[yt-users] yt on Blue Waters

Wed Apr 20 15:05:58 PDT 2016

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> 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>
> 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>
>> 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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