3.9 State File

This file should not be edited by the user. The reason for understanding the file layout is for debugging in the event of an error. The statefile is generated either in the event of a fatal error, or as a regular backup for long runs. It's purpose is to allow the program to resume running from the point at which it was interrupted. This is done using the --recover option (see -recover).

The statefile is however in a human-readable format, so it can be read in an attempt to determine the cause of the fatal error. Its format is as follows:

• Line 1 is a text string identifying the current stage of program execution. The options are:

  newx

  The program has just calculated the next set of parameters and branch lengths.
  

  hessian

  The program was in the middle of calculating the hessian.
  

  endhessian

  The program had just finished calculating the derivatives, but had not yet sorted the values out into a matrix and applied the Newton-Raphson method.

• Line 2 gives abbreviations for the types of variables stored in the file. It will normally be of the form LiLiLiLiL. This line is to allow the same code to be useable for other programs which might save different types of variables.
• Line 3 is the current set of parameter values. The parameters are orthonormalised at the start of the program, to improve convergence. Therefore, this line will not give a direct insight into the parameter values. [You could find out the actual parameter values, by running with the options --recover (see -recover) and -n0 (see -n).]
• The remaining lines come in pairs, the first of which contains the number of the site on which the program was working when it was interrupted, and the second contains a list of cumulative values for the log likelihood and its derivatives, on the sites already calculated. There should be one pair for each thread of the program. The current cumulative log-likelihood and its derivatives can be obtained by summing the relevant values for all these pairs. The sites that remain to be done are the site numbers listed in the program, and any other numbers higher than all those site numbers.