MariaDB - Crash DB: JDBC begin transaction failed

mysql
db
jdbc
mariadb
Tags: #<Tag:0x00007fe7b428e1c0> #<Tag:0x00007fe7b428e058> #<Tag:0x00007fe7b428def0> #<Tag:0x00007fe7b428dd88>

#1

Bonjour,

j’ai un petit soucis à mon avis pour la partie import en DB de l’audit :

25-10-2016 13:00:07:193 1406729 ERROR org.asqatasun.webapp.orchestrator.AsqatasunOrchestratorImpl  - AUDIT CRASHED:org.asqatasun.entity.audit.AuditImpl@b4ea32,https://XXX,1477399432
org.springframework.transaction.CannotCreateTransactionException: Could not open JPA EntityManager for transaction; nested exception is javax.persistence.PersistenceException:   org.hibernate.TransactionException: JDBC begin transaction failed:
        at org.springframework.orm.jpa.JpaTransactionManager.doBegin(JpaTransactionManager.java:427)
        at org.springframework.transaction.support.AbstractPlatformTransactionManager.getTransaction(AbstractPlatformTransactionManager.java:371)
        at org.springframework.transaction.interceptor.TransactionAspectSupport.createTransactionIfNecessary(TransactionAspectSupport.java:336)
        at org.springframework.transaction.interceptor.TransactionInterceptor.invoke(TransactionInterceptor.java:105)
        at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:172)
        at org.springframework.aop.interceptor.ExposeInvocationInterceptor.invoke(ExposeInvocationInterceptor.java:90)
        at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:172)
        at org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:202)
        at com.sun.proxy.$Proxy76.getEvidenceElement(Unknown Source)
        at org.asqatasun.processing.ProcessRemarkServiceImpl.getEvidenceElement(ProcessRemarkServiceImpl.java:571)
        at org.asqatasun.rules.elementchecker.ElementCheckerImpl.getEvidenceElement(ElementCheckerImpl.java:365)
        at org.asqatasun.rules.elementchecker.ElementCheckerImpl.getEvidenceElementCollection(ElementCheckerImpl.java:345)
        at org.asqatasun.rules.elementchecker.ElementCheckerImpl.addSourceCodeRemark(ElementCheckerImpl.java:212)
        at org.asqatasun.rules.elementchecker.element.ElementPresenceChecker.createSourceCodeRemark(ElementPresenceChecker.java:213)
        at org.asqatasun.rules.elementchecker.element.ElementPresenceChecker.checkElementPresence(ElementPresenceChecker.java:189)
        at org.asqatasun.rules.elementchecker.element.ElementPresenceChecker.doCheck(ElementPresenceChecker.java:169)
        at org.asqatasun.rules.elementchecker.ElementCheckerImpl.check(ElementCheckerImpl.java:183)
        at org.asqatasun.ruleimplementation.AbstractPageRuleWithSelectorAndCheckerImplementation.check(AbstractPageRuleWithSelectorAndCheckerImplementation.java:119)
        at org.asqatasun.ruleimplementation.AbstractPageRuleMarkupImplementation.selectAndCheck(AbstractPageRuleMarkupImplementation.java:54)
        at org.asqatasun.ruleimplementation.AbstractPageRuleDefaultImplementation.processImpl(AbstractPageRuleDefaultImplementation.java:71)
        at org.asqatasun.ruleimplementation.AbstractRuleImplementation.process(AbstractRuleImplementation.java:120)
        at org.asqatasun.processor.ProcessorImpl.run(ProcessorImpl.java:60)
        at org.asqatasun.service.ProcessorServiceImpl.process(ProcessorServiceImpl.java:78)
        at sun.reflect.GeneratedMethodAccessor184.invoke(Unknown Source)
        at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
        at java.lang.reflect.Method.invoke(Method.java:606)
        at org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:319)
        at org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:183)
        at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:150)
        at org.springframework.transaction.interceptor.TransactionInterceptor.invoke(TransactionInterceptor.java:110)
        at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:172)
        at org.springframework.aop.interceptor.ExposeInvocationInterceptor.invoke(ExposeInvocationInterceptor.java:90)
        at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:172)
        at org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:202)
        at com.sun.proxy.$Proxy86.process(Unknown Source)
        at org.asqatasun.service.command.AuditCommandImpl.process(AuditCommandImpl.java:423)
        at org.asqatasun.service.AuditServiceThreadImpl.process(AuditServiceThreadImpl.java:124)
        at org.asqatasun.service.AuditServiceThreadImpl.run(AuditServiceThreadImpl.java:97)
        at java.lang.Thread.run(Thread.java:745)
Caused by: javax.persistence.PersistenceException: org.hibernate.TransactionException: JDBC begin transaction failed:
        at org.hibernate.jpa.spi.AbstractEntityManagerImpl.convert(AbstractEntityManagerImpl.java:1763)
        at org.hibernate.jpa.spi.AbstractEntityManagerImpl.convert(AbstractEntityManagerImpl.java:1677)
        at org.hibernate.jpa.spi.AbstractEntityManagerImpl.throwPersistenceException(AbstractEntityManagerImpl.java:1771)
        at org.hibernate.jpa.internal.TransactionImpl.begin(TransactionImpl.java:64)
        at org.springframework.orm.jpa.DefaultJpaDialect.beginTransaction(DefaultJpaDialect.java:70)
        at org.springframework.orm.jpa.JpaTransactionManager.doBegin(JpaTransactionManager.java:377)
        ... 38 more
Caused by: org.hibernate.TransactionException: JDBC begin transaction failed:
        at org.hibernate.engine.transaction.internal.jdbc.JdbcTransaction.doBegin(JdbcTransaction.java:76)
        at org.hibernate.engine.transaction.spi.AbstractTransactionImpl.begin(AbstractTransactionImpl.java:162)
        at org.hibernate.internal.SessionImpl.beginTransaction(SessionImpl.java:1435)
        at org.hibernate.jpa.internal.TransactionImpl.begin(TransactionImpl.java:61)
        ... 40 more
Caused by: com.mysql.jdbc.exceptions.jdbc4.CommunicationsException: Communications link failure

The last packet successfully received from the server was 809,503 milliseconds ago.  The last packet sent successfully to the server was 0 milliseconds ago.
        at sun.reflect.NativeConstructorAccessorImpl.newInstance0(Native Method)
        at sun.reflect.NativeConstructorAccessorImpl.newInstance(NativeConstructorAccessorImpl.java:57)
        at sun.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:45)
        at java.lang.reflect.Constructor.newInstance(Constructor.java:526)
        at com.mysql.jdbc.Util.handleNewInstance(Util.java:411)
        at com.mysql.jdbc.SQLError.createCommunicationsException(SQLError.java:1129)
        at com.mysql.jdbc.MysqlIO.reuseAndReadPacket(MysqlIO.java:3720)
        at com.mysql.jdbc.MysqlIO.reuseAndReadPacket(MysqlIO.java:3609)
        at com.mysql.jdbc.MysqlIO.checkErrorPacket(MysqlIO.java:4160)
        at com.mysql.jdbc.MysqlIO.sendCommand(MysqlIO.java:2617)
        at com.mysql.jdbc.MysqlIO.sqlQueryDirect(MysqlIO.java:2778)
        at com.mysql.jdbc.ConnectionImpl.execSQL(ConnectionImpl.java:2819)
        at com.mysql.jdbc.ConnectionImpl.setAutoCommit(ConnectionImpl.java:5355)
        at com.mchange.v2.c3p0.impl.NewProxyConnection.setAutoCommit(NewProxyConnection.java:912)
        at org.hibernate.engine.transaction.internal.jdbc.JdbcTransaction.doBegin(JdbcTransaction.java:72)
        ... 43 more
Caused by: java.io.EOFException: Can not read response from server. Expected to read 4 bytes, read 0 bytes before connection was unexpectedly lost.
        at com.mysql.jdbc.MysqlIO.readFully(MysqlIO.java:3166)
        at com.mysql.jdbc.MysqlIO.reuseAndReadPacket(MysqlIO.java:3620)
        ... 51 more
25-10-2016 13:00:07:657 1407193 INFO  org.asqatasun.webapp.orchestrator.AsqatasunOrchestratorImpl  - krash email sent to [guillaume@XXX.fr] on audit n? 77
25-10-2016 13:00:12:032 1411568 INFO  org.asqatasun.webapp.orchestrator.AsqatasunOrchestratorImpl  - Audit site terminated on https://XXX

Quelques infos :

  • Je suis sous Docker.
  • J’exploire un serveur MariaDB 10…

Une idée, suis-je le seul ? J’attend un peu d’ionfo avant de lancer une migration MariaDB / MySQL.


#2

Que veux-tu dire par

?


#3

Asqatasun fait son travail (audit) une fois qu’il a fini il fait persister tout en base en 1 fois. C’est pas ça ? Car ça plante pas d’entré.


#4

Est-ce que tu as bien ajouté le paragraphe de conf spécifique MySQL (placée par le script pre-requisites.sh ?

Voici l’extrait qui nous intéresse:

[client]
default-character-set=utf8

[mysql]
default-character-set=utf8

[mysqld]
collation-server = utf8_general_ci
init-connect='SET NAMES utf8'
character-set-server = utf8
max_allowed_packet = 64M
innodb_file_per_table = 1

Le point important là dedans, c’est le max_allowed_packet


#5

Bonjour,

Alors j’ai pas copier / coller la conf mais j’ai bien un max_allowed_packet = 67 108 864 (depuis le serveur MySQL).

Pour le reste, je suis bien en UTF8 et l’innodb_file_per_table est par défaut sur MariaDB.
J’en suis a me demander si le problème ne provient pas du drivers MySQL qui serait pas MariaDB compliant…


#6

Si je comprend bien, tu arrive à ajouter des contrats ou des comptes dans ton Asqatasun : donc à persister certaines informations en DB. Par contre, quand tu lance un audit, certaines opérations de persistance en DB plantent… C’est bien cela ?

C’est valable pour tout les types d’audits ? (page, fichier, site et scénario)


#7

Je dirais gros audits de sites.


#8

Hum… Même en virant les timeouts, en mettant 128M pour la taille des packets, c’est pareil…

Pour info, une conf par défaut MariaDB, ça ressemble à ça :

# MariaDB database server configuration file.
#
# You can copy this file to one of:
# - "/etc/mysql/my.cnf" to set global options,
# - "~/.my.cnf" to set user-specific options.
#
# One can use all long options that the program supports.
# Run program with --help to get a list of available options and with
# --print-defaults to see which it would actually understand and use.
#
# For explanations see
# http://dev.mysql.com/doc/mysql/en/server-system-variables.html

# This will be passed to all mysql clients
# It has been reported that passwords should be enclosed with ticks/quotes
# escpecially if they contain "#" chars...
# Remember to edit /etc/mysql/debian.cnf when changing the socket location.
[client]
port            = 3306
socket          = /var/run/mysqld/mysqld.sock

# Here is entries for some specific programs
# The following values assume you have at least 32M ram

# This was formally known as [safe_mysqld]. Both versions are currently parsed.
[mysqld_safe]
socket          = /var/run/mysqld/mysqld.sock
nice            = 0

[mysqld]
skip-host-cache
skip-name-resolve
#
# * Basic Settings
#
user            = mysql
pid-file        = /var/run/mysqld/mysqld.pid
socket          = /var/run/mysqld/mysqld.sock
port            = 3306
basedir         = /usr
datadir         = /var/lib/mysql
tmpdir          = /tmp
lc_messages_dir = /usr/share/mysql
lc_messages     = en_US
skip-external-locking
#
# Instead of skip-networking the default is now to listen only on
# localhost which is more compatible and is not less secure.
#bind-address           = 127.0.0.1
#
# * Fine Tuning
#
max_connections         = 100
connect_timeout         = 10
wait_timeout            = 28800
max_allowed_packet      = 128M
thread_cache_size       = 128
sort_buffer_size        = 4M
bulk_insert_buffer_size = 16M
tmp_table_size          = 32M
max_heap_table_size     = 32M
#
# * MyISAM
#
# This replaces the startup script and checks MyISAM tables if needed
# the first time they are touched. On error, make copy and try a repair.
myisam_recover_options = BACKUP
key_buffer_size         = 128M
#open-files-limit       = 2000
table_open_cache        = 400
myisam_sort_buffer_size = 512M
#concurrent_insert       = 2
read_buffer_size        = 2M
read_rnd_buffer_size    = 1M
#
# * Query Cache Configuration
#
# Cache only tiny result sets, so we can fit more in the query cache.
query_cache_limit               = 128K
query_cache_size                = 64M
# for more write intensive setups, set to DEMAND or OFF
#query_cache_type               = DEMAND
#
# * Logging and Replication
#
# Both location gets rotated by the cronjob.
# Be aware that this log type is a performance killer.
# As of 5.1 you can enable the log at runtime!
#general_log_file        = /var/log/mysql/mysql.log
#general_log             = 1
#
# Error logging goes to syslog due to /etc/mysql/conf.d/mysqld_safe_syslog.cnf.
#
# we do want to know about network errors and such
#log_warnings           = 2
#
# Enable the slow query log to see queries with especially long duration
#slow_query_log[={0|1}]
slow_query_log_file     = /var/log/mysql/mariadb-slow.log
long_query_time = 10
#log_slow_rate_limit    = 1000
#log_slow_verbosity     = query_plan

#log-queries-not-using-indexes
#log_slow_admin_statements
#
# The following can be used as easy to replay backup logs or for replication.
# note: if you are setting up a replication slave, see README.Debian about
#       other settings you may need to change.
#server-id              = 1
#report_host            = master1
#auto_increment_increment = 2
#auto_increment_offset  = 1
#log_bin                        = /var/log/mysql/mariadb-bin
#log_bin_index          = /var/log/mysql/mariadb-bin.index
# not fab for performance, but safer
#sync_binlog            = 1
expire_logs_days        = 10
max_binlog_size         = 100M
# slaves
#relay_log              = /var/log/mysql/relay-bin
#relay_log_index        = /var/log/mysql/relay-bin.index
#relay_log_info_file    = /var/log/mysql/relay-bin.info
#log_slave_updates
#read_only
#
# If applications support it, this stricter sql_mode prevents some
# mistakes like inserting invalid dates etc.
#sql_mode               = NO_ENGINE_SUBSTITUTION,TRADITIONAL
#
# * InnoDB
#
# InnoDB is enabled by default with a 10MB datafile in /var/lib/mysql/.
# Read the manual for more InnoDB related options. There are many!
default_storage_engine  = InnoDB
# you can't just change log file size, requires special procedure
#innodb_log_file_size   = 50M
innodb_log_file_size    = 64M
innodb_buffer_pool_size = 256M
innodb_log_buffer_size  = 8M
innodb_file_per_table   = 1
innodb_open_files       = 400
innodb_io_capacity      = 400
innodb_flush_method     = O_DIRECT
#
# * Security Features
#
# Read the manual, too, if you want chroot!
# chroot = /var/lib/mysql/
#
# For generating SSL certificates I recommend the OpenSSL GUI "tinyca".
#
# ssl-ca=/etc/mysql/cacert.pem
# ssl-cert=/etc/mysql/server-cert.pem
# ssl-key=/etc/mysql/server-key.pem

#
# * Galera-related settings
#
[galera]
# Mandatory settings
#wsrep_on=ON
#wsrep_provider=
#wsrep_cluster_address=
#binlog_format=row
#default_storage_engine=InnoDB
#innodb_autoinc_lock_mode=2
#
# Allow server to accept connections on all interfaces.
#
#bind-address=0.0.0.0
#
# Optional setting
#wsrep_slave_threads=1
#innodb_flush_log_at_trx_commit=0

[mysqldump]
quick
quote-names
max_allowed_packet      = 64M

[mysql]
#no-auto-rehash # faster start of mysql but no tab completion

[isamchk]
key_buffer              = 16M

#
# * IMPORTANT: Additional settings that can override those from this file!
#   The files must end with '.cnf', otherwise they'll be ignored.
#
!includedir /etc/mysql/conf.d/

#9

C’est une URL dispo sur Internet ? (en MP si besoin)

Idéalement, il faudrait pouvoir lancer le même audit sur une configuration plus classique d’Asqatasun (Mysql).

De mémoire, ta configuration est l’image Docker “officielle” d’Asqatasun, avec l’export de la DB et import dans un autre conteneur type MariaDB + modif de asqatasun.conf pour changer de DB. C’est bien cela ? Si oui, c’est quelle image de MariaDB que tu utilise ?

Des audits de 10 000 pages en audit de site et plus de 3 000 pages en audit de scénario ne posent aucun problème dans la version Docker d’Asqatasun.


#10

[quote=“fabrice, post:9, topic:226”]
Idéalement, il faudrait pouvoir lancer le même audit sur une configuration plus classique d’Asqatasun (Mysql).
[/quote]Sur un MySQL 5.5 c’est nickel !


#12

@llaumgui, quel est la version de MariaDB ?

tu utilise une image Docker disponible
sur Docker Hub ou du fait maison ?


Installation d'Asqatasun sur RHEL (Red Hat)
#13

Du hub, que ce soit MySQL 5.5 (qui marche) ou MariaDB 10 (qui marche pas).

Après, il y a une lib de drivers Java pour MariaDB, c’est peut-être pas pour rien…