[yt-users] SciPy and YT problem

Roberto Iaconi trobolo.trobolo.dinni5 at gmail.com
Tue Aug 28 02:42:45 PDT 2012


I never did that before, anyway yes, I think a PPA to install YT on the
system python would be very usefull!

Roberto



2012/8/27 Matthew Turk <matthewturk at gmail.com>

> 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               *
>> *                                                                   *
>> *********************************************************************
>> _______________________________________________
>> 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
>
>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://lists.spacepope.org/pipermail/yt-users-spacepope.org/attachments/20120828/27a26647/attachment.htm>


More information about the yt-users mailing list