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Java as a cycle-stealing
computational environment
Al Globus, MRJ Technology Solutions, Inc. at
NASA Ames Research Center

Acknowledgments
• Ames: Po Chung, Creon Levit, Subash Saini
• UCSC: John Lawton, Rich McClellan, Todd Wipke
http://science.nas.nasa.gov/~globus/code/geneticGraphs/
What got done
 Java
implementation of genetic molecular design
application
• No input (Parameters.java)
• No graphics or GUI
• Computationally intensive -- O(n3)
• Many output files
 Used cycle scavenging batch system (Condor) on
NAS workstations
 Approximately 150 runs so far
http://science.nas.nasa.gov/~globus/code/geneticGraphs/
Genetic molecular design
 Randomly
generate a set of molecules
 Many times:
• Select parent molecules at random with bias
towards better performance
• Randomly rip copies of each parent in two
• Mate opposite halves
• Replace random molecules with bias towards
worse performance
 Repeat until satisfied
http://science.nas.nasa.gov/~globus/code/geneticGraphs/
Algorithm properties
 Stochastic,
embarrassingly parallel
 Robust to failure
 No guaranteed outcome
 Fitness function is crucial and non-trivial
 Performs well as cycle-scavenger using Condor,
University of Wisconsin,
http://www.cs.wisc.edu/condor
http://science.nas.nasa.gov/~globus/code/geneticGraphs/
Crossover
http://science.nas.nasa.gov/~globus/code/geneticGraphs/
Time to find small molecules
http://science.nas.nasa.gov/~globus/code/geneticGraphs/
Finding larger molecules
http://science.nas.nasa.gov/~globus/code/geneticGraphs/
Resources
 300-400
NAS workstations are idle nights and
weekends
 Provides an ideal resource if owner access is not
degraded
 University of Wisconsin experience suggests each
workstation is idle an average of 17 hours/day.
Thus NAS should have approximately 6,800
workstation hours/day or 2,448,000 workstation
hours/year available.
 This extra processing costs $0 for hardware
http://science.nas.nasa.gov/~globus/code/geneticGraphs/
Condor
 Cycle-scavenging
batch system
 Developed by University of Wisconsin
 In production since 1986
 Unix workstations (NT port in progress)
 Free from http://www.cs.wisc.edu/condor
http://science.nas.nasa.gov/~globus/code/geneticGraphs/
Some Classes
 Graph,
vertex, edge
 Molecule, atom, bond
 Breeder, Population
 FitnessFunction
 Parameters, Reporter
 Sample, DataTable
 Predicate, Procedure, ExtendedVector
 IntegerInterval, DoubleInterval
http://science.nas.nasa.gov/~globus/code/geneticGraphs/
Java advantages
 Cleaner
code than C++
 Dynamic loading eliminated input file parsing.
 CLASSPATH
• Parameters.class directory
• classes.jar
• Standard library
 Garbage collection priceless
• massive data structure manipulation
• cyclic data structures make reference counting
ineffective
http://science.nas.nasa.gov/~globus/code/geneticGraphs/
Java advantages continued
 Serialization
eases checkpointing
 Virtual machine eases cross-platform
development
• Development on WinTel
• Execution on SGI workstations
 Standard library (especially Vectors)
 Automatic html documentation integrated with
code
 Reflection enables automation of
Parameters.java toString()
 Automatic bounds checking
http://science.nas.nasa.gov/~globus/code/geneticGraphs/
Java disadvantages
JAVA with jit 50% slower than c on simple
numerical code
 Symantec Visual Café unacceptably buggy
debugger and crashed system very hard
 Supersede ok with a few bugs
 Lack of multiple inheritance sometimes irritating
 Condor cannot perform automatic checkpointing
• Condor requires relink to automate checkpointing

http://science.nas.nasa.gov/~globus/code/geneticGraphs/
Checkpointing
 Condor
jobs may be stopped at any arbitrary
time
 Virtual machine checkpointing would allow
automatic heterogeneous mobility
• stack format not defined
• heap format undefined and universal serialization
potentially problematic
• jit and optimization causes problems
• Must hack Java Virtual Machine
 Java threads cannot be truly interrupted
• suspend(), resume(), stop() depreciated
http://science.nas.nasa.gov/~globus/code/geneticGraphs/
Checkpointer.java
class application implements Checkpointable
• start(String[] arguments);
• restart();
 Application calls
• Checkpointer.ok()
• Checkpointer.checkpoint()
 Condor calls
• Checkpointer.prepareToDie()
• Checkpointer.areYouReadyToDie()
• Checkpointer.cancelDeath()
• Checkpointer.checkpointWhenPossible()

http://science.nas.nasa.gov/~globus/code/geneticGraphs/
Summary
 It
was fun
 It was productive
• 75 classes, 6389 lines of code
• one unique algorithm
• two University collaborations
• two conference presentations
• one conference poster
• one journal submission
• 400-500 CPU hours per day added to NAS batch
capability (so far)
 Java is my favorite programming language
http://science.nas.nasa.gov/~globus/code/geneticGraphs/