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6. Technical notes

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Memory management

Memory is allocated dynamically by the program, as needed; however, since repeated requests of memory from the operating system (via the C stdio library function malloc) are quite time-consuming, we have adopted a strategy in which two large initial blocks of memory are first allocated. One of these is reserved for the objects comprising the orders database and is apportioned out as needed by the function our_orders_alloc, while the other is used for all other memory requirements and is apportioned by our_alloc.

If the amounts initially allocated are insufficient, additional memory is requested from the operating system (via the library function malloc). (When this happens, a statement to that effect is printed). The default initial request of 3Mb (for our_alloc) will suffice for nearly all runs. If the program requests more memory than the operating system can provide, the program terminates with the message "ERROR: ALLOCATION FAILED IN MORECORE". If this happens, try setting the amount of memory specified in the .par file (using the parameter nb_our_alloc) to the maximum amount the operating system will allow you (and see if your system manager can increase that amount by adjusting operating system parameters). If that fails, you may need to reduce the number of loci being analyzed (often, deletion of a single locus having a large number of switches may suffice), or to split a large pedigree into subpedigrees. I would be interested to learn of cases where that is necessary, since it may be possible to improve the switch algebra algorithm to avoid it.

Underflow

When mapping large numbers of loci, the individual family likelihoods involve products of many factors numerically less than 1, and so can become quite small. If possible, at compilation time you should select an option for representation of floating point numbers which allows them to be as small as possible. With VAX C, this is done by using the /g_float option with the compile command cc, and then linking with the vaxcrtlg library.

16 bit integers

C compilers usually represent integer variables with either 16 or 32 bits. The source code provided to you assumes that you have a "32 bit" compiler. If, when you first try to run the program, it terminates prematurely, displaying the message "Your compiler uses a different size for integers; see documentation for changes that will have to be made in the source code", then you have a 16 bit compiler. To get the program to run correctly you must then make the following two changes in the source code and recompile:

1. in the file "defs.h", replace the line

   	       typedef int INT;
   	    

   by

                  typedef long INT;
   
   	    

2. Consult the manual for your compiler and determine the name of a library memory allocation function which takes long integers, instead of integers, as arguments (the function malloc takes integer arguments). The name of this function will be something like "mlalloc" (Lightspeed C) or "_halloc" (Microsoft C, ver 4.0 or later). Whatever it is, substitute it for "malloc" throughout the source files our_allo.c and our_orde.c. If your compiler does not have such a function, you will be unable to run CRI-MAP.

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