Installing Mb-System on Fedora 17

MB-System is the only fully open-source software I am aware of for swath sonar data including multibeam and sidescan backscatter. As such, I'm really hoping using it works out for me!

Compiling it on a fresh install of Fedora 17 wasn't that straight-forward (took me about 5 hours to figure all this out), so I thought I'd put together a little how-to for the benefit of myself, and hopefully you.

I've broken it down into a few stages so some sort of semblance of order can be imposed on this random collection of installation notes.

Step 1: download the software from ftp server here

In the terminal:

	cd ~/Downloads
	tar xvzf MB-System.tar.gz

view raw mb1.sh hosted with ❤ by GitHub

For me this created a folder called 'mbsystem-5.3.1982'

Step 2: install pre-requisites

A) Generic Mapping Tools (GMT). You need to go to the Downloads tab, then click on the INSTALL FORM link. This will take you to a page where you can download the installation script, and fill in an online form of your parameter settings which you can submit and save the resulting page as a textfile which becomes the input to the bash script. Sounds confusing, but it's not - the instructions on the page are adequate. I opted to allow GMT to install netCDF for me. Then in the terminal I did this:

	sudo mkdir /usr/local/GMT
	sudo sh install_gmt.sh GMT[45]param.txt
	export NETCDFHOME=/home/me/Downloads/netcdf-3.6.3
	export PATH=/usr/local/GMT/bin:$PATH

view raw mb2.sh hosted with ❤ by GitHub

B) Perl parallel forkmanager:

sudo yum install perl-Parallel-ForkManager.noarch

view raw mb3.sh hosted with ❤ by GitHub

C) X11

sudo yum groupinstall "X Software Development"

view raw mb4.sh hosted with ❤ by GitHub

D) openmotif

sudo yum install openmotif-clients.x86_64 openmotif.x86_64 openmotif-demos.x86_64

view raw mb5.sh hosted with ❤ by GitHub

E) fftw

sudo yum install fftw.x86_64 fftw-devel.x86_64

view raw mb6.sh hosted with ❤ by GitHub

F) ghostview - I had to install this indirectly using kde3:

sudo yum install kdebase3.x86_64

view raw mb6b.sh hosted with ❤ by GitHub

(Note to Fedora - why oh why oh why are B, C, and F above not installed by default!?)

G)  OTPSnc tidal prediction software: download from here

untar, and cd to the directory

first double check that ncdump and ncgen are installed (which ncdump ncgen)

then edit the makefile so it reads:

	FC = gfortran
	NCLIB = /usr/lib64
	NCINCLUDE = /usr/include
	NCLIBS= -lnetcdf -lnetcdff

view raw mb7.sh hosted with ❤ by GitHub

then in the terminal issue:

	make extract_HC
	make extract_predict_tide

view raw mb8.sh hosted with ❤ by GitHub

Hopefully this compiles without errors, then I moved them to a executable directory:

	sudo mv extract_HC /usr/bin/
	sudo mv predict_tide /usr/bin/

view raw mb9.sh hosted with ❤ by GitHub

H) openGL libraries (again I had to do this indirectly, this time through mesa):

sudo yum install mesa*

view raw mb10.sh hosted with ❤ by GitHub

Step 3: prepare mbsystem makefiles

cd mbsystem-5.3.1982/

You have to go in and point install_makefiles to where all your libraries are. This is time-consuming and involves a lot of ls, which, and whereis!

Here's a copy of the lines I edited in my install_makefiles parameters:

	$MBSYSTEM_HOME = "/home/me/Downloads/mbsystem-5.3.1982";
	$OS = "LINUX";
	$CFLAGS = "-Wall -g -I/usr/include/X11";
	$LFLAGS = "-Wall -lm -bind_at_load -Wl,-dylib_file,/usr/lib64/libGL.so";
	$NETCDFLIBDIR = "/usr/local/lib";
	$NETCDFINCDIR = "/usr/include";
	$GMTLIBDIR = "/usr/local/GMT/lib";
	$GMTINCDIR = "/usr/local/GMT/include";
	$LEVITUS = "$MBSYSTEM_HOME/share/annual";
	$PROJECTIONS = "$MBSYSTEM_HOME/share/Projections.dat";
	$FFTWLIBDIR = "/usr/lib64";
	$FFTWINCDIR = "/usr/include";
	$MOTIFINCDIR = "/usr/include/openmotif/";
	$MOTIFLIBS = "-L/usr/lib64/openmotif -L/usr/lib64/X11 -lXm -lXt -lX11";
	$LEVITUS = "$MBSYSTEM_HOME/share/annual";
	$OTPSDIR = "/usr/bin";
	$CC = "gcc";

view raw mb12.sh hosted with ❤ by GitHub

Then in the terminal

Step 3: install mbsystem

first I had to do this (but you may not need to)

	sudo cp /usr/lib64/libfftw3.so /usr/lib64/libfftw3.a
	#then
	make all
	#assuming all worked ... I copied the man and bin files into somewhere more logical/permanent:
	sudo mkdir /usr/local/mbsystem
	sudo mkdir /usr/local/mbsystem/bin
	sudo cp ~/Downloads/mbsystem-5.3.1982/bin/* /usr/local/mbsystem/bin
	sudo cp -R ~/Downloads/mbsystem-5.3.1982/man/ /usr/local/mbsystem/

view raw mb14.sh hosted with ❤ by GitHub

I then updated my ~/.bashrc so the computer can find all these lovely new files:

	MANPATH=$MANPATH:/usr/local/GMT/man:/usr/local/mbsystem/man
	export MANPATH
	PATH=$PATH:/usr/local/GMT/bin:/usr/local/mbsystem/bin
	export PATH

view raw mb15.sh hosted with ❤ by GitHub

Test the install by issuing

	man gmt
	man mbfilter

view raw mb16.sh hosted with ❤ by GitHub

you should see the manual pages come up. Right, now down to the business of multibeam analysis!