November 2024 - Nektar-users

Restarting the solution from previous time-step
by Nande, Ishan A. 28 Nov '24

28 Nov '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 am solving Linearized Euler Equations using the AcousticSolver on the cluster and I have encountered an issue. I am running initial calculations using a few time steps. The last time-step's field files are provided as an initial condition for the solution sampling phase of calculations. Let's say that the initial run's total simulation time is t_init and the same for next phase of simulations is t_sampling. These are the key-points of my setup : 1. In my initial run's session file the FinTime is set as t_init. For the sampling run, the FinTime is set as t_init + t_sampling 2. I am running the calculations in parallel and hence, the last time-step's folder( which has .chk in it's name) from the initial run is supplied to the InitialConditions field in the session of sampling run. 3. The time step for initial and sampling runs is the same. With the previously outlined setup, I have found that while the sampling phase of simulation run's for the desired total time of t_init + t_sampling , it gives the following error: Fatal : Level 0 assertion violation m_timestep < 0 I have replicated the exact same setup on one of the example cases and it results in the same error. What does this error mean ? Can someone please comment on what could be going wrong ? Regards, Ishan PGR

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Element u_11 is 0 from dsptrf
by Alexander Schukmann 18 Nov '24

18 Nov '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 all, when I run a 2.5D simulation using the incompressible NS solver the following error message appears with e.g. 480 CPUs after reading the initial state file, so the run immediately crashes: Fatal : Level 0 assertion violation ERROR: Element u_11 is 0 from dsptrf However, when switching to a lower CPU count such as 128 CPUs, it works. I have a region of local P-refinement in my domain, where the polynomial order is 7. Outside this region I coarsened the spatial resolution to P = 3 and suspect that it has something to do with this. Why does this happen? All the best Alex Sicher versendet mit [Proton Mail](https://proton.me/mail/home).

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NekMesh: msh to xml wrong space dimension
by Alexander Schukmann 14 Nov '24

14 Nov '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 all, when converting the attached 2D Gmsh mesh from msh to xml using NekMesh, I receive the following error: [InputGmsh] Reading Gmsh file: 'mesh.msh' [InputGmsh] Finished reading mesh. [InputGmsh] - Element dimension : 2 [InputGmsh] - Space dimension : 1 [InputGmsh] - No. of nodes : 2211 [InputGmsh] - No. of 2D elements : 2000 [InputGmsh] - No. of boundary elements : 420 [InputGmsh] - Elapsed time: 0.00769036s. [OutputNekpp] Writing Nektar++ file 'mesh.xml' Fatal : Level 0 assertion violation Coordinate dimension should be at least 2 for a 2D geometry terminate called after throwing an instance of 'Nektar::ErrorUtil::NekError' what(): Level 0 assertion violation Coordinate dimension should be at least 2 for a 2D geometry Aborted (core dumped) NekMesh does not read the correct space dimension for some reason. The mesh was created with ICEM, exported as cgns and converted to msh format with Gmsh version 4.5.2. I use this approach regularly and this is the first time this issue showed up. Any help will be very much appreciated! All the best Alex Sicher versendet mit [Proton Mail](https://proton.me/mail/home).

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Openmp slow in Nektar
by Gao 11 Nov '24

11 Nov '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 run the Compressible solver in parallel, when I used 120 cores, it was slower than 68 cores. I used the commond that "mpirun -n 64 CmpressibleSolver Cyl.xml ". Could someone give me some advice? The computer has 128 cores, 2 NUMA. With best regards

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Get source from CFD
by Gao 10 Nov '24

10 Nov '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 want to simulate the 2D cylinder in a crossflow in CAA. First, I need to compute the cylinder case by Compressible solver, then use the result of Compressible solver as the source of Acoustic solver. But how can I get the Lamb vector in CFD simulation? I think the Lamb vector in 2D is zero, am I right？ Could someone give me some advice? With best regards

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Dimension of geometric curvature to include for a 3D simulation
by Debbahi Saad 10 Nov '24

10 Nov '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 Nektar users, I hope you're all doing fine, i'm using the incompressible navier-stokes solver, in fully 3D case with modified basis, and I have a question about the level at which adding curved geometry information, under <CURVED>....</CURVED> xml node, should be done. *Question:* is it necessary to add surface curvature information or should one be just fine with adding curved edges information only? Regarding this, I have noticed that exporting gmsh higher order mesh produces curved edges and curved faces under <CURVED>....</CURVED> section, which typically reads: > <E ID="45953" EDGEID="26270" NUMPOINTS="3" > TYPE="PolyEvenlySpaced">2.54571429e-01 -7.50000000e-03 -6.42857143e-04 > 2.50785714e-01 -7.50000000e-03 -6.96428571e-04 2.47000000e-01 > -7.50000000e-03 -7.50000000e-04 </E> > <F ID="45954" FACEID="26260" NUMPOINTS="9" > TYPE="PolyEvenlySpaced">-1.46714286e-01 7.50000000e-03 3.00000000e-02 > -1.50500000e-01 7.50000000e-03 3.00000000e-02 -1.54285714e-01 > 7.50000000e-03 3.00000000e-02 -1.46714286e-01 1.12500000e-02 > 3.00000000e-02 -1.50500000e-01 1.12500000e-02 3.00000000e-02 > -1.54285714e-01 1.12500000e-02 3.00000000e-02 -1.46714286e-01 > 1.50000000e-02 3.00000000e-02 -1.50500000e-01 1.50000000e-02 > 3.00000000e-02 -1.54285714e-01 1.50000000e-02 3.00000000e-02 </F> > Since I'm adding curvature information using an external python script, should I be worried about explicitly adding the face curvature as produced inside an auto-generated session file through NekMesh? A first naïve thought I had was that the Edges curvature information would propagate the curvature to higher dimensions through the tensor product !? However, I'm not even close to being formal on this statement. Thank you all in advance, Kind regards, Saad

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Failed to calculate the z-direction force in pipe flow
by 小已 05 Nov '24

05 Nov '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 Nektar++ developers and users I am a phd student from BIT(Beijing institute of technology), and I am using nektar++ to simulat turbulent pipe flow recently. my simulation is a 3DH1D.The mesh is a circular. The flow direction is z-direction and expand with Fourier transform.The caculation only outputs the forces in the x and y directions and the moment of the z-direction. However,I want to get the force in the z-direction on the wall and the program is unable to output. Is there any methods to solve it? The mesh and parameter files are attached.

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Defining a Restart File
by Selman BAYSAL 05 Nov '24

05 Nov '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 am modeling laminar-to-turbulent transition in oscillatory boundary layers using IncNavierStokesSolver. I run this model for an half-period and intend to set the output obtained (say&nbsp;test.chk) as the "Initial Condition" in the subsequent model. To achieve this, I execute the following command:mpirun -np 28 FieldConvert test.xml test.chk test.fldThen, in the XML file (say&nbsp;new.xml), I define&lt;FUNCTION NAME="InitialConditions"&gt;&lt;F FILE="test.fld"&gt;&lt;/FUNCTION&gt;However, when I checked the wall shear stress (wss) outputs, I noticed that the second run may ignore the initial condition (test.fld). What might be causing this issue? What is the proper way to define a restart file? What are the possible solutions (e.g., if there is any other file format that I can use as an initial condition to restart the model, would you please explain how to obtain this format)?&nbsp;Attached is an example of the wall shear stress signal (x-component) signal. This curve should be sinusoidal when the flow is laminar. One can see in the red-circled area that the flow behaves as the model starts from the very beginning (as in the blue-circled area) like there is no initial condition file.&nbsp;Thank you very much for your time and intention.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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Question about Hybird CAA
by feigao2024 05 Nov '24

05 Nov '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 saw some posts regarding the CAA in Nektar, I have some questions. Also, I want to couple the Compressible solver and Acoustic solver. First, how can I get the Lamb vector in Compressible solver? Second, if I export the result average file from the thirdparty CFD solver, then how can I transform the result file to .fld or .pts? Is there anything else I should be aware of about CAA in Nektar? With best regards

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Failed to read nek5000 data
by Wei He 04 Nov '24

04 Nov '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 Nektar++ developers and users, I am planing to use 3D flow datas generated by nek5000. When I run the command on a centos machine, the process fails with errors, as shown below: FieldConvert roCyl_half0.f00100 cyl.fld -------------------------------------------------------------------------- WARNING: There was an error initializing an OpenFabrics device. Local host: master Local device: mlx5_0 -------------------------------------------------------------------------- Field contains unknown variable: X [master:42932] *** Process received signal *** [master:42932] Signal: Aborted (6) [master:42932] Signal code: (-6) [master:42932] [ 0] /lib64/libpthread.so.0(+0xf630)[0x7f85cfcf4630] [master:42932] [ 1] /lib64/libc.so.6(gsignal+0x37)[0x7f85cf94d387] [master:42932] [ 2] /lib64/libc.so.6(abort+0x148)[0x7f85cf94ea78] [master:42932] [ 3] /share/home/user1/nektar++/build/dist/lib64/libFieldUtils.so.5.6.0(_ZN6Nektar10FieldUtils12InputNek50009v_ProcessERN5boost15program_options13variables_mapE+0xe70)[0x7f85d3db2590] [master:42932] [ 4] FieldConvert[0x41e615] [master:42932] [ 5] FieldConvert[0x41b47e] [master:42932] [ 6] /lib64/libc.so.6(__libc_start_main+0xf5)[0x7f85cf939555] [master:42932] [ 7] FieldConvert[0x41dad2] [master:42932] *** End of error message *** Aborted (core dumped) While I also tried a 2D case on my laptop, it neither doesn't pass the procession. I wonder if I did the correct things, and thank you in advance! regards, Wei FieldConvert cylinder2D0.f00100 cyl.fld Field contains unknown variable: X [Harqin:55513] *** Process received signal *** [Harqin:55513] Signal: Abort trap: 6 (6) [Harqin:55513] Signal code: (0) [Harqin:55513] [ 0] 0 libsystem_platform.dylib 0x00000001878fe584 _sigtramp + 56 [Harqin:55513] [ 1] 0 libsystem_pthread.dylib 0x00000001878cdc20 pthread_kill + 288 [Harqin:55513] [ 2] 0 libsystem_c.dylib 0x00000001877daa30 abort + 180 [Harqin:55513] [ 3] 0 libFieldUtils.5.5.0.dylib 0x0000000100a784dc _ZN6Nektar10FieldUtils12InputNek50009v_ProcessERN5boost15program_options13variables_mapE + 5284 [Harqin:55513] [ 4] 0 FieldConvert 0x00000001002f7b5c _Z9RunModuleNSt3__110shared_ptrIN6Nektar10FieldUtils6ModuleEEERN5boost15program_options13variables_mapEb + 820 [Harqin:55513] [ 5] 0 FieldConvert 0x00000001002f24e8 main + 18272 [Harqin:55513] [ 6] 0 dyld 0x0000000187543154 s tart + 2476 [Harqin:55513] *** End of error message *** zsh: abort FieldConvert cylinder2D0.f00100 cyl.fld

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