Re: [Users] HDF5 compile issues w/ or w/o CactusExternal/HDF5

Hi Scott,

in order to use HDF5, as far as I know:

- thorn CactusExternal/HDF5 must be compiled in (irrespective of the option settings)

- you must never set HDF5 = YES (do not set 'HDF5=' at all)

- you can either set HDF5_DIR = <your installation directory> or leave also this setting out of your option list; in the latter case Cactus will build its own HDF5 libraries from source.

Hope this helps,

Luca

On 19/6/11 6:53 AM, Scott Hawley wrote:

Hi. I'm unable to get HDF5 capability to install. If I set HDF5_DIR=/sw, which is the installation already on my machine, I get the error message that I need a thorn that implements HDF5. ("CST error 1: -> Thorn 'CarpetIOHDF5' requires the capability 'HDF5'. Please add a thorn that provides 'HDF5' to your ThornList or remove 'CarpetIOHDF5' from it !")

If I leave HDF5_DIR unset (and all other "HDF5" flags unset as well) and include CactusExternal/HDF5 in my Thornlist, then I also get an error message saying it's unable to compile, as shown below.

To be clear, the options settings which are either left in the file or commented out via "#", are:

HDF5 = YES HDF5_DIR = /sw ZLIB_DIR = /sw

I tried searching online for previous users messages about this or instructions and have not found them.

What am I doing wrong? Thanks, -Scott

example of compilation with no HDF5 flags set:

% gmake texmex

...skipping...

• echo 'HDF5 selected, but HDF5_DIR not set. Checking some places...'
• echo 'END MESSAGE'

++ '[' gfortran '!=' none ']' ++ echo lib/libhdf5_fortran.a

• FILES='include/hdf5.h lib/libhdf5.a lib/libhdf5_cpp.a lib/libhdf5_fortran.a lib/libhdf5_hl.a lib/libhdf5_hl_cpp.a'
• DIRS='/usr /usr/local /usr/local/hdf5 /usr/local/packages/hdf5 /usr/local/apps/hdf5 /opt/local /Users/shawley /Users/shawley/hdf5 c:/packages/hdf5'
• for dir in '$DIRS'
• HDF5_DIR=/usr
• for file in '$FILES'
• '[' '!' -r /usr/include/hdf5.h ']'
• unset HDF5_DIR
• break
• '[' -n '' ']'
• for dir in '$DIRS'
• HDF5_DIR=/usr/local
• for file in '$FILES'
• '[' '!' -r /usr/local/include/hdf5.h ']'
• unset HDF5_DIR
• break
• '[' -n '' ']'
• for dir in '$DIRS'
• HDF5_DIR=/usr/local/hdf5
• for file in '$FILES'
• '[' '!' -r /usr/local/hdf5/include/hdf5.h ']'
• unset HDF5_DIR
• break
• '[' -n '' ']'
• for dir in '$DIRS'
• HDF5_DIR=/usr/local/packages/hdf5
• for file in '$FILES'
• '[' '!' -r /usr/local/packages/hdf5/include/hdf5.h ']'
• unset HDF5_DIR
• break
• '[' -n '' ']'
• for dir in '$DIRS'
• HDF5_DIR=/usr/local/apps/hdf5
• for file in '$FILES'
• '[' '!' -r /usr/local/apps/hdf5/include/hdf5.h ']'
• unset HDF5_DIR
• break
• '[' -n '' ']'
• for dir in '$DIRS'
• HDF5_DIR=/opt/local
• for file in '$FILES'
• '[' '!' -r /opt/local/include/hdf5.h ']'
• unset HDF5_DIR
• break
• '[' -n '' ']'
• for dir in '$DIRS'
• HDF5_DIR=/Users/shawley
• for file in '$FILES'
• '[' '!' -r /Users/shawley/include/hdf5.h ']'
• unset HDF5_DIR
• break
• '[' -n '' ']'
• for dir in '$DIRS'
• HDF5_DIR=/Users/shawley/hdf5
• for file in '$FILES'
• '[' '!' -r /Users/shawley/hdf5/include/hdf5.h ']'
• unset HDF5_DIR
• break
• '[' -n '' ']'
• for dir in '$DIRS'
• HDF5_DIR=c:/packages/hdf5
• for file in '$FILES'
• '[' '!' -r c:/packages/hdf5/include/hdf5.h ']'
• unset HDF5_DIR
• break
• '[' -n '' ']'
• '[' -z '' ']'
• echo 'BEGIN MESSAGE'
• echo 'HDF5 not found'
• echo 'END MESSAGE'
• '[' -z '' -o '' = BUILD ']'
• echo 'BEGIN MESSAGE'
• echo 'Building HDF5...'
• echo 'END MESSAGE'
• THORN=HDF5
• NAME=hdf5-1.8.6

++ dirname /Users/shawley/Cactus/arrangements/ExternalLibraries/HDF5/HDF5.sh

• SRCDIR=/Users/shawley/Cactus/arrangements/ExternalLibraries/HDF5
• BUILD_DIR=/Users/shawley/Cactus/configs/texmex/scratch/build/HDF5
• INSTALL_DIR=/Users/shawley/Cactus/configs/texmex/scratch/external/HDF5
• DONE_FILE=/Users/shawley/Cactus/configs/texmex/scratch/done/HDF5
• HDF5_DIR=/Users/shawley/Cactus/configs/texmex/scratch/external/HDF5
• exec
• set -x
• set -e
• cd /Users/shawley/Cactus/configs/texmex/scratch
• '[' -e /Users/shawley/Cactus/configs/texmex/scratch/done/HDF5 -a /Users/shawley/Cactus/configs/texmex/scratch/done/HDF5 -nt /Users/shawley/Cactus/arrangements/ExternalLibraries/HDF5/dist/hdf5-1.8.6.tar.gz -a /Users/shawley/Cactus/configs/texmex/scratch/done/HDF5 -nt /Users/shawley/Cactus/arrangements/ExternalLibraries/HDF5/HDF5.sh ']'
• echo 'HDF5: Building enclosed HDF5 library'

HDF5: Building enclosed HDF5 library ++ gmake --help ++ echo make

• MAKE=make

++ gtar --help ++ echo gtar

• TAR=gtar
• '[' -z patch ']'
• '[' gfortran = none ']'
• export FC=gfortran
• FC=gfortran
• export FCFLAGS=-m64
• FCFLAGS=-m64
• export LDFLAGS
• unset LIBS
• unset RPATH
• echo '' rucs
• grep 64
• echo 'HDF5: Preparing directory structure...'

HDF5: Preparing directory structure...

• mkdir build external done
• true
• rm -rf /Users/shawley/Cactus/configs/texmex/scratch/build/HDF5 /Users/shawley/Cactus/configs/texmex/scratch/external/HDF5
• mkdir /Users/shawley/Cactus/configs/texmex/scratch/build/HDF5 /Users/shawley/Cactus/configs/texmex/scratch/external/HDF5
• echo 'HDF5: Unpacking archive...'

HDF5: Unpacking archive...

• pushd /Users/shawley/Cactus/configs/texmex/scratch/build/HDF5

~/Cactus/configs/texmex/scratch/build/HDF5 ~/Cactus/configs/texmex/scratch

• gtar xzf /Users/shawley/Cactus/arrangements/ExternalLibraries/HDF5/dist/hdf5-1.8.6.tar.gz
• patch -p0

patching file hdf5-1.8.6/test/dt_arith.c

• echo 'HDF5: Configuring...'

HDF5: Configuring...

• cd hdf5-1.8.6

++ '[' -n gfortran ']' ++ echo '' --enable-fortran

• ./configure --prefix=/Users/shawley/Cactus/configs/texmex/scratch/external/HDF5 --with-zlib=/Users/shawley/Cactus/configs/texmex/scratch/external/zlib --enable-cxx --enable-fortran

checking for a BSD-compatible install... usage: install installation-prefix

Example: install /usr/local

Note: See script source for user-modifiable environment variables that may need to be tailored to your desired compilation environment. /usr/bin/install -c checking whether build environment is sane... yes checking for a thread-safe mkdir -p... bin/install-sh -c -d checking for gawk... gawk checking whether make sets $(MAKE)... yes checking whether to enable maintainer-specific portions of Makefiles... no checking build system type... i386-apple-darwin10.7.4 checking host system type... i386-apple-darwin10.7.4 checking shell variables initial values... done checking if basename works... yes checking if xargs works... yes checking for cached host... none checking for config i386-apple-darwin10.7.4... no checking for config i386-apple-darwin10.7.4... no checking for config apple-darwin10.7.4... no checking for config apple-darwin10.7.4... no checking for config i386-darwin10.7.4... no checking for config i386-darwin10.7.4... no checking for config i386-apple... no checking for config darwin10.7.4... no checking for config darwin10.7.4... no checking for config apple... found compiler '/sw/bin/mpicc' is GNU gcc-4.2.1 compiler 'gfortran' is GNU gfortran-4.4.4 Warning: shared libraries are not supported with Fortran Disabling shared libraries No match to get cc_version_info for /sw/bin/mpicc No match to get cxx_version_info for /sw/bin/mpic++ checking for config ./config/site-specific/host-provision.local... no checking for config ./config/site-specific/host-local... no checking for gcc... /sw/bin/mpicc checking whether the C compiler works... yes checking for C compiler default output file name... a.out checking for suffix of executables... checking whether we are cross compiling... no checking for suffix of object files... o checking whether we are using the GNU C compiler... yes checking whether /sw/bin/mpicc accepts -g... yes checking for /sw/bin/mpicc option to accept ISO C89... none needed checking for style of include used by make... GNU checking dependency style of /sw/bin/mpicc... gcc3 checking if Fortran interface enabled... yes checking whether we are using the GNU Fortran compiler... yes checking whether gfortran accepts -g... yes checking for Fortran flag to compile .f90 files... none checking whether we are using the GNU Fortran compiler... (cached) yes checking whether gfortran accepts -g... (cached) yes checking what gfortran does with modules... MODULE.mod checking how gfortran finds modules... -I checking how to get verbose linking output from gfortran... -v checking for Fortran libraries of gfortran... -L/sw/lib -L/Users/shawley/lib -L/Users/shawley/texmex/lib -L/sw/lib/gcc4.4/lib/ -L/sw/lib/gcc4.4/lib/gcc/x86_64-apple-darwin10.7.3/4.4.4 -L/sw/lib/gcc4.4/lib/gcc/x86_64-apple-darwin10.7.3/4.4.4/../../.. -lgfortranbegin -lgfortran checking for dummy main to link with Fortran libraries... none checking for Fortran name-mangling scheme... lower case, underscore, no extra underscore checking if Fortran compiler supports intrinsic SIZEOF... yes checking if Fortran default REAL is DOUBLE PRECISION... no checking whether we are using the GNU C++ compiler... yes checking whether /sw/bin/mpic++ accepts -g... yes checking dependency style of /sw/bin/mpic++... gcc3 checking how to run the C++ preprocessor... /sw/bin/mpic++ -E checking if c++ interface enabled... yes checking if /sw/bin/mpic++ needs old style header files in includes... no checking if /sw/bin/mpic++ can handle namespaces... yes checking if /sw/bin/mpic++ supports std... yes checking if /sw/bin/mpic++ supports bool types... yes checking if /sw/bin/mpic++ has offsetof extension... yes checking if /sw/bin/mpic++ can handle static cast... yes checking for perl... perl checking whether make sets $(MAKE)... (cached) yes checking for tr... /usr/bin/tr checking if srcdir= and time commands work together... yes checking for mpiexec... none checking how to print strings... printf checking for a sed that does not truncate output... /usr/bin/sed checking for grep that handles long lines and -e... /usr/bin/grep checking for egrep... /usr/bin/grep -E checking for fgrep... /usr/bin/grep -F checking for ld used by /sw/bin/mpicc... /sw/bin/mpic++ checking if the linker (/sw/bin/mpic++) is GNU ld... no checking for BSD- or MS-compatible name lister (nm)... /usr/bin/nm checking the name lister (/usr/bin/nm) interface... BSD nm checking whether ln -s works... yes checking the maximum length of command line arguments... 196608 checking whether the shell understands some XSI constructs... yes checking whether the shell understands "+="... yes checking for /sw/bin/mpic++ option to reload object files... -r checking for objdump... no checking how to recognize dependent libraries... pass_all checking for ar... ar checking for strip... strip checking for ranlib... ranlib checking command to parse /usr/bin/nm output from /sw/bin/mpicc object... ok checking for dsymutil... dsymutil checking for nmedit... nmedit checking for lipo... lipo checking for otool... otool checking for otool64... no checking for -single_module linker flag... yes checking for -exported_symbols_list linker flag... yes checking for -force_load linker flag... yes checking how to run the C preprocessor... /usr/bin/cpp checking for ANSI C header files... yes checking for sys/types.h... yes checking for sys/stat.h... yes checking for stdlib.h... yes checking for string.h... yes checking for memory.h... yes checking for strings.h... yes checking for inttypes.h... yes checking for stdint.h... yes checking for unistd.h... yes checking for dlfcn.h... yes checking for objdir... .libs checking if /sw/bin/mpicc supports -fno-rtti -fno-exceptions... no checking for /sw/bin/mpicc option to produce PIC... -fno-common -DPIC checking if /sw/bin/mpicc PIC flag -fno-common -DPIC works... yes checking if /sw/bin/mpicc static flag -static works... no checking if /sw/bin/mpicc supports -c -o file.o... yes checking if /sw/bin/mpicc supports -c -o file.o... (cached) yes checking whether the /sw/bin/mpicc linker (/sw/bin/mpic++) supports shared libraries... yes checking dynamic linker characteristics... darwin10.7.4 dyld checking how to hardcode library paths into programs... immediate checking for dlopen in -ldl... yes checking whether a program can dlopen itself... yes checking whether a statically linked program can dlopen itself... yes checking whether stripping libraries is possible... yes checking if libtool supports shared libraries... yes checking whether to build shared libraries... no checking whether to build static libraries... yes checking how to run the C++ preprocessor... /sw/bin/mpic++ -E checking for ld used by /sw/bin/mpic++... /sw/bin/mpic++ checking if the linker (/sw/bin/mpic++) is GNU ld... no checking whether the /sw/bin/mpic++ linker (/sw/bin/mpic++) supports shared libraries... yes checking for /sw/bin/mpic++ option to produce PIC... -fno-common -DPIC checking if /sw/bin/mpic++ PIC flag -fno-common -DPIC works... yes checking if /sw/bin/mpic++ static flag -static works... no checking if /sw/bin/mpic++ supports -c -o file.o... yes checking if /sw/bin/mpic++ supports -c -o file.o... (cached) yes checking whether the /sw/bin/mpic++ linker (/sw/bin/mpic++) supports shared libraries... yes checking dynamic linker characteristics... darwin10.7.4 dyld checking how to hardcode library paths into programs... immediate checking if libtool supports shared libraries... yes checking whether to build shared libraries... no checking whether to build static libraries... yes checking for gfortran option to produce PIC... -fno-common checking if gfortran PIC flag -fno-common works... yes checking if gfortran static flag -static works... no checking if gfortran supports -c -o file.o... yes checking if gfortran supports -c -o file.o... (cached) yes checking whether the gfortran linker (/sw/bin/mpic++) supports shared libraries... yes checking dynamic linker characteristics... darwin10.7.4 dyld checking how to hardcode library paths into programs... immediate checking if we should install only statically linked executables... no checking if -Wl,-rpath should be used to link shared libs in nondefault directories... yes checking make... checking how make searches directories... VPATH=DIR1 DIR2 ... checking whether make will build with undefined variables... yes checking for production mode... production checking for ceil in -lm... yes checking for ANSI C header files... (cached) yes checking whether time.h and sys/time.h may both be included... yes checking for difftime... yes checking for gettimeofday... yes checking sys/resource.h usability... yes checking sys/resource.h presence... yes checking for sys/resource.h... yes checking sys/time.h usability... yes checking sys/time.h presence... yes checking for sys/time.h... yes checking for unistd.h... (cached) yes checking sys/ioctl.h usability... yes checking sys/ioctl.h presence... yes checking for sys/ioctl.h... yes checking for sys/stat.h... (cached) yes checking sys/socket.h usability... yes checking sys/socket.h presence... yes checking for sys/socket.h... yes checking for sys/types.h... (cached) yes checking stddef.h usability... yes checking stddef.h presence... yes checking for stddef.h... yes checking setjmp.h usability... yes checking setjmp.h presence... yes checking for setjmp.h... yes checking features.h usability... no checking features.h presence... no checking for features.h... no checking for stdint.h... (cached) yes checking io.h usability... no checking io.h presence... no checking for io.h... no checking winsock.h usability... no checking winsock.h presence... no checking for winsock.h... no checking sys/timeb.h usability... yes checking sys/timeb.h presence... yes checking for sys/timeb.h... yes checking if configure should try to set up large file support... yes checking for special C compiler options needed for large files... no checking for _FILE_OFFSET_BITS value needed for large files... no checking if large (64-bit) files are supported on this system.... yes skipping test for lseek64(), fseeko64 , ftello64, ftruncate64() because off64_t is not defined checking for fseeko... yes checking for ftello... yes checking for stat64... yes checking for fstat64... yes checking for off_t... yes checking for size_t... yes checking for ssize_t... yes checking for ptrdiff_t... yes checking whether byte ordering is bigendian... no checking size of char... 1 checking size of short... 2 checking size of int... 4 checking size of unsigned... 4 checking size of long... 8 checking size of long long... 8 checking size of __int64... 0 checking size of float... 4 checking size of double... 8 checking size of long double... 16 checking size of int8_t... 1 checking size of uint8_t... 1 checking size of int_least8_t... 1 checking size of uint_least8_t... 1 checking size of int_fast8_t... 1 checking size of uint_fast8_t... 1 checking size of int16_t... 2 checking size of uint16_t... 2 checking size of int_least16_t... 2 checking size of uint_least16_t... 2 checking size of int_fast16_t... 2 checking size of uint_fast16_t... 2 checking size of int32_t... 4 checking size of uint32_t... 4 checking size of int_least32_t... 4 checking size of uint_least32_t... 4 checking size of int_fast32_t... 4 checking size of uint_fast32_t... 4 checking size of int64_t... 8 checking size of uint64_t... 8 checking size of int_least64_t... 8 checking size of uint_least64_t... 8 checking size of int_fast64_t... 8 checking size of uint_fast64_t... 8 checking size of size_t... 8 checking size of ssize_t... 8 checking size of ptrdiff_t... 8 checking size of off_t... 8 checking size of off64_t... 0 checking if dev_t is scalar... yes checking for dmalloc library... suppressed checking zlib.h usability... yes checking zlib.h presence... yes checking for zlib.h... yes checking for compress2 in -lz... yes checking for compress2... yes checking for szlib... suppressed checking for pthread... suppressed checking for thread safe support... no checking for tm_gmtoff in struct tm... yes checking for __tm_gmtoff in struct tm... no checking for global timezone variable... yes checking whether struct tm is in sys/time.h or time.h... time.h checking for struct tm.tm_zone... yes checking for struct timezone... yes checking whether gettimeofday() gives timezone... yes checking for st_blocks in struct stat... yes checking for _getvideoconfig... no checking for gettextinfo... no checking for GetConsoleScreenBufferInfo... no checking for _scrsize... no checking for ioctl... yes checking for struct videoconfig... no checking for struct text_info... no checking for TIOCGWINSZ... yes checking for TIOCGETD... yes checking for alarm... yes checking for BSDgettimeofday... no checking for fork... yes checking for frexpf... yes checking for frexpl... yes checking for gethostname... yes checking for getpwuid... yes checking for getrusage... yes checking for lstat... yes checking for rand_r... yes checking for random... yes checking for setsysinfo... no checking for signal... yes checking for longjmp... yes checking for setjmp... yes checking for siglongjmp... yes checking for sigsetjmp... yes checking for sigprocmask... yes checking for snprintf... yes checking for srandom... yes checking for strdup... yes checking for symlink... yes checking for system... yes checking for tmpfile... yes checking for vasprintf... yes checking for waitpid... yes checking for vsnprintf... yes checking if vsnprintf returns correct value... yes checking if lone colon can be used as an argument... yes checking for an ANSI C-conforming const... yes checking for inline... inline checking for __attribute__ extension... yes checking for __func__ extension... yes checking for __FUNCTION__ extension... yes checking for C99 designated initialization support... yes checking how to print long long... %ld and %lu checking Threads support system scope... yes checking for gpfs... suppressed checking for debug flags... none checking whether function stack tracking is enabled... no checking whether metadata trace file code is enabled... no checking for API tracing... no checking for instrumented library... no checking whether to clear file buffers... yes checking whether a memory checking tool will be used... no configure: error: An MPI compiler is being used; --enable-cxx is not allowed

• (( 1 ))
• echo 'BEGIN ERROR'
• echo 'Error while building HDF5. Aborting.'
• echo 'END ERROR'
• exit 1

HDF5 selected, but HDF5_DIR not set. Checking some places... HDF5 not found Building HDF5...

CST error 1: -> Configuration script for thorn HDF5 returned exit code 1 Error message: 'Error while building HDF5. Aborting.'

Checking consistency... Creating Thorn-Flesh bindings... Creating implementation bindings... Creating parameter bindings... Creating variable bindings... Creating schedule bindings... Creating function bindings...

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There was 1 error during execution of the CST This must be corrected before compilation can proceed

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Warnings were generated during execution of the CST

CST error 1: -> Configuration script for thorn HDF5 returned exit code 1 Error message: 'Error while building HDF5. Aborting.'

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make[1]: *** [/Users/shawley/Cactus/configs/texmex/config-data/make.thornlist] Error 1 make: *** [texmex] Error 2 provision.local 19>

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