There is no --with-CMake-dir option. If its in your PATH it should be picked up. Or you can use --with-cmake=/path/to/cmake-binary
Or use --download-cmake Also suggest using --download-scalapack If you are still having trouble installing petsc - send the relavent logs to petsc-maint Satish On Wed, 17 Apr 2013, Jin, Shuangshuang wrote: > Ok, I spent a long time trying to install SuperLU_DIST and MUMPS, but so far > with no luck. It took a long time for every ./configure I made. And it kept > on complaining about "UNABLE to CONFIGURE with GIVEN OPTIONS" each time for > this and that package. > > And the latest one I got was: > > [d3m956 at olympus petsc-dev.4.17.13]$ ./configure --with-scalar-type=complex > --with-clanguage=C++ PETSC_ARCH=arch-complex --with-fortran-kernels=generic > --download-superlu_dist --download-mumps > --with-scalapack-dir=/share/apps/modules/Modules/3.2.8/modulefiles/development/tools/scalapack/ > --download-parmetis --download-metis > --with-CMake-dir=/share/apps/modules/Modules/3.2.8/modulefiles/development/tools/cmake > =============================================================================== > Configuring PETSc to compile on your system > =============================================================================== > TESTING: configureLibrary from > PETSc.packages.metis(config/BuildSystem/config/package.py:464) > ******************************************************************************* > UNABLE to CONFIGURE with GIVEN OPTIONS (see configure.log for > details): > ------------------------------------------------------------------------------- > CMake > 2.5 is needed to build METIS > ******************************************************************************* > > Can you see anything wrong with my configuration command? > > Thanks, > Shuangshuang > > > -----Original Message----- > From: petsc-users-bounces at mcs.anl.gov [mailto:petsc-users-bounces at > mcs.anl.gov] On Behalf Of Barry Smith > Sent: Wednesday, April 17, 2013 2:49 PM > To: PETSc users list > Subject: Re: [petsc-users] ksp for AX=B system > > > On Apr 17, 2013, at 1:53 PM, "Jin, Shuangshuang" <Shuangshuang.Jin at > pnnl.gov> wrote: > > > Hello, Barry, I got a new question here. > > > > I have integrated the AX=B solver into my code using the example from > > ex125.c. The only major difference between my code and the example is the > > input matrix. > > > > In the example ex125.c, the A matrix is created by loading the data from a > > binary file. In my code, I passed in the computed A matrix and the B matrix > > as arguments to a user defined solvingAXB() function: > > > > static PetscErrorCode solvingAXB(Mat A, Mat B, PetscInt n, PetscInt > > nrhs, Mat X, const int me); > > > > I noticed that A has to be stored as an MATAIJ matrix and the B as a > > MATDENSE matrix. So I converted their storage types inside the solvingAXB > > as below (They were MPIAIJ type before): > > Note that MATAIJ is MATMPIAIJ when rank > 1 and MATSEQAIJ when rank == 1. > > > > > ierr = MatConvert(A, MATAIJ, MAT_REUSE_MATRIX, &A); // A has to be MATAIJ > > for built-in PETSc LU! > > MatView(A, PETSC_VIEWER_STDOUT_WORLD); > > > > ierr = MatConvert(B, MATDENSE, MAT_REUSE_MATRIX, &B); // B has to be a > > SeqDense matrix! > > MatView(B, PETSC_VIEWER_STDOUT_WORLD); > > > > With this implementation, I can run the code with expected results when 1 > > processor is used. > > > > However, when I use 2 processors, I get a run time error which I guess is > > still somehow related to the matrix format but cannot figure out how to fix > > it. Could you please take a look at the following error message? > > PETSc doesn't have a parallel LU solver, you need to install PETSc with > SuperLU_DIST or MUMPS (preferably both) and then pass in one of those names > when you call MatGetFactor(). > > Barry > > > > > [d3m956 at olympus ss08]$ mpiexec -n 2 dynSim -i 3g9b.txt Matrix Object: > > 1 MPI processes > > type: mpiaij > > row 0: (0, 0 - 16.4474 i) (3, 0 + 17.3611 i) row 1: (1, 0 - 8.34725 i) > > (7, 0 + 16 i) row 2: (2, 0 - 5.51572 i) (5, 0 + 17.0648 i) row 3: (0, > > 0 + 17.3611 i) (3, 0 - 39.9954 i) (4, 0 + 10.8696 i) (8, 0 + 11.7647 > > i) row 4: (3, 0 + 10.8696 i) (4, 0.934 - 17.0633 i) (5, 0 + 5.88235 i) > > row 5: (2, 0 + 17.0648 i) (4, 0 + 5.88235 i) (5, 0 - 32.8678 i) (6, 0 > > + 9.92063 i) row 6: (5, 0 + 9.92063 i) (6, 1.03854 - 24.173 i) (7, 0 + > > 13.8889 i) row 7: (1, 0 + 16 i) (6, 0 + 13.8889 i) (7, 0 - 36.1001 i) > > (8, 0 + 6.21118 i) row 8: (3, 0 + 11.7647 i) (7, 0 + 6.21118 i) (8, > > 1.33901 - 18.5115 i) Matrix Object: 1 MPI processes > > type: mpidense > > 0.0000000000000000e+00 + -1.6447368421052630e+01i > > 0.0000000000000000e+00 + 0.0000000000000000e+00i > > 0.0000000000000000e+00 + 0.0000000000000000e+00i > > 0.0000000000000000e+00 + 0.0000000000000000e+00i > > 0.0000000000000000e+00 + -8.3472454090150254e+00i > > 0.0000000000000000e+00 + 0.0000000000000000e+00i > > 0.0000000000000000e+00 + 0.0000000000000000e+00i > > 0.0000000000000000e+00 + 0.0000000000000000e+00i > > 0.0000000000000000e+00 + -5.5157198014340878e+00i > > 0.0000000000000000e+00 + 0.0000000000000000e+00i > > 0.0000000000000000e+00 + 0.0000000000000000e+00i > > 0.0000000000000000e+00 + 0.0000000000000000e+00i > > 0.0000000000000000e+00 + 0.0000000000000000e+00i > > 0.0000000000000000e+00 + 0.0000000000000000e+00i > > 0.0000000000000000e+00 + 0.0000000000000000e+00i > > 0.0000000000000000e+00 + 0.0000000000000000e+00i > > 0.0000000000000000e+00 + 0.0000000000000000e+00i > > 0.0000000000000000e+00 + 0.0000000000000000e+00i > > 0.0000000000000000e+00 + 0.0000000000000000e+00i > > 0.0000000000000000e+00 + 0.0000000000000000e+00i > > 0.0000000000000000e+00 + 0.0000000000000000e+00i > > 0.0000000000000000e+00 + 0.0000000000000000e+00i > > 0.0000000000000000e+00 + 0.0000000000000000e+00i > > 0.0000000000000000e+00 + 0.0000000000000000e+00i > > 0.0000000000000000e+00 + 0.0000000000000000e+00i > > 0.0000000000000000e+00 + 0.0000000000000000e+00i 0.0000000000000000e+00 + > > 0.0000000000000000e+00i PETSC LU: > > [0]PETSC ERROR: --------------------- Error Message > > ------------------------------------ > > [0]PETSC ERROR: No support for this operation for this object type! > > [0]PETSC ERROR: Matrix format mpiaij does not have a built-in PETSc LU! > > [0]PETSC ERROR: > > ---------------------------------------------------------------------- > > -- [0]PETSC ERROR: Petsc Development HG revision: > > 6e0ddc6e9b6d8a9d8eb4c0ede0105827a6b58dfb HG Date: Mon Mar 11 22:54:30 > > 2013 -0500 [0]PETSC ERROR: See docs/changes/index.html for recent updates. > > [0]PETSC ERROR: See docs/faq.html for hints about trouble shooting. > > [0]PETSC ERROR: See docs/index.html for manual pages. > > [0]PETSC ERROR: > > ---------------------------------------------------------------------- > > -- [0]PETSC ERROR: dynSim on a arch-complex named olympus.local by > > d3m956 Wed Apr 17 11:38:12 2013 [0]PETSC ERROR: Libraries linked from > > /pic/projects/ds/petsc-dev/arch-complex/lib > > [0]PETSC ERROR: Configure run at Tue Mar 12 14:32:37 2013 [0]PETSC > > ERROR: Configure options --with-scalar-type=complex > > --with-clanguage=C++ PETSC_ARCH=arch-complex > > --with-fortran-kernels=generic [0]PETSC ERROR: > > ---------------------------------------------------------------------- > > -- [0]PETSC ERROR: MatGetFactor() line 3949 in > > src/mat/interface/matrix.c [0]PETSC ERROR: solvingAXB() line 880 in > > "unknowndirectory/"reducedYBus.C End! > > [1]PETSC ERROR: > > ---------------------------------------------------------------------- > > -- [1]PETSC ERROR: Caught signal number 15 Terminate: Somet process > > (or the batch system) has told this process to end [1]PETSC ERROR: Try > > option -start_in_debugger or -on_error_attach_debugger [1]PETSC ERROR: > > or see > > http://www.mcs.anl.gov/petsc/documentation/faq.html#valgrind[1]PETSC > > ERROR: or try http://valgrind.org on GNU/linux and Apple Mac OS X to > > find memory corruption errors [1]PETSC ERROR: likely location of > > problem given in stack below [1]PETSC ERROR: --------------------- > > Stack Frames ------------------------------------ > > [1]PETSC ERROR: Note: The EXACT line numbers in the stack are not available, > > [1]PETSC ERROR: INSTEAD the line number of the start of the function > > [1]PETSC ERROR: is given. > > [1]PETSC ERROR: [1] PetscSleep line 35 src/sys/utils/psleep.c [1]PETSC > > ERROR: [1] PetscTraceBackErrorHandler line 172 > > src/sys/error/errtrace.c [1]PETSC ERROR: [1] PetscError line 361 > > src/sys/error/err.c [1]PETSC ERROR: [1] MatGetFactor line 3932 > > src/mat/interface/matrix.c [1]PETSC ERROR: --------------------- Error > > Message ------------------------------------ > > [1]PETSC ERROR: Signal received! > > [1]PETSC ERROR: > > ---------------------------------------------------------------------- > > -- [1]PETSC ERROR: Petsc Development HG revision: > > 6e0ddc6e9b6d8a9d8eb4c0ede0105827a6b58dfb HG Date: Mon Mar 11 22:54:30 > > 2013 -0500 [1]PETSC ERROR: See docs/changes/index.html for recent updates. > > [1]PETSC ERROR: See docs/faq.html for hints about trouble shooting. > > [1]PETSC ERROR: See docs/index.html for manual pages. > > [1]PETSC ERROR: > > ---------------------------------------------------------------------- > > -- [1]PETSC ERROR: dynSim on a arch-complex named olympus.local by > > d3m956 Wed Apr 17 11:38:12 2013 [1]PETSC ERROR: Libraries linked from > > /pic/projects/ds/petsc-dev/arch-complex/lib > > [1]PETSC ERROR: Configure run at Tue Mar 12 14:32:37 2013 [1]PETSC > > ERROR: Configure options --with-scalar-type=complex > > --with-clanguage=C++ PETSC_ARCH=arch-complex > > --with-fortran-kernels=generic [1]PETSC ERROR: > > ---------------------------------------------------------------------- > > -- [1]PETSC ERROR: User provided function() line 0 in unknown > > directory unknown file > > ---------------------------------------------------------------------- > > ---- > > > > Thanks, > > Shuangshuang > > > > > > -----Original Message----- > > From: petsc-users-bounces at mcs.anl.gov > > [mailto:petsc-users-bounces at mcs.anl.gov] On Behalf Of Barry Smith > > Sent: Tuesday, April 16, 2013 5:50 PM > > To: PETSc users list > > Subject: Re: [petsc-users] ksp for AX=B system > > > > > > Shuangshuang > > > > This is what I was expecting, thanks for the confirmation. For these > > size problems you definitely want to use a direct solver (often parallel > > but not for smaller matrices) and solve multiple right hand sides. This > > means you actually will not use the KSP solver that is standard for most > > PETSc work, instead you will work directly with the MatGetFactor(), > > MatGetOrdering(), MatLUFactorSymbolic(), MatLUFactorNumeric(), > > MatMatSolve() paradigm where the A matrix is stored as an MATAIJ matrix and > > the B (multiple right hand side) as a MATDENSE matrix. > > > > An example that displays this paradigm is > > src/mat/examples/tests/ex125.c > > > > Once you have something running of interest to you we would like to work > > with you to improve the performance, we have some "tricks" we haven't yet > > implemented to make these solvers much faster than they will be by default. > > > > Barry > > > > > > > > On Apr 16, 2013, at 7:38 PM, "Jin, Shuangshuang" <Shuangshuang.Jin at > > pnnl.gov> wrote: > > > >> Hi, Barry, thanks for your prompt reply. > >> > >> We have various size problems, from (n=9, m=3), (n=1081, m = 288), to > >> (n=16072, m=2361) or even larger ultimately. > >> > >> Usually the dimension of the square matrix A, n is much larger than the > >> column dimension of B, m. > >> > >> As you said, I'm using the loop to deal with the small (n=9, m=3) case. > >> However, for bigger problem, I do hope there's a better approach. > >> > >> This is a power flow problem. When we parallelized it in OpenMP > >> previously, we just parallelized the outside loop, and used a direct > >> solver to solve it. > >> > >> We are now switching to MPI and like to use PETSc ksp solver to solve it > >> in parallel. However, I don't know what's the best ksp solver I should use > >> here? Direct solver or try a preconditioner? > >> > >> I appreciate very much for your recommendations. > >> > >> Thanks, > >> Shuangshuang > >> > >> > >
