## Group Williams

Group Description |
Matrices used by S. Williams et al for sparse matrix multiplication on GPUs. 14 matrices were used in the following paper: S. Williams, L. Oliker, R. Vuduc, J. Shalf, K. Yelick, J. Demmel, "Optimization of Sparse Matrix-Vector Multiplication on Emerging Multicore Platforms", Parallel Computing Volume 35, Issue 3, March 2009, Pages 178-194. Special issue on Revolutionary Technologies for Acceleration of Emerging Petascale Applications. https://hpcrd.lbl.gov/~swwilliams/research/papers/parco08_spmv.pdf http://dx.doi.org/10.1016/j.parco.2008.12.006 This same set of 14 matrices was also used in a subsequent technical report by NVIDIA: http://www.nvidia.com/object/nvidia_research_pub_001.html "Efficient Sparse Matrix-Vector Multiplication on CUDA" Nathan Bell and Michael Garland, in, "NVIDIA Technical Report NVR-2008-004", December 2008 file Name dim* nnz description dense2 Dense 2K 4.0M dense matrix in sparse format pdb1HYS Protein 36K 4.3M protein data bank 1HYS consph FEM/Spheres 83K 6.0M FEM concentric spheres cant FEM/Cantilever 62K 4.0M FEM cantilever pwtk Wind Tunnel 218K 11.6M pressurized wind tunnel rma10 FEM/Harbor 47K 2.37M 3D CFD of Charleston Harbor qcd5_4 QCD 49K 1.90M quark propagators (QCD/LGT) shipsec1 FEM/Ship 141K 3.98M FEM Ship section / detail mac_econ_fwd500 Economics 207K 1.27M Macroeconomic model mc2depi Epidemiology 526K 2.1M 2D Markov model of epidemic cop20k_A FEM/Accelerator 121K 2.62M Accelerator cavity design scircuit Circuit 171K 959K Motorola circuit simulation webbase-1M webbase 1M 3.1M Web connectivity matrix rail4284 LP 4Kx1.1M 11.3M Railways set cover, constraint matrix (*) the matrix is square if only one dimension listed. Six of the matrices are nearly identical to the matrices already in the UF Collection. They are thus not included in the UF Collection: pwtk Boeing/pwtk. The matrix here differs in only 2 entries. The pattern is the same. The norm of the difference between the two is round-off error (5e-26). Tim Davis obtained the matrix directly from Roger Grimes, and was careful to preserve each significant bit. The Boeing/pwtk matrix in the UF Collection is thus the correct one. qcd5_4 this is the binary pattern of QCD/conf5_4-* and QCD/conf6_0-*, ids: 1598:1604 in the UF Collection. These are from B. Medeke, and were orginally collected by R. Boisvert et al. for the Matrix Market. rma10 Bova/rma10. The matrix here is binary; Bova/rma10 is not. The rma10 matrix here is binary pattern of Problem.A + Problem.Zeros in the UF Collection. Tim Davis obtained Bova/rma10 directly from the matrix creator, Steve Bova. scircuit Hamm/scircuit. The pattern is the same. The 1-norm of the difference is 5e-10, which is round-off error. This matrix was obtained by Tim Davis from Steve Hamm (at Motorola) directly, and thus the Hamm/scircuit matrix already in the UF Collection is the correct version. shipsec1 similar to DNVS/shipsec1, but different patterns. It appears that the shipsec1 matrix here is missing many entries in the lower right quadrant. The pattern differs by 0.9M entries. The matrix is from C. Damhaug, collected by J. Koster. rail4284 an exact submatrix of Mittelmann/rail4284. The UF matrix has exactly 4284 more columns than the rail4284 matrix in this collection. Let A1 be the Mittelman/rail4284 matrix, and let A2 be the rail4284 matrix in this collection. Then A2 is identical to A1(:,m+1:end). The submatrix A1(:,1:4284) of the matrix in the UF collection is exactly equal to -speye(m). Tim Davis obtained the matrix directly from Mittelmann's test set. It's possible that multiple versions exist, or that the identity was added as the initial basis. In any case, the rail4284 matrix from Williams' test set is not added to the UF Collection. The remaining eight matrices are unique to this set of matrices, but one is of no interest (dense2). Thus, there are seven matrices in the Williams/ group in the UF Collection: pdb1HYS consph cant mac_econ_fwd500 mc2depi cop20k_A webbase-1M I presume the pdb1HYS matrix comes from this source: http://www.rcsb.org/pdb/explore.do?structureId=1HYS http://dx.doi.org/10.2210/pdb1hys/pdb Crystal structure of HIV-1 reverse transcriptase in complex with a polypurine tract RNA:DNA. Sarafianos, S.G., Das, K., Tantillo, C., Clark Jr., A.D., Ding, J., Whitcomb, J.M., Boyer, P.L., Hughes, S.H., Arnold, E. Journal: (2001) EMBO J. 20: 1449-1461 PubMed: 11250910 PubMedCentral: PMC145536 DOI: 10.1093/emboj/20.6.1449 Search Related Articles in PubMed PubMed Abstract: We have determined the 3.0 A resolution structure of wild-type HIV-1 reverse transcriptase in complex with an RNA:DNA oligonucleotide whose sequence includes a purine-rich segment from the HIV-1 genome called the polypurine tract (PPT). The PPT is resistant to ribonuclease... [ Read More & Search PubMed Abstracts ] We have determined the 3.0 A resolution structure of wild-type HIV-1 reverse transcriptase in complex with an RNA:DNA oligonucleotide whose sequence includes a purine-rich segment from the HIV-1 genome called the polypurine tract (PPT). The PPT is resistant to ribonuclease H (RNase H) cleavage and is used as a primer for second DNA strand synthesis. The 'RNase H primer grip', consisting of amino acids that interact with the DNA primer strand, may contribute to RNase H catalysis and cleavage specificity. Cleavage specificity is also controlled by the width of the minor groove and the trajectory of the RNA:DNA, both of which are sequence dependent. An unusual 'unzipping' of 7 bp occurs in the adenine stretch of the PPT: an unpaired base on the template strand takes the base pairing out of register and then, following two offset base pairs, an unpaired base on the primer strand re-establishes the normal register. The structural aberration extends to the RNase H active site and may play a role in the resistance of PPT to RNase H cleavage. |
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Displaying

**all 7**collection matricesId | Name | Group | Rows | Cols | Nonzeros | Kind | Date | Download File |
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2373 | pdb1HYS | Williams | 36,417 | 36,417 | 4,344,765 | Weighted Undirected Graph | 2008 | MATLAB Rutherford Boeing Matrix Market |

2374 | consph | Williams | 83,334 | 83,334 | 6,010,480 | 2D/3D Problem | 2008 | MATLAB Rutherford Boeing Matrix Market |

2375 | cant | Williams | 62,451 | 62,451 | 4,007,383 | 2D/3D Problem | 2008 | MATLAB Rutherford Boeing Matrix Market |

2376 | mac_econ_fwd500 | Williams | 206,500 | 206,500 | 1,273,389 | Economic Problem | 2008 | MATLAB Rutherford Boeing Matrix Market |

2377 | mc2depi | Williams | 525,825 | 525,825 | 2,100,225 | 2D/3D Problem | 2008 | MATLAB Rutherford Boeing Matrix Market |

2378 | cop20k_A | Williams | 121,192 | 121,192 | 2,624,331 | 2D/3D Problem | 2008 | MATLAB Rutherford Boeing Matrix Market |

2379 | webbase-1M | Williams | 1,000,005 | 1,000,005 | 3,105,536 | Weighted Directed Graph | 2008 | MATLAB Rutherford Boeing Matrix Market |