<div dir="ltr">has anyone asked NERSC whether they'd be willing to install it sitewide as a loadable module on hopper? I'm sure there are lots of us who would want to use yt there.</div><div class="gmail_extra"><br>
<br><div class="gmail_quote">On Sat, Feb 1, 2014 at 6:16 PM, Andrew Myers <span dir="ltr"><<a href="mailto:atmyers2@gmail.com" target="_blank">atmyers2@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"><div><div>Hi Hilary,<br><br>Thanks for the suggestion. Unfortunately, it didn't work for me - if I install ipython manually, it still fails with the same error message. <br><br></div>I think I'll try to ask this at StackOverflow as well, as per Nathan's suggestion.<br>
<br></div>Thanks,<br>Andrew<br></div><div class="gmail_extra"><br><br><div class="gmail_quote">On Sat, Feb 1, 2014 at 10:09 AM, Hilary Egan <span dir="ltr"><<a href="mailto:hilaryye@gmail.com" target="_blank">hilaryye@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">I saw the same problem when I was installing on CU's janus machine. I'm pretty sure that I got around it by building just ipython by hand and making sure I was on the compile node when I tried it- no idea if there is an equivalent for Hopper.<div>
<br><div>-download and untar<span style="font-size:13px;font-family:Arial"> ipython.tar.gz (</span><font face="Arial"><a href="http://archive.ipython.org/release/" target="_blank">http://archive.ipython.org/release/</a>)</font></div>
<div>
<span style="font-size:13px;font-family:Arial">-cd ipython</span><br>
<span style="font-size:13px;font-family:Arial">-python setup.py install</span><br>
<span style="font-size:13px;font-family:Arial">-touch done</span></div></div><div><span style="font-size:13px;font-family:Arial"><br></span></div><div><span style="font-size:13px;font-family:Arial">Caveat: I have no idea why this worked when the install script didn't, and I'm just basing my answer on the note I jotted down a few months ago. There's definitely some sort of discussion out there already about this being a problem in some versions in pyzmq (</span><font face="Arial"><a href="https://github.com/zeromq/pyzmq/pull/218" target="_blank">https://github.com/zeromq/pyzmq/pull/218</a>). </font><span style="font-family:Arial;font-size:13px"> Hope that helps!</span></div>
<div><span style="font-family:Arial;font-size:13px"><br></span></div><div><span style="font-family:Arial;font-size:13px">-Hilary</span></div></div><div class="gmail_extra"><br><br><div class="gmail_quote"><div><div>
On Sat, Feb 1, 2014 at 10:49 AM, Nathan Goldbaum <span dir="ltr"><<a href="mailto:nathan12343@gmail.com" target="_blank">nathan12343@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>Hi Andrew,<div><br></div><div>Unfortunately I'm not sure what the issue is.</div>
<div><br></div><div>You might try asking this question on StackOverflow (tagging it with IPython and ZMQ) <span></span>or the IPython-dev mailing list, some of the ZMQ/IPy devs will be more likely to see it.</div>
<span><font color="#888888">
<div><br></div></font></span><div><span><font color="#888888">Nathan</font></span><div><div><br><div><br>On Saturday, February 1, 2014, Andrew Myers <<a href="mailto:atmyers2@gmail.com" target="_blank">atmyers2@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"><span style="font-family:arial,sans-serif;font-size:13px">Hi Folks,</span><div style="font-family:arial,sans-serif;font-size:13px"><br></div><div style="font-family:arial,sans-serif;font-size:13px">I'm trying to install the development version of yt-2.7 on NERSC's Hopper machine using the install script. I get to the part where it tries to build IPython, and then the script fails with the following error message:</div>
<div style="font-family:arial,sans-serif;font-size:13px"><br></div><blockquote style="font-family:arial,sans-serif;font-size:13px;margin:0px 0px 0px 40px;border:none;padding:0px"><div>============================================================================</div>
<div>BUILDING IPYTHON</div><div> python: 2.7.6 (default, Jan 31 2014, 21:52:04) [GCC 4.8.1</div><div> 20130531 (Cray Inc.)]</div><div> platform: linux2</div><div><br></div>
<div>OPTIONAL DEPENDENCIES</div><div> sphinx: Not found (required for docs and nbconvert)</div><div> pygments: Not found (required for docs and nbconvert)</div><div> nose: 1.3.0</div>
<div> pexpect: no (required for running standalone doctests)</div><div>Traceback (most recent call last):</div><div> File "setup.py", line 342, in <module></div><div> check_for_dependencies()</div>
<div> File "/global/u2/a/atmyers/yt-x86_64/src/ipython-1.1.0/setupbase.py", line 376, in check_for_dependencies</div><div> check_for_pyzmq()</div><div> File "/global/u2/a/atmyers/yt-x86_64/src/ipython-1.1.0/setupext/setupext.py", line 118, in check_for_pyzmq</div>
<div> import zmq</div><div> File "/global/homes/a/atmyers/yt-x86_64/lib/python2.7/site-packages/zmq/__init__.py", line 35, in <module></div><div> _libzmq = ctypes.CDLL(bundled[0], mode=ctypes.RTLD_GLOBAL)</div>
<div> File "/global/homes/a/atmyers/yt-x86_64/lib/python2.7/ctypes/__init__.py", line 365, in __init__</div><div> self._handle = _dlopen(self._name, mode)</div><div>OSError: /global/homes/a/atmyers/yt-x86_64/lib/python2.7/site-packages/zmq/libzmq.so: undefined symbol: clock_gettime</div>
<div><br></div></blockquote><span style="font-family:arial,sans-serif;font-size:13px">Both ZeroMQ and pyzmq appear to have been installed without errors, but then ZeroMQ can't find some of the definitions it needs. Googling around, it looks like clock_gettime is supposed to be found in librt. </span><div style="font-family:arial,sans-serif;font-size:13px">
<br></div><div style="font-family:arial,sans-serif;font-size:13px">Has anyone seen this before? Or, relatedly, has anyone been able to build yt on the NERSC machines? I know that ZeroMQ isn't strictly necessary, but I'd like to be able to use the notebooks. </div>
<div style="font-family:arial,sans-serif;font-size:13px"><br></div><div style="font-family:arial,sans-serif;font-size:13px">My complete yt_install.log is <a href="https://www.dropbox.com/s/pmdq3a9vfrbtwj9/yt_install.log" target="_blank">here</a>.</div>
<div style="font-family:arial,sans-serif;font-size:13px"><br></div><div style="font-family:arial,sans-serif;font-size:13px">Thanks,</div><div style="font-family:arial,sans-serif;font-size:13px">Andrew </div></div>
</blockquote></div></div></div></div>
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<br></blockquote></div><br><br clear="all"><div><br></div>-- <br><div>Michael Zingale</div><div>Associate Professor</div><div><br></div><div>Dept. of Physics & Astronomy • Stony Brook University • Stony Brook, NY 11794-3800</div>
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