Re: [Yade-dev] Odp: Re: Yade for LTS Ubuntu 18.04
Hi Anton, I confirm that your latest commit fixes the polyhedra crush problem :) Do you know what caused the freeze? best regards Janek Dnia 16 lutego 2018 23:12 Anton Gladky gladky.an...@gmail.com napisał(a): Dear all, thanks all for the effective and fast contribution resolving CGAL issue! I will try to fix polyhedron-crash test as soon as possible and release the new minor Yade version. Best regards Anton On Feb 16, 2018 17:27, Luc Scholteslscholte...@gmail.com wrote: Hi guys, Just a remark: the latest fix seems to solve the random behavior observed several months ago with the FlowEngine: answers.launchpad.net answers.launchpad.net yade/+question/659557 This is great :) However, now, DFNFlow does not give the expected behavior: it seems that the fractured cells are not identified correctly. Ill try to work on it asap. Best Luc 2018-02-14 15:12 GMT+01:00 Janek Kozicki (yade-dev) janek_li...@wp.pl : This is awesome. Thank you very much. I have just compiled the latest version, and I confirm that DEM-PFV test works. Finding uninitialized variables can be a super difficult job, hence: congratulations! And I must say that I am surprised why there was no warning about this variable. I specifically fixed all the remaining warnings in my second commit, just in hope of avoiding this kind of situation. The only warnings that I get right now are from external libraries: vtk and numpy. There must be some missing compiler flag, which allowed this uninitialized variable without a warning. Maybe we could try to find this missing compiler flag to enable uninitialized warning. Or maybe the problem was that this part of code was not instatinated in time when the warning could trigger. Regarding the checkPolyhedraCrush.py, for the time being I have locally (without a commit) commented out those four lines of code at the end which invoke O.Run(). That makes all tests to pass and debian package is successfully built. Of course I am not committing this commenting out. We need to think about this a bit. For the moment I am only 100% sure that the problem is due to CGAL 4.11, because it always works in 4.9. If we cannot fix this, then perhaps we release yade with cgal 4.11 support, but without polyhedra crush support. best regards Janek On 14 Feb 2018, 11:19 +0100, Bruno Chareyre bruno.chareyre@grenoble-inp.f r , wrote: Hi Robert, Congrats for finding the bug and thanks for fixing. On 02/13/2018 11:55 PM, Robert Caulk wrote: the issue was compiler related. GCC 5.4 on ubuntu 16.04 initialized factorizeOnly to false by default, while GCC 7.2 on ubuntu 18.04 did not do this. Thats a good example of undefined behavior when using non-initialized variables... Definitely a nasty bug. Therefore, the only necessary change ended up being the explicit initialization of factorizeOnly=false. Indeed. :) In addition to the bug fix, I edited the solvers so flow.useSolvers=3 and 4 can now be used with the default CPU build. I can confirm that flow.useSolver=4 enables multicore CPU factorization, while flow.useSolver=3 sticks to 1 core factorization :-). Excellent. FYI multicore CPU factorization was faster than single core in my benchmarks, but multicore solve phase (using the factorized form) was not, it was even a bit slower than single core. Hence the distinct attributes numFactorizeThreads and numSolveThreads. Cheers Bruno _ _ Mailing list: launchpad.net launchpad.net v Post to :yade-dev@lists.launchpad.net Unsubscribe : launchpad.net launchpad.net v More help : help.launchpad.net help.launchpad.net tHelp __ _ Mailing list: launchpad.net launchpad.net v Post to :yade-dev@lists.launchpad.net Unsubscribe : launchpad.net launchpad.net v More help : help.launchpad.net help.launchpad.net tHelp __ _ Mailing list: launchpad.net launchpad.net dev Post to :yade-dev@lists.launchpad.net Unsubscribe : launchpad.net launchpad.net dev More help : help.launchpad.net help.launchpad.net ListHelp __ Mailing list: launchpad.net launchpad.net Post to : yade-dev@lists.launchpad.net Unsubscribe : launchpad.net launchpad.net More help : help.launchpad.net help.launchpad.net ___ Mailing list: https://launchpad.net/~yade-dev Post to : yade-dev@lists.launchpad.net Unsubscribe : https://launchpad.net/~yade-dev More help : https://help.launchpad.net/ListHelp
Re: [Yade-dev] Yade with CGAL 4.11
Uh, Bruno :-) I was thinking to ask you whether you have given my diff to Anton after you have modified it. Please do it, or just confirm that the one which I sent is good to go (which isn’t optimal due to too many #ifdefs as you mentioned earlier). best regards Janek On 27 Nov 2017, 20:04 +0100, Anton Gladky <gladky.an...@gmail.com>, wrote: > Hi all, > > is there any progress on fixing this issue? I have disabled CGAL for > Debian builds, but it would be good to switch it on again. > > Also the stable Yade version is almost one year old. It is time to release > something newer soon. If there are some volunteers to go through > existing bugs on launchpad [1] and fix/close/react on some of them, > it would be good. > > I will probably be able to prepare a release at the beginning of 2018. > > [1] https://bugs.launchpad.net/yade > > Best regards > > Anton > > > 2017-11-07 19:35 GMT+01:00 Bruno Chareyre <bruno.chare...@grenoble-inp.fr>: > > > > > > On 11/07/2017 06:47 PM, Janek Kozicki wrote: > > > > > > I just feel a little uneasy about cross_product of two > > > (sphere-sphere) pairs ;) > > > > > > Well... after admitting that spheres can be mutually orthogonal (which is > > really the case) cross product is fine... :) > > But you are right, here cross product is really ordinary cross_product. > > Bruno > > > > > > > > > > _______ > > Mailing list: https://launchpad.net/~yade-dev > > Post to : yade-dev@lists.launchpad.net > > Unsubscribe : https://launchpad.net/~yade-dev > > More help : https://help.launchpad.net/ListHelp > > ___ > Mailing list: https://launchpad.net/~yade-dev > Post to : yade-dev@lists.launchpad.net > Unsubscribe : https://launchpad.net/~yade-dev > More help : https://help.launchpad.net/ListHelp ___ Mailing list: https://launchpad.net/~yade-dev Post to : yade-dev@lists.launchpad.net Unsubscribe : https://launchpad.net/~yade-dev More help : https://help.launchpad.net/ListHelp
Re: [Yade-dev] : Compilation on K/Ubuntu 18.04
> CGAL::Regular_triangulation_cell_base_3 >, > CGAL::Boolean_tag, CGAL::Boolean_tag >, CGAL::Sequential_tag>; > Lock_data_structure_ = CGAL::Default; CGAL::Triangulation_3<GT, Tds, > Lock_data_structure>::Cell_handle = > CGAL::internal::CC_iterator<CGAL::Compact_container<CGAL::Alpha_shape_cell_base_3<CGAL::Epick, > CGAL::Triangulation_cell_base_with_info_3<DFNCellInfo, CGAL::Epick, > CGAL::Regular_triangulation_cell_base_3<CGAL::Epick, > CGAL::Triangulation_cell_base_3<CGAL::Epick, > CGAL::Triangulation_ds_cell_base_3<CGAL::Triangulation_data_structure_3<CGAL::Alpha_shape_vertex_base_3<CGAL::Epick, > CGAL::Triangulation_vertex_base_with_info_3<DFNVertexInfo, CGAL::Epick, > CGAL::Regular_triangulation_vertex_base_3 >, > CGAL::Boolean_tag, CGAL::Boolean_tag >, > CGAL::Alpha_shape_cell_base_3<CGAL::Epick, > CGAL::Triangulation_cell_base_with_info_3<DFNCellInfo, CGAL::Epick, > CGAL::Regular_triangulation_cell_base_3 >, > CGAL::Boolean_tag, CGAL::Boolean_tag >, CGAL::Sequential_tag> > > >, CGAL::Hidden_points_memory_policy<CGAL::Boolean_tag >, > std::__cxx11::list<CGAL::Weighted_point_3, > std::allocator<CGAL::Weighted_point_3 > > > >, > CGAL::Boolean_tag, CGAL::Boolean_tag >, CGAL::Default, > CGAL::Default, CGAL::Default>, false>; CGAL::Triangulation_3<GT, Tds, > Lock_data_structure>::Point = CGAL::Weighted_point_3; > CGAL::Triangulation_3<GT, Tds, Lock_data_structure>::Vertex_handle = > CGAL::internal::CC_iterator<CGAL::Compact_container<CGAL::Alpha_shape_vertex_base_3<CGAL::Epick, > CGAL::Triangulation_vertex_base_with_info_3<DFNVertexInfo, CGAL::Epick, > CGAL::Regular_triangulation_vertex_base_3<CGAL::Epick, > CGAL::Triangulation_ds_vertex_base_3<CGAL::Triangulation_data_structure_3<CGAL::Alpha_shape_vertex_base_3<CGAL::Epick, > CGAL::Triangulation_vertex_base_with_info_3<DFNVertexInfo, CGAL::Epick, > CGAL::Regular_triangulation_vertex_base_3 >, > CGAL::Boolean_tag, CGAL::Boolean_tag >, > CGAL::Alpha_shape_cell_base_3<CGAL::Epick, > CGAL::Triangulation_cell_base_with_info_3<DFNCellInfo, CGAL::Epick, > CGAL::Regular_triangulation_cell_base_3 >, > CGAL::Boolean_tag, CGAL::Boolean_tag >, CGAL::Sequential_tag> > > > >, CGAL::Boolean_tag, CGAL::Boolean_tag >, CGAL::Default, > CGAL::Default, CGAL::Default>, false>] > locate(const Point & p, Vertex_handle hint, > ^~ > > > The installed version of CGAL is 4.11, see below: > > yade@ubuntu-yade:~$ dpkg -l | grep cgal > ii libcgal-dev:amd64 4.11-2build1 > amd64 C++ library for computational geometry (development files) > ii libcgal13:amd64 4.11-2build1 > amd64 C++ library for computational geometry > > So my question here is if someone else run into this problem or not. And did > someone fix it? > > Note that when deactivating PFVFLOW and TWOPHASEFLOW compilation is just fine. > > Once this is solved I would be happy to update the install instructions for > 18.04 as this is probably what most users will be using now. But I am not > familiar with DFNFlow nor CGAL. > > Cheers, > Klaus > > ___ > Mailing list: https://launchpad.net/~yade-dev > Post to : yade-dev@lists.launchpad.net > Unsubscribe : https://launchpad.net/~yade-dev > More help : https://help.launchpad.net/ListHelp > ___ Mailing list: https://launchpad.net/~yade-dev Post to : yade-dev@lists.launchpad.net Unsubscribe : https://launchpad.net/~yade-dev More help : https://help.launchpad.net/ListHelp
Re: [Yade-dev] Yade related publication?
Hi Robert, I think that it’s a great idea. Especially if we could use it to directly improve the documentation. I suppose that virtually everything that we could write about using yade could be somehow fit into the sphinx docs. Like in Jerome said, my specific answers to two of your questions are "no” at the moment. Mostly because whatever I do, I plan to release it either as a paper, or on the documentation. However some specific scripts to calculate this, or that - they usually grow organically over time, and I guess that those would fit greatly into what you are proposing to do. best regards Janek On 5 Feb 2018, 16:40 +0100, Bruno Chareyre <bruno.chare...@grenoble-inp.fr>, wrote: > Hi Robert, > > On 02/02/2018 07:37 PM, Robert Caulk wrote: > > Hey Yade Devs, > > > > I am wondering if we have the demand to create a Yade related white > > paper publication. The publication would document very Yade specific > > functionalities and I imagine some papers might even highlight pieces > > code. I think the format would be very flexible, some releases might > > be 3 pages with brief summary and figures, while others might be > > formatted similarly to a conference paper. In all cases, I think we > > could maintain a quality archive by incorporating CrossRef, reviewing > > the writing/work, and laying out the documents consistently. > > > I think it makes complete sense, I would support the initiative, thanks. > I would point out one risk though: it may distract one from writing an > actual documentation (with sphinx) while we know that writing the doc is > of highest importance. > I feel that the benefits could be more than the risk, but the issue > should be kept in mind. Actually the possibility of converting some of > these white papers into sphinx documents (to be included directly as doc > pages) could be systematically considered, and the white paper could be > just a step in that direction. > > This page is a good example of a short paper that was converted into a > doc page. > https://yade-dem.org/doc/FEMxDEM.html > > I think you know this one to: ;) > https://yade-dem.org/doc/amazonEC2.html > > Bruno > > > > _______ > Mailing list: https://launchpad.net/~yade-dev > Post to : yade-dev@lists.launchpad.net > Unsubscribe : https://launchpad.net/~yade-dev > More help : https://help.launchpad.net/ListHelp _______ Mailing list: https://launchpad.net/~yade-dev Post to : yade-dev@lists.launchpad.net Unsubscribe : https://launchpad.net/~yade-dev More help : https://help.launchpad.net/ListHelp
Re: [Yade-dev] Yade for LTS Ubuntu 18.04
This is a great effort, I saw you squashed dozens of bugs yesterday. Great! Regarding compiling yade with CGAL 4.11, I can look into it on Saturday, if my last patches didn't work for you? I am currently on a trip and have with me just a small laptop. The last patches I've sent is what I currently have at the moment. Yade was compiling, and seemed to work, except that one test after the compilation was hanging idefinitely. Not sure why - I still didn't look into it. Did you try to reproduce what I reported? best regards Janek On 6 Feb 2018, 10:02 +0100, Bruno Chareyre <bruno.chare...@grenoble-inp.fr>, wrote: > > > On 02/05/2018 08:42 PM, Anton Gladky wrote: > > I also want to ask everybody to have a look at the bug-tracker [1]. > Good point. I'll check the one you mentioned at least. > It would be great to fix some more. > B > > > > > ___ > Mailing list: https://launchpad.net/~yade-dev > Post to : yade-dev@lists.launchpad.net > Unsubscribe : https://launchpad.net/~yade-dev > More help : https://help.launchpad.net/ListHelp _______ Mailing list: https://launchpad.net/~yade-dev Post to : yade-dev@lists.launchpad.net Unsubscribe : https://launchpad.net/~yade-dev More help : https://help.launchpad.net/ListHelp
Re: [Yade-dev] Yade for LTS Ubuntu 18.04
Hi Anton and Bruno, I am glad that I can help, and use this opportunity to get back in track ;) So I will do this entire Saturday after I get back home on friday night. Should I work on latest yade trunk? BTW: I'm writing this from an airport ;) Best regards, Janek On 8 Feb 2018, 19:10 +0100, Anton Gladky <gladky.an...@gmail.com>, wrote: > Hi Bruno, > > CGAL_ 4.11 is the only version now for Debian (testing) [1] > and upcoming Ubuntu 18.04 [2]. The shipped Yade does > not support CGAL due to compilation problems. > > I am preparing the new Yade upload, but we have a chance > to patch the Yade within the next two weeks or prepare > the 2018.02b release with CGAL-support and upload it. > > [1] https://tracker.debian.org/pkg/cgal > [2] https://launchpad.net/ubuntu/+source/cgal > > Anton > > > 2018-02-08 18:45 GMT+01:00 Bruno Chareyre <bruno.chare...@grenoble-inp.fr>: > > Hi Anton, > > Thank you very much. > > I'm not so sure what we are speaking about here. > > Yade 2018.02a is the candidate source code for producing a binary > > yade-stable in Ubuntu 18.04, correct (approximately)? > > If yes, can we build yade-stable with CGAL at the moment? > > Bruno > > > > > > > > On 02/08/2018 06:35 PM, Anton Gladky wrote: > > > > > > Well, if we find a way to fix it within the next 2 weeks, > > > I think there is a chance to get it pushed into Debian->Ubuntu. > > > > > > Regards > > > > > > Anton > > > > > > > > > 2018-02-08 15:23 GMT+01:00 Bruno Chareyre > > > <bruno.chare...@grenoble-inp.fr>: > > > > > > > > > > > > On 02/07/2018 05:35 PM, Janek Kozicki (yade-dev) wrote: > > > > > > > > > > > > > > > Regarding compiling yade with CGAL 4.11, I can look into it on > > > > > Saturday, > > > > > if my last patches didn't work for you? > > > > > > > > I did not test it yet I'm afraid. :-/ > > > > It sounds like a critical issue for a 18.04 release. Is it? > > > > Would that mean to skip the whole CGAL related code in the binary > > > > release? > > > > I'll go back to this asap, thanks for pinging. > > > > > > > > Bruno > > > > > > > > > > > > > > > > > > > > ___ > > > > Mailing list: https://launchpad.net/~yade-dev > > > > Post to : yade-dev@lists.launchpad.net > > > > Unsubscribe : https://launchpad.net/~yade-dev > > > > More help : https://help.launchpad.net/ListHelp > > > > > > > > > > _______ > > Mailing list: https://launchpad.net/~yade-dev > > Post to : yade-dev@lists.launchpad.net > > Unsubscribe : https://launchpad.net/~yade-dev > > More help : https://help.launchpad.net/ListHelp > > ___ > Mailing list: https://launchpad.net/~yade-dev > Post to : yade-dev@lists.launchpad.net > Unsubscribe : https://launchpad.net/~yade-dev > More help : https://help.launchpad.net/ListHelp ___ Mailing list: https://launchpad.net/~yade-dev Post to : yade-dev@lists.launchpad.net Unsubscribe : https://launchpad.net/~yade-dev More help : https://help.launchpad.net/ListHelp
Re: [Yade-dev] Odp: Re: Yade for LTS Ubuntu 18.04
Awesome! Thank you! :-) On 22 Feb 2018, 21:12 +0100, Anton Gladky <gladky.an...@gmail.com>, wrote: > Dear Yade developers, > > the new minor Yade 2018.02b was released on 20-th of February. > It allows us to compile Yade against CGAL_4.11 and fixes some > bugs. Tarballs are available on GitHub [1] and Launchpad [2]. > > Also the new version was uploaded to Debian [3] and even synced > into the Ubuntu LTS 18.04 Bionic [4] and successfully built for all > relevant platforms. > > Thanks all for the great work! > > [1] https://github.com/yade/trunk/releases > [2] https://launchpad.net/yade/+download > [3] https://buildd.debian.org/status/package.php?p=yade > [4] https://launchpad.net/ubuntu/+source/yade/2018.02b-1 > > Anton > > _______ > Mailing list: https://launchpad.net/~yade-dev > Post to : yade-dev@lists.launchpad.net > Unsubscribe : https://launchpad.net/~yade-dev > More help : https://help.launchpad.net/ListHelp _______________ Mailing list: https://launchpad.net/~yade-dev Post to : yade-dev@lists.launchpad.net Unsubscribe : https://launchpad.net/~yade-dev More help : https://help.launchpad.net/ListHelp
Re: [Yade-dev] Ip2_FrictMat_FrictMat_FrictPhys doc
> > YADE_CLASS_BASE_DOC_ATTRS(Ip2_FrictMat_FrictMat_FrictPhys,IPhysFunctor,"Create
> > > a :yref:`FrictPhys` from two :yref:`FrictMats`. The compliance
> > > of one sphere under point load is defined here as $1/(E.D)$, with $E$ the
> > > stiffness of the sphere and $D$ its diameter. The compliance of the
> > > contact itself will be the sum of compliances from each sphere, i.e.
> > > $1/(E_1.D_1)+1/(E_2.D_2)$ in the general case, or $2/(E.D)$ in the
> > > special case of equal sizes and equal stiffness. Note that summing
> > > compliances corresponds to an harmonic average of stiffnesss (as in e.g.
> > > [Scholtes2009a]_), which is how kn is actually computed in the
> > > :yref:`Ip2_FrictMat_FrictMat_FrictPhys` functor:\n\n $k_n =
> > > \\frac{E_1D_1*E_2D_2}{E_1D_1+E_2D_2}=\\frac{k_1*k_2}{k_1+k_2}$, with
> > > $k_i=E_iD_i$.\n\n The shear stiffness ks of one sphere is defined via the
> > > material parameter :yref:`ElastMat::poisson`, as ks=poisson*kn, and the
> > > resulting shear stiffness of the interaction will be also an harmonic
> > > average. In the case of a contact between a :yref:`ViscElMat` and a
> > > :yref:`FrictMat`, be sure to set :yref:`FrictMat::young` and
> > > :yref:`FrictMat::poisson`, otherwise the default value will be used.",
> > > +
> > > YADE_CLASS_BASE_DOC_ATTRS(Ip2_FrictMat_FrictMat_FrictPhys,IPhysFunctor,"Create
> > > a :yref:`FrictPhys` from two :yref:`FrictMats` as per the
> > > following expressions: \n\n$k_n = \\frac{E_1D_1*E_2D_2}{E_1D_1+E_2D_2}$
> > > where $k_n=$ :yref:`FrictPhys.kn`, the $E_i$ are :yref:`FrictMat.young`
> > > for each contacting body $i=1;2$, and the $D_i$ are the bodies'
> > > (equivalent) diameters\n\n$k_s =
> > > \\frac{E_1D_1P_1*E_2D_2P_2}{E_1D_1P_1+E_2D_2P_2}$ where $k_s=$
> > > :yref:`FrictPhys.ks` and the $P_i$ are the bodies'
> > > :yref:`FrictMat.poisson`\n\n$\\mu = \\tan(min(\\phi_1,\\phi_2))$ by
> > > default (see :yref:`frictAngle
> > > attribute`), where $\\mu=$
> > > :yref:`FrictPhys.tangensOfFrictionAngle` and the $\\phi_i$ are the
> > > bodies' :yref:`FrictMat.frictionAngle`.",
> > >
> > > --
> > > Chargé de Recherche / Research Associate
> > > Irstea, RECOVER
> > > 3275 route de Cézanne – CS 40061 13182 Aix-en-Provence Cedex 5 FRANCE
> > > +33 (0)4 42 66 99 21
> > >
> > > A free DEM conference in April: https://2ndyadeworkshop.sciencesconf.org/
> > >
> > >
> > > ___
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