When analyzing a large number of trajectory files (~160) using multiple threads (~8), gorder v1.4.1 exits with a ReadTrajError::FileNotFound error, e.g.:
error: file '../3_md/storage/md0146.xtc' was not found or could not be read as a trajectory file
On rerun, a different file is reported as unreadable. The files themselves appear valid - molly reads them without error and molly --info returns correct trajectory properties.
This happens because we are hitting a file descriptor limit. On Linux, this can be avoided by setting this limit to a higher value, e.g. ulimit -n 4096.
When analyzing a large number of trajectory files (~160) using multiple threads (~8),
gorder v1.4.1exits with aReadTrajError::FileNotFounderror, e.g.:On rerun, a different file is reported as unreadable. The files themselves appear valid -
mollyreads them without error andmolly --inforeturns correct trajectory properties.This happens because we are hitting a file descriptor limit. On Linux, this can be avoided by setting this limit to a higher value, e.g.
ulimit -n 4096.