June 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

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Petsc matrices in Matlab
by Manav Bhatia 18 Sep '09

18 Sep '09

Hi, Is there a way to directly read a Petsc sequential sparse matrix in Matlab using a Matlab script? I vaguely remember doing this a couple of years ago, and the script possibly was a part of the Petsc distribution. Is that still the case? I am, otherwise, aware of the methods outlined in chapter 9 of the Petsc users guide. Thanks, Manav

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MPI-layout of PETSc
by Rolf Kuiper 04 Jul '09

04 Jul '09

Hi PETSc users, I ran into trouble in combining my developed PETSc application with another code (based on another library called "ArrayLib"). The problem is the parallel layout for MPI, e.g. in 2D with 6 cpus the ArrayLib code gives the names/ranks of the local cpus first in y- direction, than in x (from last to first, in the same way the MPI arrays are called, like 3Darray[z][y][x]): y ^ | 2-4-6 | 1-3-5 |--------> x If I call DACreate() from PETSc, it will assume an ordering according to names/ranks first set in x-direction, than in y: y ^ | 4-5-6 | 1-2-3 |--------> x Of course, if I now communicate the boundary values, I mix up the domain (build by the other program). Is there a possibility / a flag to set the name of the ranks? Due to the fact that my application is written and working in curvilinear coordinates and not in cartesian, I cannot just switch the directions. Thanks a lot for your help, Rolf

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MatGetArrayF90 returns 2d array
by Stephan Kramer 02 Jul '09

02 Jul '09

Hello, Why is it that MatGetArrayF90 returns a pointer to a 2d scalar array, instead of 1d as stated in the documentation? In fact it seems to always return a nrows x ncolumns array. Is this to deal with the MATDENSE case? Would it not be more elegant to always return a 1d array, so you get what you expect for the sparse matrices, and return a 1d array of length nrows*ncolumns in the case of MATDENSE? Cheers Stephan Kramer -- Stephan Kramer Applied Modelling and Computation Group, Department of Earth Science and Engineering, Imperial College London

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MUMPS and PETSc
by Keita Teranishi 30 Jun '09

30 Jun '09

Hi, Just a quick question, does PETSc call any MUMPS's I/O functions? I believe it just calls MUMPS's solver functions. Thanks, ================================ Keita Teranishi Scientific Library Group Cray, Inc. keita(a)cray.com ================================

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no parallel speedup with slepc krylovschur
by Christian May 30 Jun '09

30 Jun '09

Dear readers, I want to solve the following generalized eigenvalue problem in parallel: http://www.phys.ethz.ch/~cmay/binaryoutput.tgz (gnu zipped tar of the binaryoutput you get using -eps_view_binary) I know the approximate value of the lowest eigenvalues I'm interested in, so I'm using shift-and-invert with the following options: -eps_type krylovschur -st_type sinvert -st_shift -0.228 -eps_ncv 32 -eps_nev 16 -eps_tol 1e-10 However, when I use multiple CPUs, I cannot see any speedup. I am not sure whether this is a problem of the matrix or of my system. Can anybody please have a look? Thanks Christian

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PCNN-preconditioner and "floating domains"
by Andreas Grassl 29 Jun '09

29 Jun '09

Hello again, the issues from my last request regarding VecView and data distribution among the different processors are solved, but I'm experiencing still great problems on the performance of the actual preconditioner. I have an implementation of the BNN-algorithm in Matlab from a previous project which is performing very well (about 5 iterations vs. 200 for plain-cg) for a long linear elastic beam fixed at one end and loaded at the other end, discretized with solid cubic bricks (8 nodes, 24 DOF's). condition of the Matrix: 1.5e7 I now modeled a similar beam in DIANA (a bit shorter, less elements due to restrictions of DIANA-preprocessor) and tried to solve with PETSc-solver. The condition of the Matrix is of the same magnitude: ~3e7 (smallest singular value: ~1e-3, largest sv: ~4e4), number of iterations for plain-cg seems reasonable (437), but for the preconditioned system I get completely unexpected values: condition: ~7e12 (smallest sv: ~1, largest sv: ~7e12) and therefore 612 iterations for cg. The beam is divided in 4 subdomains. For more subdomains ksp ran out of iterations (Converged_Reason -3). I can imagine this is a problem of properly setting the null space, because only the first subdomain is touching the boundary, but I have no idea how to specify the null space. So far I didn't regard this issue at all. Do I have to define a function which calculates the weights of the interface DOF's and applies in a some way to create an orthonormal basis? How do I realize that? Is there anywhere an example? Cheers, ando -- /"\ Grassl Andreas \ / ASCII Ribbon Campaign Uni Innsbruck Institut f. Mathematik X against HTML email Technikerstr. 13 Zi 709 / \ +43 (0)512 507 6091

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mpiexec
by Yixun Liu 25 Jun '09

25 Jun '09

Hi, My PETSc based application can work correctly, but after system updating when I use the same commands: >lamboot >mpiexec -np 4 application It seems only one processor works. Then I test it using the following code, ********** PetscErrorCode ierr = MPI_Comm_rank(PETSC_COMM_WORLD,&rank);CHKERRQ(ierr); COUT << "This is processor : " << rank << ENDL; Use command: mpiexec -np 4 application, The output is: This is processor : 0 This is processor : 0 This is processor : 0 This is processor : 0 ********* Thanks for your help. Yixun

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fortran 90 program with PETSc
by tsjb00 24 Jun '09

24 Jun '09

Hi! I am trying to parallelize a fortran 90 program with PETSc. The original program uses a lot of global variables defined using fortran 90 modules. My question is: Can I use 'include PETSc include file' and 'use MyModule' in the program at the same time? If so, in what sequence should I put 'include XXX', 'use XXX' and 'implicit' statements? Another general question is whether I can use fortran 90 features such as 'module' and dynamic allocation on a parallel system of MPI-1 standard? Any reference on such programming work will be also appreciated. Many thanks in advance! _________________________________________________________________ 约会说不清地方？来试试微软地图最新msn互动功能！ http://ditu.live.com/?form=TL&swm=1

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Petsc configure error
by Ryan Yan 24 Jun '09

24 Jun '09

Hi all, I got configuration errors, when I trying to built PETSC with Tau. Basically, I followed the instruction on the installation webpage of PETSc. In the attached file, please find the configure log. I do built TAU and PDT seperately, and TAU with mpi and PDT. If any more information is needed, please let me know. Thanks, Yan

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