October 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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Re: [Nektar-users] FW: Nektar++ installation in a cluster
by Amitvikram Dutta 05 Nov '18

05 Nov '18

Hi Nitish, Did you turn off the BUILD_THIRDPARTY options on the ccmake screen? I had a similar problem. I placed a ThirdParty folder containing the tarballs of all the thirdparty dependencies in the NEKTAR_SRC directory (which contains the build dir) and turned off the options that I mentioned above. That worked for me. Sincerely, On Tue, Oct 30, 2018 at 9:23 AM Amitvikram Dutta < amitvikram.dutta(a)uwaterloo.ca> wrote: > > ------------------------------ > *From:* nektar-users-bounces(a)imperial.ac.ukOn Behalf OfNitish Arya > *Sent:* October 30, 2018 8:21:04 AM (UTC-05:00) Eastern Time (US & Canada) > *To:* nektar-users(a)imperial.ac.uk > *Subject:* [Nektar-users] Nektar++ installation in a cluster > > Hello. > > I am planning to use APE solver included in the nektar framework. I have > to configure the MPI using Intel MPI which is available in the cluster, > while dependencies are installed using an internet connection. The internet > connection is only available at the head node in which I am unable to > invoke the Intel MPI. So it means that I have to compile the dependencies > separately. I tried compiling the ThirdParty dependencies separately but > when I compiled Nektar, it was again searching for the dependencies via > http or https ( both of the protocols are also not working ). > > Is there any way I can install Nektar without the installer searching for > the dependencies in the internet. > > > Sincerely, > Nitish > -- *Amitvikram Dutta* Graduate Research Assistant Fluid Mechanics Research Lab Multi-Physics Interaction Lab University of Waterloo

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Re: [Nektar-users] FW: Questions regarding APE Solver
by Amitvikram Dutta 04 Nov '18

04 Nov '18

Thanks a lot Killian, Is there a tentative release date for Nektar 5? On Fri, Oct 26, 2018, 3:58 AM Amitvikram Dutta < amitvikram.dutta(a)uwaterloo.ca> wrote: > > > > ________________________________________ > From: nektar-users-bounces(a)imperial.ac.ukOn Behalf OfKilian Lackhove > Sent: October 26, 2018 3:58:07 AM (UTC-05:00) Eastern Time (US & Canada) > To: Amitvikram Dutta; nektar-users > Subject: Re: [Nektar-users] Questions regarding APE Solver > > Hi Amitvikram, > > 1. Yes, only the lamb vector was used, so the RHS of the pressure > equation is zero. > > 2. It seems the userguide is out of date. In Nektar++ 4.4 the RHS are > specified using forcings (see the userguide). See e.g. > APE_2DPulseAdv_WeakDG_MODIFIED.xml example how this is set up in the xml > file. In short, you would have something like this: > > <CONDITIONS> > ... > <FUNCTION NAME="Source"> > <E VAR="p" VALUE="0"/> > <E VAR="u" VALUE="define lamb vector here"/> > <E VAR="v" VALUE="define lamb vector here"/> > <E VAR="w" VALUE="define lamb vector here"/> > </FUNCTION> > </CONDITIONS> > <FORCING> > <FORCE TYPE="Field"> > <FIELDFORCE> Source <FIELDFORCE/> > </FORCE> > </FORCING> > > 3. The next Nektar++ major release will ship a fieldfromstring module, > which should be able to compute the source terms without the pts detour. > Until then you can just use "FieldConvert foo.xml foo.chk bar.pts" to > obtain a pts file with the values at the quadrature points. > > In general, Nektar++ 5.0.0 will contain many changes and improvements to > the acoustics solver, in particular with regard to hybdrid CAA > cosimulations, so you might want to give it a try once its released. > > Cheers, > > Kilian > > > Am 26.10.18 um 04:55 schrieb Amitvikram Dutta: > > Hi everyone, > > > > I'm trying to use the APE Solver in nektar++ to predict sound generation > > from a particular industrial flow. The work is similar in scope to that > > published in this recent paper : > > http://www.iccfd.org/iccfd10/papers/ICCFD10-248-Paper.pdf. > > I'm particularly interested in how to define the source term. If I > > understand the work correctly, in a flow dominated by coherent > > structures, the Lamb vector becomes the dominant source. > > This leads to my first question : > > 1.In the APE-4 formulation there are 2 coupled equations with seperate > > source terms - one for the pressure fluctuations and one for the > > velocity fluctuations. In the above paper when the authors state that > > only the lamb vector was considered as a source, was the source for the > > RHS of the pressure fluctuations set to zero? > > 2. If this was the case, how was this specified in the .xml file? The > > only example I have come across is in the user guide which shows > > > > <FUNCTION NAME="Source"> > > <E VAR="S" VALUE="0" /> > > </FUNCTION> > > > > If one wanted to specify the pressure and velocity source terms > > seperately how would one do it in the .xml file? > > > > 3. From older posts in the mailing list I have seen suggestions of a > > workflow where the .chk/.fld files are written into a .pts file and then > > post processed to obtain the acoustic source. Is there a relevant filter > > or an extension the FieldConvert module that allows direct conversion > > from a .fld/.chk to a .pts format? I know of the interppoints extension > > that allows export to a .dat format but not the .pts? > > > > Sorry for the lengthy post. > > Thanks in advance! > > -- > > > > *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 > > > > -- > Dr.-Ing. Kilian Lackhove > Fachgebiet für Energie- und Kraftwerkstechnik > L1|08 114 > Technische Universität Darmstadt > Otto-Berndt-Straße 3 > D-64287 Darmstadt > Germany > > Tel.: +49 6151 16 - 28915 > Fax: +49 6151 16 - 6555 > e-mail: lackhove(a)ekt.tu-darmstadt.de > > _______________________________________________ > 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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Nektar++ installation in a cluster
by Nitish Arya 30 Oct '18

30 Oct '18

Hello. I am planning to use APE solver included in the nektar framework. I have to configure the MPI using Intel MPI which is available in the cluster, while dependencies are installed using an internet connection. The internet connection is only available at the head node in which I am unable to invoke the Intel MPI. So it means that I have to compile the dependencies separately. I tried compiling the ThirdParty dependencies separately but when I compiled Nektar, it was again searching for the dependencies via http or https ( both of the protocols are also not working ). Is there any way I can install Nektar without the installer searching for the dependencies in the internet. Sincerely, Nitish

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Re: [Nektar-users] FW: FW: Questions regarding APE Solver
by Amitvikram Dutta 30 Oct '18

30 Oct '18

Hi Killian, I was hoping to get your take on my setup for the APESolver with forcing from pts files and baseflow from fld files The appropriate sections in my .xml file are as follows * <BOUNDARYCONDITIONS> <FUNCTION NAME="Baseflow">  <F VAR="*" TIMEDEPENDENT="1" FILE="nzs1_%4.fld"/> </FUNCTION> <FUNCTION NAME="Source"> <E VAR="p" VALUE="0"/> <F VAR="u" TIMEDEPENDENT="1" FILE="nzs1_vort_ptslamb_%4.pts:L_x"/> <F VAR="v" TIMEDEPENDENT="1" FILE="nzs1_vort_ptslamb_%4.pts:L_y"/> <F VAR="w" TIMEDEPENDENT="1" FILE="nzs1_vort_ptslamb_%4.pts:L_z"/> </FUNCTION> </BOUNDARYCONDITIONS> <FUNCTION NAME="InitialConditions"> <F VAR="*" FILE="nzs1_1500.fld" /></FUNCTION></CONDITIONS><FORCING> <FORCE TYPE="Field"> <FIELDFORCE> Source <FIELDFORCE/> </FORCE> </FORCING>* Where the base flow is taken from files from an incompressible simulation that was run earlier (named as nzs1_1500.fld - nzs1_1503.fld), and the forcing from .pts files which contain the lamb vector fluctuations (named as nzs1_vort_ptslamb_1500.pts-nzs1_vort_ptslamb_1503.pts). The solver fails with a segmentation fault (text shown below), which seems rather strange to me as none of the files involved are particularly large (10 Mb or so). *[nia0412:347383:0:347383] Caught signal 11 (Segmentation fault: address not mapped to object at address 0x10)==== backtrace ==== 0 0x000000000019b649 Nektar::MultiRegions::ExpList::GetBoundaryCondition() ???:0 1 0x000000000016cac5 Nektar::MultiRegions::DisContField2D::GenerateBoundaryConditionExpansion() ???:0 2 0x00000000001730d5 Nektar::MultiRegions::DisContField2D::DisContField2D() ???:0 3 0x000000000013ea91 Nektar::MemoryManager<Nektar::MultiRegions::DisContField2D>::Allocate<boost::shared_ptr<Nektar::LibUtilities::SessionReader>, boost::shared_ptr<Nektar::SpatialDomains::MeshGraph>, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > >() ???:0 4 0x00000000001360c6 Nektar::SolverUtils::EquationSystem::v_InitObject() ???:0 5 0x000000000017b6c3 Nektar::SolverUtils::UnsteadySystem::v_InitObject() ???:0 6 0x00000000004378ac Nektar::APE::v_InitObject() ???:0 7 0x000000000043ada6 Nektar::APE::create() ???:0 8 0x000000000011608a Nektar::LibUtilities::NekFactory<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, Nektar::SolverUtils::EquationSystem, boost::shared_ptr<Nektar::LibUtilities::SessionReader> const&, Nektar::LibUtilities::none, Nektar::LibUtilities::none, Nektar::LibUtilities::none, Nektar::LibUtilities::none, Nektar::LibUtilities::none>::CreateInstance() ???:0 9 0x0000000000115062 Nektar::SolverUtils::Driver::v_InitObject() ???:010 0x000000000012651e Nektar::SolverUtils::DriverStandard::create() ???:011 0x000000000042f926 Nektar::LibUtilities::NekFactory<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, Nektar::SolverUtils::Driver, boost::shared_ptr<Nektar::LibUtilities::SessionReader> const&, Nektar::LibUtilities::none, Nektar::LibUtilities::none, Nektar::LibUtilities::none, Nektar::LibUtilities::none, Nektar::LibUtilities::none>::CreateInstance() ???:012 0x0000000000423b99 main() ???:013 0x0000000000021c05 __libc_start_main() ???:014 0x0000000000426dcd _start() ???:0===================Segmentation fault* Any insight would be greatly appreciated. Sincerely, On Fri, Oct 26, 2018 at 7:58 AM Amitvikram Dutta < amitvikram.dutta(a)uwaterloo.ca> wrote: > *From:* nektar-users-bounces(a)imperial.ac.ukOn Behalf OfAmitvikram Dutta > *Sent:* October 26, 2018 7:57:47 AM (UTC-05:00) Eastern Time (US & Canada) > *To:* nektar-users > *Subject:* Re: [Nektar-users] FW: Questions regarding APE Solver > > Thanks a lot Killian, > > Is there a tentative release date for Nektar 5? > > On Fri, Oct 26, 2018, 3:58 AM Amitvikram Dutta < > amitvikram.dutta(a)uwaterloo.ca> wrote: > >> >> >> >> ________________________________________ >> From: nektar-users-bounces(a)imperial.ac.ukOn Behalf OfKilian Lackhove >> Sent: October 26, 2018 3:58:07 AM (UTC-05:00) Eastern Time (US & Canada) >> To: Amitvikram Dutta; nektar-users >> Subject: Re: [Nektar-users] Questions regarding APE Solver >> >> Hi Amitvikram, >> >> 1. Yes, only the lamb vector was used, so the RHS of the pressure >> equation is zero. >> >> 2. It seems the userguide is out of date. In Nektar++ 4.4 the RHS are >> specified using forcings (see the userguide). See e.g. >> APE_2DPulseAdv_WeakDG_MODIFIED.xml example how this is set up in the xml >> file. In short, you would have something like this: >> >> <CONDITIONS> >> ... >> <FUNCTION NAME="Source"> >> <E VAR="p" VALUE="0"/> >> <E VAR="u" VALUE="define lamb vector here"/> >> <E VAR="v" VALUE="define lamb vector here"/> >> <E VAR="w" VALUE="define lamb vector here"/> >> </FUNCTION> >> </CONDITIONS> >> <FORCING> >> <FORCE TYPE="Field"> >> <FIELDFORCE> Source <FIELDFORCE/> >> </FORCE> >> </FORCING> >> >> 3. The next Nektar++ major release will ship a fieldfromstring module, >> which should be able to compute the source terms without the pts detour. >> Until then you can just use "FieldConvert foo.xml foo.chk bar.pts" to >> obtain a pts file with the values at the quadrature points. >> >> In general, Nektar++ 5.0.0 will contain many changes and improvements to >> the acoustics solver, in particular with regard to hybdrid CAA >> cosimulations, so you might want to give it a try once its released. >> >> Cheers, >> >> Kilian >> >> >> Am 26.10.18 um 04:55 schrieb Amitvikram Dutta: >> > Hi everyone, >> > >> > I'm trying to use the APE Solver in nektar++ to predict sound generation >> > from a particular industrial flow. The work is similar in scope to that >> > published in this recent paper : >> > http://www.iccfd.org/iccfd10/papers/ICCFD10-248-Paper.pdf. >> > I'm particularly interested in how to define the source term. If I >> > understand the work correctly, in a flow dominated by coherent >> > structures, the Lamb vector becomes the dominant source. >> > This leads to my first question : >> > 1.In the APE-4 formulation there are 2 coupled equations with seperate >> > source terms - one for the pressure fluctuations and one for the >> > velocity fluctuations. In the above paper when the authors state that >> > only the lamb vector was considered as a source, was the source for the >> > RHS of the pressure fluctuations set to zero? >> > 2. If this was the case, how was this specified in the .xml file? The >> > only example I have come across is in the user guide which shows >> > >> > <FUNCTION NAME="Source"> >> > <E VAR="S" VALUE="0" /> >> > </FUNCTION> >> > >> > If one wanted to specify the pressure and velocity source terms >> > seperately how would one do it in the .xml file? >> > >> > 3. From older posts in the mailing list I have seen suggestions of a >> > workflow where the .chk/.fld files are written into a .pts file and then >> > post processed to obtain the acoustic source. Is there a relevant filter >> > or an extension the FieldConvert module that allows direct conversion >> > from a .fld/.chk to a .pts format? I know of the interppoints extension >> > that allows export to a .dat format but not the .pts? >> > >> > Sorry for the lengthy post. >> > Thanks in advance! >> > -- >> > >> > *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 >> > >> >> -- >> Dr.-Ing. Kilian Lackhove >> Fachgebiet für Energie- und Kraftwerkstechnik >> L1|08 114 >> Technische Universität Darmstadt >> Otto-Berndt-Straße 3 >> D-64287 Darmstadt >> Germany >> >> Tel.: +49 6151 16 - 28915 <+49%206151%201628915> >> Fax: +49 6151 16 - 6555 <+49%206151%20166555> >> e-mail: lackhove(a)ekt.tu-darmstadt.de >> >> _______________________________________________ >> 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 > -- *Amitvikram Dutta* Graduate Research Assistant Fluid Mechanics Research Lab Multi-Physics Interaction Lab University of Waterloo

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Regarding BiGlobal stability in Nektar++
by Abhishek Kumar 26 Oct '18

26 Oct '18

Hi, I am trying to understand the session file "PPF_R15000_3D_VCS.xml." I have two confusion: 1) Since modeType is HalfMode than why "HomModesZ" is set to 2. I think this should be 1. 2) Since the base flow is 2D2C, then is it necessary to include variable "w" in the base flow? In general, can we use a base flow generated from DNS which only have variables (uvp) in the session file having FIELDS = (uvwp)? 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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Questions regarding APE Solver
by Amitvikram Dutta 26 Oct '18

26 Oct '18

Hi everyone, I'm trying to use the APE Solver in nektar++ to predict sound generation from a particular industrial flow. The work is similar in scope to that published in this recent paper : http://www.iccfd.org/iccfd10/papers/ICCFD10-248-Paper.pdf. I'm particularly interested in how to define the source term. If I understand the work correctly, in a flow dominated by coherent structures, the Lamb vector becomes the dominant source. This leads to my first question : 1.In the APE-4 formulation there are 2 coupled equations with seperate source terms - one for the pressure fluctuations and one for the velocity fluctuations. In the above paper when the authors state that only the lamb vector was considered as a source, was the source for the RHS of the pressure fluctuations set to zero? 2. If this was the case, how was this specified in the .xml file? The only example I have come across is in the user guide which shows <FUNCTION NAME="Source"> <E VAR="S" VALUE="0" /> </FUNCTION> If one wanted to specify the pressure and velocity source terms seperately how would one do it in the .xml file? 3. From older posts in the mailing list I have seen suggestions of a workflow where the .chk/.fld files are written into a .pts file and then post processed to obtain the acoustic source. Is there a relevant filter or an extension the FieldConvert module that allows direct conversion from a .fld/.chk to a .pts format? I know of the interppoints extension that allows export to a .dat format but not the .pts? Sorry for the lengthy post. Thanks in advance! -- *Amitvikram Dutta* Graduate Research Assistant Fluid Mechanics Research Lab Multi-Physics Interaction Lab University of Waterloo

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Regarding base flow for HalfMode
by Abhishek Kumar 23 Oct '18

23 Oct '18

Hi, I am trying to do linear stability analysis using HalfMode, with the two-dimensional base flow and three-dimensional perturbation for the buoyancy-driven problem. I provide a base flow with (u,v,c,p), where c is a scalar. I am getting the following error: "For half mode, expect 2D2C base flow." Is there any solution to include a variable "c" in the base flow? With regards Abhishek --------------------------------------------------------------------------------------- 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 linear stability solver in parallel
by Abhishek Kumar 23 Oct '18

23 Oct '18

Hi, I am trying to test the linear stability solver in parallel. I did a simple test with the channel flow with a single processor and on 8 processors. I observed the following: Time taken per 1000 steps for single processor = 2.76512s Time taken per 1000 steps for 8 processors = 24.7811s I expected a reduction in the computational time while running parallel. Is there any issue in the parallel implementation of the linear stability solver? Is something related with the eigenvalue solver? 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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Routine to create *chk
by WEI HE 19 Oct '18

19 Oct '18

Dear all, Does anyone know how to load *vtu files by. nektar++? Or the rules to export the binary check file *.chk? Thanks, Regards, Wei

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