Changes between Version 4 and Version 5 of HpcInfo


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Timestamp:
Jan 25, 2012, 6:53:17 PM (12 years ago)
Author:
dzollars
Comment:

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  • HpcInfo

    v4 v5  
    1212== Laboratory Information Management System (LIMS) ==
    1313
    14 The purpose of this system it to interface with the user to specify an analysis type,
    15 such as the Genetic Algorithm (GA) or Two Dimensional Spectrum Analysis (2DSA), and
    16 the needed parameters for the analysis to the HPC system.  After the user specifies the needed
    17 data, the data is packaged into a control.xml package.  The command-line program
    18 grid-submit is then invoked.   
     14The purpose of this system is to interface with the user to specify an analysis type, such as the Genetic Algorithm (GA) or Two Dimensional Spectrum Analysis (2DSA), as well as the needed parameters for the analysis to the HPC system.  After the user specifies the needed data, the data is packaged into a common data directory, uslims3.uthscsa.edu:/srv/www/htdocs/uslims3/uslims3_data. For this analysis request LIMS creates a new GUID, associates it with the analysis data, and creates a new record in the HPCAnalysisRequest database table. This record is the parent record for everything relating to this HPC analysis, and this GUID serves as the common identifier of this analysis. For instance, this GUID is the name of the subdirectory in the common data directory where all the files relating to this particular analysis are stored when the job is submitted to the HPC system. Another example: LIMS prepends the string "US3-" to this guid and it becomes the gfacID, used by the GFAC system to identify the job, and used in the listen script and grid control program to identify the job. The database name and gfacID is how the grid control program associates the HPC job with the analysis request record in the LIMS database.
    1915
    20 The contents of the control.xml file will include a generated AnalysisGroupGUID and
    21 all needed child HPCAnlysisRequest records. 
    22 
    23 Specific data in the control.xml file will be specified here once we agree on this
    24 top level design.
    25 
    26 The database tables HPCAnalysisGroup, HPCAnalysisRequest, and appropriate Settings tables
    27 are populated by LIMS before calling grid-submit.php.
    28 
     16=== Contents of the data directory ===
    2917
    3018[wiki:Us3HpcDb US3 HPC Database Tables]
    3119
    32 LIMS is currently a Web interface.  In the future, it's functionality may be ported
    33 to the !UltraScan client.
    34 
    35 === grid-submit ===
    36 
    37 grid-submit.php is a command line tool that creates the initial HPCAnalysisResult table
    38 entry with a queue status of 'Submitted'.  It copies control.xml and all files that it specifies
    39 to the HPC system using the gsiscp utility.
    40 
    41 It then uses the submission technique needed for the specified supercomputer cluster
    42 to queue the job.
     20=== The LIMS job submit process ===
    4321
    4422== Supercomputer Queue ==