[ncl-talk] installing ncl on Debian Linux 10
Brian Thomas
brian.thomas at washburn.edu
Wed Apr 22 12:03:41 MDT 2020
I had an install issue a while back and I found that using “conda” made things much easier.
https://www.ncl.ucar.edu/Download/conda.shtml
----------------------------------------------------------------------
Message: 1
Date: Wed, 22 Apr 2020 03:52:57 +0000
From: Francesco Trotta <francesco.trotta4 at unibo.it<mailto:francesco.trotta4 at unibo.it>>
To: NCL Talk <ncl-talk at ucar.edu<mailto:ncl-talk at ucar.edu>>, Gus Correa <gus at ldeo.columbia.edu<mailto:gus at ldeo.columbia.edu>>
Subject: [ncl-talk] R: installing ncl on Debian Linux 10
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Dear Gus Correa
I tried to create a link libgfortran.so.3 to libgfortran.so.5
but I got another error
ncl: /usr/lib/x86_64-linux-gnu/libgfortran.so.3: version `GFORTRAN_1.4' not found (required by ncl)
I would like to not use the virtual environment for now
SO I tried to compile and install from the source code ncarg-6.6.2
following the step-by-step instructor from the website
After I installed all the necessary package on the /usr/local/ and
run the command: make Everything >& make-output
I end up with the below executables:
But there is not 'ncl'
bash: ncl: command not found
What did I miss?
Many Thanks
Francesco
surf at surf:/usr/local/ncl_ncarg/ncl_ncarg-6.6.2/bin$ tree -L 2 ./
./
??? cgm2ncgm
??? ConvertMapData
??? ctlib
??? fcaps
??? findg
??? fontc
??? gcaps
??? graphc
??? idt
??? med
??? ncargcc
??? ncargex
??? ncargf77
??? ncargf90
??? ncargfile
??? ncargpath
??? ncargrun
??? ncargversion
??? ncargworld
??? ncarlogo2ps
??? ncarvversion
??? ncgm2cgm
??? ncgmstat
??? ncl_convert2nc
??? ncl_filedump
??? ncl_grib2nc
??? ncl_quicklook
??? ng4ex
??? nhlcc
??? nhlf77
??? nhlf90
??? pre2ncgm
??? pre2ncgm.prog
??? psblack
??? psplit
??? pswhite
??? pwritxnt
??? scrip_check_input
??? tgks0a
??? tlocal
??? WRAPIT
??? wrapit77
??? WriteLineFile
??? WriteNameFile
??? WritePlotcharData
________________________________
Da: ncl-talk <ncl-talk-bounces at ucar.edu<mailto:ncl-talk-bounces at ucar.edu>> per conto di Gus Correa via ncl-talk <ncl-talk at ucar.edu<mailto:ncl-talk at ucar.edu>>
Inviato: luned? 20 aprile 2020 03:57
A: NCL Talk <ncl-talk at ucar.edu<mailto:ncl-talk at ucar.edu>>
Oggetto: Re: [ncl-talk] installing ncl on Debian Linux 10
Hi Francesco
Have you checked if your Debian distribution has a "compat" (compatibility) package for gfortran/libgfortran
between libgfortran.5 and libgfortran.3 ?
Apt-get may have a way to check if it is available.
I don't use Debian, but CentOS-7, which has an older kernel and older libraries.
However, I have libgfortran.3 along with a "compat" package that provides compatibility with libgfortran.1, for example.
An alternative is to install NCL using Anaconda Python.
This is currently the recommended method (argh!):
https://www.ncl.ucar.edu/Download/
That is self-contained, doesn't depend on the system libraries.
In my experience it has other problems, particularly a sensitive dependency on other Anaconda Python packages
that change by the hour, and don't give a damn to backward compatibility, which can easily break functionality.
So, if you install this way, be careful with any conda packages updates, or simply don't update.
I hope this helps,
Gus Correa
On Sun, Apr 19, 2020 at 5:25 PM Francesco Trotta via ncl-talk <ncl-talk at ucar.edu<mailto:ncl-talk at ucar.edu>> wrote:
Dear ncl team
I upgraded my operating system to Debian GNU/Linux 10 buster
This new Debian has GNU Fortran (Debian 8.3.0-6) 8.3.0 installed
Now, when I run ncl it gives me the error:
ncl: error while loading shared libraries: libgfortran.so.3: cannot open shared object file: No such file or directory
The new Debian has libgfortran.so.5
/usr/lib/x86_64-linux-gnu/libgfortran.so.5
so I upgraded ncl using to the last precompiled binary
ncl_ncarg-6.6.2-Debian9.8_64bit_nodap_gnu630.tar.gz
bu I got the same error.
I can I use ncl in Debian 10?
Many Thanks
Francesco
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Message: 2
Date: Wed, 22 Apr 2020 01:17:22 -0400
From: Gus Correa <gus at ldeo.columbia.edu>
To: NCL Talk <ncl-talk at ucar.edu>
Subject: Re: [ncl-talk] installing ncl on Debian Linux 10
Message-ID:
<CA+TEG=XT0dRqJnUfQRBdYkqpxZ2mw5fY-5s2EVT6nBMqrC3NRA at mail.gmail.com>
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Hi Francesco
I haven't tried to build NCL from source for a long time.
So, I am afraid I cannot help much, but please see two suggestions at the
end of this message.
**
Unfortunately NCAR phased out the standard NCL code in favor of the
Python-based code.
They've been recommending the Anaconda Python installation of NCL as the
preferred way to install.
The traditional NCL code development has been frozen, at least that is what
they told this mailing list a year or so ago.
Actually it is specific the Anaconda Python, which makes it even more
restrictive and less open
then Python alone (or PIP), since Anaconda is a company, a private
business, which is already
advertising and selling "pro" versions of their "conda" software, after
luring users with the "community" version for a while.
I think that was a terrible decision.
It alienated a huge user base (in the USA and worldwide).
It trashed an enormous number of research- and production-level NCL scripts
that will eventually have to be re-written.
It requires users to have to learn the NCL replacement language and rewrite
all their scripts with no tangible gain,
just to stay exactly where they were before.
It made NCL depend on corporate decisions (of Anaconda.com) that neither
the community nor NCAR has any control of,
and that do not necessarily serve the atmospheric/climate/oceans community
best interests.
We were told that the original NCL code development was frozen/killed:
don't expect new versions, there will be no updates in the downloadable
binaries, etc.
This is sure to make everything in the traditional NCL become obsolete, and
eventually go extinct.
I still have NCL installed from packages in the LInux distribution I use
(CentOS 7),
and that I install in a number of computers in the university to serve
researchers, students, and faculty.
However, since the NCL code development is frozen and killed, these
packages are bound to
become incompatible with new Linux developments, and therefore are sure to
disappear from future
LInux updates (e.g. in CentOS 8 and so on), as you are experiencing with
your new version of Debian.
I and other NCL users voiced in this mailing list
our protest against the decision of phasing out the NCL code development,
to no avail.
I wish the NCAR leadership had listened, given a second thought to this
matter,
and reconsidered their terrible decision, which really didn't take into
account the best interests of the user community.
**
As for the specifics of your email, I would check the log file of your
build, i.e.,
the make-output file, and search for errors.
I would guess that it didn't really succeed, but stumbled on errors before
it could build ncl itself.
Maybe there is a clue there on where and why the build is failing.
With respect to the soft link that you made from libgfortran.so.3 to
libgfortran.so.5,
I would not expect it to work. That is why I suggested the use of a
"compat" package
that may reconcile the differences in libgfortran versions 3 and 5.
I am not familiar with Debian, and I don't know if such a package is
available in Debian.
I use CentOS (a derivative of Red Hat Enterprise), and in general they keep
some "compat"
packages available, to allow a smooth transition from older to newer
versions of gcc, gfortran,
etc.
Sincerely,
Gus Correa
On Tue, Apr 21, 2020 at 11:52 PM Francesco Trotta <
francesco.trotta4 at unibo.it> wrote:
Dear Gus Correa
I tried to create a link libgfortran.so.3 to libgfortran.so.5
but I got another error
ncl: /usr/lib/x86_64-linux-gnu/libgfortran.so.3: version `GFORTRAN_1.4'
not found (required by ncl)
I would like to not use the virtual environment for now
SO I tried to compile and install from the source code ncarg-6.6.2
following the step-by-step instructor from the website
After I installed all the necessary package on the /usr/local/ and
run the command: make Everything >& make-output
I end up with the below executables:
But there is not 'ncl'
bash: ncl: command not found
What did I miss?
Many Thanks
Francesco
surf at surf:/usr/local/ncl_ncarg/ncl_ncarg-6.6.2/bin$ tree -L 2 ./
./
??? cgm2ncgm
??? ConvertMapData
??? ctlib
??? fcaps
??? findg
??? fontc
??? gcaps
??? graphc
??? idt
??? med
??? ncargcc
??? ncargex
??? ncargf77
??? ncargf90
??? ncargfile
??? ncargpath
??? ncargrun
??? ncargversion
??? ncargworld
??? ncarlogo2ps
??? ncarvversion
??? ncgm2cgm
??? ncgmstat
??? ncl_convert2nc
??? ncl_filedump
??? ncl_grib2nc
??? ncl_quicklook
??? ng4ex
??? nhlcc
??? nhlf77
??? nhlf90
??? pre2ncgm
??? pre2ncgm.prog
??? psblack
??? psplit
??? pswhite
??? pwritxnt
??? scrip_check_input
??? tgks0a
??? tlocal
??? WRAPIT
??? wrapit77
??? WriteLineFile
??? WriteNameFile
??? WritePlotcharData
------------------------------
*Da:* ncl-talk <ncl-talk-bounces at ucar.edu> per conto di Gus Correa via
ncl-talk <ncl-talk at ucar.edu>
*Inviato:* luned? 20 aprile 2020 03:57
*A:* NCL Talk <ncl-talk at ucar.edu>
*Oggetto:* Re: [ncl-talk] installing ncl on Debian Linux 10
Hi Francesco
Have you checked if your Debian distribution has a "compat"
(compatibility) package for gfortran/libgfortran
between libgfortran.5 and libgfortran.3 ?
Apt-get may have a way to check if it is available.
I don't use Debian, but CentOS-7, which has an older kernel and older
libraries.
However, I have libgfortran.3 along with a "compat" package that provides
compatibility with libgfortran.1, for example.
An alternative is to install NCL using Anaconda Python.
This is currently the recommended method (argh!):
https://www.ncl.ucar.edu/Download/
That is self-contained, doesn't depend on the system libraries.
In my experience it has other problems, particularly a sensitive
dependency on other Anaconda Python packages
that change by the hour, and don't give a damn to backward compatibility,
which can easily break functionality.
So, if you install this way, be careful with any conda packages updates,
or simply don't update.
I hope this helps,
Gus Correa
On Sun, Apr 19, 2020 at 5:25 PM Francesco Trotta via ncl-talk <
ncl-talk at ucar.edu> wrote:
Dear ncl team
I upgraded my operating system to Debian GNU/Linux 10 buster
This new Debian has GNU Fortran (Debian 8.3.0-6) 8.3.0 installed
Now, when I run ncl it gives me the error:
ncl: error while loading shared libraries: libgfortran.so.3: cannot
open shared object file: No such file or directory
The new Debian has libgfortran.so.5
/usr/lib/x86_64-linux-gnu/libgfortran.so.5
so I upgraded ncl using to the last precompiled binary
ncl_ncarg-6.6.2-Debian9.8_64bit_nodap_gnu630.tar.gz
bu I got the same error.
I can I use ncl in Debian 10?
Many Thanks
Francesco
_______________________________________________
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ncl-talk at ucar.edu
List instructions, subscriber options, unsubscribe:
http://mailman.ucar.edu/mailman/listinfo/ncl-talk
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Message: 3
Date: Wed, 22 Apr 2020 07:43:42 -0600
From: Rick Brownrigg <brownrig at ucar.edu>
To: Francesco Trotta <francesco.trotta4 at unibo.it>
Cc: NCL Talk <ncl-talk at ucar.edu>
Subject: Re: [ncl-talk] R: installing ncl on Debian Linux 10
Message-ID:
<CAGKRhbGR4xN5s0u=4CXARzO1E4krshDxXEJs3KvZ2W0GY5OPcQ at mail.gmail.com>
Content-Type: text/plain; charset="utf-8"
HI Francesco,
As Gus recommends, check out the log from the build. Inevitably, when you
end up with a .../bin directory as you described, it's because the ncl
binary failed at the link stage. Search for a string such as "-o ncl" and
that should get you right to where the problem occurred.
Rick
On Tue, Apr 21, 2020 at 9:53 PM Francesco Trotta via ncl-talk <
ncl-talk at ucar.edu> wrote:
Dear Gus Correa
I tried to create a link libgfortran.so.3 to libgfortran.so.5
but I got another error
ncl: /usr/lib/x86_64-linux-gnu/libgfortran.so.3: version `GFORTRAN_1.4'
not found (required by ncl)
I would like to not use the virtual environment for now
SO I tried to compile and install from the source code ncarg-6.6.2
following the step-by-step instructor from the website
After I installed all the necessary package on the /usr/local/ and
run the command: make Everything >& make-output
I end up with the below executables:
But there is not 'ncl'
bash: ncl: command not found
What did I miss?
Many Thanks
Francesco
surf at surf:/usr/local/ncl_ncarg/ncl_ncarg-6.6.2/bin$ tree -L 2 ./
./
??? cgm2ncgm
??? ConvertMapData
??? ctlib
??? fcaps
??? findg
??? fontc
??? gcaps
??? graphc
??? idt
??? med
??? ncargcc
??? ncargex
??? ncargf77
??? ncargf90
??? ncargfile
??? ncargpath
??? ncargrun
??? ncargversion
??? ncargworld
??? ncarlogo2ps
??? ncarvversion
??? ncgm2cgm
??? ncgmstat
??? ncl_convert2nc
??? ncl_filedump
??? ncl_grib2nc
??? ncl_quicklook
??? ng4ex
??? nhlcc
??? nhlf77
??? nhlf90
??? pre2ncgm
??? pre2ncgm.prog
??? psblack
??? psplit
??? pswhite
??? pwritxnt
??? scrip_check_input
??? tgks0a
??? tlocal
??? WRAPIT
??? wrapit77
??? WriteLineFile
??? WriteNameFile
??? WritePlotcharData
------------------------------
*Da:* ncl-talk <ncl-talk-bounces at ucar.edu> per conto di Gus Correa via
ncl-talk <ncl-talk at ucar.edu>
*Inviato:* luned? 20 aprile 2020 03:57
*A:* NCL Talk <ncl-talk at ucar.edu>
*Oggetto:* Re: [ncl-talk] installing ncl on Debian Linux 10
Hi Francesco
Have you checked if your Debian distribution has a "compat"
(compatibility) package for gfortran/libgfortran
between libgfortran.5 and libgfortran.3 ?
Apt-get may have a way to check if it is available.
I don't use Debian, but CentOS-7, which has an older kernel and older
libraries.
However, I have libgfortran.3 along with a "compat" package that provides
compatibility with libgfortran.1, for example.
An alternative is to install NCL using Anaconda Python.
This is currently the recommended method (argh!):
https://www.ncl.ucar.edu/Download/
That is self-contained, doesn't depend on the system libraries.
In my experience it has other problems, particularly a sensitive
dependency on other Anaconda Python packages
that change by the hour, and don't give a damn to backward compatibility,
which can easily break functionality.
So, if you install this way, be careful with any conda packages updates,
or simply don't update.
I hope this helps,
Gus Correa
On Sun, Apr 19, 2020 at 5:25 PM Francesco Trotta via ncl-talk <
ncl-talk at ucar.edu> wrote:
Dear ncl team
I upgraded my operating system to Debian GNU/Linux 10 buster
This new Debian has GNU Fortran (Debian 8.3.0-6) 8.3.0 installed
Now, when I run ncl it gives me the error:
ncl: error while loading shared libraries: libgfortran.so.3: cannot
open shared object file: No such file or directory
The new Debian has libgfortran.so.5
/usr/lib/x86_64-linux-gnu/libgfortran.so.5
so I upgraded ncl using to the last precompiled binary
ncl_ncarg-6.6.2-Debian9.8_64bit_nodap_gnu630.tar.gz
bu I got the same error.
I can I use ncl in Debian 10?
Many Thanks
Francesco
_______________________________________________
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ncl-talk at ucar.edu
List instructions, subscriber options, unsubscribe:
http://mailman.ucar.edu/mailman/listinfo/ncl-talk
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Brian C. Thomas, PhD
Professor, Physics and Astronomy, Washburn University
785-670-2144<tel:(785)%20670-2144>
brian.thomas at washburn.edu<mailto:brian.thomas at washburn.edu>
Web: http://www.washburn.edu/faculty/bthomas/
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ResearchGate profile: https://www.researchgate.net/profile/Brian_Thomas
Department of Physics and Astronomy
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