[ncl-install] Mac OS X 10.11 Incompatability

Thu Dec 17 07:40:03 MST 2015

Hi Mary,

No, I haven't built from source yet. I'm going to try first with the
standard packages I can get/have from MacPorts - it seems like everything
is there, if you include the g2clib within GDAL. It also seems that GDAL
made a major update back in September and not sure if any of your
fixes/alterations to g2clib would've snuck in there or been fixed otherwise.

(text above written yesterday)

Build finished after I left work yesterday, successfully. Interestingly,
the source tarball I downloaded seems to be quite old! It contains NCL
6.1.0-beta, a version that was outdated before I even purchased the
computer. The executables are all dated 24 May 2012, which appears to be
consistent with when such a build may have been released.

Regardless, I ran the example - gsun01n.ncl, and it immediately segfaults.
I think this has to do with me not being able to easily get some of the X11
development libraries for Mac, which is more on me than anything. Changing
the wks_type to png immediately allowed the script to run successfully.
Other libraries I didn't/couldn't get via port include HDF-EOS5 and the
patched g2clib. All other external software was included and built based
only on the MacPorts versions available.

Still not sure how the source code contains 6.1.0-beta when downloaded from
https://www.earthsystemgrid.org/dataset/ncl.630.2.html (I can confirm the
file size matches the one listed for 6.3.0 source). But regardless, build
from scratch seems to work well on 10.11 when the appropriate paths are
provided in the Q&A section of the config.

Kyle

----------------------------------------
Kyle S. Griffin
Department of Atmospheric and Oceanic Sciences
University of Wisconsin - Madison
Room 1407
1225 W Dayton St, Madison, WI 53706
Email: ksgriffin2 at wisc.edu

On Wed, Dec 16, 2015 at 12:38 PM, Mary Haley <haley at ucar.edu> wrote:

> Hi Kyle,
>
> We try to remove as many of these shared library dependencies as possible,
> and we've been able to get by with this situation with previous versions of
> MacOS.
>
> It doesn't surprise me that Apple has changed things up a bit, and
> unfortunately, I don't have a 10.11 system to test on yet.  I have to be
> careful about upgrading right away because this usually breaks my ability
> to run VPN from home, which is critical for work.
>
> I'm going to see if it's safe for me to upgrade to 10.11, and then I'll
> give the NCL build a try.
>
> I do appreciate you offering to be a guinea pig.  Have you actually tried
> building NCL from source code?
>
> --Mary
>
>
> On Mon, Dec 14, 2015 at 9:37 AM, Kyle Griffin <ksgriffin2 at wisc.edu> wrote:
>
>> Hi all,
>>
>> I wanted to highlight the result of a bit of research I've had to do
>> after upgrading a Mac from 10.9 to 10.11 - specifically, that
>> DYLD_LIBRARY_PATH and DYLD_FALLBACK_LIBRARY_PATH are no longer supported by
>> default in OS X. While they can be set, this setting is not recognized in
>> any automated (cron) calls to scripts. Here's on example output, where I
>> print the contents of both environmental variables before attempting to run
>> an NCL script. One environmental variable is set in .profile (manually
>> sourced at start of the script) and one is set within the script itself.
>> Both are ignored.
>>
>> /opt/local/lib/gcc49:/opt/local/lib/gcc
>>
>> /opt/local/lib/gcc49:/opt/local/lib/gcc
>>
>> dyld: Library not loaded: /usr/local/lib/libquadmath.0.dylib
>>
>>   Referenced from: /Users/ksgriffin2/ncl6.3.0.1010/bin/ncl
>>
>>   Reason: image not found
>>
>> The dyld:... error was originally missing libgfortran.3.dylib, but I
>> manually created a link in /usr/local/lib to the version in
>> /opt/local/lib/gcc49 try and tackle this problem. It appears that linking
>> libgfortran.3.dylib, libquadmath.0.dylib, and libgomp.1.dylib does the
>> trick to allow NCL to function as a workaround, but could be problematic
>> long-term I would guess? The binary in use here is the Mac 10.10/gcc4.9.2
>> binary.
>>
>> Apple now claims that any software relying on this should, essentially,
>> not rely on these techniques any more or place them all in /usr/local/ (I'm
>> using MacPorts, putting things /opt/local/) [see under last heading on the
>> page]:
>>
>> https://developer.apple.com/library/mac/documentation/Security/Conceptual/System_Integrity_Protection_Guide/FileSystemProtections/FileSystemProtections.html#//apple_ref/doc/uid/TP40016462-CH2-DontLinkElementID_2
>>
>> This can, in theory, be fixed by accessing the system recovery and
>> disabling the new "System Integrity Protection" feature that eliminates
>> these issues, but I feel that is not an appropriate fix for this problem.
>> For testing purposes, the simple process of disabling SIP is presented at
>> the bottom of this article:
>> http://www.macworld.com/article/2986118/security/how-to-modify-system-integrity-protection-in-el-capitan.html
>>
>> I should note the NCL appears to work fine from the command line,
>> although I have to test it in depth.
>>
>> So it appears going forward that significant changes may need to be made
>> to the NCL binaries for OS X in order for them to be functional at all.
>> I'll be happy to serve as a guinea pig for fixes if a 10.11 system isn't
>> available for testing...
>>
>>
>> Kyle
>> ----------------------------------------
>> Kyle S. Griffin
>> Department of Atmospheric and Oceanic Sciences
>> University of Wisconsin - Madison
>> Room 1407
>> 1225 W Dayton St, Madison, WI 53706
>> Email: ksgriffin2 at wisc.edu
>>
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>
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