Implementation of a Parallel NetCDF Interface for Seamless Collective Remote I/O

In scientific applications, netCDF [1] was developed to support a view of data as a collection of self-describing, portable, and array-oriented objects that can be accessed through a simple interface. Its parallel I/O interface named parallel netCDF (hereafter PnetCDF) was developed with the help of an MPI-I/O library [2] such as ROMIO [3], and the PnetCDF succeeded in scientific computation [4]. But the same operations among computers which have different MPI libraries each other have not been available. To realize this mechanism, a remote MPI-I/O mechanism of a Stampi library [5] has been implemented in a PnetCDF library as an underlying MPI-I/O layer. The Stampi library was originally developed to support seamless MPI communications among different MPI libraries by deploying its wrapper interface library between a user program and an underlying communication library [6]. It intermediates MPI communications among different MPI libraries and hides complexity and heterogeneity in communication mechanisms among different platforms. It also supports MPI-I/O operations not only inside a computer using an underlying MPI library but also among computers which have different MPI libraries [5]. MPI-I/O calls in a user program are switched to corresponding Stampi's MPI-I/O functions in the wrapper library, and it considers which I/O operation is appropriate, local or remote I/O, automatically according to a target computer name and so on which are specified in an info object. A PnetCDF library has been linked with the Stampi's MPI-I/O functions to support seamless remote I/O operations via a PnetCDF API without paying attention to complexity and heterogeneity in underlying communication and I/O systems. When a PnetCDF function is called in a user program, the I/O call is translated into several Stampi's MPI function calls. In local I/O operations, parallel I/O operations are carried out using vendor's MPI library according to those function calls. If the vendor's one is not available, UNIX I/O functions are used instead of it. On the other hand, MPI-I/O processes are invoked on a remote computer in remote I/O operations by using a remote shell command (rsh or ssh) when ncmpi create() or ncmpi open() is called, followed by a function call of MPI File open() inside them. An I/O request from each user process is transfered to the corresponding MPI-I/O process, and each MPI-I/O