
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...), 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

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@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...), 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@lists.spacepope.org http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org

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@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@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...), 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@lists.spacepope.org http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
_______________________________________________ yt-users mailing list yt-users@lists.spacepope.org http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org

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@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@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@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...), 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@lists.spacepope.org http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
_______________________________________________ yt-users mailing list yt-users@lists.spacepope.org http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
_______________________________________________ yt-users mailing list yt-users@lists.spacepope.org http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org

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@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@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@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@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...), 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@lists.spacepope.org http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
_______________________________________________ yt-users mailing list yt-users@lists.spacepope.org http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
_______________________________________________ yt-users mailing list yt-users@lists.spacepope.org http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
_______________________________________________ yt-users mailing list yt-users@lists.spacepope.org http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
-- ********************************************************************* * * * Dr. Michael Kuhlen Theoretical Astrophysics Center * * email: mqk@astro.berkeley.edu UC Berkeley * * cell phone: (831) 588-1468 B-116 Hearst Field Annex # 3411 * * skype username: mikekuhlen Berkeley, CA 94720 * * * *********************************************************************

Hi Mike, Thank you very much for the suggestion, I will try this way. Cheers, Roberto 2012/8/26 Michael Kuhlen <mqk@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
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
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" <
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
libraries should be already in the system?
Thanks, Roberto
2012/8/25 j s oishi <jsoishi@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@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
On Sat, Aug 25, 2012 at 8:45 AM, j s oishi <jsoishi@gmail.com> wrote: sources. trobolo.trobolo.dinni5@gmail.com> those 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... ), 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@lists.spacepope.org http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
_______________________________________________ yt-users mailing list yt-users@lists.spacepope.org http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
_______________________________________________ yt-users mailing list yt-users@lists.spacepope.org http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
_______________________________________________ yt-users mailing list yt-users@lists.spacepope.org http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
-- ********************************************************************* * * * Dr. Michael Kuhlen Theoretical Astrophysics Center * * email: mqk@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@lists.spacepope.org http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org

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@gmail.com>
Hi Mike,
Thank you very much for the suggestion, I will try this way.
Cheers, Roberto
2012/8/26 Michael Kuhlen <mqk@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
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
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" <
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
libraries should be already in the system?
Thanks, Roberto
2012/8/25 j s oishi <jsoishi@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@yahoo.it> wrote:
Dear YT users,
I have a problem in installing the SciPy library when using YT
what happens is that:
-when installing from packages, also after activating yt (i.e.
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
On Sat, Aug 25, 2012 at 8:45 AM, j s oishi <jsoishi@gmail.com> wrote: sources. trobolo.trobolo.dinni5@gmail.com> those python, through 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... ), 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@lists.spacepope.org http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
_______________________________________________ yt-users mailing list yt-users@lists.spacepope.org http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
_______________________________________________ yt-users mailing list yt-users@lists.spacepope.org http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
_______________________________________________ yt-users mailing list yt-users@lists.spacepope.org http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
-- ********************************************************************* * * * Dr. Michael Kuhlen Theoretical Astrophysics Center * * email: mqk@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@lists.spacepope.org http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org

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@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@gmail.com>
Hi Mike,
Thank you very much for the suggestion, I will try this way.
Cheers, Roberto
2012/8/26 Michael Kuhlen <mqk@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@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@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@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@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...), > 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@lists.spacepope.org > http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org >
_______________________________________________ yt-users mailing list yt-users@lists.spacepope.org http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
_______________________________________________ yt-users mailing list yt-users@lists.spacepope.org http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
_______________________________________________ yt-users mailing list yt-users@lists.spacepope.org http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
-- ********************************************************************* * * * Dr. Michael Kuhlen Theoretical Astrophysics Center * * email: mqk@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@lists.spacepope.org http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
_______________________________________________ yt-users mailing list yt-users@lists.spacepope.org http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org

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-pro... 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@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@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@gmail.com>
Hi Mike,
Thank you very much for the suggestion, I will try this way.
Cheers, Roberto
2012/8/26 Michael Kuhlen <mqk@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@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@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@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@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...), >> 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@lists.spacepope.org >> http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org >> > > _______________________________________________ > yt-users mailing list > yt-users@lists.spacepope.org > http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org >
_______________________________________________ yt-users mailing list yt-users@lists.spacepope.org http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
_______________________________________________ yt-users mailing list yt-users@lists.spacepope.org http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
-- ********************************************************************* * * * Dr. Michael Kuhlen Theoretical Astrophysics Center * * email: mqk@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@lists.spacepope.org http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
_______________________________________________ yt-users mailing list yt-users@lists.spacepope.org http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
_______________________________________________ yt-users mailing list yt-users@lists.spacepope.org http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
-- ********************************************************************* * * * Dr. Michael Kuhlen Theoretical Astrophysics Center * * email: mqk@astro.berkeley.edu UC Berkeley * * cell phone: (831) 588-1468 B-116 Hearst Field Annex # 3411 * * skype username: mikekuhlen Berkeley, CA 94720 * * * *********************************************************************

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@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-pro... https://wiki.ubuntu.com/PackagingGuide/Complete https://help.launchpad.net/Packaging/PPA/Uploading
Would you like me to give it a try?
Mike
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@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@gmail.com>
Hi Mike,
Thank you very much for the suggestion, I will try this way.
Cheers, Roberto
2012/8/26 Michael Kuhlen <mqk@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@gmail.com> wrote:
The libraries may be, but the headers necessary to build them
are not. If you're on ubuntu, you may need to install the blas-dev
On Mon, Aug 27, 2012 at 1:49 PM, Matthew Turk <matthewturk@gmail.com> wrote: probably 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@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@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@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... ), >>> 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@lists.spacepope.org >>> http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org >>> >> >> _______________________________________________ >> yt-users mailing list >> yt-users@lists.spacepope.org >> http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org >> > > > _______________________________________________ > yt-users mailing list > yt-users@lists.spacepope.org > http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org >
_______________________________________________ yt-users mailing list yt-users@lists.spacepope.org http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
-- ********************************************************************* * * * Dr. Michael Kuhlen Theoretical Astrophysics Center * * email: mqk@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@lists.spacepope.org http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
_______________________________________________ yt-users mailing list yt-users@lists.spacepope.org http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
_______________________________________________ yt-users mailing list yt-users@lists.spacepope.org http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
-- ********************************************************************* * * * Dr. Michael Kuhlen Theoretical Astrophysics Center * * email: mqk@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@lists.spacepope.org http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org

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@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@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-pro... https://wiki.ubuntu.com/PackagingGuide/Complete https://help.launchpad.net/Packaging/PPA/Uploading
Would you like me to give it a try?
Mike
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@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@gmail.com>
Hi Mike,
Thank you very much for the suggestion, I will try this way.
Cheers, Roberto
2012/8/26 Michael Kuhlen <mqk@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
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@gmail.com> wrote: > The libraries may be, but the headers necessary to build them
> are > not. If you're on ubuntu, you may need to install the blas-dev
> 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@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@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@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
>>>> 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... ), >>>> 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@lists.spacepope.org >>>> http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org >>>> >>> >>> _______________________________________________ >>> yt-users mailing list >>> yt-users@lists.spacepope.org >>> http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org >>> >> >> >> _______________________________________________ >> yt-users mailing list >> yt-users@lists.spacepope.org >> http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org >> > > _______________________________________________ > yt-users mailing list > yt-users@lists.spacepope.org > http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org >
-- ********************************************************************* * * * Dr. Michael Kuhlen Theoretical Astrophysics Center * * email: mqk@astro.berkeley.edu UC Berkeley
* cell phone: (831) 588-1468 B-116 Hearst Field Annex # 3411
On Mon, Aug 27, 2012 at 1:49 PM, Matthew Turk <matthewturk@gmail.com> wrote: those probably package python, * *
* skype username: mikekuhlen Berkeley, CA 94720 * * * ********************************************************************* _______________________________________________ yt-users mailing list yt-users@lists.spacepope.org http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
_______________________________________________ yt-users mailing list yt-users@lists.spacepope.org http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
_______________________________________________ yt-users mailing list yt-users@lists.spacepope.org http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
-- ********************************************************************* * * * Dr. Michael Kuhlen Theoretical Astrophysics Center * * email: mqk@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@lists.spacepope.org http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
_______________________________________________ yt-users mailing list yt-users@lists.spacepope.org http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
participants (6)
-
j s oishi
-
Matthew Turk
-
Michael Kuhlen
-
roberto iaconi
-
Roberto Iaconi
-
trobolo dinni