Here you go:
> ldd
> <INSTALL_PATH>/anaconda/envs/fenics27/lib/python2.7/site-packages/dolfin/cpp/_common.so
> | grep libbz2
> ldd: warning: you do not have execution permission for
> `<INSTALL_PATH>/anaconda/envs/fenics27/lib/python2.7/site-packages/dolfin/cpp/_common.so'
> <INSTALL_PATH>/anaconda/envs/fenics27/lib/python2.7/site-packages/dolfin/cpp/_common.so:
> /lib64/libc.so.6: version `GLIBC_2.14' not found (required by
> <INSTALL_PATH>/anaconda/envs/fenics27/lib/python2.7/site-packages/dolfin/cpp/../../../../libboost_filesystem.so.1.55.0)
> <INSTALL_PATH>/anaconda/envs/fenics27/lib/python2.7/site-packages/dolfin/cpp/_common.so:
> /lib64/libc.so.6: version `GLIBC_2.14' not found (required by
> <INSTALL_PATH>/anaconda/envs/fenics27/lib/python2.7/site-packages/dolfin/cpp/../../../../libboost_program_options.so.1.55.0)
> libbz2.so.1.0 => not found
>
and
bash-4.1$ find /{,usr/}lib* -name "libbz2*"
> /lib/libbz2.so.1
> /lib/libbz2.so.1.0.4
> /lib64/libbz2.so.1
> /lib64/libbz2.so.1.0.4
> /usr/lib/libbz2.so
> find: `/usr/lib64/audit': Permission denied
> /usr/lib64/libbz2.so
>
and for future reference:
> ldd --version
> ldd (GNU libc) 2.12
> Copyright (C) 2010 Free Software Foundation, Inc.
> ...
>
Hope this will help?
Greetings,
Maarten
On 26 January 2015 at 21:17, Juan Luis Cano <[email protected]> wrote:
> On 2015-01-26 19:21, Maarten wrote:
>
> 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
>
>
> This one isn't part of conda, but I wonder how come your system cannot
> locate that library. Could you please post the contents of this? (in Bash,
> just in case)
>
> $ ldd
> <INSTALL_PATH>/anaconda/envs/fenics27/lib/python2.7/site-packages/dolfin/cpp/_common.so
> | grep libbz2
> $ find /{,usr/}lib* -name "libbz2*"
>
> In theory they should be part of the system, but as they don't come with
> conda, installing them with the native package manager is compulsory. In
> your case:
>
> $ sudo yum install bzip2-libs bzip2-devel
>
> I checked the output of ldd and I think no other libraries are needed, but
> who knows!
>
> Regards,
>
> Juan Luis
>
>
>
> 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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