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NPE in Basex8.4.4

Monday, 1 August 2016 · 7 messages
PB
Panagiotis Bailis1 Aug 2016 12:37 #
Hi all, I am using Basex 8.4.4 through the JAVA API and I noticed quite a few occurrences of the following NPE and AIOOB exceptions in the logs: ------------------------------------------------------------------------
java.lang.NullPointerException
        at org.basex.data.DiskData.write(DiskData.java:126)
        at org.basex.data.DiskData.close(DiskData.java:140)
        at org.basex.core.Datas.close(Datas.java:84)
        at org.basex.core.Context.close(Context.java:155)
------------------------------------------------------------------------ org.basex.core.BaseXException: Improper use? Potential bug? Your feedback is welcome: Contact: basex-talk at mailman.uni-konstanz.de Version: BaseX 8.4.4 Java: Oracle Corporation, 1.8.0_66 OS: Linux, amd64 Stack Trace: java.lang.NullPointerException at org.basex.data.DiskData.write(DiskData.java:120) at org.basex.data.DiskData.flush(DiskData.java:235) at org.basex.data.DiskData.finishUpdate(DiskData.java:225) at org.basex.core.Command.finishUpdate(Command.java:341) at org.basex.core.cmd.ACreate.finishUpdate(ACreate.java:87) at org.basex.core.cmd.Replace.run(Replace.java:59) at org.basex.core.Command.run(Command.java:398) at org.basex.core.Command.execute(Command.java:100) at org.basex.core.Command.execute(Command.java:123) ------------------------------------------------------------------------ org.basex.core.BaseXException: Improper use? Potential bug? Your feedback is welcome: Contact: basex-talk at mailman.uni-konstanz.de Version: BaseX 8.4.4 Java: Oracle Corporation, 1.8.0_66 OS: Linux, amd64 Stack Trace:
java.lang.ArrayIndexOutOfBoundsException: 0
    at org.basex.io.random.TableDiskAccess.fpre(TableDiskAccess.java:501)
    at org.basex.io.random.TableDiskAccess.setPage(TableDiskAccess.java:473)
    at org.basex.io.random.TableDiskAccess.readPage(TableDiskAccess.java:482)
    at org.basex.io.random.TableDiskAccess.insert(TableDiskAccess.java:316)
    at org.basex.data.Data.insert(Data.java:901)
    at org.basex.data.Data.insert(Data.java:727)
    at org.basex.query.up.atomic.Insert.apply(Insert.java:44)
    at org.basex.query.up.atomic.AtomicUpdateCache.applyUpdates(AtomicUpdateCache.java:297)
    at org.basex.query.up.atomic.AtomicUpdateCache.execute(AtomicUpdateCache.java:281)
    at org.basex.core.cmd.Replace.replace(Replace.java:106)
    at org.basex.core.cmd.Replace.run(Replace.java:57)
    at org.basex.core.Command.run(Command.java:398)
    at org.basex.core.Command.execute(Command.java:100)
    at org.basex.core.Command.execute(Command.java:123)
------------------------------------------------------------------------ The collection files are stored to NFS, but the above exceptions seem to appear at random while trying to update an existing collection. Unfortunately, I do not have a clear pattern as to what causes the above, or any errors during initialization. *Thank you* in advance, Panagiotis
CG
Christian Grün1 Aug 2016 12:46 #
Hi Panagiotis,
Quoted text · Panagiotis Bailis · 2 lines
> Unfortunately, I do not have a clear pattern as to what causes the above, or > any errors during initialization.
Difficult to say what might be the problem. Are you working with multiple threads? If there’s any chance for you to provide us with a reproducible example, feel free to do so. Christian
Quoted text · Panagiotis Bailis · 72 lines
On Mon, Aug 1, 2016 at 12:37 PM, Panagiotis Bailis <pmpailis at gmail.com> wrote: > Hi all, > > I am using Basex 8.4.4 through the JAVA API and I noticed quite a few > occurrences of the following NPE and AIOOB exceptions in the logs: > > ------------------------------------------------------------------------ > > java.lang.NullPointerException > at org.basex.data.DiskData.write(DiskData.java:126) > at org.basex.data.DiskData.close(DiskData.java:140) > at org.basex.core.Datas.close(Datas.java:84) > at org.basex.core.Context.close(Context.java:155) > > ------------------------------------------------------------------------ > > org.basex.core.BaseXException: Improper use? Potential bug? Your feedback is > welcome: > Contact: basex-talk at mailman.uni-konstanz.de > Version: BaseX 8.4.4 > Java: Oracle Corporation, 1.8.0_66 > OS: Linux, amd64 > Stack Trace: > java.lang.NullPointerException > at org.basex.data.DiskData.write(DiskData.java:120) > at org.basex.data.DiskData.flush(DiskData.java:235) > at org.basex.data.DiskData.finishUpdate(DiskData.java:225) > at org.basex.core.Command.finishUpdate(Command.java:341) > at org.basex.core.cmd.ACreate.finishUpdate(ACreate.java:87) > at org.basex.core.cmd.Replace.run(Replace.java:59) > at org.basex.core.Command.run(Command.java:398) > at org.basex.core.Command.execute(Command.java:100) > at org.basex.core.Command.execute(Command.java:123) > > ------------------------------------------------------------------------ > > org.basex.core.BaseXException: Improper use? Potential bug? Your feedback is > welcome: > Contact: basex-talk at mailman.uni-konstanz.de > Version: BaseX 8.4.4 > Java: Oracle Corporation, 1.8.0_66 > OS: Linux, amd64 > Stack Trace: > java.lang.ArrayIndexOutOfBoundsException: 0 > at org.basex.io.random.TableDiskAccess.fpre(TableDiskAccess.java:501) > at org.basex.io.random.TableDiskAccess.setPage(TableDiskAccess.java:473) > at > org.basex.io.random.TableDiskAccess.readPage(TableDiskAccess.java:482) > at org.basex.io.random.TableDiskAccess.insert(TableDiskAccess.java:316) > at org.basex.data.Data.insert(Data.java:901) > at org.basex.data.Data.insert(Data.java:727) > at org.basex.query.up.atomic.Insert.apply(Insert.java:44) > at > org.basex.query.up.atomic.AtomicUpdateCache.applyUpdates(AtomicUpdateCache.java:297) > at > org.basex.query.up.atomic.AtomicUpdateCache.execute(AtomicUpdateCache.java:281) > at org.basex.core.cmd.Replace.replace(Replace.java:106) > at org.basex.core.cmd.Replace.run(Replace.java:57) > at org.basex.core.Command.run(Command.java:398) > at org.basex.core.Command.execute(Command.java:100) > at org.basex.core.Command.execute(Command.java:123) > > ------------------------------------------------------------------------ > > The collection files are stored to NFS, but the above exceptions seem to > appear at random while trying to update an existing collection. > Unfortunately, I do not have a clear pattern as to what causes the above, or > any errors during initialization. > > > Thank you in advance, > Panagiotis
PB
Panagiotis Bailis1 Aug 2016 12:56 #
Hi Christian, Thanks for the quick reply! No, all the ADD/REPLACE/DELETE operations are executed sequentially by a single thread. For example, even if I try to add 2000 documents the above exceptions might occur after the first 1000 have been updated successfully. If I do manage to create a reproducible example, I will of course share it with the community. Could this instability be simply related to NFS? What kind of handling/workaround would you suggest? Thanks, Panagiotis
Quoted text · Christian Grün · 98 lines
On 1 August 2016 at 13:46, Christian Grün <christian.gruen at gmail.com> wrote: > Hi Panagiotis, > > > Unfortunately, I do not have a clear pattern as to what causes the > above, or > > any errors during initialization. > > Difficult to say what might be the problem. Are you working with > multiple threads? > > If there’s any chance for you to provide us with a reproducible > example, feel free to do so. > > Christian > > > > On Mon, Aug 1, 2016 at 12:37 PM, Panagiotis Bailis <pmpailis at gmail.com> > wrote: > > Hi all, > > > > I am using Basex 8.4.4 through the JAVA API and I noticed quite a few > > occurrences of the following NPE and AIOOB exceptions in the logs: > > > > ------------------------------------------------------------------------ > > > > java.lang.NullPointerException > > at org.basex.data.DiskData.write(DiskData.java:126) > > at org.basex.data.DiskData.close(DiskData.java:140) > > at org.basex.core.Datas.close(Datas.java:84) > > at org.basex.core.Context.close(Context.java:155) > > > > ------------------------------------------------------------------------ > > > > org.basex.core.BaseXException: Improper use? Potential bug? Your > feedback is > > welcome: > > Contact: basex-talk at mailman.uni-konstanz.de > > Version: BaseX 8.4.4 > > Java: Oracle Corporation, 1.8.0_66 > > OS: Linux, amd64 > > Stack Trace: > > java.lang.NullPointerException > > at org.basex.data.DiskData.write(DiskData.java:120) > > at org.basex.data.DiskData.flush(DiskData.java:235) > > at org.basex.data.DiskData.finishUpdate(DiskData.java:225) > > at org.basex.core.Command.finishUpdate(Command.java:341) > > at org.basex.core.cmd.ACreate.finishUpdate(ACreate.java:87) > > at org.basex.core.cmd.Replace.run(Replace.java:59) > > at org.basex.core.Command.run(Command.java:398) > > at org.basex.core.Command.execute(Command.java:100) > > at org.basex.core.Command.execute(Command.java:123) > > > > ------------------------------------------------------------------------ > > > > org.basex.core.BaseXException: Improper use? Potential bug? Your > feedback is > > welcome: > > Contact: basex-talk at mailman.uni-konstanz.de > > Version: BaseX 8.4.4 > > Java: Oracle Corporation, 1.8.0_66 > > OS: Linux, amd64 > > Stack Trace: > > java.lang.ArrayIndexOutOfBoundsException: 0 > > at org.basex.io.random.TableDiskAccess.fpre(TableDiskAccess.java:501) > > at > org.basex.io.random.TableDiskAccess.setPage(TableDiskAccess.java:473) > > at > > org.basex.io.random.TableDiskAccess.readPage(TableDiskAccess.java:482) > > at > org.basex.io.random.TableDiskAccess.insert(TableDiskAccess.java:316) > > at org.basex.data.Data.insert(Data.java:901) > > at org.basex.data.Data.insert(Data.java:727) > > at org.basex.query.up.atomic.Insert.apply(Insert.java:44) > > at > > > org.basex.query.up.atomic.AtomicUpdateCache.applyUpdates(AtomicUpdateCache.java:297) > > at > > > org.basex.query.up.atomic.AtomicUpdateCache.execute(AtomicUpdateCache.java:281) > > at org.basex.core.cmd.Replace.replace(Replace.java:106) > > at org.basex.core.cmd.Replace.run(Replace.java:57) > > at org.basex.core.Command.run(Command.java:398) > > at org.basex.core.Command.execute(Command.java:100) > > at org.basex.core.Command.execute(Command.java:123) > > > > ------------------------------------------------------------------------ > > > > The collection files are stored to NFS, but the above exceptions seem to > > appear at random while trying to update an existing collection. > > Unfortunately, I do not have a clear pattern as to what causes the > above, or > > any errors during initialization. > > > > > > Thank you in advance, > > Panagiotis >
CG
Christian Grün1 Aug 2016 13:04 #
Quoted text · Panagiotis Bailis · 1 line
> Could this instability be simply related to NFS?
Well, it could be ;) I haven’t experienced a similar pattern so far (maybe someone else on the list did), so I am afraid I cannot really help. Did you try BaseX 8.5.2?
Quoted text · Christian Grün · 101 lines
> On 1 August 2016 at 13:46, Christian Grün <christian.gruen at gmail.com> wrote: >> >> Hi Panagiotis, >> >> > Unfortunately, I do not have a clear pattern as to what causes the >> > above, or >> > any errors during initialization. >> >> Difficult to say what might be the problem. Are you working with >> multiple threads? >> >> If there’s any chance for you to provide us with a reproducible >> example, feel free to do so. >> >> Christian >> >> >> >> On Mon, Aug 1, 2016 at 12:37 PM, Panagiotis Bailis <pmpailis at gmail.com> >> wrote: >> > Hi all, >> > >> > I am using Basex 8.4.4 through the JAVA API and I noticed quite a few >> > occurrences of the following NPE and AIOOB exceptions in the logs: >> > >> > ------------------------------------------------------------------------ >> > >> > java.lang.NullPointerException >> > at org.basex.data.DiskData.write(DiskData.java:126) >> > at org.basex.data.DiskData.close(DiskData.java:140) >> > at org.basex.core.Datas.close(Datas.java:84) >> > at org.basex.core.Context.close(Context.java:155) >> > >> > ------------------------------------------------------------------------ >> > >> > org.basex.core.BaseXException: Improper use? Potential bug? Your >> > feedback is >> > welcome: >> > Contact: basex-talk at mailman.uni-konstanz.de >> > Version: BaseX 8.4.4 >> > Java: Oracle Corporation, 1.8.0_66 >> > OS: Linux, amd64 >> > Stack Trace: >> > java.lang.NullPointerException >> > at org.basex.data.DiskData.write(DiskData.java:120) >> > at org.basex.data.DiskData.flush(DiskData.java:235) >> > at org.basex.data.DiskData.finishUpdate(DiskData.java:225) >> > at org.basex.core.Command.finishUpdate(Command.java:341) >> > at org.basex.core.cmd.ACreate.finishUpdate(ACreate.java:87) >> > at org.basex.core.cmd.Replace.run(Replace.java:59) >> > at org.basex.core.Command.run(Command.java:398) >> > at org.basex.core.Command.execute(Command.java:100) >> > at org.basex.core.Command.execute(Command.java:123) >> > >> > ------------------------------------------------------------------------ >> > >> > org.basex.core.BaseXException: Improper use? Potential bug? Your >> > feedback is >> > welcome: >> > Contact: basex-talk at mailman.uni-konstanz.de >> > Version: BaseX 8.4.4 >> > Java: Oracle Corporation, 1.8.0_66 >> > OS: Linux, amd64 >> > Stack Trace: >> > java.lang.ArrayIndexOutOfBoundsException: 0 >> > at >> > org.basex.io.random.TableDiskAccess.fpre(TableDiskAccess.java:501) >> > at >> > org.basex.io.random.TableDiskAccess.setPage(TableDiskAccess.java:473) >> > at >> > org.basex.io.random.TableDiskAccess.readPage(TableDiskAccess.java:482) >> > at >> > org.basex.io.random.TableDiskAccess.insert(TableDiskAccess.java:316) >> > at org.basex.data.Data.insert(Data.java:901) >> > at org.basex.data.Data.insert(Data.java:727) >> > at org.basex.query.up.atomic.Insert.apply(Insert.java:44) >> > at >> > >> > org.basex.query.up.atomic.AtomicUpdateCache.applyUpdates(AtomicUpdateCache.java:297) >> > at >> > >> > org.basex.query.up.atomic.AtomicUpdateCache.execute(AtomicUpdateCache.java:281) >> > at org.basex.core.cmd.Replace.replace(Replace.java:106) >> > at org.basex.core.cmd.Replace.run(Replace.java:57) >> > at org.basex.core.Command.run(Command.java:398) >> > at org.basex.core.Command.execute(Command.java:100) >> > at org.basex.core.Command.execute(Command.java:123) >> > >> > ------------------------------------------------------------------------ >> > >> > The collection files are stored to NFS, but the above exceptions seem to >> > appear at random while trying to update an existing collection. >> > Unfortunately, I do not have a clear pattern as to what causes the >> > above, or >> > any errors during initialization. >> > >> > >> > Thank you in advance, >> > Panagiotis > >
PB
Panagiotis Bailis1 Aug 2016 13:14 #
Quoted text · Christian Grün · 1 line
> Did you try BaseX 8.5.2?
Not yet. Planning to upgrade within the week, but if I recall correctly the same errors were also appearing (sparingly) in BaseX 8.3.1. Once I upgrade to the newest version, should the same issues arise again, I'll let you know.
Quoted text · Christian Grün · 119 lines
On 1 August 2016 at 14:04, Christian Grün <christian.gruen at gmail.com> wrote: > > Could this instability be simply related to NFS? > > Well, it could be ;) I haven’t experienced a similar pattern so far > (maybe someone else on the list did), so I am afraid I cannot really > help. Did you try BaseX 8.5.2? > > > > > On 1 August 2016 at 13:46, Christian Grün <christian.gruen at gmail.com> > wrote: > >> > >> Hi Panagiotis, > >> > >> > Unfortunately, I do not have a clear pattern as to what causes the > >> > above, or > >> > any errors during initialization. > >> > >> Difficult to say what might be the problem. Are you working with > >> multiple threads? > >> > >> If there’s any chance for you to provide us with a reproducible > >> example, feel free to do so. > >> > >> Christian > >> > >> > >> > >> On Mon, Aug 1, 2016 at 12:37 PM, Panagiotis Bailis <pmpailis at gmail.com> > >> wrote: > >> > Hi all, > >> > > >> > I am using Basex 8.4.4 through the JAVA API and I noticed quite a few > >> > occurrences of the following NPE and AIOOB exceptions in the logs: > >> > > >> > > ------------------------------------------------------------------------ > >> > > >> > java.lang.NullPointerException > >> > at org.basex.data.DiskData.write(DiskData.java:126) > >> > at org.basex.data.DiskData.close(DiskData.java:140) > >> > at org.basex.core.Datas.close(Datas.java:84) > >> > at org.basex.core.Context.close(Context.java:155) > >> > > >> > > ------------------------------------------------------------------------ > >> > > >> > org.basex.core.BaseXException: Improper use? Potential bug? Your > >> > feedback is > >> > welcome: > >> > Contact: basex-talk at mailman.uni-konstanz.de > >> > Version: BaseX 8.4.4 > >> > Java: Oracle Corporation, 1.8.0_66 > >> > OS: Linux, amd64 > >> > Stack Trace: > >> > java.lang.NullPointerException > >> > at org.basex.data.DiskData.write(DiskData.java:120) > >> > at org.basex.data.DiskData.flush(DiskData.java:235) > >> > at org.basex.data.DiskData.finishUpdate(DiskData.java:225) > >> > at org.basex.core.Command.finishUpdate(Command.java:341) > >> > at org.basex.core.cmd.ACreate.finishUpdate(ACreate.java:87) > >> > at org.basex.core.cmd.Replace.run(Replace.java:59) > >> > at org.basex.core.Command.run(Command.java:398) > >> > at org.basex.core.Command.execute(Command.java:100) > >> > at org.basex.core.Command.execute(Command.java:123) > >> > > >> > > ------------------------------------------------------------------------ > >> > > >> > org.basex.core.BaseXException: Improper use? Potential bug? Your > >> > feedback is > >> > welcome: > >> > Contact: basex-talk at mailman.uni-konstanz.de > >> > Version: BaseX 8.4.4 > >> > Java: Oracle Corporation, 1.8.0_66 > >> > OS: Linux, amd64 > >> > Stack Trace: > >> > java.lang.ArrayIndexOutOfBoundsException: 0 > >> > at > >> > org.basex.io.random.TableDiskAccess.fpre(TableDiskAccess.java:501) > >> > at > >> > org.basex.io.random.TableDiskAccess.setPage(TableDiskAccess.java:473) > >> > at > >> > org.basex.io.random.TableDiskAccess.readPage(TableDiskAccess.java:482) > >> > at > >> > org.basex.io.random.TableDiskAccess.insert(TableDiskAccess.java:316) > >> > at org.basex.data.Data.insert(Data.java:901) > >> > at org.basex.data.Data.insert(Data.java:727) > >> > at org.basex.query.up.atomic.Insert.apply(Insert.java:44) > >> > at > >> > > >> > > org.basex.query.up.atomic.AtomicUpdateCache.applyUpdates(AtomicUpdateCache.java:297) > >> > at > >> > > >> > > org.basex.query.up.atomic.AtomicUpdateCache.execute(AtomicUpdateCache.java:281) > >> > at org.basex.core.cmd.Replace.replace(Replace.java:106) > >> > at org.basex.core.cmd.Replace.run(Replace.java:57) > >> > at org.basex.core.Command.run(Command.java:398) > >> > at org.basex.core.Command.execute(Command.java:100) > >> > at org.basex.core.Command.execute(Command.java:123) > >> > > >> > > ------------------------------------------------------------------------ > >> > > >> > The collection files are stored to NFS, but the above exceptions seem > to > >> > appear at random while trying to update an existing collection. > >> > Unfortunately, I do not have a clear pattern as to what causes the > >> > above, or > >> > any errors during initialization. > >> > > >> > > >> > Thank you in advance, > >> > Panagiotis > > > > >
LV
Lizzi, Vincentin reply to Christian Grün, 1 Aug 2016, 13:041 Aug 2016 13:16 #
This sounds similar to a problem I ran into previously, when adding several thousand documents an exception would occur after a somewhat consistent number of documents were added. The number might have been 1000. I suspected the antivirus program might be interfering with BaseX, though couldn't confirm this was the problem, and ran the import on a different machine that had a fresh install of Windows. This was over a year ago, and I don't recall the specifics. Maybe this is helpful in some way. Vincent
Quoted text · basex-talk-bounces at mailman.uni-konstanz.de · 110 lines
From: basex-talk-bounces at mailman.uni-konstanz.de <basex-talk-bounces at mailman.uni-konstanz.de> on behalf of Christian Grün <christian.gruen at gmail.com> Sent: Monday, August 1, 2016 7:04:26 AM To: Panagiotis Bailis Cc: BaseX Subject: Re: [basex-talk] NPE in Basex8.4.4 > Could this instability be simply related to NFS? Well, it could be ;) I haven’t experienced a similar pattern so far (maybe someone else on the list did), so I am afraid I cannot really help. Did you try BaseX 8.5.2? > On 1 August 2016 at 13:46, Christian Grün <christian.gruen at gmail.com> wrote: >> >> Hi Panagiotis, >> >> > Unfortunately, I do not have a clear pattern as to what causes the >> > above, or >> > any errors during initialization. >> >> Difficult to say what might be the problem. Are you working with >> multiple threads? >> >> If there’s any chance for you to provide us with a reproducible >> example, feel free to do so. >> >> Christian >> >> >> >> On Mon, Aug 1, 2016 at 12:37 PM, Panagiotis Bailis <pmpailis at gmail.com> >> wrote: >> > Hi all, >> > >> > I am using Basex 8.4.4 through the JAVA API and I noticed quite a few >> > occurrences of the following NPE and AIOOB exceptions in the logs: >> > >> > ------------------------------------------------------------------------ >> > >> > java.lang.NullPointerException >> > at org.basex.data.DiskData.write(DiskData.java:126) >> > at org.basex.data.DiskData.close(DiskData.java:140) >> > at org.basex.core.Datas.close(Datas.java:84) >> > at org.basex.core.Context.close(Context.java:155) >> > >> > ------------------------------------------------------------------------ >> > >> > org.basex.core.BaseXException: Improper use? Potential bug? Your >> > feedback is >> > welcome: >> > Contact: basex-talk at mailman.uni-konstanz.de >> > Version: BaseX 8.4.4 >> > Java: Oracle Corporation, 1.8.0_66 >> > OS: Linux, amd64 >> > Stack Trace: >> > java.lang.NullPointerException >> > at org.basex.data.DiskData.write(DiskData.java:120) >> > at org.basex.data.DiskData.flush(DiskData.java:235) >> > at org.basex.data.DiskData.finishUpdate(DiskData.java:225) >> > at org.basex.core.Command.finishUpdate(Command.java:341) >> > at org.basex.core.cmd.ACreate.finishUpdate(ACreate.java:87) >> > at org.basex.core.cmd.Replace.run(Replace.java:59) >> > at org.basex.core.Command.run(Command.java:398) >> > at org.basex.core.Command.execute(Command.java:100) >> > at org.basex.core.Command.execute(Command.java:123) >> > >> > ------------------------------------------------------------------------ >> > >> > org.basex.core.BaseXException: Improper use? Potential bug? Your >> > feedback is >> > welcome: >> > Contact: basex-talk at mailman.uni-konstanz.de >> > Version: BaseX 8.4.4 >> > Java: Oracle Corporation, 1.8.0_66 >> > OS: Linux, amd64 >> > Stack Trace: >> > java.lang.ArrayIndexOutOfBoundsException: 0 >> > at >> > org.basex.io.random.TableDiskAccess.fpre(TableDiskAccess.java:501) >> > at >> > org.basex.io.random.TableDiskAccess.setPage(TableDiskAccess.java:473) >> > at >> > org.basex.io.random.TableDiskAccess.readPage(TableDiskAccess.java:482) >> > at >> > org.basex.io.random.TableDiskAccess.insert(TableDiskAccess.java:316) >> > at org.basex.data.Data.insert(Data.java:901) >> > at org.basex.data.Data.insert(Data.java:727) >> > at org.basex.query.up.atomic.Insert.apply(Insert.java:44) >> > at >> > >> > org.basex.query.up.atomic.AtomicUpdateCache.applyUpdates(AtomicUpdateCache.java:297) >> > at >> > >> > org.basex.query.up.atomic.AtomicUpdateCache.execute(AtomicUpdateCache.java:281) >> > at org.basex.core.cmd.Replace.replace(Replace.java:106) >> > at org.basex.core.cmd.Replace.run(Replace.java:57) >> > at org.basex.core.Command.run(Command.java:398) >> > at org.basex.core.Command.execute(Command.java:100) >> > at org.basex.core.Command.execute(Command.java:123) >> > >> > ------------------------------------------------------------------------ >> > >> > The collection files are stored to NFS, but the above exceptions seem to >> > appear at random while trying to update an existing collection. >> > Unfortunately, I do not have a clear pattern as to what causes the >> > above, or >> > any errors during initialization. >> > >> > >> > Thank you in advance, >> > Panagiotis > >
PB
Panagiotis Bailis1 Aug 2016 13:35 #
Hi Vincent, The difference in this case is that there doesn't appear to be some sort of consistency between the number of documents or the specifics of each exception (which is rather annoying!). However, the next step could be somewhat similar to yours, in the sense that I could move from the NFS to the local FS, in order to simply see if the problem re-occurs. Thanks, Panagiotis
Quoted text · Vincent · 142 lines
On 1 August 2016 at 14:16, Lizzi, Vincent < Vincent.Lizzi at taylorandfrancis.com> wrote: > This sounds similar to a problem I ran into previously, when adding > several thousand documents an exception would occur after a somewhat > consistent number of documents were added. The number might have been 1000. > I suspected the antivirus program might be interfering with BaseX, though > couldn't confirm this was the problem, and ran the import on a different > machine that had a fresh install of Windows. This was over a year ago, and > I don't recall the specifics. Maybe this is helpful in some way. > > > Vincent > > > ------------------------------ > *From:* basex-talk-bounces at mailman.uni-konstanz.de < > basex-talk-bounces at mailman.uni-konstanz.de> on behalf of Christian Grün < > christian.gruen at gmail.com> > *Sent:* Monday, August 1, 2016 7:04:26 AM > *To:* Panagiotis Bailis > *Cc:* BaseX > *Subject:* Re: [basex-talk] NPE in Basex8.4.4 > > > Could this instability be simply related to NFS? > > Well, it could be ;) I haven’t experienced a similar pattern so far > (maybe someone else on the list did), so I am afraid I cannot really > help. Did you try BaseX 8.5.2? > > > > > On 1 August 2016 at 13:46, Christian Grün <christian.gruen at gmail.com> > wrote: > >> > >> Hi Panagiotis, > >> > >> > Unfortunately, I do not have a clear pattern as to what causes the > >> > above, or > >> > any errors during initialization. > >> > >> Difficult to say what might be the problem. Are you working with > >> multiple threads? > >> > >> If there’s any chance for you to provide us with a reproducible > >> example, feel free to do so. > >> > >> Christian > >> > >> > >> > >> On Mon, Aug 1, 2016 at 12:37 PM, Panagiotis Bailis <pmpailis at gmail.com> > >> wrote: > >> > Hi all, > >> > > >> > I am using Basex 8.4.4 through the JAVA API and I noticed quite a few > >> > occurrences of the following NPE and AIOOB exceptions in the logs: > >> > > >> > > ------------------------------------------------------------------------ > >> > > >> > java.lang.NullPointerException > >> > at org.basex.data.DiskData.write(DiskData.java:126) > >> > at org.basex.data.DiskData.close(DiskData.java:140) > >> > at org.basex.core.Datas.close(Datas.java:84) > >> > at org.basex.core.Context.close(Context.java:155) > >> > > >> > > ------------------------------------------------------------------------ > >> > > >> > org.basex.core.BaseXException: Improper use? Potential bug? Your > >> > feedback is > >> > welcome: > >> > Contact: basex-talk at mailman.uni-konstanz.de > >> > Version: BaseX 8.4.4 > >> > Java: Oracle Corporation, 1.8.0_66 > >> > OS: Linux, amd64 > >> > Stack Trace: > >> > java.lang.NullPointerException > >> > at org.basex.data.DiskData.write(DiskData.java:120) > >> > at org.basex.data.DiskData.flush(DiskData.java:235) > >> > at org.basex.data.DiskData.finishUpdate(DiskData.java:225) > >> > at org.basex.core.Command.finishUpdate(Command.java:341) > >> > at org.basex.core.cmd.ACreate.finishUpdate(ACreate.java:87) > >> > at org.basex.core.cmd.Replace.run(Replace.java:59) > >> > at org.basex.core.Command.run(Command.java:398) > >> > at org.basex.core.Command.execute(Command.java:100) > >> > at org.basex.core.Command.execute(Command.java:123) > >> > > >> > > ------------------------------------------------------------------------ > >> > > >> > org.basex.core.BaseXException: Improper use? Potential bug? Your > >> > feedback is > >> > welcome: > >> > Contact: basex-talk at mailman.uni-konstanz.de > >> > Version: BaseX 8.4.4 > >> > Java: Oracle Corporation, 1.8.0_66 > >> > OS: Linux, amd64 > >> > Stack Trace: > >> > java.lang.ArrayIndexOutOfBoundsException: 0 > >> > at > >> > org.basex.io.random.TableDiskAccess.fpre(TableDiskAccess.java:501) > >> > at > >> > org.basex.io.random.TableDiskAccess.setPage(TableDiskAccess.java:473) > >> > at > >> > org.basex.io.random.TableDiskAccess.readPage(TableDiskAccess.java:482) > >> > at > >> > org.basex.io.random.TableDiskAccess.insert(TableDiskAccess.java:316) > >> > at org.basex.data.Data.insert(Data.java:901) > >> > at org.basex.data.Data.insert(Data.java:727) > >> > at org.basex.query.up.atomic.Insert.apply(Insert.java:44) > >> > at > >> > > >> > > org.basex.query.up.atomic.AtomicUpdateCache.applyUpdates(AtomicUpdateCache.java:297) > >> > at > >> > > >> > > org.basex.query.up.atomic.AtomicUpdateCache.execute(AtomicUpdateCache.java:281) > >> > at org.basex.core.cmd.Replace.replace(Replace.java:106) > >> > at org.basex.core.cmd.Replace.run(Replace.java:57) > >> > at org.basex.core.Command.run(Command.java:398) > >> > at org.basex.core.Command.execute(Command.java:100) > >> > at org.basex.core.Command.execute(Command.java:123) > >> > > >> > > ------------------------------------------------------------------------ > >> > > >> > The collection files are stored to NFS, but the above exceptions seem > to > >> > appear at random while trying to update an existing collection. > >> > Unfortunately, I do not have a clear pattern as to what causes the > >> > above, or > >> > any errors during initialization. > >> > > >> > > >> > Thank you in advance, > >> > Panagiotis > > > > > >

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