how to make hollow square marks with matplotlib in python

Setting markerfacecolor='white' does not actually make them hollow, it makes them white. In order to make them hollow, you need to set markerfacecolor='none'. Additionally, you need to set markeredgecolor to the color you want. So:

pylab.semilogy(xaxis, pq_averages, 'ks-',color='black',
       label='DCTCP-PQ47.5', markerfacecolor='none', markeredgecolor='black')

Will do the job for you.

Try adding markerfacecolor like so:

pylab.semilogy(xaxis, pq_averages, 'ks-', markerfacecolor='none', label='DCTCP-PQ47.5')