Adjusted retest scripts to write aprun output to .running file.

lammps/15May15/cle5.2_gnu5.1.0/retest

milc-nsf/v1/cle5.2_gnu4.9.3/retest

namd/2.10/cle5.2_gnu5.1.0/retest

nwchem/6.6/cle5.2_gnu5.1.0/retest