Re: [deal.II] Query Regarding Direct Import of Dream3D Synthetic Microstructures into Deal.II
Thank you Now it's working. Initially, I defined *feature_id1_at_all_dof* as *std::vector*, but later I recognized that it should be defined as *dealii::Vector*. thank you. On Wednesday, March 13, 2024 at 7:01:28 PM UTC+5:30 ME20D503 NEWTON wrote: > Dear everyone, I would greatly appreciate any assistance you can provide > with the following issue. > > I am trying to use this function to interpolate the feature ID from FE > space 1(linear) to FE space 2(quadratic). (please see the trailing mail for > a better understanding of my problem) > > interpolate() [4/4] > templatehttps://www.dealii.org/9.4.0/doxygen/deal.II/classint.html> > dim, class InVector , class OutVector , int > <https://www.dealii.org/9.4.0/doxygen/deal.II/classint.html> spacedim> > > void VectorTools::interpolate > ( > const DoFHandler > <https://www.dealii.org/9.4.0/doxygen/deal.II/classDoFHandler.html>< dim, > spacedim > & *dof_1*, > const DoFHandler > <https://www.dealii.org/9.4.0/doxygen/deal.II/classDoFHandler.html>< dim, > spacedim > & *dof_2*, > const FullMatrix > <https://www.dealii.org/9.4.0/doxygen/deal.II/classFullMatrix.html>< > double > & *transfer*, > const InVector & *data_1*, > OutVector & *data_2* > ) > > *my function which i am using in my code is:* > > VectorTools::interpolate(dof_handler_dream3d, dof_handler_eta, > transfer_matrix ,feature_id1_at_all_dof, solution_xi1); > > VectorTools::interpolate(dof_handler_dream3d, dof_handler_eta, > transfer_matrix ,feature_id2_at_all_dof, solution_xi2); > > *but i am getting error like :* > > [ 66%] Linking CXX executable PhaseField > > CMakeFiles/PhaseField.dir/PhaseField.cc.o:PhaseField.cc:function > PhaseField::Solid<2>::run(): error: undefined reference to 'void > dealii::VectorTools::interpolate<2, std::vector std::allocator >, dealii::Vector, 2>(dealii::DoFHandler<2, > 2> const&, dealii::DoFHandler<2, 2> const&, dealii::FullMatrix > const&, std::vector > const&, > dealii::Vector&)' > > CMakeFiles/PhaseField.dir/PhaseField.cc.o:PhaseField.cc:function > PhaseField::Solid<2>::run(): error: undefined reference to 'void > dealii::VectorTools::interpolate<2, std::vector std::allocator >, dealii::Vector, 2>(dealii::DoFHandler<2, > 2> const&, dealii::DoFHandler<2, 2> const&, dealii::FullMatrix > const&, std::vector > const&, > dealii::Vector&)' > > collect2: error: ld returned 1 exit status > > make[3]: *** [CMakeFiles/PhaseField.dir/build.make:228: PhaseField] Error 1 > > make[2]: *** [CMakeFiles/Makefile2:90: CMakeFiles/PhaseField.dir/all] > Error 2 > > make[1]: *** [CMakeFiles/Makefile2:123: CMakeFiles/run.dir/rule] Error 2 > > make: *** [Makefile:137: run] Error 2 > > "make run" terminated with exit code 2. Build might be incomplete. > > 17:58:08 Build Failed. 4 errors, 63 warnings. (took 20s.439ms) > > > Thank you. > > On Monday, March 11, 2024 at 5:01:25 PM UTC+5:30 ME20D503 NEWTON wrote: > >> Dear Prof. Bangerth, >> >> Thank you for the reply. >> >> I have successfully managed to read the .vtk file in Deal.II and extract >> the feature IDs along with their corresponding coordinate points by >> manually parsing the vtk file (using std::getline(file, line)). >> >> *However, I am now encountering another difficulty for which I require >> your guidance.* >> >> *>> When I use linear elements, I can visualize my initial structure as >> desired. However, when I switch to using quadratic elements, five >> additional nodes are added to each cell. Since I only have information >> about the feature IDs at the four corners of the cell, I lack data >> for these extra five nodes. Is there a method to interpolate the feature >> IDs for these additional nodes using the four at the corners of the cell?* >> >> Please refer to the attached figure for a better understanding of my >> issue. >> >> Thank you. >> On Thursday, March 7, 2024 at 12:38:34 PM UTC+5:30 Wolfgang Bangerth >> wrote: >> >>> On 3/5/24 00:46, ME20D503 NEWTON wrote: >>> > 1. >>> > >>> > In the final .vtk file format, I don't have information about the >>> element >>> > type (linear or quadratic). Is it possible to assign the element type >>> in >>> > deal.II after reading the .vtk file? >>> >>> I think you already solved that (along with the next problem), but just >>> for >>> completeness: t
Re: [deal.II] Query Regarding Direct Import of Dream3D Synthetic Microstructures into Deal.II
Dear everyone, I would greatly appreciate any assistance you can provide with the following issue. I am trying to use this function to interpolate the feature ID from FE space 1(linear) to FE space 2(quadratic). (please see the trailing mail for a better understanding of my problem) interpolate() [4/4] templatehttps://www.dealii.org/9.4.0/doxygen/deal.II/classint.html> dim, class InVector , class OutVector , int <https://www.dealii.org/9.4.0/doxygen/deal.II/classint.html> spacedim> void VectorTools::interpolate ( const DoFHandler <https://www.dealii.org/9.4.0/doxygen/deal.II/classDoFHandler.html>< dim, spacedim > & *dof_1*, const DoFHandler <https://www.dealii.org/9.4.0/doxygen/deal.II/classDoFHandler.html>< dim, spacedim > & *dof_2*, const FullMatrix <https://www.dealii.org/9.4.0/doxygen/deal.II/classFullMatrix.html>< double > & *transfer*, const InVector & *data_1*, OutVector & *data_2* ) *my function which i am using in my code is:* VectorTools::interpolate(dof_handler_dream3d, dof_handler_eta, transfer_matrix ,feature_id1_at_all_dof, solution_xi1); VectorTools::interpolate(dof_handler_dream3d, dof_handler_eta, transfer_matrix ,feature_id2_at_all_dof, solution_xi2); *but i am getting error like :* [ 66%] Linking CXX executable PhaseField CMakeFiles/PhaseField.dir/PhaseField.cc.o:PhaseField.cc:function PhaseField::Solid<2>::run(): error: undefined reference to 'void dealii::VectorTools::interpolate<2, std::vector >, dealii::Vector, 2>(dealii::DoFHandler<2, 2> const&, dealii::DoFHandler<2, 2> const&, dealii::FullMatrix const&, std::vector > const&, dealii::Vector&)' CMakeFiles/PhaseField.dir/PhaseField.cc.o:PhaseField.cc:function PhaseField::Solid<2>::run(): error: undefined reference to 'void dealii::VectorTools::interpolate<2, std::vector >, dealii::Vector, 2>(dealii::DoFHandler<2, 2> const&, dealii::DoFHandler<2, 2> const&, dealii::FullMatrix const&, std::vector > const&, dealii::Vector&)' collect2: error: ld returned 1 exit status make[3]: *** [CMakeFiles/PhaseField.dir/build.make:228: PhaseField] Error 1 make[2]: *** [CMakeFiles/Makefile2:90: CMakeFiles/PhaseField.dir/all] Error 2 make[1]: *** [CMakeFiles/Makefile2:123: CMakeFiles/run.dir/rule] Error 2 make: *** [Makefile:137: run] Error 2 "make run" terminated with exit code 2. Build might be incomplete. 17:58:08 Build Failed. 4 errors, 63 warnings. (took 20s.439ms) Thank you. On Monday, March 11, 2024 at 5:01:25 PM UTC+5:30 ME20D503 NEWTON wrote: > Dear Prof. Bangerth, > > Thank you for the reply. > > I have successfully managed to read the .vtk file in Deal.II and extract > the feature IDs along with their corresponding coordinate points by > manually parsing the vtk file (using std::getline(file, line)). > > *However, I am now encountering another difficulty for which I require > your guidance.* > > *>> When I use linear elements, I can visualize my initial structure as > desired. However, when I switch to using quadratic elements, five > additional nodes are added to each cell. Since I only have information > about the feature IDs at the four corners of the cell, I lack data > for these extra five nodes. Is there a method to interpolate the feature > IDs for these additional nodes using the four at the corners of the cell?* > > Please refer to the attached figure for a better understanding of my issue. > > Thank you. > On Thursday, March 7, 2024 at 12:38:34 PM UTC+5:30 Wolfgang Bangerth wrote: > >> On 3/5/24 00:46, ME20D503 NEWTON wrote: >> > 1. >> > >> > In the final .vtk file format, I don't have information about the >> element >> > type (linear or quadratic). Is it possible to assign the element type >> in >> > deal.II after reading the .vtk file? >> >> I think you already solved that (along with the next problem), but just >> for >> completeness: the .vtk file only contains the *mesh*. You have to choose >> what >> element to use on it. These are independent questions. >> >> >> > 2. >> > >> > In the final .vtk file format, there is no information regarding the >> scale >> > I'm working with. I intend to create a nanoscale sample, but the >> > dimensions I set in DREAM.3D are unitless. Is it possible to scale it >> down >> > in deal.II after reading the .vtk file? >> >> You will want to use GridTools::scale(). >> >> >> > 3. >> > >> > The final .vtk file includes information like featureId (please see the >> > attached figure). After reading this .vtk file, I wan
Re: [deal.II] Query Regarding Direct Import of Dream3D Synthetic Microstructures into Deal.II
Dear Bangerth, I've successfully solved points 1 and 2. However, I'm encountering difficulties with point 3. Could you assist me in understanding how to extract the feature IDs from the .vtk file after reading it in dealii, and then perform further operations based on these feature IDs in dealii? Thank you. On Tuesday, March 5, 2024 at 1:16:21 PM UTC+5:30 ME20D503 NEWTON wrote: > Dear Bangerth, I'm facing difficulties with the following issues, and I > would appreciate your input: > > I'm working on processing a .vtk file exported from DREAM.3D using > PRISMS-PF scripts( > https://github.com/prisms-center/phaseField/tree/master/applications/grainGrowth_dream3d) > > to convert it into a .vtk file format with UNSTRUCTURED_GRID dataset, > making it compatible with deal.II. > > Here are my specific doubts: > >1. > >In the final .vtk file format, I don't have information about the >element type (linear or quadratic). Is it possible to assign the element >type in deal.II after reading the .vtk file? >2. > >In the final .vtk file format, there is no information regarding the >scale I'm working with. I intend to create a nanoscale sample, but the >dimensions I set in DREAM.3D are unitless. Is it possible to scale it down >in deal.II after reading the .vtk file? >3. > >The final .vtk file includes information like featureId (please see >the attached figure). After reading this .vtk file, I want to assign some >variables to the featureId. Is it possible to extract the value and assign >variables to it in deal.II? > > I am attaching all the files. > > *trial1.vtk* a rectilinear grid cell data output from DREAM.3D > *microstructure_RL_resampled.vtk *point data (using prismPF script) > *microstructure_US.vtk *UNSTRUCTURED_GRID dataset type(using prismPF > script) > > Thank you. > > On Friday, March 1, 2024 at 3:04:32 AM UTC+5:30 Wolfgang Bangerth wrote: > >> On 2/29/24 02:08, ME20D503 NEWTON wrote: >> > However, I'm facing some confusion regarding the appropriate file >> format for >> > exporting from Dream3D to Deal. II. Additionally, I've come across >> another >> > open-source software, PRISM-PF ( >> https://prisms-center.github.io/phaseField/ >> > < >> https://nam10.safelinks.protection.outlook.com/?url=https%3A%2F%2Fprisms-center.github.io%2FphaseField%2F=05%7C02%7CWolfgang.Bangerth%40colostate.edu%7C46793158b282404d8f3b08dc39060bcc%7Cafb58802ff7a4bb1ab21367ff2ecfc8b%7C0%7C0%7C638447949240491605%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C6%7C%7C%7C=NqzE83il7FWP%2FAwG6sGvfP%2BPUPNxuESv244YD3kpQtE%3D=0>), >> >> which has successfully achieved a similar process and is built upon Deal. >> II. >> > >> > I would greatly appreciate any guidance or insights you could provide >> on this >> > matter. >> >> If PRISM-PR does what you want, by all means go with it! As for the >> Dream3d >> format: You need to explain in more detail what "I'm facing some >> confusion" >> means in concrete terms :-) >> >> Best >> W. >> >> >> -- >> >> Wolfgang Bangerth email: bang...@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/e2a0e46b-37dd-48d9-b1cd-bc4cd9f04acdn%40googlegroups.com.
Re: [deal.II] Query Regarding Direct Import of Dream3D Synthetic Microstructures into Deal.II
Dear Dr. Bangerth, I am currently working on generating a synthetic microstructure of polycrystalline material using Dream3D, an open-source software (accessible at https://dream3d.bluequartz.net/). My intention is to import this microstructure into Deal.II for further simulations, such as discretization and solving phase field equations. However, I'm facing some confusion regarding the appropriate file format for exporting from Dream3D to Deal. II. Additionally, I've come across another open-source software, PRISM-PF ( https://prisms-center.github.io/phaseField/), which has successfully achieved a similar process and is built upon Deal. II. I would greatly appreciate any guidance or insights you could provide on this matter. Thank you. On Thursday, February 29, 2024 at 1:36:12 PM UTC+5:30 Wolfgang Bangerth wrote: > On 2/28/24 21:21, ME20D503 NEWTON wrote: > > I am writing to inquire about the feasibility of directly importing > Dream3D > > synthetic microstructures into Deal.II. If this is indeed possible, > could you > > kindly provide guidance on the required file format? > > @Newton: > I'm not sure anyone here has heard of that file format (or, indeed, what > it > represents) before. What is it? What does it represent? Where is it > documented? > > In general, people read in all sorts of file formats in their programs. > But it > all starts from understanding what the data means and how it is > represented. > > Best > W. > > -- > > Wolfgang Bangerth email: bang...@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/a32843e6-1dbe-4973-aa1a-bb3c09361db3n%40googlegroups.com.
[deal.II] Query Regarding Direct Import of Dream3D Synthetic Microstructures into Deal.II
Dear all, I am writing to inquire about the feasibility of directly importing Dream3D synthetic microstructures into Deal.II. If this is indeed possible, could you kindly provide guidance on the required file format? thanks. -- 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/10665a37-23d5-4455-89ac-208283f15782n%40googlegroups.com.
Re: [deal.II] I am experiencing varying execution speeds when running my code with different configurations of Ubuntu and Deal.II. Here are the observed speeds for the same code on different systems
Thanks, Daniel I got the problem. There is no problem with the Versions. I was using Debug mode to run the code in the terminal. I was using directly "cmake run" to run my code which i had to use "make release" then "make run'. On Mon, Sep 25, 2023 at 6:16 PM Daniel Arndt wrote: > What is your code doing and how do you configure deal.II in all of these > cases? Are you running in Release mode when comparing the run time of your > program with different configurations? > I would be very surprised to find that vastly different runtimes are a > result of using different Ubuntu versions. > > Best, > Daniel > > On Mon, Sep 25, 2023 at 1:29 AM ME20D503 NEWTON > wrote: > >> >> >> "I am experiencing varying execution speeds when running my code with >> different configurations of Ubuntu and Deal.II. Here are the observed >> speeds for the same code on different systems: >> >> 1. Ubuntu 22.04.2 LTS, Deal.II 9.5.1, 32GB RAM, Intel Xeon Silver 4208 >> CPU @ 2.10GHz x 16 cores: The code runs very fast on this system. >> >> 2. Ubuntu 22.04.1 LTS, Deal.II 9.5.1, 32GB RAM, Intel Xeon Silver 4208 >> CPU @ 2.10GHz x 16 cores: The code runs very slow on this system. >> >> 3. Ubuntu 20.04.3 LTS, Deal.II 9.4.2, 64GB RAM, Intel Xeon Silver 4208 >> CPU @ 2.10GHz x 40 cores: The code runs very slow on this system. >> >> 4. Ubuntu 22.04.3 LTS, Deal.II 9.5.1, 32GB RAM, Intel Xeon Silver 4208 >> CPU @ 2.10GHz x 16 cores: The code runs very slow on this system. >> >> I am seeking assistance to understand why there is such a significant >> difference in code execution speed across these configurations." >> >> Thank you. >> >> regards >> >> -- >> 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/d657d4ed-a443-4282-9993-93e580977f99n%40googlegroups.com >> <https://groups.google.com/d/msgid/dealii/d657d4ed-a443-4282-9993-93e580977f99n%40googlegroups.com?utm_medium=email_source=footer> >> . >> > -- > 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 a topic in the > Google Groups "deal.II User Group" group. > To unsubscribe from this topic, visit > https://groups.google.com/d/topic/dealii/x6pTZ3rWeRI/unsubscribe. > To unsubscribe from this group and all its topics, send an email to > dealii+unsubscr...@googlegroups.com. > To view this discussion on the web visit > https://groups.google.com/d/msgid/dealii/CAOYDWbJTJq_dMCsaMJj2r9Y1bDYtHqef%2BYSxr%3DPtr-EO6oBzhw%40mail.gmail.com > <https://groups.google.com/d/msgid/dealii/CAOYDWbJTJq_dMCsaMJj2r9Y1bDYtHqef%2BYSxr%3DPtr-EO6oBzhw%40mail.gmail.com?utm_medium=email_source=footer> > . > -- 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/CAM2td%3DXX_%3D2HfpNSyNNa_UGR7CwCBD8uQWrFE91T3hNasziMuw%40mail.gmail.com.
[deal.II] I am experiencing varying execution speeds when running my code with different configurations of Ubuntu and Deal.II. Here are the observed speeds for the same code on different systems
"I am experiencing varying execution speeds when running my code with different configurations of Ubuntu and Deal.II. Here are the observed speeds for the same code on different systems: 1. Ubuntu 22.04.2 LTS, Deal.II 9.5.1, 32GB RAM, Intel Xeon Silver 4208 CPU @ 2.10GHz x 16 cores: The code runs very fast on this system. 2. Ubuntu 22.04.1 LTS, Deal.II 9.5.1, 32GB RAM, Intel Xeon Silver 4208 CPU @ 2.10GHz x 16 cores: The code runs very slow on this system. 3. Ubuntu 20.04.3 LTS, Deal.II 9.4.2, 64GB RAM, Intel Xeon Silver 4208 CPU @ 2.10GHz x 40 cores: The code runs very slow on this system. 4. Ubuntu 22.04.3 LTS, Deal.II 9.5.1, 32GB RAM, Intel Xeon Silver 4208 CPU @ 2.10GHz x 16 cores: The code runs very slow on this system. I am seeking assistance to understand why there is such a significant difference in code execution speed across these configurations." Thank you. regards -- 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/d657d4ed-a443-4282-9993-93e580977f99n%40googlegroups.com.
Re: [deal.II] i am trying to get Tau(kirchoff stress) in the cook memebrane problem in the output_results() but getting error
degree);
std::ostringstream filename;
filename << "solution-" << time.get_timestep() << ".vtk";
std::ofstream output(filename.str().c_str());
data_out.write_vtk(output);
}
..
...
*error i am getting*
make all
Consolidate compiler generated dependencies of target cook_membrane
[ 50%] Building CXX object CMakeFiles/cook_membrane.dir/cook_membrane.cc.o
/home/newton/dealii-candi/deal.II-v9.4.2/examples/cook_membrane/cook_membrane.cc:
In instantiation of ‘void Cook_Membrane::Solid::output_results() const [with int dim = 3; NumberType =
Sacado::Fad::Exp::GeneralFad >]’:
/home/newton/dealii-candi/deal.II-v9.4.2/examples/cook_membrane/cook_membrane.cc:1006:5:
required from ‘void Cook_Membrane::Solid::run() [with int
dim = 3; NumberType =
Sacado::Fad::Exp::GeneralFad >]’
/home/newton/dealii-candi/deal.II-v9.4.2/examples/cook_membrane/cook_membrane.cc:2421:23:
required from here
/home/newton/dealii-candi/deal.II-v9.4.2/examples/cook_membrane/cook_membrane.cc:2288:62:
error: cannot convert ‘std::vector > >, std::allocator > > > >’ to ‘std::vector,
std::allocator > >&’
2288 | scratch.solution_grads_u_total);
| ^~
| |
| std::vector > >, std::allocator > > > >
In file included from /home/newton/dealii-candi/deal.II-v9.4.2/include/deal.
II/grid/grid_tools.h:33,
from /home/newton/dealii-candi/deal.II
-v9.4.2/examples/cook_membrane/cook_membrane.cc:40:
/home/newton/dealii-candi/deal.II-v9.4.2/include/deal.II/fe/fe_values.h:1180:10:
note: initializing argument 2 of ‘void dealii::FEValuesViews::Vector::get_function_gradients(const InputVector&, std::vector >::type>&) const [with InputVector = dealii::BlockVector;
int dim = 3; int spacedim = 3; typename dealii::ProductType >::type =
dealii::Tensor<2,
3, double>; typename InputVector::value_type = double]’
1179 | std::vector>
| ~
1180 | ) const;
| ~^
/home/newton/dealii-candi/deal.II-v9.4.2/examples/cook_membrane/cook_membrane.cc:2307:44:
error: cannot convert ‘dealii::internal::SymmetricTensorAccessors::Accessor<2,
3, true, 1,
Sacado::Fad::Exp::GeneralFad > >::reference’ {aka
‘Sacado::Fad::Exp::GeneralFad >’} to ‘double’ in assignment
2307 | local_history_values_at_qpoints[i][j](q) = tau[i][j]; // tau_locally
stored
| ~^
/home/newton/dealii-candi/deal.II-v9.4.2/examples/cook_membrane/cook_membrane.cc:
In instantiation of ‘void Cook_Membrane::Solid::output_results() const [with int dim = 3; NumberType =
Sacado::Rad::ADvar > >]’:
/home/newton/dealii-candi/deal.II-v9.4.2/examples/cook_membrane/cook_membrane.cc:1006:5:
required from ‘void Cook_Membrane::Solid::run() [with int
dim = 3; NumberType =
Sacado::Rad::ADvar > >]’
/home/newton/dealii-candi/deal.II-v9.4.2/examples/cook_membrane/cook_membrane.cc:2434:23:
required from here
/home/newton/dealii-candi/deal.II-v9.4.2/examples/cook_membrane/cook_membrane.cc:2288:62:
error: cannot convert ‘std::vector > > >, std::allocator > > > > >’ to ‘std::vector,
std::allocator > >&’
2288 | scratch.solution_grads_u_total);
| ^~
| |
| std::vector > > >, std::allocator > > > > >
In file included from /home/newton/dealii-candi/deal.II-v9.4.2/include/deal.
II/grid/grid_tools.h:33,
from /home/newton/dealii-candi/deal.II
-v9.4.2/examples/cook_membrane/cook_membrane.cc:40:
/home/newton/dealii-candi/deal.II-v9.4.2/include/deal.II/fe/fe_values.h:1180:10:
note: initializing argument 2 of ‘void dealii::FEValuesViews::Vector::get_function_gradients(const InputVector&, std::vector >::type>&) const [with InputVector = dealii::BlockVector;
int dim = 3; int spacedim = 3; typename dealii::ProductType >::type =
dealii::Tensor<2,
3, double>; typename InputVector::value_type = double]’
1179 | std::vector>
| ~
1180 | ) const;
| ~^
/home/newton/dealii-candi/deal.II-v9.4.2/examples/cook_membrane/cook_membrane.cc:2307:44:
error: cannot convert ‘dealii::internal::SymmetricTensorAccessors::Accessor<2,
3, true, 1,
Sacado::Rad::ADvar > > >::reference’ {aka
‘Sacado::Rad::ADvar > >’} to ‘double’ in assignment
2307 | local_history_values_at_qpoints[i][j](q) = tau[i][j]; // tau_locally
stored
| ~~~~~^
make[2]: *** [CMakeFiles/cook_membrane.dir/build.make:76:
CMakeFiles/cook_membrane.dir/cook_membrane.cc.o] Error 1
make[1]: *** [CMakeFiles/Makefile2:90: CMakeFiles/cook_membrane.dir/all]
Error 2
make: *** [Makefile:91: all] Error 2
"make all" terminated with exit code 2. Build might be incomplete.
--
On Tue, Jun 20, 2023 at 9:43 AM Wolfgang Bangerth
[deal.II] i am trying to get Tau(kirchoff stress) in the cook memebrane problem in the output_results() but getting error
template
void Solid::output_results() const
{
DataOut data_out;
data_out.attach_dof_handler(dof_handler_ref);
std::vector solution_names;
solution_names.emplace_back("u_x");
solution_names.emplace_back("u_y");
solution_names.emplace_back("u_z");
data_out.add_data_vector(solution_n, solution_names);
next part calculates Kirchhoff stress using scratch and pertaskdata
FE_DGQ history_fe (1);
DoFHandler history_dof_handler (triangulation);
history_dof_handler.distribute_dofs (history_fe);
std::vector< std::vector< Vector > >
history_field (dim, std::vector< Vector >(dim)),
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 qpoint_to_dof_matrix (history_fe.dofs_per_cell,
qf_cell.size());
FETools::compute_projection_from_quadrature_points_matrix
(history_fe,
qf_cell, qf_cell,
qpoint_to_dof_matrix);
typename DoFHandler::active_cell_iterator cell = dof_handler_ref.
begin_active(),
endc = dof_handler_ref.end(),
dg_cell = history_dof_handler.begin_active();
for (; cell!=endc; ++cell, ++dg_cell)
{
/// added to define scratch and pertaskdata
//
const UpdateFlags uf_cell(update_gradients |
update_JxW_values);
const UpdateFlags uf_face(update_values |
update_JxW_values);
typename Assembler_Base::PerTaskData_ASM data(this);
typename Assembler_Base::ScratchData_ASM scratch(fe, qf_cell,
uf_cell, qf_face, uf_face, solution_n);
const FEValuesExtractors::Vector _fe = data.solid->u_fe;
data.reset();
scratch.reset();
scratch.fe_values_ref.reinit(cell);
cell->get_dof_indices(data.local_dof_indices);
const std::vector > >
lqph =
const_cast *>(data.solid)->
quadrature_point_history.get_data(cell);
Assert(lqph.size() == n_q_points, ExcInternalError());
scratch.fe_values_ref[u_fe].get_function_gradients(scratch.solution_total,
scratch.solution_grads_u_total);
///
for (unsigned int i=0; i _u = scratch.solution_grads_u_total[q];
const Tensor<2,dim,NumberType> F = Physics::Elasticity::Kinematics::F
(grad_u);
const NumberType det_F = determinant(F);
const Tensor<2,dim,NumberType> F_bar = Physics::Elasticity::Kinematics::
F_iso(F);
const SymmetricTensor<2,dim,NumberType> b_bar =
Physics::Elasticity::Kinematics::b(F_bar);
const SymmetricTensor<2,dim,NumberType> tau = lqph[q]->get_tau(det_F,b_bar);
//
local_history_values_at_qpoints[i][j](q) = tau[i][j]; // tau_locally stored
}
qpoint_to_dof_matrix.vmult (local_history_fe_values[i][j],
local_history_values_at_qpoints[i][j]); // q_point to node extrapolation
dg_cell->set_dof_values (local_history_fe_values[i][j],
history_field[i][j]); // local to global dof transfer
}
}
data_out.add_data_vector(history_dof_handler,history_field[0][0],
"Kirchhoff_st_xx");
data_out.add_data_vector(history_dof_handler,history_field[1][1],
"Kirchhoff_st_yy");
data_out.add_data_vector(history_dof_handler,history_field[2][2],
"Kirchhoff_st_zz");
data_out.add_data_vector(history_dof_handler,history_field[0][1],
"Kirchhoff_st_xy");
data_out.add_data_vector(history_dof_handler,history_field[0][2],
"Kirchhoff_st_xz");
data_out.add_data_vector(history_dof_handler,history_field[1][2],
"Kirchhoff_st_yz");
// Since we are dealing with a large deformation problem, it would be nice
// to display the result on a displaced grid! The MappingQEulerian class
// linked with the DataOut class provides an interface through which this
// can be achieved without physically moving the grid points in the
// Triangulation object ourselves. We first need to copy the solution to
// a temporary vector and then create the Eulerian mapping. We also
// specify the polynomial degree to the DataOut object in order to produce
// a more refined output data set when higher order polynomials are used.
Vector soln(solution_n.size());
for (unsigned int i = 0; i < soln.size(); ++i)
soln(i) = solution_n(i);
MappingQEulerian q_mapping(degree, dof_handler_ref, soln);
data_out.build_patches(q_mapping, degree);
std::ostringstream filename;
filename << "solution-" << time.get_timestep() << ".vtk";
std::ofstream output(filename.str().c_str());
data_out.write_vtk(output);
}
..
*error i am getting*
make all
Consolidate compiler generated dependencies of target cook_membrane
[ 50%] Building CXX object CMakeFiles/cook_membrane.dir/cook_membrane.cc.o
/home/newton/dealii-candi/deal.II-v9.4.2/examples/cook_membrane/cook_membrane.cc:
In instantiation of ‘void Cook_Membrane::Solid::output_results() const [with int dim = 3; NumberType =
Sacado::Fad::Exp::GeneralFad >]’:
/home/newton/dealii-candi/deal.II-v9.4.2/examples/cook_membrane/cook_membrane.cc:1006:5:
required from ‘void
Re: [deal.II] Re: trying to install dealii 9.1.1 using candi.
Dear Bruno, i tried adding as suggested by you and tried to change the boost version also but getting the same error. Thank you. On Wednesday, March 8, 2023 at 7:06:24 PM UTC+5:30 bruno.t...@gmail.com wrote: > Do you need to use Boost in your own project? If you don't, try adding > -DDEAL_II_FORCE_BUNDLED_BOOST=ON to your configuration. > > Best, > > Bruno > > Le mer. 8 mars 2023 à 00:02, ME20D503 NEWTON a > écrit : > >> Dear Bruno, >> i am using ubuntu 22.04.1 and g++ (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0. >> >> Thank you. >> >> >> On Wednesday, March 8, 2023 at 3:18:47 AM UTC+5:30 bruno.t...@gmail.com >> wrote: >> >>> Hello, >>> >>> It looks like the error is from boost. Which version are you using? >>> What's your compiler? >>> >>> Best, >>> >>> Bruno >>> >>> On Tuesday, March 7, 2023 at 12:58:10 AM UTC-5 me20...@iittp.ac.in >>> wrote: >>> >>>> Dear Sir/Ma'am, >>>> trying to install dealii-9.1.1 version using candi command. i just >>>> change the version in candi.cfg from 9.4.2 to 9.1.1 as suggested.then uses >>>> candi commands to install. But i am getting error. >>>> please help me out. >>>> >>>> Thank you. >>>> >>>> usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx/intracomm.h:101:22: >>>> >>>> warning: ‘virtual MPI::Intracomm& MPI::Intracomm::Clone() const’ can be >>>> marked override [-Wsuggest-override] >>>> 101 | virtual Intracomm& Clone() const; >>>> | ^ >>>> In file included from /usr/lib/x86_64-linux-gnu/ >>>> openmpi/include/openmpi/ompi/mpi/cxx/mpicxx.h:227, >>>> from /usr/lib/x86_64-linux-gnu/ >>>> openmpi/include/mpi.h:2887, >>>> from /home/newton/dealii-candi/tmp/ >>>> build/deal.II-v9.1.1/include/deal.II/base/config.h:439, >>>> from /home/newton/dealii-candi/tmp/ >>>> unpack/deal.II-v9.1.1/include/deal.II/base/tensor.h:19, >>>> from /home/newton/dealii-candi/tmp/ >>>> unpack/deal.II-v9.1.1/include/deal.II/base/derivative_form.h:19, >>>> from /home/newton/dealii-candi/tmp/ >>>> unpack/deal.II-v9.1.1/include/deal.II/numerics/vector_tools. >>>> templates.h:20, >>>> from /home/newton/dealii-candi/tmp/ >>>> unpack/deal.II-v9.1.1/source/numerics/vector_tools_boundary.cc:17: >>>> /usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx/topology.h:65:21: >>>> >>>> warning: ‘virtual MPI::Cartcomm& MPI::Cartcomm::Clone() const’ can be >>>> marked override [-Wsuggest-override] >>>>65 | virtual Cartcomm& Clone() const; >>>> | ^ >>>> /usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx/topology.h:143:22: >>>> >>>> warning: ‘virtual MPI::Graphcomm& MPI::Graphcomm::Clone() const’ can be >>>> marked override [-Wsuggest-override] >>>> 143 | virtual Graphcomm& Clone() const; >>>> | ^ >>>> In file included from /usr/lib/x86_64-linux-gnu/ >>>> openmpi/include/openmpi/ompi/mpi/cxx/mpicxx.h:228, >>>> from /usr/lib/x86_64-linux-gnu/ >>>> openmpi/include/mpi.h:2887, >>>> from /home/newton/dealii-candi/tmp/ >>>> build/deal.II-v9.1.1/include/deal.II/base/config.h:439, >>>> from /home/newton/dealii-candi/tmp/ >>>> unpack/deal.II-v9.1.1/include/deal.II/base/tensor.h:19, >>>> from /home/newton/dealii-candi/tmp/ >>>> unpack/deal.II-v9.1.1/include/deal.II/base/derivative_form.h:19, >>>> from /home/newton/dealii-candi/tmp/ >>>> unpack/deal.II-v9.1.1/include/deal.II/numerics/vector_tools. >>>> templates.h:20, >>>> from /home/newton/dealii-candi/tmp/ >>>> unpack/deal.II-v9.1.1/source/numerics/vector_tools_boundary.cc:17: >>>> /usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx/intercomm.h:75:22: >>>> >>>> warning: ‘virtual MPI::Intercomm& MPI::Intercomm::Clone() const’ can be >>>> marked override [-Wsuggest-override] >>>>75 | virtual Intercomm& Clone() const; >>>> | ^
[deal.II] Re: trying to install dealii 9.1.1 using candi.
Dear Bruno, i am using ubuntu 22.04.1 and g++ (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0. Thank you. On Wednesday, March 8, 2023 at 3:18:47 AM UTC+5:30 bruno.t...@gmail.com wrote: > Hello, > > It looks like the error is from boost. Which version are you using? What's > your compiler? > > Best, > > Bruno > > On Tuesday, March 7, 2023 at 12:58:10 AM UTC-5 me20...@iittp.ac.in wrote: > >> Dear Sir/Ma'am, >> trying to install dealii-9.1.1 version using candi command. i just change >> the version in candi.cfg from 9.4.2 to 9.1.1 as suggested.then uses candi >> commands to install. But i am getting error. >> please help me out. >> >> Thank you. >> >> usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx/intracomm.h:101:22: >> >> warning: ‘virtual MPI::Intracomm& MPI::Intracomm::Clone() const’ can be >> marked override [-Wsuggest-override] >> 101 | virtual Intracomm& Clone() const; >> | ^ >> In file included from /usr/lib/x86_64-linux-gnu/ >> openmpi/include/openmpi/ompi/mpi/cxx/mpicxx.h:227, >> from /usr/lib/x86_64-linux-gnu/ >> openmpi/include/mpi.h:2887, >> from /home/newton/dealii-candi/tmp/ >> build/deal.II-v9.1.1/include/deal.II/base/config.h:439, >> from /home/newton/dealii-candi/tmp/ >> unpack/deal.II-v9.1.1/include/deal.II/base/tensor.h:19, >> from /home/newton/dealii-candi/tmp/ >> unpack/deal.II-v9.1.1/include/deal.II/base/derivative_form.h:19, >> from /home/newton/dealii-candi/tmp/ >> unpack/deal.II-v9.1.1/include/deal.II/numerics/vector_tools. >> templates.h:20, >> from /home/newton/dealii-candi/tmp/ >> unpack/deal.II-v9.1.1/source/numerics/vector_tools_boundary.cc:17: >> /usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx/topology.h:65:21: >> >> warning: ‘virtual MPI::Cartcomm& MPI::Cartcomm::Clone() const’ can be >> marked override [-Wsuggest-override] >>65 | virtual Cartcomm& Clone() const; >> | ^ >> /usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx/topology.h:143:22: >> >> warning: ‘virtual MPI::Graphcomm& MPI::Graphcomm::Clone() const’ can be >> marked override [-Wsuggest-override] >> 143 | virtual Graphcomm& Clone() const; >> | ^ >> In file included from /usr/lib/x86_64-linux-gnu/ >> openmpi/include/openmpi/ompi/mpi/cxx/mpicxx.h:228, >> from /usr/lib/x86_64-linux-gnu/ >> openmpi/include/mpi.h:2887, >> from /home/newton/dealii-candi/tmp/ >> build/deal.II-v9.1.1/include/deal.II/base/config.h:439, >> from /home/newton/dealii-candi/tmp/ >> unpack/deal.II-v9.1.1/include/deal.II/base/tensor.h:19, >> from /home/newton/dealii-candi/tmp/ >> unpack/deal.II-v9.1.1/include/deal.II/base/derivative_form.h:19, >> from /home/newton/dealii-candi/tmp/ >> unpack/deal.II-v9.1.1/include/deal.II/numerics/vector_tools. >> templates.h:20, >> from /home/newton/dealii-candi/tmp/ >> unpack/deal.II-v9.1.1/source/numerics/vector_tools_boundary.cc:17: >> /usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx/intercomm.h:75:22: >> >> warning: ‘virtual MPI::Intercomm& MPI::Intercomm::Clone() const’ can be >> marked override [-Wsuggest-override] >>75 | virtual Intercomm& Clone() const; >> | ^ >> In file included from /usr/lib/x86_64-linux-gnu/ >> openmpi/include/openmpi/ompi/mpi/cxx/mpicxx.h:277, >> from /usr/lib/x86_64-linux-gnu/ >> openmpi/include/mpi.h:2887, >> from /home/newton/dealii-candi/tmp/ >> build/deal.II-v9.1.1/include/deal.II/base/config.h:439, >> from /home/newton/dealii-candi/tmp/ >> unpack/deal.II-v9.1.1/include/deal.II/base/tensor.h:19, >> from /home/newton/dealii-candi/tmp/ >> unpack/deal.II-v9.1.1/include/deal.II/base/derivative_form.h:19, >> from /home/newton/dealii-candi/tmp/ >> unpack/deal.II-v9.1.1/include/deal.II/numerics/vector_tools. >> templates.h:20, >> from /home/newton/dealii-candi/tmp/ >> unpack/deal.II-v9.1.1/source/numerics/vector_tools_boundary.cc:17: >> /usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx/op_inln.h: >> In member function ‘virtual void MPI::Op::Init(void (*)(const void*, void*, >> int, const MPI::Datatype&), bool)’: >> /usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx/op_inln.h:121:25: >> >> warning: cast between incompatible function types from ‘void (*)(void*, >> void*, int*, ompi_datatype_t**, void (*)(void*, void*, int*, >> ompi_datatype_t**))’ to ‘void (*)(void*, void*, int*, ompi_datatype_t**)’ >> [-Wcast-function-type] >> 121 | (void)MPI_Op_create((MPI_User_function*) >> ompi_mpi_cxx_op_intercept, >> | ^~ >> >>
[deal.II] trying to install dealii 9.1.1 using candi.
Dear Sir/Ma'am, trying to install dealii-9.1.1 version using candi command. i just change the version in candi.cfg from 9.4.2 to 9.1.1 as suggested.then uses candi commands to install. But i am getting error. please help me out. Thank you. usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx/intracomm.h:101:22: warning: ‘virtual MPI::Intracomm& MPI::Intracomm::Clone() const’ can be marked override [-Wsuggest-override] 101 | virtual Intracomm& Clone() const; | ^ In file included from /usr/lib/x86_64-linux-gnu/ openmpi/include/openmpi/ompi/mpi/cxx/mpicxx.h:227, from /usr/lib/x86_64-linux-gnu/openmpi/include/mpi.h:2887, from /home/newton/dealii-candi/tmp/ build/deal.II-v9.1.1/include/deal.II/base/config.h:439, from /home/newton/dealii-candi/tmp/ unpack/deal.II-v9.1.1/include/deal.II/base/tensor.h:19, from /home/newton/dealii-candi/tmp/ unpack/deal.II-v9.1.1/include/deal.II/base/derivative_form.h:19, from /home/newton/dealii-candi/tmp/ unpack/deal.II-v9.1.1/include/deal.II/numerics/vector_tools.templates.h:20, from /home/newton/dealii-candi/tmp/ unpack/deal.II-v9.1.1/source/numerics/vector_tools_boundary.cc:17: /usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx/topology.h:65:21: warning: ‘virtual MPI::Cartcomm& MPI::Cartcomm::Clone() const’ can be marked override [-Wsuggest-override] 65 | virtual Cartcomm& Clone() const; | ^ /usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx/topology.h:143:22: warning: ‘virtual MPI::Graphcomm& MPI::Graphcomm::Clone() const’ can be marked override [-Wsuggest-override] 143 | virtual Graphcomm& Clone() const; | ^ In file included from /usr/lib/x86_64-linux-gnu/ openmpi/include/openmpi/ompi/mpi/cxx/mpicxx.h:228, from /usr/lib/x86_64-linux-gnu/openmpi/include/mpi.h:2887, from /home/newton/dealii-candi/tmp/ build/deal.II-v9.1.1/include/deal.II/base/config.h:439, from /home/newton/dealii-candi/tmp/ unpack/deal.II-v9.1.1/include/deal.II/base/tensor.h:19, from /home/newton/dealii-candi/tmp/ unpack/deal.II-v9.1.1/include/deal.II/base/derivative_form.h:19, from /home/newton/dealii-candi/tmp/ unpack/deal.II-v9.1.1/include/deal.II/numerics/vector_tools.templates.h:20, from /home/newton/dealii-candi/tmp/ unpack/deal.II-v9.1.1/source/numerics/vector_tools_boundary.cc:17: /usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx/intercomm.h:75:22: warning: ‘virtual MPI::Intercomm& MPI::Intercomm::Clone() const’ can be marked override [-Wsuggest-override] 75 | virtual Intercomm& Clone() const; | ^ In file included from /usr/lib/x86_64-linux-gnu/ openmpi/include/openmpi/ompi/mpi/cxx/mpicxx.h:277, from /usr/lib/x86_64-linux-gnu/openmpi/include/mpi.h:2887, from /home/newton/dealii-candi/tmp/ build/deal.II-v9.1.1/include/deal.II/base/config.h:439, from /home/newton/dealii-candi/tmp/ unpack/deal.II-v9.1.1/include/deal.II/base/tensor.h:19, from /home/newton/dealii-candi/tmp/ unpack/deal.II-v9.1.1/include/deal.II/base/derivative_form.h:19, from /home/newton/dealii-candi/tmp/ unpack/deal.II-v9.1.1/include/deal.II/numerics/vector_tools.templates.h:20, from /home/newton/dealii-candi/tmp/ unpack/deal.II-v9.1.1/source/numerics/vector_tools_boundary.cc:17: /usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx/op_inln.h: In member function ‘virtual void MPI::Op::Init(void (*)(const void*, void*, int, const MPI::Datatype&), bool)’: /usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx/op_inln.h:121:25: warning: cast between incompatible function types from ‘void (*)(void*, void*, int*, ompi_datatype_t**, void (*)(void*, void*, int*, ompi_datatype_t**))’ to ‘void (*)(void*, void*, int*, ompi_datatype_t**)’ [-Wcast-function-type] 121 | (void)MPI_Op_create((MPI_User_function*) ompi_mpi_cxx_op_intercept, | ^~ /usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx/op_inln.h:123:38: warning: cast between incompatible function types from ‘void (*)(const void*, void*, int, const MPI::Datatype&)’ to ‘void (*)(void*, void*, int*, ompi_datatype_t**)’ [-Wcast-function-type] 123 | ompi_op_set_cxx_callback(mpi_op, (MPI_User_function*) func); | ^ In file included from /usr/include/boost/smart_ptr/ detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/ detail/spinlock_gcc_atomic.hpp:14, from
[deal.II] error while running code dependent on step-44
Dear all, i am getting error while running a code based on step-44. i am not able to understand the error output, can anyone please help me out ? thanks in advance. Exception on processing: An error occurred in line <953> of file in function void dealii::Vector::block_read(std::istream&) [with Number = double; std::istream = std::basic_istream] The violated condition was: in Additional information: An input/output error has occurred. There are a number of reasons why this may be happening, both for reading and writing operations. If this happens during an operation that tries to read data: First, you may be trying to read from a file that doesn't exist or that is not readable given its file permissions. Second, deal.II uses this error at times if it tries to read information from a file but where the information in the file does not correspond to the expected format. An example would be a truncated file, or a mesh file that contains not only sections that describe the vertices and cells, but also sections for additional data that deal.II does not understand. If this happens during an operation that tries to write data: you may be trying to write to a file to which file or directory permissions do not allow you to write. A typical example is where you specify an output file in a directory that does not exist. -- 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/8ae95a1a-0330-44f7-a7cc-d485e90fe732n%40googlegroups.com.
Re: [deal.II] Re: Trouble getting UMFPACK to work
figure/configure_2_metis.cmake
-- METIS_LIBRARY not found! Call:
-- FIND_LIBRARY(METIS_LIBRARY NAMES metis HINTS PATH_SUFFIXES lib lib64
lib build/Linux-x86_64/libmetis)
-- METIS_INCLUDE_DIR not found! Call:
-- FIND_PATH(METIS_INCLUDE_DIR metis.h HINTS PATH_SUFFIXES metis
include/metis include)
-- METIS_LIBRARIES: *** Required variable "METIS_LIBRARY" set to NOTFOUND
***
-- METIS_INCLUDE_DIRS: *** Required variable "METIS_INCLUDE_DIR" set to
NOTFOUND ***
-- METIS_USER_INCLUDE_DIRS: *** Required variable "METIS_INCLUDE_DIR" set
to NOTFOUND ***
-- Could NOT find METIS
-- DEAL_II_WITH_METIS has unmet external dependencies.
--
-- Include
/home/newton/fem/dealii-9.2.0/cmake/configure/configure_2_trilinos.cmake
-- EPETRA_CONFIG_H not found! Call:
-- FIND_FILE(EPETRA_CONFIG_H Epetra_config.h HINTS NO_DEFAULT_PATH
NO_CMAKE_ENVIRONMENT_PATH NO_CMAKE_PATH NO_SYSTEM_ENVIRONMENT_PATH
NO_CMAKE_SYSTEM_PATH NO_CMAKE_FIND_ROOT_PATH)
-- TRILINOS_LIBRARIES:
-- TRILINOS_INCLUDE_DIRS: *** Required variable "Trilinos_INCLUDE_DIRS"
empty ***
-- TRILINOS_USER_INCLUDE_DIRS: *** Required variable
"Trilinos_INCLUDE_DIRS" empty ***
-- TRILINOS_LINKER_FLAGS:
-- Could NOT find TRILINOS
-- DEAL_II_WITH_TRILINOS has unmet external dependencies.
--
-- Include
/home/newton/fem/dealii-9.2.0/cmake/configure/configure_2_umfpack.cmake
CMake Error at cmake/macros/macro_configure_feature.cmake:196 (MESSAGE):
DEAL_II_WITH_UMFPACK has unmet configuration requirements:
DEAL_II_WITH_LAPACK has to be set to "ON".
Call Stack (most recent call first):
cmake/configure/configure_2_umfpack.cmake:46 (CONFIGURE_FEATURE)
cmake/macros/macro_verbose_include.cmake:19 (INCLUDE)
CMakeLists.txt:124 (VERBOSE_INCLUDE)
-- Configuring incomplete, errors occurred!
See also "/home/newton/fem/dealii-9.2.0/CMakeFiles/CMakeOutput.log".
See also "/home/newton/fem/dealii-9.2.0/CMakeFiles/CMakeError.log".
On Tuesday, July 5, 2022 at 9:35:36 PM UTC+5:30 d.arnd...@gmail.com wrote:
> What does the log for running
> cmake -DDEAL_II_WITH_UMFPACK=ON .
> look like? The summary printed at the end should tell you if `UMFPACK`
> really was found. N=Any problems in finding a compatible library should be
> contained in the output printed when running the CMake command.
>
> Best,
> Daniel
>
> On Mon, Jul 4, 2022 at 12:25 PM ME20D503 NEWTON
> wrote:
>
>> Hello everyone,
>> which command i have to use to check whether UMFPACK is enabled or not??
>> if it is OFF how to turn it ON??
>>
>> Thank you in advance.
>>
>> On Thursday, August 31, 2017 at 9:28:52 PM UTC+5:30 John wrote:
>>
>>> Hello everyone,
>>>
>>> I am currently using Deal II version 8.0.0. When I try to run a project
>>> I am getting the following:
>>>
>>>
>>> Exception on processing:
>>>
>>>
>>> An error occurred in line <379> of file
>>>
>>> in function
>>> void dealii::SparseDirectUMFPACK::factorize(const Matrix&) [with
>>> Matrix = dealii::SparseMatrix]
>>> The violated condition was:
>>> false
>>> The name and call sequence of the exception was:
>>> ExcMessage("To call this function you need UMFPACK, but configured
>>> deal.II without passing the necessary switch to 'cmake'. Please consult the
>>> installation instructions in doc/readme.html.")
>>> Additional Information:
>>> To call this function you need UMFPACK, but configured deal.II without
>>> passing the necessary switch to 'cmake'. Please consult the installation
>>> instructions in doc/readme.html.
>>>
>>> Stacktrace:
>>> ---
>>> #0 /Downloads/deal.II/lib/libdeal_II.so.8.0.0: void
>>> dealii::SparseDirectUMFPACK::factorize
>>> >(dealii::SparseMatrix const&)
>>> #1 step-3: TmsProblem::solve()
>>> #2 step-3: TmsProblem::run()
>>> #3 step-3: main
>>>
>>>
>>> Aborting!
>>>
>>> CMake Error at CMakeFiles/run_target.cmake:6 (MESSAGE):
>>>
>>>
>>> Program terminated with exit code: 1
>>>
>>>
>>> CMakeFiles/run.dir/build.make:57: recipe for target 'CMakeFiles/run'
>>> failed
>>> make[3]: *** [CMakeFiles/run] Error 1
>>> CMakeFiles/Makefile2:264: recipe for target 'CMakeFiles/run.dir/all'
>>> failed
>>> make[2]: *** [CMakeF
Re: [deal.II] UMFPACK ISSUE.
Dear Luca, can help me out, what this error is trying to tell me? To call this function you need UMFPACK, but you configured deal.II without passing the necessary switch to 'cmake'. Please consult the installation instructions in doc/readme.html. On Tuesday, July 5, 2022 at 12:41:03 PM UTC+5:30 luca@gmail.com wrote: > This part of the message contains all the information you need to fix the > issue. > > Luca > > > Il giorno 5 lug 2022, alle ore 06:46, ME20D503 NEWTON < > me20...@iittp.ac.in> ha scritto: > > > > Additional information: > > To call this function you need UMFPACK, but you configured deal.II > > without passing the necessary switch to 'cmake'. Please consult the > > installation instructions in doc/readme.html. > -- 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/3f7a8855-f572-4145-8454-0a8dc97bb532n%40googlegroups.com.
[deal.II] UMFPACK ISSUE.
Dear Deal.ii group, i am trying to run a code but i am getting errors related to UMFPACK. please find the error below. Thanks . Exception on processing: An error occurred in line <635> of file in function void dealii::SparseDirectUMFPACK::factorize(const Matrix&) [with Matrix = dealii::SparseMatrix] The violated condition was: false Additional information: To call this function you need UMFPACK, but you configured deal.II without passing the necessary switch to 'cmake'. Please consult the installation instructions in doc/readme.html. Aborting! CMakeFiles/run.dir/build.make:57: recipe for target 'CMakeFiles/run' failed make[3]: *** [CMakeFiles/run] Error 1 CMakeFiles/Makefile2:131: recipe for target 'CMakeFiles/run.dir/all' failed make[2]: *** [CMakeFiles/run.dir/all] Error 2 CMakeFiles/Makefile2:138: recipe for target 'CMakeFiles/run.dir/rule' failed make[1]: *** [CMakeFiles/run.dir/rule] Error 2 Makefile:144: recipe for target 'run' failed make: *** [run] Error 2 -- 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/d1f55d5d-c73e-4685-b839-a31880a6051cn%40googlegroups.com.
[deal.II] Re: Trouble getting UMFPACK to work
Hello everyone,
which command i have to use to check whether UMFPACK is enabled or not?? if
it is OFF how to turn it ON??
Thank you in advance.
On Thursday, August 31, 2017 at 9:28:52 PM UTC+5:30 John wrote:
> Hello everyone,
>
> I am currently using Deal II version 8.0.0. When I try to run a project I
> am getting the following:
>
>
> Exception on processing:
>
>
> An error occurred in line <379> of file
>
> in function
> void dealii::SparseDirectUMFPACK::factorize(const Matrix&) [with
> Matrix = dealii::SparseMatrix]
> The violated condition was:
> false
> The name and call sequence of the exception was:
> ExcMessage("To call this function you need UMFPACK, but configured
> deal.II without passing the necessary switch to 'cmake'. Please consult the
> installation instructions in doc/readme.html.")
> Additional Information:
> To call this function you need UMFPACK, but configured deal.II without
> passing the necessary switch to 'cmake'. Please consult the installation
> instructions in doc/readme.html.
>
> Stacktrace:
> ---
> #0 /Downloads/deal.II/lib/libdeal_II.so.8.0.0: void
> dealii::SparseDirectUMFPACK::factorize
> >(dealii::SparseMatrix const&)
> #1 step-3: TmsProblem::solve()
> #2 step-3: TmsProblem::run()
> #3 step-3: main
>
>
> Aborting!
>
> CMake Error at CMakeFiles/run_target.cmake:6 (MESSAGE):
>
>
> Program terminated with exit code: 1
>
>
> CMakeFiles/run.dir/build.make:57: recipe for target 'CMakeFiles/run' failed
> make[3]: *** [CMakeFiles/run] Error 1
> CMakeFiles/Makefile2:264: recipe for target 'CMakeFiles/run.dir/all' failed
> make[2]: *** [CMakeFiles/run.dir/all] Error 2
> CMakeFiles/Makefile2:271: recipe for target 'CMakeFiles/run.dir/rule'
> failed
> make[1]: *** [CMakeFiles/run.dir/rule] Error 2
> Makefile:196: recipe for target 'run' failed
> make: *** [run] Error 2
>
>
>
> I have tried "*cmake -DDEAL_II_WITH_UMFPACK=ON*" and "*cmake
> -DDEAL_II_WITH_UMFPACK=ON -DUMFPACK_DIR=/Downloads/deal.II/bundled/umfpack
> .*" and also "*cmake -DDEAL_II_WITH_UMFPACK=ON
> -DUMFPACK_DIR=/Downloads/deal.II/bundled/umfpack/UMFPACK .*" and then
> following each of these with "*make*" and "*make run*". However, all of
> these still end up giving me the same error as above. Can anyone help me
> with getting umfpack to work? Thank you in advance.
>
--
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https://groups.google.com/d/forum/dealii?hl=en
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Re: [deal.II] deal.ii installation problem
Thank you so much professor. I successfully installed the deal. ii in my system. On Sunday, June 12, 2022 at 3:59:11 AM UTC+5:30 Wolfgang Bangerth wrote: > > > i am facing some problem while installing deal.ii. installation has been > > completed upto 100% but in the last i got some error.please find the > attachment. > > The error message actually says everything you need to know: > cannot create directory /usr/local/... Maybe you need administrative > privileges. > > What is happening is that you called cmake without saying where you wanted > deal.II to be installed (which you would do with the > -DCMAKE_INSTALL_PREFIX=... switch). The default for installation is > /usr/local > which is a directory only the 'root' user can write to, but not the iittp > user > you apparently are. > > Unless you are a sysadmin, people generally install deal.II into a > location in > their home directory by specifying -DCMAKE_INSTALL_PREFIX=... when calling > cmake -- see also the installation instructions at > https://dealii.org/developer/readme.html > > Best > W. > > > -- > > Wolfgang Bangerth email: bang...@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/5430d190-b71b-48b2-aa9d-cfd57987344dn%40googlegroups.com.
