Matthias K. Gobbert

MPI under Linux in the Math Department

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Purpose of this Document

This document tries to explain how to get started using MPI on our department's Linux cluster math-cluster4. We are running the mpich implementation of MPI, and all explanations pertain to that.

My intention is to expand or modify this page during the semester in order to include other information as needed. If you find mistakes on this page or have suggestions, please contact me.

General Information and Login Procedure

Let me start by explaining the setup of the cluster: It consists of four dual-processor Linux PCs. They are called,,, and I will refer to them as pc51, node2, node3, and node4, respectively, in the following.

Each machine has two 1000 MHz Intel Pentium III processors and 1 GB of memory. The four nodes of math-cluster4 are connected by 100 Mbps ethernet cables and a dedicated switch; therefore, the cluster is called a Beowulf cluster. The cables and the switch are off-the-shelf commodity products. All four computers access the central SCSI harddisk on pc51.

The only machine with a connection to the outside network is pc51. The department uses the port number 49207 for ssh connections, so you would log in to pc51

  ssh -p 49207
where username denotes your username on math-cluster4. Here, 49207 with the -p flag specifies the port number. You may want to try that you can connect to the other machines like node2 from pc51 using ssh node2 for instance. You will need to enter a password every time; this fact makes parallel computing impractical, and you must implement the following instructions to overcome this problem.

Setup on the Operating System Level

To eliminate the need to enter a password every time, set up the RSA key control, as follows; this needs to be done only once. Log in to pc51 and start by saying in your home directory
  ssh-keygen -t dsa
at the Linux prompt; do not choose any passphrase, rather just hit RETURN. Then copy .ssh/ to .ssh/authorized_keys2 by
  cp .ssh/ .ssh/authorized_keys2
Try to see that you can now log onto the other machines from pc51 just by saying ssh node2 without being prompted for a password.

Finally, set up one environment variable and add the MPI directory to the path, as follows. Add the following two lines to your .cshrc file:

  setenv MPIHOME /usr/local/mpich
  set path = ( $path $MPIHOME/bin )
Do a source .cshrc to activate the changes in .cshrc in your current shell. To be precise, you will have to enter your password once to enable the automatic authentication; to this end, you may want to ssh to all machines (node2, node3, and node4) manually at this time. From then on, you should be able to log in to these other machines as well as run your parallel code without entering your password.

Compiling and Linking MPI Code Using mpich

Let's assume that you have a C code sample.c that contains some MPI commands. Compile and link the MPI code by
  mpicc -o sample sample.c
The script mpicc (located in directory $MPIHOME/bin) works on the surface just like the regular compiler gcc. For instance, the option -o sample chooses the name of the output file (here the executable file), and mpicc compiles and links in one (apparent) step.

If your code includes mathematical functions (like exp, cos, etc.), you need to link to the mathematics library This is done, just like for serial compiling, by adding -lm to the end of your compile command, that is,

  mpicc -o sample sample.c -lm
In a similar fashion, other libraries can be linked.

More formally, I could also separate the compile from the link step. That is, the C file sample.c is first compiled into object code sample.o, which then gets linked to the required libraries to obtain the executable sample. The sequence of the two commands

  mpicc -c sample.c
  mpicc -o sample sample.o -lm
accomplishes this, where the option -c stands for "compile-only".

See the man page of mpicc for more information by saying

  man mpicc

Running of MPI Code Using mpich

After compiling and linking, proceed to run the code using, for instance,
  mpirun -np 4 sample
Again, mpirun is a script located in $MPIHOME/bin. The last argument sample is the name of the executable file, and the option -np 4 gives the number of processors that you requesting for this MPI run.

The processors, on which your code is run, are taken from the default machinefile given by $MPIHOME/share/machines.LINUX. You can inspect its contents by saying

  more $MPIHOME/share/machines.LINUX

If you wish to control more precisely, which machines your code is run on, you should create your own machinefile called, for instance, machines.sample. If this file is placed in your current directory along with the executable sample, you use it by saying

  mpirun -machinefile machines.sample -np 4 sample
Using -np 4 assumes of course that your machinefile contains a list of at least processors.

Notice that it clearly does not make sense to use more than 8 processors on our system, since it consists only of four dual PCs. See the man page of mpirun for more information by saying

  man mpirun

Good Running Habits

The script mpirun does not check, whether the processors given in the machinefile (default or custom) are available for use. That is, if someone else is already running a job on one or more processors, it will still run your job, as requested. This has two main disadvantages: (1) You are stepping on someone else and impeding his/her running of code, and (2) your code will run slower than necessary, if another processor is available.

While the second issue above should be reason enough to be more careful, the first issue is more important: We rely on all users to be courteous to other users by not stepping on them and impeding their work. There is no automatic scheduler set up on our system. Rather, scheduling is on a first-come first-serve basis. That means that it is your obligation before starting your job to make sure that all desired processors are available!

This means usually that you need to manually ssh to all desired machines and use the command top to assess the system status. Only then is it okay to start your parallel job. If you do not adhere to these common-sense rules of courtesy to other users, the department reserves the right to suspend or revoke your user privileges on this system without notice!

Other Useful Information

The Beowulf cluster including pc51 only allows secure connection from the outside. Hence, the above instructions referred to ssh. Correspondingly, to transfer files in and out of the machine, you must use scp or similar secure software. You will need to do this to print out code written on the cluster, for instance.

Let me explain the use of scp by the following example: The user username has a file hello.c in directory math627/hw1. To copy the file to the current diretory on another Unix/Linux system with scp installed, e.g., other machines in the departmental computer lab, use

  scp -P 49207 .
The period "." at the end of the above sample command is significant; it signifies that you want the file copied to your current directory (without changing the name of the file). Here, 49207 is the port number, which is given by the -P option of scp; notice carefully that this is different from the -p for ssh. (As a side note, -p for scp stands for "preserve" and preserves the date stamp and other settings.)

As with ssh, you can leave out the username@, if your username agrees on both machines. If issuing the command from within the Mathematics domain, you can also abbreviate the machine name to pc51.

Copyright © 2001-2006 by Matthias K. Gobbert. All Rights Reserved.
This page version 1.6, September 2006.