Abstract: Method and system for moving an object from a source partition server to a target partition server in a distributed file system having multiple partition servers. Each object has at least one associated and linked parent object, and each partition server owns a subset of objects of the file system. The object migration is accomplished by creating a copy in a target partition server of a selected object from a source partition server. At the source partition server, a forwarding link is created that references the copy in the target partition server. The copy is linked to the parent object of the selected object, and requests for access to the selected object are responded to with the forwarding link.

Abstract: Method and system for migrating a logical volumes in a distributed file system having multiple partitions servers. Each partition server owns one or more volumes, and each volume including a subset of logically related objects of the file system. In response to a migration request that requests migration of a selected logical volume from a source partition server to the target partition server, an ownership map is updated to indicate the selected logical volume is owned by the target partition server. At the source partition server, forwarding information is stored to reference the target partition server. When the source partition server receives a request for access to the object, the forwarding information is transmitted to the requester.

Abstract: The present invention provides methods and systems for performing improved implementations of the BLAST algorithm for high-speed sequence database searching, e.g., on commodity Beowulf-class parallel computing hardware. The present invention also provides methods and systems for query packing, dynamic database division, and improved hit extension.

Abstract: Data coherency and lock services for distributed physical file systems. Client applications are coupled to a virtual file system, which is coupled to one or more physical file systems. A lock agent is coupled to one or more lock servers and to the virtual file system. The virtual file system, in response to a file access request from a client application, submits a data validation request to the lock agent. The lock agent, in turn, submits a lease request to the lock server. When the lock server grants the lease, the lease and a validation code are returned to the lock agent. The validation code indicates whether the data in the buffer cache of the virtual file system are valid. The lock agent then returns the lease to the virtual file system, which then submits the file access request to a selected one of the physical file systems.

Abstract: Namespace service in a distributed file system using a database management system. A namespace database is configured on a namespace server with namespace identifiers and associated file location information. The namespace server is separate from the data servers in the distributed file system. A client proxy arrangement interfaces with client applications and with the namespace server to obtain from the namespace server location information associated with files referenced in file access requests and submit storage access requests to the appropriate data servers. The separate namespace server and data servers enhances scalability of the distributed file system.

Abstract: A system and method for providing a plurality of client applications access to data in a distributed file system. In various embodiments, read requests are separated from write requests and the read requests are processed by dedicated read servers. A plurality of read servers are coupled to the client applications and each read server reads file data from the distributed file system and returns the file data to the client applications. A write server writes data to the distributed file system. Various embodiments are described for separating read requests from write requests and transmitting read requests to the read servers write requests to the write server.

Abstract: Apparatus and method for extending a standard-based remote file access protocol and maintaining compatibility with the standard protocol stack. Network file system (NFS) remote procedure calls (RPCs) that are submitted by an NFS client application are intercepted in a manner that is transparent to the client operating system. The intercepted NFS-RPCs are sent to a file interface card. The file interface card includes a processor that executes code that implements the standard NFS-RPC protocol, along with extensions to the standard NFS-RPC protocol. Non-NFS RPCs are sent to a conventional network interface card for processing.

Abstract: A computer system having a checkpoint error recovery system. The computer system includes a first computer having a first memory and a second computer having a second memory and a buffer. The first and second memories are updated by memory updates that include an address specifying a location and data to be written to the memory receiving the update at the location. The computer system also includes an interface for providing the second computer with a copy of each memory update received by the first memory. Upon receiving each of the copies of the memory updates, the second computer generates a recovery memory update corresponding to that copy of the memory update. The recovery memory update includes the data stored in the second memory at the address specified in the first memory update and the address specified in the received copy.