The final two steps are to run the install_makefiles.yourfile script, and to compile the software. Run install_makefiles.yourfile simply with

./install_makefiles.yourfile

Parameters defined for Makefiles:
Mb-System Home:            /usr/local/mbsystem/mbsystem5b31
Operating System:          LINUX
Byte swapping:             enabled
C Compiler:                cc
C Compile Flags:           -g -w -DLINUX -DBYTESWAPPED -DGMT3_3
Load Flags:                -lm -L/usr/local/gmt/netcdf-3.5.0/lib -lnetcdf
Library Archiver:          ar rcv
Graphical Utilities:       enabled
Motif Include Location:    /usr/X11R6/LessTif/Motif1.2/include
Motif Libraries:           -L/usr/X11R6/LessTif/Motif1.2/lib -lXm -L/usr/X11R6/lib -lXt -lX11
GMT Library Location:      /usr/local/gmt
GMT Include Location:      /usr/local/gmt
NetCDF Library Location:   /usr/local/gmt/netcdf-3.5.0/lib
NetCDF Include Location:   /usr/local/gmt/netcdf-3.5.0/include
Levitus Data Location:     /usr/local/mbsystem/mbsystem5b31/share/LevitusAnnual.dat
Projections Data Location: /usr/local/mbsystem/mbsystem5b31/share/Projections.dat

Makefile Template: Makefile.template
Output Makefile:   ./Makefile

Makefile Template: src/gmt/Makefile.template
Output Makefile:   src/gmt/Makefile

Makefile Template: src/gsf/Makefile.template
Output Makefile:   src/gsf/Makefile

Makefile Template: src/macros/Makefile.template
Output Makefile:   src/macros/Makefile

Makefile Template: src/Makefile.template
Output Makefile:   src/Makefile

Makefile Template: src/mbaux/Makefile.template
Output Makefile:   src/mbaux/Makefile

Makefile Template: src/mbedit/Makefile.template
Output Makefile:   src/mbedit/Makefile

Makefile Template: src/mbeditold/Makefile.template
Output Makefile:   src/mbeditold/Makefile

Makefile Template: src/mbio/Makefile.template
Output Makefile:   src/mbio/Makefile

Makefile Template: src/mbnavadjust/Makefile.template
Output Makefile:   src/mbnavadjust/Makefile

Makefile Template: src/mbnavedit/Makefile.template
Output Makefile:   src/mbnavedit/Makefile

Makefile Template: src/mbnaveditold/Makefile.template
Output Makefile:   src/mbnaveditold/Makefile

Makefile Template: src/mbvelocitytool/Makefile.template
Output Makefile:   src/mbvelocitytool/Makefile

Makefile Template: src/mr1pr/Makefile.template
Output Makefile:   src/mr1pr/Makefile

Makefile Template: src/proj/Makefile.template
Output Makefile:   src/proj/Makefile

Makefile Template: src/surf/Makefile.template
Output Makefile:   src/surf/Makefile

Makefile Template: src/utilities/Makefile.template
Output Makefile:   src/utilities/Makefile

All done!

If your output looked something like above (of course with your specific parameters) then you are ready to compile. To compile MB-System™ execute

make

Now go get a cup of coffee. The make command will descend recursively down through the directory structure, compiling source files, linking object files, and copying executables and manual pages to the appropriate directories. The executables will be placed in mbsystem/bin, the libraries in mbsystem/lib, and the manual pages in mbsystem/man/man1.

If there is an error, scroll back through the output and see if you can find the source. If there are no overt errors when the process completes, you are probably ready to take things for a spin. It's a good idea to try things out with mbm_plot, and mbedit as these will utilize enough of the software that you are likely to catch any major problems.

Now that you've compiled (and installed) MB-System™ you should edit your PATH variable, typically in .cshrc for c-shell or .bash_profile for the bash shell.

Finally, you may also want to specify the default viewer for postscript files (which is called automatically from utilities such as mbm_plot). This can be set as an environment variable (PS_VIEWER), or with the mbdefaults utility, which will store the value (and any other changes from the installed default) in their $HOME/.mbdio_defaults. The default for the postscript viewer is ghostview, usually executed with gv on unix machines.