<div dir="ltr">Hi Nathan,<br><br>Thank you for the quick response! <div><br></div><div>On Smic: Where is this "clean.sh" file? In the old yt3, it is under yt-x86_64/src/yt-hg, but I cannot find it in the new "/yt-conda/".<div><br></div><div>On Comet, after reinstalling yt following your instructions, I am able to update yt now. However, when I submit a job, I get this error at "import yt":</div><div><div>...</div><div><div> File "/home/yuan/source/yt-conda/src/yt-hg/yt/__init__.py", line 78, in <module></div><div> import numpy as np # For modern purposes</div></div><div>...</div><div>from . import multiarray</div><div>AttributeError: PyCapsule_Import "datetime.datetime_CAPI" is not valid</div><div><br></div><div><br></div><div>Any suggestions on how to fix this?</div></div></div><div><br></div><div>Yuan</div></div><div class="gmail_extra"><br><div class="gmail_quote">On Wed, Jun 15, 2016 at 2:50 PM, 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"><div dir="ltr"><br><div class="gmail_extra"><br><div class="gmail_quote"><span class="">On Wed, Jun 15, 2016 at 1:42 PM, Yuan Li <span dir="ltr"><<a href="mailto:yuan@astro.columbia.edu" target="_blank">yuan@astro.columbia.edu</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"><div>Hi all,</div><div><br></div><div>I am having trouble installing/running the latest yt on Xsede Smic and Comet clusters. I used to have yt3 on both machines and they were working fine. Recently, after failing to update yt, I decided to delete the old one and install the latest version. I am using the unmodified file from <a href="http://bitbucket.org/yt_analysis/yt/raw/yt/doc/install_script.sh" target="_blank">http://bitbucket.org/yt_analysis/yt/raw/yt/doc/install_script.sh</a></div><div><br></div><div><br></div><div>Here are the problems I have:</div><div><b>On Smic</b></div><div>When I do "yt update" on the login node, or when I try to submit a yt job, I get this error message</div><div>...</div>ValueError: numpy.dtype has the wrong size, try recompiling<br><div><br></div><div>I have seen this error message before and fixed it somehow, but I do not remember how...</div></div></blockquote><div><br></div></span><div>Navigate to the checkout of the yt mercurial repository and do:</div><div><br></div><div>$ ./clean.sh</div><div>$ python setup.py develop</div><span class=""><div> </div><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div dir="ltr"><div><br></div><div><br></div><div><b>On Comet</b></div><div>When I do "yt update", I get this error message:</div><div>...</div><div><div>YT site-packages not in path, so you must</div><div>update this installation manually by committing and</div><div>merging your modifications to the code before</div><div>updating to the newest changeset.</div></div><div><br></div><div>I manually set YT_DEST in my bash_profile, but that does not seem to help. I can however submit a yt job and it will run fine, but not in parallel. Before I reinstalled yt, I was able to run yt3 in parallel on Comet after loading mpi4py.<br></div><div><br></div><div><div>Also, when I do</div><div>"source ~/source/yt-conda/bin/activate" I get this error message:</div><div>Error: no environment provided.</div></div><div>and it seems that I do not even need to activate yt anymore (is it because I have "export PATH=/home/yuanli/source/yt-conda/bin:$PATH" in my bash_profile?). Maybe I missed something in the doc. I am very confused. </div></div></blockquote><div><br></div></span><div>It looks like you ran the install script with INST_YT_SOURCE=0 (the default). Try again with INST_YT_SOURCE=1. You will also likely need to do "pip install mpi4py" to get an mpi4py installation linked against comet's MPI libraries.</div><div><br></div><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div dir="ltr"><div><br></div><div><br></div><div>Thanks in advance!</div><span><font color="#888888"><div>Yuan</div></font></span></div>
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