[yt-users] SciPy and YT problem

Matthew Turk matthewturk at gmail.com
Mon Aug 27 14:56:27 PDT 2012


Hi Mike,

I actually haven't ever made one either! If you are up for the first shot
at it, that would be awesome! Thanks!

-Matt
On Aug 27, 2012 5:25 PM, "Michael Kuhlen" <mqk at astro.berkeley.edu> wrote:

> If you've done this before, or know how to do it quickly, yes please!
> I imagine a PPA would be useful for quite a few users.
>
> I've never made a PPA myself. But from a quick googling I found the
> following docs, with which I could probably figure it out:
>
>
> http://askubuntu.com/questions/28562/how-do-i-create-a-ppa-for-a-working-program
> https://wiki.ubuntu.com/PackagingGuide/Complete
> https://help.launchpad.net/Packaging/PPA/Uploading
>
> Would you like me to give it a try?
>
> Mike
>
>
> On Mon, Aug 27, 2012 at 1:49 PM, Matthew Turk <matthewturk at gmail.com>
> wrote:
> > Hi Roberto and Mike,
> >
> > Would it be worthwhile to try to make PPAs on Ubuntu for this?
> >
> > -Matt
> >
> > On Mon, Aug 27, 2012 at 5:32 AM, trobolo dinni
> > <trobolo.trobolo.dinni5 at gmail.com> wrote:
> >> The installation worked fine and I can now import yt while in the system
> >> python as a standard library. Now I'll check if every feature works
> fine.
> >> Thank you very much for the help Mike!
> >>
> >> Cheers,
> >>                Roberto
> >>
> >>
> >>
> >> 2012/8/26 trobolo dinni <trobolo.trobolo.dinni5 at gmail.com>
> >>>
> >>> Hi Mike,
> >>>
> >>> Thank you very much for the suggestion, I will try this way.
> >>>
> >>> Cheers,
> >>>                Roberto
> >>>
> >>>
> >>> 2012/8/26 Michael Kuhlen <mqk at astro.berkeley.edu>
> >>>>
> >>>> Hi Roberto
> >>>>
> >>>> This is one reason why I typically install yt manually using the
> >>>> system's python installation, instead of running the yt install
> >>>> script. It's really quite straightforward, just go to $YTDIR/ and do
> >>>> "python ./setup.py build", followed by "python ./setup.py install
> >>>> --prefix=$HOME/local", and then make sure that your PYTHONPATH
> >>>> environment variable includes $HOME/local/lib/python2.7/site-packages.
> >>>> Of course with this approach you also have to install all the other
> >>>> yt-dependencies using you system's python (using apt-get,
> >>>> easy_install, pip, or whatever). If you decide to go down this route
> >>>> you may want to start from scratch with your yt installation, since if
> >>>> you did run the yt install script then it probably installed all those
> >>>> packages with the yt-provided python. YMMV.
> >>>>
> >>>> Apologies to the yt dev's if I'm giving non-standard recommendations
> >>>> here, but this works for me.
> >>>>
> >>>> Mike
> >>>>
> >>>>
> >>>> On Sat, Aug 25, 2012 at 8:45 AM, j s oishi <jsoishi at gmail.com> wrote:
> >>>> > The libraries may be, but the headers necessary to build them
> probably
> >>>> > are
> >>>> > not. If you're on ubuntu, you may need to install the blas-dev
> package
> >>>> > or
> >>>> > whatever it may be called. Or you could build Blas and atlas from
> >>>> > sources.
> >>>> > This difficulty with building is why we avoid shipping scipy with
> yt.
> >>>> > Sorry
> >>>> > it's such a pain!
> >>>> >
> >>>> > I am away from my computer, so I am afraid I can't help further.
> >>>> >
> >>>> > On Aug 25, 2012 11:11 AM, "trobolo dinni"
> >>>> > <trobolo.trobolo.dinni5 at gmail.com>
> >>>> > wrote:
> >>>> >>
> >>>> >> Hi Jeff,
> >>>> >>
> >>>> >> I already tried that way and I get the same error about Alias and
> Blas
> >>>> >> libraries missing (attached)...
> >>>> >> My question is: since SciPy works fine with the system python,
> don't
> >>>> >> those
> >>>> >> libraries should be already in the system?
> >>>> >>
> >>>> >>
> >>>> >> Thanks,
> >>>> >>                 Roberto
> >>>> >>
> >>>> >>
> >>>> >> 2012/8/25 j s oishi <jsoishi at gmail.com>
> >>>> >>>
> >>>> >>> Hi Roberto,
> >>>> >>>
> >>>> >>> Try activating yt and then typing
> >>>> >>>
> >>>> >>> pip install scipy
> >>>> >>>
> >>>> >>> I am not sure that will work, but if it does, scipy will
> certainly be
> >>>> >>> in
> >>>> >>> the right place.
> >>>> >>>
> >>>> >>> Jeff
> >>>> >>>
> >>>> >>> On Aug 25, 2012 10:42 AM, "roberto iaconi" <
> robertoiaconi at yahoo.it>
> >>>> >>> wrote:
> >>>> >>>>
> >>>> >>>> Dear YT users,
> >>>> >>>>
> >>>> >>>> I have a problem in installing the SciPy library when using YT
> >>>> >>>> python,
> >>>> >>>> what happens is that:
> >>>> >>>>
> >>>> >>>> -when installing from packages, also after activating yt (i.e.
> >>>> >>>> through
> >>>> >>>> the command sudo apt-get install python-scipy) I get the
> >>>> >>>> confirmation that
> >>>> >>>> SciPy is correctly installed but i cannot import it in YT python,
> >>>> >>>> since
> >>>> >>>> probably the installation is connected to the system python
> instead.
> >>>> >>>> -when installing from source (by downloading the packages) I get
> a
> >>>> >>>> lot
> >>>> >>>> of errors concerning missing libraries (mainly blas and atlas).
> >>>> >>>> I installed them and added the paths to a "site.cfg" file, but I
> am
> >>>> >>>> still getting the same error.
> >>>> >>>>
> >>>> >>>> Also, I appended the system SciPy path through the
> sys.path.append()
> >>>> >>>> function, in this way I can succesfully import SciPy, but I
> cannot
> >>>> >>>> import
> >>>> >>>> any sublibrary such as SciPy.optimize (which is the one I
> >>>> >>>> particularly
> >>>> >>>> need).
> >>>> >>>>
> >>>> >>>> By browsing the YT Mailing List I found a user with a similar
> >>>> >>>> problem
> >>>> >>>>
> >>>> >>>> (
> http://lists.spacepope.org/htdig.cgi/yt-users-spacepope.org/2011-July/001694.html
> ),
> >>>> >>>> but there are no suggestions in reply.
> >>>> >>>>
> >>>> >>>> I would like to ask if there is a way to get SciPy installed
> under
> >>>> >>>> YT or
> >>>> >>>> make it available to be included.
> >>>> >>>>
> >>>> >>>> Cheers,
> >>>> >>>>                 Roberto
> >>>> >>>>
> >>>> >>>> _______________________________________________
> >>>> >>>> yt-users mailing list
> >>>> >>>> yt-users at lists.spacepope.org
> >>>> >>>> http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
> >>>> >>>>
> >>>> >>>
> >>>> >>> _______________________________________________
> >>>> >>> yt-users mailing list
> >>>> >>> yt-users at lists.spacepope.org
> >>>> >>> http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
> >>>> >>>
> >>>> >>
> >>>> >>
> >>>> >> _______________________________________________
> >>>> >> yt-users mailing list
> >>>> >> yt-users at lists.spacepope.org
> >>>> >> http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
> >>>> >>
> >>>> >
> >>>> > _______________________________________________
> >>>> > yt-users mailing list
> >>>> > yt-users at lists.spacepope.org
> >>>> > http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
> >>>> >
> >>>>
> >>>>
> >>>>
> >>>> --
> >>>> *********************************************************************
> >>>> *                                                                   *
> >>>> *  Dr. Michael Kuhlen              Theoretical Astrophysics Center  *
> >>>> *  email: mqk at astro.berkeley.edu   UC Berkeley                      *
> >>>> *  cell phone: (831) 588-1468      B-116 Hearst Field Annex # 3411  *
> >>>> *  skype username: mikekuhlen      Berkeley, CA 94720               *
> >>>> *                                                                   *
> >>>> *********************************************************************
> >>>> _______________________________________________
> >>>> yt-users mailing list
> >>>> yt-users at lists.spacepope.org
> >>>> http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
> >>>
> >>>
> >>
> >>
> >> _______________________________________________
> >> yt-users mailing list
> >> yt-users at lists.spacepope.org
> >> http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
> >>
> > _______________________________________________
> > yt-users mailing list
> > yt-users at lists.spacepope.org
> > http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
>
>
>
> --
> *********************************************************************
> *                                                                   *
> *  Dr. Michael Kuhlen              Theoretical Astrophysics Center  *
> *  email: mqk at astro.berkeley.edu   UC Berkeley                      *
> *  cell phone: (831) 588-1468      B-116 Hearst Field Annex # 3411  *
> *  skype username: mikekuhlen      Berkeley, CA 94720               *
> *                                                                   *
> *********************************************************************
> _______________________________________________
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> http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
>
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