January 2021 - Nektar-users

external meshes
by Cimpoeru, Ionut Andrei 28 Jan '21

28 Jan '21

******************* 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, I have a linear multiblock structured mesh generated in Icem Hexa and I would like to know if NekMesh could be used to curve external linear meshes. Thanks a lot and looking forward to hearing from you. Cheers, Andrei Not Subject to Export Control This information is provided by Rolls-Royce in good faith based upon the latest information available to it; no warranty or representation is given; no contractual or other binding commitment is implied. (c) 2021 Rolls-Royce The data contained in, or attached to, this e-mail, may contain confidential information. If you have received it in error you should notify the sender immediately by reply e-mail, delete the message from your system and contact +44 (0) 3301235850 (Security Operations Centre) if you need assistance. Please do not copy it for any purpose, or disclose its contents to any other person. An e-mail response to this address may be subject to interception or monitoring for operational reasons or for lawful business practices. (c) 2021 Rolls-Royce plc Registered office: Kings Place, 3rd Floor 90 York Way, London, N1 9FX Company number: 1003142. Registered in England

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Launching a solver in parallel
by Eli Frydman 28 Jan '21

28 Jan '21

******************* 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, I have an issue running the incompressible solver in parallel. I compiled Nektar++ with the flag NEKTAR_USE_MPI set to ON but when I execute my case with the command: mpirun -np 8 IncNavierStokesSolver session_s1223.xml I got the following error message: Fatal : Level 0 assertion violation A parallel solver must be used when run in parallel. ------------------------------------------------------- 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: [[30155,1],0] Exit code: 1 Can you please help me to resolve this issue? Regards, Eli

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Nektar++ 5.0.1 Released
by Chris Cantwell 22 Jan '21

22 Jan '21

Dear all, We are pleased to announce the release of Nektar++ v5.0.1. With this update, we now have binary packages for a range of Linux distributions including recent versions of Debian, Ubuntu, CentOS and Fedora, which will continue to be updated with each new release. Installation instructions for our binary packages are available in the user guide. This release includes a number of bug fixes to the 5.0 release: **Library** - Fix incorrect coordinate dimension used in history point filter (!1118) - Added checked conversion from double to int in SessionReader (!1113) - Fix compile errors with GCC 9.x (!1108) - Correct the Energy/Enstropy integral for the 3DH1 flow (!1132) - Added IsRealEqual method to compare real numbers with relative tolerance. Started using it in SharedArray and in NekMesh to fix peralign-extrude tool chain (!1134) - Fix Collection unit tests (!1160) - Fix periodic boundary conditions with HDF5 input file (!1163) - Fix performance of GetExp(coord) by using octree lookup (!1165) - Fix DESTDIR issues for MacPorts (!1179) **IncNavierStokesSolver** - Change the baseflow time in the Adjoint advection (!1133) **FieldConvert** - Fix OutputTecplot skipping final plane in 3DH1D (!1016) **NekMesh** - Fix compile errors when using intel cc (!1114) **Documentation** - Fix error in compilation of developer guide (!1136) **CI** - Added checked conversion from double to int in SessionReader (!1113) - Switched to Gitlab CI (!1120, !1120, !1128, !1129, !1131, !1141) - Updated bullseye build to remove UCX components (!1203) - Added automated packaging for Linxu distributions (!1206) 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 Senior Lecturer in Aeronautics Department of Aeronautics Imperial College London South Kensington Campus London SW7 2AZ Tel: +44 (0)20 759 45050 Email: c.cantwell(a)imperial.ac.uk www.imperial.ac.uk/people/c.cantwell

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NekMesh error message
by Eli Frydman 21 Jan '21

21 Jan '21

******************* 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 Please don't take account my previous email, there is a solution to my issue on the forum. Thanks Mr Frydman

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NekMesh error message with mcf type file
by Eli Frydman 20 Jan '21

20 Jan '21

******************* 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, I tried to get a mesh for the naca airfoil example in the directory nektar++-5.0.0/utilities/NekMesh/Tests/MeshGen/NACA using the command : NekMesh -v 2d_bl.mcf mesh.xml But i got the following error message: terminate called after throwing an instance of 'Nektar::ErrorUtil::NekError' what(): Level 0 assertion violation No such module: Input: mcf Can you please help me with this issue. Thank you Mr Frydman

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Power Kernel
by Vishal Saini 17 Jan '21

17 Jan '21

******************* 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, Hope you're keeping well. I was trying to understand the working of the Power Kernel in the context of SVV. The input coefficient related to this kernel is to be scaled by *a*h/P* (according to Moura's original paper) where *a* is some measure of local elemental velocity and *h/P* gives local mesh size. So, I ventured into VelocityCorrectionScheme.cpp. Now, 1. I could see where *h/P* is multiplied but not *a *(I imagined that *a* would vary in space but seems like a=1 for the whole domain). Could someone kindly point out where that would be? 2. I noticed that the said scaling takes place just once, in the beginning of the simulation. Is that correct? Thank you in advance. --- *Vishal SAINI*

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Filters Time writing problem
by Moto Light 07 Jan '21

07 Jan '21

******************* 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, happy new year for all of you, Just a small question. Whenever I am using filters like (AeroForces) or using probes and set the OutputFrequancy =1 sometimes the written files are repeating time in the output, please see the forces file written data. <FILTER TYPE="AeroForces"> <PARAM NAME="OutputFile">stats/stats4/CylinderForces3D</PARAM> <PARAM NAME="OutputFrequency">*1*</PARAM> <PARAM NAME="Boundary"> B[6] </PARAM> </FILTER> //////////////////////////////////// the written forces file looks like # Time F1-press F1-visc F1-total F2-press F2-visc F2-total 1821.08 4.1827904 0.4123355 4.5951259 0.45330259 -0.49524554 -0.041942954 1821.08 4.5897777 0.4169459 5.0067236 0.5086121 -0.49606064 0.012551456 1821.08 3.2548159 0.41033032 3.6651462 0.39509326 -0.4935032 -0.098409937 1821.08 4.6163333 0.41190927 5.0282425 0.37645971 -0.49545957 -0.11899986 1821.08 4.01314 0.41139674 4.4245367 0.52263137 -0.4956953 0.026936074 As you see the written time is fixed and after 15 steps changes to be 1821.09, can we control the written time to increase the number of floating digits written by filters. Regards, Reda

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FieldConvert -m gradient seg-fault
by G. D. McBain 04 Jan '21

04 Jan '21

******************* 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. ******************* I'm just starting to learn Nektar++ from the tutorials and User Guide and mostly it's going very well, but I'm having trouble with FieldConvert -m gradient, hitting a segmentation fault. I'm wondering whether I'm misunderstanding its use. For example, after successfully running the basics-helmholtz example https://doc.nektar.info/tutorials/latest/basics/helmholtz/basics-helmholtz.… gmsh -2 Helm_mesh.geo Nekmesh Helm_mesh.msh Helm_mesh.xml ADRSolver -v Helm_mesh.xml Helm_conditions.xml FieldConvert Helm_mesh.xml Helm_conditions.xml Helm_mesh.fld Helm_mesh.vtu to produce Helm_mesh.fld and Helm_mesh.vtu, I tried FieldConvert -m gradient Helm_mesh.xml Helm_conditions.xml Helm_mesh.fld Helm-grad.fld following the documentation at https://doc.nektar.info/userguide/latest/user-guidese22.html#x35-1480005.5.… but this raised [levy:58744] *** Process received signal *** [levy:58744] Signal: Segmentation fault (11) [levy:58744] Signal code: Address not mapped (1) [levy:58744] Failing at address: 0xb0 [levy:58744] [ 0] /lib/x86_64-linux-gnu/libc.so.6(+0x3f040)[0x7f9d682b1040] [levy:58744] [ 1] /usr/lib/x86_64-linux-gnu/libFieldUtils.so.5.0.0(_ZN6Nektar10FieldUtils11ProcessGrad7ProcessERN5boost15program_options13variables_mapE+0x6cc)[0x7f9d6a1aa7ac] [levy:58744] [ 2] FieldConvert(_Z9RunModuleSt10shared_ptrIN6Nektar10FieldUtils6ModuleEERN5boost15program_options13variables_mapEb+0x3f)[0x55c3dbf99b8f] [levy:58744] [ 3] FieldConvert(main+0x176c)[0x55c3dbf95e5c] [levy:58744] [ 4] /lib/x86_64-linux-gnu/libc.so.6(__libc_start_main+0xe7)[0x7f9d68293bf7] [levy:58744] [ 5] FieldConvert(_start+0x2a)[0x55c3dbf9956a] [levy:58744] *** End of error message *** Segmentation fault (core dumped) That's on Ubuntu 18.04, where I had installed nektar++ from http://www.nektar.info/ubuntu-bionic bionic/contrib, but I also get the same error on CentOS 7.7.1908, using the docker image nektarpp/nektar:244f4842. What I was wanting to use the gradient module in my own project fpr was having solved for a steady incompressible potential flow with ADRSolver (EQTYPE "Laplace") to compute the velocity field as the gradient of the potential. Thank you, Geordie McBain Sent from [ProtonMail](https://protonmail.com), Swiss-based encrypted email.

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