Re: [deal.II] Re: .msh file triangulation failed

2020-09-22 Thread yuesu jin
Dear Bruno,
  Sorry for the late reply. Here is flooding, I was driving home hours
before. You are right, in the linux version of gmsh, it always gives the
error message that cannot find the corresponding vertex, but actually I do
nothing on the cell. It is the 1e-7 rounding error that makes the system
very unstable. Thank you again for your patience and kindness. Have a good
day!
Best regards,
Yuesu

On Tue, Sep 22, 2020 at 10:55 AM Bruno Turcksin 
wrote:

> Honestly I don't know. I wonder if the terms -1e-07 are the problem. I
> told you to remove  SetFactory("OpenCASCADE") because it was the only
> difference with my .geo files.
>
> Bruno
>
> Le mar. 22 sept. 2020 à 11:20, yuesu jin  a écrit :
> >
> > Dear Bruno,
> >   The problem was solved after I removed the
> 'SetFactory("OpenCASCADE")'.  Here are two mesh files with and without
> 'SetFactory("OpenCASCADE")'. Could you tell me why this command made the
> system unable to work? Thank you very much for your help!
> > Best regards,
> > Yuesu
> >
> >
> >
> > On Tue, Sep 22, 2020 at 10:01 AM Bruno Turcksin <
> bruno.turck...@gmail.com> wrote:
> >>
> >> Hmmm. Can you try without the SetFactory("OpenCASCADE"); and can you
> >> send me your .msh
> >>
> >> Bruno
> >>
> >> Le mar. 22 sept. 2020 à 10:45, yuesu jin  a
> écrit :
> >> >
> >> > Dear Bruno,
> >> >I did some modification according to your suggestion :
> >> > 
> >> > Physical Volume("4") = {1};
> >> > //+
> >> > Physical Surface("0") = {4, 3, 2, 5, 1, 6};
> >> > 
> >> > I add all external surfaces in one physical group and the volume in
> another group. But the error message remains the same.  I tried a few types
> of grouping combinations, the error message did not change.
> >> > Best regards,
> >> > Yuesu
> >> >
> >> > On Tue, Sep 22, 2020 at 9:30 AM Bruno Turcksin <
> bruno.turck...@gmail.com> wrote:
> >> >>
> >> >> You don't want to set the physical groups for the curves and the
> >> >> points. This means nothing in deal.II. A vertex does not have a
> >> >> boundary ID. You need all the external surfaces and the volume to
> have
> >> >> a physical group. That's it.
> >> >>
> >> >> Bruno
> >> >>
> >> >> Le mar. 22 sept. 2020 à 10:24, yuesu jin  a
> écrit :
> >> >> >
> >> >> > Dear Bruno,
> >> >> >   Thank you for your help! I added physical groups for volume,
> surfaces, curves, and points. But the problem remains the same.  The
> modified geo file is attached below.
> >> >> > Best regards,
> >> >> > Yuesu
> >> >> >
> >> >> > On Tue, Sep 22, 2020 at 7:55 AM Bruno Turcksin <
> bruno.turck...@gmail.com> wrote:
> >> >> >>
> >> >> >>
> >> >> >> Yuesu,
> >> >> >>
> >> >> >> I had the same problem recently. Our gmsh reader assumes that the
> user has set boundary id and material id to the mesh. It looks like you
> don't have those and so the file is read incorrectly.
> >> >> >>
> >> >> >> Best,
> >> >> >>
> >> >> >> Bruno
> >> >> >> On Tuesday, September 22, 2020 at 2:04:17 AM UTC-4
> jinyu...@gmail.com wrote:
> >> >> >>>
> >> >> >>> Dear all,
> >> >> >>>   I have one problem when I try to input the .msh file with
> grid_in function. The error message is :
> >> >> >>>
> >> >> >>> *
> >> >> >>>
> >> >> >>> Exception on processing:
> >> >> >>>
> >> >> >>> 
> >> >> >>> An error occurred in line <3139> of file
>  in function
> >> >> >>> static void
> dealii::internal::TriangulationImplementation::Implementation::create_triangulation(const
> std::vector >&, const std::vector,
> std::allocator > >&, const dealii::SubCellData&,
> dealii::Triangulation<3, spacedim>&) [with int spacedi

Re: [deal.II] Re: .msh file triangulation failed

2020-09-22 Thread yuesu jin
Dear Bruno,
   I did some modification according to your suggestion :



*Physical Volume("4") = {1};//+Physical Surface("0") = {4, 3, 2, 5, 1, 6};*

I add all external surfaces in one physical group and the volume in another
group. But the error message remains the same.  I tried a few types of
grouping combinations, the error message did not change.
Best regards,
Yuesu

On Tue, Sep 22, 2020 at 9:30 AM Bruno Turcksin 
wrote:

> You don't want to set the physical groups for the curves and the
> points. This means nothing in deal.II. A vertex does not have a
> boundary ID. You need all the external surfaces and the volume to have
> a physical group. That's it.
>
> Bruno
>
> Le mar. 22 sept. 2020 à 10:24, yuesu jin  a écrit :
> >
> > Dear Bruno,
> >   Thank you for your help! I added physical groups for volume, surfaces,
> curves, and points. But the problem remains the same.  The modified geo
> file is attached below.
> > Best regards,
> > Yuesu
> >
> > On Tue, Sep 22, 2020 at 7:55 AM Bruno Turcksin 
> wrote:
> >>
> >>
> >> Yuesu,
> >>
> >> I had the same problem recently. Our gmsh reader assumes that the user
> has set boundary id and material id to the mesh. It looks like you don't
> have those and so the file is read incorrectly.
> >>
> >> Best,
> >>
> >> Bruno
> >> On Tuesday, September 22, 2020 at 2:04:17 AM UTC-4 jinyu...@gmail.com
> wrote:
> >>>
> >>> Dear all,
> >>>   I have one problem when I try to input the .msh file with grid_in
> function. The error message is :
> >>>
> >>> *
> >>>
> >>> Exception on processing:
> >>>
> >>> 
> >>> An error occurred in line <3139> of file
>  in function
> >>> static void
> dealii::internal::TriangulationImplementation::Implementation::create_triangulation(const
> std::vector >&, const std::vector,
> std::allocator > >&, const dealii::SubCellData&,
> dealii::Triangulation<3, spacedim>&) [with int spacedim = 3]
> >>> The violated condition was:
> >>> false
> >>> Additional information:
> >>> While trying to assign a boundary indicator to a line: the line
> with end vertices -1 and 0 does not exist.
> >>> 
> >>>
> >>> I attached the gmsh .geo file in this email. There is no vertex -1
> actually. Could you tell me what's wrong with my mesh generation?
> >>>
> >>> Thank you very much!
> >>> Best regards,
> >>>
> >>> --
> >>> Yuesu Jin,
> >>> Ph.D student,
> >>> University of Houston,
> >>> College of Natural Sciences and Mathematics,
> >>> Department of Earth and Atmospheric Sciences,
> >>> Houston, Texas 77204-5008
> >>> 346-404-2062
> >>>
> >> --
> >> 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.
> >> To unsubscribe from this group and stop receiving emails from it, send
> an email to dealii+unsubscr...@googlegroups.com.
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> https://groups.google.com/d/msgid/dealii/5bf5008c-865d-47df-a49f-e4408028ef1dn%40googlegroups.com
> .
> >
> >
> >
> > --
> > Yuesu Jin,
> > Ph.D student,
> > University of Houston,
> > College of Natural Sciences and Mathematics,
> > Department of Earth and Atmospheric Sciences,
> > Houston, Texas 77204-5008
> > 346-404-2062
> >
> > --
> > 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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> > To view this discussion o

Re: [deal.II] Re: .msh file triangulation failed

2020-09-22 Thread yuesu jin
Dear Bruno,
  Thank you for your help! I added physical groups for volume, surfaces,
curves, and points. But the problem remains the same.  The modified geo
file is attached below.
Best regards,
Yuesu

On Tue, Sep 22, 2020 at 7:55 AM Bruno Turcksin 
wrote:

>
> Yuesu,
>
> I had the same problem recently. Our gmsh reader assumes that the user has
> set boundary id and material id to the mesh. It looks like you don't have
> those and so the file is read incorrectly.
>
> Best,
>
> Bruno
> On Tuesday, September 22, 2020 at 2:04:17 AM UTC-4 jinyu...@gmail.com
> wrote:
>
>> Dear all,
>>   I have one problem when I try to input the .msh file with grid_in
>> function. The error message is :
>>
>> *
>>
>> Exception on processing:
>>
>> 
>> An error occurred in line <3139> of file
>>  in function
>> static void
>> dealii::internal::TriangulationImplementation::Implementation::create_triangulation(const
>> std::vector >&, const std::vector,
>> std::allocator > >&, const dealii::SubCellData&,
>> dealii::Triangulation<3, spacedim>&) [with int spacedim = 3]
>> The violated condition was:
>> false
>> Additional information:
>>  *   While trying to assign a boundary indicator to a line: the line
>> with end vertices -1 and 0 does not exist.*
>> --------
>>
>> I attached the gmsh .geo file in this email. There is no vertex -1
>> actually. Could you tell me what's wrong with my mesh generation?
>>
>> Thank you very much!
>> Best regards,
>>
>> --
>> Yuesu Jin,
>> Ph.D student,
>> University of Houston,
>> College of Natural Sciences and Mathematics,
>> Department of Earth and Atmospheric Sciences,
>> Houston, Texas 77204-5008
>> 346-404-2062 <(346)%20404-2062>
>>
>> --
> 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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> .
>


-- 
Yuesu Jin,
Ph.D student,
University of Houston,
College of Natural Sciences and Mathematics,
Department of Earth and Atmospheric Sciences,
Houston, Texas 77204-5008
346-404-2062

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tank.geo
Description: Binary data


[deal.II] .msh file triangulation failed

2020-09-22 Thread yuesu jin
Dear all,
  I have one problem when I try to input the .msh file with grid_in
function. The error message is :

*

Exception on processing:


An error occurred in line <3139> of file
 in function
static void
dealii::internal::TriangulationImplementation::Implementation::create_triangulation(const
std::vector >&, const std::vector,
std::allocator > >&, const dealii::SubCellData&,
dealii::Triangulation<3, spacedim>&) [with int spacedim = 3]
The violated condition was:
false
Additional information:
 *   While trying to assign a boundary indicator to a line: the line with
end vertices -1 and 0 does not exist.*


I attached the gmsh .geo file in this email. There is no vertex -1
actually. Could you tell me what's wrong with my mesh generation?

Thank you very much!
Best regards,

-- 
Yuesu Jin,
Ph.D student,
University of Houston,
College of Natural Sciences and Mathematics,
Department of Earth and Atmospheric Sciences,
Houston, Texas 77204-5008
346-404-2062

-- 
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tank.geo
Description: Binary data


Re: [deal.II] What is the first and second index of the gradient tensor

2020-09-07 Thread yuesu jin
Dear Dr.Bangerth,
  I found it just before, it is on  the page of FEValuesView (
https://www.dealii.org/current/doxygen/deal.II/classFEValuesViews_1_1Vector.html).
Thank you very much!
Best regards,
Yuesu

On Mon, Sep 7, 2020 at 11:00 PM Wolfgang Bangerth 
wrote:

> On 9/7/20 6:21 PM, yuesu jin wrote:
> >I want to contract the gradient tensor with another vector, such as
> > T_ij*n_j, the gradient tensor is d_j u_i (d is the partial differential
> > operator). I am wondering what is the first index of gradient tensor, i
> or j?
>
> I believe it is
>T_ij = d_j u_i
> I know I documented this somewhere (maybe in FEValues::gradient() or
> FEValuesView::Vector::gradient) but if you can't find it, it would be nice
> if
> you could just try out and maybe suggest a place where this should be
> documented.
>
> 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/
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> .
>


-- 
Yuesu Jin,
Ph.D student,
University of Houston,
College of Natural Sciences and Mathematics,
Department of Earth and Atmospheric Sciences,
Houston, Texas 77204-5008
346-404-2062

-- 
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[deal.II] What is the first and second index of the gradient tensor

2020-09-07 Thread yuesu jin
Dear all,
  I want to contract the gradient tensor with another vector, such as
T_ij*n_j, the gradient tensor is d_j u_i (d is the partial differential
operator). I am wondering what is the first index of gradient tensor, i or
j? Thank you !
Best regards,
Yuesu

-- 
Yuesu Jin,
Ph.D student,
University of Houston,
College of Natural Sciences and Mathematics,
Department of Earth and Atmospheric Sciences,
Houston, Texas 77204-5008
346-404-2062

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Re: [deal.II] Question about fe_value.divergence

2020-09-03 Thread yuesu jin
Dear Dr. Bangerth,
  I read the step.20 again. It solves my question. I didn't understand what
the non-primitive element talks about, now I know the necessity of that.
Thank you!
Best regards,
Yuesu


On Thu, Sep 3, 2020 at 5:38 PM yuesu jin  wrote:

> Dear Dr. Bangerth,
>   Thank you very much! I was confused about the shape function in the
> vector case.
>   In step.8 we use the FEValue::shape_grad(index of shape function,index
> of quadrature point) and get a vector as the gradient of shape function.
> However, in step.20 and step.22, when we take the gradient of 
> FESystem[vector_indices]::gradient(index
> of shape function, index of quadrature point) we get a rank-2 tensor. If
> the shape function is a vector, FEValue::shape_grad(index of shape
> function,index of quadrature point) should give a tensor as well. Does it
> mean that the shape_grad gives the gradient of the non-zero component in
> the vector shape function such that it is a vector?
>   Thank you again!
> Best regards,
>
> On Thu, Sep 3, 2020 at 3:11 PM Wolfgang Bangerth 
> wrote:
>
>> On 9/3/20 1:28 PM, yuesu jin wrote:
>> >I am working on vector value finite element modeling. I read the
>> pages
>> >
>> https://www.dealii.org/current/doxygen/deal.II/group__vector__valued.html
>> > <
>> https://nam01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.dealii.org%2Fcurrent%2Fdoxygen%2Fdeal.II%2Fgroup__vector__valued.html=02%7C01%7CWolfgang.Bangerth%40colostate.edu%7Cb30f39009c8c49c8fc8108d8503f8631%7Cafb58802ff7a4bb1ab21367ff2ecfc8b%7C0%7C0%7C637347581059635256=w%2BABjRZ1fzUdFfCQvw49JwLF7Inl3iEG4XR78VwlgoA%3D=0>
>>  which
>>
>> > uses the fe_values.divergence and fe_value.grad, but I cannot find
>> these two
>> > member functions in the FEValues\FESystem\FEValueBase categories. Could
>> you
>> > give me the documentation page about these two functions?
>>
>> These functions only exist in FEValuesViews::Vector and
>> FEValuesViews::Tensor.
>> You get that if you have something like
>>
>>FEValuesExtractors::Vector velocities(0);
>>fe_values[velocities].divergence (...);
>>
>> step-22 shows how this works in practice.
>>
>> 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
>> ---
>> You received this message because you are subscribed to the Google Groups
>> "deal.II User Group" group.
>> To unsubscribe from this group and stop receiving emails from it, send an
>> email to dealii+unsubscr...@googlegroups.com.
>> To view this discussion on the web visit
>> https://groups.google.com/d/msgid/dealii/79b2e60e-86e5-b310-9b28-c5c96c3eb364%40colostate.edu
>> .
>>
>
>
> --
> Yuesu Jin,
> Ph.D student,
> University of Houston,
> College of Natural Sciences and Mathematics,
> Department of Earth and Atmospheric Sciences,
> Houston, Texas 77204-5008
> 346-404-2062
>
>

-- 
Yuesu Jin,
Ph.D student,
University of Houston,
College of Natural Sciences and Mathematics,
Department of Earth and Atmospheric Sciences,
Houston, Texas 77204-5008
346-404-2062

-- 
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Re: [deal.II] Question about fe_value.divergence

2020-09-03 Thread yuesu jin
Dear Dr. Bangerth,
  Thank you very much! I was confused about the shape function in the
vector case.
  In step.8 we use the FEValue::shape_grad(index of shape function,index of
quadrature point) and get a vector as the gradient of shape function.
However, in step.20 and step.22, when we take the gradient of
FESystem[vector_indices]::gradient(index
of shape function, index of quadrature point) we get a rank-2 tensor. If
the shape function is a vector, FEValue::shape_grad(index of shape
function,index of quadrature point) should give a tensor as well. Does it
mean that the shape_grad gives the gradient of the non-zero component in
the vector shape function such that it is a vector?
  Thank you again!
Best regards,

On Thu, Sep 3, 2020 at 3:11 PM Wolfgang Bangerth 
wrote:

> On 9/3/20 1:28 PM, yuesu jin wrote:
> >I am working on vector value finite element modeling. I read the
> pages
> >
> https://www.dealii.org/current/doxygen/deal.II/group__vector__valued.html
> > <
> https://nam01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.dealii.org%2Fcurrent%2Fdoxygen%2Fdeal.II%2Fgroup__vector__valued.html=02%7C01%7CWolfgang.Bangerth%40colostate.edu%7Cb30f39009c8c49c8fc8108d8503f8631%7Cafb58802ff7a4bb1ab21367ff2ecfc8b%7C0%7C0%7C637347581059635256=w%2BABjRZ1fzUdFfCQvw49JwLF7Inl3iEG4XR78VwlgoA%3D=0>
>  which
>
> > uses the fe_values.divergence and fe_value.grad, but I cannot find these
> two
> > member functions in the FEValues\FESystem\FEValueBase categories. Could
> you
> > give me the documentation page about these two functions?
>
> These functions only exist in FEValuesViews::Vector and
> FEValuesViews::Tensor.
> You get that if you have something like
>
>FEValuesExtractors::Vector velocities(0);
>fe_values[velocities].divergence (...);
>
> step-22 shows how this works in practice.
>
> 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/
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> .
>


-- 
Yuesu Jin,
Ph.D student,
University of Houston,
College of Natural Sciences and Mathematics,
Department of Earth and Atmospheric Sciences,
Houston, Texas 77204-5008
346-404-2062

-- 
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[deal.II] Question about fe_value.divergence

2020-09-03 Thread yuesu jin
Dear all,
  I am working on vector value finite element modeling. I read the pages
https://www.dealii.org/current/doxygen/deal.II/group__vector__valued.html which
uses the fe_values.divergence and fe_value.grad, but I cannot find these
two member functions in the FEValues\FESystem\FEValueBase categories. Could
you give me the documentation page about these two functions?
Best regards,


-- 
Yuesu Jin,
Ph.D student,
University of Houston,
College of Natural Sciences and Mathematics,
Department of Earth and Atmospheric Sciences,
Houston, Texas 77204-5008
346-404-2062

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Re: [deal.II] PETSc iteration does not converge

2020-08-17 Thread yuesu jin
OK, I see. I will do it, thank you! I will let you know if I get any result.

On Mon, Aug 17, 2020 at 7:06 PM Wolfgang Bangerth 
wrote:

> On 8/17/20 6:01 PM, yuesu jin wrote:
> >  I did nothing to verify those properties. because the single thread
> CG
> > solver converged well. I used  different preconditioners in parallel
> version
> > and single thread version. In the parallel version I used block Jacobi
> and in
> > the single thread version I used Jacobi. How can I check if the parallel
> > blocked sparse matrix is/ isn't symmetrical and positive definite?
>
> Think of tests such as this:
> * run on 1 processor, multiply a vector w of all 1s from the right, and
> output
> the resulting vector v=Aw on all processors
> * run on >1 processors and repeat
> Are the vectors the same for both cases? The matrix should be the same
> regardless of partitioning, but is it?
>
> * repeat the same with Tvmult (multiplication from the left)
>
> You can probably come up with many similar tests that check properties of
> the
> matrix, comparing between the single-processor and multiple-processor
> cases.
> The point is that you may not know the exact answer, but you know that the
> two
> cases should result in the same output.
>
> Best
>   W.
>
> --
> 
> Wolfgang Bangerth  email: bange...@colostate.edu
> www: http://www.math.colostate.edu/~bangerth/
>
> --
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> .
>


-- 
Yuesu Jin,
Ph.D student,
University of Houston,
College of Natural Sciences and Mathematics,
Department of Earth and Atmospheric Sciences,
Houston, Texas 77204-5008
346-404-2062

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Re: [deal.II] PETSc iteration does not converge

2020-08-17 Thread yuesu jin
Dear Dr.Bangerth,
I did nothing to verify those properties. because the single thread CG
solver converged well. I used  different preconditioners in parallel
version and single thread version. In the parallel version I used block
Jacobi and in the single thread version I used Jacobi. How can I check if
the parallel blocked sparse matrix is/ isn't symmetrical and positive
definite?
Best regards,
Yuesu

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Re: [deal.II] Question about complex value finite element

2020-08-16 Thread yuesu jin
Sure, I will add my progress following this email.
Best regards,

On Sun, Aug 16, 2020 at 7:47 PM Wolfgang Bangerth 
wrote:

> On 8/16/20 6:38 PM, yuesu jin wrote:
> > Thank you very much! I found step-62 yesterday and I have
> compared the
> > difference between them.  I want to write two versions and compare their
> CPU
> > time to get an exact result.
>
> That would be interesting to hear about -- please let us know what you
> find!
> Best
>   W.
>
> --
> 
> Wolfgang Bangerth  email: bange...@colostate.edu
> www: http://www.math.colostate.edu/~bangerth/
>
> --
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> .
>


-- 
Yuesu Jin,
Ph.D student,
University of Houston,
College of Natural Sciences and Mathematics,
Department of Earth and Atmospheric Sciences,
Houston, Texas 77204-5008
346-404-2062

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Re: [deal.II] PETSc iteration does not converge

2020-08-16 Thread yuesu jin
Dear Dr.Bangerth,
   I tried both, first I tried 1e-4*system_rhs.l2_norm(), it failed. Then I
tried with exact precision limits, from 1e-3 to 1e-8, all of them cannot
converge.  If I set the precision level as 1e-4, with or without L2 norm it
stopped at step-42 with the residue 0.0113395.
Best regards,
Yuesu

On Sun, Aug 16, 2020 at 7:20 PM Wolfgang Bangerth 
wrote:

> On 8/14/20 9:20 PM, yuesu jin wrote:
> > I tried a few levels of the tolerance, 1e-3, 1e-4 ,1e-6 and 1e-8. 1e-3
> > converged because that is in the same level with the solution. Error
> occurs
> > below 1e-4.  I have tried the Jacobi preconditioner instead of SSOR in
> the
> > single thread CG version, it converged as well.
>
> Is this 1e-4 * system_rhs.l2_norm(), or just 1e-4? If the latter, what is
> the
> size of system_rhs.l2_norm()? You should choose a tolerance that is
> proportional to the norm of the right hand side.
>
> Best
>   W.
>
>
> --
> 
> Wolfgang Bangerth  email: bange...@colostate.edu
> www: http://www.math.colostate.edu/~bangerth/
>
> --
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> .
>


-- 
Yuesu Jin,
Ph.D student,
University of Houston,
College of Natural Sciences and Mathematics,
Department of Earth and Atmospheric Sciences,
Houston, Texas 77204-5008
346-404-2062

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Re: [deal.II] Question about complex value finite element

2020-08-16 Thread yuesu jin
Dear Dr. Bangerth,
   Thank you very much! I found step-62 yesterday and I have compared the
difference between them.  I want to write two versions and compare their
CPU time to get an exact result.
Best regards,
Yuesu

On Sun, Aug 16, 2020 at 7:19 PM Wolfgang Bangerth 
wrote:

> Yuesu,
>
> >I am adding an absorbing boundary condition like step-24 did in the
> > frequency domain, in which the time derivative gives a complex term.  I
> also
> > found the complex acoustic wave problem step-29 which splits the complex
> wave
> > function into two real parts.
> >What I want to know is what if I directly set up the matrix and rhs
> vector
> > as complex ? Why does step-29 says "/it is often more convenient
> to
> > split complex valued functions into their real and imaginary parts and
> use
> > separate scalar finite element fields for discretizing each one of
> them/" ?
>
> The problem is that we don't have iterative solvers for problems in which
> the
> matrix and vectors store complex values. We can, however, use PETSc's
> complex-valued solvers as well as the SparseDirectUMFPACK solver. I think
> you
> probably want to look at step-62 and step-58 for other options.
>
> 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/
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> .
>


-- 
Yuesu Jin,
Ph.D student,
University of Houston,
College of Natural Sciences and Mathematics,
Department of Earth and Atmospheric Sciences,
Houston, Texas 77204-5008
346-404-2062

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[deal.II] Question about complex value finite element

2020-08-14 Thread yuesu jin
Dear all,
  I am adding an absorbing boundary condition like step-24 did in the
frequency domain, in which the time derivative gives a complex term.  I
also found the complex acoustic wave problem step-29 which splits the
complex wave function into two real parts.
  What I want to know is what if I directly set up the matrix and rhs
vector as complex ? Why does step-29 says "*it is often more
convenient to split complex valued functions into their real and imaginary
parts and use separate scalar finite element fields for discretizing each
one of them*" ?
Best wishes,

-- 
Yuesu Jin,
Ph.D student,
University of Houston,
College of Natural Sciences and Mathematics,
Department of Earth and Atmospheric Sciences,
Houston, Texas 77204-5008
346-404-2062

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Re: [deal.II] PETSc iteration does not converge

2020-08-14 Thread yuesu jin
Dear Dr. Bangerth,
  I tried a few levels of the tolerance, 1e-3, 1e-4 ,1e-6 and 1e-8. 1e-3
converged because that is in the same level with the solution. Error occurs
below 1e-4.  I have tried the Jacobi preconditioner instead of SSOR in the
single thread CG version, it converged as well.
Best regards,
Yuesu


On Fri, Aug 14, 2020 at 10:14 PM Wolfgang Bangerth 
wrote:

> On 8/14/20 5:53 PM, yuesu jin wrote:
> >
> > I also wrote a single thread CG version, which converges well. The
> > preconditioner in the parallel version is blockJacobi but the single
> thread
> > version I used is SSOR. Does it matter to the convergence? Thank you!
>
> Yes, in exactly the ways the error message shows: If you are using a
> different
> preconditioner, you should expect different convergence behavior.
>
> Whether you should expect one or the other method to work (or fail)
> depends on
> the properties of the matrix you are trying to solve. I'd also check
> whether
> the residual 0.00295038 is large or small compared to the initial
> residual.
> What is the tolerance you are using in the SolverControl object?
>
> 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/
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> .
>


-- 
Yuesu Jin,
Ph.D student,
University of Houston,
College of Natural Sciences and Mathematics,
Department of Earth and Atmospheric Sciences,
Houston, Texas 77204-5008
346-404-2062

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[deal.II] PETSc iteration does not converge

2020-08-14 Thread yuesu jin
Dear all,
  I am working on acoustic wave simulation through PETSc wrapper, it gives
the error message:
**
Mesh Info
Dimensions2
No.cells:5144
Number of active cells:5144
Number of degrees of freedom:20833


*
Exception on processing:


An error occurred in line <148> of file
 in function
void dealii::PETScWrappers::SolverBase::solve(const
dealii::PETScWrappers::MatrixBase&, dealii::PETScWrappers::VectorBase&,
const dealii::PETScWrappers::VectorBase&, const
dealii::PETScWrappers::PreconditionerBase&)
The violated condition was:
false
Additional information:
Iterative method reported convergence failure in step 65. The residual in
the last step was 0.00295038.

This error message can indicate that you have simply not allowed a
sufficiently large number of iterations for your iterative solver to
converge. This often happens when you increase the size of your problem. In
such cases, the last residual will likely still be very small, and you can
make the error go away by increasing the allowed number of iterations when
setting up the SolverControl object that determines the maximal number of
iterations you allow.

The other situation where this error may occur is when your matrix is not
invertible (e.g., your matrix has a null-space), or if you try to apply the
wrong solver to a matrix (e.g., using CG for a matrix that is not symmetric
or not positive definite). In these cases, the residual in the last
iteration is likely going to be large.


Aborting
***
I also wrote a single thread CG version, which converges well. The
preconditioner in the parallel version is blockJacobi but the single thread
version I used is SSOR. Does it matter to the convergence? Thank you!
Best regards,
-- 
Yuesu Jin,
Ph.D student,
University of Houston,
College of Natural Sciences and Mathematics,
Department of Earth and Atmospheric Sciences,
Houston, Texas 77204-5008
346-404-2062

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[deal.II] A small question about subdomain renumbering

2020-08-05 Thread yuesu jin
Dear all,
  I have a question about DoFRenumbering::subdomain_wise(dof_handler). In
step-17 tutorial for example, this function doesn't use the argument of
n_mpi_processes, how does it know how many subdomains it should divide the
dofs into?
After we renumbered the subdomain and get the
locally_owned_dofs_per_subomain, we can already use this_mpi_process to
access the partition vector, which means the subdomain partition has been
done according to the n_mpi_processes.
Best regards,
-- 
Yuesu Jin,
Ph.D student,
University of Houston,
College of Natural Sciences and Mathematics,
Department of Earth and Atmospheric Sciences,
Houston, Texas 77204-5008
346-404-2062

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Re: [deal.II] Re: Set up boundary id in gmsh

2020-08-05 Thread yuesu jin
Dear Bruno,
  Thank you very much!!! This solved my problem. This is very helpful!
Best regards,
Yuesu

On Wed, Aug 5, 2020 at 9:33 PM Bruno Blais  wrote:

> The best way to proceed is to set the boundary conditions using Physical
> Entities in GMSH.
> An example is always better. For example, the following GMSH code :
>
>  lc = 2.0e-1;
>  lf = 2.0e-1;
>  RO=1;
>  RI=0.25;
>
>  Point(0) = {0, 0, 0, lc};
>  Point(1) = {RO, 0, 0, lc};
>  Point(2) = {0, -RO , 0, lc};
>  Point(3) = {-RO, 0, 0, lc};
>  Point(4) = {0, RO, 0, lc};
>
>  Point(5) = {RI, 0, 0, lf};
>  Point(6) = {0, -RI , 0, lf};
>  Point(7) = {-RI, 0, 0, lf};
>  Point(8) = {0, RI, 0, lf};
>
>  Circle(1)={1,0,2};
>  Circle(2)={2,0,3};
>  Circle(3)={3,0,4};
>  Circle(4)={4,0,1};
>
>  Circle(5)={5,0,6};
>  Circle(6)={6,0,7};
>  Circle(7)={7,0,8};
>  Circle(8)={8,0,5};
>
>  Line Loop(1) = {1,2,3,4};
>  Line Loop(2) = {5,6,7,8};
>
>  Plane Surface(1) = {1,2} ;
>  //Transfinite Surface{1}={1,2,3,4};
>  Recombine Surface{1,2};
>
>  // Creates a physical entity 1 (i.e. for a BC)
>  //Physical Point(1) = {1,2} ;
>  Physical Line(0)={1,2,3,4};
>  Physical Line(1)={5,6,7,8};
>
>  Physical Surface(0) = {1};
>
>
> Produces a 2D mesh of a single surface with id 0. It has two boundary
> conditions (0) and (1). One on the outer circle and the other on the inner
> circle. We use it to simulate a Taylor-Couette flow.
> If you wanted to use a 3D mesh, then you would make a Physical Volume(0)
> and you would use the Physical Surface for the boundary conditions
>
> Best
> Bruno
>
>
>
> On Wednesday, 5 August 2020 20:36:09 UTC-4, yuesu jin wrote:
>>
>> Dear all,
>>   I want to set up one Dirchlet boundary condition and one Neumann
>> boundary condition on a 2d  mesh, which is generated by gmsh. How can I set
>> up the mesh file in order to tell dealii with the boundary id when I input
>> the .msh file into dealii? Thanks!
>> Best regards,
>> --
>> Yuesu Jin,
>> Ph.D student,
>> University of Houston,
>> College of Natural Sciences and Mathematics,
>> Department of Earth and Atmospheric Sciences,
>> Houston, Texas 77204-5008
>> 346-404-2062
>>
>> --
> The deal.II project is located at http://www.dealii.org/
> For mailing list/forum options, see
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> .
>


-- 
Yuesu Jin,
Ph.D student,
University of Houston,
College of Natural Sciences and Mathematics,
Department of Earth and Atmospheric Sciences,
Houston, Texas 77204-5008
346-404-2062

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[deal.II] Set up boundary id in gmsh

2020-08-05 Thread yuesu jin
Dear all,
  I want to set up one Dirchlet boundary condition and one Neumann boundary
condition on a 2d  mesh, which is generated by gmsh. How can I set up the
mesh file in order to tell dealii with the boundary id when I input the
.msh file into dealii? Thanks!
Best regards,
-- 
Yuesu Jin,
Ph.D student,
University of Houston,
College of Natural Sciences and Mathematics,
Department of Earth and Atmospheric Sciences,
Houston, Texas 77204-5008
346-404-2062

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Re: [deal.II] Question about the numbering of DoFs

2020-08-03 Thread yuesu jin
Dear Jimmy,
  Thank you! Your answer solved my question. I had the wrong impression
that higher-order polynomials will give more base functions. Shape
functions just play the role of interpolation and construct the solution
space. It could be a high-order polynomial but only one base function per
node.  Thank you very much!
Best regards

On Sun, Aug 2, 2020 at 11:50 PM Jimmy Ho  wrote:

> Hi Yuesu,
>
> To be more precise: Yes, you do have two sets of basis functions in each
> element. A quadratic one for interpolating the vector components, and a
> linear one for interpolating the scalar. But when calculating DOFs
> associated with the vector components, you should only count the basis
> functions that interpolate those components, which is one basis function
> per node.
>
> Hope this helps!
>
> Best,
> Jimmy
>
> --
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> .
>


-- 
Yuesu Jin,
Ph.D student,
University of Houston,
College of Natural Sciences and Mathematics,
Department of Earth and Atmospheric Sciences,
Houston, Texas 77204-5008
346-404-2062

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Re: [deal.II] Question about the numbering of DoFs

2020-08-02 Thread yuesu jin
Dear Jimmy,
 Thank you for your reply. Yes, I can set up only one base function for
each node. But the problem is that the example sets up two base functions
for a two-component vector. FESystems fe_basis(FE_Q (2),dim,FE_Q
(1),1), which the (2) means the vector has order-2 base functions.
Best regards,
Yuesu

On Sun, Aug 2, 2020 at 10:09 PM Jimmy Ho  wrote:

> Hi Yuesu,
>
> When you have a vector-valued finite element, different components of the
> vector are still interpolated using the same basis functions. So you can
> have two DOFs on each node, but there's only one basis function associated
> with this node.
>
> Hope that helps!
>
> Best,
> Jimmy
>
> --
> The deal.II project is located at http://www.dealii.org/
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> .
>


-- 
Yuesu Jin,
Ph.D student,
University of Houston,
College of Natural Sciences and Mathematics,
Department of Earth and Atmospheric Sciences,
Houston, Texas 77204-5008
346-404-2062

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[deal.II] Question about the numbering of DoFs

2020-08-02 Thread yuesu jin
Dear all,
  I am reading the page :
https://www.dealii.org/current/doxygen/deal.II/classFiniteElement.html.
I feel confused by the numbering of the degrees of freedom. For example:

FESystem
<https://www.dealii.org/current/doxygen/deal.II/classFESystem.html>
fe_basis(FE_Q
<https://www.dealii.org/current/doxygen/deal.II/classFE__Q.html>(2), dim,
FE_Q <https://www.dealii.org/current/doxygen/deal.II/classFE__Q.html>
(1),1);

As mentioned in Glossary:

Describing "degrees of freedom" in this context requires us to simply
*enumerate* the basis functions of the space *V**h*. For *Q*1 elements this
means simply enumerating the vertices of the mesh in some way, but for
higher elements one also has to enumerate the shape functions that are
associated with edges, faces, or cell interiors of the mesh.


We have a vector u which has 2 components defined on 9 nodes. On each node,
there are 2 base functions, so the degrees of freedom are 9*2*2 = 36. And
we have a scalar p which has 1 component defined on 4 nodes. On each node,
there is one base function, so the degrees of freedom are 4*1*1=4. The
total degrees of freedom should be 36+4=40.

In the webpage, it gives 2*9+4*1=22 degrees of freedom, it equals the base
function with the vector components.
[image: image.png]

u(0) should have two base element [phi(0),0] and [phi(0) 0], u(1) should
have two base elements as well [0 phi(0)] [0 phi(1)], so here should be 4
rather than 2 degrees of freedom.

Best regards,

-- 
Yuesu Jin,
Ph.D student,
University of Houston,
College of Natural Sciences and Mathematics,
Department of Earth and Atmospheric Sciences,
Houston, Texas 77204-5008
346-404-2062

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Re: [deal.II] METIS partition error

2020-07-27 Thread yuesu jin
Dear David,
 Thank you! It solved the problem.
Best wishes,
Yuesu

On Mon, Jul 27, 2020 at 8:48 AM David Wells  wrote:

> Hi Yuesu,
>
> Essentially, yes. If you look at the code for partition_triangulation you
> will find
>
> // check for an easy return
> if (n_partitions == 1)
>   {
> for (const auto  : triangulation.active_cell_iterators())
>   cell->set_subdomain_id(0);
> return;
>   }
>
> Hence step-17 only tries to use metis (and, if metis is not available,
> aborts) if there are multiple partitions for the mesh.
>
> Best,
> David
>
>
> On Mon, Jul 27, 2020 at 12:37 AM yuesu jin  wrote:
>
>> Dear all,
>>   I am running step-17 by mpirun, it returns the error message below:
>> **
>> 
>> Exception on processing:
>>
>> 
>> An error occurred in line <69> of file
>>  in function
>> void dealii::SparsityTools::{anonymous}::partition_metis(const
>> dealii::SparsityPattern&, const std::vector&, unsigned int,
>> std::vector&)
>> The violated condition was:
>> false
>> Additional information:
>> The function you called requires METIS, but you did not configure
>> deal.II with METIS.
>> 
>> This message does't appear when I use a single node to run it.  Does the
>> sparsity tools  automatically overload to partition_metis under parallel
>> case?
>> Thank you!
>> Best regards
>> --
>> Yuesu Jin,
>> Ph.D student,
>> University of Houston,
>> College of Natural Sciences and Mathematics,
>> Department of Earth and Atmospheric Sciences,
>> Houston, Texas 77204-5008
>> 346-404-2062
>>
>> --
>> 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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>> <https://groups.google.com/d/msgid/dealii/CA%2B25a%3DJ2Rzk9yL0Zt%2Boq_U-MV4hWcwNJGvj-4tjjjRAqABs81Q%40mail.gmail.com?utm_medium=email_source=footer>
>> .
>>
> --
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> .
>


-- 
Yuesu Jin,
Ph.D student,
University of Houston,
College of Natural Sciences and Mathematics,
Department of Earth and Atmospheric Sciences,
Houston, Texas 77204-5008
346-404-2062

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[deal.II] METIS partition error

2020-07-26 Thread yuesu jin
Dear all,
  I am running step-17 by mpirun, it returns the error message below:
**

Exception on processing:


An error occurred in line <69> of file
 in function
void dealii::SparsityTools::{anonymous}::partition_metis(const
dealii::SparsityPattern&, const std::vector&, unsigned int,
std::vector&)
The violated condition was:
false
Additional information:
The function you called requires METIS, but you did not configure
deal.II with METIS.

This message does't appear when I use a single node to run it.  Does the
sparsity tools  automatically overload to partition_metis under parallel
case?
Thank you!
Best regards
-- 
Yuesu Jin,
Ph.D student,
University of Houston,
College of Natural Sciences and Mathematics,
Department of Earth and Atmospheric Sciences,
Houston, Texas 77204-5008
346-404-2062

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Re: [deal.II] Point receivers

2020-07-26 Thread yuesu jin
Dear Daniel,
  Thank you very much! It solves my question!
Best wishes,
Yuesu

On Sun, Jul 26, 2020 at 5:55 PM Daniel Arndt  wrote:

> Yuesu,
>
> Have a look at FEFieldFunction (
> https://www.dealii.org/current/doxygen/deal.II/classFunctions_1_1FEFieldFunction.html)
> for the case that the interpolation points don't coincide with support
> points for nodal elements.
> Otherwise, you can use DoFTools::map_dofs_to_support_points (
> https://www.dealii.org/current/doxygen/deal.II/namespaceDoFTools.html#a5c7b6729af729af6d7deb67885467a79)
> and search fo the corresponding degree of freedom.
>
> Best,
> Daniel
>
> Am So., 26. Juli 2020 um 16:58 Uhr schrieb yuesu jin  >:
>
>> Dear all,
>>   I am working on an elastic wave simulation code which needs to set up
>> receivers on the surface boundaries to record the waveform.  In this case,
>> how can I link the point coordinate with the dof handlers and extract
>> values from the solution vector? Thank you!
>> Best regards,
>>
>>
>> --
>> Yuesu Jin,
>>
>>
>> --
>> 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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>> <https://groups.google.com/d/msgid/dealii/CA%2B25a%3D%2BY%2BVVdKMEds6HRFdt%2BmrdMR4ZdWrwtdx3YQgHBfCpt5A%40mail.gmail.com?utm_medium=email_source=footer>
>> .
>>
> --
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> .
>


-- 
Yuesu Jin,
Ph.D student,
University of Houston,
College of Natural Sciences and Mathematics,
Department of Earth and Atmospheric Sciences,
Houston, Texas 77204-5008
346-404-2062

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[deal.II] Point receivers

2020-07-26 Thread yuesu jin
Dear all,
  I am working on an elastic wave simulation code which needs to set up
receivers on the surface boundaries to record the waveform.  In this case,
how can I link the point coordinate with the dof handlers and extract
values from the solution vector? Thank you!
Best regards,


-- 
Yuesu Jin,

-- 
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Re: [deal.II] Cannot find local compiled petsc library

2020-07-24 Thread yuesu jin
Dear all,
  This problem has been solved. I copied the petscversion.h file to the
arch/include folder therefore cmake found all petsc files and finished
compilation.
Best regards

On Fri, Jul 24, 2020 at 3:17 PM yuesu jin  wrote:

> Dear Daniel,
>  Thank you for the instruction! I gave the architecture directory, which
> is a sub-directory : /home/yjin6/petsc/arch-linux-c-debug. It returns
> message like this:
>
> ***
> -- Include
> /home/yjin6/Deal.II/dealii-9.2.0/cmake/configure/configure_3_petsc.cmake
> -- Found PETSC_LIBRARY
> -- Found PETSC_INCLUDE_DIR_ARCH
> -- PETSC_INCLUDE_DIR_COMMON not found! Call:
> -- FIND_PATH(PETSC_INCLUDE_DIR_COMMON petscversion.h HINTS
> /home/yjin6/petsc/arch-linux-c-debug /home/yjin6/petsc/arch-linux-c-debug/
> PATH_SUFFIXES petsc include include/petsc)
> -- Found PETSC_PETSCVARIABLES
> -- Found PETSC_LIBRARY_flapack
> -- Found PETSC_LIBRARY_fblas
> -- Found PETSC_LIBRARY_X11
> -- Performing Test PETSC_LIBRARY_m
> -- Performing Test PETSC_LIBRARY_m - Success
> -- Performing Test PETSC_LIBRARY_dl
> -- Performing Test PETSC_LIBRARY_dl - Success
> -- Found PETSC_LIBRARY_mpi_usempif08
> -- Found PETSC_LIBRARY_mpi_usempi_ignore_tkr
> -- Found PETSC_LIBRARY_mpi_mpifh
> -- Found PETSC_LIBRARY_mpi
> -- Performing Test PETSC_LIBRARY_gfortran
> -- Performing Test PETSC_LIBRARY_gfortran - Success
> -- Performing Test PETSC_LIBRARY_quadmath
> -- Performing Test PETSC_LIBRARY_quadmath - Success
> -- Performing Test PETSC_LIBRARY_pthread
> -- Performing Test PETSC_LIBRARY_pthread - Success
> --   PETSC_LIBRARIES:
> /home/yjin6/petsc/arch-linux-c-debug/lib/libpetsc.so;/home/yjin6/petsc/arch-linux-c-debug/lib/libflapack.a;/home/yjin6/petsc/arch-linux-c-debug/lib/libfblas.a;/usr/lib/x86_64-linux-gnu/libX11.so;m;dl;/usr/local/lib/libmpi_usempif08.so;/usr/local/lib/libmpi_usempi_ignore_tkr.so;/usr/local/lib/libmpi_mpifh.so;/usr/local/lib/libmpi.so;gfortran;m;gfortran;m;quadmath;pthread;quadmath;dl
> --   PETSC_INCLUDE_DIRS: *** Required variable "PETSC_INCLUDE_DIR_COMMON"
> set to NOTFOUND ***
> --   PETSC_USER_INCLUDE_DIRS: *** Required variable
> "PETSC_INCLUDE_DIR_COMMON" set to NOTFOUND ***
> -- Could NOT find PETSC
> -- DEAL_II_WITH_PETSC has unmet external dependencies.
>
>
> On Fri, Jul 24, 2020 at 1:39 PM Daniel Arndt 
> wrote:
>
>> Yuesun,
>>
>> Apparently, CMake was able to find the file petscvariables, but not the
>> include directories or the library.
>> Can you search for "libpetsc.so" yourself? Our CMake find module tries to
>> find this library in {PETSC_DIR}/lib or {PETSC_DIR}/lib64.
>> See if you can adjust PETSC_DIR accordingly.
>>
>> Best,
>> Daniel
>>
>> Am Fr., 24. Juli 2020 um 01:18 Uhr schrieb yuesu jin <
>> jinyues...@gmail.com>:
>>
>>> Dear all,
>>>   I am installing deal.ii with petsc on a cluster. After I compiled the
>>> petsc library (The arch folder name is arch-linux-c-debug) and gave a cmake
>>> argument -DPETSC_DIR=/home/yjin6/petsc
>>> cmake cannot find the petsc library .so file(It is in the folder), but
>>> it founds the version is 3.13.
>>> Could you tell me what's the possible reason why cmake cannot find the
>>> library?
>>> Best regards
>>> ***
>>> --- Include
>>> /home/yjin6/Deal.II/dealii-9.2.0/cmake/configure/configure_3_petsc.cmake
>>> -- PETSC_LIBRARY not found! Call:
>>> -- FIND_LIBRARY(PETSC_LIBRARY NAMES petsc libpetsc HINTS
>>> /home/yjin6/petsc /home/yjin6/petsc/ PATH_SUFFIXES lib lib64 lib)
>>> -- PETSC_INCLUDE_DIR_ARCH not found! Call:
>>> -- FIND_PATH(PETSC_INCLUDE_DIR_ARCH petscconf.h HINTS
>>> /home/yjin6/petsc /home/yjin6/petsc/ PATH_SUFFIXES petsc include
>>> include/petsc)
>>> -- Found PETSC_INCLUDE_DIR_COMMON
>>> -- Found PETSC_PETSCVARIABLES
>>> --   PETSC_VERSION: 3.13.3.0
>>> --   PETSC_LIBRARIES: *** Required variable "PETSC_LIBRARY" set to
>>> NOTFOUND ***
>>> --   PETSC_INCLUDE_DIRS: *** Required variable "PETSC_INCLUDE_DIR_ARCH"
>>> set to NOTFOUND ***
>>> --   PETSC_USER_INCLUDE_DIRS: *** Required variable
>>> "PETSC_INCLUDE_DIR_ARCH" set to NOTFOUND ***
>>> -- Could NOT find PETSC
>>> -- DEAL_II_WITH_PETSC has unmet external dependencies.
>>> --
>>> Yuesu Jin,
>>> Ph.D student,
>>> University of Houston,
>>> College of Natural Sciences and Mathematics,
>

Re: [deal.II] Cannot find local compiled petsc library

2020-07-24 Thread yuesu jin
Dear Daniel,
 Thank you for the instruction! I gave the architecture directory, which is
a sub-directory : /home/yjin6/petsc/arch-linux-c-debug. It returns message
like this:
***
-- Include
/home/yjin6/Deal.II/dealii-9.2.0/cmake/configure/configure_3_petsc.cmake
-- Found PETSC_LIBRARY
-- Found PETSC_INCLUDE_DIR_ARCH
-- PETSC_INCLUDE_DIR_COMMON not found! Call:
-- FIND_PATH(PETSC_INCLUDE_DIR_COMMON petscversion.h HINTS
/home/yjin6/petsc/arch-linux-c-debug /home/yjin6/petsc/arch-linux-c-debug/
PATH_SUFFIXES petsc include include/petsc)
-- Found PETSC_PETSCVARIABLES
-- Found PETSC_LIBRARY_flapack
-- Found PETSC_LIBRARY_fblas
-- Found PETSC_LIBRARY_X11
-- Performing Test PETSC_LIBRARY_m
-- Performing Test PETSC_LIBRARY_m - Success
-- Performing Test PETSC_LIBRARY_dl
-- Performing Test PETSC_LIBRARY_dl - Success
-- Found PETSC_LIBRARY_mpi_usempif08
-- Found PETSC_LIBRARY_mpi_usempi_ignore_tkr
-- Found PETSC_LIBRARY_mpi_mpifh
-- Found PETSC_LIBRARY_mpi
-- Performing Test PETSC_LIBRARY_gfortran
-- Performing Test PETSC_LIBRARY_gfortran - Success
-- Performing Test PETSC_LIBRARY_quadmath
-- Performing Test PETSC_LIBRARY_quadmath - Success
-- Performing Test PETSC_LIBRARY_pthread
-- Performing Test PETSC_LIBRARY_pthread - Success
--   PETSC_LIBRARIES:
/home/yjin6/petsc/arch-linux-c-debug/lib/libpetsc.so;/home/yjin6/petsc/arch-linux-c-debug/lib/libflapack.a;/home/yjin6/petsc/arch-linux-c-debug/lib/libfblas.a;/usr/lib/x86_64-linux-gnu/libX11.so;m;dl;/usr/local/lib/libmpi_usempif08.so;/usr/local/lib/libmpi_usempi_ignore_tkr.so;/usr/local/lib/libmpi_mpifh.so;/usr/local/lib/libmpi.so;gfortran;m;gfortran;m;quadmath;pthread;quadmath;dl
--   PETSC_INCLUDE_DIRS: *** Required variable "PETSC_INCLUDE_DIR_COMMON"
set to NOTFOUND ***
--   PETSC_USER_INCLUDE_DIRS: *** Required variable
"PETSC_INCLUDE_DIR_COMMON" set to NOTFOUND ***
-- Could NOT find PETSC
-- DEAL_II_WITH_PETSC has unmet external dependencies.


On Fri, Jul 24, 2020 at 1:39 PM Daniel Arndt  wrote:

> Yuesun,
>
> Apparently, CMake was able to find the file petscvariables, but not the
> include directories or the library.
> Can you search for "libpetsc.so" yourself? Our CMake find module tries to
> find this library in {PETSC_DIR}/lib or {PETSC_DIR}/lib64.
> See if you can adjust PETSC_DIR accordingly.
>
> Best,
> Daniel
>
> Am Fr., 24. Juli 2020 um 01:18 Uhr schrieb yuesu jin  >:
>
>> Dear all,
>>   I am installing deal.ii with petsc on a cluster. After I compiled the
>> petsc library (The arch folder name is arch-linux-c-debug) and gave a cmake
>> argument -DPETSC_DIR=/home/yjin6/petsc
>> cmake cannot find the petsc library .so file(It is in the folder), but it
>> founds the version is 3.13.
>> Could you tell me what's the possible reason why cmake cannot find the
>> library?
>> Best regards
>> ***
>> --- Include
>> /home/yjin6/Deal.II/dealii-9.2.0/cmake/configure/configure_3_petsc.cmake
>> -- PETSC_LIBRARY not found! Call:
>> -- FIND_LIBRARY(PETSC_LIBRARY NAMES petsc libpetsc HINTS
>> /home/yjin6/petsc /home/yjin6/petsc/ PATH_SUFFIXES lib lib64 lib)
>> -- PETSC_INCLUDE_DIR_ARCH not found! Call:
>> -- FIND_PATH(PETSC_INCLUDE_DIR_ARCH petscconf.h HINTS
>> /home/yjin6/petsc /home/yjin6/petsc/ PATH_SUFFIXES petsc include
>> include/petsc)
>> -- Found PETSC_INCLUDE_DIR_COMMON
>> -- Found PETSC_PETSCVARIABLES
>> --   PETSC_VERSION: 3.13.3.0
>> --   PETSC_LIBRARIES: *** Required variable "PETSC_LIBRARY" set to
>> NOTFOUND ***
>> --   PETSC_INCLUDE_DIRS: *** Required variable "PETSC_INCLUDE_DIR_ARCH"
>> set to NOTFOUND ***
>> --   PETSC_USER_INCLUDE_DIRS: *** Required variable
>> "PETSC_INCLUDE_DIR_ARCH" set to NOTFOUND ***
>> -- Could NOT find PETSC
>> -- DEAL_II_WITH_PETSC has unmet external dependencies.
>> --
>> Yuesu Jin,
>> Ph.D student,
>> University of Houston,
>> College of Natural Sciences and Mathematics,
>> Department of Earth and Atmospheric Sciences,
>> Houston, Texas 77204-5008
>> 346-404-2062
>>
>> --
>> 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.
>> To unsubscribe from this group and stop receiving emails from it, send an
>> email to dealii+unsubscr...@googlegroups.com.
>> To view this discussion on the web visit
>> https://groups.google.com/d/msgid/dealii/CA%

[deal.II] Cannot find local compiled petsc library

2020-07-23 Thread yuesu jin
Dear all,
  I am installing deal.ii with petsc on a cluster. After I compiled the
petsc library (The arch folder name is arch-linux-c-debug) and gave a cmake
argument -DPETSC_DIR=/home/yjin6/petsc
cmake cannot find the petsc library .so file(It is in the folder), but it
founds the version is 3.13.
Could you tell me what's the possible reason why cmake cannot find the
library?
Best regards
***
--- Include
/home/yjin6/Deal.II/dealii-9.2.0/cmake/configure/configure_3_petsc.cmake
-- PETSC_LIBRARY not found! Call:
-- FIND_LIBRARY(PETSC_LIBRARY NAMES petsc libpetsc HINTS
/home/yjin6/petsc /home/yjin6/petsc/ PATH_SUFFIXES lib lib64 lib)
-- PETSC_INCLUDE_DIR_ARCH not found! Call:
-- FIND_PATH(PETSC_INCLUDE_DIR_ARCH petscconf.h HINTS /home/yjin6/petsc
/home/yjin6/petsc/ PATH_SUFFIXES petsc include include/petsc)
-- Found PETSC_INCLUDE_DIR_COMMON
-- Found PETSC_PETSCVARIABLES
--   PETSC_VERSION: 3.13.3.0
--   PETSC_LIBRARIES: *** Required variable "PETSC_LIBRARY" set to NOTFOUND
***
--   PETSC_INCLUDE_DIRS: *** Required variable "PETSC_INCLUDE_DIR_ARCH" set
to NOTFOUND ***
--   PETSC_USER_INCLUDE_DIRS: *** Required variable
"PETSC_INCLUDE_DIR_ARCH" set to NOTFOUND ***
-- Could NOT find PETSC
-- DEAL_II_WITH_PETSC has unmet external dependencies.
-- 
Yuesu Jin,
Ph.D student,
University of Houston,
College of Natural Sciences and Mathematics,
Department of Earth and Atmospheric Sciences,
Houston, Texas 77204-5008
346-404-2062

-- 
The deal.II project is located at http://www.dealii.org/
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Re: [deal.II] Re: PETSc is not compatible with current MPI

2020-07-23 Thread yuesu jin
Dear Bruno,
Thank you very much! I am using mpi/gcc right now. I will change to
Intel mpi library.
Best regards

On Thu, Jul 23, 2020 at 9:08 PM Bruno Turcksin 
wrote:

> Yuesu Jin,
>
> You don't need to compile your own PETSc but you need to use the same MPI
> library than the one that PETSc is using. There are very hard to debug
> problems that appear when PETSc and deal.II use different MPI libraries. I
> think that you want to use this MPI library 
> project/cacds/apps/intelmpi/2019.0.117/intel64/lib/release/libmpi.so
> So you probably need to load a module to use Intel MPI.
>
> Best,
>
> Bruno
>
> On Thursday, July 23, 2020 at 7:47:23 PM UTC-4, yuesu jin wrote:
>>
>> Dear all,
>>   I installed the Deal.II on a cluster.
>>
>> The first thing I found is that, the 
>> /dealii-9.2.0/cmake/configure/configure_1_mpi.cmake
>> automatically set the DEAL_II_WITH_MPI argument as "off", therefore the
>> MPI_FOUND module cannot run. I switched it on and cmake can find the MPI
>> library.
>>
>> The second thing I found is very strange. Cmake gives the message "Could
>> not find a sufficient PETSC installation: PETSC is compiled against a
>> different MPI library than the one deal.II picked up." The PETSc library
>> is integrated in the cluster's public library, I can add it by the command
>> "module add". Does this message mean that I need to compile a new version
>> of PETSc different from the one in the public library?
>>
>> Thanks!
>> Best
>>
>>
>> **
>> -- Include
>> /home/yjin6/DEALII/dealii-9.2.0/cmake/configure/configure_3_petsc.cmake
>> -- Found PETSC_LIBRARY
>> -- Found PETSC_INCLUDE_DIR_ARCH
>> -- Found PETSC_INCLUDE_DIR_COMMON
>> -- Found PETSC_PETSCVARIABLES
>> -- Found PETSC_LIBRARY_mkl_scalapack_lp64
>> -- Found PETSC_LIBRARY_mkl_blacs_intelmpi_lp64
>> -- Found PETSC_LIBRARY_mkl_intel_lp64
>> -- Found PETSC_LIBRARY_mkl_sequential
>> -- Found PETSC_LIBRARY_mkl_core
>> -- Found PETSC_LIBRARY_umfpack
>> -- Found PETSC_LIBRARY_klu
>> -- Found PETSC_LIBRARY_cholmod
>> -- Found PETSC_LIBRARY_btf
>> -- Found PETSC_LIBRARY_ccolamd
>> -- Found PETSC_LIBRARY_colamd
>> -- Found PETSC_LIBRARY_camd
>> -- Found PETSC_LIBRARY_amd
>> -- Found PETSC_LIBRARY_suitesparseconfig
>> -- Found PETSC_LIBRARY_HYPRE
>> -- Found PETSC_LIBRARY_fftw3xc_intel_pic
>> -- Found PETSC_LIBRARY_fftw3x_cdft_lp64_pic
>> -- Found PETSC_LIBRARY_mkl_cdft_core
>> -- Found PETSC_LIBRARY_mkl_blacs_intelmpi_lp64
>> -- Found PETSC_LIBRARY_mkl_intel_lp64
>> -- Found PETSC_LIBRARY_mkl_sequential
>> -- Found PETSC_LIBRARY_mkl_core
>> -- Found PETSC_LIBRARY_mkl_intel_lp64
>> -- Found PETSC_LIBRARY_mkl_sequential
>> -- Found PETSC_LIBRARY_mkl_core
>> -- Found PETSC_LIBRARY_parmetis
>> -- Found PETSC_LIBRARY_metis
>> -- Performing Test PETSC_LIBRARY_dl
>> -- Performing Test PETSC_LIBRARY_dl - Success
>> -- Found PETSC_LIBRARY_iomp5
>> -- Performing Test PETSC_LIBRARY_pthread
>> -- Performing Test PETSC_LIBRARY_pthread - Success
>> -- Performing Test PETSC_LIBRARY_rt
>> -- Performing Test PETSC_LIBRARY_rt - Success
>> -- Found PETSC_LIBRARY_mpifort
>> -- Found PETSC_LIBRARY_mpi
>> -- Found PETSC_LIBRARY_ifport
>> -- Found PETSC_LIBRARY_ifcoremt_pic
>> -- Found PETSC_LIBRARY_imf
>> -- Found PETSC_LIBRARY_svml
>> -- Performing Test PETSC_LIBRARY_m
>> -- Performing Test PETSC_LIBRARY_m - Success
>> -- Found PETSC_LIBRARY_ipgo
>> -- Found PETSC_LIBRARY_irc
>> -- Found PETSC_LIBRARY_irc_s
>> -- Found PETSC_LIBRARY_iomp5
>> --   PETSC_VERSION: 3.10.2.0
>> --   PETSC_LIBRARIES:
>> /project/cacds/apps/easybuild/software/PETSc/3.10.2-intel-2017b/lib/libpetsc.a;/project/cacds/apps/easybuild/software/imkl/2017.4.239-iimpi-2017b/mkl/lib/intel64/libmkl_scalapack_lp64.so;/project/cacds/apps/easybuild/software/imkl/2017.4.239-iimpi-2017b/mkl/lib/intel64/libmkl_blacs_intelmpi_lp64.so;/project/cacds/apps/easybuild/software/imkl/2017.4.239-iimpi-2017b/mkl/lib/intel64/libmkl_intel_lp64.so;/project/cacds/apps/easybuild/software/imkl/2017.4.239-iimpi-2017b/mkl/lib/intel64/libmkl_sequential.so;/project/cacds/apps/easybuild/software/imkl/2017.4.239-iimpi-2017b/mkl/lib/intel64/libmkl_core.so;/project/cacds/apps/easybuild/software/SuiteSparse/5.1.2-intel-2017b-METIS-5.1.0/UMFPACK/Lib/libumfpack.a;/project/cacds/apps/easybuild/software/SuiteSparse/5.1.2-intel-2017b-METIS-5.1.0/KLU/Lib/libklu.a;/project/cacds/apps/easybuild/software/SuiteSparse/5.1.2-int

[deal.II] PETSc is not compatible with current MPI

2020-07-23 Thread yuesu jin
than the one deal.II picked up.
-- DEAL_II_WITH_PETSC has unmet external dependencies.

-- 
Yuesu Jin,
Ph.D student,
University of Houston,
College of Natural Sciences and Mathematics,
Department of Earth and Atmospheric Sciences,
Houston, Texas 77204-5008
346-404-2062

-- 
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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Re: [deal.II] Installation stopped

2020-07-23 Thread yuesu jin
Dear all,
 The problem has been solved. The GCC version was too old to compile the
new version of deal.ii. I changed the gcc to a newer version which gave a
very good result. Thanks!
Best regards

On Thu, Jul 23, 2020 at 11:56 AM yuesu jin  wrote:

> Dear Bruno,
>   Ok, I will try a new gcc for compilation. Thank you!
>
> On Thu, Jul 23, 2020 at 7:57 AM Bruno Turcksin 
> wrote:
>
>> Yuesu Lin,
>>
>> Do you have access to a newer compiler? gcc 4.8.5 is very old.
>>
>> Best,
>>
>> Bruno
>>
>> On Wednesday, July 22, 2020 at 11:26:05 PM UTC-4, yuesu jin wrote:
>>>
>>> Dear Timo,
>>>  The configuration in summary.log file is:
>>>
>>> deal.II configuration:
>>> #CMAKE_BUILD_TYPE:   DebugRelease
>>> #BUILD_SHARED_LIBS:  ON
>>> #CMAKE_INSTALL_PREFIX:   /home/yjin6/DEALII/main
>>> #CMAKE_SOURCE_DIR:   /home/yjin6/DEALII/dealii-9.2.0
>>> #(version 9.2.0)
>>> #CMAKE_BINARY_DIR:   /home/yjin6/DEALII/dealii-9.2.0/build
>>> #CMAKE_CXX_COMPILER: GNU 4.8.5 on platform Linux x86_64
>>> #/usr/bin/c++
>>>
>>> And error message is:
>>>
>>> /home/yjin6/DEALII/dealii-9.2.0/build/source/dofs/dof_tools_sparsity.inst:12118:27:
>>>   required from here
>>> /home/yjin6/DEALII/dealii-9.2.0/source/dofs/dof_tools_sparsity.cc:1352:55:
>>> error: no matching function for call to
>>> ‘make_flux_sparsity_pattern(const dealii::hp::DoFHandler<3, 3>&,
>>> dealii::BlockDynamicSparsityPattern&, dealii::AffineConstraints&,
>>> const bool&, const dealii::Table<2, dealii::DoFTools::Coupling>&, const
>>> dealii::Table<2, dealii::DoFTools::Coupling>&, const subdomain_id&,
>>> )’
>>> /home/yjin6/DEALII/dealii-9.2.0/source/dofs/dof_tools_sparsity.cc:1352:55:
>>> note: candidates are:
>>> /home/yjin6/DEALII/dealii-9.2.0/source/dofs/dof_tools_sparsity.cc:689:3:
>>> note: template void
>>> dealii::DoFTools::make_flux_sparsity_pattern(const DoFHandlerType&,
>>> SparsityPatternType&)
>>>    make_flux_sparsity_pattern(const DoFHandlerType ,
>>>^
>>>
>>> On Wed, Jul 22, 2020 at 9:28 PM Timo Heister 
>>> wrote:
>>>
>>>> Yuesu Jin,
>>>>
>>>> the error message should be higher up in the output. To see them more
>>>> clearly, you can compile again with "make -j 1". What compiler and
>>>> what version of deal.II is this? (look at your summary.log)
>>>>
>>>> On Wed, Jul 22, 2020 at 7:23 PM yuesu jin  wrote:
>>>> >
>>>> > Dear Deal.II team,
>>>> >
>>>> >   I am installing the deal.ii on a new cluster. The compiling process
>>>> stopped at 62%.
>>>> >
>>>> > [ 62%] Building CXX object
>>>> source/numerics/CMakeFiles/obj_numerics_debug.dir/vector_tools_project_qpmf.cc.o
>>>> > [ 62%] [ 62%] Building CXX object
>>>> source/fe/CMakeFiles/obj_fe_debug.dir/mapping_q1_eulerian.cc.o
>>>> > Building CXX object
>>>> source/fe/CMakeFiles/obj_fe_debug.dir/mapping_q_eulerian.cc.o
>>>> > [ 62%] Built target obj_fe_debug
>>>> > [ 62%] Built target obj_numerics_debug
>>>> >
>>>> > The last few lines are:
>>>> >
>>>> > /home/yjin6/DEALII/dealii-9.2.0/include/deal.II/base/index_set.h: In
>>>> member function ‘dealii::IndexSet::IntervalIterator
>>>> dealii::IndexSet::IntervalIterator::operator++(int)’:
>>>> >
>>>> /home/yjin6/DEALII/dealii-9.2.0/include/deal.II/base/index_set.h:1192:44:
>>>> note: synthesized method
>>>> ‘dealii::IndexSet::IntervalIterator::IntervalIterator(const
>>>> dealii::IndexSet::IntervalIterator&)’ first required here
>>>> >const IndexSet::IntervalIterator iter = *this;
>>>> > ^
>>>> > In file included from
>>>> /home/yjin6/DEALII/dealii-9.2.0/include/deal.II/lac/vector.h:24:0,
>>>> >  from
>>>> /home/yjin6/DEALII/dealii-9.2.0/include/deal.II/lac/vector_memory.h:26,
>>>> >  from
>>>> /home/yjin6/DEALII/dealii-9.2.0/include/deal.II/lac/lapack_full_matrix.h:27,
>>>> >  from
>>>> /home/yjin6/DEALII/dealii-9.2.0/in

Re: [deal.II] Installation stopped

2020-07-23 Thread yuesu jin
Dear Bruno,
  Ok, I will try a new gcc for compilation. Thank you!

On Thu, Jul 23, 2020 at 7:57 AM Bruno Turcksin 
wrote:

> Yuesu Lin,
>
> Do you have access to a newer compiler? gcc 4.8.5 is very old.
>
> Best,
>
> Bruno
>
> On Wednesday, July 22, 2020 at 11:26:05 PM UTC-4, yuesu jin wrote:
>>
>> Dear Timo,
>>  The configuration in summary.log file is:
>>
>> deal.II configuration:
>> #CMAKE_BUILD_TYPE:   DebugRelease
>> #BUILD_SHARED_LIBS:  ON
>> #CMAKE_INSTALL_PREFIX:   /home/yjin6/DEALII/main
>> #CMAKE_SOURCE_DIR:   /home/yjin6/DEALII/dealii-9.2.0
>> #(version 9.2.0)
>> #CMAKE_BINARY_DIR:   /home/yjin6/DEALII/dealii-9.2.0/build
>> #CMAKE_CXX_COMPILER: GNU 4.8.5 on platform Linux x86_64
>> #/usr/bin/c++
>>
>> And error message is:
>>
>> /home/yjin6/DEALII/dealii-9.2.0/build/source/dofs/dof_tools_sparsity.inst:12118:27:
>>   required from here
>> /home/yjin6/DEALII/dealii-9.2.0/source/dofs/dof_tools_sparsity.cc:1352:55:
>> error: no matching function for call to ‘make_flux_sparsity_pattern(const
>> dealii::hp::DoFHandler<3, 3>&, dealii::BlockDynamicSparsityPattern&,
>> dealii::AffineConstraints&, const bool&, const dealii::Table<2,
>> dealii::DoFTools::Coupling>&, const dealii::Table<2,
>> dealii::DoFTools::Coupling>&, const subdomain_id&, > function type>)’
>> /home/yjin6/DEALII/dealii-9.2.0/source/dofs/dof_tools_sparsity.cc:1352:55:
>> note: candidates are:
>> /home/yjin6/DEALII/dealii-9.2.0/source/dofs/dof_tools_sparsity.cc:689:3:
>> note: template void
>> dealii::DoFTools::make_flux_sparsity_pattern(const DoFHandlerType&,
>> SparsityPatternType&)
>>make_flux_sparsity_pattern(const DoFHandlerType ,
>>^
>>
>> On Wed, Jul 22, 2020 at 9:28 PM Timo Heister  wrote:
>>
>>> Yuesu Jin,
>>>
>>> the error message should be higher up in the output. To see them more
>>> clearly, you can compile again with "make -j 1". What compiler and
>>> what version of deal.II is this? (look at your summary.log)
>>>
>>> On Wed, Jul 22, 2020 at 7:23 PM yuesu jin  wrote:
>>> >
>>> > Dear Deal.II team,
>>> >
>>> >   I am installing the deal.ii on a new cluster. The compiling process
>>> stopped at 62%.
>>> >
>>> > [ 62%] Building CXX object
>>> source/numerics/CMakeFiles/obj_numerics_debug.dir/vector_tools_project_qpmf.cc.o
>>> > [ 62%] [ 62%] Building CXX object
>>> source/fe/CMakeFiles/obj_fe_debug.dir/mapping_q1_eulerian.cc.o
>>> > Building CXX object
>>> source/fe/CMakeFiles/obj_fe_debug.dir/mapping_q_eulerian.cc.o
>>> > [ 62%] Built target obj_fe_debug
>>> > [ 62%] Built target obj_numerics_debug
>>> >
>>> > The last few lines are:
>>> >
>>> > /home/yjin6/DEALII/dealii-9.2.0/include/deal.II/base/index_set.h: In
>>> member function ‘dealii::IndexSet::IntervalIterator
>>> dealii::IndexSet::IntervalIterator::operator++(int)’:
>>> >
>>> /home/yjin6/DEALII/dealii-9.2.0/include/deal.II/base/index_set.h:1192:44:
>>> note: synthesized method
>>> ‘dealii::IndexSet::IntervalIterator::IntervalIterator(const
>>> dealii::IndexSet::IntervalIterator&)’ first required here
>>> >const IndexSet::IntervalIterator iter = *this;
>>> > ^
>>> > In file included from
>>> /home/yjin6/DEALII/dealii-9.2.0/include/deal.II/lac/vector.h:24:0,
>>> >  from
>>> /home/yjin6/DEALII/dealii-9.2.0/include/deal.II/lac/vector_memory.h:26,
>>> >  from
>>> /home/yjin6/DEALII/dealii-9.2.0/include/deal.II/lac/lapack_full_matrix.h:27,
>>> >  from
>>> /home/yjin6/DEALII/dealii-9.2.0/include/deal.II/base/tensor.h:29,
>>> >  from
>>> /home/yjin6/DEALII/dealii-9.2.0/include/deal.II/base/point.h:23,
>>> >  from
>>> /home/yjin6/DEALII/dealii-9.2.0/include/deal.II/base/quadrature.h:22,
>>> >  from
>>> /home/yjin6/DEALII/dealii-9.2.0/include/deal.II/base/quadrature_lib.h:22,
>>> >  from
>>> /home/yjin6/DEALII/dealii-9.2.0/source/fe/mapping_q_eulerian.cc:16:
>>> >
>>> /home/yjin6/DEALII/dealii-9.2.0/include/deal.II/base/index_se

Re: [deal.II] Installation stopped

2020-07-22 Thread yuesu jin
Dear Timo,
 The configuration in summary.log file is:

deal.II configuration:
#CMAKE_BUILD_TYPE:   DebugRelease
#BUILD_SHARED_LIBS:  ON
#CMAKE_INSTALL_PREFIX:   /home/yjin6/DEALII/main
#CMAKE_SOURCE_DIR:   /home/yjin6/DEALII/dealii-9.2.0
#(version 9.2.0)
#CMAKE_BINARY_DIR:   /home/yjin6/DEALII/dealii-9.2.0/build
#CMAKE_CXX_COMPILER: GNU 4.8.5 on platform Linux x86_64
#/usr/bin/c++

And error message is:

/home/yjin6/DEALII/dealii-9.2.0/build/source/dofs/dof_tools_sparsity.inst:12118:27:
  required from here
/home/yjin6/DEALII/dealii-9.2.0/source/dofs/dof_tools_sparsity.cc:1352:55:
error:
no matching function for call to ‘make_flux_sparsity_pattern(const
dealii::hp::DoFHandler<3, 3>&, dealii::BlockDynamicSparsityPattern&,
dealii::AffineConstraints&, const bool&, const dealii::Table<2,
dealii::DoFTools::Coupling>&, const dealii::Table<2,
dealii::DoFTools::Coupling>&, const subdomain_id&, )’
/home/yjin6/DEALII/dealii-9.2.0/source/dofs/dof_tools_sparsity.cc:1352:55:
note: candidates are:
/home/yjin6/DEALII/dealii-9.2.0/source/dofs/dof_tools_sparsity.cc:689:3:
note: template void
dealii::DoFTools::make_flux_sparsity_pattern(const DoFHandlerType&,
SparsityPatternType&)
   make_flux_sparsity_pattern(const DoFHandlerType ,
   ^

On Wed, Jul 22, 2020 at 9:28 PM Timo Heister  wrote:

> Yuesu Jin,
>
> the error message should be higher up in the output. To see them more
> clearly, you can compile again with "make -j 1". What compiler and
> what version of deal.II is this? (look at your summary.log)
>
> On Wed, Jul 22, 2020 at 7:23 PM yuesu jin  wrote:
> >
> > Dear Deal.II team,
> >
> >   I am installing the deal.ii on a new cluster. The compiling process
> stopped at 62%.
> >
> > [ 62%] Building CXX object
> source/numerics/CMakeFiles/obj_numerics_debug.dir/vector_tools_project_qpmf.cc.o
> > [ 62%] [ 62%] Building CXX object
> source/fe/CMakeFiles/obj_fe_debug.dir/mapping_q1_eulerian.cc.o
> > Building CXX object
> source/fe/CMakeFiles/obj_fe_debug.dir/mapping_q_eulerian.cc.o
> > [ 62%] Built target obj_fe_debug
> > [ 62%] Built target obj_numerics_debug
> >
> > The last few lines are:
> >
> > /home/yjin6/DEALII/dealii-9.2.0/include/deal.II/base/index_set.h: In
> member function ‘dealii::IndexSet::IntervalIterator
> dealii::IndexSet::IntervalIterator::operator++(int)’:
> >
> /home/yjin6/DEALII/dealii-9.2.0/include/deal.II/base/index_set.h:1192:44:
> note: synthesized method
> ‘dealii::IndexSet::IntervalIterator::IntervalIterator(const
> dealii::IndexSet::IntervalIterator&)’ first required here
> >const IndexSet::IntervalIterator iter = *this;
> > ^
> > In file included from
> /home/yjin6/DEALII/dealii-9.2.0/include/deal.II/lac/vector.h:24:0,
> >  from
> /home/yjin6/DEALII/dealii-9.2.0/include/deal.II/lac/vector_memory.h:26,
> >  from
> /home/yjin6/DEALII/dealii-9.2.0/include/deal.II/lac/lapack_full_matrix.h:27,
> >  from
> /home/yjin6/DEALII/dealii-9.2.0/include/deal.II/base/tensor.h:29,
> >  from
> /home/yjin6/DEALII/dealii-9.2.0/include/deal.II/base/point.h:23,
> >  from
> /home/yjin6/DEALII/dealii-9.2.0/include/deal.II/base/quadrature.h:22,
> >  from
> /home/yjin6/DEALII/dealii-9.2.0/include/deal.II/base/quadrature_lib.h:22,
> >  from
> /home/yjin6/DEALII/dealii-9.2.0/source/fe/mapping_q_eulerian.cc:16:
> > /home/yjin6/DEALII/dealii-9.2.0/include/deal.II/base/index_set.h:640:5:
> warning: unused parameter ‘other’ [-Wunused-parameter]
> >  IntervalIterator(const IntervalIterator ) = default;
> >  ^
> > /home/yjin6/DEALII/dealii-9.2.0/include/deal.II/base/index_set.h: In
> member function ‘dealii::IndexSet::IntervalIterator
> dealii::IndexSet::IntervalIterator::operator++(int)’:
> >
> /home/yjin6/DEALII/dealii-9.2.0/include/deal.II/base/index_set.h:1192:44:
> note: synthesized method
> ‘dealii::IndexSet::IntervalIterator::IntervalIterator(const
> dealii::IndexSet::IntervalIterator&)’ first required here
> >const IndexSet::IntervalIterator iter = *this;
> > ^
> > make: *** [all] Error 2
> >
> > Could you give me some instructions about that? Thank you!
> > --
> > Yuesu Jin,
> > Ph.D student,
> > University of Houston,
> > College of Natural Sciences and Mathematics,
> > Department of Earth and Atmospheric Sciences,
> > Houston, Texas 77204-5008
> > 3

[deal.II] Installation stopped

2020-07-22 Thread yuesu jin
Dear Deal.II team,

  I am installing the deal.ii on a new cluster. The compiling process
stopped at 62%.

[ 62%] Building CXX object
source/numerics/CMakeFiles/obj_numerics_debug.dir/vector_tools_project_qpmf.cc.o
[ 62%] [ 62%] Building CXX object
source/fe/CMakeFiles/obj_fe_debug.dir/mapping_q1_eulerian.cc.o
Building CXX object
source/fe/CMakeFiles/obj_fe_debug.dir/mapping_q_eulerian.cc.o
[ 62%] Built target obj_fe_debug
[ 62%] Built target obj_numerics_debug

The last few lines are:

/home/yjin6/DEALII/dealii-9.2.0/include/deal.II/base/index_set.h: In member
function ‘dealii::IndexSet::IntervalIterator
dealii::IndexSet::IntervalIterator::operator++(int)’:
/home/yjin6/DEALII/dealii-9.2.0/include/deal.II/base/index_set.h:1192:44:
note: synthesized method
‘dealii::IndexSet::IntervalIterator::IntervalIterator(const
dealii::IndexSet::IntervalIterator&)’ first required here
   const IndexSet::IntervalIterator iter = *this;
^
In file included from
/home/yjin6/DEALII/dealii-9.2.0/include/deal.II/lac/vector.h:24:0,
 from
/home/yjin6/DEALII/dealii-9.2.0/include/deal.II/lac/vector_memory.h:26,
 from
/home/yjin6/DEALII/dealii-9.2.0/include/deal.II/lac/lapack_full_matrix.h:27,
 from
/home/yjin6/DEALII/dealii-9.2.0/include/deal.II/base/tensor.h:29,
 from
/home/yjin6/DEALII/dealii-9.2.0/include/deal.II/base/point.h:23,
 from
/home/yjin6/DEALII/dealii-9.2.0/include/deal.II/base/quadrature.h:22,
 from
/home/yjin6/DEALII/dealii-9.2.0/include/deal.II/base/quadrature_lib.h:22,
 from
/home/yjin6/DEALII/dealii-9.2.0/source/fe/mapping_q_eulerian.cc:16:
/home/yjin6/DEALII/dealii-9.2.0/include/deal.II/base/index_set.h:640:5:
warning: unused parameter ‘other’ [-Wunused-parameter]
 IntervalIterator(const IntervalIterator ) = default;
 ^
/home/yjin6/DEALII/dealii-9.2.0/include/deal.II/base/index_set.h: In member
function ‘dealii::IndexSet::IntervalIterator
dealii::IndexSet::IntervalIterator::operator++(int)’:
/home/yjin6/DEALII/dealii-9.2.0/include/deal.II/base/index_set.h:1192:44:
note: synthesized method
‘dealii::IndexSet::IntervalIterator::IntervalIterator(const
dealii::IndexSet::IntervalIterator&)’ first required here
   const IndexSet::IntervalIterator iter = *this;
^
make: *** [all] Error 2

Could you give me some instructions about that? Thank you!
-- 
Yuesu Jin,
Ph.D student,
University of Houston,
College of Natural Sciences and Mathematics,
Department of Earth and Atmospheric Sciences,
Houston, Texas 77204-5008
346-404-2062

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Re: [deal.II] Re: Little question about constructor

2019-09-04 Thread yuesu jin
Dear Konrad,
  Appreciating for your detailed explanation, it really helps!! Thank you!
I am learning c++ by the means of studying deal.ii, so actually I am a
layman both in deal.ii and c++. I will read the reference page and books
you recommended. Thanks again!!
Best regards,
Yuesu

On Wed, Sep 4, 2019 at 5:03 AM Konrad  wrote:

> Hi Yuesu,
>
> I think this is rather a general C++ question. Once you create an object
> all members are initialized by invoking a constructor. If you do not
> declare any constructor the compiler will silently generate a set of
> constructors. The default constructor that takes no arguments is one of
> them. This will initialize all members in the order they are given. If you
> have a member of a primitive type like double or int memory for an int or
> double will be reserved (but not initialized with a value yet). If you have
> a class member it also needs to be initialized somehow so the compiler will
> look for a default constructor.
>
> What happens in your example is that the triangulation actually does get
> initialized by invoking its default constructor which initializes an empty
> triangulation. The dof_handler then can be called with the triangulation as
> an argument to store a (smart) pointer to the triangulation.
>
> See this documentation for example:
>
>
> https://docs.microsoft.com/en-us/cpp/cpp/constructors-cpp?view=vs-2019#constructors_in_composite_classes
>
> It is often good to know what the C++ compiler (secretly) does without
> explicitly telling you and what functions it generates if you do not
> provide them explicitly (and when you must do so). I really recommend the
> book by Scott Meyers "Effective C++: 55 ways ..."
>
> Hope that helps.
>
> Best,
> Konrad
>
>
> On Wednesday, September 4, 2019 at 4:44:24 AM UTC+2, yuesu jin wrote:
>>
>> Hi all,
>>
>>   I have a question about the constructor initialization list. In some
>> tutorials, we initialize the dof_handler in the constructor with parameter
>> triangulation, however, the triangulation is initialized in some member
>> function within this class, which means when we initialize the class, we
>> have not had the triangulation yet, I don't know why this method works?
>>
>> Best regards,
>> Yuesu
>>
> --
> 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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> <https://groups.google.com/d/msgid/dealii/fd3807d1-51e6-4daa-8eed-5da2eec1336b%40googlegroups.com?utm_medium=email_source=footer>
> .
>


-- 
Yuesu Jin,
Ph.D student,
University of Houston,
College of Natural Sciences and Mathematics,
Department of Earth and Atmospheric Sciences,
Houston, Texas 77204-5008
346-404-2062

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[deal.II] Little question about constructor

2019-09-03 Thread yuesu jin
Hi all,

  I have a question about the constructor initialization list. In some
tutorials, we initialize the dof_handler in the constructor with parameter
triangulation, however, the triangulation is initialized in some member
function within this class, which means when we initialize the class, we
have not had the triangulation yet, I don't know why this method works?

Best regards,
Yuesu

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Re: [deal.II] Re: Where can I find member function of cell?

2019-08-27 Thread yuesu jin
Hi, Bruno,
  Thanks a lot! It really helps!

On Tue, Aug 27, 2019 at 7:28 AM Bruno Turcksin 
wrote:

> Yuesu,
>
> For a Triangulation, the list is here:
> https://dealii.org/current/doxygen/deal.II/classCellAccessor-members.html
> (CellAccessor)
> For a DofHandler, the list is here:
> https://dealii.org/current/doxygen/deal.II/classDoFCellAccessor-members.html
> (DofCellAccessor)
>
> Best,
>
> Bruno
>
> On Monday, August 26, 2019 at 10:42:00 PM UTC-4, yuesu jin wrote:
>>
>> Hi all,
>>   When we iterate the cell within triangulation/dof_handler, we often use
>> functions such as cell->face(), cell->vertices()  etc. Where can I find all
>> the member function in our documentation webpage? Thanks a lot!
>>
>> --
>> Yuesu Jin,
>> Ph.D student,
>> University of Houston,
>> College of Natural Sciences and Mathematics,
>> Department of Earth and Atmospheric Sciences,
>> Houston, Texas 77204-5008
>> 346-404-2062
>>
>> --
> 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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> <https://groups.google.com/d/msgid/dealii/141f7ec4-53af-4336-8bdc-5f4897d5acff%40googlegroups.com?utm_medium=email_source=footer>
> .
>


-- 
Yuesu Jin,
Ph.D student,
University of Houston,
College of Natural Sciences and Mathematics,
Department of Earth and Atmospheric Sciences,
Houston, Texas 77204-5008
346-404-2062

-- 
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[deal.II] Where can I find member function of cell?

2019-08-26 Thread yuesu jin
Hi all,
  When we iterate the cell within triangulation/dof_handler, we often use
functions such as cell->face(), cell->vertices()  etc. Where can I find all
the member function in our documentation webpage? Thanks a lot!

-- 
Yuesu Jin,
Ph.D student,
University of Houston,
College of Natural Sciences and Mathematics,
Department of Earth and Atmospheric Sciences,
Houston, Texas 77204-5008
346-404-2062

-- 
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Re: [deal.II] Re: Question about constraints

2019-08-22 Thread yuesu jin
Thank you very much, Daniel!! I appreciate your help!

On Wed, Aug 21, 2019 at 11:40 PM Daniel Arndt 
wrote:

> Yuesu,
>
>   I am learning step-7 which has the same class AffineConstraints class,
>> in step6, we use the member function ::distribute_local_to_global to put
>> the local matrix and rhs into global matrix and rhs, but in step-7, we
>> still use system_matrix.add and then use the constraint.condense on
>> system_matrix and system_rhs. Do those two procedure have the same effect?
>>
>
> You can find a discussion at
> https://www.dealii.org/9.0.1/doxygen/deal.II/group__constraints.html. In
> short: Yes, they have the same purpose, but different advantages and
> disadvantages. In general, we recommend using distribute_local_to_global
> over condensation.
>
> 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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> .
>


-- 
Yuesu Jin,
Ph.D student,
University of Houston,
College of Natural Sciences and Mathematics,
Department of Earth and Atmospheric Sciences,
Houston, Texas 77204-5008
346-404-2062

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[deal.II] Question about constraints

2019-08-21 Thread yuesu jin
Hi all,
  I am learning step-7 which has the same class AffineConstraints class, in
step6, we use the member function ::distribute_local_to_global to put the
local matrix and rhs into global matrix and rhs, but in step-7, we still
use system_matrix.add and then use the constraint.condense on system_matrix
and system_rhs. Do those two procedure have the same effect?

---
Yuesu Jin,
Ph.D student,
University of Houston,
College of Natural Sciences and Mathematics,
Department of Earth and Atmospheric Sciences,
Houston, Texas 77204-5008
346-404-2062

-- 
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Re: [deal.II] undefined symbol: mkl_blas_dsyrk

2019-08-12 Thread yuesu jin
Hi Dr.Bangerth,
   I know where is the problem. My bash is in the anaconda environment
(with (base) in front of the command line.), so all the library links are
referenced to anaconda library. I modified the bashrc scripts then all goes
well!! Thanks a lot! I have learned a lesson about linux bash. It really
cost my time!
Best regards,
Yuesu


On Mon, Aug 12, 2019 at 12:12 PM Wolfgang Bangerth 
wrote:

> On 8/12/19 11:01 AM, yuesu jin wrote:
> >
> > Installation completed, what a stupid mistake I made! Appreciate for
> > your support!
> > All the problem should be the symbol mkl_blas_dsyrk. It may be caused by
> > my anaconda package manager because the message said:
> > /*/step-5_sec: symbol lookup error:
> > /home/yjin6/anaconda3/lib/libmkl_intel_lp64.so: undefined symbol:
> > mkl_blas_dsyrk
> > */
> > I try to fix it .
>
> Yuesu,
> ok, at least now you're back in business. Linking with the MKL is
> difficult. The kind of situation you report is listed on many websites
> -- an example is here:
>
>
> https://software.intel.com/en-us/articles/symbol-lookup-error-when-linking-intel-mkl-with-gcc-on-ubuntu
>
> Can you try the following: on the command line, say
>export
> LD_PRELOAD=/path/to/libmkl_core.so:/path/to/libmkl_intel_thread.so
> where you need to replace /path/to by the directory in which the
> libmkl_core.so and libmkl_intel_thread.so libraries are located. Then
> issue the last of the commands again that led to the error above (I
> suspect that that was 'make install').
>
> 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
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> .
>


-- 
Yuesu Jin,
Ph.D student,
University of Houston,
College of Natural Sciences and Mathematics,
Department of Earth and Atmospheric Sciences,
Houston, Texas 77204-5008
346-404-2062

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Re: [deal.II] undefined symbol: mkl_blas_dsyrk

2019-08-12 Thread yuesu jin
Hi Dr.Bangerth,
   Installation completed, what a stupid mistake I made! Appreciate for
your support!
   All the problem should be the symbol mkl_blas_dsyrk. It may be caused by
my anaconda package manager because the message said:

*/step-5_sec: symbol lookup error:
/home/yjin6/anaconda3/lib/libmkl_intel_lp64.so: undefined symbol:
mkl_blas_dsyrk*
   I try to fix it .
Best regards,
Yuesu

On Mon, Aug 12, 2019 at 8:30 AM Wolfgang Bangerth 
wrote:

> On 8/11/19 9:08 PM, yuesu jin wrote:
> > AH... I understand,/*cmake -DCMAKE_INSTALL_PREFIX=[Directory you want
> to
> > install] [Directory you build the program]*/
>
> No, the second [...] block is the directory where the sources are located,
> not
> where you build the program. The directory where you build the program is
> the
> directory you are currently in when you call 'cmake'.
>
>
> > I have installed it again in a new folder, the folder now is 3.6GB,
> which
> > means something has been installed in that. But the message is still
> there:
> > **
> > [100%] Building CXX object source/CMakeFiles/deal_II.dir/dummy.cc.o
> > [100%] Linking CXX shared library ../lib/libdeal_II.so
> > [100%] Built target deal_II
> > Install the project...
> > -- Install configuration: "DebugRelease"
> > CMake Error at cmake/scripts/cmake_install.cmake:36 (file):
> >file INSTALL cannot set permissions on
> >"/path/to/install/dir/share/deal.II/scripts/normalize.pl <
> http://normalize.pl>"
>
> You still have the /path/to/install/dir/ here. Delete the build directory
> and
> start from scratch.
>
> 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
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> .
>


-- 
Yuesu Jin,
Ph.D student,
University of Houston,
College of Natural Sciences and Mathematics,
Department of Earth and Atmospheric Sciences,
Houston, Texas 77204-5008
346-404-2062

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Re: [deal.II] undefined symbol: mkl_blas_dsyrk

2019-08-11 Thread yuesu jin
AH... I understand,* cmake -DCMAKE_INSTALL_PREFIX=[Directory you want to
install] [Directory you build the program]*
I have installed it again in a new folder, the folder now is 3.6GB, which
means something has been installed in that. But the message is still there:
**
[100%] Building CXX object source/CMakeFiles/deal_II.dir/dummy.cc.o
[100%] Linking CXX shared library ../lib/libdeal_II.so
[100%] Built target deal_II
Install the project...
-- Install configuration: "DebugRelease"
CMake Error at cmake/scripts/cmake_install.cmake:36 (file):
  file INSTALL cannot set permissions on
  "/path/to/install/dir/share/deal.II/scripts/normalize.pl"
Call Stack (most recent call first):
  cmake_install.cmake:37 (include)

Makefile:61: recipe for target 'install' failed
make: *** [install] Error 1
**

And when I run make test, all the tests give the same failure message:



/home/yjin6/Deal.II/dealii/tests/quick_tests/gsl.debug: *symbol lookup
error: /home/yjin6/anaconda3/lib/libmkl_intel_lp64.so: undefined symbol:
mkl_blas_dsyrk*
tests/quick_tests/CMakeFiles/gsl.debug.run.dir/build.make:57: recipe for
target 'tests/quick_tests/CMakeFiles/gsl.debug.run' failed
CMakeFiles/Makefile2:7094: recipe for target
'tests/quick_tests/CMakeFiles/gsl.debug.run.dir/all' failed
CMakeFiles/Makefile2:7101: recipe for target
'tests/quick_tests/CMakeFiles/gsl.debug.run.dir/rule' failed
Makefile:2294: recipe for target 'gsl.debug.run' failed
#

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Re: [deal.II] undefined symbol: mkl_blas_dsyrk

2019-08-11 Thread yuesu jin
Hi Daniel,
  Thank you for your reply. I misunderstood build and install. I thought
after I setup the build folder and make install, the program should be
compiled in that build folder, because I installed the 9.0.1 version just
run the command as those in README file. Now, I first input
*cmake -DCMAKE_INSTALL_PREFIX=/**path/to/install/dir
home/yjin6/Deal.II/dealii-9.0.1  *in
*/home.yjin6/Deal.II/dealii-9.0.1/build, *
then I repeat
*cmake -DCMAKE_INSTALL_PREFIX=${HOME}**/deal.II
/home/yjin6/Deal.II/dealii-9.0.1 *
finally I make install. Is that correct?
Thanks a lot!

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Re: [deal.II] undefined symbol: mkl_blas_dsyrk

2019-08-11 Thread yuesu jin
Hello Daniel,
  Thank you very much! I make a new folder to save the compile file for
cmake, and I used the command
*cmake -DCMAKE_INSTALL_PREFIX=${HOME}**/deal.II
home/yjin6/Deal.II/dealii-9.0.1* (substituted with my directory),
but cmake gave error warning. I substitute it with
*cmake -DCMAKE_INSTALL_PREFIX=/**path/to/install/dir
home/yjin6/Deal.II/dealii-9.0.1*
Cmake gives the message that:
-- Configuring done
-- Generating done
-- Build files have been written to: /home/yjin6/Deal.II/dealii


/home/yjin6/Deal.II/dealii is my current installation directory.
Best regards
Yuesu
On Sun, Aug 11, 2019 at 5:57 PM Daniel Arndt  wrote:

>
> Thank you for your timely reply!
>>  I changed the installation direction according to the README document
>> and redirected it to the deal.ii-9.0.1 source code.
>>
>
> It seems that you still set the installation directory to a non-existent
> path. If you want to install in your home directory calling
>
> cmake -DCMAKE_INSTALL_PREFIX=${HOME}/deal.II DEAL_II_SOURCE_DIR
>
>
> in your build directory should work (you need to replace
> DEAL_II_SOURCE_DIR with the actual path to the deal.II source directory).
>
> Best,
> Daniel
> --
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>


-- 
Yuesu Jin,
Ph.D student,
University of Houston,
College of Natural Sciences and Mathematics,
Department of Earth and Atmospheric Sciences,
Houston, Texas 77204-5008
346-404-2062

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Re: [deal.II] undefined symbol: mkl_blas_dsyrk

2019-08-11 Thread yuesu jin
Hi,all
  I re-installed Deal.II-9.1.1, the message is listed below:
***
Install the project...
-- Install configuration: "DebugRelease"
CMake Error at cmake/scripts/cmake_install.cmake:36 (file):
  file INSTALL cannot set permissions on
  "/path/to/install/dir/share/deal.II/scripts/normalize.pl"
Call Stack (most recent call first):
  cmake_install.cmake:37 (include)



Makefile:61: recipe for target 'install' failed
make: *** [install] Error 1
***
I cannot figure out what is wrong there, can you tell me what is the
problem? Thanks a lot!


On Sat, Aug 10, 2019 at 9:58 PM yuesu jin  wrote:

> Hi, all,
> I am a novice of deal.II, I begun to learn deal.II since version 9.0.1,
> after I updated it from 9.0.1 to 9.1.1, I found the executable file cannot
> run, the message is:
>
>  ./step-5_sec: symbol lookup error: 
> /home/yjin6/anaconda3/lib/libmkl_intel_lp64.so:
> undefined symbol: mkl_blas_dsyrk.
>
> What is the problem? Thanks a lot!
>
> --
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> For mailing list/forum options, see
> https://groups.google.com/d/forum/dealii?hl=en
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> .
>

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[deal.II] undefined symbol: mkl_blas_dsyrk

2019-08-10 Thread yuesu jin
Hi, all,
I am a novice of deal.II, I begun to learn deal.II since version 9.0.1, 
after I updated it from 9.0.1 to 9.1.1, I found the executable file cannot 
run, the message is:

 ./step-5_sec: symbol lookup error: 
/home/yjin6/anaconda3/lib/libmkl_intel_lp64.so: undefined symbol: 
mkl_blas_dsyrk.

What is the problem? Thanks a lot!

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