R. Scott Studham, Associate Director Advanced Computing April 13, 2004 HPC At PNNL March 2004

2 HPC Systems at PNNL Molecular Science Computing Facility 11.8TF Linux based supercomputer using Intel Itanium2 processors and Elan4 interconnect A balance for our users: 500TB Disk, 6.8 TB memory PNNL Advanced Computing Center 128 Processor SGI Altix NNSA-ASC “Spray Cool” Cluster

3 William R. Wiley Environmental Molecular Sciences Laboratory Who are we? A 200,000 square-foot U.S. Department of Energy national scientific user facility Operated by Pacific Northwest National Laboratory in Richland, Washington What we provide for you Free access to over 100 state-of-the-art research instruments A peer-review proposal process Expert staff to assist or collaborate Why use EMSL? EMSL provides - under one roof - staff and instruments for fundamental research on physical, chemical, and biological processes.

4 HPCS2 Configuration Elan4 4 Login nodes with 4Gb-Enet 2 System Mgt nodes 1,976 next generation Itanium ® processors 11.8TF 6.8TB Memory … compute nodes 2Gb SAN / 53TB … Lustre Elan3 The 11.8TF system is in full operations now.

5 Who uses the MSCF, and what do they run? FY02 numbers Gaussian

6 More than 67% of the usage is for large jobs. Demand for access to this resource is high. Fewer users focused on Longer, Larger runs and Big Science. MSCF is focused on grand challenges

7 The world-class science is enabled by having systems that enable the fastest time-to-solution for our science Significant improvement (25- 45% for moderate number of processors) in time to solution by upgrading the interconnect to Elan4. Improved efficiency Improved scalability HPCS2 is a science driven computer architecture that has the fastest time-to-solution for our users science of any system we have benchmarked.

8 Accurate binding energies for large water clusters Accurate binding energies for large water clusters These results provide unique information on the transition from the cluster to the liquid and solid phases of water. Code: NWChem 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.

9 Energy calculation of a protein complex 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. Code: NWChem Kernel: Hartree-Fock 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.

10 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 HPCS1 HPCS2 HPCS3 Biogeochemistry: Membranes for Bioremediation

11 A new trend is emerging With the expansion into biology, the need for storage has drastically increased. EMSL users have stored >50TB in the past 8 months. More than 80% of the data is from experimentalists. Projected Growth Trend for Biology Log Scale! The MSCF provides a synergy between the computational and experimentalists.

12 Storage Drivers We support Three different domains with different requirements High Performance Computing – Chemistry Low storage volumes (10 TB) High performance storage (>500MB/s per client, GB/s aggregate) POSIX access High Throughput Proteomics – Biology Large storage volumes (PB’s) and exploding Write once, read rarely if used as an archive Modest latency okay (<10s to data) If analysis could be done in place it would require faster storage Atmospheric Radiation Measurement - Climate Modest side storage requirements (100’s TB) Shared with community and replicated to ORNL

13 PNNL's Lustre Implementation PNNL and the ASCI Tri-Labs are currently working with CFS and HP to develop Lustre. Lustre has been in full production since last Aug and used for aggressive IO from our supercomputer. Highly stable Still hard to manage We are expanding our use of Lustre to act as the filesystem for our archival storage. Deploying a ~400TB filesystem 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

14 Open computing requires a trust relationship between sites. User logs into siteA and ssh’s to siteB. If siteA is compromised the hacker has probably sniffed the password for siteB. Reaction #1: Teach users to minimize jumping through hosts they do not personally know are secure (why did the user trust SiteA?) Reaction #2: Implement one-time passwords (SecureID) Reaction #3: Turn off open access (Earth simulator?) SecuritySecurity

15 Thoughts about one-time-passwords A couple of different hurdles to cross: We would like to avoid having to force our users to carry a different SecureID card for each site they have access to. However the distributed nature of security (it is run by local site policy) will probably end up with something like this for the short term. As of April 8 th the MSCF has converted over to the PNNL SecureID system for all remote ssh logins. Lots of FedEx’ed SecureID cards

16 SummarySummary HPCS2 is running well and the IO capabilities of the system are enabling chemistry and biology calculations that could not be run on any other system in the world. Storage for proteomics is on a super-exponential trend. Lustre is great. 660MB/s from a single client. Building 1/2PB single filesystem. We rapidly implemented SecureID authentication methods last week.