GNU Octave is a high-level interpreted language, primarily intended for numerical computations. It provides capabilities for the numerical solution of linear and nonlinear problems, and for performing other numerical experiments. It also provides extensive graphics capabilities for data visualization and manipulation. Octave is normally used through its interactive command line interface, but it can also be used to write non-interactive programs. The Octave language is quite similar to MATLAB so that most programs are easily portable.
After connecting to iceberg (see Establishing a SSH connection), start an interactive session with either the qsh or qrsh commands.
The latest version of Octave (currently 4.0.0) is made available with the command
module load apps/gcc/5.2/octave
Alternatively, you can load a specific version with
module load apps/gcc/5.2/octave/4.0
This adds Octave to your PATH and also loads all of the supporting libraries and compilers required by the system.
Start Octave by executing the command
octave
If you are using a qsh session, the graphical user interface version will begin. If you are using a qrsh session, you will only be able to use the text-only terminal version.
Here is an example batch submission script that will run an Octave program called foo.m
#!/bin/bash
# Request 5 gigabytes of real memory
#$ -l rmem=5G
# Request 64 hours of run time
#$ -l h_rt=64:00:00
module load apps/gcc/5.2/octave/4.0
octave foo.m
Octave toolboxes are referred to as packages. To see which ones are installed, use the command ver from within Octave.
Unlike MATLAB, Octave does not load all of its packages at startup. It is necessary to load the package before its commands are available to your session. For example, as with MATLAB, the pdist command is part of the statistics package. Unlike MATLAB, pdist is not immediately available to you
octave:1> pdist([1 2 3; 2 3 4; 1 1 1])
warning: the 'pdist' function belongs to the statistics package from Octave
Forge which you have installed but not loaded. To load the package, run
`pkg load statistics' from the Octave prompt.
Please read `http://www.octave.org/missing.html' to learn how you can
contribute missing functionality.
warning: called from
__unimplemented__ at line 524 column 5
error: 'pdist' undefined near line 1 column 1
As the error message suggests, you need to load the statistics package
octave:1> pkg load statistics
octave:2> pdist([1 2 3; 2 3 4; 1 1 1])
ans =
1.7321 2.2361 3.7417
These are primarily for administrators of the system.
Octave was installed using gcc 5.2 and the following libraries:
github/usr/local/packages6/apps/gcc/5.2/octave/4.0/make_octave4.0.0.logFor full functionality, Octave requires a large number of additional libraries to be installed. We have currently not installed all of these but will do so should they be required.
For information, here is the relevant part of the Configure log that describes how Octave was configured
Source directory: .
Installation prefix: /usr/local/packages6/apps/gcc/5.2/octave/4.0
C compiler: gcc -pthread -fopenmp -Wall -W -Wshadow -Wforma
t -Wpointer-arith -Wmissing-prototypes -Wstrict-prototypes -Wwrite-strings -Wcas
t-align -Wcast-qual -I/usr/local/packages6/compilers/gcc/5.2.0/include
C++ compiler: g++ -pthread -fopenmp -Wall -W -Wshadow -Wold-s
tyle-cast -Wformat -Wpointer-arith -Wwrite-strings -Wcast-align -Wcast-qual -g -
O2
Fortran compiler: gfortran -O
Fortran libraries: -L/usr/local/packages6/compilers/gcc/5.2.0/lib -
L/usr/local/packages6/compilers/gcc/5.2.0/lib64 -L/usr/local/packages6/compilers
/gcc/5.2.0/lib/gcc/x86_64-unknown-linux-gnu/5.2.0 -L/usr/local/packages6/compile
rs/gcc/5.2.0/lib/gcc/x86_64-unknown-linux-gnu/5.2.0/../../../../lib64 -L/lib/../
lib64 -L/usr/lib/../lib64 -L/usr/local/packages6/libs/gcc/5.2/fftw/3.3.4/lib -L/
usr/local/packages6/libs/gcc/5.2/fltk/1.3.3/lib -L/usr/local/packages6/compilers
/gcc/5.2.0/lib/gcc/x86_64-unknown-linux-gnu/5.2.0/../../.. -lgfortran -lm -lquad
math
Lex libraries:
LIBS: -lutil -lm
AMD CPPFLAGS:
AMD LDFLAGS:
AMD libraries:
ARPACK CPPFLAGS:
ARPACK LDFLAGS:
ARPACK libraries:
BLAS libraries: -lblas
CAMD CPPFLAGS:
CAMD LDFLAGS:
CAMD libraries:
CARBON libraries:
CCOLAMD CPPFLAGS:
CCOLAMD LDFLAGS:
CCOLAMD libraries:
CHOLMOD CPPFLAGS:
CHOLMOD LDFLAGS:
CHOLMOD libraries:
COLAMD CPPFLAGS:
COLAMD LDFLAGS:
COLAMD libraries:
CURL CPPFLAGS:
CURL LDFLAGS:
CURL libraries: -lcurl
CXSPARSE CPPFLAGS:
CXSPARSE LDFLAGS:
CXSPARSE libraries:
DL libraries:
FFTW3 CPPFLAGS:
FFTW3 LDFLAGS:
FFTW3 libraries: -lfftw3_threads -lfftw3
FFTW3F CPPFLAGS:
FFTW3F LDFLAGS:
FFTW3F libraries: -lfftw3f_threads -lfftw3f
FLTK CPPFLAGS: -I/usr/local/packages6/libs/gcc/5.2/fltk/1.3.3/in
clude -I/usr/include/freetype2 -I/usr/local/packages6/compilers/gcc/5.2.0/includ
e -D_LARGEFILE_SOURCE -D_LARGEFILE64_SOURCE -D_THREAD_SAFE -D_REENTRANT
FLTK LDFLAGS: -L/usr/local/packages6/libs/gcc/5.2/fltk/1.3.3/li
b -Wl,-rpath,/usr/local/packages6/libs/gcc/5.2/fltk/1.3.3/lib -L/usr/local/packa
ges6/compilers/gcc/5.2.0/lib -L/usr/local/packages6/compilers/gcc/5.2.0/lib64 -l
fltk_gl -lGLU -lGL -lfltk -lXcursor -lXfixes -lXext -lXft -lfontconfig -lXineram
a -lpthread -ldl -lm -lX11
FLTK libraries:
fontconfig CPPFLAGS:
fontconfig libraries: -lfontconfig
FreeType2 CPPFLAGS: -I/usr/include/freetype2
FreeType2 libraries: -lfreetype
GLPK CPPFLAGS:
GLPK LDFLAGS:
GLPK libraries:
HDF5 CPPFLAGS:
HDF5 LDFLAGS:
HDF5 libraries: -lhdf5
Java home: /usr/local/packages6/apps/binapps/java/jre1.8.0_6
0/
Java JVM path: /usr/local/packages6/apps/binapps/java/jre1.8.0_6
0/lib/amd64/server
Java CPPFLAGS: -I/usr/local/packages6/apps/binapps/java/jre1.8.0
_60//include -I/usr/local/packages6/apps/binapps/java/jre1.8.0_60//include/linux
Java libraries:
LAPACK libraries: -llapack
LLVM CPPFLAGS:
LLVM LDFLAGS:
LLVM libraries:
Magick++ CPPFLAGS:
Magick++ LDFLAGS:
Magick++ libraries:
OPENGL libraries: -lfontconfig -lGL -lGLU
OSMesa CPPFLAGS:
OSMesa LDFLAGS:
OSMesa libraries:
PCRE CPPFLAGS:
PCRE libraries: -lpcre
PortAudio CPPFLAGS:
PortAudio LDFLAGS:
PortAudio libraries:
PTHREAD flags: -pthread
PTHREAD libraries:
QHULL CPPFLAGS:
QHULL LDFLAGS:
QHULL libraries:
QRUPDATE CPPFLAGS:
QRUPDATE LDFLAGS:
QRUPDATE libraries:
Qt CPPFLAGS: -I/usr/include/QtCore -I/usr/include/QtGui -I/usr
/include/QtNetwork -I/usr/include/QtOpenGL
Qt LDFLAGS:
Qt libraries: -lQtNetwork -lQtOpenGL -lQtGui -lQtCore
READLINE libraries: -lreadline
Sndfile CPPFLAGS:
Sndfile LDFLAGS:
Sndfile libraries:
TERM libraries: -lncurses
UMFPACK CPPFLAGS:
UMFPACK LDFLAGS:
UMFPACK libraries:
X11 include flags:
X11 libraries: -lX11
Z CPPFLAGS:
Z LDFLAGS:
Z libraries: -lz
Default pager: less
gnuplot: gnuplot
Build Octave GUI: yes
JIT compiler for loops: no
Build Java interface: no
Do internal array bounds checking: no
Build static libraries: no
Build shared libraries: yes
Dynamic Linking: yes (dlopen)
Include support for GNU readline: yes
64-bit array dims and indexing: no
OpenMP SMP multithreading: yes
Build cross tools: no
configure: WARNING:
I didn't find gperf, but it's only a problem if you need to
reconstruct oct-gperf.h
configure: WARNING:
I didn't find icotool, but it's only a problem if you need to
reconstruct octave-logo.ico, which is the case if you're building from
VCS sources.
configure: WARNING: Qhull library not found. This will result in loss of functi
onality of some geometry functions.
configure: WARNING: GLPK library not found. The glpk function for solving linea
r programs will be disabled.
configure: WARNING: gl2ps library not found. OpenGL printing is disabled.
configure: WARNING: OSMesa library not found. Offscreen rendering with OpenGL w
ill be disabled.
configure: WARNING: qrupdate not found. The QR & Cholesky updating functions wi
ll be slow.
configure: WARNING: AMD library not found. This will result in some lack of fun
ctionality for sparse matrices.
configure: WARNING: CAMD library not found. This will result in some lack of fu
nctionality for sparse matrices.
configure: WARNING: COLAMD library not found. This will result in some lack of
functionality for sparse matrices.
configure: WARNING: CCOLAMD library not found. This will result in some lack of
functionality for sparse matrices.
configure: WARNING: CHOLMOD library not found. This will result in some lack of
functionality for sparse matrices.
configure: WARNING: CXSparse library not found. This will result in some lack o
f functionality for sparse matrices.
configure: WARNING: UMFPACK not found. This will result in some lack of functio
nality for sparse matrices.
configure: WARNING: ARPACK not found. The eigs function will be disabled.
configure: WARNING: Include file <jni.h> not found. Octave will not be able to
call Java methods.
configure: WARNING: Qscintilla library not found -- disabling built-in GUI editor
configure:
Some commonly-used packages were additionally installed from Octave Forge using the following commands from within Octave
pkg install -global -forge io
pkg install -global -forge statistics
pkg install -global -forge mapping
pkg install -global -forge image
pkg install -global -forge struct
pkg install -global -forge optim
The module file is octave_4.0