dolfin team mailing list archive

[mspieg <mspieg@xxxxxxxxxxxxxxxxx>]

Hi All,
   I've been running into similar problems on macosx with the JIT  
compiler for Dolfin Functions in PyDolfin

info:
python-2.5 from the enthought distribution
OS is macosx-10.4.11 intel.
swig-1.3.36
Dolfin 0.9.1 (development version)
FFC 0.6.1 (development version)
instant (dev version etc...)


running something like the restriction-interpolation demo, I get

Calling FFC just-in-time (JIT) compiler, this may take some time... done
Creating Python extension (compiling and linking), this may take some  
time... done
Calling FFC just-in-time (JIT) compiler, this may take some time... done
Creating Python extension (compiling and linking), this may take some  
time... done
Calling DOLFIN Function just-in-time (JIT) compiler, this may take  
some time...In instant.recompile: The module did not compile, see '/ 
tmp/tmpVKDvoA2009-2-27-15-07_instant/ 
dolfin_compile_function_227f8d92341151df5a32d2c19fc7a041/compile.log'

looking at the log file, the issue seems to be that the compiler is  
using the options

g++ -arch i386 -arch ppc -isysroot /Developer/SDKs/MacOSX10.4u.sdk -g  
-bundle -undefined dynamic_lookup blah blah blah

which appends /Developer/SDKs/MacOSX10.4u.sdk/  in front of some of  
my dynamic library paths which generates missing symbols etc. etc (in  
addition, I don't want to build for ppc but that doesn't seem as  
serious)

In particular, my openmpi libraries happen to be in  /Applications/ 
mpich/openmpi-1.2.8/lib

but ld  complains:

warning can't open dynamic library: /Developer/SDKs/MacOSX10.4u.sdk/ 
Applications/mpich/openmpi-1.2.8/lib/libmpi_cxx.0.dylib
referenced from: /Users/mspieg/mspieg/hg_repositories/FEniCS/ 
srcFEniCS/dolfin/local/lib/libdolfin.dylib (checking for undefined  
symbols may be affected) (No such file or directory, errno = 2)

and then generates a pile of missing MPI symbols.

All the c++ demos work as does some of the mesh and plotting python  
demos.  Unfortunately, projection from python is just what I need  
(and I'm hoping there's an easy fix)

All help greatly appreciated
cheers
marc




On Jan 16, 2009, at 8:31 AM, Harish Narayanan wrote:

> Johan Hake wrote:
> > Hello!
> >
> > After I added shared_ptr support for PyDOLFIN things have  
> > stabelized, I
> > think... but there are some issues you should be aware of. We need  
> > swig
> > version 1.3.35 or higher. This version comes with ubuntu 08.10  
> > (intrepid).
> > Johannes are going to compile the newest swig, 1.3.37 and put it  
> > in our apt
> > repositories. I assume this also will be done for ubuntu 08.10?  
> > This last
> > version came this week, and it comes with a fix for  
> > std::tr1::shared_ptr,
> > making it possible to change back to tr1.
> >
> > The nice thing with shared_ptrs in PyDOLFIN is that we no longer  
> > have to keep
> > any references for instances we do not want to get garbage  
> > collected in
> > python, as swig now use a shared_ptr to store the underlying c++  
> > instance.
> > And of course it interact better with the c++ library which now use
> > shared_ptrs quite heavily.
>
> I am running into some troubles with the JIT compiler after these  
> recent
> changes. I have Swig 1.3.35 and have run instant-clean.
>
> When I try to run a(ny) python demo, it fails with a 'module did not
> compile' and points me to a log file. Here is its head:
>
> running build_ext
> building '_form_631c2971bc63dc564a258685317dbc7c19bb5b84' extension
> creating build
> creating build/temp.macosx-10.5-i386-2.5
> gcc -fno-strict-aliasing -Wno-long-double -mno-fused-madd -DNDEBUG -g
> -fwrapv -O3 -Wall -Wstrict-prototypes
> -I/Users/hnarayan/Work/FEniCS/build/include -I/sw/include/python2.5 -c
> form_631c2971bc63dc564a258685317dbc7c19bb5b84_wrap.cxx -o
> build/temp.macosx-10.5-i386-2.5/ 
> form_631c2971bc63dc564a258685317dbc7c19bb5b84_wrap.o
> -O0
> cc1plus: warning: command line option "-Wstrict-prototypes" is  
> valid for
> C/ObjC but not for C++
> form_631c2971bc63dc564a258685317dbc7c19bb5b84_wrap.cxx:2625:33: error:
> boost/shared_ptr.hpp: No such file or directory
> form_631c2971bc63dc564a258685317dbc7c19bb5b84_wrap.cxx:2640: error:
> ‘boost’ has not been declared
>
> ... many more related errors.
>
> The compiler flags seem to be missing a -I/where/boost/includes/are  
> and
> -L/where/boost/libs/are . They are present in the corresponding scons
> compile/link lines for the C++ demos which do not have this problem.
>
> Harish
> _______________________________________________
> DOLFIN-dev mailing list
> DOLFIN-dev@xxxxxxxxxx
> http://www.fenics.org/mailman/listinfo/dolfin-dev

----------------------------------------------------
Marc Spiegelman
Lamont-Doherty Earth Observatory
Dept. of Applied Physics/Applied Math
Columbia University
http://www.ldeo.columbia.edu/~mspieg
tel: 845 704 2323 (SkypeIn)
----------------------------------------------------