[yt-users] Problem when run yt dev in parallel on Blue Waters

Fri Nov 20 04:52:13 PST 2015

Thanks for the instruction Brian! I'll try to remember this email in case
people have questions about yt on blue waters and other cray machines in
the future.

On Friday, November 20, 2015, Brian O'Shea <bwoshea at gmail.com> wrote:

> Hi Pengfei,
>
> Sorry for the delay in response.  Here are instructions for getting yt-3
> to work on Blue Waters using mpi4py.  I believe that Rob Sisneros has
> gotten yt-3 working as a module; however, it is likely that it will not be
> updated very frequently, at least compared to the pace of yt development.
>
> --Brian
>
> -----------------------------------------------------------------------
>
> Getting yt-3 to work on Blue Waters:
>
> 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 Fri, Nov 20, 2015 at 3:46 AM, Pengfei Chen <madcpf at gmail.com
> <javascript:_e(%7B%7D,'cvml','madcpf at gmail.com');>> wrote:
>
>> Hi Brian,
>>
>> Thank you very much for your reply! No, I followed the instructions here
>>  http://yt-project.org/docs/dev/installing.html
>> <http://yt-project.org/docs/dev/installing.html>. I need the
>> yt-development, but failed when using All-in-One Installation Script to
>> install it on BW, so I used miniconda to install. Could you please send me
>> your installation instructions for yt on BW? I will try it out.
>>
>> Thanks,
>> Pengfei
>>
>> On Thu, Nov 19, 2015 at 8:45 AM, Brian O'Shea <bwoshea at gmail.com
>> <javascript:_e(%7B%7D,'cvml','bwoshea at gmail.com');>> wrote:
>>
>>> Hi Pengfei,
>>>
>>> Did you use my installation instructions for yt on Blue Waters?  If not,
>>> I can send those along.
>>>
>>> B
>>>
>>>
>>> On Thu, Nov 19, 2015 at 10:02 AM, Nathan Goldbaum <nathan12343 at gmail.com
>>> <javascript:_e(%7B%7D,'cvml','nathan12343 at gmail.com');>> wrote:
>>>
>>>> So it looks like either mpi4py isn't able to properly link against the
>>>> MPI installation on Blue waters or properly initialize itself at runtime.
>>>>
>>>> In either case, this points to the issue being a problem with mpi4py,
>>>> not yt.
>>>>
>>>> Three things to try:
>>>>
>>>> * check which version version of mpi4py you have installed in your
>>>> yt-2.x environment and install that version in your yt-3.x environment. You
>>>> may have found a bug in mpi4py 2.0, which made major changes to the mpi4py
>>>> library.
>>>>
>>>> * contact the Blue Waters sysadmins.
>>>>
>>>> * contact the mpi4py developers
>>>>
>>>> Hope that helps,
>>>>
>>>> Nathan
>>>>
>>>>
>>>> On Thursday, November 19, 2015, Pengfei Chen <madcpf at gmail.com
>>>> <javascript:_e(%7B%7D,'cvml','madcpf at gmail.com');>> wrote:
>>>>
>>>>> Hi Nathan,
>>>>>
>>>>> Thank you very much for your reply! When I run that test script in
>>>>> parallel with 16 cores, I get 16 0s. Any suggestions to fix this?
>>>>>
>>>>> Thanks,
>>>>> Pengfei
>>>>>
>>>>>
>>>>>
>>>>> On Wed, Nov 18, 2015 at 3:40 PM, Nathan Goldbaum <
>>>>> nathan12343 at gmail.com> wrote:
>>>>>
>>>>>> Hi Pengfei,
>>>>>>
>>>>>> Can you try to run the following test script in parallel? This will
>>>>>> determine if the issue is on the yt side of things or the mpi4py side of
>>>>>> things:
>>>>>>
>>>>>>     from mpi4py import MPI
>>>>>>
>>>>>>     print(MPI.COMM_WORLD.rank)
>>>>>>
>>>>>> -Nathan
>>>>>>
>>>>>> On Wed, Nov 18, 2015 at 5:36 PM, Pengfei Chen <madcpf at gmail.com>
>>>>>> wrote:
>>>>>>
>>>>>>> Hi all,
>>>>>>>
>>>>>>> I have trouble running yt in parallel on Blue Waters. I installed yt
>>>>>>> using miniconda, the version of yt is
>>>>>>>
>>>>>>> ~/miniconda/lib $yt version
>>>>>>> yt module located at:
>>>>>>>
>>>>>>> /u/sciteam/madcpf/miniconda/lib/python2.7/site-packages/yt-3.3.dev0-py2.7-linux-x86_64.egg
>>>>>>> The current version and changeset for the code is:
>>>>>>> ---
>>>>>>> Version = 3.3-dev
>>>>>>> Changeset = 90f900be7a36+ yt
>>>>>>>
>>>>>>> Then with miniconda/bin in PATH I installed mpi4py-2.0.0. But when I
>>>>>>> tried to make the following simple output in parallel, I get:
>>>>>>>
>>>>>>> import yt
>>>>>>> yt.enable_parallelism()
>>>>>>> from yt.utilities.parallel_tools.parallel_analysis_interface import\
>>>>>>>  parallel_objects, communication_system
>>>>>>>
>>>>>>> comm = communication_system.communicators[-1]
>>>>>>> print comm.rank, comm.size
>>>>>>>
>>>>>>> 0 1
>>>>>>> 0 1
>>>>>>> 0 1
>>>>>>> 0 1
>>>>>>> 0 1
>>>>>>> 0 1
>>>>>>> 0 1
>>>>>>> 0 1
>>>>>>> ...
>>>>>>>
>>>>>>> When I run a similar code but with yt-2.x also on Blue Waters, I get
>>>>>>> what I expect:
>>>>>>>
>>>>>>> 7 16
>>>>>>> 15 16
>>>>>>> 6 16
>>>>>>> 9 16
>>>>>>> 11 16
>>>>>>> 8 16
>>>>>>> 0 16
>>>>>>> 4 16
>>>>>>> ...
>>>>>>>
>>>>>>> I'm confused about it. Could anyone give me some suggestions please?
>>>>>>>
>>>>>>> Thanks,
>>>>>>> Pengfei
>>>>>>>
>>>>>>> _______________________________________________
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>>>>>>>
>>>>>>>
>>>>>>
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