<div dir="ltr"><br><div class="gmail_extra"><br><div class="gmail_quote">On Mon, Oct 19, 2015 at 4:11 PM, Mateusz Ruszkowski <span dir="ltr"><<a href="mailto:mateuszr@umich.edu" target="_blank">mateuszr@umich.edu</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div style="word-wrap:break-word"><div><br></div><div><br></div><div>Hi Nathan/Desika,</div><div><br></div><div>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><br></div><div><div>bash Miniconda3-latest-Linux-x86_64.sh<br><div><div dir="ltr">miniconda3/bin/conda install yt [instead of: miniconda3/bin/conda build conda-recipes/yt]</div></div></div><div dir="ltr">miniconda3/bin/conda install pip</div><div><div dir="ltr"><span class="">hg clone <a href="https://bitbucket.org/yt_analysis/yt" target="_blank">https://bitbucket.org/yt_analysis/yt</a><br>cd yt/<br></span>hg up yt<br>python setup.py develop</div><div dir="ltr"><br></div><span class=""><div dir="ltr"><div dir="ltr"><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"><div><div><span><div>Cython is a build-time requirement for the source tree of yt.<br>Please either install yt from a provided, release tarball,<br>or install Cython (version 0.22 or higher).<br>You may be able to accomplish this by typing:<br> pip install -U Cython<br></div></span></div></div></div></blockquote></div></div></div></div><div dir="ltr"><br></div></span><div dir="ltr">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><br></div><div>Yes, that is possible.</div><div><br></div><div>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> </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"><div><div><div dir="ltr"><br></div><div dir="ltr"> Thanks,</div><div dir="ltr"> Mateusz</div><div dir="ltr"><br></div><div dir="ltr"><br> <br> </div></div></div><div><div class="h5"><div><br></div>
<br><div><blockquote type="cite"><div>On Oct 19, 2015, at 5:05 PM, Nathan Goldbaum <<a href="mailto:nathan12343@gmail.com" target="_blank">nathan12343@gmail.com</a>> wrote:</div><br><div><div dir="ltr"><br><div class="gmail_extra"><br><div class="gmail_quote">On Mon, Oct 19, 2015 at 1:42 PM, Mateusz Ruszkowski <span dir="ltr"><<a href="mailto:mateuszr@umich.edu" target="_blank">mateuszr@umich.edu</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div style="word-wrap:break-word"><div><br></div><div><br></div><div> Hi Nathan,</div><div><br></div><div>Thanks for your help. I think also this almost works ... I downloaded the latest miniconda and followed this procedure:</div><div><br></div><div><br></div><div><div>bash Miniconda3-latest-Linux-x86_64.sh<br>miniconda3/bin/conda build conda-recipes/yt<br></div></div></div></blockquote><div><br></div><div>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><br></div><div>As desika mentioned, you can also install pip with "conda install pip".</div><div><br></div><div>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> </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"><div><div>hg clone <a href="https://bitbucket.org/yt_analysis/yt" target="_blank">https://bitbucket.org/yt_analysis/yt</a><br></div>cd yt/<br>hy up yt<br>python setup.py develop<br><br></div>This resulted in:<div> <br><div><span><div>Cython is a build-time requirement for the source tree of yt.<br>Please either install yt from a provided, release tarball,<br>or install Cython (version 0.22 or higher).<br>You may be able to accomplish this by typing:<br> pip install -U Cython<br><br></div></span><div>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><br></div><div><br></div><div> Thanks,</div><div> Mateusz</div><div><div><div><br></div><div><br></div><div><br>
</div>
<br><div><blockquote type="cite"><div>On Oct 19, 2015, at 2:26 PM, Nathan Goldbaum <<a href="mailto:nathan12343@gmail.com" target="_blank">nathan12343@gmail.com</a>> wrote:</div><br><div><div dir="ltr">Hi Mateusz<div><br></div><div>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><br></div><div>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><br></div><div>Personally, I set up my python environment on Pleiades using miniconda.</div><div><br></div><div>-Nathan</div></div><div class="gmail_extra"><br><div class="gmail_quote">On Mon, Oct 19, 2015 at 11:23 AM, Mateusz Ruszkowski <span dir="ltr"><<a href="mailto:mateuszr@umich.edu" target="_blank">mateuszr@umich.edu</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div style="word-wrap:break-word"><div><br></div><div> Hi,</div><div><br></div><div>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><br></div><div> Thanks,</div><div> Mateusz</div><div><br></div><div>
<div style="letter-spacing:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;word-wrap:break-word"><div>------------------------------------------------</div><div><div><div>Dr. Mateusz Ruszkowski</div><div>Associate Professor</div><div><br></div><div>University of Michigan </div><div>Department of Astronomy</div><div>301C West Hall</div><div>1085 South University Ave. </div><div>Ann Arbor, MI 48109-1107, USA</div><div><br></div><div>e-mail: <a href="mailto:mateuszr@umich.edu" target="_blank">mateuszr@umich.edu</a></div></div></div><div><br></div></div><br>————————————————————————
</div>
<br><div><div><div dir="ltr">% module load pkgsrc/2014Q3<br>% module load python/2.7.9<br>% hg clone <a href="https://bitbucket.org/yt_analysis/yt" target="_blank">https://bitbucket.org/yt_analysis/yt</a><br>warning: <a href="http://bitbucket.org/" target="_blank">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>destination directory: yt<br>requesting all changes<br>adding changesets<br>adding manifests<br>adding file changes<br>added 17568 changesets with 36510 changes to 3053 files (+3 heads)<br>updating to bookmark @ on branch stable<br>1209 files updated, 0 files merged, 0 files removed, 0 files unresolved<br>% cd yt<br>% hg update yt<br>317 files updated, 0 files merged, 148 files removed, 0 files unresolved<br>(leaving bookmark @)<br>% python setup.py install --user --prefix=/nobackupnfs2/mruszkow<br>Cython is a build-time requirement for the source tree of yt.<br>Please either install yt from a provided, release tarball,<br>or install Cython (version 0.22 or higher).<br>You may be able to accomplish this by typing:<br> pip install -U Cython<br>% pip install -U Cython<br>Downloading/unpacking Cython from <a href="https://pypi.python.org/packages/source/C/Cython/Cython-0.23.4.tar.gz#md5=157df1f69bcec6b56fd97e0f2e057f6e" target="_blank">https://pypi.python.org/packages/source/C/Cython/Cython-0.23.4.tar.gz#md5=157df1f69bcec6b56fd97e0f2e057f6e</a><br> Downloading Cython-0.23.4.tar.gz (1.6MB): 1.6MB downloaded<br> Running setup.py (path:/tmp/pip_build_mruszkow/Cython/setup.py) egg_info for package Cython<br> Unable to find pgen, not compiling formal grammar.<br> <br> warning: no files found matching '*.pyx' under directory 'Cython/Debugger/Tests'<br> warning: no files found matching '*.pxd' under directory 'Cython/Debugger/Tests'<br> warning: no files found matching '*.h' under directory 'Cython/Debugger/Tests'<br> warning: no files found matching '*.pxd' under directory 'Cython/Utility'<br>Installing collected packages: Cython<br> Found existing installation: Cython 0.21.1<br> Uninstalling Cython:<br>Cleaning up...<br>Exception:<br>Traceback (most recent call last):<br> File "/nasa/pkgsrc/2014Q4/lib/python2.7/site-packages/pip/basecommand.py", line 122, in main<br> status = self.run(options, args)<br> File "/nasa/pkgsrc/2014Q4/lib/python2.7/site-packages/pip/commands/install.py", line 283, in run<br> requirement_set.install(install_options, global_options, root=options.root_path)<br> File "/nasa/pkgsrc/2014Q4/lib/python2.7/site-packages/pip/req.py", line 1431, in install<br> requirement.uninstall(auto_confirm=True)<br> File "/nasa/pkgsrc/2014Q4/lib/python2.7/site-packages/pip/req.py", line 598, in uninstall<br> paths_to_remove.remove(auto_confirm)<br> File "/nasa/pkgsrc/2014Q4/lib/python2.7/site-packages/pip/req.py", line 1836, in remove<br> renames(path, new_path)<br> File "/nasa/pkgsrc/2014Q4/lib/python2.7/site-packages/pip/util.py", line 295, in renames<br> shutil.move(old, new)<br> File "/nasa/pkgsrc/2014Q4/lib/python2.7/shutil.py", line 300, in move<br> rmtree(src)<br> File "/nasa/pkgsrc/2014Q4/lib/python2.7/shutil.py", line 247, in rmtree<br> rmtree(fullname, ignore_errors, onerror)<br> File "/nasa/pkgsrc/2014Q4/lib/python2.7/shutil.py", line 252, in rmtree<br> onerror(os.remove, fullname, sys.exc_info())<br> File "/nasa/pkgsrc/2014Q4/lib/python2.7/shutil.py", line 250, in rmtree<br> os.remove(fullname)<br>OSError: [Errno 30] Read-only file system: '/nasa/pkgsrc/2014Q4/lib/python2.7/site-packages/Cython/Build/BuildExecutable.py'<br><br>Storing debug log for failure in /u/mruszkow/.pip/pip.log<br>% <br></div>
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