From: softlib.cs.rice.edu
Last mod: August 20, 1994
fastlink, version 3.0P

Memory Requirements

This file discusses memory requirements for FASTLINK. See the top level README file for a roadmap to all FASTLINK documentation.

Memory Requirements

The FASTLINK programs can require large amounts of memory. For instance linkmap as configured in this distribution and compiled with 
  make linkmap
requires about 29 Mb. Of course the amount of memory required is very dependent on the number of loci and the number of alleles at each locus. However even 100 Mb is not a problem to run under Sun OS for instance, because this is a virtual memory operating system. Ideally one would want to run a program of this size on a machine with 32 Mb of memory, but in our experience it is possible to run on machines with as little as 12 Mb.

Of course it is necessary to have a swap file with sufficient space to run the OS and have enough free space for the program.

To see how much space a program requires in version 2.0 or earlier, it was possible to use the unix command: 

	size
for instance using linkmap from FASTLINK, 2.0: 
	unix> /usr/bin/size linkmap

	text    data    bss     	dec     	hex
        139264	8192	28719480	28866936	1b87978
This value under "dec" is the decimal number of bytes for the whole program. So we see in this case that 28.9 Mbytes is required.

Then compare this with the unix pstat command: 

	unix> /etc/pstat -s
	14880k allocated + 3712k reserved = 18592k used, 169000k available
This indicates that a total of 187592 Kbytes or 187 Mb has been allocated on this system for swap space, and with the current job mix, 18.5 Mb are used and 169 Mb are available. So in this case linkmap will be able to run.

To enlarge the swap space consult your local system administrator. For a single user system running FASTLINK we recommend 150Mb total swap space as a minimum.

Alternatively, use the "slow" versions of the programs. The term slow is a little misleading in that these versions will still be significantly faster than the originals. In the case of linkmap, the version compiled with 

  make slowlinkmap
with the current constant settings is less than 1 Mb in size. Any unix system should have a swap file large enough for this.

Starting in version 2.1 of FASTLINK a lot of the memory allocation is done dynamically (See README.updates ). In version 2.2 and beyond, almost all the large data structures are allocated dynamically. This means that you will not be able to detect before running whether you have enough memory. If you do not have enough, the program should exit politely with an explanation, shortly after startup. The advantage of doing the memory allocation at runtime is that it may be possible to use significantly less memory based on knowledge of certain parameters that are available only at runtime.

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