[yt-users] install error
Matthew Turk
matthewturk at gmail.com
Fri Jul 13 09:01:30 PDT 2012
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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>>>>> yt-users at lists.spacepope.org
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>>>>>
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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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>>
>>
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