A deposition system for depositing a thin film photovoltaic cell on a flexible substrate, comprising: a) an enclosure comprising a fluid space that is fluidically isolated from an environment external to said enclosure; b) a plurality of deposition chambers in said fluid space, wherein at least one deposition chamber of said plurality of deposition chambers comprises a magnetron sputtering apparatus that directs a material flux of one or more target materials towards a portion of said flexible substrate that is disposed in said at least one deposition chamber of said plurality of deposition chambers; b1) wherein each of said deposition chambers that comprises a magnetron sputtering apparatus includes openings through which said flexible substrate passes and adjustable conductance limiters arranged at said openings to form a gap between said substrate and said conductance limiter; c) a substrate payout roller and a substrate take-up roller in said enclosure, wherein said substrate payout roller provides a flexible substrate that is directed through each of said plurality of deposition chambers to said substrate take-up roller; and d) at least one guide roller in said enclosure, wherein said guide roller is configured to direct said flexible substrate to or from a given deposition chamber among said plurality of deposition chambers; wherein said at least one deposition chamber comprises a magnetron sputtering apparatus comprising: a rotatable magnetron adjacent to a planar magnetron; and one or more shields forming a sub-chamber between said rotatable magnetron and said planar magnetron, wherein said planar magnetron is configured to contain a liquid target having a first material and provide a material flux having said first material towards said rotatable magnetron, and wherein said rotatable magnetron is configured to rotate a solid target having a second material in relation to said planar magnetron and provide a material flux having said first and second materials towards said flexible substrate. a) an enclosure comprising a fluid space that is fluidically isolated from an environment external to said enclosure; b) a plurality of deposition chambers in said fluid space, wherein at least one deposition chamber of said plurality of deposition chambers comprises a magnetron sputtering apparatus that directs a material flux of one or more target materials towards a portion of said flexible substrate that is disposed in said at least one deposition chamber of said plurality of deposition chambers; b1) wherein each of said deposition chambers that comprises a magnetron sputtering apparatus includes openings through which said flexible substrate passes and adjustable conductance limiters arranged at said openings to form a gap between said substrate and said conductance limiter; b1) wherein each of said deposition chambers that comprises a magnetron sputtering apparatus includes openings through which said flexible substrate passes and adjustable conductance limiters arranged at said openings to form a gap between said substrate and said conductance limiter; c) a substrate payout roller and a substrate take-up roller in said enclosure, wherein said substrate payout roller provides a flexible substrate that is directed through each of said plurality of deposition chambers to said substrate take-up roller; and d) at least one guide roller in said enclosure, wherein said guide roller is configured to direct said flexible substrate to or from a given deposition chamber among said plurality of deposition chambers; wherein said at least one deposition chamber comprises a magnetron sputtering apparatus comprising: a rotatable magnetron adjacent to a planar magnetron; and one or more shields forming a sub-chamber between said rotatable magnetron and said planar magnetron, wherein said planar magnetron is configured to contain a liquid target having a first material and provide a material flux having said first material towards said rotatable magnetron, and wherein said rotatable magnetron is configured to rotate a solid target having a second material in relation to said planar magnetron and provide a material flux having said first and second materials towards said flexible substrate. a rotatable magnetron adjacent to a planar magnetron; and one or more shields forming a sub-chamber between said rotatable magnetron and said planar magnetron, wherein said planar magnetron is configured to contain a liquid target having a first material and provide a material flux having said first material towards said rotatable magnetron, and wherein said rotatable magnetron is configured to rotate a solid target having a second material in relation to said planar magnetron and provide a material flux having said first and second materials towards said flexible substrate.