[Dune-devel] [GSoC2016]Spline topic discussion
Oliver Sander
oliver.sander at tu-dresden.de
Wed Mar 23 06:32:41 CET 2016
Hi Xinyun, hi Maikel,
Maikel, thanks for all these explanations, there isn't really anything I have to
add here.
Xinyun, do have a look at dune-geometry/dune/geometry/axisalignedgeometry.hh.
The interface in there is what you need to replicate. The documentation in
dune-localfunctions-manual.pdf is okay, but may be a bit outdated.
Enjoy,
Oliver
On 22.03.2016 13:20, Maikel Nadolski wrote:
> Hi Xinyun,
>
> On 21.03.2016 14:04, Xinyun wrote:
>> Hi Maikel,
>>
>> Hope you enjoyed your vacation. :-)
>
> Thanks! I had a great time for St. Patricks Day in Ireland. :o)
>
>> Now I have installed Ubunte on my laptop. You are correct that all my
>> problems result from the operating system. Then I followed you
>> instructions and It seems I can build it now.
>> But I still have some doubts .
>
> Good!
>
>> １. Where can I get the results and how can I visualize them? I think I
>> should get two files called "bsplincure" and "bsplinesurface". But I
>> didn't see them. Also, I didn't get any print out message, for example,
>> "done with curve". Does this mean I didn't build successfully? Or I
>> forgot some further commands?
>
> Try to use the program `paraview` on the files which get generated by
> the test binary. It simply worked for me and you get to see one 3d curve
> and one surface.
>
>> 2. I don't quite understand what the "bsplinebasis" file is intended
>> for. This file is much harder for me to understand than the
>> "bsplinepatch". And the test code don't use any function from the this
>> file.
>
> BSplineBasis implements the very basic and first things which you need
> to implement a geometry. Look back to the first email I wrote about
> this, because I am kinda repeating myself.
>
> My answer from last week didnt change:
>
> "The pdf
>
> http://www.dune-project.org/doc/localfunctions/dune-localfunctions-manual.pdf
>
> was really helpful for me, also
>
> http://www.dune-project.org/doc/grid-howto/grid-howto.pdf
>
> Im orienting myself on the grid/geometry implementations in the
> dune-grid and dune-geometry module. I look for simple examples like
> AxisAlignedCubeGeometry or onedgrid."
>
>
>> 3. Where is best to start? What does the Geometry interface mean in the
>> task description? I somehow feel the geometry interface is related to
>> the "bsplinebasis" code. But the basic B-spline algorithm should lie in
>> the BSplineGeometry class. What's your understanding?
>
> The thing is, that Dune uses the Barton-Nackman trick to emulate
> 'interfaces'. This is also described in the PDFs. One could say, that we
> use "soft" Template Meta Programming and trait classes to enforce
> interfaces. This is because of the performance problems of virtual
> tables, which matter to some users (vtable data is layouted in front
> blocking the cache and such things, i believe). But that is also why it
> might seem unsual to you.
>
> I think a mentor could answer your questions better to what function you
> should concentrate on. That is why I forwarded the message to Oliver. I
> hope that is ok. I also think these informations could benefit more
> people and maybe you should make these questions more public. It also
> shows what furtherdocumentation might be needed. Like a tutorial on how
> to implement an interface? I would say for now: try to look at the
> existent simple implementations.
>
> I have to finish my master thesis util next friday so I can't really
> help more than that for now. From april on we can dive together into the
> code.
>
> Until then, happy coding!
>
>> Thanks,
>> Xinyun
>>
>>
>>
>> On 03/16/2016 01:29 PM, Maikel Nadolski wrote:
>>> No, no. i wont apply! Take your chances. Im just offering my help.
>>>
>>> On 03/16/2016 01:28 PM, Xinyun Li wrote:
>>>> Hey Maikel,
>>>>
>>>> That would be super nice if I can work with you. I had a quick look at
>>>> their code and I think a lot can be done. I would ask the mentors later
>>>> if they have any suitable prior job for this topic.
>>>> I'm not sure if we can apply together. But I would still be very eager
>>>> to assist you if they can only pick one student for this topic in the
>>>> end. Please update your code so I'm not doing redundant work. Or we may
>>>> have discussion later on more detail and separate the tasks.
>>>>
>>>> Best,
>>>> Xinyun
>>>>
>>>>
>>>>
>>>> 2016-03-16 11:40 GMT+01:00 Maikel Nadolski <nadolski at math.fu-berlin.de
>>>> <mailto:nadolski at math.fu-berlin.de>>:
>>>>
>>>> Hey Xinyun,
>>>>
>>>> dont worry, it doesn't bother me. I am interested in the spline
>>>> implementation too. Actually I already started on some
>>>> improvements of
>>>> the prototype. If you need any help dont shy to ask. Oliver
>>>> Sander is
>>>> the mentor of the project: ask him too!
>>>>
>>>> I strongly dislike that solo aspect of GSoC. I love working in a
>>>> team,
>>>> so maybe we can work together on the implementations. If you
>>>> keep your
>>>> fork updated (maybe even better on dunes gitlab) I might review
>>>> your
>>>> code. ;-)
>>>>
>>>> Maikel
>>>>
>>>> On 03/15/2016 10:20 PM, Xinyun Li wrote:
>>>> > Hi Maikel,
>>>> >
>>>> > I'll try to make a virtual machine and build again. I hope I
>>>> don't
>>>> need to bother you again.
>>>> >
>>>> > I'm very interested in machine learning and deep learning. But
>>>> nowadays it's so hot and everyone likes it. So it's also highly
>>>> competitive; that's why I didn't search for any project related to
>>>> that. :‑D
>>>> > I always want to do some projects on machine learning but I
>>>> always
>>>> get something on computer graphics. But the good side is it’s less
>>>> competitive. Haha, I feel there are less students interested in the
>>>> B-Spline topic.
>>>> > Deep learning is not totally different from machine learning, I
>>>> think it’s more like derived from machine learning and specialized
>>>> on neutral networks. If you have knowledge on machine learning, it
>>>> would be much easier for you to understand deep learning. You
>>>> already know minimization techniques and markov models, that's very
>>>> necessary for deep learning.
>>>> >
>>>> > Enjoy your vacation, the weather is getting nice now.
>>>> >
>>>> > Best,
>>>> > Xinyun
>>>> >
>>>> > -----Original Message-----
>>>> > From: Maikel Nadolski [mailto:nadolski at math.fu-berlin.de
>>>> <mailto:nadolski at math.fu-berlin.de>]
>>>> > Sent: Tuesday, March 15, 2016 9:39 PM
>>>> > To: Xinyun Li <xinyun.li at fau.de <mailto:xinyun.li at fau.de>>
>>>> > Subject: Re: [Dune-devel] [GSoC2016]Spline topic discussion
>>>> >
>>>> > Hi Xinyun,
>>>> >
>>>> > On 03/15/2016 07:25 PM, Xinyun Li wrote:
>>>> >> Hi Maikel,
>>>> >>
>>>> >> Thanks for your nice explanation. ^_^
>>>> >> Sorry to reply you late because I have to work during daytime.
>>>> >
>>>> > No problem. I am working during daytime too ... well at least
>>>> most
>>>> of the time :-)
>>>> >
>>>> > I will be traveling until sunday and wont be able to answer
>>>> regularly.
>>>> >
>>>> >> I'm really inexperienced with cmake under UNIX, I normally
>>>> use Visual
>>>> >> Stuidio to work with C++ project. Now I have downloaded the
>>>> modules
>>>> >> you mentioned separately (in different subfolders) and I
>>>> tried to
>>>> run "
>>>> >> ./dune-common/bin/dunecontrol --module=dune-iga all". But I
>>>> got some
>>>> >> error message. Actually this command looks very strange to me as
>>>> >> "dunecontrol" is not a executable. Can you share me with your
>>>> >> successful experience building DUNE? Any information is welcome.
>>>> Maybe
>>>> >> I should get a UNIX environment first.
>>>> >
>>>> > I am really not sure if the project works under Windows at
>>>> all. Go
>>>> ahead and ask on the mailing list, but i highly doubt it.
>>>> > For example `dunecontrol` should be executable but it is actually
>>>> a bash script. Just open it in an editor and look into it ;-). That
>>>> especially means you need a bash terminal to execute it, and i dont
>>>> know if that is possible in windows (does cygwin provide something
>>>> like that?) I had the impression that Christoph Grüninger,
>>>> christoph.grueninger at iws.uni-stuttgart.de
>>>> <mailto:christoph.grueninger at iws.uni-stuttgart.de>, has most
>>>> insight
>>>> into the build system (and Dune in general tbh). You can ask him
>>>> probably for details.
>>>> >
>>>> > In the end the installation boils down to having the modules in a
>>>> folder and executing `dunecontrol all`. That will configure and
>>>> compile everything. You can install it locally with make install
>>>> then (with root privileges). If you, like myself, lack root rights
>>>> on your system (in the university) there also ways to install them
>>>> locally. But that is a little bit more complicated. But I would
>>>> also
>>>> recommend to not install dune-iga while you develop it. I do things
>>>> like this:
>>>> >
>>>> > $ ls -l
>>>> > total 20
>>>> > drwxr-xr-x 12 maikel maikel 4096 Mar 9 06:56 dune-common/
>>>> drwxr-xr-x 8 maikel maikel 4096 Mar 9 07:23 dune-geometry/
>>>> drwxr-xr-x 10 maikel maikel 4096 Mar 9 07:24 dune-grid/ drwxr-xr-x
>>>> 10 maikel maikel 4096 Mar 11 23:07 dune-iga/ drwxr-xr-x 8 maikel
>>>> maikel 4096 Mar 11 21:47 dune-istl/
>>>> >
>>>> > $ ./dune-common/bin/dunecontrol --module=dune-grid all
>>>> >
>>>> > [...]
>>>> >
>>>> > $ sudo ./dune-common/bin/dunecontrol --module=dune-grid make
>>>> install
>>>> >
>>>> > [...]
>>>> >
>>>> > $ cd dune-iga/
>>>> > $ cmake .
>>>> >
>>>> > [ ... ]
>>>> >
>>>> > $ make
>>>> >
>>>> > [ ... ]
>>>> >
>>>> > Profit!
>>>> >
>>>> >> Do you know Chinese pinyin? Ha, it's interesting you know
>>>> weiqi. I am
>>>> >> also exicted about this match. Lee Seedol lost today's last
>>>> match.
>>>> >> AlphaGo is really amazing and I have read some paper on their
>>>> >> algorithm. They didn't use much go related feature so it can be
>>>> >> further improved. Deep learning is super coooool.
>>>> >
>>>> > Haha, no, no. I do not really know pinyin. Before my study I was
>>>> just a rather active go player and know that it is called weiqi in
>>>> china and baduk in korea. And i have to admit, that I know more
>>>> about japanese or korean go players than chinese ones. Although I
>>>> really liked replaying Nie Weiping games.
>>>> >
>>>> > Do you have interest especially in deep learning? AFAIK that is
>>>> different from machine learning in general, right? All I know about
>>>> topics roughly in that direction are just general minimization
>>>> methods, linear regression stuff and theory about discrete markov
>>>> processes and such things. When I have time after my thesis i
>>>> wanted
>>>> to take a look into that direction too.
>>>> >
>>>> >> Cheers,
>>>> >> Xinyun
>>>> >>
>>>> >>
>>>> >> -----Original Message-----
>>>> >> From: Maikel Nadolski [mailto:nadolski at math.fu-berlin.de
>>>> <mailto:nadolski at math.fu-berlin.de>]
>>>> >> Sent: Monday, March 14, 2016 10:45 PM
>>>> >> To: Xinyun Li <xinyun.li at fau.de <mailto:xinyun.li at fau.de>>
>>>> >> Subject: Re: [Dune-devel] [GSoC2016]Spline topic discussion
>>>> >>
>>>> >> Dune consist of several core modules. Dune-iga depends on
>>>> dune-common
>>>> >> and i think on dune-geometry and dune-grid (not sure tho).
>>>> >>
>>>> >> In dune-iga you find a test in the src folder and important
>>>> sources in
>>>> >> the include/dune/iga folder.
>>>> >>
>>>> >> Don't panick if you do not understand dune's build system
>>>> immediately.
>>>> >> It took my 2 days or so until i understood everything and
>>>> could play
>>>> >> around with it and I am really experienced with that kind of
>>>> stuff.
>>>> >>
>>>> >> The core modules are mirrored on github:
>>>> >>
>>>> >> https://github.com/dune-project
>>>> >>
>>>> >> But i checked it again and I think you can access their gitlab
>>>> >> directly here
>>>> >>
>>>> >> https://gitlab.dune-project.org/groups/core
>>>> >>
>>>> >> https://gitlab.dune-project.org/core/dune-common
>>>> >> https://gitlab.dune-project.org/core/dune-geometry
>>>> >> https://gitlab.dune-project.org/core/dune-grid
>>>> >>
>>>> >> etc.
>>>> >>
>>>> >> Do you know Weiqi? Have you followed the match of AlphaGo
>>>> against Lee
>>>> >> Seedol? Great stuff. 5th match incoming.
>>>> >>
>>>> >> On 03/14/2016 10:13 PM, Xinyun Li wrote:
>>>> >>> Hi Maikel,
>>>> >>>
>>>> >>> I just downloaded the code. Thanks again for your effort. :) Is
>>>> there
>>>> >>> only one small piece of code? (dune-iga.cc). Do I need to
>>>> >> download
>>>> >>> other packages?
>>>> >>>
>>>> >>> Cheers,
>>>> >>> Xinyun
>>>> >>>
>>>> >>> -----Original Message-----
>>>> >>> From: Maikel Nadolski [mailto:nadolski at math.fu-berlin.de
>>>> <mailto:nadolski at math.fu-berlin.de>]
>>>> >>> Sent: Monday, March 14, 2016 9:58 PM
>>>> >>> To: Xinyun Li <xinyun.li at fau.de <mailto:xinyun.li at fau.de>>
>>>> >>> Subject: Re: [Dune-devel] [GSoC2016]Spline topic discussion
>>>> >>>
>>>> >>> Hey Xinyun,
>>>> >>>
>>>> >>> I still have to calculate it through, but it might simply be
>>>> less
>>>> >>> than social welfare.. I will probably start my PhD in that time
>>>> >>> anyway so i do not know if I have time throughout the summer.
>>>> >>>
>>>> >>> Just feel free to ask questions. The people on the mailing
>>>> list are
>>>> >>> all nice.
>>>> >>>
>>>> >>> Cheers,
>>>> >>> Maikel
>>>> >>>
>>>> >>> On 03/14/2016 09:45 PM, Xinyun Li wrote:
>>>> >>>> Hi Maikel,
>>>> >>>>
>>>> >>>> Thanks a lot. It's very nice of you :) I think you can
>>>> postpone
>>>> your
>>>> >>>> graduate and apply for the Gsoc. Did you already register at
>>>> >>>> university?
>>>> >>>> I will try downloading from Github and give you feedback.
>>>> >>>>
>>>> >>>> Thanks,
>>>> >>>> Xinyun
>>>> >>>>
>>>> >>>> -----Original Message-----
>>>> >>>> From: Maikel Nadolski [mailto:nadolski at math.fu-berlin.de
>>>> <mailto:nadolski at math.fu-berlin.de>]
>>>> >>>> Sent: Monday, March 14, 2016 9:38 PM
>>>> >>>> To: Xinyun Li <xinyun.li at fau.de <mailto:xinyun.li at fau.de>>
>>>> >>>> Subject: Re: [Dune-devel] [GSoC2016]Spline topic discussion
>>>> >>>>
>>>> >>>> https://github.com/maikel/dune-iga
>>>> >>>>
>>>> >>>> Tell me if it works!
>>>> >>>>
>>>> >>>> On 03/14/2016 09:33 PM, Maikel Nadolski wrote:
>>>> >>>>> Oh, I am not sure, but Dune's Gitlab might be "private". That
>>>> >>>>> means, you need to create an account at
>>>> >>>>> https://gitlab.dune-project.org/ and wait for an
>>>> administrator
>>>> to accept.
>>>> >>>>>
>>>> >>>>> I will mirror the respository to Github give me a second.
>>>> >>>>>
>>>> >>>>> On 03/14/2016 09:24 PM, Xinyun Li wrote:
>>>> >>>>>> Hello Maikel,
>>>> >>>>>>
>>>> >>>>>> Thanks a lot for your quick and helpful reply. I'm now
>>>> still
>>>> >> struggling
>>>> >>>>>> with downloading the code. I'm sorry to bother you with
>>>> these
>>>> >>>>>> stupid question. But I think you have some experience and
>>>> really
>>>> >>>>>> wish you can
>>>> >>>> help.
>>>> >>>>>
>>>> >>>>> Actually, I just started looking into Dune a week ago. In two
>>>> weeks
>>>> >>>>> i finish my master thesis in numerics and lose my student
>>>> status...
>>>> >>>>> unfortunately I think I can not participate in GSoC ... ;-(
>>>> >>>>>
>>>> >>>>>> The system of my personal laptop is Windows so I tried to
>>>> remotely
>>>> >> login
>>>> >>>>>> into our Linux machine.
>>>> >>>>>
>>>> >>>>> I do not have any experience with Windows, sorry. :-(
>>>> >>>>>
>>>> >>>>>> After typing in " git clone
>>>> >>>>>>
>>>> ssh://git@gitlab.dune-project.org:22022/oliver.sander/dune-iga.git
>>>>
>>>> <http://git@gitlab.dune-project.org:22022/oliver.sander/dune-iga.git>
>>>> >>>>>> ", I got the following error:
>>>> >>>>>> " ECDSA key fingerprint is
>>>> >>>> cb:15:d3:92:f0:b0:36:c4:83:d7:1d:8b:ae:d6:73:c0.
>>>> >>>>>> Are you sure you want to continue connecting (yes/no)? yes
>>>> >>>>>> Warning: Permanently added
>>>> >>>>>> '[gitlab.dune-project.org
>>>> <http://gitlab.dune-project.org>]:22022,[129.206.107.252]:22022'
>>>> (ECDSA)
>>>> >>>>>> to
>>>> >> the
>>>> >>>>>> list of known hosts.
>>>> >>>>>> Permission denied (publickey).
>>>> >>>>>> fatal: Could not read from remote repository."
>>>> >>>>>
>>>> >>>>> If you already have access to Gitlab, you have to add your
>>>> public
>>>> >>>>> ssh key in your profile. Under SSH-Keys. Do you need a
>>>> tutorial? I
>>>> >>>>> think i can look for one.
>>>> >>>>>
>>>> >>>>>> Afterwards, I came back to the GitGUI under Windows. I
>>>> tried to
>>>> >>>>>> add and fetch but got similar access error. Could you
>>>> please
>>>> tell
>>>> >>>>>> me where I
>>>> >>> was
>>>> >>>>>> wrong or how you made it successfully?
>>>> >>>>>
>>>> >>>>> Wait a sec. Im cloning to Github.
>>>> >>>>>
>>>> >>>>>> Thanks for your time in advance.
>>>> >>>>>> Best regards,
>>>> >>>>>> Xinyun
>>>> >>>>>>
>>>> >>>>>>
>>>> >>>>>> -----Original Message-----
>>>> >>>>>> From: Maikel Nadolski [mailto:nadolski at math.fu-berlin.de
>>>> <mailto:nadolski at math.fu-berlin.de>]
>>>> >>>>>> Sent: Monday, March 14, 2016 2:32 PM
>>>> >>>>>> To: Xinyun Li <xinyun.li at fau.de <mailto:xinyun.li at fau.de>>;
>>>> dune-devel at dune-project.org <mailto:dune-devel at dune-project.org>
>>>> >>>>>> Subject: Re: [Dune-devel] [GSoC2016]Spline topic discussion
>>>> >>>>>>
>>>> >>>>>> Oh i take the part with De Boors algorithm back. What is
>>>> >>>>>> implemented is actually a straight bottom-up implementation
>>>> of the
>>>> >>>>>> recursive Cox De Boor formula.
>>>> >>>>>>
>>>> >>>>>> On 14.03.2016 14:20, Maikel Nadolski wrote:
>>>> >>>>>>> Hi Xinyun,
>>>> >>>>>>>
>>>> >>>>>>> I try to answer as a student interested in GSoC myself,
>>>> because I
>>>> >> think
>>>> >>>>>>> I had to overcome similar barriers and feel with you :-)
>>>> >>>>>>>
>>>> >>>>>>>> The project tasks sound clear to me. But I have some
>>>> problem
>>>> >>>>>>>> with accessing your source code.
>>>> >>>>>>>
>>>> >>>>>>> Can you clone the prototype
>>>> >>>>>>>
>>>> >>>>>>>
>>>> ssh://git@gitlab.dune-project.org:22022/oliver.sander/dune-iga.git
>>>>
>>>> <http://git@gitlab.dune-project.org:22022/oliver.sander/dune-iga.git> ?
>>>> >>>>>>>
>>>> >>>>>>>
>>>> >>>>>>>> Could you please kindly give me some tutorial? Also, it
>>>> seems
>>>> >>>>>>>> you already have the BSplineGeometry class.
>>>> >>>>>>>
>>>> >>>>>>> AFAIK there is no "complete" Geometry class yet. But the
>>>> >>>>>>> prototype
>>>> >> does
>>>> >>>>>>> implement a few things already (for example the De Boor
>>>> Algorithm).
>>>> >>>>>>> Thats why you can start with implementing any function
>>>> needed for
>>>> >>>>>>> the interface. The pdf
>>>> >>>>>>>
>>>> >>>>>>>
>>>> >>>>>>
>>>> >>>>
>>>> >>>
>>>> >>
>>>>
>>>> http://www.dune-project.org/doc/localfunctions/dune-localfunctions-man
>>>> >> ual.pd
>>>> >>>>>> f
>>>> >>>>>>>
>>>> >>>>>>> was really helpful for me, also
>>>> >>>>>>>
>>>> >>>>>>> http://www.dune-project.org/doc/grid-howto/grid-howto.pdf
>>>> >>>>>>>
>>>> >>>>>>> Im orienting myself on the grid/geometry implementations
>>>> in the
>>>> >>>>>>> dune-grid and dune-geometry module. I look for simple
>>>> examples
>>>> >>>>>>> like AxisAlignedCubeGeometry or onedgrid.
>>>> >>>>>>>
>>>> >>>>>>> I
>>>> >>>>>>>> assume you already have the basis functions of
>>>> B-splines so the
>>>> >>> splines
>>>> >>>>>>>> can be easily built given the knot vector and the control
>>>> >>>>>>>> points. I
>>>> >>>> have
>>>> >>>>>>>> some thoughts on "small projects to get started". Some
>>>> functions
>>>> >>>>>>>> that can be implemented:
>>>> >>>>>>>>
>>>> >>>>>>>> 1. Evalution at a certain parameter (de Boor Algorithm)
>>>> >>>>>>>>
>>>> >>>>>>>> 2. Knot addtiton and deletion (Boehm Algorithm)
>>>> >>>>>>>>
>>>> >>>>>>>> 3. Fitting to a list of points(global or local
>>>> interpolation)
>>>> >>>>>>>>
>>>> >>>>>>>>
>>>> >>>>>>>>
>>>> >>>>>>>> Thanks for your time and hope to hear from you soon!
>>>> >>>>>>>
>>>> >>>>>>>
>>>> >>>>>>> HTH, Maikel
>>>> >>>>>>>
>>>> >>>>>
>>>>
>>>>
>
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