September 2009 - petsc-users - mailman3.cels.anl.gov

Some basic questions about PETSC
by Ben Tay 19 Jan '11

19 Jan '11

Hi, I'm still relatively new to PETSC but I've finally managed to solve my own poisson eqn using it in about a week's time.Thank you for writing such a good solver. However, I have some questions still about PETSC: 1. Are petscscaler the same as real nos.? I am writing in double precision or real(8). So are these 2 interchangeable? (same as petscint and integer). 2. while linking in compaq visual fortran, I get the warning message about conflict library with LIBCMT. Is it important or can I just ignore it? 3. I am writing in f90 free form format. When I modify from fixed f77 format to f90, it gives me a lot of error, which seems to be the include file error. So, is it possible to write in f90 format? 4. I am writing a Navier stokes solver and I'm using PETSC to solve the poisson eqn. If only the RHS changes with each time step, do I need to call VecCreateSeq <insert values in RHS b> VecAssemblyBegin VecAssemblyEnd VecDestroy at each time step? I don't think I can (or I should) change values of b after VecAssemblyBegin,VecAssemblyEnd, or can I? Thank you very much and have a nice day Regards, Ben

4 8

SNES and internal variables
by Lukasz Kaczmarczyk 30 Sep '09

30 Sep '09

Hello, I like to use SNES to solve nonlinear system of equations. For my problem, I have to update some internal variables for computed newtons increments of primary unknowns, before I update residual (right hand side) and Jacobian. I found function SNESSetUpdate which is called at the beginning o every iteration. But I am not sure enough if that function is proper for updating internal variables. Can You advise me if it is right to use internal variables, f.e. increments of plastic strain at gauss points. Lukasz Kaczmarczyk

2 2

SNES and internar variables
by Lukasz Kaczmarczyk 30 Sep '09

30 Sep '09

Hello, I like to use SNES to solve nonlinear system of equations. For my problem, I have to update some internal variables for computed newtons increments of primary unknowns, before I update residual (right hand side) and Jacobian. I found function SNESSetUpdate which is called at the beginning o every iteration. But I am not sure enough if that function is proper for updating internal variables. Can You advise me if it is right to use internal variables, f.e. increments of plastic strain at gauss points. Such problems exist in solid mechanics when increment of plastic strain and plastic multiplayer have to be computed. Another example is for hybrid/mixed FE discretisation having some variables approximated with C(-1) continuity. Unknowns associated to C(-1) continuos approximations can be statically condensed , see attached file. As a results at each iteration step increments for statically condense variables have to be updated. Lukasz Kaczmarczyk

1 0

PETSC memory usage
by Matt Funk 29 Sep '09

29 Sep '09

Hi, i have another question regarding how petsc uses memory w.r.t caching in MatSetValues . My code does the standard stuff: 1) i preallocate the memory 2) i insert the values via MatSetValues 3)i assemble it. Say, for example i declare a 100x100 matrix with 10 NZ entries per row. After 1), will the memory used for the matrix be 100^2*10*sizeof(double)? After 2), will the memory used be 100^2*10*sizeof(double) from the prealloc PLUS 100^2*10*sizeof(double) form the caching of values After 3), will the memory then be reduced back to 100^2*10*sizeof(double)? My concern is step 2). If it is using memory for prealloc and seperately for caching, then is there a way to flush the cached values to the preallocated slots? I tried finding stuff in the manual pages but i am not quite sure if i can or not. thanks matt

2 2

Schur decomposition
by Marco Schauer 29 Sep '09

29 Sep '09

Dear PETSc developers, I translate a sequential Fortran code, which uses LAPACK into a parallel c++ code based on PETSc 3.0.0-p7. The Fortran code uses a function called DGEES to calculate Schur decomposition. I have absolutely no idea how to do this in PETSc. Is there a PETSc example of this problem? Every hint is very welcome to me. Best regards Marco -- Dipl. Ing. Marco Schauer Technische Universität Carolo-Wilhelmina zu Braunschweig Institut für Angewandte Mechanik Spielmannstraße 11 D-38106 Braunschweig, Germany phone +49 (0) 531 391 7108 fax +49 (0) 531 391 5843 email m.schauer(a)tu-braunschweig.de web http://www.infam.tu-braunschweig.de

3 2

errors in make test (petsc 3.0.0 p8 with complex)
by Yujie 29 Sep '09

29 Sep '09

Hi, PETSc Developers I am trying to compile the latest version (3.0.0 p8) of PETSc in my PC (AMD 64bits, GCC4.2). My configure command is: config/configure.py --with-mpi-dir=/home/yujie/codes/mpich127/ --with-clanguage=C++ --with-debugging=1 --with-shared=1 --with-scalar-type=complex --with-spooles=1 --download-spooles=1 --with-parmetis=1 --download-parmetis=1 --with-superlu_dist=1 --download-superlu_dist=1 --with-mumps=1 --download-mumps=1 --with-scalapack=1 --download-scalapack=1 --with-plapack=1 --download-plapack=1 --download-f-blas-lapack=1 --with-blacs --download-blacs=1 I can configure and make PETSc. However, when I make test, I got the following errros: " Running test examples to verify correct installation Possible error running C/C++ src/snes/examples/tutorials/ex19 with 1 MPI process See http://www.mcs.anl.gov/petsc/petsc-as/documentation/troubleshooting.html /home/yujie/codes/petsc-3.0.0-p8/src/snes/examples/tutorials/./ex19: symbol lookup error: /home/yujie/codes/petsc-3.0.0-p8/src/snes/examples/tutorials/./ex19: undefined symbol: _Z25DMMGSetSNESLocali_PrivatePP7_n_DMMGPFiP11DALocalInfoP10MatStencilPvPSt7complexIdES6_EPFiS3_S5_S6_S6_S6_ESD_ Possible error running C/C++ src/snes/examples/tutorials/ex19 with 2 MPI processes See http://www.mcs.anl.gov/petsc/petsc-as/documentation/troubleshooting.html /home/yujie/codes/petsc-3.0.0-p8/src/snes/examples/tutorials/./ex19: symbol lookup error: /home/yujie/codes/petsc-3.0.0-p8/src/snes/examples/tutorials/./ex19: undefined symbol: _Z25DMMGSetSNESLocali_PrivatePP7_n_DMMGPFiP11DALocalInfoP10MatStencilPvPSt7complexIdES6_EPFiS3_S5_S6_S6_S6_ESD_ /home/yujie/codes/petsc-3.0.0-p8/src/snes/examples/tutorials/./ex19: symbol lookup error: /home/yujie/codes/petsc-3.0.0-p8/src/snes/examples/tutorials/./ex19: undefined symbol: _Z25DMMGSetSNESLocali_PrivatePP7_n_DMMGPFiP11DALocalInfoP10MatStencilPvPSt7complexIdES6_EPFiS3_S5_S6_S6_S6_ESD_ Error running Fortran example src/snes/examples/tutorials/ex5f with 1 MPI process See http://www.mcs.anl.gov/petsc/petsc-as/documentation/troubleshooting.html /home/yujie/codes/petsc-3.0.0-p8/src/snes/examples/tutorials/./ex5f: symbol lookup error: /home/yujie/codes/petsc-3.0.0-p8/src/snes/examples/tutorials/./ex5f: undefined symbol: mpi_comm_size_ Completed test examples " Could you give me some help? Thanks a lot. Regards, Yujie

2 2

Petsc and .Net
by Michel Cancelliere 28 Sep '09

28 Sep '09

Hi Petsc Users, I'm trying to use petsc in a .Net app but i'm experiencing problem when linking (ijw/native module detected; cannot link with pure modules). Has somebody managed to do that? Thank you in advance, Michel Cancelliere

2 1

KSP advice
by tsjb00 25 Sep '09

25 Sep '09

Hi! I am looking for suggestion for KSP solvers. I need to solve a multi-component reactive transport problem with KSP solver. The problem involves wide range of time and length scales. Which KSP method would be my best choice? Many thanks in advance! _________________________________________________________________ 上Windows Live 中国首页，下载最新版Messenger！ http://www.windowslive.cn

2 2

Parallel graph coloring heuristics to color large-scale general jacobian matrices
by Rafael Santos Coelho 24 Sep '09

24 Sep '09

Hello to everyone, I've been working for some time on this piece of code for estimating large-scale and general jacobian matrices via finite differences whose sparsity patterns can be determined a priori. It basically uses a parallel graph coloring heuristic to find a good vertex coloring for the column intersection graph relative to the jacobian matrix at hand. Now, I'd like to integrate that code into PETSc, but the problem is that I don't know exactly how. So after spending a lot of time sifting through and trying to grasp "the logic" of PETSc source code, especially, the source code to the MatFDColoring module, I came up with a "tacky" solution proposal: firstly, I would call my code in order to obtain the coloring in parallel, and then I would have a routine (which would have to be embedded in PETSc code base) that, on each processor, would build the "MatFDColoring" data structure based on two things, the coloring found and the sparsity pattern of the jacobian matrix in question. It seems to me that this might work out, though I'm not entirely sure. What do you guys think? Is there an easier and/or more "elegant" way to do this? Thanks in advance, Rafael

3 4

MATMPIAIJ preallocation may not be cleaned by MatDestroy?
by xiaoyin ji 24 Sep '09

24 Sep '09

Hi all, I've finally fixed the problem with the increasing solving time for iterative call of ksp solver. The way is set mat type as MATAIJ instead of MATMPIAIJ. Here is the new codes of mat construction. MatCreate(PETSC_COMM_WORLD,&A); MatSetSizes(A,PETSC_DECIDE,PETSC_DECIDE,ngridtot,ngridtot); MatSetType(A,MATAIJ); MatSetFromOptions(A); MPI_Comm_size(PETSC_COMM_WORLD,&size); if (size > 1){ MatMPIAIJSetPreallocation(A,7,PETSC_NULL,2,PETSC_NULL); } else { MatSeqAIJSetPreallocation(A,7,PETSC_NULL); } The older version is like this, mat type is defined seperately based on the system size as MATMPIAIJ and MATSEQAIJ respectively. This code works ok in Fortran subroutines, but in C++ it will cause ksp solver getting slower and slower like a parabola, which may be a memory leak. MatCreate(world,&A); MatSetSizes(A,PETSC_DECIDE,PETSC_DECIDE,ngridtot,ngridtot); // setup sparse matrix in either MATMPIAIJ or MATSEQAIJ format MPI_Comm_size(world,&size); if (size > 1) { MatSetType(A,MATMPIAIJ); MatSetFromOptions(A); MatMPIAIJSetPreallocation(A,7,PETSC_NULL,2,PETSC_NULL); } else { MatSetType(A,MATSEQAIJ); MatSetFromOptions(A); MatSeqAIJSetPreallocation(A,7,PETSC_NULL); } However, I think petsc library still have problem, as both codes should work in C++ or Fortran. Thanks. Best, Xiaoyin Ji

3 3