August 2018 - Nektar-users

"PressureInflowFile" BC template
by Arash Nouri 24 Aug '18

24 Aug '18

Hi all, Is there anyone here who have an uncompressed template of "PressureInflowFile" BC for the compressible flow solver? Thanks in advance, Arash --------------------------------- Arash G. Nouri Research Scientist Computational Modeling & Simulation (http://cmsp.pitt.edu/) 1127 Benedum Hall University of Pittsburgh Pittsburgh, PA 15261, USA E-mail: arn36(a)pitt.edu

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Compiling nektar on Blue Gene / Q
by Fatih Ertinaz 23 Aug '18

23 Aug '18

Hello everyone I'm trying to compile nektar++-4.4.1 on a BG/Q cluster. So far my attempts are unsuccessful. I found this post quite helpful however still ended up with some errors: https://www.nektar.info/nektar-on-mira-cluster/ I've updated "$srcdir/cmake/ThirdPartyZlib.cmake" as it is written in that post. Then from $builddir I am running the following cmake: > > cmake $srcdir \ > > -DNEKTAR_USE_MPI=ON \ > > -DTHIRDPARTY_BUILD_ZLIB=OFF \ > > -DNEKTAR_USE_SYSTEM_BLAS_LAPACK=ON \ > > -DCMAKE_INSTALL_PREFIX=$prf > zlib and lapack are already installed on this cluster therefore I want to use those versions. This is the cmake output: > > -- The C compiler identification is GNU 4.8.1 > > -- The CXX compiler identification is GNU 4.8.1 > > -- Check for working C compiler: /....../gcc/4.8.1/mpi/bin/mpicc > > -- Check for working C compiler: /....../gcc/4.8.1/mpi/bin/mpicc -- works > > -- Detecting C compiler ABI info > > -- Detecting C compiler ABI info - done > > -- Check for working CXX compiler: /....../gcc/4.8.1/mpi/bin/mpicxx > > -- Check for working CXX compiler: /....../gcc/4.8.1/mpi/bin/mpicxx -- > > works > > -- Detecting CXX compiler ABI info > > -- Detecting CXX compiler ABI info - done > > -- Looking for a Fortran compiler > > -- Looking for a Fortran compiler - /....../gcc/4.8.1/mpi/bin/mpif90 > > -- The Fortran compiler identification is GNU > > -- Check for working Fortran compiler: /....../gcc/4.8.1/mpi/bin/mpif90 > > -- Check for working Fortran compiler: > > /....../gcc/4.8.1/mpi/bin/mpif90 -- works > > -- Detecting Fortran compiler ABI info > > -- Detecting Fortran compiler ABI info - done > > -- Checking whether /....../gcc/4.8.1/mpi/bin/mpif90 supports Fortran 90 > > -- Checking whether /....../gcc/4.8.1/mpi/bin/mpif90 supports Fortran > > 90 -- yes > > -- Build TinyXML: > > > /....../nektar/nektar++-4.4.1-build/ThirdParty/dist/lib/nektar++-4.4.1/libtinyxml.a > > -- Build Loki: > /....../nektar/nektar++-4.4.1-build/ThirdParty/dist/include > > -- Build Metis: > > > /....../nektar/nektar++-4.4.1-build/ThirdParty/dist/lib/nektar++-4.4.1/libmetis.a > *> -- Found Zlib: /usr/lib64/libz.so (version 1.2.3)* > > -- Searching for Boost: > > -- -- Pre-installed Boost thread library not found > > -- -- Pre-installed Boost iostreams library not found > > -- -- Pre-installed Boost date_time library not found > > -- -- Pre-installed Boost filesystem library not found > > -- -- Pre-installed Boost system library not found > > -- -- Pre-installed Boost program_options library not found > > -- -- Pre-installed Boost regex library not found > > -- -- Pre-installed Boost timer library not found > > -- -- Pre-installed Boost chrono library not found > > -- Build boost libs: thread, iostreams, date_time, filesystem, system, > > program_options, regex, timer, chrono > > -- Looking for include file mpi.h > > -- Looking for include file mpi.h - found > > -- Looking for MPI_Send > > -- Looking for MPI_Send - found > > -- Found MPI: built in > > -- Build GSMPI: > > /....../nektar/nektar++-4.4.1-build/ThirdParty/dist/lib/libgsmpi.a > > -- Build XXT: > > /....../nektar/nektar++-4.4.1-build/ThirdParty/dist/lib/libxxt.a > > -- Build blas: > > > /....../nektar/nektar++-4.4.1-build/ThirdParty/dist/lib/nektar++-4.4.1/libblas.a > > -- Build lapack: > > > /....../nektar/nektar++-4.4.1-build/ThirdParty/dist/lib/nektar++-4.4.1/lapack.a > > CMake Warning (dev) at library/LibUtilities/CMakeLists.txt:422 > > (TARGET_LINK_LIBRARIES): > > Link library type specifier "debug" is followed by specifier > "optimized" > > instead of a library name. The first specifier will be ignored. > > This warning is for project developers. Use -Wno-dev to suppress it. > > > > CMake Error at library/LibUtilities/CMakeLists.txt:422 > > (TARGET_LINK_LIBRARIES): > > The "optimized" argument must be followed by a library. > > > > -- Configuring incomplete, errors occurred! > > See also > "/....../nektar/nektar++-4.4.1-build/CMakeFiles/CMakeOutput.log". > I've added the cmake.log as well. First thing I am confused is this line: > > -- Build lapack: > > > /....../nektar/nektar++-4.4.1-build/ThirdParty/dist/lib/nektar++-4.4.1/lapack.a > I've specified: > > -DNEKTAR_USE_SYSTEM_BLAS_LAPACK=ON \ > but it looks like somehow cmake is configured to use the third-party version. I can see both libblas.a and liblapack.a (created a symlink lapack.a too) are in my environment. Do they have to be shared libs? Should I update my LD_LIBRARY_PATH as well? Another thing is at the end of the cmake output above: > > CMake Error at library/LibUtilities/CMakeLists.txt:422 > > (TARGET_LINK_LIBRARIES): > > The "optimized" argument must be followed by a library. > I don't see any files in "nektar++-4.4.1-build/library/LibUtilities/CMakeFiles/". Therefore I have no idea why it says optimized argument must be followed by a library. When I search for optimized, this is all I get: > > bgqdev-fen1-$ grep -rn "optimized" * > > CMakeCache.txt:105:// /Ot /Oy /Gs will produce slightly less optimized > > but smaller > > CMakeCache.txt:125:// /Ot /Oy /Gs will produce slightly less optimized > > but smaller > > CMakeCache.txt:163:// /Ot /Oy /Gs will produce slightly less optimized > > but smaller > So, I don't know how to proceed any further at the moment. One last thing. Scaling achieved on Mira cluster looks impressive: https://www.nektar.info/nektar-strong-scaling-performance-on-mira/ Was it obtained using gcc or xl compilers? Any help is highly appreciated. // Fatih Ertinaz

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Dong Outflow BCs
by Amitvikram Dutta 20 Aug '18

20 Aug '18

Hi all, I have been trying to implement the stabilised outflow BCs as given by DOng and included in the User guide as follows <R VAR="u" USERDEFINEDTYPE="HOutflow" VALUE="0" PRIMCOEFF="D0/TimeStep"/> <R VAR="v" USERDEFINEDTYPE="HOutflow" VALUE="0" PRIMCOEFF="D0/TimeStep"/> <R VAR="p" USERDEFINEDTYPE="HOutflow" VALUE="0" PRIMCOEFF="1.0/(D0*Kinvis)"/> What does the parameter Do represent? Is it a flow quantity?Also, how do I set it within the xml file? Sincerely, -- *Amitvikram Dutta* Graduate Research Assistant Fluid Mechanics Research Lab Multi-Physics Interaction Lab University of Waterloo

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Extracting data from a plane over multiple timesteps
by Amitvikram Dutta 09 Aug '18

09 Aug '18

Hi all, I'm postprocessing a simulation and require data from a plane within my computational domain. I'm currently using the *FieldConvert -m interppoints* command to extract data from individual .chk/.fld files. Is there a variation of this command that allows a user to extract data from multiple .chk/.fld files thus obtaining the required data over a range of timesteps? Or is the simplest solution to write a bash script that executes this command multiple times in a loop over the desired range of filenames? Note, I'm also aware of the history points option, but since the number of points on the plane i require is quite large (over 1500), I have discounted this option for the present. Sincerely, -- *Amitvikram Dutta* Graduate Research Assistant Fluid Mechanics Research Lab Multi-Physics Interaction Lab University of Waterloo

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help
by Rubini R. 01 Aug '18

01 Aug '18

Good morning, I'm currently using nektar++, as a user, for my research. In the near future I would like to implement some extra functionalities in the already existing library. In order not to spam anyone I would like to know if this is the right mailing list where to ask questions about the developing aspects of the software. Thanks for any info! Have a good day! Best regards, Riccardo

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