March 2023 - Nektar-users - imperial.ac.uk

Installing Nektar++ 5.2.0 on a cluster
by Ehsan Asgari 09 Mar '23

09 Mar '23

******************* 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 Everyone, I am trying to install the latest version of Nektar on a cluster. However, I get the following error at some point: ../../library/SpatialDomains/libSpatialDomains.so.5.3.0: error: undefined > reference to '__intel_sse2_strlen' > ../../library/SpatialDomains/libSpatialDomains.so.5.3.0: error: undefined > reference to '_intel_fast_memcpy' > ../../library/SpatialDomains/libSpatialDomains.so.5.3.0: error: undefined > reference to '_intel_fast_memset' > collect2: error: ld returned 1 exit status > make[2]: *** [utilities/NekMesh/CMakeFiles/NekMesh.dir/build.make:106: > utilities/NekMesh/NekMesh] Error 1 > make[1]: *** [CMakeFiles/Makefile2:1647: > utilities/NekMesh/CMakeFiles/NekMesh.dir/all] Error 2 > make: *** [Makefile:141: all] Error 2 I had "NEKTAR_USE_SYSTEM_BLAS_LAPACK:BOOL=ON " and "THIRDPARTY_BUILD_BLAS_LAPACK:BOOL=ON" in the ccmake as per suggested in the user archives. I appreciate your kind help. Kind regards syavash

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(no subject)
by Ehsan Asgari 08 Mar '23

08 Mar '23

******************* 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 Everyone, I had two questions: 1-Is it possible to specify the output field overwrite using a parameter? For example, keeping only the last two time fields. I searched through the user-guide but couldn't find it. 2-What is the difference between "MODIFIED" and "GLL_LAGRANGE" under TYPE in the incompressible solver? I appreciate your kind responses. syavash

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Standard way of handling large mesh in parallel run
by Ehsan Asgari 08 Mar '23

08 Mar '23

******************* 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 Everyone I've been trying to import a mesh generated in a third-party package and run it in the incompressible solver. First, I tried a smaller mesh with a size of 10MB and 32 cores on an HPC with 3GB ram specified for each core. It worked and I proceeded to the main larger mesh with a size of 75MB and 128 cores. However, I found it can be quite challenging to establish a simulation as I often get MPI-related errors at the very beginning. I was wondering if this is the standard way of handling large mesh files in parallel using mpirun: mpirun -np 128 IncNavierStokesSolver condition.xml grid.xml I am new to nektar++ so my question might seem trivial. Kind regards syavash

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Questions about simulations of a flexible cylinder by Nektar++
by Zhipeng Yu 05 Mar '23

05 Mar '23

******************* 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 Professor Hope this email finds you well. My name is Zhipeng Yu, and I am a PhD student of Tsinghua University, China. Recently, I encountered some problems when I used Nektar++ to carry out simulations of a flexible cylinder. The problems are shown as follows: 1. Can we define the natural frequency of a flexible cylinder in the in.xml file? Besides, could you tell me the relationship between EI and fn? It seems the definition of some parameters is different from other references, such as the mass ratio. 2. During post-processing, the real displacement of a cylinder cannot be seen by using "FieldConvert in.xml in.fld out.dat". Are there any ways to show the transformed coordinates of the cylinder in tecplot? 3. How to turn the DNS to LES by Nektar++? Thank you for your patient. Best regards. Zhipeng Yu

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Setting a maximum artificial viscosity value
by Andrew Barnes 03 Mar '23

03 Mar '23

******************* 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'm trying to run a complex transonic case in the CompressibleFlowSolver which keeps diverging at a specific point in flow time no matter which settings I put in, including using a few different meshes for that geometry. After playing around with an alternative solver I noticed that the stability of the simulation was highly dependent on the maximum artificial viscosity setting for the shock capture method. So I was wondering if there is an equivalent option in Nektar++? Ideally one which applies to the NonSmooth capture method but I can switch to Physical if necessary. Kind regards, Andrew

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T-S tutorial
by Ehsan Asgari 02 Mar '23

02 Mar '23

******************* 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 am new to Nektar++ and when examining the T-S tutorial I couldn't find the associated input files, particularly the mesh file. Am I missing something? Thanks syavash

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