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There are a few problems that you might have:
You will know this is the case, because after the Makefile.pl script has completed it will tell you that it has not encountered your system before. In this case, you will need to create a Makefile for your machine and operating system. You should read the Section called What you can do if a site_config file does not exist for your system>.
You will know this is the case if you see many messages involving unresolved symbol. Refer to the Section called Compiling the BLAS and LAPACK libraries>.
These are usually indicated by messages like fatal error, insufficient virtual memory, or no message at all with the generation of a core file. There is very little that can be done about fatal errors, but they may be solved by reducing the compilation language level from Fortran95 to Fortran90 by using the -DLANGUAGE_FORTRAN_90 preprocessor option, or by reducing the compilation level to using the -FDEBUG compilation option, or changing the compilation options so that no optimisation is performed. See the chapter "Compiling customised version of TONTO". Messages such as insufficient memory can be solved by adding more memory to your computer, or increasing the virtual memory or swap space. You should consult an expert for your system in this case. For example, on COMPAQ systems, memory problems can often be solved by increasing the stacksize and other limits using the limit or ulimit command.
These are indicated when compiler messages involving the words subroutine, incorrect syntax, unknown syntax or undeclared variable. Usually, a line of Fortran code will also be printed. If you know Fortran and also the foo preprocessor, you should alter the corresponding line in the .foo source file, found in the foofiles directory. These problems are quite rare and usually indicate a non-compliant compiler. The problem may be removed by reducing the compilation language level using the -DLANGUAGE_FORTRAN_90 preprocessor option.