[ncl-install] ncl -V error: dyld: Library not loaded: @rpath/libstdc++.6.dylib
Kevin Hallock
hallock at ucar.edu
Thu Oct 25 10:31:33 MDT 2018
Hi Matthew,
I’m sorry to hear you’re still getting the same error.
Could you please run “conda list -n ncl_stable” and reply with the output? I would like to try to reproduce this issue by installing all of the same packages that you have in your “ncl_stable” environment.
You might be able to run “conda install -c conda-forge -n ncl_stable libgcc” in order to install the “libgcc” package that contains the file “libstdc++.6.dylib”. However, even if that fixes things I’m still very interested in determining the cause of the original installation problem.
Thanks,
Kevin
> On Oct 25, 2018, at 6:16 AM, Little, Matthew Benjamin <littlema18 at students.ecu.edu> wrote:
>
> Hi Kevin,
>
> You are right, I am trying to use conda to install/run NCL; I forgot to mention that in my first message.
>
> The following occurs when issuing the commands reccommended:
> $ source activate ncl_stable
> $ conda update --all -c conda-forge
>
> ## Package Plan ##
>
> environment location: /Users/littlema18/miniconda2/envs/ncl_stable
>
>
> The following packages will be downloaded:
>
> package | build
> ---------------------------|-----------------
> ncl-6.5.0 |blas_openblash59bd76f_3 58.5 MB conda-forge
>
> The following packages will be UPDATED:
>
> ncl: 6.5.0-blas_openblash59bd76f_2 conda-forge [blas_openblas] --> 6.5.0-blas_openblash59bd76f_3 conda-forge [blas_openblas]
>
> Proceed ([y]/n)? y
>
>
> Downloading and Extracting Packages
> ncl-6.5.0 | 58.5 MB | ##################################### | 100%
> Preparing transaction: done
> Verifying transaction: done
> Executing transaction: done
> $ ncl -V
> dyld: Library not loaded: @rpath/libstdc++.6.dylib
> Referenced from: /Users/littlema18/miniconda2/envs/ncl_stable/bin/ncl
> Reason: image not found
> Abort trap: 6
>
> So, the problem appears to persist at this time.
>
> Matthew B. Little
> From: Kevin Hallock <hallock at ucar.edu>
> Sent: Wednesday, October 24, 2018 2:28:26 PM
> To: Little, Matthew Benjamin
> Cc: ncl-install at ucar.edu
> Subject: Re: [ncl-install] ncl -V error: dyld: Library not loaded: @rpath/libstdc++.6.dylib
>
> Hi Matthew,
>
> Are you trying to run a version of NCL installed through conda or are you compiling your own build? Clang vs GCC can be an issue if you’re building NCL yourself, but the conda NCL package is available as a pre-compiled binary and should include all of the necessary libraries.
>
> Based on the directories I can see in the command output below, it looks like you’re using conda. With your “ncl_stable” conda environment activated, could you please try running “conda update --all -c conda-forge” and then “ncl -V” again?
>
> Thanks,
> Kevin
>
>> On Oct 24, 2018, at 11:27 AM, Little, Matthew Benjamin via ncl-install <ncl-install at ucar.edu <mailto:ncl-install at ucar.edu>> wrote:
>>
>> Hello NCL install group,
>>
>> I am currently trying to install NCL on MacOS. I initially was using clang, however, I encountered installation problems with clang I switched to gcc. Nevertheless, the problem that I saw when using clang persists when I issue the command:
>> $ ncl -V
>> dyld: Library not loaded: @rpath/libstdc++.6.dylib
>> Referenced from: /Users/littlema18/miniconda2/envs/ncl_stable/bin/ncl
>> Reason: image not found
>> Abort trap: 6
>>
>> This seems to be a common problem from what I can tell, but I feel I have hit a wall with my limited knowledge. Below are
>>
>>
>> $ sw_vers -productVersion
>> 10.13.3
>> which gcc
>> /usr/local/bin/gcc
>> $ which gfortran
>> /usr/local/bin/gfortran
>> $ gcc --version
>> gcc (GCC) 8.1.0
>> 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.
>> $ gfortran --version
>> GNU Fortran (GCC) 8.1.0
>> 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.
>> $ env | grep NCARG
>> OLD_NCARG_ROOT=/usr/local/ncl-current
>> NCARG_ROOT=/Users/littlema18/miniconda2/envs/ncl_stable
>> $ env | grep LD
>> OLD_NCARG_ROOT=/usr/local/ncl-current
>> $ which ncl
>> /Users/littlema18/miniconda2/envs/ncl_stable/bin/ncl
>> $ otool -L `which ncl`
>> /Users/littlema18/miniconda2/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)
>>
>> Thanks for any advice,
>>
>> Matthew B. Little
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