1. Using Paraguin to Create Parallel Programs
Assignment 2
Using Paraguin to Create Parallel Programs

2. Cluster at UNCW Submit Host: babbage Head Node: harpua
User
Computers
Dedicated Cluster
Ethernet interface
Master node
Submit Host: babbage
Switch
Head Node: harpua
Compute nodes
Compute Nodes: compute-0-0, compute-0-1, compute-0-2, …
9/4/2012

3. Cluster at UNCW
We use the Sun Grid Engine (SGE) to schedule jobs on the cluster
This is to allow users to have exclusive use of the compute nodes so that users’ applications don’t interfere with the performance of others
The scheduler (SGE) is responsible for allocating compute nodes to jobs exclusively
Compile as normal:
$ mpicc hello.c –o hello
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4. SGE But running is done through a job submission file
Some SGE commands:
qsub <job submission file> – submits a job to the schedule to run
qstat – see the status of submitted jobs (waiting, queued, running, terminated, etc.)
qdel <#> - deletes a job (by number) from the system
qhost – see a list of hosts
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5. SGE Example job submission file (hello.sge): #!/bin/sh
# Usage: qsub hello.sge
#$ -S /bin/sh
#$ -pe orte # Specify how many processors we want
# -- our name ---
#$ -N Hello # Name for the job
#$ -l h_rt=00:01:00 # Request 1 minute to execute
#$ -cwd # Make sure that the .e and .o file arrive in the working directory
#$ -j y # Merge the standard out and standard error to one file
mpirun -np $NSLOTS ./hello
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6. SGE Example job submission file (hello.sge): #!/bin/sh
# Usage: qsub hello.sge
#$ -S /bin/sh
#$ -pe orte # Specify how many processors we want
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7. SGE Example job submission file (hello.sge): # -- our name ---
#$ -N Hello # Name for the job
#$ -l h_rt=00:01:00 # Request 1 minute to execute
The name of the job plus the name of the output files: Hello.o### and Hello.op###
Indicates that the job will need only a minute. This is important so that SGE will clean up if the program hangs or terminates incorrectly. May need to increase the time for longer programs or it will terminate the program before it has completed.
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8. SGE Example job submission file (hello.sge):
#$ -cwd # Make sure that the .e and .o file arrive in the working directory
#$ -j y # Merge the standard out and standard error to one file
Do the job in the current directory
SGE will create 3 files: Hello.o##, Hello.e##, and Hello.op##. The –j y command will merge the Hello.o and Hello.e files (std out and error).
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9. SGE Example job submission file (hello.sge):
mpirun -np $NSLOTS ./hello
And finally the command to run the MPI program. $NSLOTS is the same number given with the #$ -pe orte 16 line.
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10. SGE Example
$ qstat $ qsub hello.sge Your job 106 ("Hello") has been submitted job-ID prior name user state submit/start at queue slots ja-task-ID Hello cferner qw 09/04/ :08:38 16 $
The state of “qw” means queued and waiting.
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11. SGE Example
$ qstat job-ID prior name user state submit/start at queue slots ja-task-ID Hello cferner r 09/04/ :11:43 16 mpi_assign]$
The state of “r” means running
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12. SGE Example
$ ls hello hello.c Hello.o106 Hello.po106 hello.sge ring ring.c ring.sge test test.c test.sge $ cat Hello.o106 Hello world from master process 0 running on compute-0-2.local Message from process = 1 : Hello world from process 1 running on compute-0-2.local Message from process = 2 : Hello world from process 2 running on compute-0-2.local …
You will want to clean up the output files when you are done with them or you will end up with a bunch of clutter.
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13. Deleting a job
$ qstat job-ID prior name user state submit/start at queue slots ja-task-ID Hello cferner qw 09/04/ :18:20 16 $ qdel 108 cferner has registered the job 108 for deletion $
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14. Assignment 2 Setup (Do this only once)
Put these lines in the file .bash_profile
export MACHINE=x86_64-redhat-linux
export SUIFHOME=/share/apps/suifhome
export COMPILER_NAME=gcc
`perl $SUIFHOME/setup_suif -sh`
Run the command:
$ . .bash_profile
Notice the 2 periods and the space between them

15. Hello World Program Program is given to you
You simply need to compile it and run it (using a job submission file)
Try running it on my processors
Produce documentation of compiling and running the program

16. Matrix Multiplication
Matrix Multiplication skeleton program is given to you in Appendix
Includes:
Opening the input file
Reading the input
Taking a time stamp
Taking a 2nd time stamp
Computing the elapsed time between the time stamps
Printing the results

17. Matrix Multiplication
You need to:
Broadcast the error to the processors and exit in necessary
Scatter the input
Compute the partial results
Gather the partial results

18. Heat Distribution
Using the stencil pattern, model the distribution of heat in a room that has a fireplace along one wall

19. Heat Distribution
The newly computed values will be the average of its neighbors (diagonals also) as well as its own old value
So each value at location i,j should be the average of 9 values
This reduces oscillations

20. Producing a Visual of the Output
Produced with X11 Graphics
Produced with Excel

21. Producing a Visual of the Output
See the document signments/X11GraphicsNotes.pdf for help with creating graphics using X11.
The Excel Graph is a surface plot

22. Monte Carlo Estimation of π (required for Graduates/optional for Undergraduates)
Scatter/Gather pattern, but uses broadcast and reduce
This is not a workflow pattern
π can also be estimated by integrating the function , but you aren’t asked to do this.

23. Questions?