We report results of a deep all-sky search for periodic gravitational waves from isolated neutron stars in data from the S6 LIGO science run. The search was possible thanks to the computing power provided by the volunteers of the Einstein@Home distributed computing project. We find no significant signal candidate and set the most stringent upper limits to date on the amplitude of gravitational wave signals from the target population. At the frequency of best strain sensitivity, between $170.5$ and $171$ Hz we set a 90% confidence upper limit of ${5.5}^{-25}$, while at the high end of our frequency range, around 505 Hz, we achieve upper limits $\simeq {10}^{-24}$. At $230$ Hz we can exclude sources with ellipticities greater than $10^{-6}$ within 100 pc of Earth with fiducial value of the principal moment of inertia of $10^{38} \textrm{kg m}^2$. If we assume a higher (lower) gravitational wave spindown we constrain farther (closer) objects to higher (lower) ellipticities.
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