Help installing OpenMRS

[Michael Koontz]

Hello,

I'm new to using Linux and very new to OpenMRS standalone and enterprise (first time installing it) and have ran in to some installation issues with the enterprise version.
I am not installing it locally.  I have 2 different VPS that I am using.  The server is running CentOS 6 with Java 1.6 and Tomcat6 installed.  I have gotten as far as deploying the OpenMRS installation on both VPS which is where I have run in to the errors.

With the first server, from the Tomcat Manager html page I have deployed the OpenMRS package by uploading it.  After some time the page refreshed and under "Applications" I see /openmrs.  When I click on /openmrs it brings me to the OpenMRS installation wizard page.  I make sure English is selected and check the box next to "remember this choice".  When I click the arrow to continue I get the following error message:

Error!
A runtime properties file is needed for OpenMRS to start up consistently.
OpenMRS is unable to create this file : /var/lib/OpenMRS/openmrs-runtime.properties
Because of this error : Permission denied

You must correct this before continuing.

With the second server I actually get much further to the point where I tell it to proceed with the installation.  I see it going the the "Tasks to Execute" and it completes all of them except for the last one "Update the Database".  It hangs there at 55%.  When I view the Output Details I see the following error messages:

Updating database tables to latest version (289/526): Author: wyclif Comments: Setting the concept name type for short names Description: Update Data, Delete Data (x2)

Number of actions completed so far: 718

Server log file output: WARN - OpenmrsUtil.getRuntimePropertiesFilePathName(2597) |2014-12-16 05:11:21,708| Unable to find properties file: /usr/share/tomcat6/.OpenMRS/openmrs-runtime.properties
WARN - OpenmrsUtil.getRuntimeProperties(2534) |2014-12-16 05:11:21,709| Unable to find a runtime properties file. Initial setup is needed. View the webapp to run the setup wizard.
WARN - OpenmrsUtil.getRuntimePropertiesFilePathName(2571) |2014-12-16 05:18:28,338| Unable to find a runtime properties file at /usr/share/tomcat6/openmrs-runtime.properties
WARN - OpenmrsUtil.getRuntimePropertiesFilePathName(2597) |2014-12-16 05:18:28,340| Unable to find properties file: /usr/share/tomcat6/.OpenMRS/openmrs-runtime.properties
ERROR - Context.getServiceContext(255) |2014-12-16 06:18:57,420| serviceContext is null. Creating new ServiceContext()

I've tried searching the web for answers on how to solve these issues but I am not having any luck.  If anyone here could help me I would greatly appreciate it.

regards,

Michael

[Daniel Kayiwa]

Which version of OpenMRS are you trying to install?

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[Michael Koontz]

Hello Daniel,

Thank you for the reply.  The version I'm trying to install is OpenMRS Platform 1.10.1 WAR (for Enterprise) downloaded directly from this page http://openmrs.org/download/.

Is there another version I should be installing on a CentOS server?

regards,

Michael

[Michael Koontz]

I have a quick update here.  I went back through and looked at some things and tried working with the permissions for OpenMRS installation on Server 1.

I logged in as root to the server and performed the following commands:

mkdir /usr/share/tomcat6/.OpenMRS/
chown -R tomcat:root /usr/share/tomcat6/.OpenMRS/
cd /usr/share/tomcat6/.OpenMRS/
vi openmrs-runtime.properties
chown -R tomcat:root /usr/share/tomcat6/.OpenMRS/openmrs-runtime.properties

I added a single space to the file openmrs-runtime.properties before doing chown on it.
After doing all of that the installation proceeded much further but then I ended up with the following error messages.

There was an error while updating the database to the latest. file: liquibase-update-to-latest.xml. Error: Error executing SQL SELECT FILENAME,AUTHOR,ID,MD5SUM,DATEEXECUTED,ORDEREXECUTED,TAG,EXECTYPE FROM `liquibasechangelog` ORDER BY DATEEXECUTED ASC, ORDEREXECUTED ASC: Out of memory (Needed 411312 bytes) Error while trying to update to the latest database version

There was an error while updating the database to the latest. file: liquibase-schema-only.xml. Error: Error executing SQL SELECT FILENAME,AUTHOR,ID,MD5SUM,DATEEXECUTED,ORDEREXECUTED,TAG,EXECTYPE FROM `liquibasechangelog` ORDER BY DATEEXECUTED ASC, ORDEREXECUTED ASC: Out of memory (Needed 411312 bytes) See the error log for more details

On the second server I tried the same thing and this time it looked like it completed successfully but I wasn't taken to the OpenMRS front page.  Instead it stayed on the final install page.  When I went back to the Tomcat html manager and tried to start OpenMRS I received a whole host of errors.

The following error occurred at startup:

Error occurred while trying to get the updates needed for the database. Unable to get a connection to the database. Please check your openmrs runtime properties file and make sure you have the correct connection.username and connection.password set

java.lang.RuntimeException: Error occurred while trying to get the updates needed for the database. Unable to get a connection to the database.  Please check your openmrs runtime properties file and make sure you have the correct connection.username and connection.password set
	at org.openmrs.util.DatabaseUpdater.getUnrunDatabaseChanges(DatabaseUpdater.java:631)
	at org.openmrs.util.DatabaseUpdater.getUnrunDatabaseChanges(DatabaseUpdater.java:590)
	at org.openmrs.util.DatabaseUpdater.updatesRequired(DatabaseUpdater.java:262)
	at org.openmrs.web.Listener.setupNeeded(Listener.java:171)
	at org.openmrs.web.Listener.contextInitialized(Listener.java:143)
	at org.apache.catalina.core.StandardContext.listenerStart(StandardContext.java:4210)
	at org.apache.catalina.core.StandardContext.start(StandardContext.java:4709)
	at org.apache.catalina.core.ContainerBase.addChildInternal(ContainerBase.java:791)
	at org.apache.catalina.core.ContainerBase.addChild(ContainerBase.java:771)
	at org.apache.catalina.core.StandardHost.addChild(StandardHost.java:526)
	at org.apache.catalina.startup.HostConfig.deployDescriptor(HostConfig.java:637)
	at org.apache.catalina.startup.HostConfig.deployDescriptors(HostConfig.java:563)
	at org.apache.catalina.startup.HostConfig.deployApps(HostConfig.java:498)
	at org.apache.catalina.startup.HostConfig.start(HostConfig.java:1277)
	at org.apache.catalina.startup.HostConfig.lifecycleEvent(HostConfig.java:321)
	at org.apache.catalina.util.LifecycleSupport.fireLifecycleEvent(LifecycleSupport.java:142)
	at org.apache.catalina.core.ContainerBase.start(ContainerBase.java:1053)
	at org.apache.catalina.core.StandardHost.start(StandardHost.java:722)
	at org.apache.catalina.core.ContainerBase.start(ContainerBase.java:1045)
	at org.apache.catalina.core.StandardEngine.start(StandardEngine.java:443)
	at org.apache.catalina.core.StandardService.start(StandardService.java:516)
	at org.apache.catalina.core.StandardServer.start(StandardServer.java:710)
	at org.apache.catalina.startup.Catalina.start(Catalina.java:593)
	at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
	at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:57)
	at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
	at java.lang.reflect.Method.invoke(Method.java:622)
	at org.apache.catalina.startup.Bootstrap.start(Bootstrap.java:289)
	at org.apache.catalina.startup.Bootstrap.main(Bootstrap.java:414)
Caused by: java.lang.Exception: Unable to get a connection to the database.  Please check your openmrs runtime properties file and make sure you have the correct connection.username and connection.password set
	at org.openmrs.util.DatabaseUpdater.getLiquibase(DatabaseUpdater.java:368)
	at org.openmrs.util.DatabaseUpdater.getUnrunDatabaseChanges(DatabaseUpdater.java:617)
	... 28 more
Caused by: com.mysql.jdbc.exceptions.jdbc4.MySQLNonTransientConnectionException: Could not create connection to database server. Attempted reconnect 3 times. Giving up.
	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:534)
	at com.mysql.jdbc.Util.handleNewInstance(Util.java:411)
	at com.mysql.jdbc.Util.getInstance(Util.java:386)
	at com.mysql.jdbc.SQLError.createSQLException(SQLError.java:1015)
	at com.mysql.jdbc.SQLError.createSQLException(SQLError.java:989)
	at com.mysql.jdbc.SQLError.createSQLException(SQLError.java:975)
	at com.mysql.jdbc.SQLError.createSQLException(SQLError.java:920)
	at com.mysql.jdbc.ConnectionImpl.connectWithRetries(ConnectionImpl.java:2395)
	at com.mysql.jdbc.ConnectionImpl.createNewIO(ConnectionImpl.java:2316)
	at com.mysql.jdbc.ConnectionImpl.(ConnectionImpl.java:834)
	at com.mysql.jdbc.JDBC4Connection.(JDBC4Connection.java:47)
	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:534)
	at com.mysql.jdbc.Util.handleNewInstance(Util.java:411)
	at com.mysql.jdbc.ConnectionImpl.getInstance(ConnectionImpl.java:416)
	at com.mysql.jdbc.NonRegisteringDriver.connect(NonRegisteringDriver.java:347)
	at java.sql.DriverManager.getConnection(DriverManager.java:615)
	at java.sql.DriverManager.getConnection(DriverManager.java:195)
	at org.openmrs.util.DatabaseUpdater.getConnection(DatabaseUpdater.java:427)
	at org.openmrs.util.DatabaseUpdater.getLiquibase(DatabaseUpdater.java:365)
	... 29 more
Caused by: java.sql.SQLException: Access denied for user 'test'@'localhost' (using password: YES)
	at com.mysql.jdbc.SQLError.createSQLException(SQLError.java:1086)
	at com.mysql.jdbc.MysqlIO.checkErrorPacket(MysqlIO.java:4237)
	at com.mysql.jdbc.MysqlIO.checkErrorPacket(MysqlIO.java:4169)
	at com.mysql.jdbc.MysqlIO.checkErrorPacket(MysqlIO.java:928)
	at com.mysql.jdbc.MysqlIO.secureAuth411(MysqlIO.java:4736)
	at com.mysql.jdbc.MysqlIO.doHandshake(MysqlIO.java:1342)
	at com.mysql.jdbc.ConnectionImpl.coreConnect(ConnectionImpl.java:2493)
	at com.mysql.jdbc.ConnectionImpl.connectWithRetries(ConnectionImpl.java:2334)
	... 43 more

See the server log for full output.

Once again, any help solving these issues would be greatly appreciated.

regards,

Michael

[Daniel Kayiwa]

Can you increase your tomcat memory as per this page? https://wiki.openmrs.org/display/docs/Troubleshooting+Memory+Errors

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[prateek pandey]

Hey,
In your first method, you have to use 'sudo' command before executing other commands. This is done to give apt permission for the file to install.
This is done for every installation you do if you are not working as a root user.

Prateek Pandey

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[prateek pandey]

[Harsha Kumara]

Hi Michael Koontz,

Shall we do a fresh installation. First you will need to drop the openmrs db if it created in your mysql server. And then remove the OpenMRS directory file in either in var/lib or home directory as a hidden file. 

Make sure you give mydql root user with a password. By default mysql root user doesn't have a password and you will need to setup a one.

The exception shows, error while connecting to the database.

Thanks,

Harrsha

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Harsha Kumara

Software Engineer

WSO2 Inc.

Sri Lanka.

[Michael Koontz]

Thanks everyone for all the responses!

I decided to start from scratch and had the vps reinstall the OS.  I then proceeded to install Java 1.6, MySQL and Tomcat6.  I deployed the OpenMRS.war file by uploading it through the Tomcat6 html manager page.

When I clicked on /openmrs to start the installation it went to the end and got to where it said "Update the Database" and got stuck at 28% !
The output details were as follows:

Updating database tables to latest version (147/526): Author: bwolfe Comments: Creating unique index on concept_description.uuid column Description: Create Index

Number of actions completed so far: 576

Server log file output: WARN - OpenmrsUtil.getRuntimePropertiesFilePathName(2571) |2014-12-17 12:21:55,010| Unable to find a runtime properties file at /usr/share/tomcat6/openmrs-runtime.properties
WARN - OpenmrsUtil.getRuntimePropertiesFilePathName(2597) |2014-12-17 12:21:55,010| Unable to find properties file: /var/lib/OpenMRS/openmrs-runtime.properties
WARN - OpenmrsUtil.getRuntimePropertiesFilePathName(2571) |2014-12-17 12:27:07,038| Unable to find a runtime properties file at /usr/share/tomcat6/openmrs-runtime.properties
WARN - OpenmrsUtil.getRuntimePropertiesFilePathName(2597) |2014-12-17 12:27:07,039| Unable to find properties file: /var/lib/OpenMRS/openmrs-runtime.properties
ERROR - Context.getServiceContext(255) |2014-12-17 12:30:33,784| serviceContext is null. Creating new ServiceContext()

So far it's just sitting there not going past 28%.  I'm really at a loss here.  Again thank you for any and all help.

regards,

Michael

[Daniel Kayiwa]

Can you paste the contents of your tomcat log at http://pastebin.com/?

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[Michael Koontz]

Daniel,

I used your suggestion and increased the tomcat memory without any problems.  Thank you for that tip as I stopped running in to the memory issues.

regards,

Michael

[Harsha Kumara]

Hi Michael,

Did you gave the read write permissions for the /var/lib/OpenMRS/ directory? Seems like runtime property file is not created.

Thanks,

Harsha

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[Michael Koontz]

Daniel,

Please excuse my ignorance.  Can you give me a link to a resource on where to find the log file for tomcat?

Harsha,

I did the following for the permissions:

sudo chown -R tomcat:root /var/lib/OpenMRS/
sudo chown -R tomcat:root /var/lib/OpenMRS

Is that suffecient?

regards,

Michael

[Daniel Kayiwa]

You could look for a file named catalina.out in /usr/share/tomcat6/logs

[Michael Koontz]

Daniel,

I don't have any kind of gui, only command line.  I've found the file no problem and can view it but I'm having trouble copying everything out of the file.  Can you give me some tips on how to copy the file or the contents of the file so I can put them on pastebin.

regards,

Michael

[Daniel Kayiwa]

Try copying the file from the server to your local current directory with something like below:

scp username@server:/usr/share/tomcat6/logs/catalina.out catalina.out

[Michael Koontz]

Thanks for the help Daniel,  While I have my MCSE & MCSA and have done several things in DOS in the years past I'm really not used to doing things in Linux/Unix command line without a gui.  Anyways, I ended up uploading the file via ftp from the linux vps to my webhost where I downloaded it.  Here's the link to the catalina.out file contents on pastebin.
http://pastebin.com/JeaUZmL8

regards,

Michael

[Daniel Kayiwa]

According to this line from your log: "There is insufficient memory for the Java Runtime Environment to continue."

Your server does not have enough memory for Java.

NB: You correctly set the Java memory options. So no need to set these again for now.

You could either boost your server with more memory, or try to restart it, just in case there is some process eating it up.

By the way, how much total memory does your server have?

If these two do not work, then i will give you one extra option before i run out of ideas. :)

[Michael Koontz]

Daniel,

Thank you for reviewing the information.  I am using a VPS from Interserver.  I guess I would need to upgrade to get more memory.

Storage 25GB

Memory 1024MB

Transfer 1TB

What is the minimum amount of memory required to run OpenMRS?

regards,

Michael

[Daniel Kayiwa]

There are some guidelines here: https://wiki.openmrs.org/display/docs/System+Requirements

[Michael Koontz]

For what I'm doing the server requirements should be enough as I'm just trying to install and I won't have anywhere near 10,000 patients.  What was your other idea?

[Lluis Martinez]

Hi Michael

256 MB seems very optimistic to me. Even with a very small database the amount of RAM needed for the JRE + the webapp will be  bigger. 256MB could be ok just for the heap.

Cheers

[Michael Koontz]

Hello Everyone,

I'm still having trouble installing the Enterprise version of OpenMRS.  I gave up on trying to use an online Virtual Machine as they weren't offering enough memory or CPU speed.  I've since resorted to using VMWare and CentOS 6.6 x86_64 with 2Gb of ram.  I've tried installing OpenMRS many different ways but always seem to run in to some trouble.  Could someone please provide me a definitive step by step guide for installing OpenMRS?  Please keep in mind that I am new to Linux so even the smallest command that you might take for granted might fly over my head.

Here is a list of tutorials I have tried thus far for installing OpenMRS:
https://wiki.openmrs.org/pages/viewpage.action?pageId=38635088
http://www.unixmen.com/install-openmrs-open-medical-record-system-centos-6-5/

My last attempt and thus far most successful attempt still left me with more error messages.  This last time I actually got past the installation process but when OpenMRS tried to open index.htm page for the first time I got some kind of java error (http://pastebin.com/tJfZ60B5)

I've tried using the commands to just simply install Java with what CentOS 6 ships with and I've tried downloading it and installing it directly upgrading Java.  I'm guessing since I got Tomcat6 working, and the

java -version

command shows me that I'm running Java 1.6.0.45 I did things correctly.  I also made sure that I removed Java versions 1.5 & 1.7.

So now on to Tomcat 6.  Instead of installing it the way described in the tutorial I already linked above:
http://www.unixmen.com/install-openmrs-open-medical-record-system-centos-6-5/
I installed it by following the directions found here
http://tecadmin.net/steps-to-install-tomcat-server-on-centos-rhel/
adjusting of course for the fact that I was using Tomcat 6 instead of version 7 used in their directions.

Also, I'd like to ask if this code, found here listed under "other operating systems" has an error in it

sudo useradd tomcat6
cd /opt
sudo tar zxvf apache-tomcat-6.0.29.tar.gz
sudo ln -s apache-tomcat-6.0.29 tomcat6
sudo chown tomcat6.tomcat6 apache-tomcat-6.0.29

Where is says tomcat6.tomcat6, should the . be replaced by a : ?  I ask because if I type it in like that I receive an error that the user does not exist but if I replace the . with a : it works with no errors.

It seems each time I do a search there are different ways to install either Java, Tomcat, etc... in order to get OpenMRS up and running and I'm really getting confused as to what is the proper way.  There has got to be some ultimate source on how to do it properly that I just can't find.  If anyone could help me out with that resource I would be most appreciative!

regards,

Michael

[Daniel Kayiwa]

Hi Michael,

Your pastebin.com error looks familiar. Can you restart tomcat and then try again?

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[Daniel Kayiwa]

By "try again" i mean log in OpenMRS again.

[TCHEUTCHOUA SALDEU STEVE LIONEL]

hi Mikael ,

You can always change the default version your linux system uses for java using the command

sudo update-alternatives --config java

You could also try installing openmrs following help from https://wiki.openmrs.org/display/docs/Installing+OpenMRS

If the only problem you are facing now is installing tomcat, you can also download it from http://tomcat.apache.org/download-80.cgi and run the startup.sh script in the bin directory.

I followed the procedure from the first link above and successfully installed openmrs two days ago.

Hope it helps.

[Michael Koontz]

Hello Daniel,

That worked!  Not sure why but OpenMRS started after restarting Tomcat.  However I now have 2 new problems.
The less important problem, which I'm sure I can fix is the fact that Tomcat is not recognized as a service how I set it up so I have to go in to th! directory and manually do a shutdown and startup.
The more important problem is that even though OpenMRS started and prompted me to login it is not recognizing the admin password I set.  I found this thread explaining how to reset the admin password which I will try to work on tomorrow:
https://answers.openmrs.org/questions/135/how-do-i-change-password-on-database-backend
If that doesn't work I will just try to undeploy and redeploy.

Thanks again for the suggestion and all the help!

regards,

Michael

[Michael Koontz]

OK, I undeployed OpenMRS and uninstalled Tomcat 6 just to reinstall them and run in to the same errors.  Once again restarting Tomcat solved the error again but OpenMRS still didn't recognize the password I set during the installation.  I tried the default password of "test" and it let me login as admin.  Not sure why that happened but I was able to log in and change the admin password.  I also created a new admin/provider account.  Now I just have to figure out how to use this to it's fullest potential.

Thank for all the replies and the help!

regards,

Michael

[Daniel Kayiwa]

Just in case you had not seen this: http://flossmanuals.net/openmrs-guide/

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[Wyclif Luyima]

Hi Michael,

I think there is something strange about our install wizard, when you choose to install add demo data, the scripts actually overwrite your users table in the DB meaning the password for the admin account is that in the demo data which is test. I think we need to fix the wizard not to ask the user for the username and password when they choose to add demo data since it gets ignored. I have created TRUNK-4564 to get it fixed and avoid the confusion

Wyclif

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[Michael Koontz]

Hello Wyclif,

Thank you for the reply however I did not choose to install the demo data.

regards,

Michael