Building 2.0+

classic Classic list List threaded Threaded
4 messages Options
Reply | Threaded
Open this post in threaded view
|

Building 2.0+

Paulo Nuin
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
Reply | Threaded
Open this post in threaded view
|

Re: Building 2.0+

sergio contrino-2
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.

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)

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
_______________________________________________
dev mailing list
[hidden email]
https://lists.intermine.org/mailman/listinfo/dev
Reply | Threaded
Open this post in threaded view
|

Re: Building 2.0+

Paulo Nuin
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

_______________________________________________
dev mailing list
[hidden email]
https://lists.intermine.org/mailman/listinfo/dev
Reply | Threaded
Open this post in threaded view
|

Re: Building 2.0+

sergio contrino-2
hi paulo,
please add this to your gradle_opts if is not yet there:

-Dorg.gradle.daemon=false

(like in
-server -Xmx20g -XX:+UseParallelGC -Xms1700m
-XX:SoftRefLRUPolicyMSPerMB=1 -XX:MaxHeapFreeRatio=99
-Dorg.gradle.daemon=false
)

please let me know if it was already present.
thanks!
sergio


On 20/12/2018 17:45, Paulo Nuin wrote:

> 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
>

--
sergio contrino                  InterMine, University of Cambridge
https://sergiocontrino.github.io           http://www.intermine.org
_______________________________________________
dev mailing list
[hidden email]
https://lists.intermine.org/mailman/listinfo/dev