[ncl-install] Install issues on OS X

Kwesi Akumenyi Quagraine starskykwesi at gmail.com
Tue Nov 7 07:25:38 MST 2017 

Great to hear that!

Cheers!
Kwesi
--------
Try not to become a man of success but rather a man of value-Albert Einstein

Kwesi A. Quagraine
Department of Physics, 
School of Physical Sciences, 
College of Agriculture and Natural Sciences
University of Cape Coast
Cape Coast, Ghana

Alt. Email: kwesi at csag.uct.ac.za  
Web: http://www.recycleupghana.org/
office: +27 21 650 3164
skype: quagraine_cwasi


> On 07 Nov 2017, at 2:08 PM, Johnson, Henry <henry_johnson at brown.edu> wrote:
> 
> Thanks so much Kwesi!
> 
> It does indeed seem to work, even with OS X 10.13.1 (High Sierra). Even "idt" works.
> 
> Cheers
> 
> 
> On Mon, Nov 6, 2017 at 5:21 PM, Kwesi Akumenyi Quagraine <starskykwesi at gmail.com <mailto:starskykwesi at gmail.com>> wrote:
> Hello Mary, Hello Johnson,
> 
> I had the same problem as Johnson, this is how I got around it on Mac OS X High Sierra with GNU v7.2.0.
> 
> I realised from Mary’s earlier post that gsl version was an issue so I decided to force the ncl installation with the gsl package version 2.2.1 and also on the error you are getting, it seems gdal version installed by default is not compatible the libkea default. 
> 
> conda create -n ncl_stable -c conda-forge ncl=6.4.0 gsl=2.2.1 libgdal=2.2.2
> 
> Everything works fine now after testing the installation with;
> 
> ng4ex xy05n -clean -W png
> 
> Hope it helps!
> Cheers!
> 
> Kwesi
> --------
> Try not to become a man of success but rather a man of value-Albert Einstein
> 
> Kwesi A. Quagraine
> Department of Physics, 
> School of Physical Sciences, 
> College of Agriculture and Natural Sciences
> University of Cape Coast
> Cape Coast, Ghana
> 
> Alt. Email: kwesi at csag.uct.ac.za <mailto:kwesi at csag.uct.ac.za>  
> Web: http://www.recycleupghana.org/ <http://www.recycleupghana.org/>
> office: +27 21 650 3164 <tel:+27%2021%20650%203164>
> skype: quagraine_cwasi
> 
> 
>> On 02 Nov 2017, at 8:49 PM, Mary Haley <haley at ucar.edu <mailto:haley at ucar.edu>> wrote:
>> 
>> Hi Henry,
>> 
>> Sorry for the delay in response.  We are having issues with the conda-forge release of NCL. The administrators changed some of the packages that NCL depends on, and now they are broken. 
>> 
>> For now, we are going to recommend that people NOT use conda to install NCL, but rather the ESG binaries.
>> 
>> As for the ESG version of NCL, if you google this error message:
>> 
>> Internal Error: get_unit(): Bad internal unit KIND
>> 
>> You will see some threads that refer to GNU V7.1 being the issue, which is the version you have installed.  We built NCL with V6.​1​.0 and V5.4.0, so would you be able to install GNU​ V6.x and try this instead?​
>> 
>> Thanks,
>> 
>> --Mary
>> 
>> 
>> On Wed, Nov 1, 2017 at 9:03 AM, Johnson, Henry <henry_johnson at brown.edu <mailto:henry_johnson at brown.edu>> wrote:
>> Hi,
>> 
>> I provide support for our group, and we have seem to have a problem with getting NCL running on either OS X 10.12 or 10.13 (Sierra and High Sierra)
>> 
>> Using "conda" I can get a functional NCL 6.3.0 install working. However, the present conda images (or whatever you call them, environments?) for 6.4.0 have a whole slew of unmet dependencies. I managed to update GSL, only to be then bit by a libkea version mismatch.
>> 
>> Anyway, leaving conda behind (at least we can run 6.3.0, but not NCAR Graphics), here's a run down on some of my initial troubleshooting with installation of 6.4.0 on the latest OS X (10.13.1) box. I've installed gcc and am using that instead of the Xcode stuff. The same stuff happens with OS X 10.12.
>> 
>> Using gcc-7.1-bin.tar, gfortran-7.1-bin.tar and ncl_ncarg-6.4.0-MacOS_10.12_64bit_gnu530.tar.gz
>> 
>> IBES4iMac:Desktop hj11$ which ncl
>> 
>> /usr/local/ncl-6.4.0/bin/ncl
>> 
>> IBES4iMac:Desktop hj11$ ncl -V
>> 
>> 6.4.0
>> 
>> IBES4iMac:Desktop hj11$ otool -L `which ncl`
>> 
>> /usr/local/ncl-6.4.0/bin/ncl:
>> 
>> /usr/lib/libcurl.4.dylib (compatibility version 7.0.0, current version 9.0.0)
>> 
>> /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)
>> 
>> /usr/lib/libiconv.2.dylib (compatibility version 7.0.0, current version 7.0.0)
>> 
>> /opt/X11/lib/libfontconfig.1.dylib (compatibility version 11.0.0, current version 11.2.0)
>> 
>> /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/libgfortran.3.dylib (compatibility version 4.0.0, current version 4.0.0)
>> 
>> /usr/local/lib/libquadmath.0.dylib (compatibility version 1.0.0, current version 1.0.0)
>> 
>> /usr/local/lib/libstdc++.6.dylib (compatibility version 7.0.0, current version 7.21.0)
>> 
>> /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 1238.0.0)
>> 
>> /usr/local/lib/libgcc_s.1.dylib (compatibility version 1.0.0, current version 1.0.0)
>> 
>> IBES4iMac:Desktop hj11$ env | grep NCARG
>> 
>> NCARG_ROOT=/usr/local/ncl-6.4.0
>> 
>> IBES4iMac:Desktop hj11$ which gcc
>> 
>> /usr/local//bin/gcc
>> 
>> IBES4iMac:Desktop hj11$ which gfortran
>> 
>> /usr/local//bin/gfortran
>> 
>> IBES4iMac:Desktop hj11$ gfortran --version
>> 
>> GNU Fortran (GCC) 7.1.0
>> 
>> Copyright (C) 2017 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.
>> 
>> IBES4iMac:Desktop hj11$ gcc --version
>> 
>> gcc (GCC) 7.1.0
>> 
>> Copyright (C) 2017 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.
>> 
>> 
>> But to get "ncl -V" to work, which it didn't with either the 10.12 or 10.13 OS X installs,  I did:
>> 
>> IBES4iMac:Desktop hj11$ ncl -V
>> 
>> dyld: Library not loaded: /usr/local/lib/libgfortran.3.dylib
>> 
>>   Referenced from: /usr/local/ncl-6.4.0/bin/ncl
>> 
>>   Reason: image not found
>> 
>> Abort trap: 6
>> 
>> IBES4iMac:Desktop hj11$ sudo bash
>> 
>> bash-3.2# cd /usr/local/lib
>> 
>> bash-3.2# ln libgfortran.3.dylib libgfortran.dylib
>> 
>> ln: libgfortran.3.dylib: No such file or directory
>> 
>> bash-3.2# ln libgfortran.dylib libgfortran.3.dylib
>> 
>> bash-3.2# exit
>> 
>> exit
>> 
>> IBES4iMac:Desktop hj11$ ncl -V
>> 
>> 6.4.0
>> 
>> IBES4iMac:Desktop hj11$ ng4ex xy02n -clean
>> 
>> 
>> 
>> NCAR Graphics NCL Example <xy02n>
>> 
>> 
>> 
>>   Copying xy02n.ncl
>> 
>>   Copying xy02.res
>> 
>> 
>> 
>> Running NCL...
>> 
>>  Copyright (C) 1995-2017 - All Rights Reserved
>> 
>>  University Corporation for Atmospheric Research
>> 
>>  NCAR Command Language Version 6.4.0
>> 
>>  The use of this software is governed by a License Agreement.
>> 
>>  See http://www.ncl.ucar.edu/ <http://www.ncl.ucar.edu/> for more details.
>> 
>> At line 382 of file ngseti.f
>> 
>> Internal Error: get_unit(): Bad internal unit KIND
>> 
>> 
>> 
>> ncl failed.
>> 
>> 
>> I get the Internal Error thing with gcc and the Xcode version of gcc. 
>> 
>> And if I use conda (after I've updated gsl) I get this:
>> 
>> IBES4iMac:Desktop hj11$ source activate ncl_stable
>> (ncl_stable) IBES4iMac:Desktop hj11$ ncl -V
>> dyld: Library not loaded: @rpath/libkea.1.4.7.dylib
>>   Referenced from: /Users/hj11/miniconda3/envs/ncl_stable/lib/libgdal.20.dylib
>>   Reason: Incompatible library version: libgdal.20.dylib requires version 1.4.7 or later, but libkea.1.4.7.dylib provides version 1.4.0
>> Abort trap: 6
>> 
>> Cheers
>> 
>> -- 
>> Henry Johnson, Ph.D
>> Systems Manager
>> Institute at Brown for Environment and Society <http://www.brown.edu/academics/institute-environment-society/>
>> IBES RM 258
>> 401 863 5431 <tel:(401)%20863-5431>
>> 
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> 
> 
> 
> 
> -- 
> Henry Johnson, Ph.D
> Systems Manager
> Institute at Brown for Environment and Society <http://www.brown.edu/academics/institute-environment-society/>
> IBES RM 258
> 401 863 5431

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