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5.1 Configuration Macros

The following macros can be set for compilation using the make optionname=value syntax. They can also be modified in the file configvars.template. The default values are listed here:

NUMTHREADS 4


BUFFERSIZE 50


DEFAULTPARAMS parametermatrices


DEFAULTVARIABLES .variables


DEFAULTMATRIX ECMq.txt


DEFAULTNUMTIMES 100


DEFAULTTREE testtrees


DEFAULTDATA testdata


DEFAULTMASKFILE masks


DEFAULTMODELFILE models

The only options that are likely to need to be changed are NUMTHREADS, which should probably be set to the number of available processors, but might need to be smaller if memory is a problem (see Number of Threads, for more detail); DEFAULTDATA, which could be changed to a database stored on your system; and DEFAULTTREE which could be set to a file containing the trees that you are particularly interested in. Other default files are specific to cold, and the user could just edit the default files instead.

The runtime configuration file can also be modified using the makefile. This time type make config optionname=value. The following options can be modified:

Alternatively, the variables file (called .variables by default) can be directly modified.