Thank you for your quick replies. I downgraded boost; here is the next
ImportError (another library to downgrade?)
>>> import dolfin
> Traceback (most recent call last):
> File "<stdin>", line 1, in <module>
> File
> "<INSTALL_PATH>/anaconda/envs/fenics27/lib/python2.7/site-packages/dolfin/__init__.py",
> line 16, in <module>
> import cpp
> File
> "<INSTALL_PATH>/anaconda/envs/fenics27/lib/python2.7/site-packages/dolfin/cpp/__init__.py",
> line 42, in <module>
> exec("import %s" % module_name)
> File "<string>", line 1, in <module>
> File
> "<INSTALL_PATH>/anaconda/envs/fenics27/lib/python2.7/site-packages/dolfin/cpp/common.py",
> line 32, in <module>
> _common = swig_import_helper()
> File
> "<INSTALL_PATH>/anaconda/envs/fenics27/lib/python2.7/site-packages/dolfin/cpp/common.py",
> line 28, in swig_import_helper
> _mod = imp.load_module('_common', fp, pathname, description)
> ImportError: libbz2.so.1.0: cannot open shared object file: No such file
> or directory
>
Thanks,
Maarten
On 26 January 2015 at 18:55, Juan Luis Cano <[email protected]> wrote:
> On 2015-01-26 14:50, Maarten wrote:
>
> I tried these commands to install FEniCS on a CentOS 6.6 system. Here
> is the result:
>
> > which python
> <INSTALL_PATH>/anaconda/envs/fenics27/bin/python
>
>
>
> However:
>
> >>> import dolfin
> Traceback (most recent call last):
> File "<stdin>", line 1, in <module>
> File
> "<INSTALL_PATH>/anaconda/envs/fenics27/lib/python2.7/site-packages/dolfin/__init__.py",
> line 16, in <module>
> import cpp
> File
> "<INSTALL_PATH>/anaconda/envs/fenics27/lib/python2.7/site-packages/dolfin/cpp/__init__.py",
> line 42, in <module>
> exec("import %s" % module_name)
> File "<string>", line 1, in <module>
> File
> "<INSTALL_PATH>/anaconda/envs/fenics27/lib/python2.7/site-packages/dolfin/cpp/common.py",
> line 32, in <module>
> _common = swig_import_helper()
> File
> "<INSTALL_PATH>/anaconda/envs/fenics27/lib/python2.7/site-packages/dolfin/cpp/common.py",
> line 28, in swig_import_helper
> _mod = imp.load_module('_common', fp, pathname, description)
> ImportError: libboost_filesystem.so.1.55.0: cannot open shared object
> file: No such file or directory
>
>
> So no succes yet.
>
> Regards,
>
> Maarten
>
>
> Hello Maarten,
>
> I see what happened: conda installed boost from the default channel, which
> is a different version of what I used to compile DOLFIN (perhaps it should
> look for libboost_*.so instead of attaching the version number?)
>
> The workaround is forcing conda to install boost from my channel once
> again:
>
> $ (fenics27) $ conda install "boost=1.55" --channel
> https://conda.binstar.org/juanlu001/channel/fenics:1.4.0:centos
>
> This will downgrade boost and give you a working FEniCS :) Hopefully!
>
> I just updated the FEniCS recipe accordingly so the installation procedure
> should work from the first step now.
>
> Regards,
>
> Juan Luis
>
>
>
>
> On 15 January 2015 at 23:14, Juan Luis Cano <[email protected]> wrote:
>
>> I finally polished the recipes, adding test running and checksums for
>> both 1.4.0 and 1.5.0. I also uploaded compiled versions of FEniCS to
>> Binstar.
>>
>> Here is the source of the recipes (check the maint-1.4.0 branch too) with
>> non-very-rigorous instructions on installing and building:
>>
>> https://github.com/juanlu001/fenics-recipes
>>
>> To install FEniCS in CentOS 6 these commands should work:
>>
>> $ bash
>> $ conda create -n fenics27 python=2.7
>> $ source activate fenics27
>> (fenics27) $ conda install "fenics=1.4.0" mkl --channel
>> https://conda.binstar.org/juanlu001/channel/fenics:1.4.0:centos
>>
>> I still find that installing the packages in a different distribution
>> that the one used for building them has its problems (e.g. some hardcoded
>> paths in instant and ffc, at least in 1.4.0, that require manual fixing)
>> but still these recipes work wonderfully as a build system. I have compiled
>> all the libraries like thirty times in the past two weeks but in the end I
>> reached my goal, which was using FEniCS in my native system. Hope they are
>> useful :)
>>
>> Best regards,
>>
>> Juan Luis
>>
>>
>> On 2015-01-11 21:38, Juan Luis Cano wrote:
>>
>>> Hello all,
>>>
>>> I just wanted to say that I finally got VTK plotting to work.
>>> Fortunately there was a VTK conda package, so I switched my build system to
>>> a Linux Mint with a proper graphical server and it worked. I tested the
>>> package both in Mint and Arch Linux and I can claim success :)
>>>
>>> Let me repeat the commands:
>>>
>>> $ conda create --name py27 python=2.7
>>> $ source activate py27
>>> (py27)$ conda install fenics --channel juanlu001
>>>
>>>
>>> I will repeat the process with the first 1.5 release with updated
>>> requirements, and by then I will probably put all the conda recipes in an
>>> independent Bitbucket repo. Again, any feedback is welcome.
>>>
>>> Best regards,
>>>
>>> Juan Luis
>>>
>>> On 2015-01-05 22:32, Garth N. Wells wrote:
>>>
>>>> I think is is great.
>>>>
>>>> I haven’t tested yet, but a suggestion to make the process simpler is
>>>> to let PETSc build suitesparse, etc. PETSc is a C library but can be
>>>> installed with pip (it has a Python-based build system). It can take care
>>>> of a number of dependencies (solvers, graph partitioners, etc).
>>>>
>>>> I’ve copied Andy Terrel at Conitnuum Analytics who might have something
>>>> to chip in with.
>>>>
>>>> Garth
>>>>
>>>>
>>>> On 5 Jan 2015, at 13:07, Juan Luis Cano <[email protected]> wrote:
>>>>>
>>>>> Hello all,
>>>>>
>>>>> My name is Juan Luis Cano, I'm studying a MSc in Aerospace Engineering
>>>>> in Madrid and I started recently to play with FEniCS for my final degree
>>>>> project. For my day to day work I am using a virtualized Linux Mint and
>>>>> everything works like a charm thanks to the Ubuntu PPA, but as it is not
>>>>> the distribution which I normally use I tried to build a conda package
>>>>> these holidays.
>>>>>
>>>>> I noticed there are a couple of build systems out there (dorsal,
>>>>> hashdist) but, as the Anaconda distribution[1] is getting popular in the
>>>>> scientific Python world these days, I really wanted to try to provide
>>>>> FEniCS packages for it (at least in Linux). For those who don't know it,
>>>>> Anaconda's package manager, conda, is open source[2] and provides a nice
>>>>> build system[3].
>>>>>
>>>>> You can try out my progress so far with a Linux 64 bit box and a
>>>>> Python 2.7 environment:
>>>>>
>>>>> $ conda create --name py27 python=2.7
>>>>> $ source activate py27
>>>>> (py27)$ conda install fenics --channel juanlu001
>>>>>
>>>>> The build process itself was painful because I knew very little about
>>>>> FEniCS dependencies a week ago but right now I managed to run the
>>>>> `demo_poisson.py` (_without_ plotting, see below). The results seem OK
>>>>> from
>>>>> Paraview.
>>>>>
>>>>> The good thing is that I made the builds in an Ubuntu Server box but
>>>>> it works the same in an Arch Linux machine too. I didn't try to compile it
>>>>> against PETSc, Trilinos and such yet because I wanted some feedback from
>>>>> the community first, and know if this is something useful for anybody!
>>>>>
>>>>> The trick here was avoiding the Ubuntu packages (via apt-get) and
>>>>> compile the dependencies in the form of conda packages themselves. I did
>>>>> such with boost and suitesparse, for instance[4]. This way there are no
>>>>> linking problems across different Linux distros. I am stuck with VTK
>>>>> though
>>>>> because it seems to look for libGL.so, which in turn pulls from X11... and
>>>>> everythings gets messy very quickly[5].
>>>>>
>>>>> So if I can get some feedback about how does this work in others'
>>>>> computers, if this is any useful and which packages should I try to build
>>>>> next that would be great. Anybody can reproduce the build process using my
>>>>> conda-recipes fork.
>>>>>
>>>>> Kind regards and happy new year!
>>>>>
>>>>> Juan Luis
>>>>>
>>>>> [1] https://store.continuum.io/cshop/anaconda
>>>>> [2] https://github.com/conda/
>>>>> [3] http://conda.pydata.org/docs/build.html
>>>>> [4] https://binstar.org/juanlu001/
>>>>> [5]
>>>>> https://github.com/Juanlu001/conda-recipes/commit/a18cedc56e330ba09961b8ddaeb86f580e22f3cc
>>>>> _______________________________________________
>>>>> fenics-support mailing list
>>>>> [email protected]
>>>>> http://fenicsproject.org/mailman/listinfo/fenics-support
>>>>>
>>>>
>>>
>>
>
>
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