[yt-users] install error

[Matthew Turk]

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> 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> 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>>
>> >>> 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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