[deal.II] Re: Accuracy of shape function gradients

2016-10-04 Thread Praveen C
Please ignore my message. I implemented the fix for grad(phi_i) within my code but that still does not solve my problem. Best praveen On Wed, Oct 5, 2016 at 10:42 AM, Praveen C wrote: > Dear all > > While a solving a conservation law with DG, I find that total mass is not > conserved. To get to

Re: [deal.II] Neumann bc in step-20

2016-10-04 Thread Erik Svensson
The 'VectorTools::project_boundary_values_div_conforming' worked very well. Thanks a lot Wolfgang! /Erik 2016-09-30 7:39 GMT+02:00 Erik Svensson : > Ok, thanks Wolfgang and Daniel! > > I will follow your advise and post updates on this issue. > > /Erik > > 2016-09-30 5:54 GMT+02:00 Wolfgang Bang

[deal.II] Accuracy of shape function gradients

2016-10-04 Thread Praveen C
Dear all While a solving a conservation law with DG, I find that total mass is not conserved. To get total mass conservation, we need sum_(i=0,1,...ndofs-1) grad(phi_i(xq, yq, zq)) = 0 where phi_i are shape functions and ndofs = fe.dofs_per_cell and above equation must hold at every quadrature

Re: [deal.II] Re: Issue with Trilinos installation (issue with blas?)

2016-10-04 Thread Matt Weller
As am I. Okay I tried as you suggested, and same issue. It can't find -l/usr/lib64/libblas.so.3.6.1 . There is something off with the library but I have not the foggiest what it is. Also, did somehow click respond privately as I was heading out the door earlier. I'm beginning to suspect I did

Re: [deal.II] how to use solution.

2016-10-04 Thread hanks0227
2016년 10월 5일 수요일 오전 1시 17분 31초 UTC+9, Wolfgang Bangerth 님의 말: > > On 10/04/2016 09:12 AM, hank...@gmail.com wrote: > > > > template > > void Step6::get_profile () > > { > > const QGauss quadrature_formula(3); > > FEValues fe_values (fe, quadrature_formula, > >

Re: [deal.II] Re: Issue with Trilinos installation (issue with blas?)

2016-10-04 Thread Wolfgang Bangerth
On 10/04/2016 06:01 PM, Matt Weller wrote: So, I upgraded to Trilinos 12.8.1, and the same problem happens. [ 10%] Linking CXX shared library libteuchosnumerics.so /usr/bin/ld: cannot find -l/usr/lib64/libblas.so.3.6.1 I'm at a loss, and not an expert in Trilinos anyway. What happens if you h

Re: [deal.II] Re: Issue with Trilinos installation (issue with blas?)

2016-10-04 Thread Matt Weller
So, I upgraded to Trilinos 12.8.1, and the same problem happens. [ 10%] Linking CXX shared library libteuchosnumerics.so /usr/bin/ld: cannot find -l/usr/lib64/libblas.so.3.6.1 collect2: error: ld returned 1 exit status packages/teuchos/numerics/src/CMakeFiles/teuchosnumerics.dir/build.make:307:

Re: [deal.II] Re: Issue with Trilinos installation (issue with blas?)

2016-10-04 Thread Wolfgang Bangerth
On 10/04/2016 04:52 PM, Matt Weller wrote: Why are you using such an old version of Trilinos? Blas and Lapack support is better in recent version of Trilinos. I am working on installing Aspect v1.40, the recommendation of the manual is to use Trilinos version 1.4.x (which I assumed there to be

[deal.II] Re: Issue with Trilinos installation (issue with blas?)

2016-10-04 Thread Matt Weller
Why are you using such an old version of Trilinos? Blas and Lapack support is better in recent version of Trilinos. I am working on installing Aspect v1.40, the recommendation of the manual is to use Trilinos version 1.4.x (which I assumed there to be specific reason for that recommendation,

[deal.II] Re: Running deal.ii with METIS

2016-10-04 Thread Chenchen Liu
Thank you Bruno for the reply. First, I did not modify step-17. I just try to run the original code with no modification. The memory I requested is huge. It is really wired. Second, for "#PBS -l nodes=1:ppn=x", no matter what the value x is, the error always exists. Third, I don't know what is

[deal.II] Re: Running deal.ii with METIS

2016-10-04 Thread Bruno Turcksin
Chenchen, On Tuesday, October 4, 2016 at 5:16:12 PM UTC-4, Chenchen Liu wrote: > > > ***Memory allocation failed for SetupCtrl: maxvwgt. Requested size: > 18446744073709551608 bytes > This line says that you are asking for 18446744073 GB of memory... > It is said that there is a bottleneck for

[deal.II] Running deal.ii with METIS

2016-10-04 Thread Chenchen Liu
Dear all, I am trying to run deal.ii with METIS on cluster such as step-17 and step-18. There are some technical errors occurs, and it always shows ***Memory allocation failed for SetupCtrl: maxvwgt. Requested size: 18446744073709551608 bytes Current memory used: 384 bytes Max

[deal.II] Re: Issue with Trilinos installation (issue with blas?)

2016-10-04 Thread Bruno Turcksin
Matt, On Tuesday, October 4, 2016 at 4:49:28 PM UTC-4, Matt Weller wrote: > > packages/teuchos/numerics/src/CMakeFiles/teuchosnumerics.dir/build.make:280: > recipe for target > 'packages/teuchos/numerics/src/libteuchosnumerics.so.11.4.2' failed > Why are you using such an old version of Trilinos

Re: [deal.II] Issue with Trilinos installation (issue with blas?)

2016-10-04 Thread Matt Weller
It's readable and executable (not completely writable) -rwxr-xr-x. 1 root root 355288 Jul 6 14:26 /usr/lib64/libblas.so.3.6.1 ~M On Tuesday, October 4, 2016 at 3:59:41 PM UTC-5, Wolfgang Bangerth wrote: > > On 10/04/2016 02:49 PM, Matt Weller wrote: > > > > libblas.so.3.6.1 is absolutely

Re: [deal.II] Issue with Trilinos installation (issue with blas?)

2016-10-04 Thread Wolfgang Bangerth
On 10/04/2016 02:49 PM, Matt Weller wrote: libblas.so.3.6.1 is absolutely present and accounted for "ls /usr/lib64/libblas.so.3.6.1 /usr/lib64/libblas.so.3.6.1" So, I really am not sure where the malfunction is. Is it readable? Executable? Can you do 'ls -l' instead? W. -- -

[deal.II] Issue with Trilinos installation (issue with blas?)

2016-10-04 Thread Matt Weller
Hi all, I am trying to get trilinous up and running on Fedora 24, but keep running into issues with Blas and Lapack libraries. I've managed to suss out most of these, but the latest has left me scratching my head a bit (dynamic and static libraries, which - I think- I fixed). Scanning depen

Re: [deal.II] Derivatives (gradients) of Symmetric Tensors

2016-10-04 Thread Daniel Arndt
Metin, I understand that the components are in space (x/y/z), > and (*shape_gradient_ptr++)[d] would be derivative of phi in each > direction; is that correct? > Yes, that is the derivative of the dth component in direction d. > > (compared to vectors) the implementation of divergence function

Re: [deal.II] how to use solution.

2016-10-04 Thread Wolfgang Bangerth
On 10/04/2016 09:12 AM, hanks0...@gmail.com wrote: template void Step6::get_profile () { const QGauss quadrature_formula(3); FEValues fe_values (fe, quadrature_formula, update_values| update_gradients | update_quadrature_points |

[deal.II] how to use solution.

2016-10-04 Thread hanks0227
Hi, I'm trying to study how to use solution after the calculation is done. So, What I'm trying to do in step6 tutorial program is to calculate f=x*solution+y; So I add the following class.(that almost comes from assemble_system()) template void Step6::get_profile () { const QGauss quadratu

Re: [deal.II] Re: how to get 3D structured mesh from rotated 2D mesh in dealii

2016-10-04 Thread Daniel Arndt
Marek, Only the vertices with indices in considered_vertices are tested for >> equality. This speeds up the algorithm, which is quadratic and thus quite >> slow to begin with. However, if you wish to consider all vertices, simply >> pass an empty vector. >> > > i.e. I have assumed it is called

Re: [deal.II] Derivatives (gradients) of Symmetric Tensors

2016-10-04 Thread Metin Cakircali
Daniel, thank you for the explanation. I understand that the components are in space (x/y/z), and (*shape_gradient_ptr++)[d] would be derivative of phi in each direction; is that correct? (compared to vectors) the implementation of divergence function for the tensors is as following;