On 28 October 2011 23:08, Johan Hake <email address hidden> wrote:
> On Friday October 28 2011 13:02:36 Kristian B. Ølgaard wrote:
>> On 28 October 2011 21:16, Johan Hake <email address hidden> wrote:
>> > On Friday October 28 2011 10:00:15 Martin Sandve Alnæs wrote:
>> >> Just a few quick comments here:
>> >>
>> >> cmath is fully standard, which makes it not comparable to boost math for
>> >> these issues.
>> >
>> > Ok.
>> >
>> >> The issue is mainly from python because from C++ there will be a build
>> >> system to handle libraries.
>> >
>> > But who tells the build system to provide the library? Should that be a
>> > user tweaking the local CMakeList.txt. I think it would be nice if UFC
>> > provided a generic FindUFC.cmake including all dependencies by default,
>> > or FFC provided such a file (FindSomething.cmake), which then could be
>> > problem dependent.
>>
>> If UFC has to provide all possible dependencies for all possible
>> compilers, we end up with an infinite list of libraries which a
>> specific code generated by a specific form compiler might not even
>> need.
>
> I see that theoretically this might be the case, but in practice?
>
>> The form compiler e.g., FFC generates the code and therefore knows
>> which special libraries are needed.
>> It would therefore make sense if FFC could provide the flags for all
>> special libraries that it _might_ need, and then only in those cases
>> where it is actually needed should they be added to the standard
>> flags.
>
> I see this take on it.
>
>> This approach will work well with Python but is more troublesome to
>> integrate with C++ and compiling a header file against DOLFIN.
>
> Yes, then FFC need to provide some sort of CMake file to take care of the
> extra flags.
>
>> >> I think boost math is comparable to boost shared_ptr, in fact they are
>> >> both tr1 and light weight. Configuring one more boost library in ufc
>> >> would not be so bad.
>> >
>> > Ok.
>> >
>> >> But it is more robust if it is optional and not linked with unless
>> >> needed.
>> >
>> > Sure but then we rely on user interaction, and we need to provide a
>> > consistant and robust interface for that. If I have not missed anything
>> > I see two ideal solutions:
>> >
>> >  1) UFC provides everything for us:
>> >
>> >       Python : Everything just works
>> >       C++    : We include all flags in FindUFC.cmake
>>
>> As I write above, this could easily get out of hand if many compilers
>> start using different libraries.
>
> Sure.
>
>> >  2) FFC provides optional dependecies for us. For this to be automated
>> > FFC need to scan a form for the use of non standard functions this
>> > information is then propagated:
>> >
>> >       Python : to the ufc provided JIT compilation
>> >       C++    : to a local CMakeFile (not sure what name we should have),
>> >                which a user manually should include in the local
>> > CMakeFile, or (optimally) is already included in the local
>> > CMakeFiles.txt through some fancy include path.
>>
>> Python is easy, C++ is not in this case.
>
> I think C++ is incorporated into my suggestion. We just need FFC to generate
> some sort of general CMakeFile, which is included in the CMakeFile of each
> poject.
>
>> > Other suggestions? I am open for both solutions. 1) is the easiest to
>> > implement and is the least disruptive to the present functionality.
>>
>> Since we're currently just talking about adding one extra boost
>> dependency in DOLFIN and UFC, I think we should go with option 1).
>
> If this is what we land on I can try to hack the CMake of UFC and add it
> there. If I fail I might ask some CMake guro to help out. I can also add
> configuration of the libmath from boost to the compilation of the python
> extension module.

Yes, let's go with this approach for now and see if we can avoid
making things too general/complex.

Kristian

> Johan
>
>>
>> Kristian
>>
>> > Johan
>> >
>> >> Martin
>> >> Den 28. okt. 2011 17.41 skrev "Johan Hake" <email address hidden>
>> >>
>> >> følgende:
>> >> > On Friday October 28 2011 02:37:34 Kristian B. Ølgaard wrote:
>> >> > > On 28 October 2011 01:03, Johan Hake <email address hidden>
> wrote:
>> >> > > > On Thursday October 27 2011 12:02:35 Kristian B. Ølgaard wrote:
>> >> > > >> On 27 October 2011 19:38, Johan Hake <email address hidden>
>> >> >
>> >> > wrote:
>> >> > > >> > On Thursday October 27 2011 10:25:22 Garth Wells wrote:
>> >> > > >> >> I don't think that it's a fix. We need to search for right
>> >> > > >> >> library. It may be in a non-standard location, and in my case
>> >> > > >> >> it should link to
>> >> > > >>
>> >> > > >> It was just meant as a pointer to where the problem lies, not a
>> >> > > >> proper fix.
>> >> > > >>
>> >> > > >> >>     libboost_math_tr1-mt.so
>> >> > > >> >>
>> >> > > >> >> and not
>> >> > > >> >>
>> >> > > >> >>     libboost_math_tr1.so
>> >> > > >> >>
>> >> > > >> >> Perhaps UFC should supply the build flags?
>> >> > > >>
>> >> > > >> That could work for this case, but since UFC is not concerned
>> >> > > >> about how the functions are implemented it seems more natural
>> >> > > >> that the form compiler supplies the additional flags needed for
>> >> > > >> the generated code.
>> >> > > >
>> >> > > > Sure, but we actually moved from a situation where the actuall
>> >> > > > compilation were done in FFC to UFC. It simplified the interface
>> >> > > > to the JIT compilations alot.
>> >> > > >
>> >> > > >> > There are already logic in the building of extension modules to
>> >> > > >> > find the boost libraries, or more precise the boost header for
>> >> >
>> >> > shared_ptr.
>> >> >
>> >> > > >> > So it is not unatural to add logic for finding the correct
>> >> > > >> > boost
>> >> >
>> >> > math
>> >> >
>> >> > > >> > library.
>> >> > > >>
>> >> > > >> But should it be? shared_ptr is not used in native UFC AFAIK, it
>> >> > > >> is used for the DOLFIN wrapper code generated by FFC which again
>> >> > > >> suggests that FFC supplies the additional flags.
>> >> > > >
>> >> > > > Well, it provides a shared_ptr interface of UFC objects. DOLFIN
>> >> > > > depends on this but it is not tied to DOLFIN per se. Other
>> >> > > > programs can use
>> >> >
>> >> > this
>> >> >
>> >> > > > wrapper to include UFC modules.
>> >> > >
>> >> > > There are no shared_ptr in ufc.h, but I guess you're talking about
>> >> > > the swig generated modules?
>> >> >
>> >> > Yes, and the decission of letting ufc handle its own JIT compilation
>> >> > made it
>> >> > important to have a configure step where we found boost.
>> >> >
>> >> > > >> So with this argument, FFC could use the DOLFIN configuration to
>> >> > > >> get the correct include dirs and libraries?
>> >> > > >
>> >> > > > I think FFC generated UFC code should not have to depend on DOLFIN
>> >> >
>> >> > flags.
>> >> >
>> >> > > > The most natural thing is to include the flags in a
>> >> > > > UFCCmake/pkg-config file I guess. Unfortunatly this will give us
>> >> > > > the libs each time also when we do not use them. Not sure this is
>> >> > > > a problem though.
>> >> > >
>> >> > > No, but what should happen when 'ffc -l dolfin foo.ufl' is used?
>> >> > > Then the output is wrapped for DOLFIN and it would be natural to
>> >> > > use the DOLFIN flags. If, on the other hand, pure UFC is generated
>> >> > > and the presence of bessel functions demand the boost_math_tr
>> >> > > library, we should get the flags directly from FFC. We can't get
>> >> > > the flags from UFC, as UFC cannot know which libraries the form
>> >> > > compilers might need for their code.
>> >> >
>> >> > Sure, but my point is that ufc should provide all possible libraries a
>> >> > form compiler can use.
>> >> >
>> >> > > But for now, it will be simpler to require users to supply a list of
>> >> > > libraries, when needed, using the parameter system in FFC.
>> >> > > This will only be needed for the Python interface, and users can
>> >> > > decide for themselves if they will use 'libboost_math_tr1-mt.so' or
>> >> > >
>> >> > >  'libboost_math_tr1.so'.
>> >> >
>> >> > Why is this only needed for the Python compilation? If nost_math is
>> >> > included
>> >> > in DOLFIN now we have to include any "exotic" libraries in the future
>> >> > to DOLFIN too.
>> >> >
>> >> > > >> If FFC is used from the command line to generate a header file
>> >> > > >> which is included in a DOLFIN program, I would expect Garth's
>> >> > > >> fix to work for the C++ version.
>> >> > > >
>> >> > > > That is true. But ufc code should be able to be integrated with
>> >> > > > any software, and optimally it should be self contained. But
>> >> > > > introducing boost dependencies we drop that.
>> >> > > >
>> >> > > > For a cleaner dependency chain I suggest UFC provide everything it
>> >> >
>> >> > needs
>> >> >
>> >> > > > to compile UFC code (and python extensions) and then form
>> >> > > > compilers
>> >> >
>> >> > have
>> >> >
>> >> > > > to limit them self to what UFC provides. Whenever a formcompiler
>> >> > > > want something new and fancy we need to update UFC to make that
>> >> > > > happen.
>> >> > >
>> >> > > Yes, this will be the simplest solution, but it means that whenever
>> >> > > a random form compiler decides to implement e.g., the dof
>> >> > > evaluation by calling some exotic library, we have to update UFC to
>> >> > > use that library, while most other form compilers will generate
>> >> > > code which doesn't need it.
>> >> >
>> >> > Would this be a problem? In a way this is what we do in
>> >> > compile_expressions.
>> >> > Here we make cmath functions and also complex expression available. I
>> >> > see that
>> >> > this might constrain the user.
>> >> >
>> >> > Johan
>> >> >
>> >> > > Kristian
>> >> > >
>> >> > > > Johan
>> >> > > >
>> >> > > >> Kristian
>> >> > > >>
>> >> > > >> > What do you mean with UFC supply build flags?
>> >> > > >> >
>> >> > > >> > Johan
>> >> > > >> >
>> >> > > >> >> Garth
>> >> > > >> >
>> >> > > >> > --
>> >> > > >> > You received this bug notification because you are a member of
>> >> >
>> >> > DOLFIN
>> >> >
>> >> > > >> > Core Team, which is subscribed to DOLFIN.
>> >> > > >> > https://bugs.launchpad.net/bugs/882560
>> >> > > >> >
>> >> > > >> > Title:
>> >> > > >> >  tr1::cyl_bessel_* functions are not found at linking stage of
>> >> > > >> > jit
>> >> > > >> >
>> >> > > >> > Status in DOLFIN:
>> >> > > >> >  Confirmed
>> >> > > >> >
>> >> > > >> > Bug description:
>> >> > > >> >  When a jit compiled module using bessel functions is imported
>> >> > > >> >  into python, it fails with an undefined symbol error. Probably
>> >> > > >> >  because
>> >> >
>> >> > the
>> >> >
>> >> > > >> >  boost math tr1 library is not linked in.
>> >> >
>> >> >  ImportError:/home/martinal/.instant/cache/d003d0ea29ed9346265963000f1
>> >> >
>> >> > > >> > a90 648953f6a6/_d003d0ea29ed9346265963000f1a90648953f6a6.so:
>> >> > undefined
>> >> >
>> >> > > >> > symbol: boost_cyl_bessel_j;
>> >> > > >> >
>> >> > > >> >  Code to reproduce:
>> >> > > >> >
>> >> > > >> >  from dolfin import *
>> >> > > >> >  mesh = Interval(10, 0.1, 2.0)
>> >> > > >> >  V = FunctionSpace(mesh, "CG", 1)
>> >> > > >> >  x = interval.x
>> >> > > >> >  f = bessel_J(0, x)
>> >> > > >> >  g = project(f, V)
>> >> > > >> >  plot(g, mesh=mesh)
>> >> > > >> >  interactive()
>> >> > > >> >
>> >> > > >> > To manage notifications about this bug go to:
>> >> > > >> > https://bugs.launchpad.net/dolfin/+bug/882560/+subscriptions
>> >> > > >
>> >> > > > --
>> >> > > > You received this bug notification because you are a member of
>> >> > > > DOLFIN Core Team, which is subscribed to DOLFIN.
>> >> > > > https://bugs.launchpad.net/bugs/882560
>> >> > > >
>> >> > > > Title:
>> >> > > >  tr1::cyl_bessel_* functions are not found at linking stage of jit
>> >> > > >
>> >> > > > Status in DOLFIN:
>> >> > > >  Confirmed
>> >> > > >
>> >> > > > Bug description:
>> >> > > >  When a jit compiled module using bessel functions is imported
>> >> > > > into python, it fails with an undefined symbol error. Probably
>> >> > > > because the boost math tr1 library is not linked in.
>> >> >
>> >> >  ImportError:/home/martinal/.instant/cache/d003d0ea29ed9346265963000f1
>> >> > a90
>> >> >
>> >> > > > 648953f6a6/_d003d0ea29ed9346265963000f1a90648953f6a6.so: undefined
>> >> > > > symbol: boost_cyl_bessel_j;
>> >> > > >
>> >> > > >  Code to reproduce:
>> >> > > >
>> >> > > >  from dolfin import *
>> >> > > >  mesh = Interval(10, 0.1, 2.0)
>> >> > > >  V = FunctionSpace(mesh, "CG", 1)
>> >> > > >  x = interval.x
>> >> > > >  f = bessel_J(0, x)
>> >> > > >  g = project(f, V)
>> >> > > >  plot(g, mesh=mesh)
>> >> > > >  interactive()
>> >> > > >
>> >> > > > To manage notifications about this bug go to:
>> >> > > > https://bugs.launchpad.net/dolfin/+bug/882560/+subscriptions
>> >> >
>> >> > --
>> >> > You received this bug notification because you are a member of DOLFIN
>> >> > Core Team, which is subscribed to DOLFIN.
>> >> > https://bugs.launchpad.net/bugs/882560
>> >> >
>> >> > Title:
>> >> >  tr1::cyl_bessel_* functions are not found at linking stage of jit
>> >> >
>> >> > Status in DOLFIN:
>> >> >  Confirmed
>> >> >
>> >> > Bug description:
>> >> >  When a jit compiled module using bessel functions is imported into
>> >> >  python, it fails with an undefined symbol error. Probably because the
>> >> >  boost math tr1 library is not linked in.
>> >> >
>> >> >
>> >> >  ImportError:/home/martinal/.instant/cache/d003d0ea29ed9346265963000f1
>> >> > a90 648953f6a6/_d003d0ea29ed9346265963000f1a90648953f6a6.so: undefined
>> >> > symbol: boost_cyl_bessel_j;
>> >> >
>> >> >
>> >> >  Code to reproduce:
>> >> >
>> >> >  from dolfin import *
>> >> >  mesh = Interval(10, 0.1, 2.0)
>> >> >  V = FunctionSpace(mesh, "CG", 1)
>> >> >  x = interval.x
>> >> >  f = bessel_J(0, x)
>> >> >  g = project(f, V)
>> >> >  plot(g, mesh=mesh)
>> >> >  interactive()
>> >> >
>> >> > To manage notifications about this bug go to:
>> >> > https://bugs.launchpad.net/dolfin/+bug/882560/+subscriptions
>> >
>> > --
>> > You received this bug notification because you are a member of DOLFIN
>> > Core Team, which is subscribed to DOLFIN.
>> > https://bugs.launchpad.net/bugs/882560
>> >
>> > Title:
>> >  tr1::cyl_bessel_* functions are not found at linking stage of jit
>> >
>> > Status in DOLFIN:
>> >  Confirmed
>> >
>> > Bug description:
>> >  When a jit compiled module using bessel functions is imported into
>> >  python, it fails with an undefined symbol error. Probably because the
>> >  boost math tr1 library is not linked in.
>> >
>> >  ImportError:/home/martinal/.instant/cache/d003d0ea29ed9346265963000f1a90
>> > 648953f6a6/_d003d0ea29ed9346265963000f1a90648953f6a6.so: undefined
>> > symbol: boost_cyl_bessel_j;
>> >
>> >
>> >  Code to reproduce:
>> >
>> >  from dolfin import *
>> >  mesh = Interval(10, 0.1, 2.0)
>> >  V = FunctionSpace(mesh, "CG", 1)
>> >  x = interval.x
>> >  f = bessel_J(0, x)
>> >  g = project(f, V)
>> >  plot(g, mesh=mesh)
>> >  interactive()
>> >
>> > To manage notifications about this bug go to:
>> > https://bugs.launchpad.net/dolfin/+bug/882560/+subscriptions
>
> --
> You received this bug notification because you are a member of DOLFIN
> Core Team, which is subscribed to DOLFIN.
> https://bugs.launchpad.net/bugs/882560
>
> Title:
>  tr1::cyl_bessel_* functions are not found at linking stage of jit
>
> Status in DOLFIN:
>  Confirmed
>
> Bug description:
>  When a jit compiled module using bessel functions is imported into
>  python, it fails with an undefined symbol error. Probably because the
>  boost math tr1 library is not linked in.
>
>  ImportError:/home/martinal/.instant/cache/d003d0ea29ed9346265963000f1a90648953f6a6/_d003d0ea29ed9346265963000f1a90648953f6a6.so:
>  undefined symbol: boost_cyl_bessel_j;
>
>
>  Code to reproduce:
>
>  from dolfin import *
>  mesh = Interval(10, 0.1, 2.0)
>  V = FunctionSpace(mesh, "CG", 1)
>  x = interval.x
>  f = bessel_J(0, x)
>  g = project(f, V)
>  plot(g, mesh=mesh)
>  interactive()
>
> To manage notifications about this bug go to:
> https://bugs.launchpad.net/dolfin/+bug/882560/+subscriptions
>