Parallel Processing: A KISS Approach - University of North Dakota

17. “#PBS –l” Sets limits on the job execution. This example specifies 4 nodes with 1
process per node. Note that there are many options. Do a “Man pbs_resources”
for more info (see text box below).
18. “./mst” Instructs the batch scheduler to run the example program. You must
change this argument to specify your process.
In general, parallelizing a job across a number of nodes and processes per node is
not as obvious as it may first seem. Fortunately, if you have a task that this
example was designed to manage, you can probably specify as many nodes as you
have data files (however, the heuristic is to specify, at most, half as many nodes as
data files). Specifying the processes per node is not as obvious. Here’s another
heuristic: If your processing requires mainly computations and little IO, specify 2
processes per node and reduce the number of nodes requested. If your processing
involves a lot of IO, you may want to only specify 1 process per node.
Finally, remember that this example implements a master-slave paradigm.
Therefore, 1 entire node (regardless of the number of processes per node
specified) will be allocated to the master. For example, in this example only 3
slave processes will be created even though 4 processes have been requested via
“#PBS –l”
7. Running the program:
Once you have PVM configured and a batch submission script configured you can
execute the derived program using the command:
qsub ./name_of_batch_script
Note that when using the batch scheduler no output is displayed on the computer
screen, but is written to an output file (see “#PBS –o” and “#PBS –e” above).
To summarize, modify your .bash_profile file to include PVM paths, edit mstSlave.cpp
and mst.cpp according to your task, compile mstSlave.cpp and mst.cpp using the Makefile
(and optional “build” script) shown above, and then run the example derived program
using the batch scheduler.
Since the program gets the list of nodes to execute on from the batch scheduler each time
it is executed, you can change the number of nodes or processes per node in the batch
submission script and any example derived program will adjust the load balancing
accordingly.
Finally, the load balancing mechanism is master-slave and naïve. Since it does not have
any information regarding the processing time of any partition, it may very well end up
waiting for a single long-to-process partition to be completed while all of the other
partitions have long finished. An informed scheduler would process long-to-process
partitions first.
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