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Linking with PETSc [message #703783]

Wed, 27 July 2011 22:50

Matt Bockman

Messages: 1
Registered: July 2011

Junior Member

Hi,

I am running Ubuntu 11.04 and Eclipse 3.5.2. I have compiled the PETSc library in my home directory.

I have an existing C++ project in Eclipse with automatically generated makefiles. The problem is that I cannot seem to link to the PETSc library. A lot of this stuff is way over my head so I'm trying to learn as much as possible but it is a lot to absorb.

Here is the error that I get from Eclipse:

**** Build of configuration Debug for project quad_FEM_svn ****

make all 
Building file: ../SparseMatrixPetsc.c
Invoking: GCC C Compiler
/home/mdbockman/Documents/Research/codes/petsc/petsc-3.1-p8/linux-gnu-c-debug/bin/mpicc -I/home/mdbockman/Documents/Research/codes/petsc/petsc-3.1-p8/linux-gnu-c-debug/include -I/home/mdbockman/Documents/Research/codes/petsc/petsc-3.1-p8/include -I/home/mdbockman/Documents/Research/codes/petsc/petsc-3.1-p8/linux-gnu-c-debug/include -O0 -g3 -pg -p -Wall -MMD -MP -MF"SparseMatrixPetsc.d" -MT"SparseMatrixPetsc.d" -o"SparseMatrixPetsc.o" "../SparseMatrixPetsc.c"
/usr/lib/x86_64-linux-gnu/gcc/x86_64-linux-gnu/4.5.2/../../../gcrt1.o: In function `_start':
(.text+0x20): undefined reference to `main'
/tmp/ccZLkAIH.o: In function `solveMatrix':
/home/mdbockman/Documents/Research/codes/quadrilateral_FEM/quad_FEM_svn_local/quad_FEM_svn/Debug/../SparseMatrixPetsc.c:24: undefined reference to `PetscInitialize'
/home/mdbockman/Documents/Research/codes/quadrilateral_FEM/quad_FEM_svn_local/quad_FEM_svn/Debug/../SparseMatrixPetsc.c:24: undefined reference to `PetscError'
/home/mdbockman/Documents/Research/codes/quadrilateral_FEM/quad_FEM_svn_local/quad_FEM_svn/Debug/../SparseMatrixPetsc.c:25: undefined reference to `PetscOptionsSetValue'
/home/mdbockman/Documents/Research/codes/quadrilateral_FEM/quad_FEM_svn_local/quad_FEM_svn/Debug/../SparseMatrixPetsc.c:25: undefined reference to `PetscError'
/home/mdbockman/Documents/Research/codes/quadrilateral_FEM/quad_FEM_svn_local/quad_FEM_svn/Debug/../SparseMatrixPetsc.c:32: undefined reference to `MatCreateSeqAIJ'
/home/mdbockman/Documents/Research/codes/quadrilateral_FEM/quad_FEM_svn_local/quad_FEM_svn/Debug/../SparseMatrixPetsc.c:32: undefined reference to `PetscError'
/home/mdbockman/Documents/Research/codes/quadrilateral_FEM/quad_FEM_svn_local/quad_FEM_svn/Debug/../SparseMatrixPetsc.c:33: undefined reference to `VecCreateSeq'
/home/mdbockman/Documents/Research/codes/quadrilateral_FEM/quad_FEM_svn_local/quad_FEM_svn/Debug/../SparseMatrixPetsc.c:33: undefined reference to `PetscError'
/home/mdbockman/Documents/Research/codes/quadrilateral_FEM/quad_FEM_svn_local/quad_FEM_svn/Debug/../SparseMatrixPetsc.c:34: undefined reference to `VecDuplicate'
/home/mdbockman/Documents/Research/codes/quadrilateral_FEM/quad_FEM_svn_local/quad_FEM_svn/Debug/../SparseMatrixPetsc.c:34: undefined reference to `PetscError'
/home/mdbockman/Documents/Research/codes/quadrilateral_FEM/quad_FEM_svn_local/quad_FEM_svn/Debug/../SparseMatrixPetsc.c:37: undefined reference to `MatSetValues'
/home/mdbockman/Documents/Research/codes/quadrilateral_FEM/quad_FEM_svn_local/quad_FEM_svn/Debug/../SparseMatrixPetsc.c:37: undefined reference to `PetscError'
/home/mdbockman/Documents/Research/codes/quadrilateral_FEM/quad_FEM_svn_local/quad_FEM_svn/Debug/../SparseMatrixPetsc.c:39: undefined reference to `VecSetValues'
/home/mdbockman/Documents/Research/codes/quadrilateral_FEM/quad_FEM_svn_local/quad_FEM_svn/Debug/../SparseMatrixPetsc.c:39: undefined reference to `PetscError'
/home/mdbockman/Documents/Research/codes/quadrilateral_FEM/quad_FEM_svn_local/quad_FEM_svn/Debug/../SparseMatrixPetsc.c:40: undefined reference to `VecSetValues'
/home/mdbockman/Documents/Research/codes/quadrilateral_FEM/quad_FEM_svn_local/quad_FEM_svn/Debug/../SparseMatrixPetsc.c:40: undefined reference to `PetscError'
/home/mdbockman/Documents/Research/codes/quadrilateral_FEM/quad_FEM_svn_local/quad_FEM_svn/Debug/../SparseMatrixPetsc.c:44: undefined reference to `VecSetValues'
/home/mdbockman/Documents/Research/codes/quadrilateral_FEM/quad_FEM_svn_local/quad_FEM_svn/Debug/../SparseMatrixPetsc.c:44: undefined reference to `PetscError'
/home/mdbockman/Documents/Research/codes/quadrilateral_FEM/quad_FEM_svn_local/quad_FEM_svn/Debug/../SparseMatrixPetsc.c:48: undefined reference to `MatSetValues'
/home/mdbockman/Documents/Research/codes/quadrilateral_FEM/quad_FEM_svn_local/quad_FEM_svn/Debug/../SparseMatrixPetsc.c:48: undefined reference to `PetscError'
/home/mdbockman/Documents/Research/codes/quadrilateral_FEM/quad_FEM_svn_local/quad_FEM_svn/Debug/../SparseMatrixPetsc.c:49: undefined reference to `MatSetValues'
/home/mdbockman/Documents/Research/codes/quadrilateral_FEM/quad_FEM_svn_local/quad_FEM_svn/Debug/../SparseMatrixPetsc.c:49: undefined reference to `PetscError'
/home/mdbockman/Documents/Research/codes/quadrilateral_FEM/quad_FEM_svn_local/quad_FEM_svn/Debug/../SparseMatrixPetsc.c:52: undefined reference to `MatSetValues'
/home/mdbockman/Documents/Research/codes/quadrilateral_FEM/quad_FEM_svn_local/quad_FEM_svn/Debug/../SparseMatrixPetsc.c:52: undefined reference to `PetscError'
/home/mdbockman/Documents/Research/codes/quadrilateral_FEM/quad_FEM_svn_local/quad_FEM_svn/Debug/../SparseMatrixPetsc.c:53: undefined reference to `MatSetValues'
/home/mdbockman/Documents/Research/codes/quadrilateral_FEM/quad_FEM_svn_local/quad_FEM_svn/Debug/../SparseMatrixPetsc.c:53: undefined reference to `PetscError'
/home/mdbockman/Documents/Research/codes/quadrilateral_FEM/quad_FEM_svn_local/quad_FEM_svn/Debug/../SparseMatrixPetsc.c:54: undefined reference to `MatAssemblyBegin'
/home/mdbockman/Documents/Research/codes/quadrilateral_FEM/quad_FEM_svn_local/quad_FEM_svn/Debug/../SparseMatrixPetsc.c:54: undefined reference to `PetscError'
/home/mdbockman/Documents/Research/codes/quadrilateral_FEM/quad_FEM_svn_local/quad_FEM_svn/Debug/../SparseMatrixPetsc.c:55: undefined reference to `MatAssemblyEnd'
/home/mdbockman/Documents/Research/codes/quadrilateral_FEM/quad_FEM_svn_local/quad_FEM_svn/Debug/../SparseMatrixPetsc.c:55: undefined reference to `PetscError'
/home/mdbockman/Documents/Research/codes/quadrilateral_FEM/quad_FEM_svn_local/quad_FEM_svn/Debug/../SparseMatrixPetsc.c:56: undefined reference to `VecAssemblyBegin'
/home/mdbockman/Documents/Research/codes/quadrilateral_FEM/quad_FEM_svn_local/quad_FEM_svn/Debug/../SparseMatrixPetsc.c:56: undefined reference to `PetscError'
/home/mdbockman/Documents/Research/codes/quadrilateral_FEM/quad_FEM_svn_local/quad_FEM_svn/Debug/../SparseMatrixPetsc.c:57: undefined reference to `VecAssemblyEnd'
/home/mdbockman/Documents/Research/codes/quadrilateral_FEM/quad_FEM_svn_local/quad_FEM_svn/Debug/../SparseMatrixPetsc.c:57: undefined reference to `PetscError'
/home/mdbockman/Documents/Research/codes/quadrilateral_FEM/quad_FEM_svn_local/quad_FEM_svn/Debug/../SparseMatrixPetsc.c:59: undefined reference to `MatView'
/home/mdbockman/Documents/Research/codes/quadrilateral_FEM/quad_FEM_svn_local/quad_FEM_svn/Debug/../SparseMatrixPetsc.c:63: undefined reference to `VecView'
/home/mdbockman/Documents/Research/codes/quadrilateral_FEM/quad_FEM_svn_local/quad_FEM_svn/Debug/../SparseMatrixPetsc.c:65: undefined reference to `VecView'
/home/mdbockman/Documents/Research/codes/quadrilateral_FEM/quad_FEM_svn_local/quad_FEM_svn/Debug/../SparseMatrixPetsc.c:73: undefined reference to `KSPCreate'
/home/mdbockman/Documents/Research/codes/quadrilateral_FEM/quad_FEM_svn_local/quad_FEM_svn/Debug/../SparseMatrixPetsc.c:73: undefined reference to `PetscError'
/home/mdbockman/Documents/Research/codes/quadrilateral_FEM/quad_FEM_svn_local/quad_FEM_svn/Debug/../SparseMatrixPetsc.c:74: undefined reference to `KSPSetOperators'
/home/mdbockman/Documents/Research/codes/quadrilateral_FEM/quad_FEM_svn_local/quad_FEM_svn/Debug/../SparseMatrixPetsc.c:74: undefined reference to `PetscError'
/home/mdbockman/Documents/Research/codes/quadrilateral_FEM/quad_FEM_svn_local/quad_FEM_svn/Debug/../SparseMatrixPetsc.c:76: undefined reference to `KSPSetType'
/home/mdbockman/Documents/Research/codes/quadrilateral_FEM/quad_FEM_svn_local/quad_FEM_svn/Debug/../SparseMatrixPetsc.c:76: undefined reference to `PetscError'
/home/mdbockman/Documents/Research/codes/quadrilateral_FEM/quad_FEM_svn_local/quad_FEM_svn/Debug/../SparseMatrixPetsc.c:77: undefined reference to `KSPSetInitialGuessNonzero'
/home/mdbockman/Documents/Research/codes/quadrilateral_FEM/quad_FEM_svn_local/quad_FEM_svn/Debug/../SparseMatrixPetsc.c:77: undefined reference to `PetscError'
/home/mdbockman/Documents/Research/codes/quadrilateral_FEM/quad_FEM_svn_local/quad_FEM_svn/Debug/../SparseMatrixPetsc.c:83: undefined reference to `KSPGetPC'
/home/mdbockman/Documents/Research/codes/quadrilateral_FEM/quad_FEM_svn_local/quad_FEM_svn/Debug/../SparseMatrixPetsc.c:83: undefined reference to `PetscError'
/home/mdbockman/Documents/Research/codes/quadrilateral_FEM/quad_FEM_svn_local/quad_FEM_svn/Debug/../SparseMatrixPetsc.c:84: undefined reference to `PCSetType'
/home/mdbockman/Documents/Research/codes/quadrilateral_FEM/quad_FEM_svn_local/quad_FEM_svn/Debug/../SparseMatrixPetsc.c:84: undefined reference to `PetscError'
/home/mdbockman/Documents/Research/codes/quadrilateral_FEM/quad_FEM_svn_local/quad_FEM_svn/Debug/../SparseMatrixPetsc.c:87: undefined reference to `KSPSetFromOptions'
/home/mdbockman/Documents/Research/codes/quadrilateral_FEM/quad_FEM_svn_local/quad_FEM_svn/Debug/../SparseMatrixPetsc.c:87: undefined reference to `PetscError'
/home/mdbockman/Documents/Research/codes/quadrilateral_FEM/quad_FEM_svn_local/quad_FEM_svn/Debug/../SparseMatrixPetsc.c:88: undefined reference to `KSPSetUp'
/home/mdbockman/Documents/Research/codes/quadrilateral_FEM/quad_FEM_svn_local/quad_FEM_svn/Debug/../SparseMatrixPetsc.c:88: undefined reference to `PetscError'
/home/mdbockman/Documents/Research/codes/quadrilateral_FEM/quad_FEM_svn_local/quad_FEM_svn/Debug/../SparseMatrixPetsc.c:95: undefined reference to `PCFactorGetMatrix'
/home/mdbockman/Documents/Research/codes/quadrilateral_FEM/quad_FEM_svn_local/quad_FEM_svn/Debug/../SparseMatrixPetsc.c:95: undefined reference to `PetscError'
/home/mdbockman/Documents/Research/codes/quadrilateral_FEM/quad_FEM_svn_local/quad_FEM_svn/Debug/../SparseMatrixPetsc.c:96: undefined reference to `VecDuplicate'
/home/mdbockman/Documents/Research/codes/quadrilateral_FEM/quad_FEM_svn_local/quad_FEM_svn/Debug/../SparseMatrixPetsc.c:96: undefined reference to `PetscError'
/home/mdbockman/Documents/Research/codes/quadrilateral_FEM/quad_FEM_svn_local/quad_FEM_svn/Debug/../SparseMatrixPetsc.c:97: undefined reference to `MatGetDiagonal'
/home/mdbockman/Documents/Research/codes/quadrilateral_FEM/quad_FEM_svn_local/quad_FEM_svn/Debug/../SparseMatrixPetsc.c:97: undefined reference to `PetscError'
/home/mdbockman/Documents/Research/codes/quadrilateral_FEM/quad_FEM_svn_local/quad_FEM_svn/Debug/../SparseMatrixPetsc.c:98: undefined reference to `VecView'
/home/mdbockman/Documents/Research/codes/quadrilateral_FEM/quad_FEM_svn_local/quad_FEM_svn/Debug/../SparseMatrixPetsc.c:105: undefined reference to `KSPSolve'
/home/mdbockman/Documents/Research/codes/quadrilateral_FEM/quad_FEM_svn_local/quad_FEM_svn/Debug/../SparseMatrixPetsc.c:105: undefined reference to `PetscError'
/home/mdbockman/Documents/Research/codes/quadrilateral_FEM/quad_FEM_svn_local/quad_FEM_svn/Debug/../SparseMatrixPetsc.c:106: undefined reference to `KSPGetConvergedReason'
/home/mdbockman/Documents/Research/codes/quadrilateral_FEM/quad_FEM_svn_local/quad_FEM_svn/Debug/../SparseMatrixPetsc.c:106: undefined reference to `PetscError'
/home/mdbockman/Documents/Research/codes/quadrilateral_FEM/quad_FEM_svn_local/quad_FEM_svn/Debug/../SparseMatrixPetsc.c:113: undefined reference to `KSPGetIterationNumber'
/home/mdbockman/Documents/Research/codes/quadrilateral_FEM/quad_FEM_svn_local/quad_FEM_svn/Debug/../SparseMatrixPetsc.c:113: undefined reference to `PetscError'
/home/mdbockman/Documents/Research/codes/quadrilateral_FEM/quad_FEM_svn_local/quad_FEM_svn/Debug/../SparseMatrixPetsc.c:118: undefined reference to `VecDestroy'
/home/mdbockman/Documents/Research/codes/quadrilateral_FEM/quad_FEM_svn_local/quad_FEM_svn/Debug/../SparseMatrixPetsc.c:118: undefined reference to `PetscError'
/home/mdbockman/Documents/Research/codes/quadrilateral_FEM/quad_FEM_svn_local/quad_FEM_svn/Debug/../SparseMatrixPetsc.c:119: undefined reference to `VecDestroy'
/home/mdbockman/Documents/Research/codes/quadrilateral_FEM/quad_FEM_svn_local/quad_FEM_svn/Debug/../SparseMatrixPetsc.c:119: undefined reference to `PetscError'
/home/mdbockman/Documents/Research/codes/quadrilateral_FEM/quad_FEM_svn_local/quad_FEM_svn/Debug/../SparseMatrixPetsc.c:120: undefined reference to `VecDestroy'
/home/mdbockman/Documents/Research/codes/quadrilateral_FEM/quad_FEM_svn_local/quad_FEM_svn/Debug/../SparseMatrixPetsc.c:120: undefined reference to `PetscError'
/home/mdbockman/Documents/Research/codes/quadrilateral_FEM/quad_FEM_svn_local/quad_FEM_svn/Debug/../SparseMatrixPetsc.c:121: undefined reference to `MatDestroy'
/home/mdbockman/Documents/Research/codes/quadrilateral_FEM/quad_FEM_svn_local/quad_FEM_svn/Debug/../SparseMatrixPetsc.c:121: undefined reference to `PetscError'
/home/mdbockman/Documents/Research/codes/quadrilateral_FEM/quad_FEM_svn_local/quad_FEM_svn/Debug/../SparseMatrixPetsc.c:122: undefined reference to `KSPDestroy'
/home/mdbockman/Documents/Research/codes/quadrilateral_FEM/quad_FEM_svn_local/quad_FEM_svn/Debug/../SparseMatrixPetsc.c:122: undefined reference to `PetscError'
/home/mdbockman/Documents/Research/codes/quadrilateral_FEM/quad_FEM_svn_local/quad_FEM_svn/Debug/../SparseMatrixPetsc.c:123: undefined reference to `PetscFinalize'
collect2: ld returned 1 exit status
make: *** [SparseMatrixPetsc.o] Error 1

Here is the file I am trying to compile:

/*
 * SparseMatrixPetsc.c
 *
 *  Created on: Jul 26, 2011
 *      Author: mdbockman
 */

#include "SparseMatrixPetsc.h"
#include "petscksp.h"
#include "petscsys.h"

int solveMatrix(int argc,char **argv)
{
  KSP                solver;
  PC                 prec;
  Mat                A,M;
  Vec                X,B,D;
  MPI_Comm           comm;
  PetscScalar        v;
  KSPConvergedReason reason;
  PetscInt           i,j,its;
  PetscErrorCode     ierr;

  ierr = PetscInitialize(&argc,&argv,0,0);CHKERRQ(ierr);
  ierr = PetscOptionsSetValue("-options_left",PETSC_NULL);CHKERRQ(ierr);
  comm = MPI_COMM_SELF;

  /*
   * Construct the Kershaw matrix
   * and a suitable rhs / initial guess
   */
  ierr = MatCreateSeqAIJ(comm,4,4,4,0,&A);CHKERRQ(ierr);
  ierr = VecCreateSeq(comm,4,&B);CHKERRQ(ierr);
  ierr = VecDuplicate(B,&X);CHKERRQ(ierr);
  for (i=0; i<4; i++) {
    v=3;
    ierr = MatSetValues(A,1,&i,1,&i,&v,INSERT_VALUES);CHKERRQ(ierr);
    v=1;
    ierr = VecSetValues(B,1,&i,&v,INSERT_VALUES);CHKERRQ(ierr);
    ierr = VecSetValues(X,1,&i,&v,INSERT_VALUES);CHKERRQ(ierr);
  }

  i=0; v=0;
  ierr = VecSetValues(X,1,&i,&v,INSERT_VALUES);CHKERRQ(ierr);

  for (i=0; i<3; i++) {
    v=-2; j=i+1;
    ierr = MatSetValues(A,1,&i,1,&j,&v,INSERT_VALUES);CHKERRQ(ierr);
    ierr = MatSetValues(A,1,&j,1,&i,&v,INSERT_VALUES);CHKERRQ(ierr);
  }
  i=0; j=3; v=2;
  ierr = MatSetValues(A,1,&i,1,&j,&v,INSERT_VALUES);CHKERRQ(ierr);
  ierr = MatSetValues(A,1,&j,1,&i,&v,INSERT_VALUES);CHKERRQ(ierr);
  ierr = MatAssemblyBegin(A,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr);
  ierr = MatAssemblyEnd(A,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr);
  ierr = VecAssemblyBegin(B);CHKERRQ(ierr);
  ierr = VecAssemblyEnd(B);CHKERRQ(ierr);
  printf("\nA:\n");
MatView(A,0);
//printf("M:\n");
//MatView(M,0);
printf("X:\n");
VecView(X,0);
printf("B:\n");
VecView(B,0);
//printf("D:\n");
//VecView(D,0);

  /*
   * A Conjugate Gradient method
   * with ILU(0) preconditioning
   */
  ierr = KSPCreate(comm,&solver);CHKERRQ(ierr);
  ierr = KSPSetOperators(solver,A,A,SAME_NONZERO_PATTERN);CHKERRQ(ierr);

  ierr = KSPSetType(solver,KSPCG);CHKERRQ(ierr);
  ierr = KSPSetInitialGuessNonzero(solver,PETSC_TRUE);CHKERRQ(ierr);

  /*
   * ILU preconditioner;
   * this will break down unless you add the Shift line,
   * or use the -pc_factor_shift_positive_definite option */
  ierr = KSPGetPC(solver,&prec);CHKERRQ(ierr);
  ierr = PCSetType(prec,PCILU);CHKERRQ(ierr);
  /* ierr = PCFactorSetShiftType(prec,MAT_SHIFT_POSITIVE_DEFINITE);CHKERRQ(ierr); */

  ierr = KSPSetFromOptions(solver);CHKERRQ(ierr);
  ierr = KSPSetUp(solver);CHKERRQ(ierr);

  /*
   * Now that the factorisation is done, show the pivots;
   * note that the last one is negative. This in itself is not an error,
   * but it will make the iterative method diverge.
   */
  ierr = PCFactorGetMatrix(prec,&M);CHKERRQ(ierr);
  ierr = VecDuplicate(B,&D);CHKERRQ(ierr);
  ierr = MatGetDiagonal(M,D);CHKERRQ(ierr);
  printf("\nPivots:\n\n"); VecView(D,0);

  /*
   * Solve the system;
   * without the shift this will diverge with
   * an indefinite preconditioner
   */
  ierr = KSPSolve(solver,B,X);CHKERRQ(ierr);
  ierr = KSPGetConvergedReason(solver,&reason);CHKERRQ(ierr);
  if (reason==KSP_DIVERGED_INDEFINITE_PC) {
    printf("\nDivergence because of indefinite preconditioner;\n");
    printf("Run the executable again but with '-pc_factor_shift_type POSITIVE_DEFINITE' option.\n");
  } else if (reason<0) {
    printf("\nOther kind of divergence: this should not happen.\n");
  } else {
    ierr = KSPGetIterationNumber(solver,&its);CHKERRQ(ierr);
    printf("\nConvergence in %d iterations.\n",(int)its);
  }
  printf("\n");

  ierr = VecDestroy(X);CHKERRQ(ierr);
  ierr = VecDestroy(B);CHKERRQ(ierr);
  ierr = VecDestroy(D);CHKERRQ(ierr);
  ierr = MatDestroy(A);CHKERRQ(ierr);
  ierr = KSPDestroy(solver);CHKERRQ(ierr);
  PetscFinalize();
  return 0;
}

Which is a C file. I haven't yet included this file in any of my other files, but I eventually will. I understand that I need to use some special magic to use C functions in a C++ context.

Also, that code is copied from an example file (except in the example file, the function is called main). The makefile for that example is here:

CFLAGS	        = 
FFLAGS          =
CPPFLAGS        =
FPPFLAGS        =
LOCDIR          = src/ksp/pc/examples/tutorials/
EXAMPLESC       = ex1.c ex2.c ex3.c
EXAMPLESF       =
MANSEC          = PC

include ${PETSC_DIR}/conf/variables
include ${PETSC_DIR}/conf/rules

ex1: ex1.o  chkopts
	-${CLINKER}  -o ex1 ex1.o ${PETSC_KSP_LIB} 
	echo ${PETSC_KSP_LIB}
	${RM} ex1.o

ex2: ex2.o  chkopts
	-${CLINKER}  -o ex2 ex2.o ${PETSC_KSP_LIB} 
	${RM} ex2.o

ex3: ex3.o  chkopts
	-${CLINKER}  -o ex3 ex3.o ${PETSC_KSP_LIB} 
	${RM} ex3.o
#------------------------------------------------------------------------------------
runex3:
	-@${MPIEXEC} -n 1 ./ex3 -ksp_monitor_short > ex3_inode.out 2>&1;
	-@${MPIEXEC} -n 1 ./ex3 -ksp_monitor_short -mat_no_inode > ex3.tmp 2>&1; \
	if (${DIFF} ex3_inode.out ex3.tmp) then true; \
	   else echo "Possible problem with ex3, diffs above"; fi; \
	   ${RM} -f ex3_inode.out; ${RM} -f ex3.tmp

runex3_pd:
	-@${MPIEXEC} -n 1 ./ex3 -ksp_monitor_short -pc_factor_shift_type POSITIVE_DEFINITE > ex3_inode.out 2>&1;
	-@${MPIEXEC} -n 1 ./ex3 -ksp_monitor_short -pc_factor_shift_type POSITIVE_DEFINITE -mat_no_inode > ex3.tmp 2>&1; \
	if (${DIFF} ex3_inode.out ex3.tmp) then true; \
	   else echo "Possible problem with ex3, diffs above"; fi; \
	   ${RM} -f ex3_inode.out; ${RM} -f ex3.tmp

TESTEXAMPLES_C	   = ex3.PETSc runex3 runex3_pd ex3.rm 
TESTEXAMPLES_C_X11 = ex2.PETSc ex2.rm

include ${PETSC_DIR}/conf/test

I understand that I can create my own makefile. Indeed I have compiled the example by itself using a separate project and creating my own makefile. However, it would be really painful to have to make my own makefile for this project and I'm hoping there is a better way to include a library.

Thanks in advance for your help,
Matt

(BTW, I originally tried to use pastebin but the forum does not allow any links during the first 5 posts, I know it's a lot of code!)

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Re: Linking with PETSc [message #707398 is a reply to message #703783]

Mon, 01 August 2011 15:42

lokuz Mising name

Messages: 3
Registered: August 2011

Junior Member

Did you find a solution to this problem?

Report message to a moderator

Re: Linking with PETSc [message #707855 is a reply to message #703783]

Tue, 02 August 2011 06:30

Axel Mueller

Messages: 1973
Registered: July 2009

Senior Member

http://wiki.eclipse.org/CDT/User/FAQ#Adding_C.2FC.2B.2B_External_Libraries

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Re: Linking with PETSc [message #709733 is a reply to message #707855]

Thu, 04 August 2011 08:37

lokuz Mising name

Messages: 3
Registered: August 2011

Junior Member

Thanks for your answer. The problem is not adding a normal lib to the project settings. The troublemaker is the

include ${PETSC_DIR}/conf/variables
include ${PETSC_DIR}/conf/rules

part of the makefile below. Of course you can set the whole stuff in there by hand, but this is really tedious. AFAIK there is no possiblily to add autmatically insert line to the CDT generated makefile.

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