- Nektar-users - imperial.ac.uk

PDF of a variable in Nektar++
by Shervin Sammak 14 Oct '18

14 Oct '18

Hi all, Is there any filter to get the probability density function of a variable from Nektar++? Thanks, Shervin -- ----------------------------------------------------------- Shervin Sammak, Ph.D. Research Assistant Professor Mechanical Engineering and Materials Science Center for Research Computing University of Pittsburgh, 312I Schenley Place Pittsburgh, PA 15213, USA E-mail: shervin.sammak(a)pitt.edu Website: https://www.engineering.pitt.edu/People/Faculty/Profiles/Shervin-Sammak/

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Re: [Nektar-users] FW: Problem while installing nektar++ with lapack
by Amitvikram Dutta 12 Oct '18

12 Oct '18

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: 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

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Re: [Nektar-users] FW: Problem while installing nektar++ with lapack
by Amitvikram Dutta 12 Oct '18

12 Oct '18

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

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Problem while installing nektar++ with lapack
by Amitvikram Dutta 12 Oct '18

12 Oct '18

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

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Re: [Nektar-users] TGV- L2 norm analysis
by Sherwin, Spencer J 18 Sep '18

18 Sep '18

Dear Cheng, Many thanks for confirming this and good to know it is running correctly (up to the time step error). Cheers, Spencer. On 18 Sep 2018, at 19:15, Xiao, Chengnian <CHX33(a)pitt.edu<mailto:CHX33@pitt.edu>> wrote: Dear all, Many thanks for your helpful responses. I have followed your recommendations and reduced the time step, and the L_2 error has indeed been reduced by a factor of around the square of the time step ratio, indicative of a second order temporal scheme. There appears to be no error with the analytic solution formula. Best regards, Cheng ________________________________ From: Cassinelli, Andrea <andrea.cassinelli15(a)imperial.ac.uk<mailto:andrea.cassinelli15@imperial.ac.uk>> Sent: Tuesday, September 18, 2018 9:51:37 AM To: Sherwin, Spencer J; Shervin Sammak Cc: nektar-users; Xiao, Chengnian Subject: Re: [Nektar-users] TGV- L2 norm analysis Hi Shervin, Spencer, I have actually not looked into the TGV problem to date. However, I agree with Spencer as to me it would look like there might be a discrepancy with the exact solution, especially if at P higher than 6 no further change is observed. Cheers, Andrea From: "Sherwin, Spencer J" <s.sherwin(a)imperial.ac.uk<mailto:s.sherwin@imperial.ac.uk>> Date: Tuesday, 18 September 2018 at 11:50 To: Shervin Sammak <shervin.sammak(a)gmail.com<mailto:shervin.sammak@gmail.com>> Cc: nektar-users <nektar-users(a)imperial.ac.uk<mailto:nektar-users@imperial.ac.uk>>, "Xiao, Chengnian" <chx33(a)pitt.edu<mailto:chx33@pitt.edu>>, "Cassinelli, Andrea" <andrea.cassinelli15(a)imperial.ac.uk<mailto:andrea.cassinelli15@imperial.ac.uk>> Subject: Re: [Nektar-users] TGV- L2 norm analysis HI Shervin, I do not recall if this has been explored previously. I am guessing it is saturating due to an formulation issue possibly as you suggest to do with the exact solution. However is this saturation also related to the time discretisation error or are you hitting that error boundary? Have you tried reducing the time step. @Andrea: you were looking at this recently, have you seen this issue before? Cheers, Spencer On 17 Sep 2018, at 19:52, Shervin Sammak <shervin.sammak(a)gmail.com<mailto:shervin.sammak@gmail.com>> wrote: Dear all, Here at Pitt, we are trying to solve the 2D Taylor Green Vortex solution from the tutorial and study the effect of resolution on L2 norm. As it is shown in the attached file, it appears that there is no difference at all between p=5 and p=6. It also looks like that the L2-error cannot be reduced below approx. 7e-6. I assume that the L2 norm provided at the end of simulation output is the comparison to the exact solution of the TGV. Are we missing something? Regards, Shervin -- ----------------------------------------------------------- Shervin Sammak Research Assistant Professor Center for Research Computing University of Pittsburgh 4420 Bayard St Pittsburgh, PA 15213 E-mail: shervin.sammak(a)pitt.edu<mailto:shervin.sammak@pitt.edu> Website: www.crc.pitt.edu<http://www.crc.pitt.edu/> ~ You chase quality and quantity will chase you. <l2-u.jpeg>_______________________________________________ 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/<https://na01.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.imperia…> 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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TGV- L2 norm analysis
by Shervin Sammak 18 Sep '18

18 Sep '18

Dear all, Here at Pitt, we are trying to solve the 2D Taylor Green Vortex solution from the tutorial and study the effect of resolution on L2 norm. As it is shown in the attached file, it appears that there is no difference at all between p=5 and p=6. It also looks like that the L2-error cannot be reduced below approx. 7e-6. I assume that the L2 norm provided at the end of simulation output is the comparison to the exact solution of the TGV. Are we missing something? Regards, Shervin -- ----------------------------------------------------------- Shervin Sammak Research Assistant Professor Center for Research Computing University of Pittsburgh 4420 Bayard St Pittsburgh, PA 15213 E-mail: shervin.sammak(a)pitt.edu Website: www.crc.pitt.edu ~ You chase quality and quantity will chase you.

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Compilation of Nektar++ 4.4.1 fails with "DSO missing from command line"
by Mikkel Bue Lykkegaard 13 Sep '18

13 Sep '18

Hi all I am trying to install Nektar++ for the first time, on Linux 4.18.6 with CMake version 3.12.1. The compilation fails with: [ 66%] Linking CXX executable CardiacEPSolver /usr/bin/ld: CMakeFiles/CardiacEPSolver.dir/CellModels/CellModel.cpp.o: undefined reference to symbol 'pthread_condattr_setclock@@GLIBC_2.3.3' /usr/bin/ld: /usr/lib/libpthread.so.0: error adding symbols: DSO missing from command line collect2: error: ld returned 1 exit status make[2]: *** [solvers/CardiacEPSolver/CMakeFiles/CardiacEPSolver.dir/build.make:465: solvers/CardiacEPSolver/CardiacEPSolver] Error 1 make[1]: *** [CMakeFiles/Makefile2:2907: solvers/CardiacEPSolver/CMakeFiles/CardiacEPSolver.dir/all] Error 2 make: *** [Makefile:163: all] Error 2 if I disable CardiacEPSolver in the configuration, I get a similar error: [ 70%] Linking CXX executable CompressibleFlowSolver /usr/bin/ld: CMakeFiles/CompressibleFlowSolver.dir/ArtificialDiffusion/ArtificialDiffusion.cpp.o: undefined reference to symbol 'pthread_condattr_setclock@@GLIBC_2.3.3' /usr/bin/ld: /usr/lib/libpthread.so.0: error adding symbols: DSO missing from command line collect2: error: ld returned 1 exit status make[2]: *** [solvers/CompressibleFlowSolver/CMakeFiles/CompressibleFlowSolver.dir/build.make:615: solvers/CompressibleFlowSolver/CompressibleFlowSolver] Error 1 make[1]: *** [CMakeFiles/Makefile2:2925: solvers/CompressibleFlowSolver/CMakeFiles/CompressibleFlowSolver.dir/all] Error 2 make: *** [Makefile:163: all] Error 2 Can someone point me in the right direction? Thanks, Mikkel

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Buildbot updated
by Chris Cantwell 09 Sep '18

09 Sep '18

Dear all, Our continuous integration system (Buildbot) has now been updated to the latest version with a range of improvements with increased automation and integration with Gitlab. Buildbot is our system for testing the Nektar++ code compiles and runs successfully on a range of architectures and operating systems as we add new developments. It is available at https://buildbot.nektar.info. The main changes in the latest version are: - Automatic builds on pushes to the main repository; - Automatic builds on new merge requests, or updates to existing merge requests; - Authentication via a Gitlab account (required to initiate manual (re)builds); - Automatic status updates to Gitlab. Build status of the master branch is available on the projects page (https://gitlab.nektar.info/dashboard/projects) and for merge requests on the merge requests listing (https://gitlab.nektar.info/nektar/nektar/merge_requests) One notable feature regression is that it is no longer possible to force a build on all builders at once (only individual builders). However, with the automation above, this should hopefully not be a problem. Remember to authenticate (where it says 'anonymous' in top-right) to initiate a forced build. There are a few outstanding teething issues with a couple of the workers, which will be fixed in due course, but please let me know if you encounter any other problems. Cheers, Chris -- 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

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Error building on windows 10 with MS Visual Studio 14 Win64
by Dr. Madhukar M. Rao 04 Sep '18

04 Sep '18

I am unable to build nektar 4.4.1 on MS Windows 10 using Visual Studio 14 win64. The error comes from Loki: Loki::ClassLevelLockable The actual error messages are reproduced below: ======================================================================== "C:\CFD\nektar\build\INSTALL.vcxproj" (default target) (1) -> "C:\CFD\nektar\build\ALL_BUILD.vcxproj" (default target) (3) -> "C:\CFD\nektar\build\solvers\ADRSolver\ADRSolver.vcxproj" (default target) (4) -> "C:\CFD\nektar\build\library\SolverUtils\SolverUtils.vcxproj" (default target) (17) -> (ClCompile target) -> C:\CFD\nektar\nektar441\library\SolverUtils\EquationSystem.cpp(88): error C2039: 'ClassLevelLocka ble': is not a member of 'Loki' [C:\CFD\nektar\build\library\SolverUtils\SolverUtils.vcxproj] C:\CFD\nektar\nektar441\library\SolverUtils\EquationSystem.cpp(88): error C2065: 'ClassLevelLocka ble': undeclared identifier [C:\CFD\nektar\build\library\SolverUtils\SolverUtils.vcxproj] ======================================================================== BOOST_HOME is c:\local\boost_1_61_0 (along with the modifications suggested in the user guide for version 4.4.1) Please let me know if any additional information is required. Thank you for your help. Madhu Rao

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"PressureInflowFile" BC template
by Arash Nouri 24 Aug '18

24 Aug '18

Hi all, Is there anyone here who have an uncompressed template of "PressureInflowFile" BC for the compressible flow solver? Thanks in advance, Arash --------------------------------- Arash G. Nouri Research Scientist Computational Modeling & Simulation (http://cmsp.pitt.edu/) 1127 Benedum Hall University of Pittsburgh Pittsburgh, PA 15261, USA E-mail: arn36(a)pitt.edu

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