February 2019 - Nektar-users

creating user defined libraries in Nektar++
by Nitish Arya 20 Feb '19

20 Feb '19

Hi everyone, I am trying to link APE solver with a separate solver for an aero-acoustic simulation. For this purpose, I have to access the data structures during runtime which can be achieved by creating a new user-defined library(".so"). Is it possible to create a user-defined library which would facilitate me to have a coupled simulation if the library path is included in the session file; or a stand-alone simulation if it is not included? If yes, I would really appreciate if someone can guide me to build it as I am new and uncomfortable with cmake structure. Sincerely, Nitish

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compiling and installation issue of Nektar++ 4.4.1
by zxiong＠sas.upenn.edu 20 Feb '19

20 Feb '19

Dear officer, I can't successfully install Nektar++ 4.4.1 on my macOS Mojave(10.14.3) laptop by following the installation tutorial on user-guide-4.4.1. In the last step of installation is type command 'test', but it showed many lines of 'not Run'. Also, I tried installation tutorial from the web page: https://www.nektar.info/installing-nektar-on-os-x-through-macports-or-homeb… by using home-brew. However, it's still not working. My Xcode version is 10.1. Could you help me to fix this problem? If you need more information to know better my issue, please let me know. Thank you very much and expecting your response. Best, Zhen

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Re: [Nektar-users] FW: Adding a non analytic velocity inlet profile
by Amitvikram Dutta 14 Feb '19

14 Feb '19

Thanks Sherwin, The workflow is clear to me now! On Thu, Feb 14, 2019 at 8:39 AM Amitvikram Dutta < amitvikram.dutta(a)uwaterloo.ca> wrote: > > ------------------------------ > *From:* nektar-users-bounces(a)imperial.ac.ukOn Behalf OfSherwin, Spencer J > *Sent:* February 14, 2019 8:39:13 AM (UTC-05:00) Eastern Time (US & > Canada) > *To:* Amitvikram Dutta > *Cc:* nektar-users > *Subject:* Re: [Nektar-users] Adding a non analytic velocity inlet profile > > Hi Amit, > > It is possible to specify a .fld file as a boundary condition. In the past > I have used RANS data. > > The process is that you need to extract the surface from your domain using > Nekmesh with the -m extract module. You will need to specify the composite > as an argument. I.e :surf=2 > > Once you have the surface you can get a set of x,y,z points from this > surface using FieldConvert. You will then need to work out how to > interpolate your data to these points. There is then a module to project > the interpolated points back to a surface fld file. I do not recall this > off the top of my head but it should be in the user guide. > > Having successfully generates a surface fld file you can then specify this > in the xml boundary condition. Rather than using > > VALUE=“x*y” > > You can specify > > FILE=“myfile.fld” > > Cheers, > Spencer > > > > Sent from my iPhone > > On 14 Feb 2019, at 02:03, Amitvikram Dutta <amitvdutta23(a)gmail.com> wrote: > > Hi all, > > I'm re-asking a question I posed a few weeks ago since the email may have > gotten lost in the clutter. Is it possible to add a non analytic profile to > a boundary, if one does not have a .bc file. For example if One has > experimental data on a series of points over a domain, would it be possible > to interpolate that data to a boundary region of the mesh? > > > Sincerely, > -- > > *Amitvikram Dutta* > > Graduate Research Assistant > > Fluid Mechanics Research Lab > > Multi-Physics Interaction Lab > > University of Waterloo > > _______________________________________________ > Nektar-users mailing list > Nektar-users(a)imperial.ac.uk > https://mailman.ic.ac.uk/mailman/listinfo/nektar-users > > -- *Amitvikram Dutta* Graduate Research Assistant Fluid Mechanics Research Lab Multi-Physics Interaction Lab University of Waterloo

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Adding a non analytic velocity inlet profile
by Amitvikram Dutta 14 Feb '19

14 Feb '19

Hi all, I'm re-asking a question I posed a few weeks ago since the email may have gotten lost in the clutter. Is it possible to add a non analytic profile to a boundary, if one does not have a .bc file. For example if One has experimental data on a series of points over a domain, would it be possible to interpolate that data to a boundary region of the mesh? Sincerely, -- *Amitvikram Dutta* Graduate Research Assistant Fluid Mechanics Research Lab Multi-Physics Interaction Lab University of Waterloo

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How can I open or see Nektar documents?
by Dongmyung Suh 01 Feb '19

01 Feb '19

Hello, Nektar community, I installed Nektar from source code. After installation, I found developer-guide, doxygen, and user-guide in docs folder. But I don't know how to open and see them. Please let me know how to read them. Thank you Dongmyung Suh

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Nektar hangs on NFS
by Fatih Ertinaz 01 Feb '19

01 Feb '19

Hello I deploy a small cluster on the cloud (not on IB). I setup the VMs, keys etc. and I use NFS for shared storage. This is a small cluster intended for 1-2 users, so presumably NFS should be fine. At least that's what I thought. Currently I am testing the tutorial case "basics-advection-diffusion". It runs when executed in serial or parallel using 1 node (4 cores). However, when I use 2 nodes it hangs during: > Initial Conditions: > - Field u: sin(k*x)*cos(k*y) > Writing: "ADR_mesh_aligned_0.chk" (0.0199919s, XML) I see that "ADR_mesh_aligned_0" and its content written successfully, however next directory cannot be created and solver remains idle. > mpirun -np 8 -mca btl_tcp_if_include eth0 -hostfile hosts \ > $NEKTAR_BIN/ADRSolver ADR_mesh_aligned.xml ADR_conditions.xml I tested a simple hostname command and an mpi parallel file write, both worked fine on two nodes with mpirun. Any suggestions highly appreciated. Thank you // Fatih

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'std::bad_alloc' error in several tests
by Kurt Sansom 01 Feb '19

01 Feb '19

Hi am trying to compile the master branch, but when I go to test it everything works except for about some tests. it appears that they are all related to the code throwing 'std::bad_alloc'. Can anyone point me to something that might help me resolve this? Ubuntu 16.04, openmpi, most modules in cmake are on except python, CCM, CFI, Metis, petsc are off. using external OCE, and vtk. I tried a clean rebuild, and several other variants without there being any change. I tried to debug one of the tests using gdb without much clarity. 1 - NekMesh_Nektar++/InvalidTetFace (Failed) 2 - NekMesh_Nektar++/InvalidQuads (Failed) 3 - NekMesh_Nektar++/Tube45Refinement (Failed) 4 - NekMesh_Nektar++/Tube45Refinement_extractsurf (Failed) 5 - NekMesh_Nektar++/CylQuadBl (Failed) 35 - NekMesh_MeshGen/cylinder (Failed) 36 - NekMesh_MeshGen/sphere (Failed) 37 - NekMesh_MeshGen/2d-cad (Failed) 38 - NekMesh_MeshGen/2d-naca (Failed) 39 - NekMesh_MeshGen/geo (Failed) 40 - NekMesh_MeshGen/t106c (Failed) 41 - NekMesh_MeshGen/t106step (Failed) 43 - FieldConvert_chan3D_interppointsplane (Failed) 44 - FieldConvert_chan3D_interppointsbox (Failed) 46 - FieldConvert_bfs_probe (Failed) 52 - FieldConvert_chan3D_csv (Failed) 53 - FieldConvert_chan3D_pts (Failed) 58 - FieldConvert_chan3D_probe (Failed) 63 - FieldConvert_interpfield (Failed) 72 - FieldConvert_chan3D_interppointsplane_par (Failed) 73 - FieldConvert_chan3D_interppointsbox_par (Failed) 329 - IncNavierStokesSolver_Cyl_AdaptiveSFD (Failed) 558 - tutorial_basics-advection-diffusion-msh-align (Failed) 568 - tutorial_fundamentals-integration-std1D-python (Failed) 569 - tutorial_fundamentals-integration-std2D-python (Failed) 570 - tutorial_fundamentals-integration-loc2D-python (Failed) 571 - tutorial_fundamentals-differentiation-std1D-python (Failed) 572 - tutorial_fundamentals-differentiation-std2D-python (Failed) 573 - tutorial_fundamentals-differentiation-loc2D-python (Failed) 583 - tutorial_mesh-generation-2d-step (Failed) Regards, ~Kurt -- Kurt Sansom

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Segmentation fault in the advectiondiffusion.xml
by Dongmyung Suh 01 Feb '19

01 Feb '19

Dear Nektar community, After I installed Nektar4.4.1 in my Ubuntu (18.04) by source code, I successfully run the two examples (1D Advection equ and 2D Helmholtz problem) in User guide, Chapter 6. But when I tried the third example (AdvectionDiffusion.xml, in 6.4.3 Advection dominated mass transport in a pipe), I bumped into a segmentation error. I am a newbie in Nektar, So I could not find which one is a problem in the input xml file. Could you give me an idea to solve the problem? I really want to learn Nektar. Thank you. Dongmyung Suh ---------------------------------------------------------------------------------------------------------------- T5500:~/Desktop/Nektar_exercise/AdvectionDiffusion$ ADRSolver AdvectionDiffusion.xml Warning: Level 0 assertion violation Using Default variable expansion definition for field: u [T5500:03146] *** Process received signal *** [T5500:03146] *Signal: Segmentation fault (11)* [T5500:03146] Signal code: Address not mapped (1) [T5500:03146] Failing at address: 0x8 [T5500:03146] [ 0] /lib/x86_64-linux-gnu/libc.so.6(+0x3ef20)[0x7fbe5b148f20] [T5500:03146] [ 1] /home/dongmyung/Software/nektar++-4.4.1/build/dist/lib64/nektar++-4.4.1/libSolverUtils.so.4.4.1(_ZN6Nektar11SolverUtils14UnsteadySystem17v_GenerateSummaryERSt6vectorISt4pairINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEES9_ESaISA_EE+0x28f)[0x7fbe5e33f9af] [T5500:03146] [ 2] /home/dongmyung/Software/nektar++-4.4.1/build/dist/lib64/nektar++-4.4.1/libSolverUtils.so.4.4.1(_ZN6Nektar11SolverUtils14DriverStandard9v_ExecuteERSo+0x4a4)[0x7fbe5e2e3b14] [T5500:03146] [ 3] ADRSolver(main+0x177)[0x55d5de973037] [T5500:03146] [ 4] /lib/x86_64-linux-gnu/libc.so.6(__libc_start_main+0xe7)[0x7fbe5b12bb97] [T5500:03146] [ 5] ADRSolver(_start+0x2a)[0x55d5de98329a] [T5500:03146] *** End of error message *** Segmentation fault (core dumped) ---------------------------------------------------------------------------------------------------------------------

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L2 error
by Amitvikram Dutta 01 Feb '19

01 Feb '19

Hi all, I'd like to clear up a point that has been bugging me for some time. Are the L2 and Linf norms in nektar++ always defined with respect to a given analytical solution for a problem? What do these terms represent in a case for which a solution is not specified? Sincerely, -- *Amitvikram Dutta* Graduate Research Assistant Fluid Mechanics Research Lab Multi-Physics Interaction Lab University of Waterloo

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