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

Scott Hawley scott.hawley at belmont.edu
Sat Jun 18 16:53:36 CDT 2011 

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...


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



------------------------------------------------------
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.'

------------------------------------------------------

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

-------------- next part --------------
A non-text attachment was scrubbed...
Name: PGP.sig
Type: application/pgp-signature
Size: 535 bytes
Desc: This is a digitally signed message part
Url : http://lists.einsteintoolkit.org/pipermail/users/attachments/20110618/23459d93/attachment.bin

More information about the Users mailing list