- Nektar-users - imperial.ac.uk

check the file
by Moto Light 01 Dec '20

01 Dec '20

******************* This email originates from outside Imperial. Do not click on links and attachments unless you recognise the sender. If you trust the sender, add them to your safe senders list https://spam.ic.ac.uk/SpamConsole/Senders.aspx to disable email stamping for this address. *******************

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Regarding parallelisation of Nektar++
by Abhishek Kumar 24 Nov '20

24 Nov '20

******************* This email originates from outside Imperial. Do not click on links and attachments unless you recognise the sender. If you trust the sender, add them to your safe senders list https://spam.ic.ac.uk/SpamConsole/Senders.aspx to disable email stamping for this address. ******************* Dear friends, I am trying to understand the parallelisation of Nektar++. I have a question on the use of Row and Column communicator. Is both the communicators are used in the 2D mesh? Can I also get some reference of Nektar++ parallelisation strategy? With regards Abhishek -- --------------------------------------------------------------------------------------- Abhishek Kumar Assistant Professor (Research) Centre for Fluid and Complex Systems Coventry University, Coventry CV15FB The United Kingdom Phone: +44 24 7765 9150 Mobile: +44 7464026494 ---------------------------------------------------------------------------------------

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discontinuous results when using ariable polynomial order
by 王昭予 09 Nov '20

09 Nov '20

******************* This email originates from outside Imperial. Do not click on links and attachments unless you recognise the sender. If you trust the sender, add them to your safe senders list https://spam.ic.ac.uk/SpamConsole/Senders.aspx to disable email stamping for this address. ******************* Dear Prof. Sherwin Thanks for your reply. There is a problem is when I use variable polynomial order in the field, the results near the boundary between 2 domains with different polynomial order cant be smoothed by C0projection module. So how can I handle the discontinuous results in this case? Many thanks, Zhaoyu Wang Shanghai Jiao Tong University

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Nektar compile error - development version.
by Debbahi Saad 03 Nov '20

03 Nov '20

******************* This email originates from outside Imperial. Do not click on links and attachments unless you recognise the sender. If you trust the sender, add them to your safe senders list https://spam.ic.ac.uk/SpamConsole/Senders.aspx to disable email stamping for this address. ******************* Dear Nektar users, After a lot of trial and error, this is what I end up with trying to compile the fresh development version of Nektar. Here I reproducing the compile error since I encountered the same error on an hpc cluster rhel6 and Gcc-8.2.0, same thing on my workstation Gcc-8.2.0 running Centos 6.10 64bits. nevertheless, release version 5.0 does compile fine. I've been trying to compile the development version with nektar-error-on-warnings set OFF, with full build for all thirdparty packages, I also had the same error using cxxflags=-std=c++11 trying to limit the compiler features to c++11. Would you please check out the compile error output attached hereafter. Thanks to all of you. Saâd [22%] Building CXX object library/LibUtilities/CMakeFile s/LibUtilities.dir/LinearAlgebra/blas.cpp.o [ 22%] Building CXX object library/LibUtilities/CMakeFile s/LibUtilities.dir/LinearAlgebra/BlockMatrix.cpp.o In file included from /softroot/nektar++/library/Lib Utilities/Communication/CommCwipi.cpp:37: /softroot/nektar++/library/LibUtilities/Communication/CommCwipi.h:73:18: error: virtual function ‘virtual void Nektar::LibUtilities::CommCwipi::v_Finalise()’ overriding final function virtual void v_Finalise(); ^~~~~~~~~~ In file included from /softroot/nektar++/library/Lib Utilities/Communication/CommCwipi.h:41, from /softroot/nektar++/library/Lib Utilities/Communication/CommCwipi.cpp:37: /softroot/nektar++/library/LibUtilities/Communication/CommMpi.h:114:18: note: overridden function is ‘virtual void Nektar::LibUtilities::CommMpi: :v_Finalise()’ virtual void v_Finalise() final; ^~~~~~~~~~ /softroot/nektar++/library/LibUtilities/Communication/CommCwipi.cpp: In constructor ‘Nektar::LibUtilities::CommCwipi::CommCwipi(int, char**)’: /softroot/nektar++/library/LibUtilities/Communication/CommCwipi.cpp:52:55: error: no matching function for call to ‘Nektar::LibUtilities::CommMpi ::CommMpi()’ CommCwipi::CommCwipi(int narg, char *arg[]) : CommMpi() ^ In file included from /softroot/nektar++/library/Lib Utilities/Communication/CommCwipi.h:41, from /softroot/nektar++/library/Lib Utilities/Communication/CommCwipi.cpp:37: /softroot/nektar++/library/LibUtilities/Communication/CommMpi.h:112:14: note: candidate: ‘Nektar::LibUtilities::CommMpi::CommMpi(MPI_Comm)’ explicit CommMpi(MPI_Comm pComm); ^~~~~~~ /softroot/nektar++/library/LibUtilities/Communication/CommMpi.h:112:14: note: candidate expects 1 argument, 0 provided /softroot/nektar++/library/LibUtilities/Communication/CommMpi.h:103:26: note: candidate: ‘Nektar::LibUtilities::CommMpi::CommMpi(int, char**)’ LIB_UTILITIES_EXPORT CommMpi(int narg, char *arg[]); ^~~~~~~ /softroot/nektar++/library/LibUtilities/Communication/CommMpi.h:103:26: note: candidate expects 2 arguments, 0 provided /softroot/nektar++/library/LibUtilities/Communication/CommMpi.h:91:7: note: candidate: ‘Nektar::LibUtilities::CommMpi::CommMpi(const Nektar::LibUtilities::CommMpi&)’ class CommMpi : public Comm ^~~~~~~ /softroot/nektar++/library/LibUtilities/Communication/CommMpi.h:91:7: note: candidate expects 1 argument, 0 provided [ 23%] Building CXX object library/LibUtilities/CMakeFile s/LibUtilities.dir/LinearAlgebra/MatrixBase.cpp.o make[2]: *** [library/LibUtilities/CMakeFiles/LibUtilities.dir/Communication/CommCwipi.cpp.o] Error 1 make[2]: *** Waiting for unfinished jobs.... make[1]: *** [library/LibUtilities/CMakeFiles/LibUtilities.dir/all] Error 2 make: *** [all] Error 2

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how to monitor the heat flux or momentum flux along some boundary region.
by ztdepyahoo 27 Oct '20

27 Oct '20

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Nektar++ install help!
by Octavio Morales 26 Oct '20

26 Oct '20

******************* This email originates from outside Imperial. Do not click on links and attachments unless you recognise the sender. If you trust the sender, add them to your safe senders list https://spam.ic.ac.uk/SpamConsole/Senders.aspx to disable email stamping for this address. ******************* Hi Nektar team, I've been trying to install Nektar++ in my Ubuntu 20.04 LTS but nothing seems to work. If someone have succeeded at installing Nektar++ in this Ubuntu version, could you please tell me what you did so it can work? I installed the C++ compiler, CMake, BLAS/LAPACK and Scotch and nothing. Any help will be extremely appreciated!!

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How to compute the heat flux along a boundary region in nektar
by Professor Ding、 25 Oct '20

25 Oct '20

******************* This email originates from outside Imperial. Do not click on links and attachments unless you recognise the sender. If you trust the sender, add them to your safe senders list https://spam.ic.ac.uk/SpamConsole/Senders.aspx to disable email stamping for this address. ******************* Dear sir: I am using netkar 4.5 for natural convection problem. I want to know how to monitor the heat flux or momentum flux along some boundary region. Regards | | Professor Ding、 | | ztdepyahoo(a)163.com | 签名由网易邮箱大师定制

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Nektar++-5.0.0 installation on Linux
by Fatih Ertinaz 24 Oct '20

24 Oct '20

******************* This email originates from outside Imperial. Do not click on links and attachments unless you recognise the sender. If you trust the sender, add them to your safe senders list https://spam.ic.ac.uk/SpamConsole/Senders.aspx to disable email stamping for this address. ******************* Hello everyone After a couple of unsuccessful attempts, I decided to write here for some help. I've tried to build Nektar++-5.0.0 from its source using two different environments: - On a machine that has Ubuntu-16.04, GCC-9.3.0 and OpenMPI-4.0.4 - On a Docker environment (hosted on the Ubuntu machine) with CentOS-7, GCC-4.8.5 and OpenMPI-4.0.4 I initially tried using Docker because I'm preparing containers for a project I'm developing at the moment. I had some environment related troubles with GCC-7.3.0, so decided to stick with the default GCC which is 4.8. I don't have the logs right now but build failed with something like: > MMFAdvection.cpp:945:35: error: 'dF' may be used uninitialized in this > function [-Werror=maybe-uninitialized I thought this might be due to the old GCC version (which now I think it's not), and decided to complete the installation using the new GCC suite on my laptop which is the system I shared in the first item above. However, these new attempts also have failed. This my build script: > export PATH=/opt/openmpi-4.0.4/bin:$PATH > export LD_LIBRARY_PATH=/opt/openmpi-4.0.4/lib:$LD_LIBRARY_PATH > cmake .. \ # I'm in src/build > -DCMAKE_INSTALL_PREFIX=/opt/nektar++-5.0.0 \ > -DNEKTAR_BUILD_DEMOS=ON \ > -DNEKTAR_BUILD_LIBRARY=ON \ > -DNEKTAR_BUILD_SOLVERS=ON \ > -DNEKTAR_BUILD_UTILITIEs=ON \ > -DNEKTAR_USE_MPI=ON \ > -DNEKTAR_USE_OPENBLAS=ON \ > -DNEKTAR_USE_BOOST=ON \ > -DNEKTAR_USE_SCOTCH=ON \ > -DTHIRDPARTY_BUILD_OPENBLAS=ON \ > -DTHIRDPARTY_BUILD_BOOST=ON \ > -DTHIRDPARTY_BUILD_SCOTCH=ON > > make install This is the shorter script which I've excluded FFTW, HDF5, ARPACK, PETSC and METIS. When HDF5 is enabled, the build fails with: > [ 13%] Building CXX object > library/LibUtilities/CMakeFiles/LibUtilities.dir/BasicUtils/FieldIOHdf5.cpp.o > /home/fertinaz/nektar/nektar++-5.0.0/library/LibUtilities/BasicUtils/FieldIOHdf5.cpp: > In member function ‘virtual void > Nektar::LibUtilities::FieldIOHdf5::v_Import(const string&, > std::vector<std::shared_ptr<Nektar::LibUtilities::FieldDefinitions> >&, > std::vector<std::vector<double> >&, > Nektar::LibUtilities::FieldMetaDataMap&, const Nektar::Array<Nektar::OneD, > int>&)’: > /home/fertinaz/nektar/nektar++-5.0.0/library/LibUtilities/BasicUtils/FieldIOHdf5.cpp:1028:31: > error: implicitly-declared > ‘Nektar::LibUtilities::FieldIOHdf5::OffsetHelper& > Nektar::LibUtilities::FieldIOHdf5::OffsetHelper::operator=(const > Nektar::LibUtilities::FieldIOHdf5::OffsetHelper&)’ is deprecated > [-Werror=deprecated-copy] > 1028 | decompsToOffsets[i] = running; > | ^~~~~~~ So I've disabled HDF5 and a couple of others. Eventually, I want them too, but I wanted to use as little external libs as possible in the first step. Then initiated a new build which failed with the following error: > [ 20%] Building CXX object > library/SpatialDomains/CMakeFiles/SpatialDomains.dir/MeshGraph.cpp.o > /home/fertinaz/nektar/nektar++-5.0.0/library/SpatialDomains/MeshGraph.cpp: > In member function ‘void > Nektar::SpatialDomains::MeshGraph::SetExpansionsToEvenlySpacedPoints(int)’: > /home/fertinaz/nektar/nektar++-5.0.0/library/SpatialDomains/MeshGraph.cpp:1529:54: > error: implicitly-declared ‘Nektar::LibUtilities::BasisKey& > Nektar::LibUtilities::BasisKey::operator=(const > Nektar::LibUtilities::BasisKey&)’ is deprecated [-Werror=deprecated-copy] > 1529 | expIt->second->m_basisKeyVector[i] = bkeynew; Error due to "bkeynew" assignment repeats itself a couple of times and then the build exits with: > *cc1plus: all warnings being treated as errors <<<* > library/SpatialDomains/CMakeFiles/SpatialDomains.dir/build.make:254: > recipe for target > 'library/SpatialDomains/CMakeFiles/SpatialDomains.dir/MeshGraph.cpp.o' > failed > make[2]: *** > [library/SpatialDomains/CMakeFiles/SpatialDomains.dir/MeshGraph.cpp.o] > Error 1 > CMakeFiles/Makefile2:2271: recipe for target > 'library/SpatialDomains/CMakeFiles/SpatialDomains.dir/all' failed > make[1]: *** [library/SpatialDomains/CMakeFiles/SpatialDomains.dir/all] > Error 2 > Makefile:140: recipe for target 'all' failed > make: *** [all] Error 2 See the line I've highlighted. All of these errors occur because "-Werror" flag is enabled. I know this is the right way of doing things, however on a large application like Nektar I'm not sure if it must be this strict. So the question is what would be the best solution to tackle those warnings? I'm planning to disable the "Werror" flag unless there is a better idea. Thank you Fatih Ertinaz

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Visualizing deforming and moving geometry in post-processing
by Debbahi Saad 21 Oct '20

21 Oct '20

******************* This email originates from outside Imperial. Do not click on links and attachments unless you recognise the sender. If you trust the sender, add them to your safe senders list https://spam.ic.ac.uk/SpamConsole/Senders.aspx to disable email stamping for this address. ******************* Dear Nektar users, I have launched a few runs of the cylinder example demonstrating the global mapping approach for geometry deformation, using the IncNavierStokesSolver, however when trying to visualize the deformation under Paraview or Tecplot the post-processor shows no geometry alteration? Please notice that I've used the Hdf5 output format for parallel run. and batch converted the *.chk files using FieldConvert which definitely uses the same XML session file to generate the .plt and .vtu files. If it's normal to see no geometry alteration, could there be a way to alter the geometry accordingly and obtain a model that visually deforms in the post-processor? Thanks to all of you, S. Debbahi

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Torque of a rotating body under crossflow
by Victor Hugo Santiago Peron 21 Oct '20

21 Oct '20

******************* This email originates from outside Imperial. Do not click on links and attachments unless you recognise the sender. If you trust the sender, add them to your safe senders list https://spam.ic.ac.uk/SpamConsole/Senders.aspx to disable email stamping for this address. ******************* Hello all, I'm currently using the incompressible Navier-Stokes tool to measure the stability of bodies under torsional oscillation and I'm wondering if the IncNavierStokesSolver algorithm provides the value of the torque caused by the fluid in the body. Could you please provide me this information and, if possible, where to get it? Thanks in advance, Best regards. Victor Peron Department of Mechanical Engineering Escola Politécnica da Universidade de São Paulo

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