Executing parallel jobs with message passing on compute clusters

A client may submit a job to a service provider that processes a large data set and that employs a message passing interface (MPI) to coordinate the collective execution of the job on multiple compute nodes. The framework may create a MapReduce cluster (e.g., within a VPC) and may generate a single key pair for the cluster, which may be downloaded by nodes in the cluster and used to establish secure node-to-node communication channels for MPI messaging. A single node may be assigned as a mapper process and may launch the MPI job, which may fork its commands to other nodes in the cluster (e.g., nodes identified in a hostfile associated with the MPI job), according to the MPI interface. A rankfile may be used to synchronize the MPI job and another MPI process used to download portions of the data set to respective nodes in the cluster.