Amber Implicit CS 1.3
A set of Amber 9 methods has been modified to take advantage of the ClearSpeed Advance X620 and e620 acceleration. This includes the effective radius and force calculation of Amber’s Generalized Born (GB) models 1, 2, 5 and 6 (gas phase). See the downloads section below. (In order to use the modifications, you must have an Amber 9 license.) For more information on Amber please click here.
While the genborn module of Amber is a small part of the sander executable, it typically amounts for 95-97% of the CPU compute time for GB simulations. The CPU compute time is mainly spent in three loops: effective radii calculations, diagonal and off-diagonal force calculations.
The overall structure of the code was maintained. A thin layer written in C, using ClearSpeed’s CSAPI library, was added to handle the communication between the host and card.
New Release Features
The Amber Implicit CS 1.3 Release provides the following improvements over version 1.2:
- Changes include faster code for GB models
- Models 1, 2, and 5 23-33 %
- GB model 6 55-67 %
- The GB 7 model has been added
The supported options include the following:
- Constant pH
- Analytical linearized Poission Boltzmann
- Other options that do not directly change the force calculation such as NMR restraints
Is this modification right for you?
In order to see good acceleration of Amber, you must have the following conditions:
- Large and/or infinite cutoff and/or rgbmax values. At least one, but preferably both should be large
- Do not set nrespa != 1. This option imposes a fixed short cutoff on the in-between time steps.
- The work is done in batches of 768 atoms/card. Consequently, simulations with a number of atoms just below a multiple of 768 will get much better acceleration than a simulation where the number of atoms is just above.
- For large problems, such as > 5000 atoms this is less of an issue.
Scalability:
- The number of atoms is important when determining scalability in a multi card setup.
- An example is if you have 1500 atoms, this fits well on two cards, but you gain nothing by using a third
- Another example is if you have 3000 atoms will do well on 2 or 4 cards but less so on 3 or 5 cards.
Amber Implicit CS 1.3 Download
Operating System |
Amber Implicit CS 1.3 Package |
|---|---|
| Red Hat® Enterprise Linux® 3 32-bit | Download |
Each download will contain the following elements:
| AmberClearSpeedSetup.pdf | A PDF version of the Installation Guide |
bugfix.all |
Amber 9 patches to patch level 37. This is an unaltered copy from the AMBER web site: http://amber.scripps.edu/bugfixes90.html |
amber9_CS.patch |
ClearSpeed's Amber patches. |
amber_csboard.tgz |
Tarball of card-side code. |
patch_amber9_ClearSpeed.bash |
Script that patches the Amber 9 distribution, first with the Amber bug fixes, and then with ClearSpeed's modification |
build_amber9_ClearSpeed.bash |
Script to build the modified Amber 9 version for Advance X620 and e620 Accelerator card. |
amber_cs_env.bash |
Script that sets up part of the environment needed to run ClearSpeed's version of sander. |
Software Requirement
Amber Implicit CS 1.3 works only with the 2.51 release of the SDK and runtime.
Associated Documentation
ClearSpeed Amber 9 Installation Guide (PDF)
ClearSpeed Amber 10 Installation Guide (PDF)
- Instructions for installing the Amber Implicit CS 1.3 package to experience ClearSpeed Acceleration
For ClearSpeed Accelerated Amber benchmark information click here. Note that new benchmark information for Amber Implicit CS 1.3 will be updated soon.