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9.4 MPICHMessage Passing Interface Chameleon (MPICH) was developed by William Gropp and Ewing Lusk and is freely available from Argonne National Laboratory (http://www-unix.mcs.anl.gov/mpi/mpich/). Like LAM, it is both a library and an execution environment. It runs on a wide variety of Unix platforms and is even available for Windows NT. Documentation can be downloaded from the web site. There are separate manuals for each of the communication models. This chapter provides an overview of the installation process and a description of how to use MPICH. For more up-to-date and detailed information, you should consult the appropriate manual for the communications model you are using. 9.4.1 InstallingThere are five different "flavors" of MPICH reflecting the type of machine it will run on and how interprocess communication has been implemented:
The best choice for most clusters is either the ch_p4 model or ch_p4mpd model. The ch_p4mpd model assumes a homogenous architecture while ch_p4 works with mixed architectures. If you have a homogenous architecture, ch_p4mpd should provide somewhat better performance. This section will describe the ch_p4 since it is more versatile. The first step in installing MPICH is to download the source code for your system. MPICH is not available in binary (except for Windows NT). Although the available code is usually updated with the latest patches, new patches are occasionally made available, so you'll probably want to check the patch list at the site. If necessary, apply the patches to your download file following the directions supplied with the patch file. Decide where you want to install the software. This example uses /usr/local/src/mpich. Then download the source to the appropriate directory, uncompress it, and unpack it. [root@fanny src]# gunzip mpich.tar.gz [root@fanny src]# tar -xvf mpich.tar ... Expect lots of output! Change to the directory where the code was unpacked, make a directory for the installation, and run configure. [root@fanny src]# cd mpich-1.2.5.2 [root@fanny mpich-1.2.5.2]# mkdir /usr/local/mpich-1.2.5.2 [root@fanny mpich-1.2.5.2]# ./configure --prefix=/usr/local/mpich-1.2.5.2 \ > -rsh=ssh ... As with LAM, this installation configures MPICH to use SSH.[4] Other configuration options are described in the installation and user's guides.
Next, you'll make, install, and clean up. [root@fanny mpich-1.2.5.2]# make ... [root@fanny mpich-1.2.5.2]# make install ... [root@fanny mpich-1.2.5.2]# make clean ... Again, you'll see lots of output after each of these steps. The first make builds the software while the make install, which is optional, puts it in a public directory. It is also a good idea to make the tests on the head node. Before you can use MPICH, you'll need to tell it which machines to use by editing the file machine.architecture. For Linux clusters, this is the file machine.LINUX and is located in the directory ../share under installation directory. If you use the same file layout used here, the file is /usr/local/mpich-1.2.5.2/share/machines.LINUX. This file is just a simple list of machines with one hostname per line. For SMP systems, you can append a :n where n is the number of processors in the host. This file plays the same role as the schema with LAM. (You can specify a file with a different set of machines as a command-line argument when you run a program if desired.) 9.4.2 User ConfigurationSince individual users don't set up schemas for MPICH, there is slightly less you need to do compared to LAM. Besides this difference, the user setup is basically the same. You'll need to set the $PATH variable appropriately (and $MANPATH, if you wish). The same concerns apply with MPICH as with LAM-you need to distinguish between LAM and MPICH executables if you install both, and you need to ensure the path is set for both interactive and noninteractive logins. You'll also need to ensure that you can log onto each machine in the cluster using SSH without a password. (For more information on these issues, see the subsection on user configuration under LAM/MPI.) 9.4.3 Using MPICHUnlike LAM, you don't need to boot or shut down the runtime environment when running an MPICH program. With MPICH you'll just need to write, compile, and run your code. The downside is, if your program crashes, you may need to manually kill errant processes on compute nodes. But this shouldn't be a common problem. Also, you'll be able to run programs as root provided you distribute the binaries to all the nodes. (File access can be an issue if you don't export root's home directory via NFS.) The first step is to write and enter your program using your favorite text editor. Like LAM, MPICH supplies a set of wrapper programs to simplify compilation-mpicc, mpiCC, and mpif77, and mpif90 for C, C++, FORTRAN 77, and FORTRAN 90, respectively. Here is an example of compiling a C program: [sloanjd@fanny sloanjd]$ mpicc -o cpi cpi.c cpi.c is one of the sample programs included with MPICH. It can be found in the directory ../examples/basic under the source directory. You can see the options supplied by the wrapper program without executing the code by using the -show option. For example, [sloanjd@fanny sloanjd]$ mpicc -show -o cpi cpi.c gcc -DUSE_STDARG -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_UNISTD_H=1 -DHAVE_ STDARG_H=1 -DUSE_STDARG=1 -DMALLOC_RET_VOID=1 -L/opt/mpich-1.2.5.10-ch_p4-gcc/ lib -o cpi cpi.c -lmpich Obviously, you'll want to use the wrapper programs rather than type in arguments manually. To run a program, you use the mpirun command. Again, before the code will run, you must have copies of the binaries on each machine and you must be able to log into each machine with SSH without a password. Here is an example of running the code we just compiled. [sloanjd@fanny sloanjd]$ mpirun -np 4 cpi Process 0 of 4 on fanny.wofford.int pi is approximately 3.1415926544231239, Error is 0.0000000008333307 wall clock time = 0.008783 Process 2 of 4 on hector.wofford.int Process 1 of 4 on george.wofford.int Process 3 of 4 on ida.wofford.int The argument -np 4 specified running the program with four processes. If you want to specify a particular set of machines, use the -machinefile argument. [sloanjd@fanny sloanjd]$ mpirun -np 4 -machinefile machines cpi Process 0 of 4 on fanny.wofford.int pi is approximately 3.1415926544231239, Error is 0.0000000008333307 wall clock time = 0.007159 Process 1 of 4 on george.wofford.int Process 2 of 4 on fanny.wofford.int Process 3 of 4 on george.wofford.int In this example, four processes were run on the two machines listed in the file machines. Notice that each machine was used twice. You can view the mpicc(1) and mpirun(1) manpage for more details. 9.4.4 Testing the InstallationYou can test connectivity issues and the like with the MPICH-supplied script tstmachines, which is located in the ../sbin directory under the MPICH installation. This script takes the architecture as an argument. For example, [sloanjd@fanny sloanjd]$ /usr/local/mpich-1.2.5.2/sbin/tstmachines LINUX If all is well, the script runs and terminates silently. If there is a problem, it makes suggestions on how to fix the problem. If you want more reassurance that it is actually doing something, you can run it with the -v argument. For more thorough testing, MPICH provides a set of tests with the distribution. You'll find a thorough collection of tests supplied with the source files. These are in the directory ../examples/test. You run these tests by executing the command: [sloanjd@fanny test]$ make testing | tee make.log ... You'll need to do this in the test directory. This directory must be shared among all the nodes on the cluster, so you will have to either mount this directory on all the machines or copy its contents over to a mounted directory. When this runs, you'll see a lot of output as your cluster is put through its paces. The output will be copied to the file make.log, so you'll be able to peruse it at your leisure. 9.4.5 MPEThe Multi-Processing Environment (MPE) library extends MPI. MPE provides such additional facilities as libraries for creating log files, an X graphics library, graphical visualization tools, routines for serializing sections of parallel code, and debugger setup routines. While developed for use with MPICH, MPE can be used with any MPI implementation. MPE is included with MPICH and will be built and installed. MPE includes both a library for collecting information and a viewer for displaying the collected information. A user's guide is available that provides greater detail. Use of MPE is described in greater detail in Chapter 17. MPE includes four viewers-upshot, nupshot, jumpshot-2, and jumpshot-3. These are not built automatically since the software required for the build may not be present on every machine. Both upshot and nupshot require Tcl/Tk and Wish. jumpshot-2 and jumpshot-3 require Java. There are three different output formats for MPE log files-alog, an ASCII format provided for backwards compatibility; clog, alog's binary equivalent; and slog, a scalable format capable of handling very large files. upshot reads alog files, nupshot and jumpshot-2 read clog files, and jumpshot-3 reads slog files. MPE includes two utilities, clog2slog and clog2alog, to convert between formats. The basic functionality of the viewers is similar, so installing any one of them will probably meet your basic needs. Although the requirements are different, the compilation process is similar for each tool. You can build the viewers collectively or individually. For example, to compile jumpshot-3, you'll need to install Java if you don't already have it. JDK-1.1, JDK-1.2, or JDK-1.3 can be used. (jumpshot-2 compiles only with JDK-1.1.) If you don't have the appropriate Java, you can download it from http://www.blackdown.org or http://java.sun.com and follow the installation directions given at the respective site. Once Java has been installed, make sure that you add its directory to your path. Next, change to the ../mpe/viewer/jumpshot-3 subdirectory under the MPICH directory, for example, /usr/local/src/mpich-1.2.5.2/mpe/viewers/jumpshot-3. Now you can configure and build jumpshot-3. [root@fanny jumpshot-3]# ./configure ... [root@fanny jumpshot-3]# make ... [root@fanny jumpshot-3]# make install ... jumpshot-3 will be installed in the /usr/local/bin directory as jumpshot. (You will only need to install it on the head node.) For details on the installation of the other viewer, see the MPE installation and user's guide. To test your installation, you'll need to compile a program using the -mpilog option and run the code to create a log file. [sloanjd@fanny sloanjd]$ mpicc -mpilog -o cpi cpi.c [sloanjd@fanny sloanjd]$ mpirun cpi ... When you run the code, the log file cpi.clog will be created. You'll need to convert this to a format that jumpshot-3 can read. [sloanjd@fanny sloanjd]$ clog2slog cpi.clog The conversion routines are in the directory ../mpich-1.2.5.2/bin. Now you can view the output. Of course, you must have a graphical login for this to work. With this command, several windows should open on your display. [sloanjd@fanny sloanjd]$ jumpshot cpi.slog As noted, the use of MPE will be described in greater detail in Chapter 17. |
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