Building a Folding Farm - The Branches
(Page 4 of 4 )
With the tarball created and verified, it's time to power up one of the farm clients and see if we can get a net-boot to work. PXE netboot should be seamless, however, I ran into a problem here in that my theoretically bootable NICs didn't appear to be. A little research revealed that the boot capability is turned off by default and must be turned on by the utility that normally comes packaged with the card. A visit to the 3Com site and a few downloads later netted me all the manuals, patches, drivers and utilities available for my cards. I installed a few into my Windows machine and used the utilities to turn on PXE-boot.
Once I reinstalled the NIC into my client machine, I saw a line at the top of the screen saying "press ctrl+alt+b to configure" and therefore I could set the NIC up for booting off the LAN. Once I reset the machine, the system booted and I was up and running.
Routing
Here's where things get really interesting (as in I'd rather go to the dentist). The current version of Fold-Server is set up as a router. This means that every client computer makes its request to Stanford (say, to upload a new WU) and the server routes that request to the Internet server. Any data coming off the Internet server to a client address is routed by the Fold-Server to the clients.
This is fine, as long as the Internet server knows about those client addresses. The problem lies in the fact that in my setup the clients are on a subnet and their respective addresses are issued by the Fold-Server (acting as Domain Name Server, or DNS, on the sub-LAN) and not the Internet server (or whichever server acts as DNS for the regular network). Therefore, we need to create a static route for the client IP addresses through the Internet server so it doesn't drop the incoming data. The documentation for Fold-Server details how to accomplish that for a few different routers (including a general Linux one which should work with most Linux-based firewalls/proxies), and Will is more than happy to help out those who need a little more hands-on assistance.
I am a little (okay, a lot) paranoid, and thus hesitant to open up a channel bypassing my firewall, particularly for the IP range recommended in the documentation, so I chose to set the server up to do Network Address Translation (NAT). In this way, the regular network sees all requests coming from the farm as originating from the server, and the server will route the data to the appropriate client as it is received. Now all the network-savvy readers out there are wincing because double NATing is considered a very bad thing, and my firewall/proxy already provides NAT for the regular network. Funny thing is, 82% of them have no idea why it's bad, they just know it is. Yes, I just made up that statistic.
After probably much debate in various circles, Will has decided that the next iteration of Fold-Server will likely default to NAT. There will always be an option to turn it off. Here are the commands I entered in the console (note: Linux is painfully case-dependent, so if a command line entry shows an upper-case letter, then that letter needs to be upper-case. The same is true with files and directories; /Folder is different from /folder):
wget http://fold-server.sf.net/iptables -O /usr/sbin/iptables (get the prebuilt IP tables from the Fold-Server site and output them in directory/usr/sbin/iptables)
mkdir -p /usr/local/lib/iptables/ (create a directory at /usr/local/lib/iptables )
wget http://fold-server.sf.net/libipt_SNAT.so -O /usr/local/lib/iptables/libipt_SNAT.so (get the prebuilt server NAT file from the Fold-Server site and output it to the directory /usr/local/lib/iptables)
chmod +x /usr/sbin/iptables (change the file mode to executable)
chmod +x /usr/local/lib/iptables/libipt_SNAT.so (change the file mode to executable)
With the files downloaded and in their appropriate locations, I can activate the NAT:
iptables -t nat -A POSTROUTING -o eth1 -j SNAT --destination 0.0.0.0/0 --to-source 192.168.5.15
Note that the source location is the IP address of the server itself; the default is 192.168.1.15, but in my case it's the above address. That gets the NAT running for now, but we want to make sure that it's running next time the server is turned on, so we have to edit the /opt/bootlocal.sh file. In the directions, this is done using the nano text file editor. Basically, you'll want to open up the file with a text editor and place the above command at the end of the file, then save and exit. (Note that I had to preface my wget commands with the http_proxy information mentioned previously to get it to work with my firewall).
Now we should be able to turn on the branch computers and have them start folding.
Monitoring
A quick and easy way to monitor the progress of your farm is through the GUI interface. Simply log into the server from a computer on the main LAN, enter the administrator password you set during the install and select the "monitor clients" button. This will bring you to a page that lists all the clients on the farm (including the server) and their current progress.
In regard to setting up and getting the folding farm to run, this is it, we're done. I have, however, made a few changes to the way the farm operates that may be of interest to serious folders (and if you are building a farm, chances are you're serious about folding). I will cover these extra things in my next article, Customizing Your Farm.
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