Daily Lab / POC Activities

caBIG

Extramural

• Created phgrid.net domain name and associated A records: dallas.phgrid.net, ncphi.phgrid.net, tarrant.phgrid.net and pitt.phgrid.net
• Created dallas.phgrid.net host and client public and private keys and emailed public keys to HealthGrid to be signed
• Tested VNC connectivity to dallas.phgrid.net host
• Began shipping process with CDC personnel
• Uploaded software stack to ftp.phgrid.net site for future installations

Extramural Certificate Process

There are two certificates--one host certificate and one client certificate. They are created using the following commands:

$GLOBUS_LOCATION/bin/grid-cert-request -host `hostname`
$GLOBUS_LOCATION/bin/grid-cert-request

** In the first command you can see why uniquely identifiable domain names are required for each server (-host ‘hostname’).

Each of these commands creates two files--one private key and one public key. Of course, the private key remains on the server.

The public keys are emailed to cert-request@healthgrid.us. The HealthGrid folks (actually, we are working directly with one person) sign the keys then send the certificates back so that we may begin using the grid services.

Daily Lab / POC Activities

caBIG

• Received the following email from NCI

I’ve reviewed your model submission package and found that we will need one additional item. It is your FirstPass xmi file. Can you take the xmi file you sent and run it through the Semantic Connector using the SIW? When finished, it will prepend “FirstPass” to your xmi file. You can then either delete erroneous concepts mapped to your class/attributes using the “Review Annotated XMI file” in the SIW or leave it as it is and send to me. On another note, I noticed in your submission document you want to use 0.1 as a version number but your files have the version as 3.0. Should we say 3.0.1 or 1.0 maybe? The loading team recommends using 1.0 rather than 0.1. For now, I am going to name your files as listed below to follow naming protocol when I submit your package (let me know otherwise about the version number):

CDC_v3_0_1_rv1.EAP

CDC_v3_0_1_rv1.xmi

FirstPass_ CDC_v3_0_1_rv1.xmi

Submission_Form_ CDC_v3_0_1_rv1.doc

The revision number is for your and my benefit so we know what file we’re working with if edits need to be made down the road. So, go ahead and run the Semantic Connector and send me that file and I will continue from there. Please feel free to contact me if you have any questions or concerns.

Extramural

• Conference call to discuss status and establish a two hour block of time to review grid node setup. Minor technical issue with installation of SUSE on Tarrant County server. SUSE must be installed prior to grid setup session.
  

• Shared IP addresses at each four nodes for network administration at each site

• Firewall changes made for NCPHI Lab network

• Dallas grid node built. Need domain name, if available, otherwise we'll have to use another methodology to create certificates. Certificates remain to be created
  

  
  

Medicus Installation

As the globus user (works better as root), make sure $GLOBUS_LOCATION is set, and run:

$GLOBUS_LOCATION/sbin/gpt-build globus_simple_ca_ae084d2a_setup-0.19.tar.gz
$GLOBUS_LOCATION/sbin/gpt-postinstall

You will get a scary-looking message from gpt-postinstall saying that the installation didn't complete. All that means is that there's another step that you need to run as root.

As root, make sure $GLOBUS_LOCATION is set, and run:

$GLOBUS_LOCATION/setup/globus_simple_ca_ae084d2a_setup/setup-gsi -default

You should do this on each host on which you have Globus installed. At that point, you'll be able to create a host certificate request for each host by running the following as root on each host:

$GLOBUS_LOCATION/bin/grid-cert-request -host `hostname`

You can create a user certificate request by running the following as yourself:

$GLOBUS_LOCATION/bin/grid-cert-request

Then you can follow the directions about mailing the certificate requests to the CA.

Daily Lab / POC Activities

caBIG

• Received the following email from nci.nih.gov:

I’ve received your model submission files and am currently reviewing
them. I will be your main point of contact as we proceed through the
process of having your model loaded to the caDSR. At any time, please feel
free to contact me if you have any questions or concerns. I look forward
to working with you. I’ll be in touch as soon as I can after completing my
review.

Sincerely,

John
301-443-3540

Extramural

• Installed all C Compiler libraries on Dallas County grid node server
• Completed Globus install
• Tomorrow: Medicus installation and cert requests

Installation Process

• Confirm all C Compilers and supporting libraries installed
• Confirm Java JDK version: 1.5.0.14
• Confirm Ant version: 1.6.5
  
• Confirm Full Toolkit Source Download version: 4.0.5
  
• Confirm path: $PATH=./:/home/globus/java_card_kit-2_2_2/bin:/usr/local/apache-ant-1.6.5/bin:/usr/java/jdk1.5.0_14/bin:/home/globus/bin:/home/globus/bin/sbin:/usr/local/bin:/usr/local/sbin:/usr/bin:/usr/sbin:/bin:/sbin:/usr/bin/X11:/usr/X11R6/bin:/usr/games:/opt/kde3/bin:/opt/cross/bin
• Confirm environment variables:

  export GLOBUS_LOCATION=/usr/local/globus-4.0.5
  export LD_LIBRARY_PATH=/usr/lib:usr/local/lib:/usr/i586-suse-linux/lib:/lib
  export ANT_HOME=/usr/local/apache-ant-1.6.5
  export GLOBUS_LOCATION=/usr/local/globus-4.0.5
  export JAVA_HOME=/usr/java/jdk1.5.0_14

• Change directory to gt4.0.5-all-source-installer (as su) then run the following:
  
• ./configure
• make
• make install


• Medicus installation
• Certificate request
• GridFTP Test
  
  

Daily Lab / POC Activities

caBIG

• Successfully annotated test UML model and validated against Semantic Integration Workbench (without errors)
• Sent EAP & XMI files to SCI for submission to caBIG integration group for manual validation
• Hopefully, they'll be able to expedite the process

Extramural

• Status call
• University of Pittsburgh to installed VMWare on Tarrant County node computer and plans to install SUSE within the VM today
• Tarrant County place HL7 files on their node computer
• CDC successfully connected via VPN to Tarrant County node computer
• NCPHI grid node operational in lab
• NCPHI lab firewall changes have been submitted to lab management
• Grid node firewall requirements posted to this blog in order that other nodes may request similar changes to their networked firewalls
• OGSA-DAI call scheduled for first or second week in January, 2008, to discuss federating OpenMRS data model for public health use
• Two hours scheduled for Thursday, January 4th status call to walk through node setup on Tarrant County grid node
• We should be able to begin exchanging HL7 files the second week in January

Daily Lab / POC Activities

caBIG

• Annotated test Enterprise Architect model
• Had errors attempting to run it through caAdapter & Semantic Integration Workbench
• Plan to call help desk and revisit tomorrow

Extramural

• Successfully connected to Tarrant County VPN then used Windows Remote Desktop to connect to their soon-to-be-build grid node
• Ken plans to install the Tarrant County grid node online through WebEx so that everybody can see how it's done

OGSA-DAI

• Rescheduled development meeting to first week in January, 2008
• Realized that we were all looking at the OpenMRS software backwards. Decided to federate a view into the OpenMRS data model so that anybody may query multiple OpenMRS systems in a distributed fashion. This is more in line with original OGSA-DAI design principles. After this we'll look at gridifying OpenMRS.
  

Misc

• Reported both PoC's progress to CDC PMO lead
  
• Attended meeting to discuss new Diginet PoC in lab
  

Node Firewall Configuration

NAT from firewall/router to x.x.x.x all incoming traffic as specified below:

• Open up port 2811/tcp (for GridFTP control channel connection) for incoming connections to x.x.x.x
• Open up the range of ports 50000-51000 (for GridFTP data channel connections) for incoming connections to x.x.x.x
• Open up port 22/tcp (for GSI-Enabled SSH) for incoming connections to x.x.x.x
• Open up port 7512/tcp (for GridMyProxy) for incoming connections to x.x.x.x
• Open up port 2119/tcp (for GRAM) for incoming connections to x.x.x.x
• Open up port 2135/tcp (for MDS) for incoming connections to x.x.x.x

x.x.x.x = node server ip address behind firewall

GridFTP

The first grid service to be tested on the extramural research grid is GridFTP and the ability to move files between each node.

The document being used to setup GridFTP on the NCPHI node, including firewall restrictions, is located here.

Daily Lab / POC Activities

Extramural

• Requested & received user certificate under 'ken' user name
• Setup time on Tuesday morning to go over VPN access to Tarrant County

caBIG

• Attended Semantic Integration Workbench training
• Attended caCORE SDK training
• Patel, Satish (NIH/NCI) [C] [patelsat@mail.nih.gov] recommended the following:

Use SDK 4.0 version if you are planning to use it for a longer term. If you intend to use the SDK with grid in shorter timeframe then you would have to use SDK 3.2.1. You can create grid service 1.1 from it.

SDK is available for download here
SDK documentation is available here