HIMMER PFAM algorithm and parallel schemes

1
EARTH on Chiba City Cluster
Ready Queue

• DOE/ANL Chiba City Cluster
• 256 dual-CPU Pentium III 500 MHz Computing Nodes
  with 512 MB of RAM and 9G of local disk.
• Switched Fast Ethernet for file service and
  management functionality connecting all computing
  nodes.

Send Queue
EARTH Runtime Model
Token Queue
EARTH Execution Model

• adaptive, event driven fibers
• parallel function invocations
• parallel dynamic load balance
• producer-consumer parallelism - pipelining
  support

2
Comparison between RTS 2.0 and RTS 2.5
Experimental Results (On Chiba City)
Different Layouts of RTS (On Single-CPU or
Dual-CPU node)

• Lock free. (Only the last
• token in TQ needs lock)
• Stable.
• Concise message formats.
• Less system calls.

• Locks on shared resources.
• Unstable on certain benchmarks.
• Redundancies in network
• message formats.
• Excessive system calls.

• Fibonacci fine-grain, dynamic load balancing.
• Tomcatv data parallel, computation intensive,
  global reduction and barrier

3
Performance of RTS 2.5 and RTS 2.0 on various
platforms
Relative Speedup (Earthquake)
Relative Speedup (Comet)
Relative Speedup (Chiba City)
RTS2.0
RTS2.5

• Earthquake 16 nodes, 500MHz PIII, 128MB RAM,
  Fast Ethernet
• Comet 16 nodes, dual-cpu Athlon 1.4GHz, 512MB
  RAM, Fast Ethernet
• Chiba City Up to 256 nodes, dual-cpu PIII 500
  MHz, 512 MB RAM, Fast Ethernet

• Fibonacci and Nqueen fine-grain, dynamic load
  balancing problems. Both broke on RTS
• 2.0 at various problem size.
• Tomcatv data parallel, computation intensive
  app. Do global reduction and barrier.
• ATGC sequence comparison through dynamic
  programming.

4
New Parallel Schemes for HIMMER PFAM
5
EARTH 2.6 SMP LAYOUT

• POSIX-THREADS and standard TCP/IP sockets give
  portability
• Pthreads modules overlapping computation and
  communication
• SMP support without any locks, all operation
  accessing shared resources serialized by center
  managers like token manager in SM, SU in EM
• Satisfying remote data and token request
  immediately
• Internal token balancer balances tokens among
  local EMs, and outside load balancer try to
  balance work load among all physical nodes

6
Plan for benchmarking to test EARTH 2.6
Preliminary Results

• Existing Benchmarks
• N-Queen, Fibonacci, tomcatv, cannon,
  Ping-Pong, Paraffins, ATGC
• New Benchmark
• HMMER PFAM
• Porting THREADED-C 1.0 benchmarks
• shortpath, wave2d, gauss elimination, pivot,
  parallel Astar, etc.