Mysql error while building standalone

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Ben Wolfe (openmrs) Ben Wolfe (openmrs)
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Mysql error while building standalone

Darius, I have checked out the standalone code on my machine and built it with success. 

However, when I try to build it on a remote server I get the mysql error below.  Have you seen this before?  Anything I can do to debug it?

(mysql is installed.  Running as root gets the same problem. port 3326 is not in use. that mysqld executable file does exist)

~/standalone$ mvn -e clean package
+ Error stacktraces are turned on.
[INFO] Scanning for projects...
[INFO] ------------------------------------------------------------------------
[INFO] Building standalone
[INFO]    task-segment: [clean, package]
[INFO] ------------------------------------------------------------------------
[INFO] [clean:clean {execution: default-clean}]
[INFO] Deleting file set: /home/bwolfe/standalone/target (included: [**], excluded: [])
[INFO] [resources:resources {execution: default-resources}]
[INFO] Using 'UTF-8' encoding to copy filtered resources.
[INFO] Copying 1 resource
[INFO] [liquibase:update {execution: empty-db-create-schema}]
[INFO] ------------------------------------------------------------------------
[INFO] Loading artfacts into URLClassLoader
[INFO]   artifact: file:/home/bwolfe/.m2/repository/org/apache/tomcat/catalina/6.0.26/catalina-6.0.26.jar
[INFO]   artifact: file:/home/bwolfe/.m2/repository/org/apache/tomcat/coyote/6.0.26/coyote-6.0.26.jar
[INFO]   artifact: file:/home/bwolfe/.m2/repository/org/apache/tomcat/jasper/6.0.26/jasper-6.0.26.jar
[INFO]   artifact: file:/home/bwolfe/.m2/repository/mysql/mysql-connector-java/5.1.8/mysql-connector-java-5.1.8.jar
[INFO]   artifact: file:/home/bwolfe/.m2/repository/com/mysql/mysql-connector-mxj/5.0.11/mysql-connector-mxj-5.0.11.jar
[INFO]   artifact: file:/home/bwolfe/.m2/repository/com/mysql/mysql-connector-mxj-dbfiles/5.0.11/mysql-connector-mxj-dbfiles-5.0.11.jar
[INFO]   artifact: file:/home/bwolfe/standalone/target/classes/
[INFO] ------------------------------------------------------------------------
[INFO] Settings----------------------------
[INFO]     driver: com.mysql.jdbc.Driver
[INFO]     url: jdbc:mysql:mxj://127.0.0.1:3326/openmrs?autoReconnect=true&sessionVariables=storage_engine=InnoDB&useUnicode=true&characterEncoding=UTF-8&server.initialize-user=true&createDatabaseIfNotExist=true&server.basedir=emptydatabase&server.datadir=emptydatabase/data&server.collation-server=utf8_general_ci&server.character-set-server=utf8&server.max_allowed_packet=32M
[INFO]     username: openmrs
[INFO]     password: test
[INFO]     use empty password: false
[INFO]     properties file: null
[INFO]     properties file will override? false
[INFO]     prompt on non-local database? true
[INFO]     clear checksums? false
[INFO]     changeLogFile: liquibase-schema-only.xml
[INFO]     drop first? false
[INFO]     context(s): null
[INFO]     number of changes to apply: 0
[INFO] ------------------------------------------------------------------------
[/home/bwolfe/standalone/emptydatabase/bin/mysqld][--no-defaults][--port=3326][--collation-server=utf8_general_ci][--max_allowed_packet=32M][--character-set-server=utf8][--socket=mysql.sock][--basedir=/home/bwolfe/standalone/emptydatabase][--datadir=/home/bwolfe/standalone/emptydatabase/data][--pid-file=/home/bwolfe/standalone/emptydatabase/data/MysqldResource.pid]
[MysqldResource] launching mysqld (driver_launched_mysqld_1)
Exception in thread "driver_launched_mysqld_1" com.mysql.management.util.WrappedException: java.io.IOException: Cannot run program "/home/bwolfe/standalone/emptydatabase/bin/mysqld": java.io.IOException: error=2, No such file or directory
    at com.mysql.management.util.Exceptions.toRuntime(Exceptions.java:55)
    at com.mysql.management.util.Exceptions$Block.exec(Exceptions.java:89)
    at com.mysql.management.util.RuntimeI$Default.exec(RuntimeI.java:180)
    at com.mysql.management.util.Shell$Default.run(Shell.java:140)
    at java.lang.Thread.run(Thread.java:636)
Caused by: java.io.IOException: Cannot run program "/home/bwolfe/standalone/emptydatabase/bin/mysqld": java.io.IOException: error=2, No such file or directory
    at java.lang.ProcessBuilder.start(ProcessBuilder.java:475)
    at java.lang.Runtime.exec(Runtime.java:610)
    at com.mysql.management.util.RuntimeI$Default$1.inner(RuntimeI.java:177)
    at com.mysql.management.util.Exceptions$Block.exec(Exceptions.java:86)
    ... 3 more
Caused by: java.io.IOException: java.io.IOException: error=2, No such file or directory
    at java.lang.UNIXProcess.<init>(UNIXProcess.java:164)
    at java.lang.ProcessImpl.start(ProcessImpl.java:81)
    at java.lang.ProcessBuilder.start(ProcessBuilder.java:468)
    ... 6 more


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Jeremy Keiper-3 Jeremy Keiper-3
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Re: Mysql error while building standalone

So, /home/bwolfe/standalone/emptydatabase/bin/mysqld exists and permissions all along the way are good?

Jeremy Keiper
OpenMRS Core Developer
AMPATH / IU-Kenya Support


On Mon, Nov 28, 2011 at 7:33 AM, Ben Wolfe <[hidden email]> wrote:
Darius, I have checked out the standalone code on my machine and built it with success. 

However, when I try to build it on a remote server I get the mysql error below.  Have you seen this before?  Anything I can do to debug it?

(mysql is installed.  Running as root gets the same problem. port 3326 is not in use. that mysqld executable file does exist)

~/standalone$ mvn -e clean package
+ Error stacktraces are turned on.
[INFO] Scanning for projects...
[INFO] ------------------------------------------------------------------------
[INFO] Building standalone
[INFO]    task-segment: [clean, package]
[INFO] ------------------------------------------------------------------------
[INFO] [clean:clean {execution: default-clean}]
[INFO] Deleting file set: /home/bwolfe/standalone/target (included: [**], excluded: [])
[INFO] [resources:resources {execution: default-resources}]
[INFO] Using 'UTF-8' encoding to copy filtered resources.
[INFO] Copying 1 resource
[INFO] [liquibase:update {execution: empty-db-create-schema}]
[INFO] ------------------------------------------------------------------------
[INFO] Loading artfacts into URLClassLoader
[INFO]   artifact: file:/home/bwolfe/.m2/repository/org/apache/tomcat/catalina/6.0.26/catalina-6.0.26.jar
[INFO]   artifact: file:/home/bwolfe/.m2/repository/org/apache/tomcat/coyote/6.0.26/coyote-6.0.26.jar
[INFO]   artifact: file:/home/bwolfe/.m2/repository/org/apache/tomcat/jasper/6.0.26/jasper-6.0.26.jar
[INFO]   artifact: file:/home/bwolfe/.m2/repository/mysql/mysql-connector-java/5.1.8/mysql-connector-java-5.1.8.jar
[INFO]   artifact: file:/home/bwolfe/.m2/repository/com/mysql/mysql-connector-mxj/5.0.11/mysql-connector-mxj-5.0.11.jar
[INFO]   artifact: file:/home/bwolfe/.m2/repository/com/mysql/mysql-connector-mxj-dbfiles/5.0.11/mysql-connector-mxj-dbfiles-5.0.11.jar
[INFO]   artifact: file:/home/bwolfe/standalone/target/classes/
[INFO] ------------------------------------------------------------------------
[INFO] Settings----------------------------
[INFO]     driver: com.mysql.jdbc.Driver
[INFO]     url: jdbc:mysql:mxj://127.0.0.1:3326/openmrs?autoReconnect=true&sessionVariables=storage_engine=InnoDB&useUnicode=true&characterEncoding=UTF-8&server.initialize-user=true&createDatabaseIfNotExist=true&server.basedir=emptydatabase&server.datadir=emptydatabase/data&server.collation-server=utf8_general_ci&server.character-set-server=utf8&server.max_allowed_packet=32M
[INFO]     username: openmrs
[INFO]     password: test
[INFO]     use empty password: false
[INFO]     properties file: null
[INFO]     properties file will override? false
[INFO]     prompt on non-local database? true
[INFO]     clear checksums? false
[INFO]     changeLogFile: liquibase-schema-only.xml
[INFO]     drop first? false
[INFO]     context(s): null
[INFO]     number of changes to apply: 0
[INFO] ------------------------------------------------------------------------
[/home/bwolfe/standalone/emptydatabase/bin/mysqld][--no-defaults][--port=3326][--collation-server=utf8_general_ci][--max_allowed_packet=32M][--character-set-server=utf8][--socket=mysql.sock][--basedir=/home/bwolfe/standalone/emptydatabase][--datadir=/home/bwolfe/standalone/emptydatabase/data][--pid-file=/home/bwolfe/standalone/emptydatabase/data/MysqldResource.pid]
[MysqldResource] launching mysqld (driver_launched_mysqld_1)
Exception in thread "driver_launched_mysqld_1" com.mysql.management.util.WrappedException: java.io.IOException: Cannot run program "/home/bwolfe/standalone/emptydatabase/bin/mysqld": java.io.IOException: error=2, No such file or directory
    at com.mysql.management.util.Exceptions.toRuntime(Exceptions.java:55)
    at com.mysql.management.util.Exceptions$Block.exec(Exceptions.java:89)
    at com.mysql.management.util.RuntimeI$Default.exec(RuntimeI.java:180)
    at com.mysql.management.util.Shell$Default.run(Shell.java:140)
    at java.lang.Thread.run(Thread.java:636)
Caused by: java.io.IOException: Cannot run program "/home/bwolfe/standalone/emptydatabase/bin/mysqld": java.io.IOException: error=2, No such file or directory
    at java.lang.ProcessBuilder.start(ProcessBuilder.java:475)
    at java.lang.Runtime.exec(Runtime.java:610)
    at com.mysql.management.util.RuntimeI$Default$1.inner(RuntimeI.java:177)
    at com.mysql.management.util.Exceptions$Block.exec(Exceptions.java:86)
    ... 3 more
Caused by: java.io.IOException: java.io.IOException: error=2, No such file or directory
    at java.lang.UNIXProcess.<init>(UNIXProcess.java:164)
    at java.lang.ProcessImpl.start(ProcessImpl.java:81)
    at java.lang.ProcessBuilder.start(ProcessBuilder.java:468)
    ... 6 more


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Ben Wolfe (openmrs) Ben Wolfe (openmrs)
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Re: Mysql error while building standalone

Yes, it existed and the permissions were good.  I ran it as root to make sure it wasn't permissions issues.

Ultimately I never figured out what the issue was.  In comparing it to my (working) build on my laptop I saw that the "emptydatabase" build dir was supposed to be in the target folder but for some reason it was doing it at the root of the project.

I deleted the /standalone/emptydatabase folder (mvn clean wasn't removing it) and then did yet another mvn clean package and it just worked!  It put it in /standalone/target/emptydatabase this time and didn't complain at all.

Ben

On Fri, Dec 2, 2011 at 9:01 PM, Jeremy Keiper <[hidden email]> wrote:
So, /home/bwolfe/standalone/emptydatabase/bin/mysqld exists and permissions all along the way are good?

Jeremy Keiper
OpenMRS Core Developer
AMPATH / IU-Kenya Support


On Mon, Nov 28, 2011 at 7:33 AM, Ben Wolfe <[hidden email]> wrote:
Darius, I have checked out the standalone code on my machine and built it with success. 

However, when I try to build it on a remote server I get the mysql error below.  Have you seen this before?  Anything I can do to debug it?

(mysql is installed.  Running as root gets the same problem. port 3326 is not in use. that mysqld executable file does exist)

~/standalone$ mvn -e clean package
+ Error stacktraces are turned on.
[INFO] Scanning for projects...
[INFO] ------------------------------------------------------------------------
[INFO] Building standalone
[INFO]    task-segment: [clean, package]
[INFO] ------------------------------------------------------------------------
[INFO] [clean:clean {execution: default-clean}]
[INFO] Deleting file set: /home/bwolfe/standalone/target (included: [**], excluded: [])
[INFO] [resources:resources {execution: default-resources}]
[INFO] Using 'UTF-8' encoding to copy filtered resources.
[INFO] Copying 1 resource
[INFO] [liquibase:update {execution: empty-db-create-schema}]
[INFO] ------------------------------------------------------------------------
[INFO] Loading artfacts into URLClassLoader
[INFO]   artifact: file:/home/bwolfe/.m2/repository/org/apache/tomcat/catalina/6.0.26/catalina-6.0.26.jar
[INFO]   artifact: file:/home/bwolfe/.m2/repository/org/apache/tomcat/coyote/6.0.26/coyote-6.0.26.jar
[INFO]   artifact: file:/home/bwolfe/.m2/repository/org/apache/tomcat/jasper/6.0.26/jasper-6.0.26.jar
[INFO]   artifact: file:/home/bwolfe/.m2/repository/mysql/mysql-connector-java/5.1.8/mysql-connector-java-5.1.8.jar
[INFO]   artifact: file:/home/bwolfe/.m2/repository/com/mysql/mysql-connector-mxj/5.0.11/mysql-connector-mxj-5.0.11.jar
[INFO]   artifact: file:/home/bwolfe/.m2/repository/com/mysql/mysql-connector-mxj-dbfiles/5.0.11/mysql-connector-mxj-dbfiles-5.0.11.jar
[INFO]   artifact: file:/home/bwolfe/standalone/target/classes/
[INFO] ------------------------------------------------------------------------
[INFO] Settings----------------------------
[INFO]     driver: com.mysql.jdbc.Driver
[INFO]     url: jdbc:mysql:mxj://127.0.0.1:3326/openmrs?autoReconnect=true&sessionVariables=storage_engine=InnoDB&useUnicode=true&characterEncoding=UTF-8&server.initialize-user=true&createDatabaseIfNotExist=true&server.basedir=emptydatabase&server.datadir=emptydatabase/data&server.collation-server=utf8_general_ci&server.character-set-server=utf8&server.max_allowed_packet=32M
[INFO]     username: openmrs
[INFO]     password: test
[INFO]     use empty password: false
[INFO]     properties file: null
[INFO]     properties file will override? false
[INFO]     prompt on non-local database? true
[INFO]     clear checksums? false
[INFO]     changeLogFile: liquibase-schema-only.xml
[INFO]     drop first? false
[INFO]     context(s): null
[INFO]     number of changes to apply: 0
[INFO] ------------------------------------------------------------------------
[/home/bwolfe/standalone/emptydatabase/bin/mysqld][--no-defaults][--port=3326][--collation-server=utf8_general_ci][--max_allowed_packet=32M][--character-set-server=utf8][--socket=mysql.sock][--basedir=/home/bwolfe/standalone/emptydatabase][--datadir=/home/bwolfe/standalone/emptydatabase/data][--pid-file=/home/bwolfe/standalone/emptydatabase/data/MysqldResource.pid]
[MysqldResource] launching mysqld (driver_launched_mysqld_1)
Exception in thread "driver_launched_mysqld_1" com.mysql.management.util.WrappedException: java.io.IOException: Cannot run program "/home/bwolfe/standalone/emptydatabase/bin/mysqld": java.io.IOException: error=2, No such file or directory
    at com.mysql.management.util.Exceptions.toRuntime(Exceptions.java:55)
    at com.mysql.management.util.Exceptions$Block.exec(Exceptions.java:89)
    at com.mysql.management.util.RuntimeI$Default.exec(RuntimeI.java:180)
    at com.mysql.management.util.Shell$Default.run(Shell.java:140)
    at java.lang.Thread.run(Thread.java:636)
Caused by: java.io.IOException: Cannot run program "/home/bwolfe/standalone/emptydatabase/bin/mysqld": java.io.IOException: error=2, No such file or directory
    at java.lang.ProcessBuilder.start(ProcessBuilder.java:475)
    at java.lang.Runtime.exec(Runtime.java:610)
    at com.mysql.management.util.RuntimeI$Default$1.inner(RuntimeI.java:177)
    at com.mysql.management.util.Exceptions$Block.exec(Exceptions.java:86)
    ... 3 more
Caused by: java.io.IOException: java.io.IOException: error=2, No such file or directory
    at java.lang.UNIXProcess.<init>(UNIXProcess.java:164)
    at java.lang.ProcessImpl.start(ProcessImpl.java:81)
    at java.lang.ProcessBuilder.start(ProcessBuilder.java:468)
    ... 6 more


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Ben Wolfe (openmrs) Ben Wolfe (openmrs)
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Re: Mysql error while building standalone

Just to finalize this thread for anyone googling for the answer:

I just found a non-committed modification on the server where I was building this.  The fix for this was to upgrade the mysql mxj connector and dbfiles versions to 5.0.12:
https://source.openmrs.org/changelog/contrib?cs=24875

Ben

On Fri, Dec 2, 2011 at 10:05 PM, Ben Wolfe <[hidden email]> wrote:
Yes, it existed and the permissions were good.  I ran it as root to make sure it wasn't permissions issues.

Ultimately I never figured out what the issue was.  In comparing it to my (working) build on my laptop I saw that the "emptydatabase" build dir was supposed to be in the target folder but for some reason it was doing it at the root of the project.

I deleted the /standalone/emptydatabase folder (mvn clean wasn't removing it) and then did yet another mvn clean package and it just worked!  It put it in /standalone/target/emptydatabase this time and didn't complain at all.

Ben


On Fri, Dec 2, 2011 at 9:01 PM, Jeremy Keiper <[hidden email]> wrote:
So, /home/bwolfe/standalone/emptydatabase/bin/mysqld exists and permissions all along the way are good?

Jeremy Keiper
OpenMRS Core Developer
AMPATH / IU-Kenya Support


On Mon, Nov 28, 2011 at 7:33 AM, Ben Wolfe <[hidden email]> wrote:
Darius, I have checked out the standalone code on my machine and built it with success. 

However, when I try to build it on a remote server I get the mysql error below.  Have you seen this before?  Anything I can do to debug it?

(mysql is installed.  Running as root gets the same problem. port 3326 is not in use. that mysqld executable file does exist)

~/standalone$ mvn -e clean package
+ Error stacktraces are turned on.
[INFO] Scanning for projects...
[INFO] ------------------------------------------------------------------------
[INFO] Building standalone
[INFO]    task-segment: [clean, package]
[INFO] ------------------------------------------------------------------------
[INFO] [clean:clean {execution: default-clean}]
[INFO] Deleting file set: /home/bwolfe/standalone/target (included: [**], excluded: [])
[INFO] [resources:resources {execution: default-resources}]
[INFO] Using 'UTF-8' encoding to copy filtered resources.
[INFO] Copying 1 resource
[INFO] [liquibase:update {execution: empty-db-create-schema}]
[INFO] ------------------------------------------------------------------------
[INFO] Loading artfacts into URLClassLoader
[INFO]   artifact: file:/home/bwolfe/.m2/repository/org/apache/tomcat/catalina/6.0.26/catalina-6.0.26.jar
[INFO]   artifact: file:/home/bwolfe/.m2/repository/org/apache/tomcat/coyote/6.0.26/coyote-6.0.26.jar
[INFO]   artifact: file:/home/bwolfe/.m2/repository/org/apache/tomcat/jasper/6.0.26/jasper-6.0.26.jar
[INFO]   artifact: file:/home/bwolfe/.m2/repository/mysql/mysql-connector-java/5.1.8/mysql-connector-java-5.1.8.jar
[INFO]   artifact: file:/home/bwolfe/.m2/repository/com/mysql/mysql-connector-mxj/5.0.11/mysql-connector-mxj-5.0.11.jar
[INFO]   artifact: file:/home/bwolfe/.m2/repository/com/mysql/mysql-connector-mxj-dbfiles/5.0.11/mysql-connector-mxj-dbfiles-5.0.11.jar
[INFO]   artifact: file:/home/bwolfe/standalone/target/classes/
[INFO] ------------------------------------------------------------------------
[INFO] Settings----------------------------
[INFO]     driver: com.mysql.jdbc.Driver
[INFO]     url: jdbc:mysql:mxj://127.0.0.1:3326/openmrs?autoReconnect=true&sessionVariables=storage_engine=InnoDB&useUnicode=true&characterEncoding=UTF-8&server.initialize-user=true&createDatabaseIfNotExist=true&server.basedir=emptydatabase&server.datadir=emptydatabase/data&server.collation-server=utf8_general_ci&server.character-set-server=utf8&server.max_allowed_packet=32M
[INFO]     username: openmrs
[INFO]     password: test
[INFO]     use empty password: false
[INFO]     properties file: null
[INFO]     properties file will override? false
[INFO]     prompt on non-local database? true
[INFO]     clear checksums? false
[INFO]     changeLogFile: liquibase-schema-only.xml
[INFO]     drop first? false
[INFO]     context(s): null
[INFO]     number of changes to apply: 0
[INFO] ------------------------------------------------------------------------
[/home/bwolfe/standalone/emptydatabase/bin/mysqld][--no-defaults][--port=3326][--collation-server=utf8_general_ci][--max_allowed_packet=32M][--character-set-server=utf8][--socket=mysql.sock][--basedir=/home/bwolfe/standalone/emptydatabase][--datadir=/home/bwolfe/standalone/emptydatabase/data][--pid-file=/home/bwolfe/standalone/emptydatabase/data/MysqldResource.pid]
[MysqldResource] launching mysqld (driver_launched_mysqld_1)
Exception in thread "driver_launched_mysqld_1" com.mysql.management.util.WrappedException: java.io.IOException: Cannot run program "/home/bwolfe/standalone/emptydatabase/bin/mysqld": java.io.IOException: error=2, No such file or directory
    at com.mysql.management.util.Exceptions.toRuntime(Exceptions.java:55)
    at com.mysql.management.util.Exceptions$Block.exec(Exceptions.java:89)
    at com.mysql.management.util.RuntimeI$Default.exec(RuntimeI.java:180)
    at com.mysql.management.util.Shell$Default.run(Shell.java:140)
    at java.lang.Thread.run(Thread.java:636)
Caused by: java.io.IOException: Cannot run program "/home/bwolfe/standalone/emptydatabase/bin/mysqld": java.io.IOException: error=2, No such file or directory
    at java.lang.ProcessBuilder.start(ProcessBuilder.java:475)
    at java.lang.Runtime.exec(Runtime.java:610)
    at com.mysql.management.util.RuntimeI$Default$1.inner(RuntimeI.java:177)
    at com.mysql.management.util.Exceptions$Block.exec(Exceptions.java:86)
    ... 3 more
Caused by: java.io.IOException: java.io.IOException: error=2, No such file or directory
    at java.lang.UNIXProcess.<init>(UNIXProcess.java:164)
    at java.lang.ProcessImpl.start(ProcessImpl.java:81)
    at java.lang.ProcessBuilder.start(ProcessBuilder.java:468)
    ... 6 more


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