November 2018 - Nektar-users

Re: [Nektar-users] FW: Problem while installing nektar++ with lapack
by Amitvikram Dutta 22 Feb '19

22 Feb '19

Hi all, I had to use a slight workaround because the platform I was compiling on could not download the thirdparty files correctly and would always give a hash mismatched error. I downloaded the third party files on my home machine and re-uploaded them into the $NEKTAR_HOME folder. As a result when I begin the build process the ThirdParty folder is populated with the zipped versions of the third party software. Is this what what might be causing the problem? Is there any way to edit the cmake file and to get the compilation process working correctly? On Fri, Oct 12, 2018 at 2:57 PM Amitvikram Dutta < amitvikram.dutta(a)uwaterloo.ca> wrote: > *From:* nektar-users-bounces(a)imperial.ac.ukOn Behalf OfJeremy Cohen > *Sent:* October 12, 2018 2:56:43 PM (UTC-05:00) Eastern Time (US & Canada) > > *To:* Amitvikram Dutta > *Cc:* nektar-users > *Subject:* Re: [Nektar-users] Problem while installing nektar++ with > lapack > > Hi Amitvikram, > > Have you attempted to build lapack separately at any point? It's probably > worth clearing out your build directory and also all the contents of the > ThirdParty directory in the base nektar++ source directory, which I'll call > $NEKTAR_HOME, so $NEKTAR_HOME/ThirdParty and then re-running cmake in an > empty $NEKTAR_HOME/build directory and trying the build again. > > It looks like the build step is encountering a previous source tree in the > location where it's trying to build which seems strange. > > I've just had a look at the log from my clean build and I see exactly the > same messages as you in relation to lapack-3.7.0 in the same order as far > as "Checking whether /usr/bin/f95 supports Fortran 90 -- yes", however, I > then see "-- Looking for Python greater than 2.6 - " and the build of > lapack completes successfully. > > Just to confirm, I am running cmake and make in a separate build directory > under the main nektar++ source tree directory, so I'm building in > $NEKTAR_HOME/build - I assume you're doing something similar? You should > see a ThirdParty directory in $NEKTAR_HOME and another ThirdParty directory > in $NEKTAR_HOME/build/ > > I believe that the initial download of the lapack-3.7.0.tar.gz should be > placed in $NEKTAR_HOME/ThirdParty and unpacked there. Then, when the build > succeeds or stops, in $NEKTAR_HOME/build/ThirdParty, you should see > lapack-3.7.0/ where I think the build actually takes place, and then a > separate $NEKTAR_HOME/build/ThirdParty/lapack-3.7.0-tmp which should > contain a couple of lapack-3.7.0-cfgcmd.txt files that I think contain the > build command that is used - you could perhaps paste the contents of the > lapack-3.7.0-cfgcmd.txt into an email if you're still having issues and we > can see if that looks correct. > > It is, of course, possible that this is something related to the specific > configuration of the platform that you're building on, but I think the > third party lapack build should be straightforward and it sounds like for > some reason, it's attempting to build in the wrong location, or a location > where an existing source tree has ended up for some reason. > > I'm afraid I don't have a very detailed knowledge of the build system > beyond this so if none of the suggestions so far help you to resolve the > problem, maybe someone with more knowledge of the build system can provide > some advice. > > Cheers, > Jeremy > > On 12 Oct 2018, at 19:34, Amitvikram Dutta <amitvdutta23(a)gmail.com> wrote: > > Hi all, > > I tried to compile nektar using Jeremy's latest suggestions having both > THIRDPARTY_BUILD_BLAS_LAPACK and NEKTAR_USE_SYSTEM_BLAS_LAPACK turned on. > The following error occured. It seems that I might have to compile lapack > separately. Is this unusual? > > <image.png> > > On Fri, Oct 12, 2018 at 1:16 PM Amitvikram Dutta < > amitvikram.dutta(a)uwaterloo.ca> wrote: > >> *From:* nektar-users-bounces(a)imperial.ac.ukOn Behalf OfJeremy Cohen >> *Sent:* October 12, 2018 1:16:14 PM (UTC-05:00) Eastern Time (US & >> Canada) >> >> *To:* Amitvikram Dutta >> *Cc:* nektar-users >> *Subject:* Re: [Nektar-users] Problem while installing nektar++ with >> lapack >> >> Hi Amitvikram, >> >> As Chris suggests, it's probably better to use vendor supplied libraries >> if you can get those working. >> >> In addition to the further information Chris has asked to take a look at, >> one thing you could check is to whether there are any files in your >> nektar++/build/ThirdParty/lapack-3.7.0 directory (if that directory exists >> at all). >> >> I've been trying to see if I can recreate the problem and I was able to >> see something similar when setting THIRDPARTY_BUILD_BLAS_LAPACK=ON and >> NEKTAR_USE_SYSTEM_BLAS_LAPACK=OFF. In this case, I can configure >> successfully and start the build but it fails with a large number of >> undefined references that are similar to, and include, the dtpmv_ symbol >> that you mentioned. When I look in nektar++/build/ThirdParty/lapack-3.7.0, >> the directory is empty so it looks like the build system has configured on >> the basis of building its own blas/lapack but the build hasn't been carried >> out and therefore LibUtilities can't be linked against it. >> >> As a test, you could try running the build with both >> THIRDPARTY_BUILD_BLAS_LAPACK=ON and NEKTAR_USE_SYSTEM_BLAS_LAPACK=ON, if >> this isn't the setting you've been using already. When I tried this, the >> build of blas/lapack is carried out successfully and the linking is fine >> with the full build of Nektar++ completing successfully. I removed the >> system blas/lapack on my test system to be sure it was linking against the >> correct instance. >> >> Cheers, >> Jeremy >> >> On 12 Oct 2018, at 17:50, Chris Cantwell <c.cantwell(a)imperial.ac.uk> >> wrote: >> >> Hi Amitvikram, >> >> Could you send us your CMakeCache.txt file from your build directory and >> the output from running: >> make VERBOSE=1 >> for both cases. >> >> In the case of using ThirdParty LAPACK, it seems to not be linking to it. >> Probably you should be using vendor-supplied libraries if possible though >> so better if ee can get those working. >> >> Thanks, >> Chris >> >> >> >> On 12 October 2018 14:08:55 BST, Amitvikram Dutta <amitvdutta23(a)gmail.com> >> wrote: >>> >>> Hi Jeremy, >>> >>> I'm actually trying to build nektar++ on a BGQ cluster similar to Mira. >>> >>> I'm trying to build nektar++-4.4.1 and the system lapacek version is >>> 3.4.2 >>> >>> Sincerely, >>> On Fri, Oct 12, 2018 at 4:24 AM Amitvikram Dutta < >>> amitvikram.dutta(a)uwaterloo.ca> wrote: >>> >>>> >>>> ------------------------------ >>>> *From:* nektar-users-bounces(a)imperial.ac.ukOn Behalf OfJeremy Cohen >>>> *Sent:* October 12, 2018 4:24:33 AM (UTC-05:00) Eastern Time (US & >>>> Canada) >>>> *To:* Amitvikram Dutta >>>> *Cc:* nektar-users >>>> *Subject:* Re: [Nektar-users] Problem while installing nektar++ with >>>> lapack >>>> >>>> Hi Amitvikram, >>>> >>>> Can you provide some further details of the problem you're encountering. >>>> >>>> Specifically, can you confirm what platform (including version) you're >>>> building on, and if Linux, which I assume is the platform you're using, >>>> which distribution. >>>> >>>> Can you also confirm what version of Nektar++ you're trying to build, >>>> and the version of the system Lapack distribution that you're using. >>>> >>>> Thanks, >>>> >>>> Jeremy >>>> >>>> On 12 Oct 2018, at 01:05, Amitvikram Dutta <amitvdutta23(a)gmail.com> >>>> wrote: >>>> >>>> Hi all, >>>> >>>> I keep having the same problem while trying to install nektar++ with >>>> regards to the Lapack libraries. >>>> >>>> When I try to use the system Lapack installation I get the following >>>> message >>>> >>>> */scinet/bgq/Libraries/lapack/lib/liblapack.so: undefined reference to >>>> `_xlfEndIO(a)XLF_1.0'* >>>> >>>> while when I try to install using the ThirdParty Lapack supplied with >>>> the nektar++ source directory I get the following error >>>> >>>> *../../library/LibUtilities/libLibUtilities.so.4.4.1: undefined >>>> reference to `dtpmv_'* >>>> >>>> I have a feeling these errors have been encountered by the community at >>>> large before. Could someone point out where I'm going wrong? >>>> >>>> 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 >>> >> >> -- >> Chris Cantwell >> Imperial College London >> South Kensington Campus >> London SW7 2AZ >> Email: c.cantwell(a)imperial.ac.uk >> www.imperial.ac.uk/people/c.cantwell >> >> >> -- > > *Amitvikram Dutta* > > Graduate Research Assistant > > Fluid Mechanics Research Lab > > Multi-Physics Interaction Lab > > University of Waterloo > > > -- *Amitvikram Dutta* Graduate Research Assistant Fluid Mechanics Research Lab Multi-Physics Interaction Lab University of Waterloo

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BiGlobal Stability Analysis of 3D Channel Flow case at Re15000
by Xu Chu 14 Dec '18

14 Dec '18

Dear Nektarers, I am running a 3D direct stability analysis test case, the Re15000 Channel Flow from the tutorial (PPF_R15000_3D, ARPACK as the solver). As I understand, this is a BiGlobal stability analysis with 2D base flow and the spanwise wavenumber Beta. It means that for a given Beta, the Eigenvalues can be calculated. What I am seeking is the Eigenvalues under different spanwise wavenumber Beta, so I turn "Beta Set To Zero" as false (as in the PPF_R15000_3D). And the solver converged showing 4 Eigenvalues with Real and Imaginary part of each, with no information of Beta. How can I find the Eigenvalues under different spanwise wavenumber Beta? Thank you very much. Best Regards, Xu

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Re: [Nektar-users] Handling Pyramids
by Vishal Saini 07 Dec '18

07 Dec '18

Dear Spencer and David, Thanks very much for your prompt replies. 1. Defining the expansions separately still produced the "note" (in Nektar 4.4.1 Release). 2. Compiling the latest master solved the problem. However, I didn't try if defining the expansions collectively i.e. *<E COMPOSITE="C[1,10,11]" NUMMODES="3" FIELDS="u,v,w,p" TYPE="MODIFIED" /> *produces any warnings in the latest compilation. BR, Vishal --- *Vishal SAINI* On Mon, Nov 26, 2018 at 4:43 PM Moxey, David <D.Moxey(a)exeter.ac.uk> wrote: > Hi Vishal, > > You might also try a newer version of the code (i.e. latest master), I am > not sure that the pyramid collections functions were added in 4.4.1. > > Many thanks, > > Dave > > > On 26 Nov 2018, at 14:53, Sherwin, Spencer J <s.sherwin(a)imperial.ac.uk> > wrote: > > > > Dear Vishal, > > > > I do not quite recall but it may be necessary to define the expansions > for composites of different shape independently. So please try: > > > >> <E COMPOSITE=“C[1]" NUMMODES="3" FIELDS="u,v,w,p" TYPE="MODIFIED" /> > >> <E COMPOSITE=“C[10]" NUMMODES="3" FIELDS="u,v,w,p" TYPE="MODIFIED" /> > >> <E COMPOSITE="C[11]" NUMMODES="3" FIELDS="u,v,w,p" TYPE="MODIFIED" /> > > > > Possibly it is expecting to have a pyramid collection within a > tetrahedral expansion and so this is why you see this message. > > > > If this does not work can you send the xml file along. > > > > Thanks, > > Spencer. > > > > > >> On 26 Nov 2018, at 11:45, Vishal Saini <vishal.saini.nitj(a)gmail.com> > wrote: > >> > >> Hi all, > >> > >> I've imported a mesh from gmsh that contains a layer of pyramids for > transitioning between hexes and tets using: > >> NekMesh JICF_NektP2_2comp.msh JICF_NektP2_2comp.xml > >> Output: > >> Multiple elements in composite detected; remapped: > >> - Tag 1 => 11 (Tetrahedron), 10 (Pyramid), 1 (Hexahedron) > >> No problem on NekMesh level. > >> > >> Defining my expansion as: > >> <E COMPOSITE="C[1,10,11]" NUMMODES="3" FIELDS="u,v,w,p" TYPE="MODIFIED" > /> > >> > >> when I run (Nektar++ v 4.4.1) using: > >> mpirun -npernode 28 -np 56 IncNavierStokesSolver -v > JICF_NektP2_2comp_xml conditions_JICF_2D.xml > >> (using prepartitioned mesh). > >> I get the following "note": > >> Collection Implemenation for Tetrahedron ( 3 3 3 ) for ngeoms = 24960 > >> Note: Implementation does not exist: Pyramid, BwdTrans, SumFac, Modal > >> Note: Implementation does not exist: Pyramid, IProductWRTBase, SumFac, > Modal > >> Note: Implementation does not exist: Pyramid, IProductWRTDerivBase, > SumFac, Modal > >> Note: Implementation does not exist: Pyramid, PhysDeriv, SumFac, Modal > >> Note: Implementation does not exist: Pyramid, BwdTrans, SumFac, Modal > >> Note: Implementation does not exist: Pyramid, IProductWRTBase, SumFac, > Modal > >> Note: Implementation does not exist: Pyramid, IProductWRTDerivBase, > SumFac, Modal > >> Note: Implementation does not exist: Pyramid, PhysDeriv, SumFac, Modal > >> > >> What does it mean? How can I fix it? > >> Do Pyramids need to be treated in a somewhat different way? > >> > >> BR, > >> Vishal > >> > >> > >> --- > >> Vishal SAINI > >> _______________________________________________ > >> Nektar-users mailing list > >> Nektar-users(a)imperial.ac.uk > >> https://mailman.ic.ac.uk/mailman/listinfo/nektar-users > > > > Spencer Sherwin FREng, FRAeS > > Head, Aerodynamics, > > Director of Research Computing Service, > > Professor of Computational Fluid Mechanics, > > Department of Aeronautics, > > s.sherwin(a)imperial.ac.uk South > Kensington Campus, > > Phone: +44 (0)20 7594 5052 Imperial College > London, > > Fax: +44 (0)20 7594 1974 London, SW7 > 2AZ, UK > > http://www.imperial.ac.uk/people/s.sherwin/ > > > > _______________________________________________ > > Nektar-users mailing list > > Nektar-users(a)imperial.ac.uk > > https://mailman.ic.ac.uk/mailman/listinfo/nektar-users > >

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Hi all question about Possible choices for the expansion TYPE for mesh cells
by Moto Light 30 Nov '18

30 Nov '18

Hi all, i need to know what is the different between the three types in order to expansion my mesh cells Modal MODIFIED Nodal GLL_LAGRANGE Nodal SEM GLL_LAGRANGE_SEM Thanks, Regards.

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File naming convention for APESolver
by Amitvikram Dutta 27 Nov '18

27 Nov '18

Hello everyone, I'm trying to use the APESolver using a time-dependent series of files for my baseflow and my source terms. I'm having difficulty in figuring out the regex that's used to specify the format of these file names. From the tutorial the file names are specified in the .xml file as thus: APEzzz_%14.8E.pts while the actual filename this points to is : APEzzz_1.00000000E-05.pts and so on. I can't quite decipher the regex. Observation tells me that the 14 refers to the total number of characters after the underscore and 8 is the number of zeros between the decimal point and the E. However, since my input .pts file come directly from a simulation it would be easier for me if I could provide the regex to the .xml file to access filenames of the form APEzzz_1401.pts, APEzzz_1402.pts and so on. I have tried APEzzzz_%4.pts as an input but this returns an error. I'd be grateful for some further guidance in this regard. Sincerely, -- *Amitvikram Dutta* Graduate Research Assistant Fluid Mechanics Research Lab Multi-Physics Interaction Lab University of Waterloo

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Handling Pyramids
by Vishal Saini 26 Nov '18

26 Nov '18

Hi all, I've imported a mesh from gmsh that contains a layer of *pyramids* for transitioning between hexes and tets using: *NekMesh JICF_NektP2_2comp.msh JICF_NektP2_2comp.xml* Output: *Multiple elements in composite detected; remapped:- Tag 1 => 11 (Tetrahedron), 10 (Pyramid), 1 (Hexahedron)* No problem on NekMesh level. Defining my expansion as: *<E COMPOSITE="C[1,10,11]" NUMMODES="3" FIELDS="u,v,w,p" TYPE="MODIFIED" />* when I run (Nektar++ v 4.4.1) using: *mpirun -npernode 28 -np 56 IncNavierStokesSolver -v JICF_NektP2_2comp_xml conditions_JICF_2D.xml* (using prepartitioned mesh). I get the following "note": *Collection Implemenation for Tetrahedron ( 3 3 3 ) for ngeoms = 24960Note: Implementation does not exist: Pyramid, BwdTrans, SumFac, ModalNote: Implementation does not exist: Pyramid, IProductWRTBase, SumFac, ModalNote: Implementation does not exist: Pyramid, IProductWRTDerivBase, SumFac, ModalNote: Implementation does not exist: Pyramid, PhysDeriv, SumFac, ModalNote: Implementation does not exist: Pyramid, BwdTrans, SumFac, ModalNote: Implementation does not exist: Pyramid, IProductWRTBase, SumFac, ModalNote: Implementation does not exist: Pyramid, IProductWRTDerivBase, SumFac, ModalNote: Implementation does not exist: Pyramid, PhysDeriv, SumFac, Modal* What does it mean? How can I fix it? Do Pyramids need to be treated in a somewhat different way? BR, Vishal --- *Vishal SAINI*

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Re: [Nektar-users] Regarding reconstruction 3D eigenmode from biGlobal linear stability with HalfMode
by Abhishek Kumar 20 Nov '18

20 Nov '18

Dear Spencer and David, Thanks for your response. 1) Yes, I am running a passive scalar using a forcing term to couple the scalar. The code was working well for 2D base flow and 2D perturbation, but there was an issue with the HalfMode calculation. Now, this is resolved as there was a bug in “LinearisedAdvection::UpdateGradBase”. It was not including the passive scalar because of condition “if var<2” for "HalfMode". Now, when I change it to “if var < 4”, it works. 2) David: I tried your suggestion, but it doesn't work. I think we need a module to perform inverse Fourier transform in the homogeneous direction of the eigenmode obtain from the HalfMode calculation. Again thanks a lot to both for your help. With regards Abhishek On Tue, Nov 20, 2018 at 1:58 PM Moxey, David <D.Moxey(a)exeter.ac.uk> wrote: > Hi both, > > This might be possible without doing anything fancy, unless I am > forgetting how the half mode output looks like. Have you tried just doing: > > FieldConvert session.xml halfmode.fld out.vtu > > where session.xml has been set up as a 3DH1D problem? This might then just > populate the mean mode and zero the rest of the spectrum so you will get > the mean mode output. > > Cheers, > > Dave > > > On 20 Nov 2018, at 13:24, Sherwin, Spencer J <s.sherwin(a)imperial.ac.uk> > wrote: > > > > Dear Abhishek, > > > > I have just been trying to catch up on your thread with Stan. Do I > understand you have the stability now running correctly with a passive > scalar using a forcing term to couple the scalar? > > > > If I next understand your question you want to plot the output from a > half mode eigenfield as a 3D image? This certainly used to be possible > although I have not played with this bit of code for a while. Essentially > we need to add a mean mode component to the eigenmode to make it a full > 3D1H expansion and then FieldConvert should work. > > > > I will try and have a dig around and see what might allow you to do this > since I cannot see anything in the user-guide. > > > > Cheers, > > Spencer. > > > >> On 10 Nov 2018, at 07:43, Abhishek Kumar <abhishek.kir(a)gmail.com> > wrote: > >> > >> > >> Hi friends, > >> > >> I think I have not explained my problem properly in my last email. > >> > >> Actually, I am doing biGlobal linear stability analysis with HalfMode, > which yields eigenmode on a 2D plane. Now I want to reconstruct the > eigenmode in 3D, which will require inverse Fourier transform. I have > check one of the examples in the manual for the Floquet analysis of a of > flow past a cylinder. There is a plot for the eigenmode at z=2 [Figure > 10.25 of the manual]. > >> > >> Thus, I want to know which module is used to convert the eigenmode in > 3D. > >> > >> I would be highly thankful for the comments on this issue. > >> > >> > >> With regards > >> Abhishek Kumar > >> > >> > --------------------------------------------------------------------------------------- > >> Abhishek Kumar > >> Research Associate > >> Applied Mathematics Research Centre > >> Coventry University, Coventry CV1 5FB > >> The United Kingdom > >> > >> Email # ac7600(a)coventry.ac.uk, abhishek.kir(a)gmail.com > >> > --------------------------------------------------------------------------------------- > >> _______________________________________________ > >> Nektar-users mailing list > >> Nektar-users(a)imperial.ac.uk > >> https://mailman.ic.ac.uk/mailman/listinfo/nektar-users > > > > Spencer Sherwin FREng, FRAeS > > Head, Aerodynamics, > > Director of Research Computing Service, > > Professor of Computational Fluid Mechanics, > > Department of Aeronautics, > > s.sherwin(a)imperial.ac.uk South > Kensington Campus, > > Phone: +44 (0)20 7594 5052 Imperial College > London, > > Fax: +44 (0)20 7594 1974 London, SW7 > 2AZ, UK > > http://www.imperial.ac.uk/people/s.sherwin/ > > > > _______________________________________________ > > Nektar-users mailing list > > Nektar-users(a)imperial.ac.uk > > https://mailman.ic.ac.uk/mailman/listinfo/nektar-users > > -- With regards Abhishek Kumar --------------------------------------------------------------------------------------- Abhishek Kumar Research Associate Applied Mathematics Research Centre Coventry University, Coventry CV1 5FB The United Kingdom Email # ac7600(a)coventry.ac.uk, abhishek.kir(a)gmail.com ---------------------------------------------------------------------------------------

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Regarding reconstruction 3D eigenmode from biGlobal linear stability with HalfMode
by Abhishek Kumar 20 Nov '18

20 Nov '18

Hi friends, I think I have not explained my problem properly in my last email. Actually, I am doing biGlobal linear stability analysis with HalfMode, which yields eigenmode on a 2D plane. Now I want to reconstruct the eigenmode in 3D, which will require inverse Fourier transform. I have check one of the examples in the manual for the Floquet analysis of a of flow past a cylinder. There is a plot for the eigenmode at z=2 [Figure 10.25 of the manual]. Thus, I want to know which module is used to convert the eigenmode in 3D. I would be highly thankful for the comments on this issue. With regards Abhishek Kumar --------------------------------------------------------------------------------------- Abhishek Kumar Research Associate Applied Mathematics Research Centre Coventry University, Coventry CV1 5FB The United Kingdom Email # ac7600(a)coventry.ac.uk, abhishek.kir(a)gmail.com ---------------------------------------------------------------------------------------

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the bug in analytical expressions evaluation
by A.P. 19 Nov '18

19 Nov '18

Hello, I calculated a boundary condition <D VAR="u" VALUE="-y^2+1.0" /> and had found that the expression "-y^2+1.0" had calculated as "(-y)^2+1.0". The "1-y^2" and the "-(y^2)+1.0" are OK. Alexander.

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Regarding three-dimensional eigenmode
by Abhishek Kumar 09 Nov '18

09 Nov '18

Hi, I am doing biGlobal linear stability analysis with HalfMode. I want to convert the 2D eigenmode to the real space in 3D. Is there any utility to convert the eigenmode? With regards Abhishek Kumar --------------------------------------------------------------------------------------- Abhishek Kumar Research Associate Applied Mathematics Research Centre Coventry University, Coventry CV1 5FB The United Kingdom Email # ac7600(a)coventry.ac.uk, abhishek.kir(a)gmail.com ---------------------------------------------------------------------------------------

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