<div dir="ltr">Hi Brian,<div><br></div><div>Thank you very much for your reply! No, I followed the instructions here<a href="http://yt-project.org/docs/dev/installing.html"> http://yt-project.org/docs/dev/installing.html</a>. 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.</div><div><br></div><div>Thanks,</div><div>Pengfei</div></div><div class="gmail_extra"><br><div class="gmail_quote">On Thu, Nov 19, 2015 at 8:45 AM, Brian O'Shea <span dir="ltr"><<a href="mailto:bwoshea@gmail.com" target="_blank">bwoshea@gmail.com</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div dir="ltr">Hi Pengfei,<div><br></div><div>Did you use my installation instructions for yt on Blue Waters? If not, I can send those along.</div><span class="HOEnZb"><font color="#888888"><div><br></div><div>B</div><div><br></div></font></span></div><div class="HOEnZb"><div class="h5"><div class="gmail_extra"><br><div class="gmail_quote">On Thu, Nov 19, 2015 at 10:02 AM, Nathan Goldbaum <span dir="ltr"><<a href="mailto:nathan12343@gmail.com" target="_blank">nathan12343@gmail.com</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">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.<div><br></div><div>In either case, this points to the issue being a problem with<span></span> mpi4py, not yt.</div><div><br></div><div>Three things to try: </div><div><br></div><div>* 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.</div><div><br></div><div>* contact the Blue Waters sysadmins.</div><div><br></div><div>* contact the mpi4py developers</div><div><br></div><div>Hope that helps,</div><div><br></div><div>Nathan<div><div><br><br>On Thursday, November 19, 2015, Pengfei Chen <<a href="mailto:madcpf@gmail.com" target="_blank">madcpf@gmail.com</a>> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div dir="ltr">Hi Nathan,<div><br></div><div>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?</div><div><br></div><div>Thanks,</div><div>Pengfei</div><div><br></div><div><br></div></div><div class="gmail_extra"><br><div class="gmail_quote">On Wed, Nov 18, 2015 at 3:40 PM, Nathan Goldbaum <span dir="ltr"><<a>nathan12343@gmail.com</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div dir="ltr">Hi Pengfei,<div><br></div><div>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:</div><div><br></div><div> from mpi4py import MPI</div><div><br></div><div> print(MPI.COMM_WORLD.rank)</div><div><br></div><div>-Nathan</div></div><div class="gmail_extra"><br><div class="gmail_quote"><div><div>On Wed, Nov 18, 2015 at 5:36 PM, Pengfei Chen <span dir="ltr"><<a>madcpf@gmail.com</a>></span> wrote:<br></div></div><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div><div><div dir="ltr">Hi all,<div><br></div><div><div>I have trouble running yt in parallel on Blue Waters. I installed yt using miniconda, the version of yt is</div><div><br></div><div>~/miniconda/lib $yt version</div><div>yt module located at:</div><div> /u/sciteam/madcpf/miniconda/lib/python2.7/site-packages/yt-3.3.dev0-py2.7-linux-x86_64.egg</div><div>The current version and changeset for the code is:</div><div>---</div><div>Version = 3.3-dev</div><div>Changeset = 90f900be7a36+ yt</div><div><br></div><div>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:</div>
<div><br></div><div><div style="font-size:12.8px">import yt<br></div><div style="font-size:12.8px">yt.enable_parallelism()</div><div style="font-size:12.8px">from yt.utilities.parallel_tools.parallel_analysis_interface import\<br></div><div style="font-size:12.8px"> parallel_objects, communication_system</div></div><div style="font-size:12.8px"><br></div><div>comm = communication_system.communicators[-1]</div><div>print comm.rank, comm.size</div><div><br></div><div>0 1</div><div>0 1</div><div>0 1</div><div>0 1</div><div>0 1</div><div>0 1</div><div>0 1</div><div>0 1</div><div>...</div><div><br></div><div>When I run a similar code but with yt-2.x also on Blue Waters, I get what I expect:</div><div><br></div><div>7 16</div><div>15 16</div><div>6 16</div><div>9 16</div><div>11 16</div><div>8 16</div><div>0 16</div><div>4 16</div><div>...</div><div><br></div><div>I'm confused about it. Could anyone give me some suggestions please?</div><div><br></div><div>Thanks,</div><div>Pengfei</div></div></div>
<br></div></div>_______________________________________________<br>
yt-users mailing list<br>
<a>yt-users@lists.spacepope.org</a><br>
<a href="http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org" rel="noreferrer" target="_blank">http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org</a><br>
<br></blockquote></div><br></div>
<br>_______________________________________________<br>
yt-users mailing list<br>
<a>yt-users@lists.spacepope.org</a><br>
<a href="http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org" rel="noreferrer" target="_blank">http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org</a><br>
<br></blockquote></div><br></div>
</blockquote></div></div></div>
<br>_______________________________________________<br>
yt-users mailing list<br>
<a href="mailto:yt-users@lists.spacepope.org" target="_blank">yt-users@lists.spacepope.org</a><br>
<a href="http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org" rel="noreferrer" target="_blank">http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org</a><br>
<br></blockquote></div><br></div>
</div></div><br>_______________________________________________<br>
yt-users mailing list<br>
<a href="mailto:yt-users@lists.spacepope.org">yt-users@lists.spacepope.org</a><br>
<a href="http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org" rel="noreferrer" target="_blank">http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org</a><br>
<br></blockquote></div><br></div>