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MDGRAPE-3 PCI-X |
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MDGRAPE-3 was developed by Genomic Science Center in RIKEN Yokohama as a successor of MDGRAPE-2. PCI-X board mounting two MDGRAPE-3 chips has 330 Gflops speed.
You can read the technical information at the Riken, High-performance Molecular Simulation team's homepage.
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How to work |
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The MDGRAPE-3 system consists of a host computer and a MDGRAPE-3 board. The MDGRAPE-3 board calculates non-bonding forces (i.e. electrostatic and intermolecular forces), which dominates computational load. All other calculation is performed by a host computer.
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Applications Supported |
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- AMBER based codes
- CHARMM based codes (planned)
- Original simulations : using c and fortran library that Riken delivers.
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Free Boundary Benchmark |
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- Scytalone Dehydratase (2,715atoms) and waters molecules
- Free boundary, Non cutoff, NVE, Total time for 1,000 steps
- Original : Pentium4 3.2GHz
- MDGRAPE-3: PentiumD 3.0GHz (only single core is used) with one MDGRAPE-3 PCI-X(250MHz)
| # of atoms |
3,339 |
4,953 |
13,101 |
| Original(sec) |
346.73 |
884.52 |
9231.70 |
| MDGRAPE-3(sec) |
6.38 |
7.33 |
34.31 |
| Acceleration |
54 |
115 |
269 |
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Specifications |
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| MDGRAPE-3 chips |
2 |
| Performance |
330GFlops |
| Host Interface |
PCI-X 133MHz |
| SDK |
Riken delivers c and fortran library. |
| Power consumption |
40W |
| Price |
Academic : US$12,000.00
Non-Academic : US$16,000.00 |
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System Requirements |
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| Platform |
IA-32 (Pentium4/PentiumD/Xeon) |
| Chip Set |
Intel E7501, E7505, E7520, E7525, E7230, 955X |
| Power |
DC12V@4A |
| OS |
Linux (kernel 2.4/2.6, 32-bit/64-bit)
Note: Beta version of WindowsXP driver
(Non support) |
| Linux Distribution |
Fedora core 3/4,CentOS 4.1/4.2/4.3
Red Hat Enterprise WS 4.0 |
| Diskspace |
100MB |
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Notice |
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The chips mounted on MDGRAPE-3 board have very high dense circuits and generate high heat. In order to cool down this heat, there are mounted fans above 2 chips on the board. As the result of these fans, the thickness of the board is about 40mm which occupies two adjacent PCI slots, and 10mm level free space is needed next to fan top.
MDGRAPE-3 stops its processing with warning message(s) when the board temperature becomes over 48 °C. MDGRAPE chip temperature with normal use under average office environment will be kept around 35 to 45 °C however, depend on the user’s application program, it may exceed 50 °C. If your application results frequent over 50 °C, we advise to install a fan fitted in PCI slot, such as FD08025B1ME4 Exhauster.
Nevertheless, when you cannot have a good result, we recommend you to move your whole system to the computer room with air conditioning.
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