dolfin team mailing list archive

[Johan Hake <hake@xxxxxxxxx>]

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.

> 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?

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.
> >>>>>>
> >>>>>> walker@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/relea
> >>>>>>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/relea
> >>>>>>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.
> >>
> >> walker@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:
> >>
> >> walker@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:
> >>>>
> >>>> walker@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_lengt
> >>>>>>>>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
> >>>>>>>> DOLFIN-dev@xxxxxxxxxx
> >>>>>>>> http://www.fenics.org/mailman/listinfo/dolfin-dev