= HPC Communications =

 * [wiki:LIMS3SchemaOverview Overview]
 * [wiki:LIMS3SchemaDataflow1 Data Flow, step 1]
 * [wiki:LIMS3SchemaDataflow2 Data Flow, step 2]
 * [wiki:LIMS3SchemaDataflow3 Data Flow, step 3]
 * [wiki:LIMS3SchemaDataflow4 Data Flow, step 4]
 * [wiki:LIMS3SchemaDataflowAsync Data Flow, Asynchronous Step]

!UltraScan's communication with the High Performance Computer (HPC) or Grid Cluster is implemented according to the above drawings. The tasks are accomplished as described below. The original !OpenOffice document is attached to this page.

== Laboratory Information Management System (LIMS) ==

The purpose of this system it to interface with the user to specify an analysis type, 
such as the Genetic Algorithm (GA) or Two Dimensional Spectrum Analysis (2DSA), and 
the needed parameters for the analysis to the HPC system.  After the user specifies the needed
data, the data is packaged into a control.xml package.  The command-line program 
grid-submit is then invoked.   

The contents of the control.xml file will include a generated AnalysisGroupGUID and
all needed child HPCAnlysisRequest records.  

Specific data in the control.xml file will be specified here once we agree on this
top level design. 

The database tables HPCAnalysisGroup, HPCAnalysisRequest, and appropriate Settings tables 
are populated by LIMS before calling grid-submit.php.


[wiki:Us3HpcDb US3 HPC Database Tables]

LIMS is currently a Web interface.  In the future, it's functionality may be ported
to the !UltraScan client.

=== grid-submit ===

grid-submit.php is a command line tool that creates the initial HPCAnalysisResult table
entry with a queue staus of 'Submitted'.  It copies control.xml and all files that it specifies
to the HPC system using the gsiscp utility.

It then uses the submission technique needed for the specified supercomputer cluster
to queue the job.

== Supercomputer Queue ==

This task is controlled by the Supercomputer system.  It is responsible for controlling
the jobs running on that system and communication with clients.

Communication tasks include receiving tasks, returning job status, and informing the 
client when a task has been completed or aborted. 

== NNLS (!UltraScan HPC Analysis Program) ==

The NNLS program reads the control.xml file and uses that as a guide to read other data 
files as needed to populate internal data structures.  It then performs the analysis, 
writing any needed output to disk.

At the beginning of the program, periodically during execution, and at the end of of
processing, NNLS writes a UDP status datagram to a listener on the host and port specified 
in the control.xml file.  Each datagram will consist of the analysisRequestGUID and a
status (e.g. started, iteration number, finished).  This is not a reliable two-way 
communication and it is the responsibility of the listener to follow up and manage any 
missed messages.

== grid-timeout ==

This program will ether be scheduled periodically via cron, or run as a daemon.  It will
check status of jobs in the mysql database and initiate a status query for jobs 
that have overdue status updates.  If a job has been aborted, it will notify the 
grid-listen program of that status.

== grid-query ==

This is a command line program that submits a status query to the Supercomputer Queue and 
returns the result.

== grid-listen == 

This program runs as daemon receiving udp packets from the NNLS program or the grid-timeout
program.  It is responsible for updating the mysql database table HPCAnalysisResult with current 
status and, upon completion or abort of an analysis, fetches needed files from 
the supercomputer cluster, sends an email to the user, and does any other cleanup necessary.