dolfin team mailing list archive

[Marie Rognes <meg@xxxxxxxxxxx>]

Matthew Knepley wrote:
> On Wed, Aug 20, 2008 at 5:08 AM, Garth N. Wells <gnw20@xxxxxxxxx> wrote:
>   
> > Marie Rognes wrote:
> >     
> > > Garth N. Wells wrote:
> > >       
> > > > Marie Rognes wrote:
> > > >         
> > > > > I'm trying to compile dolfin with PETSc and SLEPc, but without MPI:
> > > > >
> > > > >      ./scons.local enableMpi=no withPetscDir=$PETSC_DIR
> > > > >     withSlepcDir=$SLEPC_DIR
> > > > >
> > > > > This gives the following error:
> > > > >
> > > > >           
> > > > Hopefully this is fixed now, although my PETSc is built with MPI, so I
> > > > can't be sure. Let me know if it's ok or otherwise.
> > > >         
> > > I get through the compilation stage now, so that's good :)
> > >
> > > However, if I try to "import dolfin", I get:
> > >
> > >        Python 2.5.2 (r252:60911, Jun 19 2008, 15:12:17)
> > >    [GCC 4.1.2 (Gentoo 4.1.2 p1.0.2)] on linux2
> > >    Type "help", "copyright", "credits" or "license" for more information.
> > >     >>> import dolfin
> > >    Traceback (most recent call last):
> > >      File "<stdin>", line 1, in <module>
> > >      File
> > >
> > > "/home/meg/src/dolfin/dolfin/local/lib/python2.5/site-packages/dolfin/__init__.py",
> > >
> > >    line 13, in <module>
> > >        from assemble import *
> > >      File
> > >
> > > "/home/meg/src/dolfin/dolfin/local/lib/python2.5/site-packages/dolfin/assemble.py",
> > >
> > >    line 22, in <module>
> > >        from dolfin import *
> > >      File
> > >
> > > "/home/meg/src/dolfin/dolfin/local/lib/python2.5/site-packages/dolfin/dolfin.py",
> > >
> > >    line 7, in <module>
> > >        import _dolfin
> > >    ImportError: /home/meg/src/dolfin/dolfin/local/lib/libdolfin.so:
> > >    undefined symbol: MPIUNI_TMP
> > >
> > >       
> > Looks like a linking problem to PETSc. Can you compile C++ DOLFIN programs?
> >     
>
>   

Nope. The cpp poisson demo gives:

meg in cpp >> scons
scons: Reading SConscript files ...
scons: done reading SConscript files.
scons: Building targets ...
c++ -o main.o -c -Wall -pipe -ansi -g -Werror -O2 -fno-strict-aliasing 
-pthread -DDEBUG -DNDEBUG -DPACKAGE_VERSION="0.8.0" -DHAS_PETSC=1 
-DHAS_SLEPC=1 -DHAS_UMFPACK=1 -DHAS_GTS=1 
-I/home/meg/src/dolfin/dolfin/local/include 
-I/usr/lib/python2.5/site-packages/numpy/core/include 
-I/home/meg/src/slepc -I/home/meg/src/slepc/include 
-I/usr/include/python2.5 -I/home/meg/src/petsc/bmake/linux-gnu-c-debug 
-I/home/meg/src/petsc/include 
-I/home/meg/src/petsc-2.3.3-p13/include/mpiuni -I/usr/include/libxml2 
-I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include main.cpp
c++ -o demo -Wl,-rpath,/home/meg/src/slepc/lib/linux-gnu-c-debug 
-Wl,-rpath,/home/meg/src/petsc/lib/linux-gnu-c-debug -pthread 
-Wl,--export-dynamic main.o -L/home/meg/src/dolfin/dolfin/local/lib 
-L/home/meg/src/slepc/lib/linux-gnu-c-debug -L/usr/lib/atlas 
-L/home/meg/src/petsc/lib/linux-gnu-c-debug -ldolfin -lslepc -lblas 
-lumfpack -lamd -lgts -lxml2 -lpetscts -lpetscsnes -lpetscksp -lpetscdm 
-lpetscmat -lpetscvec -lpetsc -lgthread-2.0 -lrt -lgmodule-2.0 -ldl 
-lglib-2.0
/home/meg/src/dolfin/dolfin/local/lib/libdolfin.so: undefined reference 
to `Petsc_MPI_Abort'

> Almost  certainly it is an incomplete link line when libdolfin.so is
> constructed. When PETSc
> is built without MPI, it creates an extra library (libmpiuni) which
> must be linked against to
> get these symbols.
>   

I'm not quite sure what that implies... But, I should somehow add 
-lmpiuni when linking dolfin? For instance in the pkgconfig file scons 
creates for petsc?


--
Marie E. Rognes
Ph.D Fellow, 
Centre of Mathematics for Applications, 
University of Oslo
http://folk.uio.no/meg