[ncl-install] Trouble installing on MacOS 10.14 Mojave
Kevin Hallock
hallock at ucar.edu
Fri Oct 26 10:54:27 MDT 2018
Hi Alison,
Thanks for letting us know about the installation problem and also for following up with your workaround.
Using “conda” to install NCL is supposed to make dependencies easier to deal with, so it’s interesting to me that there are still linking issues at run time. I wasn’t able to reproduce the issue on my Mac, but I’ll look into this a bit more to see if I can fix our NCL conda package to prevent this from happening in the future.
Thanks again,
Kevin
> On Oct 25, 2018, at 8:56 PM, Alison Kohout via ncl-install <ncl-install at ucar.edu> wrote:
>
> Hi again,
>
> I think I’ve solved it.
> It was a bit of a cheat, but I just linked my homebrew gcc library into the ncl_stable library.
>
> Seems to be working now.
>
> Thanks
>
>
>
>
>
> <image0244fb.PNG> <http://www.niwa.co.nz/>
>
> Dr Alison Kohout
> Hydrodynamics Scientist
> T +64-3-343-7842
> National Institute of Water & Atmospheric Research Ltd (NIWA)
> 10 Kyle Street, Riccarton, Christchurch
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>
> From: Alison Kohout <Alison.Kohout at niwa.co.nz>
> Date: Friday, 26 October 2018 at 10:08
> To: "ncl-install at ucar.edu" <ncl-install at ucar.edu>
> Subject: Trouble installing on MacOS 10.14 Mojave
>
> Hi,
>
> I’ve been trying to install ncl from conda on my macOS 10.14, but running into trouble. Originally I tried using clang gcc, but ran into trouble. I then tried the latest gcc on homebrew, still having trouble.
> It would be fantastic if you could help me out.
>
> THANKS
>
> Here are the details:
>
> [kohoutal at niwa-36847 ~]$ source activate ncl_stable
>
> (ncl_stable) [kohoutal at niwa-36847 ~]$ which ncl
> /Users/kohoutal/miniconda3/envs/ncl_stable/bin/ncl
>
> (ncl_stable) [kohoutal at niwa-36847 ~]$ ncl -V
> dyld: lazy symbol binding failed: Symbol not found: ___emutls_get_address
> Referenced from: /Users/kohoutal/miniconda3/envs/ncl_stable/lib/libgomp.1.dylib
> Expected in: /usr/lib/libSystem.B.dylib
>
> dyld: Symbol not found: ___emutls_get_address
> Referenced from: /Users/kohoutal/miniconda3/envs/ncl_stable/lib/libgomp.1.dylib
> Expected in: /usr/lib/libSystem.B.dylib
>
> Abort trap: 6
>
> (ncl_stable) [kohoutal at niwa-36847 ~]$ otool -L `which ncl`
> /Users/kohoutal/miniconda3/envs/ncl_stable/bin/ncl:
> /usr/lib/libc++.1.dylib (compatibility version 1.0.0, current version 307.5.0)
> @rpath/libnetcdf.13.dylib (compatibility version 13.0.0, current version 13.0.0)
> @rpath/libcurl.4.dylib (compatibility version 10.0.0, current version 10.0.0)
> @rpath/libhdf5_hl.100.dylib (compatibility version 102.0.0, current version 102.1.0)
> @rpath/libhdf5.103.dylib (compatibility version 104.0.0, current version 104.0.0)
> @rpath/libmfhdf.0.dylib (compatibility version 1.0.0, current version 1.0.0)
> @rpath/libdf.0.dylib (compatibility version 1.0.0, current version 1.0.0)
> @rpath/libjpeg.9.dylib (compatibility version 13.0.0, current version 13.0.0)
> @rpath/libz.1.dylib (compatibility version 1.0.0, current version 1.2.11)
> @rpath/libgdal.20.dylib (compatibility version 24.0.0, current version 24.3.0)
> @rpath/libproj.12.dylib (compatibility version 13.0.0, current version 13.0.0)
> @rpath/libudunits2.0.dylib (compatibility version 2.0.0, current version 2.0.0)
> @rpath/libexpat.1.dylib (compatibility version 8.0.0, current version 8.7.0)
> @rpath/libjasper.1.dylib (compatibility version 2.0.0, current version 2.0.0)
> @rpath/libpng16.16.dylib (compatibility version 51.0.0, current version 51.0.0)
> /opt/X11/lib/libcairo.2.dylib (compatibility version 11403.0.0, current version 11403.6.0)
> /opt/X11/lib/libfontconfig.1.dylib (compatibility version 11.0.0, current version 11.2.0)
> /opt/X11/lib/libpixman-1.0.dylib (compatibility version 35.0.0, current version 35.0.0)
> /opt/X11/lib/libfreetype.6.dylib (compatibility version 19.0.0, current version 19.6.0)
> /opt/X11/lib/libXrender.1.dylib (compatibility version 5.0.0, current version 5.0.0)
> @rpath/libiconv.2.dylib (compatibility version 9.0.0, current version 9.0.0)
> @rpath/libbz2.dylib (compatibility version 0.0.0, current version 0.0.0)
> @rpath/libgsl.19.dylib (compatibility version 22.0.0, current version 22.0.0)
> @rpath/libopenblas.dylib (compatibility version 0.0.0, current version 0.0.0)
> /opt/X11/lib/libXpm.4.dylib (compatibility version 16.0.0, current version 16.0.0)
> /opt/X11/lib/libX11.6.dylib (compatibility version 10.0.0, current version 10.0.0)
> /opt/X11/lib/libXext.6.dylib (compatibility version 11.0.0, current version 11.0.0)
> @rpath/libgfortran.3.dylib (compatibility version 4.0.0, current version 4.0.0)
> @rpath/libquadmath.0.dylib (compatibility version 1.0.0, current version 1.0.0)
> @rpath/libstdc++.6.dylib (compatibility version 7.0.0, current version 7.19.0)
> @rpath/libgomp.1.dylib (compatibility version 2.0.0, current version 2.0.0)
> /usr/lib/libSystem.B.dylib (compatibility version 1.0.0, current version 1238.60.2)
> @rpath/libgcc_s.1.dylib (compatibility version 1.0.0, current version 1.0.0)
>
> (ncl_stable) [kohoutal at niwa-36847 ~]$ env | grep NCARG
> NCARG_ROOT=/Users/kohoutal/miniconda3/envs/ncl_stable
>
> (ncl_stable) [kohoutal at niwa-36847 ~]$ which gcc
> /usr/local/bin/gcc
>
> (ncl_stable) [kohoutal at niwa-36847 ~]$ which gfortran
> /usr/local/bin/gfortran
>
> (ncl_stable) [kohoutal at niwa-36847 ~]$ gfortran --version
> GNU Fortran (Homebrew GCC 8.2.0) 8.2.0
> Copyright (C) 2018 Free Software Foundation, Inc.
> This is free software; see the source for copying conditions. There is NO
> warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
>
> (ncl_stable) [kohoutal at niwa-36847 ~]$ gcc --version
> gcc (Homebrew GCC 8.2.0) 8.2.0
> Copyright (C) 2018 Free Software Foundation, Inc.
> This is free software; see the source for copying conditions. There is NO
> warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
>
>
>
>
>
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