Changes between Initial Version and Version 1 of HpcInfo

Timestamp:

Jan 23, 2012, 10:49:06 PM (12 years ago)

Author:

dzollars

Comment:

--

HpcInfo

@@ +1 @@
+= HPC Communications =
+
+[[Image(sc-comm.png)]]
+
+!UltraScan's communication with the High Performance Computer (HPC) or Grid Cluster is 
+in accordance with the above drawing.   The following tasks will be accomplished by the 
+elements as described below.
+
+== 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.
+