[ncl-install] Error on Mac when testing NCL
Dominikus Heinzeller
climbfuji at ymail.com
Sat Jan 7 07:23:06 MST 2017
Hi Benedikt & Kwesi,
I had a similar problem a while ago. On Mac OS X, you can use a command such as
install_name_tool -change /usr/local/opt/gcc/lib/gcc/5/libgfortran.3.dylib /usr/local/lib/libgfortran.3.dylib /usr/local/opt/mpich/lib/libmpi.12.dylib
to change the symbolic libraries an application is looking for:
install_name_tool -h
install_name_tool [-change old new] ... [-rpath old new] ... [-add_rpath new] ... [-delete_rpath old] ... [-id name] input
Hope this helps.
Cheers, Dom
> On 7/01/2017, at 2:25 PM, Kwesi Quagraine <starskykwesi at gmail.com> wrote:
>
> Great news. Cheers!!
>
> On Jan 7, 2017 3:22 PM, "Benedikt Becsi" <benedikt.becsi at boku.ac.at <mailto:benedikt.becsi at boku.ac.at>> wrote:
> Hey Kwesi,
>
> thanks again for your advice. It still ran into the same problem when I softlinked the library in /ncl_6.3.0/lib/. With some additional testing I found out the following:
> NCL only started when I put export DYLD_FALLBACK_LIBRARY_PATH=/usr/local/Cellar/gcc/6.3.0_1/lib/gcc/6 into my .bashrc file. Removing this line I received the same error as when I try to run the test script ng4ex gsun01n -clean so I assumed that the problem was with the libstdc++.6.dylib library in my /usr/lib/ folder. Originally it was only a softlink to the libstdc++.6.0.9.dylib library in the same folder. Since NCL was able to start when I put the export DYLD_FALLBACK_LIBRARY_PATH line into my .bashrc-file, but ng4ex produced the error, it is obvious that the ng4ex bin does not use the library specified in the .bashrc file, but rather the default on in /usr/lib/. So for now I got it to run by disabling the mac System Integrity Protection (SIP) and replacing the libstdc++.6.dylib softlink with the full library in usr/local/Cellar/gcc/6.3.0_1/lib/gcc/6/, which is a homebrew gcc version I installed. Now it works perfectly, also ncl does start without the export DYLD_FALLBACK_LIBRARY_PATH line in my .bashrc-file.
> However, this can't be an optimal solution, since I don't know which programs accessed the softlink in /usr/lib/ and can't get redirected to libstdc++.6.0.9.dylib anymore because i deleted the softlink. The real solution should be that I can tell ng4ex and ncl and all the other bins in the ncl environment that they have to access the library I specify in my .bashrc-file. Does anybody know if that's possible? From my testing I conclude that the .bashrc file only tells the NCL bin what to do.
>
> Thanks to all for your help!
>
> >>> Kwesi Quagraine <starskykwesi at gmail.com <mailto:starskykwesi at gmail.com>> 05.01.17 17.11 Uhr >>>
> Kindly go into this folder rather;
>
> cd /usr/local/ncl_6.3.0/lib
>
> sudo ln -s /location/given/by/locating/libstdc++.6.dylib .
>
> Also remember to exit your terminal and re-enter your terminal before starting ncl
>
> Hope it helps. Cheer!!
>
> On Thu, Jan 5, 2017 at 5:40 PM, Benedikt Becsi <benedikt.becsi at boku.ac.at <mailto:benedikt.becsi at boku.ac.at>> wrote:
> Hi Kwesi,
>
> thanks for your quick response, I created softlinks to different locations of the libstdc++.6.dylib library (three locations where located by "locate library") in your suggested folder (dind't exist btw), but unfortunately I still got the same error message every time:
>
> dyld: Symbol not found: __ZTTNSt7__cxx1118basic_stringstreamIcSt11char_traitsIcESaIcEEE
> Referenced from: /usr/local/ncl_6.3.0/bin/ncl
> Expected in: /usr/lib/libstdc++.6.dylib
> in /usr/local/ncl_6.3.0/bin/ncl
>
> Any other idea?
> Thank you very much!
>
> >>> Kwesi Quagraine <starskykwesi at gmail.com <mailto:starskykwesi at gmail.com>> 05.01.17 13.57 Uhr >>>
> Hello Benedikt, try these from your terminal;
>
> locate libstdc++.6.dylib library
>
> cd /usr/local/ncl_6.3.0/bin/lib
>
> sudo ln -s /location/given/by/locating/libstdc++.6.dylib .
>
> Kindly remember to put the dot at the end of the last command, it is just soft linking the location of the file to the current directory.
>
> Hope it helps. Cheer!!
>
> On Thu, Jan 5, 2017 at 1:54 PM, Benedikt Becsi <benedikt.becsi at boku.ac.at <mailto:benedikt.becsi at boku.ac.at>> wrote:
> Dear all,
>
> installing ncl on Mac did work, but when I try to run the test script ng4ex gsun01n -clean I get the following error message:
>
> dyld: Symbol not found: __ZTTNSt7__cxx1118basic_stringstreamIcSt11char_traitsIcESaIcEEE
> Referenced from: /usr/local/ncl_6.3.0/bin/ncl
> Expected in: /usr/lib/libstdc++.6.dylib
> in /usr/local/ncl_6.3.0/bin/ncl
>
> here are the details about my setup environment:
>
> Benedikts-MacBook-Pro:bin ich$ which ncl
> /usr/local/ncl_6.3.0/bin/ncl
> Benedikts-MacBook-Pro:bin ich$ ncl -V
> 6.3.0
> Benedikts-MacBook-Pro:bin ich$ otool -L `which ncl`
> /usr/local/ncl_6.3.0/bin/ncl:
> /usr/lib/libssl.0.9.8.dylib (compatibility version 0.9.8, current version 0.9.8)
> /usr/lib/libcrypto.0.9.8.dylib (compatibility version 0.9.8, current version 0.9.8)
> /System/Library/Frameworks/LDAP.framework/Versions/A/LDAP (compatibility version 1.0.0, current version 2.4.0)
> /opt/X11/lib/libfontconfig.1.dylib (compatibility version 10.0.0, current version 10.0.0)
> /usr/lib/libiconv.2.dylib (compatibility version 7.0.0, current version 7.0.0)
> /opt/X11/lib/libXrender.1.dylib (compatibility version 5.0.0, current version 5.0.0)
> /usr/lib/libbz2.1.0.dylib (compatibility version 1.0.0, current version 1.0.5)
> /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)
> /usr/local/lib/libstdc++.6.dylib (compatibility version 7.0.0, current version 7.22.0)
> /usr/local/lib/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 1226.10.1)
> /usr/local/lib/libgcc_s.1.dylib (compatibility version 1.0.0, current version 1.0.0)
> Benedikts-MacBook-Pro:bin ich$ env | grep NCARG
> NCARG_ROOT=/usr/local/ncl_6.3.0
> Benedikts-MacBook-Pro:bin ich$ which gcc
> /usr/local/Cellar/gcc/6.3.0_1/bin/gcc
> Benedikts-MacBook-Pro:bin ich$ which gfortran
> /usr/local/Cellar/gcc/6.3.0_1/bin/gfortran
> Benedikts-MacBook-Pro:bin ich$ gfortran --version
> GNU Fortran (Homebrew GCC 6.3.0_1) 6.3.0
> Copyright (C) 2016 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.
>
> Benedikts-MacBook-Pro:bin ich$ gcc --version
> gcc (Homebrew GCC 6.3.0_1) 6.3.0
> Copyright (C) 2016 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.
>
> I put the following lines into my .bashrc file:
>
> export NCARG_ROOT=/usr/local/ncl_6.3.0
> export PATH=$NCARG_ROOT/bin:$PATH
> export PATH=/usr/local/Cellar/gcc/6.3.0_1/bin:$PATH
> export DYLD_FALLBACK_LIBRARY_PATH=/usr/local/Cellar/gcc/6.3.0_1/lib/gcc/6
>
> There seems to be a problem with my libstdc++.6.dylib library. The file in the /usr/lib/ directory is just an alias and points to a file named libstdc++.6.0.9.dylib. Could it be that ncl has problems with that version of the library?
>
> Thank you very much for the help!
> All the best,
> Benedikt Becsi
>
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> University of Cape Coast|College of Agriculture and Natural Sciences|Department of Physics|
> Team Leader|Recycle Up! Ghana|Technology Without Borders|
> Other emails: kwesi.quagraine at ucc.edu.gh <mailto:kwesi.quagraine at ucc.edu.gh>|kwesi.quagraine at teog.de <mailto:kwesi.quagraine at teog.de>|
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> --
> Try not to become a man of success but rather a man of value-Albert Einstein
>
> University of Cape Coast|College of Agriculture and Natural Sciences|Department of Physics|
> Team Leader|Recycle Up! Ghana|Technology Without Borders|
> Other emails: kwesi.quagraine at ucc.edu.gh <mailto:kwesi.quagraine at ucc.edu.gh>|kwesi.quagraine at teog.de <mailto:kwesi.quagraine at teog.de>|
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