June 2015 - petsc-users - mailman3.cels.anl.gov

MatGetDiagonal
by Nachiket Gokhale 09 Dec '19

09 Dec '19

Any chance of making this work in serial? http://www.mcs.anl.gov/petsc/petsc-current/docs/manualpages/Mat/MatGetDiago… Not a show stopper, I am trying to get the diagonal of some small projected, dense matrices (which come from large sparse matrices). I am running in serial because 1) Since my projected matrices are small, and 2) PETSc does not do certain matrix multiplications involving a dense matrix in parallel, -Nachiket

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monitoring the convergence of fieldsplit 0 and 1
by Klaij, Christiaan 15 May '18

15 May '18

A question when using PCFieldSplit: for each linear iteration of the system, how many iterations for fielsplit 0 and 1? One way to find out is to run with -ksp_monitor, -fieldsplit_0_ksp_monitor and -fieldsplit_0_ksp_monitor. This gives the complete convergence history. Another way, suggested by Matt, is to use -ksp_monitor, -fieldsplit_0_ksp_converged_reason and -fieldsplit_1_ksp_converged_reason. This gives only the totals for fieldsplit 0 and 1 (but without saying for which one). Both ways require to somehow process the output, which is a bit inconvenient. Could KSPGetResidualHistory perhaps return (some) information on the subsystems' convergence for processing inside the code? Chris dr. ir. Christiaan Klaij CFD Researcher Research & Development E mailto:[email protected] T +31 317 49 33 44 MARIN 2, Haagsteeg, P.O. Box 28, 6700 AA Wageningen, The Netherlands T +31 317 49 39 11, F +31 317 49 32 45, I www.marin.nl

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How to use class function in SNESSetFunction
by behzad baghapour 20 Mar '17

20 Mar '17

Dear developers, In my code, the function "residual" used in SNESSetFunction() for calculating Nonlinear function is a member of a class called "solver". When compiling with Petsc, I received the error: error: argument of type ‘PetscErrorCode (solver::)(_p_SNES*, _p_Vec*, _p_Vec*, void*)’ does not match ‘PetscErrorCode (*)(_p_SNES*, _p_Vec*, _p_Vec*, void*)’ How can I access that class member function is SNESSetFunction()? I need to keep my code structure as before. Thanks, BB.

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Column #j is wrong in parallel from message "Inserting a new nonzero (i, j) into matrix"
by Eric Chamberland 21 Oct '16

21 Oct '16

Hi, while looking for where in the world do I insert the (135,9) entry in my matrix, I have discovered that the column # shown is wrong in parallel! I am using PETsc 3.5.3. The full error message is: [0]PETSC ERROR: MatSetValues_MPIAIJ() line 564 in /home/mefpp_ericc/petsc-3.5.3/src/mat/impls/aij/mpi/mpiaij.c Inserting a new nonzero (135, 9) into matrix This line code is a call to a #defined macro: MatSetValues_SeqAIJ_B_Private(row,col,value,addv); where the "col" parameter is not equal to "in[j]"!!! in gdb, printing "in[j]" gave me: print in[j] $6 = 537 while "col" is: print col $7 = 9 So, I expected to have a message telling me that (135,537) and not (135,9) is a new entry matrix!!! Would it be a big work to fix this so that the col # displayed is correct? Thanks! Eric

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Allocating memory for off-diagonal matrix blocks when using DMComposite
by Gautam Bisht 28 Apr '16

28 Apr '16

Hi, The comment on line 419 of SNES ex 28.c <http://www.mcs.anl.gov/petsc/petsc-current/src/snes/examples/tutorials/ex28…> says that the approach used in this example is not the best way to allocate off-diagonal blocks. Is there an example that shows a better way off allocating memory for off-diagonal matrix blocks when using DMComposite? Thanks, -Gautam.

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Integrating TAO into SNES and TS
by Justin Chang 01 Sep '15

01 Sep '15

Hi everyone, I have a two part question regarding the integration of the following optimization problem min 1/2 u^T*K*u + u^T*f S.T. u >= 0 into SNES and TS 1) For SNES, assuming I am working with a linear FE equation, I have the following algorithm/steps for solving my problem a) Set an initial guess x b) Obtain residual r and jacobian A through functions SNESComputeFunction() and SNESComputeJacobian() respectively c) Form vector b = r - A*x d) Set Hessian equal to A, gradient to A*x, objective function value to 1/2*x^T*A*x + x^T*b, and variable (lower) bounds to a zero vector e) Call TaoSolve This works well at the moment, but my question is there a more "efficient" way of doing this? Because with my current setup, I am making a rather bold assumption that my problem would converge in one SNES iteration without the bounded constraints and does not have any unexpected nonlinearities. 2) How would I go about doing the above for time-stepping problems? At each time step, I want to solve a convex optimization subject to the lower bounds constraint. I plan on using backward euler and my resulting jacobian should still be compatible with the above optimization problem. Thanks, -- Justin Chang PhD Candidate, Civil Engineering - Computational Sciences University of Houston, Department of Civil and Environmental Engineering Houston, TX 77004 (512) 963-3262

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TSSolve problems
by Li, Xinya 23 Jul '15

23 Jul '15

Dear Sir, I am using the ts solver to solve a set of ODE and DAE. The Jacobian matrix is a 1152 *1152 sparse complex matrix. Each TSStep in TSSolve is taking nearly 1 second. Thus, I need to improve the speed of TSSolve. Which parts should be taking into account to accelerate TSSolve? Thank you very much. Regards __________________________________________________ Xinya Li Scientist EED/Hydrology Pacific Northwest National Laboratory 902 Battelle Boulevard P.O. Box 999, MSIN K9-33 Richland, WA 99352 USA Tel: 509-372-6248<tel:509-372-6248> Fax: 509-372-6089<tel:509-372-6089> Xinya.Li(a)pnl.gov<mailto:[email protected]>

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Fieldsplit PC null pointer error on getksp
by Sander Land 16 Jul '15

16 Jul '15

I am trying to use the Schur complement preconditioner in petsc, but am encountering a null argument error calling PCFieldSplitGetSubKSP. This only happens on PC_COMPOSITE_SCHUR, the multiplicative/additive options do return a KSP array. Error message: [0]PETSC ERROR: --------------------- Error Message -------------------------------------------------------------- [0]PETSC ERROR: Null argument, when expecting valid pointer [0]PETSC ERROR: Null Object: Parameter # 1 [0]PETSC ERROR: See http://www.mcs.anl.gov/petsc/documentation/faq.html for trouble shooting. [0]PETSC ERROR: Petsc Release Version 3.6.0, Jun, 09, 2015 [0]PETSC ERROR: ./elecmech on a arch-linux2-cxx-debug [0]PETSC ERROR: Configure options --with-shared-libraries=1 --with-debugging=1 --download-openmpi=1 --with-clanguage=c++ --download-fblaslapack=1 --download-scalapack=1 --download-blacs=1 --download-suitesparse=1 --download-pastix=1 --download-superlu=1 --dowload-essl=1 --download-ptscotch=1 --download-mumps=1 --download-lusol=1 [0]PETSC ERROR: #1 MatSchurComplementGetKSP() line 317 in petsc-3.6/src/ksp/ksp/utils/schurm.c [0]PETSC ERROR: #2 PCFieldSplitGetSubKSP_FieldSplit_Schur() line 1264 in petsc-3.6/src/ksp/pc/impls/fieldsplit/fieldsplit.c [0]PETSC ERROR: #3 PCFieldSplitGetSubKSP() line 1668 in petsc-3.6/src/ksp/pc/impls/fieldsplit/fieldsplit.c Code snippet: ISCreateGeneral(PETSC_COMM_SELF,xp_dofs,&ii[0],PETSC_COPY_VALUES,&is_xp); ISCreateGeneral(PETSC_COMM_SELF,all_dofs - xp_dofs,&ii[xp_dofs],PETSC_COPY_VALUES,&is_wk); PCSetType(pc,PCFIELDSPLIT); PCFieldSplitSetType(pc,PC_COMPOSITE_SCHUR); PCFieldSplitSetIS(pc,"xp",is_xp); PCFieldSplitSetIS(pc,"wk",is_wk); int n; KSP* ksps; PC subpc; PCFieldSplitGetSubKSP(pc,&n,&ksps); ii here is simply an array with ii[i] = i. There is probably a better way to simply indicate two blocks of different size, but I couldn't find it. Thanks, Sander

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move from KSPSetNullSpace to MatSetNullSpace
by Stephan Kramer 05 Jul '15

05 Jul '15

Dear petsc devs I've been trying to move our code from using KSPSetNullSpace to use MatSetNullSpace instead. Although I appreciate the convenience of the nullspace being propagated automatically through the solver hierarchy, I'm still a little confused on how to deal with the case that mat/=pmat in a ksp. If I read the code correctly I need to call MatSetNullSpace on the pmat in order for a ksp to project that nullspace out of the residual during the krylov iteration. However the nullspaces of mat and pmat are not necessarily the same. For instance, what should I do if the system that I want to solve has a nullspace (i.e. the `mat` has a null vector), but the preconditioner matrix does not. As an example of existing setups that we have for which this is the case: take a standard Stokes velocity, pressure system - where we want to solve for pressure through a Schur complement. Suppose the boundary conditions are Dirichlet for velocity on all boundaries, then the pressure equation has the standard, constant nullspace. A frequently used preconditioner is the "scaled pressure mass matrix" where G^T K^{-1} G is approximated by a pressure mass matrix that is scaled by the value of the viscosity. So in this case the actual system has a nullspace, but the preconditioner matrix does not. The way we previously used to solve this is by setting the nullspace on the ksp of the Schur system, where the mat comes from MatCreateSchurComplement and the pmat is the scaled mass matrix. We then set the pctype to PCKSP and do not set a nullspace on its associated ksp. I don't really see how I can do this using only MatSetNullSpace - unless I create a copy of the mass matrix and have one copy with and one copy without a nullspace so that I could use the one with the nullspace for the pmat of the Schur ksp (and thus the mat of the pcksp) and the copy without the nullspace as the pmat for the pcksp. We would very much appreciate some guidance on what the correct way to deal with this kind of situation is Cheers Stephan

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Weird behavior for log_summary
by Michele Rosso 01 Jul '15

01 Jul '15

Hi, I am checking the performances of my code via -log_summary, but the output is incomplete (please see attached) file. I configured petsc with the following options: if __name__ == '__main__': import sys import os sys.path.insert(0, os.path.abspath('config')) import configure configure_options = [ '--with-batch=1 ', '--known-mpi-shared=0 ', '--known-mpi-shared-libraries=0', '--known-memcmp-ok ', '--with-blas-lapack-lib=-L/opt/acml/5.3.1/gfortran64/lib -lacml', '--COPTFLAGS=-march=bdver1 -fopenmp -O3 -ffast-math -fPIC ', '--FOPTFLAGS=-march=bdver1 -fopenmp -O3 -ffast-math -fPIC ', '--CXXOPTFLAGS=-march=bdver1 -fopenmp -O3 -ffast-math -fPIC ', '--with-x=0 ', '--with-debugging=0', '--with-clib-autodetect=0 ', '--with-cxxlib-autodetect=0 ', '--with-fortranlib-autodetect=0 ', '--with-shared-libraries=0 ', '--with-mpi-compilers=1 ', '--with-cc=cc ', '--with-cxx=CC ', '--with-fc=ftn ', # '--with-64-bit-indices', '--download-hypre=1', '--download-blacs=1 ', '--download-scalapack=1 ', '--download-superlu_dist=1 ', '--download-metis=1 ', '--download-parmetis=1 ', ] configure.petsc_configure(configure_options) Any idea about this issue? Thanks, Michele

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