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caGrid Production VM Release Notes

The following steps describe how to install the cagrid-production virtual machine.

Acquire the VM

Download the vm image tarball to the VM image hosting location on your platform
```
wget http://138.26.125.70/vm/cagrid-production-0.1.tar.gz
```
Unpack the image
```
tar -xzf cagrid-production-0.1.tar.gz
```
This will create a directory cagrid-production that contains the VM description file cagrid-production.vmx.
Add this to your VM collection by opening the vmx file via your VM console interface

Configure the VM

In order to configure the VM, it's necessary to first boot into single user mode in order to customize the IP address and host name configuration for your environment.

Start the newly loaded VM
At the Grub boot prompt press ESC to stop the default boot process
- Press e to edit the selected (default) boot entry
- Scroll to the line that begins with kernel and press e to edit the boot parameters
- Add the word single to the end of the boot arguments
- Press enter to save the changes
- Press b to begin the boot process
The VM will complete the boot into single user mode and present a command-line for root. It is now ready for the following configuration steps.

Network Configuration

Change the IP address and host name at the following locations

/etc/hosts (ip addr + hostname)
/etc/sysconfig/network-scripts/ifcfg-eth0 (ip addr)
/etc/sysconfig/network (hostname)

The host firewall is pre-configured with the following ports open to support the production services of the VM. You need to ensure that other network firewalls are configured to reflect this port profile.

Standard system service ports
- 5353 (DNS)
- 123 (NTP)
- 22 (SSH)
End-user web applications for demonstration caBIG applications (caArray and User Provisioning Tool (UPT))
- 38080 (caArray)
- 46210 (UPT)
caGrid data services for the production caGrid environment (these are the interfaces accessed from caBIG).
- 8080 (Labkey)
- 18080 (caArray)

After making sure the firewall is configured, need to bring up the machine with the network service on. Building the services without the network connection results in a build failure. A bug on this failure has been documented here.

Boot the machine at this point in multi user mode,. which will bring up the network service.

init 3

VMWare Tools Configuration

Sync the VM time with the ESXi Server Time

From the ESXi Server GUI, select the cagrid VM, right-click, and select Install VMware Tools
Open the VM console and login as root
Mount the virtual cdrom device
```
mount /dev/cdrom /mnt
```
Install the VMWare Tools
```
rpm -ivh /mnt/VMWareTools.........rpm
```
Execute the vmware tools script and change/keep the guest x resolution
```
vmware-config-tools.pl
```
The script adds the vmware tools as a system service and starts the service. Check for the service
```
chkconfig --list | grep -i vm
```

caArray Service

The caArray service embeds the host name and IP address in its binaries. Therefore, whenever we change these values for the host we need to rebuild caArray so the binaries use the new values.

Backup the Database

Before rebuilding the caArray service, we need to back up the existing caArray database since it is destroyed during the rebuild.

cd /usr/local/mysql/data
date=`date +"%Y%m%d"`
tar -cf caarray-backup-$date.tar caarray

After the data is protected, we can drop the existing database to ensure a clean build

mysql -u root -p
mysql> drop database caarray;

Rebuild caArray

The rebuild requires that we change IP address in the services install.properties file to the new IP address of your host.

Change to the caArray account
```
su - caarray
cd src/caarray2
```

Set a variable with the new IP address and patch the file

newip=12.34.56.78 # this is whatever your new IP address is

patch --ignore-whitespace --backup install.properties << EOF
4c4
< application.host.ipaddr=138.26.125.99
---
> application.host.ipaddr=$newip
EOF

Rebuild the service
```
ant
```
Exit from the caarray account
```
exit
```

Restore the Database

Restore the caarray database so that it contains the test data to query the caArray service from the caBIG portal

cd /usr/local/mysql/data
tar -xf caarray-backup-$date.tar caarray

Change Service Metadata

Re-building of caBig services (caArray/caTissue), changes the service metadata, by overwriting the Point of Contact information with those of NCI's. Hence, after re-building the caArray/caTissue, need to edit serviceMetadata.xml to contain the following point of contact information

  <ns1:hostingResearchCenter>
  <ns15:ResearchCenter displayName="UAB Comprehensive Cancer Center" shortName="UAB-CCC" xmlns:ns15="gme://caGrid.caBIG/1.0/gov.nih.nc
i.cagrid.metadata.common">
   <ns15:Address country="US" locality="Birmingham" postalCode="35233" stateProvince="AL" street1="1802 6th Avenue South" street2=""/>
   <ns15:pointOfContactCollection>
    <ns15:PointOfContact affiliation="Staff" email="John.Sandefur@ccc.uab.edu" firstName="John" lastName="Sandefur" phoneNumber="205-9
96-5236" role="Information Systems Manager/caBIG Deployment Lead"/>
    <ns15:PointOfContact affiliation="Staff" email="bebrake@.uab.edu" firstName="Bobby" lastName="Brake" phoneNumber="205-934-4980" ro
le="Assistant Director, Infrastructure Services"/>
   </ns15:pointOfContactCollection>
  </ns15:ResearchCenter>
 </ns1:hostingResearchCenter>

For caArray

su - caarray
cd /home/caarray/apps/caarray2/jboss-4.0.4.GA/server/default/deploy/wsrf.war/WEB-INF/etc/cagrid_CaArraySvc/

Edit serviceMetadata.xml with the above point of contact information

Change System Passwords

Before starting the VM you should change the default passwords delivered with the VM. The passwords for root, cagrid, and the JBoss containers should be changed at this point. The UPT and caArray passwords should be changed after reboot.

System passwords
```
passwd root
passwd cagrid
```

Jboss container passwords - edit the following files to change the passwords contained in those files (Note: these passwords are maintain in clear text so simply replace the password values with the new ones

For caArray WebApp:

/home/caarray/apps/caarray2/jboss-4.0.5.GA/server/default/conf/props/jmx-console-users.properties 
/home/caarray/apps/caarray2/jboss-4.0.5.GA/server/default/conf/props/web-console-users.properties

For caArray data service:

/home/caarray/apps/caarray2/jboss-4.0.4.GA/server/default/conf/props/jmx-console-users.properties 
/home/caarray/apps/caarray2/jboss-4.0.4.GA/server/default/conf/props/web-console-users.properties

For UPT:

/home/upt/apps/upt/jboss-4.0.4.GA/server/default/conf/props/jmx-console-users.properties 
/home/upt/apps/upt/jboss-4.0.4.GA/server/default/conf/props/web-console-users.properties

Reboot the VM

The VM is now ready to be brought into full operation. Enter reboot at the command prompt and wait for the machine to enter full operation.

Working with the VM

By default, booting the VM turns on all necessary caBIG services which automatically register themselves with the caBIG portal. After the machine has booted completely, the services registered with the new IP address should show up on the map in the portal.

With the machine in full operation you will be able to access the caArray and UPT applications via your browser at

You should change the default passwords for the UPT superadmin and caarray accounts and use UPT to change the passwords for the existing caArray demo accounts or to create new accounts. Information on UPT can be found here.

Diagnostics Checks for Grid Services

Once the grid services for caArray/caTissue/Labkey are configured and their respective publish containers started, we can perform some diagnostics checks.

From the cagrid Portal:

Go to the caGrid Services tab
At the Service Diagnostics section, type the url in the Service URL field

For caArray, the service url is:

http://your.host.name:18080/wsrf/services/cagrid/CaArraySvc

For Labkey, the service url is:

http://your.host.name:8080/wsrf/services/cagrid/Cpas

* We can replace the hostname with the IP address as well

From command line, using Globus commands. We have a Globus container in /home/labkey. Hence, we can execute all our queries from labkey account. So, switch to labkey first. All the below commands are from caBig Portal Troubleshoot Guide

su - labkey

Verify your Grid service is registering with the Index service

$GLOBUS_LOCATION/bin/wsrf-query -a -z none -s http://cagrid-index.nci.nih.gov:8080/wsrf/services/DefaultIndexService | grep "<ns8:Address xmlns:ns8" | cut -d'>' -f2 | cut -d'<' -f1 | sort > all_grid_services.txt

grep for uab in the output file all_grid_services.txt

Make sure the service's metadata is accessible

For caArray service:

$GLOBUS_LOCATION/bin/wsrf-get-property -a -z none -s http://your.host.name:18080/wsrf/services/cagrid/CaArraySvc {gme://caGrid.caBIG/1.0/gov.nih.nci.cagrid.metadata}ServiceMetadata

For labkey service:

$GLOBUS_LOCATION/bin/wsrf-get-property -a -z none -s http://your.host.name:8080/wsrf/services/cagrid/Cpas {gme://caGrid.caBIG/1.0/gov.nih.nci.cagrid.metadata}ServiceMetadata

Make sure the service's Domain Model is accessible (if the service is a Data Service)