Co-processors for speeding up drug design algorithms Advait Jain Priyanka Jindal Pulkit Gambhir

Objective To design FPGA based hardware accelerators for speeding up the energy minimization process.

Bottleneck Functions Iterate over list of bonds {O(N) elements} Iterate over list of angles {O(N) elements} Iterate over list of dihedrals {O(N) elements} Iterate over list of non-bonded pairs {O(N 2 ) elements} Eval energyEval Energy for stepDiff energy

Mathematical operations EvalEnergy_for_step() DiffEnergy()

Non-bonded List Node structure Float A, B, C (4*3 bytes) Int a1, a2 C is a function of charge q1 and q2 of atoms. 471,282 distinct Cs (3 bytes) A, B Are a function of radius and epsilon of atoms. 192 distinct pairs of A,B (1 byte)

New Data Structure Vector of Distinct Cs Vector of Distinct (A,B) pairs New Node structure 3d coordinates of atoms Int a1, a2 Unsigned common_index 3 1

Generating the proposed Data Structure Given q1, q2 Calculate C Insert (C, C_index) Into the Hash table Key: C, Data: C_Index Node.Common index = C_Index (corresponding to C) Repeat for all non- bonded pairs

Hash Table to distinct C vector (C_index, C)(C, C_index) Hash table Vector of Distinct Cs

Result of new data structure Molecule Size: 2008 VanderList: 2,008,417 AB_Vander list: 136 C_Vanderlist: 21,651 Old DatastructureNew Datastructure 2,008,417 * 20 = 40,168,340 bytes 2,008,417 * * ,651 * 4 = 24,188,696 bytes

Cache Profiling (old vs new) D1 misses: 3,158,603,092 ( 3,152,690,177 rd + 5,912,915 wr) D1 misses: 2,872,958,414 ( 2,868,217,925 rd + 4,740,489 wr) L2d misses: 1,270,584,560 ( 1,266,933,599 rd + 3,650,961 wr) L2d misses: 503,167,419 ( 500,920,315 rd + 2,247,104 wr) L2 misses: 1,270,606,180 ( 1,266,955,219 rd + 3,650,961 wr) L2 misses: 503,188,994 ( 500,941,890 rd + 2,247,104 wr)

Bottleneck Functions Iterate over list of bonds {O(N) elements} Iterate over list of angles {O(N) elements} Iterate over list of dihedrals {O(N) elements} Iterate over list of non-bonded pairs {O(N 2 ) elements} Eval energyEval Energy for stepDiff energy

Split Up code Eval_Energy_for _step(%) Diff_Energy(%) Non-bonded pairs Dihedrals Angles Bonded00.00

Ongoing Work  Multiple threads operating on the Non- bonded list together.  Floating point precision requirement.

Tentative Schedule  Software Profiling August  No. of calls  Cache misses  Effect of parameters  Control Flow Analysis August - September  Flow Diagram  Data parallelism  Floating point precision requirement  Exploring H/W Options September - October  Platform Selection  S/W H/W Partitioning  Implementation October onwards  Analysis