May 2007 - 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

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Preallocation for external direct solvers
by Paul T. Bauman 02 Oct '07

02 Oct '07

Hello, I'm developing some code and am using direct solvers (for the moment), in particular MUMPS and SuperLU. I noticed that PETSc is not preallocating the memory for it even though I specify maximum number of entries per row. call MatCreateSeqAIJ(PETSC_COMM_WORLD,total_num_dofs,total_num_dofs, & max_number_nonzeros_row,PETSC_NULL_INTEGER, J ,ierr) call MatSetFromOptions(J,ierr) call SNESSetJacobian(snes,J,J,FormJacobian,PETSC_NULL_OBJECT,ierr) When I print -info: [0] User provided function(): (Fortran):PETSc successfully started: procs 1 [0] User provided function(): Running on machine: dhcp-67-30.ices.utexas.edu [0] PetscCommDuplicate(): Duplicating a communicator 1140850688 -2080374784 max tags = 2147483647 [0] PetscCommDuplicate(): Using internal PETSc communicator 1140850688 -2080374784 [0] PetscCommDuplicate(): Using internal PETSc communicator 1140850688 -2080374784 [0] PetscCommDuplicate(): Using internal PETSc communicator 1140850688 -2080374784 [0] PetscCommDuplicate(): Using internal PETSc communicator 1140850688 -2080374784 [0] MatConvert_AIJ_AIJMUMPS(): Using MUMPS for LU factorization and solves. [0] PetscCommDuplicate(): Using internal PETSc communicator 1140850688 -2080374784 0 SNES Function norm 8.500000000000e-01 [0] MatSetUpPreallocation(): Warning not preallocating matrix storage So, of course, this really slows down the code for even small problems (20000 dof). Same story for SuperLU. Should I use a different call to do the preallocation? Thanks for any suggestions. Best, Paul

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python-petsc in Debian
by Ondrej Certik 28 May '07

28 May '07

Hi, I packaged the python bindings to petsc: http://code.google.com/p/petsc4py/ and it is already in Debian unstable now: http://packages.debian.org/unstable/python/python-petsc It should get into Debian testing in around 10 days and into Ubuntu Gutsy in a few days automatically. Ondrej

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Re: [PETSC #16200] Petsc Performance on Dual- and Quad-core systems
by Barry Smith 27 May '07

27 May '07

Carlos, We don't have any particular numbers for these systems. There are two main things to keep in mind. 1) Ideally the MPI you use will take advantage of the local shared memory within a node to lower the communication time. MPICH for example can be compiled with certain options to help this. 2) The memory bandwidth is often shared among several of the cores. Since sparse matrices computations are almost totally bounded by memory bandwidth the most important thing to consider when buying a system like this is how much totally memory bandwidth does it have and how much is really usable for each core. Ideally you'd like to see a 6++ gigabytes per second peak memory bandwith per core. Barry On Wed, 23 May 2007, Carlos Erik Baumann wrote: > > > Hello Everyone, > > > > Do you have any performance number on Petsc solving typical heat > transfer / laplace / poisson problems using dual and/or quad-core > workstations ? > > > > I am interested in speedup based on problem size, etc. > > > > Looking forward to your reply. > > > > Best, > > > > --Carlos > > > > Carlos Baumann Altair Engineering, Inc. > > Cell 512-657-4348, Ph. 512-467-0618(x512) > > > > > > > >

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about mkl_p4p.dll not found
by Yixun Liu 26 May '07

26 May '07

Hi, My program is based on PETSC. Its compiler and link is ok, but when execute a error was generated. The error is: "MKL FATAL ERROR: Cannot load neither mkl_p4p.dll nor mkl_def.dllPress any key to continue" I can find the mkl_p4p.dll in "D:\MyVC\petsc-2.3.2-p3\externalpackages\w_mkl_serial_p_8.1.001\mkl_serial_8.1\mkl_8.1_serial\ia32\bin". Do I need to set the environment variable? Hope your help. Best, Yixun

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Re: New PETSc release 2.3.3
by yaron＠oak-research.com 24 May '07

24 May '07

Barry- When will the manual (http://www-unix.mcs.anl.gov/petsc/petsc-as/snapshots/petsc-current/docs/man…) be updated? Thanks Yaron -------Original Message------- From: Barry Smith Subject: New PETSc release 2.3.3 Sent: 24 May '07 14:20 ---------------------------------------------------------------------------- Portable, Extensible Toolkit for Scientific Computation (PETSc) ---------------------------------------------------------------------------- [LINK: http://www.mcs.anl.gov/petsc] http://www.mcs.anl.gov/petsc We are pleased to announce the release of the PETSc 2.3.3 parallel software libraries for the implicit solution of PDEs and related problems. There are a couple of MAJOR interface changes, listed at [LINK: http://www-unix.mcs.anl.gov/petsc/petsc-as/documentation/changes/233.html] http://www-unix.mcs.anl.gov/petsc/petsc-as/documentation/changes/233.html please check these changes before compiling your codes. In particular the calling sequence for VecScatterBegin/End() now takes the scatter context as the first argument not the last. You can download from [LINK: http://www-unix.mcs.anl.gov/petsc/petsc-as/download/index.html] http://www-unix.mcs.anl.gov/petsc/petsc-as/download/index.html and and the installataion instructions are at [LINK: http://www-unix.mcs.anl.gov/petsc/petsc-as/documentation/installation.html] http://www-unix.mcs.anl.gov/petsc/petsc-as/documentation/installation.html As always, please send bug reports, questions, and requests for new features to [LINK: http://webmail.oak-research.com/[email protected]] petsc-maint(a)mcs.anl.gov Thanks for your continued support. The PETSc developers, Satish, Lisandro, Matt, Victor, Barry and Hong

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New PETSc release 2.3.3
by Barry Smith 24 May '07

24 May '07

---------------------------------------------------------------------------- Portable, Extensible Toolkit for Scientific Computation (PETSc) ---------------------------------------------------------------------------- http://www.mcs.anl.gov/petsc We are pleased to announce the release of the PETSc 2.3.3 parallel software libraries for the implicit solution of PDEs and related problems. There are a couple of MAJOR interface changes, listed at http://www-unix.mcs.anl.gov/petsc/petsc-as/documentation/changes/233.html please check these changes before compiling your codes. In particular the calling sequence for VecScatterBegin/End() now takes the scatter context as the first argument not the last. You can download from http://www-unix.mcs.anl.gov/petsc/petsc-as/download/index.html and and the installataion instructions are at http://www-unix.mcs.anl.gov/petsc/petsc-as/documentation/installation.html As always, please send bug reports, questions, and requests for new features to petsc-maint(a)mcs.anl.gov Thanks for your continued support. The PETSc developers, Satish, Lisandro, Matt, Victor, Barry and Hong

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Question about two Factorization functions
by junwang＠uwm.edu 23 May '07

23 May '07

Hi, I am trying to know the difference bewteen the following two functions: MatCholeskyFactorNumeric_SeqSBAIJ_2(Mat A,MatFactorInfo *info,Mat *B); MatCholeskyFactorNumeric_SeqSBAIJ_2_NaturalOrdering(Mat A,MatFactorInfo *info,Mat *B); Suppose I have a matrix "mat" stored in the SBAIJ format, the block size is 2. When i am running the following code, it seems it calling the second NatrualOrdering function: ierr = MatCreateSeqSBAIJ(PETSC_COMM_SELF,2,6,6,0,nnz,&mat);CHKERRQ(ierr); IS perm,colp; MatGetOrdering(mat,MATORDERING_NATURAL,&perm,&colp); ierr = ISDestroy(colp);CHKERRQ(ierr); MatFactorInfo info; info.fill=1.0; Mat result; ierr = MatCholeskyFactorSymbolic(mat,perm,&info,&result); CHKERRQ(ierr); ierr = MatCholeskyFactorNumeric(mat,&info,&result);CHKERRQ(ierr); However, since the first function is not naturalordering, does that mean i don't have to call the MatGetOrdering before I call MatCholeskyFactor....(). If so, does that mean, it will reduce the time cost since it doesn't have to do the ordering part. Is anyone can give any idea and give me a example for calling the first function to do the factorization. Thank you very mcuh! Jun

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Calling hypre
by Ben Tay 23 May '07

23 May '07

Hi, presently I am using ./a.out -pc_type hypre -pc_hypre_type boomeramg to use hypre. However, I have 2 matrix to solve and now I only want one of them to use hypre, while the other use jacobi + bcgs. for the solver using hypre, initially it's just: call PCSetType(pc,PCLU,ierr) - direct solver I now changed to call PCSetType(pc,hypre,ierr) call PCHYPRESetType(pc,boomeramg,ierr) However, I got the error msg: fortcom: Error: petsc_sub.F, line 125: This name does not have a type, and must have an explicit type. [HYPRE] call PCSetType(pc,hypre,ierr) Sorry I don't really understand the eg. hyppilut.c since my knowledge of the c language is very basic. So how should I set the options to use hypre? Thank you.

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Can't read MPIRUN_HOST
by Ben Tay 22 May '07

22 May '07

Hi, I tried to compile PETSc and there's no problem. I also used the *--with-batch=1 *option since my server is using a job scheduler. There's no shared library and I'm installing hypre too. However, when after sending the job for ex1f, I got the error msg: Can't read MPIRUN_HOST. So what's the problem? thanks

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