[yt-users] install error

Nathan Goldbaum nathan12343 at gmail.com
Fri Jul 13 09:38:02 PDT 2012 

There's no need, 10.5 comes with GCC 4.2.



On Jul 13, 2012, at 9:02 AM, Matthew Turk <matthewturk at gmail.com> wrote:

> On Fri, Jul 13, 2012 at 8:58 AM, Andrew Myers <atmyers at berkeley.edu> wrote:
>> Is it actually true that yt still works with the xcode gcc from 10.5? I
>> though that compiler didn't support openmp, which is now required.
>
> Hmm.  We could possibly try to detect whether the -fopenmp option is
> available or not, but I'm not sure how to do that.  This might require
> modifying distutils or using an env var.
>
>>
>> -Andrew M
>>
>> On Fri, Jul 13, 2012 at 8:53 AM, Sam Skillman <samskillman at gmail.com> 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> 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>
>>>>> 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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>>>>>
>>>>
>>>> --
>>>> 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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