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The embedded database used in EMAN2 (which stores most of your image data and information about your projects in a set
of EMAN2DB directories) has a
number of very important limitations and restrictions associated with it. Failure to be aware of these restrictions
could result in data loss and waste of your valuable time. Those of you accustomed to working with normal image files
and moving them around manually need to be aware that you cannot do this with a database system as EMAN2 uses.
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 (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 :
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 * The e2bdb.py program can help to manipulate databases in certain ways. 'e2bdb.py -c' is an important command to be aware of.
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 * '''Beware of network mounted filesystems'''. ie - if your home directory is on a network volume, rather than the local machine, you need to be very very cautious. This can be done safely, but only with care. The EMAN2 database is safe for running multiple programs on a single machine. It is NOT safe for simultaneous access by multiple machines. ie - if you run an EMAN2 program accessing a particular database on one machine, and simultaneously access the database on another machine via NFS, you may get very unpredictable results, and if you write to the database from both machines, you could cause corruption.
 * '''If you wish to switch running jobs from one machine to another''', you must run 'e2bdb.py' on the first machine, and insure that EMAN2 programs are closed before opening programs on the other machine.
 * '''If you wish to switch running jobs from one machine to another''', you must run 'e2bdb.py -c' on the first machine, and insure that EMAN2 programs are closed before opening programs on the other machine.
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 * '''To use EMAN2 images with other programs''' Most files are stored in the internal database by default. If you need to use EMAN2 images with another program, you can simply export them into any of the standard [[Eman2DataStorage|cryoEM formats]]. You can treat exported image files like any other file, it's only information in EMAN2DB you need to be careful about. You can get files out of the database using the 'e2display.py' GUI or the browser in 'e2workflow.py' by right clicking on the file and selecting 'save as', or using 'e2proc2d.py' or 'e2proc3d.py' from the command-line.  * '''To use EMAN2 images with other programs''' Most files are stored in the internal database by default. If you need to use EMAN2 images with another program, you can simply export them into any of the standard [[Eman2DataStorage|cryoEM formats]]. You can get files out of the database using the 'e2display.py' GUI or the browser in 'e2workflow.py' by right clicking on the file and selecting 'save as', or using 'e2proc2d.py' or 'e2proc3d.py' from the command-line.
 * '''Beware of network mounted filesystems'''. ie - if your home directory is on a network volume, rather than the local machine, you need to be very very cautious. This CAN be done safely, but only with care. The EMAN2 database is safe for running multiple programs on a single machine. It is NOT safe for simultaneous access by multiple machines. ie - if you run an EMAN2 program accessing a particular database on one machine, and simultaneously access the database on another machine via NFS, you may get very unpredictable results, and if you write to the database from both machines, you could cause corruption. Note that this is not unique to EMAN2 database files. If you write to a regular file (SPIDER, IMAGIC, etc.) from 2 different machines at once, you will also often cause corruption.

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 (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 :

  • The e2bdb.py program can help to manipulate databases in certain ways. 'e2bdb.py -c' is an important command to be aware of.
  • Do NOT move files within an EMAN2DB directory around. These are not normal image files that you can access or transport between machines. They are the internal files generated by an embedded database system. Don't mess with them !

  • exception to the above statement: If you need to remove files from an EMAN2DB directory (taking up too much space and aren't needed, etc.), you can do so, but ONLY after running 'e2bdb.py -c' on the machine first

  • If you wish to switch running jobs from one machine to another, you must run 'e2bdb.py -c' on the first machine, and insure that EMAN2 programs are closed before opening programs on the other machine.

  • If you DO get a message saying there is a database error and corruption may have resulted: first try running 'e2bdb.py -c'. 90% of the time that will fix the problem. If that doesn't work, then you may have to resort to removing the cache directory in /tmp. This may be a risky operation which could result in data loss, and is only a last resort.

  • To use EMAN2 images with other programs Most files are stored in the internal database by default. If you need to use EMAN2 images with another program, you can simply export them into any of the standard cryoEM formats. You can get files out of the database using the 'e2display.py' GUI or the browser in 'e2workflow.py' by right clicking on the file and selecting 'save as', or using 'e2proc2d.py' or 'e2proc3d.py' from the command-line.

  • Beware of network mounted filesystems. ie - if your home directory is on a network volume, rather than the local machine, you need to be very very cautious. This CAN be done safely, but only with care. The EMAN2 database is safe for running multiple programs on a single machine. It is NOT safe for simultaneous access by multiple machines. ie - if you run an EMAN2 program accessing a particular database on one machine, and simultaneously access the database on another machine via NFS, you may get very unpredictable results, and if you write to the database from both machines, you could cause corruption. Note that this is not unique to EMAN2 database files. If you write to a regular file (SPIDER, IMAGIC, etc.) from 2 different machines at once, you will also often cause corruption.

Brief technical explanation

Details on the database are discussed in Eman2DataStorage

EMAN2 uses an embedded database to store information about a project, as well as much of the actual image data. This choice was made for a number of reasons including performance, flexibility, and dealing with projects with thousands of micrographs and hundreds of thousands of particles. 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 machines 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. Just like you wouldn't create a MySQL database and go moving around its database files wily-nily, you shouldn't mess with files in the EMAN2DB directory, particularly if there is an active cache.

EMAN2/DatabaseWarning (last edited 2014-04-22 14:49:36 by SteveLudtke)