Install OpenEMR on Ubuntu 14.04 server

1) Install apache2
#apt-get install apache2
2) Install php5(atleast 5.4 version for OpenEMR)
#apt-get install php5
check the version of th php installed 
#php -v
PHP 5.5.9-1ubuntu4.14 (cli) (built: Oct 28 2015 01:34:46)
Copyright (c) 1997-2014 The PHP Group
Zend Engine v2.5.0, Copyright (c) 1998-2014 Zend Technologies
    with Zend OPcache v7.0.3, Copyright (c) 1999-2014, by Zend Technologies
 
3) Install mysql
#apt-get install mysql-server-5.5
 
4) Install php5-mysql mysql-client
#apt-get install php5-mysql mysql-client

 Modify the php.ini file according to the following
max_execution_time = 60
        max_input_time = 90
        memory_limit = 128M
        display_errors = Off
        log_errors = On
        register_globals = Off
        post_max_size = 30M
        file_uploads = On
        upload_max_filesize = 30M
        error_reporting = E_ALL & ~E_NOTICE & ~E_STRICT & ~E_DEPRECATED
        max_input_vars = 3000
        extension_mysql = mysql.so

       
5) download the OpenEMR from sourceforge.
http://sourceforge.net/projects/openemr/files/OpenEMR%20Current/4.2.0.3/openemr-4.2.0.tar.gz/download

6) Extract the tar file
 tar -pxvzf openemr-4.2.0.tar.gz

7) Move extracted files to apache web location
 mv openemr-4.2.0 /var/www/html/openemr

8) Then after go to the local site that is been deployed 
http://localhost/openemr 
        or
http://{ubuntu-server-ip}/openemr

Follow the screens mentioned in the below link
http://www.open-emr.org/wiki/index.php/OpenEMR_4.2.0_Linux_Installation

 

 

Install OpenMRS on Ubuntu 14.04 server

1) Install Java
    Download Java from Oracle site
http://www.oracle.com/technetwork/java/javase/downloads/java-archive-javase8-2177648.html

extract the tar file

tar -zxvf jdk-7*

Install java 

mv jdk1* /usr/local/
ln -s /usr/local/jdk1* /usr/local/java

After this step type java in terminal if you get "command not found error" then execute following commands based on the location you specified in above step.

#To update java command alternatives
update-alternatives --install "/usr/bin/java" "java" "/usr/local/java/bin/java" 1
#To update javac command alternatives
update-alternatives --install "/usr/bin/javac" "javac" "/usr/local/java/bin/javac" 1
#To udate javaws command alternatives
update-alternatives --install "/usr/bin/javaws" "javaws" "/usr/local/java/bin/javaws" 1

2) Install Tomcat

Download tomcat latest tar file for linux and do the following steps

Extract the tar file.

tar -zxvf apache-tomcat-*

Move the extracted files to the specific location.

mv apache-tomcat-* /usr/local/

Create Symlink for tomcat files/

ln -s /usr/local/apache-tomcat-7.0.52 /usr/local/tomcat 

Add user for the tomcat

/usr/sbin/adduser tomcat

3) Install Mysql
apt-get install mysql-server-5.5

An intermediate GUI appears to provide mysql root user  password. Please provide the password and repeat the same password again in the next screen.

4) Download and deploy OpenMRS
http://openmrs.org/download/
download platform war file in the above visited page.

5) Create the properties file in 
/usr/local/apache-tomcat-7.0.52/bin/openmrs-runtime.properties
The contents of the properties file should be like

### Database connection properties

connection.username=root

connection.password=root

6) Copy the openmrs.war file into tomcat webapps folder.
cp openmrs.war /usr/local/tomcat/webapps/

7) open the browser and go to your local openmrs application.
http://localhost:8080/openmrs
or
http://{Ubuntu-serverip}:8080/openmrs.

8) The initial setup wizard will appear to create the database schema and to load the sample data to the openmrs application. Follow the instructions.

Request for removal of a page from Google search engine

https://www.google.com/webmasters/tools/removals?pli=1

https://support.google.com/webmasters/answer/63758

Openclinica 3.8 installation on ubuntu 14.04 server

This week we worked on installing Openclinica for one of our client. The wiki page gives detailed steps but some things need to be added to that.

Here I am going to give detailed steps. Most of the steps copied from the wiki page.

1) The prerequisites are
ubuntu machine with following softwares installed
vim
unzip
tar
You require "root" user access. Run all commands in the installation instructions using root-level permission.

2) Install Java
Openclinica is based on Java.

#Create folder if it doesn't exist
mkdir -p /usr/local/oc/install 

#Change to this folder:
cd /usr/local/oc/install

#Download jdk into the above folder
#find the 32-bit version here: https://openclinica.app.box.com/oc-downloads/1/2186650849
#find the 64-bit version here: https://openclinica.app.box.com/oc-downloads/1/2186651363 

#Install Java by running:
tar -zxvf jdk-7* 

#Install Java in the operating system by running:
mv jdk1* /usr/local/
ln -s /usr/local/jdk1* /usr/local/java

After above steps test java installed by typing java and javac. If the command not found error occurs.
Then you need to update the alternatives by following commands
#To update java command alternatives
update-alternatives --install "/usr/bin/java" "java" "/usr/local/java/bin/java" 1
#To update javac command alternatives
update-alternatives --install "/usr/bin/javac" "javac" "/usr/local/java/bin/javac" 1
#To udate javaws command alternatives
update-alternatives --install "/usr/bin/javaws" "javaws" "/usr/local/java/bin/javaws" 1

3) Install tomcat

#Create folder if it doesn't exist
mkdir -p /usr/local/oc/install

#Change to this folder:
cd /usr/local/oc/install

#Download tomcat into the above folder
wget https://dev.openclinica.com/oc/software/OpenClinica-3.2/linux/apache-tomcat-7.0.52.tar.gz

#Install Tomcat by running the following:
tar -zxvf apache-tomcat-*
mv apache-tomcat-* /usr/local/
ln -s /usr/local/apache-tomcat-7.0.52 /usr/local/tomcat
/usr/sbin/adduser tomcat

#Update the File Path parameter to the correct value
chown -R tomcat /usr/local/tomcat/*
chown -R tomcat /usr/local/apache-*

4) Install PostgreSql 

We have installed postgresql 9.3. Observed that 8.4 does not work with OpenClinica 3.8.

#Install postgresql

apt-get install postgresql

Then enter into the database to create a role and database for the openclinica.

# to connect to the localhost psql

psql -U postgres
If you get following error
psql: FATAL:  Peer authentication failed for user "postgres"
then
#Edit the /etc/postgresql/9.1/main/pg_hba.conf
local   all   postgres     peer
Should be
local   all   postgres     md5
 And restart the postgresql service
service postgresql restart
sudo -i -u postgres
psql

#Enter the password that is given at the time of installation

#Create role clinica with password clinica

CREATE ROLE clinica LOGIN ENCRYPTED PASSWORD 'clinica' SUPERUSER NOINHERIT NOCREATEDB NOCREATEROLE;
#Create database openclinica
CREATE DATABASE openclinica WITH ENCODING='UTF8' OWNER=clinica;

#To change the password of 'clinica' role

ALTER USER clinica WITH PASSWORD 'newpassword';
#Exit the psql command prompt by typing

\q

5) Deploying OpenClinica within tomcat

#Create folder if it doesn't exist
mkdir -p /usr/local/oc/install

#Change to this folder:
cd /usr/local/oc/install

# Download the OpenClinica software from the OpenClinica 

# website: https://community.openclinica.com/project/openclinica. 

# To download the software, you need an OpenClinica community user account, 

# which is free to create; you will be required to log in to the account to download the

# OpenClinica software.

#Run the following commands. In the commands, v.x is your version of OpenClinica:
unzip OpenClinica-v.x*
cd OpenClinica-v.x*/distribution
unzip OpenClinica.war -d OpenClinica
cp -rf OpenClinica* /usr/local/tomcat/webapps

6) Configure the Openclinica application

If you followed all the previous instructions exactly, there is only one property in the configuration file, datainfo.properties, that you may need to change in order for OpenClinica to start. There are other properties in the configuration file you will probably want to modify for your system.
The first time you install OpenClinica you will configure datainfo.properties here: /usr/local/tomcat/webapps/OpenClinica/WEB-INF/classes/datainfo.properties. Consequent configuration changes SHOULD be made here /usr/local/tomcat/webapps/openclinica.config.

1. Open the configuration file: /usr/local/tomcat/webapps/OpenClinica/WEB-INF/classes/datainfo.properties
2. Edit values for the properties in the datainfo.properties file. You must change the value for dbPass to the password you selected in Set Up the PostgreSQL Database. Change the values for any other properties, then save the file.
3. Update the filePath parameter to the right value.
4. Run the following commands:

7) Start the tomcat

#To set Tomcat to start automatically on system startup, run the following: 

cp /usr/local/oc/install/OpenClinica-v.x*/install-docs/linux/tomcat /etc/init.d/
cd /etc/init.d
chmod a+x /etc/init.d/tomcat

#update the rc.d

update-rc.d tomcat defaults

service tomcat start

8) Go to http://{ubuntu-server-ip}:8080/OpenClinica/
default username : root
default password  : 12345678

After creating a user the password is shown under alerts&messages left panel.

Setting static IP in ubuntu

Login as sudo user or root user

$# sudo vi /etc/network/interfaces
replace following two lines

auto eth0
iface eth0 inet dhcp

With

auto eth0
iface eth0 inet static
address 192.168.100.109
netmask 255.255.255.0
gateway 192.168.100.1
write and quit(:wq) from the vi editor.

restart machine to take effect. If needed modify /etc/resolv.conf for dns servers information.
 

SFlow and Ganglia integration

For monitoring large clusters Ganglia is a robust open source tool. For a customer we have worked on the Ganglia.

We followed this blog to install Ganglia on ubuntu servers. This blog is also good one to start withGanglia contains three components.
1) gmetad
2) gmond
3) ganglia-webfront

We have installed gmetad on ubuntu 14.04. The Ganglia version is 3.6.0.
In other versions of ubuntu systems like 13.04,12.04 and 11.04, we first updated the repositories by sudo apt-get update.
We faced some issues in  updating 12.04 fresh os installation. We solved by replacing in.archive.ubuntu.com and security.ubuntu.com with oldreleases.ubuntu.com in /etc/apt/sources.list file.

after that we installed ganglia-monitor i.e., gmond by using sudo apt-get install ganglia-monitor.

The configuration changes are same as in the blog.

Time Synchronization is very important in these type of tools where master: slave or collector:sender type of installations.

It is essential that all hosts participating in the Ganglia monitoring system have a synchronized clock. Proactively deploying network time protocol (NTP) is highly recommended.

Due to the time issue we have seen this log in /var/log/syslog of gmond on ubuntu 12.04,13.04 and 11.04 servers. 
/usr/sbin/gmetad[2782]:RRD_update (/var/lib/ganglia/rrds/...metric.rrd): illegal attempt to
update using time 1329950002 when last update time is 1329950002
(minimum one second step)

After that for more metrics we have integrated the Sflow with Ganglia.
For installing Sflow we followed this blog. 

After installing Sflow we need to configure Sflow to send the metrics to gmond. we also need to configure gmond to receive metrics from the Sflow. There are two configurations we need to include in the gmetad server's gmond configuration file /etc/ganglia/gmond.conf. The configurations are

/* sFlow channel */
udp_recv_channel {
  port = 6343
}

sflow{
  accept_vm_metrics = yes
}

More about these configurations you can find below blog posts.
Ganglia-Sflow-VM-monitoring-Configuration
Ganglia-Configurations

VMware tools installation in ubuntu 11.10,12.10,14.04

Installing VMware tools on the VMware virtual machines is important.
I followed the blog post from VMware
VMware-Tools-Install

Some times while installing VMware tools in 11.10 you may get issues. For that before initiating installation of VMware tools from the VMware vsphere client, you need to select client device in device settings of the virtual machine

After that you can initiate the VMware tools installation.
In the Virtualmachine console
step1
$# sudo mkdir /mnt/cdrom
$# sudo mount /dev/cdrom /mnt/cdrom
$# tar xzvf /mnt/cdrom/VMwareTools-x.x.x-xxxx.tar.gz -C /tmp/
$# cd /tmp/vmware-tools-distrib/
$# sudo ./vmware-install.pl -d

Then reboot the virtualmachine
Now you can see the vmware tools running in the vsphere client.