How to create OPENMPI CLUSTER ?

Setting Up an MPICH2 Cluster in Ubuntu

This guide describes how to build a simple MPICH cluster in ubuntu.
To understand the guide, a basic knowledge of command line usage and the principle mpich
& clustering is assumed.
Here we have 4 nodes running Ubuntu server 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
or like this:
127.0.0.1     localhost
127.0.1.1     ub0
192.168.133.101 ub1
192.168.133.102 ub2
192.168.133.103 ub3
otherwise other hosts will try to connect to localhost when they try to reach ub0.

2. Installing NFS
NFS allows us to create a folder on the master node and have it synced on all the other nodes.
https://help.ubuntu.com/community/MpichCluster

MpichCluster ­ Community Help Wiki
This folder can be used to store programs. To Install NFS just run this in the master node's
terminal:








omid@ub0:~$ sudo apt‐get install nfs‐server






To install the client program on other nodes run this command on each of them:
omid@ub1:~$ sudo apt‐get install nfs‐client


Note: if you want to be more efficient in controlling several nodes using same
commands, ClusterSSH is a nice tool and you can find a basic two­line tutorial here.
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 the contents of this folder located on the master node to all the other
nodes. In order to do this we first edit the /etc/exports file on the master node to contain the
additional line
/mirror *(rw,sync)
This can be done using a text editor such as vim or by issuing this command:


omid@ub0:~$ echo "/mirror *(rw,sync)" | sudo tee ‐a /etc/exports
Now restart the nfs service on the master node to parse this configuration once again.

omid@ub0:~$ sudo service nfs‐kernel‐server restart

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
Now all we need to do is to mount the folder on the other nodes. This can be done manually
each time like this:
omid@ub1:~$ sudo mount ub0:/mirror /mirror
omid@ub2:~$ sudo mount ub0:/mirror /mirror
omid@ub3:~$ sudo mount ub0:/mirror /mirror
But it's better to change fstab in order to mount it on every boot. We do this by editing
/etc/fstab and adding this line:
ub0:/mirror    /mirror    nfs
and remounting all partitions by issuing this on all the slave nodes:
omid@ub1:~$ sudo mount ‐a
omid@ub2:~$ sudo mount ‐a
omid@ub3:~$ sudo mount ‐a

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.
https://help.ubuntu.com/community/MpichCluster

MpichCluster ­ Community Help Wiki
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 openssh‐server
‐

7. Setting up passwordless SSH for communication
between nodes
First we login with our new user to the master node:
omid@ub0:~$ su ‐ mpiu
Then we generate an RSA key pair for mpiu:
mpiu@ub0:~$ ssh keygen  t rsa
‐
‐
You can keep the default ~/.ssh/id_rsa location. It is suggested to enter a strong passphrase for
security reasons.
Next, we add this key to authorized keys:
mpiu@ub0:~$ cd .ssh
mpiu@ub0:~/.ssh$ cat id_rsa.pub >> 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. If you didn't mirror the home directory, though, you can use
ssh‐copy‐id <hostname> to copy a public key to another machine's authorized_keys file
safely.

To test SSH run:
mpiu@ub0:~$ ssh ub1 hostname
 
If you are asked to enter a passphrase every time, you need to set up a keychain. This is done
easily by installing... Keychain.
mpiu@ub0:~$ sudo apt‐get install keychain
 
And to tell it where your keys are and to start an ssh­agent automatically edit your ~/.bashrc
file to contain the following lines (where id_rsa is the name of your private key file):
if type keychain >/dev/null 2>/dev/null; then
  keychain ‐‐nogui ‐q id_rsa
  [ ‐f ~/.keychain/${HOSTNAME}‐sh ] && . ~/.keychain/${HOSTNAME}‐sh
  [ ‐f ~/.keychain/${HOSTNAME}‐sh‐gpg ] && . ~/.keychain/${HOSTNAME}‐sh‐gpg
fi
Exit and login once again or do a source ~/.bashrc for the changes to take effect.
Now your hostname via ssh command should return the other node's hostname without asking
for a password or a passphrase. Check that this works for all the slave nodes.


8. Installing GCC
https://help.ubuntu.com/community/MpichCluster

MpichCluster ­ Community Help Wiki
To be able to compile all the code on our master node (it's sufficient to do it only there if we
do it inside the /mirror folder and all the libraries are in place on other machines) we need a
compiler.
You can get gcc and other necessary stuff by installing the build­essential 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 you may install other compilers such as Inter Fortran, SGI compiler , ...


10. Installing MPICH2
Now the last ingredient we need installed on all the machines is the MPI implementation. You
can install MPICH2 using Synaptic by typing:
sudo apt‐get install mpich2
Alternatively, MPICH2 can be installed from source as explained in the MPICH installer
guide or you can try using some other implementation such as OpenMPI.
To test that the program did indeed install successfully enter this on all the machines:
mpiu@ub0:~$  which mpiexec
mpiu@ub0:~$  which mpirun

11. setting up a machinefile
Create a file called "machinefile" in mpiu's home directory with node names followed by a
colon and a number of processes to spawn:
ub3:4  # this will spawn 4 processes on ub3
ub2:2  # this will spawn 2 processes on ub2
ub1    # this will spawn 1 process on ub1
ub0    # this will spawn 1 process on ub0

11. Testing
Change directory to your mirror folder and write this MPI helloworld program in a file
mpi_hello.c (courtesy of this blog):

#include <stdio.h>
#include <mpi.h>
int main(int argc, char** argv) {
    int myrank, nprocs;
    MPI_Init(&argc, &argv);
    MPI_Comm_size(MPI_COMM_WORLD, &nprocs);
    MPI_Comm_rank(MPI_COMM_WORLD, &myrank);
    printf("Hello from processor %d of %d\n", myrank, nprocs);
    MPI_Finalize();
    return 0;
}
 
https://help.ubuntu.com/community/MpichCluster
MpichCluster ­ Community Help Wiki
Compile it:
mpiu@ub0:~$ mpicc mpi_hello.c ‐o mpi_hello
and run it (the parameter next to ­n specifies the number of processes to spawn and distribute
among nodes):

mpiu@ub0:~$ mpiexec ‐n 8 ‐f machinefile ./mpi_hello
 
You should now see output similar to this:
Hello from processor 0 of 8
Hello from processor 1 of 8
Hello from processor 2 of 8
Hello from processor 3 of 8
Hello from processor 4 of 8
Hello from processor 5 of 8
Hello from processor 6 of 8
Hello from processor 7 of 8
Congratulations! You have a working MPI platform
References
For more information visit:
The official MPICH webpage
The official MPICH documentation
SSHing without a key
Using Keychain to store passphrases
A blog post explaining single­node installation of OpenMPI
MpichCluster (last edited 2015­05­25 20:51:36 by heemayl @
119.30.38.159[119.30.38.159]:heemayl)
https://help.ubuntu.com/community/MpichCluster
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