On Einstein@Home we have "sticky" files, i.e. files that are used for several Tasks and thus stay on the participants machines for quite some time (some of them may be more than a year old).
Our S5R2 App suffers from various Client Errors some of which we could track to come from corrupted files, in particular the ones that are pretty old ("earth" and "sun" ephemeris files). We do some sanity checking of the files in the App, but all it can do if it finds a file being broken is to terminate with a client error.
Therefore we now enabled verify_files_on_app_start. With BOINC Core Client verion 5.6 or newer the Client will check the consistency (length, md5 sum) every time before starting a new task (and should download a file again if it's found to be corrupted).
So people observing mysterious client errors (especially if the first one happens after restarting in the middle of a task and every following task terminates with a client error in the very first seconds) are encouraged to upgrade to a recent Client.
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Client Errors & sticky files
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The main reason for the "penalty" has been eliminated in App version 4.24. Manually patching an App 4.24 or newer should give an effect below 5% in speed. See the old 4.24 thread.
If you think you need to, I suggest to patch the current Beta 4.30 and run it with the app_info.xml of the package on anonymous platform.
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