On 03/09/13 20:26, nadav hoze wrote:
OK the bottom line is that I must somehow free memory to prevent such a
huge performance degradation.
The stress tests we did are of course extreme and what we got in couple of
hours will be on client side after couple of weeks.
This means that we can somehow from time to time clear data not used.
You do not need to do anything - the internal caches are LRU and the
operating system will manage memory mapped files.
I read in
http://jena.apache.org/documentation/tdb/architecture.html#caching-on-32-and-64-bit-java-systems
that on 64-bit "TDB uses memory mapped files, accessed 8M segments, and the
operating system handles caching between RAM and disk"
and on 32 bit "TDB provides an in-heap LRU cache of B+Tree blocks" can I
force jena to use this cache on 64 bit ? (does the set of the file access
mode already does that?)
Yes - call
SystemTDB.setFileMode(FileMode.direct) ;
before anything else calls jena especially TDB.
Unfortunately, you can't resize the caches easily. In theory, there is
a properties file named by "tdb:settings" or
"com.hp.hpl.jena.tdb.settings". You'll need to look in teh code for
SystemTDB.
Let me know if this has any effect, useful or otherwise.
Andy
Thanks,
Nadav
Thanks,
On Tue, Sep 3, 2013 at 5:43 PM, Andy Seaborne <[email protected]> wrote:
On 03/09/13 07:01, nadav hoze wrote:
1. Regarding VM when I said varies from client to client I meant that
some uses VM and some don't but the 12GB is always for a single machine.
Also forgot to state that of course other processes works on that machine
beside this service that uses jena, but this service get his shared part
and I don't think it's a lack of resources issue.
What I have seen happening on other systems is that the VM configuration
is limiting the growth of the VM, causing it to not use as much of the
machine as it might.
Can you see that the whole 12G is being used at all?
Network drives don't help.
2. about the matching pattern here it is again, hopes it's OK now (I also
attached it):
This :
FILTER NOT EXISTS { ?ontologyConcept schema:isDeleted true }
is better than:
OPTIONAL{?ontologyConcept schema:isDeleted ?ontologyConceptDeleted}
FILTER(!bound(?**ontologyConceptDeleted) || (bound(?**ontologyConceptDeleted)
&& ?ontologyConceptDeleted = false))
Just a short explanation before you read the matching pattern:
this query should fetch all the triplets with relation subClassOf to a
given ontologyConcept. it's identifiers are @concept.code and
@concept.codeSystemId which are basically placeholders which we replace in
our service.
The OPTIONAL parts you see in the query are for ignoring concepts which
are marked as deleted or not bound to the schema.
?ontologyConcept schema:code @concept.code^^xsd:string .
?ontologyConcept schema:codeSystemId @concept.codeSystemId^^xsd:**string
OPTIONAL{?ontologyConcept schema:isDeleted ?ontologyConceptDeleted}
FILTER(!bound(?**ontologyConceptDeleted) || (bound(?**ontologyConceptDeleted)
&& ?ontologyConceptDeleted = false))
{
?child relations:subClassOf ?ontologyConcept .
OPTIONAL{?child schema:isDeleted ?childDeleted}
FILTER(!bound(?childDeleted) || (bound(?childDeleted) && ?childDeleted =
false))
?concept relations:equalsTo ?child .
OPTIONAL{?concept schema:isDeleted ?conceptDeleted}
FILTER(!bound(?conceptDeleted) || (bound(?conceptDeleted) &&
?conceptDeleted = false))
?concept rdf:type schema:Concept
}
UNION
{
?concept relations:equalsTo ?ontologyConcept .
?concept rdf:type schema:Concept
OPTIONAL{?concept schema:isDeleted ?conceptDeleted}
FILTER(!bound(?conceptDeleted) || (bound(?conceptDeleted) &&
?conceptDeleted = false))
}
3. About the direct mode, we already use it so no effect there, is there
a way to clear the memory cache from the model ?
No but I doubt it would make much difference. If you clear the cache,
there machine has to go to disk to fetch the data just as if it's doing
cache replacement.
Thanks,
Nadav
On Mon, Sep 2, 2013 at 6:21 PM, Andy Seaborne <[email protected] <mailto:
[email protected]>> wrote:
On 02/09/13 14:33, nadav hoze wrote:
Machine size: 12 GB
OS: Windows Server 2008 <tel:2008> 64 bit
I don't have much experience of Windows 64 bit and mmap files -
you may find running with 32 bit mode a useful datapoint (this
does not use memory mapped files which, from reading around the
web, and anecdotal evidence on users@, do not have the same
benefits as on Linux).
VM: varies from client to client.
Does this mean that several VMs for running on the same 12G hardware?
If so, how much RAM is allocate to each VM?
data (in triples): 20,000,000 (3.6 GB)
Heap size: 2 GB
How big does the entire JVM process get? At that scale, the
entire DB should be mapped into memory
Driver program : ? (didn't understand)
You say the test program issuing TDB directly so it must be in the
same JVM.
It may be useful to you to run on native hardware to see what
effect VM's are having. It can range from no measurable effect to
very significant.
No the database is on a network shared drive (different server).
pattern matching (where clause):
Sorry - this is unreadable and being a partial extract, I can't
reformat it.
Andy
*?ontologyConcept schema:code @concept.code^^xsd:string .*
*?ontologyConcept schema:codeSystemId
@concept.codeSystemId^^xsd:**string*
*OPTIONAL{?ontologyConcept schema:isDeleted
?ontologyConceptDeleted}
FILTER(!bound(?**ontologyConceptDeleted) ||
(bound(?**ontologyConceptDeleted)
&& ?ontologyConceptDeleted = false))*
*{*
* ?child relations:subClassOf ?ontologyConcept .*
* OPTIONAL{?child schema:isDeleted ?childDeleted}
FILTER(!bound(?childDeleted) || (bound(?childDeleted) &&
?childDeleted =
false))*
* ?concept relations:equalsTo ?child .*
* OPTIONAL{?concept schema:isDeleted ?conceptDeleted}
FILTER(!bound(?conceptDeleted) || (bound(?conceptDeleted) &&
?conceptDeleted = false))*
* ?concept rdf:type schema:Concept*
*}*
*UNION*
*{*
* ?concept relations:equalsTo ?ontologyConcept .*
* ?concept rdf:type schema:Concept*
* OPTIONAL{?concept schema:isDeleted ?conceptDeleted}
FILTER(!bound(?conceptDeleted) || (bound(?conceptDeleted) &&
?conceptDeleted = false))*
*}*
basically all this big fuss is to find all child concepts of a
specified
parent concept identified by concept.code and
concept.codeSystemId.
so the @concept.code and @concept.codeSystemId you see are
replaced in
runtime to actual values.
all of the optional sections you see are to ignore deleted
(logically) or
not bound concepts.
Thanks,
Nadav
On Mon, Sep 2, 2013 <tel:2013> at 4:14 PM, Andy Seaborne
<[email protected] <mailto:[email protected]>> wrote:
On 02/09/13 12:51, nadav hoze wrote:
hi,
We are doing stress tests to our service which it's
underlying data layer
is jena TDB.
one of our tests is tor run heavy queries for long
time (about 6 Hrs) and
afterwards run light queries. (we have clients which
are in that mode).
What we witness is a huge performance degradation,
light queries which
usually took around 0.1-0.2 sec after the heavy
queries execution took
more
than 3 seconds.
Not surprising - the heavy queries will have taken over the OS
cache.(assuming 64 bit - a similar effect occurs on 32
bit). The
light-after-heavy is effectively running cold.
Also the heavy query execution had a huge performance
degradation after
only one minute:
each heavy query fetched around 35000 triplets and
for the first minutes
it took between 10-40 seconds (which is OK),
afterwards it peaked to
200-8000 seconds.
Same thing memory wise, after a minute it peaked from
200mg to 2.2g.
What I would like to know is if there could be memory
leak in jena, or
whether jena objects are cached in some way and maybe
we can release them.
Here are important details for answering:
*jena version: 2.6.4*
*tdb version: 0.8.9*
*arq: 2.8.7*
*we use a single model and no datasets.*
Also can an upgrade to jena latest stable version help
us here ?
You should upgrade anyway. There are bug fixes. And a
different license.
Help is much appreciated :)
All depends on what the heavy query touches in the
database (the pattern
matching part), the size of the machine, whether anything
else is running
on the machine, ...
There are many, many factors:
What size of the machine?
What OS?
Is it a VM?
How much data (in triples) is there in the DB?
Heap size?
The driver program is on What
the same machine as the database - does this matter?
...
Andy
Thanks,
Nadav
