[deal.II] Memory loss in system solver

2020-07-24 Thread Alberto Salvadori
Dear community I have written the simple code below for solving a system using PETSc, having defined Vector incremental_displacement; Vector accumulated_displacement; in the class LargeStrainMechanicalProblem_OneField. It turns out that this code produces a memory loss, quite significant

Re: [deal.II] KDTree implementation error

2020-07-24 Thread luca.heltai
KDTree needs nanoflann to be available. Did you compile deal.II with nanoflann exnabled? Check in the summary.log if DEAL_II_WITH_NANOFLANN is ON. RTree, on the other hand, does not require nanoflann, as it is included with boost (and it is faster than nanoflann). L. > On 24 Jul 2020, at

Re: [deal.II] KDTree implementation error

2020-07-24 Thread luca.heltai
Dear Heena, here is a snippet to achieve what you want: #include namespace bgi = boost::geometry::index; … Point<2> p0; const auto tree = pack_rtree(tria.get_vertices()); for (const auto : tree | bgi::adaptors::queried(bgi::nearest(p0, 3))) // do something with p

Re: [deal.II] Cannot find local compiled petsc library

2020-07-24 Thread Daniel Arndt
Yuesun, Apparently, CMake was able to find the file petscvariables, but not the include directories or the library. Can you search for "libpetsc.so" yourself? Our CMake find module tries to find this library in {PETSC_DIR}/lib or {PETSC_DIR}/lib64. See if you can adjust PETSC_DIR accordingly.

Re: [deal.II] Accessing nodal values of a FEM solution

2020-07-24 Thread Xuefeng Li
On Thu, Jul 23, 2020 at 5:14 PM Daniel Arndt wrote: > > You can do similarly, > > Quadrature q(fe.get_unit_support_points()); > FEValues fe_values (..., q, update_q_points); > for (const auto& cell) > ... > points = fe_values.get_quadrature_points(); >

Re: [deal.II] KDTree implementation error

2020-07-24 Thread heena patel
Dear Luca, Thank you very much. It now works in both ways. Thanks for advice. Regards, Heena On Fri, Jul 24, 2020 at 12:31 PM luca.heltai wrote: > KDTree needs nanoflann to be available. Did you compile deal.II with > nanoflann exnabled? Check in the summary.log if

[deal.II] Re: Memory loss in system solver

2020-07-24 Thread Alberto Salvadori
Dear community, if I am not mistaking my analysis, it turned out that the memory loss is caused by this call: BiCG.solve (this->system_matrix, distributed_incremental_displacement, this->system_rhs, preconditioner); because if I turn it off the top command shows no change in the RES at all.

Re: [deal.II] Cannot find local compiled petsc library

2020-07-24 Thread yuesu jin
Dear Daniel, Thank you for the instruction! I gave the architecture directory, which is a sub-directory : /home/yjin6/petsc/arch-linux-c-debug. It returns message like this: ***

Re: [deal.II] Re: Memory loss in system solver

2020-07-24 Thread Daniel Arndt
Alberto, Have you tried running valgrind (in parallel) on your code? Admittedly, I expect quite a bit of false-positives from the MPI library but it should still help. Best, Daniel Am Fr., 24. Juli 2020 um 12:07 Uhr schrieb Alberto Salvadori < alberto.salvad...@unibs.it>: > Dear community, > >

Re: [deal.II] Cannot find local compiled petsc library

2020-07-24 Thread yuesu jin
Dear all, This problem has been solved. I copied the petscversion.h file to the arch/include folder therefore cmake found all petsc files and finished compilation. Best regards On Fri, Jul 24, 2020 at 3:17 PM yuesu jin wrote: > Dear Daniel, > Thank you for the instruction! I gave the

Re: [deal.II] Accessing nodal values of a FEM solution

2020-07-24 Thread Wolfgang Bangerth
On 7/23/20 12:07 PM, Xuefeng Li wrote: Well, the above function calculates the gradients of a finite element at the quadrature points of a cell, not at the nodal points of a cell. Such a need arises in the following situation. for ( x in vector_of_nodal_points )   v(x) = g(x, u(x), grad

Re: [deal.II] Location for Boundary Condition Application

2020-07-24 Thread Wolfgang Bangerth
On 7/23/20 11:47 AM, Daniel Arndt wrote: McKenzie, I'm interested in applying a non-homogeneous Dirichlet boundary condition to a specific edge. However, I'm unsure how to identify or specify a particular edge or face to add the boundary condition to. Could you help clear this

Re: [deal.II] Memory loss in system solver

2020-07-24 Thread Wolfgang Bangerth
On 7/24/20 3:32 AM, Alberto Salvadori wrote: It turns out that this code produces a memory loss, quite significant since I am solving my system thousands of times, eventually inducing the run to fail. I am not sure what is causing this issue and how to solve it, maybe more experienced users

Re: [deal.II] Re: KDTree implementation error

2020-07-24 Thread heena patel
Dear Luca, I am using 9.2 version and the implementation I try to follow from your presentation at SISSA 2018 but it gives me error. Following are the lines I added to step-1. I want to implement K nearest neighbor. I will work on your suggestion. *#include *

Re: [deal.II] Re: KDTree implementation error

2020-07-24 Thread Luca Heltai
If you are using version 9.3pre of deal.II, kdtree was removed. Use RTree instead, which is faster and more flexible. Luca > Il giorno 24 lug 2020, alle ore 05:41, heena patel ha > scritto: > >  > Dear Bruno, >I had already added kdree.h header file, check