Note: I have two nodes - one master (beryllium) and one slave (lithium). These names will be used in the examples
Once all the hardware was assembled and linux up and running, I installed a host of programs that I'd be using:
Cluster tools:
sudo apt-get install mpich2 vnstat sinfo ganglia-monitor openmpi-*
For compiling:
sudo apt-get install build-essential gfortran gpp cpp
Generally useful software:
sudo apt-get install gnuplot mpqc-openmpi gromacs-mpich gomacs-mpich octave octave-parallel qtoctave gnome-activity-journal maxima
I downloaded the nwchem source from here. We'll deal with the compilation and installation in the next post.
I followed this post to get up and running (scroll down) with nfs. Here's my take on it:
On the master node:
sudo apt-get install nfs-kernel-server nfs-common portmap
We don't want portmap to use 127.0.0.1, so
sudo dpkg-reconfigure portmap
sudo /etc/init.d/portmap restart
sudo mkdir /work
sudo chmod a+wrx /work
sudo nano /etc/exports
Add the following line to the end of the file:
/work *(rw,sync)
sudo /etc/init.d/nfs-kernel-server restart
sudo exportfs -a
One the slave node:
sudo apt-get install portmap nfs-common
sudo mkdir /work
sudo nano /etc/fstab
Add the following line:
beryllium:/work /work nfs rw 0 0
To get it up and running immediately
sudo mount /work
Next, create a file called mpd.hosts - you can use the /work directory or the home directory. List the hosts/nodes and add, without spaces, the number of processors on each node:
lithium:3
beryllium:3
On beryllium
mpd --ncpus=3 &
mpdtrace -l
which returns something akin to beryllium_12345 (192.168.1.3). 12345 is the port number, which will change each time you start mpd
On lithium
mpd --ncpus=3 -h beryllium -p 12345 &
NOTE: I had problems before specifying --ncpus - gave an error about mpich2 consecutive number/IDs. The down-side is that when you submit a job it fills up the master node, then starts jobs on the slave node(s).
Once all the hardware was assembled and linux up and running, I installed a host of programs that I'd be using:
Cluster tools:
sudo apt-get install mpich2 vnstat sinfo ganglia-monitor openmpi-*
For compiling:
sudo apt-get install build-essential gfortran gpp cpp
Generally useful software:
sudo apt-get install gnuplot mpqc-openmpi gromacs-mpich gomacs-mpich octave octave-parallel qtoctave gnome-activity-journal maxima
I downloaded the nwchem source from here. We'll deal with the compilation and installation in the next post.
I followed this post to get up and running (scroll down) with nfs. Here's my take on it:
On the master node:
sudo apt-get install nfs-kernel-server nfs-common portmap
We don't want portmap to use 127.0.0.1, so
sudo dpkg-reconfigure portmap
sudo /etc/init.d/portmap restart
sudo mkdir /work
sudo chmod a+wrx /work
sudo nano /etc/exports
Add the following line to the end of the file:
/work *(rw,sync)
sudo /etc/init.d/nfs-kernel-server restart
sudo exportfs -a
One the slave node:
sudo apt-get install portmap nfs-common
sudo mkdir /work
sudo nano /etc/fstab
Add the following line:
beryllium:/work /work nfs rw 0 0
To get it up and running immediately
sudo mount /work
Next, create a file called mpd.hosts - you can use the /work directory or the home directory. List the hosts/nodes and add, without spaces, the number of processors on each node:
lithium:3
beryllium:3
On beryllium
mpd --ncpus=3 &
mpdtrace -l
which returns something akin to beryllium_12345 (192.168.1.3). 12345 is the port number, which will change each time you start mpd
On lithium
mpd --ncpus=3 -h beryllium -p 12345 &
NOTE: I had problems before specifying --ncpus - gave an error about mpich2 consecutive number/IDs. The down-side is that when you submit a job it fills up the master node, then starts jobs on the slave node(s).
This is dummy text. It is not meant to be read. Accordingly, it is difficult to figure out when to end it. But then, this is dummy text. It is not meant to be read. Period.
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