Parallelize loops using gnu-parallel to speed up file checking

[gdevenyi]

Scinet I/O wait is painful, parallel offers "sem" which allows parallel things to be running.

Should be able to wrap the center of the loops in this to speed them up.

Concern: how does impact writing script files, will there be contention?

[gdevenyi]

https://www.gnu.org/software/parallel/sem.html

http://unix.stackexchange.com/a/216466

[gdevenyi]

Also important, fix bash's clever buffering https://www.gnu.org/software/coreutils/manual/html_node/stdbuf-invocation.html

I think this will prevent bash from writing to the jobfile until the loop is done.

[gdevenyi]

Don't need to fix bash's buffering, we'll use pipes for qbatch commands.