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

Sat Jun 18 19:07:54 CDT 2011

Thanks Luca.  When I compile in CactusExternal/HDF5 and don't set any options, then I get the error shown at the bottom of that run log I included in the message.

%Sent from my iPhone

On Jun 18, 2011, at 6:41 PM, "Luca Baiotti" <baiotti at ile.osaka-u.ac.jp> wrote:

> 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...
>>
>>
>> ------------------------------------------------------
>> 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>
>>
>>
>>
>>
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>
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