Well, yes, there shouldn’t be, but that wasn’t what Andy suggested/asked.
Have you verified that nothing else is holding references to those files in any way e.g. lsof | grep /path/to/your/db And checked that only a single Java process is listed in the output? We don’t know your deployment environment, it could be some mundane background process (e.g. anti-virus, search indexer) running on your system, it could be a bug in the particular JVM you are using, or something else entirely but without any more details we can only guess at possibilities Another long shot is that it could be a hardware issue, if you’re running the database on an SSD it could be driver optimisation to not actually delete files until the holding process exits to avoid unnecessary write operations and prolong the life of the drive Rob From: Mikael Pesonen <[email protected]> Date: Monday, 11 September 2023 at 12:17 To: [email protected] <[email protected]> Subject: Re: Jena hangs on deleted files There should not be other processes accessing the files. When jena is restarted, space from deleted files is released. On 09/09/2023 18.56, Andy Seaborne wrote: > This situation could be related to the other issues you're reported > (corrupted node tables) if some other Linux process,not nece3ssarily > java) is accessing the files. > > A process holding them open will stop them becoming recyclable by the OS. > > Andy > > On 08/09/2023 13:09, Mikael Pesonen wrote: >> Just on a command line (dev system) >> >> /usr/bin/java -Xmx8G -jar fuseki-server.jar --update --port 3030 >> --config=../jena_config/fuseki_config.ttl >> >> >> On 08/09/2023 11.47, Andy Seaborne wrote: >>> In a container? As a VM? >>> >>> On 08/09/2023 07:36, Mikael Pesonen wrote: >>>> We are using Ubuntu. >>>> >>>> On Thu, 7 Sept 2023 at 16:33, Andy Seaborne <[email protected]> wrote: >>>> >>>>> Are the database files on a MS Windows filesystem? >>>>> >>>>> There is a long-standing Java issue that memory mapped files on MS >>>>> Windows do not get freed until the JVM exists. >>>>> >>>>> Various bugs in the OpenJDK bug database such as: >>>>> >>>>> https://bugs.openjdk.org/browse/JDK-4715154 >>>>> >>>>> Andy >>>>> >>>>> On 07/09/2023 13:06, Mikael Pesonen wrote: >>>>>> >>>>>> We used deleteOld param. The 50 gigs are ghost files that are >>>>>> deleted >>>>>> but not released, that's what I meant by hanging on deleted files. >>>>>> Restarting jena releases them and now for example freed 50 gigs >>>>>> of space. >>>>>> >>>>>> On 07/09/2023 15.02, Øyvind Gjesdal wrote: >>>>>>> What does the content of the tdb2 folder look like? >>>>>>> >>>>>>> I think compact by default never deletes the old data, but you have >>>>>>> parameters for making it delete the old content on completion. >>>>>>> >>>>>>> `--deleteOld` can be supplied to the tdb2.tdbcompact command >>>>>>> line tool >>>>>>> and >>>>>>> `?deleteOld=true` can be supplied to the administration api when >>>>>>> calling >>>>>>> compact >>>>>>> >>>>> https://jena.apache.org/documentation/fuseki2/fuseki-server-protocol.html#compact >>>>> >>>>>>> >>>>>>> You can also delete the Data-NNNN that isn't the latest one in the >>>>>>> database folder. >>>>>>> >>>>>>> Best regards, >>>>>>> Øyvind >>>>>>> >>>>>>> On Thu, Sep 7, 2023 at 1:33 PM Mikael Pesonen >>>>>>> <[email protected]> >>>>>>> wrote: >>>>>>> >>>>>>>> After a while 25 gigs of files on data folder becomes 80 gigs >>>>>>>> of disk >>>>>>>> usage because Jena (4.6.1) doen't release files. Same with >>>>>>>> compact. Is >>>>>>>> this fixed in newer versions? >>>>>>>> >>>>>> >>>>> >>>> >>
