<html><head></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; ">I'm not yet sure if this is the problem (the student I was helping scooted off for the day). <div><br></div><div>But, I did read the below messages and I think what might not have been clear was that we might have had two gcc installations and it was imperative to get the Xcode one, not the macports one (unless it's the apple-fied macports option). </div><div><br></div><div>Perhaps just an extra line citing that as an example?</div><div><br></div><div><br></div><div><br><div><div>On Jul 14, 2012, at 12:53 AM, Sam Skillman wrote:</div><br class="Apple-interchange-newline"><blockquote type="cite">Here's what the install script current spits out:<br><div><br></div><div><div>Looks like you're running on Mac OSX.</div><div><br></div><div>NOTE: you must have the Xcode command line tools installed.</div><div><br>
</div><div>OS X 10.5: download Xcode 3.0 from the mac developer tools</div><div>website</div><div><br></div><div>OS X 10.6: download Xcode 3.2 from the mac developer tools</div><div>website</div><div><br></div><div>OS X 10.7: download Xcode 4.0 from the mac app store or</div>
<div>alternatively download the Xcode command line tools from</div><div>the mac developer tools website</div><div><br></div><div>NOTE: You may have problems if you are running OSX 10.6 (Snow</div><div>Leopard) or newer. If you do, please set the following</div>
<div>environment variables, remove any broken installation tree, and</div><div>re-run this script verbatim.</div><div><br></div><div>$ export CC=gcc-4.2</div><div>$ export CXX=g++-4.2</div><div><br></div><br><div class="gmail_quote">
On Fri, Jul 13, 2012 at 9:48 AM, Cameron Hummels <span dir="ltr"><<a href="mailto:chummels@astro.columbia.edu" target="_blank">chummels@astro.columbia.edu</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
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.<br>
<br>
Cameron<div class="HOEnZb"><div class="h5"><br>
<br>
<br>
On 07/13/2012 11:38 AM, Matthew Turk wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
Hi Casey,<br>
<br>
Thanks for the summary of the options -- perhaps we should make the<br>
warning more explicit in the install_script?<br>
<br>
With respect to things being far behind, I think the situation will<br>
only get worse. Apple stopped updating gcc when they moved to GPLv3,<br>
and have started shipping their own stack based on LLVM. Perhaps a<br>
brainstorming session of options -- the Xcode gcc, AT&T research<br>
gfortran, Macports, other binary installers, etc etc -- would be<br>
helpful over on yt-dev for addressing how to keep up to date with GCC<br>
as well as ensure compatibility with as much as possible.<br>
<br>
-Matt<br>
<br>
On Fri, Jul 13, 2012 at 8:17 AM, Casey W. Stark <<a href="mailto:caseywstark@gmail.com" target="_blank">caseywstark@gmail.com</a>> wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
That's a good point Sam. I've seen a lot of people reccomend the hpc for Mac<br>
compilers, but they don't support many Darwin specific flags, causing common<br>
build systems to break. This took way too long to figure out as a new Mac<br>
user. Much better to stick with Xcode gcc and get the AT&T research<br>
gfortran.<br>
<br>
If you really want a new version of gnu compilers (kind of amazing how far<br>
behind they are), I think macports has newer versions built to have the<br>
apple flags.<br>
<br>
- Casey<br>
<br>
<br>
On Friday, July 13, 2012, Sam Skillman wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
Beware -- updating gcc to anything past 4.2 will likely break the compile<br>
on a mac. You want to make sure to use the Xcode gcc, which you should be<br>
able to do by setting:<br>
<br>
export CC=gcc-4.2<br>
export CXX=g++-4.2<br>
<br>
or the equivaltent command in csh if you aren't a bash person. If you had<br>
done that, then I'm not sure what the problem would be. You'll likely have<br>
to wipe the existing install for those exports to do you any good.<br>
<br>
Sam<br>
<br>
On Fri, Jul 13, 2012 at 1:33 AM, Elizabeth Tasker<br>
<<a href="mailto:tasker@astro1.sci.hokudai.ac.jp" target="_blank">tasker@astro1.sci.hokudai.ac.<u></u>jp</a>> wrote:<br>
<br>
Hi Nathan,<br>
<br>
This is also a mac - but I'll suggest we update gcc. Thanks!<br>
<br>
Elizabeth<br>
<br>
<br>
On Jul 13, 2012, at 4:21 PM, Nathan Goldbaum wrote:<br>
<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
Hi Elizabeth,<br>
<br>
I tried running the install script on my mac laptop after your e-mail.<br>
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<br>
you're trying to build yt on. In particular, I think you'll run into issues<br>
if you're using an old version of gcc that doesn't support OpenMP. Version<br>
4.2 or newer should work.<br>
<br>
-Nathan<br>
<br>
<br>
On 7/13/12 12:16 AM, Elizabeth Tasker wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
Hi Andrew,<br>
<br>
We ran the install script from scratch, so I assume it would have<br>
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>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
Hi Elizabeth,<br>
<br>
I saw errors like this when I tried to use an older version of Cython.<br>
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<br>
<<a href="mailto:tasker@astro1.sci.hokudai.ac.jp" target="_blank">tasker@astro1.sci.hokudai.ac.<u></u>jp</a> <mailto:<a href="mailto:tasker@astro1.sci.hokudai.ac.jp" target="_blank">tasker@astro1.sci.<u></u>hokudai.ac.jp</a>>><br>
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/<u></u>PointsInVolume.c<br>
building extension "yt.utilities.lib.QuadTree" sources<br>
cythonc:> yt/utilities/lib/QuadTree.c<br>
building extension "yt.utilities.lib.<u></u>RayIntegrators" sources<br>
cythonc:> yt/utilities/lib/<u></u>RayIntegrators.c<br>
building extension "yt.utilities.lib.<u></u>VolumeIntegrator" sources<br>
cythonc:> yt/utilities/lib/<u></u>VolumeIntegrator.c<br>
building extension "yt.utilities.lib.grid_<u></u>traversal" sources<br>
cythonc:> yt/utilities/lib/grid_<u></u>traversal.c<br>
<br>
Error compiling Cython file:<br>
------------------------------<u></u>------------------------------<br>
...<br>
if im.vd_strides[0] == -1:<br>
with nogil, parallel(num_threads = num_threads):<br>
idata = <ImageAccumulator *><br>
malloc(sizeof(<u></u>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,<br>
schedule="static",chunksize=1)<u></u>:<br>
^<br>
------------------------------<u></u>------------------------------<br>
<br>
yt/utilities/lib/grid_<u></u>traversal.pyx:368:31: Invalid keyword<br>
argument: chunksize<br>
<br>
Error compiling Cython file:<br>
------------------------------<u></u>------------------------------<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>
</blockquote></blockquote></blockquote></blockquote>
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<br></div></div><span class="HOEnZb"><font color="#888888">
-- <br>
Cameron Hummels<br>
PhD Candidate, Astronomy Department of Columbia University<br>
Public Outreach Director, Astronomy Department of Columbia University<br>
NASA IYA New York State Student Ambassador<br>
<a href="http://outreach.astro.columbia.edu/" target="_blank">http://outreach.astro.<u></u>columbia.edu</a><br>
PGP: 0x06F886E3</font></span><div class="HOEnZb"><div class="h5"><br>
<br>
<br>
<br>
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