October 2018 - Nektar-users

Re: [Nektar-users] Problem with msh to xml conversion using NekMesh
by Oliviu Sugar 18 Oct '18

18 Oct '18

Hi Dave, I checked out the latest version of Master from the repository yesterday. I also ran the NekMesh regression tests including the gmsh version 4 files, and all test completed successfully. This is what led me to think I might have made a mistake with the geo file, but if this is the case it is not evident. Best,Oliviu On Wednesday, October 17, 2018, 9:00:25 PM GMT+1, David Moxey <D.Moxey(a)exeter.ac.uk> wrote: Hi Oliviu, The problem is likely gmsh 4, which was only recently released and changed the msh file format. Thanks to Julian, one of our PhD students, we have recently added support for this to NekMesh: https://gitlab.nektar.info/nektar/nektar/merge_requests/964 However you will need to upgrade/compile your own version of the latest Nektar++ master to get this functionality. Alternatively you can use Gmsh v3.x to generate your msh file instead. Many thanks, Dave > On 17 Oct 2018, at 20:43, Oliviu Sugar <oliviu_sugar(a)yahoo.com> wrote: > > Hi Stanislaw, > > All lines and surfaces in the gmsh script have been defined as transfinite, in order to force a structured mesh generation, and I have verified that all elements are quads. > > Best regards, > Oliviu > > On Wednesday, October 17, 2018, 8:38:33 PM GMT+1, Stanisław Gepner <sgepner(a)meil.pw.edu.pl> wrote: > > > Hi, a wild guess would be that you have a mix of triangles and quads in a composite. From what I remember this is not supported. > Pozdrawiam, > Stanisław Gepner > > Dnia 17 października 2018 21:32:19 CEST, Oliviu Sugar <oliviu_sugar(a)yahoo.com> napisał(a): > Dear all, > > I've run into some problems when trying to convert a msh file (generated using gmsh 4.0.2) into a xml file, using NekMesh. > The script geo file used with gmsh is attached. > The error encountered by NekMesh is: "Different types of elements in same composite!" > Any advice on what needs to be changed in the geo file to resolve this issue would be much appreciated. > > Best regards, > Oliviu > > _______________________________________________ > Nektar-users mailing list > Nektar-users(a)imperial.ac.uk > https://mailman.ic.ac.uk/mailman/listinfo/nektar-users

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Problem with msh to xml conversion using NekMesh
by Oliviu Sugar 17 Oct '18

17 Oct '18

Dear all, I've run into some problems when trying to convert a msh file (generated using gmsh 4.0.2) into a xml file, using NekMesh.The script geo file used with gmsh is attached.The error encountered by NekMesh is: "Different types of elements in same composite!" Any advice on what needs to be changed in the geo file to resolve this issue would be much appreciated. Best regards,Oliviu

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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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