scholarly journals Autogeneration and Autotuning of 3D Stencil Codes on Homogeneous and Heterogeneous GPU Clusters

2013 ◽  
Vol 24 (3) ◽  
pp. 417-427 ◽  
Author(s):  
Yongpeng Zhang ◽  
Frank Mueller
Keyword(s):  
Gpu Clusters ◽  
Stencil Codes

scholarly journals Two Decades of 4D-QSAR: A Dying Art or Staging a Comeback?

2021 ◽  
Vol 22 (10) ◽  
pp. 5212
Author(s):  
Andrzej Bak
Keyword(s):  
Molecular Conformation ◽  
Graphics Processing Unit ◽  
Processing Unit ◽  
Diverse Range ◽  
Current State ◽  
Gpu Clusters ◽  
Pharmacophore Hypothesis ◽  
Rising Power ◽  
Graphics Processing ◽  
Ligand Conformation

A key question confronting computational chemists concerns the preferable ligand geometry that fits complementarily into the receptor pocket. Typically, the postulated ‘bioactive’ 3D ligand conformation is constructed as a ‘sophisticated guess’ (unnecessarily geometry-optimized) mirroring the pharmacophore hypothesis—sometimes based on an erroneous prerequisite. Hence, 4D-QSAR scheme and its ‘dialects’ have been practically implemented as higher level of model abstraction that allows the examination of the multiple molecular conformation, orientation and protonation representation, respectively. Nearly a quarter of a century has passed since the eminent work of Hopfinger appeared on the stage; therefore the natural question occurs whether 4D-QSAR approach is still appealing to the scientific community? With no intention to be comprehensive, a review of the current state of art in the field of receptor-independent (RI) and receptor-dependent (RD) 4D-QSAR methodology is provided with a brief examination of the ‘mainstream’ algorithms. In fact, a myriad of 4D-QSAR methods have been implemented and applied practically for a diverse range of molecules. It seems that, 4D-QSAR approach has been experiencing a promising renaissance of interests that might be fuelled by the rising power of the graphics processing unit (GPU) clusters applied to full-atom MD-based simulations of the protein-ligand complexes.

CUDA-DTM: Distributed Transactional Memory for GPU Clusters

2019 ◽  
pp. 183-199 ◽  
Author(s):  
Samuel Irving ◽  
Sui Chen ◽  
Lu Peng ◽  
Costas Busch ◽  
Maurice Herlihy ◽  
...  
Keyword(s):  
Transactional Memory ◽  
Gpu Clusters

scholarly journals Stencil codes on a vector length agnostic architecture

2018 ◽  
Author(s):  
Adrià Armejach ◽  
Helena Caminal ◽  
Juan M. Cebrian ◽  
Rekai González-Alberquilla ◽  
Chris Adeniyi-Jones ◽  
...  
Keyword(s):  
Vector Length ◽  
Stencil Codes
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