[deal.II] Re: which version of trilinos for dealii-8.4.1

Hi Roc, I just built [1] deal.II 8.4.1. with Trilinos 12.6.3 using Spack https://github.com/LLNL/spack which also includes as tests running Step-40 with Trilinos and (1) iterative solver (2) direct Superlu_Dist (3) direct MUMPS. So as far as I can tell it works ok. [1] I will create a PR on

Re: [deal.II] Transfer of quadrature point history data after mesh refinement.

Hi > On 14 Jun 2016, at 16:51, dealii.gr...@gmail.com wrote: > > Hi > > I am solving a problem using Trilinos and parallel::distributed > > triangulation. It

[deal.II] Re: Elasticity

It appears that you are solving small strain non-linear elasticity. Then you need to study step-44 and linearize your problem. Regards, Denis. On Tuesday, June 14, 2016 at 5:07:05 PM UTC+2, benhour@gmail.com wrote: > > Dear all, > Thanks very much for your response and help. If I can make

[deal.II] Re: Elasticity

Hi Benhour, I am afraid that not many people would be able to answer such a general question, that does not look to be specific to deal.II per se. Just a general advise, i would suggest you to first research on what you are trying to implement in deal.II, which system of equations you solve (if

[deal.II] Re: Reuse factorization in Trilinos direct solver

p.s. if the issue is resolved, please mark it as such ;-) -- 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

[deal.II] Re: "Make test" failure following Trilinos installation with Mesquite

p.s. one can also make Clang + gfortran work, but this is de-factor mixing of compilers and requires hacking two-three lines to work properly. For starters you can try pure GCC build. -- The deal.II project is located at http://www.dealii.org/ For mailing list/forum options, see

[deal.II] Re: "Make test" failure following Trilinos installation with Mesquite

Hi Oded, Here are instructions again with a bit more explanation as I noticed that you don't follows them exactly: (0) add the following to ~/.bash_profile (DO NOT RUN IN TERMINAL) ``` SPACK_ROOT=/path/to/spack export PATH=$SPACK_ROOT/bin:$PATH ``` Run new terminal window and install GCC and

Re: [deal.II] Re: PETScWrappers::SparseDirectMUMPS for symmetry system matrix and factorization resue

Hi Alexander, > On 26 Jul 2016, at 09:40, Alexander wrote: > > > @Denis: I agree, the logic is somewhat deficient. I also think documentation > and interface itself (e.g. I have no idea why does method set_solver_type >

Re: [deal.II] Re: global dof renumbering with parallel triangulation and trilinos direct solver (Bug ?)

You test worked for me with DoFRenumbering::Cuthill_McKee(dof_handler); I will see if I can spot any issues with renubmer() part... > On 10 Aug 2016, at 16:19, Daniel Jodlbauer wrote: > > Here it is. > > First run is without renumbering, second one with dof renumbering. >

Re: Re: [deal.II] global dof renumbering with parallel triangulation and trilinos direct solver (Bug ?)

I debugged locally owned DoFs for 2 cores and 1 global refinement and I see: core=1: DEAL::n_dofs = 9 DEAL::before renumbering: DEAL::{[0,2]} DEAL::after renumbering: DEAL::{[6,8]} core=2: DEAL::n_dofs = 9 DEAL::before renumbering: DEAL::{[3,8]} DEAL::after renumbering: DEAL::{[0,5]} which

Re: [deal.II] Re: global dof renumbering with parallel triangulation and trilinos direct solver (Bug ?)

Are you sure that you reinitialise all involved vectors and matrices after renumbering? Regards, Denis. > On 10 Aug 2016, at 13:47, Daniel Jodlbauer wrote: > > Ok, if I use SolverGMRES<>, it reports the error "Column map of matrix does > not fit with vector map!", however,

[deal.II] Re: PETScWrappers::SparseDirectMUMPS solver error

Hi Rajat, On Tuesday, July 12, 2016 at 8:37:11 AM UTC+2, RAJAT ARORA wrote: > > Hello Jean, > > Thanks for the reply. > I understand your concern for the lack of proper information but this is > all I have. > > The error occurs after around 900 iterations of solving 5 coupled > equations so it

[deal.II] Re: PETScWrappers::SparseDirectMUMPS solver error

On Wednesday, July 13, 2016 at 10:56:27 PM UTC+2, RAJAT ARORA wrote: > > Hello Denis, > > Thanks for your reply. > > Candi looks like a good option to use to install all the libraries. > However, I also need mumps which Petsc installs for me when I install > libraries separately. > I looked at

[deal.II] Re: On the use of MappingFEField

I suppose this is a duplicate post and can be deleted? On Monday, May 30, 2016 at 8:02:06 AM UTC+2, Praveen C wrote: > > Dear all > > I have problems involving airfoil geometry where the cells have high > aspect ratio in the boundary layer. Due to this, it is not enough to just > use curved

[deal.II] Re: Embedding a Python script

Hi Oded, On Tuesday, August 9, 2016 at 10:36:39 AM UTC+2, Oded Yaakobi wrote: > > > However, if I want to keep the functionality of switching the build types > between "Debug" and "Release" versions, how can I do it now? > I just do -DCMAKE_BUILD_TYPE=Debug or Release you can also probably try

Re: [deal.II] Stresses at support point locations

Indeed, one commonly for stress recovery used approach is nodal averaging. See for example Zienkiewicz and Zhu "A Simple Estimator and Adaptive Procedure for Practical Engineering Analysis" http://onlinelibrary.wiley.com/doi/10.1002/nme.1620240206/abstract You can obtain the best fit in L2 norm

[deal.II] Re: How to input an argument of Fe_Enriched constructor

Hi, On Tuesday, January 31, 2017 at 5:27:10 AM UTC+1, Edith Sotelo wrote: > > > Hi, >> So far I just worked with the simple Fe_Enriched constructor, However I >> want to use more enrichment functions and I am having problems to >> understand the third argument of this constructor (below).

[deal.II] Re: bool ParameterHandler::read_input (const std::string &, const bool, const bool, const std::string &) DEAL_II_DEPRECATED

I am glad that it worked out. Please mark some answer as "correct/bast" so that this topic is marked as "Answered" in the google group list. Cheers, Denis. On Tuesday, January 31, 2017 at 7:27:17 PM UTC+1, Vinayak Gholap wrote: > > Hello, > > Yes it worked. > @Jean-Paul: Yes I use the

[deal.II] Re: How to input an argument of Fe_Enriched constructor

If there are no further questions on this topic, please mark some answer as "correct/best" so that this topic is displayed as "Answered" in the google group list. Cheers, Denis. On Tuesday, January 31, 2017 at 10:01:38 AM UTC+1, Denis Davydov wrote: > > Hi, > > O

[deal.II] WorkStream + hp : resizing members of Copy/Scratch data

Hi all, That's a question, probably, to Wolfgang and/or Bruno. It's not explicitly mention in the documentation whether or not parts of the Copy/Scratch data classes can be resized during cell assembly. Obviously, in the hp-FEM case, one would need to resize local matrices according to a FE

Re: [deal.II] Re: How to input an argument of Fe_Enriched constructor

Hi Edith, I would certainly run in debugger to see what’s going on. >From the code you show, it looks like you initialize your functions **after** >you actually pass them to constructor of FE_Enriched. To be on the safe side, i would move those above. Cheers, Denis. > On 3 Feb 2017, at 15:29,

[deal.II] Re: interpolation in a finer mesh with enriched elements

Hi Edith, Assuming that the all children of coarse enriched element are also marked for enrichment, then everything could work out-of-the-box. But I must admit i have not tried it and there are no tests in deal.II which would verify it. If you are interested, you can try verifying it and add a

[deal.II] Re: CXX flags for SIMD and other optimization flags (GCC@6)

), but nothing to be worried about, as far as i can tell. ps. The continuous tester "GNU-5.3.0-master-optimized" on CDash appears to be adding -march=native -pipe to all flags and -Ofast to release flags. Regards, Denis On Thursday, September 15, 2016 at 2:04:58 PM UT

[deal.II] Re: bug in program only with adaptive mesh refinement

Hi Daniel, The vectors you have in this equation P(u+h*v) =..., which of those have constrains distributed and which zeroed? If you assembly matrices with ConstraintMatrix.distribute_local_to_global() the diagonal elements corresponding to constrained DoFs will be dummy (and positive) just to

[deal.II] Re: More questions about FE_enriched & PUM FEM

On Friday, February 10, 2017 at 4:00:25 PM UTC+1, Edith Sotelo wrote: > > > A follow up about this post: > > This is the way I went on implementing the strong bc.: > Assigned the Boundary value to the non-enriched dof, and assigned Zero to > the enriched dofs.. it worked for me. > I used

Re: [deal.II] Re: More questions about FE_enriched & PUM FEM

or system_to_base_index().first.first > On 13 Feb 2017, at 18:06, Denis Davydov <davyd...@gmail.com> wrote: > > > > On Friday, February 10, 2017 at 4:00:25 PM UTC+1, Edith Sotelo wrote: > > A follow up about this post: > > This is the way I went on implem

[deal.II] hp and SolutionTransfer -- ExcInterpolationNotImplemented ?!

Hi all, Apparently, a long discussion on this topic in 2015 here https://groups.google.com/forum/?fromgroups#!searchin/dealii/hp|sort:relevance/dealii/a7RipcMRI5s/r5pQOr9FSf0J is not enough for myself. I came across an issue which I don't think I saw before.

[deal.II] test stage for compiling deal.II suite in Spack 0.10 (and later 1.0)

Dear all, Supercomputer PACKage manager currently has a test stage for the upcoming 0.10 release (*), see this comment . If you are using Spack, it's* good time to test that nothing is broken*

[deal.II] Re: Reference article for modified Kelly Estimator

Hi Deepak, There are a few references, but they are all problem specific (simple Laplace equation, or the eigenpairs of the Laplace operator, etc). I can't really give a single one to cite. Instead, i would suggest you to do a quick literature review on hp-FEM in your application area and most

[deal.II] Re: Help with the weak form

Hi Dragan, Did you do a literature review to see what researchers are doing in your field? Most likely you need to linearize it w.r.t. to "c" so that you will be solving for \Delta c around some points c_0 employing something like Newton-Raphson method. Regards, Denis. On Thursday, September

[deal.II] Re: CXX flags for SIMD and other optimization flags (GCC@6)

Thanks Bruno and Martin for the swift reply. For starters i will try with -march=native . Cheers, Denis. On Thursday, September 15, 2016 at 2:04:58 PM UTC+2, Denis Davydov wrote: > > Dear all, > > From the matrix-free tutorials 37 and 48, I see that the recommended flags > for V

Re: [deal.II] a few questions about matrix-free

Hi Martin, both of your posts helped a lot to clarify things. Thanks a lot! Would you mind adding the discussion on using MatrixFree with different operators to the documentation of MatrixFree class? Essentially copy-pasting of what you wrote in the two e-mails related to update flags and alike

[deal.II] CXX flags for SIMD and other optimization flags (GCC@6)

Dear all, >From the matrix-free tutorials 37 and 48, I see that the recommended flags for VectorizedArrays with GCC are -DCMAKE_CXX_FLAGS="-march=native" How about using -O3, -ffast-math, -funroll-loops ? Any other recommended flags for GCC? Regards, Denis. -- The deal.II project is

[deal.II] Re: PARPACK issues

p.s. Alternatively, you can check those tests in 8.4. https://github.com/dealii/dealii/tree/dealii-8.4 branch -- 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

[deal.II] Re: PARPACK issues

Hi Ehsan, On Monday, September 19, 2016 at 9:04:35 AM UTC+2, Ehsan Mihankhah wrote: > > Hi, > > I have been working with Dealii 8.3 for a while and I have been using the > modified version of step-36 to solve eigenvalue problem with ARPACK. I > noticed that there is a possibility of working

[deal.II] Re: macOS Sierra dynamic linker limit

after digging more i found out that it has to do with extra not needed LC_RPATH load commands added by Spack https://github.com/LLNL/spack/issues/1874 On Wednesday, September 28, 2016 at 5:58:07 PM UTC+2, Denis Davydov wrote: > > I am hitting run-time error of the form: > > 36: d

[deal.II] a few questions about matrix-free

Dear all, I have accumulated a few matrix-free related questions which i would like to clarify ask. (1) FEEvaluation has read_dof_values (const std::vector< VectorType > , const unsigned int first_index=0), but i don’t see a function to get to values of each DoF vector at quadrature points.

Re: [deal.II] a few questions about matrix-free

Hi Martin, > On 30 Sep 2016, at 16:49, Martin Kronbichler > wrote: > > There are two possibilities for doing things. One is like you say, you loop > over the components in the input vector or create two FEEvaluation objects > and let them do similar things. Note

[deal.II] LA::distributed::Vector initialized with MatrixFree and Kelly estimator

There is a complication of using LA::distributed::Vector initialized with MatrixFree::initialize_dof_vector() in Kelly estimator. A naïve usage would lead to a problem which obviously has to do with locally relevant cells and their dofs: Number

[deal.II] Re: More questions about FE_enriched & PUM FEM

Hi Edith, On Monday, November 28, 2016 at 7:19:56 PM UTC+1, Edith Sotelo wrote: > > Hi all, > I have more questions regarding Fe_enriched & PUM > > 1) Are enriched functions shifted, so that the enriched part evaluates to > zero at the mesh nodes? > no, nothing is shifted. Enrichment

Re: [deal.II] Cluster with Infiniband network

On Wednesday, November 16, 2016 at 3:11:08 PM UTC+1, Wolfgang Bangerth wrote: > > Our rule of thumb is usually to use about 100,000 > unknowns per MPI process. @Woflgang: maybe this should be added to a stand-along page in https://www.dealii.org/developer/index.html within the "Information

Re: [deal.II] Re: Interfacing dealii-8.4.1 with trilinos-12.6.2 - make test failed

On Wednesday, November 9, 2016 at 11:44:30 PM UTC+1, Joaquin wrote: > > Apparently I used the same MPI by default for both of them. > Not necessarily. You need to check logs to see what is picked up by Trilinos and what is picked up by deal.II. To make sure both use the same MPI you can do:

[deal.II] Re: Issues with Fe_Enriched constructor

Hi, If you look at the documentation https://www.dealii.org/developer/doxygen/deal.II/classFE__Enriched.html#ada373a36db9791fa6e6440987e8ce258 then the constructor takes a pointer to the function, not the function itself. So you need to create your object Enrichment() and then pass a pointer to

[deal.II] reuse FEEvaluation within a cell for RHS-like calculation

I wonder if it possible to re-use FEEvaluation within each cell to calculate integrals of multiple right-hand-side like vectors. Something along these lines: for (unsigned int cell=0; cell

Re: [deal.II] reuse FEEvaluation within a cell for RHS-like calculation

Hi Martin, Cool, thanks for the prompt reply. Kind regards, Denis > On 15 Nov 2016, at 14:59, Martin Kronbichler > wrote: > > Hi Denis, > > > >> I wonder if it possible to re-use FEEvaluation within each cell to calculate >> integrals of multiple

Re: [deal.II] Re: Problems in handling the userdata of Distributed Triangulation

I see. In serial mode all is doable because u can go from current cell to neighbors to quadrature data and do whatever. For the case of MPI you would still need to somehow ship the data to ghost cells. Because at some point neighbors of locally owned cells will be ghost cells. I think it is

Re: [deal.II] Re: Problems in handling the userdata of Distributed Triangulation

Hi Jack, One more approach: you first loop over all locally owned cells and determine the local flag (tru/false). Then you still need to ship this to ghost cells on other MPI processors. On doing that you can do your assembly as usual. Kind regards, Denis > On 3 Nov 2016, at 10:12, Jack

[deal.II] Re: deal.II cmake stuck at "Performing Test DEAL_II_HAVE_USABLE_FLAGS_DEBUG"

Hi Praveen, I am glad that you at least have the whole stack of packages installed via Spack (although with minor issues due to missing "patch" on the system). As for the compilation of your own deal.II from github, the simplest way is supposed to be `spack setup dealii@develop` (see

[deal.II] Re: deal.II cmake stuck at "Performing Test DEAL_II_HAVE_USABLE_FLAGS_DEBUG"

On Friday, December 16, 2016 at 4:34:29 AM UTC+1, Praveen C wrote: > > Additionally I added Fortran compiler and fixed "suitesparse" to > "suite-sparse", but I am still stuck at the same place as before. > > Should I use "Filesystem View" to compile my own dealii with spack > packages ? > > If

Re: [deal.II] obtaining solution values at any point using Quadrature< dim >::Quadrature(const Point< dim > & point)

Jiaqi, please don't forget to mark the topic as Answered by choosing the best reply. This helps us see which topics still require attention. Regards, Denis. On Friday, December 16, 2016 at 6:15:30 AM UTC+1, Jiaqi ZHANG wrote: > > Got it. Thanks so much, Dr. Bangerth. > > Jiaqi > > 2016-12-16

Re: [deal.II] Re: GitHub: make developers team public and add @dealii to ping all

Please delete it then, i will re-post. Sorry for troubles. > On 6 Dec 2016, at 17:47, Jean-Paul Pelteret <jppelte...@gmail.com> wrote: > > No way to move it, but I can delete it if you want? > > On Tuesday, December 6, 2016 at 5:41:32 PM UTC+1, Denis Davydov wrote: &g

[deal.II] Re: GitHub: make developers team public and add @dealii to ping all

wrong forum, sorry, i meant to post it here https://groups.google.com/forum/?fromgroups#!forum/dealii-developers If there is a way to move the post, feel free. On Tuesday, December 6, 2016 at 5:40:49 PM UTC+1, Denis Davydov wrote: > > I think it would be better if deal.II's GitHub accou

[deal.II] Re: Best application to plot

Hi, Don't know about Visit, but in Paraview you can also plot-over-line and then export the data and re-plot it using Gnuplot with right styles, lines, fonts, etc. But otherwise, I never cam across any instance where Vist and/or Paraview would not be enough. Cheers, Denis. On Wednesday,

Re: [deal.II] Re: deal.II cmake stuck at "Performing Test DEAL_II_HAVE_USABLE_FLAGS_DEBUG"

Alternative, is to add the view to your path, i.e. PATH=${DEAL_II_VIEW}/bin:${PATH} then -DCMAKE_C_COMPILER="mpicc" would also be ok. On Saturday, December 17, 2016 at 12:52:44 PM UTC+1, Denis Davydov wrote: > > To clarify with FileSystem views, you would need to do > &g

Re: [deal.II] Re: deal.II cmake stuck at "Performing Test DEAL_II_HAVE_USABLE_FLAGS_DEBUG"

> On 17 Dec 2016, at 12:59, Praveen C wrote: > > I used instructions on wiki like this > > DEAL_II_VIEW=/home/soft > > cmake \ > -DCMAKE_FIND_FRAMEWORK=LAST \ > -DCMAKE_INSTALL_RPATH_USE_LINK_PATH=FALSE \ > -DCMAKE_INSTALL_RPATH=${DEAL_II_VIEW} \ >

Re: [deal.II] Re: deal.II cmake stuck at "Performing Test DEAL_II_HAVE_USABLE_FLAGS_DEBUG"

t; > On Fri, Dec 16, 2016 at 6:28 PM, Denis Davydov <davy...@gmail.com > > wrote: > >> >> >> On Friday, December 16, 2016 at 4:34:29 AM UTC+1, Praveen C wrote: >>> >>> Additionally I added Fortran compiler and fixed "suitesparse" to >&

Re: [deal.II] Re: deal.II cmake stuck at "Performing Test DEAL_II_HAVE_USABLE_FLAGS_DEBUG"

That looks like something is wrong in deal.II configuration tests. Correct me if I am wrong, but 8.4.2 installs ok for you with Spack but the current @develop fails, so the changes must have been introduced after 8.4.2 release. @all: any ideas on how to debug it further or what could be the

[deal.II] Re: can I used unstructured quadrilateral meshes?

Hi Chaman, yes, you can. Step-1 already shows you such meshes https://www.dealii.org/developer/doxygen/deal.II/step_1.html You can NOT use triangles/tetrahedra, see https://github.com/dealii/dealii/wiki/Frequently-Asked-Questions#can-i-useimplement-trianglestetrahedra-in-dealii Regards, Denis.

[deal.II] Re: p::d::SolutionTransfer::interpolate fails with LA::distributed::Vector's in the specific case

bfb5b8, all_out=size=120) + 2451 at solution_transfer.cc:183 but that's not really helpful. On Monday, January 2, 2017 at 5:50:32 PM UTC+1, Denis Davydov wrote: > > Hi all, > > I came across a very weird problem today. When using > p::d::SolutionTransfer during refinement I get t

[deal.II] Re: compute sign of the determinant of the global tangent stiffness matrix

Hi Pasha, It looks like what you need is to know whether the matrix is positive-definite or negative-definite. I don't think there is way to calculate a determinant of an arbitrary huge sparse matrix such as Epetra_CrsMatrix, that is wrapped in TrilinosWrappers. I gave a quick look at

Re: [deal.II] Re: deal.II cmake stuck at "Performing Test DEAL_II_HAVE_USABLE_FLAGS_DEBUG"

On Tuesday, December 20, 2016 at 5:20:20 AM UTC+1, Praveen C wrote: > > I removed all the libraries and do > > /home/spack/opt/spack/linux-opensuse20161217-x86_64/gcc-6/openmpi-2.0.1-asdjmd22cnyktv2athcx3ouhrozknk22/bin/mpic++ > > -DDEAL_II_HAVE_USABLE_FLAGS_DEBUG -pedantic -fPIC -Wall

Re: [deal.II] Re: deal.II cmake stuck at "Performing Test DEAL_II_HAVE_USABLE_FLAGS_DEBUG"

> On 19 Dec 2016, at 18:09, Wolfgang Bangerth wrote: > > On 12/19/2016 07:26 AM, Praveen C wrote: >> >> [ 50%] Linking CXX executable cmTC_4e156 >> >> /home/spack/opt/spack/linux-opensuse20161217-x86_64/gcc-6/cmake-3.7.1-erobxw7bh6cbnaqfzaqwvzk6crnj5ojy/bin/cmake >> -E

Re: [deal.II] Re: deal.II cmake stuck at "Performing Test DEAL_II_HAVE_USABLE_FLAGS_DEBUG"

r system. Regards, Denis. On Saturday, December 17, 2016 at 4:16:08 PM UTC+1, Praveen C wrote: > > > > On Sat, Dec 17, 2016 at 8:41 PM, Denis Davydov <davy...@gmail.com > > wrote: > >> That looks like something is wrong in deal.II configuration tests.

Re: [deal.II] Re: deal.II cmake stuck at "Performing Test DEAL_II_HAVE_USABLE_FLAGS_DEBUG"

I second Wolfagng’s suggestion to remove flags one-by-one from the command line and see which one make ld hang. That’s also bisection in a sense, instead of working out which commit breaks it, you investigate which flag breaks it. My best guess is that some extra checks have been added to

Re: [deal.II] Re: deal.II cmake stuck at "Performing Test DEAL_II_HAVE_USABLE_FLAGS_DEBUG"

> On 20 Dec 2016, at 11:32, Praveen C wrote: > > Without Trilinos, the linking takes 0.307s > > So I am adding one library from Trilinos after another. I find that as I add > more Trilinos libraries, the linking takes increasing time. > > until libifpack.so ==> 3m 47s >

Re: [deal.II] Re: deal.II cmake stuck at "Performing Test DEAL_II_HAVE_USABLE_FLAGS_DEBUG"

Hi Praveen, > On 20 Dec 2016, at 13:52, Praveen C wrote: > > Hello Denis > > I am not able to do either > > spack install dealii@develop~python > > or > > spack install dealii@8.4.2 > > It fails at Boost > > ==> Using cached archive: >

Re: [deal.II] restart/checkpoint strategies in user applications/libraries

Hi Timo, > On 24 Dec 2016, at 22:00, Timo Heister wrote: > > Denis, > > we do a mixture in ASPECT: > We have a "resume computation = true" setting in the prm and ASPECT > will first load all settings from the ParameterHandler and then resume > from the last snapshot by

Re: [deal.II] Re: Evaluating the gradient of the solution at the centroid of the element

> On 22 Dec 2016, at 17:10, cmhame...@gmail.com wrote: > > The thing is though that I don't actually need to integrate at these points. > The method still employ a 4node quad element in 2d or an 8 node hex element > in 3d but only uses the element centroid to calculate the deformation >

Re: [deal.II] Re: make test

please don't forget to mark the reply that helped as "Best Answer" so that the topic is shown as "Answered". Regards, Denis. On Tuesday, December 20, 2016 at 4:19:14 PM UTC+1, Sudarshan Kumar wrote: > > > Dear Heister, > > The problem was that I did not choose corerct mpi compiler, now the >

Re: [deal.II] Re: deal.II cmake stuck at "Performing Test DEAL_II_HAVE_USABLE_FLAGS_DEBUG"

mailto:openblas@0.2.19.> > > Maybe I will uninstall everything and do a fresh install of dealii@develop. > > Best > praveen > > On Sun, Dec 18, 2016 at 9:00 PM, Denis Davydov <davyd...@gmail.com > <mailto:davyd...@gmail.com>> wrote: >

Re: [deal.II] Re: deal.II cmake stuck at "Performing Test DEAL_II_HAVE_USABLE_FLAGS_DEBUG"

> -Wno-unused-local-typedefs -Og -ggdb -Wa,--compress-debug-sections > CMakeFiles/cmTC_4e156.dir/src.cxx.o -o cmTC_4e156 .. > > and never finishes. > > All the flags should be available in these files, right ? Would it help to > look into these ? > > Best &g

[deal.II] Re: Evaluating the gradient of the solution at the centroid of the element

Hi On Thursday, December 22, 2016 at 5:47:24 AM UTC+1, cmha...@gmail.com wrote: > > I have gone through some of the tutorials previously and thought it was > about time I actually tried to implement something on my own in the > library. > > I am attempting to implement a finite strain code

[deal.II] Re: Installation using Spack fails during 'ncurses' installation

On Thursday, March 16, 2017 at 6:43:13 PM UTC+1, Bruno Turcksin wrote: > > Steve, > > I have tried to use spack several times on two clusters and it never > worked for me (but it works fine on my own machine). I usually have to > patch a bunch of things and at the > p.s. maybe a good idea is

[deal.II] Re: Installation using Spack fails during 'ncurses' installation

p.p.s. Just to be sure, i wiped my installations of Spack on Ubuntu16.04+gcc5.4.0 PC and Centos7+gcc4.8.5 cluster and reinstalled everything from scratch using commit 1124bdc99ee84c26201c40536d9b04dac74d7f6a (this is the current HEAD in Spack, I updated dealii's wiki to mention it). I still

[deal.II] An issue in compiling on a cluster

Bruno is right, you definitely don't want compile MPI yourself in a cluster. At the very top of the WiKi there is an example of how to configure Spack on a cluster with external MPI https://github.com/dealii/dealii/wiki/deal.II-in-Spack Probably you missed this. I will edit the WiKi to stress

Re: [deal.II] Re: An issue in compiling on a cluster

HI Alberto, On Tuesday, April 4, 2017 at 10:58:39 PM UTC+2, Alberto Salvadori wrote: > > Sorry, I am a bit confused. > > "you need to make sure that building mpich is set to false." > - where I can set "building mpich" to false? Shall I edit a file > ~/.spack/packages.yaml that BTW currently

[deal.II] Re: An issue in compiling on a cluster

p.s. it's a bit of a learning curve to set things up with Spack, but hopefully it does not take too much as there is a lot of documentation. On the positive side, a lot of developers now give more and more attention to Spack and maintain their packages. I know that PETSc and Trilinos guys keep

Re: [deal.II] Re: fe_enriched and step-47

> On 12 Apr 2017, at 14:54, Sean McGovern wrote: > > >> Would the general point be that if one can go to higher resolutions with >> distributed parallelism that the enhanced accuracy of the enrichment >> functions can be compensated for? > > Sorry, i did not get what you

Re: [deal.II] Re: fe_enriched and step-47

> On 7 Apr 2017, at 03:09, Wolfgang Bangerth wrote: > > On 04/06/2017 06:14 AM, Daniel Arndt wrote: >>I don't know if Wolfgang, the author of the tutorial, plan to finish it. >>Maybe we can team up here. >> >> step-47 seems to be completed in the paper On the

Re: [deal.II] Re: fe_enriched and step-47

Hi On Sunday, April 9, 2017 at 10:20:13 AM UTC+2, Simon Sticko wrote: > > Hi. > Regarding this: > > > On Thursday, April 6, 2017 at 1:51:41 PM UTC+2, Denis Davydov wrote: > > > > The issue with integrating and quadrature would still remain. > > > I've bee

[deal.II] Re: Crack propagation

es I actually made. Won't happen again. ;) > > Regarding the speedup, I just figured out how to make use of the > CellDataStorage function which has been recently implemented within > deal.II. First of all, I want to thank Denis Davydov and Jean-Paul Pelteret > for implementing

Re: [deal.II] Re: Crack propagation

(). The same resasons pack_values() are NOT called pack_scalars() etc Regards, Denis. > On 10 Apr 2017, at 11:30, 'Seyed Ali Mohseni' via deal.II User Group > <dealii@googlegroups.com> wrote: > > Dear Denis Davydov, > > I am trying to implement the pack_values() and u

[deal.II] Error using dealii with spack .../binutils-2.27 collect2: error:ld returned 1 exit status

Try using Ubuntu's compiler (gcc5.4, make sure u install gfortran). I successfully run the full dealii suite on ubuntu16.04 a few weeks back and had zero issues with Spack. Binutil issue with Spack's build GCC should probably be reported on Spack's github issues page. Regards, Denis -- The

[deal.II] Re: Error using dealii with spack .../binutils-2.27 collect2: error:ld returned 1 exit status

Hi Phil Quick follow up. I was setting up a fresh installation of Ubuntu 16.04 LTS and had zero issues building/running. I updated instructions on how to get *gfortran* on ubuntu and that you would need *curl*. See https://github.com/dealii/dealii/wiki/deal.II-in-Spack Make sure you do `*git

[deal.II] Re: Interpolate selected components

I think it's easier if you create another 4-compoennt Function class which wraps your 5-component function. Regards, Denis. On Sunday, March 12, 2017 at 2:03:42 PM UTC+1, Praveen C wrote: > > Dear all > > I have an FESystem with 4 components and a Function with 5 components. Is > it possible

[deal.II] Re: fe_enriched and step-47

Hi Sean, Hopefully someone get to finish step-47 with XFEM. I am really interested in digging there and I put it on my own TODO list. I don't know if Wolfgang, the author of the tutorial, plan to finish it. Maybe we can team up here. My understanding that step-47 did all the book-keeping of

Re: [deal.II] Re: Superlu_dist usage in dealii

> On 18 Apr 2017, at 21:39, Kartik Jujare wrote: > > Thank you Uwe and Dennis dor your additions > > However Dennis, I have a supplementary question. How does one make you of the > arguments inside the program specifically inside solve function? currently you can’t,

[deal.II] Re: Superlu_dist usage in dealii

for completeness, you can also use superlu_dist from PETSc using command-line argument, along the lines: -pc_type lu -pc_factor_mat_solver_package superlu_dist On Monday, April 17, 2017 at 1:08:29 PM UTC+2, Kartik Jujare wrote: > > Hello, > > Can anyone please provide an implementation example

Re: [deal.II] Installation didn't give any errors but when I tried make test, it failed all tests

Hi Japan, I am happy to hear that it worked and you resolved your problem! Sincerely, Denis. > On 14 Aug 2017, at 04:13, Japan Patel wrote: > > Hey everyone, > > Thanks Dr. Bangerth and thanks Denis!! > > I was able to run step-1. I installed using spack. It took a while

Re: [deal.II] Installation didn't give any errors but when I tried make test, it failed all tests

Hi, Usually, one compiles some MPI provider (i.e. Openmpi) and then use its compiler wrappers in majority of dealii' dependencies. Alternativelt ou can give Spack https://github.com/dealii/dealii/wiki/deal.II-in-Spack a try which guarantees that the whole toolchain is consistent: a single

Re: [deal.II] segmentation fault when calling make_vectorized_array

Hi Martin, > On 13 Jul 2017, at 09:13, Martin Kronbichler > wrote: > >> >> no, it's just a member variable VectorizedArray: >> >> VectorizedArray a; > > But then the class/struct that holds this member variable is not properly > aligned, you probably have it

Re: [deal.II] segmentation fault when calling make_vectorized_array

Hi Martin, On Wednesday, July 12, 2017 at 6:05:30 PM UTC+2, Martin Kronbichler wrote: > > Hi Denis, > > what is a? Is it an element of an array? If yes, is the array of type > AlignedVector (or derived from that). > no, it's just a member variable VectorizedArray: VectorizedArray a; >

Re: [deal.II] segmentation fault when calling make_vectorized_array

Thanks a lot for your help, Martin! Cheers, Denis > On 13 Jul 2017, at 11:02, Martin Kronbichler > wrote: > > Hi Denis, > >> While on the topic of alignment, do I need to be more careful about using >> >> template >> struct QPData >> { >>Table<2,

[deal.II] Re: Status of support for complex equations?

Have a look at this issue which aggregates efforts in this direction: https://github.com/dealii/dealii/issues/2033 Essentially, the main missing piece is ConstraintMatrix https://github.com/dealii/dealii/issues/1760 which Matthias wanted to do over the weekend in July 2016 :-) I think there is

[deal.II] Re: About constructor FE_Enriched

Hi, On Friday, April 28, 2017 at 10:22:07 PM UTC+2, Edith Sotelo wrote: > > Hi. > I want to use several enrichment and incorporate them through a loop in > the constructor. I came up with this piece of code (see below) . But I had > to create a vector of FE_Enriched though I do not need > >

Re: [deal.II] AssertDimension (partition_blocks[partition], task_info.n_blocks) when calling MatrixFree::reinit() for finest level in GMG

Correct! > On 14 May 2017, at 10:50, Daniel Arndt > wrote: > > Denis, > > this is solved by https://github.com/dealii/dealii/pull/4376, isn't it? > > -- > The deal.II project is located at http://www.dealii.org/ > > For mailing

Re: [deal.II] AssertDimension (partition_blocks[partition], task_info.n_blocks) when calling MatrixFree::reinit() for finest level in GMG

Just to confirm my sanity, I can reproduce the error by loading in the p::d::Tria and setting up GMG objects. Of course, that does not really help anyone to try this as the refinement history in p::d::Tria::save() is written as a binary file... :-( On Saturday, May 6, 2017 at 8:00:36 AM

[deal.II] Re: Parallel GridIn of large file - PETSC Error

It could be whatever. PETSc intercepts error and always print such things even when it happens outside of PETSc, which I find very inconvenient. Try compiling and running in Debug mode. On Tuesday, May 9, 2017 at 12:40:22 PM UTC+2, Mathias Mentler wrote: > > Hi everybody, > > I am currently

[deal.II] Re: Trouble with integrating Trilinos with Deal II

To check that I installed 8.4.1 with Spack (see https://github.com/dealii/dealii/wiki/deal.II-in-Spack ) on our Centos 7 cluster, and step-32 links perfectly fine with 8.4.1 and Trilinos 12.10.1. $ ldd step-32 | grep dealii libdeal_II.g.so.8.4.1 =>

[deal.II] Re: Parallel GridIn of large file - PETSC Error

p.s. could also be this https://groups.google.com/forum/#!topic/dealii/zSC33HFN9AA -- 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

  1   2   >