[yt-users] install error

Andrew Myers atmyers at berkeley.edu
Fri Jul 13 08:58:07 PDT 2012 

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.

-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 <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<tasker at astro1.sci.hokudai.ac.jp><mailto:
>>>>>>>> tasker at astro1.sci.**hokudai.ac.jp <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 <http://outreach.astro.columbia.edu>
>> PGP: 0x06F886E3
>>
>>
>>
>>
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