<div><div dir="auto">Also if this is a cluster, make sure you have any modules unloaded. I think your HDF5 issue might be because h5py is picking up a system HDF5 installation.</div><br><div class="gmail_quote"><div>On Tue, Jun 20, 2017 at 8:05 AM Carla Bernhardt <<a href="mailto:carla.j.bernhardt@gmail.com">carla.j.bernhardt@gmail.com</a>> wrote:<br></div><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div>I did delete the previous partial installations of yt before each attempt at installation. I previously tried installing rockstar manually for a conda-based environment, but I don't remember what went wrong, so I will try that again and let you know. Either way, thank you for your insights.<div><br></div><div>Cheers,</div><div>Carla</div></div><div class="gmail_extra"><br><div class="gmail_quote">2017-06-20 14:59 GMT+02:00 Nathan Goldbaum <span><<a href="mailto:nathan12343@gmail.com" target="_blank">nathan12343@gmail.com</a>></span>:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div><div dir="auto">Are you running the install script from scratch in this situation? That means removing the older partial installations before rerunning the install script.</div><div dir="auto"><br></div><div dir="auto">If that's not the problem I'm not sure what the issue is.</div><div dir="auto"><br></div><div dir="auto">You could try setting up a python environment outside the install script and set up rockstar manually following the instructions for conda-based environments here:</div><div dir="auto"><br></div><div dir="auto"><a href="http://yt-project.org/docs/dev/installing.html#installing-yt-using-anaconda" target="_blank">http://yt-project.org/docs/dev/installing.html#installing-yt-using-anaconda</a></div><div><div class="m_-1549681192845968354h5"><br><div class="gmail_quote"><div>On Tue, Jun 20, 2017 at 6:31 AM Carla Bernhardt <<a href="mailto:carla.j.bernhardt@gmail.com" target="_blank">carla.j.bernhardt@gmail.com</a>> wrote:<br></div><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div>Hi Nathan,<div><br></div><div>Likely independent from the Cython discrepancy, when I try installing yt with rockstar enabled (from source only), I get this error: <span style="font-variant-ligatures:no-common-ligatures;color:rgb(0,0,0);font-family:Menlo;font-size:11px">ValueError: HDF5 version string must be in X.Y.Z format </span>(more of the error <a href="https://pastebin.com/ci3QMtRL" target="_blank">here</a>).<span style="font-variant-ligatures:no-common-ligatures;color:rgb(0,0,0);font-family:Menlo;font-size:11px"> </span>So I tried installing with a different hdf5--same result. I tried disabling h5py, but then I get this error:<span style="font-variant-ligatures:no-common-ligatures;color:rgb(0,0,0);font-family:Menlo;font-size:11px"> </span><span style="font-variant-ligatures:no-common-ligatures;color:rgb(0,0,0);font-family:Menlo;font-size:11px">ImportError: cannot import name 'print_line' </span>(more of the error <a href="https://pastebin.com/61haGr3T" target="_blank">here</a>). I also tried installing yt with both INST_CONDA =1 and INST_YT_SOURCE=1 as listed in my previous email, but just for good measure, I retried with the new install script (<a href="https://pastebin.com/xgXyzBQx" target="_blank">same result</a>). Any suggestions?</div><div><br></div><div>Cheers,</div><div>Carla</div>
</div><div class="gmail_extra"><br><div class="gmail_quote">2017-06-19 16:45 GMT+02:00 Nathan Goldbaum <span><<a href="mailto:nathan12343@gmail.com" target="_blank">nathan12343@gmail.com</a>></span>:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div>Done:<div><br></div><div><a href="https://github.com/yt-project/yt/pull/1458/files" target="_blank">https://github.com/yt-project/yt/pull/1458/files</a><br></div><div><br></div><div>You should be able to get an updated install script by downloading it from my fork:</div><div><br></div><div>$ wget <a href="https://raw.githubusercontent.com/ngoldbaum/yt/27dafcdaf068829c78f34c4c7211f6dd56beea0d/doc/install_script.sh" target="_blank">https://raw.githubusercontent.com/ngoldbaum/yt/27dafcdaf068829c78f34c4c7211f6dd56beea0d/doc/install_script.sh</a></div><span class="m_-1549681192845968354m_-7626620402216893229m_8354112871211616689HOEnZb"><font color="#888888"><div><br></div><div>-Nathan</div></font></span></div><div class="m_-1549681192845968354m_-7626620402216893229m_8354112871211616689HOEnZb"><div class="m_-1549681192845968354m_-7626620402216893229m_8354112871211616689h5"><div class="gmail_extra"><br><div class="gmail_quote">On Mon, Jun 19, 2017 at 9:31 AM, Carla Bernhardt <span><<a href="mailto:carla.j.bernhardt@gmail.com" target="_blank">carla.j.bernhardt@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>Hi Nathan,<div><br></div><div>I don't mind waiting, I think you will do a better job updating the script. I tried before, but the installation still failed. I am not using MacOS, I am on a server using Redhat.</div><div><br></div><div>Cheers,</div><div>Carla</div></div><div class="m_-1549681192845968354m_-7626620402216893229m_8354112871211616689m_4026905994419121853HOEnZb"><div class="m_-1549681192845968354m_-7626620402216893229m_8354112871211616689m_4026905994419121853h5"><div class="gmail_extra"><br><div class="gmail_quote">2017-06-19 15:43 GMT+02:00 Nathan Goldbaum <span><<a href="mailto:nathan12343@gmail.com" target="_blank">nathan12343@gmail.com</a>></span>:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div><div dir="auto">No, I haven't seen that error before.</div><div dir="auto"><br></div><div dir="auto">I'll be heading into the office shortly and will update the install script when I get in. If you can't wait on me, you could try updating it yourself to download the latest cython release from e.g. pypi.</div><div dir="auto"><br></div><div dir="auto">By the way, do you happen to be using the latest version of MacOS? In that case building rockstar from source will not work:</div><div dir="auto"><br></div><div dir="auto"><a href="https://github.com/yt-project/yt/issues/1289" target="_blank">https://github.com/yt-project/yt/issues/1289</a></div><span class="m_-1549681192845968354m_-7626620402216893229m_8354112871211616689m_4026905994419121853m_-428581865868733695HOEnZb"><font color="#888888"><div dir="auto"><br></div><div dir="auto">Nathan</div></font></span><div><div class="m_-1549681192845968354m_-7626620402216893229m_8354112871211616689m_4026905994419121853m_-428581865868733695h5"><br><div class="gmail_quote"><div>On Mon, Jun 19, 2017 at 8:32 AM Carla Bernhardt <<a href="mailto:carla.j.bernhardt@gmail.com" target="_blank">carla.j.bernhardt@gmail.com</a>> wrote:<br></div><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div>Hi Nathan,<div><br></div><div>I did try running with rockstar install enabled, INST_CONDA=1 and INST_YT_SOURCE=1 and I got <a href="https://pastebin.com/EWXsbzCx" target="_blank">this strange error</a> that I don't have the file "libisl.so.10". Any suggestions on that? I wasn't able to find anything helpful about this online. I just want to get a working version of yt going with rockstar enabled, it doesn't have to be from source.</div><div><br></div><div>Cheers,</div><div>Carla</div>
</div><div class="gmail_extra"><br><div class="gmail_quote">2017-06-19 15:17 GMT+02:00 Nathan Goldbaum <span><<a href="mailto:nathan12343@gmail.com" target="_blank">nathan12343@gmail.com</a>></span>:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div><div dir="auto">Hi Carla,</div><div dir="auto"><br></div><div dir="auto">I think we need to update the install script for the case with INST_CONDA=0. For now you should be able to set INST_CONDA=1 and still get rockstar setup, we made it so you can use rockstar with a conda-based install a while back.</div><div dir="auto"><br></div><div dir="auto">Nathan</div><br><div class="gmail_quote"><div><div class="m_-1549681192845968354m_-7626620402216893229m_8354112871211616689m_4026905994419121853m_-428581865868733695m_8075718787077433509m_5730497828985017502h5"><div>On Mon, Jun 19, 2017 at 6:34 AM Carla Bernhardt <<a href="mailto:carla.j.bernhardt@gmail.com" target="_blank">carla.j.bernhardt@gmail.com</a>> wrote:<br></div></div></div><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div><div class="m_-1549681192845968354m_-7626620402216893229m_8354112871211616689m_4026905994419121853m_-428581865868733695m_8075718787077433509m_5730497828985017502h5"><div>Dear yt-users,<div><br></div><div>I am trying to compile yt with rockstar enabled, so I am having yt install itself from source. The code downloads Cython 0.23.5, but later then requires Cython 0.24+. I tried downloading Cython-0.25.2, but this failed (I probably did it wrong). What do I need to change to make the install_script.sh work with Cython?</div><div><br></div><div>Here is a piece of the failure report I got:</div><div><br></div><div><font face="monospace, monospace">Installing GitPython-2.1.3<br>Installing sympy-1.0<br>Building Rockstar<br>Installing yt<br>********************************************<br> FAILURE REPORT:<br>********************************************<br><br> File "/home/hd/hd_hd/hd_ri129/yt-x86_64/lib/python3.5/site-packages/setuptools-20.6.7-py3.5.egg/setuptools/command/sdist.py", line 132, in add_defaults<br> File "/home/hd/hd_hd/hd_ri129/yt-x86_64/lib/python3.5/distutils/cmd.py", line 299, in get_finalized_command<br> cmd_obj.ensure_finalized()<br> File "/home/hd/hd_hd/hd_ri129/yt-x86_64/lib/python3.5/distutils/cmd.py", line 107, in ensure_finalized<br> self.finalize_options()<br> File "setup.py", line 308, in finalize_options<br> cython.__version__)<br>RuntimeError: Building yt from source requires Cython 0.24 or newer but<br>Cython 0.23.5 is installed. Please update Cython using the appropriate<br>package manager for your python environment.<br><br>********************************************<br>********************************************</font></div><div><br></div><div>Cheers,</div><div>Carla Bernhardt</div><div>PhD Student</div><div>ZAH Institut für Theoretische Astrophysik</div><div>Universität Heidelberg</div>
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