Re: [petsc-users] MatZeroRowsColumnsLocal for MatNest

f specifying everything in terms of local indices, though it > could be implemented. > > "Garth N. Wells" <gn...@cam.ac.uk> writes: > > > Should MatZeroRowsColumnsLocal work for matrices of type MATNEST? > > > > Garth >

[petsc-users] MatZeroRowsColumnsLocal for MatNest

Should MatZeroRowsColumnsLocal work for matrices of type MATNEST? Garth

Re: [petsc-dev] Config failure

esting (we've been using https://circleci.com/) has taken our success rate for full next testing from around 60% to over 90%. It would pick up errors like this one within a minute of pushing to a branch. Garth > Satish > > On Wed, 31 Jan 2018, Garth N. Wells wrote: > > > The gree

[petsc-dev] Config failure

The green bits here: https://bitbucket.org/petsc/petsc/commits/b9693abc333a4cb54c29596de4de4a2160c61cc0 ain't proper Python. Breaks config. Not sure how this gets past your testing . . . . Garth

Re: [petsc-dev] CMake: make, install, find_package ?

On 7 November 2017 at 09:17, Franck Houssen wrote: > Seems you really had a very bad experience with CMake. Not gonna fight. :D > (joking) > I'll stick to pkg-config: that's fine to me. > Here is an example FindPETSc.cmake file that extracts data from petsc.pc via

Re: [petsc-users] Multigrid coarse grid solver

0 > [0]PETSC ERROR: ./ex56 on a arch-macosx-gnu-g named MarksMac-5.local by > markadams Wed Apr 26 17:46:28 2017 > [0]PETSC ERROR: Configure options --with-cc=clang --with-cc++=clang++ > COPTFLAGS="-g -O0 -mavx2" CXXOPTFLAGS="-g -O0 -mavx2" F > > > On Thu, A

Re: [petsc-users] Multigrid coarse grid solver

hase of > the communication for each V cycle since every process has the entire > solution it just grabs from itself the values it needs without communication. > > > > >> On Apr 26, 2017, at 5:25 PM, Garth N. Wells <gn...@cam.ac.uk> wrote: >> >> I'm a bit c

Re: [petsc-users] petsc4py bool type

On 26 April 2017 at 09:06, Lisandro Dalcin <dalc...@gmail.com> wrote: > On 25 April 2017 at 19:48, Garth N. Wells <gn...@cam.ac.uk> wrote: >> I'm seeing some behaviour with bool types in petsc4py that I didn't >> expect. In the Python interface, returned Booleans ha

[petsc-users] petsc4py bool type

I'm seeing some behaviour with bool types in petsc4py that I didn't expect. In the Python interface, returned Booleans have type '', where I expected them to have type ' '. Below program illustrates issue. Seems to be related to bint in cython. Am I doing something wrong? Garth from petsc4py

Re: [petsc-dev] Problem with petsc.pc when configured with --with-single-library=0

On 5 March 2017 at 06:15, Jed Brown <j...@jedbrown.org> wrote: > "Garth N. Wells" <gn...@cam.ac.uk> writes: > >>> How do you ensure that you find the correct shared versus static >>> libraries? Does the above really work for static? >>

Re: [petsc-dev] Problem with petsc.pc when configured with --with-single-library=0

On 4 March 2017 at 16:07, Jed Brown <j...@jedbrown.org> wrote: > "Garth N. Wells" <gn...@cam.ac.uk> writes: > >> On 4 March 2017 at 15:43, Jed Brown <j...@jedbrown.org> wrote: >>> "Garth N. Wells" <gn...@cam.ac.uk> writes: >&

Re: [petsc-dev] Problem with petsc.pc when configured with --with-single-library=0

On 4 March 2017 at 15:43, Jed Brown <j...@jedbrown.org> wrote: > "Garth N. Wells" <gn...@cam.ac.uk> writes: > >> On 1 March 2017 at 16:22, Jed Brown <j...@jedbrown.org> wrote: >>> Barry and Garth, should we include RPATH flags in the Libs

Re: [petsc-dev] Problem with petsc.pc when configured with --with-single-library=0

esn't > risk namespace collision. > > Jed Brown <j...@jedbrown.org> writes: > >> Garth, I put a fix in 'next'. Dolfin configures for me now. >> >> Barry, the fact that PETSc.pc has been broken for four years is why >> someone might use FindPETSc.cmake. (

[petsc-dev] Problem with petsc.pc when configured with --with-single-library=0

When configuring PETSc with "--with-single-library=0", my installed petsc.pc file looks like: prefix=/home/garth/local/packages/petsc-test exec_prefix=${prefix} includedir=${prefix}/include libdir=/home/garth/local/packages/petsc-test/lib ccompiler=mpicc fcompiler=mpif90 blaslapacklibs=-llapack

[petsc-dev] PaStiX build broken

I get a PaStiX build failure with '--download-pastix': In file included from sopalin/src/murge.c:364:0, from sopalin/src/zmurge.c:54: sopalin/src/variable_csc.c: In function ‘vcsc_add_node’: sopalin/src/variable_csc.c:138:13: error: non-floating-point argument in call to function

[petsc-dev] Parallel LU solvers without ParMETIS

It would be helpful if solvers for which ParMETIS is an optional dependency, e.g. MUMPS, could optionally be built with/without ParMETIS. The problem is that ParMETIS screws up the licensing and precludes commercial use. Garth

[petsc-dev] Build system failure - undeclared variable

I commented on a change that breaks the build systems at: https://bitbucket.org/petsc/petsc/commits/a2e251dc20fc908bc93fbeeecda5467a0fda289e?at=master#chg-config/configure.py Garth

Re: [petsc-dev] Install step broken

On 28 January 2016 at 15:40, Matthew Knepley <knep...@gmail.com> wrote: > On Wed, Jan 27, 2016 at 9:10 AM, Garth N. Wells <gn...@cam.ac.uk> wrote: > >> The 'install' step for master is broken for me since Matt's >> change ddc4758 ( >> https

[petsc-dev] Install step broken

The 'install' step for master is broken for me since Matt's change ddc4758 ( https://bitbucket.org/petsc/petsc/commits/ddc47588dc986180af4263ab160cc4a555099aa9). I can build and install c502958 fine. Error at 'make install' is: No cached configure in RDict at

[petsc-dev] SuperLU build error

I've reported before that SuperLU has a bug that causes compile failures: util.c:32:18: error: format not a string literal and no format arguments [-Werror=format-security] fprintf(stderr, msg); I usually fix this by hand, but the way PETSc since very recently resets user changes in

Re: [petsc-dev] SuperLU build error

with the Ubuntu MPICH package. Garth > Jeff > > > On Thursday, December 17, 2015, Garth N. Wells <gn...@cam.ac.uk> wrote: > >> I've reported before that SuperLU has a bug that causes compile failures: >> >> util.c:32:18: error: format not a string

Re: [petsc-dev] SuperLU build error

>Satish, > > I thought this was now fully resolved? > > Barry > > > On Dec 18, 2015, at 2:52 AM, Garth N. Wells <gn...@cam.ac.uk> wrote: > > > > I've reported before that SuperLU has a bug that causes compile failures: > > > > ut

Re: [petsc-dev] SuperLU build error

tch? > > > https://bitbucket.org/petsc/pkg-superlu/commits/0342e0bb6526fa61e40db44bd70bd0802e9b32a2 > > Thanks, > Satish > > On Fri, 18 Dec 2015, Garth N. Wells wrote: > > > On 18 December 2015 at 16:45, Barry Smith <bsm...@mcs.anl.gov> wrote: > > > > > > >

Re: [FEniCS-support] [IMPORTANT] New mailing lists

On 9 November 2015 at 15:46, Anders Logg wrote: > Dear all, > > For a couple of weeks now we have had severe problems with users being > unsubscribed from our mailing lists due to excessive bouncing. > > This seems to be related to users forwarding their email to Gmail, but >

Re: [FEniCS] [FEniCS-support] [IMPORTANT] New mailing lists

-- > *From:* fenics-boun...@fenicsproject.org [fenics-boun...@fenicsproject.org] > on behalf of Garth N. Wells [gn...@cam.ac.uk] > *Sent:* 10 November 2015 10:50 > *To:* Anders Logg > *Cc:* fenics-supp...@fenicsproject.org; fenics@fenicsproject.org > *Sub

[FEniCS] FFC time extension status

What's the status of the FFC time extension? In working on improving the documentation for FFC, the documentation builder is failing because the time extension module is imported by some FFC code (ffc/timeelements.py), but the extension is not installed. I presume this means that it's not working

Re: [FEniCS] Remove Qt dependency from DOLFIN

On 30 October 2015 at 19:03, Jan Blechta <blec...@karlin.mff.cuni.cz> wrote: > On Fri, 30 Oct 2015 17:56:56 + > "Garth N. Wells" <gn...@cam.ac.uk> wrote: > > > I'd like to flag this up again. I get problems building DOLFIN when I > > have Qt dev p

Re: [FEniCS-support] problem with make dolfin version 1.6

It looks like you have an old version of UFC (which is distributed with FFC). Check that you have a matching version of DOLFIn and FFC, i.e. DOLFIN and FFC 1.6, or DOLFIN and FFC dev. Also check that you don't have an old ufc.h lying around somewhere. Garth On 19 October 2015 at 13:36, Björn

Re: [FEniCS] Boundary conditions for H(div) elements

lly need to specify. Better then to specify a function of the same > value dimension and say that this function should agree for all the dofs on > the facet. > > -- > Anders > > > fre 9 okt. 2015 kl 22:32 skrev Garth N. Wells <gn...@cam.ac.uk>: > >> I thought you mig

Re: [FEniCS] mpi4py

few calls, I think it's fine to wrap them and to make mpi4py a dijitso dependency in parallel. Garth > 1. okt. 2015 12:54 skrev "Garth N. Wells" <gn...@cam.ac.uk>: > >> >> On 1 October 2015 at 11:33, Martin Sandve Alnæs <marti...@simula.no> >&

Re: [FEniCS] mpi4py

On 1 October 2015 at 10:44, Martin Sandve Alnæs wrote: > Can we make mpi4py a required dependency for fenics? Any reasons not to? > > To keep it simple, I presume it would mean making MPI a dependency for FEniCS (?), which is not presently the case. Garth > Martin > >

Re: [FEniCS] Expose new function through swig

i Oslo >> >> >> ___ >> fenics mailing list >> fenics@fenicsproject.org >> <javascript:_e(%7B%7D,'cvml','fenics@fenicsproject.org');> >> http://fenicsproject.org/mailman/listinfo/fenics >> > -- Garth N. Wells Department of Engineering, University of Cambridge http://www.eng.cam.ac.uk/~gnw20 ___ fenics mailing list fenics@fenicsproject.org http://fenicsproject.org/mailman/listinfo/fenics

Re: [FEniCS] Binaries for CentOS-Linux

On 10 September 2015 at 08:58, Maria Schuette < maria.schue...@uni-paderborn.de> wrote: > Dear all, > > are there any binaries for CentOS-Linux (FEniCS version 1.5) available for > download? > > No. Garth > > Best regards, > > Maria Schuette > -- > Maria Schuette > Wissenschaftliche

[FEniCS] PETSc version bump

I would like to propose that we switch to DOLFIN supporting PETSc 3.6 only. Martin has just reported a number of bugs that in all likelihood are due to bugs in the Ubuntu/Debian PETSc 3.4 package, or in old versions of PETSc dependencies. Finding work-arounds for these is not a good use of

Re: [FEniCS-support] manual installation on OS X

As a work-around, try using -DDOLFIN_ENABLE_MUMPS=False when building DOLFIN. I'm not aware of any FEniCS developers using MacPorts for dependencies (I use Homebrew), so support will be patchy. Garth On 28 August 2015 at 00:41, Gideon Simpson gideon.simp...@gmail.com wrote: Hi, I’m trying to

Re: [FEniCS-support] manual installation on OS X

. MUMPSLUSolver is toggled by #ifdef PETSC_HAVE_MUMPS There is a linking problem to $PETSC_DIR/lib/libdmumps.a. Ensure that the object is visible to linker. Jan On Fri, 28 Aug 2015 09:36:43 +0100 Garth N. Wells gn...@cam.ac.uk wrote: As a work-around, try using -DDOLFIN_ENABLE_MUMPS=False when

Re: [FEniCS-support] ECCN Needed before use can be approved of SCOTCH

Information on SCOTCH is available on the SCOTCH web page: https://www.labri.fr/perso/pelegrin/scotch/. Garth On 31 July 2015 at 19:29, Carney, Katherine D katherine.d.car...@exxonmobil.com wrote: I need to confirm the Export Controls Classification Number for Scotch 6.X provided on the

Re: [FEniCS] Multi-thread issue when using dolfin Function

region? Garth thanks in advance for any help Alvaro Diez From: Garth N. Wells [gn...@cam.ac.uk] Sent: 25 August 2015 14:22 To: Alvaro Diez Gonzalez-Pardo Cc: fenics@fenicsproject.org Subject: Re: [FEniCS] Multi-thread issue when using dolfin

Re: [FEniCS] Multi-thread issue when using dolfin Function

It looks like the 'auto' build and caching of the bounding box tree is not thread-safe (we can add this to the reasons why I think the user should be tasked with managing the bounding box tree initialisation). Try calling Mesh::bounding_box_tree() before any calls to Function::eval. Garth On

Re: [FEniCS] Buildbot failures

On 20 August 2015 at 15:21, Martin Sandve Alnæs marti...@simula.no wrote: The iteration number assertions that keep failing here: http://fenicsproject.org:8010/builders/dolfin-master-full-trusty-amd64-py3 http://fenicsproject.org:8010/builders/dolfin-master-full-wheezy-amd64 Are they caused

Re: [FEniCS] Buildbot failures

On 20 August 2015 at 16:02, Johannes Ring joha...@simula.no wrote: On Thu, Aug 20, 2015 at 4:39 PM Garth N. Wells gn...@cam.ac.uk wrote: On 20 August 2015 at 15:21, Martin Sandve Alnæs marti...@simula.no wrote: The iteration number assertions that keep failing here: http

[petsc-dev] Seg fault after changeset aa6a8e1

I get a seg fault on master since changeset aa6a8e1 ( https://bitbucket.org/petsc/petsc/commits/aa6a8e194ee3df4b7fc8e67a3c63e52c695f2de4?at=master) when I call KSPMonitorSet(ksp, KSPMonitorTrueResidualNorm, NULL, NULL). Is there a problem with the changeset? Garth

Re: [FEniCS-support] Guidance for solving Pressure-Poisson with many processes (poor scaling)

Start with P1 elements, and make sure your matrix is symmetric-positive definite and use CG. Also, to start use 50k - 500k dofs per process. Make sure that the iteration count grows only very mildly with problem size and is (almost) independent of the number of processes. Garth On 9 August 2015

Re: [FEniCS-support] bjacobi preconditioner not found after installing 1.6?

in there. It looked like it was missing parameter sets for the various preconditioners and a parameter on the solver to specify which one to use? Perhaps a demo for Stokes iterative with block Jacobi? Thank you again, Charles *From:* Garth N. Wells [mailto:gn...@cam.ac.uk

Re: [FEniCS-support] bjacobi preconditioner not found after installing 1.6?

the values but they had no change on the solver call. Charles *From:* Garth N. Wells [mailto:gn...@cam.ac.uk] *Sent:* Monday, August 3, 2015 10:21 AM *To:* Charles Cook char...@rodbourn.com *Cc:* fenics-support@fenicsproject.org *Subject:* Re: [FEniCS-support] bjacobi preconditioner

Re: [FEniCS-support] bjacobi preconditioner not found after installing 1.6?

On 2 August 2015 at 00:11, Jan Blechta blec...@karlin.mff.cuni.cz wrote: The issue has already been discovered, see http://fenicsproject.org/pipermail/fenics/2015-July/002875.html Should we consider patching this by 1.6.1 release, Garth? We could, although 'jacobi' is the only one I'd like

Re: [FEniCS] Preconditioners missing?

On 31 July 2015 at 08:42, Mikael Mortensen mikael.morten...@gmail.com wrote: On 30 Jul 2015, at 17:13, Garth N. Wells gn...@cam.ac.uk wrote: On 30 July 2015 at 13:19, Mikael Mortensen mikael.morten...@gmail.com wrote: On 30 Jul 2015, at 13:54, Jan Blechta blec...@karlin.mff.cuni.cz wrote

Re: [FEniCS] Preconditioners missing?

On 30 July 2015 at 12:18, Mikael Mortensen mikael.morten...@gmail.com wrote: Hi Back from vacation and very pleased :-) to find that I can update my Fenics installation to version 1.6 in less than 10 minutes! Used to take at least a few days. Now I’m trying to upgrade my applications to

Re: [FEniCS] Release status?

of PETSc. Neither case is worth fixing. Garth mån 27 juli 2015 kl 12:42 skrev Garth N. Wells gn...@cam.ac.uk: On 27 July 2015 at 11:37, Anders Logg anders.l...@gmail.com wrote: Yes, fixing this assertion error in one of the unit tests on one of the buildbots: http://fenicsproject.org

Re: [FEniCS] PETSc SNES code in NonlinearVariationalSolver

allows user to bring his own nonlinear solver to NonlinearVariationalSolver, and accessing it back using a method. At the same time it will also solve Garth's original complaint. Any comments? Jan On Thu, 18 Jun 2015 10:43:50 +0100 Garth N. Wells gn...@cam.ac.uk wrote: I'll pin

Re: [FEniCS] gmsh meshes failing in facet-wise assembly through SystemAssembler

I've pushed a fix for this to master. Cian, could you test it? Longer term the assembly code in question needs some re-factoring. Garth On 20 March 2015 at 11:05, Garth N. Wells gn...@cam.ac.uk wrote: So this doesn't get lost, I've registered it as an issue: https://bitbucket.org

Re: [FEniCS] Release status?

I think we're ready now for the 1.6 release. Garth On 9 July 2015 at 22:54, Cian Wilson cwil...@ldeo.columbia.edu wrote: Done. See: https://bitbucket.org/tferma/dolfin/branch/systemassemblerfix-master Cheers, Cian On 07/08/2015 04:03 AM, Garth N. Wells wrote: On 25 June 2015 at 21

Re: [FEniCS] Release status?

could bring your branch up-to-date with master. Thanks. Garth Cheers, Cian On 06/25/2015 04:14 PM, Garth N. Wells wrote: On 25 June 2015 at 19:36, Anders Logg l...@chalmers.se wrote: What is the status of the upcoming release? Which are the current blockers? This one is a blocker

Re: [petsc-dev] Julia Petsc Wrapper

On 6 July 2015 at 16:59, Matthew Knepley knep...@gmail.com wrote: On Mon, Jul 6, 2015 at 10:56 AM, Garth N. Wells gn...@cam.ac.uk wrote: On 6 July 2015 at 14:56, Matthew Knepley knep...@gmail.com wrote: On Mon, Jul 6, 2015 at 8:40 AM, Patrick Sanan patrick.sa...@gmail.com wrote: On Mon

Re: [petsc-dev] Julia Petsc Wrapper

On 6 July 2015 at 14:56, Matthew Knepley knep...@gmail.com wrote: On Mon, Jul 6, 2015 at 8:40 AM, Patrick Sanan patrick.sa...@gmail.com wrote: On Mon, Jul 6, 2015 at 3:02 PM, Matthew Knepley knep...@gmail.com wrote: On Mon, Jul 6, 2015 at 4:59 AM, Patrick Sanan patrick.sa...@gmail.com

Re: [FEniCS] Release status?

On 25 June 2015 at 19:36, Anders Logg l...@chalmers.se wrote: What is the status of the upcoming release? Which are the current blockers? This one is a blocker: https://bitbucket.org/fenics-project/dolfin/issue/494 Garth -- Anders ___

Re: [FEniCS] Get rid of Mesh::bounding_box_tree (WAS: PointSource::apply)

On 23 June 2015 at 14:02, Martin Sandve Alnæs marti...@simula.no wrote: On 23 June 2015 at 14:13, Jan Blechta blec...@karlin.mff.cuni.cz wrote: On Tue, 23 Jun 2015 12:18:05 +0100 Garth N. Wells gn...@cam.ac.uk wrote: On 23 June 2015 at 10:43, Martin Sandve Alnæs marti...@simula.no wrote

Re: [FEniCS] next accidentally merged into master

On 19 June 2015 at 17:21, Jan Blechta blec...@karlin.mff.cuni.cz wrote: Next has been (at least once) accidentally merged into master. $ git branch --contains 832946b * master morandini/add-matrix-get-diagonal next $ git show --oneline 832946b 832946b Merge branch 'logg/fix-issue-328'

[FEniCS] PETSc SNES code in NonlinearVariationalSolver

When did PETSc SNES code slip into NonlinearVariationalSolver? It obviously shouldn't be in there because NonlinearVariationalSolver is not specific to a linear algebra backend. Garth ___ fenics mailing list fenics@fenicsproject.org

Re: [petsc-users] Parameter to pick KSP for estimating eigenvalues for Chebyshev

to the patched version of PETSc. Will the patch find its way into the dev version? Garth Barry On Jun 17, 2015, at 12:59 PM, Garth N. Wells gn...@cam.ac.uk wrote: On 17 June 2015 at 15:43, Barry Smith bsm...@mcs.anl.gov wrote: I introduced a bug in my cleanup. The kspest eigenestimator

Re: [petsc-users] Parameter to pick KSP for estimating eigenvalues for Chebyshev

me know how it goes. I've applied the patch, but I still can't change the Krylov method for estimating the eigenvalues. Garth Barry On Jun 17, 2015, at 6:24 AM, Garth N. Wells gn...@cam.ac.uk wrote: It used to be possible to pick the Krylov solver used to estimate the eigenvalues

[petsc-users] Parameter to pick KSP for estimating eigenvalues for Chebyshev

It used to be possible to pick the Krylov solver used to estimate the eigenvalues for Chebyshev, via the parameter system (mg_levels_est_ksp_type and gamg_est_ksp_type). I know there was some clean-up, with the parameters becoming mg_levels_ksp_chebyshev_esteig_foo, but an option to pick the

[FEniCS] Remove BinaryFile and TimeSeries

Any objections to removing the classes BinaryFile and TimeSeries, and then renaming TimeSeriesHDF - TimeSeries? We have an HDF5 interface that provides the same functionality as BinaryFile, but is portable, faster, self-documenting, works in parallel, . . . . Garth

Re: [FEniCS] Deprecations in MeshGeometry

On 15 June 2015 at 17:34, Chris Richardson ch...@bpi.cam.ac.uk wrote: Dear all, I've been looking at: https://bitbucket.org/fenics-project/fenics-developer-tools/wiki/Parameterized_geometries today. It seems like it might be a good idea to rewrite the interface to MeshGeometry in some

Re: [FEniCS] Deprecations in MeshGeometry

On 15 June 2015 at 19:47, Anders Logg anders.l...@gmail.com wrote: MeshGeometry::x(std::size_t n) means give me the x-coordinate for vertex n. Nope, the full signature is double* MeshGeometry::x(std::size_t n); so it gives a pointer to the coordinate values of vertex n. Garth Shouldn't

[petsc-dev] ML via --download-ml

I've noticed very different performance with ML when I (a) link PETSc to a Trilinos installation; or (b) use --download-ml. I observe - Case (a): solver behaves exactly as I would expect. Iteration counts very close to GAMG iteration counts, minimal dependency on problem size. - Case (b):

[FEniCS-support] Post-doc position at University of Cambridge

I have an opening for a post-doc (two-year position) on a project that involves FEniCS use and development, and in particular high performance computing. The advertisement, with information on how to apply, is at http://www.jobs.cam.ac.uk/job/7120/. Contact me for informal enquiries. Garth

Re: [FEniCS] Remove uBLAS backend from DOLFIN

I've made a pull request at https://bitbucket.org/fenics-project/dolfin/pull-request/22. I'd like to merge asap to avoid untangling conflicts. Garth On 1 June 2015 at 09:40, Anders Logg anders.l...@gmail.com wrote: ok for me. -- Anders mån 1 juni 2015 kl 10:40 skrev Garth N. Wells gn

Re: [FEniCS-support] [FEniCS] FEniCS with Linux containers

On 30 May 2015 at 12:29, Juan Luis Cano juanlu...@gmail.com wrote: On 2015-05-30 13:20, Garth N. Wells wrote: A collection of images for running FEniCS inside Linux containers using Docker (https://www.docker.com/) are now available. With a container image, a FEniCS environment can be quickly

[FEniCS] FEniCS with Linux containers

A collection of images for running FEniCS inside Linux containers using Docker (https://www.docker.com/) are now available. With a container image, a FEniCS environment can be quickly and reliably created with just one line. There is no performance difference with respect to a 'native

[FEniCS-support] FEniCS with Linux containers

A collection of images for running FEniCS inside Linux containers using Docker (https://www.docker.com/) are now available. With a container image, a FEniCS environment can be quickly and reliably created with just one line. There is no performance difference with respect to a 'native

Re: [FEniCS] GenericMatrix::set/get_diagonal

On 12 May 2015 at 04:40, Marco Morandini marco.morand...@polimi.it wrote: Currently only GenericMatrix::set_diagonal is defined and implemented for most of the la backends. Would you object to a patch introducing get_diagonal ? What data structure do you suggest the function returns, e.g. a

Re: [FEniCS-support] [FEniCS] help for Fenics-dorsal installation

On Wed, Apr 8, 2015 at 10:51 AM, Jan Blechta blec...@karlin.mff.cuni.cz wrote: [Please, keep fenics-support@fenicsproject.org in CC.] On Wed, 8 Apr 2015 03:10:27 + 송 의환 ehs...@clunix.com wrote: Hello, Jan Thank you for the reply. I really appreciate it. Since this machine is RHEL6.5

Re: [FEniCS] Tests in FIAT land

On Wed, Apr 1, 2015 at 5:12 PM, Robert Kirby robert_ki...@baylor.edu wrote: David, The right choice is, of course, c.) Write tests for everything However, if you'd like to write tests for your own additions, just use the Framework of Your Choice. Use pytest since we've been moving other

Re: [FEniCS] Performance regressions

\ --with-superlu_dist-dir=$SUPERLU_DIST_DIR \ --download-mumps=1 \ --download-scalapack=1 \ --download-blacs=1 \ --download-ml=1 -- Anders mån 30 mars 2015 kl 17:05 skrev Garth N. Wells gn...@cam.ac.uk: On Mon, Mar 30, 2015 at 1:34 PM, Anders Logg l...@chalmers.se wrote

[FEniCS-support] DOLFIN package in Ubuntu

I've seen the below error message a load of times on the mailing list, but trying the Ubuntu package for this first time I get it too. What's wrong with the package (Ubuntu 14.10)? Garth Traceback (most recent call last): File demo_cahn-hilliard.py, line 27, in module from dolfin import

Re: [FEniCS-support] FEniCS virtual machine images

25 mars 2015 kl 13:00 skrev Garth N. Wells gn...@cam.ac.uk: A virtual image has been added to the array of methods for running FEniCS. The latest image is available at http://fenicsproject.org/pub/virtual/fenics-latest.ova. The image can be useful in a number of scenarios, perhaps most notably

Re: [FEniCS] [FEniCS-support] FEniCS virtual machine images

25 mars 2015 kl 13:00 skrev Garth N. Wells gn...@cam.ac.uk: A virtual image has been added to the array of methods for running FEniCS. The latest image is available at http://fenicsproject.org/pub/virtual/fenics-latest.ova. The image can be useful in a number of scenarios, perhaps most notably

[FEniCS] FEniCS virtual machine images

A virtual image has been added to the array of methods for running FEniCS. The latest image is available at http://fenicsproject.org/pub/virtual/fenics-latest.ova. The image can be useful in a number of scenarios, perhaps most notably in teaching and courses using FEniCS. Some simple instructions

[FEniCS-support] FEniCS virtual machine images

A virtual image has been added to the array of methods for running FEniCS. The latest image is available at http://fenicsproject.org/pub/virtual/fenics-latest.ova. The image can be useful in a number of scenarios, perhaps most notably in teaching and courses using FEniCS. Some simple instructions

Re: [FEniCS] PETSc preconditioner reuse

Call ‘set_operator' when you want the preconditioner to be updated. Garth On 21 Mar 2015, at 18:54, Mikael Mortensen mikael.morten...@gmail.com wrote: Hi, Seems like there is a problem with preconditioner reuse in dolfin 1.5:

Re: [FEniCS] PETSc preconditioner reuse

. The difference (2.43 vs 2.32) is too small to be significant, at least without averaging over a number of runs. The options different_nonzero_pattern and same” were removed from PETS 3.5. Garth Mikael On 21 Mar 2015, at 20:09, Garth N. Wells gn...@cam.ac.uk wrote: Call ‘set_operator

Re: [FEniCS] gmsh meshes failing in facet-wise assembly through SystemAssembler

So this doesn't get lost, I've registered it as an issue: https://bitbucket.org/fenics-project/dolfin/issue/494 Garth On Tue, Feb 10, 2015 at 4:28 PM, Garth N. Wells gn...@cam.ac.uk wrote: On Tue, Feb 10, 2015 at 3:48 AM, Cian Wilson cwil...@ldeo.columbia.edu wrote: Hello, Just

[FEniCS] Python 3

Has anyone built DOLFIN with Python 3 on Ubuntu? I use ./cmake.local -DPYTHON_EXECUTABLE=python3 and get -- Could NOT find PythonInterp: Found unsuitable version 1.4, but required is at least 3 (found /home/garth/code/fenics/dev/dolfin.d/dolfin-2/build.master/python3) It also fails at

Re: [FEniCS] bitbucket issue tracker 'component' field

On Fri, Mar 13, 2015 at 9:23 AM, Martin Sandve Alnæs marti...@simula.no wrote: There's a new field that can be set up in the repository settings called 'component', we can add a list of valid strings and get a new box in the issue setup to group issues. Looks like I don't have admin rights

Re: [FEniCS] Transition to SWIG 3

On Fri, Mar 13, 2015 at 9:17 AM, Martin Sandve Alnæs marti...@simula.no wrote: Agree. Go ahead. Yes, just go ahead. Garth Martin On 13 March 2015 at 10:10, Jan Blechta blec...@karlin.mff.cuni.cz wrote: On Thu, 12 Mar 2015 15:20:05 +0100 Johannes Ring joha...@simula.no wrote: On Thu,

[FEniCS] DOLFIN IO inconsistencies, mesh data, parallel

We have some inconsistencies with how more elaborate IO is handled in serial and parallel with XML formats. It would take considerable work to sort this out and would add complexity, all for a format that is inherently unsuited to parallel simulation. I therefore propose that: - We support only

Re: [FEniCS] Transition to SWIG 3

I don't really mind either way between 3.0.2 and 3.0.3. I'm all for minimising developer effort, so if there's no real difference in that respect let's go with 3.0.2. Otherwise, let's require 3.0.3. Garth On Mon, Mar 9, 2015 at 8:36 PM, Johan Hake hake@gmail.com wrote: Ahh, yes I missed

Re: [FEniCS] Interface consistencies in future ufc changes

anders.l...@gmail.com: An additional point is that run-time performance may also be affected by needing to copy stuff into flattened arrays on the DOLFIN side so in some cases flattening may not be the most effecient option. -- Anders fre 6 mars 2015 kl 11:52 skrev Garth N. Wells gn

Re: [petsc-dev] Recent changes to Chebyshev

and the prefixes. The functions related to this all have EigEst and the prefix _eigest for Eigenvalue Estimator Barry On Mar 5, 2015, at 1:29 PM, Garth N. Wells gn...@cam.ac.uk wrote: I see there have been some recent changes relating to Chebyshev. What should I now use in place

[petsc-dev] Recent changes to Chebyshev

I see there have been some recent changes relating to Chebyshev. What should I now use in place of the old options -mg_est_ksp_type -gamg_est_ksp_type ? Garth

Re: [FEniCS] [FEniCS-support] integral equations in FEniCS

On Mon, Mar 2, 2015 at 11:21 AM, Miroslav Kuchta mi...@math.uio.no wrote: Hi, I wrote a simple script which shows how FEniCS can be used to solve integral equations. At the moment FEniCS is combined with numpy to solve the problem, so I’d be grateful for pointers on how to solve the

Re: [FEniCS-support] integral equations in FEniCS

On Mon, Mar 2, 2015 at 11:21 AM, Miroslav Kuchta mi...@math.uio.no wrote: Hi, I wrote a simple script which shows how FEniCS can be used to solve integral equations. At the moment FEniCS is combined with numpy to solve the problem, so I’d be grateful for pointers on how to solve the

Re: [FEniCS] slow petsc cholesky factorization

this? Thanks. Regards, Miro -- Garth N. Wells Department of Engineering, University of Cambridge http://www.eng.cam.ac.uk/~gnw20 ___ fenics mailing list fenics@fenicsproject.org http://fenicsproject.org/mailman/listinfo/fenics

Re: [FEniCS] Naming of dofs

On Wed, Feb 25, 2015 at 12:27 PM, Martin Sandve Alnæs marti...@simula.no wrote: On 25 February 2015 at 13:14, Garth N. Wells gn...@cam.ac.uk wrote: On Wed, Feb 25, 2015 at 12:07 PM, Martin Sandve Alnæs marti...@simula.no wrote: We might actually want to have both 'domain dofs' (which I

Re: [FEniCS] Naming of dofs

On Wed, Feb 25, 2015 at 12:07 PM, Martin Sandve Alnæs marti...@simula.no wrote: We might actually want to have both 'domain dofs' (which I don't know how to identify with domains in ufc yet) and 'universal dofs' (without a domain association). Wouldn't these 'universal dofs' be associated

Re: [FEniCS] Object views in DOLFIN

2015 at 11:04, Garth N. Wells gn...@cam.ac.uk wrote: We have some objects in DOLFIN that can contain data or can be a view into another object, e.g. DofMap, FunctionSpace, Function. It's often not clear what is what, and it tends to complicate the code for classes that can either own data

[FEniCS] Object views in DOLFIN

We have some objects in DOLFIN that can contain data or can be a view into another object, e.g. DofMap, FunctionSpace, Function. It's often not clear what is what, and it tends to complicate the code for classes that can either own data or provide a view. We've settled on adding a MeshView

Re: [FEniCS] Naming of dofs

On Wed, Feb 25, 2015 at 8:57 AM, Martin Sandve Alnæs marti...@simula.no wrote: I've started working on this issue: https://bitbucket.org/fenics-project/ffc/issue/61/global-dofs-aka-reals-should-not-be Can we agree on a target convention for naming of dofs in FEniCS? I'd like to clean it up,

[FEniCS] Hashdist questions and comments

I'm trying to use Hashdist to build FEniCS inside a Docker container. I have a few comments and questions: - The script at http://fenicsproject.org/fenics-install.sh takes an incredibly long time to run because it builds *so* many libraries, e.g. do we really need to be building openssl,

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