Macs in Chemistry

Insanely Great Science

Khronos Releases OpenGL 4.6 with SPIR-V Support


The Khronos™ Group, an open consortium of leading hardware and software companies, announced at the SIGGRAPH 2017 Conference the immediate public availability of the OpenGL® 4.6 specification. OpenGL 4.6 integrates the functionality of numerous ARB and EXT extensions created by Khronos members AMD, Intel, and NVIDIA into core, including the capability to ingest SPIR-V™ shaders.

The OpenGL 4.6 specification can be found at The GLSL to SPIR-V compiler glslang has been updated with GLSL 4.60 support, and can be found at


Khronos Releases OpenCL 2.2


I see that OpenCL 2.2 has been released and reading through the press release there are a couple of notes that might be of wider interest.

By finalizing OpenCL 2.2, Khronos has delivered on its promise to make C++ a first-class kernel language in the OpenCL standard,” said Neil Trevett, OpenCL chair and Khronos president. “The OpenCL working group is now free to continue its work with SYCL, to converge the power of single source parallel C++ programming with standard ISO C++, and to explore new markets and opportunities for OpenCL — such as embedded vision and inferencing. We are also working to converge with, and leverage, the Khronos Vulkan API — merging advanced graphics and compute into a single API.

Vulkan is a new generation graphics and compute API that provides high-efficiency, cross-platform access to modern GPUs used in a wide variety of devices from computers and consoles to mobile phones and embedded platforms.

There is page of GPU accelerated applications in science applications here


Updated the GPU Science page


I've just updated the GPU Science page adding a couple of new applications including cyroSPARC.


Amber16 and AmberTools16 released


AmberTools consists of several independently developed packages that work well by themselves, and with Amber itself. The suite can also be used to carry out complete molecular dynamics simulations, with either explicit water or generalized Born solvent models.

The AmberTools suite is free of charge, and its components are mostly released under the GNU General Public License (GPL). A few components are included that are in the public domain or which have other, open-source, licenses. The sander program now has the LGPL license. AmberTools is distributed in source code format, and must be compiled in order to be used. You will need C, C++ and Fortran90 compilers

The Amber16 package builds on AmberTools16 by adding the pmemd program, which resembles the sander (molecular dynamics) code in AmberTools, but provides (much) better performance on multiple CPUs, and dramatic speed improvements on GPUs. Major new features include:

Semi-Isotropic Pressure Scaling (GPU)
Charmm VDW Force Switch (CPU, GPU)
Enhanced NMR Restraint support + R^6 averaging support (GPU)
Gaussian Accelerated Molecular Dynamics (CPU, GPU)
Support for external electric fields (CPU)
Expanded umbrella sampling support (GPU)
Constant pH supported with replica exchange along pH coordinate (GPU)
Support for gas phase MD (igb=6) (CPU, GPU)
Support and significant performance improvements for the latest Kepler, Maxwell and Pascal GPUs from NVIDIA.


GPU-Accelerated Scientific Applications


There has been a discussion about GPU-Accelerated Scientific Applications on CCL so I thought it was a good time to update the GPU Science page.

Many thanks to all those who contributed.


OLCF’s second OpenACC hackathon


The GPU Science page is always pretty popular so I thought I'd thought I'd mention an upcoming event.

OLCF’s second OpenACC hackathon will take place the week of October 19th, 2015

The goal of each hackathon is for current or prospective user groups of large hybrid CPU-GPU systems to send teams of 3-6 developers along with either (1) a (potentially) scalable application that needs to be ported to GPU accelerators, or (2) an application running on accelerators which needs optimization. There will be intensive mentoring during this 5-day hands-on workshop, with the goal that the teams leave with applications running on GPUs, or at least with a clear roadmap of how to get there. Our mentors come from national laboratories, universities and vendors, and besides having extensive experience in programming with OpenACC, many of them develop the OpenACC-capable compilers and help define the OpenACC standard.

The application period is now open and closes on 3 July, 2015. Space will be limited to a maximum of eight teams, with two mentors for each team. Groups will be notified about acceptance or rejection of their application by Friday, July 31, 2015. See below how to apply. Prior GPU experience is not required! Those groups whose application successfully passes the selection process will receive further information regarding registration.


Vulkan: New graphics API


The Khronos group have announced a series of lectures describing Vulcan the new cross-platform Graphics API Vulkan: High-Efficiency GPU Graphics and Compute. Also known as the Next Generation OpenGL Initiative.

There are more details on the Kronos website.


CUDA for Mac


Nvidia have released CUDA driver 6.0.51 which is required for CUDA support on Mac OS X 10.9 Mavericks. Note: Quadro FX for Mac or GeForce for Mac must be installed prior to CUDA 6.0.51 installation

An alternative method to download the latest CUDA driver is within Mac OS environment.  Access the latest driver through System Preferences > Other > CUDA.  Click 'Install CUDA Update'.

There are a number of GPU-accelerated science applications described on the GPU Science Page.




I’ve just been sent details of this webinar.

An Overview of AMBER 14 - Creating the World's Fastest Molecular Dynamics Software Package Tuesday, May 13, 2014 9:00 AM - 10:00 AM PDT

This webinar will provide an overview of the AMBER Molecular Dynamics Software package with focus on what is new with regards to GPU acceleration in the recently released version 14. This includes details of peer-to-peer support and optimizations, which have resulted in version 14 being the fastest MD software package on commodity hardware. Benchmarks will be provided, along with recommended hardware choices. In addition, an overview of the new GPU centric features in AMBER 14 will be covered, including support for multi-dimensional replica exchange MD, hydrogen mass repartitioning, accelerated MD, Scaled MD, and support-as-a-service on Amazon Web Services. This is a joint webinar by Ross C. Walker, University of California San Diego, Scott Le Grand, Amazon Web Services, and Adrian Roitberg, University of Florida.


OpenCL training course


Simon McIntosh-Smith has just released a new OpenCL training course “HandsOnOpenCL" via Github. It Includes a comprehensive set of exercises and solutions in C, C++ & Python.

There is a list of GPU-accelerated scientific applications here.