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

Brian O'Shea bwoshea at gmail.com
Thu Nov 19 08:45:29 PST 2015


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>
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> 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
>>>>
>>>> _______________________________________________
>>>> yt-users mailing list
>>>> yt-users at lists.spacepope.org
>>>> http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
>>>>
>>>>
>>>
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>>>
>>
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