Namd on BGQ

A parameter study was undertaken to test simulation performance and efficiency of NAMD on the Blue Gene/Q cluster, BGQ, with attention to NAMD performance tuning documentation. Determining optimal parameters for a NAMD simulation on this system is more difficult as there are only certain simulation sizes that have optimal topologies (512, 1024, etc). The system of study is a 246,000 atom membrane protein simulation (Cytochrome c Oxidase embedded in a TIP3P solvated DPPC bilayer) using the CHARMM36 forcefield (protein and lipids). The unit cell is cubic with box dimensions 144 x 144 x 117 Angstroms and the simulation time-step was 2fs.

Performance Tuning Benchmarks

Efficiency is measured with respect to the 16 ranks-per-node 512 core simulation. All simulations are started using a restart file from a pre-equilibrated snapshot. Performance in nanoseconds per day is based on the geometric mean of the three "Benchmark time" lines at the beginning of the simulation's standard output. In this section, the PME patch grid was manually doubled in either the X, Y, or Z directions. Default PME patch doubling in NAMD 2.9 is generally recommended (twoAway parameters need not be specified in the configuration file).

Ranks	Cores	NAMD Config Options	ns/day	Efficiency
16	512		2.79	1.00
16	1024		5.05	0.91
16	1024	twoAwayX (default)	5.62	1.01
16	2048	twoAwayX (default)	10.07	0.90
16	2048	twoAwayXY	10.59	0.95
16	4096	twoAwayX	14.32	0.64
16	4096	twoAwayXY (default)	17.63	0.79
16	4096	twoAwayXYZ	16.79	0.75
16	8192	twoAwayX	23.52	0.53
16	8192	twoAwayXY (default)	25.00	0.56
16	16384	twoAwayX	23.67	0.27
16	16384	twoAwayXY	28.31	0.32
16	16384	twoAwayXYZ (default)	27.98	0.31

PME Pencils

A "pencil-based" PME decomposition may be more efficient than the default "slab-based decomposition". In this study PME pencil grids are created for both dedicated PME nodes (lblUnload=yes) and non-dedicated PME nodes. Fine-tuning of PMEPencils resulted in insignificant performance gains for this study.

Ranks	Cores	NAMD Config Options	ns/day	Efficiency
16	4096	twoAwayXY, PMEPencils=8, lblUnload=yes	12.93	0.58
16	4096	twoAwayXY, PMEPencils=12, lblUnload=yes	17.27	0.77
16	4096	twoAwayXY, PMEPencils=16, lblUnload=yes	16.02	0.72
16	4096	twoAwayXY, PMEPencils=20, lblUnload=yes	15.41	0.69
16	4096	twoAwayXY, PMEPencils=12	16.21	0.73
16	4096	twoAwayXY, PMEPencils=16	17.92	0.80
16	4096	twoAwayXY, PMEPencils=20	17.99	0.81
16	4096	twoAwayXY, PMEPencils=24	17.83	0.80
16	4096	twoAwayXY, PMEPencils=36	16.97	0.76
8	4096	twoAwayXY, PMEPencils=20	18.24	0.82
16	4096	twoAwayXY, PMEPencils=20	17.99	0.81
32	4096	twoAwayXY, PMEPencils=20	13.94	0.63

Ranks-Per-Node Study

The "ranks-per-node" or simply the number of processes per compute node is a Blue Gene/Q runjob command parameter. In this study, memory requirements were too large to use 64 due to memory errors, and also resulted in out of memory errors for 16384 core simulations of 32 ranks per node. The following efficiency estimates are measured with respect to the 16 ranks per node results for the same number of nodes.

Ranks	Cores	NAMD Config Options	ns/day	Efficiency
32	1024		4.46	1.6
32	2048		8.01	1.43
32	4096		13.74	1.3
16	8192		19.81	1.12

Incorrect Particle-Mesh Ewald Grid

Long-range electrostatics are computed using PME for all simulations above with PME grid spacing set to be generated automatically with the "pmeGridSpacing 1.0" setting. A poor choice in PME grid spacing (i.e. not a multiple of 2,3, and 5) can result in increasingly large performance degradation due to the matrix size requirements in the FFT algorithm. Below is an example of the type of performance degradation that one may expect with none of the grid dimensions are divisible by 5. One can draw a comparison to a more correct PME choice in the Performance Tuning Benchmarks above.

Ranks	Cores	NAMD Config Options	ns/day	Efficiency
16	512	Poor PME Multiple (144x144x111)	2.70	0.97
16	1024	Poor PME Multiple (144x144x111)	5.13	0.92
16	2048	Poor PME Multiple (144x144x111)	8.61	0.77
16	4096	Poor PME Multiple (144x144x111)	13.93	0.62
16	8192	Poor PME Multiple (144x144x111)	17.08	0.38
16	16384	Poor PME Multiple (144x144x111)	17.64	0.20

Documentation

1. NAMD 2.9 User Guide
2. NAMD Performance Tuning Wiki