My project

I have finally decided to get new dedicated hardware for my pet projects. This is not a conventional server, workstation or a desktop - this is pure computational machine. All I really want is:

• huge amount of RAM
• fast processor
• fast bus
• fast disk

I don't really need anything else because my pet projects are typically about pushing the limits of computation. I don't care about other bell and whistles like sound or video card quality. Just give me memory and CPU... Well, I do care about one more thing - the price in hope that $700-800 should do the trick.

One quickly discovers that motherboards that support above 8G of RAM are quite rare and expensive. Also typical 32 bit OS (Windows or Linux) can't handle memory above 4G. This means that I have to get into 64bit computing.

I don't want to pay for 64bit Windows Advanced Server and I will go with Linux. While any 64bit OS today will have issues something tells me that 64 bit Linux is safer than Windows. Most of my pet projects are in Java with MySQL InnoDB. I do hope that both of these are stable on 64bit Linux.

My new hardware

I have bought this new barebone system from http://www.portatech.com. I took almost two weeks and US$799 to get it. Very typical barebone system vendor, nothing fancy, no complaints. Here it is:

Fast CPU = AMD Athlon 64 X2 6000+ (Dual Core)

8GB of Memory = 4 sticks of 2GB Dual Channel Capable PC6400 DDR2-800 Memory Modules

Fast Front-Side Bus Motherboard = Mfr Part Number: M2A-VM(GREEN) * CPU: Socket AM2 support AMD Athlon64 FX/ Athlon64 X2/ Athlon64/ Sempron processors; AMD Cool 'n' Quiet Technology; AMD64 architecture enables simultaneous 32-bit and 64-bit computing; AMD Live! Ready; FSB 2000/1600 MT/s * Chipset: AMD 690G & ATI SB600 * Memory: 4x 240pin DDR2-800/667/533 DIMMs, Dual Channel, un-buffered ECC and Non-ECC, Max capacity 8GB * Slots: 1x PCI-Express x16 slot; 1x PCI-Express x1 slots; 2x PCI slots * IDE/SATA: 1x ATA-133 channels, 4x SATA2 ports support RAID 0, 1 and 10 * Audio: ALC883 6-channel High Definition Audio CODEC * Video: Integrated ATI Radeon X1250-based Graphics Controller, shared upto 256MB memory * LAN: Intergated PCI-Express Gigabit Ethernet Controller * Ports: 10x USB 2.0 ports (4 rear, 6 by headers); 2x PS/2 ports; 1x Parallel port; 1x VGA port; 1x DVI-D port; 1x RJ45 LAN port; Audio I/O jacks * Power Connector: 1x 24pin main power, 1x 4pin CPU power * Form Factor: Micro ATX, 9.6 x 9 inch / 24.5 x 22.9 cm * Package: Retail * RoHS Compliant

SATA II (300 MB/s) Disk = 160GB 7200RPM SATA II U300 - Hard Drive

Ubuntu 6.06 & 7.10 desktop or server

Ubuntu installer started, but failed to begin installation because it could not find a CD disk. It was kind of funny because it was actually running from the CD disk, but just could not re-mount it to read the rest of the install packages. The CD/DVD drive in my system is on SATA interface, which I guess is the root of the problem.

Fedora 8

Fedora 8 failed to even to boot the install image. Right after BIOS message goes away DVD boot was initiated couple of messages got printed on the console and the thing prints "Failed to start" and dies.

CentOS 4.6 x86_64

CentOS 4.6 run and installed everything! I was so happy, but... The installation run fine from beginning to the end, but two major problems came up right after that.

First of all, the installation onto SATA disk did not work. It did recognize the disk, partitioned and installed onto it, but would fail to boot. The exact text of the error I do not have, but it looked similar to this:

	ata4.00: exception Emask 0x0 SAct 0x0 SErr 0x0 action 0x2 frozen
	ata4.00: cmd ea/00:00:00:00:00/00:00:00:00:00/a0 tag 0 cdb 0x0 data 0 out

The same message would repeat several times for about 5 minutes and system would eventually slowly boot. Maybe this is "normal", but not for me...

Second problem was that the network card was not detected. At this point I gave up. I could have looked for the driver and so on, but I really did not want to kernel compilation.

openSUSE 10.3

openSuse 10.3 installer started and run fine. By this time I was already frustrated and ready to give up. And then I noticed how much different this installer was. It actually had dedicated hardware detection screen that I used to review my hardware before the installation. Here I saw that my SATA and IDE drives were properly discovered. The network card, audio, video - it all was properly detected. Great job!

Another thing I likes is the ability to fully configure installed packaged, view package dependencies and so on. Other installers I tried give you this opportunity as well, but not with the level of detailed I found in SUSE.

After all said and done openSUSE installed and worked great. Installation takes long time, much longer than CentOS, but I did not care. Finally, I was able to install and fully configure the hardware without any fiddling with it. Linux works, man!

Running MySQL 5.0.45 on 64 bit Linux

Installed and run great. I was able to use 7GB of RAM for MySQL without a problem using --innodb-buffer-pool variable. The data files were placed both on SATA and IDE disk and worked fine on both. No complaints here.

64bit Java 1.5.0_13 SDK from Sun

Installed and run great. No complaints here.

Running Eclipse on 64bit Linux

Eclipse did not run on 64bit Linux exiting with the Exit code=13. Here it the error message:

	JVM terminated. Exit code=13
	/oy/au_node/jdk1.5.0_13/bin/java
	-Dosgi.requiredJavaVersion=1.5
	-Xms40m
	-Xmx256m
	-jar /oy/au_node/eclipse-java-europa-fall2-linux-gtk/eclipse
		/plugins/org.eclipse.equinox.launcher_1.0.1.R33x_v20070828.jar
	-os linux
	-ws gtk
	-arch x86
	-showsplash
	-launcher /oy/au_node/eclipse-java-europa-fall2-linux-gtk/eclipse/eclipse
	-name Eclipse
	--launcher.library /oy/au_node/eclipse-java-europa-fall2-linux-gtk/eclipse
		/plugins/org.eclipse.equinox.launcher.gtk.linux.x86_1.0.2.R331_v20071019/eclipse_1021.so
	-startup /oy/au_node/eclipse-java-europa-fall2-linux-gtk/eclipse
		/plugins/org.eclipse.equinox.launcher_1.0.1.R33x_v20070828.jar
	-exitdata 90002
	-vm /oy/au_node/jdk1.5.0_13/bin/java
	-vmargs
	-Dosgi.requiredJavaVersion=1.5
	-Xms40m
	-Xmx256m
	-jar /oy/au_node/eclipse-java-europa-fall2-linux-gtk/eclipse
		/plugins/org.eclipse.equinox.launcher_1.0.1.R33x_v20070828.jar  

I have looked around and many people report that Eclipse's SWT (Standard Window  Toolkit) uses native code that is 32 bit. I am sure there are "official" workarounds, but I will simply not run Eclipse for now.

Measuring performance with SciMark

SciMark 2.0 is a Java benchmark for scientific and numerical computing. It uses several numeric methods to measure the composite MFlops score. I run SciMark for both the server and the client JVM's from the command line like this:

	java -server -cp scimark2lib.jar jnt.scimark2.commandline
	java -client -cp scimark2lib.jar jnt.scimark2.commandline

New system score (client JVM performs better) is quite respectable:

	SciMark 2.0a
 
	Composite Score: 709.5588785447046
	FFT (1024): 560.3086048901283
	SOR (100x100):   969.0495393131292
	Monte Carlo : 82.16573593238223
	Sparse matmult (N=1000, nz=5000): 529.7979030420823
	LU (100x100): 1406.4726095458013
	
	java.vendor: Sun Microsystems Inc.
	java.version: 1.5.0_12
	os.arch: amd64
	os.name: Linux
	os.version: 2.6.22.5-31-default

For comparison, my M1210 Dell XPS laptop score (server JVM performs better) is here:

	SciMark 2.0a

	Composite Score: 477.50727979704214
	FFT (1024): 330.2235173390862
	SOR (100x100):   708.9606526769663
	Monte Carlo : 30.68535111475739
	Sparse matmult (N=1000, nz=5000): 367.86977640512555
	LU (100x100): 949.7971014492753
	
	java.vendor: Sun Microsystems Inc.
	java.version: 1.4.2
	os.arch: x86
	os.name: Windows XP
	os.version: 5.1

The Final Word

One thing I would recommend if you are going into 64bit is to choose a proven motherboard. In the old days the only thing the motherboard had was a CPU, memory and extension slots. So nothing could really go wrong. These days, when motherboards come with all the things soldered on including RAID controller, you got to pay attention to it. So many things can go wrong... You will be flashing that BIOS till the end of the days...

It looks like Linux on 64bit is accessible, stable and mature OS. I finally have huge amounts of RAM and speed I need for my projects. And all of this can be had for $799 and accessed remotely via VNC and SSH from anywhere. Beats the hell out of my programmable calculator way back from 1987...  Very very cool!