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Re: petsc interface to other packages

On 08/11/17 08:33, Drew Parsons wrote:

On Tue, 2017-11-07 at 12:07 +0100, Matteo Semplice wrote:

On 07/11/17 04:12, Drew Parsons wrote:

You've got 4 options:

1) scotch support is activated. scotch provides the same
functionality
as parmetis. Can you use it instead?

In principle, yes, anything better than the "simple" partitioner
would
be ok for me at present. In practice, however, it does not seem to
work.


...

Here I guess that the issue is that petsc 3.7 does not include
scotch
support
(http://www.mcs.anl.gov/petsc/petsc-3.7/docs/manualpages/DM/PetscPart
itionerType.html),
whereas 3.8 does include it.

Unless I am doing something wrong here, for this option I would need
3.8
and since this is not in debian yet, I would need to compile it
locally
from source.

Annoying if it doesn't work easily.  3.7 should have scotch support
already, we'd need to debug more deeply to understand what's wrong.
Perhaps you mean specifically the PETSCPARTITIONERPTSCOTCH interface.
3.8 is on it's way in. In the meantime you could build the debian
packages from the repo at
https://anonscm.debian.org/cgit/debian-science/packages/petsc.git/
(experimental branch)


2) scotch provides a compatibility interface that parmetis clients
are
supposed to be able to link against, see libscotchparmetis-dev.

This would be probably the best solution for stable (and testing, if
3.8
will not get into it).

I installed libscotchparmetis-dev which replaced libparmetis-dev, but
it
must not be sufficient,

Yeah, it will be the same problem actually: PETSc will need to be built
with parmetis support (even if provided by scotch).

Sadly I tested it.  petsc doesn't (yet) build cleanly against
libscotchparmetis-dev.  Looks like the scotchparmetis interface only
provides partial compatibility, but PETSc demands full compatibility.
Might need some dedicated hacking time to sort out.



3) Rebuild petsc locally, with parmetis support activated.
     - this actually should not be difficult to do. We can write
       the instructions into our petsc build scripts if needed.

Depending on the petsc config on the cluster I'll be making the real
runs on, I might end up having to build petsc in my home directory
for
the final code, but I'd prefer a debian solution for the code
development since both myself and my collaborators are running
debian
stable.

It will be a debian solution: what I mean by rebuilding is to build a
local copy of the deb packages.  Then you can install them for the
system in place of the official package.

The basic procedure is

$ apt-get source petsc

... hack debian/rules to add
           --with-metis --with-metis-include=/usr/include --with-metis-lib="-lmetis" \
           --with-parmetis --with-parmetis-include=/usr/include --with-parmetis-lib="-lparmetis" \
to CONFIGURATION_OPTIONS.

$ dch --nmu
   (add a comment to the changelog)

$ dpkg-buildpackage


That's pretty much it (obviously, install the packages for apt-get,
dch, dpkg-buildpackage and build-depends).

(same idea for building 3.8, but start with git clone in place of
apt-get source)


I recommend trying to build the 3.8 deb package with parmetis support
activated.  Then you can test PETSCPARTITIONERPTSCOTCH again using 3.8,
but will have parmetis support in any case.

Drew


Hi Drew,
    I cloned the git repo, switched to experimental branch, branched off again to "local" to make my changes but it does not compile. So I returned to experimental and realized that I cannot even compile the experimental branch without modifications: 

matteo@signalkuppe:~/software/petsc$ git branch -vv
* experimental 4b7653fcb [origin/experimental] upload 3.8.0+dfsg1-1exp1 to experimental 
  local        4b7653fcb upload 3.8.0+dfsg1-1exp1 to experimental
  master       f4811ce9c [origin/master] upload 3.7.7+dfsg1-2 to unstable
matteo@signalkuppe:~/software/petsc$ git diff
matteo@signalkuppe:~/software/petsc$ dpkg-buildpackage
dpkg-buildpackage: info: source package petsc
dpkg-buildpackage: info: source version 3.8.0+dfsg1-1exp1
dpkg-buildpackage: info: source distribution experimental
dpkg-buildpackage: info: source changed by Drew Parsons <dparsons@debian.org> 
dpkg-buildpackage: info: host architecture amd64
 dpkg-source --before-build petsc
 fakeroot debian/rules clean
dh clean --with python2
   dh_testdir
   debian/rules override_dh_auto_clean
make[1]: ingresso nella directory "/home/matteo/software/petsc"
if [ -d x86_64-linux-gnu-real-debug ]; then \
  dh_auto_clean -plibpetsc-real3.8-dbg -ppetsc3.8-doc -- \
    PETSC_DIR=/home/matteo/software/petsc PETSC_ARCH=x86_64-linux-gnu-real-debug; \ 
fi
        make -j8 distclean PETSC_DIR=/home/matteo/software/petsc PETSC_ARCH=x86_64-linux-gnu-real-debug 
make[2]: ingresso nella directory "/home/matteo/software/petsc"
makefile:15: x86_64-linux-gnu-real-debug/lib/petsc/conf/petscvariables: File o directory non esistente /home/matteo/software/petsc/lib/petsc/conf/variables:118: /home/matteo/software/petsc/x86_64-linux-gnu-real-debug/lib/petsc/conf/petscvariables: File o directory non esistente /home/matteo/software/petsc/lib/petsc/conf/rules:972: /home/matteo/software/petsc/x86_64-linux-gnu-real-debug/lib/petsc/conf/petscrules: File o directory non esistente make[2]: ***  Nessuna regola per generare l'obiettivo "/home/matteo/software/petsc/x86_64-linux-gnu-real-debug/lib/petsc/conf/petscrules". Arresto. 
make[2]: uscita dalla directory "/home/matteo/software/petsc"
dh_auto_clean: make -j8 distclean PETSC_DIR=/home/matteo/software/petsc PETSC_ARCH=x86_64-linux-gnu-real-debug returned exit code 2 debian/rules:121: set di istruzioni per l'obiettivo "override_dh_auto_clean" non riuscito 
make[1]: *** [override_dh_auto_clean] Errore 2
make[1]: uscita dalla directory "/home/matteo/software/petsc"
debian/rules:118: set di istruzioni per l'obiettivo "clean" non riuscito
make: *** [clean] Errore 2
dpkg-buildpackage: error: fakeroot debian/rules clean gave error exit status 2 

I am sorry for the italian in the output, but
make[2]: ***  Nessuna regola per generare l'obiettivo "/home/matteo/software/petsc/x86_64-linux-gnu-real-debug/lib/petsc/conf/petscrules". Arresto. 

should be somthing like
make[2]: ***  No rule to generate "/home/matteo/software/petsc/x86_64-linux-gnu-real-debug/lib/petsc/conf/petscrules". Stopping. 

and
debian/rules:121: set di istruzioni per l'obiettivo "override_dh_auto_clean" non riuscito 
means
debian/rules:121: instruction set for "override_dh_auto_clean" did not succeed 

I am no expert of build-package... Would you have any suggestion?

    Matteo
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