<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="">You were right that I didn’t have python from miniconda in my PATH and so I was picking up the (old) system version of python. I prepended PATH variable and “which python” now points to the right version of python from miniconda. Nevertheless, the problem remains as illustrated below. I am puzzled why this is happening ... </div><div class=""><br class=""></div>% pwd<br class="">/nobackupnfs2/mruszkow<br class="">% ls<br class="">Miniconda3-latest-Linux-x86_64.sh<br class="">% bash Miniconda3-latest-Linux-x86_64.sh <br class="">% setenv PATH /nobackupnfs2/mruszkow/miniconda3/bin:${PATH}<br class="">% echo $PATH<br class="">% which python<br class="">% conda install yt<br class="">% module load pkgsrc/2015Q2<br class="">% hg clone <a href="https://bitbucket.org/yt_analysis/yt" class="">https://bitbucket.org/yt_analysis/yt</a><br class="">% ls<br class="">Miniconda3-latest-Linux-x86_64.sh miniconda3 yt<br class="">% pwd<br class="">/nobackupnfs2/mruszkow<br class="">% cd yt/<br class="">% hg up yt<br class="">% which python<br class="">/nobackupnfs2/mruszkow/miniconda3/bin/python<br class="">% python setup.py develop<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=""><div apple-content-edited="true" class="">
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<br class=""><div><blockquote type="cite" class=""><div class="">On Oct 19, 2015, at 7:53 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="">You don't have the python from miniconda in your PATH and are picking up a version of python 2.6 or older from the operating system on Pleiades.<div class=""><br class=""></div><div class="">What's the output of "which python"? If the path returned by that command doesn't have "miniconda" in it, it's the wrong python executable. You might need to manually add miniconda's bin directory to your PATH environment variable.</div></div><div class="gmail_extra"><br class=""><div class="gmail_quote">On Mon, Oct 19, 2015 at 4:51 PM, 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=""><br class=""></div><div class=""><br class=""></div><div class="">The reason I originally loaded python_2.7.2 was to avoid the error message below. Now that python_2.7.2 is unloaded this message is back ...</div><div class=""><br class=""></div><div class="">% module unload python_2.7.2<br class="">% python setup.py develop<br class="">yt currently requires Python version 2.7<br class="">certain features may fail unexpectedly and silently with older versions.</div><div class="">%</div><div class=""><br class=""></div><div class="">As the next step I will try to repeat the whole process from scratch w/o using module load pkgsrc/2015Q2. Instead, I will just use standalone mercurial installation to see if this helps.</div><div class=""><div class="h5"><div class=""><br class=""></div><div class=""><br class=""></div><div class=""><br class=""><br class="">
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<br class=""><div class=""><blockquote type="cite" class=""><div class="">On Oct 19, 2015, at 7:31 PM, Nathan Goldbaum <<a href="mailto:nathan12343@gmail.com" target="_blank" class="">nathan12343@gmail.com</a>> wrote:</div><br class=""><div class=""><div dir="ltr" class=""><br class=""><div class="gmail_extra"><br class=""><div class="gmail_quote">On Mon, Oct 19, 2015 at 4:11 PM, 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=""><br class=""></div><div class="">Hi Nathan/Desika,</div><div class=""><br class=""></div><div class="">Thanks! Following your suggestions, I replaced "conda build conda-recipes/yt" with "conda install yt.” I am also able to do "conda install pip" w/o problem. But I nevertheless get the same error message when I execute the last command in this series:</div><div class=""><br class=""></div><div class=""><div class="">bash Miniconda3-latest-Linux-x86_64.sh<br class=""><div class=""><div dir="ltr" class="">miniconda3/bin/conda install yt [instead of: miniconda3/bin/conda build conda-recipes/yt]</div></div></div><div dir="ltr" class="">miniconda3/bin/conda install pip</div><div class=""><div dir="ltr" class=""><span class="">hg clone <a href="https://bitbucket.org/yt_analysis/yt" target="_blank" class="">https://bitbucket.org/yt_analysis/yt</a><br class="">cd yt/<br class=""></span>hg up yt<br class="">python setup.py develop</div><div dir="ltr" class=""><br class=""></div><span class=""><div dir="ltr" class=""><div dir="ltr" class=""><div class="gmail_extra"><div class="gmail_quote"><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left-width:1px;border-left-color:rgb(204,204,204);border-left-style:solid;padding-left:1ex"><div style="word-wrap:break-word" class=""><div class=""><div class=""><span 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=""></div></span></div></div></div></blockquote></div></div></div></div><div dir="ltr" class=""><br class=""></div></span><div dir="ltr" class="">Is there anything obvious in the above command sequence that is wrong? I am wondering if this problem has anything to do with how you setup various modules on Pleiades. For example, in order to use mercuria,l I do "module load pkgsrc/2015Q2” I also do “module load python_2.7.2” The pkgsrc/2015Q2 package loads a number of obsolete modules and perhaps they are messing things up?</div></div></div></div></blockquote><div class=""><br class=""></div><div class="">Yes, that is possible.</div><div class=""><br class=""></div><div class="">You want to make sure that you are running the miniconda python and not the python loaded by the module. You can check by doing "which python". If you're using miniconda, you want to unload the python_2.7.2 module.</div><div class=""> </div><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=""><div class=""><div dir="ltr" class=""><br class=""></div><div dir="ltr" class=""> Thanks,</div><div dir="ltr" class=""> Mateusz</div><div dir="ltr" class=""><br class=""></div><div dir="ltr" class=""><br class=""> <br class=""> </div></div></div><div class=""><div class=""><div class=""><br class=""></div>
<br class=""><div class=""><blockquote type="cite" class=""><div class="">On Oct 19, 2015, at 5:05 PM, Nathan Goldbaum <<a href="mailto:nathan12343@gmail.com" target="_blank" class="">nathan12343@gmail.com</a>> wrote:</div><br class=""><div class=""><div dir="ltr" class=""><br class=""><div class="gmail_extra"><br class=""><div class="gmail_quote">On Mon, Oct 19, 2015 at 1:42 PM, 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=""><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=""></div></div></div></blockquote><div class=""><br class=""></div><div class="">Here you want to do "conda install yt" to get all of yt's dependencies. From there you can install the development version of yt. You can "conda install" must python packages.</div><div class=""><br class=""></div><div class="">As desika mentioned, you can also install pip with "conda install pip".</div><div class=""><br class=""></div><div class="">I'd caution against using the full anaconda distribution since anaconda's MPI will shadow the system MPI installation unless you explicitly remove it.</div><div class=""> </div><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=""><div class="">hg clone <a href="https://bitbucket.org/yt_analysis/yt" target="_blank" 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=""><span 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></span><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=""><div class=""><div class=""><br class=""></div><div class=""><br class=""></div><div class=""><br class="">
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<br class=""><div class=""><blockquote type="cite" class=""><div class="">On Oct 19, 2015, at 2:26 PM, Nathan Goldbaum <<a href="mailto:nathan12343@gmail.com" target="_blank" class="">nathan12343@gmail.com</a>> wrote:</div><br class=""><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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