[yt-users] install error

Cameron Hummels chummels at astro.columbia.edu
Fri Jul 13 08:59:48 PDT 2012


Never mind, I guess that looks explicit enough!

Cameron

On 07/13/2012 11:53 AM, Sam Skillman wrote:
> Here's what the install script current spits out:
>
> Looks like you're running on Mac OSX.
>
> NOTE: you must have the Xcode command line tools installed.
>
> OS X 10.5: download Xcode 3.0 from the mac developer tools
> website
>
> OS X 10.6: download Xcode 3.2 from the mac developer tools
> website
>
> OS X 10.7: download Xcode 4.0 from the mac app store or
> alternatively download the Xcode command line tools from
> the mac developer tools website
>
> NOTE: You may have problems if you are running OSX 10.6 (Snow
> Leopard) or newer.  If you do, please set the following
> environment variables, remove any broken installation tree, and
> re-run this script verbatim.
>
> $ export CC=gcc-4.2
> $ export CXX=g++-4.2
>
>
> On Fri, Jul 13, 2012 at 9:48 AM, Cameron Hummels 
> <chummels at astro.columbia.edu <mailto:chummels at astro.columbia.edu>> wrote:
>
>     I'm +1 on making things more explicit in the install_script
>     message to users (particularly of mac).  I think most people treat
>     it like a black box and hope for the best.  And if it breaks they
>     come here. If something popped up and said, *make sure you have
>     xcode gcc installed*, it might be better for all involved.
>
>     Cameron
>
>
>
>     On 07/13/2012 11:38 AM, Matthew Turk wrote:
>
>         Hi Casey,
>
>         Thanks for the summary of the options -- perhaps we should
>         make the
>         warning more explicit in the install_script?
>
>         With respect to things being far behind, I think the situation
>         will
>         only get worse.  Apple stopped updating gcc when they moved to
>         GPLv3,
>         and have started shipping their own stack based on LLVM.
>          Perhaps a
>         brainstorming session of options -- the Xcode gcc, AT&T research
>         gfortran, Macports, other binary installers, etc etc -- would be
>         helpful over on yt-dev for addressing how to keep up to date
>         with GCC
>         as well as ensure compatibility with as much as possible.
>
>         -Matt
>
>         On Fri, Jul 13, 2012 at 8:17 AM, Casey W. Stark
>         <caseywstark at gmail.com <mailto:caseywstark at gmail.com>> wrote:
>
>             That's a good point Sam. I've seen a lot of people
>             reccomend the hpc for Mac
>             compilers, but they don't support many Darwin specific
>             flags, causing common
>             build systems to break. This took way too long to figure
>             out as a new Mac
>             user. Much better to stick with Xcode gcc and get the AT&T
>             research
>             gfortran.
>
>             If you really want a new version of gnu compilers (kind of
>             amazing how far
>             behind they are), I think macports has newer versions
>             built to have the
>             apple flags.
>
>             - Casey
>
>
>             On Friday, July 13, 2012, Sam Skillman wrote:
>
>                 Beware -- updating gcc to anything past 4.2 will
>                 likely break the compile
>                 on a mac.  You want to make sure to use the Xcode gcc,
>                 which you should be
>                 able to do by setting:
>
>                 export CC=gcc-4.2
>                 export CXX=g++-4.2
>
>                 or the equivaltent command in csh if you aren't a bash
>                 person.  If you had
>                 done that, then I'm not sure what the problem would
>                 be.  You'll likely have
>                 to wipe the existing install for those exports to do
>                 you any good.
>
>                 Sam
>
>                 On Fri, Jul 13, 2012 at 1:33 AM, Elizabeth Tasker
>                 <tasker at astro1.sci.hokudai.ac.jp
>                 <mailto:tasker at astro1.sci.hokudai.ac.jp>> wrote:
>
>                 Hi Nathan,
>
>                 This is also a mac - but I'll suggest we update gcc.
>                 Thanks!
>
>                 Elizabeth
>
>
>                 On Jul 13, 2012, at 4:21 PM, Nathan Goldbaum wrote:
>
>                     Hi Elizabeth,
>
>                     I tried running the install script on my mac
>                     laptop after your e-mail.
>                     I was able to build yt from the install script
>                     with no problems.
>
>                     It would help if you could let us know a bit more
>                     about the system
>                     you're trying to build yt on.  In particular, I
>                     think you'll run into issues
>                     if you're using an old version of gcc that doesn't
>                     support OpenMP.  Version
>                     4.2 or newer should work.
>
>                     -Nathan
>
>
>                     On 7/13/12 12:16 AM, Elizabeth Tasker wrote:
>
>                         Hi Andrew,
>
>                         We ran the install script from scratch, so I
>                         assume it would have
>                         installed the version of cython it needed?
>
>                         Elizabeth
>
>
>                         On Jul 13, 2012, at 1:59 PM, Andrew Myers wrote:
>
>                             Hi Elizabeth,
>
>                             I saw errors like this when I tried to use
>                             an older version of Cython.
>                             Are you sure that you're using version 0.16?
>
>                             -Andrew M
>
>                             On Thu, Jul 12, 2012 at 9:55 PM, Elizabeth
>                             Tasker
>                             <tasker at astro1.sci.hokudai.ac.jp
>                             <mailto:tasker at astro1.sci.hokudai.ac.jp>
>                             <mailto:tasker at astro1.sci.hokudai.ac.jp
>                             <mailto:tasker at astro1.sci.hokudai.ac.jp>>>
>                             wrote:
>
>                                 Hi,
>
>                                 We've had some problems installing yt
>                             via the install script.
>
>                                 Initially it did not download
>                             distribute, which we did by hand.
>                                 Then, it couldn't get pip, so I
>                             commented that line out and now
>                                 it's died on cython with:
>
>
>
>                                 cythonc:>
>                             yt/utilities/lib/PointsInVolume.c
>                                 building extension
>                             "yt.utilities.lib.QuadTree" sources
>                                 cythonc:> yt/utilities/lib/QuadTree.c
>                                 building extension
>                             "yt.utilities.lib.RayIntegrators" sources
>                                 cythonc:>
>                             yt/utilities/lib/RayIntegrators.c
>                                 building extension
>                             "yt.utilities.lib.VolumeIntegrator" sources
>                                 cythonc:>
>                             yt/utilities/lib/VolumeIntegrator.c
>                                 building extension
>                             "yt.utilities.lib.grid_traversal" sources
>                                 cythonc:>
>                             yt/utilities/lib/grid_traversal.c
>
>                                 Error compiling Cython file:
>                                
>                             ------------------------------------------------------------
>                                 ...
>                                         if im.vd_strides[0] == -1:
>                                             with nogil,
>                             parallel(num_threads = num_threads):
>                                                 idata =
>                             <ImageAccumulator *>
>                                 malloc(sizeof(ImageAccumulator))
>                                                 idata.supp_data =
>                             self.supp_data
>                                                 v_pos = <np.float64_t
>                             *> malloc(3 *
>                                 sizeof(np.float64_t))
>                                                 for j in prange(size,
>                             schedule="static",chunksize=1):
>                                                               ^
>                                
>                             ------------------------------------------------------------
>
>                                
>                             yt/utilities/lib/grid_traversal.pyx:368:31: Invalid
>                             keyword
>                                 argument: chunksize
>
>                                 Error compiling Cython file:
>                                
>                             ------------------------------------------------------------
>                                 ...
>                                                 idata.supp_data =
>                             self.supp_data
>                                                 v_pos = <np.float64_t
>                             *> malloc(3 *
>                                 sizeof(np.float64_t))
>                                                 v_dir = <np.float64_t
>                             *> malloc(3 *
>                                 sizeof(np.float64_t))
>                                                 # If we do not have a
>                             simple image plane, we have
>                                 to cast all
>                                                 # our rays
>                                                 for j in prange(size,
>                             schedule="dynamic",
>                                 chunksize=100):
>                                                               ^
>
>
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>
>
>     -- 
>     Cameron Hummels
>     PhD Candidate, Astronomy Department of Columbia University
>     Public Outreach Director, Astronomy Department of Columbia University
>     NASA IYA New York State Student Ambassador
>     http://outreach.astro.columbia.edu
>     PGP: 0x06F886E3
>
>
>
>
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-- 
Cameron Hummels
PhD Candidate, Astronomy Department of Columbia University
Public Outreach Director, Astronomy Department of Columbia University
NASA IYA New York State Student Ambassador
http://outreach.astro.columbia.edu
PGP: 0x06F886E3



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