[yt-users] mpi4py and yt
Britton Smith
brittonsmith at gmail.com
Sat Feb 14 13:12:06 PST 2009
On Sat, Feb 14, 2009 at 1:56 PM, rsoares <dlleuz at xmission.com> wrote:
> I meant that I use mpich2 on all my computers, some which are "server"
> only, no gui stuff.
I don't really see what this has to do with anything.
I think I've covered this already, but I'll say it again. Openmpi works.
It installs, it runs with both enzo and yt.
It works.
I use it.
If you can get mpich2 to work, then use that. If not, I've given you an
alternative that I know works.
>
> rsoares wrote:
>
>> Yt /python2.6 is of course compatible with openmpi then?
>>
>> Britton Smith wrote:
>>
>>> Here's how it works.
>>> mpi4py is a module like any other. You build it with the python
>>> installation that you built all the other modules with, ala python setup.py
>>> build and install. In order for that to work, you need some mpi libraries
>>> installed. As I said, I prefer openmpi for this because they were the
>>> easiest for me to install and build mpi4py with. Before you do python build
>>> install in the mpi4py directory, you'll need to edit the .cfg file (can't
>>> remember exactly what it's called) so that the installation has the proper
>>> paths to your mpi install.
>>>
>>> When you've got mpi4py properly built, you will be able to run some yt
>>> operations in parallel in the following manner.
>>> 1. Whatever you want to do needs to be in some python script. As far as
>>> I know, you can't do parallel entering lines directly into the interpreter.
>>> Here's an example:
>>>
>>> ### Start
>>> from yt.mods import *
>>> from yt.config import ytcfg
>>> pf = EnzoStaticOutput("EnzoRuns/cool_core_rediculous/DD0252/DD0252")
>>> pc = PlotCollection(pf,center=[0.5,0.5,0.5])
>>> pc.add_projection("Density",0)
>>>
>>> if ytcfg.getint("yt","__parallel_rank") == 0:
>>> pc.save("DD0252")
>>> ### End
>>> That if statement at the end assures that the final image save is done by
>>> the root process only. The nice thing is this script can be run in exactly
>>> the same form in serial, too.
>>>
>>> 2. Let's say this script is called proj.py. You'll run it like this:
>>> mpirun -np 4 python proj.py --parallel
>>>
>>> If you don't unclude the --parallel, you'll see 4 instances of your
>>> proj.py script running separately, but each one doing the entire projection
>>> and not working together.
>>>
>>> Hope that helps,
>>>
>>> Britton
>>>
>>> On Fri, Feb 13, 2009 at 11:15 PM, rsoares <dlleuz at xmission.com <mailto:
>>> dlleuz at xmission.com>> wrote:
>>>
>>> What Python do you parallelize to install mpi4py into - or do you
>>> build /use mpi4py without python, then how?
>>>
>>> R.Soares
>>>
>>> Britton Smith wrote:
>>>
>>> I recommend using openmpi. I have been able to build openmpi
>>> on multiple platforms and then build mpi4py with it without
>>> any customization. As Matt has said, though, you won't see
>>> any benefit to using parallel until your simulations are at
>>> least 256^3 cells or more.
>>>
>>> On Thu, Feb 12, 2009 at 8:16 PM, Matthew Turk
>>> <matthewturk at gmail.com <mailto:matthewturk at gmail.com>
>>> <mailto:matthewturk at gmail.com <mailto:matthewturk at gmail.com>>>
>>> wrote:
>>>
>>> Hi again,
>>>
>>> I just realized that I should say a couple important caveats --
>>>
>>> 1. We haven't released 'yt-trunk' as 1.5 yet because it's
>>> not quite
>>> done or stable. It's going well, and many people use it for
>>> production-quality work, but it's not really
>>> stamped-and-completed.
>>> 2. I should *also* note that you won't really get a lot out of
>>> parallel yt unless you have relatively large datasets or
>>> relatively
>>> large amounts of computation on each cell while creating a
>>> derived
>>> field. It might end up being a bit more work than you're
>>> looking for,
>>> if you just want to get some plots out quickly.
>>>
>>> -Matt
>>>
>>> On Thu, Feb 12, 2009 at 7:12 PM, Matthew Turk
>>> <matthewturk at gmail.com <mailto:matthewturk at gmail.com>
>>> <mailto:matthewturk at gmail.com <mailto:matthewturk at gmail.com>>>
>>> wrote:
>>> > Hi!
>>> >
>>> > yt-trunk is now parallelized. Not all tasks work in
>>> parallel, but
>>> > projections, profiles (if done in 'lazy' mode) and halo
>>> finding (if
>>> > you use the SS_HopOutput module) are now parallelized.
>>> Slices are
>>> > almost done, and the new covering grid will be. It's not
>>> documented,
>>> > but those tasks should all run in parallel. We will be
>>> rolling
>>> out a
>>> > 1.5 release relatively soon, likely shortly after I
>>> defend my thesis
>>> > in April, that will have documentation and so forth.
>>> >
>>> > I'm surprised you can't compile against the mpich
>>> libraries in a
>>> > shared fashion. Unfortunately, I'm not an expert on MPI
>>> > implementations, so I can't quite help out there. In my
>>> personal
>>> > experience, using OpenMPI, I have needed to except when
>>> running on
>>> > some form of linux without a loader -- the previous
>>> discussion about
>>> > this was related to Kraken, which runs a Cray-specific
>>> form of linux
>>> > called "Compute Node Linux." I don't actually know
>>> offhand (anybody
>>> > else?) of any non-Cray machines at supercomputing out
>>> there require
>>> > static linking as opposed to a standard installation of
>>> Python.
>>> (I'm
>>> > sure they do, I just don't know of them!)
>>> >
>>> > As for the second part, usually when instantiating you
>>> have to
>>> run the
>>> > executable via mpirun. (On other MPI implementations,
>>> this could be
>>> > something different.) One option for this -- if you're
>>> running off
>>> > trunk -- would be to do something like:
>>> >
>>> > mpirun -np 4 python my_script.py --parallel
>>> >
>>> > where the file my_script.py has something like:
>>> >
>>> > --
>>> > from yt.mods import *
>>> > pf = EnzoStaticOutput("my_output")
>>> > pc = PlotCollection(pf, center=[0.5,0.5,0.5])
>>> > pc.add_projection("Density",0)
>>> > pc.save("hi_there")
>>> > --
>>> >
>>> > The projection would be executed in parallel, in this case.
>>> (There is
>>> > a command line interface called 'yt' that also works in
>>> parallel, but
>>> > it's still a bit in flux.) You can't just run "python"
>>> because
>>> of the
>>> > way the stdin and stdout streams work; you have to supply a
>>> script, so
>>> > that it can proceed without input from the user. (IPython's
>>> parallel
>>> > fanciness notwithstanding, which we do not use in yt.)
>>> >
>>> > But, keep in mind, running "mpirun -np 4" by itself,
>>> wihtout setting
>>> > up a means of distributing tasks (usually via a tasklist)
>>> will run
>>> > them all on the current machine. I am, unfortunately,
>>> not really
>>> > qualified to speak to setting up MPI implementations.
>>> But please do
>>> > let us know if you have problems with the yt aspects of this!
>>> >
>>> > -Matt
>>> >
>>> > On Thu, Feb 12, 2009 at 6:59 PM, rsoares
>>> <dlleuz at xmission.com <mailto:dlleuz at xmission.com>
>>> <mailto:dlleuz at xmission.com <mailto:dlleuz at xmission.com>>>
>>> wrote:
>>> >> Hi,
>>> >>
>>> >> I'm trying to run mpi4py on my 4 machines, but I need a
>>> parallelized version
>>> >> of Python. Tried to compile one with Python 2.5 and
>>> mpich2 but
>>> mpich2 won't
>>> >> let me built dynamic /shares libraries which it needs.
>>> Trying
>>> with the
>>> >> static ones involves alot of headers errors from both.
>>> >> Is yt-trunk capable of doing python in parallel?
>>> >>
>>> >> Without parallel-python, I mpdboot -n 4 then
>>> >>
>>> >> python
>>> >>>>>import MPI
>>> >>>>> rank, size = MPI.COMM_WORLD.rank, MPI.COMM_WORLD.size
>>> >>>>> print 'Hello World! I am process', rank, 'of', size
>>> >> Hello World! I am process 0 of 1
>>> >>>>>
>>> >>
>>> >> not 4 processes, and mpirun -np 4 python just hangs.
>>> mpi4py
>>> installed on
>>> >> all 4 nodes.
>>> >>
>>> >> Thanks.
>>> >>
>>> >> R.Soares
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