Computer hardware: Difference between revisions

From CCP4 wiki
Jump to navigation Jump to search
No edit summary
(throw away the old stuff)
 
(6 intermediate revisions by 2 users not shown)
Line 1: Line 1:
== April 2008: a machine that may serve as a Linux workstation ==
== 2020 ==


A Dell Vostro 400 MT costs 549,- € (plus tax and shipping, but on the other hand Dell gives a discount to universities) in Germany. It comes by default with a (high-end!) NVidia GeForce 8800GT graphics card, 3 GB of memory, a 500 GB disk, and a quadcore Q6600 CPU running @ 2.4GHz. If most of your data reside on a fileserver, then you might want to put an additional GB ethernet card (5-10€) into one of the two empty PCI slots.
The recent [https://en.wikipedia.org/wiki/Ryzen#CPUs:_Matisse_(Ryzen)_and_Castle_Peak_(Ryzen_Threadripper) Ryzen Threadripper 3xxx series processors] with up to 64 cores (128 threads) have a significantly better cost/performance ratio than other processor families. For example, a TR 3970X workstation can be bought for less than 5000€, and offers 64 threads.  


This machine is very cheap, fast, small, and quiet - we have four of those. But as we ordered them in March they "only" have the 8600 GTS graphics (in practice even a GeForce 5200 is fast enough for [[coot]], [[O]] and [[pymol]]).
Make sure to buy DDR4-3200 JEDEC memory, but observe the following [https://www.guru3d.com/articles-pages/amd-ryzen-threadripper-3990x-review,2.html table],  
Memory  Rank Official JEDEC frequency support
4x8 Single DDR4-3200
8x8 Single DDR4-2933
4x16 Dual DDR4-3200
8x16 Dual DDR4-2667
4x32 Dual DDR4-3200
8x32 Dual DDR4-2667
which shows that the maximum speed with which the memory controller can drive the RAM may be less than that of DDR4-3200.  


This GeForce NVidia card is quite suitable for crystallographic visualization, but - being GeForce and not Quadro - it does not support [[stereo]]. But a 22" TFT monitor (about 250,- €) does not support stereo either.
The data transfer may become the bottleneck in keeping the cores busy; but 10Gb networking ports may be used, using the PCIe 4.0 bus.


It is a good idea to switch (in the BIOS) the SATA mode from IDE (the default) to RAID ''before'' you install Linux, because this activates the very good Linux AHCI driver and makes the use of the Linux kernel option "irqpoll" unnecessary. (This hint applies to all modern chipsets featuring SATA disks; "IDE", "legacy IDE" and "enhanced IDE" are often not the best setups for Linux - depending on the distribution's kernel - , whereas "AHCI" and "RAID" are good. This option can be found in the BIOS, often under "Integral peripherals" or the like.) It is also a good idea to check in the BIOS if the power-saving option of the CPUs is switched on - it is probably called "Speedstep" or "Intel Enhanced SpeedStep" or the like and should be enabled.
The [https://en.wikipedia.org/wiki/Epyc#Second_generation_Epyc_(Rome) 2nd generation AMD Epyc "Rome" processors] are the server variant of the Threadripper 3xxx workstation processors. They are more expensive and not quite as fast, but offer 8-channel memory and a higher maximum amount of memory than Threadripper.
 
 
----
 
Update: we replaced the graphics card in one of the machines with a stereo-capable Quadro card (I believe a FX 1400) which cost about € 400,-, and have now a stereo workstation for about € 1000,- .
 
== September/October 2008 ==
 
The Vostro has changed its model number (410), comes with a GB-ethernet card, and should be ordered with a 8800 GT card. The system that I would order would cost € 699,-, so unfortunately Dell seems to have raised the price significantly.
 
== February 2009 ==
 
We purchased 3 identical core i7 940 machines; this represents the second-fastest CPU currently available (it's a quad-core with Hyperthreading - look at the benchmarks at [http://www.spec.org/cpu2006/results]!). Their configuration (with MSI X58 Pro motherboard, 6 GB memory, large disk, and a cheap NVidia graphics card) was established at http://www.hardwareversand.de (I'm not affiliated with this company but I bought my son's PC there, and he's happy with it); the price of such a machine is slightly below 1000,-€, including sales tax and 20,-€ cost for putting the pieces together!
The BIOS has lots of things that one can adjust; at least the IDE mode should be set to AHCI. After installing the 64bit version of CentOS 5.2 we discovered that the network adapter is not well supported by the slightly old installation kernel. So we grabbed one of the kernel (plus kernel-devel and kernel-headers) RPM packages from the site http://people/redhat.com/dzickus (at least version 128) and installed those with the help of a USB stick. This worked beautifully and we now have three machines that are really fast, for 1000€ a piece.

Latest revision as of 20:06, 20 February 2020

2020[edit | edit source]

The recent Ryzen Threadripper 3xxx series processors with up to 64 cores (128 threads) have a significantly better cost/performance ratio than other processor families. For example, a TR 3970X workstation can be bought for less than 5000€, and offers 64 threads.

Make sure to buy DDR4-3200 JEDEC memory, but observe the following table, 

Memory  Rank	Official JEDEC frequency support
4x8	Single	DDR4-3200
8x8	Single	DDR4-2933
4x16	Dual	DDR4-3200
8x16	Dual	DDR4-2667
4x32	Dual	DDR4-3200
8x32	Dual	DDR4-2667

which shows that the maximum speed with which the memory controller can drive the RAM may be less than that of DDR4-3200.

The data transfer may become the bottleneck in keeping the cores busy; but 10Gb networking ports may be used, using the PCIe 4.0 bus.

The 2nd generation AMD Epyc "Rome" processors are the server variant of the Threadripper 3xxx workstation processors. They are more expensive and not quite as fast, but offer 8-channel memory and a higher maximum amount of memory than Threadripper.

Retrieved from "https://wiki.uni-konstanz.de/ccp4/index.php?title=Computer_hardware&oldid=2682"