On Wed, Mar 12, 2014 at 2:11 PM, Johannes Ring <[email protected]> wrote:
> On Wed, Mar 12, 2014 at 2:06 PM, Bishesh Khanal <[email protected]> > wrote: > > > > > > > > On Wed, Mar 12, 2014 at 1:14 PM, Johannes Ring <[email protected]> > wrote: > >> > >> On Tue, Mar 11, 2014 at 3:51 PM, Bishesh Khanal <[email protected]> > >> wrote: > >> > Dear all, > >> > I'm a beginner and trying to install fenics for the first time. I use > >> > fedora > >> > core 16 on a 64-bit machine. Having seen dorsal being supported only > up > >> > to > >> > fedora 15, I tried to install all the required components > individually. > >> > I installed FFC, FIAT, INSTANT, and UFL using: > >> > $python setup.py install > >> > > >> > > --prefix=/home/bkhanal/Documents/softwares/fenicsComponents/installDirectory/ > >> > > >> > I did not install UFC because it is said to be deprecated and > integrated > >> > to > >> > FFC. > >> > > >> > I got stuck at when trying to install dolfin. > >> > I use: > >> > ccmake > >> > > >> > > -DCMAKE_INSTALL_PREFIX=/home/bkhanal/Documents/softwares/fenicsComponents/ > >> > > >> > For some of the errors, I had manually set the path for the libraries > >> > such > >> > as boost, petsc etc. > >> > I also put the following in my .bashrc file: > >> > > >> > export > >> > > >> > > PATH=$PATH:/home/bkhanal/Documents/softwares/fenicsComponents/installDirectory/bin/ > >> > export > >> > > >> > > PYTHONPATH=/home/bkhanal/Documents/softwares/fenicsComponents/installDirectory/lib/python2.7/site-packages/:$PYTHONPATH > >> > > >> > However, now the cmake gives the following error (and the warning if > >> > it's > >> > important): > >> > > >> > CMake Warning at dolfin/CMakeLists.txt:316 (message): > >> > Unable to import UFC. Install latest UFC or check that PYTHONPATH > is > >> > set > >> > appropriately. Python will be disabled. > >> > > >> > CMake Error at CMakeLists.txt:793 (message): > >> > Generation of form files failed: > >> > > >> > Traceback (most recent call last): > >> > > >> > File "/home/bkhanal/Documents/ > >> > softwares/fenicsComponents/installDirectory/bin/ffc", line 45, in > >> > <module> > >> > from ffc.log import info > >> > > >> > ImportError: No module named ffc.log > >> > > >> > Traceback (most recent call last): > >> > > >> > File > >> > > >> > > "/home/bkhanal/Documents/softwares/fenicsComponents/fenics-project-dolfin-ed58f6bd083b/cmake/scripts/generate-form-files", > >> > line 73, in <module> > >> > raise RuntimeError, "Unable to compile form: %s/%s" % (root, f) > >> > > >> > RuntimeError: Unable to compile form: dolfin/ale/Poisson3D.ufl > >> > >> It looks like some of the FEniCS components was not installed > >> correctly or that PYTHONPATH was not set correctly. What is the > >> contents of this directory: > >> > >> > >> > /home/bkhanal/Documents/softwares/fenicsComponents/installDirectory/lib/python2.7/site-packages > >> > >> ? > > > > > > Thanks for the reply. Here are the contents of that directory: > > FIAT FIAT-1.3.0_-py2.7.egg-info instant instant-1.3.0_-py2.7.egg-info > > ufl UFL-1.3.0_-py2.7.egg-info > > I suspected something was wrong because I didn't see ffc here, but then I > > realized that there was also this directory > > ../installDirectory/lib64/python2.7/site-packages with following > contents: > > ffc FFC-1.3.0_-py2.7.egg-info ufc > > So now, I added this path lib64/python2.7/site-packages to PYTHONPATH. > > This eliminated the previous error and the warning about ufc. However, > now I > > have the following error during the cmake: > > > > > ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ > > > > CMake Error at CMakeLists.txt:793 (message): > > Generation of form files failed: > > > > Traceback (most recent call last): > > > > File > > > "/home/bkhanal/Documents/softwares/fenicsComponents/installDirectory/bin/ffc", > > line 45, in <module> > > from ffc.log import info > > File > > > "/home/bkhanal/Documents/softwares/fenicsComponents/installDirectory/lib64/python2.7/site-packages/ffc/__init__.py", > > line 18, in <module> > > from ffc.compiler import compile_form, compile_element > > File > > > "/home/bkhanal/Documents/softwares/fenicsComponents/installDirectory/lib64/python2.7/site-packages/ffc/compiler.py", > > line 127, in <module> > > from ffc.analysis import analyze_forms, analyze_elements > > File > > > "/home/bkhanal/Documents/softwares/fenicsComponents/installDirectory/lib64/python2.7/site-packages/ffc/analysis.py", > > line 42, in <module> > > from ffc.quadratureelement import default_quadrature_degree > > File > > > "/home/bkhanal/Documents/softwares/fenicsComponents/installDirectory/lib64/python2.7/site-packages/ffc/quadratureelement.py", > > line 27, in <module> > > from FIAT.functional import PointEvaluation > > File > > > "/home/bkhanal/Documents/softwares/fenicsComponents/installDirectory/lib/python2.7/site-packages/FIAT/__init__.py", > > line 11, in <module> > > from FIAT.finite_element import FiniteElement > > File > > > "/home/bkhanal/Documents/softwares/fenicsComponents/installDirectory/lib/python2.7/site-packages/FIAT/finite_element.py", > > line 19, in <module> > > from .polynomial_set import PolynomialSet > > File > > > "/home/bkhanal/Documents/softwares/fenicsComponents/installDirectory/lib/python2.7/site-packages/FIAT/polynomial_set.py", > > line 29, in <module> > > from . import expansions > > File > > > "/home/bkhanal/Documents/softwares/fenicsComponents/installDirectory/lib/python2.7/site-packages/FIAT/expansions.py", > > line 34, in <module> > > """) > > > > Exception: Unable to import the Python Scientific module required by > > FIAT. > > > > Consider installing the package python-scientific. > > > > > > Traceback (most recent call last): > > > > File > > > "/home/bkhanal/Documents/softwares/fenicsComponents/fenics-project-dolfin-ed58f6bd083b/cmake/scripts/generate-form-files", > > line 73, in <module> > > raise RuntimeError, "Unable to compile form: %s/%s" % (root, f) > > > > RuntimeError: Unable to compile form: dolfin/ale/Poisson3D.ufl > > > ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ > > > > I tried searching for the python-scientific package but it seems it is > > rather a collection of other packages (please correct me if I'm wrong, > I'm > > new to all of this and python). I installed the following: > > yum install numpy scipy python-matplotlib ipython python-pandas sympy > > python-nose > > where it installed everything except python-pandas for which it didn't > find > > any suitable distribution. > > I think the package you need to install is called ScientificPython: > > yum install ScientificPython > Thanks, it seems to be fine now with no errors although there are some warnings. I'll try to do the make install now and see if it works. Thank you. > > Johannes > > > I tried searching for cause of error I posted above, on the internet and > I > > found this link where installing python-netcdf is suggested: > > https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=674014 > > I tried searching for the package, but didn't find it. I found > > netcdf4-python and installed it with : yum install netcdf4-python > > But the same error I posted above persists. > > > > > > > >> > >> Johannes > > > > >
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