC_ENTER_NOAPI_NOINIT_NOERR - - HDassert(file); - HDassert(H5FD_MPIPOSIX == file->pub.driver_id); - - FUNC_LEAVE_NOAPI(MAX(file->eof, file->eoa)) -} /* end H5FD_mpiposix_get_eof() */ - - -/*------------------------------------------------------------------------- - * Function: H5FD_mpiposix_get_handle - * - * Purpose: Returns the file handle of MPI-POSIX file driver. - * - * Returns: SUCCEED/FAIL - * - * Programmer: Raymond Lu - * Sept. 16, 2002 - * - *------------------------------------------------------------------------- - */ -static herr_t -H5FD_mpiposix_get_handle(H5FD_t *_file, hid_t UNUSED fapl, void** file_handle) -{ - H5FD_mpiposix_t *file = (H5FD_mpiposix_t *)_file; - herr_t ret_value = SUCCEED; - - FUNC_ENTER_NOAPI_NOINIT - - if(!file_handle) - HGOTO_ERROR(H5E_ARGS, H5E_BADVALUE, FAIL, "file handle not valid") - - *file_handle = &(file->fd); - -done: - FUNC_LEAVE_NOAPI(ret_value) -} - - -/*------------------------------------------------------------------------- - * Function: H5FD_mpiposix_read - * - * Purpose: Reads SIZE bytes of data from FILE beginning at address ADDR - * into buffer BUF according to data transfer properties in - * DXPL_ID using potentially complex file and buffer types to - * effect the transfer. - * - * Reading past the end of the file returns zeros instead of - * failing. - * - * Return: Success: Non-negative. Result is stored in caller-supplied - * buffer BUF. - * Failure: Negative, Contents of buffer BUF are undefined. - * - * Programmer: Quincey Koziol - * Thursday, July 11, 2002 - * - *------------------------------------------------------------------------- - */ -static herr_t -H5FD_mpiposix_read(H5FD_t *_file, H5FD_mem_t UNUSED type, hid_t UNUSED dxpl_id, - haddr_t addr, size_t size, void *buf/*out*/) -{ - H5FD_mpiposix_t *file = (H5FD_mpiposix_t*)_file; - ssize_t nbytes; /* Number of bytes read each I/O call */ - herr_t ret_value = SUCCEED; - - FUNC_ENTER_NOAPI_NOINIT - - HDassert(file); - HDassert(H5FD_MPIPOSIX == file->pub.driver_id); - HDassert(buf); - - /* Check for overflow conditions */ - if (HADDR_UNDEF == addr) - HGOTO_ERROR(H5E_ARGS, H5E_BADVALUE, FAIL, "addr undefined") - if (REGION_OVERFLOW(addr, size)) - HGOTO_ERROR(H5E_ARGS, H5E_OVERFLOW, FAIL, "addr overflow") - if((addr + size) > file->eoa) - HGOTO_ERROR(H5E_ARGS, H5E_OVERFLOW, FAIL, "addr overflow") - -#ifdef REPORT_IO - { - int commrank; - MPI_Comm_rank(MPI_COMM_WORLD, &commrank); - HDfprintf(stderr, "read: rank=%d file=0x%08lx type=%d, addr=%a size=%Zu\n", - commrank, (unsigned long)file, (int)type, addr, size); - } -#endif - - /* Seek to the correct location */ - if(addr != file->pos || OP_READ != file->op) { - if(HDlseek(file->fd, (HDoff_t)addr, SEEK_SET) < 0) - HGOTO_ERROR(H5E_IO, H5E_SEEKERROR, FAIL, "unable to seek to proper position") - } /* end if */ - - /* Read data, being careful of interrupted system calls, partial results, - * and the end of the file. - */ - 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 */ - - /* Trying to read more bytes than the return type can handle is - * undefined behavior in POSIX. - */ - if(size > H5_POSIX_MAX_IO_BYTES) - bytes_in = H5_POSIX_MAX_IO_BYTES; - else - bytes_in = (h5_posix_io_t)size; - - do { - bytes_read = HDread(file->fd, buf, bytes_in); - } 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, 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->fd, myerrno, HDstrerror(myerrno), buf, (unsigned long long)size, (unsigned long long)bytes_in, (unsigned long long)bytes_read, (unsigned long long)myoffset); - } /* end if */ - - if(0 == bytes_read) { - /* end of file but not end of format address space */ - HDmemset(buf, 0, size); - break; - } /* end if */ - - HDassert(bytes_read >= 0); - HDassert((size_t)bytes_read <= size); - - size -= (size_t)bytes_read; - addr += (haddr_t)bytes_read; - buf = (char *)buf + bytes_read; - } /* end while */ - - /* Update current position */ - file->pos = addr; - file->op = OP_READ; - -done: - /* Check for error */ - if(ret_value < 0) { - /* Reset last file I/O information */ - file->pos = HADDR_UNDEF; - file->op = OP_UNKNOWN; - } /* end if */ - - FUNC_LEAVE_NOAPI(ret_value) -} /* end H5FD_mpiposix_read() */ - - -/*------------------------------------------------------------------------- - * Function: H5FD_mpiposix_write - * - * Purpose: Writes SIZE bytes of data to FILE beginning at address ADDR - * from buffer BUF according to data transfer properties in - * DXPL_ID using potentially complex file and buffer types to - * effect the transfer. - * - * Return: SUCCEED/FAIL - * - * Programmer: Quincey Koziol - * Thursday, July 11, 2002 - * - *------------------------------------------------------------------------- - */ -static herr_t -H5FD_mpiposix_write(H5FD_t *_file, H5FD_mem_t type, hid_t dxpl_id, haddr_t addr, - size_t size, const void *buf) -{ - H5FD_mpiposix_t *file = (H5FD_mpiposix_t*)_file; -#if 0 /* JRM */ - int mpi_code; /* MPI return code */ -#endif /* JRM */ - ssize_t nbytes; /* Number of bytes written each I/O call */ - H5P_genplist_t *plist; /* Property list pointer */ - herr_t ret_value = SUCCEED; /* Return value */ - - FUNC_ENTER_NOAPI_NOINIT - - HDassert(file); - HDassert(H5FD_MPIPOSIX == file->pub.driver_id); - HDassert(H5I_GENPROP_LST == H5I_get_type(dxpl_id)); - HDassert(TRUE == H5P_isa_class(dxpl_id,H5P_DATASET_XFER)); - HDassert(buf); - - /* Check for overflow conditions */ - if (HADDR_UNDEF == addr) - HGOTO_ERROR(H5E_ARGS, H5E_BADVALUE, FAIL, "addr undefined") - if (REGION_OVERFLOW(addr, size)) - HGOTO_ERROR(H5E_ARGS, H5E_OVERFLOW, FAIL, "addr overflow") - if ((addr + size) > file->eoa) - HGOTO_ERROR(H5E_ARGS, H5E_OVERFLOW, FAIL, "addr overflow") - - /* Obtain the data transfer properties */ - if(NULL == (plist = H5I_object(dxpl_id))) - HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "not a file access property list") - - /* Metadata specific actions */ - /* All metadata is now written from process 0 -- thus this function - * needs to be re-written to reflect this. For now I have simply - * commented out the code that attempts to synchronize metadata - * writes between processes, but we should really just flag an error - * whenever any process other than process 0 attempts to write - * metadata. - * -- JRM 9/1/05 - */ - if(type != H5FD_MEM_DRAW) { - unsigned block_before_meta_write = 0; /* Whether to block before a metadata write */ - - /* Check if we need to synchronize all processes before attempting - * metadata write (Prevents race condition where the process writing - * the metadata goes ahead and writes the metadata to the file before - * all the processes have read the data, "transmitting" data from the - * "future" to the reading process. -QAK ) - * - * The only time we don't want to block before a metadata write is when - * we are flushing out a bunch of metadata. Then, we block before the - * first write and don't block for further writes in the sequence. - */ - if(H5P_exist_plist(plist,H5AC_BLOCK_BEFORE_META_WRITE_NAME) > 0) - if(H5P_get(plist,H5AC_BLOCK_BEFORE_META_WRITE_NAME,&block_before_meta_write) < 0) - HGOTO_ERROR(H5E_PLIST, H5E_CANTGET, FAIL, "can't get H5AC property") - -#if 0 /* JRM */ - if(block_before_meta_write) - if (MPI_SUCCESS != (mpi_code = MPI_Barrier(file->comm))) - HMPI_GOTO_ERROR(FAIL, "MPI_Barrier failed", mpi_code) -#endif /* JRM */ - -#if 0 /* JRM -- 3/23/10 */ /* this is no longer always the case */ - /* Only one process will do the actual write if all procs in comm write same metadata */ - if (file->mpi_rank != H5_PAR_META_WRITE) - HGOTO_DONE(SUCCEED) /* skip the actual write */ -#endif /* JRM */ - } /* end if */ - -#ifdef REPORT_IO - { - int commrank; - MPI_Comm_rank(MPI_COMM_WORLD, &commrank); - HDfprintf(stderr, "write: rank=%d file=0x%08lx type=%d, addr=%a size=%Zu %s\n", - commrank, (unsigned long)file, (int)type, addr, size, - 0 == file->naccess ? "(FIRST ACCESS)" : ""); - } -#endif - - if (0 == file->naccess++) { - /* First write access to this file */ -#ifdef H5_HAVE_GPFS - if (file->use_gpfs) { - struct { - gpfsFcntlHeader_t hdr; - gpfsMultipleAccessRange_t mar; - } hint; - HDmemset(&hint, 0, sizeof hint); - hint.hdr.totalLength = sizeof hint; - hint.hdr.fcntlVersion = GPFS_FCNTL_CURRENT_VERSION; - hint.mar.structLen = sizeof hint.mar; - hint.mar.structType = GPFS_MULTIPLE_ACCESS_RANGE; - hint.mar.accRangeCnt = 1; - hint.mar.accRangeArray[0].blockNumber = addr / file->blksize; - hint.mar.accRangeArray[0].start = addr % file->blksize; - hint.mar.accRangeArray[0].length = MIN(file->blksize-hint.mar.accRangeArray[0].start, size); - hint.mar.accRangeArray[0].isWrite = 1; - if (gpfs_fcntl(file->fd, &hint)<0) - HGOTO_ERROR(H5E_FILE, H5E_FCNTL, NULL, "failed to send hints to GPFS") - } -#endif /* H5_HAVE_GPFS */ - } - - /* Seek to the correct location */ - 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 */ - - /* Write data, being careful of interrupted system calls, partial results, - * and the end of the file. - */ - while(size > 0) { - - h5_posix_io_t bytes_in = 0; /* # of bytes to write */ - h5_posix_io_ret_t bytes_wrote = -1; /* # of bytes actually written */ - - /* Trying to write more bytes than the return type can handle is - * undefined behavior in POSIX. - */ - if(size > H5_POSIX_MAX_IO_BYTES) - bytes_in = H5_POSIX_MAX_IO_BYTES; - else - bytes_in = (h5_posix_io_t)size; - - do { - bytes_wrote = HDwrite(file->fd, buf, bytes_in); - } 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_READERROR, FAIL, "file write failed: time = %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->fd, myerrno, HDstrerror(myerrno), buf, (unsigned long long)size, (unsigned long long)bytes_in, (unsigned long long)bytes_wrote, (unsigned long long)myoffset); - } /* end if */ - - if(0 == bytes_wrote) { - /* end of file but not end of format address space */ - HDmemset(buf, 0, size); - break; - } /* end if */ - - HDassert(bytes_wrote >= 0); - HDassert((size_t)bytes_wrote <= size); - - size -= (size_t)bytes_wrote; - addr += (haddr_t)bytes_wrote; - buf = (char *)buf + bytes_wrote; - } /* end while */ - - /* Update current position */ - file->pos = addr; - file->op = OP_WRITE; - -done: - /* Check for error */ - if(ret_value < 0) { - /* Reset last file I/O information */ - file->pos = HADDR_UNDEF; - file->op = OP_UNKNOWN; - } /* end if */ -#if 0 /* JRM */ - /* Since metadata writes are now done by process 0 only, this broadcast - * is no longer needed. I leave it in and commented out to remind us - * that we need to re-work this function to reflect this reallity. - * - * -- JRM 9/1/05 - */ - - /* Guard against getting into metadata broadcast in failure cases */ - else { - /* when only one process writes, need to broadcast the ret_value to other processes */ - if (type != H5FD_MEM_DRAW) { - if (MPI_SUCCESS != (mpi_code= MPI_Bcast(&ret_value, sizeof(ret_value), MPI_BYTE, H5_PAR_META_WRITE, file->comm))) - HMPI_GOTO_ERROR(FAIL, "MPI_Bcast failed", mpi_code) - } /* end if */ - } /* end else */ -#endif /* JRM */ - - FUNC_LEAVE_NOAPI(ret_value) -} /* end H5FD_mpiposix_write() */ - - -/*------------------------------------------------------------------------- - * Function: H5FD_mpiposix_truncate - * - * Purpose: Makes sure that the true file size is the same (or larger) - * than the end-of-address. - * - * Return: SUCCEED/FAIL - * - * Programmer: Quincey Koziol - * Thursday, July 11, 2002 - * - *------------------------------------------------------------------------- - */ -static herr_t -H5FD_mpiposix_truncate(H5FD_t *_file, hid_t UNUSED dxpl_id, hbool_t UNUSED closing) -{ - H5FD_mpiposix_t *file = (H5FD_mpiposix_t*)_file; - herr_t ret_value = SUCCEED; /* Return value */ - int mpi_code; /* MPI return code */ - - FUNC_ENTER_NOAPI_NOINIT - - HDassert(file); - HDassert(H5FD_MPIPOSIX == file->pub.driver_id); - - /* Extend the file to make sure it's large enough */ - if(file->eoa > file->last_eoa) { - /* Use the round-robin process to truncate (extend) the file */ - if(file->mpi_rank == H5_PAR_META_WRITE) { - -#ifdef H5_HAVE_WIN32_API - LARGE_INTEGER li; /* 64-bit (union) integer for SetFilePointer() call */ - DWORD dwPtrLow; /* Low-order pointer bits from SetFilePointer() - * Only used as an error code here. - */ - DWORD dwError; /* DWORD error code from GetLastError() */ - BOOL bError; /* Boolean error flag */ - - /* Windows uses this odd QuadPart union for 32/64-bit portability */ - li.QuadPart = (__int64)file->eoa; - - /* Extend the file to make sure it's large enough. - * - * Since INVALID_SET_FILE_POINTER can technically be a valid return value - * from SetFilePointer(), we also need to check GetLastError(). - */ - dwPtrLow = SetFilePointer(file->hFile, li.LowPart, &li.HighPart, FILE_BEGIN); - if(INVALID_SET_FILE_POINTER == dwPtrLow) { - dwError = GetLastError(); - if(dwError != NO_ERROR ) - HGOTO_ERROR(H5E_FILE, H5E_FILEOPEN, FAIL, "unable to set file pointer") - } - - bError = SetEndOfFile(file->hFile); - if(0 == bError) - HGOTO_ERROR(H5E_IO, H5E_SEEKERROR, FAIL, "unable to extend file properly") -#else /* H5_HAVE_WIN32_API */ -#ifdef H5_VMS - /* Reset seek offset to the beginning of the file, so that the file isn't - * re-extended later. This may happen on Open VMS. */ - if(-1 == HDlseek(file->fd, (HDoff_t)0, SEEK_SET)) - HSYS_GOTO_ERROR(H5E_IO, H5E_SEEKERROR, FAIL, "unable to seek to proper position") -#endif /* H5_VMS */ - if(-1 == HDftruncate(file->fd, (HDoff_t)file->eoa)) - HSYS_GOTO_ERROR(H5E_IO, H5E_SEEKERROR, FAIL, "unable to extend file properly") -#endif /* H5_HAVE_WIN32_API */ - } /* end if */ - - /* Don't let any proc return until all have extended the file. - * (Prevents race condition where some processes go ahead and write - * more data to the file before all the processes have finished making - * it the shorter length, potentially truncating the file and dropping - * the new data written) - */ - if(MPI_SUCCESS != (mpi_code = MPI_Barrier(file->comm))) - HMPI_GOTO_ERROR(FAIL, "MPI_Barrier failed", mpi_code) - - /* Update the 'last' eoa and eof values */ - file->last_eoa = file->eoa; - file->eof = file->eoa; - - /* Reset last file I/O information */ - file->pos = HADDR_UNDEF; - file->op = OP_UNKNOWN; - } /* end if */ - -done: - FUNC_LEAVE_NOAPI(ret_value) -} /* end H5FD_mpiposix_truncate() */ - - -/*------------------------------------------------------------------------- - * Function: H5FD_mpiposix_mpi_rank - * - * Purpose: Returns the MPI rank for a process - * - * Return: MPI rank. Cannot report failure. - * - * Programmer: Quincey Koziol - * Thursday, July 11, 2002 - * - *------------------------------------------------------------------------- - */ -static int -H5FD_mpiposix_mpi_rank(const H5FD_t *_file) -{ - const H5FD_mpiposix_t *file = (const H5FD_mpiposix_t*)_file; - - FUNC_ENTER_NOAPI_NOINIT_NOERR - - HDassert(file); - HDassert(H5FD_MPIPOSIX == file->pub.driver_id); - - FUNC_LEAVE_NOAPI(file->mpi_rank) -} /* end H5FD_mpiposix_mpi_rank() */ - - -/*------------------------------------------------------------------------- - * Function: H5FD_mpiposix_mpi_size - * - * Purpose: Returns the number of MPI processes - * - * Return: The number of MPI processes. Cannot report failure. - * - * Programmer: Quincey Koziol - * Thursday, July 11, 2002 - * - *------------------------------------------------------------------------- - */ -static int -H5FD_mpiposix_mpi_size(const H5FD_t *_file) -{ - const H5FD_mpiposix_t *file = (const H5FD_mpiposix_t*)_file; - - FUNC_ENTER_NOAPI_NOINIT_NOERR - - HDassert(file); - HDassert(H5FD_MPIPOSIX == file->pub.driver_id); - - FUNC_LEAVE_NOAPI(file->mpi_size) -} /* end H5FD_mpiposix_mpi_size() */ - - -/*------------------------------------------------------------------------- - * Function: H5FD_mpiposix_communicator - * - * Purpose: Returns the MPI communicator for the file. - * - * Return: The MPI communicator. Cannot report failure. - * - * Programmer: Quincey Koziol - * Thursday, July 11, 2002 - * - *------------------------------------------------------------------------- - */ -static MPI_Comm -H5FD_mpiposix_communicator(const H5FD_t *_file) -{ - const H5FD_mpiposix_t *file = (const H5FD_mpiposix_t*)_file; - - FUNC_ENTER_NOAPI_NOINIT_NOERR - - HDassert(file); - HDassert(H5FD_MPIPOSIX == file->pub.driver_id); - - FUNC_LEAVE_NOAPI(file->comm) -} /* end H5FD_mpi_posix_communicator() */ - -#endif /*H5_HAVE_PARALLEL*/ diff --git a/src/H5FDmpiposix.h b/src/H5FDmpiposix.h deleted file mode 100644 index 12ff206..0000000 --- a/src/H5FDmpiposix.h +++ /dev/null @@ -1,51 +0,0 @@ -/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * - * Copyright by The HDF Group. * - * Copyright by the Board of Trustees of the University of Illinois. * - * All rights reserved. * - * * - * This file is part of HDF5. The full HDF5 copyright notice, including * - * terms governing use, modification, and redistribution, is contained in * - * the files COPYING and Copyright.html. COPYING can be found at the root * - * of the source code distribution tree; Copyright.html can be found at the * - * root level of an installed copy of the electronic HDF5 document set and * - * is linked from the top-level documents page. It can also be found at * - * http://hdfgroup.org/HDF5/doc/Copyright.html. If you do not have * - * access to either file, you may request a copy from help@hdfgroup.org. * - * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */ - -/* - * Programmer: Quincey Koziol <koziol@hdfgroup.org> - * Thursday, July 11, 2002 - * - * Purpose: The public header file for the mpiposix driver. - */ - -#ifndef __H5FDmpiposix_H -#define __H5FDmpiposix_H - -#ifdef H5_HAVE_PARALLEL -# define H5FD_MPIPOSIX (H5FD_mpiposix_init()) -#else -# define H5FD_MPIPOSIX (-1) -#endif - -/* Macros */ - -#ifdef H5_HAVE_PARALLEL - -/* Function prototypes */ -#ifdef __cplusplus -extern "C" { -#endif - -H5_DLL hid_t H5FD_mpiposix_init(void); -H5_DLL herr_t H5Pset_fapl_mpiposix(hid_t fapl_id, MPI_Comm comm, hbool_t use_gpfs); -H5_DLL herr_t H5Pget_fapl_mpiposix(hid_t fapl_id, MPI_Comm *comm/*out*/, hbool_t *use_gpfs/*out*/); - -#ifdef __cplusplus -} -#endif - -#endif /*H5_HAVE_PARALLEL*/ - -#endif /* __H5FDmpiposix_H */ diff --git a/src/H5FDprivate.h b/src/H5FDprivate.h index 600cae1..6e4df22 100644 --- a/src/H5FDprivate.h +++ b/src/H5FDprivate.h @@ -43,9 +43,6 @@ #define IS_H5FD_MPIO(f) /* (H5F_t *f) */ \ (H5FD_MPIO==H5F_DRIVER_ID(f)) -#define IS_H5FD_MPIPOSIX(f) /* (H5F_t *f) */ \ - (H5FD_MPIPOSIX==H5F_DRIVER_ID(f)) - #ifdef H5_HAVE_PARALLEL /* ======== Temporary data transfer properties ======== */ /* Definitions for memory MPI type property */ diff --git a/src/H5HFman.c b/src/H5HFman.c index 882d2ba..58dab10 100644 --- a/src/H5HFman.c +++ b/src/H5HFman.c @@ -312,12 +312,14 @@ H5HF_man_op_real(H5HF_hdr_t *hdr, hid_t dxpl_id, const uint8_t *id, /* Decode the object offset within the heap & its length */ UINT64DECODE_VAR(id, obj_off, hdr->heap_off_size); UINT64DECODE_VAR(id, obj_len, hdr->heap_len_size); - HDassert(obj_off > 0); - HDassert(obj_len > 0); /* Check for bad offset or length */ + if(obj_off == 0) + HGOTO_ERROR(H5E_HEAP, H5E_BADRANGE, FAIL, "invalid fractal heap offset") if(obj_off > hdr->man_size) HGOTO_ERROR(H5E_HEAP, H5E_BADRANGE, FAIL, "fractal heap object offset too large") + if(obj_len == 0) + HGOTO_ERROR(H5E_HEAP, H5E_BADRANGE, FAIL, "invalid fractal heap object size") if(obj_len > hdr->man_dtable.cparam.max_direct_size) HGOTO_ERROR(H5E_HEAP, H5E_BADRANGE, FAIL, "fractal heap object size too large for direct block") if(obj_len > hdr->max_man_size) diff --git a/src/H5HGdbg.c b/src/H5HGdbg.c index 74044cb..16d8c49 100644 --- a/src/H5HGdbg.c +++ b/src/H5HGdbg.c @@ -91,9 +91,8 @@ H5HG_debug(H5F_t *f, hid_t dxpl_id, haddr_t addr, FILE *stream, int indent, unsigned u, nused, maxobj; unsigned j, k; H5HG_heap_t *h = NULL; - char buf[64]; uint8_t *p = NULL; - herr_t ret_value=SUCCEED; /* Return value */ + herr_t ret_value = SUCCEED; /* Return value */ FUNC_ENTER_NOAPI(FAIL) @@ -107,66 +106,69 @@ H5HG_debug(H5F_t *f, hid_t dxpl_id, haddr_t addr, FILE *stream, int indent, if(NULL == (h = H5HG_protect(f, dxpl_id, addr, H5AC_READ))) HGOTO_ERROR(H5E_HEAP, H5E_CANTPROTECT, FAIL, "unable to protect global heap collection"); - fprintf(stream, "%*sGlobal Heap Collection...\n", indent, ""); - fprintf(stream, "%*s%-*s %d\n", indent, "", fwidth, + HDfprintf(stream, "%*sGlobal Heap Collection...\n", indent, ""); + HDfprintf(stream, "%*s%-*s %d\n", indent, "", fwidth, "Dirty:", (int)(h->cache_info.is_dirty)); - fprintf(stream, "%*s%-*s %lu\n", indent, "", fwidth, + HDfprintf(stream, "%*s%-*s %lu\n", indent, "", fwidth, "Total collection size in file:", (unsigned long)(h->size)); - for (u=1, nused=0, maxobj=0; u<h->nused; u++) { - if (h->obj[u].begin) { + for(u = 1, nused = 0, maxobj = 0; u < h->nused; u++) + if(h->obj[u].begin) { nused++; - if (u>maxobj) maxobj = u; + if (u>maxobj) + maxobj = u; } - } - fprintf (stream, "%*s%-*s %u/%lu/", indent, "", fwidth, + HDfprintf(stream, "%*s%-*s %u/%lu/", indent, "", fwidth, "Objects defined/allocated/max:", - nused, (unsigned long)h->nalloc); + nused, + (unsigned long)h->nalloc); if(nused) - fprintf(stream, "%u\n", maxobj); + HDfprintf(stream, "%u\n", maxobj); else - fprintf(stream, "NA\n"); + HDfprintf(stream, "NA\n"); - fprintf (stream, "%*s%-*s %lu\n", indent, "", fwidth, + HDfprintf(stream, "%*s%-*s %lu\n", indent, "", fwidth, "Free space:", (unsigned long)(h->obj[0].size)); - for (u=1; u<h->nused; u++) { - if (h->obj[u].begin) { - sprintf (buf, "Object %u", u); - fprintf (stream, "%*s%s\n", indent, "", buf); - fprintf (stream, "%*s%-*s %lu\n", indent+3, "", MIN(fwidth-3, 0), + for(u = 1; u < h->nused; u++) + if(h->obj[u].begin) { + char buf[64]; + + HDsnprintf(buf, sizeof(buf), "Object %u", u); + HDfprintf(stream, "%*s%s\n", indent, "", buf); + HDfprintf(stream, "%*s%-*s %lu\n", indent + 3, "", MIN(fwidth - 3, 0), "Obffset in block:", (unsigned long)(h->obj[u].begin - h->chunk)); - fprintf (stream, "%*s%-*s %d\n", indent+3, "", MIN(fwidth-3, 0), + HDfprintf(stream, "%*s%-*s %d\n", indent + 3, "", MIN(fwidth - 3, 0), "Reference count:", h->obj[u].nrefs); - fprintf (stream, "%*s%-*s %lu/%lu\n", indent+3, "", - MIN(fwidth-3, 0), + HDfprintf(stream, "%*s%-*s %lu/%lu\n", indent + 3, "", + MIN(fwidth - 3, 0), "Size of object body:", (unsigned long)(h->obj[u].size), (unsigned long)H5HG_ALIGN(h->obj[u].size)); - p = h->obj[u].begin + H5HG_SIZEOF_OBJHDR (f); - for (j=0; j<h->obj[u].size; j+=16) { - fprintf (stream, "%*s%04u: ", indent+6, "", j); - for (k=0; k<16; k++) { - if (8==k) fprintf (stream, " "); - if (j+k<h->obj[u].size) { - fprintf (stream, "%02x ", p[j+k]); - } else { + p = h->obj[u].begin + H5HG_SIZEOF_OBJHDR(f); + for(j = 0; j < h->obj[u].size; j += 16) { + HDfprintf(stream, "%*s%04u: ", indent + 6, "", j); + for(k = 0; k < 16; k++) { + if(8 == k) + HDfprintf(stream, " "); + if(j + k < h->obj[u].size) + HDfprintf(stream, "%02x ", p[j + k]); + else HDfputs(" ", stream); - } } - for (k=0; k<16 && j+k<h->obj[u].size; k++) { - if (8==k) fprintf (stream, " "); - HDfputc(p[j+k]>' ' && p[j+k]<='~' ? p[j+k] : '.', stream); + for(k = 0; k < 16 && j + k < h->obj[u].size; k++) { + if(8 == k) + HDfprintf(stream, " "); + HDfputc(p[j + k]>' ' && p[j + k] <= '~' ? p[j + k] : '.', stream); } - fprintf (stream, "\n"); + HDfprintf(stream, "\n"); } } - } done: if (h && H5AC_unprotect(f, dxpl_id, H5AC_GHEAP, addr, h, H5AC__NO_FLAGS_SET) < 0) diff --git a/src/H5HLdbg.c b/src/H5HLdbg.c index 29d5c82..4ac22b8 100644 --- a/src/H5HLdbg.c +++ b/src/H5HLdbg.c @@ -54,8 +54,8 @@ herr_t H5HL_debug(H5F_t *f, hid_t dxpl_id, haddr_t addr, FILE * stream, int indent, int fwidth) { H5HL_t *h = NULL; - int i, overlap, free_block; - H5HL_free_t *freelist = NULL; + int free_block; + H5HL_free_t *freelist; uint8_t *marker = NULL; size_t amount_free = 0; herr_t ret_value = SUCCEED; /* Return value */ @@ -72,8 +72,8 @@ H5HL_debug(H5F_t *f, hid_t dxpl_id, haddr_t addr, FILE * stream, int indent, int if(NULL == (h = (H5HL_t *)H5HL_protect(f, dxpl_id, addr, H5AC_READ))) HGOTO_ERROR(H5E_HEAP, H5E_CANTLOAD, FAIL, "unable to load heap") - fprintf(stream, "%*sLocal Heap...\n", indent, ""); - fprintf(stream, "%*s%-*s %lu\n", indent, "", fwidth, + HDfprintf(stream, "%*sLocal Heap...\n", indent, ""); + HDfprintf(stream, "%*s%-*s %lu\n", indent, "", fwidth, "Header size (in bytes):", (unsigned long)h->prfx_size); HDfprintf(stream, "%*s%-*s %a\n", indent, "", fwidth, @@ -90,34 +90,36 @@ H5HL_debug(H5F_t *f, hid_t dxpl_id, haddr_t addr, FILE * stream, int indent, int if(NULL == (marker = (uint8_t *)H5MM_calloc(h->dblk_size))) HGOTO_ERROR(H5E_HEAP, H5E_CANTALLOC, FAIL, "memory allocation failed") - fprintf(stream, "%*sFree Blocks (offset, size):\n", indent, ""); - + HDfprintf(stream, "%*sFree Blocks (offset, size):\n", indent, ""); for(free_block = 0, freelist = h->freelist; freelist; freelist = freelist->next, free_block++) { char temp_str[32]; - sprintf(temp_str,"Block #%d:",free_block); + HDsnprintf(temp_str, sizeof(temp_str), "Block #%d:", free_block); HDfprintf(stream, "%*s%-*s %8Zu, %8Zu\n", indent+3, "", MAX(0,fwidth-9), temp_str, freelist->offset, freelist->size); if((freelist->offset + freelist->size) > h->dblk_size) - fprintf(stream, "***THAT FREE BLOCK IS OUT OF BOUNDS!\n"); + HDfprintf(stream, "***THAT FREE BLOCK IS OUT OF BOUNDS!\n"); else { - for(i = overlap = 0; i < (int)(freelist->size); i++) { + int overlap = 0; + size_t i; + + for(i = 0; i < freelist->size; i++) { if(marker[freelist->offset + i]) overlap++; marker[freelist->offset + i] = 1; } /* end for */ if(overlap) - fprintf(stream, "***THAT FREE BLOCK OVERLAPPED A PREVIOUS ONE!\n"); + HDfprintf(stream, "***THAT FREE BLOCK OVERLAPPED A PREVIOUS ONE!\n"); else amount_free += freelist->size; } /* end for */ } /* end for */ if(h->dblk_size) - fprintf(stream, "%*s%-*s %.2f%%\n", indent, "", fwidth, + HDfprintf(stream, "%*s%-*s %.2f%%\n", indent, "", fwidth, "Percent of heap used:", - (100.0 * (double)(h->dblk_size - amount_free) / (double)h->dblk_size)); + ((double)100.0f * (double)(h->dblk_size - amount_free) / (double)h->dblk_size)); /* * Print the data in a VMS-style octal dump. @@ -864,7 +864,6 @@ H5I_register(H5I_type_t type, const void *object, hbool_t app_ref) */ if(type_ptr->wrapped) { H5I_wrap_ud_t udata; /* User data for iteration */ - hid_t previd; /* Previous ID value */ herr_t iter_status; /* Iteration status */ /* Set up user data for iteration */ @@ -1287,7 +1286,7 @@ H5I__remove_common(H5I_id_type_t *type_ptr, hid_t id) HDassert(type_ptr); /* Get the ID node for the ID */ - if(NULL == (curr_id = H5SL_remove(type_ptr->ids, &id))) + if(NULL == (curr_id = (H5I_id_info_t *)H5SL_remove(type_ptr->ids, &id))) HGOTO_ERROR(H5E_ATOM, H5E_CANTDELETE, NULL, "can't remove ID node from skip list") /* (Casting away const OK -QAK) */ @@ -1320,7 +1319,6 @@ void * H5I_remove(hid_t id) { H5I_id_type_t *type_ptr; /*ptr to the atomic type */ - H5I_id_info_t *curr_id; /*ptr to the current atom */ H5I_type_t type; /*atom's atomic type */ void * ret_value; /*return value */ @@ -1418,7 +1416,7 @@ H5I_dec_ref(hid_t id) HGOTO_ERROR(H5E_ARGS, H5E_BADRANGE, FAIL, "invalid type number") /* General lookup of the ID */ - if(NULL == (id_ptr = H5SL_search(type_ptr->ids, &id))) + if(NULL == (id_ptr = (H5I_id_info_t *)H5SL_search(type_ptr->ids, &id))) HGOTO_ERROR(H5E_ATOM, H5E_BADATOM, FAIL, "can't locate ID") /* @@ -1620,7 +1618,7 @@ H5I_inc_ref(hid_t id, hbool_t app_ref) HGOTO_ERROR(H5E_ATOM, H5E_BADGROUP, FAIL, "invalid type") /* General lookup of the ID */ - if(NULL == (id_ptr = H5SL_search(type_ptr->ids, &id))) + if(NULL == (id_ptr = (H5I_id_info_t *)H5SL_search(type_ptr->ids, &id))) HGOTO_ERROR(H5E_ATOM, H5E_BADATOM, FAIL, "can't locate ID") /* Adjust reference counts */ @@ -1705,7 +1703,7 @@ H5I_get_ref(hid_t id, hbool_t app_ref) HGOTO_ERROR(H5E_ATOM, H5E_BADGROUP, FAIL, "invalid type") /* General lookup of the ID */ - if(NULL == (id_ptr = H5SL_search(type_ptr->ids, &id))) + if(NULL == (id_ptr = (H5I_id_info_t *)H5SL_search(type_ptr->ids, &id))) HGOTO_ERROR(H5E_ATOM, H5E_BADATOM, FAIL, "can't locate ID") /* Set return value */ @@ -2287,7 +2285,7 @@ H5I__find_id(hid_t id) HGOTO_DONE(NULL); /* Locate the ID node for the ID */ - ret_value = H5SL_search(type_ptr->ids, &id); + ret_value = (H5I_id_info_t *)H5SL_search(type_ptr->ids, &id); done: FUNC_LEAVE_NOAPI(ret_value) diff --git a/src/H5Lexternal.c b/src/H5Lexternal.c index 6ac1bdf..cc8fdae 100644 --- a/src/H5Lexternal.c +++ b/src/H5Lexternal.c @@ -210,6 +210,7 @@ H5L_extern_traverse(const char UNUSED *link_name, hid_t cur_group, char *parent_group_name = NULL;/* Temporary pointer to group name */ char local_group_name[H5L_EXT_TRAVERSE_BUF_SIZE]; /* Local buffer to hold group name */ char *temp_file_name = NULL; /* Temporary pointer to file name */ + size_t temp_file_name_len; /* Length of temporary file name */ char *actual_file_name = NULL; /* Parent file's actual name */ H5P_genplist_t *fa_plist; /* File access property list pointer */ H5F_close_degree_t fc_degree = H5F_CLOSE_WEAK; /* File close degree for target file */ @@ -314,6 +315,7 @@ H5L_extern_traverse(const char UNUSED *link_name, hid_t cur_group, /* Copy the file name to use */ if(NULL == (temp_file_name = H5MM_strdup(file_name))) HGOTO_ERROR(H5E_RESOURCE, H5E_NOSPACE, FAIL, "memory allocation failed") + temp_file_name_len = HDstrlen(temp_file_name); /* target file_name is an absolute pathname: see RM for detailed description */ if(H5_CHECK_ABSOLUTE(file_name) || H5_CHECK_ABS_PATH(file_name)) { @@ -331,7 +333,8 @@ H5L_extern_traverse(const char UNUSED *link_name, hid_t cur_group, ptr++; /* Copy into the temp. file name */ - HDstrncpy(temp_file_name, ptr, HDstrlen(ptr) + 1); + HDstrncpy(temp_file_name, ptr, temp_file_name_len); + temp_file_name[temp_file_name_len - 1] = '\0'; } /* end if */ } /* end if */ else if(H5_CHECK_ABS_DRIVE(file_name)) { @@ -341,7 +344,8 @@ H5L_extern_traverse(const char UNUSED *link_name, hid_t cur_group, H5E_clear_stack(NULL); /* strip "<drive-letter>:" */ - HDstrncpy(temp_file_name, &file_name[2], (HDstrlen(file_name) - 2) + 1); + HDstrncpy(temp_file_name, &file_name[2], temp_file_name_len); + temp_file_name[temp_file_name_len - 1] = '\0'; } /* end if */ } /* end if */ @@ -600,9 +604,9 @@ H5Lcreate_external(const char *file_name, const char *obj_name, /* Encode the external link information */ p = (uint8_t *)ext_link_buf; *p++ = (H5L_EXT_VERSION << 4) | H5L_EXT_FLAGS_ALL; /* External link version & flags */ - HDstrncpy((char *)p, file_name, file_name_len); /* Name of file containing external link's object */ + HDstrncpy((char *)p, file_name, buf_size - 1); /* Name of file containing external link's object */ p += file_name_len; - HDstrncpy((char *)p, norm_obj_name, norm_obj_name_len); /* External link's object */ + HDstrncpy((char *)p, norm_obj_name, buf_size - (file_name_len + 1)); /* External link's object */ loc_params.type = H5VL_OBJECT_BY_NAME; loc_params.loc_data.loc_by_name.name = link_name; diff --git a/src/H5Oattr.c b/src/H5Oattr.c index b8e6b32..2269bd3 100644 --- a/src/H5Oattr.c +++ b/src/H5Oattr.c @@ -793,7 +793,7 @@ H5O_attr_debug(H5F_t *f, hid_t dxpl_id, const void *_mesg, FILE * stream, int in { const H5A_t *mesg = (const H5A_t *)_mesg; const char *s; /* Temporary string pointer */ - char buf[256]; /* Temporary string buffer */ + char buf[128]; /* Temporary string buffer */ herr_t ret_value = SUCCEED; /* Return value */ FUNC_ENTER_NOAPI_NOINIT @@ -804,7 +804,7 @@ H5O_attr_debug(H5F_t *f, hid_t dxpl_id, const void *_mesg, FILE * stream, int in HDassert(indent >= 0); HDassert(fwidth >= 0); - fprintf(stream, "%*s%-*s \"%s\"\n", indent, "", fwidth, + HDfprintf(stream, "%*s%-*s \"%s\"\n", indent, "", fwidth, "Name:", mesg->shared->name); switch(mesg->shared->encoding) { @@ -830,17 +830,17 @@ H5O_attr_debug(H5F_t *f, hid_t dxpl_id, const void *_mesg, FILE * stream, int in case H5T_CSET_RESERVED_13: case H5T_CSET_RESERVED_14: case H5T_CSET_RESERVED_15: - sprintf(buf, "H5T_CSET_RESERVED_%d", (int)(mesg->shared->encoding)); + HDsnprintf(buf, sizeof(buf), "H5T_CSET_RESERVED_%d", (int)(mesg->shared->encoding)); s = buf; break; case H5T_CSET_ERROR: default: - sprintf(buf, "Unknown character set: %d", (int)(mesg->shared->encoding)); + HDsnprintf(buf, sizeof(buf), "Unknown character set: %d", (int)(mesg->shared->encoding)); s = buf; break; } /* end switch */ - fprintf(stream, "%*s%-*s %s\n", indent, "", fwidth, + HDfprintf(stream, "%*s%-*s %s\n", indent, "", fwidth, "Character Set of Name:", s); HDfprintf(stream, "%*s%-*s %t\n", indent, "", fwidth, @@ -856,18 +856,18 @@ H5O_attr_debug(H5F_t *f, hid_t dxpl_id, const void *_mesg, FILE * stream, int in "Creation Index:", (unsigned)mesg->shared->crt_idx); - fprintf(stream, "%*sDatatype...\n", indent, ""); - fprintf(stream, "%*s%-*s %lu\n", indent+3, "", MAX(0,fwidth-3), + HDfprintf(stream, "%*sDatatype...\n", indent, ""); + HDfprintf(stream, "%*s%-*s %lu\n", indent + 3, "", MAX(0,fwidth - 3), "Encoded Size:", (unsigned long)(mesg->shared->dt_size)); if((H5O_MSG_DTYPE->debug)(f, dxpl_id, mesg->shared->dt, stream, indent + 3, MAX(0, fwidth - 3)) < 0) HGOTO_ERROR(H5E_OHDR, H5E_WRITEERROR, FAIL, "unable to display datatype message info") - fprintf(stream, "%*sDataspace...\n", indent, ""); - fprintf(stream, "%*s%-*s %lu\n", indent+3, "", MAX(0, fwidth - 3), + HDfprintf(stream, "%*sDataspace...\n", indent, ""); + HDfprintf(stream, "%*s%-*s %lu\n", indent + 3, "", MAX(0, fwidth - 3), "Encoded Size:", (unsigned long)(mesg->shared->ds_size)); - if(H5S_debug(f, dxpl_id, mesg->shared->ds, stream, indent+3, MAX(0, fwidth - 3)) < 0) + if(H5S_debug(f, dxpl_id, mesg->shared->ds, stream, indent + 3, MAX(0, fwidth - 3)) < 0) HGOTO_ERROR(H5E_OHDR, H5E_WRITEERROR, FAIL, "unable to display dataspace message info") done: diff --git a/src/H5Odbg.c b/src/H5Odbg.c index 5901c61..b91a51a 100644 --- a/src/H5Odbg.c +++ b/src/H5Odbg.c @@ -455,30 +455,32 @@ H5O_debug_real(H5F_t *f, hid_t dxpl_id, H5O_t *oh, haddr_t addr, FILE *stream, i hbool_t flag_printed = FALSE; if(oh->mesg[i].flags & H5O_MSG_FLAG_SHARED) { - HDfprintf(stream, "%s%s", (flag_printed ? ", " : "<"), "S"); + HDfprintf(stream, "<S"); flag_printed = TRUE; } /* end if */ if(oh->mesg[i].flags & H5O_MSG_FLAG_CONSTANT) { - HDfprintf(stream, "%s%s", (flag_printed ? ", " : "<"), "C"); + HDfprintf(stream, "%sC", (flag_printed ? ", " : "<")); flag_printed = TRUE; } /* end if */ if(oh->mesg[i].flags & H5O_MSG_FLAG_DONTSHARE) { - HDfprintf(stream, "%s%s", (flag_printed ? ", " : "<"), "DS"); + HDfprintf(stream, "%sDS", (flag_printed ? ", " : "<")); flag_printed = TRUE; } /* end if */ if(oh->mesg[i].flags & H5O_MSG_FLAG_FAIL_IF_UNKNOWN) { - HDfprintf(stream, "%s%s", (flag_printed ? ", " : "<"), "FIU"); + HDfprintf(stream, "%sFIU", (flag_printed ? ", " : "<")); flag_printed = TRUE; } /* end if */ if(oh->mesg[i].flags & H5O_MSG_FLAG_MARK_IF_UNKNOWN) { - HDfprintf(stream, "%s%s", (flag_printed ? ", " : "<"), "MIU"); + HDfprintf(stream, "%sMIU", (flag_printed ? ", " : "<")); flag_printed = TRUE; } /* end if */ if(oh->mesg[i].flags & H5O_MSG_FLAG_WAS_UNKNOWN) { HDassert(oh->mesg[i].flags & H5O_MSG_FLAG_MARK_IF_UNKNOWN); - HDfprintf(stream, "%s%s", (flag_printed ? ", " : "<"), "WU"); + HDfprintf(stream, "%sWU", (flag_printed ? ", " : "<")); flag_printed = TRUE; } /* end if */ + if(!flag_printed) + HDfprintf(stream, "-"); HDfprintf(stream, ">\n"); if(oh->mesg[i].flags & ~H5O_MSG_FLAG_BITS) HDfprintf(stream, "%*s%-*s 0x%02x\n", indent + 3,"", MAX(0, fwidth - 3), diff --git a/src/H5Oefl.c b/src/H5Oefl.c index 487b6f4..c6db7c3 100644 --- a/src/H5Oefl.c +++ b/src/H5Oefl.c @@ -545,7 +545,6 @@ H5O_efl_debug(H5F_t UNUSED *f, hid_t UNUSED dxpl_id, const void *_mesg, FILE * s int indent, int fwidth) { const H5O_efl_t *mesg = (const H5O_efl_t *) _mesg; - char buf[64]; size_t u; FUNC_ENTER_NOAPI_NOINIT_NOERR @@ -565,8 +564,10 @@ H5O_efl_debug(H5F_t UNUSED *f, hid_t UNUSED dxpl_id, const void *_mesg, FILE * s mesg->nused, mesg->nalloc); for(u = 0; u < mesg->nused; u++) { - sprintf (buf, "File %u", (unsigned)u); - HDfprintf (stream, "%*s%s:\n", indent, "", buf); + char buf[64]; + + HDsnprintf(buf, sizeof(buf), "File %u", (unsigned)u); + HDfprintf(stream, "%*s%s:\n", indent, "", buf); HDfprintf(stream, "%*s%-*s \"%s\"\n", indent+3, "", MAX (fwidth-3, 0), "Name:", @@ -576,11 +577,11 @@ H5O_efl_debug(H5F_t UNUSED *f, hid_t UNUSED dxpl_id, const void *_mesg, FILE * s "Name offset:", (unsigned long)(mesg->slot[u].name_offset)); - HDfprintf (stream, "%*s%-*s %lu\n", indent+3, "", MAX (fwidth-3, 0), + HDfprintf(stream, "%*s%-*s %lu\n", indent+3, "", MAX (fwidth-3, 0), "Offset of data in file:", (unsigned long)(mesg->slot[u].offset)); - HDfprintf (stream, "%*s%-*s %lu\n", indent+3, "", MAX (fwidth-3, 0), + HDfprintf(stream, "%*s%-*s %lu\n", indent+3, "", MAX (fwidth-3, 0), "Bytes reserved for data:", (unsigned long)(mesg->slot[u].size)); } /* end for */ diff --git a/src/H5Olink.c b/src/H5Olink.c index 4dda5fe..184f6b9 100644 --- a/src/H5Olink.c +++ b/src/H5Olink.c @@ -484,6 +484,9 @@ H5O_link_size(const H5F_t *f, hbool_t UNUSED disable_shared, const void *_mesg) FUNC_ENTER_NOAPI_NOINIT_NOERR + /* Sanity check */ + HDcompile_assert(sizeof(uint64_t) >= sizeof(size_t)); + /* Get name's length */ name_len = (uint64_t)HDstrlen(lnk->name); @@ -500,7 +503,7 @@ H5O_link_size(const H5F_t *f, hbool_t UNUSED disable_shared, const void *_mesg) /* Set return value */ ret_value = 1 + /* Version */ 1 + /* Link encoding flags */ - (lnk->type != H5L_TYPE_HARD ? 1 : 0) + /* Link type */ + (lnk->type != H5L_TYPE_HARD ? (size_t)1 : 0) + /* Link type */ (lnk->corder_valid ? 8 : 0) + /* Creation order */ (lnk->cset != H5T_CSET_ASCII ? 1 : 0) + /* Character set */ name_size + /* Name length */ diff --git a/src/H5Pdxpl.c b/src/H5Pdxpl.c index b5d688b..472700a 100644 --- a/src/H5Pdxpl.c +++ b/src/H5Pdxpl.c @@ -165,7 +165,7 @@ #define H5D_XFER_DIRECT_CHUNK_WRITE_FILTERS_DEF 0 #define H5D_XFER_DIRECT_CHUNK_WRITE_OFFSET_SIZE sizeof(hsize_t *) #define H5D_XFER_DIRECT_CHUNK_WRITE_OFFSET_DEF NULL -#define H5D_XFER_DIRECT_CHUNK_WRITE_DATASIZE_SIZE sizeof(size_t) +#define H5D_XFER_DIRECT_CHUNK_WRITE_DATASIZE_SIZE sizeof(uint32_t) #define H5D_XFER_DIRECT_CHUNK_WRITE_DATASIZE_DEF 0 /******************/ @@ -267,7 +267,7 @@ static const void *H5D_def_xfer_xform_g = H5D_XFER_XFORM_DEF; /* Defaul static const hbool_t H5D_def_direct_chunk_flag_g = H5D_XFER_DIRECT_CHUNK_WRITE_FLAG_DEF; /* Default value for the flag of direct chunk write */ static const uint32_t H5D_def_direct_chunk_filters_g = H5D_XFER_DIRECT_CHUNK_WRITE_FILTERS_DEF; /* Default value for the filters of direct chunk write */ static const hsize_t *H5D_def_direct_chunk_offset_g = H5D_XFER_DIRECT_CHUNK_WRITE_OFFSET_DEF; /* Default value for the offset of direct chunk write */ -static const size_t H5D_def_direct_chunk_datasize_g = H5D_XFER_DIRECT_CHUNK_WRITE_DATASIZE_DEF; /* Default value for the datasize of direct chunk write */ +static const uint32_t H5D_def_direct_chunk_datasize_g = H5D_XFER_DIRECT_CHUNK_WRITE_DATASIZE_DEF; /* Default value for the datasize of direct chunk write */ /*------------------------------------------------------------------------- @@ -1493,8 +1493,9 @@ H5Pset_btree_ratios(hid_t plist_id, double left, double middle, H5TRACE4("e", "iddd", plist_id, left, middle, right); /* Check arguments */ - if(left < 0.0 || left > 1.0 || middle < 0.0 || middle > 1.0 || - right < 0.0 || right > 1.0) + if(left < (double)0.0f || left > (double)1.0f + || middle < (double)0.0f || middle > (double)1.0f + || right < (double)0.0f || right > (double)1.0f) HGOTO_ERROR(H5E_ARGS, H5E_BADVALUE, FAIL, "split ratio must satisfy 0.0<=X<=1.0") /* Get the plist structure */ diff --git a/src/H5Ppublic.h b/src/H5Ppublic.h index 882b195..4d60c5c 100644 --- a/src/H5Ppublic.h +++ b/src/H5Ppublic.h @@ -160,11 +160,10 @@ typedef enum H5D_mpio_no_collective_cause_t { H5D_MPIO_SET_INDEPENDENT = 0x01, H5D_MPIO_DATATYPE_CONVERSION = 0x02, H5D_MPIO_DATA_TRANSFORMS = 0x04, - H5D_MPIO_SET_MPIPOSIX = 0x08, + H5D_MPIO_MPI_OPT_TYPES_ENV_VAR_DISABLED = 0x08, H5D_MPIO_NOT_SIMPLE_OR_SCALAR_DATASPACES = 0x10, - H5D_MPIO_POINT_SELECTIONS = 0x20, - H5D_MPIO_NOT_CONTIGUOUS_OR_CHUNKED_DATASET = 0x40, - H5D_MPIO_FILTERS = 0x80 + H5D_MPIO_NOT_CONTIGUOUS_OR_CHUNKED_DATASET = 0x20, + H5D_MPIO_FILTERS = 0x40 } H5D_mpio_no_collective_cause_t; /********************/ @@ -67,10 +67,6 @@ static H5S_t *H5S_decode(const unsigned char *buf); /*****************************/ /* Library Private Variables */ /*****************************/ -#ifdef H5_HAVE_PARALLEL -/* Global vars whose value can be set from environment variable also */ -hbool_t H5S_mpi_opt_types_g = TRUE; -#endif /* H5_HAVE_PARALLEL */ /*******************/ @@ -120,15 +116,6 @@ H5S_init_interface(void) if(H5I_register_type(H5I_DATASPACE_CLS) < 0) HGOTO_ERROR(H5E_DATASPACE, H5E_CANTINIT, FAIL, "unable to initialize interface") -#ifdef H5_HAVE_PARALLEL - { - /* Allow MPI buf-and-file-type optimizations? */ - const char *s = HDgetenv ("HDF5_MPI_OPT_TYPES"); - if (s && HDisdigit(*s)) - H5S_mpi_opt_types_g = (hbool_t)HDstrtol (s, NULL, 0); - } -#endif /* H5_HAVE_PARALLEL */ - done: FUNC_LEAVE_NOAPI(ret_value) } /* end H5S_init_interface() */ diff --git a/src/H5Smpio.c b/src/H5Smpio.c index 77e902f..284e16f 100644 --- a/src/H5Smpio.c +++ b/src/H5Smpio.c @@ -43,6 +43,14 @@ static herr_t H5S_mpio_all_type(const H5S_t *space, size_t elmt_size, MPI_Datatype *new_type, int *count, hbool_t *is_derived_type); static herr_t H5S_mpio_none_type(MPI_Datatype *new_type, int *count, hbool_t *is_derived_type); +static herr_t H5S_mpio_create_point_datatype(size_t elmt_size, hsize_t num_points, + MPI_Aint *disp, MPI_Datatype *new_type); +static herr_t H5S_mpio_point_type(const H5S_t *space, size_t elmt_size, + MPI_Datatype *new_type, int *count, hbool_t *is_derived_type, + hbool_t do_permute, hsize_t **permute_map, hbool_t *is_permuted); +static herr_t H5S_mpio_permute_type(const H5S_t *space, size_t elmt_size, + hsize_t **permute_map, MPI_Datatype *new_type, int *count, + hbool_t *is_derived_type); static herr_t H5S_mpio_hyper_type(const H5S_t *space, size_t elmt_size, MPI_Datatype *new_type, int *count, hbool_t *is_derived_type); static herr_t H5S_mpio_span_hyper_type(const H5S_t *space, size_t elmt_size, @@ -131,6 +139,335 @@ H5S_mpio_none_type(MPI_Datatype *new_type, int *count, hbool_t *is_derived_type) /*------------------------------------------------------------------------- + * Function: H5S_mpio_create_point_datatype + * + * Purpose: Create a derived datatype for point selections. + * + * Return: non-negative on success, negative on failure. + * + * Outputs: *new_type the MPI type corresponding to the selection + * + * Programmer: Mohamad Chaarawi + * + *------------------------------------------------------------------------- + */ +static herr_t +H5S_mpio_create_point_datatype (size_t elmt_size, hsize_t num_points, + MPI_Aint *disp, MPI_Datatype *new_type) +{ + MPI_Datatype elmt_type; /* MPI datatype for individual element */ + hbool_t elmt_type_created = FALSE; /* Whether the element MPI datatype was created */ + int mpi_code; /* MPI error code */ + int *blocks = NULL; /* Array of block sizes for MPI hindexed create call */ + hsize_t u; /* Local index variable */ + herr_t ret_value = SUCCEED; /* Return value */ + + FUNC_ENTER_NOAPI_NOINIT + + /* Create an MPI datatype for an element */ + if(MPI_SUCCESS != (mpi_code = MPI_Type_contiguous((int)elmt_size, MPI_BYTE, &elmt_type))) + HMPI_GOTO_ERROR(FAIL, "MPI_Type_contiguous failed", mpi_code) + elmt_type_created = TRUE; + + /* Allocate block sizes for MPI datatype call */ + if(NULL == (blocks = (int *)H5MM_malloc(sizeof(int) * num_points))) + HGOTO_ERROR(H5E_DATASPACE, H5E_CANTALLOC, FAIL, "can't allocate array of blocks") + + /* Would be nice to have Create_Hindexed_block to avoid this array of all ones */ + for(u = 0; u < num_points; u++) + blocks[u] = 1; + + /* Create an MPI datatype for the whole point selection */ + if(MPI_SUCCESS != (mpi_code = MPI_Type_create_hindexed((int)num_points, blocks, disp, elmt_type, new_type))) + HMPI_GOTO_ERROR(FAIL, "MPI_Type_create_indexed_block failed", mpi_code) + + /* Commit MPI datatype for later use */ + if(MPI_SUCCESS != (mpi_code = MPI_Type_commit(new_type))) + HMPI_GOTO_ERROR(FAIL, "MPI_Type_commit failed", mpi_code) + +done: + if(elmt_type_created) + MPI_Type_free(&elmt_type); + if(blocks) + H5MM_free(blocks); + + FUNC_LEAVE_NOAPI(ret_value) +} /* H5S_mpio_create_point_datatype() */ + + +/*------------------------------------------------------------------------- + * Function: H5S_mpio_point_type + * + * Purpose: Translate an HDF5 "point" selection into an MPI type. + * Create a permutation array to handle out-of-order point selections. + * + * Return: non-negative on success, negative on failure. + * + * Outputs: *new_type the MPI type corresponding to the selection + * *count how many objects of the new_type in selection + * (useful if this is the buffer type for xfer) + * *is_derived_type 0 if MPI primitive type, 1 if derived + * *permute_map the permutation of the displacements to create + * the MPI_Datatype + * *is_permuted 0 if the displacements are permuted, 1 if not + * + * Programmer: Mohamad Chaarawi + * + *------------------------------------------------------------------------- + */ +static herr_t +H5S_mpio_point_type(const H5S_t *space, size_t elmt_size, MPI_Datatype *new_type, + int *count, hbool_t *is_derived_type, hbool_t do_permute, hsize_t **permute, + hbool_t *is_permuted) +{ + MPI_Aint *disp = NULL; /* Datatype displacement for each point*/ + H5S_pnt_node_t *curr = NULL; /* Current point being operated on in from the selection */ + hssize_t snum_points; /* Signed number of elements in selection */ + hsize_t num_points; /* Sumber of points in the selection */ + hsize_t u; /* Local index variable */ + herr_t ret_value = SUCCEED; /* Return value */ + + FUNC_ENTER_NOAPI_NOINIT + + /* Check args */ + HDassert(space); + + /* Get the total number of points selected */ + if((snum_points = (hssize_t)H5S_GET_SELECT_NPOINTS(space)) < 0) + HGOTO_ERROR(H5E_DATASPACE, H5E_CANTCOUNT, FAIL, "can't get number of elements selected") + num_points = (hsize_t)snum_points; + + /* Allocate array for element displacements */ + if(NULL == (disp = (MPI_Aint *)H5MM_malloc(sizeof(MPI_Aint) * num_points))) + HGOTO_ERROR(H5E_DATASPACE, H5E_CANTALLOC, FAIL, "can't allocate array of displacements") + + /* Allocate array for element permutation - returned to caller */ + if(do_permute) + if(NULL == (*permute = (hsize_t *)H5MM_malloc(sizeof(hsize_t) * num_points))) + HGOTO_ERROR(H5E_DATASPACE, H5E_CANTALLOC, FAIL, "can't allocate permutation array") + + /* Iterate through list of elements */ + curr = space->select.sel_info.pnt_lst->head; + for(u = 0 ; u < num_points ; u++) { + /* calculate the displacement of the current point */ + disp[u] = H5VM_array_offset(space->extent.rank, space->extent.size, curr->pnt); + disp[u] *= elmt_size; + + /* This is a File Space used to set the file view, so adjust the displacements + * to have them monotonically non-decreasing. + * Generate the permutation array by indicating at each point being selected, + * the position it will shifted in the new displacement. Example: + * Suppose 4 points with corresponding are selected + * Pt 1: disp=6 ; Pt 2: disp=3 ; Pt 3: disp=0 ; Pt 4: disp=4 + * The permute map to sort the displacements in order will be: + * point 1: map[0] = L, indicating that this point is not moved (1st point selected) + * point 2: map[1] = 0, indicating that this point is moved to the first position, + * since disp_pt1(6) > disp_pt2(3) + * point 3: map[2] = 0, move to position 0, bec it has the lowest disp between + * the points selected so far. + * point 4: map[3] = 2, move the 2nd position since point 1 has a higher disp, + * but points 2 and 3 have lower displacements. + */ + if(do_permute) { + if(u > 0 && disp[u] < disp[u - 1]) { + unsigned s = 0, l = u, m = u / 2; + + *is_permuted = TRUE; + do { + if(disp[u] > disp[m]) + s = m + 1; + else if(disp[u] < disp[m]) + l = m; + else + break; + m = s + ((l - s) / 2); + } while(s < l); + + if(m < u) { + MPI_Aint temp; + + temp = disp[u]; + HDmemmove(disp + m + 1, disp + m, (u - m) * sizeof(MPI_Aint)); + disp[m] = temp; + } /* end if */ + (*permute)[u] = m; + } /* end if */ + else + (*permute)[u] = num_points; + } /* end if */ + /* this is a memory space, and no permutation is necessary to create + the derived datatype */ + else { + ;/* do nothing */ + } /* end else */ + + /* get the next point */ + curr = curr->next; + } /* end for */ + + /* Create the MPI datatype for the set of element displacements */ + if(H5S_mpio_create_point_datatype(elmt_size, num_points, disp, new_type) < 0) + HGOTO_ERROR(H5E_DATASPACE, H5E_BADTYPE, FAIL, "couldn't create an MPI Datatype from point selection") + + /* Set values about MPI datatype created */ + *count = 1; + *is_derived_type = TRUE; + +done: + if(NULL != disp) + H5MM_free(disp); + + /* Release the permutation buffer, if it wasn't used */ + if(!(*is_permuted) && (*permute)) { + H5MM_free(*permute); + *permute = NULL; + } /* end if */ + + FUNC_LEAVE_NOAPI(ret_value) +} /* H5S_mpio_point_type() */ + + +/*------------------------------------------------------------------------- + * Function: H5S_mpio_permute_type + * + * Purpose: Translate an HDF5 "all/hyper/point" selection into an MPI type, + * while applying the permutation map. This function is called if + * the file space selection is permuted due to out-of-order point + * selection and so the memory datatype has to be permuted using the + * permutation map created by the file selection. + * + * Note: This routine is called from H5S_mpio_space_type(), which is + * called first for the file dataspace and creates + * + * Return: non-negative on success, negative on failure. + * + * Outputs: *new_type the MPI type corresponding to the selection + * *count how many objects of the new_type in selection + * (useful if this is the buffer type for xfer) + * *is_derived_type 0 if MPI primitive type, 1 if derived + * + * Programmer: Mohamad Chaarawi + * + *------------------------------------------------------------------------- + */ +static herr_t +H5S_mpio_permute_type(const H5S_t *space, size_t elmt_size, hsize_t **permute, + MPI_Datatype *new_type, int *count, hbool_t *is_derived_type) +{ + MPI_Aint *disp = NULL; /* Datatype displacement for each point*/ + H5S_sel_iter_t sel_iter; /* Selection iteration info */ + hbool_t sel_iter_init = FALSE; /* Selection iteration info has been initialized */ + hsize_t off[H5D_IO_VECTOR_SIZE]; /* Array to store sequence offsets */ + size_t len[H5D_IO_VECTOR_SIZE]; /* Array to store sequence lengths */ + hssize_t snum_points; /* Signed number of elements in selection */ + hsize_t num_points; /* Number of points in the selection */ + size_t max_elem; /* Maximum number of elements allowed in sequences */ + hsize_t u; /* Local index variable */ + herr_t ret_value = SUCCEED; /* Return value */ + + FUNC_ENTER_NOAPI_NOINIT + + /* Check args */ + HDassert(space); + + /* Get the total number of points selected */ + if((snum_points = (hssize_t)H5S_GET_SELECT_NPOINTS(space)) < 0) + HGOTO_ERROR(H5E_DATASPACE, H5E_CANTCOUNT, FAIL, "can't get number of elements selected") + num_points = (hsize_t)snum_points; + + /* Allocate array to store point displacements */ + if(NULL == (disp = (MPI_Aint *)H5MM_malloc(sizeof(MPI_Aint) * num_points))) + HGOTO_ERROR(H5E_DATASPACE, H5E_CANTALLOC, FAIL, "can't allocate array of displacements") + + /* Initialize selection iterator */ + if(H5S_select_iter_init(&sel_iter, space, elmt_size) < 0) + HGOTO_ERROR(H5E_DATASPACE, H5E_CANTINIT, FAIL, "unable to initialize selection iterator") + sel_iter_init = TRUE; /* Selection iteration info has been initialized */ + + /* Set the number of elements to iterate over */ + H5_ASSIGN_OVERFLOW(max_elem, num_points, hsize_t, size_t); + + /* Loop, while elements left in selection */ + u = 0; + while(max_elem > 0) { + hsize_t off[H5D_IO_VECTOR_SIZE]; /* Array to store sequence offsets */ + size_t len[H5D_IO_VECTOR_SIZE]; /* Array to store sequence lengths */ + size_t nelem; /* Number of elements used in sequences */ + size_t nseq; /* Number of sequences generated */ + size_t curr_seq; /* Current sequence being worked on */ + + /* Get the sequences of bytes */ + if(H5S_SELECT_GET_SEQ_LIST(space, 0, &sel_iter, (size_t)H5D_IO_VECTOR_SIZE, max_elem, &nseq, &nelem, off, len) < 0) + HGOTO_ERROR(H5E_DATASPACE, H5E_UNSUPPORTED, FAIL, "sequence length generation failed") + + /* Loop, while sequences left to process */ + for(curr_seq = 0; curr_seq < nseq; curr_seq++) { + hsize_t curr_off; /* Current offset within sequence */ + size_t curr_len; /* Length of bytes left to process in sequence */ + + /* Get the current offset */ + curr_off = off[curr_seq]; + + /* Get the number of bytes in sequence */ + curr_len = len[curr_seq]; + + /* Loop, while bytes left in sequence */ + while(curr_len > 0) { + /* Set the displacement of the current point */ + disp[u] = curr_off; + + /* This is a memory displacement, so for each point selected, + * apply the map that was generated by the file selection */ + if((*permute)[u] != num_points) { + MPI_Aint temp = disp[u]; + + HDmemmove(disp + (*permute)[u] + 1, disp + (*permute)[u], + (u - (*permute)[u]) * sizeof(MPI_Aint)); + disp[(*permute)[u]] = temp; + } /* end if */ + + /* Advance to next element */ + u++; + + /* Increment offset in dataspace */ + curr_off += elmt_size; + + /* Decrement number of bytes left in sequence */ + curr_len -= elmt_size; + } /* end while */ + } /* end for */ + + /* Decrement number of elements left to process */ + max_elem -= nelem; + } /* end while */ + + /* Create the MPI datatype for the set of element displacements */ + if(H5S_mpio_create_point_datatype(elmt_size, num_points, disp, new_type) < 0) + HGOTO_ERROR(H5E_DATASPACE, H5E_BADTYPE, FAIL, "couldn't create an MPI Datatype from point selection") + + /* Set values about MPI datatype created */ + *count = 1; + *is_derived_type = TRUE; + +done: + /* Release selection iterator */ + if(sel_iter_init) + if(H5S_SELECT_ITER_RELEASE(&sel_iter) < 0) + HDONE_ERROR(H5E_DATASPACE, H5E_CANTRELEASE, FAIL, "unable to release selection iterator") + + /* Free memory */ + if(disp) + H5MM_free(disp); + if(*permute) { + H5MM_free(*permute); + *permute = NULL; + } /* end if */ + + FUNC_LEAVE_NOAPI(ret_value) +} /* H5S_mpio_permute_type() */ + + +/*------------------------------------------------------------------------- * Function: H5S_mpio_hyper_type * * Purpose: Translate an HDF5 hyperslab selection into an MPI type. @@ -478,7 +815,7 @@ done: /*------------------------------------------------------------------------- - * Function: H5S_obtain datatype + * Function: H5S_obtain_datatype * * Purpose: Obtain an MPI derived datatype based on span-tree * implementation @@ -673,8 +1010,9 @@ done: *------------------------------------------------------------------------- */ herr_t -H5S_mpio_space_type(const H5S_t *space, size_t elmt_size, - MPI_Datatype *new_type, int *count, hbool_t *is_derived_type) +H5S_mpio_space_type(const H5S_t *space, size_t elmt_size, MPI_Datatype *new_type, + int *count, hbool_t *is_derived_type, hbool_t do_permute, hsize_t **permute_map, + hbool_t *is_permuted) { herr_t ret_value = SUCCEED; /* Return value */ @@ -684,44 +1022,75 @@ H5S_mpio_space_type(const H5S_t *space, size_t elmt_size, HDassert(space); HDassert(elmt_size); - /* Creat MPI type based on the kind of selection */ + /* Create MPI type based on the kind of selection */ switch(H5S_GET_EXTENT_TYPE(space)) { case H5S_NULL: case H5S_SCALAR: case H5S_SIMPLE: - switch(H5S_GET_SELECT_TYPE(space)) { - case H5S_SEL_NONE: - if(H5S_mpio_none_type(new_type, count, is_derived_type) < 0) - HGOTO_ERROR(H5E_DATASPACE, H5E_BADTYPE, FAIL,"couldn't convert 'none' selection to MPI type") - break; - - case H5S_SEL_ALL: - if(H5S_mpio_all_type(space, elmt_size, new_type, count, is_derived_type) < 0) - HGOTO_ERROR(H5E_DATASPACE, H5E_BADTYPE, FAIL,"couldn't convert 'all' selection to MPI type") - break; - - case H5S_SEL_POINTS: - /* not yet implemented */ - ret_value = FAIL; - break; - - case H5S_SEL_HYPERSLABS: - if((H5S_SELECT_IS_REGULAR(space) == TRUE)) { - if(H5S_mpio_hyper_type(space, elmt_size, new_type, count, is_derived_type) < 0) - HGOTO_ERROR(H5E_DATASPACE, H5E_BADTYPE, FAIL,"couldn't convert regular 'hyperslab' selection to MPI type") - } /* end if */ - else { - if(H5S_mpio_span_hyper_type(space, elmt_size, new_type, count, is_derived_type) < 0) - HGOTO_ERROR(H5E_DATASPACE, H5E_BADTYPE, FAIL,"couldn't convert irregular 'hyperslab' selection to MPI type") - } /* end else */ - break; - - case H5S_SEL_ERROR: - case H5S_SEL_N: - default: - HDassert("unknown selection type" && 0); - break; - } /* end switch */ + /* If the file space has been permuted previously due to + * out-of-order point selection, then permute this selection which + * should be a memory selection to match the file space permutation. + */ + if(TRUE == *is_permuted) { + switch(H5S_GET_SELECT_TYPE(space)) { + case H5S_SEL_NONE: + if(H5S_mpio_none_type(new_type, count, is_derived_type) < 0) + HGOTO_ERROR(H5E_DATASPACE, H5E_BADTYPE, FAIL, "couldn't convert 'none' selection to MPI type") + break; + + case H5S_SEL_ALL: + case H5S_SEL_POINTS: + case H5S_SEL_HYPERSLABS: + /* Sanity check */ + HDassert(!do_permute); + + if(H5S_mpio_permute_type(space, elmt_size, permute_map, new_type, count, is_derived_type) < 0) + HGOTO_ERROR(H5E_DATASPACE, H5E_BADTYPE, FAIL, "couldn't convert 'all' selection to MPI type") + break; + + case H5S_SEL_ERROR: + case H5S_SEL_N: + default: + HDassert("unknown selection type" && 0); + break; + } /* end switch */ + } /* end if */ + /* the file space is not permuted, so do a regular selection */ + else { + switch(H5S_GET_SELECT_TYPE(space)) { + case H5S_SEL_NONE: + if(H5S_mpio_none_type(new_type, count, is_derived_type) < 0) + HGOTO_ERROR(H5E_DATASPACE, H5E_BADTYPE, FAIL,"couldn't convert 'none' selection to MPI type") + break; + + case H5S_SEL_ALL: + if(H5S_mpio_all_type(space, elmt_size, new_type, count, is_derived_type) < 0) + HGOTO_ERROR(H5E_DATASPACE, H5E_BADTYPE, FAIL,"couldn't convert 'all' selection to MPI type") + break; + + case H5S_SEL_POINTS: + if(H5S_mpio_point_type(space, elmt_size, new_type, count, is_derived_type, do_permute, permute_map, is_permuted) < 0) + HGOTO_ERROR(H5E_DATASPACE, H5E_BADTYPE, FAIL, "couldn't convert 'point' selection to MPI type") + break; + + case H5S_SEL_HYPERSLABS: + if((H5S_SELECT_IS_REGULAR(space) == TRUE)) { + if(H5S_mpio_hyper_type(space, elmt_size, new_type, count, is_derived_type) < 0) + HGOTO_ERROR(H5E_DATASPACE, H5E_BADTYPE, FAIL,"couldn't convert regular 'hyperslab' selection to MPI type") + } /* end if */ + else { + if(H5S_mpio_span_hyper_type(space, elmt_size, new_type, count, is_derived_type) < 0) + HGOTO_ERROR(H5E_DATASPACE, H5E_BADTYPE, FAIL,"couldn't convert irregular 'hyperslab' selection to MPI type") + } /* end else */ + break; + + case H5S_SEL_ERROR: + case H5S_SEL_N: + default: + HDassert("unknown selection type" && 0); + break; + } /* end switch */ + } /* end else */ break; case H5S_NO_CLASS: diff --git a/src/H5Sprivate.h b/src/H5Sprivate.h index 0e67af1..44cd6c3 100644 --- a/src/H5Sprivate.h +++ b/src/H5Sprivate.h @@ -268,16 +268,13 @@ H5_DLL herr_t H5S_select_iter_next(H5S_sel_iter_t *sel_iter, size_t nelem); H5_DLL herr_t H5S_select_iter_release(H5S_sel_iter_t *sel_iter); #ifdef H5_HAVE_PARALLEL -/* Global vars whose value comes from environment variable */ -/* (Defined in H5S.c) */ -H5_DLLVAR hbool_t H5S_mpi_opt_types_g; - -H5_DLL herr_t -H5S_mpio_space_type( const H5S_t *space, size_t elmt_size, - /* out: */ - MPI_Datatype *new_type, - int *count, - hbool_t *is_derived_type ); +H5_DLL herr_t H5S_mpio_space_type(const H5S_t *space, size_t elmt_size, + /* out: */ MPI_Datatype *new_type, + int *count, + hbool_t *is_derived_type, + hbool_t do_permute, + hsize_t **permute_map, + hbool_t * is_permuted); #endif /* H5_HAVE_PARALLEL */ #endif /* _H5Sprivate_H */ diff --git a/src/H5Sselect.c b/src/H5Sselect.c index 44688b6..2cb4b38 100644 --- a/src/H5Sselect.c +++ b/src/H5Sselect.c @@ -34,8 +34,8 @@ /* Local functions */ #ifdef LATER -static herr_t H5S_select_iter_block (const H5S_sel_iter_t *iter, hsize_t *start, hsize_t *end); -static htri_t H5S_select_iter_has_next_block (const H5S_sel_iter_t *iter); +static herr_t H5S_select_iter_block(const H5S_sel_iter_t *iter, hsize_t *start, hsize_t *end); +static htri_t H5S_select_iter_has_next_block(const H5S_sel_iter_t *iter); static herr_t H5S_select_iter_next_block(H5S_sel_iter_t *iter); #endif /* LATER */ @@ -922,7 +922,7 @@ H5S_select_iter_init(H5S_sel_iter_t *sel_iter, const H5S_t *space, size_t elmt_s REVISION LOG --------------------------------------------------------------------------*/ herr_t -H5S_select_iter_coords (const H5S_sel_iter_t *sel_iter, hsize_t *coords) +H5S_select_iter_coords(const H5S_sel_iter_t *sel_iter, hsize_t *coords) { herr_t ret_value; /* return value */ @@ -964,7 +964,7 @@ H5S_select_iter_coords (const H5S_sel_iter_t *sel_iter, hsize_t *coords) REVISION LOG --------------------------------------------------------------------------*/ static herr_t -H5S_select_iter_block (const H5S_sel_iter_t *iter, hsize_t *start, hsize_t *end) +H5S_select_iter_block(const H5S_sel_iter_t *iter, hsize_t *start, hsize_t *end) { herr_t ret_value; /* return value */ @@ -1004,7 +1004,7 @@ H5S_select_iter_block (const H5S_sel_iter_t *iter, hsize_t *start, hsize_t *end) REVISION LOG --------------------------------------------------------------------------*/ hsize_t -H5S_select_iter_nelmts (const H5S_sel_iter_t *sel_iter) +H5S_select_iter_nelmts(const H5S_sel_iter_t *sel_iter) { hsize_t ret_value; /* return value */ @@ -1043,7 +1043,7 @@ H5S_select_iter_nelmts (const H5S_sel_iter_t *sel_iter) REVISION LOG --------------------------------------------------------------------------*/ static htri_t -H5S_select_iter_has_next_block (const H5S_sel_iter_t *iter) +H5S_select_iter_has_next_block(const H5S_sel_iter_t *iter) { herr_t ret_value; /* return value */ @@ -1217,24 +1217,13 @@ H5S_select_iterate(void *buf, hid_t type_id, const H5S_t *space, H5D_operator_t H5T_t *dt; /* Datatype structure */ H5S_sel_iter_t iter; /* Selection iteration info */ hbool_t iter_init = FALSE; /* Selection iteration info has been initialized */ - uint8_t *loc; /* Current element location in buffer */ - hsize_t coords[H5O_LAYOUT_NDIMS]; /* Coordinates of element in dataspace */ hssize_t nelmts; /* Number of elements in selection */ hsize_t space_size[H5O_LAYOUT_NDIMS]; /* Dataspace size */ - hsize_t off[H5D_IO_VECTOR_SIZE]; /* Array to store sequence offsets */ - hsize_t curr_off; /* Current offset within sequence */ - hsize_t tmp_off; /* Temporary offset within sequence */ - size_t len[H5D_IO_VECTOR_SIZE]; /* Array to store sequence lengths */ - size_t curr_len; /* Length of bytes left to process in sequence */ - size_t nseq; /* Number of sequences generated */ - size_t curr_seq; /* Current sequnce being worked on */ - size_t nelem; /* Number of elements used in sequences */ size_t max_elem; /* Maximum number of elements allowed in sequences */ size_t elmt_size; /* Datatype size */ unsigned ndims; /* Number of dimensions in dataspace */ - int i; /* Local Index variable */ - herr_t user_ret=0; /* User's return value */ - herr_t ret_value=SUCCEED; /* Return value */ + herr_t user_ret = 0; /* User's return value */ + herr_t ret_value = SUCCEED; /* Return value */ FUNC_ENTER_NOAPI(FAIL) @@ -1274,12 +1263,21 @@ H5S_select_iterate(void *buf, hid_t type_id, const H5S_t *space, H5D_operator_t /* Loop, while elements left in selection */ while(max_elem > 0 && user_ret == 0) { + hsize_t off[H5D_IO_VECTOR_SIZE]; /* Array to store sequence offsets */ + size_t len[H5D_IO_VECTOR_SIZE]; /* Array to store sequence lengths */ + size_t nelem; /* Number of elements used in sequences */ + size_t nseq; /* Number of sequences generated */ + size_t curr_seq; /* Current sequence being worked on */ + /* Get the sequences of bytes */ if(H5S_SELECT_GET_SEQ_LIST(space, 0, &iter, (size_t)H5D_IO_VECTOR_SIZE, max_elem, &nseq, &nelem, off, len) < 0) HGOTO_ERROR(H5E_INTERNAL, H5E_UNSUPPORTED, FAIL, "sequence length generation failed") /* Loop, while sequences left to process */ - for(curr_seq=0; curr_seq<nseq && user_ret==0; curr_seq++) { + for(curr_seq = 0; curr_seq < nseq && user_ret == 0; curr_seq++) { + hsize_t curr_off; /* Current offset within sequence */ + size_t curr_len; /* Length of bytes left to process in sequence */ + /* Get the current offset */ curr_off = off[curr_seq]; @@ -1288,6 +1286,11 @@ H5S_select_iterate(void *buf, hid_t type_id, const H5S_t *space, H5D_operator_t /* Loop, while bytes left in sequence */ while(curr_len > 0 && user_ret == 0) { + hsize_t coords[H5O_LAYOUT_NDIMS]; /* Coordinates of element in dataspace */ + hsize_t tmp_off; /* Temporary offset within sequence */ + uint8_t *loc; /* Current element location in buffer */ + int i; /* Local Index variable */ + /* Compute the coordinate from the offset */ for(i = (int)ndims, tmp_off = curr_off; i >= 0; i--) { coords[i] = tmp_off % space_size[i]; @@ -1298,22 +1301,22 @@ H5S_select_iterate(void *buf, hid_t type_id, const H5S_t *space, H5D_operator_t loc = (unsigned char *)buf + curr_off; /* Call user's callback routine */ - user_ret=(*op)(loc,type_id,ndims,coords,operator_data); + user_ret = (*op)(loc, type_id, ndims, coords, operator_data); /* Increment offset in dataspace */ - curr_off+=elmt_size; + curr_off += elmt_size; /* Decrement number of bytes left in sequence */ - curr_len-=elmt_size; + curr_len -= elmt_size; } /* end while */ } /* end for */ /* Decrement number of elements left to process */ - max_elem-=nelem; + max_elem -= nelem; } /* end while */ /* Set return value */ - ret_value=user_ret; + ret_value = user_ret; done: /* Release selection iterator */ diff --git a/src/H5Tconv.c b/src/H5Tconv.c index 45304da..673698c 100644 --- a/src/H5Tconv.c +++ b/src/H5Tconv.c @@ -8043,9 +8043,9 @@ H5T__conv_float_schar (hid_t src_id, hid_t dst_id, H5T_cdata_t *cdata, size_t UNUSED bkg_stride, void *buf, void UNUSED *bkg, hid_t UNUSED dxpl_id) { -GCC_DIAG_OFF(float-equal) +H5_GCC_DIAG_OFF(float-equal) H5T_CONV_Fx(FLOAT, SCHAR, float, signed char, SCHAR_MIN, SCHAR_MAX); -GCC_DIAG_ON(float-equal) +H5_GCC_DIAG_ON(float-equal) } @@ -8070,9 +8070,9 @@ H5T__conv_float_uchar (hid_t src_id, hid_t dst_id, H5T_cdata_t *cdata, size_t UNUSED bkg_stride, void *buf, void UNUSED *bkg, hid_t UNUSED dxpl_id) { -GCC_DIAG_OFF(float-equal) +H5_GCC_DIAG_OFF(float-equal) H5T_CONV_Fx(FLOAT, UCHAR, float, unsigned char, 0, UCHAR_MAX); -GCC_DIAG_ON(float-equal) +H5_GCC_DIAG_ON(float-equal) } @@ -8097,9 +8097,9 @@ H5T__conv_double_schar (hid_t src_id, hid_t dst_id, H5T_cdata_t *cdata, size_t UNUSED bkg_stride, void *buf, void UNUSED *bkg, hid_t UNUSED dxpl_id) { -GCC_DIAG_OFF(float-equal) +H5_GCC_DIAG_OFF(float-equal) H5T_CONV_Fx(DOUBLE, SCHAR, double, signed char, SCHAR_MIN, SCHAR_MAX); -GCC_DIAG_ON(float-equal) +H5_GCC_DIAG_ON(float-equal) } @@ -8124,9 +8124,9 @@ H5T__conv_double_uchar (hid_t src_id, hid_t dst_id, H5T_cdata_t *cdata, size_t UNUSED bkg_stride, void *buf, void UNUSED *bkg, hid_t UNUSED dxpl_id) { -GCC_DIAG_OFF(float-equal) +H5_GCC_DIAG_OFF(float-equal) H5T_CONV_Fx(DOUBLE, UCHAR, double, unsigned char, 0, UCHAR_MAX); -GCC_DIAG_ON(float-equal) +H5_GCC_DIAG_ON(float-equal) } @@ -8152,9 +8152,9 @@ H5T__conv_ldouble_schar (hid_t src_id, hid_t dst_id, H5T_cdata_t *cdata, size_t UNUSED bkg_stride, void *buf, void UNUSED *bkg, hid_t UNUSED dxpl_id) { -GCC_DIAG_OFF(float-equal) +H5_GCC_DIAG_OFF(float-equal) H5T_CONV_Fx(LDOUBLE, SCHAR, long double, signed char, SCHAR_MIN, SCHAR_MAX); -GCC_DIAG_ON(float-equal) +H5_GCC_DIAG_ON(float-equal) } #endif /* H5T_CONV_INTERNAL_LDOUBLE_INTEGER */ @@ -8181,9 +8181,9 @@ H5T__conv_ldouble_uchar (hid_t src_id, hid_t dst_id, H5T_cdata_t *cdata, size_t UNUSED bkg_stride, void *buf, void UNUSED *bkg, hid_t UNUSED dxpl_id) { -GCC_DIAG_OFF(float-equal) +H5_GCC_DIAG_OFF(float-equal) H5T_CONV_Fx(LDOUBLE, UCHAR, long double, unsigned char, 0, UCHAR_MAX); -GCC_DIAG_ON(float-equal) +H5_GCC_DIAG_ON(float-equal) } #endif /* H5T_CONV_INTERNAL_LDOUBLE_INTEGER */ @@ -8209,9 +8209,9 @@ H5T__conv_float_short (hid_t src_id, hid_t dst_id, H5T_cdata_t *cdata, size_t UNUSED bkg_stride, void *buf, void UNUSED *bkg, hid_t UNUSED dxpl_id) { -GCC_DIAG_OFF(float-equal) +H5_GCC_DIAG_OFF(float-equal) H5T_CONV_Fx(FLOAT, SHORT, float, short, SHRT_MIN, SHRT_MAX); -GCC_DIAG_ON(float-equal) +H5_GCC_DIAG_ON(float-equal) } @@ -8236,9 +8236,9 @@ H5T__conv_float_ushort (hid_t src_id, hid_t dst_id, H5T_cdata_t *cdata, size_t UNUSED bkg_stride, void *buf, void UNUSED *bkg, hid_t UNUSED dxpl_id) { -GCC_DIAG_OFF(float-equal) +H5_GCC_DIAG_OFF(float-equal) H5T_CONV_Fx(FLOAT, USHORT, float, unsigned short, 0, USHRT_MAX); -GCC_DIAG_ON(float-equal) +H5_GCC_DIAG_ON(float-equal) } @@ -8263,9 +8263,9 @@ H5T__conv_double_short (hid_t src_id, hid_t dst_id, H5T_cdata_t *cdata, size_t UNUSED bkg_stride, void *buf, void UNUSED *bkg, hid_t UNUSED dxpl_id) { -GCC_DIAG_OFF(float-equal) +H5_GCC_DIAG_OFF(float-equal) H5T_CONV_Fx(DOUBLE, SHORT, double, short, SHRT_MIN, SHRT_MAX); -GCC_DIAG_ON(float-equal) +H5_GCC_DIAG_ON(float-equal) } @@ -8290,9 +8290,9 @@ H5T__conv_double_ushort (hid_t src_id, hid_t dst_id, H5T_cdata_t *cdata, size_t UNUSED bkg_stride, void *buf, void UNUSED *bkg, hid_t UNUSED dxpl_id) { -GCC_DIAG_OFF(float-equal) +H5_GCC_DIAG_OFF(float-equal) H5T_CONV_Fx(DOUBLE, USHORT, double, unsigned short, 0, USHRT_MAX); -GCC_DIAG_ON(float-equal) +H5_GCC_DIAG_ON(float-equal) } @@ -8318,9 +8318,9 @@ H5T__conv_ldouble_short (hid_t src_id, hid_t dst_id, H5T_cdata_t *cdata, size_t UNUSED bkg_stride, void *buf, void UNUSED *bkg, hid_t UNUSED dxpl_id) { -GCC_DIAG_OFF(float-equal) +H5_GCC_DIAG_OFF(float-equal) H5T_CONV_Fx(LDOUBLE, SHORT, long double, short, SHRT_MIN, SHRT_MAX); -GCC_DIAG_ON(float-equal) +H5_GCC_DIAG_ON(float-equal) } #endif /*H5T_CONV_INTERNAL_LDOUBLE_INTEGER*/ @@ -8347,9 +8347,9 @@ H5T__conv_ldouble_ushort (hid_t src_id, hid_t dst_id, H5T_cdata_t *cdata, size_t UNUSED bkg_stride, void *buf, void UNUSED *bkg, hid_t UNUSED dxpl_id) { -GCC_DIAG_OFF(float-equal) +H5_GCC_DIAG_OFF(float-equal) H5T_CONV_Fx(LDOUBLE, USHORT, long double, unsigned short, 0, USHRT_MAX); -GCC_DIAG_ON(float-equal) +H5_GCC_DIAG_ON(float-equal) } #endif /* H5T_CONV_INTERNAL_LDOUBLE_INTEGER */ @@ -8375,9 +8375,9 @@ H5T__conv_float_int (hid_t src_id, hid_t dst_id, H5T_cdata_t *cdata, size_t UNUSED bkg_stride, void *buf, void UNUSED *bkg, hid_t UNUSED dxpl_id) { -GCC_DIAG_OFF(float-equal) +H5_GCC_DIAG_OFF(float-equal) H5T_CONV_Fx(FLOAT, INT, float, int, INT_MIN, INT_MAX); -GCC_DIAG_ON(float-equal) +H5_GCC_DIAG_ON(float-equal) } @@ -8402,9 +8402,9 @@ H5T__conv_float_uint (hid_t src_id, hid_t dst_id, H5T_cdata_t *cdata, size_t UNUSED bkg_stride, void *buf, void UNUSED *bkg, hid_t UNUSED dxpl_id) { -GCC_DIAG_OFF(float-equal) +H5_GCC_DIAG_OFF(float-equal) H5T_CONV_Fx(FLOAT, UINT, float, unsigned int, 0, UINT_MAX); -GCC_DIAG_ON(float-equal) +H5_GCC_DIAG_ON(float-equal) } @@ -8429,9 +8429,9 @@ H5T__conv_double_int (hid_t src_id, hid_t dst_id, H5T_cdata_t *cdata, size_t UNUSED bkg_stride, void *buf, void UNUSED *bkg, hid_t UNUSED dxpl_id) { -GCC_DIAG_OFF(float-equal) +H5_GCC_DIAG_OFF(float-equal) H5T_CONV_Fx(DOUBLE, INT, double, int, INT_MIN, INT_MAX); -GCC_DIAG_ON(float-equal) +H5_GCC_DIAG_ON(float-equal) } @@ -8456,9 +8456,9 @@ H5T__conv_double_uint (hid_t src_id, hid_t dst_id, H5T_cdata_t *cdata, size_t UNUSED bkg_stride, void *buf, void UNUSED *bkg, hid_t UNUSED dxpl_id) { -GCC_DIAG_OFF(float-equal) +H5_GCC_DIAG_OFF(float-equal) H5T_CONV_Fx(DOUBLE, UINT, double, unsigned int, 0, UINT_MAX); -GCC_DIAG_ON(float-equal) +H5_GCC_DIAG_ON(float-equal) } @@ -8484,9 +8484,9 @@ H5T__conv_ldouble_int (hid_t src_id, hid_t dst_id, H5T_cdata_t *cdata, size_t UNUSED bkg_stride, void *buf, void UNUSED *bkg, hid_t UNUSED dxpl_id) { -GCC_DIAG_OFF(float-equal) +H5_GCC_DIAG_OFF(float-equal) H5T_CONV_Fx(LDOUBLE, INT, long double, int, INT_MIN, INT_MAX); -GCC_DIAG_ON(float-equal) +H5_GCC_DIAG_ON(float-equal) } #endif /* H5T_CONV_INTERNAL_LDOUBLE_INTEGER */ @@ -8513,9 +8513,9 @@ H5T__conv_ldouble_uint (hid_t src_id, hid_t dst_id, H5T_cdata_t *cdata, size_t UNUSED bkg_stride, void *buf, void UNUSED *bkg, hid_t UNUSED dxpl_id) { -GCC_DIAG_OFF(float-equal) +H5_GCC_DIAG_OFF(float-equal) H5T_CONV_Fx(LDOUBLE, UINT, long double, unsigned int, 0, UINT_MAX); -GCC_DIAG_ON(float-equal) +H5_GCC_DIAG_ON(float-equal) } #endif /* H5T_CONV_INTERNAL_LDOUBLE_UINT */ @@ -8541,9 +8541,9 @@ H5T__conv_float_long (hid_t src_id, hid_t dst_id, H5T_cdata_t *cdata, size_t UNUSED bkg_stride, void *buf, void UNUSED *bkg, hid_t UNUSED dxpl_id) { -GCC_DIAG_OFF(float-equal) +H5_GCC_DIAG_OFF(float-equal) H5T_CONV_Fx(FLOAT, LONG, float, long, LONG_MIN, LONG_MAX); -GCC_DIAG_ON(float-equal) +H5_GCC_DIAG_ON(float-equal) } @@ -8568,9 +8568,9 @@ H5T__conv_float_ulong (hid_t src_id, hid_t dst_id, H5T_cdata_t *cdata, size_t UNUSED bkg_stride, void *buf, void UNUSED *bkg, hid_t UNUSED dxpl_id) { -GCC_DIAG_OFF(float-equal) +H5_GCC_DIAG_OFF(float-equal) H5T_CONV_Fx(FLOAT, ULONG, float, unsigned long, 0, ULONG_MAX); -GCC_DIAG_ON(float-equal) +H5_GCC_DIAG_ON(float-equal) } @@ -8595,9 +8595,9 @@ H5T__conv_double_long (hid_t src_id, hid_t dst_id, H5T_cdata_t *cdata, size_t UNUSED bkg_stride, void *buf, void UNUSED *bkg, hid_t UNUSED dxpl_id) { -GCC_DIAG_OFF(float-equal) +H5_GCC_DIAG_OFF(float-equal) H5T_CONV_Fx(DOUBLE, LONG, double, long, LONG_MIN, LONG_MAX); -GCC_DIAG_ON(float-equal) +H5_GCC_DIAG_ON(float-equal) } @@ -8622,9 +8622,9 @@ H5T__conv_double_ulong (hid_t src_id, hid_t dst_id, H5T_cdata_t *cdata, size_t UNUSED bkg_stride, void *buf, void UNUSED *bkg, hid_t UNUSED dxpl_id) { -GCC_DIAG_OFF(float-equal) +H5_GCC_DIAG_OFF(float-equal) H5T_CONV_Fx(DOUBLE, ULONG, double, unsigned long, 0, ULONG_MAX); -GCC_DIAG_ON(float-equal) +H5_GCC_DIAG_ON(float-equal) } @@ -8650,9 +8650,9 @@ H5T__conv_ldouble_long (hid_t src_id, hid_t dst_id, H5T_cdata_t *cdata, size_t UNUSED bkg_stride, void *buf, void UNUSED *bkg, hid_t UNUSED dxpl_id) { -GCC_DIAG_OFF(float-equal) +H5_GCC_DIAG_OFF(float-equal) H5T_CONV_Fx(LDOUBLE, LONG, long double, long, LONG_MIN, LONG_MAX); -GCC_DIAG_ON(float-equal) +H5_GCC_DIAG_ON(float-equal) } #endif /*H5T_CONV_INTERNAL_LDOUBLE_INTEGER*/ @@ -8679,9 +8679,9 @@ H5T__conv_ldouble_ulong (hid_t src_id, hid_t dst_id, H5T_cdata_t *cdata, size_t UNUSED bkg_stride, void *buf, void UNUSED *bkg, hid_t UNUSED dxpl_id) { -GCC_DIAG_OFF(float-equal) +H5_GCC_DIAG_OFF(float-equal) H5T_CONV_Fx(LDOUBLE, ULONG, long double, unsigned long, 0, ULONG_MAX); -GCC_DIAG_ON(float-equal) +H5_GCC_DIAG_ON(float-equal) } #endif /* H5T_CONV_INTERNAL_LDOUBLE_INTEGER */ @@ -8708,9 +8708,9 @@ H5T__conv_float_llong (hid_t src_id, hid_t dst_id, H5T_cdata_t *cdata, size_t UNUSED bkg_stride, void *buf, void UNUSED *bkg, hid_t UNUSED dxpl_id) { -GCC_DIAG_OFF(float-equal) +H5_GCC_DIAG_OFF(float-equal) H5T_CONV_Fx(FLOAT, LLONG, float, long long, LLONG_MIN, LLONG_MAX); -GCC_DIAG_ON(float-equal) +H5_GCC_DIAG_ON(float-equal) } #endif /* H5T_CONV_INTERNAL_FP_LLONG */ @@ -8764,9 +8764,9 @@ H5T__conv_double_llong (hid_t src_id, hid_t dst_id, H5T_cdata_t *cdata, size_t UNUSED bkg_stride, void *buf, void UNUSED *bkg, hid_t UNUSED dxpl_id) { -GCC_DIAG_OFF(float-equal) +H5_GCC_DIAG_OFF(float-equal) H5T_CONV_Fx(DOUBLE, LLONG, double, long long, LLONG_MIN, LLONG_MAX); -GCC_DIAG_ON(float-equal) +H5_GCC_DIAG_ON(float-equal) } #endif /*H5T_CONV_INTERNAL_FP_LLONG*/ @@ -8820,9 +8820,9 @@ H5T__conv_ldouble_llong (hid_t src_id, hid_t dst_id, H5T_cdata_t *cdata, size_t UNUSED bkg_stride, void *buf, void UNUSED *bkg, hid_t UNUSED dxpl_id) { -GCC_DIAG_OFF(float-equal) +H5_GCC_DIAG_OFF(float-equal) H5T_CONV_Fx(LDOUBLE, LLONG, long double, long long, LLONG_MIN, LLONG_MAX); -GCC_DIAG_ON(float-equal) +H5_GCC_DIAG_ON(float-equal) } #endif /*H5T_CONV_INTERNAL_LDOUBLE_LLONG*/ @@ -664,7 +664,13 @@ H5Zfilter_avail(H5Z_filter_t id) HGOTO_ERROR (H5E_ARGS, H5E_BADVALUE, FAIL, "invalid filter identification number") if((ret_value = H5Z_filter_avail(id)) < 0) - HGOTO_ERROR(H5E_PLINE, H5E_NOTFOUND, FAIL, "unable to check the availability of the filter") + HGOTO_ERROR(H5E_PLINE, H5E_NOTFOUND, FAIL, "unable to check the availability of the filter") + else if(ret_value == FALSE) { + const H5Z_class2_t *filter_info; + + if(NULL != (filter_info = (const H5Z_class2_t *)H5PL_load(H5PL_TYPE_FILTER, (int)id))) + ret_value = TRUE; + } /* end if */ done: FUNC_LEAVE_API(ret_value) @@ -1324,22 +1330,20 @@ H5Z_pipeline(const H5O_pline_t *pline, unsigned flags, */ if((fclass_idx = H5Z_find_idx(pline->filter[idx].id)) < 0) { hbool_t issue_error = FALSE; - - /* Check for "no plugins" indicated" */ - const H5Z_class2_t *filter_info; - - /* Try loading the filter */ - if(NULL != (filter_info = (const H5Z_class2_t *)H5PL_load(H5PL_TYPE_FILTER, (int)(pline->filter[idx].id)))) { - /* Register the filter we loaded */ - if(H5Z_register(filter_info) < 0) - HGOTO_ERROR(H5E_PLINE, H5E_CANTINIT, FAIL, "unable to register filter") - - /* Search in the table of registered filters again to find the dynamic filter just loaded and registered */ - if((fclass_idx = H5Z_find_idx(pline->filter[idx].id)) < 0) - issue_error = TRUE; - } /* end if */ - else - issue_error = TRUE; + const H5Z_class2_t *filter_info; + + /* Try loading the filter */ + if(NULL != (filter_info = (const H5Z_class2_t *)H5PL_load(H5PL_TYPE_FILTER, (int)(pline->filter[idx].id)))) { + /* Register the filter we loaded */ + if(H5Z_register(filter_info) < 0) + HGOTO_ERROR(H5E_PLINE, H5E_CANTINIT, FAIL, "unable to register filter") + + /* Search in the table of registered filters again to find the dynamic filter just loaded and registered */ + if((fclass_idx = H5Z_find_idx(pline->filter[idx].id)) < 0) + issue_error = TRUE; + } /* end if */ + else + issue_error = TRUE; /* Check for error */ if(issue_error) { diff --git a/src/H5Zdeflate.c b/src/H5Zdeflate.c index f318c2f..82ad1ba 100644 --- a/src/H5Zdeflate.c +++ b/src/H5Zdeflate.c @@ -51,7 +51,7 @@ const H5Z_class2_t H5Z_DEFLATE[1] = {{ H5Z_filter_deflate, /* The actual filter function */ }}; -#define H5Z_DEFLATE_SIZE_ADJUST(s) (HDceil(((double)(s))*1.001)+12) +#define H5Z_DEFLATE_SIZE_ADJUST(s) (HDceil(((double)(s)) * (double)1.001f) + 12) /*------------------------------------------------------------------------- diff --git a/src/H5Zshuffle.c b/src/H5Zshuffle.c index 90509b0..4a67839 100644 --- a/src/H5Zshuffle.c +++ b/src/H5Zshuffle.c @@ -81,7 +81,7 @@ H5Z_set_local_shuffle(hid_t dcpl_id, hid_t type_id, hid_t UNUSED space_id) HGOTO_ERROR(H5E_ATOM, H5E_BADATOM, FAIL, "can't find object for ID") /* Get datatype */ - if(NULL == (type = H5I_object_verify(type_id, H5I_DATATYPE))) + if(NULL == (type = (const H5T_t *)H5I_object_verify(type_id, H5I_DATATYPE))) HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "not a datatype") /* Get the filter's current parameters */ diff --git a/src/H5config.h.in b/src/H5config.h.in index 02bafd8..76de6c6 100644 --- a/src/H5config.h.in +++ b/src/H5config.h.in @@ -174,12 +174,6 @@ /* Define to 1 if you have the `get_fpc_csr' function. */ #undef HAVE_GET_FPC_CSR -/* Define if we have GPFS support */ -#undef HAVE_GPFS - -/* Define to 1 if you have the <gpfs.h> header file. */ -#undef HAVE_GPFS_H - /* Define if library will contain instrumentation to detect correct optimization operation */ #undef HAVE_INSTRUMENTED_LIBRARY diff --git a/src/H5detect.c b/src/H5detect.c index 0f8d051..aed7514 100644 --- a/src/H5detect.c +++ b/src/H5detect.c @@ -332,7 +332,7 @@ precision (detected_t *d) if(_v1 != _v2) \ _pad_mask[_i] |= _byte_mask; \ _buf1[_i] ^= _byte_mask; \ - } /* enf for */ \ + } /* end for */ \ \ /* Byte Order */ \ for(_i = 0, _v1 = 0.0, _v2 = 1.0; _i < (int)sizeof(TYPE); _i++) { \ diff --git a/src/H5private.h b/src/H5private.h index 859f518..89bff47 100644 --- a/src/H5private.h +++ b/src/H5private.h @@ -439,8 +439,8 @@ /* * Maximum & minimum values for our typedefs. */ -#define HSIZET_MAX ((hsize_t)ULLONG_MAX) -#define HSSIZET_MAX ((hssize_t)LLONG_MAX) +#define HSIZET_MAX ((hsize_t)ULLONG_MAX) +#define HSSIZET_MAX ((hssize_t)LLONG_MAX) #define HSSIZET_MIN (~(HSSIZET_MAX)) /* @@ -2363,25 +2363,6 @@ func_init_failed: \ #define HDcompile_assert(e) do { typedef struct { unsigned int b: (e); } x; } while(0) */ -/* Macros for enabling/disabling particular GCC warnings */ -/* (see the following web-sites for more info: - * http://www.dbp-consulting.com/tutorials/SuppressingGCCWarnings.html - * http://gcc.gnu.org/onlinedocs/gcc/Diagnostic-Pragmas.html#Diagnostic-Pragmas - */ -/* These pragmas are only implemented usefully in gcc 4.6+ */ -#if ((__GNUC__ * 100) + __GNUC_MINOR__) >= 406 - #define GCC_DIAG_STR(s) #s - #define GCC_DIAG_JOINSTR(x,y) GCC_DIAG_STR(x ## y) - #define GCC_DIAG_DO_PRAGMA(x) _Pragma (#x) - #define GCC_DIAG_PRAGMA(x) GCC_DIAG_DO_PRAGMA(GCC diagnostic x) - - #define GCC_DIAG_OFF(x) GCC_DIAG_PRAGMA(push) GCC_DIAG_PRAGMA(ignored GCC_DIAG_JOINSTR(-W,x)) - #define GCC_DIAG_ON(x) GCC_DIAG_PRAGMA(pop) -#else - #define GCC_DIAG_OFF(x) - #define GCC_DIAG_ON(x) -#endif - /* Private functions, not part of the publicly documented API */ H5_DLL herr_t H5_init_library(void); H5_DLL void H5_term_library(void); diff --git a/src/H5public.h b/src/H5public.h index 5bfc909..9312f15 100644 --- a/src/H5public.h +++ b/src/H5public.h @@ -72,13 +72,32 @@ extern "C" { #endif +/* Macros for enabling/disabling particular GCC warnings */ +/* (see the following web-sites for more info: + * http://www.dbp-consulting.com/tutorials/SuppressingGCCWarnings.html + * http://gcc.gnu.org/onlinedocs/gcc/Diagnostic-Pragmas.html#Diagnostic-Pragmas + */ +/* These pragmas are only implemented usefully in gcc 4.6+ */ +#if ((__GNUC__ * 100) + __GNUC_MINOR__) >= 406 + #define H5_GCC_DIAG_STR(s) #s + #define H5_GCC_DIAG_JOINSTR(x,y) H5_GCC_DIAG_STR(x ## y) + #define H5_GCC_DIAG_DO_PRAGMA(x) _Pragma (#x) + #define H5_GCC_DIAG_PRAGMA(x) H5_GCC_DIAG_DO_PRAGMA(GCC diagnostic x) + + #define H5_GCC_DIAG_OFF(x) H5_GCC_DIAG_PRAGMA(push) H5_GCC_DIAG_PRAGMA(ignored H5_GCC_DIAG_JOINSTR(-W,x)) + #define H5_GCC_DIAG_ON(x) H5_GCC_DIAG_PRAGMA(pop) +#else + #define H5_GCC_DIAG_OFF(x) + #define H5_GCC_DIAG_ON(x) +#endif + /* Version numbers */ #define H5_VERS_MAJOR 1 /* For major interface/format changes */ #define H5_VERS_MINOR 9 /* For minor interface/format changes */ -#define H5_VERS_RELEASE 172 /* For tweaks, bug-fixes, or development */ +#define H5_VERS_RELEASE 176 /* For tweaks, bug-fixes, or development */ #define H5_VERS_SUBRELEASE "" /* For pre-releases like snap0 */ /* Empty string for real releases. */ -#define H5_VERS_INFO "HDF5 library version: 1.9.172" /* Full version string */ +#define H5_VERS_INFO "HDF5 library version: 1.9.176" /* Full version string */ #define H5check() H5check_version(H5_VERS_MAJOR,H5_VERS_MINOR, \ H5_VERS_RELEASE) @@ -148,8 +167,10 @@ typedef long long ssize_t; * type. */ #if H5_SIZEOF_LONG_LONG >= 8 +H5_GCC_DIAG_OFF(long-long) typedef unsigned long long hsize_t; typedef signed long long hssize_t; +H5_GCC_DIAG_ON(long-long) # define H5_SIZEOF_HSIZE_T H5_SIZEOF_LONG_LONG # define H5_SIZEOF_HSSIZE_T H5_SIZEOF_LONG_LONG #else @@ -313,6 +334,7 @@ H5_DLL herr_t H5get_libversion(unsigned *majnum, unsigned *minnum, unsigned *relnum); H5_DLL herr_t H5check_version(unsigned majnum, unsigned minnum, unsigned relnum); +H5_DLL herr_t H5free_memory(void *mem); #ifdef __cplusplus } diff --git a/src/H5system.c b/src/H5system.c index 614b8b9..437a004 100644 --- a/src/H5system.c +++ b/src/H5system.c @@ -200,20 +200,28 @@ HDfprintf(FILE *stream, const char *fmt, ...) case 'H': if(sizeof(hsize_t) < sizeof(long)) modifier[0] = '\0'; - else if(sizeof(hsize_t) == sizeof(long)) - HDstrncpy(modifier, "l", (size_t)2); - else - HDstrncpy(modifier, H5_PRINTF_LL_WIDTH, HDstrlen(H5_PRINTF_LL_WIDTH) + 1); + else if(sizeof(hsize_t) == sizeof(long)) { + HDstrncpy(modifier, "l", sizeof(modifier)); + modifier[sizeof(modifier) - 1] = '\0'; + } /* end if */ + else { + HDstrncpy(modifier, H5_PRINTF_LL_WIDTH, sizeof(modifier)); + modifier[sizeof(modifier) - 1] = '\0'; + } /* end else */ break; case 'Z': case 'z': if(sizeof(size_t) < sizeof(long)) modifier[0] = '\0'; - else if(sizeof(size_t) == sizeof(long)) - HDstrncpy(modifier, "l", (size_t)2); - else - HDstrncpy(modifier, H5_PRINTF_LL_WIDTH, HDstrlen(H5_PRINTF_LL_WIDTH) + 1); + else if(sizeof(size_t) == sizeof(long)) { + HDstrncpy(modifier, "l", sizeof(modifier)); + modifier[sizeof(modifier) - 1] = '\0'; + } /* end if */ + else { + HDstrncpy(modifier, H5_PRINTF_LL_WIDTH, sizeof(modifier)); + modifier[sizeof(modifier) - 1] = '\0'; + } /* end else */ break; default: diff --git a/src/H5trace.c b/src/H5trace.c index 6dcabd0..a293c4d 100644 --- a/src/H5trace.c +++ b/src/H5trace.c @@ -544,48 +544,45 @@ H5_trace(const double *returning, const char *func, const char *type, ...) } /* end if */ else { H5D_mpio_no_collective_cause_t nocol_cause_mode = (H5D_mpio_no_collective_cause_t)va_arg(ap, int); + hbool_t flag_already_displayed = FALSE; - switch(nocol_cause_mode) { - case H5D_MPIO_COLLECTIVE: - fprintf(out, "H5D_MPIO_COLLECTIVE"); - break; - - case H5D_MPIO_SET_INDEPENDENT: - fprintf(out, "H5D_MPIO_SET_INDEPENDENT"); - break; - - case H5D_MPIO_DATATYPE_CONVERSION: - fprintf(out, "H5D_MPIO_DATATYPE_CONVERSION"); - break; - - case H5D_MPIO_DATA_TRANSFORMS: - fprintf(out, "H5D_MPIO_DATA_TRANSFORMS"); - break; - - case H5D_MPIO_SET_MPIPOSIX: - fprintf(out, "H5D_MPIO_SET_MPIPOSIX"); - break; - - case H5D_MPIO_NOT_SIMPLE_OR_SCALAR_DATASPACES: - fprintf(out, "H5D_MPIO_NOT_SIMPLE_OR_SCALAR_DATASPACES"); - break; - - case H5D_MPIO_POINT_SELECTIONS: - fprintf(out, "H5D_MPIO_POINT_SELECTIONS"); - break; - - case H5D_MPIO_NOT_CONTIGUOUS_OR_CHUNKED_DATASET: - fprintf(out, "H5D_MPIO_NOT_CONTIGUOUS_OR_CHUNKED_DATASET"); - break; - - case H5D_MPIO_FILTERS: - fprintf(out, "H5D_MPIO_FILTERS"); - break; + /* Check for all bit-flags which might be set */ + if(nocol_cause_mode & H5D_MPIO_COLLECTIVE) { + fprintf(out, "H5D_MPIO_COLLECTIVE"); + flag_already_displayed = TRUE; + } /* end if */ + if(nocol_cause_mode & H5D_MPIO_SET_INDEPENDENT) { + fprintf(out, "%sH5D_MPIO_SET_INDEPENDENT", flag_already_displayed ? " | " : ""); + flag_already_displayed = TRUE; + } /* end if */ + if(nocol_cause_mode & H5D_MPIO_DATATYPE_CONVERSION) { + fprintf(out, "%sH5D_MPIO_DATATYPE_CONVERSION", flag_already_displayed ? " | " : ""); + flag_already_displayed = TRUE; + } /* end if */ + if(nocol_cause_mode & H5D_MPIO_DATA_TRANSFORMS) { + fprintf(out, "%sH5D_MPIO_DATA_TRANSFORMS", flag_already_displayed ? " | " : ""); + flag_already_displayed = TRUE; + } /* end if */ + if(nocol_cause_mode & H5D_MPIO_MPI_OPT_TYPES_ENV_VAR_DISABLED) { + fprintf(out, "%sH5D_MPIO_MPI_OPT_TYPES_ENV_VAR_DISABLED", flag_already_displayed ? " | " : ""); + flag_already_displayed = TRUE; + } /* end if */ + if(nocol_cause_mode & H5D_MPIO_NOT_SIMPLE_OR_SCALAR_DATASPACES) { + fprintf(out, "%sH5D_MPIO_NOT_SIMPLE_OR_SCALAR_DATASPACES", flag_already_displayed ? " | " : ""); + flag_already_displayed = TRUE; + } /* end if */ + if(nocol_cause_mode & H5D_MPIO_NOT_CONTIGUOUS_OR_CHUNKED_DATASET) { + fprintf(out, "%sH5D_MPIO_NOT_CONTIGUOUS_OR_CHUNKED_DATASET", flag_already_displayed ? " | " : ""); + flag_already_displayed = TRUE; + } /* end if */ + if(nocol_cause_mode & H5D_MPIO_FILTERS) { + fprintf(out, "%sH5D_MPIO_FILTERS", flag_already_displayed ? " | " : ""); + flag_already_displayed = TRUE; + } /* end if */ - default: - fprintf(out, "%ld", (long)nocol_cause_mode); - break; - } /* end switch */ + /* Display '<none>' if there's no flags set */ + if(!flag_already_displayed) + fprintf(out, "<none>"); } /* end else */ break; diff --git a/src/Makefile.am b/src/Makefile.am index 7e843a0..f021b7c 100644 --- a/src/Makefile.am +++ b/src/Makefile.am @@ -61,7 +61,7 @@ libhdf5_la_SOURCES= H5.c H5checksum.c H5dbg.c H5system.c H5timer.c H5trace.c \ H5VL.c H5VLint.c H5VLnative.c \ H5FD.c H5FDcore.c \ H5FDdirect.c H5FDfamily.c H5FDint.c H5FDlog.c H5FDmpi.c H5FDmpio.c \ - H5FDmpiposix.c H5FDmulti.c H5FDsec2.c H5FDspace.c H5FDstdio.c \ + H5FDmulti.c H5FDsec2.c H5FDspace.c H5FDstdio.c \ H5FL.c H5FO.c H5FS.c H5FScache.c H5FSdbg.c H5FSsection.c H5FSstat.c H5FStest.c \ H5G.c H5Gbtree2.c H5Gcache.c \ H5Gcompact.c H5Gdense.c H5Gdeprec.c H5Gent.c \ @@ -114,8 +114,9 @@ libhdf5_la_SOURCES= H5.c H5checksum.c H5dbg.c H5system.c H5timer.c H5trace.c \ include_HEADERS = hdf5.h H5api_adpt.h H5overflow.h H5pubconf.h H5public.h H5version.h \ H5Apublic.h H5ACpublic.h \ H5Cpublic.h H5Dpublic.h \ - H5Epubgen.h H5Epublic.h H5Fpublic.h H5FDpublic.h H5FDcore.h H5FDdirect.h \ - H5FDfamily.h H5FDlog.h H5FDmpi.h H5FDmpio.h H5FDmpiposix.h \ + H5Epubgen.h H5Epublic.h H5Fpublic.h \ + H5FDpublic.h H5FDcore.h H5FDdirect.h \ + H5FDfamily.h H5FDlog.h H5FDmpi.h H5FDmpio.h \ H5FDmulti.h H5FDsec2.h H5FDstdio.h \ H5VLpublic.h H5VLnative.h \ H5Gpublic.h H5Ipublic.h H5Lpublic.h \ diff --git a/src/Makefile.in b/src/Makefile.in index 8408524..5e002b4 100644 --- a/src/Makefile.in +++ b/src/Makefile.in @@ -1,7 +1,7 @@ -# Makefile.in generated by automake 1.12.3 from Makefile.am. +# Makefile.in generated by automake 1.14.1 from Makefile.am. # @configure_input@ -# Copyright (C) 1994-2012 Free Software Foundation, Inc. +# Copyright (C) 1994-2013 Free Software Foundation, Inc. # This Makefile.in is free software; the Free Software Foundation # gives unlimited permission to copy and/or distribute it, @@ -35,23 +35,51 @@ VPATH = @srcdir@ -am__make_dryrun = \ - { \ - am__dry=no; \ +am__is_gnu_make = test -n '$(MAKEFILE_LIST)' && test -n '$(MAKELEVEL)' +am__make_running_with_option = \ + case $${target_option-} in \ + ?) ;; \ + *) echo "am__make_running_with_option: internal error: invalid" \ + "target option '$${target_option-}' specified" >&2; \ + exit 1;; \ + esac; \ + has_opt=no; \ + sane_makeflags=$$MAKEFLAGS; \ + if $(am__is_gnu_make); then \ + sane_makeflags=$$MFLAGS; \ + else \ case $$MAKEFLAGS in \ *\\[\ \ ]*) \ - echo 'am--echo: ; @echo "AM" OK' | $(MAKE) -f - 2>/dev/null \ - | grep '^AM OK$$' >/dev/null || am__dry=yes;; \ - *) \ - for am__flg in $$MAKEFLAGS; do \ - case $$am__flg in \ - *=*|--*) ;; \ - *n*) am__dry=yes; break;; \ - esac; \ - done;; \ + bs=\\; \ + sane_makeflags=`printf '%s\n' "$$MAKEFLAGS" \ + | sed "s/$$bs$$bs[$$bs $$bs ]*//g"`;; \ esac; \ - test $$am__dry = yes; \ - } + fi; \ + skip_next=no; \ + strip_trailopt () \ + { \ + flg=`printf '%s\n' "$$flg" | sed "s/$$1.*$$//"`; \ + }; \ + for flg in $$sane_makeflags; do \ + test $$skip_next = yes && { skip_next=no; continue; }; \ + case $$flg in \ + *=*|--*) continue;; \ + -*I) strip_trailopt 'I'; skip_next=yes;; \ + -*I?*) strip_trailopt 'I';; \ + -*O) strip_trailopt 'O'; skip_next=yes;; \ + -*O?*) strip_trailopt 'O';; \ + -*l) strip_trailopt 'l'; skip_next=yes;; \ + -*l?*) strip_trailopt 'l';; \ + -[dEDm]) skip_next=yes;; \ + -[JT]) skip_next=yes;; \ + esac; \ + case $$flg in \ + *$$target_option*) has_opt=yes; break;; \ + esac; \ + done; \ + test $$has_opt = yes +am__make_dryrun = (target_option=n; $(am__make_running_with_option)) +am__make_keepgoing = (target_option=k; $(am__make_running_with_option)) pkgdatadir = $(datadir)/@PACKAGE@ pkgincludedir = $(includedir)/@PACKAGE@ pkglibdir = $(libdir)/@PACKAGE@ @@ -70,13 +98,13 @@ PRE_UNINSTALL = : POST_UNINSTALL = : build_triplet = @build@ host_triplet = @host@ -DIST_COMMON = $(include_HEADERS) $(srcdir)/H5config.h.in \ - $(srcdir)/Makefile.am $(srcdir)/Makefile.in \ - $(srcdir)/libhdf5.settings.in $(top_srcdir)/bin/depcomp \ - $(top_srcdir)/bin/mkinstalldirs \ - $(top_srcdir)/config/commence.am \ - $(top_srcdir)/config/conclude.am \ - $(top_srcdir)/config/lt_vers.am COPYING +DIST_COMMON = $(top_srcdir)/config/commence.am \ + $(top_srcdir)/config/lt_vers.am \ + $(top_srcdir)/config/conclude.am $(srcdir)/Makefile.in \ + $(srcdir)/Makefile.am $(srcdir)/H5config.h.in \ + $(top_srcdir)/bin/mkinstalldirs $(srcdir)/libhdf5.settings.in \ + $(top_srcdir)/bin/depcomp $(include_HEADERS) \ + $(top_srcdir)/bin/test-driver COPYING noinst_PROGRAMS = H5detect$(EXEEXT) H5make_libsettings$(EXEEXT) TESTS = subdir = src @@ -137,13 +165,13 @@ am_libhdf5_la_OBJECTS = H5.lo H5checksum.lo H5dbg.lo H5system.lo \ H5FAdblkpage.lo H5FAhdr.lo H5FAstat.lo H5FAtest.lo H5VL.lo \ H5VLint.lo H5VLnative.lo H5FD.lo H5FDcore.lo H5FDdirect.lo \ H5FDfamily.lo H5FDint.lo H5FDlog.lo H5FDmpi.lo H5FDmpio.lo \ - H5FDmpiposix.lo H5FDmulti.lo H5FDsec2.lo H5FDspace.lo \ - H5FDstdio.lo H5FL.lo H5FO.lo H5FS.lo H5FScache.lo H5FSdbg.lo \ - H5FSsection.lo H5FSstat.lo H5FStest.lo H5G.lo H5Gbtree2.lo \ - H5Gcache.lo H5Gcompact.lo H5Gdense.lo H5Gdeprec.lo H5Gent.lo \ - H5Gint.lo H5Glink.lo H5Gloc.lo H5Gname.lo H5Gnode.lo H5Gobj.lo \ - H5Goh.lo H5Groot.lo H5Gstab.lo H5Gtest.lo H5Gtraverse.lo \ - H5HF.lo H5HFbtree2.lo H5HFcache.lo H5HFdbg.lo H5HFdblock.lo \ + H5FDmulti.lo H5FDsec2.lo H5FDspace.lo H5FDstdio.lo H5FL.lo \ + H5FO.lo H5FS.lo H5FScache.lo H5FSdbg.lo H5FSsection.lo \ + H5FSstat.lo H5FStest.lo H5G.lo H5Gbtree2.lo H5Gcache.lo \ + H5Gcompact.lo H5Gdense.lo H5Gdeprec.lo H5Gent.lo H5Gint.lo \ + H5Glink.lo H5Gloc.lo H5Gname.lo H5Gnode.lo H5Gobj.lo H5Goh.lo \ + H5Groot.lo H5Gstab.lo H5Gtest.lo H5Gtraverse.lo H5HF.lo \ + H5HFbtree2.lo H5HFcache.lo H5HFdbg.lo H5HFdblock.lo \ H5HFdtable.lo H5HFhdr.lo H5HFhuge.lo H5HFiblock.lo H5HFiter.lo \ H5HFman.lo H5HFsection.lo H5HFspace.lo H5HFstat.lo H5HFtest.lo \ H5HFtiny.lo H5HG.lo H5HGcache.lo H5HGdbg.lo H5HGquery.lo \ @@ -230,12 +258,199 @@ am__can_run_installinfo = \ esac DATA = $(settings_DATA) HEADERS = $(include_HEADERS) +am__tagged_files = $(HEADERS) $(SOURCES) $(TAGS_FILES) \ + $(LISP)H5config.h.in +# Read a list of newline-separated strings from the standard input, +# and print each of them once, without duplicates. Input order is +# *not* preserved. +am__uniquify_input = $(AWK) '\ + BEGIN { nonempty = 0; } \ + { items[$$0] = 1; nonempty = 1; } \ + END { if (nonempty) { for (i in items) print i; }; } \ +' +# Make sure the list of sources is unique. This is necessary because, +# e.g., the same source file might be shared among _SOURCES variables +# for different programs/libraries. +am__define_uniq_tagged_files = \ + list='$(am__tagged_files)'; \ + unique=`for i in $$list; do \ + if test -f "$$i"; then echo $$i; else echo $(srcdir)/$$i; fi; \ + done | $(am__uniquify_input)` ETAGS = etags CTAGS = ctags am__tty_colors_dummy = \ mgn= red= grn= lgn= blu= brg= std=; \ am__color_tests=no -am__tty_colors = $(am__tty_colors_dummy) +am__tty_colors = { \ + $(am__tty_colors_dummy); \ + if test "X$(AM_COLOR_TESTS)" = Xno; then \ + am__color_tests=no; \ + elif test "X$(AM_COLOR_TESTS)" = Xalways; then \ + am__color_tests=yes; \ + elif test "X$$TERM" != Xdumb && { test -t 1; } 2>/dev/null; then \ + am__color_tests=yes; \ + fi; \ + if test $$am__color_tests = yes; then \ + red='[0;31m'; \ + grn='[0;32m'; \ + lgn='[1;32m'; \ + blu='[1;34m'; \ + mgn='[0;35m'; \ + brg='[1m'; \ + std='[m'; \ + fi; \ +} +am__recheck_rx = ^[ ]*:recheck:[ ]* +am__global_test_result_rx = ^[ ]*:global-test-result:[ ]* +am__copy_in_global_log_rx = ^[ ]*:copy-in-global-log:[ ]* +# A command that, given a newline-separated list of test names on the +# standard input, print the name of the tests that are to be re-run +# upon "make recheck". +am__list_recheck_tests = $(AWK) '{ \ + recheck = 1; \ + while ((rc = (getline line < ($$0 ".trs"))) != 0) \ + { \ + if (rc < 0) \ + { \ + if ((getline line2 < ($$0 ".log")) < 0) \ + recheck = 0; \ + break; \ + } \ + else if (line ~ /$(am__recheck_rx)[nN][Oo]/) \ + { \ + recheck = 0; \ + break; \ + } \ + else if (line ~ /$(am__recheck_rx)[yY][eE][sS]/) \ + { \ + break; \ + } \ + }; \ + if (recheck) \ + print $$0; \ + close ($$0 ".trs"); \ + close ($$0 ".log"); \ +}' +# A command that, given a newline-separated list of test names on the +# standard input, create the global log from their .trs and .log files. +am__create_global_log = $(AWK) ' \ +function fatal(msg) \ +{ \ + print "fatal: making $@: " msg | "cat >&2"; \ + exit 1; \ +} \ +function rst_section(header) \ +{ \ + print header; \ + len = length(header); \ + for (i = 1; i <= len; i = i + 1) \ + printf "="; \ + printf "\n\n"; \ +} \ +{ \ + copy_in_global_log = 1; \ + global_test_result = "RUN"; \ + while ((rc = (getline line < ($$0 ".trs"))) != 0) \ + { \ + if (rc < 0) \ + fatal("failed to read from " $$0 ".trs"); \ + if (line ~ /$(am__global_test_result_rx)/) \ + { \ + sub("$(am__global_test_result_rx)", "", line); \ + sub("[ ]*$$", "", line); \ + global_test_result = line; \ + } \ + else if (line ~ /$(am__copy_in_global_log_rx)[nN][oO]/) \ + copy_in_global_log = 0; \ + }; \ + if (copy_in_global_log) \ + { \ + rst_section(global_test_result ": " $$0); \ + while ((rc = (getline line < ($$0 ".log"))) != 0) \ + { \ + if (rc < 0) \ + fatal("failed to read from " $$0 ".log"); \ + print line; \ + }; \ + printf "\n"; \ + }; \ + close ($$0 ".trs"); \ + close ($$0 ".log"); \ +}' +# Restructured Text title. +am__rst_title = { sed 's/.*/ & /;h;s/./=/g;p;x;s/ *$$//;p;g' && echo; } +# Solaris 10 'make', and several other traditional 'make' implementations, +# pass "-e" to $(SHELL), and POSIX 2008 even requires this. Work around it +# by disabling -e (using the XSI extension "set +e") if it's set. +am__sh_e_setup = case $$- in *e*) set +e;; esac +# Default flags passed to test drivers. +am__common_driver_flags = \ + --color-tests "$$am__color_tests" \ + --enable-hard-errors "$$am__enable_hard_errors" \ + --expect-failure "$$am__expect_failure" +# To be inserted before the command running the test. Creates the +# directory for the log if needed. Stores in $dir the directory +# containing $f, in $tst the test, in $log the log. Executes the +# developer- defined test setup AM_TESTS_ENVIRONMENT (if any), and +# passes TESTS_ENVIRONMENT. Set up options for the wrapper that +# will run the test scripts (or their associated LOG_COMPILER, if +# thy have one). +am__check_pre = \ +$(am__sh_e_setup); \ +$(am__vpath_adj_setup) $(am__vpath_adj) \ +$(am__tty_colors); \ +srcdir=$(srcdir); export srcdir; \ +case "$@" in \ + */*) am__odir=`echo "./$@" | sed 's|/[^/]*$$||'`;; \ + *) am__odir=.;; \ +esac; \ +test "x$$am__odir" = x"." || test -d "$$am__odir" \ + || $(MKDIR_P) "$$am__odir" || exit $$?; \ +if test -f "./$$f"; then dir=./; \ +elif test -f "$$f"; then dir=; \ +else dir="$(srcdir)/"; fi; \ +tst=$$dir$$f; log='$@'; \ +if test -n '$(DISABLE_HARD_ERRORS)'; then \ + am__enable_hard_errors=no; \ +else \ + am__enable_hard_errors=yes; \ +fi; \ +case " $(XFAIL_TESTS) " in \ + *[\ \ ]$$f[\ \ ]* | *[\ \ ]$$dir$$f[\ \ ]*) \ + am__expect_failure=yes;; \ + *) \ + am__expect_failure=no;; \ +esac; \ +$(AM_TESTS_ENVIRONMENT) $(TESTS_ENVIRONMENT) +# A shell command to get the names of the tests scripts with any registered +# extension removed (i.e., equivalently, the names of the test logs, with +# the '.log' extension removed). The result is saved in the shell variable +# '$bases'. This honors runtime overriding of TESTS and TEST_LOGS. Sadly, +# we cannot use something simpler, involving e.g., "$(TEST_LOGS:.log=)", +# since that might cause problem with VPATH rewrites for suffix-less tests. +# See also 'test-harness-vpath-rewrite.sh' and 'test-trs-basic.sh'. +am__set_TESTS_bases = \ + bases='$(TEST_LOGS)'; \ + bases=`for i in $$bases; do echo $$i; done | sed 's/\.log$$//'`; \ + bases=`echo $$bases` +RECHECK_LOGS = $(TEST_LOGS) +AM_RECURSIVE_TARGETS = check recheck +TEST_SUITE_LOG = test-suite.log +am__test_logs1 = $(TESTS:=.log) +am__test_logs2 = $(am__test_logs1:@EXEEXT@.log=.log) +TEST_LOGS = $(am__test_logs2:.sh.log=.log) +SH_LOG_DRIVER = $(SHELL) $(top_srcdir)/bin/test-driver +SH_LOG_COMPILE = $(SH_LOG_COMPILER) $(AM_SH_LOG_FLAGS) $(SH_LOG_FLAGS) +am__set_b = \ + case '$@' in \ + */*) \ + case '$*' in \ + */*) b='$*';; \ + *) b=`echo '$@' | sed 's/\.log$$//'`; \ + esac;; \ + *) \ + b='$*';; \ + esac DISTFILES = $(DIST_COMMON) $(DIST_SOURCES) $(TEXINFOS) $(EXTRA_DIST) ACLOCAL = @ACLOCAL@ ADD_PARALLEL_FILES = @ADD_PARALLEL_FILES@ @@ -307,7 +522,6 @@ FC_VERSION = @FC_VERSION@ FGREP = @FGREP@ FILTERS = @FILTERS@ FSEARCH_DIRS = @FSEARCH_DIRS@ -GPFS = @GPFS@ GREP = @GREP@ H5_CFLAGS = @H5_CFLAGS@ H5_CPPFLAGS = @H5_CPPFLAGS@ @@ -520,7 +734,7 @@ CHECK_CLEANFILES = *.chkexe *.chklog *.clog # Add libtool shared library version numbers to the HDF5 library # See libtool versioning documentation online. LT_VERS_INTERFACE = 6 -LT_VERS_REVISION = 162 +LT_VERS_REVISION = 166 LT_VERS_AGE = 0 # Our main target, the HDF5 library @@ -556,7 +770,7 @@ libhdf5_la_SOURCES = H5.c H5checksum.c H5dbg.c H5system.c H5timer.c H5trace.c \ H5VL.c H5VLint.c H5VLnative.c \ H5FD.c H5FDcore.c \ H5FDdirect.c H5FDfamily.c H5FDint.c H5FDlog.c H5FDmpi.c H5FDmpio.c \ - H5FDmpiposix.c H5FDmulti.c H5FDsec2.c H5FDspace.c H5FDstdio.c \ + H5FDmulti.c H5FDsec2.c H5FDspace.c H5FDstdio.c \ H5FL.c H5FO.c H5FS.c H5FScache.c H5FSdbg.c H5FSsection.c H5FSstat.c H5FStest.c \ H5G.c H5Gbtree2.c H5Gcache.c \ H5Gcompact.c H5Gdense.c H5Gdeprec.c H5Gent.c \ @@ -609,8 +823,9 @@ libhdf5_la_SOURCES = H5.c H5checksum.c H5dbg.c H5system.c H5timer.c H5trace.c \ include_HEADERS = hdf5.h H5api_adpt.h H5overflow.h H5pubconf.h H5public.h H5version.h \ H5Apublic.h H5ACpublic.h \ H5Cpublic.h H5Dpublic.h \ - H5Epubgen.h H5Epublic.h H5Fpublic.h H5FDpublic.h H5FDcore.h H5FDdirect.h \ - H5FDfamily.h H5FDlog.h H5FDmpi.h H5FDmpio.h H5FDmpiposix.h \ + H5Epubgen.h H5Epublic.h H5Fpublic.h \ + H5FDpublic.h H5FDcore.h H5FDdirect.h \ + H5FDfamily.h H5FDlog.h H5FDmpi.h H5FDmpio.h \ H5FDmulti.h H5FDsec2.h H5FDstdio.h \ H5VLpublic.h H5VLnative.h \ H5Gpublic.h H5Ipublic.h H5Lpublic.h \ @@ -647,7 +862,7 @@ all: H5config.h $(MAKE) $(AM_MAKEFLAGS) all-am .SUFFIXES: -.SUFFIXES: .c .lo .o .obj +.SUFFIXES: .c .lo .log .o .obj .sh .sh$(EXEEXT) .trs $(srcdir)/Makefile.in: @MAINTAINER_MODE_TRUE@ $(srcdir)/Makefile.am $(top_srcdir)/config/commence.am $(top_srcdir)/config/lt_vers.am $(top_srcdir)/config/conclude.am $(am__configure_deps) @for dep in $?; do \ case '$(am__configure_deps)' in \ @@ -681,8 +896,8 @@ $(ACLOCAL_M4): @MAINTAINER_MODE_TRUE@ $(am__aclocal_m4_deps) $(am__aclocal_m4_deps): H5config.h: stamp-h1 - @if test ! -f $@; then rm -f stamp-h1; else :; fi - @if test ! -f $@; then $(MAKE) $(AM_MAKEFLAGS) stamp-h1; else :; fi + @test -f $@ || rm -f stamp-h1 + @test -f $@ || $(MAKE) $(AM_MAKEFLAGS) stamp-h1 stamp-h1: $(srcdir)/H5config.h.in $(top_builddir)/config.status @rm -f stamp-h1 @@ -696,6 +911,7 @@ distclean-hdr: -rm -f H5config.h stamp-h1 libhdf5.settings: $(top_builddir)/config.status $(srcdir)/libhdf5.settings.in cd $(top_builddir) && $(SHELL) ./config.status $(subdir)/$@ + install-libLTLIBRARIES: $(lib_LTLIBRARIES) @$(NORMAL_INSTALL) @list='$(lib_LTLIBRARIES)'; test -n "$(libdir)" || list=; \ @@ -730,6 +946,7 @@ clean-libLTLIBRARIES: echo rm -f $${locs}; \ rm -f $${locs}; \ } + libhdf5.la: $(libhdf5_la_OBJECTS) $(libhdf5_la_DEPENDENCIES) $(EXTRA_libhdf5_la_DEPENDENCIES) $(AM_V_CCLD)$(libhdf5_la_LINK) -rpath $(libdir) $(libhdf5_la_OBJECTS) $(libhdf5_la_LIBADD) $(LIBS) @@ -741,9 +958,11 @@ clean-noinstPROGRAMS: list=`for p in $$list; do echo "$$p"; done | sed 's/$(EXEEXT)$$//'`; \ echo " rm -f" $$list; \ rm -f $$list + H5detect$(EXEEXT): $(H5detect_OBJECTS) $(H5detect_DEPENDENCIES) $(EXTRA_H5detect_DEPENDENCIES) @rm -f H5detect$(EXEEXT) $(AM_V_CCLD)$(LINK) $(H5detect_OBJECTS) $(H5detect_LDADD) $(LIBS) + H5make_libsettings$(EXEEXT): $(H5make_libsettings_OBJECTS) $(H5make_libsettings_DEPENDENCIES) $(EXTRA_H5make_libsettings_DEPENDENCIES) @rm -f H5make_libsettings$(EXEEXT) $(AM_V_CCLD)$(LINK) $(H5make_libsettings_OBJECTS) $(H5make_libsettings_LDADD) $(LIBS) @@ -822,7 +1041,6 @@ distclean-compile: @AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/H5FDlog.Plo@am__quote@ @AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/H5FDmpi.Plo@am__quote@ @AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/H5FDmpio.Plo@am__quote@ -@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/H5FDmpiposix.Plo@am__quote@ @AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/H5FDmulti.Plo@am__quote@ @AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/H5FDsec2.Plo@am__quote@ @AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/H5FDspace.Plo@am__quote@ @@ -1028,14 +1246,14 @@ distclean-compile: @am__fastdepCC_TRUE@ $(AM_V_at)$(am__mv) $(DEPDIR)/$*.Tpo $(DEPDIR)/$*.Po @AMDEP_TRUE@@am__fastdepCC_FALSE@ $(AM_V_CC)source='$<' object='$@' libtool=no @AMDEPBACKSLASH@ @AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@ -@am__fastdepCC_FALSE@ $(AM_V_CC@am__nodep@)$(COMPILE) -c $< +@am__fastdepCC_FALSE@ $(AM_V_CC@am__nodep@)$(COMPILE) -c -o $@ $< .c.obj: @am__fastdepCC_TRUE@ $(AM_V_CC)$(COMPILE) -MT $@ -MD -MP -MF $(DEPDIR)/$*.Tpo -c -o $@ `$(CYGPATH_W) '$<'` @am__fastdepCC_TRUE@ $(AM_V_at)$(am__mv) $(DEPDIR)/$*.Tpo $(DEPDIR)/$*.Po @AMDEP_TRUE@@am__fastdepCC_FALSE@ $(AM_V_CC)source='$<' object='$@' libtool=no @AMDEPBACKSLASH@ @AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@ -@am__fastdepCC_FALSE@ $(AM_V_CC@am__nodep@)$(COMPILE) -c `$(CYGPATH_W) '$<'` +@am__fastdepCC_FALSE@ $(AM_V_CC@am__nodep@)$(COMPILE) -c -o $@ `$(CYGPATH_W) '$<'` .c.lo: @am__fastdepCC_TRUE@ $(AM_V_CC)$(LTCOMPILE) -MT $@ -MD -MP -MF $(DEPDIR)/$*.Tpo -c -o $@ $< @@ -1092,26 +1310,15 @@ uninstall-includeHEADERS: files=`for p in $$list; do echo $$p; done | sed -e 's|^.*/||'`; \ dir='$(DESTDIR)$(includedir)'; $(am__uninstall_files_from_dir) -ID: $(HEADERS) $(SOURCES) $(LISP) $(TAGS_FILES) - list='$(SOURCES) $(HEADERS) $(LISP) $(TAGS_FILES)'; \ - unique=`for i in $$list; do \ - if test -f "$$i"; then echo $$i; else echo $(srcdir)/$$i; fi; \ - done | \ - $(AWK) '{ files[$$0] = 1; nonempty = 1; } \ - END { if (nonempty) { for (i in files) print i; }; }'`; \ - mkid -fID $$unique -tags: TAGS - -TAGS: $(HEADERS) $(SOURCES) H5config.h.in $(TAGS_DEPENDENCIES) \ - $(TAGS_FILES) $(LISP) +ID: $(am__tagged_files) + $(am__define_uniq_tagged_files); mkid -fID $$unique +tags: tags-am +TAGS: tags + +tags-am: $(TAGS_DEPENDENCIES) $(am__tagged_files) set x; \ here=`pwd`; \ - list='$(SOURCES) $(HEADERS) H5config.h.in $(LISP) $(TAGS_FILES)'; \ - unique=`for i in $$list; do \ - if test -f "$$i"; then echo $$i; else echo $(srcdir)/$$i; fi; \ - done | \ - $(AWK) '{ files[$$0] = 1; nonempty = 1; } \ - END { if (nonempty) { for (i in files) print i; }; }'`; \ + $(am__define_uniq_tagged_files); \ shift; \ if test -z "$(ETAGS_ARGS)$$*$$unique"; then :; else \ test -n "$$unique" || unique=$$empty_fix; \ @@ -1123,15 +1330,11 @@ TAGS: $(HEADERS) $(SOURCES) H5config.h.in $(TAGS_DEPENDENCIES) \ $$unique; \ fi; \ fi -ctags: CTAGS -CTAGS: $(HEADERS) $(SOURCES) H5config.h.in $(TAGS_DEPENDENCIES) \ - $(TAGS_FILES) $(LISP) - list='$(SOURCES) $(HEADERS) H5config.h.in $(LISP) $(TAGS_FILES)'; \ - unique=`for i in $$list; do \ - if test -f "$$i"; then echo $$i; else echo $(srcdir)/$$i; fi; \ - done | \ - $(AWK) '{ files[$$0] = 1; nonempty = 1; } \ - END { if (nonempty) { for (i in files) print i; }; }'`; \ +ctags: ctags-am + +CTAGS: ctags +ctags-am: $(TAGS_DEPENDENCIES) $(am__tagged_files) + $(am__define_uniq_tagged_files); \ test -z "$(CTAGS_ARGS)$$unique" \ || $(CTAGS) $(CTAGSFLAGS) $(AM_CTAGSFLAGS) $(CTAGS_ARGS) \ $$unique @@ -1140,9 +1343,10 @@ GTAGS: here=`$(am__cd) $(top_builddir) && pwd` \ && $(am__cd) $(top_srcdir) \ && gtags -i $(GTAGS_ARGS) "$$here" +cscopelist: cscopelist-am -cscopelist: $(HEADERS) $(SOURCES) $(LISP) - list='$(SOURCES) $(HEADERS) $(LISP)'; \ +cscopelist-am: $(am__tagged_files) + list='$(am__tagged_files)'; \ case "$(srcdir)" in \ [\\/]* | ?:[\\/]*) sdir="$(srcdir)" ;; \ *) sdir=$(subdir)/$(srcdir) ;; \ @@ -1158,6 +1362,151 @@ cscopelist: $(HEADERS) $(SOURCES) $(LISP) distclean-tags: -rm -f TAGS ID GTAGS GRTAGS GSYMS GPATH tags +# Recover from deleted '.trs' file; this should ensure that +# "rm -f foo.log; make foo.trs" re-run 'foo.test', and re-create +# both 'foo.log' and 'foo.trs'. Break the recipe in two subshells +# to avoid problems with "make -n". +.log.trs: + rm -f $< $@ + $(MAKE) $(AM_MAKEFLAGS) $< + +# Leading 'am--fnord' is there to ensure the list of targets does not +# expand to empty, as could happen e.g. with make check TESTS=''. +am--fnord $(TEST_LOGS) $(TEST_LOGS:.log=.trs): $(am__force_recheck) +am--force-recheck: + @: + +$(TEST_SUITE_LOG): $(TEST_LOGS) + @$(am__set_TESTS_bases); \ + am__f_ok () { test -f "$$1" && test -r "$$1"; }; \ + redo_bases=`for i in $$bases; do \ + am__f_ok $$i.trs && am__f_ok $$i.log || echo $$i; \ + done`; \ + if test -n "$$redo_bases"; then \ + redo_logs=`for i in $$redo_bases; do echo $$i.log; done`; \ + redo_results=`for i in $$redo_bases; do echo $$i.trs; done`; \ + if $(am__make_dryrun); then :; else \ + rm -f $$redo_logs && rm -f $$redo_results || exit 1; \ + fi; \ + fi; \ + if test -n "$$am__remaking_logs"; then \ + echo "fatal: making $(TEST_SUITE_LOG): possible infinite" \ + "recursion detected" >&2; \ + else \ + am__remaking_logs=yes $(MAKE) $(AM_MAKEFLAGS) $$redo_logs; \ + fi; \ + if $(am__make_dryrun); then :; else \ + st=0; \ + errmsg="fatal: making $(TEST_SUITE_LOG): failed to create"; \ + for i in $$redo_bases; do \ + test -f $$i.trs && test -r $$i.trs \ + || { echo "$$errmsg $$i.trs" >&2; st=1; }; \ + test -f $$i.log && test -r $$i.log \ + || { echo "$$errmsg $$i.log" >&2; st=1; }; \ + done; \ + test $$st -eq 0 || exit 1; \ + fi + @$(am__sh_e_setup); $(am__tty_colors); $(am__set_TESTS_bases); \ + ws='[ ]'; \ + results=`for b in $$bases; do echo $$b.trs; done`; \ + test -n "$$results" || results=/dev/null; \ + all=` grep "^$$ws*:test-result:" $$results | wc -l`; \ + pass=` grep "^$$ws*:test-result:$$ws*PASS" $$results | wc -l`; \ + fail=` grep "^$$ws*:test-result:$$ws*FAIL" $$results | wc -l`; \ + skip=` grep "^$$ws*:test-result:$$ws*SKIP" $$results | wc -l`; \ + xfail=`grep "^$$ws*:test-result:$$ws*XFAIL" $$results | wc -l`; \ + xpass=`grep "^$$ws*:test-result:$$ws*XPASS" $$results | wc -l`; \ + error=`grep "^$$ws*:test-result:$$ws*ERROR" $$results | wc -l`; \ + if test `expr $$fail + $$xpass + $$error` -eq 0; then \ + success=true; \ + else \ + success=false; \ + fi; \ + br='==================='; br=$$br$$br$$br$$br; \ + result_count () \ + { \ + if test x"$$1" = x"--maybe-color"; then \ + maybe_colorize=yes; \ + elif test x"$$1" = x"--no-color"; then \ + maybe_colorize=no; \ + else \ + echo "$@: invalid 'result_count' usage" >&2; exit 4; \ + fi; \ + shift; \ + desc=$$1 count=$$2; \ + if test $$maybe_colorize = yes && test $$count -gt 0; then \ + color_start=$$3 color_end=$$std; \ + else \ + color_start= color_end=; \ + fi; \ + echo "$${color_start}# $$desc $$count$${color_end}"; \ + }; \ + create_testsuite_report () \ + { \ + result_count $$1 "TOTAL:" $$all "$$brg"; \ + result_count $$1 "PASS: " $$pass "$$grn"; \ + result_count $$1 "SKIP: " $$skip "$$blu"; \ + result_count $$1 "XFAIL:" $$xfail "$$lgn"; \ + result_count $$1 "FAIL: " $$fail "$$red"; \ + result_count $$1 "XPASS:" $$xpass "$$red"; \ + result_count $$1 "ERROR:" $$error "$$mgn"; \ + }; \ + { \ + echo "$(PACKAGE_STRING): $(subdir)/$(TEST_SUITE_LOG)" | \ + $(am__rst_title); \ + create_testsuite_report --no-color; \ + echo; \ + echo ".. contents:: :depth: 2"; \ + echo; \ + for b in $$bases; do echo $$b; done \ + | $(am__create_global_log); \ + } >$(TEST_SUITE_LOG).tmp || exit 1; \ + mv $(TEST_SUITE_LOG).tmp $(TEST_SUITE_LOG); \ + if $$success; then \ + col="$$grn"; \ + else \ + col="$$red"; \ + test x"$$VERBOSE" = x || cat $(TEST_SUITE_LOG); \ + fi; \ + echo "$${col}$$br$${std}"; \ + echo "$${col}Testsuite summary for $(PACKAGE_STRING)$${std}"; \ + echo "$${col}$$br$${std}"; \ + create_testsuite_report --maybe-color; \ + echo "$$col$$br$$std"; \ + if $$success; then :; else \ + echo "$${col}See $(subdir)/$(TEST_SUITE_LOG)$${std}"; \ + if test -n "$(PACKAGE_BUGREPORT)"; then \ + echo "$${col}Please report to $(PACKAGE_BUGREPORT)$${std}"; \ + fi; \ + echo "$$col$$br$$std"; \ + fi; \ + $$success || exit 1 +recheck: all + @test -z "$(TEST_SUITE_LOG)" || rm -f $(TEST_SUITE_LOG) + @set +e; $(am__set_TESTS_bases); \ + bases=`for i in $$bases; do echo $$i; done \ + | $(am__list_recheck_tests)` || exit 1; \ + log_list=`for i in $$bases; do echo $$i.log; done`; \ + log_list=`echo $$log_list`; \ + $(MAKE) $(AM_MAKEFLAGS) $(TEST_SUITE_LOG) \ + am__force_recheck=am--force-recheck \ + TEST_LOGS="$$log_list"; \ + exit $$? +.sh.log: + @p='$<'; \ + $(am__set_b); \ + $(am__check_pre) $(SH_LOG_DRIVER) --test-name "$$f" \ + --log-file $$b.log --trs-file $$b.trs \ + $(am__common_driver_flags) $(AM_SH_LOG_DRIVER_FLAGS) $(SH_LOG_DRIVER_FLAGS) -- $(SH_LOG_COMPILE) \ + "$$tst" $(AM_TESTS_FD_REDIRECT) +@am__EXEEXT_TRUE@.sh$(EXEEXT).log: +@am__EXEEXT_TRUE@ @p='$<'; \ +@am__EXEEXT_TRUE@ $(am__set_b); \ +@am__EXEEXT_TRUE@ $(am__check_pre) $(SH_LOG_DRIVER) --test-name "$$f" \ +@am__EXEEXT_TRUE@ --log-file $$b.log --trs-file $$b.trs \ +@am__EXEEXT_TRUE@ $(am__common_driver_flags) $(AM_SH_LOG_DRIVER_FLAGS) $(SH_LOG_DRIVER_FLAGS) -- $(SH_LOG_COMPILE) \ +@am__EXEEXT_TRUE@ "$$tst" $(AM_TESTS_FD_REDIRECT) + distdir: $(DISTFILES) @srcdirstrip=`echo "$(srcdir)" | sed 's/[].[^$$\\*]/\\\\&/g'`; \ topsrcdirstrip=`echo "$(top_srcdir)" | sed 's/[].[^$$\\*]/\\\\&/g'`; \ @@ -1218,6 +1567,9 @@ install-strip: fi mostlyclean-generic: -test -z "$(MOSTLYCLEANFILES)" || rm -f $(MOSTLYCLEANFILES) + -test -z "$(TEST_LOGS)" || rm -f $(TEST_LOGS) + -test -z "$(TEST_LOGS:.log=.trs)" || rm -f $(TEST_LOGS:.log=.trs) + -test -z "$(TEST_SUITE_LOG)" || rm -f $(TEST_SUITE_LOG) clean-generic: @@ -1303,21 +1655,21 @@ uninstall-am: uninstall-includeHEADERS uninstall-libLTLIBRARIES \ .MAKE: all check-am install-am install-strip -.PHONY: CTAGS GTAGS all all-am all-local check check-TESTS check-am \ - clean clean-generic clean-libLTLIBRARIES clean-libtool \ - clean-noinstPROGRAMS cscopelist ctags distclean \ - distclean-compile distclean-generic distclean-hdr \ - distclean-libtool distclean-tags distdir dvi dvi-am html \ - html-am info info-am install install-am install-data \ - install-data-am install-dvi install-dvi-am install-exec \ - install-exec-am install-html install-html-am \ +.PHONY: CTAGS GTAGS TAGS all all-am all-local check check-TESTS \ + check-am clean clean-generic clean-libLTLIBRARIES \ + clean-libtool clean-noinstPROGRAMS cscopelist-am ctags \ + ctags-am distclean distclean-compile distclean-generic \ + distclean-hdr distclean-libtool distclean-tags distdir dvi \ + dvi-am html html-am info info-am install install-am \ + install-data install-data-am install-dvi install-dvi-am \ + install-exec install-exec-am install-html install-html-am \ install-includeHEADERS install-info install-info-am \ install-libLTLIBRARIES install-man install-pdf install-pdf-am \ install-ps install-ps-am install-settingsDATA install-strip \ installcheck installcheck-am installdirs maintainer-clean \ maintainer-clean-generic mostlyclean mostlyclean-compile \ mostlyclean-generic mostlyclean-libtool mostlyclean-local pdf \ - pdf-am ps ps-am tags uninstall uninstall-am \ + pdf-am ps ps-am recheck tags tags-am uninstall uninstall-am \ uninstall-includeHEADERS uninstall-libLTLIBRARIES \ uninstall-settingsDATA diff --git a/src/hdf5.lnt b/src/hdf5.lnt index 90af778..2ccc1f5 100644 --- a/src/hdf5.lnt +++ b/src/hdf5.lnt @@ -92,6 +92,5 @@ macros cleaned up, but have not been linted due to their dependencies on features that we don't support on Windows: H5FDmpio.c - H5FDmpiposix.c H5FDstream.c */ diff --git a/src/libhdf5.settings.in b/src/libhdf5.settings.in index b594cc2..27df560 100644 --- a/src/libhdf5.settings.in +++ b/src/libhdf5.settings.in @@ -69,7 +69,6 @@ Features: Clear file buffers before write: @CLEARFILEBUF@ Using memory checker: @USINGMEMCHECKER@ Function Stack Tracing: @CODESTACK@ - GPFS: @GPFS@ Strict File Format Checks: @STRICT_FORMAT_CHECKS@ Optimization Instrumentation: @INSTRUMENT@ Large File Support (LFS): @LARGEFILE@ |