[yt-users] yt on Pleiades
Mateusz Ruszkowski
mateuszr at umich.edu
Mon Oct 19 11:23:37 PDT 2015
Hi,
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?
Thanks,
Mateusz
------------------------------------------------
Dr. Mateusz Ruszkowski
Associate Professor
University of Michigan
Department of Astronomy
301C West Hall
1085 South University Ave.
Ann Arbor, MI 48109-1107, USA
e-mail: mateuszr at umich.edu <mailto:mateuszr at umich.edu>
————————————————————————
% module load pkgsrc/2014Q3
% module load python/2.7.9
% hg clone https://bitbucket.org/yt_analysis/yt <https://bitbucket.org/yt_analysis/yt>
warning: bitbucket.org <http://bitbucket.org/> 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)
destination directory: yt
requesting all changes
adding changesets
adding manifests
adding file changes
added 17568 changesets with 36510 changes to 3053 files (+3 heads)
updating to bookmark @ on branch stable
1209 files updated, 0 files merged, 0 files removed, 0 files unresolved
% cd yt
% hg update yt
317 files updated, 0 files merged, 148 files removed, 0 files unresolved
(leaving bookmark @)
% python setup.py install --user --prefix=/nobackupnfs2/mruszkow
Cython is a build-time requirement for the source tree of yt.
Please either install yt from a provided, release tarball,
or install Cython (version 0.22 or higher).
You may be able to accomplish this by typing:
pip install -U Cython
% pip install -U Cython
Downloading/unpacking Cython from https://pypi.python.org/packages/source/C/Cython/Cython-0.23.4.tar.gz#md5=157df1f69bcec6b56fd97e0f2e057f6e <https://pypi.python.org/packages/source/C/Cython/Cython-0.23.4.tar.gz#md5=157df1f69bcec6b56fd97e0f2e057f6e>
Downloading Cython-0.23.4.tar.gz (1.6MB): 1.6MB downloaded
Running setup.py (path:/tmp/pip_build_mruszkow/Cython/setup.py) egg_info for package Cython
Unable to find pgen, not compiling formal grammar.
warning: no files found matching '*.pyx' under directory 'Cython/Debugger/Tests'
warning: no files found matching '*.pxd' under directory 'Cython/Debugger/Tests'
warning: no files found matching '*.h' under directory 'Cython/Debugger/Tests'
warning: no files found matching '*.pxd' under directory 'Cython/Utility'
Installing collected packages: Cython
Found existing installation: Cython 0.21.1
Uninstalling Cython:
Cleaning up...
Exception:
Traceback (most recent call last):
File "/nasa/pkgsrc/2014Q4/lib/python2.7/site-packages/pip/basecommand.py", line 122, in main
status = self.run(options, args)
File "/nasa/pkgsrc/2014Q4/lib/python2.7/site-packages/pip/commands/install.py", line 283, in run
requirement_set.install(install_options, global_options, root=options.root_path)
File "/nasa/pkgsrc/2014Q4/lib/python2.7/site-packages/pip/req.py", line 1431, in install
requirement.uninstall(auto_confirm=True)
File "/nasa/pkgsrc/2014Q4/lib/python2.7/site-packages/pip/req.py", line 598, in uninstall
paths_to_remove.remove(auto_confirm)
File "/nasa/pkgsrc/2014Q4/lib/python2.7/site-packages/pip/req.py", line 1836, in remove
renames(path, new_path)
File "/nasa/pkgsrc/2014Q4/lib/python2.7/site-packages/pip/util.py", line 295, in renames
shutil.move(old, new)
File "/nasa/pkgsrc/2014Q4/lib/python2.7/shutil.py", line 300, in move
rmtree(src)
File "/nasa/pkgsrc/2014Q4/lib/python2.7/shutil.py", line 247, in rmtree
rmtree(fullname, ignore_errors, onerror)
File "/nasa/pkgsrc/2014Q4/lib/python2.7/shutil.py", line 252, in rmtree
onerror(os.remove, fullname, sys.exc_info())
File "/nasa/pkgsrc/2014Q4/lib/python2.7/shutil.py", line 250, in rmtree
os.remove(fullname)
OSError: [Errno 30] Read-only file system: '/nasa/pkgsrc/2014Q4/lib/python2.7/site-packages/Cython/Build/BuildExecutable.py'
Storing debug log for failure in /u/mruszkow/.pip/pip.log
%
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://lists.spacepope.org/pipermail/yt-users-spacepope.org/attachments/20151019/8c72d7b7/attachment.htm>
More information about the yt-users
mailing list