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]
<mailto:[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]
<mailto:[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]
<mailto:[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
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