[dune-pdelab] Reg: terminal freezes at vtk output
sgupta@geomar.de
sgupta at geomar.de
Thu Oct 18 13:33:36 CEST 2018
So once again... I tried my dune 2.5 code with no blocking for the vector back-end.. Now I get the same issues with the linear solver in 2.5 too!
So, my question is, how can I specify a fixed blocking in dune 2.6 for my model, given that I use P0 fem space ?
Thanks again, and best wishes, Shubhangi
----- Reply message -----
From: "Shubhangi Gupta" <sgupta at geomar.de>
To: "Steffen Müthing" <steffen.muething at iwr.uni-heidelberg.de>
Cc: <dune-pdelab at lists.dune-project.org>
Subject: [dune-pdelab] Reg: terminal freezes at vtk output
Date: Thu, Oct 18, 2018 12:30
Not sure if this is relevant, but here's a bit more information,
I am constructing a composite grid function space as following:
typedef typename GV::Grid::ctype Coord;
typedef Dune::PDELab::P0ParallelConstraints CON0;
using VBE0 = Dune::PDELab::ISTL::VectorBackend<>;
// default block size: 1
typedef Dune::PDELab::P0LocalFiniteElementMap<Coord,RF,dim>
FEM0; // basis function
FEM0 fem0(Dune::GeometryType(Dune::GeometryType::cube,dim));
typedef Dune::PDELab::GridFunctionSpace<GV, FEM0, CON0, VBE0>
GFS0;
GFS0 gfs0(gv, fem0);
using VBE =
Dune::PDELab::ISTL::VectorBackend<Dune::PDELab::ISTL::Blocking::none>;
using GFS =
Dune::PDELab::CompositeGridFunctionSpace<VBE,Dune::PDELab::EntityBlockedOrderingTag,GFS0,GFS0,GFS0,GFS0,GFS0,GFS0,GFS0>;
GFS gfs(gfs0,gfs0,gfs0,gfs0,gfs0,gfs0,gfs0);
Best wishes, Shubhangi
On 18.10.18 11:52, Shubhangi Gupta
wrote:
Dear Steffen,
I thought of changing to dune 2.6 and see if I run into the
same problem.
But now, with dune 2.6 I have another problem. Basically, its
exactly the same test setting as before, but now the linear
solver does not solve in parallel any more.
The only difference between my code in 2.5 and 2.6 versions is
in the vector backend blocking. In 2.5 I had "using VBE =
Dune::PDELab::ISTL::VectorBackend<Dune::PDELab::ISTL::Blocking::fixed,
num_of_variables>;"
whereas, in 2.6, I have "using VBE =
Dune::PDELab::ISTL::VectorBackend<Dune::PDELab::ISTL::Blocking::none>;".
If I try to use a fixed blocking in 2.6, I get the following
error:
/dune/dune-pdelab/dune/pdelab/backend/istl/vectorhelpers.hh:323:9:
error: static assertion failed: You requested static blocking,
but at least one leaf space has a finite element that does not
support automatic block size extraction. Please specify the
block size with the second template parameter of that space's
vector backend.
FYI, In dune 2.5, the following linear solver was solving quite
fine:
typedef
Dune::PDELab::ISTLBackend_OVLP_GMRES_ILU0<GFS,CC> LS;
LS ls(gfs,cc,5000,1,200);
But now somehow it does not work. I also tried the following
linear solvers, but none seems to solve...
typedef
Dune::PDELab::ISTLBackend_BCGS_AMG_SSOR<IGO> LS;
LS ls(gfs,5000,1,true,true);
typedef Dune::PDELab::ISTLBackend_BCGS_AMG_ILU0<IGO>
LS;
LS ls(gfs,5000,0, false, true);
typedef
Dune::PDELab::ISTLBackend_OVLP_BCGS_SSORk<GFS,CC> LS;
LS ls(gfs,cc,5000,1,1);
I am not sure what I am doing wrong here, and I'll be really
grateful if somebody can help me out!
Thanks, and best wishes, Shubhangi
On 10.10.18 14:54, Steffen Müthing
wrote:
Hi Shubhangi,
that version contains the fix that makes sure you always get an error message. Does your
program also hang in sequential runs? My next step would probably be to run a debug build
and see if that hangs as well. If it does, I'd attach a debugger to the hanging process to see
where exactly the problem is happening.
Steffen
Am 10.10.2018 um 13:07 schrieb Shubhangi Gupta <sgupta at geomar.de>:
Hi Stefan,
I am running version 2.5. The program just silently freezes. There are no error messages.
On 10.10.2018 13:05, Steffen Müthing wrote:
HI Shubhangi,
Am 09.10.2018 um 21:35 schrieb Shubhangi Gupta <sgupta at geomar.de>:
Hi Steffen,
Thanks a lot for your reply! This is happening on my laptop, and also on the cluster... hmmm... I am not sure what to do next... DO you maybe have any suggestions?
what version of Dune are you running? Errors before the start of VTK output are often related to missing
directories for the files, and there were some bug fixes in recent Dune versions. Do you get any kind
of error message, or does the program just silently freeze?
Steffen
Thanks again, and best wishes, Shubhangi
On 09.10.2018 21:02, Steffen Müthing wrote:
Hi Shubhangi,
Am 09.10.2018 um 16:32 schrieb Shubhangi Gupta <sgupta at geomar.de>:
Dear all,
I am currently experiencing a really strange problem during the execution of my dune program... When I run the problem in parallel, the program execution freezes in the terminal just before writing the vtk output file... the freeze occurs randomly, sometimes right before the first output, but sometimes after 5, 20, or even 500 outputs, even though I don't change anything about my problem setting! I am really puzzled, and I'll be very thankful for suggestions for solving/debugging this!
that really sounds strange. The one explanation I can think of is a race condition. Are you running this on a cluster with a network file system?
In that case, there might be an issue where one rank tries to write to a per-timestep subdirectory before the creation of that subdirectory has
been flushed from rank 0 to the file server and the other compute nodes, but that’s just guessing right now (but that might explain the freeze if
the program crash is not properly propagated by your MPI / batch system).
Steffen
Thanks in advance, and best wishes, Shubhangi
PS: So far, this problem occurs only in parallel. I write vtk output as follows:
int subsampling = 0;
typedef Dune::SubsamplingVTKWriter<GV> VTKWRITER;
VTKWRITER vtkwriter(gv,subsampling,(int)0);
typedef Dune::VTKSequenceWriter<GV> VTKSEQUENCEWRITER;
VTKSEQUENCEWRITER vtkSequenceWriter( std::make_shared<
VTKWRITER (vtkwriter), fileName, pathName,"" );
.....
.....
vtkSequenceWriter.write(time,Dune::VTK::appendedraw);
--
Dr. Shubhangi Gupta
Marine Geosystems
GEOMAR Helmholtz Center for Ocean Research
Wischhofstraße 1-3,
D-24148 Kiel
Room: 12-206
Phone: +49 431 600-1402
Email:
sgupta at geomar.de
_______________________________________________
dune-pdelab mailing list
dune-pdelab at lists.dune-project.org
https://lists.dune-project.org/mailman/listinfo/dune-pdelab
--
Dr. Shubhangi Gupta
Marine Geosystems
GEOMAR Helmholtz Center for Ocean Research
Wischhofstraße 1-3,
D-24148 Kiel
Room: 12-206
Phone: +49 431 600-1402
Email: sgupta at geomar.de
--
Dr. Shubhangi Gupta
Marine Geosystems
GEOMAR Helmholtz Center for Ocean Research
Wischhofstraße 1-3,
D-24148 Kiel
Room: 12-206
Phone: +49 431 600-1402
Email: sgupta at geomar.de
--
Dr. Shubhangi Gupta
Marine Geosystems
GEOMAR Helmholtz Center for Ocean Research
Wischhofstraße 1-3,
D-24148 Kiel
Room: 12-206
Phone: +49 431 600-1402
Email: sgupta at geomar.de
_______________________________________________
dune-pdelab mailing list
dune-pdelab at lists.dune-project.org
https://lists.dune-project.org/mailman/listinfo/dune-pdelab
--
Dr. Shubhangi Gupta
Marine Geosystems
GEOMAR Helmholtz Center for Ocean Research
Wischhofstraße 1-3,
D-24148 Kiel
Room: 12-206
Phone: +49 431 600-1402
Email: sgupta at geomar.de
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