[deal.II] Re: Untraceable "not implemented" error in GDB

2016-09-16 Thread Alex Zimmerman
Yep that does it! Thanks for your patience :)

On Friday, September 16, 2016 at 7:28:41 PM UTC+2, Bruno Turcksin wrote:
>
> Alex,
>
> before the run command, you need to use: catch throw 
>
> Best,
>
> Bruno
>
> On Friday, September 16, 2016 at 1:21:41 PM UTC-4, Alex Zimmerman wrote:
>>
>> A couple of times now I have encountered GDB output similar to my 
>> attached snapshot.
>>
>> The previous time I had only made a very small change to my code, so it 
>> was easy enough for me to figure out on my own. Presently I'm trying to run 
>> a 1D version of my code for the first time. So far I've only ran 2D 
>> problems, though I have been attempting to employ the dimension independent 
>> programming found throughout the library.
>>
>> So I imagine that there is some templated method I'm using which simply 
>> has not been implemented in 1D. Any tips on how to quickly narrow down 
>> which specific method(s) is/are throwing this exception? Is it extremely 
>> odd that this exception doesn't point me to the source code?
>>
>> I'm on Ubuntu 14.04 and using a debug build of a 8.5.0-pre version of 
>> deal.II at commit 0752c81b84c7f9c737ef62ac09932853bb976f8d
>>
>> As shown in the snapshot, GDB has consistently been throwing a couple of 
>> warnings. I always get those warnings and this is only the second time I've 
>> had an untraceable error, both of which are related to the "not 
>> implemented" cases; so I'm guessing that it's unrelated, but I could be 
>> entirely wrong about that.
>>
>> Any ideas? Thanks!
>>
>

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Re: [deal.II] Help with Vector template instantiations

2016-09-16 Thread dragnikolic
True, I've checked in the master and it is templated for the 
Function too. I use 8.4.1.
It's fine then. Thanks. 

On Friday, September 16, 2016 at 5:39:33 PM UTC+1, Wolfgang Bangerth wrote:
>
> On 09/15/2016 05:12 AM, dragn...@gmail.com  wrote: 
> > 
> > One more question, in fact a small inconsistency that is of my interest: 
> > the function VectorTools::interpolate_boundary_values is not templated 
> > for the generic Number type but for double only (argument 
> > std::map& boundary_values). Is there a 
> > reason for that? 
>
> Which version of deal.II are you using? In the current development 
> version, this is properly templated so that the value type of the 
> Function object is the same as the value type of the boundary_values map. 
>
> Best 
>   Wolfgang 
>
> -- 
>  
> Wolfgang Bangerth  email: bang...@colostate.edu 
>  
> www: http://www.math.colostate.edu/~bangerth/ 
>

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[deal.II] Re: Untraceable "not implemented" error in GDB

2016-09-16 Thread Bruno Turcksin
Alex,

before the run command, you need to use: catch throw 

Best,

Bruno

On Friday, September 16, 2016 at 1:21:41 PM UTC-4, Alex Zimmerman wrote:
>
> A couple of times now I have encountered GDB output similar to my attached 
> snapshot.
>
> The previous time I had only made a very small change to my code, so it 
> was easy enough for me to figure out on my own. Presently I'm trying to run 
> a 1D version of my code for the first time. So far I've only ran 2D 
> problems, though I have been attempting to employ the dimension independent 
> programming found throughout the library.
>
> So I imagine that there is some templated method I'm using which simply 
> has not been implemented in 1D. Any tips on how to quickly narrow down 
> which specific method(s) is/are throwing this exception? Is it extremely 
> odd that this exception doesn't point me to the source code?
>
> I'm on Ubuntu 14.04 and using a debug build of a 8.5.0-pre version of 
> deal.II at commit 0752c81b84c7f9c737ef62ac09932853bb976f8d
>
> As shown in the snapshot, GDB has consistently been throwing a couple of 
> warnings. I always get those warnings and this is only the second time I've 
> had an untraceable error, both of which are related to the "not 
> implemented" cases; so I'm guessing that it's unrelated, but I could be 
> entirely wrong about that.
>
> Any ideas? Thanks!
>

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[deal.II] Untraceable "not implemented" error in GDB

2016-09-16 Thread Alex Zimmerman
A couple of times now I have encountered GDB output similar to my attached 
snapshot.

The previous time I had only made a very small change to my code, so it was 
easy enough for me to figure out on my own. Presently I'm trying to run a 
1D version of my code for the first time. So far I've only ran 2D problems, 
though I have been attempting to employ the dimension independent 
programming found throughout the library.

So I imagine that there is some templated method I'm using which simply has 
not been implemented in 1D. Any tips on how to quickly narrow down which 
specific method(s) is/are throwing this exception? Is it extremely odd that 
this exception doesn't point me to the source code?

I'm on Ubuntu 14.04 and using a debug build of a 8.5.0-pre version of 
deal.II at commit 0752c81b84c7f9c737ef62ac09932853bb976f8d

As shown in the snapshot, GDB has consistently been throwing a couple of 
warnings. I always get those warnings and this is only the second time I've 
had an untraceable error, both of which are related to the "not 
implemented" cases; so I'm guessing that it's unrelated, but I could be 
entirely wrong about that.

Any ideas? Thanks!

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Re: [deal.II] Help with Vector template instantiations

2016-09-16 Thread Wolfgang Bangerth

On 09/15/2016 05:12 AM, dragniko...@gmail.com wrote:


One more question, in fact a small inconsistency that is of my interest:
the function VectorTools::interpolate_boundary_values is not templated
for the generic Number type but for double only (argument
std::map& boundary_values). Is there a
reason for that?


Which version of deal.II are you using? In the current development 
version, this is properly templated so that the value type of the 
Function object is the same as the value type of the boundary_values map.


Best
 Wolfgang

--

Wolfgang Bangerth  email: bange...@colostate.edu
   www: http://www.math.colostate.edu/~bangerth/

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Re: [deal.II] Re: Failing to set up simple test configuration

2016-09-16 Thread Alex Zimmerman
Timo, when I looked into this before posting my question, it seemed to be a 
pretty clear issue with the perl command not working on the Windows 
filesystem. Per my recent reply to Wolfgang, I have moved forward with a 
simple work-around (which simply does not involve running ctest on the 
Windows file system). I imagine at some point in the not-so-distant future 
I'll be interested in fixing this. Of course please do let me know if 
you're interested and want to to reproduce the log for the group's purposes.

Thanks.

On Wednesday, September 7, 2016 at 6:44:09 PM UTC+2, Timo Heister wrote:
>
> Hey Alex, 
>
> I am not surprised you are running into issues, because you are the 
> first one to try "ubuntu on windows" to compile deal.II with (at least 
> as far as I know). 
>
> It could be a permission problem that you are running into, who knows. 
> Would you mind sharing you deal.II detailed.log? 
>
> On Wed, Sep 7, 2016 at 9:32 AM, Jean-Paul Pelteret  > wrote: 
> > Hi Alex, 
> > 
> > Great, many thanks for your useful feedback. I've alerted the other 
> > developers to your comments so that they can be considered in the 
> discussion 
> > about getting deal.II to properly on windows. 
> > 
> > Cheers, 
> > J-P 
> > 
> > 
> > On Wednesday, September 7, 2016 at 2:56:10 PM UTC+2, Alex Zimmerman 
> wrote: 
> >> 
> >> The recent Windows 10 "Anniversary Update" included an entire built-in 
> >> Ubuntu (14.04) subsystem: 
> >> 
> https://urldefense.proofpoint.com/v2/url?u=https-3A__msdn.microsoft.com_en-2Dus_commandline_wsl_about&d=CwIBaQ&c=Ngd-ta5yRYsqeUsEDgxhcqsYYY1Xs5ogLxWPA_2Wlc4&r=4k7iKXbjGC8LfYxVJJXiaYVu6FRWmEjX38S7JmlS9Vw&m=WDpmF-SkGP5uKyQ0vKXcggIG-I_RfG1fLlDteZEDQ_s&s=iVn3ecqjKuFP2DxDo7Q8ippSqeZvU8HaFT57rzJEvRQ&e=
>  
> >> 
> >> I've built a few different versions of deal.II on this system, 
> including 
> >> the candi build with Trilinos, p4est, etc. This was all painless, so 
> >> definitely try it out if you can use the latest version of Windows. 
> >> 
> >> It's actually called "Bash on Ubuntu on Windows", and it's marketed as 
> >> just being a bash prompt useful for command line tools; but it appears 
> much 
> >> more capable than that. Also it can read/write from/to the entire 
> Windows C: 
> >> drive, which is the "/mnt/c" path in my question. This has been useful 
> so 
> >> that I can use Notepad++ and Paraview from Windows. "Bash on Ubuntu on 
> >> Windows" currently isn't very good at forwarding graphics. Even gedit 
> >> doesn't forward very well. There might be some low level magic that 
> >> Microsoft has performed to make all of this work. Presently it appears 
> that 
> >> my issue is related to MS-DOS not allowing my ctest to do some inline 
> file 
> >> editing on my C: drive. But this is indeed to first issue I've had, so 
> the 
> >> system looks quite promising. 
> >> 
> >> After some brief Googling, I think I might even be able to fix this 
> issue 
> >> if I could find where the code is that is causing the error "Can't do 
> >> inplace edit on 
> >> 
> /mnt/c/Users/Alexander/UbuntuShared/dimice-heat-dealii/build/tests/cylinder.debug/output:
>  
>
> >> No such file or directory." Unfortunately I'm completely unfamiliar 
> with the 
> >> test system and I have not a clue. 
> >> 
> >> 
> >> On Wednesday, September 7, 2016 at 10:29:54 AM UTC+2, Jean-Paul 
> Pelteret 
> >> wrote: 
> >>> 
> >>> Great, glad that you sorted it out! 
> >>> 
> >>> By the way, there's recently been a discussion on GitHub related to 
> >>> running deal.II on windows. Its interesting to hear that you've got it 
> >>> running on Windows 10. Out of curiosity, how have you configured 
> deal.II? Do 
> >>> you link it against any external libraries? 
> >>> 
> >>> On Wednesday, September 7, 2016 at 10:07:06 AM UTC+2, Alex Zimmerman 
> >>> wrote: 
>  
>  This might be a problem with my file system. I've been successfully 
>  using the Ubuntu subsystem on Windows 10 for the past few weeks, and 
> that's 
>  where the odd "/mnt/c/Users..." path comes from in my question. 
>  
>  I just tried this again at my home directory, and it worked. I 
> thought I 
>  had tried running the test on my user project in my home directory, 
> but I'm 
>  fairly sure I never tried this simple step-1 example there. 
>  
>  So now this is working: 
>  
>  $ ctest 
>  
>  
> > 
> > Test project /home/zimmerman/temp/step-1/build 
> > Start 1: tests/my_test.debug 
> > 1/1 Test #1: tests/my_test.debug ..   Passed5.51 sec 
> > 100% tests passed, 0 tests failed out of 1 
> > Total Test time (real) =   5.52 sec 
>  
>  
>  
>  One of these days I'll ask a question that I don't answer myself a 
> few 
>  minutes later :) 
>  
>  
>  On Wednesday, September 7, 2016 at 9:57:33 AM UTC+2, Alex Zimmerman 
>  wrote: 
> > 
> > Maybe this is a bug, but I think it's more likely that I'm doing 
> > somethin

Re: [deal.II] Re: Failing to set up simple test configuration

2016-09-16 Thread Alex Zimmerman
Wolfgang, thanks for pointing me to this part of the code. I'm not sure 
when I'll try to fix the problem, because it was very simple to just only 
ever run ctest on the Linux filesystem, completely circumventing it. I'll 
make sure to post an update if I ever fix this so that I can run ctest on 
the Windows filesystem (from the bash prompt).

On Wednesday, September 7, 2016 at 10:36:21 PM UTC+2, Wolfgang Bangerth 
wrote:
>
> On 09/07/2016 06:56 AM, Alex Zimmerman wrote: 
> > 
> > After some brief Googling, I think I might even be able to fix this 
> issue if I 
> > could find where the code is that is causing the error "Can't do inplace 
> edit 
> > on 
> > 
> /mnt/c/Users/Alexander/UbuntuShared/dimice-heat-dealii/build/tests/cylinder.debug/output:
>  
>
> > No such file or directory." Unfortunately I'm completely unfamiliar with 
> the 
> > test system and I have not a clue. 
>
> This happens in cmake/macros/macro_deal_ii_add_test.cmake, around line 
> 240: 
>
>ADD_CUSTOM_COMMAND(OUTPUT ${_test_directory}/output 
>  COMMAND sh 
> ${DEAL_II_PATH}/${DEAL_II_SHARE_RELDIR}/scripts/run_test.sh 
>run "${_test_full}" "${_run_command}" "${_test_diff}" 
>"${DIFF_EXECUTABLE}" "${_comparison_file}" 
>  COMMAND ${PERL_EXECUTABLE} 
>-pi ${DEAL_II_PATH}/${DEAL_II_SHARE_RELDIR}/scripts/
> normalize.pl 
>${_test_directory}/output 
>  WORKING_DIRECTORY 
>${_test_directory} 
>  DEPENDS 
>${_target} 
>${DEAL_II_PATH}/${DEAL_II_SHARE_RELDIR}/scripts/normalize.pl 
>  VERBATIM 
>  ) 
>
> We here call "perl -pi  ". 
>
> Best 
>   W. 
>
> -- 
>  
> Wolfgang Bangerth  email: bang...@colostate.edu 
>  
> www: http://www.math.colostate.edu/~bangerth/ 
>
>

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[deal.II] Re: 1D version of step3

2016-09-16 Thread Weixiong Zheng
Bruno,

Yeah, I noticed an old discussion with the same problem and solved it.

Thanks,
Weixiong



在 2016年9月16日星期五 UTC-5上午10:42:30,Bruno Turcksin写道:
>
> Weixong,
>
> On Friday, September 16, 2016 at 11:35:09 AM UTC-4, Weixiong Zheng wrote:
>>
>> When running the program, the solution is zero on the left side as 
>> expected. However, the right side solution is something nonzero. Since I am 
>> using the same apply_boundary_condition settings, I am supposed to get zero 
>> solution on both boundaries, right? 
>>
> I don't think so. I think that in 1D, the left side has always a 
> boundary_id of 0 and the right side has a boundary_id of 1.
>
> Best,
>
> Bruno
>

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[deal.II] Re: 1D version of step3

2016-09-16 Thread Bruno Turcksin
Weixong,

On Friday, September 16, 2016 at 11:35:09 AM UTC-4, Weixiong Zheng wrote:
>
> When running the program, the solution is zero on the left side as 
> expected. However, the right side solution is something nonzero. Since I am 
> using the same apply_boundary_condition settings, I am supposed to get zero 
> solution on both boundaries, right? 
>
I don't think so. I think that in 1D, the left side has always a 
boundary_id of 0 and the right side has a boundary_id of 1.

Best,

Bruno

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[deal.II] 1D version of step3

2016-09-16 Thread Weixiong Zheng
Dear all,

I just tried to modify step-3 to 1D. The changes are minor.

The equation is changed to be with a small reaction.

The mesh is generated with subdivided_hyper_cube (triangulation, 50, 0, 
10); I changed all the <2>, the dimension, to <1>.

When running the program, the solution is zero on the left side as 
expected. However, the right side solution is something nonzero. Since I am 
using the same apply_boundary_condition settings, I am supposed to get zero 
solution on both boundaries, right? Am I missing something?

Thanks in advance.
Weixiong

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Re: [deal.II] Parasitic stress in corners with periodic boundary conditions

2016-09-16 Thread David F
Hi, sorry for this late reply. I missed it and realized just now. I found 
the problem, which is simply that if the whole system is fully periodic ( I 
mean, for example from plane to torus topology) then the 4 corners become 
effectively fixed (the other possibility would be rigid body motion). The 
fact that this 4 nodes become fixed, makes that when some eigenstrain is 
prescribed somewhere, unexpected stress appears close to the corners as the 
system can't fully relax there. I think this is something one was to live 
with. I didn't see it with other FEM packages because the solution suffered 
some post processing before I got it, which smoothed the result and somehow 
hide this.


On Monday, 2 June 2014 00:59:11 UTC+2, Wolfgang Bangerth wrote:
>
> On 05/28/2014 10:29 AM, David F wrote: 
> > Hello, my problem is the following: 
> > 
> > I prescribe an eigenstrain value in one element of the grid (i.e., an 
> inner 
> > element undergoes a certain transformation and this introduces strain 
> and 
> > stress in the rest of the grid), and everything works fine for normal 
> > boundaries and periodic boundaries. However, if one pays close 
> attention, for 
> > the periodic boundary solution in the corners of the grid one can see 
> some 
> > parasitic stress that shouldn't be there. 
> > 
> > I think the reason is the following: prescribing, let's say, a shear 
> > eigenstrain in one element, the four corners (in 2D) of the grid deform 
> in 
> > opositte directions if the boundary is not periodic, therefore when it 
> is 
> > periodic the four corners are in fact "the same", and these 4 opposite 
> > displacements would add up to 0, effectively fixing the "corner node". 
> This 
> > seems to me a natural problem of FEM and periodicity, so I have no clue 
> how to 
> > correct this with code. 
> > 
> > I have used other FEM packages for solving exactly the same problem I 
> > described, and somehow this is not happening, so there must be a way to 
> avoid 
> > this. I am not sure if it has to do with my implementation of the 
> periodic 
> > boundaries, or maybe the way in which deal.ii deals with periodicity is 
> the 
> > reason, or maybe I have to apply some kind of postprocessing correction 
> of 
> > which I am not aware yet. 
> > 
> > Does anyone know why could this be? 
>
> I don't know myself. Maybe someone else does. But I'd like to point out 
> that 
> using periodic boundary conditions is equivalent to looking at a problem 
> where 
> you have periodic array of sources. Is the element where you prescribe the 
> eigenstrain by chance close to a corner of your domain? If so, I would 
> expect 
> there to be some strain close to the opposite corner as well, simply 
> because 
> there is a source (outside your domain) close to that opposite corner. 
>
> It may be worthwhile sending a picture that shows what you are observing. 
>
>
> > P.S.: my periodic boundary implementation is a direct extension of 
> step-45 and 
> > everything but these small parasitic stress in the corners is pretty 
> accurate, 
> > so probably a problem in the code is not reason. Should I try with 
> > DoFTools::make_periodicity_constraints or do you the problem will be 
> exactly 
> > the same? 
>
> Hard to tell. It's probably worth a try. 
>
> Best 
>   W. 
> -- 
>  
> Wolfgang Bangerth   email:bang...@math.tamu.edu 
>  
>  www: http://www.math.tamu.edu/~bangerth/ 
>
>

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

2016-09-16 Thread David Wells
A useful flag that I use in release mode is -funsafe-loop-optimizations, 
which assumes that loop counters cannot overflow and other such things. I 
don't remember the exact numbers but I do remember that using this flag 
made a small, but measurable, performance improvement.

On Thursday, September 15, 2016 at 8:04:58 AM UTC-4, Denis Davydov wrote:
>
> 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.
>

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Re: [deal.II] Re: Help with time stepping methods

2016-09-16 Thread Bruno Turcksin
I have created a pull request here: https://github.com/dealii/dealii/pull/3123

Thanks again

Bruno

2016-09-16 10:01 GMT-04:00 Bruno Turcksin :
> 2016-09-16 9:22 GMT-04:00 Vaibhav Palkar :
>>
>> The error being exactly zero is indeed intriguing. I'm still looking out for
>> the reason why that is happening. I didn't understand what you meant by a
>> "ramp in time". Could you please elaborate?
> Since you are using a low order method in time, I am just wondering if
> the solution is linear in time. This is one way to have the exact
> solution at each time step and it could explain why the error is zero
> (assuming that there is no spatial error)
>
>> Step-52 works fine, I'm getting exactly the same results as the online
>> documentation. I looked at time_stepping.templates.h, I think there is a bug
>> around line 730, delta_t_guess should be assigned the value of new_delta_t
>> (the coarsened time step) rather than delta_t (old time step).
> Good catch!! Patch incoming.
>
> Thanks
>
> Bruno

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Re: [deal.II] Re: Help with time stepping methods

2016-09-16 Thread Bruno Turcksin
2016-09-16 9:22 GMT-04:00 Vaibhav Palkar :
>
> The error being exactly zero is indeed intriguing. I'm still looking out for
> the reason why that is happening. I didn't understand what you meant by a
> "ramp in time". Could you please elaborate?
Since you are using a low order method in time, I am just wondering if
the solution is linear in time. This is one way to have the exact
solution at each time step and it could explain why the error is zero
(assuming that there is no spatial error)

> Step-52 works fine, I'm getting exactly the same results as the online
> documentation. I looked at time_stepping.templates.h, I think there is a bug
> around line 730, delta_t_guess should be assigned the value of new_delta_t
> (the coarsened time step) rather than delta_t (old time step).
Good catch!! Patch incoming.

Thanks

Bruno

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Re: [deal.II] Re: Help with time stepping methods

2016-09-16 Thread Vaibhav Palkar

On Friday, September 16, 2016 at 1:38:57 AM UTC+5:30, Bruno Turcksin wrote:

> I don't see anything wrong. The output says that your error is zero, 
> are you doing a simple ramp in time? It's very strange that the error 
> is exactly zero. What happens if you just use the default parameters? 
> Does step-52 work correctly? The delta_t_guess is computed around line 
> 715 in include/dealii/base/time_stepping.templates.h You could put a 
> couple of cout there to see what's happening (you will need to 
> recompile deal though) 
>

The error being exactly zero is indeed intriguing. I'm still looking out 
for the reason why that is happening. I didn't understand what you meant by 
a "ramp in time". Could you please elaborate?

Step-52 works fine, I'm getting exactly the same results as the online 
documentation. I looked at time_stepping.templates.h, I think there is a 
bug around line 730, delta_t_guess should be assigned the value of 
new_delta_t (the coarsened time step) rather than delta_t (old time step).

Thanks,
Vaibhav

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[deal.II] Re: How to find all the partial derivatives of the solution polynomial in deal.II

2016-09-16 Thread Daniel Arndt
Jiaqi,

Currently you can access first, second and third partial derivatives in 
FEValues. The FiniteElement class also implements fourth derivatives.
If this is sufficient for your purposes, then using 
FEValues*::third_derivative should be fine for you. I don't see a easier 
way at the moment.

Best,
Daniel

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