<html><head><meta http-equiv="Content-Type" content="text/html charset=utf-8"></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;" class=""><div class=""><br class=""></div><div class=""><br class=""></div><div class=""> Hi Nathan,</div><div class=""><br class=""></div><div class="">Thanks for your help. I think also this almost works ... I downloaded the latest miniconda and followed this procedure:</div><div class=""><br class=""></div><div class=""><br class=""></div><div class=""><div class="">bash Miniconda3-latest-Linux-x86_64.sh<br class="">miniconda3/bin/conda build conda-recipes/yt<br class="">hg clone <a href="https://bitbucket.org/yt_analysis/yt" class="">https://bitbucket.org/yt_analysis/yt</a><br class=""></div>cd yt/<br class="">hy up yt<br class="">python setup.py develop<br class=""><br class=""></div>This resulted in:<div class=""> <br class=""><div class=""><div class="">Cython is a build-time requirement for the source tree of yt.<br class="">Please either install yt from a provided, release tarball,<br class="">or install Cython (version 0.22 or higher).<br class="">You may be able to accomplish this by typing:<br class=""> pip install -U Cython<br class=""><br class=""></div><div class="">which I am not able to install via "pip install -U Cython." So this is essentially the same error message I got when I attempted to install yt using the method described in my previous e-mail. Any idea what may still be wrong?</div></div><div class=""><br class=""></div><div class=""><br class=""></div><div class=""> Thanks,</div><div class=""> Mateusz</div><div class=""><br class=""></div><div class=""><br class=""></div><div apple-content-edited="true" class=""><br class="Apple-interchange-newline">
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<br class=""><div><blockquote type="cite" class=""><div class="">On Oct 19, 2015, at 2:26 PM, Nathan Goldbaum <<a href="mailto:nathan12343@gmail.com" class="">nathan12343@gmail.com</a>> wrote:</div><br class="Apple-interchange-newline"><div class=""><div dir="ltr" class="">Hi Mateusz<div class=""><br class=""></div><div class="">Rather than using the python module on pleiades, I'd suggest setting up your python stack on your own in your home folder.</div><div class=""><br class=""></div><div class="">By far the quickest way to do this is to install miniconda and then install yt into the miniconda environment using "conda install yt". You could also use the yt install script, although you might have issues with that if Pleiades has an older (insecure) version of OpenSSL installed, which is sadly quite common on supercomputers these days...</div><div class=""><br class=""></div><div class="">Personally, I set up my python environment on Pleiades using miniconda.</div><div class=""><br class=""></div><div class="">-Nathan</div></div><div class="gmail_extra"><br class=""><div class="gmail_quote">On Mon, Oct 19, 2015 at 11:23 AM, Mateusz Ruszkowski <span dir="ltr" class=""><<a href="mailto:mateuszr@umich.edu" target="_blank" class="">mateuszr@umich.edu</a>></span> wrote:<br class=""><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div style="word-wrap:break-word" class=""><div class=""><br class=""></div><div class=""> Hi,</div><div class=""><br class=""></div><div class="">I am trying to install yt on Pleiades. I was able to complete a number installation steps but I eventually got an error message related to Cython (Cython seems to be installed though). The error message is attached below. Does anybody have an idea what needs to be done to complete this installation? </div><div class=""><br class=""></div><div class=""> Thanks,</div><div class=""> Mateusz</div><div class=""><br class=""></div><div class="">
<div style="letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; word-wrap: break-word;" class=""><div class="">------------------------------------------------</div><div class=""><div class=""><div class="">Dr. Mateusz Ruszkowski</div><div class="">Associate Professor</div><div class=""><br class=""></div><div class="">University of Michigan </div><div class="">Department of Astronomy</div><div class="">301C West Hall</div><div class="">1085 South University Ave. </div><div class="">Ann Arbor, MI 48109-1107, USA</div><div class=""><br class=""></div><div class="">e-mail: <a href="mailto:mateuszr@umich.edu" target="_blank" class="">mateuszr@umich.edu</a></div></div></div><div class=""><br class=""></div></div><br class="">————————————————————————
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<br class=""><div class=""><div class=""><div dir="ltr" class="">% module load pkgsrc/2014Q3<br class="">% module load python/2.7.9<br class="">% hg clone <a href="https://bitbucket.org/yt_analysis/yt" target="_blank" class="">https://bitbucket.org/yt_analysis/yt</a><br class="">warning: <a href="http://bitbucket.org/" target="_blank" class="">bitbucket.org</a> certificate with fingerprint 46:de:34:e7:9b:18:cd:7f:ae:fd:8b:e3:bc:f4:1a:5e:38:d7:ac:24 not verified (check hostfingerprints or web.cacerts config setting)<br class="">destination directory: yt<br class="">requesting all changes<br class="">adding changesets<br class="">adding manifests<br class="">adding file changes<br class="">added 17568 changesets with 36510 changes to 3053 files (+3 heads)<br class="">updating to bookmark @ on branch stable<br class="">1209 files updated, 0 files merged, 0 files removed, 0 files unresolved<br class="">% cd yt<br class="">% hg update yt<br class="">317 files updated, 0 files merged, 148 files removed, 0 files unresolved<br class="">(leaving bookmark @)<br class="">% python setup.py install --user --prefix=/nobackupnfs2/mruszkow<br class="">Cython is a build-time requirement for the source tree of yt.<br class="">Please either install yt from a provided, release tarball,<br class="">or install Cython (version 0.22 or higher).<br class="">You may be able to accomplish this by typing:<br class=""> pip install -U Cython<br class="">% pip install -U Cython<br class="">Downloading/unpacking Cython from <a href="https://pypi.python.org/packages/source/C/Cython/Cython-0.23.4.tar.gz#md5=157df1f69bcec6b56fd97e0f2e057f6e" target="_blank" class="">https://pypi.python.org/packages/source/C/Cython/Cython-0.23.4.tar.gz#md5=157df1f69bcec6b56fd97e0f2e057f6e</a><br class=""> Downloading Cython-0.23.4.tar.gz (1.6MB): 1.6MB downloaded<br class=""> Running setup.py (path:/tmp/pip_build_mruszkow/Cython/setup.py) egg_info for package Cython<br class=""> Unable to find pgen, not compiling formal grammar.<br class=""> <br class=""> warning: no files found matching '*.pyx' under directory 'Cython/Debugger/Tests'<br class=""> warning: no files found matching '*.pxd' under directory 'Cython/Debugger/Tests'<br class=""> warning: no files found matching '*.h' under directory 'Cython/Debugger/Tests'<br class=""> warning: no files found matching '*.pxd' under directory 'Cython/Utility'<br class="">Installing collected packages: Cython<br class=""> Found existing installation: Cython 0.21.1<br class=""> Uninstalling Cython:<br class="">Cleaning up...<br class="">Exception:<br class="">Traceback (most recent call last):<br class=""> File "/nasa/pkgsrc/2014Q4/lib/python2.7/site-packages/pip/basecommand.py", line 122, in main<br class=""> status = self.run(options, args)<br class=""> File "/nasa/pkgsrc/2014Q4/lib/python2.7/site-packages/pip/commands/install.py", line 283, in run<br class=""> requirement_set.install(install_options, global_options, root=options.root_path)<br class=""> File "/nasa/pkgsrc/2014Q4/lib/python2.7/site-packages/pip/req.py", line 1431, in install<br class=""> requirement.uninstall(auto_confirm=True)<br class=""> File "/nasa/pkgsrc/2014Q4/lib/python2.7/site-packages/pip/req.py", line 598, in uninstall<br class=""> paths_to_remove.remove(auto_confirm)<br class=""> File "/nasa/pkgsrc/2014Q4/lib/python2.7/site-packages/pip/req.py", line 1836, in remove<br class=""> renames(path, new_path)<br class=""> File "/nasa/pkgsrc/2014Q4/lib/python2.7/site-packages/pip/util.py", line 295, in renames<br class=""> shutil.move(old, new)<br class=""> File "/nasa/pkgsrc/2014Q4/lib/python2.7/shutil.py", line 300, in move<br class=""> rmtree(src)<br class=""> File "/nasa/pkgsrc/2014Q4/lib/python2.7/shutil.py", line 247, in rmtree<br class=""> rmtree(fullname, ignore_errors, onerror)<br class=""> File "/nasa/pkgsrc/2014Q4/lib/python2.7/shutil.py", line 252, in rmtree<br class=""> onerror(os.remove, fullname, sys.exc_info())<br class=""> File "/nasa/pkgsrc/2014Q4/lib/python2.7/shutil.py", line 250, in rmtree<br class=""> os.remove(fullname)<br class="">OSError: [Errno 30] Read-only file system: '/nasa/pkgsrc/2014Q4/lib/python2.7/site-packages/Cython/Build/BuildExecutable.py'<br class=""><br class="">Storing debug log for failure in /u/mruszkow/.pip/pip.log<br class="">% <br class=""></div>
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