The Charm++ Programming Model and NAMD Abhinav S Bhatele Department of Computer Science University of Illinois at Urbana-Champaign

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Presentation transcript:

The Charm++ Programming Model and NAMD Abhinav S Bhatele Department of Computer Science University of Illinois at Urbana-Champaign

Feb 13th, 2009Abhinav S Bhatele2 University of Illinois Urbana-Champaign, Illinois, USA

Processor Virtualization User ViewSystem View Programmer: Decomposes the computation into objects Runtime: Maps the computation on to the processors Feb 13th, 20093Abhinav S Bhatele

Benefits of the Charm++ Model Software Engineering – Number of VPs independent of physical processors – Different sets of VPs for different computations Dynamic Mapping – Load balancing – Change the set of processors used Message-driven execution – Compositionality – Predictability Feb 13th, 20094Abhinav S Bhatele

Charm++ and CSE Applications Feb 13th, 20095Abhinav S Bhatele Gordon Bell Award, SC 2002 Fine-grained CPAIMD Cosmological Simulations

Adaptive MPI (AMPI) Feb 13th, 2009Abhinav S Bhatele6 MPI “Processes” - Implemented as virtual “processes” (light-weight user level migratable threads)

Load Balancing Based on Principle of Persistence Runtime instrumentation – Measures communication volume and computation time Measurement based load balancers – Use the instrumented data-base periodically to make new decisions – Many alternative strategies can use the database Centralized vs distributed Greedy improvements vs complete reassignments Taking communication into account Feb 13th, 2009Abhinav S Bhatele7

NAMD Feb 13th, 2009Abhinav S Bhatele8 NAnoscale Molecular Dynamics Simulates the life of bio-molecules Simulation window broken down into a large number of time steps (typically 1 fs each) Forces on each atom calculated every step Positions and velocities updated and atoms migrated to their new positions

Parallelization of NAMD Hybrid Decomposition Feb 13th, 2009Abhinav S Bhatele9

Control Flow Feb 13th, 2009Abhinav S Bhatele10

Feb 13th, 2009Abhinav S Bhatele11 Non-bonded Work Bonded Work Integration PME Communication

Optimizations on MareNostrum Fixes to the CVS version – Crash due to a xlc compiler bug Performance analysis – Using Projections performance analysis tool Performance tuning – Configuration parameters for NAMD to enable high parallelization Feb 13th, 2009Abhinav S Bhatele12

Performance Tuning Increasing the number of objects – twoAway{X, Y, Z} options Choice of PME implementation – Slab (1D) vs. Pencil (2D) decomposition Offloading processors doing PME Use of spanning tree for communication Feb 13th, 2009Abhinav S Bhatele13

DD on MareNostrum Feb 13th, Abhinav S Bhatele

DD with Slab PME Feb 13th, 2009Abhinav S Bhatele15

DD with Pencil PME Feb 13th, 2009Abhinav S Bhatele16

Problem? Feb 13th, 2009Abhinav S Bhatele ms

Feb 13th, 2009Abhinav S Bhatele18

Nucleosome on MareNostrum Feb 13th, Abhinav S Bhatele

Membrane on MareNostrum Feb 13th, Abhinav S Bhatele

Similar Problem? Feb 13th, 2009Abhinav S Bhatele21 16 ms Bandwidth on Myrinet: 250 MB/s Expected Latency for 6-10 KB messages < 0.1 ms

Optimizations on the Xe Cluster Getting the CVS version running (over mpi) Trying a development version of charm – Runs directly over Infiniband (ibverbs) – Currently unstable Feb 13th, 2009Abhinav S Bhatele22

DD on Xeon Cluster Feb 13th, Abhinav S Bhatele

Thank You!