Re: [FEniCS-support] Install on SLES SP3

Wed, 24 Sep 2014 08:57:21 -0700 

Dear Johannes,

Getting closer...

[SCOTCH problem]

> Try cleaning out the cmake build cache for DOLFIN.
> When using Dorsal, you can do this by removing the dorsal_build_dir in the DOLFIN source directory. 

That made it.

["-fPIC" problem]

> It not DOLFIN that needs to be recompiled with -fPIC, it is Python.
> Either do that or recompile Python with shared libraries.

I manually installed python with "--enable-shared" and it made it too.

I now get this problem at build time (the full dorsal output is attached):
---------------
[...]
[ 97%] Swig source
/home/zatopek/Fenics/MyInstall/Downloads/dolfin-1.4.0/dolfin/swig/shared_ptr_classes.i:47: Error: Unable to find 'swig/ufc_shared_ptr_classes.i' 
make[2]: *** [dolfin/swig/modules/mesh/modulePYTHON_wrap.cxx] Error 1
--------------
However, the "ufc_shared_ptr_classes.i" file is present in the dorsal-downloaded ffc package: 
------------
> ll /home/zatopek/Fenics/MyInstall/Downloads/ffc-1.4.0/ufc/ufc_shared_ptr_classes.i -rw-r--r-- 1 zatopek users 377 Jun 2 16:10 /home/zatopek/Fenics/MyInstall/Downloads/ffc-1.4.0/ufc/ufc_shared_ptr_classes.i 
------------
I guess the problem might be that "ufc_shared_ptr_classes.i" is not in a directory "swig/" as "shared_ptr_classes.i" requests it. What would be a nice way to go over this? And please note, if it may play a role, that I am using my own self-compiled swig.3.0.2 version. 

Thanks again,
Serge



Found configuration for project FEniCS.
Skipping parmetis-4.0.2
Skipping scotch_6.0.0_esmumps
Skipping ScientificPython-2.8
Skipping fiat-1.4.0
Skipping ufl-1.4.0
Skipping ffc-1.4.0
Skipping instant-1.4.0
Fetching dolfin-1.4.0
Verifying dolfin-1.4.0
dolfin-1.4.0.tar.gz: OK
Unpacking dolfin-1.4.0
Building dolfin-1.4.0
-- The C compiler identification is GNU 4.9.1
-- The CXX compiler identification is GNU 4.9.1
-- Check for working C compiler: /home/zatopek/gcc/MyInstall/bin/gcc
-- Check for working C compiler: /home/zatopek/gcc/MyInstall/bin/gcc -- works
-- Detecting C compiler ABI info
-- Detecting C compiler ABI info - done
-- Check for working CXX compiler: /home/zatopek/gcc/MyInstall/bin/g++
-- Check for working CXX compiler: /home/zatopek/gcc/MyInstall/bin/g++ -- works
-- Detecting CXX compiler ABI info
-- Detecting CXX compiler ABI info - done
fatal: Not a git repository (or any parent up to mount point /home)
Stopping at filesystem boundary (GIT_DISCOVERY_ACROSS_FILESYSTEM not set).
-- Performing Test HAVE_PIPE
-- Performing Test HAVE_PIPE - Success
-- Performing Test HAVE_PEDANTIC
-- Performing Test HAVE_PEDANTIC - Success
-- Performing Test HAVE_STD_CPP11
-- Performing Test HAVE_STD_CPP11 - Success
-- Performing Test HAVE_DEBUG
-- Performing Test HAVE_DEBUG - Success
-- Performing Test HAVE_O2_OPTIMISATION
-- Performing Test HAVE_O2_OPTIMISATION - Success
-- The Fortran compiler identification is GNU
-- Check for working Fortran compiler: /home/zatopek/gcc/MyInstall/bin/gfortran
-- Check for working Fortran compiler: /home/zatopek/gcc/MyInstall/bin/gfortran 
 -- works
-- Detecting Fortran compiler ABI info
-- Detecting Fortran compiler ABI info - done
-- Checking whether /home/zatopek/gcc/MyInstall/bin/gfortran supports Fortran 90
-- Checking whether /home/zatopek/gcc/MyInstall/bin/gfortran supports Fortran 
90 -- yes
-- Looking for sys/types.h
-- Looking for sys/types.h - found
-- Looking for stdint.h
-- Looking for stdint.h - found
-- Looking for stddef.h
-- Looking for stddef.h - found
-- Check size of size_t
-- Check size of size_t - done
-- Found MPI_C: 
/opt/openmpi/lib/libmpi.so;/usr/lib64/libdl.so;/usr/lib64/libm.so;/usr/lib64/librt.so;/usr/lib64/libnsl.so;/usr/lib64/libutil.so
  
-- Found MPI_CXX: 
/opt/openmpi/lib/libmpi_cxx.so;/opt/openmpi/lib/libmpi.so;/usr/lib64/libdl.so;/usr/lib64/libm.so;/usr/lib64/librt.so;/usr/lib64/libnsl.so;/usr/lib64/libutil.so
  
-- Found MPI_Fortran: 
/opt/openmpi/lib/libmpi_f90.so;/opt/openmpi/lib/libmpi_f77.so;/opt/openmpi/lib/libmpi.so;/usr/lib64/libdl.so;/usr/lib64/libm.so;/usr/lib64/librt.so;/usr/lib64/libnsl.so;/usr/lib64/libutil.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: 1.56.0
-- Found the following Boost libraries:
--   filesystem
--   program_options
--   system
--   thread
--   iostreams
-- UFC version: 1.4.0
-- Found Eigen3: /home/zatopek/Eigen3/eigen-eigen-1306d75b4a21 (Required is at 
least version "3.0.0") 
-- Found LibXml2: /usr/lib64/libxml2.so (found version "2.7.6") 
-- Found PythonInterp: /home/zatopek/Python/MyInstall/bin/python (found 
suitable version "2.7.8", minimum required is "2") 
-- NumPy header version 1.8.1 found
-- Found SWIG: /home/zatopek/swig-3.0.2/MyInstall/bin/swig (found version 
"3.0.2") 
-- Checking for package 'PETSc'
-- PETSC_DIR is /opt/petsc/petsc-3.4.3-opt
-- PETSC_ARCH is arch-linux2-c-opt
-- Found petscconf.h
-- Performing test PETSC_TEST_RUNS - Success
-- Performing Test PETSC_CUSP_FOUND
-- Performing Test PETSC_CUSP_FOUND - Failed
-- PETSc configured without Cusp support
-- Found PETSc: /opt/petsc/petsc-3.4.3-opt/arch-linux2-c-opt/lib/libpetsc.so 
(Required is at least version "3.3") 
-- Checking for package 'SLEPc'
-- SLEPC_DIR is SLEPC_DIR-NOTFOUND
-- SLEPc could not be found. Be sure to set SLEPC_DIR, PETSC_DIR, and 
PETSC_ARCH. (missing:  SLEPC_LIBRARIES SLEPC_DIR SLEPC_INCLUDE_DIRS 
SLEPC_TEST_RUNS SLEPC_VERSION SLEPC_VERSION_OK) (Required is at least version 
"3.3")
-- Checking for package 'PETSc4Py'
-- Performing Test PARMETIS_TEST_RUNS
-- Performing Test PARMETIS_TEST_RUNS - Success
-- Found ParMETIS: 
/home/zatopek/Fenics/MyInstall/lib/libparmetis.so;/home/zatopek/Fenics/MyInstall/lib/libmetis.so
 (Required is at least version "4.0.2") 
-- Checking for package 'SCOTCH-PT'
-- Found SCOTCH (version 6.0.0)
-- Performing test SCOTCH_TEST_RUNS
-- Performing test SCOTCH_TEST_RUNS - Success
-- Found SCOTCH: 
/home/zatopek/Fenics/MyInstall/lib/libptscotch.a;/home/zatopek/Fenics/MyInstall/lib/libscotch.a;/home/zatopek/Fenics/MyInstall/lib/libptscotcherr.a
  
-- Checking for package 'AMD'
-- Looking for Fortran sgemm
-- Looking for Fortran sgemm - found
-- Looking for include file pthread.h
-- Looking for include file pthread.h - found
-- Looking for pthread_create
-- Looking for pthread_create - found
-- Found Threads: TRUE  
-- Checking for package 'UMFPACK'
-- Checking for package 'AMD'
-- Checking for package 'CHOLMOD'
-- Checking for package 'AMD'
-- A library with BLAS API found.
-- Looking for Fortran cheev
-- Looking for Fortran cheev - found
-- Checking for package 'CHOLMOD'
-- Checking for package 'AMD'
-- A library with BLAS API found.
-- Found HDF5: 
/usr/lib64/libhdf5.so;/usr/lib64/libpthread.so;/usr/lib64/libz.so;/usr/lib64/librt.so;/usr/lib64/libm.so
  
-- HDF5 has been found, but is missing parallel support. It will not be enabled.
-- PASTIX_LIBRARIES 
PASTIX_LIBRARY-NOTFOUND;/usr/lib64/librt.so;/usr/lib64/libm.so
-- A library with BLAS API found.
-- PaStiX could not be found. Be sure to set PASTIX_DIR. (missing:  
PASTIX_INCLUDE_DIRS PASTIX_TEST_RUNS PASTIX_VERSION PASTIX_VERSION_OK) 
-- Checking for Trilinos
-- Unable to find Trilinos (>= 11.0.0)
-- Trilinos could not be found
-- 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) 
(Required is at least version "4.1")
-- Found ZLIB: /usr/lib64/libz.so (found version "1.2.7") 
-- Found PkgConfig: /usr/bin/pkg-config (found version "0.23") 
-- checking for module 'cppunit'
--   package 'cppunit' not found
-- CPPUNIT could not be found. Be sure to set CPPUNIT_DIR. (missing:  
CPPUNIT_LIBRARIES CPPUNIT_INCLUDE_DIRS) 
-- Checking for package 'Sphinx'
-- Found Sphinx: /home/zatopek/Sphinx/MyInstall/bin/sphinx-build (Required is 
at least version "1.1.0") 
-- Looking for Q_WS_X11
-- Looking for Q_WS_X11 - found
-- Looking for Q_WS_WIN
-- Looking for Q_WS_WIN - not found
-- Looking for Q_WS_QWS
-- Looking for Q_WS_QWS - not found
-- Looking for Q_WS_MAC
-- Looking for Q_WS_MAC - not found
-- Found Qt4: /usr/bin/qmake (found version "4.6.3") 
-- Found VTK: /home/zatopek/VTK/MyInstall/lib/cmake/vtk-6.1 (found version 
"6.1")
-- 
-- The following optional packages were found:
-- -------------------------------------------
-- (OK) OPENMP
-- (OK) MPI
-- (OK) PETSC
-- (OK) SCOTCH
-- (OK) PARMETIS
-- (OK) ZLIB
-- (OK) PYTHON
-- (OK) SPHINX
-- (OK) VTK
-- (OK) QT
-- 
-- The following optional packages were not found:
-- -----------------------------------------------
-- (**) PETSC4PY
-- (**) SLEPC
-- (**) TRILINOS
-- (**) UMFPACK
-- (**) CHOLMOD
-- (**) PASTIX
-- (**) CGAL
-- (**) HDF5
-- 
-- 
-- Generating SWIG interface.
-- --------------------------
-- Found Qt4: /usr/bin/qmake (found version "4.6.3") 
-- Enabling generation of documentation.
-- Initializing sphinx projects
-- Enabling generation of html-documentation
-- 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/zatopek/Fenics/MyInstall/Downloads/dolfin-1.4.0/dorsal_build_dir
make: Entering directory 
`/home/zatopek/Fenics/MyInstall/Downloads/dolfin-1.4.0/dorsal_build_dir'
make[1]: Entering directory 
`/home/zatopek/Fenics/MyInstall/Downloads/dolfin-1.4.0/dorsal_build_dir'
make[2]: Entering directory 
`/home/zatopek/Fenics/MyInstall/Downloads/dolfin-1.4.0/dorsal_build_dir'
Scanning dependencies of target dolfin
make[2]: Leaving directory 
`/home/zatopek/Fenics/MyInstall/Downloads/dolfin-1.4.0/dorsal_build_dir'
make[2]: Entering directory 
`/home/zatopek/Fenics/MyInstall/Downloads/dolfin-1.4.0/dorsal_build_dir'
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Linking CXX shared library libdolfin.so
make[2]: Leaving directory 
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Scanning dependencies of target copy_swig_files
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/home/zatopek/Fenics/MyInstall/Downloads/dolfin-1.4.0/dolfin/swig/shared_ptr_classes.i:47:
 Error: Unable to find 'swig/ufc_shared_ptr_classes.i'
make[2]: *** [dolfin/swig/modules/mesh/modulePYTHON_wrap.cxx] Error 1
make[2]: Leaving directory 
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make[1]: *** [dolfin/swig/modules/mesh/CMakeFiles/_mesh.dir/all] Error 2
make[1]: Leaving directory 
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make: *** [all] Error 2
make: Leaving directory 
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Failure with exit status: 2
Exit message: There was a problem building dolfin-1.4.0.

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