March 2023 - Nektar-users - imperial.ac.uk

Reconstruct the parallel files into a single field
by Ehsan Asgari 20 Mar '23

20 Mar '23

******************* This email originates from outside Imperial. Do not click on links and attachments unless you recognise the sender. If you trust the sender, add them to your safe senders list https://spam.ic.ac.uk/SpamConsole/Senders.aspx to disable email stamping for this address. ******************* Dear all, I went through the user-guide to see how to convert the parallel files into a single field using FieldConvert. Unfortunately, I wasn't able to do it. Is there any specific command to do this? For example, I have 128 parallel fields inside a solution directory. I'd like to reconstruct them into a single file to post-process the solution. Kind regards syavash

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Question about mesh
by Ehsan Asgari 20 Mar '23

20 Mar '23

******************* This email originates from outside Imperial. Do not click on links and attachments unless you recognise the sender. If you trust the sender, add them to your safe senders list https://spam.ic.ac.uk/SpamConsole/Senders.aspx to disable email stamping for this address. ******************* Dear All, My background is in FVM and I have recently started using Nektar++ and reading about SEM. My first question is about the mesh quality in the context of SEM. Should I have a mesh with the same quality as in FVM? Is there any specific index to consider when dealing with tet and hex meshes in Nektar++? I have seen a very skewed tri mesh in one of the tutorials. Could you kindly provide some insight on this? My second question is specifically about NekMesh. Is it possible to smooth the mesh of a wall-mounted cylinder using high-order cylinder module? Or would you suggest to use spherigon module for that purpose? Kind regards syavash

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snappyHexMesh
by Ehsan Asgari 18 Mar '23

18 Mar '23

******************* This email originates from outside Imperial. Do not click on links and attachments unless you recognise the sender. If you trust the sender, add them to your safe senders list https://spam.ic.ac.uk/SpamConsole/Senders.aspx to disable email stamping for this address. ******************* Dear All, I was wondering if Nektar++ accepts mesh from snappyHexMesh (an OpenFOAM module) ? Kind regards syavash

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Compiling with AVX2 issues
by Ehsan Asgari 17 Mar '23

17 Mar '23

******************* This email originates from outside Imperial. Do not click on links and attachments unless you recognise the sender. If you trust the sender, add them to your safe senders list https://spam.ic.ac.uk/SpamConsole/Senders.aspx to disable email stamping for this address. ******************* Dear All, When I turn on the AVX2 flag in ccmake, I receive the following error messages: icpc: error #10106: Fatal error in > /***/intel/2020.1.217/compilers_and_libraries_2020.1.217/linux/bin/intel64/mcpcom, > terminated by kill signal > compilation aborted for > /home/***/Nektar/nektar++/library/UnitTests/SIMD/main.cpp (code 1) > make[2]: *** > [library/UnitTests/SIMD/CMakeFiles/VecDataUnitTests.dir/build.make:76: > library/UnitTests/SIMD/CMakeFiles/VecDataUnitTests.dir/main.cpp.o] Error 1 > make[1]: *** [CMakeFiles/Makefile2:3140: > library/UnitTests/SIMD/CMakeFiles/VecDataUnitTests.dir/all] Error 2 > make[1]: *** Waiting for unfinished jobs.... > [ 6%] Building CXX object > library/LibUtilities/CMakeFiles/LibUtilities.dir/BasicUtils/SessionReader.cpp.o > icpc: error #10106: Fatal error in > /***/intel/2020.1.217/compilers_and_libraries_2020.1.217/linux/bin/intel64/mcpcom, > terminated by kill signal > compilation aborted for > /home/***/Nektar/nektar++/library/LibUtilities/BasicUtils/FieldIO.cpp (code > 1) > make[2]: *** > [library/LibUtilities/CMakeFiles/LibUtilities.dir/build.make:132: > library/LibUtilities/CMakeFiles/LibUtilities.dir/BasicUtils/FieldIO.cpp.o] > Error 1 > make[2]: *** Waiting for unfinished jobs.... > remark #11074: Inlining inhibited by limit max-size > remark #11074: Inlining inhibited by limit max-total-size > remark #11076: To get full report use -qopt-report=4 -qopt-report-phase ipo > remark #11074: Inlining inhibited by limit max-size > remark #11074: Inlining inhibited by limit max-total-size > remark #11076: To get full report use -qopt-report=4 -qopt-report-phase ipo > remark #11074: Inlining inhibited by limit max-size > remark #11074: Inlining inhibited by limit max-total-size > remark #11076: To get full report use -qopt-report=4 -qopt-report-phase ipo > remark #11074: Inlining inhibited by limit max-size > remark #11074: Inlining inhibited by limit max-total-size > remark #11076: To get full report use -qopt-report=4 -qopt-report-phase ipo > make[1]: *** [CMakeFiles/Makefile2:2790: > library/LibUtilities/CMakeFiles/LibUtilities.dir/all] Error 2 > make: *** [Makefile:146: all] Error 2 Can anybody diagnose the problem? Kind regards syavash

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Fwd: Installing Nektar++ 5.2.0 on a cluster
by Ehsan Asgari 14 Mar '23

14 Mar '23

---------- Forwarded message --------- From: Ehsan Asgari <eh.asgari(a)gmail.com> Date: Tue, Mar 14, 2023 at 11:46 AM Subject: Re: [Nektar-users] Installing Nektar++ 5.2.0 on a cluster To: Slaughter, James W <j.slaughter19(a)imperial.ac.uk> Hi James Yes, I compiled without those flags for gcc. Are you pointing out this is the cause of the runtime difference I get? I see there are avx2 and avx512 directories on the cluster. Would you believe changing their flags will bring a noticeable speed-up? Here is the error I received when I tried to use 128 cores each with 3GB of RAM: ======================================================================= > EquationType: UnsteadyNavierStokes > Session Name: clusteredToGmsh > Spatial Dim.: 3 > Max SEM Exp. Order: 4 > Num. Processes: 64 > Expansion Dim.: 3 > Projection Type: Continuous Galerkin > Advection: explicit > Diffusion: implicit > Time Step: 0.0001 > No. of Steps: 500000 > Checkpoints (steps): 10 > Integration Type: IMEXOrder2 > Splitting Scheme: Velocity correction (strong press. form) > ======================================================================= > Initial Conditions: > - Field u: from file clusteredToGmsh.fld > - Field v: from file clusteredToGmsh.fld > - Field w: from file clusteredToGmsh.fld > - Field p: from file clusteredToGmsh.fld > Writing: "clusteredToGmsh_0.chk" (1.18025s, XML) > -------------------------------------------------------------------------- > Primary job terminated normally, but 1 process returned > a non-zero exit code. Per user-direction, the job has been aborted. > -------------------------------------------------------------------------- > -------------------------------------------------------------------------- > mpirun noticed that process rank 55 with PID 32156 on node cra710 exited > on signal 9 (Killed). > -------------------------------------------------------------------------- > 4 total processes killed (some possibly by mpirun during cleanup) Sometimes, the error happens before everything (not even showing the setup). The mesh issue has become a bottleneck, as the cluster has put me in a queue to apply for 2 hours use of 128 cores and a dedicated 125GB of RAM. It has been 1 day so far! To give more insight, I could be granted 24 hours use of 128 cores with 3GB of RAM per core almost instantly. Kind regards syavash On Tue, Mar 14, 2023 at 1:47 AM Slaughter, James W < j.slaughter19(a)imperial.ac.uk> wrote: > Hi Syavash, > > > > The compiler itself shouldn’t make a massive difference. You were > compiling by the looks of it with SSE with the chosen intel compiler. > Guessing you were then running on intel based cluster? SSE and AVX will > speed-up your simulations non-trivially then. My suspicion would be that > these you aren’t compiling with these compiler flags for gcc. > > > > The mesh is a trickier one again to troubleshoot. 750k at P3 yeh, I’d > suggest 3Gb won’t be enough. When you had the previous issue do you know > where in the simulation it fails? I.e in setup, first-timestep or a bit > further into the simulation? > > > > Kind regards, > > James. > > > > *From:* nektar-users-bounces(a)imperial.ac.uk < > nektar-users-bounces(a)imperial.ac.uk> *On Behalf Of *Ehsan Asgari > *Sent:* Monday, March 13, 2023 7:57 PM > *To:* nektar-users <nektar-users(a)imperial.ac.uk> > *Subject:* Re: [Nektar-users] Installing Nektar++ 5.2.0 on a cluster > > > > Thank you James > > > > You are quite right. I managed to install it by totally unloading the > intel-related modules and loading gcc instead. However, I found that gcc > resulted in significantly slower simulations. > > > > Regarding the mesh problem, I realized that Nektar is quite demanding in > term of memory, so I had to allocate a big sum of RAM to the larger mesh > (750K cells I sent you). In other words, the minimum 3GB of RAM was not > enough to decompose and start the solution. It can be restrictive as > resources may not be available as "whole node" on clusters. > > For now I am doing some tests to see if 128 cores with 3GB RAM per core > can do the trick. > > > > Please let me know if things can be improved. > > > > Kind regards > > syavash > > > > On Mon, Mar 13, 2023, 22:02 Slaughter, James W < > j.slaughter19(a)imperial.ac.uk> wrote: > > Hi Syavash, > > > > Can you run ldd the IncNavierStokesSolver and put module list as an extra > line in your submission script before the solver execution and run again > and send through the output? > > > > It looks like you’ve compiled at least Spatial Domains with an intel > specific instruction set and these can’t be found at runtime. > > > > Kind regards, > > James. > > > > *From:* nektar-users-bounces(a)imperial.ac.uk < > nektar-users-bounces(a)imperial.ac.uk> *On Behalf Of *Ehsan Asgari > *Sent:* Saturday, March 11, 2023 8:32 AM > *To:* nektar-users <nektar-users(a)imperial.ac.uk> > *Subject:* [Nektar-users] Installing Nektar++ 5.2.0 on a cluster > > > > Hi Parv > > > > Thank you for your kind response. > > I managed to install ver. 5.3 using intel compiler and OpenMPI 4.0.3 at > last. However, I am still getting MPI-related issues when running a > medium-sized mesh with 760K cells (success with a smaller mesh in parallel): > > > > ======================================================================= > EquationType: UnsteadyNavierStokes > Session Name: clusteredToGmsh > Spatial Dim.: 3 > Max SEM Exp. Order: 4 > Num. Processes: 32 > Expansion Dim.: 3 > Projection Type: Continuous Galerkin > Advect. advancement: explicit > Diffuse. advancement: implicit > Time Step: 0.0001 > No. of Steps: 500000 > Checkpoints (steps): 10000 > Integration Type: IMEX > Splitting Scheme: Velocity correction (strong press. form) > ======================================================================= > Initial Conditions: > - Field u: 1.0 > - Field v: 0.0 > - Field w: 0.0 > - Field p: 0.0 > -------------------------------------------------------------------------- > Primary job terminated normally, but 1 process returned > a non-zero exit code. Per user-direction, the job has been aborted. > -------------------------------------------------------------------------- > -------------------------------------------------------------------------- > mpirun noticed that process rank 0 with PID 0 on node cra1080 exited on > signal 9 (Killed). > > > > I was suspicious that it might be a problem with the inlet compiler and so > I switched to GCC 9.3 for a fresh installation. But it seems that GCC is > causing problems and I get the following error at some point: > > > > ../../SpatialDomains/libSpatialDomains.so.5.3.0: error: undefined > reference to '__intel_sse2_strcpy' > ../../SpatialDomains/libSpatialDomains.so.5.3.0: error: undefined > reference to '_intel_fast_memmove' > ../../SpatialDomains/libSpatialDomains.so.5.3.0: error: undefined > reference to '__intel_sse2_strlen' > ../../SpatialDomains/libSpatialDomains.so.5.3.0: error: undefined > reference to '_intel_fast_memcpy' > ../../SpatialDomains/libSpatialDomains.so.5.3.0: error: undefined > reference to '_intel_fast_memset' > collect2: error: ld returned 1 exit status > make[2]: *** > [library/Demos/SpatialDomains/CMakeFiles/PartitionAnalyse.dir/build.make:127: > library/Demos/SpatialDomains/PartitionAnalyse] Error 1 > make[1]: *** [CMakeFiles/Makefile2:3681: > library/Demos/SpatialDomains/CMakeFiles/PartitionAnalyse.dir/all] Error 2 > make[1]: *** Waiting for unfinished jobs.... > > > > I discussed the mesh problem with James Slaughter prior to this and he > suggested that the problem might be due to a bug in a lower version (5.0.3) > that I was working with. That is why I decided to go with the most recent > version. > > After all, I am still struggling with my parallel simulations! > > > > Kind regards > > syavash > > > > On Thu, Mar 9, 2023 at 4:57 PM Khurana, Parv <p.khurana22(a)imperial.ac.uk> > wrote: > > Hi Syavash, > > > > A few questions pop up on my mind on seeing this: > > > > 1. What compilers are you using (GCC or Intel?) > 2. Are you loading the modules which are compatible with the compiler > you are using? > 3. Do you have a version of OpenBLAS or MKL already loaded as one of > the modules on your cluster? > > > > As often is the case, the problem might be more detailed and it’ll be > great to see the modules and cmake commands you are using for you > installation in order to debug this properly. Happy to hop on a call if > needed! > > > > Best > > Parv > > > > > > *From:* nektar-users-bounces(a)imperial.ac.uk < > nektar-users-bounces(a)imperial.ac.uk> *On Behalf Of *Ehsan Asgari > *Sent:* 09 March 2023 09:54 > *To:* nektar-users <nektar-users(a)imperial.ac.uk> > *Subject:* [Nektar-users] Installing Nektar++ 5.2.0 on a cluster > > > > This email from eh.asgari(a)gmail.com originates from outside Imperial. Do > not click on links and attachments unless you recognise the sender. If you > trust the sender, add them to your safe senders list > <https://spam.ic.ac.uk/SpamConsole/Senders.aspx> to disable email > stamping for this address. > > > > Hi Everyone, > > > > I am trying to install the latest version of Nektar on a cluster. However, > I get the following error at some point: > > > > ../../library/SpatialDomains/libSpatialDomains.so.5.3.0: error: undefined > reference to '__intel_sse2_strlen' > ../../library/SpatialDomains/libSpatialDomains.so.5.3.0: error: undefined > reference to '_intel_fast_memcpy' > ../../library/SpatialDomains/libSpatialDomains.so.5.3.0: error: undefined > reference to '_intel_fast_memset' > collect2: error: ld returned 1 exit status > make[2]: *** [utilities/NekMesh/CMakeFiles/NekMesh.dir/build.make:106: > utilities/NekMesh/NekMesh] Error 1 > make[1]: *** [CMakeFiles/Makefile2:1647: > utilities/NekMesh/CMakeFiles/NekMesh.dir/all] Error 2 > make: *** [Makefile:141: all] Error 2 > > > > I had "NEKTAR_USE_SYSTEM_BLAS_LAPACK:BOOL=ON " and > "THIRDPARTY_BUILD_BLAS_LAPACK:BOOL=ON" in the ccmake as per suggested in > the user archives. > > > > I appreciate your kind help. > > > > Kind regards > > syavash > >

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Re: [Nektar-users] Installing Nektar++ 5.2.0 on a cluster
by Ehsan Asgari 13 Mar '23

13 Mar '23

> > Thank you James > > You are quite right. I managed to install it by totally unloading the > intel-related modules and loading gcc instead. However, I found that gcc > resulted in significantly slower simulations. > > Regarding the mesh problem, I realized that Nektar is quite demanding in > term of memory, so I had to allocate a big sum of RAM to the larger mesh > (750K cells I sent you). In other words, the minimum 3GB of RAM was not > enough to decompose and start the solution. It can be restrictive as > resources may not be available as "whole node" on clusters. > For now I am doing some tests to see if 128 cores with 3GB RAM per core > can do the trick. > > Please let me know if things can be improved. > > Kind regards > syavash > > On Mon, Mar 13, 2023, 22:02 Slaughter, James W < > j.slaughter19(a)imperial.ac.uk> wrote: > >> Hi Syavash, >> >> >> >> Can you run ldd the IncNavierStokesSolver and put module list as an extra >> line in your submission script before the solver execution and run again >> and send through the output? >> >> >> >> It looks like you’ve compiled at least Spatial Domains with an intel >> specific instruction set and these can’t be found at runtime. >> >> >> >> Kind regards, >> >> James. >> >> >> >> *From:* nektar-users-bounces(a)imperial.ac.uk < >> nektar-users-bounces(a)imperial.ac.uk> *On Behalf Of *Ehsan Asgari >> *Sent:* Saturday, March 11, 2023 8:32 AM >> *To:* nektar-users <nektar-users(a)imperial.ac.uk> >> *Subject:* [Nektar-users] Installing Nektar++ 5.2.0 on a cluster >> >> >> >> Hi Parv >> >> >> >> Thank you for your kind response. >> >> I managed to install ver. 5.3 using intel compiler and OpenMPI 4.0.3 at >> last. However, I am still getting MPI-related issues when running a >> medium-sized mesh with 760K cells (success with a smaller mesh in parallel): >> >> >> >> ======================================================================= >> EquationType: UnsteadyNavierStokes >> Session Name: clusteredToGmsh >> Spatial Dim.: 3 >> Max SEM Exp. Order: 4 >> Num. Processes: 32 >> Expansion Dim.: 3 >> Projection Type: Continuous Galerkin >> Advect. advancement: explicit >> Diffuse. advancement: implicit >> Time Step: 0.0001 >> No. of Steps: 500000 >> Checkpoints (steps): 10000 >> Integration Type: IMEX >> Splitting Scheme: Velocity correction (strong press. form) >> ======================================================================= >> Initial Conditions: >> - Field u: 1.0 >> - Field v: 0.0 >> - Field w: 0.0 >> - Field p: 0.0 >> -------------------------------------------------------------------------- >> Primary job terminated normally, but 1 process returned >> a non-zero exit code. Per user-direction, the job has been aborted. >> -------------------------------------------------------------------------- >> -------------------------------------------------------------------------- >> mpirun noticed that process rank 0 with PID 0 on node cra1080 exited on >> signal 9 (Killed). >> >> >> >> I was suspicious that it might be a problem with the inlet compiler and >> so I switched to GCC 9.3 for a fresh installation. But it seems that GCC is >> causing problems and I get the following error at some point: >> >> >> >> ../../SpatialDomains/libSpatialDomains.so.5.3.0: error: undefined >> reference to '__intel_sse2_strcpy' >> ../../SpatialDomains/libSpatialDomains.so.5.3.0: error: undefined >> reference to '_intel_fast_memmove' >> ../../SpatialDomains/libSpatialDomains.so.5.3.0: error: undefined >> reference to '__intel_sse2_strlen' >> ../../SpatialDomains/libSpatialDomains.so.5.3.0: error: undefined >> reference to '_intel_fast_memcpy' >> ../../SpatialDomains/libSpatialDomains.so.5.3.0: error: undefined >> reference to '_intel_fast_memset' >> collect2: error: ld returned 1 exit status >> make[2]: *** >> [library/Demos/SpatialDomains/CMakeFiles/PartitionAnalyse.dir/build.make:127: >> library/Demos/SpatialDomains/PartitionAnalyse] Error 1 >> make[1]: *** [CMakeFiles/Makefile2:3681: >> library/Demos/SpatialDomains/CMakeFiles/PartitionAnalyse.dir/all] Error 2 >> make[1]: *** Waiting for unfinished jobs.... >> >> >> >> I discussed the mesh problem with James Slaughter prior to this and he >> suggested that the problem might be due to a bug in a lower version (5.0.3) >> that I was working with. That is why I decided to go with the most recent >> version. >> >> After all, I am still struggling with my parallel simulations! >> >> >> >> Kind regards >> >> syavash >> >> >> >> On Thu, Mar 9, 2023 at 4:57 PM Khurana, Parv <p.khurana22(a)imperial.ac.uk> >> wrote: >> >> Hi Syavash, >> >> >> >> A few questions pop up on my mind on seeing this: >> >> >> >> 1. What compilers are you using (GCC or Intel?) >> 2. Are you loading the modules which are compatible with the compiler >> you are using? >> 3. Do you have a version of OpenBLAS or MKL already loaded as one of >> the modules on your cluster? >> >> >> >> As often is the case, the problem might be more detailed and it’ll be >> great to see the modules and cmake commands you are using for you >> installation in order to debug this properly. Happy to hop on a call if >> needed! >> >> >> >> Best >> >> Parv >> >> >> >> >> >> *From:* nektar-users-bounces(a)imperial.ac.uk < >> nektar-users-bounces(a)imperial.ac.uk> *On Behalf Of *Ehsan Asgari >> *Sent:* 09 March 2023 09:54 >> *To:* nektar-users <nektar-users(a)imperial.ac.uk> >> *Subject:* [Nektar-users] Installing Nektar++ 5.2.0 on a cluster >> >> >> >> This email from eh.asgari(a)gmail.com originates from outside Imperial. Do >> not click on links and attachments unless you recognise the sender. If you >> trust the sender, add them to your safe senders list >> <https://spam.ic.ac.uk/SpamConsole/Senders.aspx> to disable email >> stamping for this address. >> >> >> >> Hi Everyone, >> >> >> >> I am trying to install the latest version of Nektar on a cluster. >> However, I get the following error at some point: >> >> >> >> ../../library/SpatialDomains/libSpatialDomains.so.5.3.0: error: undefined >> reference to '__intel_sse2_strlen' >> ../../library/SpatialDomains/libSpatialDomains.so.5.3.0: error: undefined >> reference to '_intel_fast_memcpy' >> ../../library/SpatialDomains/libSpatialDomains.so.5.3.0: error: undefined >> reference to '_intel_fast_memset' >> collect2: error: ld returned 1 exit status >> make[2]: *** [utilities/NekMesh/CMakeFiles/NekMesh.dir/build.make:106: >> utilities/NekMesh/NekMesh] Error 1 >> make[1]: *** [CMakeFiles/Makefile2:1647: >> utilities/NekMesh/CMakeFiles/NekMesh.dir/all] Error 2 >> make: *** [Makefile:141: all] Error 2 >> >> >> >> I had "NEKTAR_USE_SYSTEM_BLAS_LAPACK:BOOL=ON " and >> "THIRDPARTY_BUILD_BLAS_LAPACK:BOOL=ON" in the ccmake as per suggested in >> the user archives. >> >> >> >> I appreciate your kind help. >> >> >> >> Kind regards >> >> syavash >> >>

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Installing Nektar++ 5.2.0 on a cluster
by Ehsan Asgari 13 Mar '23

13 Mar '23

Hi Parv Thank you for your kind response. I managed to install ver. 5.3 using intel compiler and OpenMPI 4.0.3 at last. However, I am still getting MPI-related issues when running a medium-sized mesh with 760K cells (success with a smaller mesh in parallel): ======================================================================= > EquationType: UnsteadyNavierStokes > Session Name: clusteredToGmsh > Spatial Dim.: 3 > Max SEM Exp. Order: 4 > Num. Processes: 32 > Expansion Dim.: 3 > Projection Type: Continuous Galerkin > Advect. advancement: explicit > Diffuse. advancement: implicit > Time Step: 0.0001 > No. of Steps: 500000 > Checkpoints (steps): 10000 > Integration Type: IMEX > Splitting Scheme: Velocity correction (strong press. form) > ======================================================================= > Initial Conditions: > - Field u: 1.0 > - Field v: 0.0 > - Field w: 0.0 > - Field p: 0.0 > -------------------------------------------------------------------------- > Primary job terminated normally, but 1 process returned > a non-zero exit code. Per user-direction, the job has been aborted. > -------------------------------------------------------------------------- > -------------------------------------------------------------------------- > mpirun noticed that process rank 0 with PID 0 on node cra1080 exited on > signal 9 (Killed). I was suspicious that it might be a problem with the inlet compiler and so I switched to GCC 9.3 for a fresh installation. But it seems that GCC is causing problems and I get the following error at some point: ../../SpatialDomains/libSpatialDomains.so.5.3.0: error: undefined reference > to '__intel_sse2_strcpy' > ../../SpatialDomains/libSpatialDomains.so.5.3.0: error: undefined > reference to '_intel_fast_memmove' > ../../SpatialDomains/libSpatialDomains.so.5.3.0: error: undefined > reference to '__intel_sse2_strlen' > ../../SpatialDomains/libSpatialDomains.so.5.3.0: error: undefined > reference to '_intel_fast_memcpy' > ../../SpatialDomains/libSpatialDomains.so.5.3.0: error: undefined > reference to '_intel_fast_memset' > collect2: error: ld returned 1 exit status > make[2]: *** > [library/Demos/SpatialDomains/CMakeFiles/PartitionAnalyse.dir/build.make:127: > library/Demos/SpatialDomains/PartitionAnalyse] Error 1 > make[1]: *** [CMakeFiles/Makefile2:3681: > library/Demos/SpatialDomains/CMakeFiles/PartitionAnalyse.dir/all] Error 2 > make[1]: *** Waiting for unfinished jobs.... I discussed the mesh problem with James Slaughter prior to this and he suggested that the problem might be due to a bug in a lower version (5.0.3) that I was working with. That is why I decided to go with the most recent version. After all, I am still struggling with my parallel simulations! Kind regards syavash On Thu, Mar 9, 2023 at 4:57 PM Khurana, Parv <p.khurana22(a)imperial.ac.uk> wrote: > Hi Syavash, > > > > A few questions pop up on my mind on seeing this: > > > > 1. What compilers are you using (GCC or Intel?) > 2. Are you loading the modules which are compatible with the compiler > you are using? > 3. Do you have a version of OpenBLAS or MKL already loaded as one of > the modules on your cluster? > > > > As often is the case, the problem might be more detailed and it’ll be > great to see the modules and cmake commands you are using for you > installation in order to debug this properly. Happy to hop on a call if > needed! > > > > Best > > Parv > > > > > > *From:* nektar-users-bounces(a)imperial.ac.uk < > nektar-users-bounces(a)imperial.ac.uk> *On Behalf Of *Ehsan Asgari > *Sent:* 09 March 2023 09:54 > *To:* nektar-users <nektar-users(a)imperial.ac.uk> > *Subject:* [Nektar-users] Installing Nektar++ 5.2.0 on a cluster > > > > This email from eh.asgari(a)gmail.com originates from outside Imperial. Do > not click on links and attachments unless you recognise the sender. If you > trust the sender, add them to your safe senders list > <https://spam.ic.ac.uk/SpamConsole/Senders.aspx> to disable email > stamping for this address. > > > > Hi Everyone, > > > > I am trying to install the latest version of Nektar on a cluster. However, > I get the following error at some point: > > > > ../../library/SpatialDomains/libSpatialDomains.so.5.3.0: error: undefined > reference to '__intel_sse2_strlen' > ../../library/SpatialDomains/libSpatialDomains.so.5.3.0: error: undefined > reference to '_intel_fast_memcpy' > ../../library/SpatialDomains/libSpatialDomains.so.5.3.0: error: undefined > reference to '_intel_fast_memset' > collect2: error: ld returned 1 exit status > make[2]: *** [utilities/NekMesh/CMakeFiles/NekMesh.dir/build.make:106: > utilities/NekMesh/NekMesh] Error 1 > make[1]: *** [CMakeFiles/Makefile2:1647: > utilities/NekMesh/CMakeFiles/NekMesh.dir/all] Error 2 > make: *** [Makefile:141: all] Error 2 > > > > I had "NEKTAR_USE_SYSTEM_BLAS_LAPACK:BOOL=ON " and > "THIRDPARTY_BUILD_BLAS_LAPACK:BOOL=ON" in the ccmake as per suggested in > the user archives. > > > > I appreciate your kind help. > > > > Kind regards > > syavash >

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restarting a parallel simulation
by Ehsan Asgari 13 Mar '23

13 Mar '23

******************* This email originates from outside Imperial. Do not click on links and attachments unless you recognise the sender. If you trust the sender, add them to your safe senders list https://spam.ic.ac.uk/SpamConsole/Senders.aspx to disable email stamping for this address. ******************* Hi Everone, I have a parallel simulation with a created directory of the initial conditions (caseName_0.chk). There are 64 processes and inside the directory, I see P0000000.fld up to P0000063.fld. Now the question is, what should I change within the session file if I'd like to restart the simulation from these initial conditions? Should it be something like: <F VAR="u,v,w,p" FILE="caseName.fld" /> I wonder if this is correct, as I have no single file named "caseName.fld". Kind regards syavash

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On the implicit integration scheme for the compressible NS equations
by Jian Yu 12 Mar '23

12 Mar '23

******************* This email originates from outside Imperial. Do not click on links and attachments unless you recognise the sender. If you trust the sender, add them to your safe senders list https://spam.ic.ac.uk/SpamConsole/Senders.aspx to disable email stamping for this address. ******************* Hi Everyone, We are trying to perform ILES for high Re flow using implicit solver of Nektar++. But we couldn't get the solver running. We feel it is the something wrong with configuration file. Could anyone please provide a valid demo case (including xml and mesh) to show how to use the implicit integration scheme with the compressible NS equations? Thanks! Best Jian

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Parameters for local time stepping
by Chengeng Qian 10 Mar '23

10 Mar '23

******************* This email originates from outside Imperial. Do not click on links and attachments unless you recognise the sender. If you trust the sender, add them to your safe senders list https://spam.ic.ac.uk/SpamConsole/Senders.aspx to disable email stamping for this address. ******************* Hi everyone, What is following parameter used for? <I PROPERTY="LocalTimeStep" VALUE="True" /> I though that it must be ture if we calculated time step using CFL. But I found that I could run case with LocalTimeStep = False. In addition, the result obtained by LocalTimeStep = Ture is more closed to the steady solution. Any comments are appreciated. Cheers, Chengeng.

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