The Collaborative International Dictionary of English v.0.48:

Penitentiary \Pen`i*ten"tia*ry\, n.; pl. Penitentiaries. [Cf.
   F. p['e]nitencier. See Penitent.]
   1. One who prescribes the rules and measures of penance.
      [Obs.] --Bacon.
      [1913 Webster]

   2. One who does penance. [Obs.] --Hammond.
      [1913 Webster]

   3. A small building in a monastery where penitents confessed.
      --Shpiley.
      [1913 Webster]

   4. That part of a church to which penitents were admitted.
      --Shipley.
      [1913 Webster]

   5. (R. C. Ch.)
      (a) An office of the papal court which examines cases of
          conscience, confession, absolution from vows, etc.,
          and delivers decisions, dispensations, etc. Its chief
          is a cardinal, called the Grand Penitentiary,
          appointed by the pope.
      (b) An officer in some dioceses since A. D. 1215, vested
          with power from the bishop to absolve in cases
          reserved to him.
          [1913 Webster]

   6. A house of correction, in which offenders are confined for
      punishment, discipline, and reformation, and in which they
      are generally compelled to labor; a prison; a jail.
      Colloquially often shortened to pen.
      [1913 Webster]