April 2016 - Nektar-users - imperial.ac.uk

Re: [Nektar-users] Parallel transposition not implemented yet for 3D-Homo-2D approach
by Asim Onder 01 Jun '16

01 Jun '16

Hi Douglas, thanks for the feedback. I was aware of --npz parallelization but was using a small number, not 1/2 or 1/4 of HomModesZ. Increasing npz really helped. I still have to try GlobalSysSoln. Now I face a memory problem for another case. The simulation runs out of memory when starting from a checkpoint file. Here is a little bit information about this case: - Mesh is made of around 16000 quad elements with p=5, i.e., NUMMODES="6" TYPE="MODIFIED" in xy, and HomModesZ=1080 in z direction. - I'm trying to run this case on 60 computing nodes each equipped with 24 processors, and a memory of 105 gb. In total, it makes 1440 procs, and 6300gb memory. - Execution command: mpirun -np 1440 IncNavierStokesSolver --npz 360 config.xml I was wondering if the memory usage of the application is scaling on different cores during IO, or using only one core. If it is only one core, than if it exceeds 105gb, it crushes I guess. Would you have maybe any suggestion/comment on this? Thanks, Asim On 04/13/2016 12:12 AM, Serson, Douglas wrote: Hi Asim, Concerning your questions: 1- Are you using the command line argument --npz? This is very important for obtaining an efficient parallel performance with the Fourier expansion, since it defines the number of partitions in the z-direction. If it is not set, only the xy plane will be partitioned and the parallelism will saturate quickly. I suggest initially setting npz to 1/2 or 1/4 of HomModesZ (note that nprocs must be a multiple of npz, since nprocs/npz is the number of partitions in the xy plane). Also, depending on your particular case and the number of partitions you have in the xy plane, your simulation may benefit from using a direct solver for the linear systems. This can be activated by adding '-I GlobalSysSoln=XxtMultiLevelStaticCond' to the command line. This is usually more efficient for a small number of partitions, but considering the large size of your problem it might be worth trying it. 2- I am not sure what could be causing that. I suppose it would help if you could send the exact commands you are using to run FieldConvert. Cheers, Douglas ________________________________ From: Asim Onder <ceeao(a)nus.edu.sg><mailto:ceeao@nus.edu.sg> Sent: 12 April 2016 06:42 To: Sherwin, Spencer J; Serson, Douglas Cc: nektar-users; Moxey, David Subject: Re: [Nektar-users] Parallel transposition not implemented yet for 3D-Homo-2D approach Dear Spencer, Douglas, Nektar-users, I'm involved now in testing of a local petascale supercomputer, and for some quite limited time I can use several thousand processors for my DNS study. My test case is oscillating flow over a rippled bed. I build up a dense unstructured grid with p=6 quadrilateral elements in x-y, and Fourier expansions in z directions. In total I have circa half billion dofs per variable. I would have a few questions about this relatively large case: 1. I noticed that scaling gets inefficient after around 500 procs, let's say parallel efficiency goes below 80%. I was wondering if you would have any general suggestions to tune the configurations for a better scaling. 2. Postprocessing vorticity and Q criterion is not working for this case. At the of the execution Fieldconvert writes some small files without the field data. What could be the reason for this? Thanks you in advance for your suggestions. Cheers, Asim On 03/21/2016 04:16 AM, Sherwin, Spencer J wrote: Hi Asim, To follow-up on Douglas’ comment we are trying to get more organised to sort out a developers guide. We are also holding a user meeting in June. If you were able to make this we could also try and have a session on getting you going on the developmental side of things. Cheers, Spencer. On 17 Mar 2016, at 14:58, Serson, Douglas <d.serson14(a)imperial.ac.uk<mailto:d.serson14@imperial.ac.uk>> wrote: Hi Asim, I am glad that your simulation is now working. About your questions: 1. We have some work done on a filter for calculating Reynolds stresses as the simulation progresses, but it is not ready yet, and it would not provide all the statistics you want. Since you already have a lot of chk files, I suppose the best way would indeed be using a script to process all of them with FieldConvert. 2. Yes, this has been recently included in FieldConvert, using the new 'meanmode' module. 3. I just checked that, and apparently this is caused by a bug when using this module without fftw. This should be fixed soon, but as an alternative this module should work if you switch fftw on (just add to you session file, if the code was compiled with support to fftw). 4. I think there is some work towards a developer guide, but I don't how advanced is the progress on that. I am sure Spencer will be able to provide you with more information on that. Cheers, Douglas ________________________________________ From: Asim Onder <ceeao(a)nus.edu.sg<mailto:ceeao@nus.edu.sg>> Sent: 17 March 2016 09:10 To: Serson, Douglas; Sherwin, Spencer J Cc: nektar-users; Moxey, David Subject: Re: [Nektar-users] Parallel transposition not implemented yet for 3D-Homo-2D approach Hi Spencer, Douglas, Thanks to your suggestions I managed to get the turbulent regime for the oscillatory channel flow. I have now completed the DNS study for one case, and built up a large database with checkpoint (*chk) files. I would like to calculate turbulent statistics using this database, especially for second order terms, e.g. Reynolds stresses and turbulent dissipation, and third order terms, e.g. turbulent diffusion terms. However, I am a little bit confused how I could achieve this. I would appreciate if you could give some hints about the following: 1. The only way I could think of to calculate turbulent statistics is to write a simple bash script to iterate over chk files, and apply various existing/extended FieldConvert operations on individual chk files. This would require some additional storage to store the intermediate steps, and therefore would be a bit cumbersome. Would it be any simpler way directly doing this directly in Nektar++? 2. I have one homogeneous direction, for which I used Fourier expansions. I would like to apply spatial averaging over this homogeneous direction. Does Nektar++ already contain such functionality? 3. I want to use 'wss' in Fieldconvert module to calculate wall shear stress. However, it returns segmentation fault. Any ideas why it could be? 4. I was wondering if there is any introductory document for basic programming in Nektar++. User guide does not contain information about programming. It would be nice to have some additional information to Doxygen documentation. Thank you very much in advance for your feedback. Cheers, Asim On 02/15/2016 11:59 PM, Serson, Douglas wrote: Hi Asim, As Spencer mentioned, svv can help in stabilizing your solution. You can find information on how to set it up in the user guide (pages 92-93), but basically all you need to do is use: You can also tune it by setting the parameters SVVCutoffRatio and SVVDiffCoeff, but I would suggest starting with the default parameters. Also, you can use the parameter IO_CFLSteps to output the CFL number. This way you can check if the time step you are using is appropriate. Cheers, Douglas From: Sherwin, Spencer J Sent: 14 February 2016 19:46 To: ceeao Cc: nektar-users; Serson, Douglas; Moxey, David Subject: Re: [Nektar-users] Parallel transposition not implemented yet for 3D-Homo-2D approach Hi Asim, Getting a flow through transition is very challenging since there is a strong localisation of shear and this can lead to aliasing issues which can then cause instabilities. Both Douglas and Dave have experienced this with recent simulations so I am cc’ing them to make some suggestions. I would be inclined to be using spectralhpdealiasing and svv. Hopefully Douglas can send you an example of how to switch this on. Cheers, Spencer. On 11 Feb 2016, at 10:32, ceeao<<mailto:ceeao@nus.edu.sg>ceeao(a)nus.edu.sg<mailto:ceeao@nus.edu.sg>> wrote: Hi Spencer, Nektar-Users, I followed the suggestion and coarsened the grid a bit. This way it worked impressively fast, but the flow is stable and remains laminar, as I didn't add any perturbations. I need to kick the transition to have turbulence. If I add white noise, even very low magnitude, conjugate gradient solver blows up again. I also tried adding some sinusoidal perturbations to boundary conditions, and again had troubles with CG. I don't really get CG's extreme sensitivity to perturbations. Any suggestion is much appreciated. Thanks in advance. Cheers, Asim On 02/08/2016 04:48 PM, Sherwin, Spencer J wrote: HI Asim, How many parallel cores are you running on. Sometime starting up these flows can be tricky especially if you are immediately jumping to a high Reynolds number. Have you tried first starting the flow at a Lower Reynolds number? Also 100 x 200 is quite a few elements in the x-y plane. Remember the polynomial order adds in more points on top of the mesh discretisation. I would perhaps recommend trying a smaller mesh to see how that goes first. Actually I note there is a file called TurbChFl_3D1H.xml in the ~/Nektar/Solvers/IncNavierStokesSolver/Examples directory which might be worth looking at. I think this was a mesh used in Ale Bolis’ thesis which you can find under: http://wwwf.imperial.ac.uk/ssherw/spectralhp/papers/PhDThesis/Bolis_Thesis.… Cheers, Spencer. On 1 Feb 2016, at 07:01, ceeao<mailto:ceeao@nus.edu.sg><ceeao(a)nus.edu.sg><mailto:ceeao@nus.edu.sg> wrote: Hi Spencer, Thank you for the quick reply and suggestion. I switched indeed to 3D homo 1D case and this time I have problems with the divergence of linear solvers. I refined the grid in the channel flow example to 100x200x64 in x-y-z directions, and left everything else the same. When I employ the default global system solver "IterativeStaticCond" with this setup, I get divergence: "Exceeded maximum number of iterations (5000)". I checked the initial fields and mesh in Paraview, everything seems to be normal. I also tried the "LowEnergyBlock" preconditioner, and apparently this one is valid only in sheer 3D cases. My knowledge in iterative solvers for hp-Fem is minimal. Therefore, I was wondering if you could suggest maybe a robust option that at least converge. My concern is getting some rough estimates for the speed of Nektar++ in my oscillating channel flow problem. If the speed will be promising, I will switch to Nektar++ from OpenFOAM, as OpenFOAM is low-order and not really suitable for DNS. Thanks again in advance. Cheers, Asim On 01/31/2016 11:53 PM, Sherwin, Spencer J wrote: Hi Asim, I think your conclusions is correct. We did some early implementation into the 2D Homogeneous expansion but have not pulled it all the way through since we did not have a full project on this topic. We have however kept the existing code running through our regression test. For now I would perhaps suggest you try the 3D homo 1D approach for your runs since you can use parallelisation in that code. Cheers, Spencer. On 29 Jan 2016, at 04:00, ceeao<mailto:ceeao@nus.edu.sg><ceeao(a)nus.edu.sg><mailto:ceeao@nus.edu.sg> wrote: Dear all, I just installed the library, and need to simulate DNS of a channel flow with oscillating pressure gradient. As I have two homogeneous directions I applied standard Fourier discretization in these directions. It seems like this case is not parallelized yet, and I got the error in the subject. I was wondering if I'm overlooking something. If not, are there maybe any plans in the future to include parallelization of 2D FFT's? Thank you in advance. Best, Asim Onder Research Fellow National University of Singapore ________________________________ Important: This email is confidential and may be privileged. If you are not the intended recipient, please delete it and notify us immediately; you should not copy or use it for any purpose, nor disclose its contents to any other person. Thank you. _______________________________________________ Nektar-users mailing list Nektar-users(a)imperial.ac.uk<mailto:Nektar-users@imperial.ac.uk> https://mailman.ic.ac.uk/mailman/listinfo/nektar-users Spencer Sherwin 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<mailto:s.sherwin@imperial.ac.uk> +44 (0) 20 759 45052 Important: This email is confidential and may be privileged. If you are not the intended recipient, please delete it and notify us immediately; you should not copy or use it for any purpose, nor disclose its contents to any other person. Thank you. Spencer Sherwin 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<mailto:s.sherwin@imperial.ac.uk> +44 (0) 20 759 45052 Important: This email is confidential and may be privileged. If you are not the intended recipient, please delete it and notify us immediately; you should not copy or use it for any purpose, nor disclose its contents to any other person. Thank you. Spencer Sherwin 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<mailto:s.sherwin@imperial.ac.uk> +44 (0) 20 759 45052 ________________________________ Important: This email is confidential and may be privileged. If you are not the intended recipient, please delete it and notify us immediately; you should not copy or use it for any purpose, nor disclose its contents to any other person. Thank you. Spencer Sherwin 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 <mailto:s.sherwin@imperial.ac.uk>s.sherwin(a)imperial.ac.uk<mailto:s.sherwin@imperial.ac.uk> +44 (0) 20 759 45052 ________________________________ Important: This email is confidential and may be privileged. If you are not the intended recipient, please delete it and notify us immediately; you should not copy or use it for any purpose, nor disclose its contents to any other person. Thank you. ________________________________ Important: This email is confidential and may be privileged. If you are not the intended recipient, please delete it and notify us immediately; you should not copy or use it for any purpose, nor disclose its contents to any other person. Thank you.

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EulerCFE - performance issue & MPI problem
by Kühnelt Helmut 20 May '16

20 May '16

Hi Spencer, hi All, I experience that CompressibleFlowSolver for EulerCFE in 1D is really slow. A computation on a grid with 5000 elements, with P=5 and a 5th order RK_SSP (self-implemented) needs ~1 s per time step on an up-to-date workstation (single core execution). (A calculation of 1e5 steps (1s with a time step = 1e-5s) needs 27 hours...) The profiler shows that 68% ot the time the code spends releasing of shared pointers, constructing and destructing Array(), lock() and unlock() and the = operator. Flat profile: Each sample counts as 0.01 seconds. % cumulative self self total time seconds seconds calls ms/call ms/call name 32.05 1.38 1.38 10032 0.14 0.14 boost::detail::sp_counted_base::release() 9.56 1.79 0.41 20514 0.02 0.02 Nektar::Array<Nektar::OneD, double const>::Array(unsigned int, double const&) 9.09 2.18 0.39 7693730 0.00 0.00 Nektar::Array<Nektar::OneD, double const>::~Array() 8.86 2.56 0.38 137658633 0.00 0.00 boost::unique_lock<boost::mutex>::lock() 8.04 2.90 0.35 137608137 0.00 0.00 boost::mutex::unlock() 7.69 3.23 0.33 20528 0.02 0.02 Nektar::Array<Nektar::OneD, double const>::operator=(Nektar::Array<Nektar::OneD, double const> const&) 7.23 3.54 0.31 2500500 0.00 0.00 Nektar::ExactSolverToro::v_PointSolve(double, double, double, double, double, double, double, double, double, double, double&, double&, double&, double&, double&) 4.31 3.73 0.19 74253 0.00 0.01 Nektar::MemPool::Allocate(unsigned long) 2.33 3.83 0.10 Nektar::Array<Nektar::OneD, int const>::~Array() ... Running CompressibleFlowSolver with MPI gives a segmentation fault somewhere in the mesh partitioning (1D mesh) MeshPartition::MeshPartition() MeshPartition::ReadGeometry() 0x15d70d0 0x15d71a0 0x15d71a0 0 [node92:28879] *** Process received signal *** [node92:28879] Signal: Segmentation fault (11) [node92:28879] Signal code: Address not mapped (1) [node92:28879] Failing at address: 0x38 [node92:28879] [ 0] /lib/x86_64-linux-gnu/libc.so.6(+0x36d40) [0x7f7e7a781d40] [node92:28879] [ 1] /home/hkuehnelt/nektar++/build/library/LibUtilities/libLibUtilities.so.4.3.0(_ZN6Nektar12LibUtilities13MeshPartition12ReadGeometryERKN5boost10shared_ptrINS0_13SessionReaderEEE+0x1268) [0x7f7e7be44118] [node92:28879] [ 2] /home/hkuehnelt/nektar++/build/library/LibUtilities/libLibUtilities.so.4.3.0(_ZN6Nektar12LibUtilities13MeshPartitionC1ERKN5boost10shared_ptrINS0_13SessionReaderEEE+0x40f) [0x7f7e7be44a5f] [node92:28879] [ 3] /home/hkuehnelt/nektar++/build/library/LibUtilities/libLibUtilities.so.4.3.0(_ZN6Nektar12LibUtilities18MeshPartitionMetisC2ERKN5boost10shared_ptrINS0_13SessionReaderEEE+0x17) [0x7f7e7be519f7] [node92:28879] [ 4] /home/hkuehnelt/nektar++/build/library/LibUtilities/libLibUtilities.so.4.3.0(_ZN6Nektar12LibUtilities18MeshPartitionMetis6createERKN5boost10shared_ptrINS0_13SessionReaderEEE+0xc5) [0x7f7e7be53505] [node92:28879] [ 5] /home/hkuehnelt/nektar++/build/library/LibUtilities/libLibUtilities.so.4.3.0(_ZN6Nektar12LibUtilities10NekFactoryISsNS0_13MeshPartitionERKN5boost10shared_ptrINS0_13SessionReaderEEENS0_4noneES9_S9_S9_E14CreateInstanceESsS8_+0x96) [0x7f7e7be77c26] [node92:28879] [ 6] /home/hkuehnelt/nektar++/build/library/LibUtilities/libLibUtilities.so.4.3.0(_ZN6Nektar12LibUtilities13SessionReader13PartitionMeshEv+0x3fd) [0x7f7e7be6cb5d] [node92:28879] [ 7] /home/hkuehnelt/nektar++/build/library/LibUtilities/libLibUtilities.so.4.3.0(_ZN6Nektar12LibUtilities13SessionReader11InitSessionEv+0x55) [0x7f7e7be6de55] [node92:28879] [ 8] /home/hkuehnelt/nektar++/build/solvers/CompressibleFlowSolver/CompressibleFlowSolver(_ZN6Nektar12LibUtilities13SessionReader14CreateInstanceEiPPc+0x14c) [0x4396bc] [node92:28879] [ 9] /home/hkuehnelt/nektar++/build/solvers/CompressibleFlowSolver/CompressibleFlowSolver(main+0x4d) [0x4291ed] [node92:28879] [10] /lib/x86_64-linux-gnu/libc.so.6(__libc_start_main+0xf5) [0x7f7e7a76cec5] [node92:28879] [11] /home/hkuehnelt/nektar++/build/solvers/CompressibleFlowSolver/CompressibleFlowSolver() [0x430b99] [node92:28879] *** End of error message *** -------------------------------------------------------------------------- mpirun noticed that process rank 0 with PID 28879 on node node92 exited on signal 11 (Segmentation fault). -------------------------------------------------------------------------- Do you have any advice how to speed up the code and to fix the MPI issue? Best regards, Helmut ________________________________________ Helmut Kühnelt Scientist Mobility Department Electric Drive Technologies AIT Austrian Institute of Technology GmbH Giefinggasse 2 | 1210 Vienna | Austria T: +43 50550-6245 | M: +43 664 815 78 38 | F: +43 50550-6595 helmut.kuehnelt(a)ait.ac.at<https://aitmail.ait.ac.at/owa/redir.aspx?C=LR7CP_NRwEmvpxwWXICJVa6k5FhGic8I…> | http://www.ait.ac.at/<https://aitmail.ait.ac.at/owa/redir.aspx?C=LR7CP_NRwEmvpxwWXICJVa6k5FhGic8I…> FN: 115980 i HG Wien | UID: ATU14703506 This email and any attachments thereto, is intended only for use by the addressee(s) named herein and may contain legally privileged and/or confidential information. If you are not the intended recipient, please notify the sender by return e-mail or by telephone and delete this message from your system and any printout thereof. Any unauthorized use, reproduction, or dissemination of this message is strictly prohibited. Please note that e-mails are susceptible to change. AIT Austrian Institute of Technology GmbH shall not be liable for the improper or incomplete transmission of the information contained in this communication, nor shall it be liable for any delay in its receipt.

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Solve scalar transport equation along with Incompressible Navier Stokes
by Siddarth Chintamani 04 May '16

04 May '16

Hello all, I am trying to study scalar mixing from a jet. I can use the incompressible Navier Stokes solver to get the velocity at every time step. I am thinking of calling the advection-diffusion solver from the Navier Stokes solver every time step and solve for the scalar mixing. I was wondering if there is any other easier approach? Is there any example that I can look into? I greatly appreciate any help regarding this problem Thank you, Siddarth

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Time dependent bodyforce
by Péter Tamás Nagy 03 May '16

03 May '16

Dear All, I have two questions in regard to the usage of the Nektar++ 4.2.0. 1. Is it possible to define time-dependent body-force for the Incompressible Navier-Stokes solver? Could anyone send me an example? 2. I read in the User Giude that the definition of the geometry can be stored in separate from the remaining configuration. It is not obvious for me how the solver will identify then the geometry or the configuration elements. In this case how should I call the IncNavierStokesSolver? Could anybody send me an example? I really appreciate any help. Best regards, Péter

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Turbulent channel flow example
by César Alegre 03 May '16

03 May '16

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Correct Designation of Boundary Conditions
by Amitvikram Dutta 26 Apr '16

26 Apr '16

Hi all, I'm having some confusion in applying appropriate boundary conditions to proper named surfaces in my mesh. I'm using v4.2.0 with the original mesh being constructed in gmsh. I subsequently use the MeshConvert utility to generate the partial xml file for the simulation. In my .msh file I have my surfaces set as $PhysicalNames 5 2 1 "Unspecified" 1 2 "Airfoil" 1 3 "Inlet" 1 4 "Outlet" 1 5 "Tandb" $EndPhysicalNames I want to apply no-slip condition to the airfoil, a velocity inlet , a constant pressure outlet and no slip wall to TandB as well. My relevant section of the xml case file is given below. I'd like to know if I'm implementing the boundary conditions correctly. <BOUNDARYREGIONS> C[2] C[3] C[4] C[5] </BOUNDARYREGIONS> <BOUNDARYCONDITIONS> <REGION REF="0"> <D VAR="u" VALUE="0" /> <D VAR="v" VALUE="0" /> <N VAR="p" USERDEFINEDTYPE="H" VALUE="0" /> </REGION> <REGION REF="1"> <D VAR="u" VALUE ="1" /> <D VAR="v" VALUE="0" /> <N VAR="p" USERDEFINEDTYPE="H" VALUE="0" /> </REGION> <REGION REF="2"> <N VAR="u" VALUE="0" /> <N VAR="v" VALUE="0" /> <D VAR="p" VALUE="0" /> </REGION> <REGION REF="3"> <D VAR="u" VALUE="0" /> <D VAR="v" VALUE="0" /> <N VAR="p" USERDEFINEDTYPE="H" VALUE="0" /> </REGION> </BOUNDARYCONDITIONS> <FUNCTION NAME="InitialConditions"> <E VAR= "u" VALUE="1" /> <E VAR="v" VALUE="0" /> <E VAR="p" VALUE="0" /> </FUNCTION> -- *Amitvikram Dutta* *MASc Candidate* *Graduate Research Assistant * *Okanagan CFD Laboratory* *University of British Columbia | Okanagan Campus*

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Nektar++ on OS X and Xcode 7.3
by David Moxey 26 Apr '16

26 Apr '16

Hi all, Just want to draw OS X users' attention to a compilation bug with METIS on OS X. If you are using Xcode 7.3 (i.e. clang -v says: Apple LLVM version 7.3.0 (clang-703.0.29)), presently there's some kind of low-level bug when compiling METIS which will yield the following error, or one like it: [ 79%] Building C object programs/CMakeFiles/cmpfillin.dir/smbfactor.c.o Linking C executable cmpfillin ld: in ../libmetis/libmetis.a(error.c.o), section __DATA/__thread_bss extends beyond end of file, for architecture x86_64 Right now there is no known workaround for this, other than to use gcc or another compiler version. I therefore thoroughly recommend avoiding Xcode 7.3 for the time being, otherwise you will not be able to compile Nektar++. If you have already upgraded, you can try to downgrade to Xcode 7.2, which continues to work fine. For reference, there is a homebrew bug report here: https://github.com/Homebrew/homebrew-science/issues/3461 and a possible LLVM bug here: https://llvm.org/bugs/show_bug.cgi?id=27059 Cheers, Dave -- David Moxey (Research Fellow) d.moxey(a)imperial.ac.uk | www.imperial.ac.uk/people/d.moxey Room 363, Department of Aeronautics, Imperial College London, London, SW7 2AZ, UK.

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Basis type for the "MODIFIED"
by Hongfu Zhang 21 Apr '16

21 Apr '16

Hi all, Look at the words in XML "<E COMPOSITE="C[0]" NUMMODES="5" FIELDS="u" TYPE="MODIFIED" />" I would like to know what the default basis type for the "MODIFIED" ? Regards! Hongfu Zhang

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FW: Requesting some help with the Adaptive SFD algorithm
by Sharma, Manish (sharmamh) 15 Apr '16

15 Apr '16

Dear All, Just checking to see if you received my email query of March 14, 2016 (appended below for your convenience). Looking forward to hearing from you soon. Thank you very much! Manish Sharma -----Original Message----- From: Sharma, Manish (sharmamh) Sent: Monday, March 14, 2016 11:41 AM To: David Moxey <d.moxey(a)imperial.ac.uk> Cc: nektar-users(a)imperial.ac.uk Subject: FW: Requesting some help with the Adaptive SFD algorithm Hi Dave, Appended below is my original email with the input files attached. Thank you very much for helping with this. Manish -----Original Message----- From: Sharma, Manish (sharmamh) Sent: Friday, March 11, 2016 12:36 AM To: nektar-users-bounces(a)imperial.ac.uk Subject: Requesting some help with the Adaptive SFD algorithm Dear All, I am fairly new to nektar++, and have been trying to simulate the flow in a lid-driven cavity using the adaptive SFD method. However, after the first stability analysis run, I get the following output and error. Iteration: 1 (residual : 8.559e-27) Writing: "SquareCavityNonuniform110x110-AdaptiveSFD1.fld" L 2 error (variable u) : 1.60644e-14 L inf error (variable u) : 3.59318e-14 L 2 error (variable v) : 1.48736e-14 L inf error (variable v) : 3.72109e-14 L 2 error (variable p) : 1.01877e-14 L inf error (variable p) : 5.76926e-17 Fatal : Level 0 assertion violation Unrecognised value. I have checked my input files thoroughly, but am unable to understand what this error of "Unrecognised value" mean, or, how it has occurred. For your convenience/reference, the Geometry/Mesh, the nonlinear problem definition, and the homogeneous linear problem files are attached. Any suggestions/solutions to resolve this issue will be greatly appreciated. Thank you, Manish

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Installation problem: Boost specification
by Victor Eijkhout 12 Apr '16

12 Apr '16

I can not find in the documentation how to specify the Boost library. 1. I’ve unzipped the tar.bz2 file in the ThirdParty directory, but nektar still tries to download the tar.bz2 file. 2. I have a boost 1.59 installed, and the bin directory is in the LD_LIBRARY_PATH but the installation is not finding or using it. Victor.

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