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Hardware Resources
Computational biochemistry is very computer-intensive research. We use
a variety of different computer systems, from regular PCs to parallel
computers and high-end graphics workstations. Most computers run
Linux or another type of UNIX operating system.
Ganglia pages of lab resources.
Availability of storage resources.
Lab workstations
Workstations are either PCs running Linux or Macs running OS-X.
sunsetcliffs is used for word processing etc. as a Windows XP/Linux
dual boot machine and is often not available under Linux.
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theshores
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2x quad-core Xeon 2.5 GHz, 8 GB, 64 bit |
Michael's computer |
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swamis
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Pentium 4 2.8 GHz, 2 GB, 32 bit |
Sabai's computer |
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blacks
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2x quad-core Xeon 2.0 GHz, 6 GB, 64 bit |
Srinivasa's computer |
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tourmaline
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Pentium 4 2.8 GHz, 1.5 GB, 32 bit |
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windansea
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Pentium 4 3.4 GHz, 1 GB, 64 bit |
Yi-Ming's computer |
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pbpier
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Pentium 4 3.4 GHz, 1 GB, 64 bit |
Shayantani's computer |
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pipes
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Dual-core Pentium 4 3.0 GHz, 2 GB, 64 bit |
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ponto
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Dual-core Pentium 4, 3.0 GHz, 2 GB, 64 bit |
Sean's computer |
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trestles
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Dual-core Pentium 4 3.0 GHz, 2 GB, 64 bit
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Maryam's computer |
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crystalpier
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Pentium 4 2.8 GHz, 2 GB, 32 bit
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Afra's computer |
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southbay
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Pentium 4 2.8 GHz, 1 GB, 32 bit |
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sunsetcliffs
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Pentium 4 2.4 GHz, 1.5 GB, 32 bit
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Windows/Linux PC |
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15thstreet
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iMAC G5 1.6 GHz, 0.5 GB
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birdrock
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iMAC G5 1.6 GHz, 0.5 GB
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| rhea |
SGI Fuel 500 MHz R14K, 512 MB |
Stereo workstation |
Blue minicluster
The blue machines were self-assembled in 2003/2004 based on the
Supermicro X5DPA-GG
motherboard and Intel Xeon CPUs. For the network connection, a low-end
gigabit switch is used. All blue machines are still running RedHat Linux 9.0
at this time.
blue2-6 are available as a limited compute resource for testing,
interactive, and small-scale calculations.
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blue2
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2x Xeon 2.8 GHz, 2 GB, 32 bit |
Compute node |
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blue3
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2x Xeon 2.8 GHz, 2 GB, 32 bit
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Compute node |
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blue4
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2x Xeon 2.8 GHz, 4 GB, 32 bit
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Compute node |
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blue5
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2x Xeon 2.8 GHz, 2 GB, 32 bit
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Compute node |
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blue6
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2x Xeon 3.06 GHz, 2 GB, 32 bit
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Compute node |
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blue7
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2x Xeon 3.06 GHz, 2 GB, 32 bit |
Compute node |
Green cluster
The cluster was delivered by
Dell in April 2004 and consists of 44 dual
Xeon nodes, 2 RAID storage servers, a master node, and 2 high-performance gigabit ethernet
switches from Nortel. A total of 94 CPUs are available with a compute power of
200 GFlops/s, as
measured by the Linpack
benchmark.
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green
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2x Xeon 3.06 GHz, 2 GB, 32 bit |
Login node |
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greencNN
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2x Xeon 3.06 GHz, 2 GB, 32 bit
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Compute nodes 01 - 44 |
Introduction into green usage
Orange cluster
The compute nodes orange2-orange13 are used for SimDB
computing and as a second lab cluster. All nodes are running
Gentoo Linux.
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orangeNN
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2x Quad-core Xeon 2.66 GHz, 8 GB, 64 bit
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Compute nodes 2-12 |
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orange13
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2x Quad-core Xeon 2.66 GHz, 16 GB
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Compute node 13 |
Servers
These are various storage servers in the Feig group.
All servers are running Gentoo Linux.
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blue1
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2x quad-core Xeon 2.0 GHz, 8 GB, 64 bit
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Lab server, Matlab |
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greens1
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2x quad-core Xeon 2.5 GHz, 8 GB, 1.2 TB, 64 bit |
Storage |
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greens3
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2x quad-core Xeon 2.5 GHz, 8 GB, 2x4 TB, 64 bit |
Storage |
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greens4
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2x Xeon 3.0 GHz, 2 GB, 1 TB, 64 bit |
Storage |
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greens5
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2x quad-core Xeon 2.66 GHz, 16 GB, 4x9 TB, 64 bit |
Storage |
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orange1
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2x Xeon 3.4 GHz, 2 GB, 4 TB, 64 bit
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SimDB storage |
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feigstore
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2x Xeon 3.0 GHz, 2 GB, 2 TB, 64 bit
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Backup server |
Biochemistry workstations
The Department of Biochemistry and Molecular Biology
has a number of workstations for teaching and research. They are connected with a Gigabit Ethernet
switch. The machines are located in BCH 202 and managed by
Kaillathe Padmanabhan (Pappan).
| minnie |
2x Quad-core Xeon 2.0 GHz, 8 GB, 64 bit |
compute node |
| mickey |
2x Quad-core Xeon 2.0 GHz, 8 GB, 64 bit |
compute node |
| jasmine |
2x Quad-core Xeon 2.0 GHz, 8 GB, 64 bit |
compute node |
| tigger |
2x Quad-core Xeon 2.0 GHz, 8 GB, 64 bit |
compute node |
| piglet |
2x Quad-core Xeon 2.0 GHz, 8 GB, 64 bit |
compute node |
| goofy |
2x Quad-core Xeon 2.0 GHz, 8 GB, 64 bit |
compute node |
| mowgli |
2x Quad-core Xeon 2.0 GHz, 8 GB, 64 bit |
compute node |
| raksha |
2x Quad-core Xeon 2.0 GHz, 8 GB, 64 bit |
compute node |
| shanty |
2x Quad-core Xeon 2.0 GHz, 8 GB, 64 bit |
compute node |
| venus |
2x Xeon 3.2 GHz, 2 GB, 64 bit |
compute node |
| mercury |
2x Xeon 3.2 GHz, 2 GB, 64 bit |
compute node |
| pluto |
2x Xeon 3.2 GHz, 2 GB, 64 bit |
compute node |
| mars |
2x Xeon 3.2 GHz, 2 GB, 64 bit |
compute node |
| hercules |
1x Quad-core Xeon 2.0 GHz, 4 GB, 1.4 TB, 64 bit |
File server |
| helios |
2x Xeon 2.66 GHz, 1 GB, 32 bit |
NIS server |
QBMI cluster
The QBMI cluster
is a shared resource available to MSU research groups participating in the
Quantitative Biology Modeling Initiative.
The cluster can be reached at neumann.cem.msu.edu.
It is administered by Paul Reed.
| neumann |
2x Xeon 2.66 GHz, 1 GB, 32 bit |
Login node |
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schroedinger
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2x Athlon 4000 (2.1 GHz), 1 GB, 64 bit
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Head node |
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compute-1-2
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2x Athlon 4000 (2.1 GHz), 1 GB, 64 bit
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Compute node |
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compute-1-6
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2x Athlon 4000 (2.1 GHz), 1 GB, 64 bit
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Compute node |
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compute-1-7
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2x Athlon 4000 (2.1 GHz), 1 GB, 64 bit
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Compute node |
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compute-1-8
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2x Athlon 4000 (2.1 GHz), 1 GB, 64 bit
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Compute node |
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compute-1-10
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2x Athlon 4000 (2.1 GHz), 1 GB, 64 bit
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Compute node |
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compute-1-11
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2x Athlon 4000 (2.1 GHz), 1 GB, 64 bit
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Compute node |
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compute-1-12
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2x Athlon 4000 (2.1 GHz), 1 GB, 64 bit
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Compute node |
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compute-1-16
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2x Athlon 4000 (2.1 GHz), 1 GB, 64 bit |
Compute node |
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compute-1-17
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2x Athlon 4000 (2.1 GHz), 1 GB, 64 bit |
Compute node |
MCBI cluster
The 64-CPU MCBI cluster
is a shared resource available to research groups participating in the
Michigan Center for Biological Information.
The cluster can be reached at mcbilin.cem.msu.edu.
It is administered by Paul Reed.
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head
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2x Xeon 2.66 GHz, 2 GB, 32 bit
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Head node |
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io
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2x Xeon 2.66 GHz, 2 GB, 32 bit
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I/O node |
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sched
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Pentium 4, 2.4 GHz, 2 GB, 32 bit
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Scheduler node |
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apps
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2x Xeon 2.66 GHz, 2 GB, 32 bit
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Applications node |
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compute-1-NN
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2x Xeon 2.66 GHz, 2 GB, 32 bit
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Compute nodes 1-32 |
MCBI SGI
The MCBI SGI is a 16-CPU shared memory Origin 2000 system. It is available
to MSU research groups participating in the
Michigan Center for Biological Information.
The host name is mcbisgi.cem.msu.edu. The system manager is
Paul Reed.
| mcbisgi |
16x 300 MHz R12K, 12 GB |
Shared memory nodes |
hbar
hbar
is a 32-CPU shared memory Origin 2000 system primarily used by the
theory group
in the
Department of Chemistry at MSU.
The host name is hbar.cem.msu.edu, and it is managed by
Paul Reed.
| hbar |
32x 400 MHz R12K, 24 GB |
Shared memory nodes |
hydra
hydra
is a 13-node cluster primarily used by the
theory group
in the
Department of Chemistry at MSU.
The host name is hydra.cem.msu.edu, and it is managed by
Paul Reed.
| hydra |
2x Dual-core AMD Opteron 1.8 GHz R12K, 4 GB |
Head node |
| c2d0-N |
2x Dual-core AMD Opteron 1.8 GHz R12K, 4 GB |
Compute nodes 0-10 |
| p0-0 |
2x Dual-core AMD Opteron 1.8 GHz R12K, 16 GB |
Big compute node |
HPC SMP machine (green)
A large SGI Altix 3700 Bx2 SMP system that is part of the
High Performance Computing center at MSU.
| green |
128 x 1.6 GHz Itanium, 576 GB |
Shared memory nodes |
HPC Opteron cluster (wilson)
A large AMD Opteron cluster that is part of the
High Performance Computing center at MSU.
| amd-NNN |
2 x Dual-core Opteron 2.2 GHz, 8 GB, 64 bit, Infiniband |
Compute nodes 1-128 |
HPC Xeon cluster (brody)
A large AMD Opteron cluster that is part of the
High Performance Computing center at MSU.
| scw-NNN |
2 x Quad-core Xeon 2.3 GHz, 8 GB, 64 bit, Infiniband |
Compute nodes 1-128 |
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