- Nektar-users - imperial.ac.uk

Team chat
by David Moxey 19 Aug '16

19 Aug '16

Hi all, One of the outcomes of our user group meeting way back in June was to trial the use of a chat-based system for developers to ask questions and collaborate on a bit more of an informal basis. The easiest option turned out to be Slack, at least for trialling this amongst our group. For those unfamiliar with Slack, you can see some of the functionality here: https://slack.com/is -- it's essentially a chat room, with apps for desktop and phone, searchable history and somewhere to put attachments. The Nektar++ signup page is here: https://nektarpp.slack.com/signup Right now you need an Imperial or Utah email address to sign up, so if you don't have this and would like an invite, just reply to this email and I will send one your way. I'd encourage as many of you to take part as possible since if this is going to be successful then it requires a critical mass of people to participate! Cheers, Dave -- David Moxey (Research and Teaching Fellow) d.moxey(a)imperial.ac.uk | www.imperial.ac.uk/people/d.moxey Room 364, Department of Aeronautics, Imperial College London, London, SW7 2AZ, UK.

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A milestone
by David Moxey 15 Aug '16

15 Aug '16

Hi all, Just another quick (and happy!) note -- I noticed that we've now passed 10,000 commits and 600 merge requests for Nektar++, which is (in my mind at least) a big milestone for us! I just wanted to say thanks to everyone that has contributed code, bug reports and their time to making this such a successful project. Cheers, Dave -- David Moxey (Research and Teaching Fellow) d.moxey(a)imperial.ac.uk | www.imperial.ac.uk/people/d.moxey Room 364, Department of Aeronautics, Imperial College London, London, SW7 2AZ, UK.

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HDF5 support
by David Moxey 15 Aug '16

15 Aug '16

Dear all, The latest master now contains a new parallel output format that is based on the HDF5 dataset format. It's hoped we can make our I/O more efficient at very large core counts as a consequence. The default format is still our directory-based structure. I'd appreciate it if you can test this out on your simulations and let me know (a) the speed difference in reading/writing and (b) any bugs you encounter. - To enable HDF5, configure CMake with the NEKTAR_USE_HDF5 setting, which also requires NEKTAR_USE_MPI. Note that most clusters have HDF5 modules available that are usually detected by the CMake configuration (e.g. on ARCHER: module load cray-hdf5-parallel) - To run a simulation using the new format: IncNavierStokesSolver --io-format Hdf5 session.xml or put into your <SOLVERINFO> section. - To convert from XML based format (either serial or parallel) to HDF5: FieldConvert in.fld out.fld:fld:format=Hdf5 Note you don't need the session file for this. - Or the other way around: FieldConvert in.fld out.fld:fld:format=Xml Thanks also to Rupert Nash and Michael Bareford at EPCC for helping get this done as part of our eCSE funding. Cheers, Dave -- David Moxey (Research and Teaching Fellow) d.moxey(a)imperial.ac.uk | www.imperial.ac.uk/people/d.moxey Room 364, Department of Aeronautics, Imperial College London, London, SW7 2AZ, UK.

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Problem in getting a parallel case to run
by Amitvikram Dutta 28 Jul '16

28 Jul '16

Hi all, I'm trying to run a simple case on a NACA airfoil on a cluster. The problem is that it keeps failing to run in parallel. The job runs perfectly in serial, but that's hardly any consolation. I know, thr parallel implementation of nektar++ has correctly been installed don the cluster, since I managed to run a test file (tet_channel_m8_par.xml) successfully. I'd be greatful if anyone could point out any obvious mistakes that I'm making in the setup of my .xml file. For further reference I have attached the .xml file for my problem (naca0018_new_par.xml), the error message that I get from the cluster(0018_pw.pbs.e.....) and the test file that I ran successfully in parallel. Sincerely, -- *Amitvikram Dutta* *MASc Candidate* *Graduate Research Assistant * *Okanagan CFD Laboratory* *University of British Columbia | Okanagan Campus*

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Traction-Free boundary condition
by mohammadali alidoost 24 Jul '16

24 Jul '16

Dear Nektar++ Developers, We are going to use a Traction-Free boundary condition as an outflow in our simulation. In addition, we intend to use “Velocity Correction Scheme” of “Incompressible Navier-Stokes Solver”. As far as we know, the Traction-Free boundary condition contains two parts which should be satisfied simultaneously: zero velocity gradient and zero pressure. Based on the scheme we are going to use, we are wondering if you could tell us if it is necessary to implement both conditions in Nektar++ or we just need to set zero pressure condition alone. Kind Regards Mohammadali Alidoost

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Gitlab update
by David Moxey 23 Jul '16

23 Jul '16

Dear all, Just a quick note that I've updated gitlab this morning. As usual there are a few interface tweaks. Let me know if you have any issues. Cheers, Dave -- David Moxey (Research and Teaching Fellow) d.moxey(a)imperial.ac.uk | www.imperial.ac.uk/people/d.moxey Room 364, Department of Aeronautics, Imperial College London, London, SW7 2AZ, UK.

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Recent updates
by David Moxey 21 Jul '16

21 Jul '16

Dear all, A couple of recent updates you should be aware of: - as of this morning, FieldConvert modules have now been moved to a separate library called FieldUtils. This allows for the use of some of the post-processing modules to be run whilst the simulation is running through the use of a filter. See the MR for more details: https://gitlab.nektar.info/nektar/nektar/merge_requests/589 - in MR !654, shared filesystems (i.e. those where all processes share a common filesystem) are now automatically detected and the --shared-filesystem command line option has been removed. Cheers, Dave -- David Moxey (Research and Teaching Fellow) d.moxey(a)imperial.ac.uk | www.imperial.ac.uk/people/d.moxey Room 364, Department of Aeronautics, Imperial College London, London, SW7 2AZ, UK.

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Coupling CompressibleFlowSolver and APESolver to simulate the acoustic of a NACA-profile
by Selbach, Fabian 20 Jul '16

20 Jul '16

Hello, i have a question about coupling two solvers. First of all i make a simulation with a NACA-profile by using the NavierStokesCFE of the CompressibleFlowSolver. The solution of this i want to use to simulate the acoustic of its by solving the APE-equation. Is there an easy way to couple both solver and to simulate the acoustic of the flow around a NACA-profile? I need the acoustic source terms (c²*qc) for the APE-Solver to simulate the sound. I should get those by the solution of the NACA flow (by the CompressibleFlowSolver), but i actually i do not see a possible to get them. Is there a way or do i have to program it's on my own into the code of the CompressibleFlowSolver to handle and couple them into the APESolver? The difference between the solver-variables p, u and v ( in the CompressibleFlowSolver the absolute values and in the APESolver the fluctuations) i solved by calculating them in form of p(APE) = p(CFS) - pInf and so on. I hope somebody can give me an answer. Thank you already! Best regards Fabian

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Simulation of flow over a NACA 0012 Airfoil
by Gipperich, Manuel 20 Jul '16

20 Jul '16

Hi all, I need help for my simulation of the flow over a NACA 0012 Airfoil. I try to simulate the flow with a mach Number of M=0.4 and a reynoldsnumber of Re=408000. In every test my simulation is terminated with the message: NaN found in variable "rhou", terminating NaN found in variable "rhov", terminating NaN found in variable "E", terminating. I started the simulation with the same mach number and a lower reynoldsnumber of 4080 and it worked. So my question is, is there any solution for that problem to fix the instability of the simulation? Here is my SolverInfo data which i entered in the .xml File. Is it possible that an other UpwindType will fix the problem? <SOLVERINFO> </SOLVERINFO> My simulation runs with a CFL-number of 0.7. Thanks for any hint. If you need more information, please let me know . Best regards Manuel Gipperich

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Nektar++ v4.3.3 Released
by Chris Cantwell 16 Jul '16

16 Jul '16

Dear all, We are pleased to announce the release of Nektar++ v4.3.3. This release includes a number of further bug fixes and minor enhancements to the 4.3 release: **Library**: - Auto-detect a shared filesystem and removed --shared-filesystem option (!654) - Fix filters when using adaptive driver to avoid output being overwritten after each adaptive update (!588) - Minor fix to suppress Xxt output unless `--verbose` is specified (!642) - Fix of DirectFull solver in case where only Neumann boundary conditions are imposed. (!655) **FieldConvert**: - Fix to avoid repeated import of field file (!649) - Fix issue with C^0 projection (!644) - Fix verbose output when using --procid (!648) **NekMesh:** - Fix namespace issue in Star-CCM+ input header in NekMesh (!661) **CompressibleFlowSolver**: - Fix issue with residual output (!647) - Issues with 1D Euler solver fixed (!565) - Fix deadlocking issue with boundary conditions (!657) **Packaging**: - Fix NekMesh dependencies for DEB package (!650) - Fix PETSc build on newer linux distributions (!646) As always, if you encounter any problems please feel free to contact us on the mailing list nektar-users(a)imperial.ac.uk. Cheers, Chris -- Chris Cantwell Imperial College London South Kensington Campus London SW7 2AZ Email: c.cantwell(a)imperial.ac.uk www.imperial.ac.uk/people/c.cantwell

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