Matrix properties
number of rows	36,417
number of columns	36,417
nonzeros	4,344,765
# strongly connected comp.	1
explicit zero entries	0
nonzero pattern symmetry	symmetric
numeric value symmetry	symmetric
type	real
structure	symmetric
Cholesky candidate?	yes
positive definite?	yes

author	S. G. Sarafianos et al
editor	S. Williams, L. Oliker, R. Vuduc, J. Shalf, K. Yelick, J. Demmel
date	2008
kind	weighted undirected graph
2D/3D problem?	no

Notes:

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.  See          
the README.txt file for this collection for details.                           
   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.                                                           

SVD-based statistics:
norm(A)	352.394
min(svd(A))	9.97039e-10
cond(A)	3.5344e+11
rank(A)	36,411
null space dimension	6
full numerical rank?	no
singular value gap	137371

singular values (MAT file):	click here
SVD method used:	s = svd (full (A))
status:	ok

For a description of the statistics displayed above, click here.

Maintained by Tim Davis, last updated 12-Mar-2014.
Matrix pictures by cspy, a MATLAB function in the CSparse package.
Matrix graphs by Yifan Hu, AT&T Labs Visualization Group.