Re: [deal.II] A data structure for distributed storage of some cell "average"
> > The problem is a mismatch of expectations. Like in many other places, when > you > pass a cell-based vector to DataOut, it assumes that on every process, the > vector has one entry for each active cell of the triangulation -- i.e., on > every process it is a *local* vector -- rather than a distributed vector > with > one entry for each globally active cell. In other words, for cell-based > vectors, we ignore the fact that the computation might be parallel. Thank you for the response, looks like I didn't do my homework properly :P. Copying the MPI vector into a Vector of size triang.n_active_cells() and adding this vector instead to DataOut works. Thanks again! On Tue, 15 Jun 2021 at 04:24, Wolfgang Bangerth wrote: > On 6/11/21 12:09 AM, vachan potluri wrote: > > > > I am having an issue in using DataOut for such vector in a parallel > process. I > > am attaching a MWE which captures my problem. I am encountering a > segmentation > > fault (signal 11). > > The problem is a mismatch of expectations. Like in many other places, when > you > pass a cell-based vector to DataOut, it assumes that on every process, the > vector has one entry for each active cell of the triangulation -- i.e., on > every process it is a *local* vector -- rather than a distributed vector > with > one entry for each globally active cell. In other words, for cell-based > vectors, we ignore the fact that the computation might be parallel. > > Best > W. > > -- > > Wolfgang Bangerth email: bange...@colostate.edu > www: http://www.math.colostate.edu/~bangerth/ > > -- > 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 > --- > You received this message because you are subscribed to the Google Groups > "deal.II User Group" group. > To unsubscribe from this group and stop receiving emails from it, send an > email to dealii+unsubscr...@googlegroups.com. > To view this discussion on the web visit > https://groups.google.com/d/msgid/dealii/88da546c-259d-aac8-89cf-598e7c1f6b33%40colostate.edu > . > -- 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 --- You received this message because you are subscribed to the Google Groups "deal.II User Group" group. To unsubscribe from this group and stop receiving emails from it, send an email to dealii+unsubscr...@googlegroups.com. To view this discussion on the web visit https://groups.google.com/d/msgid/dealii/CALAVa_wF96oKWJZ6B77e2a80VDCk_vrGXqp-3sEN0it2XwbGgw%40mail.gmail.com.
Re: [deal.II] A data structure for distributed storage of some cell "average"
On 6/11/21 12:09 AM, vachan potluri wrote: I am having an issue in using DataOut for such vector in a parallel process. I am attaching a MWE which captures my problem. I am encountering a segmentation fault (signal 11). The problem is a mismatch of expectations. Like in many other places, when you pass a cell-based vector to DataOut, it assumes that on every process, the vector has one entry for each active cell of the triangulation -- i.e., on every process it is a *local* vector -- rather than a distributed vector with one entry for each globally active cell. In other words, for cell-based vectors, we ignore the fact that the computation might be parallel. Best W. -- Wolfgang Bangerth email: bange...@colostate.edu www: http://www.math.colostate.edu/~bangerth/ -- 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 --- You received this message because you are subscribed to the Google Groups "deal.II User Group" group. To unsubscribe from this group and stop receiving emails from it, send an email to dealii+unsubscr...@googlegroups.com. To view this discussion on the web visit https://groups.google.com/d/msgid/dealii/88da546c-259d-aac8-89cf-598e7c1f6b33%40colostate.edu.
Re: [deal.II] A data structure for distributed storage of some cell "average"
Hello,
I have a small question and I think the issue lies here. Are these two
function calls equivalent?
ghosted_vector.reinit(
/*locally owned indices*/,
/*ghost indices only*/,
mpi_communicator
);
ghosted_vector.reinit(
/*locally owned indices*/,
/*relevant indices (owned + ghost)*/,
mpi_communicator
);
The program runs as expected for a serial execution. I am using the first
version here and may be that is causing a crash in a parallel execution.
Any reference to a use case of
p::d::Triangulation::global_active_cell_index_partitioner() would be very
helpful :) !
Thanks
On Friday, June 11, 2021 at 11:40:37 AM UTC+5:30 vachanpo...@gmail.com
wrote:
> Hello,
>
> I am having an issue in using DataOut for such vector in a parallel
> process. I am attaching a MWE which captures my problem. I am encountering
> a segmentation fault (signal 11).
>
> #include
> #include
> #include
> #include
> #include
> #include
> #include
> #include
> #include
> #include
>
> #include
>
> using namespace dealii;
> namespace LA
> {
> using namespace ::LinearAlgebraPETSc;
> }
>
> int main(int argc, char **argv)
> {
> Utilities::MPI::MPI_InitFinalize mpi_initialization(argc, argv, 1);
>
> constexpr int dim = 3;
>
> MPI_Comm mpi_comm(MPI_COMM_WORLD);
>
> parallel::distributed::Triangulation triang(mpi_comm);
> GridGenerator::subdivided_hyper_cube(triang, 5);
> const std::shared_ptr cell_partitioner
> =
> triang.global_active_cell_index_partitioner().lock();
> LA::MPI::Vector vec(cell_partitioner->locally_owned_range(), mpi_comm);
> LA::MPI::Vector gh_vec(
> cell_partitioner->locally_owned_range(),
> cell_partitioner->ghost_indices(),
> mpi_comm
> );
>
> DoFHandler dof_handler(triang);
> FE_DGQ fe(2);
> dof_handler.distribute_dofs(fe);
>
> for(auto : dof_handler.active_cell_iterators()){
> if(!cell->is_locally_owned()) continue;
>
> vec[cell->global_active_cell_index()] = cell->global_active_cell_index();
> }
> vec.compress(VectorOperation::insert);
>
> gh_vec = vec;
>
> DataOut data_out;
> DataOutBase::VtkFlags flags;
> flags.write_higher_order_cells = true;
> data_out.set_flags(flags);
>
> data_out.attach_dof_handler(dof_handler);
>
> data_out.add_data_vector(gh_vec, "x");
>
> data_out.build_patches(
> MappingQGeneric(2),
> 2,
> DataOut::CurvedCellRegion::curved_inner_cells
> );
>
> std::ofstream proc_file(
> "output" + Utilities::int_to_string(
> Utilities::MPI::this_mpi_process(mpi_comm),
> 2
> ) + ".vtu"
> );
> data_out.write_vtu(proc_file);
> proc_file.close();
>
> if(Utilities::MPI::this_mpi_process(mpi_comm) == 0){
> std::vector filenames;
> for(int i=0; i filenames.emplace_back(
> "output" + Utilities::int_to_string(i, 2) + ".vtu"
> );
> } // loop over processes
>
> std::ofstream master_file("output.pvtu");
> data_out.write_pvtu_record(master_file, filenames);
> master_file.close();
> }
> return 0;
> }
>
>
> I suspect I am not partitioning the ghosted vector properly hence causing
> a mismatch in what is available and what DataOut wants. Am I missing any
> other step in between?
>
> Thanking in anticipation
>
> On Tue, 8 Jun 2021 at 19:32, vachan potluri wrote:
>
>> Thank you :).
>>
>> On Tue, 8 Jun, 2021, 19:24 Wolfgang Bangerth,
>> wrote:
>>
>>> On 6/8/21 4:18 AM, vachanpo...@gmail.com wrote:
>>> > If I want to add such a vector to DataOut, will the regular
>>> > DataOut::add_data_vector() work? Or is something else required to be
>>> done?
>>>
>>> Yes, DataOut::add_data_vector() can take two kinds of vectors:
>>> * Ones that have as many entries as there are DoFs
>>> * Ones that have as many entries as there are active cells
>>>
>>> Best
>>> W.
>>>
>>> --
>>>
>>> Wolfgang Bangerth email: bang...@colostate.edu
>>> www:
>>> http://www.math.colostate.edu/~bangerth/
>>>
>>> --
>>> 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
>>> ---
>>> You received this message because you are subscribed to the Google
>>> Groups "deal.II User Group" group.
>>> To unsubscribe from this group and stop receiving emails from it, send
>>> an email to dealii+un...@googlegroups.com.
>>> To view this discussion on the web visit
>>> https://groups.google.com/d/msgid/dealii/2c89ac60-d144-8ef3-62db-f15770096bd6%40colostate.edu
>>> .
>>>
>>
--
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Re: [deal.II] A data structure for distributed storage of some cell "average"
Hello,
I am having an issue in using DataOut for such vector in a parallel
process. I am attaching a MWE which captures my problem. I am encountering
a segmentation fault (signal 11).
#include
#include
#include
#include
#include
#include
#include
#include
#include
#include
#include
using namespace dealii;
namespace LA
{
using namespace ::LinearAlgebraPETSc;
}
int main(int argc, char **argv)
{
Utilities::MPI::MPI_InitFinalize mpi_initialization(argc, argv, 1);
constexpr int dim = 3;
MPI_Comm mpi_comm(MPI_COMM_WORLD);
parallel::distributed::Triangulation triang(mpi_comm);
GridGenerator::subdivided_hyper_cube(triang, 5);
const std::shared_ptr cell_partitioner =
triang.global_active_cell_index_partitioner().lock();
LA::MPI::Vector vec(cell_partitioner->locally_owned_range(), mpi_comm);
LA::MPI::Vector gh_vec(
cell_partitioner->locally_owned_range(),
cell_partitioner->ghost_indices(),
mpi_comm
);
DoFHandler dof_handler(triang);
FE_DGQ fe(2);
dof_handler.distribute_dofs(fe);
for(auto : dof_handler.active_cell_iterators()){
if(!cell->is_locally_owned()) continue;
vec[cell->global_active_cell_index()] = cell->global_active_cell_index();
}
vec.compress(VectorOperation::insert);
gh_vec = vec;
DataOut data_out;
DataOutBase::VtkFlags flags;
flags.write_higher_order_cells = true;
data_out.set_flags(flags);
data_out.attach_dof_handler(dof_handler);
data_out.add_data_vector(gh_vec, "x");
data_out.build_patches(
MappingQGeneric(2),
2,
DataOut::CurvedCellRegion::curved_inner_cells
);
std::ofstream proc_file(
"output" + Utilities::int_to_string(
Utilities::MPI::this_mpi_process(mpi_comm),
2
) + ".vtu"
);
data_out.write_vtu(proc_file);
proc_file.close();
if(Utilities::MPI::this_mpi_process(mpi_comm) == 0){
std::vector filenames;
for(int i=0; i
wrote:
> Thank you :).
>
> On Tue, 8 Jun, 2021, 19:24 Wolfgang Bangerth,
> wrote:
>
>> On 6/8/21 4:18 AM, vachanpo...@gmail.com wrote:
>> > If I want to add such a vector to DataOut, will the regular
>> > DataOut::add_data_vector() work? Or is something else required to be
>> done?
>>
>> Yes, DataOut::add_data_vector() can take two kinds of vectors:
>> * Ones that have as many entries as there are DoFs
>> * Ones that have as many entries as there are active cells
>>
>> Best
>> W.
>>
>> --
>>
>> Wolfgang Bangerth email: bange...@colostate.edu
>> www: http://www.math.colostate.edu/~bangerth/
>>
>> --
>> 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
>> ---
>> You received this message because you are subscribed to the Google Groups
>> "deal.II User Group" group.
>> To unsubscribe from this group and stop receiving emails from it, send an
>> email to dealii+unsubscr...@googlegroups.com.
>> To view this discussion on the web visit
>> https://groups.google.com/d/msgid/dealii/2c89ac60-d144-8ef3-62db-f15770096bd6%40colostate.edu
>> .
>>
>
--
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https://groups.google.com/d/forum/dealii?hl=en
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Re: [deal.II] A data structure for distributed storage of some cell "average"
Thank you :). On Tue, 8 Jun, 2021, 19:24 Wolfgang Bangerth, wrote: > On 6/8/21 4:18 AM, vachanpo...@gmail.com wrote: > > If I want to add such a vector to DataOut, will the regular > > DataOut::add_data_vector() work? Or is something else required to be > done? > > Yes, DataOut::add_data_vector() can take two kinds of vectors: > * Ones that have as many entries as there are DoFs > * Ones that have as many entries as there are active cells > > Best > W. > > -- > > Wolfgang Bangerth email: bange...@colostate.edu > www: http://www.math.colostate.edu/~bangerth/ > > -- > 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 > --- > You received this message because you are subscribed to the Google Groups > "deal.II User Group" group. > To unsubscribe from this group and stop receiving emails from it, send an > email to dealii+unsubscr...@googlegroups.com. > To view this discussion on the web visit > https://groups.google.com/d/msgid/dealii/2c89ac60-d144-8ef3-62db-f15770096bd6%40colostate.edu > . > -- 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 --- You received this message because you are subscribed to the Google Groups "deal.II User Group" group. To unsubscribe from this group and stop receiving emails from it, send an email to dealii+unsubscr...@googlegroups.com. To view this discussion on the web visit https://groups.google.com/d/msgid/dealii/CALAVa_w-AoEfkzA2rnVtEVM-Cm7cJJpNte6N72OnCw0vVab0XA%40mail.gmail.com.
Re: [deal.II] A data structure for distributed storage of some cell "average"
On 6/8/21 4:18 AM, vachanpo...@gmail.com wrote: If I want to add such a vector to DataOut, will the regular DataOut::add_data_vector() work? Or is something else required to be done? Yes, DataOut::add_data_vector() can take two kinds of vectors: * Ones that have as many entries as there are DoFs * Ones that have as many entries as there are active cells Best W. -- Wolfgang Bangerth email: bange...@colostate.edu www: http://www.math.colostate.edu/~bangerth/ -- 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 --- You received this message because you are subscribed to the Google Groups "deal.II User Group" group. To unsubscribe from this group and stop receiving emails from it, send an email to dealii+unsubscr...@googlegroups.com. To view this discussion on the web visit https://groups.google.com/d/msgid/dealii/2c89ac60-d144-8ef3-62db-f15770096bd6%40colostate.edu.
Re: [deal.II] A data structure for distributed storage of some cell "average"
If I want to add such a vector to DataOut, will the regular DataOut::add_data_vector() work? Or is something else required to be done? On Saturday, May 29, 2021 at 8:44:01 AM UTC+5:30 vachanpo...@gmail.com wrote: > Ok, right. Will have a new installation then! > > On Sat, 29 May, 2021, 02:21 Wolfgang Bangerth, > wrote: > >> On 5/27/21 11:08 PM, vachanpo...@gmail.com wrote: >> > >> > That is exactly what I need! But unfortunately I currently use version >> 9.1.1 >> > and I think this was introduced in 9.2.0 >> > ( >> https://github.com/dealii/dealii/commit/0ec6aa676a27956a07f513585f407a954678ae52#diff-ca64fff9c161a88a3b72134cb89731e3bf3ce3b758ff386ef120d07e24312c65 >> ). >> > >> > Is there any other alternative (that I can use on 9.1.1)? Otherwise I >> will >> > have to update the installation. >> >> If you wait for a week or two, you can update to 9.3 (or just install the >> pre-release snapshot that will, for all practical purposes, be >> identical). >> Sticking with the old release would require you to write work-arounds for >> functionality that exists today, and to stick with these work-arounds for >> the >> indefinite future. >> >> Best >> W. >> >> -- >> >> Wolfgang Bangerth email: bang...@colostate.edu >> www: http://www.math.colostate.edu/~bangerth/ >> >> -- >> 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 >> --- >> You received this message because you are subscribed to the Google Groups >> "deal.II User Group" group. >> To unsubscribe from this group and stop receiving emails from it, send an >> email to dealii+un...@googlegroups.com. >> To view this discussion on the web visit >> https://groups.google.com/d/msgid/dealii/b1e38738-eead-c4e9-0530-95e099a923d6%40colostate.edu >> . >> > -- 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 --- You received this message because you are subscribed to the Google Groups "deal.II User Group" group. To unsubscribe from this group and stop receiving emails from it, send an email to dealii+unsubscr...@googlegroups.com. To view this discussion on the web visit https://groups.google.com/d/msgid/dealii/09599839-f974-4413-9f67-e3d1d9860512n%40googlegroups.com.
Re: [deal.II] A data structure for distributed storage of some cell "average"
On 5/27/21 11:08 PM, vachanpo...@gmail.com wrote: That is exactly what I need! But unfortunately I currently use version 9.1.1 and I think this was introduced in 9.2.0 (https://github.com/dealii/dealii/commit/0ec6aa676a27956a07f513585f407a954678ae52#diff-ca64fff9c161a88a3b72134cb89731e3bf3ce3b758ff386ef120d07e24312c65). Is there any other alternative (that I can use on 9.1.1)? Otherwise I will have to update the installation. If you wait for a week or two, you can update to 9.3 (or just install the pre-release snapshot that will, for all practical purposes, be identical). Sticking with the old release would require you to write work-arounds for functionality that exists today, and to stick with these work-arounds for the indefinite future. Best W. -- Wolfgang Bangerth email: bange...@colostate.edu www: http://www.math.colostate.edu/~bangerth/ -- 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 --- You received this message because you are subscribed to the Google Groups "deal.II User Group" group. To unsubscribe from this group and stop receiving emails from it, send an email to dealii+unsubscr...@googlegroups.com. To view this discussion on the web visit https://groups.google.com/d/msgid/dealii/b1e38738-eead-c4e9-0530-95e099a923d6%40colostate.edu.
Re: [deal.II] A data structure for distributed storage of some cell "average"
Wolfgang, That is exactly what I need! But unfortunately I currently use version 9.1.1 and I think this was introduced in 9.2.0 (https://github.com/dealii/dealii/commit/0ec6aa676a27956a07f513585f407a954678ae52#diff-ca64fff9c161a88a3b72134cb89731e3bf3ce3b758ff386ef120d07e24312c65). Is there any other alternative (that I can use on 9.1.1)? Otherwise I will have to update the installation. On Thursday, May 27, 2021 at 7:01:12 PM UTC+5:30 Wolfgang Bangerth wrote: > On 5/26/21 10:20 PM, vachanpo...@gmail.com wrote: > > > > I have a quantity which has a single value in a cell. Let me call this > an > > "average". I want to be able to access the average of neighbouring cells > from > > every cell. > > > > What data structure can I use? > > > > Since don't have mesh refinement, I was thinking of mapping this average > to > > the cell index and using a parallel vector for storage. However, > > LA::MPI::Vector probably will not work because cell numbering is not > > continuous within a subdomain. Also, I couldn't find any function that > can > > reorder the cells which may enable use of LA::MPI::Vector. > > > > In the worst case, I can make a regular LA::MPI::Vector (using dofs) and > set > > the average to all dofs in a cell. I hope there is an alternative. > > You are looking for cell->global_active_cell_index(), which is documented > like so: > > /** > * Return a globally unique cell index for the current cell, > * assuming it is not artificial. The value is identical to > * active_cell_index() if the cell is part of a serial > * triangulation. > * > * In the context of parallel triangulations, locally-owned cells > * are enumerated contiguously within each subdomain of the > * mesh. This ensures that the index returned by this function can > * be used as the index into vectors with a total of > * Triangulation::n_globally_active_cells() entries, and for which > * every process stores a contiguous part. If such a cell-data > * vector has been set up with > * parallel::TriangulationBase::global_active_cell_index_partitioner(), > * the index returned by this function can then be used to access > * the correct vector entry. > */ > types::global_cell_index > global_active_cell_index() const; > > Best > W. > > -- > > Wolfgang Bangerth email: bang...@colostate.edu > www: http://www.math.colostate.edu/~bangerth/ > > -- 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 --- You received this message because you are subscribed to the Google Groups "deal.II User Group" group. To unsubscribe from this group and stop receiving emails from it, send an email to dealii+unsubscr...@googlegroups.com. To view this discussion on the web visit https://groups.google.com/d/msgid/dealii/6609e416-842e-4ebf-8329-77153b051848n%40googlegroups.com.
Re: [deal.II] A data structure for distributed storage of some cell "average"
On 5/26/21 10:20 PM, vachanpo...@gmail.com wrote: I have a quantity which has a single value in a cell. Let me call this an "average". I want to be able to access the average of neighbouring cells from every cell. What data structure can I use? Since don't have mesh refinement, I was thinking of mapping this average to the cell index and using a parallel vector for storage. However, LA::MPI::Vector probably will not work because cell numbering is not continuous within a subdomain. Also, I couldn't find any function that can reorder the cells which may enable use of LA::MPI::Vector. In the worst case, I can make a regular LA::MPI::Vector (using dofs) and set the average to all dofs in a cell. I hope there is an alternative. You are looking for cell->global_active_cell_index(), which is documented like so: /** * Return a globally unique cell index for the current cell, * assuming it is not artificial. The value is identical to * active_cell_index() if the cell is part of a serial * triangulation. * * In the context of parallel triangulations, locally-owned cells * are enumerated contiguously within each subdomain of the * mesh. This ensures that the index returned by this function can * be used as the index into vectors with a total of * Triangulation::n_globally_active_cells() entries, and for which * every process stores a contiguous part. If such a cell-data * vector has been set up with * parallel::TriangulationBase::global_active_cell_index_partitioner(), * the index returned by this function can then be used to access * the correct vector entry. */ types::global_cell_index global_active_cell_index() const; Best W. -- Wolfgang Bangerth email: bange...@colostate.edu www: http://www.math.colostate.edu/~bangerth/ -- 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 --- You received this message because you are subscribed to the Google Groups "deal.II User Group" group. To unsubscribe from this group and stop receiving emails from it, send an email to dealii+unsubscr...@googlegroups.com. To view this discussion on the web visit https://groups.google.com/d/msgid/dealii/5583acf5-0104-0f2f-022b-2d5cdbb2a708%40colostate.edu.
[deal.II] A data structure for distributed storage of some cell "average"
Dear All, I have a quantity which has a single value in a cell. Let me call this an "average". I want to be able to access the average of neighbouring cells from every cell. What data structure can I use? Since don't have mesh refinement, I was thinking of mapping this average to the cell index and using a parallel vector for storage. However, LA::MPI::Vector probably will not work because cell numbering is not continuous within a subdomain. Also, I couldn't find any function that can reorder the cells which may enable use of LA::MPI::Vector. In the worst case, I can make a regular LA::MPI::Vector (using dofs) and set the average to all dofs in a cell. I hope there is an alternative. Thanking in anticipation, Vachan -- 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 --- You received this message because you are subscribed to the Google Groups "deal.II User Group" group. To unsubscribe from this group and stop receiving emails from it, send an email to dealii+unsubscr...@googlegroups.com. To view this discussion on the web visit https://groups.google.com/d/msgid/dealii/1532abbb-e114-4e7b-abd6-7ab919fae049n%40googlegroups.com.
