Going back on my previous mail:

No, actually the memory is not freed even after CREATE DB, I was watching another java process; it does vary a little at import end (to about 800M). So this problem seems to be common.

I track system memory usage, via ps / top. I don't know how to measure actual heap usage on the server, just the system memory consumed.

Dinu

On 04.11.2017 19:02, Christian Grün wrote:

Fine. One more question: How do you measure the "memory leak" on command-line, and are you sure that this value is comparable to the value that is shown in the bottom bar of the BaseX GUI?

Am 04.11.2017 5:58 nachm. schrieb "Dinu Marina" <dinumarina@gmail.com mailto:dinumarina@gmail.com>:

Indeed, I use the create function from the GUI, I just assumed
it's the same 2 separate operations.

Indeed, with CREATE DB it doesn't get out of memory at 1G. And it
also gets GC'ed and returned to system afterwards with no
additional intervention, after CREATE DB memory shrinks
immediately back to ~30M.

So confirmed, huge memory usage and memory "leak" (or whatever it
is) is linked to ADD only.

Thanks,
Dinu


On 04.11.2017 18 <tel:04.11.2017%2018>:46, Christian Grün wrote:

    Hi Dinu,

    yes, I have downloaded the file.

    Just one more question:

        2) using basexclient:

        CHECK somedb
        ADD /path/to/1_feed.zip

    If you use the GUI, do you really add your zip file to an existing
    database, or do you specify it as initial input when creating
    a new
    database? The latter option is definitely more efficient, and the
    command-line equivalent would be

       CREATE DB somedb /path/to/1_feed.zip

    For adding resources to existing databases, enabling ADDCACHE
    can help [1].

    Cheers,
    Christian

    [1] http://docs.basex.org/wiki/Options#ADDCACHE
    <http://docs.basex.org/wiki/Options#ADDCACHE>



        Result:
        Out of Main Memory.

        To reproduce 2), start server with -Xmx2048m, repeat
        operations, then drop
        db, close client, check server memory usage.

        Thanks,
        Dinu



        On 04.11.2017 18 <tel:04.11.2017%2018>:18, Christian Grün
        wrote:

                The fact is, the GUI runs with no problem with
                -Xmx512M to do the same
                thing, while basexclient fails without -Xmx2048M.

            That’s surprising indeed – mostly because I would have
            expected the
            BaseX client to always consume a small and constant
            amount of memory
            (the BaseX server instance should be the process to
            consume all the
            memory). I did some quick tests with large zipped
            input, but I failed
            to reproduce the behavior you described. Feel free to
            provide me with
            a step-by-step guide.

                I will try that, thanks, but shouldn't this be the
                case automatically?
                Since
                I assume BaseX does free references to data
                structures, at least to a
                dropped DB?

            Absolutely. Anything that’s reproducible is welcome.



                On 04.11.2017 18 <tel:04.11.2017%2018>:00,
                Christian Grün wrote:

                    Hi Dinu,

                        Question 1:

                    Memory consumption of the BaseX GUI is similar
                    as on command-line, but
                    it may be due to garbage collection that some
                    memory will be freed.
                    How do you add documents outside the GUI?

                        Question 2:

                    If a certain amount of memory is reserved by
                    Java’s virtual machine,
                    it may still be used by other applications on
                    your system (provided
                    that the memory can be freed by garbage
                    collection). You can enforce
                    some GC calls by running the following XQuery
                    expression (this should
                    only be done for testing purposes):

                         (1 to 5) ! Q{java:java.lang.System}gc()

                    Best,
                    Christian


                        After the data is extracted, it's no
                        longer needed and I DROP the DB;
                        also
                        connection is closed. But memory (the huge
                        2G mentioned above) is never
                        returned to the system.

                        The script I use to run BaseX is:

                        export BASEX_JVM="-Xmx2048m
                        -XX:MinHeapFreeRatio=10
                        -XX:MaxHeapFreeRatio=20
                        -XX:+UseSerialGC -Dorg.basex.LOG=false
                        -Dorg.basex.DBPATH=/var/basex/data
                        -Dorg.basex.REPOPATH=/var/basex/repo"
                        BaseX/bin/basexserver -S

                        So basically I tried specifying
                        MaxHeapFreeRatio and SerialGC for java,
                        but
                        it's no improvement and it doesn't help so
                        I assume the memory isn't
                        hogged
                        in java... is there a way to free up the
                        memory once operations
                        complete
                        (like mentioned above, "complete" means
                        created DB is dropped,
                        connection
                        closed, waiting for another batch to start
                        over).

                        Thanks,
                        Dinu

Ok, thanks, I'll try to shed some more light on it.

So, to make an architectural decision, can you tell me if CREATE DB is running in quasi-constant space? So that I may rely on it if feeds get 10x larger?

Dinu

Having indexes is a must, so, without disabling it, will the memory requirements grow liniar with the data size? Or does it work in batches, as I can understand from "will write to disk if memory is too low"? This would qualify for constant memory for my purpose :) The idea is, if files get 10x bigger, will I need to put in -Xmx10G? Or will the 1G still be enough?

On Nov 4, 2017 19:50, "Christian Grün" christian.gruen@gmail.com wrote:

Hi Dinu,

So, to make an architectural decision, can you tell me if CREATE DB is running in quasi-constant space?

If you create new databases, it’s mostly the indexing of texts and attributes that requires additional memory. Memory usage is not constant, but the standard value indexes will automatically write temporary data structures to disk if your memory gets low. If you disable the text and attribute index, you can build initial databases from input up to 500 GB [1].

Cheers, Christian

[1] http://docs.basex.org/wiki/Statistics

So indeed usedmemory says it's about 3M. If that's the heap size, does this mean the memory is hogged in the JVM? That's why I tried to use

-XX:MinHeapFreeRatio=10 -XX:MaxHeapFreeRatio=20 -XX:+UseSerialGC

it says here http://www.stefankrause.net/wp/?p=14 that the serial GC does return memory to the system... It would sure be a nice thing to have, since the server is idle 23 hours a day. I thought about restarting the server, but there can be async requests coming in from different clients, so a restart mechanism would probably involve an external sync mechanism.

On 04.11.2017 19:40, Christian Grün wrote:

...

No, actually the memory is not freed even after CREATE DB, I was watching another java process; it does vary a little at import end (to about 800M). So this problem seems to be common.

This behavior is common indeed, and it is not related to BaseX, but to the Java virtual machine in general. Garbage collection is a very complex process, and allocated memory won’t automatically be freed after a memory consuming thread has finised, but only if it is actually required by another thread.

...

Q{java:java.lang.System}gc() Stopped at , 1/29: Unknown command: Q{java:java.lang.System}gc(). Try HELP.

The string needs to be run as XQuery expression (see my initial mail). If you want to run it on command-line, you will need to use the XQUERY command. Find more information on BaseX commands and command-line processing in our Wiki [1,2].

The following query will give you some idea of the current memory consumption:

(1 to 3) ! Q{java:java.lang.System}gc(), string(db:system()//usedmemory)

It returns the value computed via [3] (see [4] as well). The result is just a rough guess (it’s generally difficult to compute something like the “real” memory consumption of a JVM), but it might suffice to detect real memory leaks. If it turns out that this query yields a really large value (e.g. > 1gb) after creating a database and adding a zip file, then we might need to do something about it.

Hope this helps, Christian

[1] http://docs.basex.org/wiki/Commands [2] http://docs.basex.org/wiki/Command-Line_Options [3] https://github.com/BaseXdb/basex/blob/master/basex-core/src/main/java/org/ba... [4] https://stackoverflow.com/questions/37916136/how-to-calculate-memory-usage-o...

...

Dinu

On 04.11.2017 19:02, Christian Grün wrote:

Fine. One more question: How do you measure the "memory leak" on command-line, and are you sure that this value is comparable to the value that is shown in the bottom bar of the BaseX GUI?

Am 04.11.2017 5:58 nachm. schrieb "Dinu Marina" dinumarina@gmail.com:

...

Indeed, I use the create function from the GUI, I just assumed it's the same 2 separate operations.

Indeed, with CREATE DB it doesn't get out of memory at 1G. And it also gets GC'ed and returned to system afterwards with no additional intervention, after CREATE DB memory shrinks immediately back to ~30M.

So confirmed, huge memory usage and memory "leak" (or whatever it is) is linked to ADD only.

Thanks, Dinu

On 04.11.2017 18:46, Christian Grün wrote:

...

Hi Dinu,

yes, I have downloaded the file.

Just one more question:

...

2. using basexclient:

CHECK somedb ADD /path/to/1_feed.zip

If you use the GUI, do you really add your zip file to an existing database, or do you specify it as initial input when creating a new database? The latter option is definitely more efficient, and the command-line equivalent would be

CREATE DB somedb /path/to/1_feed.zip

For adding resources to existing databases, enabling ADDCACHE can help [1].

Cheers, Christian

[1] http://docs.basex.org/wiki/Options#ADDCACHE

...

Result: Out of Main Memory.

To reproduce 2), start server with -Xmx2048m, repeat operations, then drop db, close client, check server memory usage.

Thanks, Dinu

On 04.11.2017 18:18, Christian Grün wrote:

...

> The fact is, the GUI runs with no problem with -Xmx512M to do the same > thing, while basexclient fails without -Xmx2048M. That’s surprising indeed – mostly because I would have expected the BaseX client to always consume a small and constant amount of memory (the BaseX server instance should be the process to consume all the memory). I did some quick tests with large zipped input, but I failed to reproduce the behavior you described. Feel free to provide me with a step-by-step guide.

> I will try that, thanks, but shouldn't this be the case automatically? > Since > I assume BaseX does free references to data structures, at least to a > dropped DB? Absolutely. Anything that’s reproducible is welcome.

> On 04.11.2017 18:00, Christian Grün wrote: >> Hi Dinu, >> >>> Question 1: >> Memory consumption of the BaseX GUI is similar as on command-line, >> but >> it may be due to garbage collection that some memory will be freed. >> How do you add documents outside the GUI? >> >>> Question 2: >> If a certain amount of memory is reserved by Java’s virtual machine, >> it may still be used by other applications on your system (provided >> that the memory can be freed by garbage collection). You can enforce >> some GC calls by running the following XQuery expression (this should >> only be done for testing purposes): >> >> (1 to 5) ! Q{java:java.lang.System}gc() >> >> Best, >> Christian >> >> >>> After the data is extracted, it's no longer needed and I DROP the >>> DB; >>> also >>> connection is closed. But memory (the huge 2G mentioned above) is >>> never >>> returned to the system. >>> >>> The script I use to run BaseX is: >>> >>> export BASEX_JVM="-Xmx2048m -XX:MinHeapFreeRatio=10 >>> -XX:MaxHeapFreeRatio=20 >>> -XX:+UseSerialGC -Dorg.basex.LOG=false >>> -Dorg.basex.DBPATH=/var/basex/data >>> -Dorg.basex.REPOPATH=/var/basex/repo" >>> BaseX/bin/basexserver -S >>> >>> So basically I tried specifying MaxHeapFreeRatio and SerialGC for >>> java, >>> but >>> it's no improvement and it doesn't help so I assume the memory isn't >>> hogged >>> in java... is there a way to free up the memory once operations >>> complete >>> (like mentioned above, "complete" means created DB is dropped, >>> connection >>> closed, waiting for another batch to start over). >>> >>> Thanks, >>> Dinu >>>

If you don't need to add documents to existing databases (or if you use the ADDCACHE option for that), I recommend you to simply start with the JVM defaults, create a sample database from let’s say 10 GB of XML input and see if it works out of the box. Only if it doesn’t, it may be necessary to specify -Xmx, and it may additionally be interesting to analyse if you run into troubles at all if parts of your memory are reserved by the JVM. In our own use cases (with gigabytes of XML data), we nearly always work with the JVM defaults, even if our servers are also used for other stuff (but it may very well be that there is some need to free memory in your case).

Am 04.11.2017 7:41 nachm. schrieb "Dinu Marina" dinumarina@gmail.com:

So indeed usedmemory says it's about 3M. If that's the heap size, does this mean the memory is hogged in the JVM? That's why I tried to use

-XX:MinHeapFreeRatio=10 -XX:MaxHeapFreeRatio=20 -XX:+UseSerialGC

it says here http://www.stefankrause.net/wp/?p=14 that the serial GC does return memory to the system... It would sure be a nice thing to have, since the server is idle 23 hours a day. I thought about restarting the server, but there can be async requests coming in from different clients, so a restart mechanism would probably involve an external sync mechanism.

On 04.11.2017 19:40, Christian Grün wrote:

...

No, actually the memory is not freed even after CREATE DB, I was watching

...

another java process; it does vary a little at import end (to about 800M). So this problem seems to be common.

This behavior is common indeed, and it is not related to BaseX, but to the Java virtual machine in general. Garbage collection is a very complex process, and allocated memory won’t automatically be freed after a memory consuming thread has finised, but only if it is actually required by another thread.

Q{java:java.lang.System}gc()

...

Stopped at , 1/29: Unknown command: Q{java:java.lang.System}gc(). Try HELP.

The string needs to be run as XQuery expression (see my initial mail). If you want to run it on command-line, you will need to use the XQUERY command. Find more information on BaseX commands and command-line processing in our Wiki [1,2].

The following query will give you some idea of the current memory consumption:

(1 to 3) ! Q{java:java.lang.System}gc(), string(db:system()//usedmemory)

It returns the value computed via [3] (see [4] as well). The result is just a rough guess (it’s generally difficult to compute something like the “real” memory consumption of a JVM), but it might suffice to detect real memory leaks. If it turns out that this query yields a really large value (e.g. > 1gb) after creating a database and adding a zip file, then we might need to do something about it.

Hope this helps, Christian

[1] http://docs.basex.org/wiki/Commands [2] http://docs.basex.org/wiki/Command-Line_Options [3] https://github.com/BaseXdb/basex/blob/master/basex-core/src/ main/java/org/basex/util/Performance.java#L68 [4] https://stackoverflow.com/questions/37916136/how-to-calculat e-memory-usage-of-java-program

Dinu

...

On 04.11.2017 19:02, Christian Grün wrote:

Fine. One more question: How do you measure the "memory leak" on command-line, and are you sure that this value is comparable to the value that is shown in the bottom bar of the BaseX GUI?

Am 04.11.2017 5:58 nachm. schrieb "Dinu Marina" dinumarina@gmail.com:

...

Indeed, I use the create function from the GUI, I just assumed it's the same 2 separate operations.

Indeed, with CREATE DB it doesn't get out of memory at 1G. And it also gets GC'ed and returned to system afterwards with no additional intervention, after CREATE DB memory shrinks immediately back to ~30M.

So confirmed, huge memory usage and memory "leak" (or whatever it is) is linked to ADD only.

Thanks, Dinu

On 04.11.2017 18:46, Christian Grün wrote:

...

Hi Dinu,

yes, I have downloaded the file.

Just one more question:

2. using basexclient:

...

CHECK somedb ADD /path/to/1_feed.zip

If you use the GUI, do you really add your zip file to an existing database, or do you specify it as initial input when creating a new database? The latter option is definitely more efficient, and the command-line equivalent would be

CREATE DB somedb /path/to/1_feed.zip

For adding resources to existing databases, enabling ADDCACHE can help [1].

Cheers, Christian

[1] http://docs.basex.org/wiki/Options#ADDCACHE

Result:

...

Out of Main Memory.

To reproduce 2), start server with -Xmx2048m, repeat operations, then drop db, close client, check server memory usage.

Thanks, Dinu

On 04.11.2017 18:18, Christian Grün wrote:

> The fact is, the GUI runs with no problem with -Xmx512M to do the >> same >> thing, while basexclient fails without -Xmx2048M. >> > That’s surprising indeed – mostly because I would have expected the > BaseX client to always consume a small and constant amount of memory > (the BaseX server instance should be the process to consume all the > memory). I did some quick tests with large zipped input, but I failed > to reproduce the behavior you described. Feel free to provide me with > a step-by-step guide. > > I will try that, thanks, but shouldn't this be the case >> automatically? >> Since >> I assume BaseX does free references to data structures, at least to >> a >> dropped DB? >> > Absolutely. Anything that’s reproducible is welcome. > > > > On 04.11.2017 18:00, Christian Grün wrote: >> >>> Hi Dinu, >>> >>> Question 1: >>>> >>> Memory consumption of the BaseX GUI is similar as on command-line, >>> but >>> it may be due to garbage collection that some memory will be freed. >>> How do you add documents outside the GUI? >>> >>> Question 2: >>>> >>> If a certain amount of memory is reserved by Java’s virtual >>> machine, >>> it may still be used by other applications on your system (provided >>> that the memory can be freed by garbage collection). You can >>> enforce >>> some GC calls by running the following XQuery expression (this >>> should >>> only be done for testing purposes): >>> >>> (1 to 5) ! Q{java:java.lang.System}gc() >>> >>> Best, >>> Christian >>> >>> >>> After the data is extracted, it's no longer needed and I DROP the >>>> DB; >>>> also >>>> connection is closed. But memory (the huge 2G mentioned above) is >>>> never >>>> returned to the system. >>>> >>>> The script I use to run BaseX is: >>>> >>>> export BASEX_JVM="-Xmx2048m -XX:MinHeapFreeRatio=10 >>>> -XX:MaxHeapFreeRatio=20 >>>> -XX:+UseSerialGC -Dorg.basex.LOG=false >>>> -Dorg.basex.DBPATH=/var/basex/data >>>> -Dorg.basex.REPOPATH=/var/basex/repo" >>>> BaseX/bin/basexserver -S >>>> >>>> So basically I tried specifying MaxHeapFreeRatio and SerialGC for >>>> java, >>>> but >>>> it's no improvement and it doesn't help so I assume the memory >>>> isn't >>>> hogged >>>> in java... is there a way to free up the memory once operations >>>> complete >>>> (like mentioned above, "complete" means created DB is dropped, >>>> connection >>>> closed, waiting for another batch to start over). >>>> >>>> Thanks, >>>> Dinu >>>> >>>>