Re: AW: [deal.II] step-42 clarification

2018-01-26 Thread Alberto Salvadori 
Thank you, Timo. Your remarks have been very useful.
It turned out that I made a mistake in the way the mesh was prepared,
 specifically some hanging nodes were not properly dealt with.
This caused also a related issue, that I shared here some time ago (Nov.
25).

This leads to another question, that I take the opportunity to ask. Suppose
that a run is too long for a time slot allocated on a large scale computer.
In such a case, one wants to restart the computations
from a given time. To this aim, the history of the computations up to a
certain time shall be stored. All data stored in cell->user_pointer(), data
of the loads and mesh.
How can one store information on the latter, - as for the partition and the
hanging nodes - correctly? I understand that saving the mesh in a "ucd" or
alternative form may not be the right strategy.

Thank you very much.
Alberto








*Alberto Salvadori* Dipartimento di Ingegneria Civile, Architettura,
Territorio, Ambiente e di Matematica (DICATAM)
 Universita` di Brescia, via Branze 43, 25123 Brescia
 Italy
 tel 030 3711239
 fax 030 3711312

e-mail:
 alberto.salvad...@unibs.it
web-pages:
 http://m4lab.unibs.it/faculty.html
 http://dicata.ing.unibs.it/salvadori

On Fri, Jan 19, 2018 at 3:39 PM, Timo Heister  wrote:

> > in the code and re-implemented it. In serial version, all works fine so
> far.
> > However, when running in parallel, I am seeing an issue in the method
> > PlasticityContactProblem::update_solution_and_constraints.
> >
> > In particular, it turns out that the value of
> >
> > const unsigned int index_z = dof_indices[q_point];
> >
> > might be out of the range of
>
> If you do a loop over all locally owned and locally relevant cells
> than all dof values of a ghosted vector should exist. If you see an
> error, something else must be incorrect (like the IndexSets).
>
> >   PETScWrappers::MPI::Vector lambda( this->locally_relevant_dofs,
> this->mpi_communicator);
>
> This looks suspicious. Does this really create a ghosted vector in
> PETSc? I thought this would fail (at least in debug mode).
>
> Finally, it looks like you modified it to only look at locally owned
> cells to build constraints. The problem with this is that processors
> also need to know about constraints on ghost cells, not only locally
> owned cells. You no longer compute them, which means the solution
> might become incorrect around processor boundaries. It probably
> (hopefully?) works without adaptivity because each locally owned DoF
> is within at least one locally owned cell, but imagine a case where a
> dof on a ghost cells is constrained and interacts with a hanging node
> the current processor owns. You will not handle this case correctly.
>
> I don't quite remember if there is an easy way to do this, but I
> remember writing a debug function that checks if a ConstraintMatrix is
> consistent in parallel. This was a while back, but I can try to find
> it.
>
> --
> Timo Heister
> http://www.math.clemson.edu/~heister/
>
> --
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Informativa sulla Privacy: http://www.unibs.it/node/8155

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Re: [deal.II] Re: installation error

2018-01-26 Thread Wolfgang Bangerth 

On 01/26/2018 06:59 AM, Juan Carlos Araujo Cabarcas wrote:


 From the dealii detailed.log I see that:

MPI_VERSION = 2.1
OMPI_VERSION = 1.6.5

 From the terminal:

$ mpicc --version
gcc (Ubuntu 4.8.4-2ubuntu1~14.04.3) 4.8.4

So it seems I need to upgrade to MPI 3.0.
Thanks, for having a look at this.


That's one option. You could also try to modify the place in deal.II where we 
use MPI_Comm_create_group to use MPI_Comm_create instead. The difference 
between the two functions is minor, and may be useful to keep our interface at 
MPI 2.x. Any patch would of course be appreciated!


Best
 W.

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Wolfgang Bangerth  email: bange...@colostate.edu
   www: http://www.math.colostate.edu/~bangerth/

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Re: [deal.II] Re: installation error

2018-01-26 Thread Juan Carlos Araujo Cabarcas 
Hi, when I install PETSc I allow the configuration process to download the 
necessary libraries it needs: 

./config/configure.py --with-shared=1 --with-x=0 --with-mpi=1 
--with-scalar-type=complex --download-mumps --download-metis 
--download-parmetis --download-superlu_dist --download-blacs 
--download-scalapack --download-superlu_dist

>From the dealii detailed.log I see that:

MPI_VERSION = 2.1
OMPI_VERSION = 1.6.5

>From the terminal:

$ mpicc --version
gcc (Ubuntu 4.8.4-2ubuntu1~14.04.3) 4.8.4

So it seems I need to upgrade to MPI 3.0.
Thanks, for having a look at this.

El jueves, 25 de enero de 2018, 12:29:53 (UTC-5), Wolfgang Bangerth 
escribió:
>
> On 01/24/2018 07:34 AM, Juan Carlos Araujo Cabarcas wrote: 
> > Please find the file: detailed.log attached. 
> > 
> > El martes, 23 de enero de 2018, 17:02:14 (UTC-5), Wolfgang Bangerth 
> > escribió: 
> > 
> > On 01/23/2018 02:13 PM, Bruno Turcksin wrote: 
> >  > 
> >  > mypath/dealii/source/lac/scalapack.cc:243:91: error: there 
> > are no 
> >  > arguments to ‘MPI_Comm_create_group’ that depend on a 
> > template parameter, 
> >  > so a declaration of ‘MPI_Comm_create_group’ must be available 
> > [-fpermissive] 
> >  > ierr = MPI_Comm_create_group(MPI_COMM_WORLD, 
> > group_union, 5, 
> >  > _communicator_union); 
>
> It confused me that you are compiling the scalapack file but get an 
> error message that a particular MPI function was not found. This would 
> ordinarily suggest that either scalapack.cc is missing an #include of 
>  (which is not the case) or that your installation is not 
> configured with MPI (which is the case for you). So the error did not 
> make sense to me at first. 
>
> But it turns out that the call in question, MPI_Comm_create_group is a 
> function that was only added to MPI in version 3.0. Apparently all of us 
> use an MPI installation that is sufficiently up to date. What is the 
> version you use? 
>
> Best 
>   W. 
>
> -- 
>  
> Wolfgang Bangerth  email: bang...@colostate.edu 
>  
> www: http://www.math.colostate.edu/~bangerth/ 
>

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Re: [deal.II] Re: installation error

2018-01-26 Thread Juan Carlos Araujo Cabarcas 
Hi, when I install PETSc I allow the configuration process to download the 
necessary libraries it needs: 

./config/configure.py --with-shared=1 --with-x=0 --with-mpi=1 
--with-scalar-type=complex --download-mumps --download-metis 
--download-parmetis --download-superlu_dist --download-blacs 
--download-scalapack --download-superlu_dist

>From the dealii detailed.log I see that:

MPI_VERSION = 2.1
OMPI_VERSION = 1.6.5

>From the terminal:

$ mpicc --version
gcc (Ubuntu 4.8.4-2ubuntu1~14.04.3) 4.8.4

Shall I update my system libraries?

El jueves, 25 de enero de 2018, 12:29:53 (UTC-5), Wolfgang Bangerth 
escribió:
>
> On 01/24/2018 07:34 AM, Juan Carlos Araujo Cabarcas wrote: 
> > Please find the file: detailed.log attached. 
> > 
> > El martes, 23 de enero de 2018, 17:02:14 (UTC-5), Wolfgang Bangerth 
> > escribió: 
> > 
> > On 01/23/2018 02:13 PM, Bruno Turcksin wrote: 
> >  > 
> >  > mypath/dealii/source/lac/scalapack.cc:243:91: error: there 
> > are no 
> >  > arguments to ‘MPI_Comm_create_group’ that depend on a 
> > template parameter, 
> >  > so a declaration of ‘MPI_Comm_create_group’ must be available 
> > [-fpermissive] 
> >  > ierr = MPI_Comm_create_group(MPI_COMM_WORLD, 
> > group_union, 5, 
> >  > _communicator_union); 
>
> It confused me that you are compiling the scalapack file but get an 
> error message that a particular MPI function was not found. This would 
> ordinarily suggest that either scalapack.cc is missing an #include of 
>  (which is not the case) or that your installation is not 
> configured with MPI (which is the case for you). So the error did not 
> make sense to me at first. 
>
> But it turns out that the call in question, MPI_Comm_create_group is a 
> function that was only added to MPI in version 3.0. Apparently all of us 
> use an MPI installation that is sufficiently up to date. What is the 
> version you use? 
>
> Best 
>   W. 
>
> -- 
>  
> Wolfgang Bangerth  email: bang...@colostate.edu 
>  
> www: http://www.math.colostate.edu/~bangerth/ 
>

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