On Fri, 15 May 2009, Johan Hake wrote:
> On Friday 15 May 2009 14:55:25 Shawn Walker wrote:
>> On Fri, 15 May 2009, Johan Hake wrote:
>>> On Thursday 14 May 2009 21:03:47 Shawn Walker wrote:
>>>> ok, almost there.
>>>>
>>>> I included the boost library directory into my LD_LIBRARY_PATH. I also
>>>> made those symbolic links. pkgconfig was able to find it just fine and
>>>> create the boost.pc file.
>>>
>>> pkg-config does not find anything. It just reads and parse pkg-config
>>> files, for example boost.pc. However the pkg-config file generators that
>>> comes with dolfin tries to find the dependencies for the difference
>>> packages that dolfin depends on. If found a pkg-config files for the
>>> package is created.
>>>
>>> The generators resides in
>>>
>>> scons/simula-scons/simula_scons/pkgconfiggenerators
>>>
>>> and creates pkg-config files locally in
>>>
>>> scons/pkgconfig
>>>
>>> when scons is called. These files are then installed in
>>>
>>> $PREFIX/lib/pkgconfig
>>>
>>> This directory needs to be in your PKG_CONFIG_PATH, so you also need to
>>> set this in your .bashrc or something.
>>
>> I already have this in my PKG_CONFIG_PATH.
>
> Ok.
>
>>>> Everything compiled (all demos too). But, when
>>>> I try to do `scons install' I get:
>>>>
>>>> Found optional package: umfpack
>>>> Found optional package: gts
>>>> Found optional package: cholmod
>>>> Disabling compilation of Python wrappers
>>>> scons: done reading SConscript files.
>>>> scons: Building targets ...
>>>> scons: *** [install]
>>>> /home/walker/build/include/boost-1_38/boost/algorithm: Is a directory
>>>> scons: building terminated because of errors.
>>>> install failed: Is a directory
>>>>
>>>> Now what?
>>>
>>> Beats me :(
>>>
>>> Did you just type scons install? Where are you in the directory hierarchy
>>> when you compile dolfin? Whats in scons/option.cache and
>>> scons/simula_scons.log?
>>
>> I typed: 'scons install prefix=$INSTALL_PATH'
>> where: $INSTALL_PATH = ~/build
>>
>> I compiled it under the '~/FENICS/dolfin' directory. isn't this where it
>> should be compiled?
>
> Yes, you can compile dolfin where you have your source.
>
> Do you have any sym links in ~/FENICS/dolfin pointing at
> your /home/walker/build direcory or something?
no...
> I cannot figure out why you get:
>
> scons: *** [install]
> /home/walker/build/include/boost-1_38/boost/algorithm: Is a directory
> scons: building terminated because of errors.
> install failed: Is a directory
what does this error mean?
I am still using Scons 0.98.5. Do I need to upgrade this?
- Shawn
> I would actually suggest that you install boost somewhere else than as a sub
> directory of ~/build. Then you either localy sym-link the libraries to the
> new names, as before and give scons the new dirctory, or you sym-link the
> files from the boost installation to ~/build{lib/include}, and let this be
> your boost dir. Remember to remove old boost.pc files aafter you have changed
> any directories.
>
> This last suggestion is just a gut fealing. Do not know if it will work, but
> something gets confused of boost/algorithm laying where it is, so moving it
> might help ;)
>
>> Here are the contents of those files:
>>
>> wal...@box227 ~/FENICS/dolfin/scons
>> $ more options.cache
>> prefix = '/home/walker/build'
>> enableDemos = True
>> enableMpi = False
>> enableScotch = False
>> enableTrilinos = False
>> enableMtl4 = False
>> enableParmetis = False
>> enablePython = False
>> withPetscDir = '/home/walker/src/petsc-2.3.3-p13'
>> withSlepcDir = '/home/walker/src/slepc-2.3.3'
>> withUmfpackDir = '/usr/include/suitesparse'
>> withBoostDir = '/home/walker/build/include/boost-1_38'
>>
>> wal...@box227 ~/FENICS/dolfin/scons
>> $ more simula_scons.log
>> =================== dolfin log ===================
>> 2009-05-14 15:00:23.369578
>> Using simula_scons from:
>> /home/walker/FENICS/dolfin/scons/simula-scons/simula_scons/__init__.pyc
>> resolveCompiler: No pkg-config generator for package 'ufc-1'. Assuming Ok.
>> resolveCompiler: No pkg-config generator for package 'gts'. Assuming Ok.
>
> Nothing wrong here.
>
> Johan
>> - Shawn
>>
>>>> On Thu, 14 May 2009, Johan Hake wrote:
>>>>> On Thursday 14 May 2009 15:37:14 Shawn Walker wrote:
>>>>>> On Thu, 14 May 2009, Johan Hake wrote:
>>>>>>> On Wednesday 13 May 2009 23:48:33 Shawn Walker wrote:
>>>>>>>> On Wed, 13 May 2009, Johan Hake wrote:
>>>>>>>>> On Wednesday 13 May 2009 21:34:57 Shawn Walker wrote:
>>>>>>>>>> ok, here it is. Maybe it is a problem with the name.
>>>>>>>>>>
>>>>>>>>>> wal...@box227 ~
>>>>>>>>>> $ find -name 'libboost_program_options*'
>>>>>>>>>> ./build/lib/libboost_program_options-gcc41-mt.so
>>>>>>>>>> ./build/lib/libboost_program_options-gcc41-mt-1_38.so.1.38.0
>>>>>>>>>> ./build/lib/libboost_program_options-gcc41-mt-1_38.so
>>>>>>>>>> ./build/lib/libboost_program_options-gcc41-mt-1_38.a
>>>>>>>>>> ./build/lib/libboost_program_options-gcc41-mt.a
>>>>>>>>>> ./src/boost_1_38_0/bin.v2/libs/program_options/build/gcc-4.1.2/rel
>>>>>>>>>> ea se /t hre
>>>>>>>>>> ading-multi/libboost_program_options-gcc41-mt-1_38.so.1.38.0
>>>>>>>>>> ./src/boost_1_38_0/bin.v2/libs/program_options/build/gcc-4.1.2/rel
>>>>>>>>>> ea se /l ink
>>>>>>>>>> -static/threading-multi/libboost_program_options-gcc41-mt-1_38.a
>>>>>>>>>
>>>>>>>>> Have you installed the library? Typically make install or
>>>>>>>>> something.
>>>>>>>>>
>>>>>>>>> It looks like the library only lives in the build directory. None
>>>>>>>>> of the above mentioned directories corresponds to any of the ones
>>>>>>>>> given from
>>>>>>>>>
>>>>>>>>> pkg-config --libs dolfin
>>>>>>>>>
>>>>>>>>> Following the output from pkg-config --libs dolfin I would expect
>>>>>>>>> it to be in
>>>>>>>>>
>>>>>>>>> ./src/boost_1_38_0/libs
>>>>>>>>>
>>>>>>>>> However I cannot figure out why you mannage to compile and install
>>>>>>>>> dolfin in the first place...
>>>>>>>>
>>>>>>>> Are you saying I don't know what I am doing? :) Well, you would be
>>>>>>>> right! Only recently have I started compiling things; most of what
>>>>>>>> I did in the past (and still do) is in MATLAB.
>>>>>>>
>>>>>>> He, he, you never know! Even if you would have compiled your own
>>>>>>> stuff for a while we all do simple mistakes all the time, that goes
>>>>>>> for all of us!
>>>>>>>
>>>>>>>> Yes, I installed the boost stuff with `make install'. But boost put
>>>>>>>> it into those other dirs. It also has a weird filename:
>>>>>>>> libboost_program_options-gcc41-mt-1_38 (not the one dolfin looks for
>>>>>>>> I think). Isn't that the problem? If it is, why didn't pkgconfig
>>>>>>>> auto-config the boost.pc file to look for this file?
>>>>>>>
>>>>>>> Ok, I downloaded the latests boost and looked into the documentation
>>>>>>> and boost has its owns naming convention for the installed libraries.
>>>>>>>
>>>>>>> First of all whats in your,
>>>>>>>
>>>>>>> /home/walker/build/include/boost-1_38/lib
>>>>>>>
>>>>>>> directory.
>>>>>>
>>>>>> wal...@box227 ~/build/include/boost-1_38/lib
>>>>>> $ ll
>>>>>> total 1.3M
>>>>>> -rw-------+ 1 walker walker 795K May 13 18:44
>>>>>> libboost_program_options-gcc41-mt-1_38.a
>>>>>> lrwxrwxrwx 1 walker walker 48 May 13 18:44
>>>>>> libboost_program_options-gcc41-mt-1_38.so ->
>>>>>> libboost_program_options-gcc41-mt-1_38.so.1.38.0*
>>>>>> -rwx------+ 1 walker walker 290K May 13 18:44
>>>>>> libboost_program_options-gcc41-mt-1_38.so.1.38.0*
>>>>>> lrwxrwxrwx 1 walker walker 40 May 13 18:44
>>>>>> libboost_program_options-gcc41-mt.a ->
>>>>>> libboost_program_options-gcc41-mt-1_38.a
>>>>>> lrwxrwxrwx 1 walker walker 48 May 13 18:44
>>>>>> libboost_program_options-gcc41-mt.so ->
>>>>>> libboost_program_options-gcc41-mt-1_38.so.1.38.0*
>>>>>
>>>>> Ok, this tells us that the libraries are where they should be.
>>>>>
>>>>>>> Second what does
>>>>>>>
>>>>>>> pkg-config --libs boost
>>>>>>>
>>>>>>> give you? Hopefully it will include:
>>>>>>>
>>>>>>> -L/home/walker/build/include/boost-1_38/lib
>>>>>>>
>>>>>>> meaning that the dolfin configuration system has picked up boost.
>>>>>>
>>>>>> It gives me:
>>>>>>
>>>>>> wal...@box227 ~
>>>>>> $ pkg-config --libs boost
>>>>>> -L/home/walker/build/include/boost-1_38/lib -lboost_program_options
>>>>>
>>>>> Seems to be right.
>>>>>
>>>>>>> Third why has dolfin manage to do that? Have you set any
>>>>>>> environmental variables like BOOST_DIR, pointing to that directory,
>>>>>>> or called scons with
>>>>>>> withBoostDir=/home/walker/build/include/boost-1_38?
>>>>>>
>>>>>> Yes, I set BOOST_DIR to:
>>>>>>
>>>>>> BOOST_DIR=/home/walker/build/include/boost-1_38
>>>>>>
>>>>>> BTW: my current LD_LIBRARY_PATH is:
>>>>>>
>>>>>> LD_LIBRARY_PATH=/home/walker/build/lib/vtk-5.3:/home/walker/build/lib:
>>>>>
>>>>> To be able to run any dolfin applications you need to include the boost
>>>>> path too. I would recomend that you make yourself a local directory
>>>>> where you install your compiled libraries.
>>>>>
>>>>>>> Fourth, (and here comes the suggestion to fix this ;) ), go
>>>>>>> into /home/walker/build/include/boost-1_38/lib, or another directory
>>>>>>> that is included in your LD_LIBRARY_PATH, and which you can pass to
>>>>>>> dolfin via the withBoostDir= option. I have installed all my locally
>>>>>>> compiled libraries under
>>>>>>>
>>>>>>> ~/local
>>>>>>>
>>>>>>> including all the FEhiCS packages. Then you create a link to the
>>>>>>> newly compiled boost libraries in this directory. Make sure you
>>>>>>> change name of the libraries when you link. For example:
>>>>>>>
>>>>>>> ln -fs ~/build/lib/libboost_program_options-gcc41-mt.so \
>>>>>>> libboost_program_options.so
>>>>>>> ln -fs ~/build/lib/libboost_program_options-gcc41-mt.a \
>>>>>>> libboost_program_options.a
>>>>>>
>>>>>> ok, I had thought about doing something like this, but it seemed kind
>>>>>> of hacky... Shouldn't pkg-config figure this out when it creates the
>>>>>> boost.pc file?
>>>>>
>>>>> Well, by naming the libraries like boost do boot gives the user the
>>>>> responsability to link to them in what ever way he likes to. By making
>>>>> symbolic links to these files is one way. Another way is to hard code
>>>>> the library file name into a boost pkg-config file which can be used by
>>>>> scons and dolfin.
>>>>>
>>>>>>> And voila! It should just work (cross fingers ;) )
>>>>>>
>>>>>> I will try it.
>>>>>
>>>>> I see that it didn't work out. What does scons/scons.log tell you?
>>>>>
>>>>> My thought was to keep the boost.pc file which then would have pointed
>>>>> to the right library. But you told me that you erased the boost.pc file
>>>>> and simula-scons did not pick it up again? Right?
>>>>>
>>>>> I also see that we do not link any thing in our test script (boost.py),
>>>>> whould we do that too, as Shawns trouble comes in the linking?
>>>>>
>>>>> Johan
>>>>>
>>>>>> - Shawn
>>>>>>
>>>>>>> You might include the above lines in your .bashrc file, and you
>>>>>>> should probably try to avoid link to a build directory as these tends
>>>>>>> to have a limited life.
>>>>>>>
>>>>>>> Johan
>>>>>>>
>>>>>>>> I also changed something in between. Here is a re-run of
>>>>>>>> pkg-config:
>>>>>>>>
>>>>>>>> wal...@box227 ~
>>>>>>>> $ pkg-config --libs dolfin
>>>>>>>> -pthread -Wl,--export-dynamic
>>>>>>>> -Wl,-rpath,/home/walker/src/slepc-2.3.3/lib/linux-gnu-cxx-debug
>>>>>>>> -Wl,-rpath,/home/walker/src/petsc-2.3.3-p13/lib/linux-gnu-cxx-debug
>>>>>>>> -L/home/walker/build/include/boost-1_38/lib -L/usr/lib -L/lib
>>>>>>>> -L/home/walker/build/lib
>>>>>>>> -L/home/walker/src/slepc-2.3.3/lib/linux-gnu-cxx-debug
>>>>>>>> -L/usr/lib/atlas
>>>>>>>> -L/home/walker/src/petsc-2.3.3-p13/lib/linux-gnu-cxx-debug -L/usr
>>>>>>>> -ldolfin -lslepc -lumfpack -lgts -llapack -lblas -lcholmod -lamd
>>>>>>>> -lcolamd -lboost_program_options -lxml2 -lz -lm -lpetscts
>>>>>>>> -lpetscsnes -lpetscksp -lpetscdm -lpetscmat -lpetscvec -lpetsc
>>>>>>>> -lgthread-2.0 -lgmodule-2.0 -ldl -lglib-2.0
>>>>>>>>
>>>>>>>> Though, I don't think this makes a difference.
>>>>>>>>
>>>>>>>> - Shawn
>>>>>>>>
>>>>>>>>>> On Wed, 13 May 2009, Johan Hake wrote:
>>>>>>>>>>> On Wednesday 13 May 2009 20:24:10 Shawn Walker wrote:
>>>>>>>>>>>> I am still getting this error. I'm pretty sure boost is being
>>>>>>>>>>>> included. Does anyone have any suggestions?
>>>>>>>>>>>
>>>>>>>>>>> I see from the output from your pkg-config command that you have
>>>>>>>>>>> a boost installation in
>>>>>>>>>>>
>>>>>>>>>>> /home/walker/src/boost_1_38_0
>>>>>>>>>>>
>>>>>>>>>>> Do you have several boost installations? The undefined symols you
>>>>>>>>>>> refere to here are all defined in libboost_program_options, so it
>>>>>>>>>>> should work. What does
>>>>>>>>>>>
>>>>>>>>>>> locate libboost_program_options
>>>>>>>>>>>
>>>>>>>>>>> give you?
>>>>>>>>>>>
>>>>>>>>>>> Johan
>>>>>>>>>>>
>>>>>>>>>>>> /usr/bin/ld: skipping incompatible /usr/lib/libc.so when
>>>>>>>>>>>> searching for -lc /usr/bin/ld: skipping incompatible
>>>>>>>>>>>> /usr/lib/libc.a when searching for -lc dolfin/libdolfin.so:
>>>>>>>>>>>> undefined reference to
>>>>>>>>>>>> `boost::program_options::options_description::m_default_line_len
>>>>>>>>>>>> gt h' dolfin/libdolfin.so: undefined reference to
>>>>>
>>>>> `boost::program_options::detail::cmdline::set_additional_parser(boost:
>>>>>>>>>>>> :f unc tion1<std::pair<std::basic_string<char,
>>>>>>>>>>>> : std::char_traits<char>,
>>>>>>>>>>>>
>>>>>>>>>>>> std::allocator<char> >, std::basic_string<char,
>>>>>>>>>>>> std::char_traits<char>, std::allocator<char> > >,
>>>>>>>>>>>> std::basic_string<char,
>>>>>>>>>>>> std::char_traits<char>, std::allocator<char> > const&>)'
>>>>>>>>>>>> collect2: ld returned 1 exit status
>>>>>>>>>>>> scons: *** [demo/quadrature/cpp/demo] Error 1
>>>>>>>>>>>> scons: building terminated because of errors.
>>>>>>>>>>>> demo/quadrature/cpp/demo failed: Error 1
>>>>>>>>>>>>
>>>>>>>>>>>> - Shawn
>>>>>>>>>>>> _______________________________________________
>>>>>>>>>>>> DOLFIN-dev mailing list
>>>>>>>>>>>> [email protected]
>>>>>>>>>>>> http://www.fenics.org/mailman/listinfo/dolfin-dev
>
>
>
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