ok, it seems to work now that I upgraded SCONS. I did scons -c, then
re-compiled everything (except the demos, because some are broken now). I
then installed it, and it seemed to work.
- Shawn
On Fri, 15 May 2009, Johan Hake wrote:
> On Friday 15 May 2009 15:55:37 Shawn Walker wrote:
>> 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...
>
> Ok.
>
>>> 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 do not know...
>
>> I am still using Scons 0.98.5. Do I need to upgrade this?
>
> Might help.
>
> Johan
>
>> - 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/r
>>>>>>>>>>>> el 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/r
>>>>>>>>>>>> el 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/li
>>>>>>>> b:
>>>>>>>
>>>>>>> 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-debu
>>>>>>>>>> g -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_l
>>>>>>>>>>>>>> en 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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