[deal.II] Nan for stress values

[Raghunandan Pratoori]

Hello,

I am running a code to study phase transformations in metals. The code runs 
without any problem in release mode, but gives nan when outputting stress 
values using the same code snippet as in Step-18.

When I run the same code in debug mode, it gives the following error:
An error occurred in line <2183> of file 

 
in function
dealii::types::global_dof_index 
dealii::AffineConstraints::calculate_line_index(dealii::AffineConstraints::size_type)
 
const [with number = double; dealii::types::global_dof_index = unsigned 
int; dealii::AffineConstraints::size_type = unsigned int]
The violated condition was:
local_lines.is_element(line_n)
Additional information:
The index set given to this constraints object indicates constraints
for degree of freedom 31328 should not be stored by this object, but a
constraint is being added.

Stacktrace:
---
#0  microPF_polycrystal: 
dealii::AffineConstraints::calculate_line_index(unsigned int) const
#1  microPF_polycrystal: 
dealii::AffineConstraints::is_constrained(unsigned int) const
#2 
 /home/rnp/Software/dealii-build/deal.II-v9.3.3/lib/libdeal_II.g.so.9.3.3: 
dealii::AffineConstraints::make_sorted_row_list(std::vector > const&, std::vector >&) const
#3 
 /home/rnp/Software/dealii-build/deal.II-v9.3.3/lib/libdeal_II.g.so.9.3.3: 
void 
dealii::AffineConstraints::add_entries_local_to_global(std::vector > const&, 
dealii::DynamicSparsityPattern&, bool, dealii::Table<2, bool> const&, 
std::integral_constant) const
#4 
 /home/rnp/Software/dealii-build/deal.II-v9.3.3/lib/libdeal_II.g.so.9.3.3: 
void 
dealii::AffineConstraints::add_entries_local_to_global(std::vector > const&, 
dealii::DynamicSparsityPattern&, bool, dealii::Table<2, bool> const&) const
#5 
 /home/rnp/Software/dealii-build/deal.II-v9.3.3/lib/libdeal_II.g.so.9.3.3: 
void dealii::DoFTools::make_sparsity_pattern<3, 3, 
dealii::DynamicSparsityPattern, double>(dealii::DoFHandler<3, 3> const&, 
dealii::DynamicSparsityPattern&, dealii::AffineConstraints const&, 
bool, unsigned int)
#6  microPF_polycrystal: PhaseField::Solid<3>::setup_system()
#7  microPF_polycrystal: PhaseField::Solid<3>::run()
#8  microPF_polycrystal: main


It points to a problem in defining constraints in setup_system. But I 
believe I defined the constraints correctly. I have a similar code that 
works perfectly and the only thing I have changed is adding grain 
orientations which do not effect the constraint definition.

Is my understanding of the error message correct? Is there something that I 
am missing in debugging the code?

Below is the code snippet of setup_system -
template 
void Solid::setup_system()
{
TimerOutput::Scope t(computing_timer, "setup");

dof_handler.distribute_dofs(fe);
dof_handler_c.distribute_dofs(fe_c);
history_dof_handler.distribute_dofs(history_fe);

// DoFRenumbering::Cuthill_McKee(dof_handler);

const unsigned int n_dofs   = dof_handler.n_dofs();
const unsigned int n_dofs_c = dof_handler_c.n_dofs();

// Number of active cells and DoFs
pcout   << "   Number of active cells: "
<< triangulation.n_active_cells()
<< std::endl
<< "   Number of degrees of freedom: "
<< n_dofs + n_dofs_c
<< " (" << n_dofs << '+' << n_dofs_c << ')'
<< std::endl;

locally_owned_dofs = dof_handler.locally_owned_dofs();
DoFTools::extract_locally_relevant_dofs(dof_handler, 
 locally_relevant_dofs);

constraints.clear();
constraints.reinit(locally_relevant_dofs);
{
DoFTools::make_periodicity_constraints(dof_handler, 0, 1, 0, 
constraints);
DoFTools::make_periodicity_constraints(dof_handler, 2, 3, 1, 
constraints);
DoFTools::make_periodicity_constraints(dof_handler, 4, 5, 2, 
constraints);
}
constraints.close();
// constraints.print(std::cout);

DynamicSparsityPattern dsp(locally_relevant_dofs);
DoFTools::make_sparsity_pattern(dof_handler, dsp, constraints, 
false);
Utilities::MPI::all_gather(mpi_communicator, 
dof_handler.locally_owned_dofs());
SparsityTools::distribute_sparsity_pattern (dsp, 
dof_handler.locally_owned_dofs(),
mpi_communicator, 
locally_relevant_dofs);

tangent_matrix.reinit(locally_owned_dofs, locally_owned_dofs, dsp, 
mpi_communicator);
solution.reinit(locally_owned_dofs, locally_relevant_dofs, 
mpi_communicator);
solution_update.reinit(locally_owned_dofs, locally_relevant_dofs, 
mpi_communicator);
system_rhs.reinit(locally_owned_dofs, mpi_communicator);

locally_owned_dofs_c = dof_handler_c.locally_owned_dofs();
DoFTools::extract_locally_relevant_dofs(dof_handler_c, 
 locally_relevant_dofs_c);

constraints_c.clear();
   

Re: [deal.II] Extension of Step-18

[Raghunandan Pratoori]

Hello Dr. Bangerth,

I apologize for the poor communication from my side.
Below are the changes I made to the refinement process in Step-18 in red:

typedef TrilinosWrappers::MPI::Vector vectorType;
std::vector>   history_field (dim, std::vector< 
Vector >(dim));
std::vector< std::vector< Vector > >
 local_history_values_at_qpoints (dim, std::vector< 
Vector >(dim)),
 local_history_fe_values (dim, std::vector< Vector 
>(dim));
for (unsigned int i=0; i > >’ has no member 
named ‘compress’

The above error message is expected as the compress operation is not 
defined for that datatype. However, I am unsure how to do the compress 
operation, as mentioned in Step-18. Please advice.

Best,
Raghunandan.
On Thursday, September 14, 2023 at 6:49:11 PM UTC-5 Wolfgang Bangerth wrote:

> On 9/14/23 15:50, Raghunandan Pratoori wrote:
> > 
> > It took me some time to get around to trying it out. I am unable to 
> figure out 
> > how to compress the vector.
> > The simple 'history_field.compress(VectorOperation::add);' did not work 
> as 
> > expected. Can you tell me how to use it for type 
> > std::vector>?
>
> Pratoori:
> you will have to be more specific in explaining what doesn't work. "did 
> not 
> work" is not enough for me to understand what you are doing, nor what is 
> going 
> wrong. It's as if you were saying "I've tried to prove the Riemann 
> hypothesis, 
> but the proof doesn't work. Can you tell me how to fix it?" without 
> showing 
> what you already did :-)
>
> Show us the code and the error message, and then we can perhaps help!
>
> Best
> W.
>
> -- 
> 
> Wolfgang Bangerth email: bang...@colostate.edu
> www: http://www.math.colostate.edu/~bangerth/
>
>
>

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Re: [deal.II] Extension of Step-18

[Raghunandan Pratoori]

Thank you, Dr. Bangerth, for the prompt reply.

It took me some time to get around to trying it out. I am unable to figure 
out how to compress the vector.
The simple 'history_field.compress(VectorOperation::add);' did not work as 
expected. Can you tell me how to use it for type  
std::vector>?

Best,
Raghunandan.

On Monday, September 4, 2023 at 9:59:49 PM UTC-5 Wolfgang Bangerth wrote:

> On 9/4/23 20:57, Raghunandan Pratoori wrote:
> > I want to clarify if the below is the correct implementation of it -
> > 
> > std::vector>> 
> > history_field_stress (dim, 
> > std::vector>(dim)),
> > 
> > 
> > history_field.compress(VectorOperation::add);
> > 
>
> A good first test is to try and see what happens! In fact, that's often 
> faster 
> than writing a question, and then waiting to see whether anyone answers it 
> :-)
>
> Best
> W.
>
> -- 
> 
> Wolfgang Bangerth email: bang...@colostate.edu
> www: http://www.math.colostate.edu/~bangerth/
>
>
>

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[deal.II] Extension of Step-18

[Raghunandan Pratoori]

Hello team,

I want to implement Refinement during timesteps 

 as 
described in Step-18, but for a much larger problem. I want to do this 
using a parallel vector for history_field. I want to clarify if the below 
is the correct implementation of it -

std::vector>> 
history_field_stress (dim, 
std::vector>(dim)),


history_field.compress(VectorOperation::add);


Thanks in advance,
Raghunandan.

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[deal.II] Re: Problem in installing deallii using candy command.

[Raghunandan Pratoori]

You can choose the appropriate tag depending on the version you want for 
candi. Click 'Tags' above the repository directories to check the available 
tags. Clone the repository with the appropriate release tag, and you should 
get the right version.
But, it is highly unlikely that it will solve the problem you are actually 
having - some of the dependencies have not been installed correctly. There 
is no way of knowing it unless you give the *.log file and not just the 
error message.

Also, why do you want to install it using candi, when you can install it 
using Ubuntu PPA?. It takes a total of 3-4 commands and comes with all the 
appropriate dependencies and is much easier.

Best,
Raghunandan.
On Thursday, August 10, 2023 at 2:27:07 AM UTC-5 me22...@iittp.ac.in wrote:

> Thank you, sir, for promptly responding to the email. I am interested in 
> installing Deal II version 9.4.0 using the candy command exclusively on 
> Ubuntu 22.04.3. However, I have encountered an issue where the candy 
> command installs version 9.4.2 by default, resulting in recurring errors as 
> indicated below.
>
> Could you kindly provide guidance on the procedure to install Deal II 
> version 9.4.0 utilizing the candy command exclusively?
>
>
>
> ../lib/libdeal_II.g.so.9.4.2: error: undefined reference to 'EPSCreate'
> ../lib/libdeal_II.g.so.9.4.2: error: undefined reference to 
> 'EPSSetTolerances'
> ../lib/libdeal_II.g.so.9.4.2: error: undefined reference to 'EPSDestroy'
> ../lib/libdeal_II.g.so.9.4.2: error: undefined reference to 
> 'EPSSetOperators'
> ../lib/libdeal_II.g.so.9.4.2: error: undefined reference to 'EPSSetST'
> ../lib/libdeal_II.g.so.9.4.2: error: undefined reference to 'EPSSetTarget'
> ../lib/libdeal_II.g.so.9.4.2: error: undefined reference to 
> 'EPSSetWhichEigenpairs'
> ../lib/libdeal_II.g.so.9.4.2: error: undefined reference to 
> 'EPSSetProblemType'
> ../lib/libdeal_II.g.so.9.4.2: error: undefined reference to 
> 'EPSSetDimensions'
> ../lib/libdeal_II.g.so.9.4.2: error: undefined reference to 
> 'EPSSetFromOptions'
> ../lib/libdeal_II.g.so.9.4.2: error: undefined reference to 
> 'EPSSetConvergenceTest'
> ../lib/libdeal_II.g.so.9.4.2: error: undefined reference to 'EPSSolve'
> ../lib/libdeal_II.g.so.9.4.2: error: undefined reference to 
> 'EPSGetConverged'
> ../lib/libdeal_II.g.so.9.4.2: error: undefined reference to 
> 'EPSGetIterationNumber'
> ../lib/libdeal_II.g.so.9.4.2: error: undefined reference to 
> 'EPSComputeError'
> ../lib/libdeal_II.g.so.9.4.2: error: undefined reference to 
> 'EPSGetEigenpair'
> ../lib/libdeal_II.g.so.9.4.2: error: undefined reference to 'EPSSetType'
> ../lib/libdeal_II.g.so.9.4.2: error: undefined reference to 
> 'EPSArnoldiSetDelayed'
> ../lib/libdeal_II.g.so.9.4.2: error: undefined reference to 
> 'EPSLanczosSetReorthog'
> ../lib/libdeal_II.g.so.9.4.2: error: undefined reference to 
> 'EPSGDSetDoubleExpansion'
> ../lib/libdeal_II.g.so.9.4.2: error: undefined reference to 'STCreate'
> ../lib/libdeal_II.g.so.9.4.2: error: undefined reference to 'STDestroy'
> ../lib/libdeal_II.g.so.9.4.2: error: undefined reference to 'STSetMatMode'
> ../lib/libdeal_II.g.so.9.4.2: error: undefined reference to 'STSetKSP'
> ../lib/libdeal_II.g.so.9.4.2: error: undefined reference to 'STSetType'
> ../lib/libdeal_II.g.so.9.4.2: error: undefined reference to 'STSetShift'
> ../lib/libdeal_II.g.so.9.4.2: error: undefined reference to 
> 'STCayleySetAntishift'
> ../lib/libdeal_II.g.so.9.4.2: error: undefined reference to 
> 'SlepcInitialize'
> ../lib/libdeal_II.g.so.9.4.2: error: undefined reference to 'SlepcFinalize'
> collect2: error: ld returned 1 exit status
> make[2]: *** [examples/CMakeFiles/step-1.debug.dir/build.make:234: 
> bin/step-1.debug] Error 1
> make[1]: *** [CMakeFiles/Makefile2:4217: 
> examples/CMakeFiles/step-1.debug.dir/all] 
> Error 2
> make: *** [Makefile:136: all] Error 2
> Failure with exit status: 2
> Exit message: There was a problem building dealii v9.4.2.
>
>
>
> Thanks in advance.
> On Wednesday, August 9, 2023 at 12:37:35 AM UTC+5:30 r...@iastate.edu 
> wrote:
>
>> If all you want is a standard installation of deal.ii in Ubuntu (20.04 or 
>> later), the best way is to do it with the following commands -
>> sudo apt update
>> sudo apt install libdeal.ii-dev
>> sudo apt upgrade
>>
>> You can also install previous versions using PPA as given in this link - 
>> deal.II 
>> Downloads (dealii.org) 
>>
>> Use candi only when you do not want the standard installation. Also, it 
>> is always good to give the *.log file when you have errors installing. It 
>> could be because of some improper dependencies. From the message log I can 
>> see that there's a problem with symengine. If you do not need that 
>> packages, you can comment the corresponding line in candi.cfg file and run 
>> the same commands as you did.
>>
>> Best,
>> Raghunandan.
>>
>> On Tuesday, August 8, 2023 at 12:36:44 PM UTC-5 me22...@iittp.ac.in 
>> wrote:
>>
>>> Dear all,

[deal.II] Re: Problem in installing deallii using candy command.

[Raghunandan Pratoori]

If all you want is a standard installation of deal.ii in Ubuntu (20.04 or 
later), the best way is to do it with the following commands -
sudo apt update
sudo apt install libdeal.ii-dev
sudo apt upgrade

You can also install previous versions using PPA as given in this link - 
deal.II 
Downloads (dealii.org) 

Use candi only when you do not want the standard installation. Also, it is 
always good to give the *.log file when you have errors installing. It 
could be because of some improper dependencies. From the message log I can 
see that there's a problem with symengine. If you do not need that 
packages, you can comment the corresponding line in candi.cfg file and run 
the same commands as you did.

Best,
Raghunandan.

On Tuesday, August 8, 2023 at 12:36:44 PM UTC-5 me22...@iittp.ac.in wrote:

> Dear all,
>
> I am trying to install deall.ii using candy command in ubuntu(Ubuntu 
> 22.04.3 LTS).
> I followed the process 
>
> git clone https://github.com/dealii/candi.git
> cd candi
> ./candi.sh
>
> After 5 hrs of installation i got this error. (Image is also attched)
>
> Fetching symengine 0.8.1
> Verifying symengine-0.8.1.tar.gz
> symengine-0.8.1.tar.gz: OK(md5)
> symengine-0.8.1.tar.gz already downloaded and verified.
> Unpacking symengine-0.8.1.tar.gz
> Building symengine 0.8.1
> -- The C compiler identification is GNU 11.4.0
> -- The CXX compiler identification is GNU 11.4.0
> -- Detecting C compiler ABI info
> -- Detecting C compiler ABI info - done
> -- Check for working C compiler: /usr/bin/mpicc - skipped
> -- Detecting C compile features
> -- Detecting C compile features - done
> -- Detecting CXX compiler ABI info
> -- Detecting CXX compiler ABI info - done
> -- Check for working CXX compiler: /usr/bin/mpicxx - skipped
> -- Detecting CXX compile features
> -- Detecting CXX compile features - done
> -- Performing Test NO_WARN_IMPLICIT_FALL_THROUGH_FLAG
> -- Performing Test NO_WARN_IMPLICIT_FALL_THROUGH_FLAG - Success
> -- Linker supports --exclude-libs
> -- Looking for sys/types.h
> -- Looking for sys/types.h - found
> -- Looking for stdint.h
> -- Looking for stdint.h - found
> -- Looking for stddef.h
> -- Looking for stddef.h - found
> -- Check size of long double
> -- Check size of long double - done
> CMake Error at 
> /usr/share/cmake-3.22/Modules/FindPackageHandleStandardArgs.cmake:230 
> (message):
>   Could NOT find GMP (missing: GMP_LIBRARIES GMP_INCLUDE_DIRS)
> Call Stack (most recent call first):
>   /usr/share/cmake-3.22/Modules/FindPackageHandleStandardArgs.cmake:594 
> (_FPHSA_FAILURE_MESSAGE)
>   cmake/FindGMP.cmake:19 (find_package_handle_standard_args)
>   CMakeLists.txt:375 (find_package)
>
>
> -- Configuring incomplete, errors occurred!
> See also 
> "/home/administrator/dealii-candi/tmp/build/symengine-0.8.1/CMakeFiles/CMakeOutput.log".
> Failure with exit status: 1
> Exit message: There was a problem configuring symengine 0.8.1.
>
>
>
>
>
>
>
> Any help would be appreciated.
> Thanks in advance
>  
>

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Re: [deal.II] Memory error from utilities.cc

[Raghunandan Pratoori]

Thank you for your reply Prof. Bangerth. I believe I am already using 
distributed computing in my code. But I am not sure it is true for the post 
processing part. I use write_vtu and write_pvtu_record to write the output 
files. Is that the best way to do it in distributed computing? Is there any 
example where distributed computing is implemented in the post processing 
so that I can compare my code and see if it can be improved?

Thanks in advance,
Raghunandan.

On Tuesday, August 23, 2022 at 12:06:37 PM UTC-5 Wolfgang Bangerth wrote:

> On 8/23/22 07:22, Raghunandan Pratoori wrote:
> > 
> > I have 2 sets of dof_handlers. The one that is giving me a problem has 
> 6440067 
> > dofs and it becomes 6x when initializing history_field_stress or 
> > history_field_strain. I also plan on increasing these in future 
> simulations.
>
> Well, at 8 bytes per 'double' variable, you need 6,440,067 * 6 * 8 = 
> 309,123,216 bytes = 309 MB of memory to do what you want to do for just 
> this 
> one step. If your machine does not have 309 MB left, you are bound to get 
> the 
> error you describe. There is nothing you can do about this other than (i) 
> get 
> a machine with more memory, (ii) use distributed computing where the 6M 
> unknowns are distributed across more than just one machine.
>
> Best
> W.
>
> -- 
> 
> Wolfgang Bangerth email: bang...@colostate.edu
> www: http://www.math.colostate.edu/~bangerth/
>
>

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Re: [deal.II] Memory error from utilities.cc

[Raghunandan Pratoori]

Hello Prof. Bangerth,

I have 2 sets of dof_handlers. The one that is giving me a problem has 
6440067 dofs and it becomes 6x when initializing history_field_stress or 
history_field_strain. I also plan on increasing these in future simulations.
Can this only be addressed by increasing the memory allotted for the 
simulation? Or is there a way to decrease the memory demand?

Thanks in advance,
Raghunandan.
On Monday, August 22, 2022 at 10:47:46 AM UTC-5 Wolfgang Bangerth wrote:

> On 8/20/22 12:56, Raghunandan Pratoori wrote:
> > 
> > for (unsigned int i=0; i > for (unsigned int j=0; j > {
> > history_field_stress[i][j].reinit(history_dof_handler.n_dofs());
> > 
> > local_history_values_at_qpoints[i][j].reinit(qf_cell.size());
> > 
> > local_history_fe_values[i][j].reinit(history_fe.dofs_per_cell);
> > history_field_strain[i][j].reinit(history_dof_handler.n_dofs());
> > }
>
> This does not look crazy, unless you have a large number of degrees of 
> freedom. How large is history_dof_handler.n_dofs() in your case?
>
> Best
> W.
>
> -- 
> 
> Wolfgang Bangerth email: bang...@colostate.edu
> www: http://www.math.colostate.edu/~bangerth/
>

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Re: [deal.II] Memory error from utilities.cc

[Raghunandan Pratoori]

Thank you for your suggestion Prof. Bangerth. I was able to pinpoint the 
problem in my code. I am trying to write all the stress and strain 
components to the output *vtu files. Below is how initialize the variables 
needed for that before filling them up with quadrature point history. The 
lines of code in red are where the memory error is arising from. Is there a 
better way of handling this process, or am I making some fundamental 
mistake?

//Output stress and strain componenets
std::vector>> history_field_stress(dim, 
std::vector>(dim)),

local_history_values_at_qpoints(dim, std::vector>(dim)),

local_history_fe_values(dim, std::vector>(dim));

std::vector>> history_field_strain(dim, 
std::vector>(dim));

for (unsigned int i=0; i On 8/19/22 13:29, Raghunandan Pratoori wrote:
> > 
> > I am trying to run a simulation with grid refine factor 7. I know this 
> is 
> > significantly large and any improper code will raise memory issues. I am 
> in 
> > fact getting memory issues after completion of first time step and I am 
> not 
> > able to pin point where I probably am making a mistake.
>
> Raghunandan:
> somewhere in your code, there is a place where something wants to allocate 
> 134 
> MB of memory, but your system does not have this much memory left. You 
> need to 
> find out where this is, either by strategically placing print statements 
> into 
> your code to see how far it runs, or (better!) by running the program in a 
> debugger.
>
> Best
> W.
>
> -- 
> 
> Wolfgang Bangerth email: bang...@colostate.edu
> www: http://www.math.colostate.edu/~bangerth/
>
>

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[deal.II] Memory error from utilities.cc

[Raghunandan Pratoori]

Hello team,

I am trying to run a simulation with grid refine factor 7. I know this is 
significantly large and any improper code will raise memory issues. I am in 
fact getting memory issues after completion of first time step and I am not 
able to pin point where I probably am making a mistake. The below is the 
error message.

periodic facepairs: 1
   Number of active cells: 9437
   Number of degrees of freedom: 8586756 (6440067+2146689)
 Solving for Displacement:
   rhs_norm : 0.0414408Number of CG iterations: 55
   rhs_norm : 3.98697e-05Number of CG iterations: 121
CONVERGED!
--
Primary job  terminated normally, but 1 process returned
a non-zero exit code. Per user-direction, the job has been aborted.
--

Exception on processing:
Aborting!



An error occurred in line <1055> of file 

 
in function
void dealii::Utilities::System::posix_memalign(void**, std::size_t, 
std::size_t)
The violated condition was:
ierr == 0
Additional information:
Your program tried to allocate some memory but this allocation failed.
Typically, this either means that you simply do not have enough memory
in your system, or that you are (erroneously) trying to allocate a
chunk of memory that is simply beyond all reasonable size, for example
because the size of the object has been computed incorrectly.

In the current case, the request was for 134217728 bytes.

I would highly appreciate any pointers regarding this.

Thanks in advance,
Raghunandan.

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[deal.II] Error using Operator/ in Vector and FullMatrix

[Raghunandan Pratoori]

Hello team,

I am trying to use the following equations -
r = r/theta;
OM = OM_1*cos(theta);

where r is a dealii::Vector, theta is double, OM and OM_1 are 
dealii::FullMatrix. 

According to the documentation, operator/ and operator* are implemented for 
both Vector and FullMatrix, but both throw an error "no match for 
'operator'".

I am using v9.3.0 and have included /lac/vector.h and /lac/fullmatrix.h. I 
believe I am missing something trivial. Can anyone identify what mistake I 
might be making?

Thanks in advance,
Raghunandan.

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[deal.II] Re: Cluster installation error with symengine library

[Raghunandan Pratoori]

Hi Stephanie,

I use a singularity container with deal.ii on my university cluster. I 
found it to be much simpler and working on any other cluster tried without 
any problems. I suggest you try that as it is a more reliable solution.
Also, if needed, I can give you access to the singularity container I built 
on Ubuntu 20.04 with deal.ii v9.3.0

Best,
Raghunandan.

On Tuesday, February 8, 2022 at 8:30:33 AM UTC-6 sasp...@asu.edu wrote:

> Hello,
>
> I am trying to install deal.ii on my university cluster and have been 
> successful up to this point; however, when I attempt to run examples I get 
> the following error:
>
> ./step-1: error while loading shared libraries: libsymengine.so.0.7: 
> cannot open shared object file: No such file or directory
>
> I found an entry in the FAQ regarding similar problems with linking PETSc 
> and attempted to use that fix but I'm still running into the same issue.
>
> Any help would be greatly appreciated.
>
> Thanks,
> Stephanie
>

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[deal.II] Re: Use of DoFRenumbering

[Raghunandan Pratoori]

Hi Marc,

Thanks for your reply. I use DoFRenumbering with  
parallel::distributed::Triangulation and it works for me. I wanted to know 
why it was not used in step-40. Is it that the improvement observed vs the 
time taken for renumbering does not make it worth using it in this specific 
case?

Best,
Raghunandan.

On Monday, January 10, 2022 at 6:56:55 AM UTC-6 mafe...@gmail.com wrote:

> Hi
>
> I've found application examples for parallel::distributed::Triangulation 
> in our tests. See for example 
> https://github.com/dealii/dealii/blob/master/tests/mpi/renumber_cuthill_mckee.cc
>
> As you specifically mentioned step-40, I think this is what you were 
> asking for?
>
> Best,
> Marc
>
> On Monday, January 10, 2022 at 8:19:39 AM UTC+1 r...@iastate.edu wrote:
>
>> Hello,
>>
>> I am trying to understand the effective usage of DoFRenumbering. From the 
>> examples 
>> I have looked at and the pages I have read, I seem to understand that 
>> renumbering is recommended. But I do not see it being used in few examples, 
>> say step-40. Is there a reason for not renumbering in these cases? I would 
>> appreciate any pointers regarding this.
>>
>> Thanks in advance,
>>
>> Best,
>> Raghunandan.
>>
>

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[deal.II] Re: Cannot find the header files when compiling with WSL Linux distributive in VS code

[Raghunandan Pratoori]

Hi,

I use VS Code with WSL. I followed the instructions on these 2 pages and 
was able to get it to work -
https://code.visualstudio.com/docs/cpp/config-wsl
https://code.visualstudio.com/docs/cpp/cmake-linux

Also, how did you install deal.ii in wsl? I used the PPA and it took care 
of all the paths to be added.

Best,
Raghunandan.



On Sunday, January 16, 2022 at 2:13:26 AM UTC-6 keassyguang wrote:

> Hi, everyone. I'm interested in deal.ii, but I did have trouble 
> configuring the deal.ii.
>
> I am trying to compile the program for Linux in VS code (version 1.63.2) 
> using WSL (Windows Subsystem for Linux) ubuntu 20.04.3. I successfully 
> compile the "Hello, World!" program, but when I try to compile the tutorial 
> programs shown in dell.ii documentation, such as the step-1, the 
> compilation terminated with an error message "No such file or directory". 
> Then, the system includePath in VS code has been set to "/usr/include/**" 
> and other libs as shown in the below figures, however, it dosenot work.
>
> [image: 1.png][image: 2.png]
>
> Later, I manually edit some head files. For example, as shown in the below 
> figure, I know the "Kokkos_MasterLock.hpp" file is in the directory of 
> "/usr/include/trilinos", so I modified the 55th line of 
> "Kokkos_Core_fwd.hpp" file by adding the "trilions" directory into the path 
> "#include " (the original is "#include 
> "). After that, the compiler can find the 
> "Kokkos_MasterLock.hpp" file, however, the compilation terminated with 
> another new file named "Kokkos_Macros.hpp". Truly, I can edit the path as 
> the aforementioned method, it is impossible to edit all the files using 
> this way. So, can someone tell me how to compile the program for Linux in 
> VS code using WSL? It will be of great help to me.
>
> [image: 3.png][image: 4.png][image: 5.png]
>

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[deal.II] Use of DoFRenumbering

[Raghunandan Pratoori]

Hello,

I am trying to understand the effective usage of DoFRenumbering. From the 
examples 
I have looked at and the pages I have read, I seem to understand that 
renumbering is recommended. But I do not see it being used in few examples, 
say step-40. Is there a reason for not renumbering in these cases? I would 
appreciate any pointers regarding this.

Thanks in advance,

Best,
Raghunandan.

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[deal.II] Re: Adding inhomogeneity to Periodic BC

[Raghunandan Pratoori]

I realized that the above situation is arising because of close(). Is there 
a way to add inhomogeneity without it being added again because of periodic 
condition?

Best,

On Friday, October 22, 2021 at 8:01:18 PM UTC-5 Raghunandan Pratoori wrote:

> Hello,
>
> I have a cube with periodicity in all 3 directions. I want to add 
> inhomogeneity in addition to Periodic BC on one face. Below is what I have 
> done -
>
> {
> IndexSet selected_dofs_z;
> std::set boundary_ids_z = std::set boundary_id>();
> boundary_ids_x.insert(4);
> DoFTools::extract_boundary_dofs(dof_handler, fe.component_mask
> (z_displacement),
> selected_dofs_z, 
> boundary_ids_z);
> unsigned int nb_dofs_face_z = selected_dofs_z.n_elements();
> IndexSet::ElementIterator dofs_z = selected_dofs_z.begin();
>
> double relative_displacement_z = 1e-5;
>
> for(unsigned int i = 0; i < nb_dofs_face_z; i++)
> {
> constraints.add_line(*dofs_z);
> constraints.set_inhomogeneity(*dofs_z, 
> relative_displacement_z));
> dofs_z++;
> }
> }
> When I do this on single 8 noded element, I get the constraints as -
> 2 = 0.001
> 3 0:  1
> 4 1:  1
> 5 = 0.002
> 6 0:  1
> 7 1:  1
> 8 = 0.002
> 9 0:  1
> 10 1:  1
> 11 = 0.003
> 12 0:  1
> 13 1:  1
> 14 = 0.001
> 15 0:  1
> 16 1:  1
> 17 = 0.001
> 18 0:  1
> 19 1:  1
> 20 = 0.001
> 21 0:  1
> 22 1:  1
> 23 = 0.001
> When I should be getting -
> 2 = 0.001
> 3 0:  1
> 4 1:  1
> 5 = 0.001
> 6 0:  1
> 7 1:  1
> 8 = 0.001
> 9 0:  1
> 10 1:  1
> 11 = 0.001
> 12 0:  1
> 13 1:  1
> 14 = 0.001
> 15 0:  1
> 16 1:  1
> 17 = 0.001
> 18 0:  1
> 19 1:  1
> 20 = 0.001
> 21 0:  1
> 22 1:  1
> 23 = 0.001
> Is there a mistake in how I am using set_inhomogeneity?
>
> Thanks in advance,
> Raghunandan.
>

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[deal.II] Adding inhomogeneity to Periodic BC

[Raghunandan Pratoori]

Hello,

I have a cube with periodicity in all 3 directions. I want to add 
inhomogeneity in addition to Periodic BC on one face. Below is what I have 
done -

{
IndexSet selected_dofs_z;
std::set boundary_ids_z = std::set();
boundary_ids_x.insert(4);
DoFTools::extract_boundary_dofs(dof_handler, fe.component_mask(z
_displacement),
selected_dofs_z, boundary_ids_z
);
unsigned int nb_dofs_face_z = selected_dofs_z.n_elements();
IndexSet::ElementIterator dofs_z = selected_dofs_z.begin();

double relative_displacement_z = 1e-5;

for(unsigned int i = 0; i < nb_dofs_face_z; i++)
{
constraints.add_line(*dofs_z);
constraints.set_inhomogeneity(*dofs_z, 
relative_displacement_z));
dofs_z++;
}
}
When I do this on single 8 noded element, I get the constraints as -
2 = 0.001
3 0:  1
4 1:  1
5 = 0.002
6 0:  1
7 1:  1
8 = 0.002
9 0:  1
10 1:  1
11 = 0.003
12 0:  1
13 1:  1
14 = 0.001
15 0:  1
16 1:  1
17 = 0.001
18 0:  1
19 1:  1
20 = 0.001
21 0:  1
22 1:  1
23 = 0.001
When I should be getting -
2 = 0.001
3 0:  1
4 1:  1
5 = 0.001
6 0:  1
7 1:  1
8 = 0.001
9 0:  1
10 1:  1
11 = 0.001
12 0:  1
13 1:  1
14 = 0.001
15 0:  1
16 1:  1
17 = 0.001
18 0:  1
19 1:  1
20 = 0.001
21 0:  1
22 1:  1
23 = 0.001
Is there a mistake in how I am using set_inhomogeneity?

Thanks in advance,
Raghunandan.

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[deal.II] Clarification on Periodic Boundary Conditions

[Raghunandan Pratoori]

Hello,

I am trying to apply Periodic Boundary Conditions on a cubic sample in all 
the three directions and then compress it - compression of an RVE.
The displacement I need to give is:[image: Screenshot 2021-10-20 204440.png]
For this, I first applied PBC using DoFTools::make_periodicity_constraints 
and then added displacement to the corresponding DoFs (selected them using 
DoFTools::extract_boundary_dofs) using constraints.set_inhomogeneity.

I have a few questions regarding this -
1. Am I doing this correct?
2. Also, do I need to specifically restrict rigid body motions? If yes, 
what is the best way to do this? I tried by fixing some nodes, but it is 
becoming too artificial and causing huge distortions at higher strains.

Thanks in advance,
Raghunandan.

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Re: [deal.II] Clarification in Step-45 of tutorial

[Raghunandan Pratoori]

Sure. I can do that.

On Friday, October 8, 2021 at 4:36:21 PM UTC-5 Wolfgang Bangerth wrote:

> On 10/8/21 2:21 PM, Raghunandan Pratoori wrote:
> > Sure! I would be happy to that! I will submit a pull request. I am 
> currently 
> > working on v9.3.0. Will submitting a pull request on that work or should 
> it be 
> > based on the master branch?
> > 
>
> If you can, base it on master. That's where changes should go that should 
> be 
> in future releases.
>
> Best
> W.
>
> -- 
> 
> Wolfgang Bangerth email: bang...@colostate.edu
> www: http://www.math.colostate.edu/~bangerth/
>
>

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Re: [deal.II] Clarification in Step-45 of tutorial

[Raghunandan Pratoori]

Sure! I would be happy to that! I will submit a pull request. I am 
currently working on v9.3.0. Will submitting a pull request on that work or 
should it be based on the master branch?

Best,

On Friday, October 8, 2021 at 1:52:46 PM UTC-5 Wolfgang Bangerth wrote:

> On 10/8/21 11:57 AM, Raghunandan Pratoori wrote:
> > 
> > I tried by removing the second occurrence 
> > ofVectorTools::interpolate_boundary_values and got the same results.
>
> Great, thanks for trying this out. Would you like to submit a patch to 
> deal.II that fixes this? You'd become one of the authors of deal.II this 
> way :-)
>
> Best
> W.
>
>
> -- 
> 
> Wolfgang Bangerth email: bang...@colostate.edu
> www: http://www.math.colostate.edu/~bangerth/
>

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Re: [deal.II] Clarification in Step-45 of tutorial

[Raghunandan Pratoori]

Hello Dr. Bangertt,

I tried by removing the second occurrence of 
VectorTools::interpolate_boundary_values and got the same results.

Best,

On Thursday, October 7, 2021 at 10:24:48 PM UTC-5 Wolfgang Bangerth wrote:

> On 10/7/21 8:10 PM, Raghunandan Pratoori wrote:
> > 
> > Why is VectorTools::interpolate_boundary_values 
> > <
> https://nam10.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.dealii.org%2Fcurrent%2Fdoxygen%2Fdeal.II%2FnamespaceVectorTools.html%23af27ac28c698a9ed0199faed50a204538=04%7C01%7CWolfgang.Bangerth%40colostate.edu%7C7ddff1f7c1c9426d581708d98a00d98f%7Cafb58802ff7a4bb1ab21367ff2ecfc8b%7C0%7C0%7C637692559418379919%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000=UWRTkmhaarWHXm2JZe34AUbqwqBV4kx0n7fdaju6KbU%3D=0>
>  
>
> > used twice - once before DoFTools::make_periodicity_constraints and once 
> after 
> > in setup_dofs?
>
> That seems like a mistake. Can you try what happens if you remove the 
> second 
> set of calls and whether that changes the output of the program?
>
> Best
> Wolfgang
>
> -- 
> 
> Wolfgang Bangerth email: bang...@colostate.edu
> www: http://www.math.colostate.edu/~bangerth/
>
>

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[deal.II] Clarification in Step-45 of tutorial

[Raghunandan Pratoori]

Hello,

Why is VectorTools::interpolate_boundary_values 

 
used twice - once before DoFTools::make_periodicity_constraints and once 
after in setup_dofs?

Best,
Raghunandan.

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Re: [deal.II] Viewing node numbers and cell numbers in visualization

[Raghunandan Pratoori]

I was able to do it using DoFTools::map_dofs_to_support_points.

Best,
On Wednesday, October 6, 2021 at 3:22:02 PM UTC-5 Raghunandan Pratoori 
wrote:

> Thank you for your reply Dr. Bangerth.
>
> I want to check which vertices are associated with the what DoFs. How can 
> I extract them for each individual vertex? I could not find any relevant 
> extract_<..>_dofs function to do it.
>
> Best,
> Raghunandan.
> On Tuesday, October 5, 2021 at 10:06:02 PM UTC-5 Wolfgang Bangerth wrote:
>
>> On 10/5/21 8:30 PM, Raghunandan Pratoori wrote:
>> > 
>> > I would like to see how the nodes and cells are numbered during 
>> visualization, 
>> > much like in Abaqus. I am using Paraview for visualization. How should 
>> I write 
>> > my mesh for it to store all this data?
>>
>> Neither cell nor DoF numbers are exported in any format we write. That's 
>> because with the exception of scalar Q1 elements, there is no 1:1 
>> connection 
>> between vertices and DoF indices; for everything else, there is no 
>> connection 
>> and as a consequence we don't output this information. Sorry :-(
>>
>> Best
>> W.
>>
>>
>> -- 
>> 
>> Wolfgang Bangerth email: bang...@colostate.edu
>> www: http://www.math.colostate.edu/~bangerth/
>>
>>

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Re: [deal.II] Viewing node numbers and cell numbers in visualization

[Raghunandan Pratoori]

Thank you for your reply Dr. Bangerth.

I want to check which vertices are associated with the what DoFs. How can I 
extract them for each individual vertex? I could not find any relevant 
extract_<..>_dofs function to do it.

Best,
Raghunandan.
On Tuesday, October 5, 2021 at 10:06:02 PM UTC-5 Wolfgang Bangerth wrote:

> On 10/5/21 8:30 PM, Raghunandan Pratoori wrote:
> > 
> > I would like to see how the nodes and cells are numbered during 
> visualization, 
> > much like in Abaqus. I am using Paraview for visualization. How should I 
> write 
> > my mesh for it to store all this data?
>
> Neither cell nor DoF numbers are exported in any format we write. That's 
> because with the exception of scalar Q1 elements, there is no 1:1 
> connection 
> between vertices and DoF indices; for everything else, there is no 
> connection 
> and as a consequence we don't output this information. Sorry :-(
>
> Best
> W.
>
>
> -- 
> 
> Wolfgang Bangerth email: bang...@colostate.edu
> www: http://www.math.colostate.edu/~bangerth/
>
>

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[deal.II] Viewing node numbers and cell numbers in visualization

[Raghunandan Pratoori]

Hello,

I would like to see how the nodes and cells are numbered during 
visualization, much like in Abaqus. I am using Paraview for visualization. 
How should I write my mesh for it to store all this data?

Best,
Raghunandan.

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Re: [deal.II] Deal.II programming environment

[Raghunandan Pratoori]

Hi,

I recently started using VS code with deal.ii. I found it very easy to work 
with, especially when you have a wsl installation.
All you need to do is follow the instructions on these pages -
https://code.visualstudio.com/docs/cpp/config-wsl
https://code.visualstudio.com/docs/cpp/cmake-linux

VS code actually looks through the files in your directory and suggests 
extensions you would need.

Best,
Raghunandan.
On Wednesday, July 21, 2021 at 10:15:10 AM UTC-5 Wells, David wrote:

> Hi Martin,
>
> No, that's a very good question - it's important to set up a good 
> development environment. You CAN use plain text editors and run CMake from 
> the command line (in fact, with many tools you will end up still running 
> CMake from a window inside them) but its usually better to use something 
> more sophisticated (like an IDE that can run a debugger).
>
> If you look on the wiki we have instructions for both Eclipse and QT 
> creator:
>
> https://github.com/dealii/dealii/wiki
>
> a lot of people use VS code - we don't have instructions for it, and I 
> don't use it, but since we use CMake it shouldn't be that hard to point VS 
> code at your build directory and have it extract some information. If 
> anyone actually uses VS code I would appreciate if they could weigh in here!
>
> Best,
> David Wells
> --
> *From:* dea...@googlegroups.com  on behalf of 
> Jiang Hu 
> *Sent:* Wednesday, July 21, 2021 1:22 AM
> *To:* deal.II User Group 
> *Subject:* [deal.II] Deal.II programming environment 
>  
> Hello everyone, 
>
> Quite excited to find Deal.II and its potential.
>
> I installed virtual machine with Deal.II, and run step 7 on terminal 
> without any problem.
>
> The question is if I want to compile bigger program with Deal.II , what is 
> the typical working environment? 
>
> I assume we can not with terminal for such a purpose. I saw people using 
> Nano to run Deal.II, but want to ask the standard tool for such process.
>
> Emacs or Vscode?  Do I need to connect them to Deal.II?
>
> I am very new, and this could be a quite silly question.
>
> Thanks 
>
> Martin
>
> -- 
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>  
> 
> .
>

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Re: [deal.II] Re: Using periodic boundary conditions with parallell processing

[Raghunandan Pratoori]

ed 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.
>>
>> I would appreciate any pointers on the possible mistakes I might be
>> making.
>>
>> Best regards,
>> Raghunandan.
>>
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>


-- 

*Raghunandan Pratoori*

Graduate Student

Aerospace Engineering <https://www.aere.iastate.edu/> | Iowa State
University

2048 Howe Hall |  515-708-6767

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[deal.II] Using periodic boundary conditions with parallell processing

[Raghunandan Pratoori]

Hello team,

I am running a 3D simulation with periodicity in all 3 directions.
I have defined the periodic boundary conditions using (similarly in the 
other 2 directions) - 




*DoFTools::make_periodicity_constraints(dof_handler,

/*b_id*/ 0,/*b_id*/ 
1,/*direction*/ 
0,constraints);*
and the deformation of the box using - 

























*IndexSet selected_dofs_x;   std::set< types::boundary_id > 
boundary_ids_x= std::set();   
boundary_ids_x.insert(0);   
DoFTools::extract_boundary_dofs(dof_handler,
  
fe.component_mask(y_displacement),   
selected_dofs_x,   
boundary_ids_x);   unsigned int nb_dofs_face_x = 
selected_dofs_x.n_elements();   IndexSet::ElementIterator dofs_x = 
selected_dofs_x.begin();   double relative_displacement_x = 0.0;   
if(timestep<=020)relative_displacement_x = 5e-4;   else 
if(timestep%02==0)relative_displacement_x = 2e-4;   else
relative_displacement_x = 0.0;   for(unsigned int i = 0; i < 
nb_dofs_face_x; i++)   {constraints.add_line (*dofs_x); 
constraints.set_inhomogeneity(*dofs_x, (apply_dirichlet_bc ? 
relative_displacement_x : 0.0));   dofs_x++;   }*
This works fine when run using a single process. But when increased to 2 
processes, it pauses after few time steps without any error message. When 
used more than 2 processes, it does not converge in the first time step 
itself. I am not sure what is causing the problem.

I also tested it with step-45. It works fine with 1 and 2 processes. But 
when 4 processes are used, it gives out the following error:
[100%] Built target step-45
Refinement cycle 0
   Assembling...
   Computing preconditioner...
   Solving...


Exception on processing:



Exception on processing:


An error occurred in line <457> of file 
 in function
void dealii::SolverCG::solve(const MatrixType&, 
VectorType&, const VectorType&, const PreconditionerType&) [with MatrixType 
= Step45::SchurComplement; 
PreconditionerType = dealii::TrilinosWrappers::PreconditionAMG; VectorType 
= dealii::TrilinosWrappers::MPI::Vector]
The violated condition was:
false
Additional information:
Iterative method reported convergence failure in step 65. The residual in 
the last step was 4.56146e-06.

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.

I would appreciate any pointers on the possible mistakes I might be making.

Best regards,
Raghunandan.

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