Big-Box Science

A few months ago, I wrote a piece about how you can use MPI to run a parallel program over a number of machines that are networked together. But more and more often, your plain-old desktop has more than one CPU. How best can you take advantage of the amount of power at your fingertips? When you run a parallel program on one single machine, it is called shared-memory parallel programming. Several options are available when doing shared-memory programming. The most common are pthreads and openMP. This month, I take a look at openMP and how you can use it to get the most out of your box.

openMP is a specification, which means you end up actually using an implementation. It is implemented as an extension to a compiler. So, in order to use it in your code, you simply need to add a compiler flag. There is no linking in of external libraries. openMP directives are added to your program as special comments. This means if you try to compile your program with a compiler that doesn't understand openMP, it should compile fine. The openMP directives will appear just like any other comment, and you will end up with a single-threaded program. Implementations for openMP are available under C/C++ and FORTRAN.

The most basic concept in openMP is that only sections of your code are run in parallel, and for the most part, these sections all run the same code. Outside of these sections, your program will run single-threaded. The most basic parallel section is defined by:


#pragma omp parallel

in C/C++, or:


!OMP PARALLEL

in FORTRAN. This is called a parallel openMP pragma. Almost all of the other pragmas that you are likely to use are built off this.

The most common pragma you will see is the parallel loop. In C/C++, this refers to a for loop. In FORTRAN, this is a do loop. (For the rest of this piece, I stick to C/C++ as examples. There are equivalent FORTRAN statements you can find in the specification documentation.) A C/C++ loop can be parallelized with:


<![CDATA[
#pragma omp parallel for
for (i=0; i<max; i++) {
   do_something();
   area += i;
   do_something_else();
}
]]>

The pragma tells the openMP subsystem that you want to create a parallel section defined by the for loop. What happens is that the defined number of threads get created, and the work of the loop gets divided among these threads. So, for example, if you had a quad-core CPU and had to go through 100 iterations in this for loop, each CPU core gets 25 iterations of the loop to do. So, this for loop should take approximately one-fourth the time it normally takes.

Does this work with all for loops? No, not necessarily. In order for the openMP subsystem to be able to divide up the for loop, it needs to know how many iterations are involved. This means you can't use any commands that would change the number of iterations around the for loop, including things like "break" or "return" in C/C++. Both of these drop you out of the for loop before it finishes all of the iterations. You can use a "continue" statement, however. All that does is jump over the remaining code in this iteration and places you at the beginning of the next iteration. Because this preserves iteration count, it is safe to use.

By default, all of the variables in your program have a global scope. Thus, when you enter a parallel section, like the parallel for loop above, you end up having access to all of the variables that exist in your program. Although this is very convenient, it is also very, very dangerous. If you look back at my short example, the work is being done by the line:


area += i;

You can see that the variable area is being read from and written to. What happens now if you have several threads, all trying to do this at the same time? It is not very pretty—think car pile-up on the freeway. Imagine that the variable area starts with a value of zero. Then, your program starts the parallel for loop with five threads and they all read in the initial value of zero. Then, they each add their value of i and save it back to memory. This means that only one of these five actually will be saved, and the rest essentially will be lost. So, what can you do? In openMP, there is the concept of a critical section. A critical section is a section of your code that's protected so that only one thread can execute it at a time. To fix this issue, you could place the area incrementing within a critical section. It would look like this:


<![CDATA[
#pragma omp parallel for
for (i=0; i<max; i++) {
   do_something();
#pragma omp critical
   area += i;
   do_something_else();
}
]]>

Remember that in C, a code block is defined by either a single line or a series of lines wrapped in curly braces. So in the above example, the critical section applies to the one line area += i;. If you wanted it to apply to several lines of code, it would look like this:


<![CDATA[
#pragma omp parallel for
for (i=0; i<max; i++) {
   do_something();
#pragma omp critical
   {
   area += i;
   do_something_else();
   }
}
]]>

This leads us to a more subtle way that multiple threads can abuse global variables. What if you have a nested for loop and you want to parallelize the outside loop? Then:


<![CDATA[
#pragma omp parallel for
for (i=0; i<max1; i++) {
   for (j=0; j<max2; j++) {
      do_something();
   }
}
]]>

In this case, every thread is going to have access to the global variable j. They will all be reading from and writing to it at completely random times, and you will end up with either more than max2 iterations happening or less than max2. What you actually want to see happen is that each thread does everything within each iteration of the outside loop. What is the solution? Luckily, the openMP specification has the concept of a private variable. A private variable is one where each thread gets its own private copy to work with. To privatize a variable, you simply need to add to the parallel for pragma:


#pragma omp parallel for private(j)

If you have more than one variable that needs to be privatized, you can add them to the same private() option, comma-separated. By default, these new private copies will act just like regular variables in C code on Linux. This means their initial values will be whatever junk are in those memory locations. If you want to make sure that each copy starts with the value of the original value that existed on entering the parallel section, you can add the option firstprivate(). Again, you enter the variables you want treated this way in a comma-separated list. As an example that doesn't really do anything useful, this would look like:


<![CDATA[
a = 10;
#pragma omp parallel for private(a,j) firstprivate(a)
for (i=0; i<max1; i++) {
   for (j=0; j<max2; j++) {
      a += i;
      do_something(a*j);
   }
}
]]>

So, you have a program. Now what? The first step is to compile it. Because it is an extension to the compiler itself, you need to add an option to your compilation command. For gcc, it would simply be -fopenmp. You do need to be careful about the compiler version you are using and what it supports. The openMP specification is up to version 3.0 right now, with support varying across the gcc versions. If you want to look at the support in detail, check the main gcc page at http://gcc.gnu.org. The latest versions are starting to include support for version 3.0 of openMP.

Once you have it compiled, you need to run it. If you simply run it at the command line, without doing anything else, your program will check your machine and see how many CPUs you have (a dual-core processor looks like two CPUs, in case you were wondering). It then will go ahead and use that number as the number of threads to use in any parallel sections. If you want to set the number of threads that should be used explicitly, you can set it using an environment variable. In bash, you would use this to set four threads:


export OMP_NUM_THREADS=4

You can set more threads than you have CPUs. Because they are actual threads of execution, Linux has no problem scheduling them on the available CPUs. Just remember if you have more threads than available CPUs, you will see a slowdown in the execution speed of your code, as it will be swapping with itself on the CPUs.

Why would you do this? Well, when you are testing a new piece of code, you may have bugs that don't present themselves until you reach a certain number of threads. So, in testing scenarios, it may make sense to run with a large number of threads and a small input data set. The ideal situation is to be the only process running on the machine and running one thread for each CPU. This way, you maximize usage and minimize swapping.

All of this has been only the briefest introduction. I haven't covered generic parallel sections, functional parallelism, loop scheduling or any of the other more-advanced topics. The specifications are at http://www.openmp.org along with links to tons of tutorials and other examples. Hopefully, this introduction has given you some ideas to try and provides a small taste of what may be possible. I will leave you with one last hint. If you want to start to play with parallel programs without having to think about it, add the option -ftree-parallelize-loops. This will try to analyze your code and see if it can parallelize any sections. It won't be able to catch all of the sections that can be parallelized, because it can't understand the context of your code and what it is trying to do. But, for the time it takes to add the option and recompile and test the timing, it definitely would be worthwhile.

______________________

Joey Bernard has a background in both physics and computer science. This serves him well in his day job as a computational research consultant at the University of New Brunswick. He also teaches computational physics and parallel programming.

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export OMP NUM THREADS=4

Phil M's picture

Perhaps "export OMP NUM THREADS=4" above should read "export OMP_NUM_THREADS=4"

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