Re: [deal.II] deal.II on Mac OS Sierra

2017-11-07 Thread Pawan Takhar 
Hi Uwe,

I tried installing using Candi installer, but unfortunately it did not work 
for me. The application installed without any errors. However when I use 
the following commands I get error in the second and third steps:
1) cmake .  (It is able to find the dealII-candi as I have included it in 
the path)
2) make (numerous errors/warning message on this step. I am pasting those 
below.
.3) /step-1 (does not run).

I hope someone would compile .dmg file for the macOS High Sierra.

Thanks,
Pawan

Warning/error messages:
Scanning dependencies of target step-1
[ 50%] Building CXX object CMakeFiles/step-1.dir/step-1.cc.o
In file included from 
/Users/username/Documents/deal2/examples/step1/step-1.cc:22:
/Users/user/deal.ii-candi/deal.II-v8.5.1/include/deal.II/grid/tria.h:31:1: 
warning: 
  unknown warning group '-Wunused-but-set-parameter', ignored
  [-Wunknown-warning-option]
DEAL_II_DISABLE_EXTRA_DIAGNOSTICS
^
/Users/username/deal.ii-candi/deal.II-v8.5.1/include/deal.II/base/config.h:307:66:
 
note: 
  expanded from macro 'DEAL_II_DISABLE_EXTRA_DIAGNOSTICS'
_Pragma("GCC diagnostic ignored \"-Winfinite-recursion\"")   \
 ^
:44:25: note: expanded from here
 GCC diagnostic ignored "-Wunused-but-set-parameter"
^
In file included from 
/Users/username/Documents/deal2/examples/step1/step-1.cc:22:
/Users/username/deal.ii-candi/deal.II-v8.5.1/include/deal.II/grid/tria.h:31:1: 
warning: 
  unknown warning group '-Wunused-but-set-variable', ignored
  [-Wunknown-warning-option]
/Users/username/deal.ii-candi/deal.II-v8.5.1/include/deal.II/base/config.h:311:66:
 
note: 
  expanded from macro 'DEAL_II_DISABLE_EXTRA_DIAGNOSTICS'
_Pragma("GCC diagnostic ignored \"-Wdeprecated-declarations\"")  \
 ^
:45:25: note: expanded from here
 GCC diagnostic ignored "-Wunused-but-set-variable"
^
In file included from 
/Users/username/Documents/deal2/examples/step1/step-1.cc:22:
/Users/username/deal.ii-candi/deal.II-v8.5.1/include/deal.II/grid/tria.h:31:1: 
warning: 
  unknown warning group '-Wexpansion-to-defined', ignored
  [-Wunknown-warning-option]
/Users/username/deal.ii-candi/deal.II-v8.5.1/include/deal.II/base/config.h:312:66:
 
note: 
  expanded from macro 'DEAL_II_DISABLE_EXTRA_DIAGNOSTICS'
_Pragma("GCC diagnostic ignored \"-Wunused-but-set-variable\"")  \
 ^
:45:25: note: expanded from here
 GCC diagnostic ignored "-Wexpansion-to-defined"
^
In file included from 
/Users/username/Documents/deal2/examples/step1/step-1.cc:22:
/Users/username/deal.ii-candi/deal.II-v8.5.1/include/deal.II/grid/tria.h:31:1: 
warning: 
  unknown warning group '-Wmisleading-indentation', ignored
  [-Wunknown-warning-option]
/Users/username/deal.ii-candi/deal.II-v8.5.1/include/deal.II/base/config.h:314:66:
 
note: 
  expanded from macro 'DEAL_II_DISABLE_EXTRA_DIAGNOSTICS'
_Pragma("GCC diagnostic ignored \"-Wignored-attributes\"")   \
 ^
:45:25: note: expanded from here
 GCC diagnostic ignored "-Wmisleading-indentation"
^
In file included from 
/Users/username/Documents/deal2/examples/step1/step-1.cc:22:
/Users/username/deal.ii-candi/deal.II-v8.5.1/include/deal.II/grid/tria.h:31:1: 
warning: 
  unknown warning group '-Wint-in-bool-context', ignored
  [-Wunknown-warning-option]
/Users/username/deal.ii-candi/deal.II-v8.5.1/include/deal.II/base/config.h:318:66:
 
note: 
  expanded from macro 'DEAL_II_DISABLE_EXTRA_DIAGNOSTICS'
_Pragma("GCC diagnostic ignored \"-Wimplicit-fallthrough\"") \
 ^
:45:25: note: expanded from here
 GCC diagnostic ignored "-Wint-in-bool-context"
^
5 warnings generated.
[100%] Linking CXX executable step-1

[100%] Built target step-1

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Re: [deal.II] deal.II on Mac OS Sierra

2017-11-07 Thread Pawan Takhar 
Hi Uwe,

I tried installing using Candi installer, but unfortunately it did not work 
for me. The application installed without any errors. However when I use 
the following commands I get error in the second and third steps:
1) cmake .  (It is able to find the dealII-candi as I have included it in 
the path)
2) make (numerous errors/warning message on this step. I am pasting those 
below.
.3) /step-1 (does not run).

I hope someone would compile .dmg file for the macOS High Sierra.

Thanks,
Pawan

Warning/error messages:

*Scanning dependencies of target step-1*

[ 50%] Building CXX object CMakeFiles/step-1.dir/step-1.cc.o

In file included from 
/Users/username/Documents/deal2/examples/step1/step-1.cc:22:

*/Users/user/deal.ii-candi/deal.II-v8.5.1/include/deal.II/grid/tria.h:31:1: 
**warning: *

*  unknown warning group '-Wunused-but-set-parameter', ignored*

*  [-Wunknown-warning-option]*

DEAL_II_DISABLE_EXTRA_DIAGNOSTICS

*^*

*/Users/username/deal.ii-candi/deal.II-v8.5.1/include/deal.II/base/config.h:307:66:
 
note: *

  expanded from macro 'DEAL_II_DISABLE_EXTRA_DIAGNOSTICS'

_Pragma("GCC diagnostic ignored \"-Winfinite-recursion\"")   \

* ^*

*:44:25: note: *expanded from here

 GCC diagnostic ignored "-Wunused-but-set-parameter"

*^*

In file included from 
/Users/username/Documents/deal2/examples/step1/step-1.cc:22:

*/Users/username/deal.ii-candi/deal.II-v8.5.1/include/deal.II/grid/tria.h:31:1: 
**warning: *

*  unknown warning group '-Wunused-but-set-variable', ignored*

*  [-Wunknown-warning-option]*

*/Users/username/deal.ii-candi/deal.II-v8.5.1/include/deal.II/base/config.h:311:66:
 
note: *

  expanded from macro 'DEAL_II_DISABLE_EXTRA_DIAGNOSTICS'

_Pragma("GCC diagnostic ignored \"-Wdeprecated-declarations\"")  \

* ^*

*:45:25: note: *expanded from here

 GCC diagnostic ignored "-Wunused-but-set-variable"

*^*

In file included from 
/Users/username/Documents/deal2/examples/step1/step-1.cc:22:

*/Users/username/deal.ii-candi/deal.II-v8.5.1/include/deal.II/grid/tria.h:31:1: 
**warning: *

*  unknown warning group '-Wexpansion-to-defined', ignored*

*  [-Wunknown-warning-option]*

*/Users/username/deal.ii-candi/deal.II-v8.5.1/include/deal.II/base/config.h:312:66:
 
note: *

  expanded from macro 'DEAL_II_DISABLE_EXTRA_DIAGNOSTICS'

_Pragma("GCC diagnostic ignored \"-Wunused-but-set-variable\"")  \

* ^*

*:45:25: note: *expanded from here

 GCC diagnostic ignored "-Wexpansion-to-defined"

*^*

In file included from 
/Users/username/Documents/deal2/examples/step1/step-1.cc:22:

*/Users/username/deal.ii-candi/deal.II-v8.5.1/include/deal.II/grid/tria.h:31:1: 
**warning: *

*  unknown warning group '-Wmisleading-indentation', ignored*

*  [-Wunknown-warning-option]*

*/Users/username/deal.ii-candi/deal.II-v8.5.1/include/deal.II/base/config.h:314:66:
 
note: *

  expanded from macro 'DEAL_II_DISABLE_EXTRA_DIAGNOSTICS'

_Pragma("GCC diagnostic ignored \"-Wignored-attributes\"")   \

* ^*

*:45:25: note: *expanded from here

 GCC diagnostic ignored "-Wmisleading-indentation"

*^*

In file included from 
/Users/username/Documents/deal2/examples/step1/step-1.cc:22:

*/Users/username/deal.ii-candi/deal.II-v8.5.1/include/deal.II/grid/tria.h:31:1: 
**warning: *

*  unknown warning group '-Wint-in-bool-context', ignored*

*  [-Wunknown-warning-option]*

*/Users/username/deal.ii-candi/deal.II-v8.5.1/include/deal.II/base/config.h:318:66:
 
note: *

  expanded from macro 'DEAL_II_DISABLE_EXTRA_DIAGNOSTICS'

_Pragma("GCC diagnostic ignored \"-Wimplicit-fallthrough\"") \

* ^*

*:45:25: note: *expanded from here

 GCC diagnostic ignored "-Wint-in-bool-context"

*^*

5 warnings generated.

[100%] *Linking CXX executable step-1*

[100%] Built target step-1

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Re: [deal.II] A_inverse in step-57

2017-11-07 Thread Timo Heister 
> SparseILU still seems not to work. I attached my code here, if you could
> take a look, it is very easy to reproduce the issue:
> 1. compile and run it, you will see everything works as expected
> 2. comment out line 221 and uncomment line 222, the program just hangs.

Please try to debug the problem some more. Is the inner or outer
solver not converging? How are the residuals changing over the
iterations? In which step does it hang? Can you open it in a debugger?
What happens with a simpler and smaller testproblem, etc.. While there
might be a bug in deal.II that you are running into, I doubt that this
is the case here.

-- 
Timo Heister
http://www.math.clemson.edu/~heister/

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Re: [deal.II] A few questions

2017-11-07 Thread Timo Heister 
> — Is the support for geometric multigrid dependent on Trilinons/Petsc?

In serial: no. In parallel: if you are matrix-based then only Trilinos
currently. If you are matrix-free: no dependency.

> — Can deal.II be configured with both Trilinons and Petsc interfaces at the 
> same time?

Of course.

> — Is there support for complex variables simultaneously with real valued 
> variables in the solves?

Complex scalars are still a work-in-progress. We currently advise
people to split their PDE into real and imaginary parts and do the
linear algebra purely using real values.

> — Are there any applications with immersed FEM (cut-cell, etc.) with deal.II?

There was an incomplete tutorial (step-47) about this, but I don't
remember exactly what the status of it is. Sorry.

> — Can a different set of variables be defined on two different spatial 
> regions of the mesh (eg., fluid on one and structural on the other)? Does 
> this place any restrictions on multigrid preconditioning?

While you can use different variables in different regions using the
hp-FEM functionality, I have not seen this combined with multigrid
methods. This might be a lot of work to get working.

> — How easy is it to locally add Lagrange multipliers on a sub-domain or a 
> boundary in order to impose constraints and then solve the system? Can this 
> be done dynamically through the course of computations (ie., can the spatial 
> region of this application be varying throughout the course of the 
> simulation)?

I would probably reply with "not very easy" but I let others with more
experience jump in.

-- 
Timo Heister
http://www.math.clemson.edu/~heister/

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[deal.II] A few questions

2017-11-07 Thread Manav Bhatia 

Hi! 

  I am considering deal.II for a multiphysics application. A few of questions: 

— Is the support for geometric multigrid dependent on Trilinons/Petsc? 

— Can deal.II be configured with both Trilinons and Petsc interfaces at the 
same time? 

— Is there support for complex variables simultaneously with real valued 
variables in the solves? 

— Are there any applications with immersed FEM (cut-cell, etc.) with deal.II? 

— Can a different set of variables be defined on two different spatial regions 
of the mesh (eg., fluid on one and structural on the other)? Does this place 
any restrictions on multigrid preconditioning? 

— How easy is it to locally add Lagrange multipliers on a sub-domain or a 
boundary in order to impose constraints and then solve the system? Can this be 
done dynamically through the course of computations (ie., can the spatial 
region of this application be varying throughout the course of the simulation)? 

   I would appreciate your comments. 

Thanks,
Manav


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Re: [deal.II] Re: [aspect-devel] Fwd: Aspect installation error on OS X El Capitan

2017-11-07 Thread Timo Heister 
cross-posting also here:

This is caused by the fact that the binary was compiled with
optimizations that are CPU dependent and they fail if you run on older
hardware.

We are still struggling with getting the installers to work reliable,
but I just added a .dmg file for 8.5.1 here
https://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_dealii_dealii_releases_tag_v8.5.1=DwIFaQ=Ngd-ta5yRYsqeUsEDgxhcqsYYY1Xs5ogLxWPA_2Wlc4=4k7iKXbjGC8LfYxVJJXiaYVu6FRWmEjX38S7JmlS9Vw=sVpOvXGLo7QErSsl8bimvJCJPF2SSgH1mhpX4DJ1NVE=qZdJXcdJ_RHA7I1PcIuMSFEr6wRGXEvXd6Az7ex65z0=
  that should work
provided that you are using OSX 10.12 and not "high sierra" yet.

Can you please test and confirm if it works for you?

On Mon, Nov 6, 2017 at 9:15 PM, Wolfgang Bangerth
 wrote:
>
> Hiro,
> I don't know the answer (and I don't know whether there are enough people
> with Macs using ASPECT), so let me redirect you further to the deal.II
> mailing list (CC:ed).
>
> If you're not subscribed to the deal.II mailing list, you should be able to
> find answers on the online google group for this mailing list.
>
> Best
>  W.
>
>
> On 11/06/2017 03:14 PM, Hiroaki Matsui wrote:
>>
>> Hi, all,
>>
>> I have sent this question to CIG-MC mailing list,
>> but I found that here would be better place to discuss about it.
>>
>> I found that MPI compiler and mpirun command in dealii-8.5.app does not
>> run on my macbook with El Capitan (OS X 10.11.6)
>> with the illegal instruction. And, looking at information of gcc, this
>> package seems to be built for OS X 10.12.
>>
>> I wonder if this package can work on El Capitan.
>> If so, do we have to use an older version of deal ii for El Capitan?
>> Or, do we need another deal.ii-8.5.app for the older OS X?
>>
>> Hiro.
>>
>> bash-3.2$
>> /Applications/deal.II-8.5-brew.app/Contents/Resources/brew/bin/mpicc
>> Illegal instruction: 4
>> bash-3.2$
>> /Applications/deal.II-8.5-brew.app/Contents/Resources/brew/bin/mpic++
>> Illegal instruction: 4
>> bash-3.2$
>> /Applications/deal.II-8.5-brew.app/Contents/Resources/brew/bin/mpirun
>> Illegal instruction: 4
>> bash-3.2$
>> /Applications/deal.II-8.5-brew.app/Contents/Resources/brew/bin/gcc-6 -v
>> Using built-in specs.
>>
>> COLLECT_GCC=/Applications/deal.II-8.5-brew.app/Contents/Resources/brew/bin/gcc-6
>>
>> COLLECT_LTO_WRAPPER=/Applications/deal.II-8.5-brew.app/Contents/Resources/brew/Cellar/gcc/6.3.0_1/libexec/gcc/x86_64-apple-darwin16.4.0/6.3.0/lto-wrapper
>> Target: x86_64-apple-darwin16.4.0
>> Configured with: ../configure --build=x86_64-apple-darwin16.4.0
>> --prefix=/Applications/deal.II-8.5-brew.app/Contents/Resources/brew/Cellar/gcc/6.3.0_1
>> --libdir=/Applications/deal.II-8.5-brew.app/Contents/Resources/brew/Cellar/gcc/6.3.0_1/lib/gcc/6
>> --enable-languages=c,c++,objc,obj-c++,fortran --program-suffix=-6
>> --with-gmp=/Applications/deal.II-8.5-brew.app/Contents/Resources/brew/opt/gmp
>> --with-mpfr=/Applications/deal.II-8.5-brew.app/Contents/Resources/brew/opt/mpfr
>> --with-mpc=/Applications/deal.II-8.5-brew.app/Contents/Resources/brew/opt/libmpc
>> --with-isl=/Applications/deal.II-8.5-brew.app/Contents/Resources/brew/opt/isl
>> --with-system-zlib --enable-stage1-checking --enable-checking=release
>> --enable-lto --with-build-config=bootstrap-debug --disable-werror
>> --with-pkgversion='Homebrew GCC 6.3.0_1'
>> --with-bugurl=https://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_Homebrew_homebrew-2Dcore_issues=DwIFaQ=Ngd-ta5yRYsqeUsEDgxhcqsYYY1Xs5ogLxWPA_2Wlc4=4k7iKXbjGC8LfYxVJJXiaYVu6FRWmEjX38S7JmlS9Vw=sVpOvXGLo7QErSsl8bimvJCJPF2SSgH1mhpX4DJ1NVE=qD_7V50rP04N0FOkJkChWTsuJiM7uygomqdmeNFX5uI=
>>  
>> 
>> --disable-nls --enable-multilib --with-native-system-header-dir=/usr/include
>> --with-sysroot=/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.12.sdk
>> Thread model: posix
>> gcc version 6.3.0 (Homebrew GCC 6.3.0_1)
>>
>>
>>> 転送されたメッセージ：
>>>
>>> *差出人: *Hiroaki Matsui >> >
>>> *件名: **Re: Aspect installation error*
>>> *日付: *2017年11月3日 16:43:58 GMT-7
>>> *宛先: *"Hammond, Noah" >> >, cig...@geodynamics.org
>>> 
>>>
>>> Dear Hammond,
>>>
>>> Thank you for asking the installation problem.
>>>
>>> I made the instruction with Deal II v8.2.1 and I also meet the same
>>> problem by using deal II v8.5.
>>> Then, this document becomes outdated instruction.
>>>
>>> I am solving this problem, and I also ask if anyone have already install
>>> the latest ASPECT with the latest deal ii. on the mailing list.
>>>
>>> Have a good weekend,
>>> Hiro.
>>>
 2017/11/03 12:53、Hammond, Noah

Re: [deal.II] A_inverse in step-57

2017-11-07 Thread Wolfgang Bangerth 


Jie,

I wrapped up my A preconditioner with an inner CG solver (I am using IMEX 
scheme which moves the convection term to the RHS so A is symmetric) but the 
SparseILU still seems not to work.


But if A is symmetric, then you can use AMG again, and there is likely no 
better preconditioner for that other than a geometric multigrid.



I attached my code here, if you could take 
a look, it is very easy to reproduce the issue:

1. compile and run it, you will see everything works as expected
2. comment out line 221 and uncomment line 222, the program just hangs.

Wolfgang does have a point: if I were able to use a direct solver on A then I 
might as well apply it on the whole system. I think I should get SparseILU 
working at least.


The problem with the SparseILU class is that it (i) is only an approximation 
of an inverse matrix and, as a preconditioner far worse than the direct 
solver, (ii) our implementation is neither very good nor optimized for 
performance. There is also the issue that *any* ILU implementation that is 
good will have *many* parameters, such as how to deal with fill-in, 
strengthening the diagonal, pivoting, etc.


The deal.II SparseILU class is almost certainly not good enough to deal with 
complicated problems such as yours. You may have better luck with the 
implementations in PETSc or Trilinos, but in the end as Timo already said: the 
question of what preconditioners to use for the N-S equations (at least if you 
move the advection term to the left hand side) is an active research question 
where the answer is neither obvious nor settled.


This is also part of why projection schemes are so attractive: They don't 
require solving the coupled problem.


Best
 W.


--

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

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