Re: [basex-talk] db:copy

[Ветошкин Владимир]

Yes, Result of the server instance:java.vm.compressedOopsMode: 32-bit java.vm.info: mixed mode, sharing java.vm.name: OpenJDK 64-Bit Server VM java.vm.specification.name: Java Virtual Machine Specification java.vm.specification.vendor: Oracle Corporation java.vm.specification.version: 12 java.vm.vendor: Azul Systems, Inc. java.vm.version: 12.0.2+3 Result of the standalone instance:java.vm.compressedOopsMode: 32-bitjava.vm.info: mixed mode, sharingjava.vm.name: OpenJDK 64-Bit Server VMjava.vm.specification.name: Java Virtual Machine Specificationjava.vm.specification.vendor: Oracle Corporationjava.vm.specification.version: 12java.vm.vendor: Azul Systems, Inc.java.vm.version: 12.0.2+3   16.11.2023, 15:40, "Christian Grün" :Are they use different methods to copy databases? Or that jdk bug only? It’s exactly the same; when db:copy is called, the function isn’t aware of whether it has been called by a server or standalone/client instance. Are you sure that both the server and the standalone version of BaseX use the same JRE? You can e.g. check this with the following query: for $p in proc:property-names()[starts-with(., 'java.vm.')]return $p || ': ' || proc:property($p)16.11.2023, 15:00, "Christian Grün" :Hi, this definitely looks like a bug in the JDK context. What happens if you upgrade your JDK to a newer version?Best, Christian  On Thu, Nov 16, 2023 at 12:56 PM Ветошкин Владимир  wrote: Hi everyone. Since I have changed jdk version to 12 (azul) - I get error, when I copy database (db:copy).It's only in basexserver. When I run basex - everything is ok. Error:Improper use? Potential bug? Your feedback is welcome: Contact: basex-talk@mailman.uni-konstanz.de Version: BaseX 9.1.2 Java: Azul Systems, Inc., 12.0.2 OS: Linux, amd64 Stack Trace: java.lang.NoClassDefFoundError: Could not initialize class sun.nio.fs.UnixCopyFile at java.base/sun.nio.fs.UnixFileSystemProvider.copy(UnixFileSystemProvider.java:258) at java.base/java.nio.file.Files.copy(Files.java:1297) at org.basex.io.IOFile.copyTo(IOFile.java:319) at org.basex.core.cmd.Copy.copy(Copy.java:83) at org.basex.query.up.primitives.name.DBCopy.apply(DBCopy.java:43) at org.basex.query.up.NameUpdates.apply(NameUpdates.java:58) at org.basex.query.up.ContextModifier.apply(ContextModifier.java:132) at org.basex.query.up.Updates.apply(Updates.java:156) at org.basex.query.QueryContext.iter(QueryContext.java:351) at org.basex.query.QueryProcessor.iter(QueryProcessor.java:90) at org.basex.core.cmd.AQuery.query(AQuery.java:109) at org.basex.core.cmd.XQuery.run(XQuery.java:22) at org.basex.core.Command.run(Command.java:257) at org.basex.core.Command.execute(Command.java:93) at org.basex.server.ClientListener.run(ClientListener.java:140)-- С уважением,Ветошкин Владимир Владимирович   -- С уважением,Ветошкин Владимир Владимирович   -- С уважением,Ветошкин Владимир Владимирович 

Re: [basex-talk] WG: JAVA Performance Issue under RH8 by using BASEX with NFS system

[Christian Grün]

Hi Andre,

It’s probably out of scope to give a reasonable response to your questions
via the public mailing list (feel free to ask for our commercial services),
but here’s a quick shot:

>
>- why is the whole database read even for a "small" query ? (looks
>like a missing index or bad execution plan.. ?)
>
> It may depend a lot on what the query does. Could you give us an example
for a typical “small query”?

>
>- The UNIX related question (maybe it's worth opening a ticket with
>   redhat)
>
> I guess so. I’m sorry I have no in-depth knowledge on why RHL 6 and 8
behaves differently here.

Have you already tried different JDK versions/distributions?

Best,
Christian

Re: [basex-talk] db:copy

[Christian Grün]

>
> Are they use different methods to copy databases? Or that jdk bug only?
>

It’s exactly the same; when db:copy is called, the function isn’t aware of
whether it has been called by a server or standalone/client instance.

Are you sure that both the server and the standalone version of BaseX use
the same JRE? You can e.g. check this with the following query:

for $p in proc:property-names()[starts-with(., 'java.vm.')]
return $p || ': ' || proc:property($p)




> 16.11.2023, 15:00, "Christian Grün" :
>
> Hi, this definitely looks like a bug in the JDK context. What happens if
> you upgrade your JDK to a newer version?
> Best, Christian
>
>
> On Thu, Nov 16, 2023 at 12:56 PM Ветошкин Владимир 
> wrote:
>
>
> Hi everyone.
>
> Since I have changed jdk version to 12 (azul) - I get error, when I copy
> database (db:copy).
> It's only in basexserver. When I run basex - everything is ok.
>
> Error:
> Improper use? Potential bug? Your feedback is welcome: Contact:
> basex-talk@mailman.uni-konstanz.de Version: BaseX 9.1.2 Java: Azul
> Systems, Inc., 12.0.2 OS: Linux, amd64 Stack Trace:
> java.lang.NoClassDefFoundError: Could not initialize class
> sun.nio.fs.UnixCopyFile at
> java.base/sun.nio.fs.UnixFileSystemProvider.copy(UnixFileSystemProvider.java:258)
> at java.base/java.nio.file.Files.copy(Files.java:1297) at
> org.basex.io.IOFile.copyTo(IOFile.java:319) at
> org.basex.core.cmd.Copy.copy(Copy.java:83) at
> org.basex.query.up.primitives.name.DBCopy.apply(DBCopy.java:43) at
> org.basex.query.up.NameUpdates.apply(NameUpdates.java:58) at
> org.basex.query.up.ContextModifier.apply(ContextModifier.java:132) at
> org.basex.query.up.Updates.apply(Updates.java:156) at
> org.basex.query.QueryContext.iter(QueryContext.java:351) at
> org.basex.query.QueryProcessor.iter(QueryProcessor.java:90) at
> org.basex.core.cmd.AQuery.query(AQuery.java:109) at
> org.basex.core.cmd.XQuery.run(XQuery.java:22) at
> org.basex.core.Command.run(Command.java:257) at
> org.basex.core.Command.execute(Command.java:93) at
> org.basex.server.ClientListener.run(ClientListener.java:140)
> --
> С уважением,
> Ветошкин Владимир Владимирович
>
>
>
>
> --
> С уважением,
> Ветошкин Владимир Владимирович
>
>

Re: [basex-talk] WG: JAVA Performance Issue under RH8 by using BASEX with NFS system

[Gerbatsch, Andre]

bounced by the List, re-sent after subscription
--

Hello Christian and team,

I am from IT and helped Michael to analyze and reproduce the problem.
I would like to describe what we found and maybe you have some Ideas what we 
can optimize. Any advice will be helpful 

The questions are:

  *   why is the whole database read even for a "small" query ? (looks like a 
missing index or bad execution plan.. ?)
 *   are there some tricks / best practices to optimize ?
  *   why do we use 4K blocksize performing a seek() before every read even for 
sequential reads from the database file ?
 *   can the blocksize be changed ? does it make sense ?

The UNIX related question (maybe it's worth opening a ticket with redhat)

  *   why does the UNIX kernel enforce nfs reads (slow) for the combination: 
set read lock; seek; read; ... and uses the cache (is fast) if we omit seek() 
even if the file is locked?

Thank you for your comments in advance!
Andre



Below are more details.
We performed a query (wget output about 150K) and saw in the strace the typical 
sequence:

  *   open (..tbl.basex)
  *   set read lock
  *   seek(); read() the whole file (650MB) by 4k blocks, seek() before every 
read (even for sequential read - where the position is already at the right 
place for the next read());
  *   close().

We found that all recent OS (RHEL7,8; debian12) are reproducible bypassing the 
filesystem cache if the database files on a nfs mounted filesystem.
RHEL6 uses the filesystem cache.



=== trace snippets
open(.. tbl.basex); fcntl(f, F_SETLK, {l_type=F_RDLCK}; seek(); read(f, 4k); 
seek(); read(.. 4k); close

 ..
openat(AT_FDCWD, 
"/proj/mpi_la/sb_dev/sbof/tbl.basex", O_RDWR|O_CREAT, 0666) = 51

#-- set read lock on the whole file (l_len=0).
fcntl(51, F_SETLK, {l_type=F_RDLCK, 
l_whence=SEEK_SET, l_start=0, l_len=0}) = 0

#-- lseek(), read(..,4K), lseek(), read(..,4k) -
# reading
..
13:09:30.050965 lseek(51, 0, SEEK_SET) = 0 
<0.63>
13:09:30.051900 read(51, 
"\0\0\0\0\0\0\0\0\0\0\314b\0\0\0\0001\0\1\0\0\0\0\1\0\0\314a\0\0\0\1"..., 4096) 
= 4096 <0.179836>
13:09:30.231893 lseek(51, 4096, SEEK_SET) = 
4096 <0.17>
13:09:30.232818 read(51, 
"\2\0\0\0\0\0\5\274\0\0\0\1\0\0\1\0\t\0004\0\0\0\0\5\0\0\0\2\0\0\1\1"..., 4096) 
= 4096 <0.41>
13:09:30.232923 lseek(51, 8192, SEEK_SET) = 
8192 <0.15>
13:09:30.232988 read(51, 
"\2\0\0@\0\0\n\303\0\0\0\1\0\0\2\0\t\09\0\0\0\0\6\0\0\0\2\0\0\2\1"..., 4096) = 
4096 <0.16>
..
#jump to the end and back..
13:09:30.248343 lseek(51, 192512, SEEK_SET) 
= 192512 <0.15>
13:09:30.248416 read(51, 
"\2\0\0@\0\0\250\n\0\0\0\1\0\0/\0\t\0A\0\0\0\0\25\0\0\0\2\0\0/\1"..., 4096) = 
4096 <0.0
13:09:30.248488 lseek(51, 586047488, 
SEEK_SET) = 586047488 <0.15>
13:09:30.248567 read(51, 
"\31\0j\0\0\0/\377\0\0\0(\0\0/\326\v\0\6\0\0\0 \217\0\0\0\0\0\0/\327"..., 4096) 
= 4096
13:09:30.249898 lseek(51, 196608, SEEK_SET) 
= 196608 <0.16>
13:09:30.250564 read(51, 
"\2\0\0\0\0\0\253\254\0\0\0\1\0\\0\t\08\0\0\0\0\3\0\0\0\2\0\\1"..., 
4096) = 409

close(51)

 test program to repoduce the behavior.
#!/tool/pandora64/bin/python3-latest
# test emulating the bad performance when baseX opens a database for read
#
# both conditions must be true:
# 1. set a read lock on the file
# 2. seek before reading.
#
# without lock or without seek it is fast.
#
# rhel6 - fast (<1s)
# rhel7,8 and debian12 - slow (~10s)
#   nfs -o vers=3,nolock - has no effect
#
# agerbats (Andre Gerbatsch), 11/10/2023
#

import fcntl

BS= 4096
FN= "/proj/sysadmin_scratch/agerbats/tbl.basex"

f = open(FN, "rb", buffering=0)

#-- set a read lock
fcntl.lockf(f, fcntl.LOCK_SH)
f.seek(0,2)
file_length=f.tell()

offset = 0
while  offset < file_length:

#-- seek to the next 4k position (it is semantically a noop)
f.seek(offset)
block=f.read(BS)
offset+= BS

f.close()




--
Andre


Von: Otto, Michael (Layout Analysis) 
Gesendet: Montag, 13. November 2023 18:19
An: Gerbatsch, Andre 
Betreff: WG: [basex-talk] WG: JAVA Performance Issue under RH8 by using BASEX 
with NFS system



Von: Christian Grün 
Gesendet: Montag, 13. November 2023 16:11
An: Otto, Michael (Layout Analysis) 
Cc: basex-talk@mailman.uni-konstanz.de 
Betreff: Re: [basex-talk] WG: JAVA Performance Issue under RH8 by using BASEX 
with NFS system


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…difficult to tell what might be the reason; we didn’t get similar reports so 
far. Most of the BaseX caching algorithms rely on the file system, but we don’t 
differ between Windows- and UNIX-based systems.

Does it make a difference if you change another JDK distribution?

Best,
Christian


On Mon, 

Re: [basex-talk] db:copy

[Ветошкин Владимир]

Hi, Christian. I can't check it now. Maybe later.I confuse with the fact, that basexserver failes, but basex did not.Are they use different methods to copy databases? Or that jdk bug only? 16.11.2023, 15:00, "Christian Grün" :Hi, this definitely looks like a bug in the JDK context. What happens if you upgrade your JDK to a newer version?Best, Christian  On Thu, Nov 16, 2023 at 12:56 PM Ветошкин Владимир  wrote: Hi everyone. Since I have changed jdk version to 12 (azul) - I get error, when I copy database (db:copy).It's only in basexserver. When I run basex - everything is ok. Error:Improper use? Potential bug? Your feedback is welcome: Contact: basex-talk@mailman.uni-konstanz.de Version: BaseX 9.1.2 Java: Azul Systems, Inc., 12.0.2 OS: Linux, amd64 Stack Trace: java.lang.NoClassDefFoundError: Could not initialize class sun.nio.fs.UnixCopyFile at java.base/sun.nio.fs.UnixFileSystemProvider.copy(UnixFileSystemProvider.java:258) at java.base/java.nio.file.Files.copy(Files.java:1297) at org.basex.io.IOFile.copyTo(IOFile.java:319) at org.basex.core.cmd.Copy.copy(Copy.java:83) at org.basex.query.up.primitives.name.DBCopy.apply(DBCopy.java:43) at org.basex.query.up.NameUpdates.apply(NameUpdates.java:58) at org.basex.query.up.ContextModifier.apply(ContextModifier.java:132) at org.basex.query.up.Updates.apply(Updates.java:156) at org.basex.query.QueryContext.iter(QueryContext.java:351) at org.basex.query.QueryProcessor.iter(QueryProcessor.java:90) at org.basex.core.cmd.AQuery.query(AQuery.java:109) at org.basex.core.cmd.XQuery.run(XQuery.java:22) at org.basex.core.Command.run(Command.java:257) at org.basex.core.Command.execute(Command.java:93) at org.basex.server.ClientListener.run(ClientListener.java:140)-- С уважением,Ветошкин Владимир Владимирович   -- С уважением,Ветошкин Владимир Владимирович 

Re: [basex-talk] db:copy

[Christian Grün]

Hi, this definitely looks like a bug in the JDK context. What happens if
you upgrade your JDK to a newer version?
Best, Christian


On Thu, Nov 16, 2023 at 12:56 PM Ветошкин Владимир 
wrote:

>
> Hi everyone.
>
> Since I have changed jdk version to 12 (azul) - I get error, when I copy
> database (db:copy).
> It's only in basexserver. When I run basex - everything is ok.
>
> Error:
> Improper use? Potential bug? Your feedback is welcome: Contact:
> basex-talk@mailman.uni-konstanz.de Version: BaseX 9.1.2 Java: Azul
> Systems, Inc., 12.0.2 OS: Linux, amd64 Stack Trace:
> java.lang.NoClassDefFoundError: Could not initialize class
> sun.nio.fs.UnixCopyFile at
> java.base/sun.nio.fs.UnixFileSystemProvider.copy(UnixFileSystemProvider.java:258)
> at java.base/java.nio.file.Files.copy(Files.java:1297) at
> org.basex.io.IOFile.copyTo(IOFile.java:319) at
> org.basex.core.cmd.Copy.copy(Copy.java:83) at
> org.basex.query.up.primitives.name.DBCopy.apply(DBCopy.java:43) at
> org.basex.query.up.NameUpdates.apply(NameUpdates.java:58) at
> org.basex.query.up.ContextModifier.apply(ContextModifier.java:132) at
> org.basex.query.up.Updates.apply(Updates.java:156) at
> org.basex.query.QueryContext.iter(QueryContext.java:351) at
> org.basex.query.QueryProcessor.iter(QueryProcessor.java:90) at
> org.basex.core.cmd.AQuery.query(AQuery.java:109) at
> org.basex.core.cmd.XQuery.run(XQuery.java:22) at
> org.basex.core.Command.run(Command.java:257) at
> org.basex.core.Command.execute(Command.java:93) at
> org.basex.server.ClientListener.run(ClientListener.java:140)
> --
> С уважением,
> Ветошкин Владимир Владимирович
>
>

[basex-talk] db:copy

[Ветошкин Владимир]

 Hi everyone. Since I have changed jdk version to 12 (azul) - I get error, when I copy database (db:copy).It's only in basexserver. When I run basex - everything is ok. Error:Improper use? Potential bug? Your feedback is welcome: Contact: basex-talk@mailman.uni-konstanz.de Version: BaseX 9.1.2 Java: Azul Systems, Inc., 12.0.2 OS: Linux, amd64 Stack Trace: java.lang.NoClassDefFoundError: Could not initialize class sun.nio.fs.UnixCopyFile at java.base/sun.nio.fs.UnixFileSystemProvider.copy(UnixFileSystemProvider.java:258) at java.base/java.nio.file.Files.copy(Files.java:1297) at org.basex.io.IOFile.copyTo(IOFile.java:319) at org.basex.core.cmd.Copy.copy(Copy.java:83) at org.basex.query.up.primitives.name.DBCopy.apply(DBCopy.java:43) at org.basex.query.up.NameUpdates.apply(NameUpdates.java:58) at org.basex.query.up.ContextModifier.apply(ContextModifier.java:132) at org.basex.query.up.Updates.apply(Updates.java:156) at org.basex.query.QueryContext.iter(QueryContext.java:351) at org.basex.query.QueryProcessor.iter(QueryProcessor.java:90) at org.basex.core.cmd.AQuery.query(AQuery.java:109) at org.basex.core.cmd.XQuery.run(XQuery.java:22) at org.basex.core.Command.run(Command.java:257) at org.basex.core.Command.execute(Command.java:93) at org.basex.server.ClientListener.run(ClientListener.java:140)-- С уважением,Ветошкин Владимир Владимирович