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Advanced User Support Project Overview Thomas E. Cheatham III University of Utah Jan 14th 2010

Advanced User Support Project Overview Thomas E. Cheatham III University of Utah Jan 14th 2010. By Ross C. Walker. Project Overview. The Problem: Extensive work has been undertaken to improve the performance and scalability of Molecular Dynamics (MD) packages. NAMD AMBER GROMACS LAMMPS

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Advanced User Support Project Overview Thomas E. Cheatham III University of Utah Jan 14th 2010

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  1. Advanced User SupportProject Overview Thomas E. Cheatham IIIUniversity of UtahJan 14th 2010 By Ross C. Walker

  2. Project Overview • The Problem: • Extensive work has been undertaken to improve the performance andscalability ofMolecular Dynamics(MD) packages. • NAMD • AMBER • GROMACS • LAMMPS • DESMOND

  3. Project Overview • The Problem: • Larger and Larger systemsare being simulated.(1 million + atoms now routine) • Longer and longer simulationsare being run.(100ns to 1 microsecond nowroutine) • Use of GPUs is leading to longersimulations being run on‘basic’ desktops. This is leading to an explosion in trajectory size. The analysis tools are not keeping up with this.

  4. Project OverviewDevelopment of Parallel Analysis Tools for Molecular Dynamics • Project composed of 3 sections: • Development of parallel analysis tools for MD. • Improvements in the handling of large datasets. • Development of new analysis techniques for large and/or long timescale simulations.

  5. Phase 1 Parallelization of Ptraj Analysis Suite

  6. Ptraj • Developed by Prof. Cheatham during the 1990’s at UCSF. Has been continually updated since. • Distributed as openSource in the AMBERTools package. • Supports a large range of analysis techniques on multiple file formats. (AMBER, CHARMM, NAMD etc…)

  7. Work to Date • I have written a parallel version of ptraj that uses MPI calls and MPI/IO. • It supports parallel I/O to take advantage of Lustre etc. • Version 1.0 of the parallel version released at the end of December 2009 as part of free AMBERTools 1.3.(See http://ambermd.org/AmberTools-get.html) • Multiple performance improvements also included.Random file access. Non-sequential access to frames in trajectory files etc.

  8. Version 1.0 • Current supported parallel actions are:angle, atomicfluct, average, center, checkoverlap, closest, contacts,dihedrals, distance, image, principal, pucker, radgyr, randomizeions, rms,strip, translate, watershell • For actions that are not yet parallel (e.g. hbond) the code will default back to single cpu operation.

  9. Example Performance

  10. Example Performance

  11. Random File Access Improvements • The code can now seek randomly even for ASCII trajectory files. trajin foo.mdcrd 1001 1005 1 trajin foo2.mdcrd 23000 24000 100 image origin center trajout foobar.pdb pdb 1 TB trajectory file (Ranger) Original Code: 5820 secs (97 mins) New Code: 1 cpu 37.5 secs 8 cpu 4.8 secs

  12. Current Issues • Cannot currently do random / parallel IO on compressed files. • Code currently decompresses the file by calling gzip etc and streaming it. • Suggestions? • Compressed NetCDF allows this? • Use of non-parallel action currently forces the entire run to be serial.

  13. Planned Work for the Coming Year • Complete parallelization of remaining actions. • Develop distributed memory versions of the memory hungry routines (e.g. hbond) to support larger systems. • Begin developing (in collaboration with Prof Cheatham’s lab) new analysis techniques that are more useful when looking at microsecond+ trajectories or multi-million atom simulations.

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