dolfin team mailing list archive

[Johan Hake <hake@xxxxxxxxx>]

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?

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

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