[CIG-LONG] Compile error of gale

[Walter Landry]

John Yu <johnyu at usc.edu> wrote:
> Hi Walter,
> 
> The problem is configuring gale.  I've attached the config log after I
> did a clean installation of bothe petsc 3.2 and gale using the
> instructions from INSTALL.STATIC (which has some outdated instructions
> for petsc 3.0.0).
> 
> I think the error is in the following section of the log.  I've also
> attached the output of
> 
> nm /share/apps/petsc/3.2-p7/lib/libpetsc.a > petsc.nm
> 
>   Failed to find static or shared libraries for 'PETSc'.
>   Static missing: ['petscsnes', 'petscksp', 'petscdm', 'petscmat',
>   'petscvec']
>   Shared missing: ['petscsnes', 'petscksp', 'petscdm', 'petscmat',
>   'petscvec', 'petsc']
>   Looked in: ['/share/apps/petsc/3.2-p7/lib']

The problem shows up in these lines

  /usr/bin/ld: /share/apps/petsc/3.2-p7/lib/libpetsc.a(dlimpl.c.o): undefined reference to symbol 'dlclose@@GLIBC_2.2.5'
  /usr/bin/ld: note: 'dlclose@@GLIBC_2.2.5' is defined in DSO /lib64/libdl.so.2 so try adding it to the linker command line
  /lib64/libdl.so.2: could not read symbols: Invalid operation

Is there something wrong with /lib64/libdl.so.2?  Are you using the
same compiler to build Gale and Petsc?  Can you create simple Petsc
programs manually?  There is a simple example in config.log

  #include "mpi.h"
  #include "petsc.h"
  #include "petscvec.h"
  #include "petscmat.h"
  #include "petscksp.h"
  #include "petscsnes.h"
  
  int
  main() {
    PetscInitialize(NULL, NULL, NULL, NULL);
  PetscFinalize();
  return 0;
  }

Put it in "temp.cxx" and compile it with

  mpicxx -o .sconf_temp/conftest_5.o -c  .sconf_temp/conftest_5.cpp

  mpicxx -o temp -O3 -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -O -DNDEBUG -DHAVE_LIBXML2 -DHAVE_MPI -DHAVE_HDF5 -I/usr/include/libxml2 -I/share/apps/petsc/3.2-p7/include -I/usr/include/mpich2-x86_64 -Wl,-rpath=/share/apps/petsc/3.2-p7/lib temp.cxx -L/share/apps/petsc/3.2-p7/lib -lpetsc -lhdf5 -lxml2


Cheers,
Walter Landry