[deal.II] Re: error during installation with spack on CentOS7

2019-10-04 Thread Denis Davydov
Hi Alberto, Try reporting issue on Spack Github and ping @balay . Denis. On Friday, October 4, 2019 at 12:50:24 PM UTC+2, Alberto Salvadori wrote: > > Dear community > > I apologize for this too long bothering on installing deal.ii on a linux > machine equipped with CentOS7. I am having quite

Re: [deal.II] Re: error during installation with spack on CentOS7

2019-10-04 Thread Denis Davydov
cc > > cxx: /usr/local/bin/g++ > > f77: /usr/local/bin/gfortran > > fc: /usr/local/bin/gfortran > > spec: gcc@9.2.0 > > target: x86_64 > > sorts out the issue. > > > Il giorno mercoledì 2 ottobre 2019 19:26:06 UTC+2, Denis Davyd

Re: [deal.II] Re: error during installation with spack on CentOS7

2019-10-02 Thread Denis Davydov
Hi Alberto, Looks like the issue is known to Spack community: https://github.com/spack/spack/issues/11224 where there is also a possible source of the problem you can try as a fix (un-do on-line PR). Regards, Denis. On Wednesday, October 2, 2019 at 3:14:46 PM UTC+2, Bruno Turcksin wrote: > >

[deal.II] Re: Issue with boost serialization and spack?

2019-10-02 Thread Denis Davydov
On Wednesday, October 2, 2019 at 11:50:53 AM UTC+2, Konrad Simon wrote: > > Thank you, Denis. I use a pretty stupid (but simple) workaround: I setup >>> and compile deal.ii myself since all dependencies are compiled and use the >>> cmake command used by spack. That works. And I do not get the

[deal.II] Re: Issue with boost serialization and spack?

2019-10-01 Thread Denis Davydov
Hi Konrad, On Monday, September 30, 2019 at 3:55:20 PM UTC+2, Konrad Simon wrote: > > Thank you, Denis. I use a pretty stupid (but simple) workaround: I setup > and compile deal.ii myself since all dependencies are compiled and use the > cmake command used by spack. That works. And I do not get

[deal.II] Re: error during installation with spack on CentOS7

2019-10-01 Thread Denis Davydov
Hi Alberto, Such issues should ideally be reported to Perl, because that's the issue with their package. Or at least to Spack in a hope that the community can come up with some patch to workaround the build issue in Perl. For you to go on simply tell Spack to use Perl from system: perl:

[deal.II] Re: Issue with boost serialization and spack?

2019-09-29 Thread Denis Davydov
p.s. long discussion on serialization bug in Boost is here https://github.com/boostorg/serialization/pull/79 Frankly, I would not be surprized that 1.62 has issues as well... On Saturday, September 28, 2019 at 8:02:19 PM UTC+2, Konrad Simon wrote: > > Dear deal.ii community, > > I am having a

[deal.II] Issue with boost serialization and spack?

2019-09-28 Thread Denis Davydov
Hi, Boost serializstion was broken in several versions of boost, that’s why it’s blacklisted in Spack package for some and has a patch for others. It looks like your setup of compiler/platform reveal that it’s broken in another case as well. To be sure you can check CMake log in build folder

[deal.II] Soli mechanics C++/FEM developer position in Germany, Nürnberg (Siemens SISW / JobID 123744)

2019-09-25 Thread Denis Davydov
is already happening, so please don't postpone the application if you are interested. https://jobs.siemens-info.com/jobs/123744 Sincerely, Denis Davydov -- 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

[deal.II] Re: L2 norm of distribution solution

2019-03-04 Thread Denis Davydov
Hi Jean, Minor unrelated note to your snippet of manually written L2 norm: have a look at https://www.dealii.org/developer/doxygen/deal.II/namespaceUtilities_1_1MPI.html which has plenty of template wrappers for MPI functions that can make life much much easier, including sending objects that

[deal.II] Re: command line compilation error on a linux machine using spack installation of deal.ii dev

2019-01-28 Thread Denis Davydov
Hi Nicola On Monday, January 28, 2019 at 11:35:33 AM UTC+1, Nicola Giuliani wrote: > > Dear all, > > I have just updated my spack installation of deal.ii on Linux Mint (18) > machine. > by updated you mean you pulled the recent version and installed the deal.II via Spack? What commit are you

[deal.II] Re: Trouble Installing: "undefined symbol: cblas_ctrmv"

2019-01-25 Thread Denis Davydov
Hi Kyle On Friday, January 25, 2019 at 9:11:35 AM UTC+1, ky...@math.uh.edu wrote: > > Hi Denis, > > I did see both of the issues raised on github before I posted, but it > wasn't really clear what the resolution was other than its a gsl dependency > problem. > I would say from our side we

[deal.II] Re: Trouble Installing: "undefined symbol: cblas_ctrmv"

2019-01-24 Thread Denis Davydov
Hi Kyle, According to your config, deal.II picked up gslcblas.so: GSL_LIBRARIES = /usr/lib64/libgsl.so;/usr/lib64/libgslcblas.so Could you check if it contains the missing symbol, something like: $ nm -g

[deal.II] Re: Trouble building from source on MacOS

2018-11-06 Thread Denis Davydov
On Monday, November 5, 2018 at 9:20:21 PM UTC, mrjonm...@gmail.com wrote: > > Thanks for the suggestion. I tried building with candi today, but it > failed somewhere during the p4est-2.0/FAST build from the look of it. I've > been using macports instead of homebrew, and I'm wondering if some

Re: [deal.II] Re: Function to output stress and strain

2018-11-03 Thread Denis Davydov
Hi Shawn, > 3 нояб. 2018 г., в 2:28, Yuxiang Wang > написал(а): > > Hi Denis, > > Thank you for the pointer! This is very helpful. > > The below is my understanding (and please let me know if I am wrong): > > 1. If we do the L2 projection over a domain of elements, then it smooths the >

[deal.II] Re: Error in installing deal.ii with spack on CentOs7

2018-10-24 Thread Denis Davydov
Hi Alberto, I figured out what's happening. The issue you see is NOT related to what me and JP suggested. It is a separate issues related to constraints on compilers from suite-sparse. I created a PR in spack to clarify this: https://github.com/spack/spack/pull/9622/ Once it's merged, you

Re: [deal.II] Error in installing deal.ii with spack on CentOs7

2018-10-23 Thread Denis Davydov
On Tuesday, October 23, 2018 at 6:39:46 PM UTC+2, Denis Davydov wrote: > > Unfortunately I can reproduce you error in a clean environment on my Ubuntu > machine. But I am glad that you solved the issue. I meant “can NOT reproduce”, sorry for the typo. Regards, Denis . -- Th

Re: [deal.II] Error in installing deal.ii with spack on CentOs7

2018-10-23 Thread Denis Davydov
> Alberto Salvadori > Dipartimento di Ingegneria Civile, Architettura, Territorio, Ambiente e di > Matematica (DICATAM) > Universita` di Brescia, via Branze 43, 25123 Brescia > Italy > tel 030 3711239 > fax 030 3711312 > > e-mail: > alberto.salvad...@unibs.it

Re: [deal.II] Error in installing deal.ii with spack on CentOs7

2018-10-23 Thread Denis Davydov
Alberto, Did you reset Spack to the current recommended version, namely e38f39e4eafeaa6daed580cece935141e5d8f04b (I edited the wiki 7 days ago)? I double checked that 9.0.1 has no issues with concretization there with empty packages.yaml settings. My guess would be that (i) either you used

Re: [deal.II] Error in installing deal.ii with spack on CentOs7

2018-10-22 Thread Denis Davydov
Yes, JP is correct that it has to do with incompatible requirements on suitesparse from Trilinos and latest release of PETSc. To overcome this I recently disabled suitesparse by default in Trilinos, but it could be that the commit hash we recommend currently on wiki does not have this. I will

Re: [deal.II] Question on resolving chains of constraints containing both periodic and hanging node constraints

2018-08-13 Thread Denis Davydov
Thanks for the MWE, Sambit. I created a Github issue to track this further https://github.com/dealii/dealii/issues/7053 Denis. On Monday, August 13, 2018 at 12:01:07 AM UTC+2, Sambit Das wrote: > > Dear Prof. Bangerth, > > I have now reproduced the above issue in the attached minimal example.

[deal.II] Re: Linear Elastic Fracture Mechanics

2018-05-23 Thread Denis Davydov
Hi Francesca, As for the continuous enrichment part of X-FEM (i.e. crack-tip) you can look into FE_Enriched class and the paper with implementation details. Note the key difference in point-of-view: FE_Enriched does

[deal.II] Re: Mac OS X 10.13.4 Installation problem

2018-05-11 Thread Denis Davydov
Hi Jon, Try this .dmg https://github.com/luca-heltai/dealii/releases/tag/v9.0.0-rc1 If that won't work, you can try building with Spack https://github.com/dealii/dealii/wiki/deal.II-in-Spack that's what I use on macOS. You would need to first compile gcc with it, see the wiki page. Regards,

[deal.II] Re: Mac testers wanted

2018-05-11 Thread Denis Davydov
Luca, the link does not seem to contain dmg. You probably wanted to give a link to your fork, i.e. https://github.com/luca-heltai/dealii/releases/tag/v9.0.0-rc1 Cheers, Denis On Sunday, May 6, 2018 at 11:51:19 AM UTC+2, Luca Heltai wrote: > > Sorry. The address is the following: > >

[deal.II] Re: cmake . returns error on MAC OS XI Captain version 10.11.6 upon compiling dealii-8.5.0-brew.dmg

2018-05-11 Thread Denis Davydov
dmg files > associated to previous versions of deal.ii and cmake, which was perfectly > working. > When I downloaded the new versions today, it returned these errors. > > Best, > Wakil > > On Friday, May 11, 2018 at 9:04:17 PM UTC+1, Denis Davydov wrote: >> >> Hi, >

[deal.II] Re: cmake . returns error on MAC OS XI Captain version 10.11.6 upon compiling dealii-8.5.0-brew.dmg

2018-05-11 Thread Denis Davydov
today, it returned these errors. > > Best, > Wakil > > On Friday, May 11, 2018 at 9:04:17 PM UTC+1, Denis Davydov wrote: >> >> Hi, >> >> Make sure you have XCode installed as well as command line >> tools: xcode-select --install >> >> Regards,

[deal.II] Re: cmake . returns error on MAC OS XI Captain version 10.11.6 upon compiling dealii-8.5.0-brew.dmg

2018-05-11 Thread Denis Davydov
Hi, Make sure you have XCode installed as well as command line tools: xcode-select --install Regards, Denis. On Friday, May 11, 2018 at 7:36:48 PM UTC+2, Wakil Sarfaraz wrote: > > Hi all, > I have been away from deal.ii for almost two years. > I have come back and wanted to install the most

[deal.II] Re: Why fe.shape_value( const unsigned int i, const Point< dim > & p ) return a negative number?

2018-05-05 Thread Denis Davydov
Hi, it's perfectly fine for a general FE shape functions to be negative at some points, that's clearly the case for quadratic http://hplgit.github.io/INF5620/doc/pub/sphinx-fem/._main_fem003.html#fem-approx-fe-fig-p2 Denis. On Saturday, May 5, 2018 at 3:11:24 AM UTC+2, Zhao Yidong wrote: > >

Re: [deal.II] Re: New step tutorial elastic wave equation with PMLs, complex-valued algebra

2018-04-29 Thread Denis Davydov
> On 30 Apr 2018, at 04:54, Wolfgang Bangerth <bange...@colostate.edu> wrote: > > On 04/28/2018 10:36 PM, Denis Davydov wrote: >> As far as as recall there just a few things left related to complex numbers. >> The biggest one is complex-valued Dirichlet cons

[deal.II] Re: New step tutorial elastic wave equation with PMLs, complex-valued algebra

2018-04-28 Thread Denis Davydov
Hi Daniel, Thanks for willing to contribute the tutorial. As far as as recall there just a few things left related to complex numbers. The biggest one is complex-valued Dirichlet constraints in ConstraintMatrix object https://github.com/dealii/dealii/issues/1760 That's not possible yet.

[deal.II] Re: error running after update

2018-04-24 Thread Denis Davydov
p.s. given recent updates to petsc/slepc 3.9 you would need to install a current development version of deal.II, i.e. spack install dealii@develop The soon-to-be-release 9.0 will support new petsc/slepc. On Wednesday, April 25, 2018 at 12:04:06 AM UTC+2, Denis Davydov wrote: > > @Jane >

[deal.II] Re: error running after update

2018-04-24 Thread Denis Davydov
@Jane If you need to get it going soon, try following https://github.com/dealii/dealii/wiki/deal.II-in-Spack Roughly it's only 3 steps (assuming that you have XCode and command-line tools): 1. install gcc with spack 2. configure gfortran to be used with clang

[deal.II] Re: multiply constrained dofs (hanging nodes+periodic) fails a simple test case

2018-04-11 Thread Denis Davydov
On Wednesday, April 11, 2018 at 7:00:18 PM UTC+2, Sambit Das wrote: > > Hi Denis, > > >> I don't think that's the case. The domain is indeed periodic, but this is >> completely detached from location of support/nodal points. >> Same applies to geometry, you will have different coordinates of

[deal.II] Re: multiply constrained dofs (hanging nodes+periodic) fails a simple test case

2018-04-10 Thread Denis Davydov
Hi Sambit, On Saturday, April 7, 2018 at 6:51:37 PM UTC+2, Sambit Das wrote: > > Hello dealii-team, > > I have created a failing test case in serial when hanging nodes+periodic > constraints are mixed. > > *The algorithm of the test is follows: (attached * >

[deal.II] Visual Studio Code extension for syntax highlighting in parameter files

2018-03-30 Thread Denis Davydov
Hi all, Looks like I have a new favourite editor, so I added a syntax highlighting plugin for *.prm* files https://marketplace.visualstudio.com/items?itemName=davydden.dealii-prm Regards, Denis -- The deal.II project is located at http://www.dealii.org/ For mailing list/forum options, see

[deal.II] GUI to debug MPI code in Visual Studio Code

2018-03-27 Thread Denis Davydov
Dear all, I apologise for the off-topic, but since many of you use deal.II with MPI and consequently sometimes need to debug your programs, I cross-post the information below in our group. Developers of Cpptools plugin for Visual Studio Code[1]

[deal.II] Re: dealii 8.5.1 installation issue (spack, docker, debian)

2018-03-11 Thread Denis Davydov
Marquito, A few things to add to what Bruno says: On Monday, March 12, 2018 at 2:40:37 AM UTC+1, Bruno Turcksin wrote: > > Marquito, > > On Sunday, March 11, 2018 at 9:27:40 AM UTC-4, Marquito Forrest wrote: >> >> >> In summary the situation is: >> - Debian testing image (to get recent gcc) >> -

[deal.II] Re: increment Dirichlet boundary condition

2018-02-24 Thread Denis Davydov
preconditioner); > > 5) > constraints.distribute (image_solution); > > The problem is that left boundary is fixed, up and down is under zero > force, and right boundary is displaced to the right. > The solution without 5) is zero, and with 5) it is zero everywhere outside &g

[deal.II] Re: increment Dirichlet boundary condition

2018-02-22 Thread Denis Davydov
Hi IIiya, On Thursday, February 22, 2018 at 11:55:33 AM UTC+1, Bryukhanov Ilya wrote: > > Denis, thanks a lot for the answer! > > I think that on the first step I can use usual > "interpolate_boundary_values + apply_boundary_values" functions, > the outline I gave above is agnostic to "first

[deal.II] Re: increment Dirichlet boundary condition

2018-02-21 Thread Denis Davydov
s. > > > Can you give some advice how to make it correct? > > > <https://lh3.googleusercontent.com/-O_1geVdTAOc/Wo2eOCPcdWI/A44/s_OauNpGhwcv2d4h3nmBinL40UhP7-S7ACLcBGAs/s1600/iter0.jpg> > > <https://lh3.googleusercontent.com/-wHZAFJbU0bI/Wo2egOHamAI/AAAA

[deal.II] Re: increment Dirichlet boundary condition

2018-02-20 Thread Denis Davydov
Hi Ilya, I am not away of principally simple solution, the RHS simply contains your bilinear form times interpolated values at constrained DoFs. What you can do is to loop over a subset of cells (those which are at the boundary), still assemble the local matrix and do

Re: [deal.II] Re: Error in installing deal.ii with spack on linux openSuse

2018-02-19 Thread Denis Davydov
Hi Alberto, Just a quick explanation why this happens: this is a current limitation in how Spack tries to find a configuration of packages which satisfies input request. At the point when you type: spack install dealii it does not yet know which version to use (you may have your custom

[deal.II] Re: Problem compiling deal_ii with PETSc

2018-02-14 Thread Denis Davydov
Hi, You may want to try one of the source-based installers listed here https://www.dealii.org/download.html Denis. On Wednesday, February 14, 2018 at 2:55:34 AM UTC+1, Daipayan Sarkar wrote: > > Hello All, > > I am facing difficulty to link PETSc to dealii. Following are the steps > that I

[deal.II] ECCM 2018 - High Performance Geometric Multigrid Finite Element Methods

2018-02-02 Thread Denis Davydov
Dear all, The deadline for abstract submission has passed, but it’s still possible to submit one online until Monday 05.02. Regards Denis -- 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

Re: [deal.II] Re: order of cells in two MatrixFree objects on the same Triangulation and Quadrature but different FE spaces

2018-01-29 Thread Denis Davydov
those options. Regards, Denis. On Monday, January 29, 2018 at 5:13:58 PM UTC+1, Denis Davydov wrote: > > Hi Martin, > > Thanks for confirming that it's indeed possible. > > On Monday, January 29, 2018 at 4:34:07 PM UTC+1, Martin Kronbichler wrote: >> >> Dear

Re: [deal.II] Re: order of cells in two MatrixFree objects on the same Triangulation and Quadrature but different FE spaces

2018-01-29 Thread Denis Davydov
Hi Martin, Thanks for confirming that it's indeed possible. On Monday, January 29, 2018 at 4:34:07 PM UTC+1, Martin Kronbichler wrote: > > Dear Denis, > > p.s. the mapping is the same for both cases. > > On Monday, January 29, 2018 at 4:16:48 PM UTC+1, Denis Davydov wrot

[deal.II] Re: order of cells in two MatrixFree objects on the same Triangulation and Quadrature but different FE spaces

2018-01-29 Thread Denis Davydov
p.s. the mapping is the same for both cases. On Monday, January 29, 2018 at 4:16:48 PM UTC+1, Denis Davydov wrote: > > Dear all, > > I am playing around with something in the following setup: > 1. I have a single p::d::Tria > 2. two different DoFHandler's using scalar FE_Q of

[deal.II] order of cells in two MatrixFree objects on the same Triangulation and Quadrature but different FE spaces

2018-01-29 Thread Denis Davydov
Dear all, I am playing around with something in the following setup: 1. I have a single p::d::Tria 2. two different DoFHandler's using scalar FE_Q of different degrees 3. The same quadrature rule (QGauss) used for both cases 4. Two different MatrixFree objects I am not 100% sure, but it looks

[deal.II] Re: PetSc Hybrid MPI-OPENMP Parallelization with Spack Dealii

2018-01-24 Thread Denis Davydov
Hi, On Wednesday, January 24, 2018 at 9:13:06 PM UTC+1, Sukhminder Singh wrote: > > I installed Spack package of Dealii on a machine with 32 cores (48 virtual > cores) and ran a petsc-parallel code. If I run using only one MPI process, > then I only get one core running for the solver part.

[deal.II] Re: Trouble getting deal.II working on bgq

2018-01-01 Thread Denis Davydov
Hi, Jie On Sunday, December 31, 2017 at 10:55:04 PM UTC+1, Jie Cheng wrote: > > > Is there a simple way to get deal.II working with GCC 4.7.2? If not, how > to install a newer GCC on a cross-compiling system like bgq? > you might try asking this at the SPACK (Supercomputer PACKage manager)

[deal.II] Re: Is deal.ii suitable for civil engineering problems?

2017-12-15 Thread Denis Davydov
Hi, Deal.II has been used in numerous applications, including but not limited to solid mechanics, see publication lists http://www.dealii.org/publications.html and also publications of my colleague Jean-Paul https://ltm-en.cms.rrze.uni-erlangen.de/person/pelteret-jean-paul-ph-d/ who is

[deal.II] Re: surprising results from DoFHandler.locally_owned_dofs() calls in the fully distributed triangulation

2017-12-15 Thread Denis Davydov
Hi, On Friday, December 15, 2017 at 11:14:24 PM UTC+1, Marek Čapek wrote: > > Hello, > I have downloaded and installed 8.5.1 version of dealii library > using candi. I needed to use calls of > > const IndexSet > & > DoFHandler >

Re: [deal.II] Re: Cmake-MPI

2017-12-14 Thread Denis Davydov
Or use Spack which makes sure that only note instance of each dependency (such as MPI) is used to build deal.ii and all its dependencies: https://github.com/dealii/dealii/wiki/deal.II-in-Spack Ps. As for the multiple MPI on the system, it’s perfectly valid idea as long as you know what you

[deal.II] ECCM 2018 - High Performance Geometric Multigrid Finite Element Methods

2017-12-11 Thread Denis Davydov
ration, accommodation, conference venue, technical and social programs can be found at the conference website: http://www.eccm-ecfd2018.org. We are looking forward to your contribution and to seeing you at the meeting. Best regards, Martin Kronbichler (TUM, Germany) Denis Davydov (FAU, Germany) Guido Ka

Re: [deal.II] Re: Spurious eigenvalues

2017-12-01 Thread Denis Davydov
On Friday, December 1, 2017 at 2:50:38 PM UTC+1, Timo Heister wrote: > > > They're always going to be there because we keep constrained nodes in > the > > linear system. > > If we modify the way ConstraintMatrix operates, we could work around > this though: > but there is really no need,

[deal.II] Re: Spurious eigenvalues

2017-11-30 Thread Denis Davydov
Hi Bruno, AFAIK, there is a simple solution: make initial vector (or subspace) perpendicular to those constrained entries. That is, if you do Lancoz, set random initial vector and then zero out constrained DoFs. Then being Krylov-based method it should form subspaces {x, Ax, A^2x,...}

Re: [deal.II] Re: Isogeometric analysis

2017-11-23 Thread Denis Davydov
Hi Luca, do you want to move some of those classes/functionality to deal.II? I think that would great. Cheers, Denis. On Wednesday, November 22, 2017 at 9:52:38 AM UTC+1, Luca Heltai wrote: > > Dear Yaakov, > > did you even try google? > > :) > > google search: dealii isogeometric analysis

Re: [deal.II] New Mac OSX brew package

2017-11-09 Thread Denis Davydov
> On 9 Nov 2017, at 23:12, luca.heltai wrote: > > It does not compile, anyway… > > :D > > Maybe Denis can help: I get the following when trying to compile pkg-config > using gcc installed with spack: a lot of things break on macOS when compiling with GCC. For

[deal.II] Re: New Mac OSX brew package

2017-11-09 Thread Denis Davydov
nice! @Timo: If I am not mistaken, it's Apple's Clang 9.0.0 + gfortran 7.2.0. On Thursday, November 9, 2017 at 9:41:52 AM UTC+1, Luca Heltai wrote: > > Dear All, > > I just finished uploading a new brew based package for deal.II with a > 9.0pre.1 version: > >

Re: [deal.II] How to add addtional point to enrichment functions (FE_Enriched)

2017-11-02 Thread Denis Davydov
ichment function , > xi is the dof coordinate of the i-th standard basis function. > > That’s why I think I need to look for the corresponding xi point during > assembly… > > Thank you for your patience. > > > >> On Nov 2, 2017, at 10:56 AM, Denis Davydov &l

Re: [deal.II] How to add addtional point to enrichment functions (FE_Enriched)

2017-11-02 Thread Denis Davydov
e coordinate of the dof > > > and I was also thinking that I would probably need to work with DG methods. > But I can try the 1D test you suggested first to find out the continuity of > my functions > > Thank you for your help. > > Edith > > &

[deal.II] Re: Compilation error during the use of CellDataStorage datastructure

2017-10-29 Thread Denis Davydov
Hi Phani, Jean-Paul is right that one could use a less strict assert. But that's won't help you with actually using ContinuousQuadratureDataTransfer to transfer the data. That's the main purpose of CellDataStorage -- provide association functionality between cells and collection of data objects

[deal.II] Re: hp and FE_Enriched

2017-10-20 Thread Denis Davydov
Hi Edith On Friday, October 20, 2017 at 8:06:39 AM UTC+2, Edith Sotelo wrote: > > Hello, > > I am trying to use different enrichment functions in different parts of my > domain. For that I am also using hp::FECollection. > > The issue is that my solution looks discontinuous at the interface

[deal.II] Re: Error when writing files using write_vtu_header

2017-10-17 Thread Denis Davydov
AFAIK there is no know problem. Make sure you write this only from a single MPI core, though. Otherwise you will have multiple MPI cores trying to write into the same file. Regards, Denis. On Tuesday, October 17, 2017 at 8:43:55 AM UTC+2, Maxi Miller wrote: > > > Sometimes when running my

Re: [deal.II] Re: Error when applying initial values to MPI::Vector in multiple dimensions

2017-10-16 Thread Denis Davydov
. Regards, Denis. > On 16 Oct 2017, at 21:44, 'Maxi Miller' via deal.II User Group > <dealii@googlegroups.com> wrote: > > Yes, .interpolate() works fine. But what is the difference between > interpolate() and project()? > > Am Montag, 16. Oktober 2017 08:54:02 UTC+2 schr

[deal.II] Re: Error when applying initial values to MPI::Vector in multiple dimensions

2017-10-16 Thread Denis Davydov
Or you may want to use interpolate if this is enough https://www.dealii.org/developer/doxygen/deal.II/namespaceVectorTools.html#a05db6c8cebf924b417dd92f525efe3db Regards, Denis On Friday, October 13, 2017 at 11:05:01 AM UTC+2, Maxi Miller wrote: > > I try to apply initial values to a vector

[deal.II] Re: Deal for Mac OS 10.13

2017-10-10 Thread Denis Davydov
Hi, I successfully build deal.II with all dependencies on macOS High Sierra XCode 9 with Spack https://github.com/dealii/dealii/wiki/deal.II-in-Spack (Clang 9.0 + gfortran from GCC 7.2.0) BUT you would need to wait until this PR with minor fixes is merged:

[deal.II] Re: Output the results at Gauss points

2017-10-10 Thread Denis Davydov
Hi, Please search the forum, this question has been discussed numerous times in past, for example: https://groups.google.com/forum/?fromgroups#!searchin/dealii/quadrature$20points|sort:relevance/dealii/FW9Jy5_CUGY/JK6OSFWrAQAJ

[deal.II] Re: Unit test in user project with .prm and .data input files to be read

2017-10-06 Thread Denis Davydov
Vinayak, You are mixing several things, it seems. What you should do in your unit test is something along the lines: ParameterHandler prm; MyLovelyParameters::declare_parameters(prm); // parameters std::ostringstream oss; oss << "set Something = 3"

[deal.II] Re: Vector value problem with FE_Enriched

2017-10-05 Thread Denis Davydov
Hi Edith, On Thursday, October 5, 2017 at 5:26:04 PM UTC+2, Edith Sotelo wrote: > > Hi deal ii community , > > I am trying to solve a similar problem as tutorial 29: complex valued > -Helmoholtz equation but in this case each component of my 2D vector (real, > imaginary ) is a FE-Enriched

[deal.II] Re: Unit test in user project with .prm and .data input files to be read

2017-10-04 Thread Denis Davydov
Hi Vinayak, Indeed, something like SOURCE_DIR + "/relative/path/to/auxiliary_files.dat" is what you need. Regards, Denis. On Wednesday, October 4, 2017 at 8:37:23 PM UTC+2, Daniel Arndt wrote: > > Vinayak, > > you should be able to use the SOURCE_DIR preprocessor variable for this >

Re: [deal.II] Re: about deal.II with CUDA C programming acceleration

2017-09-20 Thread Denis Davydov
Hi Chih-Che > 21 сент. 2017 г., в 6:33, Chih-Che Chueh написал(а): > > Hi Wolfgang, > > >> I think you are expecting too much of Bruno. He has a day job as well, for >> which he is paid. I think you will need to figure out the installation on >> your system yourself --

Re: [deal.II] Re: about deal.II with CUDA C programming acceleration

2017-09-20 Thread Denis Davydov
deal.II in Spack is being extended for CUDA https://github.com/LLNL/spack/pull/5402 Builds ok on Ubuntu PC with gcc 5.4.0. Chih-Che, if you still have issues, you might want to try this out. Regards, Denis. -- The deal.II project is located at http://www.dealii.org/ For mailing list/forum

[deal.II] EigenValue Problem

2017-09-19 Thread Denis Davydov
Jean-Paul is right. Most likely you don't adjust the quadrature order which breaks LU factorization of the mass matrix, used by default for Generalized Hermitian Eigenvalue Problem. Essentially your mass matrix is not positive definite anymore. Regards, Denis -- The deal.II project is

[deal.II] Re: Linking error when compiling with Trilinos

2017-09-17 Thread Denis Davydov
You might want to try one of the source-based installers for deal.II, see *Source-based Installers* https://www.dealii.org/download.html Regards, Denis. On Wednesday, September 13, 2017 at 10:58:10 AM UTC+2, Maxi Miller wrote: > > I set up a new dealII-installation on another computer, but

Re: [deal.II] Re: about deal.II with CUDA C programming acceleration

2017-09-16 Thread Denis Davydov
> On 17 Sep 2017, at 01:00, Bruno Turcksin <bruno.turck...@gmail.com> wrote: > > Denis, > > 2017-09-16 18:30 GMT-04:00 Denis Davydov <davyd...@gmail.com > <mailto:davyd...@gmail.com>>: > @Bruno I don't any experience with cuda, but do we need anyth

Re: [deal.II] Re: Workstream, number threads

2017-09-14 Thread Denis Davydov
A bit off topic: if one is not careful and mixes multithreaded Blas/Lapack + multithreading via TBB in deal.II, then calls to Lapack's invert() can take 1.371e+03s instead of 1.445e+00s ;-) p.s. threading in Spack's Openblas and friends is being reworked here

Re: [deal.II] Re: Workstream, number threads

2017-09-12 Thread Denis Davydov
On Thursday, December 29, 2016 at 11:43:15 AM UTC+1, Praveen C wrote: > > Hello Martin > > I am using openblas installed using spack. openmp seems to be disabled > > openblas@0.2.19%gcc@6~openmp+pic+shared arch=linux-opensuse20161217-x86_64 > > I think the problem was that Openblas by default

Re: [deal.II] Using deal.II logo in publication

2017-08-28 Thread Denis Davydov
FYI, this logo is done with a help of qualified (master degree) graphic designer. On Monday, August 28, 2017 at 11:09:33 PM UTC+2, Timo Heister wrote: > > Personally, I prefer the colors and font I used. I like the green dot > though! > > On Mon, Aug 28, 2017 at 5:05 PM, Deni

Re: [deal.II] Using deal.II logo in publication

2017-08-28 Thread Denis Davydov
I am fine with adjusting colours, but I like the IBM Courier font as it has relevant history behind. I believe it is this font which is currently used on a low resolution logo and to my knowledge this font is royalty free. So i would stick with it. > On 28 Aug 2017, at 17:35, Matthias Maier

Re: [deal.II] Using deal.II logo in publication

2017-08-27 Thread Denis Davydov
Paul Pelteret <jppelte...@gmail.com> > написал(а): > > Can't one just trace a quarter and mirror it? > >> On Sunday, August 27, 2017 at 10:05:00 AM UTC+2, Denis Davydov wrote: >> another take on tracing the lowres logo via Adobe Illustrator CS6. The main >> differen

Re: [deal.II] Using deal.II logo in publication

2017-08-27 Thread Denis Davydov
quarter and mirror it? > >> On Sunday, August 27, 2017 at 10:05:00 AM UTC+2, Denis Davydov wrote: >> another take on tracing the lowres logo via Adobe Illustrator CS6. The main >> difference to TImo's is the shape of yellow rim, >> which IMO is closer to the original ras

Re: [deal.II] Using deal.II logo in publication

2017-08-27 Thread Denis Davydov
another take on tracing the lowres logo via Adobe Illustrator CS6. The main difference to TImo's is the shape of yellow rim, which IMO is closer to the original raster logo. But indeed, there is no hope to keep it symmetric based on lowres input, unless someones jus draws it from scratch :-)

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

2017-08-14 Thread Denis Davydov
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

2017-08-13 Thread Denis Davydov
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

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

2017-07-25 Thread Denis Davydov
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

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

2017-07-13 Thread Denis Davydov
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,

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

2017-07-13 Thread Denis Davydov
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

2017-07-12 Thread Denis Davydov
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] Re: CMake extra libraries?

2017-06-17 Thread Denis Davydov
On Friday, June 16, 2017 at 5:43:27 PM UTC+2, Wolfgang Bangerth wrote: > > On 06/15/2017 03:32 PM, Bruno Turcksin wrote: > > The problem is that > > Trilinos botched their TrilinosConfig.cmake. What we do is load the > > TrilinosConfig.cmake to get their flags but if they don't put them in,

Re: [deal.II] Re: CMake extra libraries?

2017-06-15 Thread Denis Davydov
> On 15 Jun 2017, at 19:38, Victor Eijkhout wrote: > > You seem to be saying that I need to add something to a file that is > generated by cmake. Nope. You add things to **your** CMakeList.txt > > And even then, it seems to be about a file

[deal.II] CMake extra libraries?

2017-06-08 Thread Denis Davydov
U need to build with current master branch, look at commit message here https://github.com/dealii/dealii/pull/4437 essentially u would get the location of Trilinos used by deal.ii and link in extra libs Regards, Denis -- The deal.II project is located at http://www.dealii.org/ For mailing

[deal.II] Re: state of dealii in complex arithmetics

2017-05-23 Thread Denis Davydov
On Tuesday, May 23, 2017 at 5:22:44 PM UTC+2, Juan Carlos Araujo Cabarcas wrote: > > Dear all, > > There are features in SLEPc 3.7 that I am interested in, and will try to > make a fresh re-installation soon. > > I have been using deal.II 8.3 with complex arithmetic’s from the branch: >

[deal.II] Re: Does dell.II support comformal mesh adaption.

2017-05-18 Thread Denis Davydov
Hi, On Thursday, May 18, 2017 at 12:49:32 AM UTC+2, Peng Ding wrote: > > Dear sir: >I want to use the mesh adaptive capability of dell.II for my > incompressible flow FVM computation. I want to know that does dell.II > suport conformal mesh adaption(do not have hanging node in the

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

2017-05-14 Thread Denis Davydov
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

2017-05-11 Thread Denis Davydov
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

2017-05-09 Thread Denis Davydov
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

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

2017-05-09 Thread Denis Davydov
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

2017-05-09 Thread Denis Davydov
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] AssertDimension (partition_blocks[partition], task_info.n_blocks) when calling MatrixFree::reinit() for finest level in GMG

2017-05-05 Thread Denis Davydov
Dear all, I am hitting an AssertDimension (partition_blocks[partition], task_info.n_blocks); when initializing MatrixFree object for the finest level of the mesh. This happens at 2nd h-adaptive step with 3 a-priori global refinements. The part of the code during setup of each level is rather

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