from:"Ignacio Tomas"

[deal.II] Boundary support points

2017-06-09 Thread Ignacio Tomas

Hello everybody.

I am trying to generate a map (or vectors, whatever is more convenient) 
that gives me the ''dof coordinate'' (''support point'' in the language of 
dealii) but only for the boundary dofs. Ideally I am looking for something 
of the style

std::map< types::global_dof_index, Point< spacedim > > 
 BoundaryDofCoordinates ;

What is the most practical way to get it?

Thanks.

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Re: [deal.II] Re: making a package of PETSc vectors

2017-03-24 Thread Ignacio Tomas

I wanted to do something like (in reality I would do this with a for loop)

std::vector< std::shared_ptr > VectorPacket ;
VectorPacket.resize(3) ;
VectorPacket[0].reset(new PETScWrappers::MPI::Vector) ;
VectorPacket[1].reset(new PETScWrappers::MPI::Vector) ;
VectorPacket[2].reset(new PETScWrappers::MPI::Vector) ;

and later initialize all of them (with a for loop too). Yet this does not
seem to work. Otherwise

std::vector< std::shared_ptr > VectorPacket ;
VectorPacket.resize(3) ;
VectorPacket[0].reset() ;
VectorPacket[1].reset() ;
VectorPacket[2].reset() ;

with Vect1, Vect2 and Vect3 defined/declared/initialized a priori works
fine. But it comes with the overhead of definining these vectors separately
rather than with the the vector of shared pointers.

On Fri, Mar 24, 2017 at 1:50 AM, Jean-Paul Pelteret 
wrote:

> Dear Itomas,
>
> I would recommend going the route suggested in this recent post
> ,
> namely creating a vector of shared pointers of PETSc vectors, i.e.
> std::vector. Using shared
> pointers means that you safeguard against memory leaks, and can be stored
> as entries in a vector. That would give you the flexibility that you
> require with a minimal interface change to your code (apart from how you
> create the vectors initially, you would need to dereference these vector
> entries with the "->" operator instead of the "." operator).
>
> I hope that this helps.
> Best regards,
> Jean-Paul
>
> On Friday, March 24, 2017 at 2:37:07 AM UTC+1, ito...@tamu.edu wrote:
>>
>> Dear everybody:
>>
>> I don't have any particular problem, just trying to streamline a code. I
>> am have a mess with the interfaces of my code, in particular with the
>> functions and classes I have created, primarily because I have to handle a
>> ''packet'' of vectors, say
>>
>> PETScWrappers::MPI::Vector  Vect1;
>> PETScWrappers::MPI::Vector  Vect2;
>> PETScWrappers::MPI::Vector  Vect3;
>> PETScWrappers::MPI::Vector  Vect4;
>> …
>> PETScWrappers::MPI::Vector  Vect7;
>>
>> and use them either as input or output arguments of some functions,
>> solvers, complementary computations, etc. This is quite cumbersome, and as
>> solution I naively thought I could do the following
>>
>> std::vector  VectorPacket ;
>> VectorPacket.resize(7) ;
>> for (int i=0; i<7 ; ++i)
>>   VectorPacket[i].reinit (locally_owned_dofs, mpi_communicator ) ;
>>
>> So, now VectorPacket is really a packet, rather than seven isolated
>> vectors. It is almost needless to say that this is bad idea, std::vector
>> will demand quite a few things from the class PETScWrappers::MPI::Vector
>> which are just not there (in particular some operators). In reality the
>> size of the packet of vector is not always seven, which means that I really
>> need to use a proper container for which I can change it's size. Do you
>> have any suggestion (a.k.a. creative approach) on how to deal with an issue
>> like this one? Which container from the STL would be appropriate?
>>
>> Many thanks.
>>
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Re: [deal.II] Re: making a package of PETSc vectors

2017-03-24 Thread Ignacio Tomas

Thanks, I will definitely try it.

Ignacio.

On Fri, Mar 24, 2017 at 1:50 AM, Jean-Paul Pelteret 
wrote:

> Dear Itomas,
>
> I would recommend going the route suggested in this recent post
> ,
> namely creating a vector of shared pointers of PETSc vectors, i.e.
> std::vector. Using shared
> pointers means that you safeguard against memory leaks, and can be stored
> as entries in a vector. That would give you the flexibility that you
> require with a minimal interface change to your code (apart from how you
> create the vectors initially, you would need to dereference these vector
> entries with the "->" operator instead of the "." operator).
>
> I hope that this helps.
> Best regards,
> Jean-Paul
>
> On Friday, March 24, 2017 at 2:37:07 AM UTC+1, ito...@tamu.edu wrote:
>>
>> Dear everybody:
>>
>> I don't have any particular problem, just trying to streamline a code. I
>> am have a mess with the interfaces of my code, in particular with the
>> functions and classes I have created, primarily because I have to handle a
>> ''packet'' of vectors, say
>>
>> PETScWrappers::MPI::Vector  Vect1;
>> PETScWrappers::MPI::Vector  Vect2;
>> PETScWrappers::MPI::Vector  Vect3;
>> PETScWrappers::MPI::Vector  Vect4;
>> …
>> PETScWrappers::MPI::Vector  Vect7;
>>
>> and use them either as input or output arguments of some functions,
>> solvers, complementary computations, etc. This is quite cumbersome, and as
>> solution I naively thought I could do the following
>>
>> std::vector  VectorPacket ;
>> VectorPacket.resize(7) ;
>> for (int i=0; i<7 ; ++i)
>>   VectorPacket[i].reinit (locally_owned_dofs, mpi_communicator ) ;
>>
>> So, now VectorPacket is really a packet, rather than seven isolated
>> vectors. It is almost needless to say that this is bad idea, std::vector
>> will demand quite a few things from the class PETScWrappers::MPI::Vector
>> which are just not there (in particular some operators). In reality the
>> size of the packet of vector is not always seven, which means that I really
>> need to use a proper container for which I can change it's size. Do you
>> have any suggestion (a.k.a. creative approach) on how to deal with an issue
>> like this one? Which container from the STL would be appropriate?
>>
>> Many thanks.
>>
> --
> The deal.II project is located at http://www.dealii.org/
> 
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> forum/dealii?hl=en
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Re: [deal.II] error when trying to initialize PETSc preconditioners

2016-08-15 Thread Ignacio Tomas

Timo:

Simple question: basically, now I have to download the new file
''include/deal.II/lac/petsc_precondition.h'' from the repository, replace
it in my dealii source code and recompile deal, that should do the trick?

Ignacio.

On Sun, Aug 14, 2016 at 8:02 PM, Timo Heister <heis...@clemson.edu> wrote:

> Thanks, this should fix it: https://github.com/dealii/dealii/pull/2963
>
> On Sat, Aug 13, 2016 at 5:28 PM, Ignacio Tomas <nacho...@gmail.com> wrote:
> > This is the whole error message
> >
> >
> >
> >
> >
> > terminate called after throwing an instance of
> > 'dealii::StandardExceptions::ExcInvalidState'
> >   what():
> > 
> > An error occurred in line <68> of file
> >  lac/petsc_precondition.cc>
> > in function
> > void dealii::PETScWrappers::PreconditionerBase::create_pc()
> > The violated condition was:
> > pc == NULL
> > The name and call sequence of the exception was:
> > StandardExceptions::ExcInvalidState ()
> > Additional Information:
> > (none)
> > 
> >
> > [nachote:11234] *** Process received signal ***
> > [nachote:11234] Signal: Aborted (6)
> > [nachote:11234] Signal code:  (-6)
> > [nachote:11234] [ 0] /lib/x86_64-linux-gnu/libpthread.so.0(+0x10d10)
> > [0x7f0cacb08d10]
> > [nachote:11234] [ 1] /lib/x86_64-linux-gnu/libc.so.6(gsignal+0x37)
> > [0x7f0cac14c267]
> > [nachote:11234] [ 2] /lib/x86_64-linux-gnu/libc.so.6(abort+0x16a)
> > [0x7f0cac14deca]
> > [nachote:11234] [ 3]
> > /usr/lib/x86_64-linux-gnu/libstdc++.so.6(_ZN9__gnu_
> cxx27__verbose_terminate_handlerEv+0x16d)
> > [0x7f0cac84a06d]
> > [nachote:11234] [ 4] /usr/lib/x86_64-linux-gnu/libstdc++.so.6(+0x5eee6)
> > [0x7f0cac847ee6]
> > [nachote:11234] [ 5] /usr/lib/x86_64-linux-gnu/libstdc++.so.6(+0x5ef31)
> > [0x7f0cac847f31]
> > [nachote:11234] [ 6] /usr/lib/x86_64-linux-gnu/libstdc++.so.6(+0x5f149)
> > [0x7f0cac848149]
> > [nachote:11234] [ 7]
> > /home/nachotex/Documents/deal/deal/dealii841installation/
> lib/libdeal_II.so.8.4.1(_ZN6dealii18deal_II_exceptions9internals11issue_
> errorINS_18StandardExceptions15ExcInvalidStateEEEvNS1_
> 17ExceptionHandlingEPKciS7_S7_S7_T_+0x84)
> > [0x7f0cb0a182d4]
> > [nachote:11234] [ 8]
> > /home/nachotex/Documents/deal/deal/dealii841installation/
> lib/libdeal_II.so.8.4.1(_ZN6dealii13PETScWrappers18Prec
> onditionerBase9create_pcEv+0xf9)
> > [0x7f0cb2a72689]
> > [nachote:11234] [ 9]
> > /home/nachotex/Documents/deal/deal/dealii841installation/
> lib/libdeal_II.so.8.4.1(_ZN6dealii13PETScWrappers23Prec
> onditionBlockJacobi10initializeERKNS0_10MatrixBaseERKNS1_
> 14AdditionalDataE+0x34)
> > [0x7f0cb2a742c4]
> > [nachote:11234] [10]
> > ./main(_ZN8PsystemsILi1EE26initialize_preconditionersEv+0x2c) [0x46536c]
> > [nachote:11234] [11]
> > ./main(_ZN8PsystemsILi1EE23timeloopSSP2EVnotlumpedEv+0x36) [0x43ca76]
> > [nachote:11234] [12] ./main(_ZN8PsystemsILi1EE14validation_runEv+0x356)
> > [0x43d376]
> > [nachote:11234] [13] ./main(main+0x55) [0x4354c5]
> > [nachote:11234] [14] /lib/x86_64-linux-gnu/libc.so.
> 6(__libc_start_main+0xf0)
> > [0x7f0cac137a40]
> > [nachote:11234] [15] ./main(_start+0x29) [0x4356f9]
> > [nachote:11234] *** End of error message ***
> > CMakeFiles/run.dir/build.make:49: recipe for target 'CMakeFiles/run'
> failed
> > make[3]: *** [CMakeFiles/run] Aborted (core dumped)
> > CMakeFiles/Makefile2:130: recipe for target 'CMakeFiles/run.dir/all'
> failed
> > make[2]: *** [CMakeFiles/run.dir/all] Error 2
> > CMakeFiles/Makefile2:138: recipe for target 'CMakeFiles/run.dir/rule'
> failed
> > make[1]: *** [CMakeFiles/run.dir/rule] Error 2
> > Makefile:136: recipe for target 'run' failed
> > make: *** [run] Error 2
> >
> >
> >
> > Clearly you can see that the error happens at
> > void dealii::PETScWrappers::PreconditionerBase::create_pc()
> >
> >
> >
> > On Sat, Aug 13, 2016 at 12:03 PM, Timo Heister <heis...@clemson.edu>
> wrote:
> >>
> >> > and stops again with a
> >> > error when I make the call to initialize for the second time which is
> >> > expected since ''initialize()'' can only be called once.
> >>
> >> I would hope that calling initialize() more than once works. What is
> >> the error you are getting?
> >>
> >>
> >> --
> >> Timo Heister
> >> http://www.math.clemson.edu/~heister/
> >>
> >>

Re: [deal.II] error when trying to initialize PETSc preconditioners

2016-08-13 Thread Ignacio Tomas

This is the whole error message





terminate called after throwing an instance of
'dealii::StandardExceptions::ExcInvalidState'
  what():

An error occurred in line <68> of file

in function
void dealii::PETScWrappers::PreconditionerBase::create_pc()
The violated condition was:
pc == NULL
The name and call sequence of the exception was:
StandardExceptions::ExcInvalidState ()
Additional Information:
(none)


[nachote:11234] *** Process received signal ***
[nachote:11234] Signal: Aborted (6)
[nachote:11234] Signal code:  (-6)
[nachote:11234] [ 0] /lib/x86_64-linux-gnu/libpthread.so.0(+0x10d10)
[0x7f0cacb08d10]
[nachote:11234] [ 1] /lib/x86_64-linux-gnu/libc.so.6(gsignal+0x37)
[0x7f0cac14c267]
[nachote:11234] [ 2] /lib/x86_64-linux-gnu/libc.so.6(abort+0x16a)
[0x7f0cac14deca]
[nachote:11234] [ 3]
/usr/lib/x86_64-linux-gnu/libstdc++.so.6(_ZN9__gnu_cxx27__verbose_terminate_handlerEv+0x16d)
[0x7f0cac84a06d]
[nachote:11234] [ 4] /usr/lib/x86_64-linux-gnu/libstdc++.so.6(+0x5eee6)
[0x7f0cac847ee6]
[nachote:11234] [ 5] /usr/lib/x86_64-linux-gnu/libstdc++.so.6(+0x5ef31)
[0x7f0cac847f31]
[nachote:11234] [ 6] /usr/lib/x86_64-linux-gnu/libstdc++.so.6(+0x5f149)
[0x7f0cac848149]
[nachote:11234] [ 7]
/home/nachotex/Documents/deal/deal/dealii841installation/lib/libdeal_II.so.8.4.1(_ZN6dealii18deal_II_exceptions9internals11issue_errorINS_18StandardExceptions15ExcInvalidStateEEEvNS1_17ExceptionHandlingEPKciS7_S7_S7_T_+0x84)
[0x7f0cb0a182d4]
[nachote:11234] [ 8]
/home/nachotex/Documents/deal/deal/dealii841installation/lib/libdeal_II.so.8.4.1(_ZN6dealii13PETScWrappers18PreconditionerBase9create_pcEv+0xf9)
[0x7f0cb2a72689]
[nachote:11234] [ 9]
/home/nachotex/Documents/deal/deal/dealii841installation/lib/libdeal_II.so.8.4.1(_ZN6dealii13PETScWrappers23PreconditionBlockJacobi10initializeERKNS0_10MatrixBaseERKNS1_14AdditionalDataE+0x34)
[0x7f0cb2a742c4]
[nachote:11234] [10]
./main(_ZN8PsystemsILi1EE26initialize_preconditionersEv+0x2c) [0x46536c]
[nachote:11234] [11]
./main(_ZN8PsystemsILi1EE23timeloopSSP2EVnotlumpedEv+0x36) [0x43ca76]
[nachote:11234] [12] ./main(_ZN8PsystemsILi1EE14validation_runEv+0x356)
[0x43d376]
[nachote:11234] [13] ./main(main+0x55) [0x4354c5]
[nachote:11234] [14]
/lib/x86_64-linux-gnu/libc.so.6(__libc_start_main+0xf0) [0x7f0cac137a40]
[nachote:11234] [15] ./main(_start+0x29) [0x4356f9]
[nachote:11234] *** End of error message ***
CMakeFiles/run.dir/build.make:49: recipe for target 'CMakeFiles/run' failed
make[3]: *** [CMakeFiles/run] Aborted (core dumped)
CMakeFiles/Makefile2:130: recipe for target 'CMakeFiles/run.dir/all' failed
make[2]: *** [CMakeFiles/run.dir/all] Error 2
CMakeFiles/Makefile2:138: recipe for target 'CMakeFiles/run.dir/rule' failed
make[1]: *** [CMakeFiles/run.dir/rule] Error 2
Makefile:136: recipe for target 'run' failed
make: *** [run] Error 2



Clearly you can see that the error happens at
void dealii::PETScWrappers::PreconditionerBase::create_pc()



On Sat, Aug 13, 2016 at 12:03 PM, Timo Heister  wrote:

> > and stops again with a
> > error when I make the call to initialize for the second time which is
> > expected since ''initialize()'' can only be called once.
>
> I would hope that calling initialize() more than once works. What is
> the error you are getting?
>
>
> --
> Timo Heister
> http://www.math.clemson.edu/~heister/
>
> --
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Re: [deal.II] error when trying to initialize PETSc preconditioners

2016-08-12 Thread Ignacio Tomas

Many thanks Timo.

I tried PreconditionBlockJacobi and it worked. However, I am running a 
validation loop of progressively smaller meshes, and stops again with a 
error when I make the call to initialize for the second time (I have to do 
it, since the matrix is the same ... but has changed, I have to recompute 
the incomplete factorization), which is expected since ''initialize()'' can 
only be called once. A simple solution for this problem: declaring the 
preconditioner inside the validation loop rather than outside and pass it 
as an argument to the routine that solves the linear system. 

Yes, is there a better solution? Say for instance, as with trilinos 
preconditioners that have a ''clear()'' function member so that you can 
reinitialize it with a new matrix (this is particularly useful in 
adaptivity loops, like in step-32). 

That's all for now.

Many Thanks.

Ignacio.




On Friday, August 12, 2016 at 9:31:36 PM UTC-5, Timo Heister wrote:
>
> Hey Ignacio, 
>
> good to hear from you! 
>
> Sadly this is not documented well, but the ICC preconditioner is only 
> implemented for BAIJ matrices and not MPIAIJ (which we use even if you 
> run on one processor), see 
> https://www.mcs.anl.gov/petsc/petsc-current/docs/manualpages/PC/PCICC.html 
>
> You should be able to make it work by using a 
> PETScWrappers::SparseMatrix instead of an 
> PETScWrappers::MPI::SparseMatrix. Or, probably a better idea, just use 
> a preconditioner that works with parallel matrices like 
> PreconditionBlockJacobi. 
>
> Best, 
> Timo 
>
>
> On Fri, Aug 12, 2016 at 9:46 PM, Ignacio Tomas <nach...@gmail.com 
> > wrote: 
> > Hi, everybody. I am just trying to initialize either ICC, Jacobi or 
> > ParaSalis preconditioner from PETSc, using a PETSc matrix in parallel. 
> So 
> > far I am running just one mpi process. After the call to ''.initialize'' 
> I 
> > get: 
> > 
> > 
> > 
> > 
> > [0]PETSC ERROR: No support for this operation for this object type 
> > [0]PETSC ERROR: Matrix format mpiaij does not have a built-in PETSc ICC 
> > [0]PETSC ERROR: See http://www.mcs.anl.gov/petsc/documentation/faq.html 
> for 
> > trouble shooting. 
> > [0]PETSC ERROR: Petsc Release Version 3.5.3, Jan, 31, 2015 
> > [0]PETSC ERROR: ./main on a arch-linux2-c-opt named nachote by nachotex 
> Fri 
> > Aug 12 20:28:49 2016 
> > [0]PETSC ERROR: Configure options --download-fblaslapack=1 
> > --with-shared-libraries=1 --download-hypre=1 --download-mumps=1 
> > --download-spooles=1 --download-scalapack=1 --download-metis=1 
> > --download-parmetis=1 --download-blacs=1 --with-debugging=0 --with-x=0 
> > [0]PETSC ERROR: #1 MatGetFactor() line 3960 in 
> > 
> /home/nachotex/Documents/deal/PETSC/petsc-3.5.3/src/mat/interface/matrix.c 
> > [0]PETSC ERROR: #2 PCSetup_ICC() line 18 in 
> > 
> /home/nachotex/Documents/deal/PETSC/petsc-3.5.3/src/ksp/pc/impls/factor/icc/icc.c
>  
>
> > [0]PETSC ERROR: #3 PCSetUp() line 902 in 
> > 
> /home/nachotex/Documents/deal/PETSC/petsc-3.5.3/src/ksp/pc/interface/precon.c 
>
> > terminate called after throwing an instance of 
> > 'dealii::LACExceptions::ExcPETScError' 
> >   what(): 
> >  
> > An error occurred in line <384> of file 
> > 
> 
>  
>
> > in function 
> > void dealii::PETScWrappers::PreconditionICC::initialize(const 
> > dealii::PETScWrappers::MatrixBase&, const 
> > dealii::PETScWrappers::PreconditionICC::AdditionalData&) 
> > The violated condition was: 
> > ierr == 0 
> > The name and call sequence of the exception was: 
> > ExcPETScError(ierr) 
> > Additional Information: 
> > An error with error number 56 occurred while calling a PETSc function 
> > 
> > 
> > 
> > 
> > Any clue? Did I forget to install something? 
> > 
> > -- 
> > The deal.II project is located at http://www.dealii.org/ 
> > For mailing list/forum options, see 
> > https://groups.google.com/d/forum/dealii?hl=en 
> > --- 
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> > email to dealii+un...@googlegroups.com . 
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>
>
>
> -- 
> Timo Heister 
> http://www.math.clemson.edu/~heister/ 
>

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[deal.II] error when trying to initialize PETSc preconditioners

2016-08-12 Thread Ignacio Tomas

Hi, everybody. I am just trying to initialize either ICC, Jacobi or 
ParaSalis preconditioner from PETSc, using a PETSc matrix in parallel. So 
far I am running just one mpi process. After the call to ''.initialize'' I 
get:




[0]PETSC ERROR: No support for this operation for this object type
[0]PETSC ERROR: Matrix format mpiaij does not have a built-in PETSc ICC
[0]PETSC ERROR: See http://www.mcs.anl.gov/petsc/documentation/faq.html for 
trouble shooting.
[0]PETSC ERROR: Petsc Release Version 3.5.3, Jan, 31, 2015 
[0]PETSC ERROR: ./main on a arch-linux2-c-opt named nachote by nachotex Fri 
Aug 12 20:28:49 2016
[0]PETSC ERROR: Configure options --download-fblaslapack=1 
--with-shared-libraries=1 --download-hypre=1 --download-mumps=1 
--download-spooles=1 --download-scalapack=1 --download-metis=1 
--download-parmetis=1 --download-blacs=1 --with-debugging=0 --with-x=0
[0]PETSC ERROR: #1 MatGetFactor() line 3960 in 
/home/nachotex/Documents/deal/PETSC/petsc-3.5.3/src/mat/interface/matrix.c
[0]PETSC ERROR: #2 PCSetup_ICC() line 18 in 
/home/nachotex/Documents/deal/PETSC/petsc-3.5.3/src/ksp/pc/impls/factor/icc/icc.c
[0]PETSC ERROR: #3 PCSetUp() line 902 in 
/home/nachotex/Documents/deal/PETSC/petsc-3.5.3/src/ksp/pc/interface/precon.c
terminate called after throwing an instance of 
'dealii::LACExceptions::ExcPETScError'
  what():  

An error occurred in line <384> of file 

 
in function
void dealii::PETScWrappers::PreconditionICC::initialize(const 
dealii::PETScWrappers::MatrixBase&, const 
dealii::PETScWrappers::PreconditionICC::AdditionalData&)
The violated condition was: 
ierr == 0
The name and call sequence of the exception was:
ExcPETScError(ierr)
Additional Information: 
An error with error number 56 occurred while calling a PETSc function




Any clue? Did I forget to install something?

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[deal.II] Boundary support points

Re: [deal.II] Re: making a package of PETSc vectors

Re: [deal.II] Re: making a package of PETSc vectors

Re: [deal.II] error when trying to initialize PETSc preconditioners

Re: [deal.II] error when trying to initialize PETSc preconditioners

Re: [deal.II] error when trying to initialize PETSc preconditioners

[deal.II] error when trying to initialize PETSc preconditioners

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