Machines

Features

All of our QuantumCubeTM clusters use the latest Linux operating system, currently CentOS 6.2, and come fully configured with

a permanent license to the complete PQS software suite
X-Window system
Network File System (NFS)
Sun Grid Engine (SGE) parallel job queuing system
Parallel Virtual Machine (PVM 3.4.5)
Message Passing Interface (MPI)
- MPICH1 1.2.7
- MPICH2 1.4.1p1
- OpenMPI 1.4.3

Because of our arrangements with several third-party software vendors, we are able to preinstall their programs at no extra charge other than the standard list price of the software. These include:

ADF/BAND, COSMOtherm, Jaguar, Gaussian, MolPro, Q-Chem, PCModel and Spartan. We will also make our best effort to install any other packages you might require.

There is a single set of users and home directories on all systems (with the exception of the root and tech accounts). The user password files and the home directories reside physically on the master and are accessed transparently from the slaves.

We will preinstall user IDs on request. The machine is ready to use "straight out-of-the-box". Simply plug in and switch on (instructions provided) and you should be able to submit jobs within about ten minutes. Hard-copy manuals plus a test suite for the PQS ab initio program is included.

This is a fully operational research computer and is not restricted to running exclusively PQS software. It includes Fortran and C/C++ compilers and Java interpreters, and can be used to compile and run your own programs, and those of other software vendors.

Requirements & Design

QuantumCubeTM turnkey computational chemistry clusters are designed for office use. Power and cooling requirements do not exceed facilities found in a typical office environment. Standard 20 AMP power receptacle and residential-grade air conditioning are easily sufficient for optimal operation. Large, efficient 80 mm fans used in combination with straight air flow design reduce the heat and noise generated by the machines to below office acceptable levels (QuantumCubeTM machines are often less noisy than many desktop PCs). Its small size, low noise and relatively small heat footprint make the QuantumCubeTM an attractive solution for institutions without dedicated computing facilities.

The QuantumCubeTM clusters use two types of chassis: one with two nodes and one with four. Each node is installed on a removable tray which mounts inside of the chassis enclosure. A node consists of a motherboard, two cpus, two hard drives configured with RAID, a power supply and four 80mm cooling fans at the front of

the tray. The network and power cables are routed to the ports on the back of the base, while the power switch/led light cables and usb cables are routed to the front of the base. All nodes are connected to a KVM (keyboard/video/mouse) switch at the top rear of the chassis. Top front of the chassis contains a dvd drive and on four node chassis an additional 4 port usb hub.

Application

Routine HF & DFT geometry optimization and other jobs that are CPU bound are perfect applications for machines with high number of cores, such as the 128-core QS128-2500C-OS16 QuantumCubeTM. For calculations involving correlated wave functions, such as MP2, CCSD(T), which are I/O bound, a machine such as the 32-core QS43-2670C-XS8 is preferable. This configuration offers more computing resources (memory, disk bandwith) per core.

Intel-based QuantumCubeTM systems

2-node Intel QuantumCubeTM

Approximate dimensions of the unit are: height 26" width 8" depth 19"; weight around 55 lbs. The maximum power usage is about 600 W under load. The power and cooling requirements of our system do not exceed what is normally available in a standard office environment.

Standard Hardware Configuration:
(QS32-2000C-XS8) pricing

32 cores: 4 x 2.0 GHz 8-core Intel Xeon Sandy Bridge processors (8.0GT/sec QPI)
64 GB of DDR3 REG ECC memory (2 GB/core)
6 TB serial-ATA2 hard disk storage (enterprise class, 7200 rpm, 64 MB cache)
RAID mirroring and striping
1000 Mb/s gigabit ethernet for internal communication; 10/100/1000 Mb/s external ethernet connection
DVD-RW drive
2-port USB panel
external 1000 GB backup hard drive
video card with 3D-accelerated graphics
23" wide-screen LED monitor, keyboard and mouse
straight-through air flow, low noise design

Advanced Hardware Configuration:
(QS32-2670C-XS8) pricing

32 cores: 4 x 2.67 GHz 8-core Intel Xeon Sandy Bridge processors (8.0GT/sec QPI)
128 GB of DDR3 REG ECC memory (4 GB/core)
8 TB serial-ATA2 hard disk storage (enterprise class, 7200 rpm, 64 MB cache)
RAID mirroring and striping
1000 Mb/s gigabit ethernet for internal communication; 10/100/1000 Mb/s external ethernet connection
DVD-RW drive
2-port USB panel
external 2000 GB backup hard drive
video card with 3D-accelerated graphics
23" wide-screen LED monitor, keyboard and mouse
straight-through air flow, low noise design

4-node Intel QuantumCubeTM

AMD-based QuantumCubeTM systems

2-node AMD QuantumCubeTM

4-node AMD QuantumCubeTM

QuantumCubeTM model overview

Model	# cores	CPU clock (GHz)	Total Memory (GB)	Memory/ Core (GB)	Disk space (TB)	# compute nodes	CPU type
QS32-2000C-XS8	32	2.00	64	2	6	2	Intel
QS32-2670C-XS8	32	2.67	128	4	8	2	Intel
QS64-2000C-XS8	64	2.00	128	2	6	4	Intel
QS64-2670C-XS8	64	2.67	256	4	16	4	Intel
QS48-2600C-AD12	48	2.60	96	2	8	2	AMD
QS64-2500C-AD16	64	2.50	192	3	12	2	AMD
QS96-2600C-AD12	96	2.60	192	2	16	4	AMD
QS128-2500C-AD16	128	2.50	384	3	24	4	AMD

StereoStationTM systems

Thanks to recent advances in monitor and projector technologies, we are now able to offer a new 3D stereo enabled line of workstations - the StereoStationTM. The stereo effect is achieved through the use of active shutter glasses operating at 120Hz refresh rate. The glasses are synchronized with the display, either a projector or a monitor, producing two distinct images, one for each eye. The effect is quite breathtaking and is far superior to the earlier technologies of passive polarized and anaglyph (red/blue) glasses.

A number of scientific applications which use OpenGl libraries have been capable of displaying stereo images for some years, however the cost of the necessary hardware until recently has been prohibitive. Our systems are preconfigured to run the stereo-enabled version of the PQS suite. Stereo-enabled PyMol is also installed. Additionally we offer support in installing 3rd party applications on our machines. Please inquire about specific applications at sales@pqs-chem.com.

StereoStationTM 2 person

Intended to be used as a small personal workstation, capable of executing serial PQS jobs and stereo visualization of the results for up to 2 people.

Hardware Configuration:
(SS4-3400-I74-W2P) pricing

1 x 3.4 GHz 4-core Intel Core i7 Sandy Bridge processor
16 GB of DDR3 memory (4 GB/core)
2000 GB serial-ATA2 hard disk storage (enterprise class, 7200 rpm, 64 MB cache)
1000 Mb/s gigabit ethernet
DVD-RW drive
Nvidia GeForce GTX 260 video card
2 x Nvidia 3D vision stereo glasses with transmitter
23" wide-screen 3D monitor, 1920x1080 resolution
keyboard and mouse
Full Suite of PQS stereo-enabled software, stereo-enabled PyMol
64-bit Windows7 Professional

StereoStationTM 10 person

Intended for a classroom or research environment, capable of executing serial PQS jobs and stereo visualization of the results for up to 10 people.

Hardware Configuration:
(SS4-3400-I74-W10P) pricing

1 x 3.4 GHz 4-core Intel Core i7 Sandy Bridge processor
16 GB of DDR3 memory (4 GB/core)
2000 GB serial-ATA2 hard disk storage (enterprise class, 7200 rpm, 64 MB cache)
1000 Mb/s gigabit ethernet
DVD-RW drive
Nvidia GeForce GTX 260 video card
10 x Nvidia 3D vision stereo glasses with transmitter
3D enabled, 120Hz DLP projector, 1280x800 resolution
keyboard and mouse
Full Suite of PQS stereo-enabled software, stereo-enabled PyMol
64-bit Windows7 Professional

StereoQuantumStationTM2 person

Intended for use as a large scale workstation or add-on to an existing PQS QuantumCube^TM. 24-core, 64 GB of memory Linux node, capable of running a large fully parallel PQS caclulation. Results can be viewed in stereo by up to 2 people.

Hardware Configuration:
(SS24-2400-OI12-L2P) pricing

24 cores: 2 x 2.4 GHz 12-core AMD Opteron Interlagos processors
64 GB of DDR3 REG ECC memory (2.6 GB/core)
3000 GB serial-ATA2 hard disk storage (enterprise class, 7200 rpm, 64 MB cache)
RAID mirroring and striping
1000 Mb/s gigabit ethernet
DVD-RW drive
Nvidia Quadro FX 4600 video card
2 x Nvidia 3D vision stereo glasses with transmitter
23" wide-screen 3D monitor, 1920x1080 resolution
keyboard and mouse
Complete Suite of permanently licensed, stereo-enabled, fully parallel PQS software, stereo-enabled PyMol

Custom Configuration

Custom hardware configuration is available. Additional memory, disk storage and CPU upgrades can usually be supplied on request (at extra cost). For an official quote for a system with your specific requirements, please contact us at sales@pqs-chem.com

Warranty & Support

We offer a full, 1 year warranty on all hardware components. Should you have any problems, you can, at our discretion, either return the affected equipment to us for repair or replacement, replace components yourself following our instructions, or we will make the repair on site. This warranty can be extended to 2 years for an additional 10% of the system price.

Within your warranty period we will offer phone and email support as well as remote access (via ssh) support if such access is allowed at your site.

If an extended warranty is purchased, then any part not used after 2 years may be credited towards the cost of a new QuantumCube TM if purchased in years 3 or 4.

Parallel Quantum Solutions

SUPPORT