• Packaged MB-System distributions
• How to get the MB-System source distribution
• Access MB-System source version control system
• Other required and suggested software and data
• How to unpack an MB-System source code distribution
• How to install MB-System using the configure script

MB-System is included is several package manager systems for Mac and Linux repositories, providing an easy means for installing our software. The biggest advantage of using package managers is that the prerequisite packages are identified and installed automatically. In most cases these packages are not prepared and maintained by MB-System developers, and generally the versions available in external packages lag those available from us through source distributions (particularly in the repositories described as stable). We think that the majority of MB-System users now install the software through one of these package managers.

Poseidon Linux

MB-System is included in Poseidon Linux, the "Scientific GNU/Linux". Poseidon is an Ubuntu Linux based distribution including a selection of open source software packages intended to support scientific research. In particular, it offers several specific tools in the areas of GIS, 3D Visualization, Mathematics, Statistics and several other fields of research.

UbuntuGIS for Ubuntu Linux

MB-System is one of the packages maintained in the UbuntuGIS repository.

Fink for MacOs

MB-System has been packaged for MacOS X as part of the Fink Project. The MB-System Fink package can be found at:

If the fink package manager is installed, then MB-System and its prerequisites can be installed using this command:

HomeBrew for MacOs

MB-System has also been packaged for MacOs X as part of Homebrew. If you have Homebrew installed, then MB-System and its prerequisites can be installed using these two commands:

OSGeo-Live Distribution

The OSGeo-Live distribution includes MB-System. OSGeo-Live is a self-contained bootable DVD, USB thumb drive or Virtual Machine based on Lubuntu that includes a wide variety of open source geospatial software.

Acknowledgements

Thanks to Christian Ferreira for creating and distributing Poseidon Linux, to Johan Van de Wauw for updating the MB-System package in UbuntuGIS, to Kurt Schwehr for maintaing the Fink MB-System package, to Anthony Lukach, Simon Dreutter, and Andrew Janke for maintaining the Homebrew MB-System package, and to Hamish Bowman for maintaining the OSGeo-Live MB-System package.

The source code for MB-System is available as a compressed tar archive by anonymous ftp to the Lamont-Doherty Earth Observatory of Columbia University. This archive file is about 16 megabytes in size and, depending on the speed of your internet connection, may take a few minutes to transfer.

Click here to ftp the current MB-System release as a compressed tar archive.

Click here to get point-and-click ftp access to all of the MB-System related files available from Lamont (these may include data examples and beta distributions of MB-System ).

If access through the above links fails, try running ftp from a terminal shell. The following commands represent a typical anonymous ftp session (note that your@email.address literally means to enter your email address, and that many modern ftp clients do not require the "binary" command).

% ftp ftp.ldeo.columbia.edu
Name: anonymous
Password: your@email.address
> cd pub/MB-System
> binary
> get mbsystem-5.5.2263.tar.gz
> quit

The MB-System source code is archived and managed using Subversion, an open source version control system. The MB-System and MB-Cookbook Subversion repositories can be browsed through a web interface at:

http://svn.ilab.ldeo.columbia.edu/

 

The MB-System repository is at:

http://svn.ilab.ldeo.columbia.edu/listing.php?repname=MB-System

The entire repository, or individual files, can be downloaded through this web interface. Clicking the the link above to bring up the WebSVN interface showing the most recent revision to the MB-System code base, along with a list of paths including "branches", "tags", and "trunk". To download the entire code base, click on the "Download" link to the right of "trunk". To browse the structure and download individual files, click on the "trunk" link. Users can build MB-System using this downloaded code base, but should note that the repository stores a number of files that are not included in the MB-System distributions.

MB-System requires a number of other software packages and databases to be fully functional. If one is building and installing MB-System from the source distribution, these prerequisite packages must be installed first. Often, the easiest way to obtain the prerequisite software is through one or more package managers.

The prerequisite software includes:

• GMT version 5.2.1 or later: MB-System makes use of the Generic Mapping Tools (GMT) libraries and programs for much of its graphics. GMT also includes a detailed global coastline database. GMT has been developed by Professor Paul Wessel of SOEST (School of Ocean and Earth Science and Technology at the Univeristy of Hawaii) and Dr. Walter H. F. Smith of NOAA. The GMT source code is available from the GMT web page.
• NetCDF version 3.5.1 or later: Both GMT and MB-System require the NCAR netCDF library.
• GDAL 1.11 or later: GDAL (Geospatial Data Abstraction Library) is a translator library for raster and vector geospatial data, and is now a prerequisite for GMT. Source code and documentation are available at the GDAL web page.
• Perl version 5.0 or later: Perl is a fast, well documented scripting language used widely in the Linux/Unix world. MB-System contains a number of perl scripts used both for installation and to ease common tasks. Most of the current Unix operating systems include perl. If you need to obtain the perl source code, first check with your local system administrator - you will probably find perl already available locally. The perl source code can be obtained from the GNU software archives of the Free Software Foundation.
• Perl Parallel-Forkmanager module: this Perl module is required for the parallel processing macros mbm_multicopy, mbm_multidatalist, and mbm_multiprocess to work. An easily installed package is available from from www.cpan.org.
• X11: The interactive graphical utilities in MB-System (MBedit, MBnavedit, MBvelocitytool, MBgrdviz, MBeditviz) use and require the X11 windowing system.
• Motif: The interactive graphical utilities in MB-System (MBedit, MBnavedit, MBvelocitytool, MBgrdviz, MBeditviz) use version 2 of the Motif widget set, and Motif libraries are required for these utilities to be built and to run. Most current Unix/Linux operating systems include the required Motif libraries, either in the original proprietary form (Motif), or the not-quite-open-source form (OpenMotif). If you do not have these libraries, the OpenMotif 2 source is available through Motifzone. An old alternative open source Motif-compatible distribution called LessTif does not work with the current OpenGL based MB-System programs (MBgrdviz, MBeditviz) and should be avoided.
• FFTW: The "Fastest Fourier Transform in the West" package is used by the sonagram calculation program MBbsegypsd to calculate, well, Fast Fourier Transforms. FFTW is commonly used and thus available on or for most current Unix operating systems.
• OTPSnc: The Oregon State Ocean Tide Prediction Software package is required for the tidal modeling program MBotps (which in fact is just a convenient front end for the old-style-batch interface of OTPS). The OTPSnc package can be obtained from the tidal modeling group at Oregon State University.

MB-System produces Postscript based graphics. Most current Unix operating systems provide a program which serves as a screen-based Postscript viewer. If you do not have a Postscript viewer, one option is to obtain one of several Ghostscript-based packages from the Free Software Foundation. The best is gv:

• gv: Open source screen Postscript viewer. This tool is a bit more sophisticated than the similar alternative ghostview. In particular, gv can handle large format plots gracefully. The source code can be obtained from the GNU software archives of the Free Software Foundation.

The MB-System source code is extracted from the distribution using the tar utility:

tar xvzf mbsystem-5.5.2263.tar.gz

or for some older systems with feature-limited versions of tar, a combination of gunzip and tar:

gunzip mbsystem-5.5.2263.tar.gz
tar xvf mbsystem-5.5.2263.tar

This will create a directory called (for the 5.5.2263 distribution):

mbsystem-5.5.2263

In order to build and install MB-System from an interactive shell, you need to change your current directory to the distribution:

cd mbsystem-5.5.2263

General Instructions

The configure script has been generated using the autoconf package. The current configure script does not resolve all of the flags and locations needed to build MB-System on all platforms, but does allow for flexible installation and generation and use of shared libraries without requiring interactive editing. These improvements make MB-System distributions much more amenable to inclusion in package manager systems like Debian and Fink. We hope to improve the configure script so that less intervention is required.

The basic steps for building MB-System using the configure script are:

1. Move to the top of the MB-System distribution directory:

cd mbsystem-5.5.2263

2. Run the configure script to generate the Makefile files throughout the distribution directory structure. The command line options for configure are discussed below, and common examples for different operating systems are provided towards the bottom of this page.

[...pre-options...]./configure [...options...]

make

make install

The configure script is intended to discern the enviroment, locate prerequisite packages, and construct the makefiles with a minimum of user intervention. In practice, users generally need to set at least some options when using the configure script in order to successfully build, install, and run MB-System. If NetCDF and GMT installations cannot be located, MB-System cannot be built. If FFTW3, Motif, or OpenGL cannot be found MB-System will be built, but without the applications that depend on these packages.

Depending on how user permissions are set on your system and where the package is to be installed, it may be necessary to execute some or all of the above commands with superuser privileges. On older styles of Unix and Linux, this was typically accomplished by using the su command to become root, or superuser, a step that requires knowing the root password for the system. Following a successful invocation of su in a command shell, all commands have superuser privileges. On MacOsX and other "modern" flavors of Unix and Linux, it's more common to use the sudo command in front of other commands in order to execute them with superuser privileges. An administrator password is required for the first instance of sudo, but not for subsequent instances (at least for a period of time, typically five minutes). In this case, the commands become:

sudo ./configure
sudo make
sudo make install

The default destination is /usr/local, and so one should find the MB-System executable programs and scripts in /usr/local/bin, the shared libraries in /usr/local/lib, the manual pages in /usr/local/man, and the projection and Levitus databases accessed by MB-System in /usr/local/share/mbsystem. However, one can control the installation destination of the configure script on the command line by using a "--prefix" argument. For example, to install MB-System into /Users/caress/sandbox/mbsystem, you can use:

sudo ./configure \
--prefix=/Users/caress/sandbox/mbsystem

The complete list of configure's installation location options is:

--prefix 				This is the common installation prefix for all files.
 						If exec_prefix is defined to a different value, prefix
 						is used only for architecture-independent files.
 						[Default: /usr/local]
--exec_prefix 			The installation prefix for architecture-dependent files.
						By default it's the same as prefix. You should avoid
						installing anything directly to exec_prefix. However,
						the default value for directories containing
						architecture-dependent files should be relative to
						exec_prefix.
						[Default: ${prefix} ==> /usr/local]
--datarootdir 			The root of the directory tree for read-only architecture
						-independent data files.
						[Default: ${exec_prefix}/share ==> /usr/local/share]
--bindir 				The directory for installing executables that users run.
						[Default: ${exec_prefix}/bin ==> /usr/local/bin]
--libdir 				The directory for installing object code libraries.
						[Default: ${exec_prefix}/lib ==> /usr/local/lib]
--includedir 			The directory for installing C header files.
						[Default: ${exec_prefix}/include ==> /usr/local/include]

MB-System depends on librarys from a number of different packages, including NetCDF, GMT5, GDAL, FFTW3, X11, and Motif. Sometimes a user will have more than one installation of a package available, and specifying which is used is desirable. Also, unfortunately the configure script does not always successfully find all needed packages. Consequently, the configure script allows users to set the locations on the command line when necessary. The configure command line options controlling the locations of prerequisites are:

--with-netcdf-config 	Location of NetCDF configuration script nc-config
--with-gdal-config		Location of GDAL configuration script gdal-config
--with-gmt-config 		Location of GMT configuration script gmt-config
--with-proj-lib 		Location of PROJ libs (optional)
--with-proj-include 	Location of PROJ libs (optional)
--with-fftw-lib 		Location of FFTW3 libs (optional)
--with-fftw-include 	Location of FFTW3 headers (optional)
--with-motif-lib 		Location of Motif libs (optional)
--with-motif-include 	Location of Motif headers (optional)
--with-opengl-lib 		Location of OpenGL libs (optional)
--with-opengl-include 	Location of OpenGL headers (optional)
--with-otps-dir		Location of OTPS installation (optional)

The MB-System distribution includes the source code for the PROJ4 package. By default, the configure script seeks to link with a libproj built external to MB-System. Configure accepts the command --enable-bundledproj to build MB-System using the included PROJ4 source.

--enable-bundledproj	Build using bundled proj package - the default is to link with libproj

Note that specification of FFTW3, Motif, and OpenGL is optional. If the configure script does not find these packages and the user does not specify their locations, then some MB-System programs will not be built. Lack of FFTW3 means that mbsegypsd is not built. No OpenGL results in the visualization programs mbgrdviz and mbeditviz not being built. Lack of Motif means that no graphical programs of any type are built.

User Environment Setup

Regardless of where the MB-System programs are installed, users must have that location included in their path environment variable in order to execute the programs from a command line. If MB-System has been installed using a package manager or installed manually into a common location (e.g. /usr/local/bin), the user path probably already references the needed location. If altering the user path variable is required, it can be accomplished by editing the initialization files hidden in the user's home directory. Which files need to be edited depends on which command line shell is being used. If the user works with csh, then the .cshrc and .login files need to be changed. If the shell is bash, then the .bashrc and .profile files must be altered. See the manual pages for the relevant shell program to determine how to set the user environment. The executable perl must also be available in the user's path for most of the macros to work.

The MB-System tools mbcontour, mbswath, and mbgrdtiff are actually structured as GMT5 modules that are invoked as an argument to the program gmt:

gmt mbcontour (....various arguments.....)
gmt mbswath (....various arguments.....)
gmt mbgrdtiff (....various arguments.....)

GMT_CUSTOM_LIBS = /usr/local/lib/mbsystem.so

The parallel processing modules mbm_multiprocess, mbm_multidatalist, and mbm_multicopy require the perl module Parallel::ForkManager. This can be added to your local perl installation using the command line utility cpan:

	cpan Parallel::ForkManager 

The MB-System plotting macros mbm_grdplot, mbm_plot, etc all generate shellscripts that in turn execute a combination of GMT, MB-System, and other programs to generate and then display postscript plots or images. The MB-System program mbdefaults sets the programs you want to use to display postscript files and images on the screen. If, for instance, you want to use "gv" to display postscript and "feh" to display images, then run:

	mbdefaults -Dgv -Ifeh -V

These defaults are stored in a hidden file called ".mbio_defaults" in the user's home directory.

Many MacOsX users have their NetCDF, GDAL, PROJ, GMT5, FFTW3, and OpenMotif installations through the Fink package manager, which installs packages in /sw. To install the MB-System prerequisites:

sudo fink install \
	gmt5 gmt5-dev \
	gdal gdal-dev gdal-shlibs \
	netcdf-c7 netcdf-c7-shlibs \
	proj proj-bin proj-shlibs \
	openmotif4 openmotif4-shlibs x11 x11-dev \
	fftw3 fftw3-shlibs \
	gv libicu55-shlibs

The configure script is able to find the NetCDF, GDAL and GMT5 installations because they install the programs nc-config, gdal-config, and gmt-config, respectively, in /sw/bin. However, the configure script fails to find the PROJ, FFTW3, and OpenMotif packages in /sw, and so the user must explicitly specify those packages. The OTPS tide modeling software used by mbotps is not packaged in Fink, and so must be manually installed by a user if mbotps is to work correctly. Installation of MB-System on a Mac running MacOsX 10.9 or 10.10 will likely use a configure command that looks something like:

sudo CFLAGS="-I/opt/X11/include -L/opt/X11/lib" \
./configure \
    --with-proj-include=/sw/include \
    --with-proj-lib=/sw/lib \
    --with-fftw-include=/sw/include \
    --with-fftw-lib=/sw/lib \
    --with-motif-include=/sw/include \
    --with-motif-lib=/sw/lib \
    --with-otps-dir=/usr/local/OTPS2

As shown here, one can also add to the commands seen by the compiler ("CFLAGS") and linker ("LDFLAGS") if desired or necessary by prefacing the configure command with arguments setting the environment variables CFLAGS and LDFLAGS. Here the current location of X11 header files and libraries must be specified because the new (to MacOsX) location of X11 in /opt is not known to the configure script. Another example is that in order to compile MB-System for user with a debugger, all compiler commands must include the "-g" argument. So, to enable use of the gdb debugger, the configure command becomes:

sudo CFLAGS="-g -I/opt/X11/include -L/opt/X11/lib" \
./configure \
    --with-proj-include=/sw/include \
    --with-proj-lib=/sw/lib \
    --with-fftw-include=/sw/include \
    --with-fftw-lib=/sw/lib \
    --with-motif-include=/sw/include \
    --with-motif-lib=/sw/lib \
    --with-otps-dir=/usr/local/OTPS2

MB-System now requires GMT 5.2.1 or later. The standard Ubuntu package manager apt-get installs a current GMT on Ubuntu 16. On Ubuntu 12 and 14 the available GMT version is 5.1, with the consequence that a manual GMT installation is required before MB-System can be installed.

For Ubuntu Linux 12 or 14, the following use of the apt-get utility will install all of the MB-System prerequisites excepting GMT5 and OTPS:

sudo apt-get install xorg-dev libmotif-dev libmotif4 libxp-dev mesa-common-dev \
    libsdl1.2-dev libsdl-image1.2-dev build-essential gfortran \
    nautilus-open-terminal libfftw3-3 libfftw3-dev \
    libnetcdf-dev netcdf-bin gdal-bin gdal1-dev gv

In order to install GMT5 manually, follow the installation instructions in the GMT documentation or in the excellent GMT5 installation guide by Andrew Moody at:

http://andrewjmoodie.com/2014/12/installing-the-generic-mapping-tools-5-gmt-5-1-x-on-ubuntu-linux/

For Ubuntu Linux 16, some of the prerequisite package names have changed from previous version repositories. The following use of the apt-get utility will install all of the MB-System prerequisites excepting OTPS:

sudo apt-get install gmt libgmt5 libgmt-dev gmt-gshhg gmt-doc \
            libx11-dev xorg-dev libmotif-dev libmotif4 \
            libxp-dev mesa-common-dev libsdl1.2-dev libsdl-image1.2-dev \
            sudo apt-get install  build-essential gfortran nautilus-open-terminal \
            libfftw3-3 libfftw3-dev libnetcdf-dev netcdf-bin \
            libgdal-bin gdal-dev gv csh libgmt-dev libproj-dev

If the prerequisites have all been installed as shown above, and it is desired to install MB-System in /usr/local, then only a simple call to configure is required:

sudo ./configure

Once the makefiles have been generated by configure, build and install using:

sudo make
sudo make install

In some cases the system and/or user environment impedes the successful use of the GMT and/or MB-System shared libraries. In order to manually allow shared libraries to be found for linking or running, one can either set the CFLAGS environment variable during building or set the LD_LIBRARY_PATH environment variable at login by adding a command to the user's ~/.profile or ~/.bashrc files.

To set the CFLAGS environment variable during building include "-Wl,-rpath -Wl,LIBDIR" in the configure command as shown here:

sudo CFLAGS="-Wl,-rpath -Wl,/usr/local/lib" ./configure

To augment the LD_LIBRARY_PATH environment variable during login add a line to the ~/.bashrc or ~/.profile file as shown here:

export LD_LIBRARY_PATH=/usr/local/lib:$LD_LIBRARY_PATH

Prerequisite Installation and Configure Arguments for CentOs or Red Hat Linux

The package manager usually used on CentOs or Red Hat Linux systems is yum. To install all of the MB-System prerequisites use the command:

sudo yum install openmotif openmotif-devel fftw fftw-devel netcdf netcdf-devel \
		proj proj-devel gdal-devel gmt gmt-devel gv nedit

If the prerequisites have all been installed with yum and it is desired to install MB-System in /usr/local, then only a simple call to configure is required:

sudo ./configure

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