[yt-users] mpi4py and yt
Britton Smith
brittonsmith at gmail.com
Sat Feb 14 12:06:44 PST 2009
Well, yes.
On Sat, Feb 14, 2009 at 1:03 PM, rsoares <dlleuz at xmission.com> 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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