HPC At PNNL March 2004. R. Scott Studham, Associate Director Advanced Computing April 13, 2004. HPC Systems at PNNL. Molecular Science Computing Facility 11.8TF Linux based supercomputer using Intel Itanium2 processors and Elan4 interconnect
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HPC At PNNLMarch 2004
R. Scott Studham,
April 13, 2004
1,976 next generation Itanium® processors
928 compute nodes
2Gb SAN / 53TB
2 System Mgt nodes
4 Login nodes
The 11.8TF system is in full operations now.
Fewer users focused on Longer, Larger runs and Big Science.
More than 67% of the usage is for large jobs.
Demand for access to this resource is high.
Significant improvement (25-45% for moderate number of processors) in time to solution by upgrading the interconnect to Elan4.
HPCS2 is a science driven computer architecture that has the fastest time-to-solution for our users science of any system we have benchmarked.
These results provide unique information on the transition from the cluster to the liquid and solid phases of water.
Kernel: MP2 (Disk Bound)
Sustained Performance: ~0.6 Gflop/s per processor (10% of peak)
Choke Point: Sustained 61GB/s of Disk IO and used 400TB of scratch space.
Only took 5 hours on 1024 CPUs of the HP cluster. This is a capability class problem that could not be completed on any other system.
The Ras-RasGAP protein complex is a key switch in the signaling network initiated by the epidermal growth factor (EGF). This signal network controls cell death and differentiation, and mutations in the protein complex are responsible for 30% of all human tumors.
Time for solution:~3 hours for one iteration on 1400 processors
Computation of 107 residues of the full protein complex using approximately 15,000 basis functions. This is believed to be the largest calculation of its type.
Molecular dynamics of a lipopolysaccharide (LPS)
Classical molecular dynamics of the LPS membrane of Pseudomonas aeruginosa and mineral
Quantum mechanical/molecular mechanics molecular dynamics of membrane plus mineral
The MSCF provides a synergy between the computational and experimentalists.
Projected Growth Trend for Biology
660MB/s from a single client with a simple “dd” is faster than any local or global filesystem we have tested.
We are finally in the era where global filesystems provide faster access
A couple of different hurdles to cross:
As of April 8th the MSCF has converted over to the PNNL SecureID system for all remote ssh logins.
Lots of FedEx’ed SecureID cards