binaries for OSX 10.8 (mountain lion) needed
Hello there,
I tried installing fenics from 10.7 binaries on my macbook that came with os x 10.8 (mountain lion) pre-installed. But as expected from a previous question #204163 (which strangely is listed as solved but is actually not) it throws up incompatibility error & the installation exits.
Has anyone comeup with some solution. When can we expect 10.8 binaries or is there a workaround?
Thanks!
Question information
- Language:
- English Edit question
- Status:
- Solved
- Assignee:
- No assignee Edit question
- Solved by:
- Johannes Ring
- Solved:
- Last query:
- Last reply:
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Revision history for this message
|
#1 |
We hope to have binaries for OS X 10.8 available in the near future (within the next few weeks). In the mean time, you might want to try the development version of Dorsal, which has experimental support for OS X 10.8.
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Revision history for this message
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#2 |
Hi,
I have tried installing FEniCS on OS X 10.8 Mountain Lion with the experimental dorsal script and the mountain lion.platform file. Unfortunately, I encountered a lot of problems. Some of then which I could solve and some of them which still remain and I am lost with the remaining problems. I hope somebody here can help me and maybe that some of my comments will help others to advance in the installation process.
I installed Xcode and MacPorts and used macports to install all the necessary packages as described in the mountain lion.platform file. Then I modified the mountainlion.
# Platform specific variables
default PETSC_ARCH=
default SCOTCH_
default UMFPACK_
export CGAL_DIR=
export SCOTCH_
export PKG_CONFIG_
export DYLD_FRAMEWORK_
export CC=/usr/
export CXX=/usr/
# Platform specific setup
if [ ! -d "${INSTALL_
mkdir -p ${INSTALL_PATH}/bin
fi
for CMD in /opt/local/
do
ln -sf ${CMD} ${INSTALL_
done
# Define the packages this platform needs
PACKAGES=(
cgal
parmetis
# trilinos
petsc
slepc
armadillo
# swiginac
mtl
scotch
fiat
# ferari
ufc
ufl
ffc
# syfi
viper
instant
dolfin
)
My first fail was using cmake 2.8.9 which was unable to find boost. This I could resolve using cmake 2.8.5.
With this everything installs fine now except for dolfin. When I use the mac compilers, the cmake script does not find openmp, even when I set CC=.... and CXX=... the script seems to ignores these enviroment variables. Unfortunately I could not identify where the compilers are chosen. Does someone know how to choose the compilers and make this stick in cmake? And does someone know how to prevent clang being chosen as the standard compiler?
Then the tests for PETSC, SLEPC fail during cmake for dolfin causing them to be excluded in the configuration even though the tests run fine during the installation of PETSC and SLEPC.
I removed the PETSC_TEST_RUNS and SLEPC_TEST_RUNS in the <dolfin-
Ok so, now cmake seems to find everything except Trilinos, which is not yet installed on my machine, so that’s fine.
Now during the compilation of dolfin I first got compilation errors relating to “private member functions”, as described in the previous question https:/
( /Users/
declared private here
boost:
/Users/
'_a_star' is a private member of 'dolfin:
adapt(
since the script kept on going back to compilers I did not want it to use, I moved the standard apple compilers in /usr/bin/gcc to /usr/bin/gcc2 etc. in order to force cmake to pick up on the compilers installed via macports in /opt/local/bin/.
I then got some errors related to petsc. Dorsal installs Petsc 3.3 and some of the source files in dolfin were not compatible with pets 3.3. I had to change three things to make it work with Petsc 3.3 :
1. ParMETIS.
Fixed this by changing float to double in
int ncon = 1;
std::
std::
2. la/PETScMatrix.
3. Work/FEniCS/
compilation terminated.
make[2]: *** [dolfin/
Solution: change to #include <petsc-
This then compiles dolfin. I was already so glad that I made this that far but was then disappointed to find that trying to run a test example yields
python demo_poisson.py
Calling DOLFIN just-in-time (JIT) compiler, this may take some time.
In instant.recompile: The module did not compile, see '.instant/
Traceback (most recent call last):
File "demo_poisson.py", line 54, in <module>
f = Expression(
File "Work/FEniCS/
cpp_base, members = compile_
File "Work/FEniCS/
code_snippets), classnames)
File "Work/FEniCS/
dolfin_
File "Work/FEniCS/
return local_jit(*args, **kwargs)
File “Work/FEniCS/
**instant_
File "Work/FEniCS/
recompile(
File "Work/FEniCS/
"compile, see '%s'" % compile_
File "Work/FEniCS/
raise RuntimeError(text)
RuntimeError: In instant.recompile: The module did not compile, see '.instant/
Looking at the compile.log there are a lot of nasty errors, here an excerpt:
dolfin_
dolfin_
dolfin_
etc …
/Work/FEniCS/
/Work/
building '_dolfin_
creating build
creating build/temp.
/usr/bin/clang -fno-strict-
clang: warning: argument unused during compilation: '-fopenmp'
In file included from <built-in>:152:
<command line>:2:25: warning: missing terminating '"' character
#define DOLFIN_VERSION \"1.0.0\"
dolfin_
dolfin_
In file included from dolfin_
In file included from /Work/FEniCS/
In file included from /Work/FEniCS/
In file included from /Work/FEniCS/
In file included from /Work/FEniCS/
In file included from /Work/FEniCS/
/Work/
std::string str() const;
^
/Work/
virtual std::string str(bool verbose) const;
In file included from dolfin_
In file included from /Work/FEniCS/
In file included from /Work/FEniCS/
In file included from /Work/FEniCS/
In file included from /Work/FEniCS/
In file included from /Work/FEniCS/
In file included from /Work/FEniCS/
In file included from /Work/FEniCS/
In file included from /Work/FEniCS/
In file included from /Work/FEniCS/
In file included from /Work/FEniCS/
/Work/
mutable first_argument_
^
In file included from dolfin_
In file included from /Work/FEniCS/
In file included from /Work/FEniCS/
In file included from /Work/FEniCS/
In file included from /Work/FEniCS/
In file included from /Work/FEniCS/
In file included from /Work/FEniCS/
In file included from /Work/FEniCS/
In file included from /Work/FEniCS/
In file included from /Work/FEniCS/
In file included from /Work/FEniCS/
/Work/
mutable first_argument_
^
In file included from dolfin_
In file included from /Work/FEniCS/
In file included from /Work/FEniCS/
In file included from /Work/FEniCS/
In file included from /Work/FEniCS/
In file included from /Work/FEniCS/
In file included from /Work/FEniCS/
In file included from /Work/FEniCS/
/Work/
typedef dense_vector<Value> type;
^
/Work/
template <typename Value, typename Parameters> class dense_vector;
fatal error: too many errors emitted, stopping now [-ferror-limit=]
4 warnings and 20 errors generated.
error: command '/usr/bin/clang' failed with exit status 1
I don’t know how to resolve these issues. Hope somebody can help me. Would be so grateful for any help or ideas how to resolve this.
Thank you so much in advance.
Best wishes,
Susanne
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Revision history for this message
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#3 |
Setting CC and CXX works fine, however, you must to make sure to clear the CMake cache whenever you change these environment variables. When using Dorsal, the CMake cache files are located in a folder 'dorsal_build_dir' inside the DOLFIN source directory. Simply remove this folder to clear the CMake cache.
The DOLFIN 1.0.0 release is pretty old and does not work with the latest packages, like PETSc 3.3. Use the development version
instead by setting STABLE_BUILD=false in dorsal.cfg. The development version also has a CMake option 'DOLFIN_
Also try to set CC and CXX before running demo_poisson.py (or any PyDOLFIN programs) as noted in mountainlion.
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Revision history for this message
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#4 |
Hi,
Thank you so so much!!!! It works! :) You just made my day.
Your suggested changes work like a charm. :) Just the CGAL tests still fail but everything else is working fine :)
I will just shortly describe what I did to make it work on Mac OS X 10.8 including the helpful modifications you suggested. Hope that will help other people to install it :)
1. Install Xcode including Command Line Tools from Mac App Store
2. Install MacPorts http://
3. Install Gnu Compiler Collection 4.8 as described here:
https:/
4. Install Cmake 2.8.5:
http://
5. Install Packages as described in mountainlion.
sudo port install wget autogen readline pkgconfig libxml2 libtool \
gmp zlib python27 py27-numpy bzr bzrtools git-core \
ginac boost +python27 +openmpi vtk5 +python27 -x11 -tcltk \
suitesparse py27-scientific cppunit openmpi
6. Check out dorsal:
bzr branch lp:dorsal
7. Modify STABLE_BUILD=false in dorsal.cfg
8. Change in mountainlion.
export CC=/usr/local/bin
export CXX=/usr/local/bin
Thank you so much again!
Best wishes,
Susanne
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Revision history for this message
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#5 |
Forgot one thing I also added
export CC=/usr/local/bin
export CXX=/usr/local/bin
to the dolfin.conf file to make sure, these variables are set when I run the python examples :)
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Revision history for this message
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#6 |
I'm glad it works. To figure out why DOLFIN fails to pick up CGAL, take a look in dorsal_
BTW, I guess you mean:
export CC=/usr/
export CXX=/usr/
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Revision history for this message
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#7 |
Hi,
I tried to follow Susanne's steps. During macports packages' installation, the package 'bzrtools' threw error: Failed to install 'object-
I, however, installed everything else mentioned in 'dorsal.sh'. Next, I accidentally installed cmake 2.8.9 rather than 2.8.5.
As suggested I used STABLE_BUILD=false; export CC=/usr/
Finally, running ./dorsal.sh gave the following:
#######
Fetching CGAL-4.0.2
Unpacking CGAL-4.0.2
Building CGAL-4.0.2
-- Build CGAL from release in directory CGAL-4.0.2
-- Packagenames: CGAL-4.0.2
-- CGAL_MAJOR_
-- CGAL_MINOR_
-- CGAL_BUGFIX_
-- CGAL_SONAME_
-- CGAL_SOVERSION =9.0.0
-- CGAL_REFERENCE_
-- Building shared libraries
-- Targetting Unix Makefiles
-- Using /usr/local/bin/g++ compiler.
-- DARWIN_VERSION=12
-- Mac Leopard detected
-- USING CMake version: 2.8.9
-- System: Darwin
-- USING GCC_VERSION = '4.8.0 20120930 (experimental)'
-- Using gcc version 4 or later. Adding -frounding-math
-- Build type: Release
-- USING CXXFLAGS = ' -frounding-math -O3 -DNDEBUG'
-- USING LDFLAGS = ' '
-- GMPXX include: /opt/local/include
-- GMPXX libraries: /opt/local/
-- GMP include: /usr/local/include
-- GMP libraries: /usr/local/
-- GMP definitions:
-- USING GMP_VERSION = '4.3.1'
-- MPFR include: /usr/local/include
-- MPFR libraries: /usr/local/
-- MPFR definitions:
-- USING MPFR_VERSION = '2.4.1'
-- Boost include: /opt/local/include
-- Boost libraries: /opt/local/
-- Boost definitions:
-- USING BOOST_VERSION = '1.51.0'
-- Library config detected: Core
-- Library config detected: ImageIO
-- Library config detected: Qt3
-- Library config detected: Qt4
-- Library configs detected: CGAL;Core;
-- Configuring done
-- Generating done
-- Build files have been written to: /Users/
Scanning dependencies of target CGAL
[100%] Building CXX object src/CGAL/
In file included from /opt/local/
/opt/local/
BOOST_
Linking CXX shared library ../../lib/
[100%] Built target CGAL
[100%] Built target CGAL
Install the project...
-- Install configuration: "Release"
-- Up-to-date: /Users/
-- Up-to-date: /Users/
.
.
.
lots of CGAL stuff
.
.
.
-- Installing: /Users/
-- Up-to-date: /Users/
-- Up-to-date: /Users/
./dorsal.sh: line 548: 1351080237N: value too great for base (error token is "1351080237N")
Build finished.
Summary of timings:
#######
I don't know what to make out of it. Please help me out.
Thanks
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Revision history for this message
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#8 |
Hi Johannes,
Thank you so much for your fast and helpful reply!! I really appreciate your help! :) Here is the CMakeError.log file, which is at least very confusing for me:
Determining if the function pthread_create exists in the pthreads failed with the following output:
Change Dir: /Work/FEniCS/
Run Build Command:
/usr/bin/make -f CMakeFiles/
/usr/local/
Building C object CMakeFiles/
/usr/local/bin/gcc -DCHECK_
Linking C executable cmTryCompileExec
/usr/local/
/usr/local/bin/gcc -DCHECK_
ld: library not found for -lpthreads
collect2: error: ld returned 1 exit status
make[1]: *** [cmTryCompileExec] Error 1
make: *** [cmTryCompileEx
Performing C++ SOURCE FILE Test PETSC_CUSP_FOUND failed with the following output:
Change Dir: /Work/FEniCS/
Run Build Command:
/usr/bin/make -f CMakeFiles/
/usr/local/
Building CXX object CMakeFiles/
/usr/local/bin/g++ -DMPICH_
Linking CXX executable cmTryCompileExec
/usr/local/
/usr/local/bin/g++ -DMPICH_
Return value: 1
Source file was:
#include "petsc.h"
int main()
{
#if PETSC_HAVE_CUSP
return 0;
#else
return 1;
#endif
}
Performing C++ SOURCE FILE Test CGAL_TEST_RUNS failed with the following output:
Change Dir: /Work/FEniCS/
Linking CXX executable cmTryCompileExec
/usr/local/
/usr/local/bin/g++ -DMPICH_
ld: warning: ignoring file /usr/local/
ld: warning: ignoring file /usr/local/
Undefined symbols for architecture x86_64:
"___gmpq_add", referenced from:
CGAL:
"___gmpq_
CGAL:
"___gmpq_clear", referenced from:
CGAL:
"___gmpq_cmp", referenced from:
CGAL:
"___gmpq_cmp_si", referenced from:
CGAL:
CGAL:
CGAL:
"___gmpq_div", referenced from:
CGAL:
"___gmpq_equal", referenced from:
CGAL:
"___gmpq_init", referenced from:
CGAL:
"___gmpq_mul", referenced from:
CGAL:
"___gmpq_neg", referenced from:
CGAL:
"___gmpq_set_si", referenced from:
CGAL:
"___gmpq_sub", referenced from:
CGAL:
"___gmpz_clear", referenced from:
CGAL:
"___gmpz_cmp", referenced from:
CGAL:
CGAL:
"___gmpz_cmp_si", referenced from:
CGAL:
"___gmpz_
CGAL:
"___gmpz_gcd", referenced from:
CGAL:
"___gmpz_init", referenced from:
CGAL:
"___gmpz_
CGAL:
"___gmpz_
CGAL:
"___gmpz_mul", referenced from:
CGAL:
"___gmpz_neg", referenced from:
CGAL:
"___gmpz_set", referenced from:
CGAL:
"_mpfr_clear", referenced from:
CGAL:
CGAL:
"_mpfr_get_d", referenced from:
CGAL:
CGAL:
"_mpfr_init2", referenced from:
CGAL:
CGAL:
"_mpfr_set_q", referenced from:
CGAL:
"_mpfr_set_z", referenced from:
CGAL:
ld: symbol(s) not found for architecture x86_64
collect2: error: ld returned 1 exit status
make[1]: *** [cmTryCompileExec] Error 1
make: *** [cmTryCompileEx
Return value: 1
Source file was:
// CGAL test program from Andre Massing
#include <CGAL/AABB_tree.h> // *Must* be inserted before kernel!
#include <CGAL/AABB_
#include <CGAL/AABB_
#include <CGAL/Simple_
#include <CGAL/Exact_
#include <CGAL/Exact_
#include <CGAL/Bbox_3.h>
#include <CGAL/Point_3.h>
#include <CGAL/Nef_
#include <CGAL/Polyhedro
typedef CGAL::Simple_
typedef CGAL::Exact_
typedef CGAL::Exact_
typedef CGAL::Nef_
typedef SCK::FT FT;
typedef SCK::Ray_3 Ray;
typedef SCK::Line_3 Line;
typedef SCK::Point_3 Point;
typedef SCK::Triangle_3 Triangle;
typedef std::list<
typedef CGAL::AABB_
typedef CGAL::AABB_
typedef CGAL::AABB_
typedef Nef_polyhedron_
typedef Nef_polyhedron_
typedef Nef_polyhedron_
typedef Nef_polyhedron_
typedef CGAL::Polyhedro
int main()
{
//CGAL exact points
Point_3 p1(0,0,0);
Point_3 p2(1,0,0);
Point_3 p3(0,1,0);
Point_3 p4(0,0,1);
Polyhedron_3 P;
P.make_
Nef_polyhedron_3 NP(P);
NP.transform(
//Inexact points
Point a(1.0, 0.0, 0.0);
Point b(0.0, 1.0, 0.0);
Point c(0.0, 0.0, 1.0);
Point d(0.0, 0.0, 0.0);
std::
triangles.
triangles.
triangles.
// constructs AABB tree
Tree tree(triangles.
// counts #intersections
Ray ray_query(a,b);
std::cout << tree.number_
<< " intersections(s) with ray query" << std::endl;
// compute closest point and squared distance
Point point_query(2.0, 2.0, 2.0);
Point closest_point = tree.closest_
return 0;
}
Do you have any ideas on how to fix this? Thank you so much for your help again. Would be lost without it.
Best wishes,
Susanne
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Revision history for this message
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#9 |
Hi Neeraj,
I got rid of the cmake 2.8.9 using
sudo mv /usr/bin/cmake /usr/bin/cmake2
to forcefully move cmake 2.8.9 out of the way. Might not be the best or most elegant solution but it works. :)
To dorsal.sh. I checked out the latest version and I get the same error as you. Seems like some recent update has broken the dorsal script. Try checking out the revision number 741. Thats the one I used. You can check it out by
bzr branch lp:dorsal -r 741
Hope that helps.
Best wishes,
Susanne
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Revision history for this message
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#10 |
@Neeraj: The bzr problem looks to be a MacPorts problem and should be reported there. The problem at the end of dorsal.sh has been fixed in the latest Dorsal (revision 760).
@Susanne: Your problem with cgal seems to be that the libraries /usr/local/
ld: warning: ignoring file /usr/local/
ld: warning: ignoring file /usr/local/
This leads to the undefined symbols.
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Revision history for this message
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#11 |
I tried running the latest Dorsal (rev 760). This time the script goes through but halts while building dolfin. I have tried both cmake 2.8.5 and 2.8.9 while making sure to clear cmake cache as pointed by Johannes earlier. Here's what I get:
#######
.
.
.
Building dolfin
-- The C compiler identification is GNU 4.8.0
-- The CXX compiler identification is GNU 4.8.0
-- Checking whether C compiler has -isysroot
-- Checking whether C compiler has -isysroot - yes
-- Checking whether C compiler supports OSX deployment target flag
-- Checking whether C compiler supports OSX deployment target flag - yes
-- Check for working C compiler: /usr/local/bin/gcc
-- Check for working C compiler: /usr/local/bin/gcc -- works
-- Detecting C compiler ABI info
-- Detecting C compiler ABI info - done
-- Checking whether CXX compiler has -isysroot
-- Checking whether CXX compiler has -isysroot - yes
-- Checking whether CXX compiler supports OSX deployment target flag
-- Checking whether CXX compiler supports OSX deployment target flag - yes
-- Check for working CXX compiler: /usr/local/bin/g++
-- Check for working CXX compiler: /usr/local/bin/g++ -- works
-- 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_STD
-- Performing Test HAVE_STD - Success
-- Performing Test HAVE_DEBUG
-- Performing Test HAVE_DEBUG - Success
-- Performing Test HAVE_O2_
-- Performing Test HAVE_O2_
-- The Fortran compiler identification is GNU
-- Check for working Fortran compiler: /usr/local/
-- Check for working Fortran compiler: /usr/local/
-- Detecting Fortran compiler ABI info
-- Detecting Fortran compiler ABI info - done
-- Checking whether /usr/local/
-- Checking whether /usr/local/
-- Found MPI_C: /opt/local/
-- Found MPI_CXX: /opt/local/
-- Found MPI_Fortran: /opt/local/
-- Try OpenMP C flag = [-fopenmp]
-- Performing Test OpenMP_
-- Performing Test OpenMP_
-- Try OpenMP CXX flag = [-fopenmp]
-- Performing Test OpenMP_
-- Performing Test OpenMP_
-- Found OpenMP: -fopenmp
-- Performing Test OPENMP_
-- Performing Test OPENMP_
-- Boost version: 1.51.0
-- Found the following Boost libraries:
-- filesystem
-- program_options
-- system
-- thread
-- iostreams
-- math_tr1
-- mpi
-- serialization
-- Boost version: 1.51.0
-- Found the following Boost libraries:
-- timer
-- UFC version: 2.0.5
-- Checking for package 'Armadillo'
-- Looking for Fortran dgemm
-- Looking for Fortran dgemm - 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
-- A library with BLAS API found.
-- A library with BLAS API found.
-- Looking for Fortran cheev
-- Looking for Fortran cheev - found
-- A library with LAPACK API found.
-- Performing Test ARMADILLO_TEST_RUNS
-- Performing Test ARMADILLO_TEST_RUNS - Success
-- Found Armadillo: /Users/
-- Found LibXml2: /opt/local/
-- Found PythonInterp: /opt/local/
-- Found PythonLibs: /usr/lib/
-- NumPy headers found
-- Found SWIG: /opt/local/bin/swig (found version "2.0.8")
-- Performing Test PARMETIS_TEST_RUNS
-- Performing Test PARMETIS_TEST_RUNS - Success
-- Found ParMETIS: /Users/
-- Checking for package 'SCOTCH-PT'
-- Performing test SCOTCH_TEST_RUNS
-- Performing test SCOTCH_TEST_RUNS - Success
-- Found SCOTCH: /Users/
-- Checking for package 'AMD'
-- Checking for package 'UMFPACK'
-- Checking for package 'AMD'
-- Checking for package 'CHOLMOD'
-- Checking for package 'AMD'
-- A library with BLAS API found.
-- Performing Test CHOLMOD_TEST_RUNS
-- Performing Test CHOLMOD_TEST_RUNS - Success
-- Performing Test UMFPACK_TEST_RUNS
-- Performing Test UMFPACK_TEST_RUNS - Success
-- Checking for package 'CHOLMOD'
-- Checking for package 'AMD'
-- A library with BLAS API found.
-- Found HDF5: debug;/
-- HDF5 has been found, but is missing parallel support. It will not be enabled.
-- A library with BLAS API found.
-- PaStiX could not be found. Be sure to set PASTIX_DIR. (missing: PASTIX_INCLUDE_DIRS PASTIX_TEST_RUNS)
-- Checking for Trilinos
-- Trilinos could not be found
-- Checking for package 'PETSc'
-- PETSC_DIR is PETSC_DIR-NOTFOUND
-- PETSC_ARCH is empty
-- Unable to find petscconf.h
-- PETSc could not be found. Be sure to set PETSC_DIR and PETSC_ARCH. (missing: PETSC_LIBRARIES PETSC_DIR PETSC_INCLUDE_DIRS PETSC_TEST_RUNS PETSC_VERSION PETSC_VERSION_OK) (Required is at least version "3.2")
-- Checking for package 'CGAL'
-- Performing Test CGAL_TEST_RUNS
-- Performing Test CGAL_TEST_RUNS - Success
-- Found CGAL: /Users/
-- Found ZLIB: /usr/lib/libz.dylib (found version "1.2.5")
-- Found PkgConfig: /opt/local/
-- checking for module 'cppunit'
-- found cppunit, version 1.12.1
-- Found CPPUNIT: /opt/local/
-- Checking for package 'Sphinx'
-- Could NOT find Sphinx (missing: SPHINX_EXECUTABLE SPHINX_VERSION_OK) (Required is at least version "1.0.7")
-- Found VTK: /opt/local/
--
-- The following optional packages were found:
-- -------
-- (OK) OPENMP
-- (OK) MPI
-- (OK) UMFPACK
-- (OK) CHOLMOD
-- (OK) SCOTCH
-- (OK) PARMETIS
-- (OK) CGAL
-- (OK) ZLIB
-- (OK) PYTHON
-- (OK) VTK
--
-- The following optional packages could not be found:
-- -------
-- (**) PETSC
-- (**) SLEPC
-- (**) TRILINOS
-- (**) PASTIX
-- (**) SPHINX
-- (**) HDF5
--
CMake Warning at CMakeLists.txt:660 (message):
Disabling generation of documentation because Sphinx is missing.
-- Configuring done
-- Generating done
-- Build files have been written to: /Users/
Scanning dependencies of target dolfin
[ 0%] Building CXX object dolfin/
[ 0%] Building CXX object dolfin/
[ 1%] Building CXX object dolfin/
.
.
.
goes on till 27%
.
.
.
[ 27%] Building CXX object dolfin/
In file included from /Users/
/Users/
/Users/
Exact_
^
/Users/
Exact_
/Users/
/Users/
Exact_
^
/Users/
Exact_
/Users/
/Users/
Exact_
^
/Users/
Exact_
/Users/
/Users/
Exact_
^
/Users/
Exact_
/Users/
/Users/
Exact_
^
/Users/
Exact_
/Users/
/Users/
Exact_
^
/Users/
Exact_
In file included from /Users/
/Users/
/Users/
EK:
^
/Users/
^
/Users/
/Users/
EK:
^
/Users/
^
/Users/
/Users/
EK:
^
/Users/
^
In file included from /Users/
/Users/
/Users/
/Users/
/Users/
/Users/
/Users/
/Users/
/Users/
/Users/
/Users/
/Users/
/Users/
/Users/
/Users/
Exact_
^
/Users/
/Users/
/Users/
/Users/
/Users/
/Users/
/Users/
/Users/
/Users/
/Users/
/Users/
/Users/
/Users/
/Users/
/Users/
/Users/
Exact_
^
/Users/
/Users/
return back_from_
/Users/
/Users/
/Users/
/Users/
/Users/
/Users/
/Users/
/Users/
/Users/
/Users/
/Users/
/Users/
/Users/
/Users/
Exact_
^
/Users/
/Users/
make[2]: *** [dolfin/
make[1]: *** [dolfin/
make: *** [all] Error 2
Failure with exit status: 2
Exit message: There was a problem building dolfin.
#######
Sorry for such a messy post. But, I couldn't figure out the relevant part of the error message.
Thanks
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Revision history for this message
|
#12 |
@Neeraj: There are lots of errors, maybe because you are using GCC 4.8. I'm afraid I can't help you with that.
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Revision history for this message
|
#13 |
@Johannes: I tried using macports gcc4.5 and 4.7 but the CGAL build didn't go through. So, I reverted to using gcc that comes with mountain lion (Xcode). Here's the output:
#######
Building dolfin
-- The C compiler identification is GNU 4.2.1
-- The CXX compiler identification is GNU 4.2.1
-- Checking whether C compiler has -isysroot
-- Checking whether C compiler has -isysroot - yes
-- Checking whether C compiler supports OSX deployment target flag
-- Checking whether C compiler supports OSX deployment target flag - yes
-- 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
-- Checking whether CXX compiler has -isysroot
-- Checking whether CXX compiler has -isysroot - yes
-- Checking whether CXX compiler supports OSX deployment target flag
-- Checking whether CXX compiler supports OSX deployment target flag - yes
-- Check for working CXX compiler: /usr/bin/g++
-- Check for working CXX compiler: /usr/bin/g++ -- works
-- 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_STD
-- Performing Test HAVE_STD - Success
-- Performing Test HAVE_DEBUG
-- Performing Test HAVE_DEBUG - Success
-- Performing Test HAVE_O2_
-- Performing Test HAVE_O2_
-- The Fortran compiler identification is GNU
-- Check for working Fortran compiler: /usr/local/
-- Check for working Fortran compiler: /usr/local/
-- Detecting Fortran compiler ABI info
-- Detecting Fortran compiler ABI info - done
-- Checking whether /usr/local/
-- Checking whether /usr/local/
-- Found MPI_C: /opt/local/
-- Found MPI_CXX: /opt/local/
-- Found MPI_Fortran: /opt/local/
-- Try OpenMP C flag = [-fopenmp]
-- Performing Test OpenMP_
-- Performing Test OpenMP_
-- Try OpenMP CXX flag = [-fopenmp]
-- Performing Test OpenMP_
-- Performing Test OpenMP_
-- Found OpenMP: -fopenmp
-- Performing Test OPENMP_
-- Performing Test OPENMP_
-- Boost version: 1.51.0
-- Found the following Boost libraries:
-- filesystem
-- program_options
-- system
-- thread
-- iostreams
-- math_tr1
-- mpi
-- serialization
-- Boost version: 1.51.0
-- Found the following Boost libraries:
-- timer
-- UFC version: 2.0.5
-- Checking for package 'Armadillo'
-- Looking for Fortran dgemm
-- Looking for Fortran dgemm - 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
-- A library with BLAS API found.
-- A library with BLAS API found.
-- Looking for Fortran cheev
-- Looking for Fortran cheev - found
-- A library with LAPACK API found.
-- Performing Test ARMADILLO_TEST_RUNS
-- Performing Test ARMADILLO_TEST_RUNS - Success
-- Found Armadillo: /Users/
-- Found LibXml2: /opt/local/
-- Found PythonInterp: /opt/local/
-- Found PythonLibs: /usr/lib/
-- NumPy headers found
-- Found SWIG: /opt/local/bin/swig (found version "2.0.8")
-- Performing Test PARMETIS_TEST_RUNS
-- Performing Test PARMETIS_TEST_RUNS - Success
-- Found ParMETIS: /Users/
-- Checking for package 'SCOTCH-PT'
-- Performing test SCOTCH_TEST_RUNS
-- Performing test SCOTCH_TEST_RUNS - Success
-- Found SCOTCH: /Users/
-- Checking for package 'AMD'
-- Checking for package 'UMFPACK'
-- Checking for package 'AMD'
-- Checking for package 'CHOLMOD'
-- Checking for package 'AMD'
-- A library with BLAS API found.
-- Performing Test CHOLMOD_TEST_RUNS
-- Performing Test CHOLMOD_TEST_RUNS - Success
-- Performing Test UMFPACK_TEST_RUNS
-- Performing Test UMFPACK_TEST_RUNS - Success
-- Checking for package 'CHOLMOD'
-- Checking for package 'AMD'
-- A library with BLAS API found.
-- Found HDF5: debug;/
-- HDF5 has been found, but is missing parallel support. It will not be enabled.
-- A library with BLAS API found.
-- PaStiX could not be found. Be sure to set PASTIX_DIR. (missing: PASTIX_INCLUDE_DIRS PASTIX_TEST_RUNS)
-- Checking for Trilinos
CMake Warning at CMakeLists.txt:321 (message):
Unable to find Trilinos (>= 10.8.1)
-- Trilinos could not be found
-- Checking for package 'PETSc'
-- PETSC_DIR is /Users/
-- PETSC_ARCH is empty
-- Found petscconf.h
-- Looking for XOpenDisplay in /opt/local/
-- Looking for XOpenDisplay in /opt/local/
-- Looking for gethostbyname
-- Looking for gethostbyname - found
-- Looking for connect
-- Looking for connect - found
-- Looking for remove
-- Looking for remove - found
-- Looking for shmat
-- Looking for shmat - found
-- Looking for IceConnectionNumber in ICE
-- Looking for IceConnectionNumber in ICE - found
-- Found X11: /opt/local/
-- Performing Test PETSC_TEST_RUNS
-- Performing Test PETSC_TEST_RUNS - Success
-- PETSc test runs
-- Performing Test PETSC_CUSP_FOUND
-- Performing Test PETSC_CUSP_FOUND - Failed
-- PETSc configured without Cusp support
-- Found PETSc: /Users/
-- Checking for package 'SLEPc'
-- SLEPC_DIR is /Users/
-- Performing Test SLEPC_TEST_RUNS
-- Performing Test SLEPC_TEST_RUNS - Success
-- SLEPc test runs
-- Found SLEPc: /Users/
-- Checking for package 'CGAL'
-- Performing Test CGAL_TEST_RUNS
-- Performing Test CGAL_TEST_RUNS - Success
-- Found CGAL: /Users/
-- Found ZLIB: /usr/lib/libz.dylib (found version "1.2.5")
-- Found PkgConfig: /opt/local/
-- checking for module 'cppunit'
-- found cppunit, version 1.12.1
-- Found CPPUNIT: /opt/local/
-- Checking for package 'Sphinx'
-- Could NOT find Sphinx (missing: SPHINX_EXECUTABLE SPHINX_VERSION_OK) (Required is at least version "1.0.7")
-- Found VTK: /opt/local/
--
-- The following optional packages were found:
-- -------
-- (OK) OPENMP
-- (OK) MPI
-- (OK) PETSC
-- (OK) SLEPC
-- (OK) UMFPACK
-- (OK) CHOLMOD
-- (OK) SCOTCH
-- (OK) PARMETIS
-- (OK) CGAL
-- (OK) ZLIB
-- (OK) PYTHON
-- (OK) VTK
--
-- The following optional packages could not be found:
-- -------
-- (**) TRILINOS
-- (**) PASTIX
-- (**) SPHINX
-- (**) HDF5
--
CMake Warning at CMakeLists.txt:670 (message):
Disabling generation of documentation because Sphinx is missing.
-- Configuring done
-- Generating done
-- Build files have been written to: /Users/
Scanning dependencies of target dolfin
[ 0%] Building CXX object dolfin/
[ 0%] Building CXX object dolfin/
.
.
.
[ 93%] Building CXX object dolfin/
[ 94%] Building CXX object dolfin/
Linking CXX shared library libdolfin.dylib
ld: illegal text-relocation to ___gmp_
collect2: ld returned 1 exit status
make[2]: *** [dolfin/
make[1]: *** [dolfin/
make: *** [all] Error 2
#######
Please help.
Thanks
|
Revision history for this message
|
#14 |
/usr/local/
|
Revision history for this message
|
#15 |
CGAL from MacPorts solved my problem. I am able to build everything and it works great without any issues. I could also export dolfin.conf to .profile to setup dolfin automatically while using my preferred python IDE py-spyder (also from MacPorts). Thanks a lot Johannes, Susanne and Chris Tiee for your kind help.
Although the question was about the availability of the binaries but the solution is just as good, so we can close it now.
Cheers!
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Revision history for this message
|
#16 |
Dear all,
Sorry to open this discussion again but I still don't have CGAL working.
@Neeraj: Which compiler did you use in the end? Did you use the complete CGAL version from MacPorts? not just changed the libgmp.a?
Thank you in advance for your help.
Best wishes
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Revision history for this message
|
#17 |
@Susanne: I used the default compiler from OSX that came with Xcode command line tools, i.e. gcc version 4.2.1 (Based on Apple Inc. build 5658) (LLVM build 2336.11.00).
I also didn't allow dolfin.sh to download cgal for me by commenting it out in 'mountainlion.
I hope this helps,
Best regards
|
Revision history for this message
|
#18 |
Thanks Johannes Ring, that solved my question.
