dolfin team mailing list archive

[Shawn Walker <walker@xxxxxxxxxxxxxxx>]

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:
> >
> > 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
> > > > > > > > > > > > _______________________________________________
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