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小 （新页面: {{From|https://help.ubuntu.com/community/MpichCluster}} {{Languages|UbuntuHelp:MpichCluster}} == Setting Up an MPICH2 Cluster in Ubuntu == Creator: '''[[UbuntuHelp:OmidAlemi| Omid Alemi...）
 
小
第2行： 第2行：
 
{{Languages|UbuntuHelp:MpichCluster}}
 
{{Languages|UbuntuHelp:MpichCluster}}
 
== Setting Up an MPICH2 Cluster in Ubuntu  ==
 
== Setting Up an MPICH2 Cluster in Ubuntu  ==
−
 
 
Creator: '''[[UbuntuHelp:OmidAlemi| Omid Alemi]]'''
 
Creator: '''[[UbuntuHelp:OmidAlemi| Omid Alemi]]'''
−
 
 
omid.alemi@gmail.com
 
omid.alemi@gmail.com
−
 
−
 
 
This guide describes how to building a simple MPICH cluster in ubuntu.  
 
This guide describes how to building a simple MPICH cluster in ubuntu.  
−
 
 
Before , you need an basic knowledge about mpich & clustering.
 
Before , you need an basic knowledge about mpich & clustering.
−
 
 
Here we have 4 nodes running ubuntu 7.04 with these host names: ub0,ub1,ub2,ub3;
 
Here we have 4 nodes running ubuntu 7.04 with these host names: ub0,ub1,ub2,ub3;
−
 
−
 
−
 
 
=== 1. Defining hostnames in etc/hosts/ ===
 
=== 1. Defining hostnames in etc/hosts/ ===
−
 
 
Edit /etc/hosts like these:
 
Edit /etc/hosts like these:
−
 
−
 
 
<pre><nowiki>
 
<pre><nowiki>
 
127.0.0.1    localhost
 
127.0.0.1    localhost
第28行： 第16行：
 
192.168.133.103 ub3
 
192.168.133.103 ub3
 
</nowiki></pre>
 
</nowiki></pre>
−
 
−
 
 
Note that the file shouldn't be like this:
 
Note that the file shouldn't be like this:
−
 
−
 
 
<pre><nowiki>
 
<pre><nowiki>
 
127.0.0.1    localhost
 
127.0.0.1    localhost
第41行： 第25行：
 
192.168.133.103 ub3
 
192.168.133.103 ub3
 
</nowiki></pre>
 
</nowiki></pre>
−
 
−
 
 
=== 2. Installing NFS ===
 
=== 2. Installing NFS ===
−
 
 
To Install NFS just run this in terminal:
 
To Install NFS just run this in terminal:
−
 
−
 
 
<pre><nowiki>
 
<pre><nowiki>
 
omid@ub0:~$ sudo apt-get install nfs-kernel-server
 
omid@ub0:~$ sudo apt-get install nfs-kernel-server
 
</nowiki></pre>
 
</nowiki></pre>
−
 
 
=== 3. Sharing Master Folder ===
 
=== 3. Sharing Master Folder ===
 
Make a folder in all nodes, we'll store our data and programs in this folder.
 
Make a folder in all nodes, we'll store our data and programs in this folder.
−
 
−
 
 
<pre><nowiki>
 
<pre><nowiki>
 
omid@ub0:~$ sudo mkdir /mirror
 
omid@ub0:~$ sudo mkdir /mirror
 
</nowiki></pre>
 
</nowiki></pre>
−
 
−
 
 
And then we share it over nodes on the master node.
 
And then we share it over nodes on the master node.
−
 
−
 
 
<pre><nowiki>
 
<pre><nowiki>
 
omid@ub0:~$ sudo echo  /mirror *(rw,sync) >> /etc/exports
 
omid@ub0:~$ sudo echo  /mirror *(rw,sync) >> /etc/exports
 
</nowiki></pre>
 
</nowiki></pre>
−
 
−
 
−
 
−
 
 
Note than we store out data and programs only in master node and other nodes will access them with NFS.
 
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 ===
 
=== 4. Mounting /master in nodes ===
−
 
 
<pre><nowiki>
 
<pre><nowiki>
 
omid@ub1:~$sudo mount ub0:/mirror /mirror
 
omid@ub1:~$sudo mount ub0:/mirror /mirror
第79行： 第46行：
 
omid@ub3:~$sudo mount ub0:/mirror /mirror
 
omid@ub3:~$sudo mount ub0:/mirror /mirror
 
</nowiki></pre>
 
</nowiki></pre>
−
 
−
 
 
it's better to change fstab in order to mount it on every boot.
 
it's better to change fstab in order to mount it on every boot.
−
 
 
=== 5. Defining a user for running MPI programs ===
 
=== 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.
 
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:
 
Here we name it "mpiu"! Also we change the owner of /mirror to mpiu:
−
 
 
<pre><nowiki>
 
<pre><nowiki>
 
omid@ub0:~$ sudo chown mpiu /mirror
 
omid@ub0:~$ sudo chown mpiu /mirror
 
</nowiki></pre>
 
</nowiki></pre>
−
 
−
 
−
 
 
=== 6. Installing SSH Server ===
 
=== 6. Installing SSH Server ===
 
Run this command in all nodes in order to install OpenSSH Server
 
Run this command in all nodes in order to install OpenSSH Server
−
 
−
 
 
<pre><nowiki>
 
<pre><nowiki>
 
omid@ub0:~$ sudo apt­-get install openssh­server
 
omid@ub0:~$ sudo apt­-get install openssh­server
 
</nowiki></pre>
 
</nowiki></pre>
−
 
−
 
 
=== 7. Setting up SSH with no pass phrase for communication between nodes ===
 
=== 7. Setting up SSH with no pass phrase for communication between nodes ===
 
First we login with our new user:
 
First we login with our new user:
−
 
−
 
 
<pre><nowiki>
 
<pre><nowiki>
 
omid@ub0:~$ su - mpiu
 
omid@ub0:~$ su - mpiu
 
</nowiki></pre>
 
</nowiki></pre>
−
 
−
 
 
Then we generate DSA key for mpiu:
 
Then we generate DSA key for mpiu:
−
 
−
 
−
 
 
<pre><nowiki>
 
<pre><nowiki>
 
mpiu@ub0:~$ ssh­-keygen ­-t dsa
 
mpiu@ub0:~$ ssh­-keygen ­-t dsa
 
</nowiki></pre>
 
</nowiki></pre>
−
 
−
 
 
Leave passphrase empty.
 
Leave passphrase empty.
−
 
 
Next we add this key to authorized keys:
 
Next we add this key to authorized keys:
−
 
−
 
 
<pre><nowiki>
 
<pre><nowiki>
 
mpiu@ub0:~$ cd .ssh
 
mpiu@ub0:~$ cd .ssh
 
mpiu@ub0:~/.ssh$ cat id_pub.dsa >> authorized_keys
 
mpiu@ub0:~/.ssh$ cat id_pub.dsa >> authorized_keys
 
</nowiki></pre>
 
</nowiki></pre>
−
 
−
 
 
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.
 
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:
 
To test SSH run:
−
 
−
 
 
<pre><nowiki>
 
<pre><nowiki>
 
mpiu@ub0:~$ ssh ub1 hostname
 
mpiu@ub0:~$ ssh ub1 hostname
 
</nowiki></pre>
 
</nowiki></pre>
−
 
−
 
 
It should return remote hostname without asking for passphrase.
 
It should return remote hostname without asking for passphrase.
−
 
 
=== 8. Installing GCC ===
 
=== 8. Installing GCC ===
 
Install build-essential package:
 
Install build-essential package:
−
 
−
 
 
<pre><nowiki>
 
<pre><nowiki>
 
mpiu@ub0:~$ sudo apt-get install build-essential
 
mpiu@ub0:~$ sudo apt-get install build-essential
 
</nowiki></pre>
 
</nowiki></pre>
−
 
−
 
 
=== 9.Installing Other Compilers ===
 
=== 9.Installing Other Compilers ===
 
Other prefered compilers should be installed before installing MPICH.
 
Other prefered compilers should be installed before installing MPICH.
−
 
 
In this step we install other compilers such as Inter Fortran, SGI compiler , ... .
 
In this step we install other compilers such as Inter Fortran, SGI compiler , ... .
−
 
 
=== 10. Installing  MPICH2 ===
 
=== 10. Installing  MPICH2 ===
 
Download MPICH2 source code from http://www-unix.mcs.anl.gov/mpi/mpich .
 
Download MPICH2 source code from http://www-unix.mcs.anl.gov/mpi/mpich .
−
 
 
Extract .tar.bz2 file in /mirror. Also make a folder for MPICH installation.
 
Extract .tar.bz2 file in /mirror. Also make a folder for MPICH installation.
−
 
 
<pre><nowiki>
 
<pre><nowiki>
 
mpiu@ub3:/mirror$ mkidr mpich2
 
mpiu@ub3:/mirror$ mkidr mpich2
第171行： 第98行：
 
mpiu@ub3:/mirror/mpich2­-1.0.5p3$ sudo make install
 
mpiu@ub3:/mirror/mpich2­-1.0.5p3$ sudo make install
 
</nowiki></pre>
 
</nowiki></pre>
−
 
−
 
 
For more information about compilation see README file in source package.
 
For more information about compilation see README file in source package.
−
 
 
After successfully compiling and installing mpich, add these lines to  "/mirror/mpiu/.bashrc/"
 
After successfully compiling and installing mpich, add these lines to  "/mirror/mpiu/.bashrc/"
−
 
 
<pre><nowiki>
 
<pre><nowiki>
 
export PATH=/mirror/mpich2/bin:$PATH
 
export PATH=/mirror/mpich2/bin:$PATH
第183行： 第106行：
 
export LD_LIBRARY_PATH
 
export LD_LIBRARY_PATH
 
</nowiki></pre>
 
</nowiki></pre>
−
 
−
 
 
Next we run this command in order to define MPICH installation path to SSH.
 
Next we run this command in order to define MPICH installation path to SSH.
−
 
−
 
 
<pre><nowiki>
 
<pre><nowiki>
 
mpiu@ub0:~$ sudo echo /mirror/mpich2/bin >> /etc/environment
 
mpiu@ub0:~$ sudo echo /mirror/mpich2/bin >> /etc/environment
 
</nowiki></pre>
 
</nowiki></pre>
−
 
 
For testing our installation run:
 
For testing our installation run:
−
 
 
<pre><nowiki>
 
<pre><nowiki>
 
mpiu@ub0:~$  which mpd
 
mpiu@ub0:~$  which mpd
第199行： 第116行：
 
mpiu@ub0:~$  which mpirun
 
mpiu@ub0:~$  which mpirun
 
</nowiki></pre>
 
</nowiki></pre>
−
 
−
 
−
 
 
=== 11. setting up MPD ===
 
=== 11. setting up MPD ===
 
Create mpd.hosts in mpiu's home directory with nodes names:
 
Create mpd.hosts in mpiu's home directory with nodes names:
−
 
−
 
 
<pre><nowiki>
 
<pre><nowiki>
 
ub3
 
ub3
第212行： 第124行：
 
ub0
 
ub0
 
</nowiki></pre>
 
</nowiki></pre>
−
 
 
and run :
 
and run :
−
 
 
<pre><nowiki>
 
<pre><nowiki>
 
mpiu@ub0:~$ echo secretword=something  >> ~/.mpd.conf
 
mpiu@ub0:~$ echo secretword=something  >> ~/.mpd.conf
 
mpiu@ub0:~$ chmod 600 .mpd.conf
 
mpiu@ub0:~$ chmod 600 .mpd.conf
 
</nowiki></pre>
 
</nowiki></pre>
−
 
−
 
 
To test MPD run above commands. The output should be the current hostname.
 
To test MPD run above commands. The output should be the current hostname.
−
 
−
 
 
<pre><nowiki>
 
<pre><nowiki>
 
mpiu@ub0:~$ mpd &
 
mpiu@ub0:~$ mpd &
第229行： 第135行：
 
mpiu@ub0:~$ mpdallexit
 
mpiu@ub0:~$ mpdallexit
 
</nowiki></pre>
 
</nowiki></pre>
−
 
−
 
 
After all run mpd daemon:
 
After all run mpd daemon:
−
 
 
<pre><nowiki>
 
<pre><nowiki>
 
mpiu@ub0:~$ mpdboot ­-np 4
 
mpiu@ub0:~$ mpdboot ­-np 4
 
mpiu@ub0:~$ mpdtrace
 
mpiu@ub0:~$ mpdtrace
 
</nowiki></pre>
 
</nowiki></pre>
−
 
−
 
 
The output should be name of all nodes.
 
The output should be name of all nodes.
−
 
 
There are some examples in "mpich2-1.0.5/examples", we'll run one :
 
There are some examples in "mpich2-1.0.5/examples", we'll run one :
−
 
−
 
 
<pre><nowiki>
 
<pre><nowiki>
 
mpiu@ub0:~$ mpiexec -n 4 cpi
 
mpiu@ub0:~$ mpiexec -n 4 cpi
 
</nowiki></pre>
 
</nowiki></pre>
−
 
−
 
−
 
 
That's it!
 
That's it!
 
------
 
------
 
For more information visit:
 
For more information visit:
−
 
−
 
 
http://www-unix.mcs.anl.gov/mpi/mpich/
 
http://www-unix.mcs.anl.gov/mpi/mpich/
  
 
[[category:UbuntuHelp]]
 
[[category:UbuntuHelp]]

2007年11月30日 (五) 20:22的版本

Geographylogo.png 文章出处: 

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

Geographylogo.png 点击翻译: 

English

请不要直接编辑翻译本页，本页将定期与来源同步。

Setting Up an MPICH2 Cluster in Ubuntu

Creator: Omid Alemi omid.alemi@gmail.com This guide describes how to building a simple MPICH cluster in ubuntu. Before , you need an basic knowledge about mpich & 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 http://www-unix.mcs.anl.gov/mpi/mpich . 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!

For more information visit: http://www-unix.mcs.anl.gov/mpi/mpich/

取自“https://wiki.ubuntu.org.cn/index.php?title=UbuntuHelp:MpichCluster&oldid=37570”