[yt-users] Matplotlib installation failure on OS X

Tue May 21 12:38:44 PDT 2013

For others listening in, this fix will be included in the next stable
release in ~10 days.

On Tue, May 21, 2013 at 12:37 PM, Paul La Plante <plaplant at andrew.cmu.edu>wrote:

> Hi Nathan,
>
> Thanks for the tip! Switching to the developer version fixed this.
>
> -Paul
>
> On May 21, 2013, at 1:10 PM, Nathan Goldbaum <nathan12343 at gmail.com>
> wrote:
>
> Hi Paul,
>
> This is due to an issue that has been fixed in the latest development
> version of yt.
>
> Can you try installing that instead?  The development install script is
> here:
>
> http://hg.yt-project.org/yt/raw/yt/doc/install_script.sh
>
> -Nathan
>
> On May 21, 2013, at 10:07 AM, Paul La Plante <plaplant at andrew.cmu.edu>
> wrote:
>
> Thanks for your assistance. As Britton suggested, I used the
> Apple-provided compilers. But as Chris noted, I had trouble with sed while
> trying to export CC, so I made a symbolic link instead (to llvm-gcc, I'm
> not sure if it matters). Now it crashes on the 'Installing yt' step. The
> error message is included below. It looks like it can't link against gomp.
>
> I am currently running again using Apple-provided non-llvm gcc to see if
> this fixes the problem.
>
> -Paul
>
> ********************************************
>         FAILURE REPORT:
> ********************************************
>
> ld: warning: directory not found for option
> '-L/Users/plaplant/Documents/school/grad/Second_Year/Spring_13/yt-x86_64/lib64/'
> ld: library not found for -lgomp
> clang: error: linker command failed with exit code 1 (use -v to see
> invocation)
> ld: warning: directory not found for option
> '-L/Users/plaplant/Documents/school/grad/Second_Year/Spring_13/yt-x86_64/lib64/'
> ld: warning: directory not found for option
> '-L/Users/plaplant/Documents/school/grad/Second_Year/Spring_13/yt-x86_64/lib64/'
> ld: warning: directory not found for option
> '-L/Users/plaplant/Documents/school/grad/Second_Year/Spring_13/yt-x86_64/lib64/'
> ld: warning: directory not found for option
> '-L/Users/plaplant/Documents/school/grad/Second_Year/Spring_13/yt-x86_64/lib64/'
> ld: library not found for -lgomp
> clang: error: linker command failed with exit code 1 (use -v to see
> invocation)
> error: Command "/usr/bin/clang -bundle -undefined dynamic_lookup
> -L/Users/plaplant/Documents/school/grad/Second_Year/Spring_13/yt-x86_64/lib/
> -L/Users/plaplant/Documents/school/grad/Second_Year/Spring_13/yt-x86_64/lib64/
> -L/Users/plaplant/Documents/school/grad/Second_Year/Spring_13/yt-x86_64/lib/
> -L/Users/plaplant/Documents/school/grad/Second_Year/Spring_13/yt-x86_64/lib64/
> -L/Users/plaplant/Documents/school/grad/Second_Year/Spring_13/yt-x86_64/lib/
> -L/Users/plaplant/Documents/school/grad/Second_Year/Spring_13/yt-x86_64/lib64/
> -L/Users/plaplant/Documents/school/grad/Second_Year/Spring_13/yt-x86_64/lib/
> -L/Users/plaplant/Documents/school/grad/Second_Year/Spring_13/yt-x86_64/lib64/
> -mmacosx-version-min=10.7
> build/temp.macosx-10.4-x86_64-2.7/yt/utilities/lib/geometry_utils.o -lm -o
> yt/utilities/lib/geometry_utils.so -fopenmp" failed with exit status 1
>
> ********************************************
> ********************************************
>
> On May 21, 2013, at 12:57 PM, Chris Malone <chris.m.malone at gmail.com>
> wrote:
>
> Just a comment:
>
> Using the full path to the compilers (e.g. using /usr/bin/gcc instead of
> gcc) will fail because of a sed command (line 329 in install_script.sh)
> using the forward slash as a separator.  If the compilers are in your bath,
> you might want to specify them directly by name, rather than the full
> pathname.
>
> The install script should probably be changed to use something other than
> forward slash as the delimiter, at least in this case where it might get
> mangled with pathnames.  Something like changing
>
> ... -e "s/CC=gcc/CC=${CC}/ ...
>
> to
>
> ... -e "s|CC=gcc|CC=${CC}| ...
>
> Chris
>
>
> On Tue, May 21, 2013 at 7:58 AM, Britton Smith <brittonsmith at gmail.com>wrote:
>
>> Hi Paul,
>>
>> Welcome to yt!
>>
>> We have had a number of problems in the past using gnu compilers that are
>> not the ones installed with xcode.  I recommend you try again with those
>> compilers.  To do that, you should be able to just do:
>> export CC=/usr/bin/gcc
>> export CXX=/usr/bin/g++
>>
>> Please, let us know if that doesn't work.  Also, if it doesn't, please
>> just send us the last 10 or 20 lines of the output log from the install
>> script.  That should be enough to diagnose the problem.
>>
>> Britton
>>
>>
>> On Tue, May 21, 2013 at 10:19 AM, Paul La Plante <plaplant at andrew.cmu.edu
>> > wrote:
>>
>>> Hi,
>>>
>>> I am having trouble installing yt on my personal machine using the
>>> install script. I downloaded the script from the suggested website (
>>> http://hg.yt-project.org/yt/raw/stable/doc/install_script.sh) and
>>> attempted to execute it with `bash install_script.sh.' I have tried a few
>>> different combinations of install options, but it always seems to fail
>>> while building matplotlib. My system is OS X 10.8.3, and gcc version 4.8.0
>>> (installed from MacPorts). I have attached my yt_install.log.
>>>
>>> Thanks in advance for any help!
>>>
>>> Best regards,
>>> Paul
>>>
>>>
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>>>
>>>
>>
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