[ncl-install] ncl -V error: dyld: Library not loaded: @rpath/libstdc++.6.dylib
Kevin Hallock
hallock at ucar.edu
Fri Oct 26 14:29:25 MDT 2018
Hi Matthew,
You’re welcome! Thanks for sharing the “conda list” output; it should hopefully be enough to reproduce your environment and the error message you saw.
I’m not sure why libgcc was not installed by default, but I’ll try to fix the NCL conda package so that it’s no longer necessary to manually install libgcc in the future.
Kevin
> On Oct 26, 2018, at 12:11 PM, Little, Matthew Benjamin <littlema18 at students.ecu.edu> wrote:
>
> Hi Kevin,
>
> Thank you for the suggestions. It appears that installing the libgcc package fixed the error I was getting at this time. If you still are interested in reproducing the error, I will be available to provide you with more information if you need it. Commands and output listed below. Thank you again.
>
>
> $ conda list -n ncl_stable
> # packages in environment at /Users/littlema18/miniconda2/envs/ncl_stable:
> #
> # Name Version Build Channel
> blas 1.1 openblas conda-forge
> boost-cpp 1.67.0 h3a22d5f_0 conda-forge
> bzip2 1.0.6 1 conda-forge
> ca-certificates 2018.10.15 ha4d7672_0 conda-forge
> cairo 1.14.12 he6fea26_5 conda-forge
> curl 7.61.1 h74213dd_2 conda-forge
> esmf 7.1.0r h35eb876_3 conda-forge
> expat 2.2.5 hfc679d8_2 conda-forge
> fontconfig 2.13.1 hce039c3_0 conda-forge
> freetype 2.9.1 h6debe1e_4 conda-forge
> freexl 1.0.5 h470a237_2 conda-forge
> geos 3.6.2 hfc679d8_3 conda-forge
> geotiff 1.4.2 h700e5ad_4 conda-forge
> gettext 0.19.8.1 h1f1d5ed_1 conda-forge
> giflib 5.1.4 h470a237_1 conda-forge
> glib 2.55.0 h464dc38_2 conda-forge
> gsl 2.2.1 blas_openblashddceaf2_6 [blas_openblas] conda-forge
> hdf4 4.2.13 h951d187_2 conda-forge
> hdf5 1.10.3 hc401514_2 conda-forge
> hdfeos2 2.20 h7a90ae3_0 conda-forge
> hdfeos5 5.1.16 h7423906_3 conda-forge
> icu 58.2 hfc679d8_0 conda-forge
> jasper 1.900.1 hff1ad4c_5 conda-forge
> jpeg 9c h470a237_1 conda-forge
> json-c 0.12.1 h470a237_1 conda-forge
> kealib 1.4.10 hb88cf67_0 conda-forge
> krb5 1.16.1 hbb41f41_0 conda-forge
> libcurl 7.61.1 hbdb9355_2 conda-forge
> libdap4 3.19.1 h18059cb_1 conda-forge
> libedit 3.1.20170329 haf1bffa_1 conda-forge
> libffi 3.2.1 hfc679d8_5 conda-forge
> libgdal 2.2.4 hd83b57f_10 conda-forge
> libgfortran 3.0.0 1 conda-forge
> libiconv 1.15 h470a237_3 conda-forge
> libkml 1.3.0 hccc92b1_8 conda-forge
> libnetcdf 4.6.1 h350cafa_11 conda-forge
> libpng 1.6.35 ha92aebf_2 conda-forge
> libpq 10.5 hf16a0db_0 conda-forge
> libspatialite 4.3.0a h3b29d86_23 conda-forge
> libssh2 1.8.0 h5b517e9_2 conda-forge
> libtiff 4.0.9 he6b73bb_2 conda-forge
> libxml2 2.9.8 h422b904_5 conda-forge
> mpi 1.0 mpich conda-forge
> mpich 3.2.1 h26a2512_5 conda-forge
> ncl 6.5.0 blas_openblash59bd76f_3 [blas_openblas] conda-forge
> ncurses 6.1 hfc679d8_1 conda-forge
> netcdf-fortran 4.4.4 h71ea97b_10 conda-forge
> openblas 0.3.3 ha44fe06_1 conda-forge
> openjpeg 2.3.0 h316dc23_3 conda-forge
> openssl 1.0.2p h470a237_1 conda-forge
> pcre 8.41 hfc679d8_3 conda-forge
> pixman 0.34.0 h470a237_3 conda-forge
> poppler 0.67.0 h4d7e492_3 conda-forge
> poppler-data 0.4.9 0 conda-forge
> postgresql 10.5 ha408888_0 conda-forge
> proj4 4.9.3 h470a237_8 conda-forge
> readline 7.0 haf1bffa_1 conda-forge
> sqlite 3.25.2 hb1c47c0_0 conda-forge
> tk 8.6.8 ha92aebf_0 conda-forge
> udunits2 2.2.27.6 h3a4f0e9_1 conda-forge
> xerces-c 3.2.0 h5d6a6da_2 conda-forge
> xz 5.2.4 h470a237_1 conda-forge
> zlib 1.2.11 h470a237_3 conda-forge
>
> $ conda install -c conda-forge -n ncl_stable libgcc
> Solving environment: done
>
> ## Package Plan ##
>
> environment location: /Users/littlema18/miniconda2/envs/ncl_stable
>
> added / updated specs:
> - libgcc
>
>
> The following packages will be downloaded:
>
> package | build
> ---------------------------|-----------------
> libgfortran-3.0.1 | h93005f0_2 495 KB
> libgcc-4.8.5 | hdbeacc1_10 302 KB conda-forge
> ------------------------------------------------------------
> Total: 797 KB
>
> The following NEW packages will be INSTALLED:
>
> libgcc: 4.8.5-hdbeacc1_10 conda-forge
>
> The following packages will be UPDATED:
>
> libgfortran: 3.0.0-1 conda-forge --> 3.0.1-h93005f0_2
>
> Proceed ([y]/n)? y
>
>
> Downloading and Extracting Packages
> libgfortran-3.0.1 | 495 KB | ##################################### | 100%
> libgcc-4.8.5 | 302 KB | ##################################### | 100%
> Preparing transaction: done
> Verifying transaction: done
> Executing transaction: done
> (ncl_stable) bd206-m01:~ littlema18$ ncl -V
> 6.5.0
>
>
>
>
>
>
> Matthew B. Little
> From: Kevin Hallock <hallock at ucar.edu>
> Sent: Thursday, October 25, 2018 12:31:33 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,
>
> 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 <mailto: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 <mailto:hallock at ucar.edu>>
>> Sent: Wednesday, October 24, 2018 2:28:26 PM
>> To: Little, Matthew Benjamin
>> Cc: ncl-install at ucar.edu <mailto: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
>>> _______________________________________________
>>> ncl-install mailing list
>>> List instructions, subscriber options, unsubscribe:
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