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

[Pengfei Chen]

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> 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>
> 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
>>>>>
>>>>>
>>>>
>>>> _______________________________________________
>>>> yt-users mailing list
>>>> yt-users at lists.spacepope.org
>>>> http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
>>>>
>>>>
>>>
>> _______________________________________________
>> yt-users mailing list
>> yt-users at lists.spacepope.org
>> http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
>>
>>
>
> _______________________________________________
> yt-users mailing list
> yt-users at lists.spacepope.org
> http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
>
>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://lists.spacepope.org/pipermail/yt-users-spacepope.org/attachments/20151120/fa7044eb/attachment.htm>