Shell – Redirect and pipe output

What you've written in the first line looks like a complete command (a “(compound) list” in shell terminology), so the shell treats it as a complete command. Since there's a here-document start marker (<<END), the shell then reads the here-document contents, and then starts a new command. If you want to put the here-document in the middle of a list, you need to indicate to the shell that the list is not finished. Here are couple of ways.

mpirun -np 6 ./laplace <<END |
…
END
tail -n 1 > output

{ mpirun -np 6 ./laplace <<END
…
END
} | tail -n 1 > output

Or, of course, you can make sure the command completely fits in the first line.

mpirun -np 6 ./laplace <<END | tail -n 1 > output
…
END

The rule to remember is that the here-document contents starts after the first unquoted newline after the <<END indicator. For example, here's another obfuscated way of writing this script:

mpirun -np 6 ./laplace <<END \
| tail -n $(
…
END
             echo 1) > output

I think what you are looking for is GNU screen. It maintains a buffer to hold the last screen full or two of output from one or more programs and lets you disconnect and come back later.