Hi Brian,

Thank you very much for your reply! No, I followed the instructions here 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@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@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@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@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@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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