9.5 Other Programming Software

Keeping in mind that your head node will also serve as a software development platform, there are other software packages that you'll want to install. One obvious utility is the ubiquitous text editor. Fortunately, most likely choices are readily available and will be part of your basic installation. Just don't forget them when you install the system. Because personal preferences vary so widely, you'll want to include the full complement.

9.5.1 Debuggers

Another essential tool is a software debugger. Let's face it, using printf to debug parallel code is usually a hopeless task. With multiple processes and buffered output, it is unlikely you'll know where the program was executing when you actually see the output. The best solution is a debugger designed specifically for parallel code. While commercial products such as TotalView are available and work well with MPI, free software is wanting. At the very least, you will want a good traditional debugger such as gdb. Programs that extend gdb, such as ddd (the Data Display Debugger), are a nice addition. (Debugging is discussed in greater detail in Chapter 16.) Since it is difficult to tell when they will be needed and just how essential they will be, try to be as inclusive as possible when installing these tools. As part of the gcc development package, gdb is pretty standard fare and should already be on your system. However, ddd may not be installed by default.

Since ddd provides a GUI for other debuggers such as gdb, there is no point installing it on a system that doesn't have X Windows and gdb a or similar debugger. ddd is often included as part of a Linux distribution; for instance, Red Hat includes it. If not, you can download it from http://www.gnu.org/software/ddd. The easiest way to install it is from an RPM.

[root@fanny root]# rpm -vih ddd-3.3.1-23.i386.rpm

warning: ddd-3.3.1-23.i386.rpm: V3 DSA signature: NOKEY, key ID db42a60e

Preparing...                ########################################### [100%]

   1:ddd                    ########################################### [100%]

Depending on what is installed on your system, you may run into a few dependencies. For example, ddd requires openmotif.

9.5.2 HDF5

Depending on the nature of the programming you do, there may be other useful libraries that you'll want to install. One such package that OSCAR includes is Hierarchical Data Format (Version 5) or HDF5. HDF5 is a freely available software package developed by the HDF5 group at the National Center for Supercomputing Applications (NCSA). The official web site is http://hdf.ncsa.uiuc.edu/HDF5/.

HDF5 is both a file format standard and a library with utilities specifically designed for storing scientific data. It supports very large files and is designed and tuned for efficient storage on parallel computing systems. Data is stored in two parts, a header and a data array. The header contains the information needed to interpret the data array. That is, it describes and annotates the data set. The data sets are essentially multidimensional arrays of items. The API is available only in C. While HDF5 is beyond the scope of this book, you should be aware it exists should you need it. An extensive tutorial, as well as other documentation, is available at the software's web site.

9.5.3 SPRNG

Scalable Parallel Random Number Generators (SPRNG) is a library that provides six different state-of-the-art random number generators for use with parallel programs. SPRNG integrates nicely with MPI. Its use is described in Chapter 15.

SPRNG is freely available from http://sprng.cs.fsu.edu/. At the time this was written, the latest version sprng2.0a.tgz. First, download the package and move it to an appropriate directory, e.g., /usr/local/src. The next step is to unpack it.

[root@amy src]# gunzip sprng2.0a.tgz

[root@amy src]# tar -xvf sprng2.0a.tar

...

Then change to the directory to where you just unpacked the source. Before you can build it, you need to edit a couple of files. In the first section of the file make.CHOICES, select the appropriate platform. Typically, this will be INTEL for Linux clusters. Make sure the line

PLAT = INTEL

is uncommented and the lines for other platforms are commented out. Because you want to use it with MPI, in the second section, uncomment the line

MPIDEF = -DSPRNG_MPI

You should also comment out the two lines in the third section if libgmp.a is not available on your system.

You should also edit the appropriate architecture file in the SRC subdirectory, typically make.INTEL. You'll need to make two sets of changes for a Linux cluster. First, change all the gcc optimization flags from -O3 to -O1. Next, change all the paths to MPI to match your machine. For the setup shown in this chapter, the following lines were changed:

MPIDIR = -L/usr/local/mpich-1.2.5.2/lib

and

CFLAGS = -O1 -DLittleEndian $(PMLCGDEF) $(MPIDEF) -D$(PLAT)  \

-I/usr/local/mpich-1.2.5.2/include -I/usr/local/mpich-1.2.5.2/include

CLDFLAGS =  -O1 

FFLAGS = -O1 $(PMLCGDEF) $(MPIDEF) -D$(PLAT)  \

-I/usr/local/mpich-1.2.5.2/include -I/usr/local/mpich-1.2.5.2/include -I.

F77LDFLAGS =  -O1

Once you've done this, run make from the root of the source tree. If you want to play with the MPI examples, run make mpi in the EXAMPLES subdirectory.

To use the library, you must adjust your compile paths to include the appropriate directories. For example, to use SPRNG with OSCAR and MPICH, the following changes should work.

MPIDIR = -L/opt/mpich-1.2.5.10-ch_p4-gcc/lib

MPILIB = -lmpich

   

# Please include mpi header file path, if needed

   

CFLAGS = -O1 -DLittleEndian $(PMLCGDEF) $(MPIDEF) -D$(PLAT)  -I/opt/mpich-

1.2.5.10-ch_p4-gcc/include -I/opt/mpich-1.2.5.10-ch_p4-gcc/include

CLDFLAGS =  -O1 

FFLAGS = -O1 $(PMLCGDEF) $(MPIDEF) -D$(PLAT)  -I/opt/mpich-1.2.5.10-ch_p4-

gcc/include -I/opt/mpich-1.2.5.10-ch_p4-gcc/include -I.

F77LDFLAGS =  -O1

Note this installation is specific to one version of MPI. See Chapter 15 for the details of using SPRNG.