> Hi Sergio
>
>> On Dec 20, 2018, at 5:13 AM, sergio contrino <
[hidden email]> wrote:
>>
>> hi paulo!
>> 1) what is the ram of your build machine?
>> i have a very similar setting on a 48G ram machine, but i have this
>> -XX:+UseParallelGC
>> instead of
>> -XX:-UseGCOverheadLimit
>> i can try to check out all the parameters of the setting.
>>
>
> Removed the GCOverheadLimit and got further, but not all to the end
>
> Retrieving go in a tgt items database
> [convertOBO] SLF4J: Class path contains multiple SLF4J bindings.
> [convertOBO] SLF4J: Found binding in [jar:file:/home/nuin/.gradle/caches/modules-2/files-2.1/org.slf4j/slf4j-simple/1.7.7/8095d0b9f7e0a9cd79a663c740e0f8fb31d0e2c8/slf4j-simple-1.7.7.jar!/org/slf4j/impl/StaticLoggerBinder.class]
> [convertOBO] SLF4J: Found binding in [jar:file:/home/nuin/.gradle/caches/modules-2/files-2.1/org.slf4j/slf4j-jdk14/1.7.10/13675a57601d9106fe82314fe9eebb9b2d9b13c6/slf4j-jdk14-1.7.10.jar!/org/slf4j/impl/StaticLoggerBinder.class]
> [convertOBO] SLF4J: See
http://www.slf4j.org/codes.html#multiple_bindings for an explanation.
> [convertOBO] SLF4J: Actual binding is of type [org.slf4j.impl.SimpleLoggerFactory]
> [convertOBO] [Task worker for ':' Thread 4] INFO com.zaxxer.hikari.HikariDataSource - db.common-tgt-items - Starting...
> [convertOBO] [Task worker for ':' Thread 4] INFO com.zaxxer.hikari.HikariDataSource - db.common-tgt-items - Start completed.
>
>
> FAILURE: Build failed with an exception.
>
> * What went wrong:
> Could not receive a message from the daemon.
>
>
>> 2)
>> i think you are following a thread regarding postgres connections, it seems that there are a couple of place in the code that need explicit closing of the connection.
>>
>> daniela added a ticket
>>
https://github.com/intermine/intermine/issues/1973>>
>> and the partial patch that joe proposed
>>
https://github.com/danielabutano/intermine/commit/87108e3e40cfb82725f994d511b0f64dd6b50893>>
>> you can try to (in order):
>> - decrease the number of connections required by your production and item dbs (looking at your
>>
>>
https://github.com/WormBase/intermine/blob/im-267/wormmine/default.intermine.integrate.properties>>
>> you could easily set the connection to 20 (it is 50 now) for the production db and 5 (it is 10 now) for the item one.
>>
>> - apply the patch
>>
>> - increase the max number of connections allowed by postgres by editing the postgresql.conf (you will need to restart the database)
>>
>
> I am less concerned by this, as it worked on a second try, but I will keep an eye on it.
>
> Cheers
> Paulo
>
>
>
>
>> please let us know how it goes.
>> thanks!
>> sergio
>>
>>
>>
>> On 20/12/2018 04:24, Paulo Nuin wrote:
>>> Hi
>>> I am having a number of problems while trying to build 2.x. Here are my GRADLE_OPTS
>>> -server -XX:MaxPermSize=1g -Xmx16g -XX:+UseParallelGC -Xms2g -XX:SoftRefLRUPolicyMSPerMB=1 -XX:MaxHeapFreeRatio=99 -XX:-UseGCOverheadLimit
>>> 1 - Loading GO data
>>> Sometimes I get this
>>> FAILURE: Build failed with an exception.
>>> * What went wrong:
>>> Execution failed for task ':dbmodel:retrieveSingleSource'.
>>>> java.lang.OutOfMemoryError: Java heap space
>>> * Try:
>>> Run with --stacktrace option to get the stack trace. Run with --info or --debug option to get more log output.
>>> * Get more help at
https://help.gradle.org>>> Sometimes I get this
>>>> Task :dbmodel:retrieveSingleSource
>>> Retrieving go in a tgt items database
>>> [convertOBO] SLF4J: Class path contains multiple SLF4J bindings.
>>> [convertOBO] SLF4J: Found binding in [jar:file:/home/nuin/.gradle/caches/modules-2/files-2.1/org.slf4j/slf4j-simple/1.7.7/8095d0b9f7e0a9cd79a663c740e0f8fb31d0e2c8/slf4j-simple-1.7.7.jar!/org/slf4j/impl/StaticLoggerBinder.class]
>>> [convertOBO] SLF4J: Found binding in [jar:file:/home/nuin/.gradle/caches/modules-2/files-2.1/org.slf4j/slf4j-jdk14/1.7.10/13675a57601d9106fe82314fe9eebb9b2d9b13c6/slf4j-jdk14-1.7.10.jar!/org/slf4j/impl/StaticLoggerBinder.class]
>>> [convertOBO] SLF4J: See
http://www.slf4j.org/codes.html#multiple_bindings for an explanation.
>>> [convertOBO] SLF4J: Actual binding is of type [org.slf4j.impl.SimpleLoggerFactory]
>>> [convertOBO] [Task worker for ':' Thread 2] INFO com.zaxxer.hikari.HikariDataSource - db.common-tgt-items - Starting...
>>> [convertOBO] [Task worker for ':' Thread 2] INFO com.zaxxer.hikari.HikariDataSource - db.common-tgt-items - Start completed.
>>> FAILURE: Build failed with an exception.
>>> * What went wrong:
>>> Execution failed for task ':dbmodel:retrieveSingleSource'.
>>>> java.lang.OutOfMemoryError: GC overhead limit exceeded
>>> * Try:
>>> Run with --stacktrace option to get the stack trace. Run with --info or --debug option to get more log output.
>>> * Get more help at
https://help.gradle.org>>> BUILD FAILED in 1m 13s
>>> 11 actionable tasks: 7 executed, 4 up-to-date
>>> So it’s either the heap or the garbage collector. What would be the approach here?
>>> 2- Loading GFF data
>>> I was having a not enough connections to Postgres while the build was running,
>>> Connection error:
>>> org.postgresql.util.PSQLException: FATAL: sorry, too many clients already
>>> at org.postgresql.Driver$ConnectThread.getResult(Driver.java:403)
>>> at org.postgresql.Driver.connect(Driver.java:261)
>>> at java.sql.DriverManager.getConnection(DriverManager.java:664)
>>> at java.sql.DriverManager.getConnection(DriverManager.java:247)
>>> at org.postgresql.ds.common.BaseDataSource.getConnection(BaseDataSource.java:94)
>>> at org.postgresql.ds.common.BaseDataSource.getConnection(BaseDataSource.java:79)
>>> at com.zaxxer.hikari.pool.PoolBase.newConnection(PoolBase.java:369)
>>> at com.zaxxer.hikari.pool.PoolBase.newPoolEntry(PoolBase.java:198)
>>> at com.zaxxer.hikari.pool.HikariPool.createPoolEntry(HikariPool.java:467)
>>> at com.zaxxer.hikari.pool.HikariPool.access$100(HikariPool.java:71)
>>> at com.zaxxer.hikari.pool.HikariPool$PoolEntryCreator.call(HikariPool.java:706)
>>> at com.zaxxer.hikari.pool.HikariPool$PoolEntryCreator.call(HikariPool.java:692)
>>> at java.util.concurrent.FutureTask.run(FutureTask.java:266)
>>> at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1149)
>>> at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:624)
>>> at java.lang.Thread.run(Thread.java:748)
>>> but on a second try it worked OK. How to avoid getting these?
>>> Thanks
>>> Paulo
>>> _______________________________________________
>>> dev mailing list
>>>
[hidden email]
>>>
https://lists.intermine.org/mailman/listinfo/dev>>
>> --
>> sergio contrino InterMine, University of Cambridge
>>
https://sergiocontrino.github.io http://www.intermine.org>
Locked
