[ncl-install] ncl -V error: dyld: Library not loaded: @rpath/libstdc++.6.dylib
Little, Matthew Benjamin
littlema18 at students.ecu.edu
Fri Oct 26 12:11:03 MDT 2018
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
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