A parallel computer system comprising: a partition, comprising: a plurality of compute nodes, the plurality of compute nodes being arranged in both a logical tree network and a logical torus network, wherein each compute node comprises reset hardware to reset a network hardware portion of the compute node separate from reset hardware (312, 316) to reset a remaining portion of the compute node that comprises a processing unit; the parallel computer system further comprising: a service node for controlling the operation of the compute nodes over a control system network, the service node including a failed hardware recovery mechanism that detects a failed compute node; wherein the failed hardware recovery mechanism is operable for resetting the remaining portion of the failed compute node without resetting the network hardware portion to recover from a fault on the failed compute node enabling an application executing on the partition and sending data between the plurality of compute nodes over the logical tree network and the logical torus network to continue without restarting after the reset of the remaining portion; and wherein the failed hardware recovery mechanism is operable for notifying the application executing on the partition and sending data between the plurality of nodes over the logical tree network and the logical torus network that a compute node has failed. a partition, comprising: a plurality of compute nodes, the plurality of compute nodes being arranged in both a logical tree network and a logical torus network, wherein each compute node comprises reset hardware to reset a network hardware portion of the compute node separate from reset hardware (312, 316) to reset a remaining portion of the compute node that comprises a processing unit; a plurality of compute nodes, the plurality of compute nodes being arranged in both a logical tree network and a logical torus network, wherein each compute node comprises reset hardware to reset a network hardware portion of the compute node separate from reset hardware (312, 316) to reset a remaining portion of the compute node that comprises a processing unit; the parallel computer system further comprising: a service node for controlling the operation of the compute nodes over a control system network, the service node including a failed hardware recovery mechanism that detects a failed compute node; wherein the failed hardware recovery mechanism is operable for resetting the remaining portion of the failed compute node without resetting the network hardware portion to recover from a fault on the failed compute node enabling an application executing on the partition and sending data between the plurality of compute nodes over the logical tree network and the logical torus network to continue without restarting after the reset of the remaining portion; and wherein the failed hardware recovery mechanism is operable for notifying the application executing on the partition and sending data between the plurality of nodes over the logical tree network and the logical torus network that a compute node has failed. a service node for controlling the operation of the compute nodes over a control system network, the service node including a failed hardware recovery mechanism that detects a failed compute node; wherein the failed hardware recovery mechanism is operable for resetting the remaining portion of the failed compute node without resetting the network hardware portion to recover from a fault on the failed compute node enabling an application executing on the partition and sending data between the plurality of compute nodes over the logical tree network and the logical torus network to continue without restarting after the reset of the remaining portion; and wherein the failed hardware recovery mechanism is operable for notifying the application executing on the partition and sending data between the plurality of nodes over the logical tree network and the logical torus network that a compute node has failed.