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This guide describes how to building a simple MPICH cluster in ubuntu.
Note: you need a basic knowledge about MPICH and clustering.
Here we have 4 nodes running ubuntu 7.04 with these host names: ub0,ub1,ub2,ub3;
1. Defining hostnames in etc/hosts/
Edit /etc/hosts like these:
127.0.0.1 localhost
192.168.133.100 ub0
192.168.133.101 ub1
192.168.133.102 ub2
192.168.133.103 ub3
Note that the file shouldn't be like this:
127.0.0.1 localhost
127.0.1.1 ub0
192.168.133.100 ub0
192.168.133.101 ub1
192.168.133.102 ub2
192.168.133.103 ub3
2. Installing NFS
To Install NFS just run this in terminal:
omid@ub0:~$ sudo apt-get install nfs-kernel-server
3. Sharing Master Folder
Make a folder in all nodes, we'll store our data and programs in this folder.
omid@ub0:~$ sudo mkdir /mirror
And then we share it over nodes on the master node.
omid@ub0:~$ sudo echo /mirror *(rw,sync) >> /etc/exports
Note than we store out data and programs only in master node and other nodes will access them with NFS.
4. Mounting /master in nodes
omid@ub1:~$ sudo mount ub0:/mirror /mirror
omid@ub2:~$ sudo mount ub0:/mirror /mirror
omid@ub3:~$ sudo mount ub0:/mirror /mirror
it's better to change fstab in order to mount it on every boot.
5. Defining a user for running MPI programs
We define a user with same name and same userid in all nodes with a home directory in /mirror.
Here we name it "mpiu"! Also we change the owner of /mirror to mpiu:
omid@ub0:~$ sudo chown mpiu /mirror
6. Installing SSH Server
Run this command in all nodes in order to install OpenSSH Server
omid@ub0:~$ sudo apt-get install opensshserver
7. Setting up SSH with no pass phrase for communication between nodes
First we login with our new user:
omid@ub0:~$ su - mpiu
Then we generate DSA key for mpiu:
mpiu@ub0:~$ ssh-keygen -t dsa
Leave passphrase empty.
Next we add this key to authorized keys:
mpiu@ub0:~$ cd .ssh
mpiu@ub0:~/.ssh$ cat id_pub.dsa >> authorized_keys
As the home directory of mpiu in all nodes is the same (/mirror/mpiu) , there is no need to run these commands on all nodes.
To test SSH run:
mpiu@ub0:~$ ssh ub1 hostname
It should return remote hostname without asking for passphrase.
8. Installing GCC
Install build-essential package:
mpiu@ub0:~$ sudo apt-get install build-essential
9.Installing Other Compilers
Other prefered compilers should be installed before installing MPICH.
In this step we install other compilers such as Inter Fortran, SGI compiler , ... .
10. Installing MPICH2
Download MPICH2 source code from https://www.mpich.org/downloads/
Extract .tar.bz2 file in /mirror. Also make a folder for MPICH installation.
mpiu@ub3:/mirror$ mkidr mpich2
mpiu@ub3:/mirror$ tar xvf mpich2-1.0.5p3.tar.gz
mpiu@ub3:/mirror$ cd mpich2-1.0.5p3
mpiu@ub3:/mirror/mpich2-1.0.5p3$ ./configure --prefix=/mirror/mpich2
mpiu@ub3:/mirror/mpich2-1.0.5p3$ make
mpiu@ub3:/mirror/mpich2-1.0.5p3$ sudo make install
For more information about compilation see README file in source package.
After successfully compiling and installing mpich, add these lines to "/mirror/mpiu/.bashrc/"
export PATH=/mirror/mpich2/bin:$PATH
export PATH
LD_LIBRARY_PATH="/mirror/mpich2/lib:$LD_LIBRARY_PATH"
export LD_LIBRARY_PATH
Next we run this command in order to define MPICH installation path to SSH.
mpiu@ub0:~$ sudo echo /mirror/mpich2/bin >> /etc/environment
For testing our installation run:
mpiu@ub0:~$ which mpd
mpiu@ub0:~$ which mpiexec
mpiu@ub0:~$ which mpirun
11. setting up MPD
Create mpd.hosts in mpiu's home directory with nodes names:
ub3
ub2
ub1
ub0
and run :
mpiu@ub0:~$ echo secretword=something >> ~/.mpd.conf
mpiu@ub0:~$ chmod 600 .mpd.conf
To test MPD run above commands. The output should be the current hostname.
mpiu@ub0:~$ mpd &
mpiu@ub0:~$ mpdtrace
mpiu@ub0:~$ mpdallexit
After all run mpd daemon:
mpiu@ub0:~$ mpdboot -np 4
mpiu@ub0:~$ mpdtrace
The output should be name of all nodes.
There are some examples in "mpich2-1.0.5/examples", we'll run one :
mpiu@ub0:~$ mpiexec -n 4 cpi
That's it!
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