[Users] HDF5 compile issues w/ or w/o CactusExternal/HDF5
Ian Hinder
ian.hinder at aei.mpg.de
Sun Jun 19 10:59:49 CDT 2011
On 19 Jun 2011, at 02:07, Scott Hawley wrote:
> 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.
You have two options:
* Since you already have HDF5 installed, you could try compiling in CactusExternal/HDF5 and setting HDF5_DIR = /sw. CactusExternal/HDF5 requires that the HDF5 installation you use has support enabled for both C++ and Fortran (even though you might not need this yourself).
* Compile in CactusExternal/HDF5 and set HDF5_DIR = BUILD (or leave it unset, as this is the default).
Since the build system has not complained about your use of the "HDF5" variable (see my other email), you can't have an up-to-date version of CactusExternal/HDF5. I recommend trying the latest versions of things (the recent ET release should be sufficient), as it's possible that bugs have been fixed since the version that you have.
You seem to have a problem with your C compiler. I don't think it's usually recommended to use the MPI wrapper scripts. These scripts call your normal compiler, adding in library etc. options necessary to build an MPI executable. However, these scripts cannot know the intricate details of the Cactus build system, so it is better to add the options manually. This process is often difficult and obtuse, so if you can find an option list where it has already been done for your system, this is better. For example, in simfactory, there is an optionlist macos-gcc-fink which might suit you.
>
> %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
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>>> 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
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>>> checking if Fortran interface enabled... yes
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>>> checking whether we are using the GNU Fortran compiler... (cached) yes
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>>> checking how gfortran finds modules... -I
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>>> checking for dummy main to link with Fortran libraries... none
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>>> checking dependency style of /sw/bin/mpic++... gcc3
>>> checking how to run the C++ preprocessor... /sw/bin/mpic++ -E
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>>> checking for perl... perl
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>>> checking for egrep... /usr/bin/grep -E
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>>> checking if the linker (/sw/bin/mpic++) is GNU ld... no
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>>> 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
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>>> checking dynamic linker characteristics... darwin10.7.4 dyld
>>> checking how to hardcode library paths into programs... immediate
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>>> checking how to run the C++ preprocessor... /sw/bin/mpic++ -E
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>>> checking if the linker (/sw/bin/mpic++) is GNU ld... no
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>>> checking dynamic linker characteristics... darwin10.7.4 dyld
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>>> 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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>>
>> --
>> Thanks for saving energy!
>> 節電のため、ご協力をお願いいたします。
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> _______________________________________________
> Users mailing list
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--
Ian Hinder
ian.hinder at aei.mpg.de
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