[yt-users] install error
Sam Skillman
samskillman at gmail.com
Fri Jul 13 08:53:31 PDT 2012
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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