11-17-2015
You're reading a 3/4 GB file four times - I don't know if disk I/O buffering will easily cater for that. Why dont you read your four .bed files into four different (multidimensional?) arrays ( 259 is not too large an array element count), then do your four independent calculations on each large file's input line, and then output to the four different result files?
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LEARN ABOUT OPENSOLARIS
setbuffer
setbuffer(3C) Standard C Library Functions setbuffer(3C)
NAME
setbuffer, setlinebuf - assign buffering to a stream
SYNOPSIS
#include <stdio.h>
void setbuffer(FILE *iop, char *abuf, size_t asize);
int setlinebuf(FILE *iop);
DESCRIPTION
The setbuffer() and setlinebuf() functions assign buffering to a stream. The three types of buffering available are unbuffered, block
buffered, and line buffered. When an output stream is unbuffered, information appears on the destination file or terminal as soon as writ-
ten; when it is block buffered, many characters are saved and written as a block; when it is line buffered, characters are saved until
either a NEWLINE is encountered or input is read from stdin. The fflush(3C) function may be used to force the block out early. Normally all
files are block buffered. A buffer is obtained from malloc(3C) upon the first getc(3C) or putc(3C) performed on the file. If the standard
stream stdout refers to a terminal, it is line buffered. The standard stream stderr is unbuffered by default.
The setbuffer() function can be used after a stream iop has been opened but before it is read or written. It uses the character array abuf
whose size is determined by the asize argument instead of an automatically allocated buffer. If abuf is the null pointer, input/output
will be completely unbuffered. A manifest constant BUFSIZ, defined in the <stdio.h> header, tells how large an array is needed:
char buf[BUFSIZ];
The setlinebuf() function is used to change the buffering on a stream from block buffered or unbuffered to line buffered. Unlike set-
buffer(), it can be used at any time that the stream iop is active.
A stream can be changed from unbuffered or line buffered to block buffered by using freopen(3C). A stream can be changed from block
buffered or line buffered to unbuffered by using freopen(3C) followed by setbuf(3C) with a buffer argument of NULL.
RETURN VALUES
The setlinebuf() function returns no useful value.
SEE ALSO
malloc(3C), fclose(3C), fopen(3C), fread(3C), getc(3C), printf(3C), putc(3C), puts(3C), setbuf(3C), setvbuf(3C)
NOTES
A common source of error is allocating buffer space as an "automatic" variable in a code block, and then failing to close the stream in the
same block.
SunOS 5.11 13 May 1997 setbuffer(3C)