November 2024 - petsc-users - mailman3.cels.anl.gov

local/global DMPlex Vec output
by Matteo Semplice 30 Jan '25

30 Jan '25

Dear petsc-users, I am having issues with output of parallel data attached to a DMPlex (or maybe more fundamental ones about DMPlex...). So I currently 1. create a DMPlex (DMPlexCreateGmshFromFile or DMPlexCreateBoxMesh) 2. partition it 3. and create a section for my data layout with DMPlexCreateSection(ctx.dmMesh, NULL, numComp, numDof, numBC, NULL, NULL, NULL, NULL, &sUavg) 4. DMSetLocalSection(ctx.dmMesh, sUavg) 5. create solLoc and solGlob vectors with DMCreateGlobalVector and DMCreateLocalVector 6. solve .... 7. VecView(ctx.solGlob, vtkViewer) on a .vtu file but when I load data in ParaView I get more cells than expected and it is as if the cells in the halo are put twice in output. (I could create a MWE if the above is not clear) I guess that the culprit is point (4), but if I replace it with DMSetGlobalSection then I cannot create the local vector at point (5). How should I handle this properly? In my code I need to create both local and global vectors, to perform at least GlobalToLocal and to save the global data. (On a side note, I tried also HDF5 but then it complains about the DM not having a DS...; really, any working solution that allows data to be explored with Paraview is fine) Thanks for any advice! Matteo Semplice

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error
by tryit88 30 Nov '24

30 Nov '24

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error
by tryit88 30 Nov '24

30 Nov '24

眾所周知犀利士Cialis是一款處方藥，必須持有醫師的處方才能購買的藥物，但是依舊有很多男性朋友都不知道。就在前不久，有一位患者來到我們網站咨詢醫師：“最近跟太太行房事時，總是半途就會軟竿，聽說犀利士效果很好，請問醫師一般藥局沒有處方箋可以買到犀利士嗎？”，其實這不是個例，大多數患者都問過這個問題，下面醫師為大家解答。 https://urldefense.us/v3/__https://blog.lowe99.com/__;!!G_uCfscf7eWS!aO_LP_… https://urldefense.us/v3/__https://priligy88.com__;!!G_uCfscf7eWS!aO_LP_BBT… https://urldefense.us/v3/__https://vaigratw.com/__;!!G_uCfscf7eWS!aO_LP_BBT… https://urldefense.us/v3/__https://levitra20mg.com/https:/*100mg.tw__;Lw!!G…

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MatZeroRows costly while applying 1st-kind Boundary Conditions
by Qiyue Lu 29 Nov '24

29 Nov '24

Hello, In the MPI context, after assembling the distributed matrix A (matmpiaij) and the right-hand-side b, I am trying to apply the 1st kind boundary condition using MatZeroRows() and VecSetValues(), for A and b respectively. The pseudo-code is: ========= for (int key = 0; key < BCNodes_Length; key++){ // retrieving the global row position pos = BCNodes[key]; // Set all elements in that row 0 except the one on the diagonal to be 1.0 MatZeroRows(A, 1, &pos, 1.0, NULL, NULL); } MatAssemblyBegin(A, MAT_FINAL_ASSEMBLY); MatAssemblyEnd(A, MAT_FINAL_ASSEMBLY); ========= For BCNodes_Length = 10^4, the FOR loop timing is 8 seconds. For BCNodes_Length = 15*10^4, the FOR loop timing is 3000 seconds. I am using two computational nodes and each having 12 cores. My questions are: 1) Is the timing plausible? Is the MatZeroRows() function so costly? 2) Any suggestions to apply the 1st kind boundary conditions for a better performance? Thanks, Qiyue Lu

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Doubt about mesh size distribution in DMDACreate3d using periodic boundary conditions
by MIGUEL MOLINOS PEREZ 27 Nov '24

27 Nov '24

Dear all: It seems that if I mesh a cubic domain with “DMDACreate3d” using 8 bricks for discretization and with periodic boundaries, each of the bricks has a different size. In contrast, if I use DM_BOUNDARY_NONE, all 8 bricks have the same size. I have used this together with the DMSWarm discretization. And as you can see the number of particles per rank is not evenly distributed: 210 420 366 732 420 840 732 1464 Am I missing something? Thanks, Miguel [cid:534265d3-3f18-41cd-8006-539cb06751f9@eurprd01.prod.exchangelabs.com]

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Problem with MatMPIAIJSetPreallocation
by Matthew Thomas 26 Nov '24

26 Nov '24

Hello, When I use MatMPIAIJSetPreallocation I get an argument out of range error, as below, [15]PETSC ERROR: Argument out of range [15]PETSC ERROR: New nonzero at (8,421) caused a malloc. Use MatSetOption(A, MAT_NEW_NONZERO_ALLOCATION_ERR, PETSC_FALSE) to turn off this check However, when I run the code again with identical parameters without MatMPIAIJSetPreallocation, there is no non-zero at the location that caused the error (8, 421). Using -mat_view I can see that row 8 only contains a single value at column 8, which is expected and what I have allocated for. I have also checked that every time I call MatSetValues that this location is not being set. I am very confident my dnnz and onnz arrays have been set correctly, do you have any idea why this new non-zero is created? I am using Petsc version 3.22.1 and Slepc version 3.22.1 with fortran. This issue does not occur with small number of processors, (1-8), however, this error is consistent when I use >8 processors. Thanks, Matt

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Unable to configure errors
by Brian Bainbridge - BGS 25 Nov '24

25 Nov '24

Hi there, I have downloaded petsc-.3.22.1 via git, but when I try to configure with the Intel compilers I get this message: [bba@kwvmxbridgeHPC petsc]$ ./configure --prefix=/home/bba/bin/petsc --with-mpi-dir=/home/bba/intel/oneapi/mpi/2021.14/ ============================================================================================= Configuring PETSc to compile on your system ============================================================================================= TESTING: checkCCompiler from config.setCompilers(config/BuildSystem/config/setCompilers.py:1457) ********************************************************************************************* UNABLE to CONFIGURE with GIVEN OPTIONS (see configure.log for details): --------------------------------------------------------------------------------------------- MPI compiler wrappers in /home/bba/intel/oneapi/mpi/2021.14/bin cannot be found or do not work. See https://urldefense.us/v3/__https://petsc.org/release/faq/*invalid-mpi-compi… ********************************************************************************************* But: [bba@kwvmxbridgeHPC petsc]$ ls /home/bba/intel/oneapi/mpi/2021.14/bin cpuinfo hydra_nameserver IMB-MPI1 IMB-MT IMB-P2P impi_cpuinfo mpicc mpiexec mpif77 mpifc mpigxx mpiicpc mpiicx mpiifx mpitune_fast hydra_bstrap_proxy hydra_pmi_proxy IMB-MPI1-GPU IMB-NBC IMB-RMA impi_info mpicxx mpiexec.hydra mpif90 mpigcc mpiicc mpiicpx mpiifort mpirun So it should work, but it doesn't! I tried to use --with-cc=/home/bba/intel/oneapi/mpi/2021.14/bin/mpiicx but that doesn't work: [bba@kwvmxbridgeHPC petsc]$ ./configure --prefix=/home/bba/bin/petsc --with-cc=/home/bba/intel/oneapi/mpi/2021.14/bin/mpiicx ============================================================================================= Configuring PETSc to compile on your system ============================================================================================= TESTING: checkCCompiler from config.setCompilers(config/BuildSystem/config/setCompilers.py:1457) ********************************************************************************************* UNABLE to CONFIGURE with GIVEN OPTIONS (see configure.log for details): --------------------------------------------------------------------------------------------- C compiler you provided with -with-cc=/home/bba/intel/oneapi/mpi/2021.14/bin/mpiicx cannot be found or does not work. If the above linker messages do not indicate failure of the compiler you can rerun with the option --ignoreLinkOutput=1 ********************************************************************************************* [bba@kwvmxbridgeHPC petsc]$ ls /home/bba/intel/oneapi/mpi/2021.14/bin/mpiicx /home/bba/intel/oneapi/mpi/2021.14/bin/mpiicx The compiler is there, can you please help me to configure the petsc please? Regards, Brian This email and any attachments are intended solely for the use of the named recipients. If you are not the intended recipient you must not use, disclose, copy or distribute this email or any of its attachments and should notify the sender immediately and delete this email from your system. UK Research and Innovation (UKRI) has taken every reasonable precaution to minimise risk of this email or any attachments containing viruses or malware but the recipient should carry out its own virus and malware checks before opening the attachments. UKRI does not accept any liability for any losses or damages which the recipient may sustain due to presence of any viruses.

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Memory Used When Reading petscrc
by David Scott 25 Nov '24

25 Nov '24

Hello, I am using the options mechanism of PETSc to configure my CFD code. I have introduced options describing the size of the domain etc. I have noticed that this consumes a lot of memory. I have found that the amount of memory used scales linearly with the number of MPI processes used. This restricts the number of MPI processes that I can use. Is there anything that I can do about this or do I need to configure my code in a different way? I have attached some code extracted from my application which demonstrates this along with the output from a running it on 2 MPI processes. Best wishes, David Scott The University of Edinburgh is a charitable body, registered in Scotland, with registration number SC005336. Is e buidheann carthannais a th’ ann an Oilthigh Dhùn Èideann, clàraichte an Alba, àireamh clàraidh SC005336.

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Cannot iterate well when using Newton iteration of SNES
by David Jiawei LUO LIANG 21 Nov '24

21 Nov '24

I am using the Newton iteration to solve a nonlinear 1D heat equation problem by using FEM. I attached my source code named "SNES_heat.cpp"  when I run the code   0 SNES Function norm 1.206289245288e+01   1 SNES Function norm 7.128802192789e+00   2 SNES Function norm 6.608812909525e+00 you can find that it only iterate 3 steps, and then do all the function evaluation and finally just stop the program.  I think it is not reasonble. I check my code, it is correct if I set it as a linear problem. it means my Jacobian and Residual function is correct. But when I set it as a nonlinear, the residual seems reduces as not expected.  I doubt that whether my understanding of the newton iteration is different from SNES's newton iteration process. David Jiawei LUO LIANG 南方科技大学/学生/研究生/2024 广东省深圳市南山区学苑大道1088号  

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Why can't I save a diagonal matrix into a binary file via petsc4py?
by 张峻溪 19 Nov '24

19 Nov '24

My version is 3.22.0 from "petsc4py.__version__" Here is the code: ```python from petsc4py import PETSc import numpy as np vec1 = PETSc.Vec().createWithArray(np.arange(30)) mat1 = PETSc.Mat().createDiagonal(vec1) mat1.assemble() viewer = PETSc.Viewer().createBinary("abcde.bin", "w") mat1.view(viewer) viewer.destroy() ``` I find it runs without any error, but no file generated However, if I convert mat1 to AIJ, it can be saved successfully

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