August 2024 - Nektar-users

Bug in IncNavierStokes solver terminal output for SVV with MPI
by Alexander Schukmann 02 Sep '24

02 Sep '24

******************* 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, I noticed some odd behavior of the IncNavierStokesSolvers terminal output regarding SVV when using MPI for Quasi-3D cases. When I try to use SVV in the spectral/hp planes only, i.e. without SVV along the homogeneous direction, the terminal output sometimes includes the SVV-Homo1D info, eventhough it's not specified under the SOLVERINFO tag in the session file! When I re-run the same case, it will randomly disappear as you can see here for two consecutive runs with identical settings: nektar@0d6fdc64e227:~/host_pwd/run$ mpirun -n 16 IncNavierStokesSolver mesh.xml session.xml ======================================================================= EquationType: UnsteadyNavierStokes Session Name: CylReD3900_quad_coarse2_Pgeo3 Spatial Dim.: 3 Max SEM Exp. Order: 4 Num. Processes: 16 Quasi-3D: Homogeneous in z-direction Expansion Dim.: 3 Num. Hom. Modes (z): 64 Hom. length (LZ): 3.14159 FFT Type: FFTW Projection Type: Continuous Galerkin Advect. advancement: explicit Diffuse. advancement: implicit Time Step: 0.004 No. of Steps: 1 Checkpoints (steps): 1 Integration Type: IMEX Splitting Scheme: Velocity correction (strong press. form) Dealiasing: Homogeneous1D + spectral/hp Smoothing-SpecHP: SVV (spectral/hp DG Kernel (diff coeff = 0.10000000000000001*Uh/p)) ======================================================================= nektar@0d6fdc64e227:~/host_pwd/run$ mpirun -n 16 IncNavierStokesSolver -f mesh.xml session.xml ======================================================================= EquationType: UnsteadyNavierStokes Session Name: CylReD3900_quad_coarse2_Pgeo3 Spatial Dim.: 3 Max SEM Exp. Order: 4 Num. Processes: 16 Quasi-3D: Homogeneous in z-direction Expansion Dim.: 3 Num. Hom. Modes (z): 64 Hom. length (LZ): 3.14159 FFT Type: FFTW Projection Type: Continuous Galerkin Advect. advancement: explicit Diffuse. advancement: implicit Time Step: 0.004 No. of Steps: 1 Checkpoints (steps): 1 Integration Type: IMEX Splitting Scheme: Velocity correction (strong press. form) Dealiasing: Homogeneous1D + spectral/hp Smoothing-SpecHP: SVV (spectral/hp DG Kernel (diff coeff = 0.10000000000000001*Uh/p)) Smoothing-Homo1D: SVV (Homogeneous1D - Exp Kernel(cut-off = 0.75, diff coeff = 0.10000000000000001))======================================================================= The first run does not output the "Smoothing-Homo1D" info, while the second one includes it, which makes it impossible to know whether it is activated or not. It'll use the SVV parameters that are set for the spectral/hp SVV if no parameters for the Homo1D-SVV are specified under the PARAMETERS tag. Otherwise the values will be overwritten, eventhough - as I said before - the feature is turned off under the SOLVERINFO tag. Running on one CPU shows the expected behavior. So it would be interesting to know whether this only concerns the terminal output or if the feature really is activated despite not being defined by the user. All the best Alex Sicher versendet mit [Proton Mail](https://proton.me/).

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Combining Time-averaged fields and History points filters
by Alexander Schukmann 27 Aug '24

27 Aug '24

******************* 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 all, I was wondering whether there is a way of combining the two filters „Time-averaged fields“ and „History Points“ in order to evaluate statistical convergence and at the same time avoid writing excessive amounts of data, thus e.g. sampling averaged quantities in a single point in space? Thanks in advance and all the best Alex Sent from [Proton Mail](https://proton.me/mail/home) for iOS

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Re: [Nektar-users] Introducing a Fluid Jet into the Quasi-3D IncNavierStokesSolver and Reynolds Stresses Filter
by Daniel Garcia 24 Aug '24

24 Aug '24

Selman, You define the time sampling with the "SampleFrequency" flag. Also, you can define output frequency with the "OutputFrequency" flag. Here it is an example: <FILTER TYPE="ReynoldsStresses"> <PARAM NAME="OutputFile"> MyAverageField </PARAM> <PARAM NAME="RestartFile">MyAverageRst.fld</PARAM>  <PARAM NAME="OutputFrequency"> 100*TimeStep </PARAM> <PARAM NAME="SampleFrequency"> 50 </PARAM> </FILTER> It will output the file each 100 time steps in order to check convergence and it will use data each 50 time steps to compute the averages. Em sáb., 24 de ago. de 2024 às 07:54, Selman BAYSAL < selmanbaysal(a)comu.edu.tr> escreveu: > Hello David, > > I'm doing well, thank you! I really appreciate your quick response. I have > been trying to define another boundary by using GMSH, however, I believe > that using boolean operators will be the most suitable approach for my > problem. > > As you mentioned, the User Guide states that the "Reynolds stress" filter > provides time-averaged values. However, I couldn't find a clear statement > in the document about which time intervals are used. My assumption is that > it utilizes the TimeStep value defined in the XML file. Still, to be > certain, I would greatly appreciate it if someone with different opinion or > knowledge could share their experince on this matter. > > Thank you once again for your time and attention! I wish you all the best > in your work! > > Regards, > > Selman Baysal > R. A. in Hydraulics > Dept. of Civil Eng'g > Çanakkale Onsekiz Mart University > -- > ITU Civil Eng., BSc. > ITU Coastal Sci. & Eng., MSc. > ------------------------------ > *Kimden:* ribeiro.danielg(a)gmail.com; > *Kime:* selmanbaysal(a)comu.edu.tr; - 23/08/24 - 14:42 > *Bilgi:* nektar-users(a)imperial.ac.uk; > *Konu:* Re: [Nektar-users] Introducing a Fluid Jet into the Quasi-3D > IncNavierStokesSolver and Reynolds Stresses Filter > > Hello Selman, how are you? > > i. I think you could do that with your boundary condition on the wall, > simply implementing the value of the velocity on the specific component. > Also, you can use boolean operators to limit the region and also time to > specify the period. There is (or are) an explanation of that in the user > guide. Also, If it's not on the boundary, you could use a body force, also > using boolean operators and a time flag for the specific period. > > ii. The Reynolds stress filter will compute the time average of your > solution as well as the time-averaged Reynolds stresses. If you compare the > results obtained from it with the ones from a history file, they will > eventually be the same, but as the average process is different for the > filter, they differ for short average periods. At least that was my > experience with it. > > I hope it helps and I wish you luck, > > Daniel. > > > > > Em sex., 23 de ago. de 2024 às 07:15, Selman BAYSAL < > selmanbaysal(a)comu.edu.tr> escreveu: > >> This email from selmanbaysal(a)comu.edu.tr 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 All, >> >> I have two different questions that I would greatly appreciate your >> insights on: >> >> >> 1. I'm currently investigating the laminar-to-turbulent transition in >> oscillatory wave boundary layers. For some time, I have been using a >> roughness element to generate initial perturbations. However, I would like >> to find out how to define a fluid jet (i.e., vertical velocity v = A where >> A is a constant) that puffs puffing for a while (e.g., from t0 to t1) from >> a specific point at the bed (e.g., x=y=z=0 at the boundary "2"). Is it >> possible to implement this in Quasi-3D approach? >> 2. I have implemented "Reynolds stresses" filter into my XML code and >> obtained output files without any problem. However, when I compared these >> output files with the original checkpoint file (*.chk), I observed >> noticeable discrepancies in the velocity and pressure variables. The raises >> concern about the accuracy of other variables such as uu, uv, vw, etc. >> Could you please clarify what exactly this filter outputs? >> >> Thank you very much for your time and intention. Any advice or >> recommendations you can provide would be greatly appreciated! >> >> Best regards, >> >> Selman Baysal >> R. A. in Hydraulics >> Dept. of Civil Eng'g >> Çanakkale Onsekiz Mart University >> -- >> ITU Civil Eng., BSc. >> ITU Coastal Sci. & Eng., MSc. >> _______________________________________________ >> Nektar-users mailing list >> Nektar-users(a)imperial.ac.uk >> https://mailman.ic.ac.uk/mailman/listinfo/nektar-users > >

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Introducing a Fluid Jet into the Quasi-3D IncNavierStokesSolver and Reynolds Stresses Filter
by Selman BAYSAL 23 Aug '24

23 Aug '24

******************* 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 All,I have two different questions that I would greatly appreciate your insights on:I'm currently investigating the laminar-to-turbulent transition in oscillatory wave boundary layers. For some time, I have been using a roughness element to generate initial perturbations. However, I would like to find out how to define a fluid jet (i.e., vertical velocity v = A where A is a constant) that puffs puffing for a while (e.g., from t0 to t1) from a specific point at the bed (e.g., x=y=z=0 at the boundary "2"). Is it possible to implement this in Quasi-3D approach?I have implemented "Reynolds stresses" filter into my XML code and obtained output files without any problem. However, when I compared these output files with the original checkpoint file (*.chk), I observed noticeable discrepancies in the velocity and pressure variables. The raises concern about the accuracy of other variables such as uu, uv, vw, etc. Could you please clarify what exactly this filter outputs?&nbsp;Thank you very much for your time and intention. Any advice or recommendations you can provide would be greatly appreciated!Best regards,Selman BaysalR. A. in HydraulicsDept. of Civil Eng'gÇanakkale Onsekiz Mart University--ITU Civil Eng., BSc.ITU Coastal Sci. &amp; Eng., MSc.

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Questions Regarding Wall Shear Stress Postprocessing
by Guillermo Suárez 19 Aug '24

19 Aug '24

******************* 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, I have solved the flow around a 2D cylinder using the IncNavierStokesSolver. Attached, you will find an image of the flow field (flowfield.png). As you can observe, there is a recirculation bubble on the upper rear of the cylinder, along with a separation point at the lower rear. I am looking to plot the wall shear stress as: sign(wss_x) * wss_mag. I’ve extracted the data using FieldConvert into a .csv file, which is also attached. I have a couple of questions regarding the postprocessing: 1) At the aft (0.5, 0), there’s an abrupt sign change in wss_x, which is not continuous. I believe this is related to how wall normals are defined in Nektar. To correct this, it seems necessary to multiply the wss_x values for the lower surface by -1. I am not sure about the (0.5, 0) itself. Is there a way to account for this sign change during postprocessing in Nektar? Or would it be possible to apply a preprocessing step in Nekmesh? 2) The simulation was performed with NUMMODES="2" and TYPE="MODIFIED." The edges of each element are duplicated in the .csv file, but the values for these duplicated points are noticeably different (e.g., (-0.4998656761, 0.01158903919) – entries 4 and 5). I suspect this is again related to the normal definitions, as the norm_y values differ significantly. Is there a way to smooth this out, perhaps with a pre- or postprocessing technique? Also, please note that the region between x = -4.35778714e-02 and 4.35778714e-02 on the upper and lower surfaces does not correspond to the cylinder, which explains the gap in the .csv file. Thank you in advance for your help. I look forward to your suggestions. Cheers, Guillermo

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Some parallel ctests hang
by Mark Dixon 14 Aug '24

14 Aug '24

******************* 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 there, We're trying to install nektar++ 5.6.0 from source on our HPC system and are having trouble passing two parallel tests: MultiRegions_Helmholtz2D_CG_P7_Modes_AllBCs_iter_ml_par3 MultiRegions_Helmholtz3D_CG_Hex_AllBCs_iter_ml_par3 In both cases they hang. Have tried openmpi, intelmpi and mvapich2. Attaching strace to the processes reveals a lot of polling and not much else. To simplify, I've reproduced this on a separate Rocky 8.10 system + EPEL packages and building against master (7b1aa23bb) in case it has already been fixed. openmpi is 4.1.1: git clone http://gitlab.nektar.info/nektar/nektar.git mkdir build cd build cmake -D NEKTAR_USE_MPI=ON ../nektar make -j24 ctest Are these tests known to be problematic, please? Thanks, Mark

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