- Nektar-users - imperial.ac.uk

Re: [Nektar-users] VCSMapping and parallel execution
by Guillermo 22 Nov '17

22 Nov '17

Hi Stan, Thanks for your quick response. I am getting this error after several steps (22290). I am attaching the session, the mesh, output and error messages files. Thanks, Guillermo On 22/11/17 08:55, Stanisław Gepner wrote: > > Hi Guillermo, > > For some reason the CG solver failed to converge. Are you getting any > iterations to execute at all, or does this happen at the very start of > the simulation? > > Not knowing your session and mesh I would start by having a look at > the TimeStep, Kinvis and the initial condition you are using. Also, > not sure here, but I think the mesh file should precede the session > file, i.e.: > > mpirun -np 8 IncNavierStokesSolver *mesh.msh.xml ****session.xml * > > Best, > Stan > > On 22.11.2017 12:43, Guillermo wrote: >> Dear all, >> >> I am using the Mapping function (VCSMapping) and it gave me some >> errors which I do not really understand the meaning. The simulation >> was executed in parallel: >> mpirun -np 8 IncNavierStokesSolver session.xml mesh.msh.xml >> >> Output message: >> ... >> CFL (zero plane): 1.15785e+20 (in elmt 520) >> CG iterations made = 5001 using tolerance of 1e-09 (error = nan, >> rhs_mag = inf) >> ------------------------------------------------------- >> Primary job terminated normally, but 1 process returned >> a non-zero exit code.. Per user-direction, the job has been aborted. >> ------------------------------------------------------- >> -------------------------------------------------------------------------- >> >> mpirun detected that one or more processes exited with non-zero >> status, thus causing >> the job to be terminated. The first process to do so was: >> >> Process name: [[36638,1],4] >> Exit code: 1 >> -------------------------------------------------------------------------- >> >> >> and the error messages are: >> >> Fatal : Level 0 assertion violation >> Exceeded maximum number of iterations >> >> >> I also have obtained a batch of error messages, however I think they >> are result of the simulation errors. Nevertheless, if you want them >> or any other file, please let me know. >> >> So please, could you explain to me why I have obtained these error? >> >> Thank you very much for your help. >> >> Regards, >> Guillermo >> >> _______________________________________________ >> Nektar-users mailing list >> Nektar-users(a)imperial.ac.uk >> https://mailman.ic.ac.uk/mailman/listinfo/nektar-users > > > > _______________________________________________ > Nektar-users mailing list > Nektar-users(a)imperial.ac.uk > https://mailman.ic.ac.uk/mailman/listinfo/nektar-users

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VCSMapping and parallel execution
by Guillermo 22 Nov '17

22 Nov '17

Dear all, I am using the Mapping function (VCSMapping) and it gave me some errors which I do not really understand the meaning. The simulation was executed in parallel: mpirun -np 8 IncNavierStokesSolver session.xml mesh.msh.xml Output message: ... CFL (zero plane): 1.15785e+20 (in elmt 520) CG iterations made = 5001 using tolerance of 1e-09 (error = nan, rhs_mag = inf) ------------------------------------------------------- Primary job terminated normally, but 1 process returned a non-zero exit code.. Per user-direction, the job has been aborted. ------------------------------------------------------- -------------------------------------------------------------------------- mpirun detected that one or more processes exited with non-zero status, thus causing the job to be terminated. The first process to do so was: Process name: [[36638,1],4] Exit code: 1 -------------------------------------------------------------------------- and the error messages are: Fatal : Level 0 assertion violation Exceeded maximum number of iterations I also have obtained a batch of error messages, however I think they are result of the simulation errors. Nevertheless, if you want them or any other file, please let me know. So please, could you explain to me why I have obtained these error? Thank you very much for your help. Regards, Guillermo

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Add transport equations to compressible flow solver
by Aidyn Aitzhan 07 Nov '17

07 Nov '17

Dear colleagues, I am planning to solve a combustion problem using Nektar++, so I have to add extra equations to compressible flow solver. Please suggest me what is good way to start? Which files I should modify? Thank you very much, Aidyn Aitzhan

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Reynolds Stresses
by wasim sarwar 06 Nov '17

06 Nov '17

Dear All, I am wondering how exactly Reynolds stresses are calculated in Nektar++. I have two questions regarding the calculation of reynolds stresses: 1) Whether these stresses are being calculated at every time step or just at the end of the simulation when we ask it to output the average field. 2) Once it outputs the average field then does it start from zero to compute the next average output field or proceed from the last saved output averaged field. Any feedback would be of great help. cheer

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How are edges used in the mesh
by Kurt Sansom 05 Nov '17

05 Nov '17

The documentation mentions mesh edges being required for 2D and 3D, but how are they used and is there some implicit connection between them and Elements? I would assume the only connection is the vertex Ids should match, but it's unclear to me if I might be missing something there. Regards, ~Kurt -- Kurt Sansom

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2D mesh conversion using NekMesh
by Oliviu Sugar 05 Nov '17

05 Nov '17

Dear all, I have a question about converting a 2D 3rd-order mesh generated using Gmsh (.msh format) into the native .xml format. The file that NekMesh outputs only contains 1D segment elements. Is there any additional option I must activate when using NekMesh in order to to correctly read the high-order quad elements from the .msh file? I am attaching the .geo file that I used with Gmsh, and the .xml file (uncompressed) that results from NekMesh after conversion.Thank you. Best regards, Oliviu

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Hi All
by Moto Light 04 Nov '17

04 Nov '17

Hi for all people here, i need to ask about something i did not find how i know the unites used in Nektar, like in velocity in pressure i tried to use it it is amazing but i need to know when i have velocity field which unit i see also for pressure is it pascal bar dynes/cm2 i need to know, i checked the user guide not clarify this point, i checked tutorials one of them the graph of the pressure is in dynes/cm2 i don't know which unit i can have and where we can define like Si system unit or something. thanks

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vtk convert .vtu to .xml
by Kurt Sansom 26 Oct '17

26 Oct '17

Hi, I am trying to convert a .vtu mesh file to the .xml format. has anyone done this already? NekMesh Doesn't have this feature, I tried implementing it myself, but am having some challenges that I need to work out with how vtk access's each cell. I am also gettting some errors like: Warning: degenerate tetrahedron, 3rd vertex is = 4.74539e-05 from face Any feedback would be of great help. ~Kurt -- Kurt Sansom

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Issue with CompressibleFlowSolver
by Oliviu Sugar 25 Oct '17

25 Oct '17

Dear all, I have run into some problems when trying to run the compressible flow solver. First, some background:- code build was complete without any issues, with all dependencies pre-installed system-wide, and without any problems in linking to these libraries - ran all regression tests, all successful- ran the Incompressible NS Solver, both serial and parallel without issues- ran the ADR Solver without issues The code was compiled and ran on a personal workstation, with Ubuntu 16.04 as the Linux distribution. I am not an advanced Linux user, having started to work in it only recently, and thus identifying the exact issue is not possible for me at this stage. The compressible flow solver always fails, even for the isentropic vortex case provided as example with the distribution. When running in serial, the error is:--------------------------------------------------------------------------------------------------------------------------------------------------------------- [salv08976-ub:03370] *** Process received signal ***[salv08976-ub:03370] Signal: Segmentation fault (11) [salv08976-ub:03370] Signal code: Address not mapped (1) [salv08976-ub:03370] Failing at address: 0x1573bc50 [salv08976-ub:03370] [ 0] /lib/x86_64-linux-gnu/libc.so.6(+0x354b0)[0x7fb38f0b04b0] [salv08976-ub:03370] [ 1] /home/local/ISDADS/sgs475/Nektar++/nektar++-4.4.1/build/dist/lib64/nektar++-4.4.1/libLibUtilities.so.4.4.1(_ZN6Nektar12LibUtilities27AnalyticExpressionEvaluator8StorePrm8run_onceEv+0xb)[0x7fb39087b39b] [salv08976-ub:03370] [ 2] /home/local/ISDADS/sgs475/Nektar++/nektar++-4.4.1/build/dist/lib64/nektar++-4.4.1/libLibUtilities.so.4.4.1(_ZN6Nektar12LibUtilities27AnalyticExpressionEvaluator8EvaluateEi+0x6e)[0x7fb39087514e] [salv08976-ub:03370] [ 3] /home/local/ISDADS/sgs475/Nektar++/nektar++-4.4.1/build/dist/lib64/nektar++-4.4.1/libSolverUtils.so.4.4.1(_ZNK6Nektar12LibUtilities8Equation8EvaluateEv+0x38)[0x7fb391cc8508] [salv08976-ub:03370] [ 4] /home/local/ISDADS/sgs475/Nektar++/nektar++-4.4.1/build/dist/lib64/nektar++-4.4.1/libLibUtilities.so.4.4.1(_ZN6Nektar12LibUtilities13SessionReader14ReadParametersEP12TiXmlElement+0x26d)[0x7fb3907bacbd] [salv08976-ub:03370] [ 5] /home/local/ISDADS/sgs475/Nektar++/nektar++-4.4.1/build/dist/lib64/nektar++-4.4.1/libLibUtilities.so.4.4.1(_ZN6Nektar12LibUtilities13SessionReader13ParseDocumentEv+0x92)[0x7fb3907c2612] [salv08976-ub:03370] [ 6] /home/local/ISDADS/sgs475/Nektar++/nektar++-4.4.1/build/dist/lib64/nektar++-4.4.1/libLibUtilities.so.4.4.1(_ZN6Nektar12LibUtilities13SessionReader11InitSessionEv+0x4f)[0x7fb3907c6aff] [salv08976-ub:03370] [ 7] ./CompressibleFlowSolver(_ZN6Nektar12LibUtilities13SessionReader14CreateInstanceEiPPc+0x16d)[0x48ef6d] [salv08976-ub:03370] [ 8] ./CompressibleFlowSolver(main+0x62)[0x454b52] [salv08976-ub:03370] [ 9] /lib/x86_64-linux-gnu/libc.so.6(__libc_start_main+0xf0)[0x7fb38f09b830] [salv08976-ub:03370] [10] ./CompressibleFlowSolver(_start+0x29)[0x463219] [salv08976-ub:03370] *** End of error message *** Segmentation fault (core dumped)--------------------------------------------------------------------------------------------------------------------------------------------------------------- When running in parallel the error is:The error message is pretty mush the same, only repeated a number of times equal to the number of processing cores, plus the following message at the end:--------------------------------------------------------------------------------------------------------------------------------------------------------------- mpirun noticed that process rank 3 with PID 13368 on node salv08976-ub exited on signal 11 (Segmentation fault).--------------------------------------------------------------------------------------------------------------------------------------------------------------- Any guidance with this issue would be much appreciated. Thank you.Oliviu

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compiling python wrapper
by Rubini R. 25 Oct '17

25 Oct '17

Dear All, I would like to compile the python interface of nektar. I follow the instruction I found on the GitLab repo. I have already compiled both Nektar++ and Boost.python without any problem. However I don't manage to get rid of this error during the compilation: /usr/local/lib/libboost_python.so: undefined reference to `PyUnicode_InternFromString' /usr/local/lib/libboost_python.so: undefined reference to `PyUnicode_FromFormat' /usr/local/lib/libboost_python.so: undefined reference to `PyUnicode_FromString' /usr/local/lib/libboost_python.so: undefined reference to `PyBytes_Size' /usr/local/lib/libboost_python.so: undefined reference to `PyUnicode_AsUTF8' /usr/local/lib/libboost_python.so: undefined reference to `PyUnicode_FromEncodedObject' /usr/local/lib/libboost_python.so: undefined reference to `PyBytes_AsString' /usr/local/lib/libboost_python.so: undefined reference to `_Py_fopen' /usr/local/lib/libboost_python.so: undefined reference to `PyModule_Create2' /usr/local/lib/libboost_python.so: undefined reference to `PyUnicode_AsWideChar' /usr/local/lib/libboost_python.so: undefined reference to `PyUnicode_AsUTF8String' /usr/local/lib/libboost_python.so: undefined reference to `PyUnicode_FromStringAndSize' collect2: error: ld returned 1 exit status libs/numpy/example/CMakeFiles/fromdata.dir/build.make:97: recipe for target 'bin/fromdata' failed make[5]: *** [bin/fromdata] Error 1 CMakeFiles/Makefile2:152: recipe for target 'libs/numpy/example/CMakeFiles/fromdata.dir/all' failed make[4]: *** [libs/numpy/example/CMakeFiles/fromdata.dir/all] Error 2 Makefile:138: recipe for target 'all' failed make[3]: *** [all] Error 2 CMakeFiles/boost-numpy.dir/build.make:110: recipe for target 'ThirdParty/stamp/boost-numpy-build' failed make[2]: *** [ThirdParty/stamp/boost-numpy-build] Error 2 CMakeFiles/Makefile2:67: recipe for target 'CMakeFiles/boost-numpy.dir/all' failed make[1]: *** [CMakeFiles/boost-numpy.dir/all] Error 2 Makefile:127: recipe for target 'all' failed make: *** [all] Error 2 I'm working on ubuntu 16.04 LST. What am I doing wrong or what am I missing ? Thank you very much for your help. Regards, Riccardo

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