dorsal team mailing list archive

[Paul Barbone <barbone@xxxxxx>]

 On 9/8/10 4:06 PM, Anders Logg wrote:
> On Wed, Sep 08, 2010 at 04:01:12PM -0400, Paul Barbone wrote:
> >   On 9/8/10 2:58 PM, Anders Logg wrote:
> > > On Wed, Sep 08, 2010 at 02:49:01PM -0400, Paul Barbone wrote:
> > > >   On 9/7/10 2:15 AM, Anders Logg wrote:
> > > > > On Mon, Sep 06, 2010 at 07:14:21PM -0400, Paul Barbone wrote:
> > > > > >   On 9/6/10 6:32 PM, Anders Logg wrote:
> > > > > > > Did you install PETSc and SLEPc yourself or did you let Dorsal build
> > > > > > > them?
> > > > > > I let dorsal build them.
> > > > > > > Did you have any old versions of any of the libraries on your system?
> > > > > > Yes, but these were in different directories, and incidentally
> > > > > > installed from an older dorsal build.   I tried to keep things
> > > > > > separate, but there is some overlap between the installations.
> > > > > > They use the same python, for example, but the PETSc and SLEPc are
> > > > > > distinct.
> > > > > Could you try locating all those libraries and (at least temporarily)
> > > > > rename or move them to a location where they can't be found?
> > > > >
> > > > > Then clean out the Dorsal build and start with a clean installation.
> > > > >
> > > > > Our scripts should be able to find the correct versions but the
> > > > > configure scripts need some more work.
> > > > Ok.  I reinstalled python, etc, via macports, deleted the old FEniCS
> > > > directory, and installed completely new.  I eventually got precisely
> > > > the same behavior.
> > > Very strange. It works fine on my Snow Leopard (including SCOTCH). I
> > > haven't done anything special. Your hope is that either someone else
> > > has the same problem and knows how to fix it, or you find out what the
> > > problem is yourself.
> > >
> > > It is not that difficult to add some debugging to the DOLFIN CMake
> > > configure scripts. They are located in the cmake/modules/ directory
> > > and named FindPETSc.cmake etc. Let us what you find out.
> > Thanks.  That's helpful.  Where is PETSC_ARCH specified?  It changes
> > from its definition in the  foo.platform file.
> It shouldn't be changed by Dorsal anywhere along the way. There is
> some code in FindPETSc.cmake that tries to figure out PETSC_DIR. Look
> for this passage:
>
>    # Try to figure out PETSC_ARCH if not set
>    if (PETSC_DIR AND NOT PETSC_ARCH)
>
> You can start by printing out the value of PETSC_ARCH prior to this
> and see if it looks ok:
>
>    message("DEBUG PETSC_ARCH = ${PETSC_ARCH}")
>
> --
> Anders
It gives PETSC_ARCH=darwin10.0.0-cxx-opt at this point, regardless of 
what this variable is set to in the *.platform file.   In my older 
installation, this variable was darwin9.2.0...  This is a difference, 
but I doubt, frankly, that it's important.

What I really don't understand and what I think is important is this:

Linking CXX shared library libdolfin.dylib
Undefined symbols:
  "_METIS_mCPartGraphRecursive2", referenced from:
      _ParMETIS_V3_PartKway in libparmetis.a(kmetis.o)
      _PartitionSmallGraph__ in libparmetis.a(weird.o)
      _Mc_InitPartition_RB__ in libparmetis.a(initpart.o)
      _Mc_InitPartition_RB__ in libparmetis.a(initpart.o)
      _Balance_Partition__ in libparmetis.a(initbalance.o)
      _Balance_Partition__ in libparmetis.a(initbalance.o)
ld: symbol(s) not found
collect2: ld returned 1 exit status

This is extracted from the dolfin build_log file, and also prints to the 
screen just before death.

-Paul