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

[Nathan Goldbaum]

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
> <javascript:_e(%7B%7D,'cvml','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
>> <javascript:_e(%7B%7D,'cvml','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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