UFC

Segmentation Fault when loading UFC (on Stallo)

Asked by Torbjørn Bækø Ness

Hi,
I'm trying to compile FEniCS from source in my home directory at the Stallo supercomputer.
I have finally been able to compile FFC, FIAT, Instant, Viper and UFL, although I don't
know if they work yet. However, when I try to compile UFC it seems I run
into trouble. I have downloaded the source to a $HOME/ufc folder.
Then I do this,

tar xzf ufc-2.0.5.tar.gz
cmake -DCMAKE_INSTALL_PREFIX=$HOME/ufc ufc-2.0.5
make
make install

afterwards I add this line to my .bashrc file:
export PYTHONPATH=$PYTHONPATH:$HOME/ufc/lib/python2.7/site-packages/

I log out and in again. If I then try to import ufc in
python I get a segmentation fault (Minnesegmentsfeil)
This also happens if I try to run python ufc.py in the folder.

I don't really even know where to start to fix this problem. Any
suggestions?

Here is the ufc.py file:

# This file was automatically generated by SWIG (http://www.swig.org).
# Version 2.0.5
#
# Do not make changes to this file unless you know what you are doing--modify
# the SWIG interface file instead.

from sys import version_info
if version_info >= (2,6,0):
    def swig_import_helper():
        from os.path import dirname
        import imp
        fp = None
        try:
            fp, pathname, description = imp.find_module('_ufc', [dirname(__file__)])
        except ImportError:
            import _ufc
            return _ufc
        if fp is not None:
            try:
                _mod = imp.load_module('_ufc', fp, pathname, description)
            finally:
                fp.close()
            return _mod
    _ufc = swig_import_helper()
    del swig_import_helper
else:
    import _ufc
del version_info
try:
    _swig_property = property
except NameError:
    pass # Python < 2.2 doesn't have 'property'.
def _swig_setattr_nondynamic(self,class_type,name,value,static=1):
    if (name == "thisown"): return self.this.own(value)
    if (name == "this"):
        if type(value).__name__ == 'SwigPyObject':
            self.__dict__[name] = value
            return
    method = class_type.__swig_setmethods__.get(name,None)
    if method: return method(self,value)
    if (not static):
        self.__dict__[name] = value
    else:
        raise AttributeError("You cannot add attributes to %s" % self)

def _swig_setattr(self,class_type,name,value):
    return _swig_setattr_nondynamic(self,class_type,name,value,0)

def _swig_getattr(self,class_type,name):
    if (name == "thisown"): return self.this.own()
    method = class_type.__swig_getmethods__.get(name,None)
    if method: return method(self)
    raise AttributeError(name)

def _swig_repr(self):
    try: strthis = "proxy of " + self.this.__repr__()
    except: strthis = ""
    return "<%s.%s; %s >" % (self.__class__.__module__, self.__class__.__name__, strthis,)

try:
    _object = object
    _newclass = 1
except AttributeError:
    class _object : pass
    _newclass = 0

SHARED_PTR_DISOWN = _ufc.SHARED_PTR_DISOWN
UFC_VERSION_MAJOR = _ufc.UFC_VERSION_MAJOR
UFC_VERSION_MINOR = _ufc.UFC_VERSION_MINOR
UFC_VERSION_MAINTENANCE = _ufc.UFC_VERSION_MAINTENANCE
interval = _ufc.interval
triangle = _ufc.triangle
quadrilateral = _ufc.quadrilateral
tetrahedron = _ufc.tetrahedron
hexahedron = _ufc.hexahedron
class mesh(_object):
    __swig_setmethods__ = {}
    __setattr__ = lambda self, name, value: _swig_setattr(self, mesh, name, value)
    __swig_getmethods__ = {}
    __getattr__ = lambda self, name: _swig_getattr(self, mesh, name)
    __repr__ = _swig_repr
    def __init__(self):
        this = _ufc.new_mesh()
        try: self.this.append(this)
        except: self.this = this
    __swig_destroy__ = _ufc.delete_mesh
    __del__ = lambda self : None;
    __swig_setmethods__["topological_dimension"] = _ufc.mesh_topological_dimension_set
    __swig_getmethods__["topological_dimension"] = _ufc.mesh_topological_dimension_get
    if _newclass:topological_dimension = _swig_property(_ufc.mesh_topological_dimension_get, _ufc.mesh_topological_dimension_set)
    __swig_setmethods__["geometric_dimension"] = _ufc.mesh_geometric_dimension_set
    __swig_getmethods__["geometric_dimension"] = _ufc.mesh_geometric_dimension_get
    if _newclass:geometric_dimension = _swig_property(_ufc.mesh_geometric_dimension_get, _ufc.mesh_geometric_dimension_set)
    __swig_setmethods__["num_entities"] = _ufc.mesh_num_entities_set
    __swig_getmethods__["num_entities"] = _ufc.mesh_num_entities_get
    if _newclass:num_entities = _swig_property(_ufc.mesh_num_entities_get, _ufc.mesh_num_entities_set)
mesh_swigregister = _ufc.mesh_swigregister
mesh_swigregister(mesh)
cvar = _ufc.cvar
UFC_VERSION = cvar.UFC_VERSION

class cell(_object):
    __swig_setmethods__ = {}
    __setattr__ = lambda self, name, value: _swig_setattr(self, cell, name, value)
    __swig_getmethods__ = {}
    __getattr__ = lambda self, name: _swig_getattr(self, cell, name)
    __repr__ = _swig_repr
    def __init__(self):
        this = _ufc.new_cell()
        try: self.this.append(this)
        except: self.this = this
    __swig_destroy__ = _ufc.delete_cell
    __del__ = lambda self : None;
    __swig_setmethods__["cell_shape"] = _ufc.cell_cell_shape_set
    __swig_getmethods__["cell_shape"] = _ufc.cell_cell_shape_get
    if _newclass:cell_shape = _swig_property(_ufc.cell_cell_shape_get, _ufc.cell_cell_shape_set)
    __swig_setmethods__["topological_dimension"] = _ufc.cell_topological_dimension_set
    __swig_getmethods__["topological_dimension"] = _ufc.cell_topological_dimension_get
    if _newclass:topological_dimension = _swig_property(_ufc.cell_topological_dimension_get, _ufc.cell_topological_dimension_set)
    __swig_setmethods__["geometric_dimension"] = _ufc.cell_geometric_dimension_set
    __swig_getmethods__["geometric_dimension"] = _ufc.cell_geometric_dimension_get
    if _newclass:geometric_dimension = _swig_property(_ufc.cell_geometric_dimension_get, _ufc.cell_geometric_dimension_set)
    __swig_setmethods__["index"] = _ufc.cell_index_set
    __swig_getmethods__["index"] = _ufc.cell_index_get
    if _newclass:index = _swig_property(_ufc.cell_index_get, _ufc.cell_index_set)
    __swig_setmethods__["local_facet"] = _ufc.cell_local_facet_set
    __swig_getmethods__["local_facet"] = _ufc.cell_local_facet_get
    if _newclass:local_facet = _swig_property(_ufc.cell_local_facet_get, _ufc.cell_local_facet_set)
    __swig_setmethods__["mesh_identifier"] = _ufc.cell_mesh_identifier_set
    __swig_getmethods__["mesh_identifier"] = _ufc.cell_mesh_identifier_get
    if _newclass:mesh_identifier = _swig_property(_ufc.cell_mesh_identifier_get, _ufc.cell_mesh_identifier_set)
cell_swigregister = _ufc.cell_swigregister
cell_swigregister(cell)

class function(_object):
    __swig_setmethods__ = {}
    __setattr__ = lambda self, name, value: _swig_setattr(self, function, name, value)
    __swig_getmethods__ = {}
    __getattr__ = lambda self, name: _swig_getattr(self, function, name)
    def __init__(self, *args, **kwargs): raise AttributeError("No constructor defined - class is abstract")
    __repr__ = _swig_repr
    __swig_destroy__ = _ufc.delete_function
    __del__ = lambda self : None;
    def evaluate(self, *args): return _ufc.function_evaluate(self, *args)
function_swigregister = _ufc.function_swigregister
function_swigregister(function)

class finite_element(_object):
    __swig_setmethods__ = {}
    __setattr__ = lambda self, name, value: _swig_setattr(self, finite_element, name, value)
    __swig_getmethods__ = {}
    __getattr__ = lambda self, name: _swig_getattr(self, finite_element, name)
    def __init__(self, *args, **kwargs): raise AttributeError("No constructor defined - class is abstract")
    __repr__ = _swig_repr
    __swig_destroy__ = _ufc.delete_finite_element
    __del__ = lambda self : None;
    def signature(self): return _ufc.finite_element_signature(self)
    def cell_shape(self): return _ufc.finite_element_cell_shape(self)
    def topological_dimension(self): return _ufc.finite_element_topological_dimension(self)
    def geometric_dimension(self): return _ufc.finite_element_geometric_dimension(self)
    def space_dimension(self): return _ufc.finite_element_space_dimension(self)
    def value_rank(self): return _ufc.finite_element_value_rank(self)
    def value_dimension(self, *args): return _ufc.finite_element_value_dimension(self, *args)
    def evaluate_basis(self, *args): return _ufc.finite_element_evaluate_basis(self, *args)
    def evaluate_basis_all(self, *args): return _ufc.finite_element_evaluate_basis_all(self, *args)
    def evaluate_basis_derivatives(self, *args): return _ufc.finite_element_evaluate_basis_derivatives(self, *args)
    def evaluate_basis_derivatives_all(self, *args): return _ufc.finite_element_evaluate_basis_derivatives_all(self, *args)
    def evaluate_dof(self, *args): return _ufc.finite_element_evaluate_dof(self, *args)
    def evaluate_dofs(self, *args): return _ufc.finite_element_evaluate_dofs(self, *args)
    def interpolate_vertex_values(self, *args): return _ufc.finite_element_interpolate_vertex_values(self, *args)
    def map_from_reference_cell(self, *args): return _ufc.finite_element_map_from_reference_cell(self, *args)
    def map_to_reference_cell(self, *args): return _ufc.finite_element_map_to_reference_cell(self, *args)
    def num_sub_elements(self): return _ufc.finite_element_num_sub_elements(self)
    def create_sub_element(self, *args): return _ufc.finite_element_create_sub_element(self, *args)
    def create(self): return _ufc.finite_element_create(self)
finite_element_swigregister = _ufc.finite_element_swigregister
finite_element_swigregister(finite_element)

class dofmap(_object):
    __swig_setmethods__ = {}
    __setattr__ = lambda self, name, value: _swig_setattr(self, dofmap, name, value)
    __swig_getmethods__ = {}
    __getattr__ = lambda self, name: _swig_getattr(self, dofmap, name)
    def __init__(self, *args, **kwargs): raise AttributeError("No constructor defined - class is abstract")
    __repr__ = _swig_repr
    __swig_destroy__ = _ufc.delete_dofmap
    __del__ = lambda self : None;
    def signature(self): return _ufc.dofmap_signature(self)
    def needs_mesh_entities(self, *args): return _ufc.dofmap_needs_mesh_entities(self, *args)
    def init_mesh(self, *args): return _ufc.dofmap_init_mesh(self, *args)
    def init_cell(self, *args): return _ufc.dofmap_init_cell(self, *args)
    def init_cell_finalize(self): return _ufc.dofmap_init_cell_finalize(self)
    def topological_dimension(self): return _ufc.dofmap_topological_dimension(self)
    def geometric_dimension(self): return _ufc.dofmap_geometric_dimension(self)
    def global_dimension(self): return _ufc.dofmap_global_dimension(self)
    def local_dimension(self, *args): return _ufc.dofmap_local_dimension(self, *args)
    def max_local_dimension(self): return _ufc.dofmap_max_local_dimension(self)
    def num_facet_dofs(self): return _ufc.dofmap_num_facet_dofs(self)
    def num_entity_dofs(self, *args): return _ufc.dofmap_num_entity_dofs(self, *args)
    def tabulate_dofs(self, *args): return _ufc.dofmap_tabulate_dofs(self, *args)
    def tabulate_facet_dofs(self, *args): return _ufc.dofmap_tabulate_facet_dofs(self, *args)
    def tabulate_entity_dofs(self, *args): return _ufc.dofmap_tabulate_entity_dofs(self, *args)
    def tabulate_coordinates(self, *args): return _ufc.dofmap_tabulate_coordinates(self, *args)
    def num_sub_dofmaps(self): return _ufc.dofmap_num_sub_dofmaps(self)
    def create_sub_dofmap(self, *args): return _ufc.dofmap_create_sub_dofmap(self, *args)
    def create(self): return _ufc.dofmap_create(self)
dofmap_swigregister = _ufc.dofmap_swigregister
dofmap_swigregister(dofmap)

class cell_integral(_object):
    __swig_setmethods__ = {}
    __setattr__ = lambda self, name, value: _swig_setattr(self, cell_integral, name, value)
    __swig_getmethods__ = {}
    __getattr__ = lambda self, name: _swig_getattr(self, cell_integral, name)
    def __init__(self, *args, **kwargs): raise AttributeError("No constructor defined - class is abstract")
    __repr__ = _swig_repr
    __swig_destroy__ = _ufc.delete_cell_integral
    __del__ = lambda self : None;
    def tabulate_tensor(self, *args): return _ufc.cell_integral_tabulate_tensor(self, *args)
cell_integral_swigregister = _ufc.cell_integral_swigregister
cell_integral_swigregister(cell_integral)

class exterior_facet_integral(_object):
    __swig_setmethods__ = {}
    __setattr__ = lambda self, name, value: _swig_setattr(self, exterior_facet_integral, name, value)
    __swig_getmethods__ = {}
    __getattr__ = lambda self, name: _swig_getattr(self, exterior_facet_integral, name)
    def __init__(self, *args, **kwargs): raise AttributeError("No constructor defined - class is abstract")
    __repr__ = _swig_repr
    __swig_destroy__ = _ufc.delete_exterior_facet_integral
    __del__ = lambda self : None;
    def tabulate_tensor(self, *args): return _ufc.exterior_facet_integral_tabulate_tensor(self, *args)
exterior_facet_integral_swigregister = _ufc.exterior_facet_integral_swigregister
exterior_facet_integral_swigregister(exterior_facet_integral)

class interior_facet_integral(_object):
    __swig_setmethods__ = {}
    __setattr__ = lambda self, name, value: _swig_setattr(self, interior_facet_integral, name, value)
    __swig_getmethods__ = {}
    __getattr__ = lambda self, name: _swig_getattr(self, interior_facet_integral, name)
    def __init__(self, *args, **kwargs): raise AttributeError("No constructor defined - class is abstract")
    __repr__ = _swig_repr
    __swig_destroy__ = _ufc.delete_interior_facet_integral
    __del__ = lambda self : None;
    def tabulate_tensor(self, *args): return _ufc.interior_facet_integral_tabulate_tensor(self, *args)
interior_facet_integral_swigregister = _ufc.interior_facet_integral_swigregister
interior_facet_integral_swigregister(interior_facet_integral)

class form(_object):
    __swig_setmethods__ = {}
    __setattr__ = lambda self, name, value: _swig_setattr(self, form, name, value)
    __swig_getmethods__ = {}
    __getattr__ = lambda self, name: _swig_getattr(self, form, name)
    def __init__(self, *args, **kwargs): raise AttributeError("No constructor defined - class is abstract")
    __repr__ = _swig_repr
    __swig_destroy__ = _ufc.delete_form
    __del__ = lambda self : None;
    def signature(self): return _ufc.form_signature(self)
    def rank(self): return _ufc.form_rank(self)
    def num_coefficients(self): return _ufc.form_num_coefficients(self)
    def num_cell_domains(self): return _ufc.form_num_cell_domains(self)
    def num_exterior_facet_domains(self): return _ufc.form_num_exterior_facet_domains(self)
    def num_interior_facet_domains(self): return _ufc.form_num_interior_facet_domains(self)
    def create_finite_element(self, *args): return _ufc.form_create_finite_element(self, *args)
    def create_dofmap(self, *args): return _ufc.form_create_dofmap(self, *args)
    def create_cell_integral(self, *args): return _ufc.form_create_cell_integral(self, *args)
    def create_exterior_facet_integral(self, *args): return _ufc.form_create_exterior_facet_integral(self, *args)
    def create_interior_facet_integral(self, *args): return _ufc.form_create_interior_facet_integral(self, *args)
form_swigregister = _ufc.form_swigregister
form_swigregister(form)

def ufc_swigversion():
  return _ufc.ufc_swigversion()
ufc_swigversion = _ufc.ufc_swigversion
__version__ = UFC_VERSION
del UFC_VERSION, UFC_VERSION_MAJOR, UFC_VERSION_MINOR

"""Code for adding swig version to ufc extension module."""
tmp = hex(ufc_swigversion())
__swigversion__ = "%d.%d.%d"%(tuple(map(int, [tmp[-5], tmp[-3], tmp[-2:]])))

del tmp, ufc_swigversion

# This file is compatible with both classic and new-style classes.

Question information

Language:
English Edit question
Status:
Solved
For:
UFC Edit question
Assignee:
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Solved by:
Johannes Ring
Solved:
Last query:
Last reply:
Revision history for this message
Johannes Ring (johannr) said : 		#1

Have you tried to use Dorsal to build FEniCS? If not, I would recommend to try that first.

Revision history for this message
Torbjørn Bækø Ness (torbjorn-ness) said : 		#2

I tried that now, but since I do not have root access, I don't get far when running the
dorsal.sh script.
Any way to do the 'yum' installing without root?

Found configuration for project FEniCS.
Building FEniCS using FEniCS/platforms/contributed/rhel5.platform.
Warning: Platform is not officially supported but may still work!
-------------------------------------------------------------------------------
 Red Hat Enterprise Linux 5

 This build script assumes that you have the following packages
 already installed via Red Hat's yum:

 yum install -y libtool libxml2 libxml2-devel pkgconfig lapack-devel \
 blas-devel gcc gcc-c++ gcc-gfortran subversion zlib-devel openssl-devel \
 glib2-devel bzip2-devel libXt-devel libX11-devel

 Before compiling VTK, you need to manually configure it using an
 interface its build system provides. Here are some of the relevant
 options:

 BUILD_SHARED_LIBS ON
 CMAKE_INSTALL_PREFIX ${INSTALL_PATH}
 VTK_DATA_ROOT ${DOWNLOAD_PATH}/VTKData
 VTK_WRAP_PYTHON ON
 VTK_USE_TK OFF

 Once you've set up VTK, you need to manually set the following
 environment variable in order for Viper to find it:

 export LD_LIBRARY_PATH=${INSTALL_PATH}/lib/vtk-5.4:${LD_LIBRARY_PATH}

 Also, if you're having difficulty building SuiteSparse, you may need
 to run (as root):

 ln -s /usr/lib64/libg2c.so.0.0.0 /usr/lib/libg2c.so

Downloading files to: ~/fenics/FEniCS/src
Installing projects in: ~/fenics/FEniCS

Building stable point-releases of FEniCS projects.
-------------------------------------------------------------------------------
Please make sure you've read the instructions above and your system
is ready for installing FEniCS. We find it easiest to copy and paste
these instructions in another terminal window.

Once ready, hit enter to continue!

Revision history for this message
Johannes Ring (johannr) said : 		#3

Yes, you can make your own platform file with the packages you need and let Dorsal build them for you.

Download the development version of Dorsal (bzr branch lp:dorsal) and look at the platform files in the FEniCS/platforms folder. Pick the one that best matches your needs, modify it and save it as (for instance) stallo.platform. Then run

  ./dorsal.sh stallo.platform

Revision history for this message
Harish Narayanan (hnarayanan) said : 		#4

Look in particular at dorsal/ FEniCS/platforms/contributed/openmpi_rootless.platform and see if that is helpful for you.

Revision history for this message
Torbjørn Bækø Ness (torbjorn-ness) said : 		#5

Hi,

Thank you for your help, but I'm not done yet. I tried to remove everything again and install with dorsal using the development branch, and this stallo.platform file:

torbness@stallo-2:~/dorsal$ more stallo.platform
# Written by Lizao Li <email address hidden>
# Tested FEniCS on the Itasca cluster (https://www.msi.umn.edu/hardware/itasca/)
# No root privilige is required
# Changelog
# Version 1.0 - Sep 30, 2011. First smooth build

# Platform specific variables
default PETSC_ARCH=linux-gnu-cxx-opt
default SCOTCH_ARCH=pc_linux2

# Define the packages this platform needs
PACKAGES=(
#sqlite
libxml2
#ipython
#cmake
#boost
#pcre
#swig
#blas
#lapack
suitesparsewithmetis_OpenMPI
#parmetis
trilinos
#petsc
slepc
armadillo
cgal
gmp
mpfr
mtl
scientificpython
fiat
ufc
ufl
ffc
instant
vtk
viper
dolfin
)

 I commented out all the dependencies I think I have preinstalled on stallo, and run the dorsal script. After quite some time I got this error message:

/home/torbness/Work/FEniCS/src/trilinos-10.8.5-Source/packages/nox/src-thyra/NOX_Thyra_Group.C(297): warning #1478: function "Thyra::apply(const Thyra::LinearOpBase<Scalar> &, Thyra::EOpTransp, const Thyra::MultiVectorBase<Scalar> &, Thyra::MultiVectorBase<Scalar> *, Scalar, Scalar) [with Scalar=double]" (declared at line 588 of "/home/torbness/Work/FEniCS/src/trilinos-10.8.5-Source/packages/thyra/core/src/interfaces/operator_vector/fundamental/Thyra_LinearOpBase_decl.hpp") was declared
          "deprecated"
    ::Thyra::apply(*shared_jacobian_->getObject(), ::Thyra::NOTRANS,
             ^

/home/torbness/Work/FEniCS/src/trilinos-10.8.5-Source/packages/nox/src-thyra/NOX_Thyra_Group.C(319): warning #1478: function "Thyra::apply(const Thyra::LinearOpBase<Scalar> &, Thyra::EOpTransp, const Thyra::MultiVectorBase<Scalar> &, Thyra::MultiVectorBase<Scalar> *, Scalar, Scalar) [with Scalar=double]" (declared at line 588 of "/home/torbness/Work/FEniCS/src/trilinos-10.8.5-Source/packages/thyra/core/src/interfaces/operator_vector/fundamental/Thyra_LinearOpBase_decl.hpp") was declared
          "deprecated"
    ::Thyra::apply(*shared_jacobian_->getObject(),
             ^

/home/torbness/Work/FEniCS/src/trilinos-10.8.5-Source/packages/nox/src-thyra/NOX_Thyra_Group.C(347): warning #1478: function "Thyra::apply(const Thyra::LinearOpBase<Scalar> &, Thyra::EOpTransp, const Thyra::MultiVectorBase<Scalar> &, Thyra::MultiVectorBase<Scalar> *, Scalar, Scalar) [with Scalar=double]" (declared at line 588 of "/home/torbness/Work/FEniCS/src/trilinos-10.8.5-Source/packages/thyra/core/src/interfaces/operator_vector/fundamental/Thyra_LinearOpBase_decl.hpp") was declared
          "deprecated"
      ::Thyra::apply(*shared_jacobian_->getObject(), ::Thyra::TRANS,
               ^

/home/torbness/Work/FEniCS/src/trilinos-10.8.5-Source/packages/nox/src-thyra/NOX_Thyra_Group.C(373): warning #1478: function "Thyra::apply(const Thyra::LinearOpBase<Scalar> &, Thyra::EOpTransp, const Thyra::MultiVectorBase<Scalar> &, Thyra::MultiVectorBase<Scalar> *, Scalar, Scalar) [with Scalar=double]" (declared at line 588 of "/home/torbness/Work/FEniCS/src/trilinos-10.8.5-Source/packages/thyra/core/src/interfaces/operator_vector/fundamental/Thyra_LinearOpBase_decl.hpp") was declared
          "deprecated"
    ::Thyra::apply(*shared_jacobian_->getObject(),
             ^

/home/torbness/Work/FEniCS/src/trilinos-10.8.5-Source/packages/nox/src-thyra/NOX_Thyra_Group.C(514): warning #1478: function "Thyra::solve(const Thyra::LinearOpWithSolveBase<Scalar> &, Thyra::EOpTransp, const Thyra::MultiVectorBase<Scalar> &, Thyra::MultiVectorBase<Scalar> *, const Thyra::SolveCriteria<Scalar> *) [with Scalar=double]" (declared at line 655 of
          "/home/torbness/Work/FEniCS/src/trilinos-10.8.5-Source/packages/thyra/core/src/interfaces/operator_solve/fundamental/Thyra_LinearOpWithSolveBase_decl.hpp") was declared "deprecated"
      ::Thyra::solve(*shared_jacobian_->getObject(),
               ^

[ 83%] Building CXX object packages/nox/src-thyra/CMakeFiles/noxthyra.dir/Thyra_NonlinearSolver_NOX.cpp.o
/home/torbness/Work/FEniCS/src/trilinos-10.8.5-Source/packages/nox/src-thyra/Thyra_NonlinearSolver_NOX.cpp(133): warning #1478: function "Thyra::V_StVpStV(Thyra::VectorBase<Scalar> *, const Scalar &, const Thyra::VectorBase<Scalar> &, const Scalar &, const Thyra::VectorBase<Scalar> &) [with Scalar=double]" (declared at line 815 of "/home/torbness/Work/FEniCS/src/trilinos-10.8.5-Source/packages/thyra/core/src/support/operator_vector/client_support/Thyra_VectorStdOps_decl.hpp") was declared
          "deprecated"
      ::Thyra::V_StVpStV<double>(delta,1.0,new_x,-1.0,*x);
               ^

/home/torbness/Work/FEniCS/src/trilinos-10.8.5-Source/packages/nox/src-thyra/Thyra_NonlinearSolver_NOX.cpp(136): warning #1478: function "Thyra::assign(Thyra::VectorBase<Scalar> *, const Thyra::VectorBase<Scalar> &) [with Scalar=double]" (declared at line 730 of "/home/torbness/Work/FEniCS/src/trilinos-10.8.5-Source/packages/thyra/core/src/support/operator_vector/client_support/Thyra_VectorStdOps_decl.hpp") was declared "deprecated"
    ::Thyra::assign(x, new_x);
             ^

Linking CXX shared library libnoxthyra.so
make[2]: Leaving directory `/home/torbness/Work/FEniCS/src/trilinos-10.8.5-Source/dorsal_build_dir'
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Scanning dependencies of target locathyra
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/home/torbness/Work/FEniCS/src/trilinos-10.8.5-Source/packages/nox/src-loca/src-thyra/LOCA_Thyra_Group.C(70): warning #1478: function "RTOpPack::SubVectorView<Scalar>::SubVectorView(RTOpPack::Ordinal={Teuchos_Ordinal={ptrdiff_t={long}}}, RTOpPack::Ordinal={Teuchos_Ordinal={ptrdiff_t={long}}}, Scalar *, ptrdiff_t={long}) [with Scalar=double]" (declared at line 302 of "/home/torbness/Work/FEniCS/src/trilinos-10.8.5-Source/packages/rtop/src/interfaces/RTOpPack_Types.hpp") was declared "deprecated"
    RTOpPack::SubVectorView<double> pv(0,params.length(),
                                       ^

/home/torbness/Work/FEniCS/src/trilinos-10.8.5-Source/packages/nox/src-loca/src-thyra/LOCA_Thyra_Group.C(80): warning #1478: function "Thyra::put_scalar(const Scalar &, Thyra::VectorBase<Scalar> *) [with Scalar=double]" (declared at line 605 of "/home/torbness/Work/FEniCS/src/trilinos-10.8.5-Source/packages/thyra/core/src/support/operator_vector/client_support/Thyra_VectorStdOps_decl.hpp") was declared "deprecated"
    ::Thyra::put_scalar(0.0, x_dot_vec.get());
             ^

/home/torbness/Work/FEniCS/src/trilinos-10.8.5-Source/packages/nox/src-loca/src-thyra/LOCA_Thyra_Group.C(95): warning #1478: function "RTOpPack::SubVectorView<Scalar>::SubVectorView(RTOpPack::Ordinal={Teuchos_Ordinal={ptrdiff_t={long}}}, RTOpPack::Ordinal={Teuchos_Ordinal={ptrdiff_t={long}}}, Scalar *, ptrdiff_t={long}) [with Scalar=double]" (declared at line 302 of "/home/torbness/Work/FEniCS/src/trilinos-10.8.5-Source/packages/rtop/src/interfaces/RTOpPack_Types.hpp") was declared "deprecated"
    RTOpPack::SubVectorView<double> pv(0,params.length(),
                                       ^

/home/torbness/Work/FEniCS/src/trilinos-10.8.5-Source/packages/nox/src-loca/src-thyra/LOCA_Thyra_Group.C(105): warning #1478: function "Thyra::put_scalar(const Scalar &, Thyra::VectorBase<Scalar> *) [with Scalar=double]" (declared at line 605 of "/home/torbness/Work/FEniCS/src/trilinos-10.8.5-Source/packages/thyra/core/src/support/operator_vector/client_support/Thyra_VectorStdOps_decl.hpp") was declared "deprecated"
    ::Thyra::put_scalar(0.0, x_dot_vec.get());
             ^

/home/torbness/Work/FEniCS/src/trilinos-10.8.5-Source/packages/thyra/core/src/interfaces/operator_solve/fundamental/Thyra_LinearOpWithSolveBase_decl.hpp(542): warning #1478: class "Thyra::BlockSolveCriteria<double>" (declared at line 385 of "/home/torbness/Work/FEniCS/src/trilinos-10.8.5-Source/packages/thyra/core/src/interfaces/operator_solve/fundamental/Thyra_SolveSupportTypes.hpp") was declared "deprecated"
    convertBlockSolveCriteriaToSolveCritiera(
    ^
          detected during instantiation of class "Thyra::LinearOpWithSolveBase<Scalar> [with Scalar=double]" at line 414 of "/home/torbness/Work/FEniCS/src/trilinos-10.8.5-Source/packages/nox/src-loca/src-thyra/LOCA_Thyra_Group.C"

/home/torbness/Work/FEniCS/src/trilinos-10.8.5-Source/packages/nox/src-loca/src-thyra/LOCA_Thyra_Group.C(413): warning #1478: function "Thyra::apply(const Thyra::LinearOpBase<Scalar> &, Thyra::EOpTransp, const Thyra::MultiVectorBase<Scalar> &, Thyra::MultiVectorBase<Scalar> *, Scalar, Scalar) [with Scalar=double]" (declared at line 588 of "/home/torbness/Work/FEniCS/src/trilinos-10.8.5-Source/packages/thyra/core/src/interfaces/operator_vector/fundamental/Thyra_LinearOpBase_decl.hpp") was
          declared "deprecated"
    ::Thyra::apply(*shared_jacobian_->getObject(), ::Thyra::NOTRANS,
             ^

/home/torbness/Work/FEniCS/src/trilinos-10.8.5-Source/packages/nox/src-loca/src-thyra/LOCA_Thyra_Group.C(429): warning #1478: function "Thyra::apply(const Thyra::LinearOpBase<Scalar> &, Thyra::EOpTransp, const Thyra::MultiVectorBase<Scalar> &, Thyra::MultiVectorBase<Scalar> *, Scalar, Scalar) [with Scalar=double]" (declared at line 588 of "/home/torbness/Work/FEniCS/src/trilinos-10.8.5-Source/packages/thyra/core/src/interfaces/operator_vector/fundamental/Thyra_LinearOpBase_decl.hpp") was
          declared "deprecated"
    ::Thyra::apply(*shared_jacobian_->getObject(),
             ^

Linking CXX shared library liblocathyra.so
make[2]: Leaving directory `/home/torbness/Work/FEniCS/src/trilinos-10.8.5-Source/dorsal_build_dir'
[ 94%] Built target locathyra
make[2]: Entering directory `/home/torbness/Work/FEniCS/src/trilinos-10.8.5-Source/dorsal_build_dir'
[ 94%] Generating swigpyrun.h
Scanning dependencies of target pytrilinos
make[2]: Leaving directory `/home/torbness/Work/FEniCS/src/trilinos-10.8.5-Source/dorsal_build_dir'
make[2]: Entering directory `/home/torbness/Work/FEniCS/src/trilinos-10.8.5-Source/dorsal_build_dir'
[ 94%] Building CXX object packages/PyTrilinos/src/CMakeFiles/pytrilinos.dir/PyTrilinos_NumPyImporter.cpp.o
[ 95%] Building CXX object packages/PyTrilinos/src/CMakeFiles/pytrilinos.dir/PyTrilinos_PythonException.cpp.o
[ 95%] Building CXX object packages/PyTrilinos/src/CMakeFiles/pytrilinos.dir/PyTrilinos_Util.cpp.o
[ 95%] Building CXX object packages/PyTrilinos/src/CMakeFiles/pytrilinos.dir/PyTrilinos_FILEstream.cpp.o
[ 95%] Building CXX object packages/PyTrilinos/src/CMakeFiles/pytrilinos.dir/PyTrilinos_Teuchos_Util.cpp.o
[ 95%] Building CXX object packages/PyTrilinos/src/CMakeFiles/pytrilinos.dir/Epetra_NumPyFEVector.cpp.o
[ 95%] Building CXX object packages/PyTrilinos/src/CMakeFiles/pytrilinos.dir/Epetra_NumPyIntSerialDenseMatrix.cpp.o
[ 95%] Building CXX object packages/PyTrilinos/src/CMakeFiles/pytrilinos.dir/Epetra_NumPyIntSerialDenseVector.cpp.o
[ 95%] Building CXX object packages/PyTrilinos/src/CMakeFiles/pytrilinos.dir/Epetra_NumPyIntVector.cpp.o
[ 95%] Building CXX object packages/PyTrilinos/src/CMakeFiles/pytrilinos.dir/Epetra_NumPyMultiVector.cpp.o
[ 95%] Building CXX object packages/PyTrilinos/src/CMakeFiles/pytrilinos.dir/Epetra_NumPySerialDenseMatrix.cpp.o
[ 95%] Building CXX object packages/PyTrilinos/src/CMakeFiles/pytrilinos.dir/Epetra_NumPySerialSymDenseMatrix.cpp.o
[ 96%] Building CXX object packages/PyTrilinos/src/CMakeFiles/pytrilinos.dir/Epetra_NumPySerialDenseVector.cpp.o
[ 96%] Building CXX object packages/PyTrilinos/src/CMakeFiles/pytrilinos.dir/Epetra_NumPyVector.cpp.o
[ 96%] Building CXX object packages/PyTrilinos/src/CMakeFiles/pytrilinos.dir/PyTrilinos_Epetra_Util.cpp.o
[ 96%] Building CXX object packages/PyTrilinos/src/CMakeFiles/pytrilinos.dir/PyTrilinos_EpetraExt_Util.cpp.o
Linking CXX shared library libpytrilinos.so
ld: rc/trilinos-10.8.5-Source/dorsal_build_dir/packages/rtop/src:: No such file: No such file or directory
make[2]: *** [packages/PyTrilinos/src/libpytrilinos.so] Error 1
make[2]: Leaving directory `/home/torbness/Work/FEniCS/src/trilinos-10.8.5-Source/dorsal_build_dir'
make[1]: *** [packages/PyTrilinos/src/CMakeFiles/pytrilinos.dir/all] Error 2
make[1]: Leaving directory `/home/torbness/Work/FEniCS/src/trilinos-10.8.5-Source/dorsal_build_dir'
make: *** [all] Error 2
make: Leaving directory `/home/torbness/Work/FEniCS/src/trilinos-10.8.5-Source/dorsal_build_dir'
Failure with exit status: 2
Exit message: There was a problem building trilinos-10.8.5-Source.

Any idea what I can do to solve this?
Do you know if anybody is using FEniCS on stallo?

Revision history for this message
Johannes Ring (johannr) said : 		#6

I'm not sure what's wrong but if you don't need Trilinos, then just disable it. If you do need it, then we will have to do some digging.

Also, if you are going to build SLEPc, you should most likely also build PETSc.

Revision history for this message
Torbjørn Bækø Ness (torbjorn-ness) said : 		#7

Okey, so this time the instalation finished at least. During the installation I got this message:

-- ParMETIS could not be found/configured. (missing: PARMETIS_TEST_RUNS PARMETIS_INCLUDE_DIRS)
-- Checking for package 'SCOTCH-PT'
-- SCOTCH could not be found. Be sure to set SCOTCH_DIR. (missing: SCOTCH_LIBRARIES SCOTCH_INCLUDE_DIRS SCOTCH_TEST_RUNS)

...

-- ParMETIS could not be found/configured. (missing: PARMETIS_TEST_RUNS PARMETIS_INCLUDE_DIRS)
-- Performing Test CHOLMOD_TEST_RUNS
-- Performing Test CHOLMOD_TEST_RUNS - Failed
-- CHOLMOD could not be found. Be sure to set CHOLMOD_DIR. (missing: CHOLMOD_TEST_RUNS)

-- ParMETIS could not be found/configured. (missing: PARMETIS_TEST_RUNS PARMETIS_INCLUDE_DIRS)
-- CHOLMOD could not be found. Be sure to set CHOLMOD_DIR. (missing: CHOLMOD_TEST_RUNS)
-- Checking for Trilinos
-- Trilinos could not be found

-- Checking for package 'PETSc'
-- PETSC_DIR is /global/apps/petsc/petsc-3.1-p2
-- PETSC_ARCH is linux-gnu-c-debug
-- Found petscconf.h
-- Performing Test PETSC_TEST_RUNS
-- Performing Test PETSC_TEST_RUNS - Failed
-- PETSc test failed
-- PETSc could not be found. Be sure to set PETSC_DIR and PETSC_ARCH. (missing: PETSC_TEST_RUNS)
-- Checking for package 'CGAL'
-- Performing Test CGAL_TEST_RUNS
-- Performing Test CGAL_TEST_RUNS - Failed
-- CGAL could not be found. Be sure to set CGAL_DIR (missing: CGAL_TEST_RUNS)
-- Found ZLIB: /usr/lib64/libz.so (found version "1.2.3")
-- Checking for package 'CPPUNIT'
-- CPPUNIT could not be found. Be sure to set CPPUNIT_DIR. (missing: CPPUNIT_LIBRARIES CPPUNIT_INCLUDE_DIRS)
-- Checking for package 'Sphinx'
-- Could NOT find Sphinx (missing: SPHINX_EXECUTABLE SPHINX_VERSION_OK) (Required is at least version "1.0.7")
--
-- The following optional packages were found:
-- -------------------------------------------
-- (OK) OPENMP
-- (OK) MPI
-- (OK) MTL4
-- (OK) UMFPACK
-- (OK) ZLIB
-- (OK) PYTHON
--
-- The following optional packages could not be found:
-- ---------------------------------------------------
-- (**) PETSC
-- (**) SLEPC
-- (**) TRILINOS
-- (**) CHOLMOD
-- (**) SCOTCH
-- (**) PARMETIS
-- (**) CGAL
-- (**) SPHINX
--
CMake Warning at dolfin/CMakeLists.txt:222 (message):
  Unable to import UFC. Install latest UFC or check that PYTHONPATH is set
  appropriately. Python will be disabled.

CMake Warning at CMakeLists.txt:584 (message):
  Disabling generation of documentation because Sphinx is missing.

-- Configuring done
-- Generating done
CMake Warning:
  Manually-specified variables were not used by the project:

    CGAL_DISABLE_ROUNDING_MATH_CHECK

-- Build files have been written to: /home/torbness/Work/FEniCS/src/dolfin-1.0.0/dorsal_build_dir
make: Entering directory `/home/torbness/Work/FEniCS/src/dolfin-1.0.0/dorsal_build_dir'
make[1]: Entering directory `/home/torbness/Work/FEniCS/src/dolfin-1.0.0/dorsal_build_dir'
make[2]: Entering directory `/home/torbness/Work/FEniCS/src/dolfin-1.0.0/dorsal_build_dir'

---
A while later the instalation ends with :

DOLFIN has now been installed in

    /home/torbness/Work/FEniCS

and the demo programs have been installed in

    /home/torbness/Work/FEniCS/share/dolfin/demo

Before rushing off to try the demos, don't forget to update your
environment variables. This can be done easily using the helper file
'dolfin.conf' which sets the appropriate variables (for users of the
Bash shell).

To update your environment variables, run the following command:

    source /home/torbness/Work/FEniCS/share/dolfin/dolfin.conf

For future reference, we recommend that you add this command to your
configuration (.bashrc, .profile or similar).
----------------------------------------------------------------------------
make: Leaving directory `/home/torbness/Work/FEniCS/src/dolfin-1.0.0/dorsal_build_dir'
Build finished.

After running the source command, I try to import dolfin and get

/home/torbness/Work/FEniCS/lib/python2.6/site-packages/dolfin/cppimports.py in <module>()
      2
      3 #--- Imports the SWIG-generated Python code (C++ interface) ---

----> 4 import dolfin.cpp as cpp
      5 __swigversion__ = cpp.__swigversion__
      6 __version__ = cpp.__dolfinversion__

ImportError: No module named cpp

If i try to import UFC I am back to the segmentation fault it all started with...
Btw, the installation seems to prefer python2.6, i.e. it installs to Work/FEniCS/lib/python2.6/site-packages/
while I am acctually using python 2.7. It doesn't appear to help to use oython 2.6 though.

Any further suggestions?

Revision history for this message
Torbjørn Bækø Ness (torbjorn-ness) said : 		#8

I guess at least part of this problem is the interactions between preinstalled software on Stallo and the dependencies of FEniCS. Through the command 'module avail', I can list all available modules on Stallo, and get

torbness@stallo-1:~$ module avail

------------------------------------------------------------- /opt/modules/Modules/versions --------------------------------------------------------------
3.2.6 3.2.8

--------------------------------------------------------- /opt/modules/Modules/3.2.8/modulefiles ---------------------------------------------------------
dot module-cvs module-info modules null use.own

---------------------------------------------------------------- /global/apps/modulefiles ----------------------------------------------------------------
ANTS/1.9.1 dalton/LSDALTON2011 hdf5/1.8.2(default) openmpi/1.2.8
CaGe/1.0 dalton/int64 hdf5/1.8.5-p1 openmpi/1.3.2
Coin3D/3.0.0 dalton/latest hdf5/1.8.8 openmpi/1.3.2_nodso
Landmark/LSM5000.0.3.1 dalton/latest-large-molecules hdf5/1.8.8_mpi openmpi/1.3.3
ProMax/5000.0.3.0(default) dalton/ls2011 hmmer/hmmer-2.3.2(default) openmpi/1.3.3_10.1
ProMax/5000.8.0.0 dalton/r11034 hmmer/hmmer-3.0 openmpi/1.3.3_gfortran
R/2.10.0 dalton/r11034-large-molecules hmmer/hmmer-3.0rc2 openmpi/1.3.3_gfortran44
R/2.11.1 dalton/r11144 hpctoolkit/1520 openmpi/1.4(default)
R/2.12.1 dalton/r11144-large-molecules hpn-ssh/5.1p1-hpn13v5 openmpi/1.4.4
R/2.13.1(default) dalton/r9029-large-molecules idl/6.4 openmpi/1.4.4_gnu
R/2.13.1_gcc diesel/1.16.1 idl/8.0 openmpi/1.5.4
R/2.8.1 dirac/10(default) intel-compiler/11.0 orca/2.6.35
R/2.9.1 dirac/latest intel-compiler/11.1(default) paraview/3.10.1(default)
R/2.9.2 dragon/6.0.18(default) intel-compiler/11.1.072 paraview/3.14.0
adf/2007.01 eigen/2.0.15 intel-compiler/11.1_ia32 parmetis/3.1.1
adf/2008.01 eigen/3.0.0 intel-compiler/12.1.0 petsc/petsc-3.1-p2
adf/2009.01 eigen/3.0.3(default) intel-compiler/12.1.2 phylip/3.68
adf/2009.01.snapshots elph/1.0.1 intel-mkl/10.1.0.015 psi/psi3
adf/2010.01(default) espresso/4.3 intel-mkl/10.2.0.013(default) python/2.5.1
adf/2010.01.snapshots espresso/4.3.2 intel-mkl/10.3.6 python/2.6.2(default)
adf/2010.02b fasta/35.4.7 intel-mkl/10.3.8 python/2.6.2_intel
adf/2010.snapshot fasta/36.3.4 intel-mpi/4.0.2.003(default) python/2.6.2_local
adf/2012.01 fftw/2.1.5 intel-tools/XE2011(default) python/2.7.1
adf/2012.01a fftw/3.1.2(default) ipm/0.982 python/2.7.2
adf/2012.fix fftw/3.2.2 itk/3.8.0 qt/4.4.3
adf/Development.snapshots freesurfer/4.0.4 java/1.6.0_10 sac/101.3b
adf/Development.trunk freesurfer/4.2.0(default) libtool/2.2.6a(default) sas/9.2
alglib/3.0 freesurfer/5.1.0 lsm/1.0.beta1 scalapack/1.8.0
amber/10(default) fsl/4.0.2 matlab/2007b schroedinger/2010-10-19_mxd
amber/11 fsl/4.0.4_64 matlab/R2009a schroedinger/2010_06_15_mx
amber/9.0.35 fsl/4.1.2(default) matlab/R2010b(default) schroedinger/2011.04.19(default)
ansys/13.0 fsl/4.1.4 mga/1.0 schroedinger/2011.09.23
antlr/2.7.7 fsl/4.1.6 mkl/10.1.0.015 schroedinger/2012.04.05
ase/3.4.1(default) fsl/4.1.8 mkl/10.2.0.013(default) scons/2.1.0
ase/3.4.1_py2.5 fsl/4.1.9 mkl/10.3.6 stata/10
atlas/3.8.2 fvcom/2.7.1 mkl/10.3.8 structure/2.3.1
bioscope/1.2.1-5 g03/e01 mmtsb/1.0 svn/1.6.17
blacs/1.1.0 g09/b01 molcas/7.4 system-manual/1.0
blast/blast-2.2.18(default) gaussian/03.e01 molden/4.6 tinker/5.1
blast/blast-2.2.19 gaussian/09.b01(default) molden/4.8(default) totalview/8.3.0-1
boost/1.42.0(default) gaussian/09.c01 molden/4.9 totalview/8.6.0-2
boost/1.46.1 gcc/4.6.20120210 mpiblast/1.5.0-pio totalview/8.6.1-1(default)
boost/1.47.0-intel geodict/2010R1 mpiexec/0.82(default) trackvis/0.5.1
camino/1010(default) gfs/080130 mpiexec/0.83 turbomole/5.10_parallel
camino/2.880 ggobi/2.1.8 mumps/4.9.2 turbomole/5.10_serial
cfour/rc1.0 gimic/2.0.1 mvapich2/1.2p1 turbomole/6.0.2_parallel
cfour/rc1.0_mpi(default) git/1.7.1 namd/2.6(default) turbomole/6.0.2_serial
chapel/1.2.0 glimmer/3.02 namd/2.6-TCP turbomole/6.2_huge_parallel
clustalw/2.0.10 gmt/4.5.6 namd/2.7b1 turbomole/6.2_huge_serial
clustalw-mpi/0.13 gold/2.1.5.0 nco/4.0.5 turbomole/6.2_parallel
cmake/2.6.2 google-perftools/1.6.0 netcdf/3.6.2 turbomole/6.3_felles
cmake/2.8.2 google-test/1.5.0(default) netcdf/4.1.1(default) turbomole/6.3_parallel
cmake/2.8.6(default) google-test/1.5.0_gcc netcdf/4.1.3 turbomole/6.3_serial
comsol/3.4 gotoblas/1.22 netlib/1.8.0 umcp/11
comsol/3.5 gpaw/0.7.2(default) nwchem/6.0 valgrind/3.5.0
comsol/4.1 gromacs/3.3.3 nwchem/6.1 valgrind/3.6.0(default)
comsol/4.2 gromacs/4.0.5 nwchem/6.1_ib(default) vasp/4.6.34(default)
comsol/4.2a(default) gromacs/4.5.5 octopus/3.2.0(default) vasp/5.2
cp2k/2.0 gsl/1.12 openbabel/2.2.0 visit/2.4.2
cplex/121 gsl/1.14(default) openfoam/1.6 vmd/vmd-1.8.7(default)
cuda/4.1.28(default) gtest/1.5.0(default) openfoam/1.6.091030 vtk/5.8.0
dacapo/07022011svn(default) gtest/1.5.0_gcc openfoam/1.6.100222 vtune/xe_2011.1
dalton/2.0 gts/0.7.6 openfoam/1.7.1 xmakemol/5.16
dalton/2011 gts/071220(default) openfoam/2.1.0(default)
dalton/DALTON2011(default) hdf5/1.6.9 openmpi/1.2.4
torbness@stallo-1:~$

If I write 'module list' I get the already loaded modules. My deafult is
torbness@stallo-1:~$ module list
Currently Loaded Modulefiles:
  1) intel-compiler/11.1 2) openmpi/1.4 3) system-manual/1.0 4) gold/2.1.5.0 5) python/2.7.2
torbness@stallo-1:~$

Revision history for this message
Johannes Ring (johannr) said : 		#9

OK, that explains the error. UFC is probably not built with the correct Python.

Are you using the Intel compilers? In that case you might want to look at the intel_mkl_rootless.platform in Dorsal. I haven't tried this platform file myself, however, I recently did an attempt at building FEniCS with the Intel compilers on a cluster with a similar setup, but I gave up after lots of struggling and loaded the GCC modules instead. Your mileage my vary, but if you decide to go for GCC I suggest you do something like this:

1. Unload the "intel-compiler", the "openmpi", and the "python" modules.
2. Load the "gcc/4.6.20120210" and the "openmpi/1.4.4_gnu" modules.
3. Run Dorsal with the openmpi_rootless.platform but add "python" before "ipython" in the list of packages to be built.

You should clean up the previous Dorsal installation before attempting this.

Revision history for this message
Torbjørn Bækø Ness (torbjorn-ness) said : 		#10

I didn't load or unload any compilers so I guess I used the intel-compiler then?

I now tried this: I removed the Work directory, logged out and in again, and then

torbness@stallo-1:~$ module unload python openmpi intel-compiler
torbness@stallo-1:~$ module load gcc/4.6.20120210 openmpi/1.4.4_gnu
torbness@stallo-1:~$ module list
Currently Loaded Modulefiles:
  1) system-manual/1.0 2) gold/2.1.5.0 3) gcc/4.6.20120210 4) openmpi/1.4.4_gnu
torbness@stallo-1:~$ cd dorsal/
torbness@stallo-1:~/dorsal$ emacs FEniCS/platforms/contributed/openmpi_rootless.platform

This is the file I used:

# Written by Lizao Li <email address hidden>
# Tested FEniCS on the Itasca cluster (https://www.msi.umn.edu/hardware/itasca/)
# No root privilige is required
# Changelog
# Version 1.0 - Sep 30, 2011. First smooth build

# Platform specific variables
default PETSC_ARCH=linux-gnu-cxx-opt
default SCOTCH_ARCH=pc_linux2

# Define the packages this platform needs
PACKAGES=(
sqlite
libxml2
python
ipython
#cmake
boost
pcre
swig
#blas
#lapack
suitesparsewithmetis_OpenMPI
parmetis
trilinos
petsc
slepc
armadillo
cgal
gmp
mpfr
mtl
scientificpython
fiat
ufc
ufl
ffc
instant
vtk
viper
dolfin
)

module load cmake
cp FEniCS/platforms/contributed/openmpi_rootless.platform ./
./dorsal.sh openmpi_rootless.platform
This ended with this error message:
...
common.copy /home/torbness/Work/FEniCS/include/boost/tr1/tr1/utility
common.copy /home/torbness/Work/FEniCS/include/boost/tr1/tr1/valarray
common.copy /home/torbness/Work/FEniCS/include/boost/tr1/tr1/vector
...failed updating 1 target...
...skipped 3 targets...
...updated 9828 targets...
Failure with exit status: 1
Exit message: There was a problem building boost_1_47_0.

Since some versions of boost are available on stallo I tried this

torbness@stallo-1:~/dorsal$ module load boost/1.46.1
boost/1.46.1(37):ERROR:150: Module 'boost/1.46.1' conflicts with the currently loaded module(s) 'openmpi/1.4.4_gnu'
boost/1.46.1(37):ERROR:102: Tcl command execution failed: conflict openmpi

torbness@stallo-1:~/dorsal$ module load boost/1.47.0-intel
boost/1.47.0-intel(37):ERROR:150: Module 'boost/1.47.0-intel' conflicts with the currently loaded module(s) 'openmpi/1.4.4_gnu'
boost/1.47.0-intel(37):ERROR:102: Tcl command execution failed: conflict openmpi

Do you know what can be the problem now?

Revision history for this message
Johannes Ring (johannr) said : 		#11

You cannot use the boost module because it must be used with the Intel compilers.

Look into dorsal_build.log (in ~/Work/FEniCS/src/boost_1_47_0) and try to figure out why it fails to build Boost. I'm guessing it cannot find bzlib.h?

Revision history for this message
Torbjørn Bækø Ness (torbjorn-ness) said : 		#12

Okey. I've pasted the start and end of the file:

Building Boost.Build engine with toolset gcc... tools/build/v2/engine/bin.linuxx86_64/b2
Detecting Python version... 2.7
Detecting Python root... /home/torbness/Work/FEniCS
Unicode/ICU support for Boost.Regex?... not found.
Generating Boost.Build configuration in project-config.jam...

Bootstrapping is done. To build, run:

    ./b2

To adjust configuration, edit 'project-config.jam'.
Further information:

   - Command line help:
     ./b2 --help

   - Getting started guide:
     http://www.boost.org/more/getting_started/unix-variants.html

   - Boost.Build documentation:
     http://www.boost.org/boost-build2/doc/html/index.html

Performing configuration checks

    - has_icu builds : no
    - ../config//has_gcc_visibility builds : yes
    - ../config//has_long_double_support builds : yes

Component configuration:

    - chrono : building
    - date_time : building
    - exception : building
    - filesystem : building
    - graph : building
    - graph_parallel : building
    - iostreams : building
    - math : building
    - mpi : building
    - program_options : building
    - python : building
    - random : building
    - regex : building
    - serialization : building
    - signals : building
    - system : building
    - test : building
    - thread : building
    - wave : building

...patience...
...patience...
...patience...
...patience...
...found 29074 targets...
...updating 9832 targets...
common.mkdir /home/torbness/Work/FEniCS/include/boost
common.copy /home/torbness/Work/FEniCS/include/boost/any.hpp

and then thousands of lines ....

common.copy /home/torbness/Work/FEniCS/include/boost/tr1/tr1/vector
...failed updating 1 target...
...skipped 3 targets...
...updated 9828 targets...

torbness@stallo-1:~/dorsal$ more ../Work/FEniCS/src/boost_1_47_0/dorsal_build.log |grep bzlib.h
libs/iostreams/src/bzip2.cpp:20:56: fatal error: bzlib.h: Ingen slik fil eller filkatalog

You seem to be right! Is that good news or bad news? Sorry I'm not very helpfull here...

Revision history for this message
Johannes Ring (johannr) said : 		#13

Well, we have at least located the error. I guess that is good news. The bad news is that you need to install bzip2 (or build Boost with NO_COMPRESSION). I have added bzip2 to Dorsal now so pull the latest Dorsal and add bzip2 before boost in the platform file. Hopefully, this will just work.

Revision history for this message
Torbjørn Bækø Ness (torbjorn-ness) said : 		#14

Okey, so now I did this,

bzr branch lp:dorsal
scp -r dorsal/ <email address hidden>:/home/torbness/
cd dorsal/
emacs FEniCS/platforms/contributed/openmpi_rootless.platform

# Written by Lizao Li <email address hidden>
# Tested FEniCS on the Itasca cluster (https://www.msi.umn.edu/hardware/itasca/)
# No root privilige is required
# Changelog
# Version 1.0 - Sep 30, 2011. First smooth build

# Platform specific variables
default PETSC_ARCH=linux-gnu-cxx-opt
default SCOTCH_ARCH=pc_linux2

# Define the packages this platform needs
PACKAGES=(
sqlite
libxml2
python
ipython
#cmake
bzip2
boost
pcre
swig
#blas
#lapack
suitesparsewithmetis_OpenMPI
parmetis
trilinos
petsc
slepc
armadillo
cgal
gmp
mpfr
mtl
scientificpython
fiat
ufc
ufl
ffc
instant
vtk
viper
dolfin
)

torbness@stallo-2:~/dorsal$ module unload python openmpi intel-compiler
torbness@stallo-2:~/dorsal$ module load gcc/4.6.20120210 openmpi/1.4.4_gnu cmake
torbness@stallo-2:~/dorsal$ ./dorsal.sh FEniCS/platforms/contributed/openmpi_rootless.platform

It then failed with this message:

Processing enabled package: PyTrilinos (Libs, )
-- Found PythonInterp: /home/torbness/Work/FEniCS/bin/python2.7 (Required is at least version "2.2")
CMake Error at packages/PyTrilinos/cmake/FindNumPy.cmake:103 (MESSAGE):
  Required NumPy python module not found
Call Stack (most recent call first):
  packages/PyTrilinos/CMakeLists.txt:156 (FIND_PACKAGE)

-- Enabled PyTrilinos modules:
-- Teuchos;Epetra;TriUtils;EpetraExt;Isorropia;Pliris;AztecOO;Galeri;Amesos;IFPACK;Komplex;Anasazi;ML;NOX
-- PyTrilinos installation path: /home/torbness/Work/FEniCS/lib/python2.7/site-packages/PyTrilinos

Exporting library dependencies ...

-- Configuring incomplete, errors occurred!
Failure with exit status: 1
Exit message: There was a problem configuring trilinos-10.8.5-Source.

Says here it didn't find numpy. Had I used module load to load python2.7 I would have had ipython,
numpy and scipy ready, so I gave it a try with this
(As far as I understand the Stallo people do not recommend to install packages that they have preinstalled):

torbness@stallo-2:~/dorsal$ module unload openmpi intel-compiler
torbness@stallo-2:~/dorsal$ module load gcc/4.6.20120210 openmpi/1.4.4_gnu
torbness@stallo-2:~/dorsal$ emacs FEniCS/platforms/contributed/openmpi_rootless.platform

File Edit Options Buffers Tools Help
# Written by Lizao Li <email address hidden>
# Tested FEniCS on the Itasca cluster (https://www.msi.umn.edu/hardware/itasca/)
# No root privilige is required
# Changelog
# Version 1.0 - Sep 30, 2011. First smooth build

# Platform specific variables
default PETSC_ARCH=linux-gnu-cxx-opt
default SCOTCH_ARCH=pc_linux2

# Define the packages this platform needs
PACKAGES=(
#sqlite
libxml2
#python
#ipython
#cmake
bzip2
boost
pcre
swig
#blas
#lapack
suitesparsewithmetis_OpenMPI
parmetis
trilinos
petsc
slepc
armadillo
cgal
gmp
mpfr
mtl
scientificpython
fiat
ufc
ufl
ffc
instant
vtk
viper
dolfin
)

torbness@stallo-2:~/dorsal$ module load cmake
torbness@stallo-2:~/dorsal$ ./dorsal.sh FEniCS/platforms/contributed/openmpi_rootless.platform

Now it got abit past the previous failiure, but stopped here instead:

[ 8%] Building CXX object packages/teuchos/src/CMakeFiles/teuchos.dir/Teuchos_MpiReductionOpSetter.cpp.o
Linking CXX shared library libteuchos.so
/usr/bin/ld: /global/apps/gcc/4.6.20120210/lib64/../lib64/libiberty.a(hashtab.o): relocation R_X86_64_32S against `a local symbol' can not be used when making a shared object; recompile with -fPIC
/global/apps/gcc/4.6.20120210/lib64/../lib64/libiberty.a: could not read symbols: Bad value
collect2: ld returned 1 exit status
make[2]: *** [packages/teuchos/src/libteuchos.so] Error 1
make[2]: Leaving directory `/home/torbness/Work/FEniCS/src/trilinos-10.8.5-Source/dorsal_build_dir'
make[1]: *** [packages/teuchos/src/CMakeFiles/teuchos.dir/all] Error 2
make[1]: Leaving directory `/home/torbness/Work/FEniCS/src/trilinos-10.8.5-Source/dorsal_build_dir'
make: *** [all] Error 2
make: Leaving directory `/home/torbness/Work/FEniCS/src/trilinos-10.8.5-Source/dorsal_build_dir'
Failure with exit status: 2
Exit message: There was a problem building trilinos-10.8.5-Source.

I thought I'd try without trilinos. I'm not sure if I need it.
I have so far only solved stationary linear electrostatic problems?

torbness@stallo-2:~/dorsal$ rm -r ../Work/

then I commented out trilinos and tried again. It seemed to come quite far,
but then ended with

-- Build files have been written to: /home/torbness/Work/FEniCS/src/CGAL-4.0/dorsal_build_dir
make: Entering directory `/home/torbness/Work/FEniCS/src/CGAL-4.0/dorsal_build_dir'
make[1]: Entering directory `/home/torbness/Work/FEniCS/src/CGAL-4.0/dorsal_build_dir'
make[2]: Entering directory `/home/torbness/Work/FEniCS/src/CGAL-4.0/dorsal_build_dir'
Scanning dependencies of target CGAL
make[2]: Leaving directory `/home/torbness/Work/FEniCS/src/CGAL-4.0/dorsal_build_dir'
make[2]: Entering directory `/home/torbness/Work/FEniCS/src/CGAL-4.0/dorsal_build_dir'
[100%] Building CXX object src/CGAL/CMakeFiles/CGAL.dir/all_files.cpp.o
In file included from /home/torbness/Work/FEniCS/src/CGAL-4.0/include/CGAL/is_convertible.h:28:0,
                 from /home/torbness/Work/FEniCS/src/CGAL-4.0/include/CGAL/Rational_traits.h:31,
                 from /home/torbness/Work/FEniCS/src/CGAL-4.0/include/CGAL/number_type_basic.h:65,
                 from /home/torbness/Work/FEniCS/src/CGAL-4.0/include/CGAL/basic.h:36,
                 from /home/torbness/Work/FEniCS/src/CGAL-4.0/src/CGAL/Geomview_stream.cpp:25,
                 from /home/torbness/Work/FEniCS/src/CGAL-4.0/dorsal_build_dir/src/CGAL/all_files.cpp:1:
/usr/include/gmpxx.h: In destructor ‘__gmp_alloc_cstring::~__gmp_alloc_cstring()’:
/usr/include/gmpxx.h:2096:59: error: ‘strlen’ was not declared in this scope
make[2]: *** [src/CGAL/CMakeFiles/CGAL.dir/all_files.cpp.o] Error 1
make[2]: Leaving directory `/home/torbness/Work/FEniCS/src/CGAL-4.0/dorsal_build_dir'
make[1]: *** [src/CGAL/CMakeFiles/CGAL.dir/all] Error 2
make[1]: Leaving directory `/home/torbness/Work/FEniCS/src/CGAL-4.0/dorsal_build_dir'
make: *** [all] Error 2
make: Leaving directory `/home/torbness/Work/FEniCS/src/CGAL-4.0/dorsal_build_dir'
Failure with exit status: 2
Exit message: There was a problem building CGAL-4.0.

I would appreciate any new suggestions!

Revision history for this message
Johannes Ring (johannr) said : 		#15

I would have tried to only load the gcc/4.6.20120210 and the openmpi/1.4.4_gnu modules and used the following set of packages:

PACKAGES=(
libxml2
python
ipython
cmake
bzip2
boost
pcre
swig
blas
lapack
suitesparsewithmetis_OpenMPI
parmetis
numpy
trilinos
petsc
slepc
armadillo
cgal
mtl
scientificpython
fiat
ufc
ufl
ffc
instant
vtk
viper
dolfin
)

You can drop trilinos if it is behaving difficulty.

Revision history for this message
Johannes Ring (johannr) said : 		#16

You can also add scipy after suitesparsewithmetis_OpenMPI.

Revision history for this message
Torbjørn Bækø Ness (torbjorn-ness) said : 		#17

I switched numpy to earlier since I got an error on installing scipy, that seems to be a result of not having numpy yet. I still ended up with an error, so I commented out Trilinos. 'Finally' I ended up with this error:

-- Library config detected: Qt3
-- Library config detected: ImageIO
-- Library config detected: Core
-- Library config detected: Qt4
-- Library configs detected: CGAL;Core;ImageIO;Qt3;Qt4
-- Configuring done
-- Generating done
-- Build files have been written to: /home/torbness/Work/FEniCS/src/CGAL-4.0/dorsal_build_dir
make: Entering directory `/home/torbness/Work/FEniCS/src/CGAL-4.0/dorsal_build_dir'
make[1]: Entering directory `/home/torbness/Work/FEniCS/src/CGAL-4.0/dorsal_build_dir'
make[2]: Entering directory `/home/torbness/Work/FEniCS/src/CGAL-4.0/dorsal_build_dir'
Scanning dependencies of target CGAL
make[2]: Leaving directory `/home/torbness/Work/FEniCS/src/CGAL-4.0/dorsal_build_dir'
make[2]: Entering directory `/home/torbness/Work/FEniCS/src/CGAL-4.0/dorsal_build_dir'
[100%] Building CXX object src/CGAL/CMakeFiles/CGAL.dir/all_files.cpp.o
In file included from /home/torbness/Work/FEniCS/src/CGAL-4.0/include/CGAL/is_convertible.h:28:0,
                 from /home/torbness/Work/FEniCS/src/CGAL-4.0/include/CGAL/Rational_traits.h:31,
                 from /home/torbness/Work/FEniCS/src/CGAL-4.0/include/CGAL/number_type_basic.h:65,
                 from /home/torbness/Work/FEniCS/src/CGAL-4.0/include/CGAL/basic.h:36,
                 from /home/torbness/Work/FEniCS/src/CGAL-4.0/src/CGAL/Geomview_stream.cpp:25,
                 from /home/torbness/Work/FEniCS/src/CGAL-4.0/dorsal_build_dir/src/CGAL/all_files.cpp:1:
/usr/include/gmpxx.h: In destructor ‘__gmp_alloc_cstring::~__gmp_alloc_cstring()’:
/usr/include/gmpxx.h:2096:59: error: ‘strlen’ was not declared in this scope
make[2]: *** [src/CGAL/CMakeFiles/CGAL.dir/all_files.cpp.o] Error 1
make[2]: Leaving directory `/home/torbness/Work/FEniCS/src/CGAL-4.0/dorsal_build_dir'
make[1]: *** [src/CGAL/CMakeFiles/CGAL.dir/all] Error 2
make[1]: Leaving directory `/home/torbness/Work/FEniCS/src/CGAL-4.0/dorsal_build_dir'
make: *** [all] Error 2
make: Leaving directory `/home/torbness/Work/FEniCS/src/CGAL-4.0/dorsal_build_dir'
Failure with exit status: 2
Exit message: There was a problem building CGAL-4.0.

Revision history for this message
Johannes Ring (johannr) said : 		#18

See if it helps if you add "gmp" and "mpfr" before "cgal" in the platform file.

Revision history for this message
Torbjørn Bækø Ness (torbjorn-ness) said : 		#19

Ok. I did that, and tried with (didn't work) and without Trilinos. Without it, it stoped at this message for three days:

Fetching dolfin-1.0.0
--2012-05-11 18:00:58-- http://launchpad.net/dolfin/1.0.x/1.0.0/+download/dolfi
Resolving launchpad.net... 91.189.89.222, 91.189.89.223
Connecting to launchpad.net|91.189.89.222|:80... connected.
HTTP request sent, awaiting response... 303 See Other
Location: https://launchpadlibrarian.net/86889750/dolfin-1.0.0.tar.gz [following
--2012-05-11 18:00:58-- https://launchpadlibrarian.net/86889750/dolfin-1.0.0.ta
Resolving launchpadlibrarian.net... 91.189.89.229, 91.189.89.228
Connecting to launchpadlibrarian.net|91.189.89.229|:443... connected.
HTTP request sent, awaiting response... 200 OK
Length: 9444169 (9.0M) [application/x-tar]
Saving to: `dolfin-1.0.0.tar.gz'

100%[===========================================================================

2012-05-11 18:01:03 (2.80 MB/s) - `dolfin-1.0.0.tar.gz' saved [9444169/9444169]

Unpacking dolfin-1.0.0
Building dolfin-1.0.0
-- The C compiler identification is GNU
-- The CXX compiler identification is GNU
-- Check for working C compiler: /global/apps/gcc/4.6.20120210/bin/gcc
-- Check for working C compiler: /global/apps/gcc/4.6.20120210/bin/gcc -- works
-- Detecting C compiler ABI info
-- Detecting C compiler ABI info - done
-- Check for working CXX compiler: /global/apps/gcc/4.6.20120210/bin/c++
-- Check for working CXX compiler: /global/apps/gcc/4.6.20120210/bin/c++ -- work
-- Detecting CXX compiler ABI info
-- Detecting CXX compiler ABI info - done
-- Performing Test HAVE_PIPE
-- Performing Test HAVE_PIPE - Success
-- Performing Test HAVE_PEDANTIC
-- Performing Test HAVE_PEDANTIC - Success
-- Performing Test HAVE_DISABLE_PEDANTIC_CHECKS
-- Performing Test HAVE_DISABLE_PEDANTIC_CHECKS - Success
-- Performing Test HAVE_STD
-- Performing Test HAVE_STD - Success
-- Performing Test HAVE_DEBUG
-- Performing Test HAVE_DEBUG - Success
-- Performing Test HAVE_O2_OPTIMISATION
-- Performing Test HAVE_O2_OPTIMISATION - Success
-- Found MPI_C: /global/apps/openmpi/1.4.4_gnu/lib/libmpi.so;/global/apps/openmpbm.so;/usr/lib64/libdl.so
-- Found MPI_CXX: /global/apps/openmpi/1.4.4_gnu/lib/libmpi_cxx.so;/global/apps/lib64/libnsl.so;/usr/lib64/libutil.so;/usr/lib64/libm.so;/usr/lib64/libdl.so
-- Try OpenMP C flag = [-fopenmp]
-- Performing Test OpenMP_FLAG_DETECTED
-- Performing Test OpenMP_FLAG_DETECTED - Success
-- Try OpenMP CXX flag = [-fopenmp]
-- Performing Test OpenMP_FLAG_DETECTED
-- Performing Test OpenMP_FLAG_DETECTED - Success
-- Found OpenMP: -fopenmp
-- Performing Test OPENMP_UINT_TEST_RUNS
-- Performing Test OPENMP_UINT_TEST_RUNS - Success
-- Boost version: 1.47.0
-- Found the following Boost libraries:
-- filesystem
-- program_options
-- system
-- thread
-- iostreams
-- math_tr1
-- mpi
-- serialization
-- UFC version: 2.0.5
-- Checking for package 'Armadillo'
-- Performing Test ARMADILLO_TEST_RUNS
-- Performing Test ARMADILLO_TEST_RUNS - Success
-- Found Armadillo: /home/torbness/Work/FEniCS/lib/libarmadillo.so
-- Found LibXml2: /home/torbness/Work/FEniCS/lib/libxml2.so
-- Found PythonInterp: /home/torbness/Work/FEniCS/bin/python2.7
-- Found PythonLibs: /home/torbness/Work/FEniCS/lib/libpython2.7.so
-- NumPy headers found
-- Found SWIG: /home/torbness/Work/FEniCS/bin/swig (found version "2.0.3")
-- Performing Test PARMETIS_TEST_RUNS

Revision history for this message
Johannes Ring (johannr) said : 		#20

So it got stuck on the PARMETIS_TEST_RUNS line? The ParMETIS test in <dolfin>/cmake/modules/FindParMETIS.cmake isn't doing much other than starting and stopping MPI:

  #include <mpi.h>
  #include <parmetis.h>

  int main()
  {
    // FIXME: Find a simple but sensible test for ParMETIS

    // Initialise MPI
    MPI::Init();

    // Finalize MPI
    MPI::Finalize();

    return 0;
  }

Can you compile and run this test program manually?

Revision history for this message
Torbjørn Bækø Ness (torbjorn-ness) said : 		#21

It's been quite some time since I did anything in C/C++ so correct me if I'm doing anything stupid here.
I logged in, made the test file parT.c in my home folder and ran these commands

 module unload intel-compiler/11.1 python openmpi
 module load openmpi/1.4.4_gnu gcc/4.6.20120210
 gcc -o testing parT.c

parT.c:1:17: fatal error: mpi.h: No such file or directory
compilation terminated.
torbness@stallo-2:~$

Is this what you meant?

Revision history for this message
Johannes Ring (johannr) said : 		#22

Try something like this:

  mpic++ -c -I/home/torbness/Work/FEniCS/include parT.c
  mpic++ -o testing parT.o -L/home/torbness/Work/FEniCS/lib -lparmetis
  mpirun -np 2 ./testing

Does that work?

Revision history for this message
Torbjørn Bækø Ness (torbjorn-ness) said : 		#23

torbness@stallo-1:~$ module unload intel-compiler/11.1 python openmpi
torbness@stallo-1:~$ module load openmpi/1.4.4_gnu gcc/4.6.20120210
torbness@stallo-1:~$ mpic++ -c -I/home/torbness/Work/FEniCS/include parT.c
torbness@stallo-1:~$ mpic++ -o testing parT.o -L/home/torbness/Work/FEniCS/lib -lparmetis
torbness@stallo-1:~$ mpirun -np 2 ./testing
libibverbs: Warning: no userspace device-specific driver found for /sys/class/infiniband_verbs/uverbs0
libibverbs: Warning: no userspace device-specific driver found for /sys/class/infiniband_verbs/uverbs0

It has been standing still here for at least an hour now I think....

Revision history for this message
Johannes Ring (johannr) said : 		#24

I guess it also fails without the ParMETIS stuff? Save the following in a file test.cpp:

include <mpi.h>

int main()
{
  // Initialise MPI
  MPI::Init();

  // Finalize MPI
  MPI::Finalize();

  return 0;
}

Then run

  mpic++ test.cpp -o test
  mpirun -np 2 ./test

This should complete within a second. If not, kill it and try to run

  export OMPI_MCA_btl=^openib

before you run the test program again (mpirun -np 2 ./test). If it still doesn't work, you should probably contact the system administrators.

If it do work however, you should add that line to your ~/.profile or ~/.bashrc file and continue with the DOLFIN installation.

Revision history for this message
Torbjørn Bækø Ness (torbjorn-ness) said : 		#25

I first got this,

torbness@stallo-2:~$ module unload intel-compiler/11.1 python openmpi
torbness@stallo-2:~$ module load openmpi/1.4.4_gnu gcc/4.6.20120210
torbness@stallo-2:~$ mpic++ test.cpp -o test

test.cpp:1:1: error: 'include' does not name a type

so I added an # before include <mpi.h>

torbness@stallo-2:~$ emacs test.cpp
torbness@stallo-2:~$ mpic++ test.cpp -o test
torbness@stallo-2:~$ mpirun -np 2 ./test

libibverbs: Warning: no userspace device-specific driver found for /sys/class/infiniband_verbs/uverbs0
libibverbs: Warning: no userspace device-specific driver found for /sys/class/infiniband_verbs/uverbs0

mpirun: killing job...
--------------------------------------------------------------------------
mpirun noticed that process rank 0 with PID 15211 on node stallo-2.
local exited on signal 0 (Unknown signal 0).

--------------------------------------------------------------------------
2 total processes killed (some possibly by mpirun during cleanup)

mpirun: clean termination accomplished

After I did this it worked:

  export OMPI_MCA_btl=^openib
after a clean-up, I ran dorsal again,
./dorsal.sh FEniCS/platforms/contributed/openmpi_rootless.platform

This ended in this error message:
...
[ 97%] Building CXX object dolfin/CMakeFiles/dolfin.dir/refinement/LocalMeshCoarsening.cpp.o
[ 98%] Building CXX object dolfin/CMakeFiles/dolfin.dir/refinement/LocalMeshRefinement.cpp.o
[ 98%] Building CXX object dolfin/CMakeFiles/dolfin.dir/refinement/RegularCutRefinement.cpp.o
[ 98%] Building CXX object dolfin/CMakeFiles/dolfin.dir/refinement/RivaraRefinement.cpp.o
[100%] Building CXX object dolfin/CMakeFiles/dolfin.dir/refinement/UniformMeshRefinement.cpp.o
[100%] Building CXX object dolfin/CMakeFiles/dolfin.dir/refinement/refine.cpp.o
Linking CXX shared library libdolfin.so
/usr/bin/ld: /usr/lib/../lib64/libmpfr.a(clear.o): relocation R_X86_64_32 against `a local symbol' can not be used when making a shared object; recompile with -fPIC
/usr/lib/../lib64/libmpfr.a: could not read symbols: Bad value
collect2: ld returned 1 exit status
make[2]: *** [dolfin/libdolfin.so.1.0.0] Error 1
make[2]: Leaving directory `/home/torbness/Work/FEniCS/src/dolfin-1.0.0/dorsal_build_dir'
make[1]: *** [dolfin/CMakeFiles/dolfin.dir/all] Error 2
make[1]: Leaving directory `/home/torbness/Work/FEniCS/src/dolfin-1.0.0/dorsal_build_dir'
make: *** [all] Error 2
make: Leaving directory `/home/torbness/Work/FEniCS/src/dolfin-1.0.0/dorsal_build_dir'
Failure with exit status: 2
Exit message: There was a problem building dolfin-1.0.0.

Revision history for this message
Johannes Ring (johannr) said : 		#26

I'm not sure why it tries to link with libmpfr.a but if possible this library should be recompiled with the -fPIC flag.

Revision history for this message
Torbjørn Bækø Ness (torbjorn-ness) said : 		#27

Do you know how I would do that?
Do you also know if anyone at Simula is using FEniCS on Stallo?

Revision history for this message
Johannes Ring (johannr) said : 		#28

No, I don't know anyone who uses Stallo. Maybe someone else knows?

IIRC, you added mpfr to your platform file? Try to add

  default CMAKE_PREFIX_PATH=${INSTALL_PATH}

to your platform file to ensure that CGAL picks up the mpfr library that was built by Dorsal. Then remove the CGAL folder in ~/Work/FEniCS/src and re-run Dorsal.

Revision history for this message
Torbjørn Bækø Ness (torbjorn-ness) said : 		#29

I checked that mpfr was in the platform file, and did this (so for once I don't remove the entire Work folder)

rm -r Work/FEniCS/src/CGAL-4.0/

then I added
default CMAKE_PREFIX_PATH=${INSTALL_PATH}
after
# Platform specific variables
default PETSC_ARCH=linux-gnu-cxx-opt
default SCOTCH_ARCH=pc_linux2

cd dorsal/
module unload intel-compiler/11.1 python openmpi
module load openmpi/1.4.4_gnu gcc/4.6.20120210
./dorsal.sh FEniCS/platforms/contributed/openmpi_rootless.platform

Fetching mpfr-2.2.0
Unpacking mpfr-2.2.0
Building mpfr-2.2.0
patching file lngamma.c
Reversed (or previously applied) patch detected! Skipping patch.
1 out of 1 hunk ignored -- saving rejects to file lngamma.c.rej
patching file tests/tlngamma.c
Reversed (or previously applied) patch detected! Skipping patch.
2 out of 2 hunks ignored -- saving rejects to file tests/tlngamma.c.rej
patching file mpfr.h
Reversed (or previously applied) patch detected! Skipping patch.
1 out of 1 hunk ignored -- saving rejects to file mpfr.h.rej
patching file tests/tset_si.c
Reversed (or previously applied) patch detected! Skipping patch.
2 out of 2 hunks ignored -- saving rejects to file tests/tset_si.c.rej
patching file configure
Reversed (or previously applied) patch detected! Skipping patch.
1 out of 1 hunk ignored -- saving rejects to file configure.rej
patching file tests/tpow.c
Reversed (or previously applied) patch detected! Skipping patch.
2 out of 2 hunks ignored -- saving rejects to file tests/tpow.c.rej
patching file cache.c
Reversed (or previously applied) patch detected! Skipping patch.
4 out of 4 hunks ignored -- saving rejects to file cache.c.rej
patching file hypot.c
Reversed (or previously applied) patch detected! Skipping patch.
3 out of 3 hunks ignored -- saving rejects to file hypot.c.rej
patching file mpfr-impl.h
Reversed (or previously applied) patch detected! Skipping patch.
5 out of 5 hunks ignored -- saving rejects to file mpfr-impl.h.rej
patching file mpfr.h
Reversed (or previously applied) patch detected! Skipping patch.
2 out of 2 hunks ignored -- saving rejects to file mpfr.h.rej
patching file round_near_x.c
Reversed (or previously applied) patch detected! Skipping patch.
5 out of 5 hunks ignored -- saving rejects to file round_near_x.c.rej
patching file tests/thypot.c
Reversed (or previously applied) patch detected! Skipping patch.
1 out of 1 hunk ignored -- saving rejects to file tests/thypot.c.rej
patching file div.c
Hunk #1 FAILED at 298.
Not setting time of file div.c (time mismatch)
1 out of 1 hunk FAILED -- saving rejects to file div.c.rej
patching file sin.c
Reversed (or previously applied) patch detected! Skipping patch.
2 out of 2 hunks ignored -- saving rejects to file sin.c.rej
patching file get_f.c
Reversed (or previously applied) patch detected! Skipping patch.
4 out of 4 hunks ignored -- saving rejects to file get_f.c.rej
patching file set_f.c
Reversed (or previously applied) patch detected! Skipping patch.
2 out of 2 hunks ignored -- saving rejects to file set_f.c.rej
patching file tests/tget_f.c
Reversed (or previously applied) patch detected! Skipping patch.
5 out of 5 hunks ignored -- saving rejects to file tests/tget_f.c.rej
patching file tests/tset_f.c
Reversed (or previously applied) patch detected! Skipping patch.
5 out of 5 hunks ignored -- saving rejects to file tests/tset_f.c.rej
patching file random2.c
Reversed (or previously applied) patch detected! Skipping patch.
2 out of 2 hunks ignored -- saving rejects to file random2.c.rej
patching file tests/trandom.c
Reversed (or previously applied) patch detected! Skipping patch.
2 out of 2 hunks ignored -- saving rejects to file tests/trandom.c.rej
patching file asin.c
Reversed (or previously applied) patch detected! Skipping patch.
1 out of 1 hunk ignored -- saving rejects to file asin.c.rej
patching file asinh.c
Reversed (or previously applied) patch detected! Skipping patch.
1 out of 1 hunk ignored -- saving rejects to file asinh.c.rej
patching file atan.c
Reversed (or previously applied) patch detected! Skipping patch.
1 out of 1 hunk ignored -- saving rejects to file atan.c.rej
patching file atanh.c
Reversed (or previously applied) patch detected! Skipping patch.
1 out of 1 hunk ignored -- saving rejects to file atanh.c.rej
patching file expm1.c
Hunk #1 FAILED at 61.
Not setting time of file expm1.c (time mismatch)
1 out of 1 hunk FAILED -- saving rejects to file expm1.c.rej
patching file log1p.c
Hunk #1 FAILED at 63.
Not setting time of file log1p.c (time mismatch)
1 out of 1 hunk FAILED -- saving rejects to file log1p.c.rej
patching file sin.c
Reversed (or previously applied) patch detected! Skipping patch.
1 out of 1 hunk ignored -- saving rejects to file sin.c.rej
patching file sinh.c
Reversed (or previously applied) patch detected! Skipping patch.
1 out of 1 hunk ignored -- saving rejects to file sinh.c.rej
patching file tan.c
Reversed (or previously applied) patch detected! Skipping patch.
1 out of 1 hunk ignored -- saving rejects to file tan.c.rej
patching file tanh.c
Reversed (or previously applied) patch detected! Skipping patch.
1 out of 1 hunk ignored -- saving rejects to file tanh.c.rej
patching file zeta.c
Reversed (or previously applied) patch detected! Skipping patch.
1 out of 1 hunk ignored -- saving rejects to file zeta.c.rej
patching file configure.in
Reversed (or previously applied) patch detected! Skipping patch.
1 out of 1 hunk ignored -- saving rejects to file configure.in.rej
patching file configure
Reversed (or previously applied) patch detected! Skipping patch.
1 out of 1 hunk ignored -- saving rejects to file configure.rej
patching file div.c
Reversed (or previously applied) patch detected! Skipping patch.
10 out of 10 hunks ignored -- saving rejects to file div.c.rej
patching file mpfr-gmp.c
Reversed (or previously applied) patch detected! Skipping patch.
1 out of 1 hunk ignored -- saving rejects to file mpfr-gmp.c.rej
patching file mpfr-impl.h
Reversed (or previously applied) patch detected! Skipping patch.
1 out of 1 hunk ignored -- saving rejects to file mpfr-impl.h.rej
patching file get_f.c
Reversed (or previously applied) patch detected! Skipping patch.
4 out of 4 hunks ignored -- saving rejects to file get_f.c.rej
patching file tests/tget_f.c
Reversed (or previously applied) patch detected! Skipping patch.
2 out of 2 hunks ignored -- saving rejects to file tests/tget_f.c.rej
patching file configure
Reversed (or previously applied) patch detected! Skipping patch.
4 out of 4 hunks ignored -- saving rejects to file configure.rej
patching file configure.in
Reversed (or previously applied) patch detected! Skipping patch.
3 out of 3 hunks ignored -- saving rejects to file configure.in.rej
patching file acinclude.m4
Reversed (or previously applied) patch detected! Skipping patch.
1 out of 1 hunk ignored -- saving rejects to file acinclude.m4.rej
patching file configure
Reversed (or previously applied) patch detected! Skipping patch.
1 out of 1 hunk ignored -- saving rejects to file configure.rej
patching file configure.in
Reversed (or previously applied) patch detected! Skipping patch.
1 out of 1 hunk ignored -- saving rejects to file configure.in.rej
patching file add1.c
Reversed (or previously applied) patch detected! Skipping patch.
1 out of 1 hunk ignored -- saving rejects to file add1.c.rej
patching file add1sp.c
Reversed (or previously applied) patch detected! Skipping patch.
1 out of 1 hunk ignored -- saving rejects to file add1sp.c.rej
patching file exceptions.c
Reversed (or previously applied) patch detected! Skipping patch.
1 out of 1 hunk ignored -- saving rejects to file exceptions.c.rej
patching file exp.c
Reversed (or previously applied) patch detected! Skipping patch.
1 out of 1 hunk ignored -- saving rejects to file exp.c.rej
patching file exp2.c
Reversed (or previously applied) patch detected! Skipping patch.
3 out of 3 hunks ignored -- saving rejects to file exp2.c.rej
patching file expm1.c
Reversed (or previously applied) patch detected! Skipping patch.
4 out of 4 hunks ignored -- saving rejects to file expm1.c.rej
patching file lngamma.c
Reversed (or previously applied) patch detected! Skipping patch.
1 out of 1 hunk ignored -- saving rejects to file lngamma.c.rej
patching file log1p.c
Reversed (or previously applied) patch detected! Skipping patch.
2 out of 2 hunks ignored -- saving rejects to file log1p.c.rej
patching file mpfr-impl.h
Reversed (or previously applied) patch detected! Skipping patch.
1 out of 1 hunk ignored -- saving rejects to file mpfr-impl.h.rej
patching file mul.c
Reversed (or previously applied) patch detected! Skipping patch.
2 out of 2 hunks ignored -- saving rejects to file mul.c.rej
patching file sub1.c
Reversed (or previously applied) patch detected! Skipping patch.
3 out of 3 hunks ignored -- saving rejects to file sub1.c.rej
patching file sub1sp.c
Reversed (or previously applied) patch detected! Skipping patch.
1 out of 1 hunk ignored -- saving rejects to file sub1sp.c.rej
patching file tests/tests.c
Reversed (or previously applied) patch detected! Skipping patch.
3 out of 3 hunks ignored -- saving rejects to file tests/tests.c.rej
patching file tests/texp2.c
Reversed (or previously applied) patch detected! Skipping patch.
6 out of 6 hunks ignored -- saving rejects to file tests/texp2.c.rej
patching file tests/tlog1p.c
Reversed (or previously applied) patch detected! Skipping patch.
1 out of 1 hunk ignored -- saving rejects to file tests/tlog1p.c.rej
patching file tests/texp2.c
Reversed (or previously applied) patch detected! Skipping patch.
4 out of 4 hunks ignored -- saving rejects to file tests/texp2.c.rej
Failure with exit status: 1
Exit message: There was a problem building mpfr-2.2.0.
torbness@stallo-2:~/dorsal$

Revision history for this message
Johannes Ring (johannr) said : 		#30

Yes, the patches for mpfr are not applied successfully the second time you build it. Remove the mpfr files in ~/Work/FEniCS/src and try again.

Revision history for this message
Torbjørn Bækø Ness (torbjorn-ness) said : 		#31

[ 59%] Building CXX object dolfin/CMakeFiles/dolfin.dir/refinement/LocalMeshRefinement.cpp.o
[ 59%] Building CXX object dolfin/CMakeFiles/dolfin.dir/refinement/RegularCutRefinement.cpp.o
[ 59%] Building CXX object dolfin/CMakeFiles/dolfin.dir/refinement/RivaraRefinement.cpp.o
[ 61%] Building CXX object dolfin/CMakeFiles/dolfin.dir/refinement/UniformMeshRefinement.cpp.o
[ 61%] Building CXX object dolfin/CMakeFiles/dolfin.dir/refinement/refine.cpp.o
Linking CXX shared library libdolfin.so
/usr/bin/ld: /home/torbness/Work/FEniCS/lib/libmpfr.a(clear.o): relocation R_X86_64_32 against `a local symbol' can not be used when making a shared object; recompile with -fPIC
/home/torbness/Work/FEniCS/lib/libmpfr.a: could not read symbols: Bad value
collect2: ld returned 1 exit status
make[2]: *** [dolfin/libdolfin.so.1.0.0] Error 1
make[2]: Leaving directory `/home/torbness/Work/FEniCS/src/dolfin-1.0.0/dorsal_build_dir'
make[1]: *** [dolfin/CMakeFiles/dolfin.dir/all] Error 2
make[1]: Leaving directory `/home/torbness/Work/FEniCS/src/dolfin-1.0.0/dorsal_build_dir'
make: *** [all] Error 2
make: Leaving directory `/home/torbness/Work/FEniCS/src/dolfin-1.0.0/dorsal_build_dir'
Failure with exit status: 2
Exit message: There was a problem building dolfin-1.0.0.

This message is quite similar to what we saw earlier, except that it reached to 61% instead of 100?

Revision history for this message
Best Johannes Ring (johannr) said : 		#32

I added a fix in Dorsal yesterday such that it builds a shared library for mpfr. Make sure you have the latest Dorsal (bzr pull) and remove the mpfr, CGAL and DOLFIN folders in ~/Work/FEniCS/src. Then re-run Dorsal.

Revision history for this message
Torbjørn Bækø Ness (torbjorn-ness) said : 		#33

It all seems to work now. Thank you so much for all your help!

For future reference, I first encountered this error

torbness@stallo-2:/global/work/torbness/fem$ python fem_test.py
*** Warning: libvtkCommonPythonD.so.5.8: cannot open shared object file: No such file or directory
*** Warning: Unable to import Viper, plotting disabled.
Loading mesh...
FEM simulations ...
Calling FFC just-in-time (JIT) compiler, this may take some time.
Traceback (most recent call last):
  File "fem_test.py", line 12, in <module>
    V = FunctionSpace(mesh, "CG", 1)
  File "/home/torbness/Work/FEniCS/lib/python2.7/site-packages/dolfin/functions/functionspace.py", line 353, in __init__
    FunctionSpaceBase.__init__(self, mesh, element)
  File "/home/torbness/Work/FEniCS/lib/python2.7/site-packages/dolfin/functions/functionspace.py", line 77, in __init__
    ufc_element, ufc_dofmap = jit(self._ufl_element)
  File "/home/torbness/Work/FEniCS/lib/python2.7/site-packages/dolfin/compilemodules/jit.py", line 66, in mpi_jit
    return local_jit(*args, **kwargs)
  File "/home/torbness/Work/FEniCS/lib/python2.7/site-packages/dolfin/compilemodules/jit.py", line 154, in jit
    return jit_compile(form, parameters=p, common_cell=common_cell)
  File "/home/torbness/Work/FEniCS/lib/python2.7/site-packages/ffc/jitcompiler.py", line 71, in jit
    return jit_element(ufl_object, parameters)
  File "/home/torbness/Work/FEniCS/lib/python2.7/site-packages/ffc/jitcompiler.py", line 178, in jit_element
    compiled_form, module, form_data, prefix = jit_form(form, parameters)
  File "/home/torbness/Work/FEniCS/lib/python2.7/site-packages/ffc/jitcompiler.py", line 145, in jit_form
    cache_dir = cache_dir)
  File "/home/torbness/Work/FEniCS/lib/python2.7/site-packages/ufc_utils/build.py", line 61, in build_ufc_module
    configure_instant(swig_binary, swig_path)
  File "/home/torbness/Work/FEniCS/lib/python2.7/site-packages/ufc_utils/build.py", line 158, in configure_instant
    """
OSError: The Boost math library was not found.
If Boost math library is installed in a nonstandard location,
set the environment variable BOOST_DIR.

It was easily fixed by adding
export BOOST_DIR=${HOME}/Work/FEniCS
in my ~/.bashrc file

One last question before I let you go: I have now installed without Trilinos, but I'm not sure I understand what this means.
I will for the time being only solve stationary linear poisson problems. Will I miss Trilinos in any way?

Once again, thank you for all your help!

Revision history for this message
Torbjørn Bækø Ness (torbjorn-ness) said : 		#34

Thanks Johannes Ring, that solved my question.

Revision history for this message
Johannes Ring (johannr) said : 		#35

I'm glad we finally got it working.

I don't think you will need Trilinos, but if you do, let us know and we could try to figure out why it doesn't build.

Could you post your .platform file for Dorsal? Then we can add it to Dorsal for others that might want to run FEniCS on Stallo.

Revision history for this message
Torbjørn Bækø Ness (torbjorn-ness) said : 		#36

# Written by Lizao Li <email address hidden>
# Tested FEniCS on the Itasca cluster (https://www.msi.umn.edu/hardware/itasca/)
# No root privilige is required
# Changelog
# Version 1.0 - Sep 30, 2011. First smooth build

# Platform specific variables
default PETSC_ARCH=linux-gnu-cxx-opt
default SCOTCH_ARCH=pc_linux2
default CMAKE_PREFIX_PATH=${INSTALL_PATH}

# Define the packages this platform needs
PACKAGES=(
sqlite
libxml2
python
ipython
numpy
cmake
bzip2
boost
pcre
swig
blas
lapack
suitesparsewithmetis_OpenMPI
scipy
parmetis
#trilinos
petsc
slepc
armadillo
gmp
mpfr
cgal
mtl
scientificpython
fiat
ufc
ufl
ffc
instant
vtk
viper
dolfin
)

Revision history for this message
Johannes Ring (johannr) said : 		#37

Thanks, I have added this now.