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Exercise 3

Overview:

1. Still logged into the workshop cluster?

If so, then continue to the next step. If not, then login as you did previously for Exercises 1 and 2.

2. Review the array decomposition example code.

First, review the serial version of this example code, either ser_array.c or ser_array.f.

After you understand what’s going on, review the parallel MPI version, either mpi_array.c or mpi_array.f. The comments explain how MPI is used to implement a parallel data decomposition on an array.

3. Compile the parallel MPI and serial versions of the array decomposition example code

As with Exercises 1 & 2, use the compiler command of your choice to compile the mpi_array example code.

Use the appropriate serial compiler command for the serial version. For example:

C:

icc ser_array.c  -o ser_array
mpicc mpi_array.c  -o mpi_array

Fortran:

ifort ser_array.f -o ser_array
mpif77 mpi_array.f -o mpi_array

4. Run the executables interactively

For the MPI executable, use the special workshop pool and 8 tasks. For example:

Serial:

ser_array

MPI:

srun -n8 -ppReserved mpi_array

Note: The srun command is covered in detail in the “Starting Jobs” section of the Linux Clusters Overview tutorial, located here. There is also a man page.

5. Compare other serial codes to their parallel version

If we had more time, you might even be able to start with a serial code or two and create your own parallel version. Feel free to try if you’d like.

6. Try any/all of the other MPI example codes

C:

make -f Makefile.MPI.c
make -f Makefile.MPI.c  mpi_mm
make -f Makefile.Ser.c

Fortran:

make -f Makefile.MPI.f
make -f Makefile.MPI.f  mpi_mm
make -f Makefile.Ser.f

Note: you can change the compiler being used by editing the Makefile.

CodeRequirement(s)
mpi_bandwidthRequires an even number of tasks.
mpi_cartesianRequires 16 MPI tasks
mpi_groupRequires 8 MPI tasks
mpi_heat2D
mpi_wave
These examples attempt to generate an Xwindows display for results. You will need to make sure that your Xwindows environment and software is setup correctly if you want to see the graphic. Ask the instructor if you have any questions.
mpi_latencyRequires only 2 MPI tasks that should be on DIFFERENT nodes

7. Compare per task and aggregate communications bandwidths

srun -N2 -n4 -ppReserved mpi_bandwidth
srun -N2 -n8 -ppReserved mpi_bandwidth
srun -N2 -n16 -ppReserved mpi_bandwidth
srun -N2 -n32 -ppReserved mpi_bandwidth
srun -N2 -n64 -ppReserved mpi_bandwidth
Explanation (Click to expand!) As the number of tasks increase, the per task bandwidth decreases because they must compete for use of the network adapter. Aggregate bandwidth will increase until it plateaus.

8. Compare blocking send/receive with non-blocking send/receive

Explanation (Click to expand!) Non-blocking send/receive operations are often significantly faster than blocking send/receive operations.

9. When things go wrong…

There are many things that can go wrong when developing MPI programs. The mpi_bug series of programs demonstrate just a few. See if you can figure out what the problem is with each case and then fix it.

Compile with the compile command(s) of your choice and run interactively using 4 tasks in the special workshop pool.

The buggy behavior will differ for each example. Some hints are provided below.

Hints (Click to expand!)
CodeBehaviorHints/Notes
mpi_bug1Hangsmpi_bug1 demonstrates how miscoding even a simple parameter like a message tag can lead to a hung program. Verify that the message sent from task 0 is not exactly what task 1 is expecting and vice versa. Matching the send tags with the receive tags solves the problem.
mpi_bug2Wrong results or abnormal terminationmpi_bug2 shows another type of miscoding. The data type of the message sent by task 0 is not what task 1 expects. Nevertheless, the message is received, resulting in wrong results or abnormal termination - depending upon the MPI library and platform. Matching the send data type with the receive data type solves the problem.
mpi_bug3Error message and/or abnormal terminationmpi_bug3 shows what happens when the MPI environment is not initialized or terminated properly. Inserting the MPI init and finalize calls in the right locations will solve the problem.
mpi_bug4Gives the wrong result for "Final sum". Compare to mpi_array Number of MPI tasks must be divisible by 4; mpi_bug4 shows what happens when a task does not participate in a collective communication call. In this case, task 0 needs to call MPI_Reduce as the other tasks do.
mpi_bug5Dies or hangs - depends upon platform and MPI library mpi_bug5 demonstrates an unsafe program, because sometimes it will execute fine, and other times it will fail. The reason why the program fails or hangs is due to buffer exhaustion on the receiving task side, as a consequence of the way an MPI library has implemented an eager protocol for messages of a certain size. One possible solution is to include an MPI_Barrier call in the both the send and receive loops.
mpi_bug6Terminates or is ignored (depends on platform/language) Requires 4 MPI tasks; mpi_bug6 has a bug that will terminate the program in some cases but be ignored in other cases. The problem is that task 2 performs a blocking operation, but then hits the MPI_Wait call near the end of the program. Only the tasks that make non-blocking calls should hit the MPI_Wait. The coding error in this case is easy to fix - simply make sure task 2 does not encounter the MPI_Wait call.
mpi_bug7Hangsmpi_bug7 performs a collective communication broadcast but erroneously codes the count argument incorrectly resulting in a hang condition.

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