Writing small volume of data (Bytes-MBs) with sync (fsync()/fdatasync()/O_SYNC/O_DSYNC) is very common for RDBMS and is needed to guarantee durability. For transactional log files, sync happens per commit. For data files, sync happens at checkpoint etc. Typically RDBMS does syncing data very frequently. In this case, overwriting is much faster than appending for most filesystems/storages. Overwrit