[yt-users] Compilation problem

[Mark Krumholz]

Thanks — upgrading setuptools did indeed fix the problem. I installed via

pip install setuptools —upgrade —user

to override the NASA-managed older version.

> On 25 Feb 2016, at 1:43 AM, Nathan Goldbaum <nathan12343 at gmail.com> wrote:
> 
> Just in case it's not clear from that thread: "pip install -U setuptools" should fix it. I'm not sure if you're going to be able to do that using the python installation you're using that's managed by Nasa, in which case I'd suggest setting up your installation using the get_yt.sh script, which installs yt into a miniconda environment:
> 
> https://bitbucket.org/yt_analysis/yt/raw/yt/doc/get_yt.sh <https://bitbucket.org/yt_analysis/yt/raw/yt/doc/get_yt.sh>
> 
> On Wed, Feb 24, 2016 at 8:02 AM, Matthew Turk <matthewturk at gmail.com <mailto:matthewturk at gmail.com>> wrote:
> Hi Mark,
> 
> I think this is because of a not-up-to-date setuptools package.  I'm
> not 100% familiar with the specifics, but this ticket goes over how to
> address it: https://bitbucket.org/yt_analysis/yt/issues/1169/document-issue-with-old-setuptools-or <https://bitbucket.org/yt_analysis/yt/issues/1169/document-issue-with-old-setuptools-or>
> 
> On Tue, Feb 23, 2016 at 10:41 PM, Mark Krumholz <mkrumhol at ucsc.edu <mailto:mkrumhol at ucsc.edu>> wrote:
> > Hi yt Users,
> >
> > I’m having a problem compiling the current development branch of yt on NASA
> > pleiades, and I’m hoping that someone can suggest what could be going wrong.
> > Here’s what I get when I try to compile:
> >
> > bridge4:yt mkrumhol$ /nasa/python/2.7.9/bin/python setup.py develop
> > --prefix=/u/mkrumhol
> > running develop
> > running egg_info
> > writing requirements to yt.egg-info/requires.txt
> > writing yt.egg-info/PKG-INFO
> > writing top-level names to yt.egg-info/top_level.txt
> > writing dependency_links to yt.egg-info/dependency_links.txt
> > writing entry points to yt.egg-info/entry_points.txt
> > reading manifest file 'yt.egg-info/SOURCES.txt'
> > reading manifest template 'MANIFEST.in'
> > warning: no previously-included files found matching
> > 'scripts/pr_backport.py'
> > no previously-included directories found matching
> > 'doc/source/reference/api/generated'
> > no previously-included directories found matching 'doc/build'
> > writing manifest file 'yt.egg-info/SOURCES.txt'
> > running build_ext
> > pyrexc yt/analysis_modules/photon_simulator/utils.pyx -->
> > yt/analysis_modules/photon_simulator/utils.c
> > /home3/mkrumhol/yt/yt/analysis_modules/photon_simulator/utils.pyx:6:17:
> > Syntax error in C variable declaration
> > building 'yt.analysis_modules.photon_simulator.utils' extension
> > gcc -fno-strict-aliasing -O2 -Wno-error -pipe -DHAVE_DB_185_H -pthread
> > -I/usr/include -I/nasa/pkgsrc/2014Q4/include/db4
> > -I/nasa/pkgsrc/2014Q4/include -DNDEBUG -O2 -Wno-error -pipe -DHAVE_DB_185_H
> > -pthread -I/usr/include -I/nasa/pkgsrc/2014Q4/include/db4
> > -I/nasa/pkgsrc/2014Q4/include -fPIC -I/nasa/pkgsrc/2014Q4/include/python2.7
> > -I/nasa/pkgsrc/2014Q4/lib/python2.7/site-packages/numpy/core/include -c
> > yt/analysis_modules/photon_simulator/utils.c -o
> > build/temp.linux-x86_64-2.7/yt/analysis_modules/photon_simulator/utils.o
> > gcc: yt/analysis_modules/photon_simulator/utils.c: No such file or directory
> > gcc: no input files
> > error: command 'gcc' failed with exit status 1
> >
> > I’m using python 2.7.9 and cython 0.23.4. The problem only occurs with the
> > development branch; the stable branch compiles fine.
> >
> > I’d appreciate any suggestions. Thanks.
> >
> > --
> > Mark Krumholz
> > http://www.mso.anu.edu.au/~krumholz/ <http://www.mso.anu.edu.au/~krumholz/>
> >
> >
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> >
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--
Mark Krumholz
http://www.mso.anu.edu.au/~krumholz/

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