Re: [deal.II] MPI_InitFinalize causes runtime error when setting the build type to release

[JxW]

Thanks a lot for the helpful advice.

If I pass a custom max_num_threads to the constructor of mpi_init, then I 
get 
the following behavior:

 - Segmentation violation, when max_num_threads = 3, 4, 
numbers::invalid_unsigned_int

 - Normal execution, when max_num_threads = 1, 2, 5, 6, 7, 8, 9, 10

P.S.: My computer has a dual core CPU with hyper-threading, so in 
/proc/cpuinfo
it shows 4 processors. 

When running in GDB, all segmentation violation cases above give the same 
message,
which points to the same position where the invalid read happens according 
to valgrind:

Thread 1 "test" received signal SIGSEGV, Segmentation fault.
tbb::internal::generic_scheduler::allocate_task 
(this=this@entry=0x7fffb8736600, 
number_of_bytes=number_of_bytes@entry=8, parent=parent@entry=0x0, 
context=context@entry=0x71e5c0a0 )
at ../../src/tbb/scheduler.cpp:315
315 ../../src/tbb/scheduler.cpp: No such file or directory.



On Friday, December 2, 2016 at 11:35:34 PM UTC+8, Wolfgang Bangerth wrote:
>
> On 12/02/2016 04:12 AM, JxW wrote: 
> > 
> > The following code reproduces this problem for me 
> > (The CMakeLists.txt simply calls the DEAL_II_INVOKE_AUTOPILOT() macro): 
> > 
> > #include  
> > #include  
> > 
> > intmain (int argc, char *argv[]) { 
> >   dealii::Utilities::MPI::MPI_InitFinalize mpi_init (argc, argv); 
> >   std::cout << "Program runs normally." << std::endl; 
> >   return 0; 
> > } 
> > 
> > Initially I suspected that the mpi_init object might be optimized away 
> by the 
> > compiler. But adding volatile to its 
> > declaration does not fix this. Now I still do not know what is causing 
> the 
> > problem. Any help or suggestion is appreciated. 
>
> Does this also happens with just a single processor? If you run this in a 
> debugger, can you get a backtrace that shows where the problem happens? 
>
> Best 
>   W. 
>
> -- 
>  
> Wolfgang Bangerth  email: bang...@colostate.edu 
>  
> www: http://www.math.colostate.edu/~bangerth/ 
>
>

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Re: [deal.II] make error

[Wolfgang Bangerth]

On 12/02/2016 08:09 PM, Peng Ding wrote:

 I met the following error after make,

  /home/ztdep/Downloads/dealii-8.4.1/source/fe/mapping_q_eulerian.cc:100:79:
warning: ‘dealii::MappingQEulerian::MappingQEulerian(unsigned int, const EulerVectorType&, const
dealii::DoFHandler&) [with int dim = 3; VectorType =
dealii::TrilinosWrappers::MPI::BlockVector; int spacedim = 3]’ is deprecated
(declared at
/home/ztdep/Downloads/dealii-8.4.1/source/fe/mapping_q_eulerian.cc:51)
[-Wdeprecated-declarations]
[100%] Built target obj_fe.debug
Makefile:149: recipe for target 'all' failed
make: *** [all] Error 2

 Could you please give me some suggestions.


This is only a warning. There must have been an error higher up. Can you post 
what that would have been?


Best
 W.

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[deal.II] make error

[Peng Ding]

Dear friends:
 I met the following error after make, 

  
/home/ztdep/Downloads/dealii-8.4.1/source/fe/mapping_q_eulerian.cc:100:79: 
warning: ‘dealii::MappingQEulerian::MappingQEulerian(unsigned int, const EulerVectorType&, const 
dealii::DoFHandler&) [with int dim = 3; VectorType = 
dealii::TrilinosWrappers::MPI::BlockVector; int spacedim = 3]’ is 
deprecated (declared at 
/home/ztdep/Downloads/dealii-8.4.1/source/fe/mapping_q_eulerian.cc:51) 
[-Wdeprecated-declarations]
[100%] Built target obj_fe.debug
Makefile:149: recipe for target 'all' failed
make: *** [all] Error 2

 Could you please give me some suggestions.
Regards

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Re: [deal.II] Trouble building dealii with p4est - undeclared variables in scope

[Wolfgang Bangerth]

Chris,


I used the following command successfully to build dealii (note Trilinos and
p4est are OFF)

|

rm -rf *&&\

cmake \
-DDEAL_II_WITH_MPI:BOOL=ON \
-DDEAL_II_WITH_PETSC:BOOL=ON \
-DDEAL_II_WITH_TRILINOS:BOOL=ON \
-DDEAL_II_WITH_METIS:BOOL=ON \
-DDEAL_II_WITH_P4EST:BOOL=OFF \


So you explicitly disable the use of p4est in deal.II...



/home/redclient04/Software/dealii/source/distributed/tria.cc:302:9: error:
‘p4est_connectivity_join_faces’ was not declared in this scope
   = p4est_connectivity_join_faces;
 ^
/home/redclient04/Software/dealii/source/distributed/tria.cc:677:9: error:
‘p8est_connectivity_join_faces’ was not declared in this scope
   = p8est_connectivity_join_faces;
 ^


...after which I am confused why you get to compile this line at all. Is 
DEAL_II_WITH_P4EST defined in your $BUILD/include/deal.II/base/config.h file? 
If so, why?


It is confusing to me that although you explicitly disabled p4est in the cmake 
call, the cmake log still shows that it was enabled...


Best
 W.

--

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

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Re: [deal.II] Re: Is deal.II for me? Or, I got burned elsewhere

[Wolfgang Bangerth]

On 12/02/2016 07:01 AM, Bruno Turcksin wrote:


2 - Are there facilities of some kind that can help in generating the
assembly code? In Fenics I just specified the weak formulations.

You need to write the code in C++ and loop over cells, quadrature points, and
basis functions yourself. So this will be more verbose than what you do in 
Fenics.


True, but not very much more so. For example, the bilinear form for Stokes is 
here:

 https://github.com/dealii/dealii/blob/master/examples/step-22/step-22.cc#L649

Best
 W.

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   www: http://www.math.colostate.edu/~bangerth/

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Re: [deal.II] Re: Modeling Stokes flow in and around a droplet using the approach of step-46

[Oded Yaakobi]

 

Hi Wolfgang,

 

I know that the typical treatment of the interface matching conditions is 
along the lines that you noted. However, it is not clear to me how to 
follow these guidelines in the particular case that I am working on, which 
is described in the file that I attached to my previous email. In 
particular, in my case,

 

a)The matching conditions involve gradients of velocity and pressure, 
and not just the velocity and pressure fields. 

b) The matching conditions involve time-dependent fields, so probably 
the explicit form of the constraints has to be updated each time step.

 

In order to address point a), I thought that maybe I should define 
additional degrees of freedom that correspond to the components of each one 
of the gradient terms that appear in my matching conditions (e.g. for the 
pressure gradient add DOFs P_i_x, P_i_y and P_i_z). I would then define the 
constraints with respect to those new DOFs, and would also have to assemble 
the corresponding equations (e.g. P_i_x = dP_i/dx).

 

Is this the recommended way to address point a), or is there another way 
which is better?

 

Thank you,

Oded

On Friday, December 2, 2016 at 5:18:22 PM UTC-5, Wolfgang Bangerth wrote:
>
> On 12/02/2016 01:13 PM, Oded Yaakobi wrote: 
> > Now I encounter another aspect of my problem that I don’t know how to 
> tackle – 
> > the matching conditions on the interface between the domains of the 
> Stokes 
> > flow in the droplet and around it. 
> > 
> > 
> > 
> > Attached is a description of the problem in detail. I would be happy to 
> know 
> > if you or anyone else has some advice. 
>
> Typically, if you convert the equations into the weak form, you multiply 
> the 
> equation by a test function and then you integrate (on each of the 
> subdomains) 
> by parts. This yields terms that live on the boundaries of the subdomains, 
> including the interface between the subdomains. This is where you then 
> need to 
> use the interface conditions. 
>
> In your code, this will lead to integrals over internal faces where these 
> faces sit at the interface. 
>
> Best 
>   W. 
>
> -- 
>  
> Wolfgang Bangerth  email: bang...@colostate.edu 
>  
> www: http://www.math.colostate.edu/~bangerth/ 
>
>

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Re: [deal.II] Re: Apply Neumann Boundary condition

[Wolfgang Bangerth]

On 12/02/2016 09:30 AM, benhour.amiria...@gmail.com wrote:

Thanks very much for your help and support. I do really appreciate your time
and know you are really busy. The fact is that my code ran just for the first
time step and can not solve for the other time step. when I refine the global
mesh twice, this problem happened, however, with increasing the number of
global refine mesh, the whole geometry is distorted. In fact, it is a
thermo-elastic problem which I should use two different Neumann B.C for the
curved side of my domain. I just want to know whether applying this type was
true or not. In addition, could you please help me more how I should use
load-following algorithm in dealii? It should be noted that I have multiplied
the Neumann magnitude by time-ramp (current_time/time_step). Looking forward
to hearing from you.


Benhour -- it is practically impossible to help you with this question. You 
mention the following topics:

* It is a time dependent problem
* There is adaptivity
* There seems to be mesh movement
* The geometry seems to be distorted
* It is a thermo-elastic problem
* There seem to be different boundary conditions
* There seem to be curved boundaries
* The boundary conditions are modified in some time dependent way
* There is mention of a "load-following" algorithm

These are 9 concepts, in 9 lines of text, all without any kind of elaboration. 
In other words, we have no real idea what you are doing, and equally 
important, we have no idea what is actually wrong. When debugging problems 
like yours, you need to learn to reduce things to the minimal case that shows 
the problem, and to look for the *first sign* where something seems to be 
going wrong. In your case, if you know that the mesh is distorted, it is no 
surprise that you cannot solve. So *why* is the mesh distorted? Have you 
inspected the mesh before and after you move it? Have you inspected the 
solution of the first time step that is presumably used to move the mesh?


These are the questions you need to ask yourself.

Best
 W.

--

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

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Re: [deal.II] Re: Modeling Stokes flow in and around a droplet using the approach of step-46

[Wolfgang Bangerth]

On 12/02/2016 01:13 PM, Oded Yaakobi wrote:

Now I encounter another aspect of my problem that I don’t know how to tackle –
the matching conditions on the interface between the domains of the Stokes
flow in the droplet and around it.



Attached is a description of the problem in detail. I would be happy to know
if you or anyone else has some advice.


Typically, if you convert the equations into the weak form, you multiply the 
equation by a test function and then you integrate (on each of the subdomains) 
by parts. This yields terms that live on the boundaries of the subdomains, 
including the interface between the subdomains. This is where you then need to 
use the interface conditions.


In your code, this will lead to integrals over internal faces where these 
faces sit at the interface.


Best
 W.

--

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

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[deal.II] Re: Apply Neumann Boundary condition

[benhour . amirian66]

Dear Jean,
Thanks very much for your help and support. I do really appreciate your 
time and know you are really busy. The fact is that my code ran just for 
the first time step and can not solve for the other time step. when I 
refine the global mesh twice, this problem happened, however, with 
increasing the number of global refine mesh, the whole geometry is 
distorted. In fact, it is a thermo-elastic problem which I should use two 
different Neumann B.C for the curved side of my domain. I just want to know 
whether applying this type was true or not. In addition, could you please 
help me more how I should use load-following algorithm in dealii? It should 
be noted that I have multiplied the Neumann magnitude by time-ramp 
(current_time/time_step). Looking forward to hearing from you.

On Friday, December 2, 2016 at 12:50:03 AM UTC-6, Jean-Paul Pelteret wrote:
>
> Dear Benhour,
>
> Thank you for taking my point heart and providing more specifics about 
> your actual problem.
>
> For the horizontal axis, I have considered the zero displacement along 
>> y-axis because of symmetry. Is it correct? Should I fix the center of the 
>> circle as well? 
>>
>
> If you don't provide at least one Dirichlet constraint for each of the 
> solution components then your problem is indeterminate. So if you only 
> constrain the x-DoFs along the y-axis and have no other Dirichlet 
> constraints then this could be the source of some troubles. 
>  
>
>> How Can I do that? In other words, How can I fix one point (vertex) in 
>> 2-D? 
>>
>
> You have to manually add such a point constraint to the constraint matrix 
> or map of boundary values. If your centre point is coincident with a vertex 
> of the triangulation then you can achieve this with the help of the 
> cell->vertex_dof_index() function. There have been plenty of posts 
> 
>  
> in the past on how this function works, so I need not explain it again in 
> detail.
>
> I should also note that for highly nonlinear problems, if your load 
> increment is too large between time steps then this could also be 
> problematic (unless you're using a load-following algorithm like the 
> arc-length method). It may be of use to reduce the magnitude of the applied 
> traction while you're debugging this.
>
> Regards,
> Jean-Paul
>

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Re: [deal.II] Re: Is deal.II for me? Or, I got burned elsewhere

[Bruno Turcksin]

Franco,

2016-12-02 10:57 GMT-05:00 Franco Milicchio :
> So can I use solvers as in Tutorial 3, for instance, and I'll be safe and
> sound?
Yes.

> However, is someone planning some additions to deal.II to make it less
> verbose, as in, for example, providing a DSL for that?
There are no plan to add DSL. There has been some work on
LinearOperator that reduces the amount of work that needs to be
written but there is nothing planned in the future.

> And just in case, is there a default eigensolver that is shipped for sure
> with the DMG?
deal.II implements the power method and the inverse iteration method.
I have never used them, though

> That is reasonable. This is very good news to me. To what infrastructure are
> you referring to?
See tutorial 9 http://dealii.org/8.4.1/doxygen/deal.II/step_9.html

Best,

Bruno

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[deal.II] Re: Is deal.II for me? Or, I got burned elsewhere

[Franco Milicchio]

Thank you Bruno for your answers, I failed to mention that I use Fenics 
with C++, not with Python, sorry about that. I just have few points to ask, 
if you can bear with me.

1 - Is it truly thread-safe? As in running a single analysis, or running 
>> several (no data sharing), without problems.
>>
> deal.II is thread-safe but PETSc is not so if you are using deal.II with 
> PETSc, your code won't be thread-safe.
>

So can I use solvers as in Tutorial 3, for instance, and I'll be safe and 
sound?

 

> 2 - Are there facilities of some kind that can help in generating the 
>> assembly code? In Fenics I just specified the weak formulations.
>>
> You need to write the code in C++ and loop over cells, quadrature points, 
> and basis functions yourself. So this will be more verbose than what you do 
> in Fenics. 
>

I don't mind at all, I started using FEMs way back, when there was no 
Fenics.

However, is someone planning some additions to deal.II to make it less 
verbose, as in, for example, providing a DSL for that?

 

> 4 - I see Trilinos is included, is it possible to avoid completely 
>> PETSc/SLEPc, since they're not AFAIK thread-safe?
>>
> Yes, you can. I am not an expert of SLEPc but I think that the anasazi 
> package from Trilinos https://trilinos.org/packages/anasazi has similar 
> capabilities However, I am not sure what is in the Mac binary. I don't know 
> if it comes with Trilinos and if it does, it may come with only the 
> packages required to run deal.II.
>

And just in case, is there a default eigensolver that is shipped for sure 
with the DMG?

 

> 5 - Is there a multithreaded linear solver and vector operations, or 
>> should I write them myself?
>>
> The linear solvers and the vector operations are multithreaded if you use 
> deal.II own solvers and vectors. Many operations done inside deal.II are 
> multithreaded but you are in charge of making sure that the code that you 
> are writing is multithreaded. There is an infrastructure to help you with 
> that though.
>  
>

That is reasonable. This is very good news to me. To what infrastructure 
are you referring to?

 

> 7 - Is eliminating binary distributions (DMGs and such) on the horizon?
>>
> No.
>
>
This is really awesome!

 
Thanks,
Franco

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Re: [deal.II] Re: Trouble building dealii with p4est - undeclared variables in scope

[Chris Coutinho]

I think you're right about my p4est build, there is something wrong with
how it's linking to and/or using Lua, see attached. I will have to
investigate this further.



On Fri, Dec 2, 2016 at 3:44 PM Bruno Turcksin 
wrote:

> 2016-12-02 9:36 GMT-05:00 Chris Coutinho :
> > What do you think, is this a p4est build error? It's not immediately
> clear
> > from the build output if this is an issue or not.
> Yes, it is hard to say but I don't think that these errors are really
> a problem but now I remember one time I installed p4est and everything
> seemed fine but later I had some problems. You can check that the
> installation was successful by going into p4est build directory and
> type make check. If some tests don't pass there is a problem.
>
> Bruno
>
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Making check in sc
make[1]: Entering directory '/home/redclient04/Downloads/p4est-build/DEBUG/sc'
make  test/sc_test_arrays test/sc_test_builtin test/sc_test_dmatrix test/sc_test_dmatrix_pool test/sc_test_pqueue test/sc_test_allgather test/sc_test_notify test/sc_test_reduce test/sc_test_search test/sc_test_sort test/sc_test_sortb test/sc_test_keyvalue
make[2]: Entering directory '/home/redclient04/Downloads/p4est-build/DEBUG/sc'
make[2]: 'test/sc_test_arrays' is up to date.
/bin/sh ./libtool --tag=CC   --mode=link mpicc  -O0 -g   -o test/sc_test_builtin test/test_builtin.o ./src/libsc.la-llua -ldl -lm 
libtool: link: mpicc -O0 -g -o test/.libs/sc_test_builtin test/test_builtin.o  ./src/.libs/libsc.so -llua -ldl -lm -Wl,-rpath -Wl,/home/redclient04/Software/p4est/p4est-0.3.4.1/DEBUG/lib64
test/test_builtin.o: In function `test_lua':
/home/redclient04/Downloads/p4est-0.3.4.1/sc/test/test_builtin.c:114: undefined reference to `lua_open'
collect2: error: ld returned 1 exit status
Makefile:1665: recipe for target 'test/sc_test_builtin' failed
make[2]: *** [test/sc_test_builtin] Error 1
make[2]: Leaving directory '/home/redclient04/Downloads/p4est-build/DEBUG/sc'
Makefile:4195: recipe for target 'check-am' failed
make[1]: *** [check-am] Error 2
make[1]: Leaving directory '/home/redclient04/Downloads/p4est-build/DEBUG/sc'
Makefile:3282: recipe for target 'check-recursive' failed
make: *** [check-recursive] Error 1

Re: [deal.II] Re: deal.ii and Reduced Basis method

[David Wells]

Hi Giulia,

I used deal.II in my thesis to do model reduction (Wolfgang was kind enough 
to include a link), but I used POD and not RB. Let me know if you have 
questions about the thesis :)

Thanks,
David Wells

On Thursday, December 1, 2016 at 8:18:56 AM UTC-5, Giulia Deolmi wrote:
>
> Dear Jean-Paul and Wolfgang,
> thanks a lot for your replies! We contacted the developers of pyMOR who 
> will help us to solve the RB problem, using deal.ii as an external software.
> Kind regards,
> Giulia
>
> Il giorno giovedì 1 dicembre 2016 13:07:58 UTC+1, Wolfgang Bangerth ha 
> scritto:
>>
>>
>> Giulia, 
>> there are also this thesis 
>>https://vtechworks.lib.vt.edu/handle/10919/52960 
>> and the pyMOR package has deal.II interfaces: 
>>http://pymor.org/ 
>>
>> Best 
>>   W. 
>>
>>
>> On 12/01/2016 01:05 AM, Jean-Paul Pelteret wrote: 
>> > Dear Giulia, 
>> > 
>> > Judging by the lack of reply it seems that no-one knows of (or has 
>> > implemented) an open-source library to specifically do model order 
>> reduction 
>> > with deal.II. However, at least one of my colleagues uses deal.II to 
>> perform 
>> > ROM via proper orthogonal decomposition, so deal.II definitely provides 
>> all of 
>> > the core functionality to implement this yourself. If its of any use to 
>> you, 
>> > here's a link to his paper (sadly during final editing his text citing 
>> deal.II 
>> > got removed without him noticing): 
>> > http://onlinelibrary.wiley.com/doi/10.1002/gamm.201610011/full 
>> > 
>> > Regards, 
>> > J-P 
>> > 
>> > On Monday, November 14, 2016 at 11:03:16 AM UTC+1, Giulia Deolmi wrote: 
>> > 
>> > Dear all, 
>> > I have implemented a parameter dependent problem in deal.ii and now 
>> I 
>> > would like to apply the Reduced Basis (RB) method to it. 
>> > Do you know if there is already some code available that I can use 
>> where 
>> > the RB has already been implemented (in deal.ii or compatible to 
>> it)? 
>> > So far I have only found a software called pyMOR for the RB method 
>> > (http://pymor.org/). In theory it should be possible to use 
>> deal.ii as an 
>> > external software. The example that is given is not so clear to me, 
>> > though. Is anyone familiar with it? 
>> > Thanks a lot in advance, 
>> > Kind regards, 
>> > Giulia Deolmi 
>> > 
>> > -- 
>> > 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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>> an 
>> > email to dealii+un...@googlegroups.com 
>> > . 
>> > For more options, visit https://groups.google.com/d/optout. 
>>
>>
>> -- 
>>  
>> Wolfgang Bangerth  email: bang...@colostate.edu 
>> www: http://www.math.colostate.edu/~bangerth/ 
>>
>>

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Re: [deal.II] MPI_InitFinalize causes runtime error when setting the build type to release

[Wolfgang Bangerth]

On 12/02/2016 04:12 AM, JxW wrote:


The following code reproduces this problem for me
(The CMakeLists.txt simply calls the DEAL_II_INVOKE_AUTOPILOT() macro):

#include 
#include 

intmain (int argc, char *argv[]) {
  dealii::Utilities::MPI::MPI_InitFinalize mpi_init (argc, argv);
  std::cout << "Program runs normally." << std::endl;
  return 0;
}

Initially I suspected that the mpi_init object might be optimized away by the
compiler. But adding volatile to its
declaration does not fix this. Now I still do not know what is causing the
problem. Any help or suggestion is appreciated.


Does this also happens with just a single processor? If you run this in a 
debugger, can you get a backtrace that shows where the problem happens?


Best
 W.

--

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

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Re: [deal.II] Re: Trouble building dealii with p4est - undeclared variables in scope

[Bruno Turcksin]

2016-12-02 9:36 GMT-05:00 Chris Coutinho :
> What do you think, is this a p4est build error? It's not immediately clear
> from the build output if this is an issue or not.
Yes, it is hard to say but I don't think that these errors are really
a problem but now I remember one time I installed p4est and everything
seemed fine but later I had some problems. You can check that the
installation was successful by going into p4est build directory and
type make check. If some tests don't pass there is a problem.

Bruno

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Re: [deal.II] Re: Trouble building dealii with p4est - undeclared variables in scope

[Chris Coutinho]

Howdy Bruno,

Thanks for the quick reply.

Something could have gone wrong when building p4est, but I'm not 100% 
certain because the config file is full of contradictory messages. For 
example, when checking c compiler validity, it uses some options that work 
and others that produce errors, but I think it's because different 
compilers (gcc, icc, etc...) have those options - not an error in gcc 
itself. For example, this snippet produces correct results as well as 
errors:

.
.
configure:3902: checking for C compiler version
configure:3911: mpicc --version >&5
gcc (SUSE Linux) 6.2.1 20161121 [gcc-6-branch revision 242657]
Copyright (C) 2016 Free Software Foundation, Inc.
This is free software; see the source for copying conditions.  There is NO
warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.

configure:3922: $? = 0
configure:3911: mpicc -v >&5
Using built-in specs.
COLLECT_GCC=/home/redclient04/bin/gcc
COLLECT_LTO_WRAPPER=/usr/lib64/gcc/x86_64-suse-linux/6/lto-wrapper
Target: x86_64-suse-linux
Configured with: ../configure --prefix=/usr --infodir=/usr/share/info 
--mandir=/usr/share/man --libdir=/usr/lib64 --libexecdir=/usr/lib64 
--enable-languages=c,c++,objc,fortran,obj-c++,java,ada,go 
--enable-offload-targets=hsa --enable-checking=release 
--with-gxx-include-dir=/usr/include/c++/6 --enable-ssp --disable-libssp 
--disable-libvtv --disable-libcc1 --disable-plugin 
--with-bugurl=http://bugs.opensuse.org/ --with-pkgversion='SUSE Linux' 
--disable-libgcj --with-slibdir=/lib64 --with-system-zlib 
--enable-__cxa_atexit --enable-libstdcxx-allocator=new 
--disable-libstdcxx-pch --with-default-libstdcxx-abi=gcc4-compatible 
--enable-version-specific-runtime-libs --enable-linker-build-id 
--enable-linux-futex --enable-gnu-indirect-function --program-suffix=-6 
--without-system-libunwind --enable-multilib --with-arch-32=x86-64 
--with-tune=generic --build=x86_64-suse-linux --host=x86_64-suse-linux
Thread model: posix
gcc version 6.2.1 20161121 [gcc-6-branch revision 242657] (SUSE Linux) 
configure:3922: $? = 0
configure:3911: mpicc -V >&5
gcc: error: unrecognized command line option '-V'
gcc: fatal error: no input files
compilation terminated.
configure:3922: $? = 1
configure:3911: mpicc -qversion >&5
gcc: error: unrecognized command line option '-qversion'; did you mean 
'--version'?
gcc: fatal error: no input files
compilation terminated.
configure:3922: $? = 1
configure:3942: checking whether the C compiler works
configure:3964: mpicc -O2 -DSC_LOG_PRIORITY=SC_LP_ESSENTIAL  conftest.c  >&5
configure:3968: $? = 0
configure:4017: result: yes
.
.

So by looking through the p4est config.log file, I'm not able to discern if 
there is a build error or not. For instance, this part when compiling 
'conftest.c' somewhat farther down seems suspicious. Initially its able to 
compile, but then it initiates the same command again and it fails (bold to 
emphasize):

.
.
configure:6560: mpicc -c -O2 -DSC_LOG_PRIORITY=SC_LP_ESSENTIAL conftest.c 
>&5
configure:6563: $? = 0
configure:7273: checking how to run the C preprocessor
configure:7304: *mpicc -E -DSC_LOG_PRIORITY=SC_LP_ESSENTIAL conftest.c*
configure:7304: $? = 0
configure:7318: *mpicc -E -DSC_LOG_PRIORITY=SC_LP_ESSENTIAL conftest.c*
conftest.c:17:28: fatal error: ac_nonexistent.h: No such file or directory
 #include 
^
compilation terminated.
configure:7318: $? = 1
configure: failed program was:
| /* confdefs.h */
| #define PACKAGE_NAME "p4est"
| #define PACKAGE_TARNAME "p4est"
| #define PACKAGE_VERSION "0.3.4.1"
| #define PACKAGE_STRING "p4est 0.3.4.1"
.
.


What do you think, is this a p4est build error? It's not immediately clear 
from the build output if this is an issue or not.




On Friday, December 2, 2016 at 2:28:25 PM UTC+1, Bruno Turcksin wrote:
>
> Chris, 
>
> I don't know why it doesn't work :-( Here is what you can try: 
>  - reinstall p4est and check that there are no error during the 
> compilation. The most probable reason for your error is that something 
> went wrong during the compilation of p4est. 
>  - use candi to install everything (https://github.com/dealii/candi). 
>  - use the development version of deal.II These functions are not 
> called in tria.cc anymore. 
>
> Sorry 
>
> Bruno 
>
> 2016-12-02 5:08 GMT-05:00 Chris Coutinho  >: 
> > Hi Bruno, 
> > 
> > Setting p4est_dir to the entire p4est-x.x.x.x directory doesn't change 
> > anything - it still fails with variables undefined in the current scope. 
> See 
> > attached cmake and make logs for detailed output, but I don't noticed 
> any 
> > difference. 
> > 
> > Regards, 
> > Chris 
> > 
> > 
> > On Thursday, December 1, 2016 at 7:54:53 PM UTC+1, Bruno Turcksin wrote: 
> >> 
> >> Chris, 
> >> 
> >> On Thursday, December 1, 2016 at 10:56:13 AM UTC-5, Chris Coutinho 
> wrote: 
> >>> 
> >>> With only p4est enabled, and P4EST_DIR pointing to the DEBUG folder of 
> >>> version 0.3.4.1, I get the following errors associated with undeclared 

[deal.II] Re: Is deal.II for me? Or, I got burned elsewhere

[Bruno Turcksin]

Franco,

I'll try to answer your questions but be aware that deal.II is a C++ 
library and that there are no python wrappers unlike Fenics:

On Friday, December 2, 2016 at 6:59:16 AM UTC-5, Franco Milicchio wrote:
>
> 1 - Is it truly thread-safe? As in running a single analysis, or running 
> several (no data sharing), without problems.
>
deal.II is thread-safe but PETSc is not so if you are using deal.II with 
PETSc, your code won't be thread-safe.
 

> 2 - Are there facilities of some kind that can help in generating the 
> assembly code? In Fenics I just specified the weak formulations.
>
You need to write the code in C++ and loop over cells, quadrature points, 
and basis functions yourself. So this will be more verbose than what you do 
in Fenics.
 

> 3 - Can I output some kind of time-dependant file, like a PVD? I see VTK, 
> but no PVD files.
>
Yes, you can 
http://dealii.org/8.4.1/doxygen/deal.II/classDataOutInterface.html#a0d247c3780325546472c006d8ef3b12d
 

> 4 - I see Trilinos is included, is it possible to avoid completely 
> PETSc/SLEPc, since they're not AFAIK thread-safe?
>
Yes, you can. I am not an expert of SLEPc but I think that the anasazi 
package from Trilinos https://trilinos.org/packages/anasazi has similar 
capabilities However, I am not sure what is in the Mac binary. I don't know 
if it comes with Trilinos and if it does, it may come with only the 
packages required to run deal.II.
 

> 5 - Is there a multithreaded linear solver and vector operations, or 
> should I write them myself?
>
The linear solvers and the vector operations are multithreaded if you use 
deal.II own solvers and vectors. Many operations done inside deal.II are 
multithreaded but you are in charge of making sure that the code that you 
are writing is multithreaded. There is an infrastructure to help you with 
that though.
 

> 6 - Can I use my MLK library without recompiling deal.II?
>
No, I don't think that you can. 

7 - Is eliminating binary distributions (DMGs and such) on the horizon?
>
No.

Best,

Bruno

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Re: [deal.II] Re: Trouble building dealii with p4est - undeclared variables in scope

[Bruno Turcksin]

Chris,

I don't know why it doesn't work :-( Here is what you can try:
 - reinstall p4est and check that there are no error during the
compilation. The most probable reason for your error is that something
went wrong during the compilation of p4est.
 - use candi to install everything (https://github.com/dealii/candi).
 - use the development version of deal.II These functions are not
called in tria.cc anymore.

Sorry

Bruno

2016-12-02 5:08 GMT-05:00 Chris Coutinho :
> Hi Bruno,
>
> Setting p4est_dir to the entire p4est-x.x.x.x directory doesn't change
> anything - it still fails with variables undefined in the current scope. See
> attached cmake and make logs for detailed output, but I don't noticed any
> difference.
>
> Regards,
> Chris
>
>
> On Thursday, December 1, 2016 at 7:54:53 PM UTC+1, Bruno Turcksin wrote:
>>
>> Chris,
>>
>> On Thursday, December 1, 2016 at 10:56:13 AM UTC-5, Chris Coutinho wrote:
>>>
>>> With only p4est enabled, and P4EST_DIR pointing to the DEBUG folder of
>>> version 0.3.4.1, I get the following errors associated with undeclared
>>> variables in scope. The rest of the output can be found in the attached
>>> make.log:
>>>
>> I haven't used the script in a while but I don't think it's necessary to
>> point to the DEBUG folder.
>>>
>>>
>>>
>>> > ./p4est-setup-dealii.sh p4est-0.3.4.1.tar.gz
>>> > /home/redclient04/Software/p4est/p4est-0.3.4.1
>>> > export P4EST_DIR=/home/redclient04/Software/p4est/p4est-0.3.4.1/DEBUG
>>>
>> Can you try export
>> P4EST_DIR=/home/redclient04/Software/p4est/p4est-0.3.4.1
>>
>> Best,
>>
>> Bruno
>
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[deal.II] Is deal.II for me? Or, I got burned elsewhere

[Franco Milicchio]

Dear all, 

after a couple of years developing with Fenics on MacOS X, I stumbled upon 
two dreary problems: it won't provide binaries anymore, and it does not 
play well with multithreading. I was then thinking about switching to 
deal.II, but I hope you can help me in dispelling some doubts.

My analyses are non-linear and parametric, hence my problems with Fenics: I 
parallelized single analyses, but I found many hidden race conditions.

So, here are my doubts about moving to deal.II:

1 - Is it truly thread-safe? As in running a single analysis, or running 
several (no data sharing), without problems.
2 - Are there facilities of some kind that can help in generating the 
assembly code? In Fenics I just specified the weak formulations.
3 - Can I output some kind of time-dependant file, like a PVD? I see VTK, 
but no PVD files.
4 - I see Trilinos is included, is it possible to avoid completely 
PETSc/SLEPc, since they're not AFAIK thread-safe?
5 - Is there a multithreaded linear solver and vector operations, or should 
I write them myself?
6 - Can I use my MLK library without recompiling deal.II?
7 - Is eliminating binary distributions (DMGs and such) on the horizon?

Thank you very much for your help on any of these points!
Franco

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[deal.II] MPI_InitFinalize causes runtime error when setting the build type to release

[JxW]

I encountered this problem on my linux machine. Everything works fine in 
debug mode; however, as soon as I switch to release mode using 
-DCMAKE_BUILD_TYPE=Release, the code still compiles, but bumps into a 
segmentation violation when it runs.

The following code reproduces this problem for me 
(The CMakeLists.txt simply calls the DEAL_II_INVOKE_AUTOPILOT() macro):

#include 
#include 

int main (int argc, char *argv[]) {
  dealii::Utilities::MPI::MPI_InitFinalize mpi_init (argc, argv);
  std::cout << "Program runs normally." << std::endl;
  return 0;
}

Initially I suspected that the mpi_init object might be optimized away by 
the compiler. But adding volatile to its 
declaration does not fix this. Now I still do not know what is causing the 
problem. Any help or suggestion is appreciated.

P.S.: I also tried running the binary in valgrind, which reports an invalid 
read. The full report is as follows:

==14930== Memcheck, a memory error detector
==14930== Copyright (C) 2002-2015, and GNU GPL'd, by Julian Seward et al.
==14930== Using Valgrind-3.12.0 and LibVEX; rerun with -h for copyright info
==14930== Command: ./test.o
==14930== 
==14930== Invalid read of size 8
==14930==at 0xADD6692: 
tbb::internal::generic_scheduler::allocate_task(unsigned long, tbb::task*, 
tbb::task_group_context*) (scheduler.cpp:315)
==14930==by 0xADD675A: 
tbb::internal::generic_scheduler::generic_scheduler(tbb::internal::market&) 
(scheduler.cpp:100)
==14930==by 0xADD8207: custom_scheduler (custom_scheduler.h:59)
==14930==by 0xADD8207: 
tbb::internal::custom_scheduler::allocate_scheduler(tbb::internal::market&)
 (custom_scheduler.h:115)
==14930==by 0xADD7051: allocate_scheduler (scheduler.cpp:42)
==14930==by 0xADD7051: 
tbb::internal::generic_scheduler::create_master(tbb::internal::arena*) 
(scheduler.cpp:1032)
==14930==by 0xADD1B53: tbb::internal::governor::init_scheduler(int, 
unsigned long, bool) (governor.cpp:206)
==14930==by 0xADD1C0B: tbb::task_scheduler_init::initialize(int, unsigned 
long) (governor.cpp:349)
==14930==by 0x97A96C2: dealii::MultithreadInfo::set_thread_limit(unsigned 
int) (in 
/home/xywei/spack/opt/spack/linux-arch-x86_64/gcc-6.2.1/dealii-develop-e5t4qkpvvpzbbomgfymanf2z5ja2yxfr/lib/libdeal_II.so.8.5.0-pre)
==14930==by 0x97A3D0B: 
dealii::Utilities::MPI::MPI_InitFinalize::MPI_InitFinalize(int&, char**&, 
unsigned int) (in 
/home/xywei/spack/opt/spack/linux-arch-x86_64/gcc-6.2.1/dealii-develop-e5t4qkpvvpzbbomgfymanf2z5ja2yxfr/lib/libdeal_II.so.8.5.0-pre)
==14930==by 0x409C77: main (in /home/xywei/release_debug/build/test.o)
==14930==  Address 0xfff7 is not stack'd, malloc'd or (recently) 
free'd
==14930== 
[0]PETSC ERROR: 

[0]PETSC ERROR: Caught signal number 11 SEGV: Segmentation Violation, probably 
memory access out of range
[0]PETSC ERROR: Try option -start_in_debugger or -on_error_attach_debugger
[0]PETSC ERROR: or see 
http://www.mcs.anl.gov/petsc/documentation/faq.html#valgrind
[0]PETSC ERROR: or try http://valgrind.org on GNU/linux and Apple Mac OS X to 
find memory corruption errors
[0]PETSC ERROR: configure using --with-debugging=yes, recompile, link, and run 
[0]PETSC ERROR: to get more information on the crash.
[0]PETSC ERROR: - Error Message 
--
[0]PETSC ERROR: Signal received
[0]PETSC ERROR: See http://www.mcs.anl.gov/petsc/documentation/faq.html for 
trouble shooting.
[0]PETSC ERROR: Petsc Release Version 3.7.4, Oct, 02, 2016 
[0]PETSC ERROR: ./test.o on a arch-linux2-c-opt named WXYZG_under_Arch by xywei 
Fri Dec  2 19:01:12 2016
[0]PETSC ERROR: Configure options 
--prefix=/home/xywei/spack/opt/spack/linux-arch-x86_64/gcc-6.2.1/petsc-3.7.4-gdocdh6szvdge7ybgtujtibhu3xdvhc6
 --with-ssl=0 --with-mpi=1 
--with-mpi-dir=/home/xywei/spack/opt/spack/linux-arch-x86_64/gcc-6.2.1/openmpi-2.0.1-tqpsaspkym4fdbxzzr2g7qfbaf52qz2u
 --with-cpp=cpp --with-cxxcpp=cpp --with-precision=double 
--with-scalar-type=real --with-shared-libraries=1 --with-debugging=0 
--with-blas-lapack-lib=/home/xywei/spack/opt/spack/linux-arch-x86_64/gcc-6.2.1/openblas-0.2.19-443ize6rvixorrj5ftlz4brlmju2lrfq/lib/libopenblas.so
 --with-metis=1 
--with-metis-dir=/home/xywei/spack/opt/spack/linux-arch-x86_64/gcc-6.2.1/metis-5.1.0-p255v6f6j47usne5perkzwkrcqjzyllg
 --with-boost=1 
--with-boost-dir=/home/xywei/spack/opt/spack/linux-arch-x86_64/gcc-6.2.1/boost-1.62.0-fmjpoz5juo2quof5vmwkxq7l64jlvam5
 --with-hdf5=1 
--with-hdf5-dir=/home/xywei/spack/opt/spack/linux-arch-x86_64/gcc-6.2.1/hdf5-1.10.0-patch1-viwtpeovrofsuhsll2wccgqulpnx4zhx
 --with-hypre=1 
--with-hypre-dir=/home/xywei/spack/opt/spack/linux-arch-x86_64/gcc-6.2.1/hypre-2.10.1-eyk2nctsm3lf5kzx67isilgboqtqkxgo
 --with-parmetis=1 
--with-parmetis-dir=/home/xywei/spack/opt/spack/linux-arch-x86_64/gcc-6.2.1/parmetis-4.0.3-dwetxnnqiilkpubh3rwzia3224ww4cqc
 --with-mumps=1 
--wi

[deal.II] Re: Trouble building dealii with p4est - undeclared variables in scope

[Chris Coutinho]

Hi Bruno,

Setting p4est_dir to the entire p4est-x.x.x.x directory doesn't change 
anything - it still fails with variables undefined in the current scope. 
See attached cmake and make logs for detailed output, but I don't noticed 
any difference.

Regards,
Chris


On Thursday, December 1, 2016 at 7:54:53 PM UTC+1, Bruno Turcksin wrote:
>
> Chris,
>
> On Thursday, December 1, 2016 at 10:56:13 AM UTC-5, Chris Coutinho wrote:
>>
>> With only p4est enabled, and P4EST_DIR pointing to the DEBUG folder of 
>> version 0.3.4.1, I get the following errors associated with undeclared 
>> variables in scope. The rest of the output can be found in the attached 
>> make.log:
>>
>> I haven't used the script in a while but I don't think it's necessary to 
> point to the DEBUG folder. 
>
>>
>>
>> > ./p4est-setup-dealii.sh p4est-0.3.4.1.tar.gz /home/redclient04/Software
>> /p4est/p4est-0.3.4.1
>> > export P4EST_DIR=/home/redclient04/Software/p4est/p4est-0.3.4.1/DEBUG
>>
>> Can you try export P4EST_DIR=/home/redclient04/Software/p4est/p4est-0.3.
> 4.1
>
> Best,
>
> Bruno
>

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-- This is CMake 3.5.2
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