I was wondering how bites works with a clustered setup. Does using bites with a clustered setup basically require you to use s3 or a remote mounted fs or are files copied to all nodes in the cluster?
You are correct. BITES stores the files only on the node which the write is performed. Changes to the RDF (and text) index will be replicated across the cluster, but the document contents are not. You will need to use S3 or a shared file system. Generally, we see files managed externally and BITES is used for processing and extracted results are stored in Stardog.
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