Unicorn install problem in Ubuntu 9.10

The parallel unicorn on fenics.org is an old experimental version, which shouldn't really be there. Most of the functionality is now in dolfin, except parallel mesh refinement and dynamic load balancing.

Anyway, the old experimental version doesn't work with the latest gnuiness of
Gcc >4.2. It works fine with mature compilers like IBM xl and MIPSpro.

----- Reply message -----
From: "amin" <email address hidden>
Date: Tue, Dec 8, 2009 05:19
Subject: [Question #93274]: Unicorn install problem in Ubuntu 9.10
To: <email address hidden>

New question #93274 on FEniCS Project:
https://answers.launchpad.net/fenics/+question/93274

Hello Everyone:
  I am interested to solve a fluid-structure interaction problem for aircraft wing. As recommended in fenics website,
I installed Ubuntu 9.10 and installed fenics using the instruction at http://www.fenics.org/wiki/Download.
Everything went fine and could compile and run some demos! I then moved on to install Unicorn (http://www.fenics.org/wiki/Unicorn). I downloaded for the parallel version and tried to install them using the "build_local.sh" script. I get errors.
To identify the errors, I ran the script line-by-line. I get error when I try to compile dolfin (i.e. when I run "scons -j $NUM_PROCS enablePydolfin=False withPetscDir=$PETSC_INSTALL enableGnuExtensions=True withParmetisDir=$PARMETIS_INSTALL prefix=$LOCALDIR install". I cut and paste the error message below. I dont know C++ much.. Does it have a fix (I am using the following version of C++: cpp (Ubuntu 4.4.1-4ubuntu8) 4.4.1

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amin@amin-laptop:~/Unicorn_fsi/unicorn-parafin-dist-2009-05-25_01/dolfin$ scons -j $NUM_PROCS enablePydolfin=False withPetscDir=$PETSC_INSTALL enableGnuExtensions=True withParmetisDir=$PARMETIS_INSTALL prefix=$LOCALDIR install
scons: Reading SConscript files ...

scons: warning: The BoolOption() function is deprecated; use the BoolVariable() function instead.
File "/home/amin/Unicorn_fsi/unicorn-parafin-dist-2009-05-25_01/dolfin/SConstruct", line 64, in <module>

scons: warning: The PathOption() function is deprecated; use the PathVariable() function instead.
File "/home/amin/Unicorn_fsi/unicorn-parafin-dist-2009-05-25_01/dolfin/SConstruct", line 93, in <module>

scons: warning: The Options class is deprecated; use the Variables class instead.
File "/home/amin/Unicorn_fsi/unicorn-parafin-dist-2009-05-25_01/dolfin/scons/simula-scons/simula_scons/__init__.py", line 237, in __init__
Using options from scons/options.cache
Checking for pkg-config... yes
Checking for numpy-1... yes
Checking for scotch... no (pkg-config file not found)
 Trying to generate pkg-config file for scotch... failed
Checking for trilinos... no (pkg-config file not found)
 Trying to generate pkg-config file for trilinos... failed
Checking for ufc-1... yes
Checking for umfpack... yes
Checking for parmetis... yes
Checking for petsc... yes
Checking for gts... yes
Checking for boost... yes
Checking for python-2... yes
Checking for slepc... no (pkg-config file not found)
 Trying to generate pkg-config file for slepc... failed
Checking for libxml-2.0... yes
Resolving compiler... done
 Some tests failed using mpic++
 Switching to use mpicxx instead.
Found optional package: petsc
Found optional package: umfpack
Found optional package: gts
Found optional package: parmetis
Unable to find optional package: slepc
Unable to find optional package: scotch
Unable to find optional package: trilinos
Disabling compilation of PyDOLFIN

scons: warning: The env.Copy() method is deprecated; use the env.Clone() method instead.
File "/home/amin/Unicorn_fsi/unicorn-parafin-dist-2009-05-25_01/dolfin/dolfin/SConscript", line 180, in <module>
scons: done reading SConscript files.
scons: Building targets ...
mpicxx -o dolfin/fem/DirichletBC.os -c -Wall -pipe -ansi -DDEBUG -g -Werror -DNDEBUG -O2 -Wno-deprecated -DENABLE_GCC_EXT -DHAS_MPI=1 -DMPICH_IGNORE_CXX_SEEK -DPACKAGE_VERSION=\"0.8.0\" -DHAS_PETSC=1 -DHAS_UMFPACK=1 -DHAS_GTS=1 -DHAS_PARMETIS=1 -fPIC -I. -I/home/amin/Unicorn_fsi/unicorn-parafin-dist-2009-05-25_01/local/include -I/usr/include/libxml2 -I/usr/lib/petscdir/2.3.3/bmake/linux-gnu-c-opt -I/usr/lib/petscdir/2.3.3/include -I/usr/lib/openmpi/include -I/usr/lib/openmpi/lib -Idolfin -I/usr/include/suitesparse -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include dolfin/fem/DirichletBC.cpp
mpicxx -o dolfin/fem/DofMap.os -c -Wall -pipe -ansi -DDEBUG -g -Werror -DNDEBUG -O2 -Wno-deprecated -DENABLE_GCC_EXT -DHAS_MPI=1 -DMPICH_IGNORE_CXX_SEEK -DPACKAGE_VERSION=\"0.8.0\" -DHAS_PETSC=1 -DHAS_UMFPACK=1 -DHAS_GTS=1 -DHAS_PARMETIS=1 -fPIC -I. -I/home/amin/Unicorn_fsi/unicorn-parafin-dist-2009-05-25_01/local/include -I/usr/include/libxml2 -I/usr/lib/petscdir/2.3.3/bmake/linux-gnu-c-opt -I/usr/lib/petscdir/2.3.3/include -I/usr/lib/openmpi/include -I/usr/lib/openmpi/lib -Idolfin -I/usr/include/suitesparse -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include dolfin/fem/DofMap.cpp
mpicxx -o dolfin/function/DiscreteFunction.os -c -Wall -pipe -ansi -DDEBUG -g -Werror -DNDEBUG -O2 -Wno-deprecated -DENABLE_GCC_EXT -DHAS_MPI=1 -DMPICH_IGNORE_CXX_SEEK -DPACKAGE_VERSION=\"0.8.0\" -DHAS_PETSC=1 -DHAS_UMFPACK=1 -DHAS_GTS=1 -DHAS_PARMETIS=1 -fPIC -I. -I/home/amin/Unicorn_fsi/unicorn-parafin-dist-2009-05-25_01/local/include -I/usr/include/libxml2 -I/usr/lib/petscdir/2.3.3/bmake/linux-gnu-c-opt -I/usr/lib/petscdir/2.3.3/include -I/usr/lib/openmpi/include -I/usr/lib/openmpi/lib -Idolfin -I/usr/include/suitesparse -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include dolfin/function/DiscreteFunction.cpp
cc1plus: warnings being treated as errors
./dolfin/mesh/MeshEntity.h: In member function ‘void dolfin::DirichletBC::computeBCGeometric(__gnu_cxx::hash_map<unsigned int, double, __gnu_cxx::hash<unsigned int>, std::equal_to<unsigned int>, std::allocator<double> >&, dolfin::BoundaryCondition::LocalData&)’:
./dolfin/mesh/MeshEntity.h:43: error: dereferencing pointer ‘<anonymous>’ does break strict-aliasing rules
./dolfin/mesh/MeshEntity.h:43: error: dereferencing pointer ‘<anonymous>’ does break strict-aliasing rules
./dolfin/mesh/MeshEntity.h:43: error: dereferencing pointer ‘<anonymous>’ does break strict-aliasing rules
./dolfin/mesh/MeshEntity.h:46: error: dereferencing pointer ‘<anonymous>’ does break strict-aliasing rules
./dolfin/mesh/MeshEntity.h:46: error: dereferencing pointer ‘<anonymous>’ does break strict-aliasing rules
./dolfin/mesh/MeshEntity.h:46: error: dereferencing pointer ‘<anonymous>’ does break strict-aliasing rules
./dolfin/mesh/MeshEntity.h:46: error: dereferencing pointer ‘<anonymous>’ does break strict-aliasing rules
./dolfin/mesh/MeshEntity.h:46: error: dereferencing pointer ‘<anonymous>’ does break strict-aliasing rules
./dolfin/mesh/MeshEntity.h:46: error: dereferencing pointer ‘<anonymous>’ does break strict-aliasing rules
./dolfin/mesh/MeshEntity.h:31: error: dereferencing pointer ‘<anonymous>’ does break strict-aliasing rules
dolfin/fem/DirichletBC.cpp:437: note: initialized from here
scons: *** [dolfin/fem/DirichletBC.os] Error 1
cc1plus: warnings being treated as errors
./dolfin/mesh/MeshEntity.h: In member function ‘virtual void dolfin::DiscreteFunction::interpolate(dolfin::real*) const’:
./dolfin/mesh/MeshEntity.h:43: error: dereferencing pointer ‘<anonymous>’ does break strict-aliasing rules
./dolfin/mesh/MeshEntity.h:43: error: dereferencing pointer ‘<anonymous>’ does break strict-aliasing rules
./dolfin/mesh/MeshEntity.h:43: error: dereferencing pointer ‘<anonymous>’ does break strict-aliasing rules
./dolfin/mesh/MeshEntity.h:46: error: dereferencing pointer ‘<anonymous>’ does break strict-aliasing rules
./dolfin/mesh/MeshEntity.h:46: error: dereferencing pointer ‘<anonymous>’ does break strict-aliasing rules
./dolfin/mesh/MeshEntity.h:46: error: dereferencing pointer ‘<anonymous>’ does break strict-aliasing rules
./dolfin/mesh/MeshEntity.h:46: error: dereferencing pointer ‘<anonymous>’ does break strict-aliasing rules
./dolfin/mesh/MeshEntity.h:46: error: dereferencing pointer ‘<anonymous>’ does break strict-aliasing rules
./dolfin/mesh/MeshEntity.h:46: error: dereferencing pointer ‘<anonymous>’ does break strict-aliasing rules
./dolfin/mesh/MeshEntity.h:31: error: dereferencing pointer ‘<anonymous>’ does break strict-aliasing rules
dolfin/function/DiscreteFunction.cpp:237: note: initialized from here
scons: *** [dolfin/function/DiscreteFunction.os] Error 1
cc1plus: warnings being treated as errors
./dolfin/mesh/MeshEntity.h: In member function ‘void dolfin::DofMap::disp() const’:
./dolfin/mesh/MeshEntity.h:43: error: dereferencing pointer ‘<anonymous>’ does break strict-aliasing rules
./dolfin/mesh/MeshEntity.h:43: error: dereferencing pointer ‘<anonymous>’ does break strict-aliasing rules
./dolfin/mesh/MeshEntity.h:43: error: dereferencing pointer ‘<anonymous>’ does break strict-aliasing rules
./dolfin/mesh/MeshEntity.h:46: error: dereferencing pointer ‘<anonymous>’ does break strict-aliasing rules
./dolfin/mesh/MeshEntity.h:46: error: dereferencing pointer ‘<anonymous>’ does break strict-aliasing rules
./dolfin/mesh/MeshEntity.h:46: error: dereferencing pointer ‘<anonymous>’ does break strict-aliasing rules
./dolfin/mesh/MeshEntity.h:46: error: dereferencing pointer ‘<anonymous>’ does break strict-aliasing rules
./dolfin/mesh/MeshEntity.h:46: error: dereferencing pointer ‘<anonymous>’ does break strict-aliasing rules
./dolfin/mesh/MeshEntity.h:46: error: dereferencing pointer ‘<anonymous>’ does break strict-aliasing rules
./dolfin/mesh/MeshEntity.h:31: error: dereferencing pointer ‘<anonymous>’ does break strict-aliasing rules
dolfin/fem/DofMap.cpp:734: note: initialized from here
./dolfin/mesh/MeshEntity.h:43: error: dereferencing pointer ‘<anonymous>’ does break strict-aliasing rules
./dolfin/mesh/MeshEntity.h:43: error: dereferencing pointer ‘<anonymous>’ does break strict-aliasing rules
./dolfin/mesh/MeshEntity.h:43: error: dereferencing pointer ‘<anonymous>’ does break strict-aliasing rules
./dolfin/mesh/MeshEntity.h:46: error: dereferencing pointer ‘<anonymous>’ does break strict-aliasing rules
./dolfin/mesh/MeshEntity.h:46: error: dereferencing pointer ‘<anonymous>’ does break strict-aliasing rules
./dolfin/mesh/MeshEntity.h:46: error: dereferencing pointer ‘<anonymous>’ does break strict-aliasing rules
./dolfin/mesh/MeshEntity.h:46: error: dereferencing pointer ‘<anonymous>’ does break strict-aliasing rules
./dolfin/mesh/MeshEntity.h:46: error: dereferencing pointer ‘<anonymous>’ does break strict-aliasing rules
./dolfin/mesh/MeshEntity.h:46: error: dereferencing pointer ‘<anonymous>’ does break strict-aliasing rules
./dolfin/mesh/MeshEntity.h:31: error: dereferencing pointer ‘<anonymous>’ does break strict-aliasing rules
dolfin/fem/DofMap.cpp:767: note: initialized from here
scons: *** [dolfin/fem/DofMap.os] Error 1
scons: building terminated because of errors.
dolfin/fem/DirichletBC.os failed: Error 1
dolfin/function/DiscreteFunction.os failed: Error 1
dolfin/fem/DofMap.os failed: Error 1
amin@amin-laptop:~/Unicorn_fsi/unicorn-parafin-dist-2009-05-25_01/dolfin$

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