July 2020 - petsc-users - mailman3.cels.anl.gov

Nodes coordinates in distributed dmplex
by Alejandro D Otero 16 Jul '22

16 Jul '22

Hi, sorry if this is an obvious question, but I cannot figure out how to recover finite element nodes coordinates once I have distributed a mesh stored as a dmplex. I am using petsc4py as interface to petsc rutines. I first created a dmplex using: dm.createFromCellList() In a sequential run I got the coordinates with: Coords = dm.getCoordinates() which gave a sequential vector with the coordinates of the mesh nodes. When I distribute the mesh with: dm.distribute() each mpi process has it own dm but the indexing of the vector resulting from getCoordinates() or getCoordinatesLocal() seems not consistent with the local numbering of the cells and nodes. Which is the correct way of doing this in PETSc philosophy? Thanks in advance, Alejandro

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How to add a source term for PETSCFV ?
by Thibault Bridel-Bertomeu 14 Apr '21

14 Apr '21

Dear all, I have been studying ex11.c from ts/tutorials to understand how to solve an hyperbolic system of equations using PETSCFV. I first worked on the Euler equations for inviscid fluids and based on what ex11.c presents, I was able to add the right PETSc instructions in an already existing in-house code with different gas models to solve the problems in parallel (MPI) and with the AMR capabilities offered by P4EST. Now my goal is to move to Navier-Stokes equations. Theoretically the system is not completely hyperbolic and can be seen as one with an hyperbolic part (identical to the Euler equations) and a parabolic part coming from the RHS diffusion terms. I have been looking into the manual and also the sources of PETSc around the DM, DMPlex, DS and FV classes but I could not find anything that speaks to me as "adding a RHS to an hyperbolic system of equations" or "adding a source term to an hyperbolic system of equations". What's more, that source term depends on the derivatives of the context variables ... I wanted to know if anyone maybe had a suggestion regarding this issue ? Thank you very much in advance, Thibault Bridel-Bertomeu — Eng, MSc, PhD Research Engineer CEA/CESTA 33114 LE BARP Tel.: (+33)557046924 Mob.: (+33)611025322 Mail: thibault.bridelbertomeu(a)gmail.com

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Tough to reproduce petsctablefind error
by Chris Hewson 03 Nov '20

03 Nov '20

Hi, I am having a bug that is occurring in PETSC with the return string: [7]PETSC ERROR: PetscTableFind() line 132 in /home/chewson/petsc-3.13.2/include/petscctable.h key 7556 is greater than largest key allowed 5693 This is using petsc-3.13.2, compiled and running using mpich with -O3 and debugging turned off tuned to the haswell architecture and occurring either before or during a KSPBCGS solve/setup or during a MUMPS factorization solve (I haven't been able to replicate this issue with the same set of instructions etc.). This is a terrible way to ask a question, I know, and not very helpful from your side, but this is what I have from a user's run and can't reproduce on my end (either with the optimization compilation or with debugging turned on). This happens when the code has run for quite some time and is happening somewhat rarely. More than likely I am using a static variable (code is written in c++) that I'm not updating when the matrix size is changing or something silly like that, but any help or guidance on this would be appreciated. *Chris Hewson* Senior Reservoir Simulation Engineer ResFrac +1.587.575.9792

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using real and complex together
by Sam Guo 28 Sep '20

28 Sep '20

Dear PETSc dev team, Can I use both real and complex versions together? Thanks, Sam

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overlap cpu and gpu?
by nicola varini 18 Aug '20

18 Aug '20

Hello, I would like to know if it is possible to overlap CPU and GPU with DMDA. I've a machine where each node has 1P100+1Haswell. I've to resolve Poisson and Ampere equation for each time step. I'm using 2D DMDA for each of them. Would be possible to compute poisson and ampere equation at the same time? One on CPU and the other on GPU? Thanks

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SUPERLU_DIST in single precision
by flw＠rzg.mpg.de 05 Aug '20

05 Aug '20

Dear PETSc support team, some time ago you told me that you are planning on releasing a version that supports SUPERLU_DIST in single-precision soon. Can you tell me roughly what time frame you had in mind? Best regards, Felix

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PETSc Make error
by Eda Oktay 31 Jul '20

31 Jul '20

Hi all, I configured petsc-3.13.2 with following options: ./configure --with-cc=gcc --with-cxx=g++ --with-fc=gfortran --download-mpich --download-openblas --download-metis --download-parmetis --download-chaco --download-slepc --with-X=1 However, I got a make error. I attached make.log and configure.log, how can I fix that problem? Thanks! Eda

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Accessing the adjoint in TSSetRHSJacobianP
by Salazar De Troya, Miguel 31 Jul '20

31 Jul '20

Hi, The jacobian of the RHS w.r.t. the parameter P is a matrix that will be multiplied by the adjoint solution within TSAdjoint(). I am interested in having access to that adjoint so I can calculate shape derivatives with firedrake_adjoint. I will have to use that adjoint function, apply it to the residual and calculate the shape derivative from the resulting 0-form to obtain my RHSJacobianP*adjoint. This is the workaround done in pyadjoint: https://github.com/dolfin-adjoint/pyadjoint/blob/e6fbd13f8ac63290804852fa2f… Is there another alternative within PETSc? Maybe using a matrix free approach? Thanks Miguel Miguel A. Salazar de Troya Postdoctoral Researcher, Lawrence Livermore National Laboratory B141 Rm: 1085-5 Ph: 1(925) 422-6411

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Error on INTEGER SIZE using DMDACreate3d
by Pierpaolo Minelli 31 Jul '20

31 Jul '20

Hi, I am trying to solve a Poisson equation on this grid: Nx = 2501 Ny = 3401 Nz = 1601 I received this error: [0]PETSC ERROR: --------------------- Error Message -------------------------------------------------------------- [0]PETSC ERROR: Overflow in integer operation: http://www.mcs.anl.gov/petsc/documentation/faq.html#64-bit-indices [0]PETSC ERROR: Mesh of 2501 by 3401 by 1 (dof) is too large for 32 bit indices [0]PETSC ERROR: See http://www.mcs.anl.gov/petsc/documentation/faq.html for trouble shooting. [0]PETSC ERROR: Petsc Release Version 3.8.3, Dec, 09, 2017 [0]PETSC ERROR: /marconi_scratch/userexternal/pminelli/PIC3D/2500_3400_1600/./PIC_3D on a arch-linux2-c-opt named r129c09s02 by pminelli Tu e May 26 20:16:34 2020 [0]PETSC ERROR: Configure options --prefix=/cineca/prod/opt/libraries/petsc/3.8.3/intelmpi--2018--binary CC=mpiicc FC=mpiifort CXX=mpiicpc F77=mpiifort F90=mpiifort --with-debugging=0 --with-blaslapack-dir=/cineca/prod/opt/compilers/intel/pe-xe-2018/binary/mkl --with-fortran=1 --with-fortran-interfaces=1 --with-cmake-dir=/cineca/prod/opt/tools/cmake/3.5.2/none --with-mpi-dir=/cineca/prod/opt/compilers/intel/pe-xe- 2018/binary/impi/2018.4.274 --download-scalapack --download-mumps=yes --download-hypre --download-superlu_dist --download-parmetis --downlo ad-metis [0]PETSC ERROR: #1 DMSetUp_DA_3D() line 218 in /marconi/prod/build/libraries/petsc/3.8.3/intelmpi--2018--binary/BA_WORK/petsc-3.8.3/src/dm/ impls/da/da3.c [0]PETSC ERROR: #2 DMSetUp_DA() line 25 in /marconi/prod/build/libraries/petsc/3.8.3/intelmpi--2018--binary/BA_WORK/petsc-3.8.3/src/dm/impl s/da/dareg.c [0]PETSC ERROR: #3 DMSetUp() line 720 in /marconi/prod/build/libraries/petsc/3.8.3/intelmpi--2018--binary/BA_WORK/petsc-3.8.3/src/dm/interf ace/dm.c forrtl: error (76): Abort trap signal I am on an HPC facility and after I loaded PETSC module, I have seen that it is configured with INTEGER size = 32 I solve my problem with these options and it works perfectly with smaller grids: -dm_mat_type hypre -pc_type hypre -pc_hypre_type boomeramg -pc_hypre_boomeramg_relax_type_all SOR/Jacobi -pc_hypre_boomeramg_coarsen_type PMIS -pc_hypre_boomeramg_interp_type FF1 -ksp_type richardson Is it possible to overcome this if I ask them to install a version with INTEGER SIZE = 64? Alternatively, is it possible to overcome this using intel compiler options? Thanks in advance Pierpaolo Minelli

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Petsc configure error (cmake)
by Eda Oktay 31 Jul '20

31 Jul '20

I am trying to download Petsc with slepc,openblas,mpich,meti,parmetis and chaco to a linux computer (probably ubuntu, I don't know because I am using it via ssh). Due to an error, for metis, I needed to download cmake, so I added this option, too. However, I got an error telling me that "Error running configure on cmake". I attached configure.log. What should I do? Where is the problem and how can ı fix it? Thank you so much for answering, Eda

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