On 2014-05-11 11:01, Imran Ali wrote:
On 2014-05-11 10:48, Imran Ali wrote:
On 2014-05-09 09:07, Johannes Ring wrote:
On Thu, May 8, 2014 at 2:20 PM, Imran Ali
<[email protected]> wrote:
I am trying to install dolfin through dorsal using rhl6, but the
install
gets stuck :
Found configuration for project FEniCS.
Fetching dolfin-1.3.0
Verifying dolfin-1.3.0
dolfin-1.3.0.tar.gz: OK
Unpacking dolfin-1.3.0
Building dolfin-1.3.0
patching file demo/undocumented/plot-qt/cpp/CMakeLists.txt
patching file dolfin/CMakeLists.txt
-- The C compiler identification is GNU
-- The CXX compiler identification is GNU
-- Check for working C compiler: /usr/bin/gcc
-- Check for working C compiler: /usr/bin/gcc -- works
-- Detecting C compiler ABI info
-- Detecting C compiler ABI info - done
-- Check for working CXX compiler: /usr/bin/c++
-- Check for working CXX compiler: /usr/bin/c++ -- works
-- Detecting CXX compiler ABI info
-- Detecting CXX compiler ABI info - done
fatal: Not a git repository (or any parent up to mount point
/uio/hume/student-u29)
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
-- 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
-- The Fortran compiler identification is GNU
-- Check for working Fortran compiler: /usr/bin/gfortran
-- Check for working Fortran compiler: /usr/bin/gfortran -- works
-- Detecting Fortran compiler ABI info
-- Detecting Fortran compiler ABI info - done
-- Checking whether /usr/bin/gfortran supports Fortran 90
-- Checking whether /usr/bin/gfortran supports Fortran 90 -- yes
-- Found MPI_C:
/uio/hume/student-u29/imranal/Work/FEniCS/lib/libmpi.so
-- Found MPI_CXX:
/uio/hume/student-u29/imranal/Work/FEniCS/lib/libmpi_cxx.so;/uio/hume/student-u29/imranal/Work/FEniCS/lib/libmpi.so
-- Found MPI_Fortran:
/uio/hume/student-u29/imranal/Work/FEniCS/lib/libmpi_usempi.so;/uio/hume/student-u29/imranal/Work/FEniCS/lib/libmpi_mpifh.so;/uio/hume/student-u29/imranal/Work/FEniCS/lib/libmpi.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: 1.51.0
-- Found the following Boost libraries:
-- filesystem
-- program_options
-- system
-- thread
-- iostreams
-- mpi
-- serialization
-- timer
-- chrono
-- UFC version: 2.3.0
-- Found Eigen3:
/uio/hume/student-u29/imranal/Work/FEniCS/include/eigen3
(Required is at least version "3.0.0")
-- Found LibXml2: /usr/lib64/libxml2.so
-- Found PythonInterp:
/uio/hume/student-u29/imranal/Work/FEniCS/bin/python
(Required is at least version "2")
CMake Warning (dev) at CMakeLists.txt:306 (find_package):
Ignoring EXACT since no version is requested.
This warning is for project developers. Use -Wno-dev to suppress
it.
-- NumPy header version 1.6.2 found
-- Found SWIG: /uio/hume/student-u29/imranal/Work/FEniCS/bin/swig
(found
version "2.0.3")
-- Checking for package 'PETSc'
-- PETSC_DIR is /uio/hume/student-u29/imranal/Work/FEniCS
-- PETSC_ARCH is empty
-- Found petscconf.h
At this point nothing happens.
I don't know but you can try to disable some packages (for instance
PETSc). You can also try to skip the build tests by adding
-DDOLFIN_SKIP_BUILD_TESTS:BOOL=ON to CONFOPTS in
FEniCS/packages/dolfin.package in Dorsal.
Johannes
I added the skip build tests to CONFOPTS, and got following output :
-- The following optional packages were found:
-- -------------------------------------------
-- (OK) OPENMP
-- (OK) MPI
-- (OK) PETSC
-- (OK) SLEPC
-- (OK) UMFPACK
-- (OK) SCOTCH
-- (OK) PARMETIS
-- (OK) CGAL
-- (OK) ZLIB
-- (OK) PYTHON
-- (OK) HDF5
-- (OK) VTK
-- (OK) QT
--
-- The following optional packages were not found:
-- -----------------------------------------------
-- (**) PETSC4PY
-- (**) TAO
-- (**) TRILINOS
-- (**) CHOLMOD
-- (**) PASTIX
-- (**) SPHINX
--
-- QVTK not found, disabling QT for plotting
--
-- Generating SWIG interface.
-- --------------------------
Traceback (most recent call last):
File
"/mn/anatu/studenter-u1/imranal/Work/FEniCS/src/dolfin-1.3.0/cmake/scripts/generate-swig-interface",
line 36, in <module>
from dolfin_utils.cppparser import *
File
"/mn/anatu/studenter-u1/imranal/Work/FEniCS/src/dolfin-1.3.0/site-packages/dolfin_utils/cppparser/__init__.py",
line 1, in <module>
from CppHeaderParser import CppHeader
File
"/mn/anatu/studenter-u1/imranal/Work/FEniCS/src/dolfin-1.3.0/site-packages/dolfin_utils/cppparser/CppHeaderParser.py",
line 51, in <module>
import ply.lex as lex
ImportError: No module named ply.lex
-- QT not found, or QT/VTK not enabled in DOLFIN. Not building
demo_plot-qt
-- Disabling generation of documentation because Sphinx is missing.
-- Configuring done
CMake Warning at
demo/documented/auto-adaptive-poisson/cpp/CMakeLists.txt:34
(add_executable):
Cannot generate a safe linker search path for target
demo_auto-adaptive-poisson because files in some directories may
conflict
with libraries in implicit directories:
link library [libhdf5.so] in /usr/lib64 may be hidden by files in:
/mn/anatu/studenter-u1/imranal/Work/FEniCS/lib
link library [libblas.so] in /usr/lib64 may be hidden by files
in:
/mn/anatu/studenter-u1/imranal/Work/FEniCS/lib
Some of these libraries may not be found correctly.
And these CMake warnings continued untill the build crashed :
included from
/mn/anatu/studenter-u1/imranal/Work/FEniCS/include/CGAL/internal/Exact_type_selector.h:39,
from
/mn/anatu/studenter-u1/imranal/Work/FEniCS/include/CGAL/Filtered_kernel.h:35,
from /mn
Imran
I managed to resolve this by installing the GMP package.
Will let you know if the build went ok.
Imran
In the message where I posted that the build crashed, I meant to paste
the following output :
-- Generating done
-- Build files have been written to:
/mn/anatu/studenter-u1/imranal/Work/FEniCS/src/dolfin-1.3.0/dorsal_build_dir
make: Entering directory
`/mn/anatu/studenter-u1/imranal/Work/FEniCS/src/dolfin-1.3.0/dorsal_build_dir'
make[1]: Entering directory
`/mn/anatu/studenter-u1/imranal/Work/FEniCS/src/dolfin-1.3.0/dorsal_build_dir'
make[2]: Entering directory
`/mn/anatu/studenter-u1/imranal/Work/FEniCS/src/dolfin-1.3.0/dorsal_build_dir'
Scanning dependencies of target dolfin
make[2]: Leaving directory
`/mn/anatu/studenter-u1/imranal/Work/FEniCS/src/dolfin-1.3.0/dorsal_build_dir'
make[2]: Entering directory
`/mn/anatu/studenter-u1/imranal/Work/FEniCS/src/dolfin-1.3.0/dorsal_build_dir'
[ 1%] Building CXX object
dolfin/CMakeFiles/dolfin.dir/generation/PolyhedronUtils.cpp.o
In file included from
/mn/anatu/studenter-u1/imranal/Work/FEniCS/include/CGAL/internal/Exact_type_selector.h:39,
from
/mn/anatu/studenter-u1/imranal/Work/FEniCS/include/CGAL/Filtered_kernel.h:35,
from
/mn/anatu/studenter-u1/imranal/Work/FEniCS/include/CGAL/Exact_predicates_exact_constructions_kernel.h:29,
from
/mn/anatu/studenter-u1/imranal/Work/FEniCS/src/dolfin-1.3.0/dolfin/generation/cgal_csg3d.h:12,
from
/mn/anatu/studenter-u1/imranal/Work/FEniCS/src/dolfin-1.3.0/dolfin/generation/PolyhedronUtils.h:29,
from
/mn/anatu/studenter-u1/imranal/Work/FEniCS/src/dolfin-1.3.0/dolfin/generation/PolyhedronUtils.cpp:29:
/mn/anatu/studenter-u1/imranal/Work/FEniCS/include/CGAL/Mpzf.h: In
function ‘CGAL::Mpzf CGAL::Mpzf_square(const CGAL::Mpzf&)’:
/mn/anatu/studenter-u1/imranal/Work/FEniCS/include/CGAL/Mpzf.h:709:
error: ‘mpn_sqr’ was not declared in this scope
make[2]: ***
[dolfin/CMakeFiles/dolfin.dir/generation/PolyhedronUtils.cpp.o] Error 1
make[2]: Leaving directory
`/mn/anatu/studenter-u1/imranal/Work/FEniCS/src/dolfin-1.3.0/dorsal_build_dir'
make[1]: *** [dolfin/CMakeFiles/dolfin.dir/all] Error 2
make[1]: Leaving directory
`/mn/anatu/studenter-u1/imranal/Work/FEniCS/src/dolfin-1.3.0/dorsal_build_dir'
make: *** [all] Error 2
make: Leaving directory
`/mn/anatu/studenter-u1/imranal/Work/FEniCS/src/dolfin-1.3.0/dorsal_build_dir'
Failure with exit status: 2
Exit message: There was a problem building dolfin-1.3.0.
Any case, googling error: ‘mpn_sqr’ was not declared in this scope led
me to the following thread :
http://cgal-discuss.949826.n4.nabble.com/Error-on-installing-CGAL-on-LINUX-CentOS-td4659148.html
where it was suggested to install GMP. For this resolved the issue.
Imran
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