- Nektar-users - imperial.ac.uk

I am new and need help
by shahab zeraati 23 Jun '18

23 Jun '18

Hi, I have just started working with Nektar++. Currently, I am trying to get familiar with it by doing the basic tutorials. But there is a major issue. Although I have compiled Nektar++ 4.3.4, and tested it successfully by "ctest" command, when I enter the command "NekMesh" in the terminal, it prints "command not found". I don't know what to do. Can you guys help me with it? Kind regards, Shahab

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Unreproducible results and NaN appears following the incompressible Navier-Stokes tutorial
by Oliver Pola 19 Jun '18

19 Jun '18

Dear Nektar-users, we, a students team at Hamburg University, are trying to follow the "Incompressible Navier-Stokes" tutorial on our HPC cluster. Suggested by the hints we extended the tutorial to the 128^3 case, have MPI plus FFTW enabled and are running via mpirun. See attached "tutorial-setup.txt" for exact setup of the extended tutorial. Intel-Parallel-Studio is used as compiler and provider for MPI and BLAS/LAPACK via MKL. We installed using spack and its recent nektar package (plus enabling MKL). Trying to analyze scaling we failed to get any reproducible results. We had a few runs completing all checkpoints without error so we consider our setup correct. But other identical runs quit most times early or sometimes late giving "NaN found during time integration" error. We successfully run earlier tutorials and the 64^3 version with default conditions on a single process. Going back to Nektar version 4.4.0 or 4.3.5 also throws NaN error. We did not start enough runs in those versions to get a successful one. I found this NaN error mentioned in the mailing list archive, but it was pointed out that this was due to an improper physical setup. This should be fine in the tutorial, right? Could anyone provide some hints how to solve this problem? Can this be considered a bug of Nektar or may there be a hidden problem in our MKL setup? Regards Oliver

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curved elements and BL splitting
by Vishal Saini 15 Jun '18

15 Jun '18

Hi all, This is regarding NekMesh utility. I would like to mesh a pipe which has coarse elements to begin with (inlet cross section shown in figure). In order to make the outer surface smooth I applied "spherigons" which worked fine (see attached). However, when I try to use "boundary layer splitting", NekMesh says: No elements detected to split. The element type on the outer surface are hexahedra. Is it the problem? Can anyone suggest a way out? Cheers, Vishal

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Basis functions for Quasi 3D formulation
by Amitvikram Dutta 15 Jun '18

15 Jun '18

Hi all, I wanted to clear up a certain confusion regarding the quasi-3D approach. As I understand it, a 2D solution is extruded in the third direction using the fourier transform as basis functions. Considering that a default 2D solver uses the Galerkin formulation as basis functions, does the use of a different basis function for the theird direction not cause conflict? I feel I'm missing a critical theoretical intuition here. I would be greatful if someone cast some light on this. Sincerely, -- *Amitvikram Dutta* Graduate Research Assistant Fluid Mechanics Research Lab Multi-Physics Interaction Lab University of Waterloo

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Re: [Nektar-users] Regarding CSV to FLD convertor
by Abhishek Kumar 13 Jun '18

13 Jun '18

Dear Kilian, Thanks a lot... This works :) With regards Abhishek On Wed, Jun 13, 2018 at 9:05 AM, Kilian Lackhove <kilian(a)lackhove.de> wrote: > Hi Abhishek, > > yes, you can use the "interppointdatatofld" module of FieldConvert. The > current version 4.4.1 only reads pts files, which use a similar syntax as > csv > (check out the userguide for a description of the format). The upcoming > version 5.0 (and the current master branch from git) support direct csv > input. > > Cheers, > > Kilian > > Am Montag, 11. Juni 2018, 16:47:26 CEST schrieb Abhishek Kumar: > > Dear friends, > > > > I am trying to modify the output of Nektar++ data. For that, I convert > the > > data to csv and done the process in python. Now, I want to convert the > > csv data to fld to run on Nektar++. > > > > Is there any way to convert csv file to fld file? > > > > > > > > With regards > > Abhishek Kumar > > > > ------------------------------------------------------------ > ---------------- > > ----------- Abhishek Kumar > > Research Associate > > Applied Mathematics Research Centre > > Coventry University, Coventry CV1 5FB > > The United Kingdom > > > > Email # ac7600(a)coventry.ac.uk, abhishek.kir(a)gmail.com > > ------------------------------------------------------------ > ---------------- > > ----------- > > > -- With regards Abhishek Kumar --------------------------------------------------------------------------------------- Abhishek Kumar Research Associate Applied Mathematics Research Centre Coventry University, Coventry CV1 5FB The United Kingdom Email # ac7600(a)coventry.ac.uk, abhishek.kir(a)gmail.com ---------------------------------------------------------------------------------------

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Regarding CSV to FLD convertor
by Abhishek Kumar 11 Jun '18

11 Jun '18

Dear friends, I am trying to modify the output of Nektar++ data. For that, I convert the data to csv and done the process in python. Now, I want to convert the csv data to fld to run on Nektar++. Is there any way to convert csv file to fld file? With regards Abhishek Kumar --------------------------------------------------------------------------------------- Abhishek Kumar Research Associate Applied Mathematics Research Centre Coventry University, Coventry CV1 5FB The United Kingdom Email # ac7600(a)coventry.ac.uk, abhishek.kir(a)gmail.com ---------------------------------------------------------------------------------------

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Failed to build thirdparty PETSc and Arpack
by #SHI ZIJI# 07 Jun '18

07 Jun '18

Dear all, I am trying to build Nektar++4.4.1 with third party PETSc and Arpack. The third party version of PETSc compiles, but it failed all of the tests. I executed the test command and it returned seg fault (seg fault for first 4 tests and exception for the rest). However, if I removed NEKTAR_USE_PETSC and THIRDPARTY_BUILD_PETSC, the tests can be passed. The command I used looks like the following: CC=mpiicc CXX=mpiicpc FC=mpiifort cmake\ -DNEKTAR_USE_MKL=ON \ -DNEKTAR_USE_PETSC=ON \ -DNEKTAR_USE_MPI=ON \ -DTHIRDPARTY_BUILD_PETSC=ON .. The test log is attached in this email. Meanwhile, may I know if Arpack can be supported with third party build? The cmake/ThirdPartyArpack.cmake is more like a FindArpack.cmake script. Many thanks in advance! Best Regards, Ziji

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boundary condintion file for CompressibleFlowSolver in neakar
by Chunhui Liu 06 Jun '18

06 Jun '18

Hi everyone, I am trying to use nektar++ for a simulation of convergence and divergence nozzle. https://www.grc.nasa.gov/www/wind/valid/cdv/cdv01/cdv01.html subsonic inlet and outlet case. From test case, my outlet bc was set as pressure out flow, followed the user guide. However my simulation always diverged. I don't know the reason. Is there anyone familar with boundary condition in nektar for a nozzle simulation? In addition, I noticed that in the source code CompressibleFlowSolver there are quite a lot boundary condition. However I don't know the syntax to write these boundary condition in .xml file. Thanks! <CONDITIONS> <PARAMETERS> TimeStep = 0.00001 NumSteps = 10 FinTime = TimeStep*NumSteps IO_CheckSteps = 1 IO_InfoSteps = 1 GasConstant = 287.058 Gamma = 1.4 pInf = 0.9617 rhoInf =0.000034471 uInf =46.77 vInf = 0.0 </PARAMETERS> <SOLVERINFO> </SOLVERINFO> <BOUNDARYREGIONS> C[2]  C[3]  C[4]  </BOUNDARYREGIONS> <BOUNDARYCONDITIONS> <REGION REF="0">  <D VAR="rho" VALUE="rhoInf" /> <D VAR="rhou" VALUE="rhoInf * uInf" /> <D VAR="rhov" VALUE="rhoInf * vInf" /> <D VAR="E" VALUE="pInf / (Gamma - 1) + 0.5 * rhoInf * (uInf * uInf + vInf * vInf)"/> </REGION> <REGION REF="1">  <D VAR="rho" USERDEFINEDTYPE="PressureOutflow" VALUE="0" /> <D VAR="rhou" USERDEFINEDTYPE="PressureOutflow" VALUE="0" /> <D VAR="rhov" USERDEFINEDTYPE="PressureOutflow" VALUE="0" /> <D VAR="E" USERDEFINEDTYPE="PressureOutflow" VALUE="0" /> </REGION> Chunhui Liu Mechanical and Mechatronics Engineering University of Waterloo

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Re: [Nektar-users] Compile the last version nektar++ shows link errors
by liuwenjie＠hit.edu.cn 06 Jun '18

06 Jun '18

Dear Dave Very thanks for your help! I tried it, but it still shows the same link errors. I guess the errors possible from "cxx11". All the best! Wenjie Liu > -----Original Messages----- > From: "David Moxey" <D.Moxey(a)exeter.ac.uk> > Sent Time: 2018-06-06 18:49:45 (Wednesday) > To: liuwenjie(a)hit.edu.cn > Cc: nektar-users(a)imperial.ac.uk > Subject: Re: [Nektar-users] Compile the last version nektar++ shows link errors > > Hi Wenjie, > > It looks like TinyXML might not have been installed correctly. One option might be for you to use the Debian package (libtinyxml-dev) and see if that is better? > > Cheers, > > Dave > > > On 6 Jun 2018, at 10:37, <liuwenjie(a)hit.edu.cn> <liuwenjie(a)hit.edu.cn> wrote: > > > > Dear all > > I compile the last version nektar++, used g++ 8.0.1 and cmake 3.11.2 in 64 ubuntu. > > I tried some suggestions. It still shows the following link errors. > > Can you given me some advice? Very thanks! > > > > > > Pde2016@ubuntu-1:~/libs/nektar++/build$ cmake -DCMAKE_INSTALL_PREFIX=/home/Pde2016/Bin/nektar-4.5.0 .. > > -- Found TinyXML: /usr/local/lib/libtinyxml.a > > -- Build Scotch: /home/Pde2016/libs/nektar++/build/ThirdParty/dist/lib/libscotch.a > > -- Found Zlib: /usr/lib/x86_64-linux-gnu/libz.so (version 1.2.8) > > -- Searching for Boost: > > -- -- Found Boost thread library: /usr/local/lib/libboost_thread.so > > -- -- Found Boost iostreams library: /usr/local/lib/libboost_iostreams.so > > -- -- Found Boost filesystem library: /usr/local/lib/libboost_filesystem.so > > -- -- Found Boost system library: /usr/local/lib/libboost_system.so > > -- -- Found Boost program_options library: /usr/local/lib/libboost_program_options.so > > -- -- Found Boost regex library: /usr/local/lib/libboost_regex.so > > -- Found BLAS and LAPACK: /usr/lib/liblapack.so;/usr/lib/libblas.so > > -- Configuring done > > -- Generating done > > -- Build files have been written to: /home/Pde2016/libs/nektar++/build > > Pde2016@ubuntu-1:~/libs/nektar++/build$ make > > [ 2%] Built target scotch-6.0.4 > > [ 2%] Built target tinyxml-2.6.2 > > [ 2%] Built target zlib-1.2.7 > > [ 2%] Built target boost > > [ 11%] Built target LibUtilities > > [ 14%] Built target StdRegions > > [ 17%] Built target SpatialDomains > > [ 19%] Built target LocalRegions > > [ 20%] Built target Collections > > [ 26%] Built target MultiRegions > > [ 28%] Built target GlobalMapping > > [ 35%] Built target FieldUtils > > [ 38%] Built target NekMeshUtils > > [ 38%] Linking CXX executable NekMesh > > ../../library/LibUtilities/libLibUtilities.so.4.5.0: undefined reference to `TiXmlDocument::TiXmlDocument(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&)' > > ../../library/LibUtilities/libLibUtilities.so.4.5.0: undefined reference to `operator>>(std::istream&, TiXmlNode&)' > > ../../library/SpatialDomains/libSpatialDomains.so.4.5.0: undefined reference to `TiXmlElement::SetAttribute(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&)' > > ../../library/LibUtilities/libLibUtilities.so.4.5.0: undefined reference to `operator<<(std::ostream&, TiXmlNode const&)' > > ../../library/SpatialDomains/libSpatialDomains.so.4.5.0: undefined reference to `TiXmlElement::TiXmlElement(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&)' > > collect2: error: ld returned 1 exit status > > utilities/NekMesh/CMakeFiles/NekMesh.dir/build.make:583: recipe for target 'utilities/NekMesh/NekMesh' failed > > make[2]: *** [utilities/NekMesh/NekMesh] Error 1 > > CMakeFiles/Makefile2:262: recipe for target 'utilities/NekMesh/CMakeFiles/NekMesh.dir/all' failed > > make[1]: *** [utilities/NekMesh/CMakeFiles/NekMesh.dir/all] Error 2 > > Makefile:140: recipe for target 'all' failed > > make: *** [all] Error 2 > > > > Thanks! All the best! > > > > Wenjie Liu > > Lecturer, > > Department of Mathematics, > > Harbin Institute of Technology > > _______________________________________________ > > Nektar-users mailing list > > Nektar-users(a)imperial.ac.uk > > https://mailman.ic.ac.uk/mailman/listinfo/nektar-users

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Compile the last version nektar++ shows link errors
by liuwenjie＠hit.edu.cn 06 Jun '18

06 Jun '18

Dear all I compile the last version nektar++, used g++ 8.0.1 and cmake 3.11.2 in 64 ubuntu. I tried some suggestions. It still shows the following link errors. Can you given me some advice? Very thanks! Pde2016@ubuntu-1:~/libs/nektar++/build$ cmake -DCMAKE_INSTALL_PREFIX=/home/Pde2016/Bin/nektar-4.5.0 .. -- Found TinyXML: /usr/local/lib/libtinyxml.a -- Build Scotch: /home/Pde2016/libs/nektar++/build/ThirdParty/dist/lib/libscotch.a -- Found Zlib: /usr/lib/x86_64-linux-gnu/libz.so (version 1.2.8) -- Searching for Boost: -- -- Found Boost thread library: /usr/local/lib/libboost_thread.so -- -- Found Boost iostreams library: /usr/local/lib/libboost_iostreams.so -- -- Found Boost filesystem library: /usr/local/lib/libboost_filesystem.so -- -- Found Boost system library: /usr/local/lib/libboost_system.so -- -- Found Boost program_options library: /usr/local/lib/libboost_program_options.so -- -- Found Boost regex library: /usr/local/lib/libboost_regex.so -- Found BLAS and LAPACK: /usr/lib/liblapack.so;/usr/lib/libblas.so -- Configuring done -- Generating done -- Build files have been written to: /home/Pde2016/libs/nektar++/build Pde2016@ubuntu-1:~/libs/nektar++/build$ make [ 2%] Built target scotch-6.0.4 [ 2%] Built target tinyxml-2.6.2 [ 2%] Built target zlib-1.2.7 [ 2%] Built target boost [ 11%] Built target LibUtilities [ 14%] Built target StdRegions [ 17%] Built target SpatialDomains [ 19%] Built target LocalRegions [ 20%] Built target Collections [ 26%] Built target MultiRegions [ 28%] Built target GlobalMapping [ 35%] Built target FieldUtils [ 38%] Built target NekMeshUtils [ 38%] Linking CXX executable NekMesh ../../library/LibUtilities/libLibUtilities.so.4.5.0: undefined reference to `TiXmlDocument::TiXmlDocument(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&)' ../../library/LibUtilities/libLibUtilities.so.4.5.0: undefined reference to `operator>>(std::istream&, TiXmlNode&)' ../../library/SpatialDomains/libSpatialDomains.so.4.5.0: undefined reference to `TiXmlElement::SetAttribute(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&)' ../../library/LibUtilities/libLibUtilities.so.4.5.0: undefined reference to `operator<<(std::ostream&, TiXmlNode const&)' ../../library/SpatialDomains/libSpatialDomains.so.4.5.0: undefined reference to `TiXmlElement::TiXmlElement(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&)' collect2: error: ld returned 1 exit status utilities/NekMesh/CMakeFiles/NekMesh.dir/build.make:583: recipe for target 'utilities/NekMesh/NekMesh' failed make[2]: *** [utilities/NekMesh/NekMesh] Error 1 CMakeFiles/Makefile2:262: recipe for target 'utilities/NekMesh/CMakeFiles/NekMesh.dir/all' failed make[1]: *** [utilities/NekMesh/CMakeFiles/NekMesh.dir/all] Error 2 Makefile:140: recipe for target 'all' failed make: *** [all] Error 2 Thanks! All the best! Wenjie Liu Lecturer, Department of Mathematics, Harbin Institute of Technology

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