Re: octave & netcdf

[Alexander Barth]

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.

Regards,

Alex

$ 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.
There is ABSOLUTELY NO WARRANTY; not even for MERCHANTABILITY or
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 http://www.octave.org.

Please contribute if you find this software useful.
For more information, visit http://www.octave.org/get-involved.html

Read http://www.octave.org/bugs.html 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    conftest.cc -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    conftest.cc -o conftest.o
yes
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
alternatives:
   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 __netcdf__.cc -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_ __netcdf__.cc -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