Thursday, December 20, 2007

Daily Lab / POC Activities

  • 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


  • 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

Wednesday, December 19, 2007

Daily Lab / POC Activities

  • Annotated test Enterprise Architect model
  • Had errors attempting to run it through caAdapter & Semantic Integration Workbench
  • Plan to call help desk and revisit tomorrow
  • 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
  • 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.
  • Reported both PoC's progress to CDC PMO lead
  • Attended meeting to discuss new Diginet PoC in lab

Tuesday, December 18, 2007

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


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.

Monday, December 17, 2007

Daily Lab / POC Activities

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


  • Attended Semantic Integration Workbench training
  • Attended caCORE SDK training
  • Patel, Satish (NIH/NCI) [C] [] 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

Friday, December 14, 2007

OGSA-DAI Conference Call (Upcoming)

Conference call Wednesday, next week, to discuss potential use cases for their distributed data model use case and to offer any help to the OGSA-DAI team as they code to grid-enable OpenMRS. The distributed data model is their stronger, more extensible use case.

Please let Ken know if you want to participate.

VM Report

The last few days this week the network interface within the VM disappeared. The first time this happened a simple stop and restart of the VM fixed the problem. The second time the network adapter had to be re-created for the VM.

  • Is this a known bug in VMWare? It is being investigated by DISS.
  • How stable is the VM for a future production environment of grid? Further research needs to occur here, especially since the model of building a public health grid using a VM node environment has many advantages.

Wednesday, December 12, 2007

Accidental Interesting Find - Grid Australia

Link here. Potentially useful resources - to be added to stack.

Daily Lab / POC Activities

  • Received certificate instruction from Laura
  • Ran the following commands successfully:

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


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

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

  • Used unique domain name for grid node (not for public consumption)
  • This command created host certificate file
  • Mailed host public key to
  • Awaiting certificate from HealthGrid.US


  • This command created client certificate file
  • Mailed client public key to
  • Should have used account on server ('ken', for example) instead of 'root'
  • Will redo this Monday, send public key to address then await client certificate
Discussed differences between client and host certificates with Laura Pearlman

To do Monday

  • Dave at Tarrant to send vpn and remote terminal instructions to be able to connect to their server
  • Connect to Tarrant server, download sample HL7 file. Stephan is ready to "load" file into Medicus
  • Create client certificate request and email to HealthGrid folks
Conference call

  • Decided to walk through grid creation process using webex & conference call so that all can watch and ask questions
  • Ken will do this on Tarrant County server to create their node in a VM
  • Jeremy will watch, take notes and ask questions then follow procedure to create his own node
  • Ken will also make VM image of NCPHI node, ship to Jeremy to try that method of node creation

  • Exported XMI file into caAdapter
  • Created mapping in caAdapter
  • Imported mapped XML back into EA
  • Exported into new combined XMI file
  • We are ready to use SDK to create test application
  • Set up two conference calls for training on how to use SDK (Monday @ 10 AM & 3 PM)
Next Steps

  • Load caCore SDK in lab
  • Train on SDK
  • Create test tables in Oracle

Monday, December 10, 2007

Daily Lab / POC Activities


  • Reviewed & validated process to create model to run through caCORE SDK with Raghu Narasimha & Scott Halpine (SCI)
  • Next steps: 1) Conference call with Claire to double validate the process, 2) Load Oracle & SDK on lab machine, 3) Create tables then 4) run model through SDK to create test application
  • Enrolled at NCI web site to take Metadata Curator - Using UML Models training
  • Sent questions to Scott to send to Claire prior to conference call


  • Discussed Globus / Medicus / HealthGrid Live connectivity & installation strategy with Laura Pearlman and decided to get base Globus working with GridFTP followed by RLS (to set logical names for files) followed by metadata catalog.
  • Will run "gridcertrequest" to request certificate from HealthGrid.US Live
  • Note: host certificates are not encrypted while user certificates are
  • Plan to simultaneously look at client version of Medicus on Mac using OSRIRX client
  • Laura to send links for downloads

Ally Hume's Summary of last week's OGSA-DAI Discussion

We plan to try to use OGSA-DAIs schema mapping to map a database in some schema X to look like a database in the schema used by OpenMRS. One possible suggestion for X is a Harvard system and Jeremy is looking into this. From our point of view it could be great to get this schema, some data in this schema and hints as to how this would map to the HL7 schema used by OpenMRS.

You may read the complete conference call notes at this link.

Friday, December 7, 2007

Daily Lab / POC Activities

  • Stephan uploaded latest version of Medicus to FTP server
  • Stephan asked Laura Pearlman to help us connect to HealthGrid Live Certificate Authority Server
  • Laura provided the following information: 1. Load Medicus, 2. Run GridCertRequest to generate certificate, 3. Make sure email address points to, 4. Each grid node should have it's own certificate, 5. Each grid client should have it's own certificate, 5. Grid map file contains connection/naming information of each grid node server
  • Conference call with OGSA-DAI, U. of Pittsburgh, Tarrant County and two CDC EA team members to discuss potential Public Health use cases.

Tuesday, December 4, 2007

Daily Lab / POC Activities


  • Installed NFS server on NCPHI grid node
  • Attached Dallas County grid node to NCHPI grid node through NFS client to access Globus installation files (removes download step)


  • Conference call with SCI to map out next steps in process. Finalized test model for proof-of-concept.
  • Downloaded and installed on office desktop caAdapter (Windows version) from NCI web site
  • Next steps (Load EA test model into caAdapter. Map object model to data model map specification. Import result back into EA. Re-export. Prepare questions for Claire Wolfe, expert on semantic integration at NCI. Take caCORE training for the Metadata Curator - Using UML Models curriculum in order to give them a background on the EVS and caDSR.
  • Conference call with Claire at end of week.
  • Recommendation to use 3.2.1 caCore SDK when developing "application"

Saturday, December 1, 2007

OGSA-DAI & Public Health Data Grid Architecture

Discussed potential architectural models for data grids for public health and existing applications with EA (Moses & Brian). Forwarded security and data taxonomy articles to them and collectively decided to engage the OGSA-DAI folks in England to drill down into deeper detail.

Sent email to Ally Hume to schedule a conference call.

Ally's Contact information
Software Architect
EPCC, The University of Edinburgh
Tel: +44 131 651 3397

Interesting Grid Software Stack

Tom found an interesting grid software stack which claims to have a quick installation pathway here

It is self-described as a computational grid but all grids are computational grids at its heart.