WARNING !

EMAN2 stores much of the data and other information during processing in an embedded database system based on BerkeleyDB. These databases exist in directories called EMAN2DB. You may be tempted to rename, delete or otherwise manipulate the files in these directories. If you feel thus tempted, you need to be aware of a number of limitations and restrictions associated with the flexibility and convenience of such database systems. Failure to heed these warnings could potentially result in data loss and a variety of apparently bizzare things happening. Regular flat files (HDF5, MRC, SPIDER, IMAGIC, etc) saved by EMAN2 are completely safe, of course, and you can do what you want with them. This warning applies strictly to the EMAN2DB directory and its contents :

Brief technical explanation

Details on the database are discussed in Eman2DataStorage

There are also some FAQ questions dealing with problem solving

Q: Why in the blankety-blank-blank did you decide to switch to this ? It's a pain to deal with !

A: Desktop computers with up to 12 cores are now becoming very common, meaning to get full performance you need to run things in parallel. Did you know that the normal flat files you deal with (Spider, MRC, IMAGIC, etc.) don't work very well in parallel environments ? If you have multiple cores trying to write to a file at the same time, you can get images corrupted in many different ways. This is particularly true if you use a shared filesystem (like NFS or windows/mac file sharing).

Traditional databases run a server process which requires maintenance, and has to be running all the time to use any programs. BDB, however, is an embedded database, which doesn't have a server, and permits multiple jobs within a single computer all to safely read and write to the database at the same time. It stores information about a project, as well as much of the actual image data. It also gives a dramatic performance boost to many tasks and permits arbitrary information to be stored with each image. So, that's why we use it...

However, it comes with a few limitations. Like most databases, it uses a memory & disk cache to give faster access to information and coordinate access to the data from multiple programs (on the same machine). This cache consists of a set of files stored in /tmp (which must be physically attached to the local machine). If you try to access the same database from two different computers at the same time via a shared network filesystem, each machine establishes an independent cache in /tmp, and both think they have exclusive access to the files. This produces a situation where the machines can easily disagree about the contents of a file, and can cause database corruption. The 'e2bdb.py -c' program will safely close the cache on one machine, so it can be reliably accessed from another machine. It is also possible in some cases to open the databases read-only from multiple machines at once, with no cache, however this is a special case used in some situations on clusters, and not a general rule.

The files in the EMAN2DB directories are not normal flat image files, but are actually proprietary database files. Moving them around or otherwise messing with them will confuse the database. If you run 'e2bdb.py -c', which closes and removes the cache, then and only then is it safe to do things like copy databases between machines, or remove or rename EMAN2DB contents. Note that when a cache is inactive, you must also NOT rename directories containing EMAN2DB directories.