1. A non-transitory computer-readable storage medium containing a program which, when executed, performs a specified collective operation on a parallel computer comprising a plurality of compute nodes, the specified collective operation comprising: performing a first collective operation by a source node on a plurality of target nodes to determine a characteristic of the target nodes, wherein the characteristic for each target node specifies whether a buffer of the respective target node is N-byte aligned, where N is a power of two; from a plurality of protocols, selecting a target protocol based on determining whether all of the target nodes are N-byte aligned; performing the specified collective operation by the source node on the plurality of target nodes using the target protocol; performing a second collective operation by one of the target nodes on a plurality of downstream nodes to determine a characteristic of each of the downstream nodes, wherein the characteristic for each downstream node specifies whether a buffer of the respective downstream node is N-byte aligned, where N is a power of two; from the plurality of protocols, selecting a downstream protocol based on determining whether all of the downstream nodes are N-byte aligned; and performing the specified collective operation by the one of the target nodes on the plurality of downstream nodes using the downstream protocol.