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Workflow automation for processing plasma fusion simulation data Norbert Podhorszki Bertram Ludäscher Scientific Computing Group Oak Ridge National Laboratory.

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Presentation on theme: "Workflow automation for processing plasma fusion simulation data Norbert Podhorszki Bertram Ludäscher Scientific Computing Group Oak Ridge National Laboratory."— Presentation transcript:

1 Workflow automation for processing plasma fusion simulation data Norbert Podhorszki Bertram Ludäscher Scientific Computing Group Oak Ridge National Laboratory University of California, Davis Scott A. Klasky

2 6/25/07Works’07 Monterey, CA Center for Plasma Edge Simulation Focus on the edge of the plasma in the tokamak Multi-scale, multi-physics simulation Edge turbulence in NSTX 100,000 frames/s) Diverted magnetic field

3 6/25/07Works’07 Monterey, CA Images plasma physicists adore Electric potential Parallel flow and particle positions

4 6/25/07Works’07 Monterey, CA Monitoring the simulation means…

5 6/25/07Works’07 Monterey, CA Multi-physics → many codes

6 6/25/07Works’07 Monterey, CA XGC simulation output Desired size of simulation (to be run on the petascale machine) –100K time steps –100 billion particles –10 attributes (double precision) per particles = 8 TB data per time step –Save (and process) 1K-10K time steps –about 5 days run on the petascale

7 6/25/07Works’07 Monterey, CA XGC simulation output Proprietary binary files (BP) –3D variables, separate file per each timestep NetCDF files containing –2D variables, all timesteps in one file M3D coupling data –to compute new equilibrium with external code (loose coupling) –to check linear stability of XGC externally

8 6/25/07Works’07 Monterey, CA What to do with those output? Proprietary binary files (BP) –Transfer to end-to-end system using bbcp –Convert to HDF5 format (with a C program) –Generate images using AVS/Express (running as service) –Archive HDF5 files in large chunks to HPSS NetCDF files containing –Transfer to end-to-end system (updating as new timesteps are written into the files) –Generate images using grace library –Archive NetCDF files at the end of simulation M3D coupling data –Transfer to end-to-end system –Execute M3D: compute new equilibrium –Transfer back the new equilibrium to XGC –Execute ELITE: compute growth rate, test linear stability –Execute M3D-MPP: to study unstable states (ELM crash)

9 6/25/07Works’07 Monterey, CA Schematic view of components Cray XT4 Opteron cluster Command & control site 40 GB/s HPSS ORNL

10 6/25/07Works’07 Monterey, CA ORNL Schematic view of components Cray XT4 Opteron cluster Command & control site 40 GB/s HPSS

11 6/25/07Works’07 Monterey, CA ORNL Schematic view of components Cray XT4 Opteron cluster Command & control site 40 GB/s HPSS NERSC Pull data

12 6/25/07Works’07 Monterey, CA Kepler workflow –to accomplish all these tasks –1239 (java) actors –4 levels of hierarchy –many instances of ProcessFile and FileWatcher composite actors “workflow templates” 43 actors, 3 levels 196 actors, 4 levels 30 actors 206 actors, 4 levels 137 actors 33 actors actors 66 actors 12 actors 243 actors, 4 levels

13 6/25/07Works’07 Monterey, CA Workflow – java - remote script - remote prg ls -l bp2h5 bbcp

14 Kepler actors for CPES Permanent SSH connection to perform tasks on a remote machine Generalized actors (sub-workflows) for specified tasks: –Watch a remote directory for simulation timesteps –Execute an external command on a remote machine –Tar and archive data in large junks to HPSS –Transfer a remote image file and display on screen –Control a running SCIRun server remotely –Job submission and control to various resource managers Above actors do logging/checkpointing –the final workflow can be stopped / restarted

15 6/25/07Works’07 Monterey, CA What Kepler features are used in CPES? Different computational models –PN for parallelism and pipeline processing –DDF for sequential workflow with if-then-else and while loop structures –SDF for efficient (static schedule) sequential execution of simple sub-workflows Stateful actors in stream processing of files SSH for remote operations –keeps the connection alive Command-line execution of the workflow –from a script (at deployment) (no GUI) –reading workflow parameters from a file

16 6/25/07Works’07 Monterey, CA ● SSH Directory Listing Java actor gives new files in a directory (once) ● This is a do-while loop where the termination condition is whether the list contains a specific element (which indicates end of simulation) FileWatcher: a data-dependent loop

17 6/25/07Works’07 Monterey, CA Modeling problem: stopping and finishing You create working pipelines finally. Fine. –How do you stop them? –How do you let intermediate actors know that they will not receive more tokens? –How do you perform something “after” the processing? We use a special token flowing through the pipelines –Always the last item in the pipeline. –Actors are implemented (extra work) to skip this token. Stop file created by the simulation –to stop the “task generator” actors in the workflow (FileWatchers) –to notify (stateful) actors in the pipeline that they should finalize (Archiver, Stop_AVS/Express) –to synchronize on two independent pipelines (NetCDF+HDF5 → archive images at the end)

18 6/25/07Works’07 Monterey, CA Role of stop file Stop

19 6/25/07Works’07 Monterey, CA Role of stop file Stop Finalize Wait for stop on both pipelines Extra work after the end

20 6/25/07Works’07 Monterey, CA Problem: how to restart this workflow? Kepler has no system-level checkpoint/restart mechanism (yet?) –seems to be difficult for large Java applications –not to mention the status of external (and remote) things. Pipeline execution –each actor is processing a different step simultaneously

21 6/25/07Works’07 Monterey, CA Our solution: user-level logging/restart We record –the successful operations at each (“heavy”) actor Those actors – are implemented to check before doing something whether that has been done already When the workflow is restarted –it starts from the very beginning, but the actors simply skip operations (files, tokens) that have already been done. We do not worry about repeating small (control related) actions within the workflow –external operations are that matter here

22 6/25/07Works’07 Monterey, CA ProcessFile core: check-perform-record

23 6/25/07Works’07 Monterey, CA Problem: failed operations What if an operation fails, e.g. one timestep cannot be transferred? Options: a) trust that they “fail” silently on missing data b)notify everybody downstream in the pipeline (to skip) –mark token as “failed” c) avoid giving tasks to them for the erroneous step Retrying later and processing that step is important but … … keeping up with the simulation on the next steps is even more important

24 6/25/07Works’07 Monterey, CA Our approach for failed operations ProcessFile and thus the workflow handles failures by discarding tokens related to failed operations from the stream Advantage: –actors need not care about failures an incoming token is a task to be done Disadvantage –rate of token production varies this can upset Kepler’s model of computation

25 6/25/07Works’07 Monterey, CA Discarding tokens on failure transfer 1 failed 2 convert 1arch 1 transfer 3convert 3arch 3

26 6/25/07Works’07 Monterey, CA After a restart… skip 1 transfer 2 skip 1 convert 2 skip 1 arch 2 skip 3

27 6/25/07Works’07 Monterey, CA Future Plans Provenance management –one main reason to use scientific workflow system e.g. in bioinformatics workflows –needed for debugging runs, interpreting results, repeat experiment, generate documentation, compare runs etc. –CPES workflow is selected as one use case for the ongoing Kepler provenance work New actors in CPES for controlling asynchronous I/O from the petascale computer towards the processing cluster

28 Thank You Questions?


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