made OMP_PER_READ_THREADS configurable and default to 1 #49
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- used CPU affinity from sched.h to correctly detect the number of allocated/available CPUs in, for example, SLURM jobs - considered OMP threads when calculating total threads
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This deals with the overloading observed in issue #30 where the total number of threads was the number of ptreads defined with
-ttimesOMP_PER_READ_THREADS. In my tests, given a fixed number of CPUs, there was no difference in runtime betweenOMP_PER_READ_THREADS=3andOMP_PER_READ_THREADS=1.sched.hto correctly detect the number of allocated/available CPUs in, for example, SLURM jobs rather than all CPUs available on a system