[yt-users] yt on Blue Waters
Jonah Miller
jonah.maxwell.miller at gmail.com
Wed Apr 20 16:19:59 PDT 2016
Ah, perfect. Thanks!
Best,
Jonah
On 16-04-20 06:05 PM, Nathan Goldbaum wrote:
> It can, but you'll need to edit the script to pull from your fork:
>
> https://bitbucket.org/yt_analysis/yt/src/248ccc5ef8b46d83682344d249c8de1c964759ab/doc/install_script.sh?at=yt&fileviewer=file-view-default#install_script.sh-1459
>
> On Wed, Apr 20, 2016 at 4:41 PM, Jonah Miller
> <jonah.maxwell.miller at gmail.com
> <mailto:jonah.maxwell.miller at gmail.com>> wrote:
>
> Hi Nathan, Matt, Brian,
>
> I see. Yes, I'll want to use the parallelism. Cool! I didn't
> realize the all-in-one script could pull from different repos.
> Thanks for your help!
>
> Best,
> Jonah
>
>
> On 16-04-20 05:39 PM, Nathan Goldbaum wrote:
>> You'll probably also want to follow Brian's instructions for
>> mpi4py if you're going t be using yt's parallelism. The install
>> script doesn't set that up since we can't assume people have an
>> MPI installation.
>>
>> On Wednesday, April 20, 2016, Matthew Turk <matthewturk at gmail.com
>> <mailto:matthewturk at gmail.com>> wrote:
>>
>> Hi Jonah,
>>
>> Just make sure you use the from-source option, and you can pull
>> whatever changesets you like into your source directory in your
>> installation.
>>
>> On Wed, Apr 20, 2016 at 4:34 PM, Jonah Miller
>> <jonah.maxwell.miller at gmail.com> wrote:
>> > Hi Brian, Matt,
>> >
>> > Thanks a lot! These instructions are exactly what I was
>> hoping for!
>> > Regarding the all-in-one install script, that won't work if
>> I want to
>> > install a fork of yt though, will it? This is to test my
>> carpet frontend on
>> > some production data.
>> >
>> > Best,
>> > Jonah
>> >
>> >
>> > On 16-04-20 05:24 PM, Matthew Turk wrote:
>> >>
>> >> I think it's a lot easier now that the new install script
>> has been merged
>> >> in:
>> >>
>> >>
>> >>
>> http://lists.spacepope.org/pipermail/yt-dev-spacepope.org/2016-April/006350.html
>> >>
>> >> -Matt
>> >>
>> >> On Wed, Apr 20, 2016 at 4:22 PM, Brian O'Shea
>> <bwoshea at gmail.com <mailto:bwoshea at gmail.com>> wrote:
>> >>>
>> >>> Yes indeed. It's a gigantic pain. Here are
>> instructions. Good luck!
>> >>>
>> >>> -----------------
>> >>>
>> >>> 0) Get the GNU software environment set up: “module swap
>> PrgEnv-cray
>> >>> PrgEnv-gnu” . This will be necessary later.
>> >>>
>> >>> 1) Install the Anaconda python distribution
>> >>> (https://store.continuum.io/cshop/anaconda/) for 64-bit
>> Linux systems.
>> >>> Refresh your path so the Anaconda python’s in your path.
>> >>>
>> >>> 2) Download mpi4py from
>> https://bitbucket.org/mpi4py/mpi4py/, or grab it
>> >>> from my home directory on Blue Waters
>> (~bwoshea/mpi4py-1.3.1.tar.gz).
>> >>>
>> >>> 3) Once you’ve unpacked it in your home directory, edit
>> the file
>> >>> mpi.cfg,
>> >>> which is in the top-level mpi4py directory, and add the
>> following chunk
>> >>> of
>> >>> text at the end of the file:
>> >>>
>> >>> [cray]
>> >>> mpicc = cc
>> >>> mpicxx = CC
>> >>> extra_link_args = -shared
>> >>>
>> >>> then, in the top-level mpi4py directory, type:
>> >>>
>> >>> python setup.py build --mpi=cray
>> >>> python setp.py install
>> >>>
>> >>> At this point, you should have a functional version of
>> mpi4py that uses
>> >>> the
>> >>> cray MPI libraries.
>> >>>
>> >>> 4) You can then install yt via source in your home
>> directory:
>> >>>
>> >>> hg clone https://bitbucket.org/yt_analysis/yt
>> >>> hg update yt
>> >>> python setup.py develop
>> >>>
>> >>> And it should work, though you’re going to need to modify
>> your
>> >>> LD_LIBRARY_PATH to point to your anaconda /lib
>> directory. You can verify
>> >>> that yt and mpi4py are playing nicely together by running
>> the scripts
>> >>> hw_MPI.py and yt_parallel_test.py, both of which are
>> sitting in my home
>> >>> directory. (Note that you can do this via batch script
>> or through the
>> >>> interactive queue, both with aprun - you can’t just do it
>> from the login
>> >>> node.)
>> >>>
>> >>> 5) and, optionally, if you want to install Rockstar using
>> yt from source,
>> >>> you do the following:
>> >>>
>> >>> hg clone http://bitbucket.org/MatthewTurk/rockstar
>> >>> cd rockstar
>> >>> hg pull
>> >>> hg up -C tip
>> >>> make lib
>> >>>
>> >>> and *then* make a file called rockstar.cfg that has a
>> single line of
>> >>> text:
>> >>> the path of the rockstar source code directory. At that
>> point, you need
>> >>> to
>> >>> run “python setup.py develop” again, and yt will
>> recognize that rockstar
>> >>> has
>> >>> been installed and play nicely with it. You will likely
>> also have to
>> >>> modify
>> >>> your LD_LIBRARY_PATH to point at your rockstar directory
>> so it can find
>> >>> the
>> >>> rockstar library (librockstar.so).
>> >>>
>> >>>
>> >>> On Wed, Apr 20, 2016 at 5:04 PM, Jonah Miller
>> >>> <jonah.maxwell.miller at gmail.com> wrote:
>> >>>>
>> >>>> Hi yt users,
>> >>>>
>> >>>> Does anybody have experience installing the development
>> version of yt on
>> >>>> blue waters (as opposed to relying on the module
>> pre-provided)? If so,
>> >>>> do
>> >>>> you have any tips or gotchas? I will be attempting an
>> installation in
>> >>>> the
>> >>>> next few days and I'm sort of hoping it's a solved problem.
>> >>>>
>> >>>> Best,
>> >>>> Jonah Miller
>> >>>> _______________________________________________
>> >>>> yt-users mailing list
>> >>>> yt-users at lists.spacepope.org
>> >>>>
>> http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
>> >>>
>> >>>
>> >>>
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