ML with OpenMPI
Jed, You can take a look at config/PETSc/packages/ml.py; essentially we call their configure with a given set of compilers (and MPI information). So I would say you have to report the bug to those folks; their configure should handle that issue, shouldn't it. Barry On Mar 21, 2008, at 5:09 PM, Jed Brown wrote: The MPI standard does not specify that MPI_Comm = int and in fact OpenMPI uses a pointer value which lets the compiler do slightly more type checking. This type checking recently caused me trouble when building with-download-ml. There is a line in ml_comm.h which defines their communicator to be an int when ML_MPI is not defined. It was not immediately clear why this is not defined, but result is that the compiler chokes when building PETSc. This patch fixes the problem as long as sizeof(int) = sizeof(MPI_Comm), but this is *not* the case on x86_64 with OpenMPI. It's not clear to me how much of this is an upstream issue and how much is a configuration issue. Jed diff -r c074838b79ed src/ksp/pc/impls/ml/ml.c --- a/src/ksp/pc/impls/ml/ml.c Thu Mar 20 17:04:05 2008 -0500 +++ b/src/ksp/pc/impls/ml/ml.c Fri Mar 21 22:50:32 2008 +0100 @@ -815,7 +815,7 @@ PetscErrorCode MatWrapML_SHELL(ML_Operat MLcomm = mlmat-comm; ierr = PetscNew(Mat_MLShell,shellctx);CHKERRQ(ierr); - ierr = MatCreateShell(MLcomm- USR_comm ,m,n,PETSC_DETERMINE,PETSC_DETERMINE,shellctx,newmat);CHKERRQ(ierr); + ierr = MatCreateShell((MPI_Comm)MLcomm- USR_comm ,m,n,PETSC_DETERMINE,PETSC_DETERMINE,shellctx,newmat);CHKERRQ(ierr); ierr = MatShellSetOperation(*newmat,MATOP_MULT,(void(*) (void))MatMult_ML);CHKERRQ(ierr); ierr = MatShellSetOperation(*newmat,MATOP_MULT_ADD,(void(*) (void))MatMultAdd_ML);CHKERRQ(ierr); shellctx-A = *newmat; @@ -844,7 +844,7 @@ PetscErrorCode MatWrapML_MPIAIJ(ML_Opera n = mlmat-invec_leng; if (m != n) SETERRQ2(PETSC_ERR_ARG_OUTOFRANGE,m %d must equal to n %d,m,n); - ierr = MatCreate(mlmat-comm-USR_comm,A);CHKERRQ(ierr); + ierr = MatCreate((MPI_Comm)mlmat-comm-USR_comm,A);CHKERRQ(ierr); ierr = MatSetSizes(A,m,n,PETSC_DECIDE,PETSC_DECIDE);CHKERRQ(ierr); ierr = MatSetType(A,MATMPIAIJ);CHKERRQ(ierr); ierr = PetscMalloc3 (m,PetscInt,nnzA,m,PetscInt,nnzB,m,PetscInt,nnz);CHKERRQ(ierr);
configuring with --prefix
I got this error at configuration time: You do not have write access to create install directory given with --prefix=/usr/local/petsc/dev/linux-gnu perhaps use --with-sudo=sudo also Then I've added, the sudo stuff and worked. However, after the configuation, the dir was not created. So the question is: in which scenario PETSc does need access to the install dir at configuration time? -- Lisandro Dalc?n --- Centro Internacional de M?todos Computacionales en Ingenier?a (CIMEC) Instituto de Desarrollo Tecnol?gico para la Industria Qu?mica (INTEC) Consejo Nacional de Investigaciones Cient?ficas y T?cnicas (CONICET) PTLC - G?emes 3450, (3000) Santa Fe, Argentina Tel/Fax: +54-(0)342-451.1594
ML with OpenMPI
Mmm... I believe this is a configuration issue... if ML_MPI were defined, then ML_USR_COMM should be MPI_Comm. But the problem is perhaps on the ML side, not the PETSc side. ml_common.h #define ML_MPI if macro HAVE_MPI is defined. In turn HAVE_MPI is at ml_config.h, and that file is surelly generated by ML configure script. For some reason ML's configure failed to found MPI with the command line stuff PETSc pass to it. Look at the 'config.log' file inside the ml-5.0 dir to find what happened. On 3/21/08, Jed Brown jed at 59a2.org wrote: The MPI standard does not specify that MPI_Comm = int and in fact OpenMPI uses a pointer value which lets the compiler do slightly more type checking. This type checking recently caused me trouble when building with-download-ml. There is a line in ml_comm.h which defines their communicator to be an int when ML_MPI is not defined. It was not immediately clear why this is not defined, but result is that the compiler chokes when building PETSc. This patch fixes the problem as long as sizeof(int) = sizeof(MPI_Comm), but this is *not* the case on x86_64 with OpenMPI. It's not clear to me how much of this is an upstream issue and how much is a configuration issue. Jed diff -r c074838b79ed src/ksp/pc/impls/ml/ml.c --- a/src/ksp/pc/impls/ml/ml.c Thu Mar 20 17:04:05 2008 -0500 +++ b/src/ksp/pc/impls/ml/ml.c Fri Mar 21 22:50:32 2008 +0100 @@ -815,7 +815,7 @@ PetscErrorCode MatWrapML_SHELL(ML_Operat MLcomm = mlmat-comm; ierr = PetscNew(Mat_MLShell,shellctx);CHKERRQ(ierr); - ierr = MatCreateShell(MLcomm-USR_comm,m,n,PETSC_DETERMINE,PETSC_DETERMINE,shellctx,newmat);CHKERRQ(ierr); + ierr = MatCreateShell((MPI_Comm)MLcomm-USR_comm,m,n,PETSC_DETERMINE,PETSC_DETERMINE,shellctx,newmat);CHKERRQ(ierr); ierr = MatShellSetOperation(*newmat,MATOP_MULT,(void(*)(void))MatMult_ML);CHKERRQ(ierr); ierr = MatShellSetOperation(*newmat,MATOP_MULT_ADD,(void(*)(void))MatMultAdd_ML);CHKERRQ(ierr); shellctx-A = *newmat; @@ -844,7 +844,7 @@ PetscErrorCode MatWrapML_MPIAIJ(ML_Opera n = mlmat-invec_leng; if (m != n) SETERRQ2(PETSC_ERR_ARG_OUTOFRANGE,m %d must equal to n %d,m,n); - ierr = MatCreate(mlmat-comm-USR_comm,A);CHKERRQ(ierr); + ierr = MatCreate((MPI_Comm)mlmat-comm-USR_comm,A);CHKERRQ(ierr); ierr = MatSetSizes(A,m,n,PETSC_DECIDE,PETSC_DECIDE);CHKERRQ(ierr); ierr = MatSetType(A,MATMPIAIJ);CHKERRQ(ierr); ierr = PetscMalloc3(m,PetscInt,nnzA,m,PetscInt,nnzB,m,PetscInt,nnz);CHKERRQ(ierr); -- Lisandro Dalc?n --- Centro Internacional de M?todos Computacionales en Ingenier?a (CIMEC) Instituto de Desarrollo Tecnol?gico para la Industria Qu?mica (INTEC) Consejo Nacional de Investigaciones Cient?ficas y T?cnicas (CONICET) PTLC - G?emes 3450, (3000) Santa Fe, Argentina Tel/Fax: +54-(0)342-451.1594
configuring with --prefix
On Mar 21, 2008, at 5:32 PM, Matthew Knepley wrote: On Fri, Mar 21, 2008 at 4:53 PM, Lisandro Dalcin dalcinl at gmail.com wrote: I got this error at configuration time: You do not have write access to create install directory given with --prefix=/usr/local/petsc/dev/linux-gnu perhaps use --with-sudo=sudo also Then I've added, the sudo stuff and worked. However, after the configuation, the dir was not created. So the question is: in which scenario PETSc does need access to the install dir at configuration time? PETSc does not NEED access until install time, however it is checking because people often screw this up. Also the eventual plan is that each external package will get installed directly to the prefix location (instead of being installed first in the petsc location and then copied over to the prefix location). This is a little funky to think config/configure.py is doing an install; but it is doing the install of the external packages you requested. Barry Matt -- Lisandro Dalc?n --- Centro Internacional de M?todos Computacionales en Ingenier?a (CIMEC) Instituto de Desarrollo Tecnol?gico para la Industria Qu?mica (INTEC) Consejo Nacional de Investigaciones Cient?ficas y T?cnicas (CONICET) PTLC - G?emes 3450, (3000) Santa Fe, Argentina Tel/Fax: +54-(0)342-451.1594 -- What most experimenters take for granted before they begin their experiments is infinitely more interesting than any results to which their experiments lead. -- Norbert Wiener
