Solution Performance

Amber* is a suite of programs for classical molecular dynamics and statistical analysis. The main MD program is PMEMD (Particle Mesh Ewald Molecular Dynamics) employs two separate algorithms for implicit (generalized born or GB)- and explicit-solvent (PME) dynamics.

Hardware at-a-glance: Intel® Xeon® Gold 6148 processor

Platform features: Intel® Advanced Vector Extensions 512 (Intel® AVX-512), more cores, increased memory bandwidth

Software tools/libraries: Intel® MPI Library, Intel® Parallel Studio XE 2017 Composer Edition (C++/Fortran)

Product and Performance Information


Amber: Version 16 with all patches applied at December, 2016. Workloads: PME Cellulose NVE(408K atoms), PME stmv(1M atoms), GB Nucleosome (25K), GB Rubisco (75K). No cut-off was used for GB workloads. Compiled with -mic2_spdp –intelmpi - openmp, –DMIC2 * defined. Tests performed on March 2017.
Baseline: Executed with 36 MPI, 2 OpenMP. 2S Intel® Xeon® processor E5-2697 v4, 2.3GHz, 36 cores, turbo and HT on, BIOS 86B0271.R00, 8x16GB 2400MHz DDR4, Red Hat Enterprise Linux* 7.2 kernel 3.10.0-327.
New: Executed with 40 MPI and 2 OpenMP. 2S Intel® Xeon® Gold 6148 processor, 2.4GHz, 40 cores, turbo on, HT on, BIOS 86B.01.00.0412.R00, 12x16GB 2666MHz DDR, Red Hat Enterprise Linux* 7.2 kernel 3.10.0-327.
-DMIC2 enable optimization for AVX512 vectorization, SPDP mixed precision, OpenMP optimization, but not any specific optimization for KNL arch.


Software and workloads used in performance tests may have been optimized for performance only on Intel® microprocessors. Performance tests, such as SYSmark* and MobileMark*, are measured using specific computer systems, components, software, operations and functions. Any change to any of those factors may cause the results to vary. You should consult other information and performance tests to assist you in fully evaluating your contemplated purchases, including the performance of that product when combined with other products. For more complete information about performance and benchmark results, visit