date:20160703

Re: [deal.II] Re: Deal.II does not pass quick tests after installation

2016-07-03 Thread Thien Binh Nguyen

Dear Mr. Wells,

Thank you very much for your prompt response, and I am also sorry for my
late reply!

When ldd either to libdeal_II.so or libdeal_II.g.so, I received the
following messages

[image: Hình ảnh nội tuyến 1]
As you noticed, I compiled Deal.II with root privilege. I was trying to
re-installed and complied Deal.II with my own account. But I still got the
same error messages.

Thank you very much!

Yours sincerely,
Nguyen Thien Binh

2016-07-01 23:42 GMT+09:00 David Wells :

> Hi there,
>
> Well that is something I have not seen before: it looks like it did not
> link correctly to your copy of libpthread.so. To confirm this, could you run
>
> ldd build-directory/lib/libdeal_II.so
>
> (where build-directory is whereever you compiled the library)
>
> and see if it did not find a particular library.
>
> Since it looks like the library is in '/root/': did you compile this as
> root? If so weird things can happen; you should build it as an unprivileged
> user.
>
> Thanks,
> David Wells
>
> On Thursday, June 30, 2016 at 2:00:22 AM UTC-4, deal.II newbie wrote:
>>
>> Hi! I am a newbie to Deal.II. After the installation, I typed the command
>> make test for running the quick tests. But all four tests failed out of
>> four. The reason listed below in the quicktests.log is the same for all 4
>> tests. I would like to ask if anyone could please help indicate what the
>> error is and how to fix it? Any help or hints would be much appreciated!
>> Thank you very much in advance!
>>
>> The error is the same for all 4 tests as follows,
>>
>> Scanning dependencies of target tbb.debug
>> [100%] Building CXX object
>> tests/quick_tests/CMakeFiles/tbb.debug.dir/tbb.cc.o
>> /root/dealii-8.4.1/tests/quick_tests/tbb.cc:49:6: warning: unused
>> parameter ‘scratch’ [-Wunused-parameter]
>> Linking CXX executable tbb.debug
>> ../../lib/libdeal_II.g.so.8.4.1: undefined reference to
>> `pthread_mutexattr_destroy'
>> ../../lib/libdeal_II.g.so.8.4.1: undefined reference to `pthread_join'
>> ../../lib/libdeal_II.g.so.8.4.1: undefined reference to `pthread_detach'
>> ../../lib/libdeal_II.g.so.8.4.1: undefined reference to
>> `pthread_barrier_wait'
>> ../../lib/libdeal_II.g.so.8.4.1: undefined reference to
>> `pthread_mutexattr_settype'
>> ../../lib/libdeal_II.g.so.8.4.1: undefined reference to
>> `pthread_mutex_trylock'
>> ../../lib/libdeal_II.g.so.8.4.1: undefined reference to
>> `pthread_barrier_init'
>> ../../lib/libdeal_II.g.so.8.4.1: undefined reference to `sem_wait'
>> ../../lib/libdeal_II.g.so.8.4.1: undefined reference to `sem_init'
>> ../../lib/libdeal_II.g.so.8.4.1: undefined reference to
>> `pthread_getspecific'
>> ../../lib/libdeal_II.g.so.8.4.1: undefined reference to
>> `pthread_setspecific'
>> ../../lib/libdeal_II.g.so.8.4.1: undefined reference to `sem_destroy'
>> ../../lib/libdeal_II.g.so.8.4.1: undefined reference to `pthread_create'
>> ../../lib/libdeal_II.g.so.8.4.1: undefined reference to
>> `pthread_key_delete'
>> ../../lib/libdeal_II.g.so.8.4.1: undefined reference to
>> `pthread_key_create'
>> ../../lib/libdeal_II.g.so.8.4.1: undefined reference to
>> `pthread_mutexattr_init'
>> ../../lib/libdeal_II.g.so.8.4.1: undefined reference to
>> `pthread_attr_getstack'
>> ../../lib/libdeal_II.g.so.8.4.1: undefined reference to
>> `pthread_barrier_destroy'
>> ../../lib/libdeal_II.g.so.8.4.1: undefined reference to `sem_post'
>> ../../lib/libdeal_II.g.so.8.4.1: undefined reference to
>> `pthread_getattr_np'
>> ../../lib/libdeal_II.g.so.8.4.1: undefined reference to
>> `pthread_attr_setstacksize'
>> collect2: error: ld returned 1 exit status
>> gmake[7]: *** [tests/quick_tests/tbb.debug] Error 1
>> gmake[6]: *** [tests/quick_tests/CMakeFiles/tbb.debug.dir/all] Error 2
>> gmake[5]: *** [tests/quick_tests/CMakeFiles/tbb.debug.run.dir/rule] Error
>> 2
>> gmake[4]: *** [tbb.debug.run] Error 2
>>
>> --
> 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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Re: [deal.II] Caught signal number 11 SEGV: Segmentation Violation, probably memory access out of range

2016-07-03 Thread Wolfgang Bangerth

On 07/03/2016 03:50 PM, Ehsan Esfahani wrote:

Dear All,

Greetings. I changed step-25 (minor changes) in order to solve my problem. Now
I want to change this code for parallel computation based on the method
mentioned in step-40. I got several errors and solved them one by one but the
following error:

/Number of active cells: 1024
//   Total number of cells: 1365
//{[0,4224]}//
//Time step #1; advancing to t = 0.1.

> [...]

//[0]PETSC ERROR: Caught signal number 11 SEGV: Segmentation Violation,
probably memory access out of range

> [...]

/
/
Eclipse gives me a backtrace in the following line of the code:
/solver.solve (system_matrix, completely_distributed_solution_update,
system_rhs,/
/  preconditioner);/
I have no idea why I got this error. The code is running properly for /fe(1)
/and /n_global_refinements (4)/ but when I change them to /fe(2)/ and
n_global_refinments (4) I got that error related to /Segmentation Violation.
/Do you know what's going on? Also, I have attached the code here . Thanks in
advance for your help.

Ehsan,

segmentation violations (SEGV) are typically easy to debug because you can get 
a backtrave in the debugger of the exact place where it happens, and you can 
then look at the local variables to see why this may have happened. Have you 
tried to run the program in a debugger and see what is going on?

Best
 W.

--

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

--
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[deal.II] Caught signal number 11 SEGV: Segmentation Violation, probably memory access out of range

2016-07-03 Thread Ehsan Esfahani

Dear All,

Greetings. I changed step-25 (minor changes) in order to solve my problem. 
Now I want to change this code for parallel computation based on the method 
mentioned in step-40. I got several errors and solved them one by one but 
the following error:
   

>
> *Number of active cells: 1024*
> *   Total number of cells: 1365**{[0,4224]}*
>
> *Time step #1; advancing to t = 0.1.*
>
> *--*
> *MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD **with 
> errorcode 59.*
>
> *NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes.*
> *You may or may not see output from other processes, depending on*
> *exactly when Open MPI kills them.*
>
> *--*
> *[0]PETSC ERROR: 
> *
> *[0]PETSC ERROR: Caught signal number 11 SEGV: Segmentation Violation, 
> probably memory access out of range*
> *[0]PETSC ERROR: Try option -start_in_debugger or 
> -on_error_attach_debugger*
> *[0]PETSC ERROR: or 
> see http://www.mcs.anl.gov/petsc/documentation/faq.html#valgrind 
> *
> *[0]PETSC ERROR: or try http://valgrind.org  on 
> GNU/linux and Apple Mac OS X to find memory corruption errors*
> *[0]PETSC ERROR: configure using --with-debugging=yes, recompile, link, 
> and run *
> *[0]PETSC ERROR: to get more information on the crash.*
> *[0]PETSC ERROR: - Error Message 
> --*
> *[0]PETSC ERROR: Signal received*
> *[0]PETSC ERROR: See http://www.mcs.anl.gov/petsc/documentation/faq.html 
>  for trouble shooting.*
> *[0]PETSC ERROR: Petsc Release Version 3.6.3, Dec, 03, 2015 *
> *[0]PETSC ERROR: 
> /home/ehsan/apps/candi/deal.II-toolchain/deal.II-v8.4.0/examples/step-25 
> (mine)/step-25 on a arch-linux2-c-opt named levitasgrad01.me.iastate.edu 
>  by ehsan Sun Jul  3 13:46:52 2016*
> *[0]PETSC ERROR: Configure options 
> --prefix=/home/ehsan/apps/candi/deal.II-toolchain/petsc-3.6.3 
> --with-debugging=0 --with-shared-libraries=1 --with-mpi=1 --with-x=0 
> --download-hypre=1 CC=mpicc CXX=mpicxx FC=mpif90**[0]PETSC ERROR: #1 User 
> provided function() line 0 in  unknown file*


Eclipse gives me a backtrace in the following line of the code:
* solver.solve (system_matrix, completely_distributed_solution_update, 
system_rhs,*
*   preconditioner); *
I have no idea why I got this error. The code is running properly for 
*fe(1) *and *n_global_refinements (4)* but when I change them to *fe(2)* and 
n_global_refinments (4) I got that error related to *Segmentation 
Violation. *Do you know what's going on? Also, I have attached the code 
here . Thanks in advance for your help.

Best Regards,
Ehsan Esfahani

-- 
The deal.II project is located at http://www.dealii.org/
For mailing list/forum options, see 
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/* -
 *
 * Copyright (C) 2006 - 2015 by the deal.II authors
 *
 * This file is part of the deal.II library.
 *
 * The deal.II library is free software; you can use it, redistribute
 * it, and/or modify it under the terms of the GNU Lesser General
 * Public License as published by the Free Software Foundation; either
 * version 2.1 of the License, or (at your option) any later version.
 * The full text of the license can be found in the file LICENSE at
 * the top level of the deal.II distribution.
 *
 * -

 *
 * Author: Ivan Christov, Wolfgang Bangerth, Texas A University, 2006
 */



#include //
#include //
#include //
#include 
#include 
#include 
#include 
#include //this and the following are dependent
namespace LA//
{
#if defined(DEAL_II_WITH_PETSC) && !(defined(DEAL_II_WITH_TRILINOS) && defined(FORCE_USE_OF_TRILINOS))
  using namespace dealii::LinearAlgebraPETSc;
#  define USE_PETSC_LA
#elif defined(DEAL_II_WITH_TRILINOS)
  using namespace dealii::LinearAlgebraTrilinos;
#else
#  error DEAL_II_WITH_PETSC or DEAL_II_WITH_TRILINOS required
#endif
}
#include 
#include 
#include 
#include //
#include 
#include 
#include 
#include 
#include //
#include //
#include //
#include //

#include 
#include 
#include 
#include 
#include 
#include 
#include 
#include 
#include 
#include //
#include 
#include 
#include 

#include //
#include //

#include 
#include 

namespace Step25
{

[deal.II] Caught signal number 11 SEGV: Segmentation Violation, probably memory access out of range

2016-07-03 Thread Ehsan Esfahani

Dear All,

Greetings. I changed step-25 (minor changes) in order to solve my problem. 
Now I want to change this code for parallel computation based on the method 
mentioned in step-40. I got several errors and solved them one by one but 
the following error:
   

>
> *Number of active cells: 1024*
> *   Total number of cells: 1365**{[0,4224]}*
>
> *Time step #1; advancing to t = 0.1.*
>
> *--*
> *MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD **with 
> errorcode 59.*
>
> *NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes.*
> *You may or may not see output from other processes, depending on*
> *exactly when Open MPI kills them.*
>
> *--*
> *[0]PETSC ERROR: 
> *
> *[0]PETSC ERROR: Caught signal number 11 SEGV: Segmentation Violation, 
> probably memory access out of range*
> *[0]PETSC ERROR: Try option -start_in_debugger or 
> -on_error_attach_debugger*
> *[0]PETSC ERROR: or 
> see http://www.mcs.anl.gov/petsc/documentation/faq.html#valgrind 
> *
> *[0]PETSC ERROR: or try http://valgrind.org  on 
> GNU/linux and Apple Mac OS X to find memory corruption errors*
> *[0]PETSC ERROR: configure using --with-debugging=yes, recompile, link, 
> and run *
> *[0]PETSC ERROR: to get more information on the crash.*
> *[0]PETSC ERROR: - Error Message 
> --*
> *[0]PETSC ERROR: Signal received*
> *[0]PETSC ERROR: See http://www.mcs.anl.gov/petsc/documentation/faq.html 
>  for trouble shooting.*
> *[0]PETSC ERROR: Petsc Release Version 3.6.3, Dec, 03, 2015 *
> *[0]PETSC ERROR: 
> /home/ehsan/apps/candi/deal.II-toolchain/deal.II-v8.4.0/examples/step-25 
> (mine)/step-25 on a arch-linux2-c-opt named levitasgrad01.me.iastate.edu 
>  by ehsan Sun Jul  3 13:46:52 2016*
> *[0]PETSC ERROR: Configure options 
> --prefix=/home/ehsan/apps/candi/deal.II-toolchain/petsc-3.6.3 
> --with-debugging=0 --with-shared-libraries=1 --with-mpi=1 --with-x=0 
> --download-hypre=1 CC=mpicc CXX=mpicxx FC=mpif90**[0]PETSC ERROR: #1 User 
> provided function() line 0 in  unknown file*


Eclipse gives me a backtrace in the following line of the code:
* solver.solve (system_matrix, completely_distributed_solution_update, 
system_rhs,*
*   preconditioner); *
I have no idea why I got this error. The code is running properly for 
*fe(1) *and *n_global_refinements (4)* but when I change them to *fe(2)* and 
n_global_refinments (4) I got that error related to *Segmentation 
Violation. *Do you know what's going on? Also, I have attached the code 
here . Thanks in advance for your help.

Best Regards,
Ehsan Esfahani

-- 
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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/* -
 *
 * Copyright (C) 2006 - 2015 by the deal.II authors
 *
 * This file is part of the deal.II library.
 *
 * The deal.II library is free software; you can use it, redistribute
 * it, and/or modify it under the terms of the GNU Lesser General
 * Public License as published by the Free Software Foundation; either
 * version 2.1 of the License, or (at your option) any later version.
 * The full text of the license can be found in the file LICENSE at
 * the top level of the deal.II distribution.
 *
 * -

 *
 * Author: Ivan Christov, Wolfgang Bangerth, Texas A University, 2006
 */



#include //
#include //
#include //
#include 
#include 
#include 
#include 
#include //this and the following are dependent
namespace LA//
{
#if defined(DEAL_II_WITH_PETSC) && !(defined(DEAL_II_WITH_TRILINOS) && defined(FORCE_USE_OF_TRILINOS))
  using namespace dealii::LinearAlgebraPETSc;
#  define USE_PETSC_LA
#elif defined(DEAL_II_WITH_TRILINOS)
  using namespace dealii::LinearAlgebraTrilinos;
#else
#  error DEAL_II_WITH_PETSC or DEAL_II_WITH_TRILINOS required
#endif
}
#include 
#include 
#include 
#include //
#include 
#include 
#include 
#include 
#include //
#include //
#include //
#include //

#include 
#include 
#include 
#include 
#include 
#include 
#include 
#include 
#include 
#include //
#include 
#include 
#include 

#include //
#include //

#include 
#include 

namespace Step25
{

[deal.II] Re: Error durind checkpoint / restart using parallel distributed solution transfer

2016-07-03 Thread RAJAT ARORA

Hello,

This is because of the vector locally_owned_x.
As per the documentation, during the serialization, the vector should be 
ghosted. 
If I make the change, the code works fine.


On Sunday, July 3, 2016 at 2:52:57 PM UTC-4, RAJAT ARORA wrote:
>
> Hello all,
>
> I am trying to use the checkpoint / restart code with the help of the 
> example given in the documentation here 
> 
> I am getting a long error while saving a parallel vector and parallel 
> distributed triangulation using the following code.
>
> Code Used:
>
>
> string triangulation_name = "mesh_restart";
>
> parallel::distributed::SolutionTransfer sol_trans_x(
> dof_handler);
> sol_trans_x.prepare_serialization(locally_owned_x);
>
> triangulation.save(triangulation_name.c_str());
>
>
> //LA::MPI::Vector corresponds to PETSC MPI Vector
> // locally_owned_x is solution vector reinitialized as 
> // locally_owned_x.reinit(locally_owned_dofs, MPI_COMM_WORLD);
>
>
>
> Error here:
>
>
> An error occurred in line <1253> of file  Libraries/deal/dealii8.3/dealii-8.3.0/include/deal.II/lac/
> petsc_vector_base.h> in function
> void dealii::PETScWrappers::VectorBase::extract_subvector_to(
> ForwardIterator, ForwardIterator, OutputIterator) const [with 
> ForwardIterator = const unsigned int*; OutputIterator = double*]
> The violated condition was: 
> index>=static_cast(begin) && index(end)
> The name and call sequence of the exception was:
> ExcInternalError()
> Additional Information: 
> This exception -- which is used in many places in the library -- usually 
> indicates that some condition which the author of the code thought must be 
> satisfied at a certain point in an algorithm, is not fulfilled. An 
> example would be that the first part of an algorithm sorts elements of an 
> array in ascending order, and a second part of the algorithm later 
> encounters an an element that is not larger than the previous one.
>
>
> There is usually not very much you can do if you encounter such an 
> exception since it indicates an error in deal.II, not in your own program. 
> Try to come up with the smallest possible program that still demonstrates 
> the error and contact the deal.II mailing lists with it to obtain help.
>
>
> Stacktrace:
> ---
> #0 
>  
> /home/rajat/Documents/Code-Libraries/deal/dealii8.3/installed-dealii/lib/libdeal_II.g.so.8.3.0:
>  
> void dealii::PETScWrappers::VectorBase::extract_subvector_to const*, double*>(unsigned int const*, unsigned int const*, double*) const
> #1 
>  
> /home/rajat/Documents/Code-Libraries/deal/dealii8.3/installed-dealii/lib/libdeal_II.g.so.8.3.0:
>  
> void dealii::DoFCellAccessor, 
> false>::get_dof_values double*>(dealii::PETScWrappers::MPI::Vector const&, double*, double*) const
> #2 
>  
> /home/rajat/Documents/Code-Libraries/deal/dealii8.3/installed-dealii/lib/libdeal_II.g.so.8.3.0:
>  
> void dealii::DoFCellAccessor, 
> false>::get_interpolated_dof_values double>(dealii::PETScWrappers::MPI::Vector const&, dealii::Vector&, 
> unsigned int) const
> #3 
>  
> /home/rajat/Documents/Code-Libraries/deal/dealii8.3/installed-dealii/lib/libdeal_II.g.so.8.3.0:
>  
> dealii::parallel::distributed::SolutionTransfer<3, 
> dealii::PETScWrappers::MPI::Vector, dealii::DoFHandler<3, 3> 
> >::pack_callback(dealii::TriaIterator > const&, 
> dealii::parallel::distributed::Triangulation<3, 3>::CellStatus, void*)
> #4 
>  
> /home/rajat/Documents/Code-Libraries/deal/dealii8.3/installed-dealii/lib/libdeal_II.g.so.8.3.0:
>  
> std::_Function_handler 3> > const&, dealii::parallel::distributed::Triangulation<3, 
> 3>::CellStatus, void*), std::_Bind dealii::PETScWrappers::MPI::Vector, dealii::DoFHandler<3, 3> 
> >::*)(dealii::TriaIterator > const&, 
> dealii::parallel::distributed::Triangulation<3, 3>::CellStatus, void*)> 
> (dealii::parallel::distributed::SolutionTransfer<3, 
> dealii::PETScWrappers::MPI::Vector, dealii::DoFHandler<3, 3> >*, 
> std::_Placeholder<1>, std::_Placeholder<2>, std::_Placeholder<3>)> 
> >::_M_invoke(std::_Any_data const&, 
> dealii::TriaIterator > const&, 
> dealii::parallel::distributed::Triangulation<3, 3>::CellStatus, void*)
> #5 
>  
> /home/rajat/Documents/Code-Libraries/deal/dealii8.3/installed-dealii/lib/libdeal_II.g.so.8.3.0:
>  
> std::function > 
> const&, dealii::parallel::distributed::Triangulation<3, 3>::CellStatus, 
> void*)>::operator()(dealii::TriaIterator > 
> const&, dealii::parallel::distributed::Triangulation<3, 3>::CellStatus, 
> void*) const
> #6 
>  
>

[deal.II] Error durind checkpoint / restart using parallel distributed solution transfer

2016-07-03 Thread RAJAT ARORA

Hello all,

I am trying to use the checkpoint / restart code with the help of the 
example given in the documentation here 

I am getting a long error while saving a parallel vector and parallel 
distributed triangulation using the following code.

Code Used:


string triangulation_name = "mesh_restart";

parallel::distributed::SolutionTransfer sol_trans_x(
dof_handler);
sol_trans_x.prepare_serialization(locally_owned_x);

triangulation.save(triangulation_name.c_str());


//LA::MPI::Vector corresponds to PETSC MPI Vector
// locally_owned_x is solution vector reinitialized as 
// locally_owned_x.reinit(locally_owned_dofs, MPI_COMM_WORLD);



Error here:


An error occurred in line <1253> of file  in function
void dealii::PETScWrappers::VectorBase::extract_subvector_to(
ForwardIterator, ForwardIterator, OutputIterator) const [with 
ForwardIterator = const unsigned int*; OutputIterator = double*]
The violated condition was: 
index>=static_cast(begin) && index, 
false>::get_dof_values(dealii::PETScWrappers::MPI::Vector const&, double*, double*) const
#2 
 
/home/rajat/Documents/Code-Libraries/deal/dealii8.3/installed-dealii/lib/libdeal_II.g.so.8.3.0:
 
void dealii::DoFCellAccessor, 
false>::get_interpolated_dof_values(dealii::PETScWrappers::MPI::Vector const&, dealii::Vector&, 
unsigned int) const
#3 
 
/home/rajat/Documents/Code-Libraries/deal/dealii8.3/installed-dealii/lib/libdeal_II.g.so.8.3.0:
 
dealii::parallel::distributed::SolutionTransfer<3, 
dealii::PETScWrappers::MPI::Vector, dealii::DoFHandler<3, 3> 
>::pack_callback(dealii::TriaIterator > const&, 
dealii::parallel::distributed::Triangulation<3, 3>::CellStatus, void*)
#4 
 
/home/rajat/Documents/Code-Libraries/deal/dealii8.3/installed-dealii/lib/libdeal_II.g.so.8.3.0:
 
std::_Function_handler > const&, dealii::parallel::distributed::Triangulation<3, 
3>::CellStatus, void*), std::_Bind::*)(dealii::TriaIterator > const&, 
dealii::parallel::distributed::Triangulation<3, 3>::CellStatus, void*)> 
(dealii::parallel::distributed::SolutionTransfer<3, 
dealii::PETScWrappers::MPI::Vector, dealii::DoFHandler<3, 3> >*, 
std::_Placeholder<1>, std::_Placeholder<2>, std::_Placeholder<3>)> 
>::_M_invoke(std::_Any_data const&, 
dealii::TriaIterator > const&, 
dealii::parallel::distributed::Triangulation<3, 3>::CellStatus, void*)
#5 
 
/home/rajat/Documents/Code-Libraries/deal/dealii8.3/installed-dealii/lib/libdeal_II.g.so.8.3.0:
 
std::function > 
const&, dealii::parallel::distributed::Triangulation<3, 3>::CellStatus, 
void*)>::operator()(dealii::TriaIterator > 
const&, dealii::parallel::distributed::Triangulation<3, 3>::CellStatus, 
void*) const
#6 
 
/home/rajat/Documents/Code-Libraries/deal/dealii8.3/installed-dealii/lib/libdeal_II.g.so.8.3.0:
 
std::_Function_handler >, dealii::parallel::distributed::Triangulation<3, 3>::CellStatus, 
void*), std::function 
> const&, dealii::parallel::distributed::Triangulation<3, 3>::CellStatus, 
void*)> >::_M_invoke(std::_Any_data const&, 
dealii::TriaIterator >, 
dealii::parallel::distributed::Triangulation<3, 3>::CellStatus, void*)
#7 
 
/home/rajat/Documents/Code-Libraries/deal/dealii8.3/installed-dealii/lib/libdeal_II.g.so.8.3.0:
 
std::function >, 
dealii::parallel::distributed::Triangulation<3, 3>::CellStatus, 
void*)>::operator()(dealii::TriaIterator >,

[deal.II] Restoring Gauss Point History during checkpoint/restart

2016-07-03 Thread RAJAT ARORA

Hello all,

This is related to checkpoint/restart using the parallel distributed 
solution transfer class. I am able to read the parallel vectors during the 
restart following the example 
of aspect here 

 and 
several other discussions in this forum. 

My question is related to restoring Gauss Point History during 
checkpoint/restart.

Just like we have serialization and deserialization for LinearAlgebra / MPI 
vectors, is there any way we can write the Quadrature point history to file 
and read it during a checkpoint/restart.
I am using parallel distributed triangulation.

The Quadrature point history is a std::vector<> of a struct PointHistory 
just like in step 18 
.

Is there any way to do this ?

Regards,
Rajat Arora

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Re: [deal.II] About MPI vectors, ghosted vectors

2016-07-03 Thread RAJAT ARORA


Hi Ehsan,

On Wednesday, June 29, 2016 at 3:28:40 PM UTC-4, Ehsan Esfahani wrote:
>
> Dear users,
>
> I'm asking my question here because I think it's somehow related to this 
> post, and I don't think it would be necessary to open a new topic. Could 
> you please tell me what are differences between these two public functions:
>
> void reinit 
> 
>  
> (const IndexSet 
>  , 
> const IndexSet 
>  , 
> const MPI_Comm  
> 
> )
> void reinit 
> 
>  
> (const IndexSet 
>  , 
> const MPI_Comm  
> 
> )
>
> for both, there are the same definitions on the doxygen 
> 
> .
> I've found out from examples that the first one make my vector ghosted but 
> the second one make it non-ghosted. Am I right?
>

Yes, you are right.
 

>
> Thanks in advance for you responses.
> Ehsan
>

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Re: [deal.II] problems with installation ; Unknown CMake command "DEAL_II_ADD_LIBRARY"

2016-07-03 Thread Timo Heister

Pablo,

can you try putting the source directory path at the end of the cmake
command as in
   cmake -DCMAKE_INSTALL_PREFIX=/home/pablo/dealii
-DOPENCASCADE_DIR=/usr/local/include/oce /home/pablo/dealii/source

On Sat, Jul 2, 2016 at 6:21 PM, Pablo Perez del Castillo
 wrote:
> I can not install dealii, it was downloaded with Git
>
> pablo@pablo-HP-Spectre-13-Ultrabook:~/dealii/build$ cmake
> -DCMAKE_INSTALL_PREFIX=/home/pablo/dealii /home/pablo/dealii/source
> -DOPENCASCADE_DIR=/usr/local/include/oce
> -- Setting up library
> CMake Error at fe/CMakeLists.txt:113 (DEAL_II_ADD_LIBRARY):
>   Unknown CMake command "DEAL_II_ADD_LIBRARY".
>
>
> CMake Warning (dev) in CMakeLists.txt:
>   No cmake_minimum_required command is present.  A line of code such as
>
> cmake_minimum_required(VERSION 2.8)
>
>   should be added at the top of the file.  The version specified may be
> lower
>   if you wish to support older CMake versions for this project.  For more
>   information run "cmake --help-policy CMP".
> This warning is for project developers.  Use -Wno-dev to suppress it.
>
> Advanced thanks
>
> Pablo
>
> --
> 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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-- 
Timo Heister
http://www.math.clemson.edu/~heister/

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Re: [deal.II] Re: Deal.II does not pass quick tests after installation

Re: [deal.II] Caught signal number 11 SEGV: Segmentation Violation, probably memory access out of range

[deal.II] Caught signal number 11 SEGV: Segmentation Violation, probably memory access out of range

[deal.II] Caught signal number 11 SEGV: Segmentation Violation, probably memory access out of range

[deal.II] Re: Error durind checkpoint / restart using parallel distributed solution transfer

[deal.II] Error durind checkpoint / restart using parallel distributed solution transfer

[deal.II] Restoring Gauss Point History during checkpoint/restart

Re: [deal.II] About MPI vectors, ghosted vectors

Re: [deal.II] problems with installation ; Unknown CMake command "DEAL_II_ADD_LIBRARY"

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