dolfin team mailing list archive

[Johan Hake <hake@xxxxxxxxx>]

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