[Pkg-scicomp-devel] Bug#487969: Bug#487969: Bug#487969: Can't reproduce this

[Ondrej Certik]

On Sat, Jul 19, 2008 at 4:36 PM, Ólafur Jens Sigurðsson
<ojsbug at gmail.com> wrote:
> On Sat, Jul 19, 2008 at 03:21:17PM +0200, Ondrej Certik wrote:
>> On Sat, Jul 19, 2008 at 3:19 PM, Ondrej Certik <ondrej at certik.cz> wrote:
>> > On Sat, Jul 19, 2008 at 2:56 PM, Ólafur Jens Sigurðsson
>> > <ojsbug at gmail.com> wrote:
>> >> On Fri, Jul 18, 2008 at 11:16:20AM -0400, Adam C Powell IV wrote:
>> >>
>> >>> I don't have this problem with ex2, or any other example.  Unfortunately
>> >>> the shlib is stripped so there are no symbols to check. :-(
>> >>>
>> >>> What's your architecture?  It's fine on amd64.
>> >>
>> >> When I follow the example I get the following:
>> >>
>> >> g++ -I/usr/include/libmesh -I/usr/include/mpi -I/usr/include/petsc -c -o ex2.o ex2.C
>> >>
>> >> so the first compile works fine
>> >>
>> >> g++ -o ex2 ex2.o -lmesh -lscotchmetis -lscotch -lscotcherr
>> >> ex2.o: In function main':
>> >> ex2.C:(.text+0x7c): undefined reference to lam_mpi_comm_world'
>> >
>> > ^^^^ This is weird. petsc is compiled against openmpi and libmesh
>> > should be too.
>> >
>> > I just tried on i386 and it works fine for me. Which architecture are
>> > you on? Do you have latest openmpi, petsc and libmesh and all
>> > depending packages from unstable installed?
>>
>> Please post the output of:
>>
>> ondra at fuji:~$ ll -d /usr/include/mpi
>> lrwxrwxrwx 1 root root 21 2008-03-09 14:58 /usr/include/mpi ->
>> /etc/alternatives/mpi
>> ondra at fuji:~$ ll -d /etc/alternatives/mpi
>> lrwxrwxrwx 1 root root 24 2008-07-03 12:41 /etc/alternatives/mpi ->
>> /usr/lib/openmpi/include
>>
>> On your system. Does it point to openmpi?
>
> Ahaa ... it is not openmpi ... by some reason it is pointing to lam
>
> ls -ld /usr/include/mpi
> lrwxrwxrwx 1 root root 21 2007-11-22 19:06 /usr/include/mpi ->
> /etc/alternatives/mpi/
>
> ls -ld /etc/alternatives/mpi
> lrwxrwxrwx 1 root root 16 2008-07-19 14:50 /etc/alternatives/mpi ->
> /usr/include/lam/

Yes, I hit this problem too, it's because of upgrading from lam to
openmpi. Purge lam, openmpi and all other mpi packages (mpich).
Then delete all links and alternatives, even by hand if necessary.
Install openmpi and make sure the links point to openmpi.

Or change it by hand. Please report back if it works. See also this
bug for more background:

http://bugs.debian.org/cgi-bin/bugreport.cgi?bug=457088

Ondrej