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#### Build Multiple Nodes for pbdMPI
This section demonstrate how to install OpenMPI and pbdMPI on multiple nodes
and form a cluster to run SPMD codes across nodes. I use VM to build the first
template machine (vb1) and clone it to second machine (vb2). With a few
modification on vb2 to avoid conflicts with vb1, I can have the same account,
local file, environment on both machines at the same, and can login/ssh from
and to both machines without password. Then, I can utilize two machines
freely to perform SPMD computing from vb1 along. Unlike
<a href="./aws_ec2.html">AWS EC2</a>,
I only do a minimun requirement manually for this task.
1. See <a href="./vm.html">Install VirtualBox</a>
to learn how to install and create a VM.
2. Download the
<a href="https://drive.google.com/file/d/0Bw33sMSttKpQc2trb0ZGZjVuLWs/view?usp=sharing"
target="_blank">multiple_nodes image (2.7GB)</a>
which contains two machines vb1 and vb2.
Import this image into the VirtualBox
as the same way in
<a href="./vm/pbdr_image.html">Install pbdR Image</a>
3. This image contains
- Xubuntu 14.04 without firewall
- vb1 at 192.168.1.1 and vb2 at 192.168.1.2
- ssh, NFS, git, r-base from Ubuntu default
- local built OpenMPI-1.8.4, pbdMPI 2.6
4. The detail steps are in the file
<a href="./download/multiple_nodes.txt"
target="_blank">multiple_nodes.txt</a>.
I test the SPMD code and it works by using two machines with a collective
call. In the same way, one can (linked) clone vb1 to other machines to form
a larger cluster easily.
In the example, I rebuild new OpenMPI and install R packages locally
(/home/pbdr/work-my/local/R_libs) which is shared by all nodes.
One may also use Ubuntu's default packages, "openmpi-bin" and "libopenmpi-dev",
to run with pbdMPI. However, it could have network routing problem if
<code>eth0</code> is for NAT/host and <code>eth1</code> is for internal MPI
communication. It will be easy to bring <code>eth0</code>
down by `<code>sudo ip link set eth0 down</code>' on all machines.
Potential extension including install NIS and rsh, drop ssh, and install all
other pbdR packages.
Also, simplification can be done by moving /etc and /home
to external disk that can reduce management.
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