date:20180918

Re: [deal.II] Can GridIn read 3D quad mesh?

2018-09-18 Thread Jean-Paul Pelteret

Dear Shawn,

The GridIn::read_abaqus() function is currently not equipped to deal with the 
codimension 1 case. I might be able to find some time to look at this in the 
next few days though. In addition to the mesh file that you’ve already given 
us, may you please construct and give us a fully structured grid in codimension 
1 (so something like a rectangle warped in the third dimension) that also has 
some boundary colouring? That would help a great deal with implementing this 
feature, and would also ensure that the assignment of boundary ID’s is possible.

Best,
Jean-Paul

> On 19 Sep 2018, at 01:38, Yuxiang Wang  wrote:
> 
> Prof. Bangerth,
> 
> Thank you for the prompt response! Yes please find attached the minimal 
> program. The main body is pretty short (see below), modified from step-49. 
> Please let me know if you cannot reproduce it!
> 
> ```
> int main ()
> {
>   Triangulation<2, 3> triangulation;
> 
>   GridIn<2, 3> gridin;
>   gridin.attach_triangulation(triangulation);
>   std::ifstream f("mesh.inp");
>   gridin.read_abaqus(f);
> 
>   GridOut gridout;
>   std::ofstream fout("mesh.vtu");
>   gridout.write_vtu(triangulation, fout);
> }
> 
> ```
> 
> 
> Shawn
> 
> On Tue, Sep 18, 2018 at 4:28 PM Wolfgang Bangerth  > wrote:
> On 09/18/2018 03:18 PM, Yuxiang Wang wrote:
> > 
> > Thank you for the pointer! I changed my code as you suggested and it 
> > finished 
> > running.
> 
> Great!
> 
> 
> > However, when I opened the output file (mesh.vtu), the 3D mesh was 
> > projected 
> > to a 2D plane of z=0, and lost its 3D features. Was that expected behavior?
> 
> No. Are you saying that if you read a mesh, then immediately output it again, 
> that the z-coordinate is lost? If that's correct, then that's a bug and it 
> would be nice to have a small program and input file that demonstrates this.
> 
> Best
>   W.
> 
> -- 
> 
> Wolfgang Bangerth  email: bange...@colostate.edu 
> 
> www: http://www.math.colostate.edu/~bangerth/ 
> 
> 
> -- 
> 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 
> 
> --- 
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> .
> 
> 
> -- 
> Yuxiang "Shawn" Wang, PhD
> yw...@virginia.edu 
> +1 (434) 284-0836
> 
> -- 
> The deal.II project is located at http://www.dealii.org/ 
> 
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> 
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Re: [deal.II] Compilation error in dealii development version (9.1.0-pre, shortrev c6b7876) using gcc/7.2.0 compiler and cuda/9.2

2018-09-18 Thread Sambit Das

It seems the issue is related to -DDEAL_II_WITH_64BIT_INDICES=ON.
If I set -DDEAL_II_WITH_64BIT_INDICES=OFF, the compilation worked fine.

Best,
Sambit

On Tuesday, September 18, 2018 at 11:17:43 PM UTC-5, Sambit Das wrote:
>
> Hi Bruno and Jean,
>
> Based on the discussion in  (https://github.com/dealii/dealii/issues/7204 
> )
>  
> I used the temporary fix of  setting 
> SET(ZLIB_INCLUDE_DIR  "/usr/local/include") in FindZLIB.cmake, which 
> addressed the above compilation issue.
>
> However, I get a new compilation error now:
>
> *[ 59%] Building CXX object 
> source/particles/CMakeFiles/obj_particle_debug.dir/particle.cc.o*
> */gpfs/gpfs0/groups/gavini/dsambit/software/dealii/dealii/include/deal.II/matrix_free/cuda_hanging_nodes_internal.h(286):
>  
> error: no suitable user-defined conversion from "std::vector std::allocator>" to "std::vector std::allocator>" exists*
> *  detected during:*
> *instantiation of "void 
> dealii::CUDAWrappers::internal::HangingNodes::setup_constraints(std::vector  
> int, std::allocator> &, const CellIterator &, unsigned int &) 
> const [with dim=2, 
> CellIterator=dealii::FilteredIterator  
> 2>, false>>>]" *
> */gpfs/gpfs0/groups/gavini/dsambit/software/dealii/dealii/include/deal.II/matrix_free/cuda_matrix_free.templates.h(288):
>  
> here*
> *instantiation of "void 
> dealii::CUDAWrappers::internal::ReinitHelper Number>::get_cell_data(const CellFilter &, unsigned int) [with dim=2, 
> Number=float, 
> CellFilter=dealii::FilteredIterator  
> 2>, false>>>]" *
> */gpfs/gpfs0/groups/gavini/dsambit/software/dealii/dealii/include/deal.II/matrix_free/cuda_matrix_free.templates.h(578):
>  
> here*
> *instantiation of "void dealii::CUDAWrappers::MatrixFree Number>::reinit(const dealii::Mapping &, const 
> dealii::DoFHandler &, const dealii::AffineConstraints &, 
> const dealii::Quadrature<1> &, dealii::CUDAWrappers::MatrixFree Number>::AdditionalData) [with dim=2, Number=float]" *
> */gpfs/gpfs0/groups/gavini/dsambit/software/dealii/dealii/source/matrix_free/cuda_matrix_free.cu
>  
> (25): here*
>
> The same error occurs with both bundled BOOST as well linking to a 
> manually installed BOOST/1.66.0. 
>
> Do you think the above compilation error is related to the original issue 
> in  (https://github.com/dealii/dealii/issues/7204 
> 
> )?
>
> Thank you,
> Sambit
>
> On Tuesday, September 18, 2018 at 1:02:07 PM UTC-5, Sambit Das wrote:
>>
>> Hi Jean-Paul,
>>
>> Thanks for referring me to the github issue (
>> https://github.com/dealii/dealii/issues/7204 
>> ).
>>  
>> It does seem they are related issues.
>> I will keep following the github issue.
>>
>> Thank you,
>> Sambit
>>
>> On Tuesday, September 18, 2018 at 11:53:17 AM UTC-5, Jean-Paul Pelteret 
>> wrote:
>>>
>>> Hi Sambit,
>>>
>>> Your new error looks like the same one reported (
>>> https://github.com/dealii/dealii/issues/7204 
>>> )
>>>  yesterday 
>>> so I don’t think that using another version of CMake will fix it. I’m not 
>>> quite sure what the answer to the problem is, since the discussion is 
>>> ongoing.
>>>
>>> Best,
>>> Jean-Paul
>>>
>>> On 18 Sep 2018, at 18:47, Sambit Das  wrote:
>>>
>>> Hi Bruno,
>>>
>>> Thank you for your reply. Now I tried CMake 3.9.6 but got the following 
>>> compilation error
>>>
>>> [ 54%] Building CUDA object 
>>> source/base/CMakeFiles/obj_base_debug.dir/cuda.cu.o
>>> In file included from 
>>> /gpfs/gpfs0/software/rhel72/packages/cuda/9.2/include/crt/math_functions.h:8853:0,
>>>  from 
>>> /gpfs/gpfs0/software/rhel72/packages/cuda/9.2/include/crt/common_functions.h:257,
>>>  from 
>>> /gpfs/gpfs0/software/rhel72/packages/cuda/9.2/include/common_functions.h:50,
>>>  from 
>>> /gpfs/gpfs0/software/rhel72/packages/cuda/9.2/include/cuda_runtime.h:115,
>>>  from :0:
>>> /gpfs/gpfs0/software/rhel72/packages/gcc/7.2.0/include/c++/7.2.0/cmath:45:15:
>>>  
>>> fatal error: math.h: No such file or directory
>>>  #include_next 
>>>^~~~
>>> compilation terminated.
>>>
>>> Should I try CMake 3.10/11?
>>>
>>> Thank you,
>>> Sambit
>>>
>>> On Tuesday, September 18, 2018 at 7:27:38 AM UTC-5, Bruno Turcksin wrote:

 Sambit,

 Can you try with a different version of CMake. We do not support CMake 
 3.12 with CUDA at the moment.

 Best,

 Bruno

 On Monday, September 17, 2018 at 8:56:31 PM UTC-4,

Re: [deal.II] Compilation error in dealii development version (9.1.0-pre, shortrev c6b7876) using gcc/7.2.0 compiler and cuda/9.2

2018-09-18 Thread Sambit Das

Hi Bruno and Jean,

Based on the discussion in  (https://github.com/dealii/dealii/issues/7204 
)
 
I used the temporary fix of  setting 
SET(ZLIB_INCLUDE_DIR  "/usr/local/include") in FindZLIB.cmake, which 
addressed the above compilation issue.

However, I get a new compilation error now:

*[ 59%] Building CXX object 
source/particles/CMakeFiles/obj_particle_debug.dir/particle.cc.o*
*/gpfs/gpfs0/groups/gavini/dsambit/software/dealii/dealii/include/deal.II/matrix_free/cuda_hanging_nodes_internal.h(286):
 
error: no suitable user-defined conversion from "std::vector>" to "std::vector>" exists*
*  detected during:*
*instantiation of "void 
dealii::CUDAWrappers::internal::HangingNodes::setup_constraints(std::vector> &, const CellIterator &, unsigned int &) 
const [with dim=2, 
CellIterator=dealii::FilteredIterator, false>>>]" *
*/gpfs/gpfs0/groups/gavini/dsambit/software/dealii/dealii/include/deal.II/matrix_free/cuda_matrix_free.templates.h(288):
 
here*
*instantiation of "void 
dealii::CUDAWrappers::internal::ReinitHelper::get_cell_data(const CellFilter &, unsigned int) [with dim=2, 
Number=float, 
CellFilter=dealii::FilteredIterator, false>>>]" *
*/gpfs/gpfs0/groups/gavini/dsambit/software/dealii/dealii/include/deal.II/matrix_free/cuda_matrix_free.templates.h(578):
 
here*
*instantiation of "void dealii::CUDAWrappers::MatrixFree::reinit(const dealii::Mapping &, const 
dealii::DoFHandler &, const dealii::AffineConstraints &, 
const dealii::Quadrature<1> &, dealii::CUDAWrappers::MatrixFree::AdditionalData) [with dim=2, Number=float]" *
*/gpfs/gpfs0/groups/gavini/dsambit/software/dealii/dealii/source/matrix_free/cuda_matrix_free.cu(25):
 
here*

The same error occurs with both bundled BOOST as well linking to a manually 
installed BOOST/1.66.0. 

Do you think the above compilation error is related to the original issue 
in  (https://github.com/dealii/dealii/issues/7204 

)?

Thank you,
Sambit

On Tuesday, September 18, 2018 at 1:02:07 PM UTC-5, Sambit Das wrote:
>
> Hi Jean-Paul,
>
> Thanks for referring me to the github issue (
> https://github.com/dealii/dealii/issues/7204 
> ).
>  
> It does seem they are related issues.
> I will keep following the github issue.
>
> Thank you,
> Sambit
>
> On Tuesday, September 18, 2018 at 11:53:17 AM UTC-5, Jean-Paul Pelteret 
> wrote:
>>
>> Hi Sambit,
>>
>> Your new error looks like the same one reported (
>> https://github.com/dealii/dealii/issues/7204 
>> )
>>  yesterday 
>> so I don’t think that using another version of CMake will fix it. I’m not 
>> quite sure what the answer to the problem is, since the discussion is 
>> ongoing.
>>
>> Best,
>> Jean-Paul
>>
>> On 18 Sep 2018, at 18:47, Sambit Das  wrote:
>>
>> Hi Bruno,
>>
>> Thank you for your reply. Now I tried CMake 3.9.6 but got the following 
>> compilation error
>>
>> [ 54%] Building CUDA object 
>> source/base/CMakeFiles/obj_base_debug.dir/cuda.cu.o
>> In file included from 
>> /gpfs/gpfs0/software/rhel72/packages/cuda/9.2/include/crt/math_functions.h:8853:0,
>>  from 
>> /gpfs/gpfs0/software/rhel72/packages/cuda/9.2/include/crt/common_functions.h:257,
>>  from 
>> /gpfs/gpfs0/software/rhel72/packages/cuda/9.2/include/common_functions.h:50,
>>  from 
>> /gpfs/gpfs0/software/rhel72/packages/cuda/9.2/include/cuda_runtime.h:115,
>>  from :0:
>> /gpfs/gpfs0/software/rhel72/packages/gcc/7.2.0/include/c++/7.2.0/cmath:45:15:
>>  
>> fatal error: math.h: No such file or directory
>>  #include_next 
>>^~~~
>> compilation terminated.
>>
>> Should I try CMake 3.10/11?
>>
>> Thank you,
>> Sambit
>>
>> On Tuesday, September 18, 2018 at 7:27:38 AM UTC-5, Bruno Turcksin wrote:
>>>
>>> Sambit,
>>>
>>> Can you try with a different version of CMake. We do not support CMake 
>>> 3.12 with CUDA at the moment.
>>>
>>> Best,
>>>
>>> Bruno
>>>
>>> On Monday, September 17, 2018 at 8:56:31 PM UTC-4, Sambit Das wrote:

 Dear all,

 I am trying to compile the latest development version of dealii 
 (9.1.0-pre, shortrev c6b7876) using gcc/7.2.0, 
 openmpi/3.0.0/gcc/7.2.0,  cuda/9.2 and cmake-3.12.2. 

 During compilation I get the following error:

 [ 57%] Building CUDA object 
 source/base/CMakeFiles/obj_base_debug.dir/cuda.cu.o
 In file included from

Re: [deal.II] Re: Can GridIn read 3D quad mesh?

2018-09-18 Thread Yuxiang Wang

Prof. Bangerth,

Thank you for the prompt response! Yes please find attached the minimal
program. The main body is pretty short (see below), modified from step-49.
Please let me know if you cannot reproduce it!

```
int main ()
{
  Triangulation<2, 3> triangulation;

  GridIn<2, 3> gridin;
  gridin.attach_triangulation(triangulation);
  std::ifstream f("mesh.inp");
  gridin.read_abaqus(f);

  GridOut gridout;
  std::ofstream fout("mesh.vtu");
  gridout.write_vtu(triangulation, fout);
}

```


Shawn

On Tue, Sep 18, 2018 at 4:28 PM Wolfgang Bangerth 
wrote:

> On 09/18/2018 03:18 PM, Yuxiang Wang wrote:
> >
> > Thank you for the pointer! I changed my code as you suggested and it
> finished
> > running.
>
> Great!
>
>
> > However, when I opened the output file (mesh.vtu), the 3D mesh was
> projected
> > to a 2D plane of z=0, and lost its 3D features. Was that expected
> behavior?
>
> No. Are you saying that if you read a mesh, then immediately output it
> again,
> that the z-coordinate is lost? If that's correct, then that's a bug and it
> would be nice to have a small program and input file that demonstrates
> this.
>
> Best
>   W.
>
> --
> 
> Wolfgang Bangerth  email: bange...@colostate.edu
> www: http://www.math.colostate.edu/~bangerth/
>
> --
> 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
> ---
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> Google Groups "deal.II User Group" group.
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>


-- 
Yuxiang "Shawn" Wang, PhD
yw...@virginia.edu
+1 (434) 284-0836

-- 
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#include 
#include 
#include 
#include 
#include 
#include 
#include 
#include 

#include 

#include 

using namespace dealii;




int main ()
{
  Triangulation<2, 3> triangulation;

  GridIn<2, 3> gridin;
  gridin.attach_triangulation(triangulation);
  std::ifstream f("mesh.inp");
  gridin.read_abaqus(f);

  GridOut gridout;
  std::ofstream fout("mesh.vtu");
  gridout.write_vtu(triangulation, fout);
}


mesh.inp
Description: Binary data
##
#  CMake script for the step-1 tutorial program:
##

# Set the name of the project and target:
SET(TARGET "step-49")

# Declare all source files the target consists of:
SET(TARGET_SRC
  ${TARGET}.cc
  # You can specify additional files here!
  )

# Usually, you will not need to modify anything beyond this point...

CMAKE_MINIMUM_REQUIRED(VERSION 2.8.8)

FIND_PACKAGE(deal.II 8.0 QUIET
  HINTS ${deal.II_DIR} ${DEAL_II_DIR} ../ ../../ $ENV{DEAL_II_DIR}
  )
IF(NOT ${deal.II_FOUND})
  MESSAGE(FATAL_ERROR "\n"
"*** Could not locate deal.II. ***\n\n"
"You may want to either pass a flag -DDEAL_II_DIR=/path/to/deal.II to 
cmake\n"
"or set an environment variable \"DEAL_II_DIR\" that contains this path."
)
ENDIF()

DEAL_II_INITIALIZE_CACHED_VARIABLES()
PROJECT(${TARGET})
DEAL_II_INVOKE_AUTOPILOT()


mesh.vtu
Description: Binary data

Re: [deal.II] Re: Can GridIn read 3D quad mesh?

2018-09-18 Thread Wolfgang Bangerth

On 09/18/2018 03:18 PM, Yuxiang Wang wrote:
> 
> Thank you for the pointer! I changed my code as you suggested and it finished 
> running.

Great!


> However, when I opened the output file (mesh.vtu), the 3D mesh was projected 
> to a 2D plane of z=0, and lost its 3D features. Was that expected behavior?

No. Are you saying that if you read a mesh, then immediately output it again, 
that the z-coordinate is lost? If that's correct, then that's a bug and it 
would be nice to have a small program and input file that demonstrates this.

Best
  W.

-- 

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

-- 
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[deal.II] PhD position on polymer electrolyte fuel cell modeling using deal.II

2018-09-18 Thread Marc Secanell Gallart

Dear deal.ii users,

I am currently looking for a PhD student to work on the development of our
open-source polymer electrolyte fuel cell simulation framework based on
deal.ii. Our research group has been developing the framework for several
years (see www.openfcst.org) and now we would like to extend our
micro-scale and macro-scale fuel cell models to account for transient
phenomena, such as start-up and degradation, as well as to extend the
framework to other electrochemical systems such as batteries. You would be
in charge of working in this area in combination with at least four other
developers.

The PhD student would have a fellowship for four-years with a minimum
stipend of $25,000/yr to  cover tuition and living expenses. The starting
date would be as early as Janaury 2019, but it could be as late as
September 2019. The position is at the Energy Systems Design Laboratory in
the Mechanical Engineering Department at the University of Alberta (One of
the top research intensive universities in Canada). Prof. Secanell would be
your primary supervisor (see https://scholar.google.ca/citations?user=
NjRIwW0J=en).

Applicants should have earned an M.Sc. degree in either Mathematics or
Mechanical/Chemical engineering in the last five years; should : a) have
experience in finite elements, deal.ii and programming in C++; b) have
strong communication and writing skills; and, c) be ready to work in a team.


If you are interested, please email your detailed CV to secan...@ualberta.ca
 along with your most significant journal/conference publication.

For more information about my research laboratory please go to:
http://www.mece.ualberta.ca/groups/energysystemsdesign/

Best,

Marc

*About the Energy Systems Design Laboratory* (http://http://esdlab.mece.
ualberta.ca)

Founded in 2009, the ESDLab is a research team at the University of Alberta
focused on the design of sustainable electrochemical energy systems. The
laboratory has both a numerical and an experimental group. The numerical
group is responsible for the development of OpenFCST, an open-source fuel
cell and electrolyzer simulation framework, and CoolIT, a wet cooling tower
analysis software. The experimental group is responsible for the
fabrication, characterization and testing of polymer electrolyte fuel cells
and electrolyzers to provide validation data to the modeling team.


*About the University of Alberta*
Founded in 1908, University of Alberta is one of Canada's foremost
research-intensive universities with an operating budget of over one
billion dollars annually; external research funding is approximately $500
million per year. The University has about 37,000 students at BSc, MSc, and
PhD levels. The Faculty of Engineering is among the top 5% in size in North
America with over 4,000 undergraduate and 1,500 graduate students. The
Department of Mechanical Engineering has more than 750 undergraduate and
over 250 graduate students. For more information see the Department of
Mechanical Engineering website.


*About the City of Edmonton*
The Greater Edmonton area has a population of over one million people and
offers a diverse array of cultural and sporting activities year round,
which has earned Edmonton the nickname of Festival City. Edmonton is an
international city, as evident by over seventy cultures from all over the
world that were represented in the recent annual Heritage Festival.
Edmonton's cost of living is competitive and favourable when compared with
other major cities in Canada. Edmonton is only few hours from the Rocky
Mountains and Jasper and Banff National Parks, which offer some of the
finest skiing, kayaking, cycling, hiking, and camping in the world. The
University is located centrally on the banks of the North Saskatchewan
River near downtown Edmonton.

-- 




Marc Secanell, Ph.D., P.Eng.

Associate Professor

Energy Systems Design Laboratory ( http://www.esdlab.mece.ualberta.ca/ )

Department of Mechanical Engineering

University of Alberta
10-358 Donadeo Innovation Centre for Engineering,
9211-116 Street NW,
Edmonton, AB, Canada T6G 1H9

Phone: (780) 490 8808 (cell)

(780) 492-6961 (office)

E-mail: secan...@ualberta.ca

Confidentiality notice: Emails sent to secan...@ualberta.ca are forwarded
to a Google-supported email account. Emails, attachments, documents and
calendaring data, stored, received and sent through this University account
may be transmitted to and stored on servers outside of the University,
Alberta or Canada. The University of Alberta cannot and does not guarantee
protection against the possible disclosure of your data including, without
limitation, against possible secret disclosures of data to a foreign
authority as a consequence of foreign laws.




-- 
The

Re: [deal.II] Re: Can GridIn read 3D quad mesh?

2018-09-18 Thread Yuxiang Wang

Hi Professor Bangerth,

Thank you for the pointer! I changed my code as you suggested and it 
finished running.

However, when I opened the output file (mesh.vtu), the 3D mesh was 
projected to a 2D plane of z=0, and lost its 3D features. Was that expected 
behavior?

Shawn

On Tuesday, September 18, 2018 at 1:56:19 PM UTC-7, Wolfgang Bangerth wrote:
>
> On 09/18/2018 02:40 PM, Yuxiang Wang wrote: 
> > 
> > Thank you for your help! I just tried a code snippet (modified step-49) 
> below 
> > and it does not work, either when I set the dim=2 or dim=3. 
>
> If you want to use quadrilateral (2d) meshes embedded in 3d, then you need 
> to use 
>Triangulation<2,3> 
>GridIn<2,3> 
> etc. 
>
> The 2 is the dimension of cells, the 3 the dimension of the space in which 
> they live. 
>
> Best 
>   W. 
>
> -- 
>  
> Wolfgang Bangerth  email: bang...@colostate.edu 
>  
> www: http://www.math.colostate.edu/~bangerth/ 
>
>

-- 
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Re: [deal.II] Re: Can GridIn read 3D quad mesh?

2018-09-18 Thread Wolfgang Bangerth

On 09/18/2018 02:40 PM, Yuxiang Wang wrote:
> 
> Thank you for your help! I just tried a code snippet (modified step-49) below 
> and it does not work, either when I set the dim=2 or dim=3.

If you want to use quadrilateral (2d) meshes embedded in 3d, then you need to 
use
   Triangulation<2,3>
   GridIn<2,3>
etc.

The 2 is the dimension of cells, the 3 the dimension of the space in which 
they live.

Best
  W.

-- 

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

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[deal.II] Re: Can GridIn read 3D quad mesh?

2018-09-18 Thread Yuxiang Wang

Oh and another detail - the mesh is not really 2D mesh because the four 
nodes of a quad element may not be co-planar. Therefore, there does not 
exist a transform that can reduce the mesh to 2D.

Shawn

On Monday, September 17, 2018 at 12:07:43 PM UTC-7, Daniel Arndt wrote:
>
> Shawn,
>
> If I understand correctly you want to read a 2D mesh embedded in a 
> three-dimensional space.
> Which mesh format are you interested in? 
> At least, GridIn::read_ucd and GridIn::read_msh should be able to do that.
>
> If you experience problems, we like to here about that as well. 
>
> Best,
> Daniel
>
>

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Re: [deal.II] Re: Can GridIn read 3D quad mesh?

2018-09-18 Thread Yuxiang Wang

Hi Daniel,

Thank you for your help! I just tried a code snippet (modified step-49)
below and it does not work, either when I set the dim=2 or dim=3.

```
int main ()
{
  Triangulation<2> triangulation;

  GridIn<2> gridin;
  gridin.attach_triangulation(triangulation);
  std::ifstream f("mesh.inp");
  gridin.read_abaqus(f);

  GridOut gridout;
  std::ofstream fout("mesh.vtu");
  gridout.write_vtu(triangulation, fout);
}
```

The complete code is attached at the end of this email. If you don't mind,
could you help provide any guesses in what potentially went wrong?

Shawn

On Mon, Sep 17, 2018 at 12:07 PM Daniel Arndt <
daniel.ar...@iwr.uni-heidelberg.de> wrote:

> Shawn,
>
> If I understand correctly you want to read a 2D mesh embedded in a
> three-dimensional space.
> Which mesh format are you interested in?
> At least, GridIn::read_ucd and GridIn::read_msh should be able to do that.
>
> If you experience problems, we like to here about that as well.
>
> Best,
> Daniel
>
> --
> 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
> ---
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-- 
Yuxiang "Shawn" Wang, PhD
yw...@virginia.edu
+1 (434) 284-0836

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##
#  CMake script for the step-1 tutorial program:
##

# Set the name of the project and target:
SET(TARGET "step-49")

# Declare all source files the target consists of:
SET(TARGET_SRC
  ${TARGET}.cc
  # You can specify additional files here!
  )

# Usually, you will not need to modify anything beyond this point...

CMAKE_MINIMUM_REQUIRED(VERSION 2.8.8)

FIND_PACKAGE(deal.II 8.0 QUIET
  HINTS ${deal.II_DIR} ${DEAL_II_DIR} ../ ../../ $ENV{DEAL_II_DIR}
  )
IF(NOT ${deal.II_FOUND})
  MESSAGE(FATAL_ERROR "\n"
"*** Could not locate deal.II. ***\n\n"
"You may want to either pass a flag -DDEAL_II_DIR=/path/to/deal.II to 
cmake\n"
"or set an environment variable \"DEAL_II_DIR\" that contains this path."
)
ENDIF()

DEAL_II_INITIALIZE_CACHED_VARIABLES()
PROJECT(${TARGET})
DEAL_II_INVOKE_AUTOPILOT()

#include 
#include 
#include 
#include 
#include 
#include 
#include 
#include 

#include 

#include 

using namespace dealii;




int main ()
{
  Triangulation<2> triangulation;

  GridIn<2> gridin;
  gridin.attach_triangulation(triangulation);
  std::ifstream f("mesh.inp");
  gridin.read_abaqus(f);

  GridOut gridout;
  std::ofstream fout("mesh.vtu");
  gridout.write_vtu(triangulation, fout);
}


mesh.inp
Description: Binary data

Re: [deal.II] Compilation error in dealii development version (9.1.0-pre, shortrev c6b7876) using gcc/7.2.0 compiler and cuda/9.2

2018-09-18 Thread Sambit Das

Hi Jean-Paul,

Thanks for referring me to the github issue (
https://github.com/dealii/dealii/issues/7204 
).
 
It does seem they are related issues.
I will keep following the github issue.

Thank you,
Sambit

On Tuesday, September 18, 2018 at 11:53:17 AM UTC-5, Jean-Paul Pelteret 
wrote:
>
> Hi Sambit,
>
> Your new error looks like the same one reported (
> https://github.com/dealii/dealii/issues/7204 
> )
>  yesterday 
> so I don’t think that using another version of CMake will fix it. I’m not 
> quite sure what the answer to the problem is, since the discussion is 
> ongoing.
>
> Best,
> Jean-Paul
>
> On 18 Sep 2018, at 18:47, Sambit Das > 
> wrote:
>
> Hi Bruno,
>
> Thank you for your reply. Now I tried CMake 3.9.6 but got the following 
> compilation error
>
> [ 54%] Building CUDA object 
> source/base/CMakeFiles/obj_base_debug.dir/cuda.cu.o
> In file included from 
> /gpfs/gpfs0/software/rhel72/packages/cuda/9.2/include/crt/math_functions.h:8853:0,
>  from 
> /gpfs/gpfs0/software/rhel72/packages/cuda/9.2/include/crt/common_functions.h:257,
>  from 
> /gpfs/gpfs0/software/rhel72/packages/cuda/9.2/include/common_functions.h:50,
>  from 
> /gpfs/gpfs0/software/rhel72/packages/cuda/9.2/include/cuda_runtime.h:115,
>  from :0:
> /gpfs/gpfs0/software/rhel72/packages/gcc/7.2.0/include/c++/7.2.0/cmath:45:15: 
> fatal error: math.h: No such file or directory
>  #include_next 
>^~~~
> compilation terminated.
>
> Should I try CMake 3.10/11?
>
> Thank you,
> Sambit
>
> On Tuesday, September 18, 2018 at 7:27:38 AM UTC-5, Bruno Turcksin wrote:
>>
>> Sambit,
>>
>> Can you try with a different version of CMake. We do not support CMake 
>> 3.12 with CUDA at the moment.
>>
>> Best,
>>
>> Bruno
>>
>> On Monday, September 17, 2018 at 8:56:31 PM UTC-4, Sambit Das wrote:
>>>
>>> Dear all,
>>>
>>> I am trying to compile the latest development version of dealii 
>>> (9.1.0-pre, shortrev c6b7876) using gcc/7.2.0, 
>>> openmpi/3.0.0/gcc/7.2.0,  cuda/9.2 and cmake-3.12.2. 
>>>
>>> During compilation I get the following error:
>>>
>>> [ 57%] Building CUDA object 
>>> source/base/CMakeFiles/obj_base_debug.dir/cuda.cu.o
>>> In file included from 
>>> /gpfs/gpfs0/groups/gavini/dsambit/software/dealii/dealii/include/deal.II/base/cuda.h:19:0,
>>>  from 
>>> /gpfs/gpfs0/groups/gavini/dsambit/software/dealii/dealii/source/base/
>>> cuda.cu:16:
>>> /gpfs/gpfs0/groups/gavini/dsambit/software/dealii/build/include/deal.II/base/config.h:421:12:
>>>  
>>> fatal error: mpi.h: No such file or directory
>>>  #  include 
>>> ^~~
>>> compilation terminated.
>>>
>>>
>>> I have attached the detailed.log file. 
>>>
>>> I have used the following configuration line:
>>> cmake  -DDEAL_II_CXX_FLAGS_RELEASE="-O3" -DDEAL_II_WITH_CXX17=OFF 
>>> -DCMAKE_C_COMPILER=mpicc -DCMAKE_CXX_COMPILER=mpicxx 
>>>  -DCMAKE_Fortran_COMPILER=mpif90 -DDEAL_II_WITH_CUDA=ON 
>>> -DDEAL_II_COMPONENT_EXAMPLES=OFF
>>>  -DDEAL_II_WITH_MPI=ON -DDEAL_II_WITH_64BIT_INDICES=ON
>>>  
>>> -DP4EST_DIR="/gpfs/gpfs0/groups/gavini/dsambit/software/p4est/installGcc7.2.0"
>>>   
>>> ../dealii
>>>
>>>  Interestingly, if I remove -DDEAL_II_WITH_CUDA=ON, compilation is 
>>> successful. I am wondering if I am missing any cuda related compilation 
>>> flags.
>>>
>>> Thanks a lot in advance,
>>>
>>> Best,
>>> Sambit
>>>
>>
> -- 
> 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
> --- 
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>
>
>

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Re: [deal.II] Compilation error in dealii development version (9.1.0-pre, shortrev c6b7876) using gcc/7.2.0 compiler and cuda/9.2

2018-09-18 Thread Jean-Paul Pelteret

Hi Sambit,

Your new error looks like the same one reported 
(https://github.com/dealii/dealii/issues/7204 
) yesterday so I don’t think that 
using another version of CMake will fix it. I’m not quite sure what the answer 
to the problem is, since the discussion is ongoing.

Best,
Jean-Paul

> On 18 Sep 2018, at 18:47, Sambit Das  wrote:
> 
> Hi Bruno,
> 
> Thank you for your reply. Now I tried CMake 3.9.6 but got the following 
> compilation error
> 
> [ 54%] Building CUDA object 
> source/base/CMakeFiles/obj_base_debug.dir/cuda.cu.o
> In file included from 
> /gpfs/gpfs0/software/rhel72/packages/cuda/9.2/include/crt/math_functions.h:8853:0,
>  from 
> /gpfs/gpfs0/software/rhel72/packages/cuda/9.2/include/crt/common_functions.h:257,
>  from 
> /gpfs/gpfs0/software/rhel72/packages/cuda/9.2/include/common_functions.h:50,
>  from 
> /gpfs/gpfs0/software/rhel72/packages/cuda/9.2/include/cuda_runtime.h:115,
>  from :0:
> /gpfs/gpfs0/software/rhel72/packages/gcc/7.2.0/include/c++/7.2.0/cmath:45:15: 
> fatal error: math.h: No such file or directory
>  #include_next 
>^~~~
> compilation terminated.
> 
> Should I try CMake 3.10/11?
> 
> Thank you,
> Sambit
> 
> On Tuesday, September 18, 2018 at 7:27:38 AM UTC-5, Bruno Turcksin wrote:
> Sambit,
> 
> Can you try with a different version of CMake. We do not support CMake 3.12 
> with CUDA at the moment.
> 
> Best,
> 
> Bruno
> 
> On Monday, September 17, 2018 at 8:56:31 PM UTC-4, Sambit Das wrote:
> Dear all,
> 
> I am trying to compile the latest development version of dealii (9.1.0-pre, 
> shortrev c6b7876) using gcc/7.2.0, openmpi/3.0.0/gcc/7.2.0,  cuda/9.2 and 
> cmake-3.12.2. 
> 
> During compilation I get the following error:
> 
> [ 57%] Building CUDA object 
> source/base/CMakeFiles/obj_base_debug.dir/cuda.cu.o
> In file included from 
> /gpfs/gpfs0/groups/gavini/dsambit/software/dealii/dealii/include/deal.II/base/cuda.h:19:0,
>  from 
> /gpfs/gpfs0/groups/gavini/dsambit/software/dealii/dealii/source/base/cuda.cu:16
>  :
> /gpfs/gpfs0/groups/gavini/dsambit/software/dealii/build/include/deal.II/base/config.h:421:12:
>  fatal error: mpi.h: No such file or directory
>  #  include 
> ^~~
> compilation terminated.
> 
> 
> I have attached the detailed.log file. 
> 
> I have used the following configuration line:
> cmake  -DDEAL_II_CXX_FLAGS_RELEASE="-O3" -DDEAL_II_WITH_CXX17=OFF 
> -DCMAKE_C_COMPILER=mpicc -DCMAKE_CXX_COMPILER=mpicxx 
>  -DCMAKE_Fortran_COMPILER=mpif90 -DDEAL_II_WITH_CUDA=ON 
> -DDEAL_II_COMPONENT_EXAMPLES=OFF
>  -DDEAL_II_WITH_MPI=ON -DDEAL_II_WITH_64BIT_INDICES=ON
>  
> -DP4EST_DIR="/gpfs/gpfs0/groups/gavini/dsambit/software/p4est/installGcc7.2.0"
>   ../dealii
> 
>  Interestingly, if I remove -DDEAL_II_WITH_CUDA=ON, compilation is 
> successful. I am wondering if I am missing any cuda related compilation flags.
> 
> Thanks a lot in advance,
> 
> Best,
> Sambit
> 
> -- 
> 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 Google Groups 
> "deal.II User Group" group.
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> email to dealii+unsubscr...@googlegroups.com 
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> .

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[deal.II] Re: Compilation error in dealii development version (9.1.0-pre, shortrev c6b7876) using gcc/7.2.0 compiler and cuda/9.2

2018-09-18 Thread Sambit Das

Hi Bruno,

Thank you for your reply. Now I tried CMake 3.9.6 but got the following 
compilation error

[ 54%] Building CUDA object 
source/base/CMakeFiles/obj_base_debug.dir/cuda.cu.o
In file included from 
/gpfs/gpfs0/software/rhel72/packages/cuda/9.2/include/crt/math_functions.h:8853:0,
 from 
/gpfs/gpfs0/software/rhel72/packages/cuda/9.2/include/crt/common_functions.h:257,
 from 
/gpfs/gpfs0/software/rhel72/packages/cuda/9.2/include/common_functions.h:50,
 from 
/gpfs/gpfs0/software/rhel72/packages/cuda/9.2/include/cuda_runtime.h:115,
 from :0:
/gpfs/gpfs0/software/rhel72/packages/gcc/7.2.0/include/c++/7.2.0/cmath:45:15: 
fatal error: math.h: No such file or directory
 #include_next 
   ^~~~
compilation terminated.

Should I try CMake 3.10/11?

Thank you,
Sambit

On Tuesday, September 18, 2018 at 7:27:38 AM UTC-5, Bruno Turcksin wrote:
>
> Sambit,
>
> Can you try with a different version of CMake. We do not support CMake 
> 3.12 with CUDA at the moment.
>
> Best,
>
> Bruno
>
> On Monday, September 17, 2018 at 8:56:31 PM UTC-4, Sambit Das wrote:
>>
>> Dear all,
>>
>> I am trying to compile the latest development version of dealii 
>> (9.1.0-pre, shortrev c6b7876) using gcc/7.2.0, 
>> openmpi/3.0.0/gcc/7.2.0,  cuda/9.2 and cmake-3.12.2. 
>>
>> During compilation I get the following error:
>>
>> [ 57%] Building CUDA object 
>> source/base/CMakeFiles/obj_base_debug.dir/cuda.cu.o
>> In file included from 
>> /gpfs/gpfs0/groups/gavini/dsambit/software/dealii/dealii/include/deal.II/base/cuda.h:19:0,
>>  from 
>> /gpfs/gpfs0/groups/gavini/dsambit/software/dealii/dealii/source/base/
>> cuda.cu:16:
>> /gpfs/gpfs0/groups/gavini/dsambit/software/dealii/build/include/deal.II/base/config.h:421:12:
>>  
>> fatal error: mpi.h: No such file or directory
>>  #  include 
>> ^~~
>> compilation terminated.
>>
>>
>> I have attached the detailed.log file. 
>>
>> I have used the following configuration line:
>> cmake  -DDEAL_II_CXX_FLAGS_RELEASE="-O3" -DDEAL_II_WITH_CXX17=OFF 
>> -DCMAKE_C_COMPILER=mpicc -DCMAKE_CXX_COMPILER=mpicxx 
>>  -DCMAKE_Fortran_COMPILER=mpif90 -DDEAL_II_WITH_CUDA=ON 
>> -DDEAL_II_COMPONENT_EXAMPLES=OFF
>>  -DDEAL_II_WITH_MPI=ON -DDEAL_II_WITH_64BIT_INDICES=ON
>>  
>> -DP4EST_DIR="/gpfs/gpfs0/groups/gavini/dsambit/software/p4est/installGcc7.2.0"
>>   
>> ../dealii
>>
>>  Interestingly, if I remove -DDEAL_II_WITH_CUDA=ON, compilation is 
>> successful. I am wondering if I am missing any cuda related compilation 
>> flags.
>>
>> Thanks a lot in advance,
>>
>> Best,
>> Sambit
>>
>

-- 
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[deal.II] Re: Compilation error in dealii development version (9.1.0-pre, shortrev c6b7876) using gcc/7.2.0 compiler and cuda/9.2

2018-09-18 Thread Bruno Turcksin

Sambit,

Can you try with a different version of CMake. We do not support CMake 3.12 
with CUDA at the moment.

Best,

Bruno

On Monday, September 17, 2018 at 8:56:31 PM UTC-4, Sambit Das wrote:
>
> Dear all,
>
> I am trying to compile the latest development version of dealii 
> (9.1.0-pre, shortrev c6b7876) using gcc/7.2.0, 
> openmpi/3.0.0/gcc/7.2.0,  cuda/9.2 and cmake-3.12.2. 
>
> During compilation I get the following error:
>
> [ 57%] Building CUDA object 
> source/base/CMakeFiles/obj_base_debug.dir/cuda.cu.o
> In file included from 
> /gpfs/gpfs0/groups/gavini/dsambit/software/dealii/dealii/include/deal.II/base/cuda.h:19:0,
>  from 
> /gpfs/gpfs0/groups/gavini/dsambit/software/dealii/dealii/source/base/
> cuda.cu:16:
> /gpfs/gpfs0/groups/gavini/dsambit/software/dealii/build/include/deal.II/base/config.h:421:12:
>  
> fatal error: mpi.h: No such file or directory
>  #  include 
> ^~~
> compilation terminated.
>
>
> I have attached the detailed.log file. 
>
> I have used the following configuration line:
> cmake  -DDEAL_II_CXX_FLAGS_RELEASE="-O3" -DDEAL_II_WITH_CXX17=OFF 
> -DCMAKE_C_COMPILER=mpicc -DCMAKE_CXX_COMPILER=mpicxx 
>  -DCMAKE_Fortran_COMPILER=mpif90 -DDEAL_II_WITH_CUDA=ON 
> -DDEAL_II_COMPONENT_EXAMPLES=OFF
>  -DDEAL_II_WITH_MPI=ON -DDEAL_II_WITH_64BIT_INDICES=ON
>  
> -DP4EST_DIR="/gpfs/gpfs0/groups/gavini/dsambit/software/p4est/installGcc7.2.0"
>   
> ../dealii
>
>  Interestingly, if I remove -DDEAL_II_WITH_CUDA=ON, compilation is 
> successful. I am wondering if I am missing any cuda related compilation 
> flags.
>
> Thanks a lot in advance,
>
> Best,
> Sambit
>

-- 
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Re: [deal.II] Can GridIn read 3D quad mesh?

Re: [deal.II] Compilation error in dealii development version (9.1.0-pre, shortrev c6b7876) using gcc/7.2.0 compiler and cuda/9.2

Re: [deal.II] Compilation error in dealii development version (9.1.0-pre, shortrev c6b7876) using gcc/7.2.0 compiler and cuda/9.2

Re: [deal.II] Re: Can GridIn read 3D quad mesh?

Re: [deal.II] Re: Can GridIn read 3D quad mesh?

[deal.II] PhD position on polymer electrolyte fuel cell modeling using deal.II

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[deal.II] Re: Can GridIn read 3D quad mesh?

Re: [deal.II] Re: Can GridIn read 3D quad mesh?

Re: [deal.II] Compilation error in dealii development version (9.1.0-pre, shortrev c6b7876) using gcc/7.2.0 compiler and cuda/9.2

Re: [deal.II] Compilation error in dealii development version (9.1.0-pre, shortrev c6b7876) using gcc/7.2.0 compiler and cuda/9.2

[deal.II] Re: Compilation error in dealii development version (9.1.0-pre, shortrev c6b7876) using gcc/7.2.0 compiler and cuda/9.2

[deal.II] Re: Compilation error in dealii development version (9.1.0-pre, shortrev c6b7876) using gcc/7.2.0 compiler and cuda/9.2

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