1. Parallel NetCDF + MASS Development
By: Sanjay Bappudi

2. Table of Contents Overview of Multi-Agent Spatial Simulation
NetCDF library
Integration work
Spring 2013
Extension with hadoop
Summer 2013

3. Spatial Simulation Simulation “places”
Each cell computes its own wave height, using its four neighboring cells’ information.
z[t][i][j] = 2.0 z[t-1][i][j] – z[t-2][i][j]
+ c2(dt/dd)2 (z[t-1][i+1][j] + z[t-1][i-1][j] + z[t-1][i][j+1] + z[t-1][i][j-1] – 4.0 z[t-1][i][j])

4. Multi Agent Simulation
Each agent represent an independent fish (prey) and shark (predator).
A model designer wants to focus on each agent design.

5. MASS

6. NetCDF
NetCDF
Machine-independent format for representing scientific data
Files store data arranged in variables
Each variable holds an array of data
netCDF wave2D {
dimensions:
x = 4, y = 4, time = 3;
variables:
float wave( x, y, time );
data:
0, 0, 0, 0, 0, 0, 0, 0, 1, 1, 1, 1, 1, 1, 1, 1,
0, 0, 0, 0, 0, 2, 2, 0, 1, 1, 1, 1, 1, 0, 0, 1,
0, 0, 0, 0, 0, 0, 0, 0, 1, 1, 1, 1, 1, 1, 1, 1 }

7. Purpose Within MASS Real-World application
Allow each simulation entity to save its own data
Make NetCDF file use simple and feasible for MASS
Maintain the benefits of a distributed environment running in parallel
Real-World application
Climate change analysis

8. How it works Creates a file for the simulation if none exists
Stores file contents in a buffer to increase read/write speed
Each processor holds the portion of the file relevant to them
A file is only opened by the first writer Place in each partition
A single instance per processor file creator and parallel reader and writer. When a simulation using paralll_netCDF is started a filename must be passed as part of the command line parameters.
If this file does not exist on disc, then the parameters used to initialize the writer are used to create a file holding a uniform grid of variables for the simulation.

9. Spring 2013 Understand previous work and gather information.
Debug and verify the NetCDF + MASS integration
Run performance tests, store, compare and analyze results
Kelsey's work runs correctly on one processor, but fails otherwise.

10. Summer 2013 Port the MASS-parallelized NetCDF library on to Hadoop
HDFS stores data on distributed disks
Useful for extremely large simulations
Weather simulations produce data upwards of 40 terabytes.

11. HDFS: Hadoop distributed file system
HDFS Client
block data
(block id, byte range)
HDFS datanode
HDFS datanode
HDFS datanode
Linux local file system
Linux local file system
Linux local file system … … …

12. Final Results Running Wave2D Simulation Size 100 for 1000 cycles
With 1 Node and 1 Thread
Without File Writes
1 File Write
Transfer to HDFS
Execution Time (s)
17.2 s
23.4 s
26.2 s
Increased Overhead
+6.2 s
+2.8 s

13. Questions?