By Marcel van der Veer
03-04-2018

Published in category Science

More on Beowulf, Computational Science, Linux

As described in an earlier post , at home I operate a modest Beowulf type cluster for embarrassingly parallel simulation runs in batch mode. With the experience from that build, I took on building a higher-performance cluster using Debian.

Even when using older machines in a cluster, combined performance can still be acceptable depending on application. A small cluster of older machines is like a freight truck - not the fastest option at low load, but maintaining speed at high load.

Mesoscopic simulation of a phospholipid micelle in water.

An alternative to segmenting a molecular dynamics simulation when the number of nodes in the cluster is small, is to run the actual simulation on one node and computational intensive post-processing on one or two others. In this way the cluster is still dedicated to solving a single problem. This scheme also avoids inter-segment communication which can become a bottleneck.

Drones start in text mode

The best machine in a Beowulf cluster should be the master node with a nice video card and display. Drones however can be started in text mode to save resources. On the net, different ways are described to start Linux in text mode. Contrary to some of those posts, in modern installations meddling with GRUB configuration is no longer necessary. Suffice giving the command

# systemctl set-default multiuser.target
# reboot

If at any time one wishes to revert to the graphical environment, issue

# systemctl set-default graphical.target

Connecting drones with the internet

My cluster is small enough to not need dhcp. The master node is connected to the world through a wireless connection to a router that connects to the internet. Not all drones have a wireless connection, but it is not hard to share the wireless connection on the master to the drones. I use ufw as front-end to ip-tables and then the procedure to make internet cluster-wide available is documented here and there in the forums - with a few small catches … first we set up ufw

# apt install ufw

and then activate the firewall … but take care when doing this in a ssh session with a drone, because a fresh firewall without rules will by default deny anything and lock you out of the drone! So we issue

# ufw enable && ufw allow ssh

and we remain connected. Then we set DEFAULT_FORWARD_POLICY with

# vi /etc/default/ufw
...
DEFAULT_FORWARD_POLICY="ACCEPT"

and then set up NAT by entering before the *filter rules. Suppose the physical wireless interface is wan on the master node.

# vi /etc/ufw/before.rules
...
# Add rules for NAT table -- MvdV
*nat
:POSTROUTING ACCEPT [0:0]
-A POSTROUTING -s 10.2.2.0/24 -o wan -j\
 MASQUERADE
COMMIT

Now every machine on with IP address 10.2.2.N can enjoy an internet connection after we restart ufw

# service ufw restart

The master node interface is 10.2.2.1. Now on the client side, say on drone 10.2.2.2 with interface eth we enter in /etc/network/interfaces a section

# vi /etc/network/interfaces
...
auto eth
iface eth inet static
address 10.2.2.2
netmask 255.255.255.0
network 10.2.2.0
gateway 10.2.2.1
dns-nameserver 8.8.8.8

In the forums, the last two lines are often forgotten (or taken for granted perhaps); without gateway you cannot connect outside the LAN since your packets are not transferred by the master node, and without a nameserver you will have an internet connection that works with IP adresses but not with URLs which is not very useful. Actually, you need to have already installed a DNS service on the drone, for instance

# apt install resolvconf

Hence connecting drones to the internet can be a chicken-egg problem - you need internet to install stuff to connect to the internet. I just used a mobile phone as AP with USB tethering during the set up.

Message Passing Interface

Various sources will tell you that there is no software package that defines a Beowulf cluster. But a Beowulf is dedicated to a single task so there must be communication between nodes, which is generally handled by a message passing interface for which there are excellent solutions available. Even so, I did not install an independent message passage interface. The cluster is dedicated to one application and I designed that application to handle inter-process communication itself. The program detects nodes that are online on the LAN, rates their performance, schedules subtasks based on that rating and synchronises them. This also facilitates sustainability: for less demanding jobs, nodes can be left in energy-saving mode which contributes to solving a problem in an energy efficient way.



All blog posts


Marcel van der Veer Algol68C on MVS revisited

04-08-2018

As the author of Algol 68 Genie I am interested in having access to other Algol 68 compilers for reference purposes. Several years ago I wrote a post on installing Algol68C on MVS. In this post I would like to give an update. [Read more]

Published in category Algol 68


Marcel van der Veer Let the music play on - vintage HiFi

05-07-2018

Lately I needed to call on some of my now rusty electronics skills since I came into some older HiFi equipment in need of attention. I consulted the world wide web in search of service manuals and found many more people with an interest in keeping older HiFi in working condition. Now I had the opportunity to combine my passion for electronics, HiFi equipment and music … and do not forget durability, since we are actually extending the life of otherwise obsolete products. [Read more]

Published in category HiFi


Marcel van der Veer Building a small Beowulf cluster II

03-04-2018

As described in an earlier post, at home I operate a modest Beowulf type cluster for embarrassingly parallel simulation runs in batch mode. With the experience from that build, I took on building a higher-performance cluster using Debian. [Read more]

Published in category Science


Marcel van der Veer Be multilingual!

28-01-2018

Every year my daughter's high school invites parents to partake in an evening of information sessions, to help students orient themselves on their future. The idea is to have parents from all walks of professional life, each parent discussing half an hour or so with small groups of students who subscribed to your sessions. You are expected to tell about your study and career, and the students are supposed to pose questions. As you will expect, some come well prepared, others must be stimulated a bit. I greatly enjoy those conversations with the next generation who have their lives ahead of them. [Read more]

Published in category Education


Marcel van der Veer Classical thermodynamics in a nutshell

18-11-2017

Recently I met during an event at my Alma Mater, the University of Nijmegen, my high school physics teacher. We discussed the chemistry curriculum and remarked that quite some chemistry students capture with difficulty the fundamental principles from thermodynamics. Needless to say that thermodynamics is one of those subjects that serve a chemist for a lifetime. In my humble opinion, one reason for this lack of retention may be the abstraction level in freshmen courses and that this might be improved by spending one or two introductory hours on the basic ideas of thermodynamics in a historic context. [Read more]

Published in category Science


Marcel van der Veer A brief history of Algol 68 Genie

27-11-2016

Being the author of Algol 68 Genie, people frequently ask me why a physical chemist wrote an Algol 68 compiler. This is an understandable question since people associate Algol 68 with the learned group of mathematicians and computer scientists that conceived the language some fifty years ago and people recall the reputation it had of being a hard to implement laguage. In this post I would like to give an account of how Algol 68 Genie came to be. [Read more]

Published in category Algol 68


Marcel van der Veer Building a small Beowulf cluster

01-10-2016

At home I operate a modest Beowulf type cluster for embarrassingly parallel simulation runs in batch mode. A master node controls several drones. Nodes in this cluster need no more than a server installation, but if a drone happens to have keyboard, mouse and monitor a small GUI is nice to have. This GUI should be lightweight, otherwise a desktop installation makes more sense. This page demonstrates how to set up a drone with GUI on Ubuntu Server including browser, document reader, image viewer and sound. [Read more]

Published in category Science


Marcel van der Veer Running Algol68C on MVS

31-10-2012

Recently, Algol68C Release 1.3039 was made public for download. This release is derived from the compiler that was in service to the mid 1990's on IBM mainframes. The new release is meant to run on either MVT or MVS. This report documents the installation of the new release on emulated MVS/370. [Read more]

Published in category Algol 68


Marcel van der Veer Revised Report on the Algorithmic Language Algol 68

01-06-2009

This is a translation of the Algol 68 Revised Report into HTML, for distribution with Algol 68 Genie, an Open Source Algol 68 interpreter. [Read more]

Published in category Algol 68