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Re: octave & netcdf

From: Alexander Barth
Subject: Re: octave & netcdf
Date: Fri, 4 Dec 2015 12:14:55 +0100

Hi Clinton,

Your issues on ubuntu 15.10 are very strange. I had a VM of this version of ubuntu and it worked for me with netcdf library from the Ubuntu repository (see below). I just noticed that Ubuntu 15.10 includes a release candidate of netcdf (4.4.0-rc2) which is a bit odd. Maybe you can use netcdf from the ubuntu repository for octave and your own netcdf library for ROMS.

Otherwise, I use ubuntu 14.04 on my desktop (but the gnome version) and it works quite well.


$ sudo apt-get install liboctave-dev libnetcdf-dev
$ octave --no-gui

GNU Octave, version 4.0.0
Copyright (C) 2015 John W. Eaton and others.
This is free software; see the source code for copying conditions.
FITNESS FOR A PARTICULAR PURPOSE.  For details, type 'warranty'.

Octave was configured for "x86_64-pc-linux-gnu".

Additional information about Octave is available at

Please contribute if you find this software useful.
For more information, visit

Read to learn how to submit bug reports.
For information about changes from previous versions, type 'news'.

>> pkg install -auto -verbose -forge netcdf
warning: creating installation directory /home/ubuntu-gnome/octave
warning: called from
    install at line 30 column 5
    pkg at line 405 column 9
mkdir (/tmp/oct-zHqVNp)
untar (/home/ubuntu-gnome/netcdf-1.0.7.tar.gz, /tmp/oct-zHqVNp)
checking for gcc... gcc
checking whether the C compiler works... yes
checking for C compiler default output file name... a.out
checking for suffix of executables...
checking whether we are cross compiling... no
checking for suffix of object files... o
checking whether we are using the GNU C compiler... yes
checking whether gcc accepts -g... yes
checking for gcc option to accept ISO C89... none needed
checking for mkoctfile... /usr/bin/mkoctfile --verbose
checking for octave-config... /usr/bin/octave-config
g++ -c -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include/octave-4.0.0/octave/.. -I/usr/include/octave-4.0.0/octave -I/usr/include/hdf5/serial -I/usr/include/mpi -pthread -fopenmp -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -o conftest.o
g++ -shared -Wl,-Bsymbolic  -o conftest.oct  conftest.o   -L/usr/lib/x86_64-linux-gnu/octave/4.0.0 -L/usr/lib/x86_64-linux-gnu -loctinterp -loctave -Wl,-Bsymbolic-functions -Wl,-z,relro 
checking for F77_FUNC... g++ -c -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include/octave-4.0.0/octave/.. -I/usr/include/octave-4.0.0/octave -I/usr/include/hdf5/serial -I/usr/include/mpi -pthread -fopenmp -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -o conftest.o
checking for octave... /usr/bin/octave
checking for VERSION in octave-config... 4.0.0
checking for CANONICAL_HOST_TYPE in octave-config... x86_64-pc-linux-gnu
checking for SHLEXT in octave-config... so
checking whether ln -s works... yes
checking for ranlib... ranlib
checking for strip... strip
checking for nc-config... nc-config
configure: creating ./config.status
config.status: creating Makeconf
  "$prefix" is /home/ubuntu-gnome/octave/netcdf-1.0.7
  "$exec_prefix" is ${prefix}

octave commands will install into the following directories:
   m-files:   /usr/share/octave/4.0.0/site/m/octave-forge
   oct-files: /usr/lib/x86_64-linux-gnu/octave/4.0.0/site/oct/x86_64-pc-linux-gnu/octave-forge
   binaries:  /usr/lib/x86_64-linux-gnu/octave/4.0.0/site/exec/x86_64-pc-linux-gnu
   m-files:   /usr/share/octave/4.0.0/site/octave-forge-alternatives/m
   oct-files: /usr/lib/x86_64-linux-gnu/octave/4.0.0/site/octave-forge-alternatives/oct/x86_64-pc-linux-gnu

shell commands will install into the following directories:
   binaries:  ${exec_prefix}/bin
   man pages: ${datarootdir}/man
   libraries: ${exec_prefix}/lib
   headers:   ${prefix}/include

octave-forge is configured with
   octave:        /usr/bin/octave (version 4.0.0)
   mkoctfile:     /usr/bin/mkoctfile --verbose for Octave 0
   octave-config: /usr/bin/octave-config for Octave 0
   netCDF compiler flags:  -I/usr/include -I/usr/include/hdf5/serial
   netCDF libraries:  -L/usr/lib -L/usr/lib/x86_64-linux-gnu/hdf5/serial -lnetcdf -lhdf5_hl -lhdf5 -lpthread -lz -ldl -lm -lcurl

make: Entering directory '/tmp/oct-zHqVNp/netcdf/src'
/usr/bin/mkoctfile --verbose -DHAVE_OCTAVE_ -v -I/usr/include -I/usr/include/hdf5/serial -L/usr/lib -L/usr/lib/x86_64-linux-gnu/hdf5/serial -lnetcdf -lhdf5_hl -lhdf5 -lpthread -lz -ldl -lm -lcurl
g++ -c -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include/octave-4.0.0/octave/.. -I/usr/include/octave-4.0.0/octave -I/usr/include/hdf5/serial -I/usr/include/mpi -pthread -fopenmp -g -O2 -fstack-protector-strong -Wformat -Werror=format-security   -I/usr/include -I/usr/include/hdf5/serial  -DHAVE_OCTAVE_ -o __netcdf__.o
g++ -shared -Wl,-Bsymbolic  -o __netcdf__.oct  __netcdf__.o   -L/usr/lib -L/usr/lib/x86_64-linux-gnu/hdf5/serial -lnetcdf -lhdf5_hl -lhdf5 -lpthread -lz -ldl -lm -lcurl -L/usr/lib/x86_64-linux-gnu/octave/4.0.0 -L/usr/lib/x86_64-linux-gnu -loctinterp -loctave -Wl,-Bsymbolic-functions -Wl,-z,relro 
make: Leaving directory '/tmp/oct-zHqVNp/netcdf/src'
copyfile /tmp/oct-zHqVNp/netcdf/src/__netcdf__.oct /tmp/oct-zHqVNp/netcdf/inst/x86_64-pc-linux-gnu-api-v50+
For information about changes from previous versions of the netcdf package, run 'news netcdf'.
>> test_netcdf
Using NetCDF library version "4.4.0-rc2 of Oct  6 2015 12:31:34 $"
run test_netcdf_constant..............   OK 
run test_netcdf_create................   OK 
run test_netcdf_low_level_interface...   OK 
run test_netcdf_unlim.................   OK 
run test_netcdf_datatypes.............   OK 
run test_netcdf_scalar_variable.......   OK 
run test_netcdf_attributes............   OK 
run test_netcdf_high_level_interface..   OK 
run test_netcdf_ncwriteschema.........   OK 
run test_netcdf_ncwriteschema_unlim...   OK 
run test_netcdf_ncwriteschema_chunking   OK 
run test_netcdf_ncwriteschema_group...   OK

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