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A JSDL Applications Repository and Data Staging Portal: Some New Parameter Sweep Developments and A JSDL Applications Repository and Data Staging Portal: Some New Parameter Sweep Developments and Data transfer Requirements David Meredith STFC e-Science Centre Daresbury Laboratory, UK david. [email protected] ac. uk Geoff Williams Oxford University Computing Lab, UK geoff. [email protected] ox. ac. uk

What it does: • Aim: Provide an easy way to access computing resources, execute What it does: • Aim: Provide an easy way to access computing resources, execute installed applications, stage/move data between different remote file systems (e. g. off and onto Grid resources). • Browse application templates in the repository according to ‘categories of interest’ (e. g bioinformatics, tutorials/examples, physics). • Templates fully describe all of the requirements of an application for execution (‘ready to run’ applications, provides a starting point for new users). • Users benefit from immediate access to the expertise, artefacts and configuration captured in application description templates (e. g. published and shared by domain-experts). • Select, load, modify / tweak, save as personal template. • Browse and perform file operations on different file systems (currently SRB, Grid. FTP, SFTP). List, upload, download, delete, rename. • Recursive data copy between different file systems. • Execute application and stage data in one action.

Example Use Case (NGS Applications Repository) Applications described using middleware agnostic Job Submission Description Example Use Case (NGS Applications Repository) Applications described using middleware agnostic Job Submission Description Language (JSDL GUI editor). Ensures community formation around a “best practice” approach (OGF), aids interoperability. Middleware specific dependencies added at run time - convert the JSDL into middleware specific scheme (e. g. RSL).

JSDL Ali Anjomshoaa, Fred Brisard, Michel Drescher, Donal K. Fellows, William Lee, An Ly, JSDL Ali Anjomshoaa, Fred Brisard, Michel Drescher, Donal K. Fellows, William Lee, An Ly, Steve Mc. Gough, Darren Pulsipher, Andreas Savva, Chris Smith § JSDL 1. 0 is an OGF standard § JSDL 1. 0 is published as GFD-R-P. 56 – http: //www. ggf. org/gf/docs/? final 1. An XML Schema language for describing the requirements of computational jobs for submission to Grids. > 2. Is agnostic of middleware - no dependencies on Globus, WSRF, g. Lite (means portal can be generic and not tied to any particular set of Grid technologies). 3. JSDL documents can be validated against the JSDL and JSDL POSIX XSD Schema to ensure its correctness gnuplot /usr/local/bin/gnuplot control. txt input. dat output 1. png ….

Pre configured Job Detail Input fields are pre-configured / filled out. Fields are taken Pre configured Job Detail Input fields are pre-configured / filled out. Fields are taken from the JSDL and JSDLPOSIX extension schemas. POSIXApplication is a JSDL extension. It defines standard POSIX elements. –stdin, stdout, stderr –Working directory –Command line arguments –Environment variables ? ? ? ? . . . …

/tmp env." src="https://present5.com/presentation/55cd55bbe004eef4317d49ebe68c5c23/image-6.jpg" alt="Pre configured Environment Variables /tmp env." /> Pre configured Environment Variables /tmp env. Var. Value 1 …. .

Pre configured Command Line Arguments <jsdl 1: Argument>fasta 34</jsdl 1: Argument> Paste and parse Pre configured Command Line Arguments fasta 34 Paste and parse command line arguments -H (space and/or line separated values) human. DNA 2. input /var/data/bioinformatics/. . S

Pre configured Named File Systems Named file systems used to declare mount points on Pre configured Named File Systems Named file systems used to declare mount points on the consuming system. File system names are referenced throughout the portal (and JSDL doc) for substituting mount points. Changes to a FS mount point will be updated automatically throughout the portal/JSDL. Used when specifying path info e. g. locations to files/dirs, stage data locations etc. /home/ngs 0024/my. Scratch. Dir /home/ngs 0024/my. Data. Dir fasta. out

JSDL Parameter Sweep Extensions http: //forge. gridforum. org/sf/projects/jsdl-wg 1. A common requirement to select JSDL Parameter Sweep Extensions http: //forge. gridforum. org/sf/projects/jsdl-wg 1. A common requirement to select a job and submit it ‘ 10, 50, 300’ times, each time making some modifications to the ‘original/master’ JSDL (e. g. args, parameters, output dir, input file whatever…). 2. The JSDL + PS extensions allows you to group the master JSDL + the required modifications (which JSDL fields require sweeping); • Saves writing multiple separate JSDL docs. • Can be any value within the JSDL document itself, • Can be any value within a named file that is referenced by the JSDL (e. g. an input file). • Actually yields multiple separate jobs (rather than solely parameter sweeps).

Recently submitted for public comment at OGF 24, Sept. Recently submitted for public comment at OGF 24, Sept.

JSDL Sweep Overview 1. Nest <Sweep> elements within a JSDL doc. JSDL 2. The JSDL Sweep Overview 1. Nest elements within a JSDL doc. JSDL 2. The identifies which set of should be swept / iterated using the given sweep . 3. + are abstract (can define different implementations as required). Select + give new values for element JSDL + PS 4. Spec v 1 Parameters: • , 5. Spec v 1 Functions: • , , PS ext

Basic Example - Modify the command line using Values and a Loop Two arguments Basic Example - Modify the command line using Values and a Loop Two arguments are swept, yielding 3 separate jobs (1, 4, again), (2, 5, again), (3, 7, again)

Portal Implementation Select which values require sweeping Portal Implementation Select which values require sweeping

Portal Implementation Build sweep: Identify which parameter Define function values Note, more interface work Portal Implementation Build sweep: Identify which parameter Define function values Note, more interface work required (e. g. upload. csv file for values)

JSDL + JSDL POSIX PS Extensions JSDL + JSDL POSIX PS Extensions

Part 2: Data Staging / File Transfer (Portal is VFS client) Portal is a Part 2: Data Staging / File Transfer (Portal is VFS client) Portal is a single interface to different remote file systems (Ftp, Srb, Grid. Ftp, Sftp). Browse and perform file operations (upload, download, delete, list, rename)

Manual Copy Data Between Different File Systems Compile data (spread over different file systems) Manual Copy Data Between Different File Systems Compile data (spread over different file systems) Copy data to target URI (e. g. SRB or wherever) Select files/dirs and ‘copy to opposite host’ Copy data between these different file systems.

Specify Data Staging Requirements of an Application List of data from across the Grid Specify Data Staging Requirements of an Application List of data from across the Grid that should be copied to the consuming system Before job: src URI After job: tgt URI JSDL does not mandate the protocol / URI format. Data is staged relative to named file systems. Mg. psf WORKINGDIR overwrite false gsiftp: //ngs. rl. ac. uk: 2811/apps/Siesta_mpi/…

Current Data Staging / File Transfer Implementation (VFS) File operations (list, upload, download, delete, Current Data Staging / File Transfer Implementation (VFS) File operations (list, upload, download, delete, rename) Single interface to different remote file systems (Srb Gsi. Ftp, Sftp). Bit pipe (byte IO stream) Portal + *VFS client Authentication tokens (un/pw, x 509) Auth tokens only in memory on one server. Self contained. SRB/ FTP *VFS: Apache Commons VFS SFTP/ GSIFTP Piping bytes via portal server is not ideal (bottleneck, single point of failure, concurrency issues).

Required / Suggested Architecture for Data Staging / File Transfer Service File operations (list, Required / Suggested Architecture for Data Staging / File Transfer Service File operations (list, upload, download, delete, rename) Portal + VFS client Bit pipe (byte IO stream) Authentication tokens (un/pw, x 509) JMS QUEUE Move file transfers to different server (farm), increase bandwidth, concurrency (large transfers). VFS clients Passing auth tokens around in messages (strong security required) Development effort / testing. SRB/ FTP SFTP/ GSIFTP

Summary Parameter Sweeping § Portal role is the JSDL Producer (author/persist JSDL with sweep Summary Parameter Sweeping § Portal role is the JSDL Producer (author/persist JSDL with sweep extensions for applications), not JSDL Consumer. § JSDL Consumers role is to enact the JSDL+PS e. g. create, submit, stage data for ‘ 1000’ jobs. This is the responsibility of OGSA BES, middleware and SAGA…. § But, middleware / SAGA support for PS extensions not yet available - May have to devise a ‘hack’ in the meantime ? 1. File Transfer / Data Staging Service • Need to support large data transfers by moving byte streaming to dedicated servers/services. • Will have to pass security tokens from portal to staging service (looking at WSS Username and Certificate profiles). • Here to explore this requirement (also for facilities work ? ) and investigate solutions….