SGE Admin

83 Pages·2009·0.99 MB·English

Grid Engine
Administration
Overview
This module covers
(cid:1) Grid Problem Types (cid:1) How it works
(cid:1) Distributed Resource (cid:1) Grid Engine Scheduling
Management
Grid Engine 6 Architecture
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Grid Engine 6 Variants
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SGE training, consulting and special projects - BioTeam Inc. - http://www.bioteam.net
Grid Problem
Types
SGE training, consulting and special projects - BioTeam Inc. - http://www.bioteam.net
“Grid” Problem Types
Tightly Coupled Embarrassingly Parallel
1 + 1 = X 1 + 1 = X
X + 2 = Y 2 + 2 = Y
Y + 3 = Z 3 + 3 = Z
N + Z = W N + N = W
SGE training, consulting and special projects - BioTeam Inc. - http://www.bioteam.net
Traditional Parallelism
Single process in which several parallel elements
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(threads) must communicate to solve a single
problem
Parallel programming is complicated and far from
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automatic
Users must explicitly use parallel programming tools
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and application environments
Speedup on clusters not guaranteed
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Depends on code, interconnect latency & the
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problem space
SGE training, consulting and special projects - BioTeam Inc. - http://www.bioteam.net
Traditional Parallelism
Used to be a much more fractured space
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PVM, LINDA, MPI, etc.
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MPI rules present day
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Infinite possibilities for admin headaches
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MPI flavor “A” using interconnect type “B” via
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integration method “C” using SGE CPU
$allocation_rule=“D”
Ouch.
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SGE training, consulting and special projects - BioTeam Inc. - http://www.bioteam.net
Embarrassingly Parallel
Also known as “Serial” or “Batch” Computing
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Large numbers of nearly identical jobs
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Possibly only the input file changes
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Identical analysis on large pools of input data
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or queries
Easily subdivided, mostly independent tasks
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SGE training, consulting and special projects - BioTeam Inc. - http://www.bioteam.net
Embarrassingly Parallel
Primary optimization focus
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Often less focus on interconnect and latency issues
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More focus on speed, size and scaling headroom of
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the storage infrastructure (or memory)
Performance tuning the grid scheduler (‘DRM’) and
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batch subsystem for high throughput
Data locality issues often important
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SGE training, consulting and special projects - BioTeam Inc. - http://www.bioteam.net
Generic Use Case
Scientist has a problem
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Embarrassingly
She does not want or need
Parallel
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to run ONE parallel
1 + 1 = X
application stretching
across a 100 CPU cluster
2 + 2 = Y
She wants to run a
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3 + 3 = Z
standalone program
100,000 or 1,000,000
N + N = W
times with slightly different
input and output values
SGE training, consulting and special projects - BioTeam Inc. - http://www.bioteam.net
Cliche Life Science use case
“database” of
DNA or Protein Result
known sequences
sequence(s) query
>Sequence1
>Sequence2 DB Result1
>Sequence3
Comparing sequences of interest to known
repositories in order to identify areas of biologically
significant similarity
SGE training, consulting and special projects - BioTeam Inc. - http://www.bioteam.net