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:<div><br></div><div>export CC=gcc-4.2</div><div>export CXX=g++-4.2</div>
<div><br></div><div>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.</div>
<div><br></div><div>Sam<br><br><div class="gmail_quote">On Fri, Jul 13, 2012 at 1:33 AM, Elizabeth Tasker <span dir="ltr"><<a href="mailto:tasker@astro1.sci.hokudai.ac.jp" target="_blank">tasker@astro1.sci.hokudai.ac.jp</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">Hi Nathan,<br>
<br>
This is also a mac - but I'll suggest we update gcc. Thanks!<br>
<span class="HOEnZb"><font color="#888888"><br>
Elizabeth<br>
</font></span><div class="HOEnZb"><div class="h5"><br>
<br>
On Jul 13, 2012, at 4:21 PM, Nathan Goldbaum wrote:<br>
<br>
> Hi Elizabeth,<br>
><br>
> 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.<br>
><br>
> 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.<br>
><br>
> -Nathan<br>
><br>
><br>
> On 7/13/12 12:16 AM, Elizabeth Tasker wrote:<br>
>> Hi Andrew,<br>
>><br>
>> We ran the install script from scratch, so I assume it would have installed the version of cython it needed?<br>
>><br>
>> Elizabeth<br>
>><br>
>><br>
>> On Jul 13, 2012, at 1:59 PM, Andrew Myers wrote:<br>
>><br>
>>> Hi Elizabeth,<br>
>>><br>
>>> 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?<br>
>>><br>
>>> -Andrew M<br>
>>><br>
>>> On Thu, Jul 12, 2012 at 9:55 PM, Elizabeth Tasker <<a href="mailto:tasker@astro1.sci.hokudai.ac.jp">tasker@astro1.sci.hokudai.ac.jp</a> <mailto:<a href="mailto:tasker@astro1.sci.hokudai.ac.jp">tasker@astro1.sci.hokudai.ac.jp</a>>> wrote:<br>
>>><br>
>>> Hi,<br>
>>><br>
>>> We've had some problems installing yt via the install script.<br>
>>><br>
>>> Initially it did not download distribute, which we did by hand.<br>
>>> Then, it couldn't get pip, so I commented that line out and now<br>
>>> it's died on cython with:<br>
>>><br>
>>><br>
>>><br>
>>> cythonc:> yt/utilities/lib/PointsInVolume.c<br>
>>> building extension "yt.utilities.lib.QuadTree" sources<br>
>>> cythonc:> yt/utilities/lib/QuadTree.c<br>
>>> building extension "yt.utilities.lib.RayIntegrators" sources<br>
>>> cythonc:> yt/utilities/lib/RayIntegrators.c<br>
>>> building extension "yt.utilities.lib.VolumeIntegrator" sources<br>
>>> cythonc:> yt/utilities/lib/VolumeIntegrator.c<br>
>>> building extension "yt.utilities.lib.grid_traversal" sources<br>
>>> cythonc:> yt/utilities/lib/grid_traversal.c<br>
>>><br>
>>> Error compiling Cython file:<br>
>>> ------------------------------------------------------------<br>
>>> ...<br>
>>> if im.vd_strides[0] == -1:<br>
>>> with nogil, parallel(num_threads = num_threads):<br>
>>> idata = <ImageAccumulator *><br>
>>> malloc(sizeof(ImageAccumulator))<br>
>>> idata.supp_data = self.supp_data<br>
>>> v_pos = <np.float64_t *> malloc(3 *<br>
>>> sizeof(np.float64_t))<br>
>>> for j in prange(size, schedule="static",chunksize=1):<br>
>>> ^<br>
>>> ------------------------------------------------------------<br>
>>><br>
>>> yt/utilities/lib/grid_traversal.pyx:368:31: Invalid keyword<br>
>>> argument: chunksize<br>
>>><br>
>>> Error compiling Cython file:<br>
>>> ------------------------------------------------------------<br>
>>> ...<br>
>>> idata.supp_data = self.supp_data<br>
>>> v_pos = <np.float64_t *> malloc(3 *<br>
>>> sizeof(np.float64_t))<br>
>>> v_dir = <np.float64_t *> malloc(3 *<br>
>>> sizeof(np.float64_t))<br>
>>> # If we do not have a simple image plane, we have<br>
>>> to cast all<br>
>>> # our rays<br>
>>> for j in prange(size, schedule="dynamic",<br>
>>> chunksize=100):<br>
>>> ^<br>
>>> ------------------------------------------------------------<br>
>>><br>
>>> yt/utilities/lib/grid_traversal.pyx:393:31: Invalid keyword<br>
>>> argument: chunksize<br>
>>><br>
>>> Error compiling Cython file:<br>
>>> ------------------------------------------------------------<br>
>>> ...<br>
>>> cdef np.float64_t px, py<br>
>>> cdef np.float64_t width[3]<br>
>>> for i in range(3):<br>
>>> width[i] = self.width[i]<br>
>>> if im.vd_strides[0] == -1:<br>
>>> with nogil, parallel(num_threads = num_threads):<br>
>>> ^<br>
>>> ------------------------------------------------------------<br>
>>><br>
>>> yt/utilities/lib/grid_traversal.pyx:364:32: Invalid value for<br>
>>> num_threads argument, expected an int<br>
>>> error: 3 errors while compiling<br>
>>> 'yt/utilities/lib/grid_traversal.pyx' with Cython<br>
>>><br>
>>><br>
>>><br>
>>> Has anyone had a similar experience?<br>
>>><br>
>>> Elizabeth<br>
>>> _______________________________________________<br>
>>> yt-users mailing list<br>
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>>><br>
>>><br>
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>><br>
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</div></div></blockquote></div><br></div>