- Nektar-users - imperial.ac.uk

gitlab update
by David Moxey 13 Jan '18

13 Jan '18

Dear all, As we're falling behind the gitlab versions again, I'll be taking the gitlab server down for an update tomorrow from around 1pm GMT. This might be a little longer than usual, as I will try to transition to the better-supported Omnibus edition, which will make future updates automatic. Cheers, Dave

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forces computation in parallel computations
by F Mellibovsky 13 Jan '18

13 Jan '18

Dear all, When running parallel (72 core) aggregate quantitities such as body forces (particularly pressure forces) seem to include a certain degree -low amplitude- of randomness in their evolution. The high frequency random oscillations seem to be of the order of the sampling period. This suggests some kind of issue with the gathering of data from all parallel processes for aggregate quantity computation. Is there some precaution that must be taken upon compilation or in defining the cluster parallel environtment to avoid this issue? I attach one such forces time-series to illustrate this. Viscous forces seem to be just fine, while pressure (and total) forces oscillate at high frequency. Cheers

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Regarding deforming mesh
by SIDHARTHA SANKAR SAMANTARAY 03 Jan '18

03 Jan '18

Hello, Does Nektar++ support deforming mesh? If so, what should I do to implement it? Regards, Sidharth -- ------------------------------ *Disclaimer: *This email and any files transmitted with it are confidential and intended solely for the use of the individual or entity to whom they are addressed. If you have received this email in error please notify the system manager. This message contains confidential information and is intended only for the individual named. If you are not the named addressee you should not disseminate, distribute or copy this e-mail. Please notify the sender immediately by e-mail if you have received this e-mail by mistake and delete this e-mail from your system. If you are not the intended recipient you are notified that disclosing, copying, distributing or taking any action in reliance on the contents of this information is strictly prohibited.

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Re: [Nektar-users] NAN time integration error
by SIDHARTHA SANKAR SAMANTARAY 20 Dec '17

20 Dec '17

Hello, Sorry I didn't know about the non-confirming mesh problem. Now I have prepared a conforming mesh (file attached). Can you please check whether it is okay? It is also showing NAN. Thanks. On Tue, Dec 19, 2017 at 7:31 PM, SIDHARTHA SANKAR SAMANTARAY < sss12(a)iitbbs.ac.in> wrote: > Hello, > Sorry I didn't know about the non-confirming mesh. Now I have prepared a > conforming mesh by just clicking on 2D mesh option in gmsh. Can you please > check whether it is okay? It is also showing NAN. I am online, so you can > ask me anything more you want. > > Thanks. > > On Tue, Dec 19, 2017 at 6:47 PM, Douglas Serson <d.serson(a)gmail.com> > wrote: > >> Hi Sidharth, >> >> Your geo file looks fine to me. However, I noticed a couple of problems >> in the mesh of the xml you just sent. >> First, composites 2 and 3 are switched compared to the geometry in the >> geo file (and to what I think makes sense in terms of boundary conditions). >> Also, the mesh near the inflow is non-conforming, as you can see in the >> attached image (i.e. one edge of the large element is connected to 3 >> different elements). This is not supported by Nektar++. >> How exactly did you generate this mesh? Using your geo file I obtained a >> completely different mesh from gmsh. >> >> Cheers, >> Douglas >> >> 2017-12-19 6:37 GMT-02:00 SIDHARTHA SANKAR SAMANTARAY <sss12(a)iitbbs.ac.in >> >: >> >>> Hi Douglas, >>> Thanks a lot for the solution. I found that line was in every code of >>> mine. But even after correcting that line, the same error can be seen with >>> a structured mesh. I am sending you the gmsh script this time. Please tell >>> me whether structured mesh has to be taken care in a special way. And >>> another thing i want to know is whether each grid should be orthogonal to >>> run the solver? >>> >>> Regards, >>> Sidharth >>> >>> On Tue, Dec 19, 2017 at 2:06 PM, SIDHARTHA SANKAR SAMANTARAY < >>> sss12(a)iitbbs.ac.in> wrote: >>> >>>> Hi Douglas, >>>> Thanks a lot for the solution. I found that line was in every code of >>>> mine. But even after correcting that line, the same error can be seen with >>>> a structured mesh. I am sending you the gmsh script this time. Please tell >>>> me whether structured mesh has to be taken care in a special way. And >>>> another thing i want to know is whether each grid should be orthogonal to >>>> run the solver? >>>> >>>> Regards, >>>> Sidharth >>>> >>>> On Tue, Dec 19, 2017 at 3:02 AM, Douglas Serson <d.serson(a)gmail.com> >>>> wrote: >>>> >>>>> Hi Sidharth, >>>>> >>>>> I checked your xml file and it is missing a </REGION> on line 90. >>>>> By fixing this I was able to start the simulation without getting a >>>>> NaN. >>>>> >>>>> Cheers, >>>>> Douglas >>>>> >>>>> 2017-12-18 9:57 GMT-02:00 SIDHARTHA SANKAR SAMANTARAY < >>>>> sss12(a)iitbbs.ac.in>: >>>>> >>>>>> Hello, >>>>>> I am seeing NAN time integration error while solving a simple problem >>>>>> with compressible NS solver. Can anyone tell me what is probably causing it? >>>>>> I have attached the screenshot of the error and the xml file running >>>>>> the solver. >>>>>> >>>>>> Thanks, >>>>>> Sidharth >>>>>> >>>>>> ------------------------------ >>>>>> *Disclaimer: *This email and any files transmitted with it are >>>>>> confidential and intended solely for the use of the individual or entity to >>>>>> whom they are addressed. If you have received this email in error please >>>>>> notify the system manager. This message contains confidential information >>>>>> and is intended only for the individual named. If you are not the named >>>>>> addressee you should not disseminate, distribute or copy this e-mail. >>>>>> Please notify the sender immediately by e-mail if you have received this >>>>>> e-mail by mistake and delete this e-mail from your system. If you are not >>>>>> the intended recipient you are notified that disclosing, copying, >>>>>> distributing or taking any action in reliance on the contents of this >>>>>> information is strictly prohibited. >>>>>> _______________________________________________ >>>>>> Nektar-users mailing list >>>>>> Nektar-users(a)imperial.ac.uk >>>>>> https://mailman.ic.ac.uk/mailman/listinfo/nektar-users >>>>>> >>>>>> >>>>> >>>> >>> >>> ------------------------------ >>> *Disclaimer: *This email and any files transmitted with it are >>> confidential and intended solely for the use of the individual or entity to >>> whom they are addressed. If you have received this email in error please >>> notify the system manager. This message contains confidential information >>> and is intended only for the individual named. If you are not the named >>> addressee you should not disseminate, distribute or copy this e-mail. >>> Please notify the sender immediately by e-mail if you have received this >>> e-mail by mistake and delete this e-mail from your system. If you are not >>> the intended recipient you are notified that disclosing, copying, >>> distributing or taking any action in reliance on the contents of this >>> information is strictly prohibited. >>> >> >> > -- ------------------------------ *Disclaimer: *This email and any files transmitted with it are confidential and intended solely for the use of the individual or entity to whom they are addressed. If you have received this email in error please notify the system manager. This message contains confidential information and is intended only for the individual named. If you are not the named addressee you should not disseminate, distribute or copy this e-mail. Please notify the sender immediately by e-mail if you have received this e-mail by mistake and delete this e-mail from your system. If you are not the intended recipient you are notified that disclosing, copying, distributing or taking any action in reliance on the contents of this information is strictly prohibited.

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NAN time integration error
by SIDHARTHA SANKAR SAMANTARAY 19 Dec '17

19 Dec '17

Hello, I am seeing NAN time integration error while solving a simple problem with compressible NS solver. Can anyone tell me what is probably causing it? I have attached the screenshot of the error and the xml file running the solver. Thanks, Sidharth -- ------------------------------ *Disclaimer: *This email and any files transmitted with it are confidential and intended solely for the use of the individual or entity to whom they are addressed. If you have received this email in error please notify the system manager. This message contains confidential information and is intended only for the individual named. If you are not the named addressee you should not disseminate, distribute or copy this e-mail. Please notify the sender immediately by e-mail if you have received this e-mail by mistake and delete this e-mail from your system. If you are not the intended recipient you are notified that disclosing, copying, distributing or taking any action in reliance on the contents of this information is strictly prohibited.

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Using a specified discrete velocity profile as a inflow boundary condition
by 李依然 03 Dec '17

03 Dec '17

Dear all, I'm now trying to define a inflow boundary condition using a specified discrete velocity profile when simulating with the IncNavierStokesSolver. Specially, the inflow velocity profile I use here is a Blasius profile. Since it is numerically solved by an external code, the profile here is in discrete form (i.e. velocity on discrete points). While from the user guide, I can see that a profile with an explicit expression can be directly implemented as a boundary condition in the .xml file, it seems that there is few examples on how to deal with a specified discrete velocity profile. I wonder if there is any way to implement this kind of boundary condition in Nektar++? P.S.: To solve this problem, I wonder if the module "interppointdatatofld" of FieldConvert should be used? If so, how to use it for the boundary? Besides, I think here a ".bc" file which is mentioned in 3.3.5.5 Boundary conditions from file in user guide might be needed, but I don't know how to construct this kind of files? Thanks in advance for the help. Best Regards, Mona

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interppoints:box in parallel
by Peltonen Petteri 25 Nov '17

25 Nov '17

Hey, I would like to run a POD on a section of my 3D field on a coarser grid. For this, I would like the section to be equidistributed cartesian box and this is exactly what the '-m interppoints:box' utility does. However, I'm having trouble running the utility in parallel. When I run the command: FieldConvert -m interppoints:fromxml=base/jet.xml:fromxml=base/mesh.xml:fromfld=base/mesh_1.chk:\ box=10,10,10,-0.001,0.001,-0.001,0.001,-0.003,0.003 box1.dat the utility does exactly what I want. When I run it in parallel: mpirun -np 3 FieldConvert \ -m interppoints:fromxml=base/jet.xml:fromxml=base/mesh.xml:fromfld=base/mesh_1.chk:\ box=10,10,10,-0.001,0.001,-0.001,0.001,-0.003,0.003 box2.dat box2.dat only contains one third of the points in the box. I also tried adding box2.dat:dat:writemultiplefiles, in which case I get the correct number of points split in three different files, but the file is still somehow corrupted when I open it with paraview. What am I doing wrong? Petteri Peltonen, (M.Sc.) Aalto University, School of Engineering Department of Mechanical Engineering PO Box 14300 FI-00076 Aalto, Finland +358 44 0554984 petteri.peltonen(a)aalto.fi

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Mesh generation manual
by Guillermo 24 Nov '17

24 Nov '17

Dear Turner, I am writing to you in order to provide you the errors I have encountered when using the mesh generation manual on Nektar 4.4.0. As requested I have attached the .mcf (nacagenerator.mcf) and the stdout** files. **I do not know exactly what does the "verbose -v flag" means. After a quick research I realized that it is just the command with the "--verbose" command line (NekMesh --verbose session.mcf mesh.xml). However this has not produced any .step file. So, on the Errors file, that I have attached, I just copied and pasted the errors shown on the terminal. Please let me know if you need any other information. Cheers, Guillermo

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Re: [Nektar-users] stabilisation/dealiasing in Compressible solver
by Vishal Saini 23 Nov '17

23 Nov '17

Hi Spencer and other members, Thanks Spencer for your reply on the issue. I think the problem was under-resolution of the vortex. Projection error seems to be relatively small. Also, the compressible flow tutorial was helpful to set the boundary conditions properly. I have another (very basic) query regarding determining the CFL (u*delT/delX) for the case. I suppose that for N=2, delX is same as the element size, but I'm not sure on how to define delX in case of N>2. Should I take into account the point distribution inside the element (GLL, Jacobi etc.) and then delX=min(dist. between the points), or should I consider a uniform point distribution inside the element (delX= element_size/(N-1))? I'm using compressible solver (DG and Runge-Kutta 4-step time integration). P.S. I do not understand the fact that if there is a non-uniform distribution of quadrature points inside an element why do I see a uniform distribution in the post-processing softwares (paraview, TecPlot etc.). Any input is highly appreciated. Sincerely, Vishal On Thu, Sep 21, 2017 at 10:13 PM, Spencer Sherwin <ssherwin69(a)googlemail.com > wrote: > Hi Vishal, > > Thank for your interest in Nektar++. > > I have to confess I am not quite sure what the status of > SpectralHpDealiasing is in the compressible solver (@Douglas, Dani, Gian: > can you clarify). I do believe we may have investigated it for some of the > convection operators but do not recall which ones. > > SVV is definitely only setup for the incompressible flow solver since the > DG naturally has this type of property. > > One can however solve with a higher number of quadrature points and a more > brute force way of realising. It would be interesting to know if this sorts > out the issue you are observing. It might also be that the initial > projection is leading to the poor approximation of the initial conditions > and then being advected over the domain. (perhaps see Expansions in the > user-guide for this). > > We have been tying to put together a tutorial on the compressible flow > solver so that we can help also demonstrate the use of artificial viscosity > which can also be very useful in starting up flows. I hope to get this > fully online some time soon! > > Cheers, > Spencer. > > PS The MSc student who wrote the tutorial has also been doing some flow > studies which might be of interest. If so I can let you have a copy of her > report. > > > > On 18 Sep 2017, at 17:55, Vishal Saini <vishal.saini.nitj(a)gmail.com> > wrote: > > Dear all, > > > I've just started using high-order CFD (using Nektar++). To begin with, > I've just been running the Isentropic vortex advection case in a 50x20 > domain using the IsentropicVortex test case provided. The issue is that > I've continually been observing spurious oscillations (a figure is > attached) in velocity field. Increasing the resolution improves the > situation a little, but I could not completely get rid of the oscillations. > > Next, I wanted to use dealiasing. However, the simulations do not even > start when I use SVV and SPECTRALHPDEALIASING. Plus, I could not find any > stabilization technique implementation in "nektar++-4.4.0/solvers/ > CompressibleFlowSolver/Utilities" folder (which is the case in > Incompressible solver). Can anyone clarify if any dealiasing technique is > implemented in Compressible Solver and if there are any future plans on > that? > > Cheers and regards, > Vishal > > --- > *Vishal SAINI* > Master of Research, > University of Cambridge. > Master in Turbulence > EC Lille, ENSIP and ENSMA France. > Contact: vs434(a)cam.ac.uk, vishal.saini.nitj(a)gmail.com > <vishal.saini.nitj(a)gmail.com> > (+44) 7 459 186 139 (UK) > (+33) 7 58 24 84 02 <+33%207%2058%2024%2084%2002> (France) > <Screenshot from 2017-09-18 17-44-57.png>_________________ > ______________________________ > Nektar-users mailing list > Nektar-users(a)imperial.ac.uk > https://mailman.ic.ac.uk/mailman/listinfo/nektar-users > > > Spencer Sherwin FREng, FRAeS > McLaren Racing/Royal Academy of Engineering Research Chair, > Professor of Computational Fluid Mechanics, > Department of Aeronautics, > Imperial College London > South Kensington Campus > London SW7 2AZ > > s.sherwin(a)imperial.ac.uk > +44 (0) 20 759 45052 > > >

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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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