December 2018 - Nektar-users

Element with max CFL
by Vishal Saini 02 Apr '20

02 Apr '20

Hi all, Quick question: Has anyone tried to check the location of a particular element in the mesh? A log file reports the maximum (?) CFL and the corresponding element as: "CFL: 0.0337915 (in elmt 94488)"? Is there a quick way to locate "elmt 94488"? Cheers, Vishal

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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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Extract surfaces from a mesh on latest version
by Guillermo 11 Jan '19

11 Jan '19

Dear all, Extracting a surface from a mesh file (.msh.xml) on the latest nektar version, 4.5.0, is not well performed. The resulting output file does not contain the corresponding elements on the CURVED section. When the same mesh file is used on a previous nektar version, 4.4.1, it is properly done, suggesting that some kind of issue with the 4.5.0 version or maybe the commands are not the same. Thank you. Cheers, Guillermo

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APE solver for aero-acoustic simulations
by Nitish Arya 29 Dec '18

29 Dec '18

Hi. I am trying to couple APE solver with a fluid solver (OpenFOAM) via coupling library. For this purpose, the time dependent sources (calculated from the fluid sover) from a particular region in the grid are sent to APE solver. This means that the source terms are read from the coupling library rather than defining them in the configuration file at each time step. Now I have the mean flow terms and the source terms at each point in a grid. I want APE solver to read this grid along with the data. Can anyone suggest me how should I proceed with this approach, or is there any documentation which can help me with this. Sincerely, Nitish Arya

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Re: [Nektar-users] Farfield boundary condition
by Sherwin, Spencer J 23 Dec '18

23 Dec '18

Begin forwarded message: From: "中华腾飞" <592835068(a)qq.com<mailto:592835068@qq.com>> Subject: [Nektar-users] compressible solver issues Date: 17 December 2018 at 07:37:07 GMT To: "nektar-users" <nektar-users(a)imperial.ac.uk<mailto:nektar-users@imperial.ac.uk>> Hi all! I want to ask about the boundray conditions.In 3D task,the variables are only rho,rhou,rhov,rhow and E? We can't set other variables,such as p(pressure),t(temperature)? In D type boundary condtions,if i give values to variables,such as ' VAR="rho" VALUE="rhoInf" after i have defined rhoInf=1.007, it means rho=1.007? In some tutorials, they set VALUE="0",rho=0 or E=0,it seems to be impossible! _______________________________________________ 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 Begin forwarded message: From: "中华腾飞" <592835068(a)qq.com<mailto:592835068@qq.com>> Subject: [Nektar-users] PressureOutflow boundary condtions Date: 19 December 2018 at 03:23:25 GMT To: "nektar-users" <nektar-users(a)imperial.ac.uk<mailto:nektar-users@imperial.ac.uk>> Hi all! I want to give static pressure on my outlet, p0eInf is the value that i have defined in parameters . Can you help me check out my example? By the way, i don't know how to set 'WallAdiabatic' boundary conditions ,can you help me check out my example? [cid:072d7b32-4a9d-4ad6-93d0-00c55fb719df@eurprd06.prod.outlook.com] [cid:ec3807d0-b91e-4cdd-a7d8-73c9ad130375@eurprd06.prod.outlook.com] Sometimes when i run the calculation,it will report an error called 'vacuum is generated by given data'.If i change the TimeStep , it will calculate some steps.How to explain it? Looking forward to your replay! _______________________________________________ Hi, We seem to have had quite a few emails last week from you. Can I first ask you to provide a name to write to since non of your emails are signed. Can I presume you have looked over the user-guide? i have not run the compressible flow solver so much so am unable to help you directly. However two of my PhD students are now working on the compressible code and so I am cc’ing them on this email since they might be able to help out. However obviously they have their own projects to work on too so please keep the emails about the most important points. Best regards Spencer. 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 Begin forwarded message: From: "中华腾飞" <592835068(a)qq.com<mailto:592835068@qq.com>> Subject: [Nektar-users] check out my boundary conditions Date: 21 December 2018 at 07:42:24 GMT To: "nektar-users" <nektar-users(a)imperial.ac.uk<mailto:nektar-users@imperial.ac.uk>> Hi all! I want to define two groups of values of rho, rhou, rhov, rhow,E on the two different inlets. You can see my example in following pictures. [cid:66f4d31f-59da-4f12-807f-e5ef891a5e06@eurprd06.prod.outlook.com] [cid:d460f3ae-2bb3-4ba5-9737-b101dd7b64a5@eurprd06.prod.outlook.com] The two boundary conditions : [cid:9ea82bbc-7c2a-4bfc-8010-7e7e6df9abb9@eurprd06.prod.outlook.com] [cid:2a749908-0bd3-4954-b9e1-033abac01326@eurprd06.prod.outlook.com] What i want to do is to keep the values of rho ,rhou ,rhov, rhow and E constant on the two boundary,but when i see the calculated results with paraview, the values on the "2" region are changing,only "0" region is constant....I don't know how to solve it.... Looking forward to your reply! _______________________________________________ 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 Begin forwarded message: From: "中华腾飞" <592835068(a)qq.com<mailto:592835068@qq.com>> Subject: [Nektar-users] PressureOutflow boundary conditions Date: 21 December 2018 at 02:05:53 GMT To: "nektar-users" <nektar-users(a)imperial.ac.uk<mailto:nektar-users@imperial.ac.uk>> Hi all! The nektar++ developers tell me that nektar++ can't define different static pressures on multiple outlets at the moment and 'VALUE' is not being used . If i just define the same static presssure on multiple outlets , how to set it? It seems that we can only set the value of rho,rhou,rhov,rhow and E,where is pressure? Looking forward to your reply! _______________________________________________ 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 Begin forwarded message: From: "中华腾飞" <592835068(a)qq.com<mailto:592835068@qq.com>> Subject: [Nektar-users] nektar++ mesh Date: 18 December 2018 at 03:38:49 GMT To: "nektar-users" <nektar-users(a)imperial.ac.uk<mailto:nektar-users@imperial.ac.uk>> Hi all! When i calculate my task , there is always an error called 'vacuum is generated by given data' .I have tried to check out my boundary conditions and initial conditions ,but it doesn't work. I want to check out my meshes .My meshes are generated by gmsh 3.0.6, all the elements are 'A' (tetrahedron) and about 36912. Can you give me some suggestions about my meshes or geometry?Looking forward to your reply! _______________________________________________ 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 Begin forwarded message: From: "中华腾飞" <592835068(a)qq.com<mailto:592835068@qq.com>> Subject: [Nektar-users] boundary conditions Date: 21 December 2018 at 02:28:36 GMT To: "nektar-users" <nektar-users(a)imperial.ac.uk<mailto:nektar-users@imperial.ac.uk>> Hi all! I want to know whether i can define different rho, rhou, rhov, rhow, E on multiple boundaries or not? Looking forward to your reply! _______________________________________________ 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 Begin forwarded message: From: "中华腾飞" <592835068(a)qq.com<mailto:592835068@qq.com>> Subject: [Nektar-users] Farfield boundary condition Date: 21 December 2018 at 08:38:17 GMT To: "nektar-users" <nektar-users(a)imperial.ac.uk<mailto:nektar-users@imperial.ac.uk>> Hi all! I want to give total temperature,total pressure and mach number on the inlet using compressible flow solver. Which kind of boundary condition should i use ? The Farfield boundary condtion? Should i calculate the static parameters? The VALUE is constant in the whole process? Can i define two inlets with different parameters using Farfield boundary condition? _______________________________________________ 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 FREng, FRAeS Head, Aerodynamics, Director of Research Computing Service, Professor of Computational Fluid Mechanics, Department of Aeronautics, s.sherwin(a)imperial.ac.uk<mailto:s.sherwin@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/

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Farfield boundary condition
by 中华腾飞 21 Dec '18

21 Dec '18

Hi all! I want to give total temperature,total pressure and mach number on the inlet using compressible flow solver. Which kind of boundary condition should i use ? The Farfield boundary condtion? Should i calculate the static parameters? The VALUE is constant in the whole process? Can i define two inlets with different parameters using Farfield boundary condition?

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check out my boundary conditions
by 中华腾飞 21 Dec '18

21 Dec '18

Hi all! I want to define two groups of values of rho, rhou, rhov, rhow,E on the two different inlets. You can see my example in following pictures. The two boundary conditions : What i want to do is to keep the values of rho ,rhou ,rhov, rhow and E constant on the two boundary,but when i see the calculated results with paraview, the values on the "2" region are changing,only "0" region is constant....I don't know how to solve it.... Looking forward to your reply!

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boundary conditions
by 中华腾飞 21 Dec '18

21 Dec '18

Hi all! I want to know whether i can define different rho, rhou, rhov, rhow, E on multiple boundaries or not? Looking forward to your reply!

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PressureOutflow boundary conditions
by 中华腾飞 21 Dec '18

21 Dec '18

Hi all! The nektar++ developers tell me that nektar++ can't define different static pressures on multiple outlets at the moment and 'VALUE' is not being used . If i just define the same static presssure on multiple outlets , how to set it? It seems that we can only set the value of rho,rhou,rhov,rhow and E,where is pressure? Looking forward to your reply!

1 0

boundary condtions
by 中华腾飞 20 Dec '18

20 Dec '18

Hi all! I am using the compressible flow solver for NS. I want to give static pressure 'p0eInf' on my outlet, i have defined its value in parameters . Can you help me check out my example? By the way, i don't know how to set 'WallAdiabatic' boundary conditions ,can you help me check out my example? Sometimes when i run the calculation,it will report an error called 'vacuum is generated by given data'.If i change the TimeStep , it will calculate some steps.How to explain it? Looking forward to your replay!

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