Re: [deal.II] InternalError in VectorTools::compute_nonzero_normal_flux_constraints

2017-02-20 Thread Wolfgang Bangerth
On 02/20/2017 07:22 PM, Lars Corbijn van Willenswaard wrote: Thanks for the reply. I tested the change and it did not work, as get_generalized_face_support_points() is also empty. The cause seems that FESystem doesn't initialize the generalized_face_support_points. To test that I added some code

Re: [deal.II] InternalError in VectorTools::compute_nonzero_normal_flux_constraints

2017-02-20 Thread Lars Corbijn van Willenswaard
Thanks for the reply. I tested the change and it did not work, as get_generalized_face_support_points() is also empty. The cause seems that FESystem doesn't initialize the generalized_face_support_points. To test that I added some code to initialize it when initialize_unit_face_support_points() 'fa

[deal.II] Re: 8.4.1 Installation failure

2017-02-20 Thread Chao
Problem solved! Thank you all : ) On Monday, February 20, 2017 at 7:58:49 PM UTC-3, Uwe Köcher wrote: > > Dear Chao, > > you may check also our download page https://www.dealii.org/download.html > > There we have an additional list for installers and binary packages. > > I suggest that you are on

Re: [deal.II] InternalError in VectorTools::compute_nonzero_normal_flux_constraints

2017-02-20 Thread Wolfgang Bangerth
After a bit of digging, I think the following happens. The basis for the problem is a system of RaviarThomas + DGQ. The RaviarThomas element has no support points, but has dofs_per_face. Therefore the same applies to the FESystem, which therefore triggers the above mentioned error. Interesting

[deal.II] Re: 8.4.1 Installation failure

2017-02-20 Thread 'Uwe Köcher' via deal . II User Group
Dear Chao, you may check also our download page https://www.dealii.org/download.html There we have an additional list for installers and binary packages. I suggest that you are on a linux machine, then you should take a look into our automated build script (with system package installation note

Re: [deal.II] Segfault in EvaluatorTensorProduct::apply when AVX is enabled

2017-02-20 Thread Stephen DeWitt
Dear Martin, Thank you, that makes sense. If I could trouble you with one more question -- I'm having a hard time using AlignedVector, and I can't find any examples of its use online. I'd like to build the AlignedVector with a series of push backs, but I get compiler errors if I try this: dea

Re: [deal.II] Segfault in EvaluatorTensorProduct::apply when AVX is enabled

2017-02-20 Thread Martin Kronbichler
Dear Stephen, The problem is data alignment: You create an std::vector that internally arranges its data under the assumption that the start address of FEEvaluation is divisible by 32 (the length of the vectorization). If you put an FEEvaluation object on the stack, the compiler will automati

[deal.II] Segfault in EvaluatorTensorProduct::apply when AVX is enabled

2017-02-20 Thread Stephen DeWitt
Hello, I recently realized that I should be using "-march=native" flag for optimal performance of matrix-free codes. The application that I've been using works fine with just SSE2, but with AVX enabled I'm getting a segfault. Step-48 works fine, so I don't think it is an installation issue. The

Re: [deal.II] 8.4.1 Installation failure

2017-02-20 Thread Matthias Maier
On Mon, Feb 20, 2017, at 07:27 CST, Chao wrote: > Hi Matthias, > > I did as you said, namely calling cmake with a path to the 'source' folder > while the current directory is 'build'. However, it still didn't work. > Here's the error message: > > -- This is CMake 3.7.1 > [...] You need to in

Re: [deal.II] Example of using MeshWorker::Assembler::MGMatrixLocalBlocksToGlobalBlocks?

2017-02-20 Thread Fred
Unfortunately, I wasn't able to figure it out. I have posted an Issue on github. Kent -- 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 th

Re: [deal.II] Extract some blocks from a sparse block matrix

2017-02-20 Thread Timo Heister
Leon, yes, each block in a BlockSparseMatrix is in fact a SparseMatrix. You can use something like BlockMatrixArray to compose sparse matrices into a different block structure without copying the matrices. On Mon, Feb 20, 2017 at 10:50 AM, wrote: > Dear all, > > I'm working on some monolithic a

[deal.II] Extract some blocks from a sparse block matrix

2017-02-20 Thread lianzhang030592
Dear all, I'm working on some monolithic and partitioned schemes of FSI problem. In a monolithic scheme, the matrix usually consists both fluid and structure parts. However in a partitioned scheme, we can use two matrices which represent the fluid and structure separably. I would like to extrac

Re: [deal.II] 8.4.1 Installation failure

2017-02-20 Thread Chao
Hi Matthias, I did as you said, namely calling cmake with a path to the 'source' folder while the current directory is 'build'. However, it still didn't work. Here's the error message: -- This is CMake 3.7.1 -- -- Include /Users/John/Documents/dealii-8.4.1/cmake/setup_external_macros.cmake

Re: [deal.II] Installing extra packages inside docker container of dealii

2017-02-20 Thread Sebastian.Gonzalez-Pintor
Thanks. It works perfectly. Regards, Sebas El lunes, 20 de febrero de 2017, 12:52:36 (UTC+1), Luca Heltai escribió: > > You should add a > > USER root > > > > USER dealii > > In the docker file before and after the install commands. > > Luca > > On 20 Feb 2017, at 12:47, Sebastian.Gonzalez

Re: [deal.II] Installing extra packages inside docker container of dealii

2017-02-20 Thread Luca Heltai
You should add a USER root USER dealii In the docker file before and after the install commands. Luca > On 20 Feb 2017, at 12:47, Sebastian.Gonzalez-Pintor > wrote: > > Hi Luca! > > I have tried and I do not know what I am missing. I have a makefile like this > > all: build > > b

Re: [deal.II] Installing extra packages inside docker container of dealii

2017-02-20 Thread Sebastian.Gonzalez-Pintor
Hi Luca! I have tried and I do not know what I am missing. I have a makefile like this all: build build: docker build -t new-dealii . and the Dockerfile as follows $ more Dockerfile #Dockerfile FROM dealii/dealii:v8.4.2-gcc-mpi-fulldepsmanual-debugrelease RUN apt-get update RUN apt-g

Re: [deal.II] Installing extra packages inside docker container of dealii

2017-02-20 Thread Luca Heltai
Yes. You should write a Dockefile with your instructions. See, for example, the Dockefile for deal2lkit (github). Luca > On 20 Feb 2017, at 11:58, Sebastian.Gonzalez-Pintor > wrote: > > > Hello! > > I am trying with the docker containers of dealii, so I downloaded one of them > and then

[deal.II] Installing extra packages inside docker container of dealii

2017-02-20 Thread Sebastian.Gonzalez-Pintor
Hello! I am trying with the docker containers of dealii, so I downloaded one of them and then I ran it $ docker pull dealii/dealii:v8.4.2-gcc-mpi-fulldepsmanual-debugrelease $ docker run -i -t dealii/dealii:v8.4.2-gcc-mpi-fulldepsmanual-debugrelease Now I want to install few things in the cont