C Systems Program - Read/Write Issues During Copy

Question 1

You read a value, size_buffer, and assign it to size and new_file_size, you also create a buffer[size] of that same size,

int size = atoi(size_buffer);
sscanf(current_header.ar_fmag, "%s", fmag_buffer);
//...
new_file_size = atoi(size_buffer);
//...
char buff[size];

Read returns a ssize_t count of bytes in range [0..new_file_size], which you set into io_size, realize that read(2) may return < new_file_size bytes, which is why you need the while loop. So you need to write everything you have read, until you reach your write limit. I have made some comments to guide you.

// from copy.c
while ((io_size = read (fd, buff, new_file_size)) > 0)
{
    read_cntr++;
    //perhaps you mean read_cntr += io_size;
    //you probably mean to write io_size bytes here, regardless
    //write(new_file_fd, buff, io_size);
    if (read_cntr > new_file_size) //probably you want >= here
        break;
    //you may have broke before you write...
    write (new_file_fd, buff, new_file_size);
}

A more typical idiom for this copy would be something where you pick a read/write buffer size, say 4*1024 (4K), 16*1024 (16K), etc, and read that blocksize, until you have less than that blocksize remaining; for example,

//decide how big to make buffer for read()
#define BUFSIZE (16*1024) //16K
//you need min(
#define min(x,y) ( ((x)<(y)) ? (x) : (y) )
ssize_t fdreader(int fd, int ofd, ssize_t new_file_size )
{
    ssize_t remaining = new_file_size;
    ssize_t readtotal = 0;
    ssize_t readcount;
    unsigned char buffer[BUFSIZE];
    for(  ; readcount=read(fd,buffer,min(sizeof(buffer),remaining));  )
    {
        readtotal += readcount;
        if( readcount > remaining ) //only keep remaining
            readcount = remaining;
        write( ofd, buffer, readcount);
        remaining -= readcount;
        if( remaining <= 0 ) break; //done
    }
    return readtotal;
}

Try this,

#include<stdio.h>
#include<stdlib.h>

void usage(char*progname)
{
    printf("need 2 files\n");
    printf("%s <infile> <outfile>\n",progname);
}

//decide how big to make buffer for read()
#define BUFSIZE (16*1024) //16K
//you need min(
#define min(x,y) ( ((x)<(y)) ? (x) : (y) )
ssize_t fdreader(int fd, int ofd, ssize_t new_file_size )
{
    ssize_t remaining = new_file_size;
    ssize_t readtotal = 0;
    ssize_t readcount;
    unsigned char buffer[BUFSIZE];
    for(  ; readcount=read(fd,buffer,min(sizeof(buffer),remaining));  )
    {
        readtotal += readcount;
        if( readcount > remaining ) //only keep remaining
            readcount = remaining;
        write( ofd, buffer, readcount);
        remaining -= readcount;
        if( remaining <= 0 ) break; //done
    }
    return readtotal;
}

int main(int argc,char**argv)
{
    int i=0; /* the infamous 'i' */
    FILE*infh;
    FILE*outfh;

    if( argc < 3 )
    {
        usage(argv[0]);
        return 0;
    }

    printf("%s %s\n",argv[1],argv[2]); fflush(stdout);
    if( !(infh=fopen(argv[1],"r")) )
    {
        printf("cannot open %s\n",argv[2]); fflush(stdout);
        return(2);
    }
    if( !(outfh=fopen(argv[2],"w+")) )
    {
        printf("cannot open %s\n",argv[3]); fflush(stdout);
        return(3);
    }

    int x = fdreader(fileno(infh), fileno(outfh), 512 );

    return 0;
}

Question 2

Your while() loop should probably have braces ({ ... }) after it, otherwise you're just incrementing read_cntr without doing anything else.