Cores

From FaHWiki

Introduction

The 'core' is the program that performs the calculations. The same core is used by various versions of the client and is automatically updated whenever necessary. This provides an easy way for the scientific calculations to be improved without requiring you to install a new version of the client.

There are several different cores:

FahCore #	Scientific Name	Project Summary Name	Special Optimizations	Client
FahCore_11	GPU2	GROGPU2	ATI CAL / NV CUDA	GPU client
FahCore_12	GPU2	ATI-DEV	ATI DEVELOPMENT	GPU client
FahCore_13	GPU2	NVIDIA-DEV	NVIDIA DEVELOPMENT	GPU client
FahCore_14	GPU2	GroGPU2-MT	NV CUDA	GPU client
FahCore_78	Gromacs	GROMACS	SSE	CPU client
FahCore_79	Double Gromacs	DGROMACS	SSE2	CPU client
FahCore_7a	GB Gromacs	GBGROMACS	SSE	CPU client
FahCore_7b	Double Gromacs B	DGROMACSB	SSE2	CPU client
FahCore_7c	Double Gromacs C	DGROMACSC	SSE2	CPU client
FahCore_80	Gromacs SREM	GROST	SSE	CPU client
FahCore_81	Gromacs Simulated Tempering	GROSIMT	SSE	CPU client
FahCore_82	Amber	AMBER	None	CPU client
FahCore_a0	Gromacs 33	GROMACS33	SSE	CPU client
FahCore_a1	Gromacs SMP (Version 1.74)	GRO-SMP	SSE, SMP multicore	SMP client
FahCore_a2	Gromacs SMP (Version 1.94)	GROCVS	SSE, SMP multicore	SMP client
Unknown	Gromacs PS3	GRO-PS3	Cell	PS3 client
...Retired...
FahCore_10	GPU	GROGPU	Retired
FahCore_65	Tinker	TINKER	Retired
FahCore_96	QMD	QMD	Retired

Note: The numbers associated with the names of the cores are arbitrary identifiers. They do not indicate a version number which can be used to tell an "old" core from a "new" one. Version 1.86 of FahCore_78 may or may not be older than Version 2.53 of FahCore_65.

See also: Core MD5 Sums

Gromacs core

Gromacs (Groningen Machine for Chemical Simulations) is a single-precision scientific core that is used for the majority of F@H calculations. It is developed by the University of Groningen under the GPL and is writen in Fortran77-based GROMOS in C. Gromacs takes advantage of SIMD, including SSE and AltiVec instructions in supported processors to provide nearly a threefold increase in calculation speed. Modern processors such as the Pentium 3, Pentium 4, Athlon XP and Athlon 64 series, as well as their mobile counterparts, are SSE capable. The PowerPC G4 and G5 series are Altivec capable.

More information can be found here:
http://folding.stanford.edu/gromacs.html
Gromacs Home page

Core Information

Core number	78
Core Name	Folding@Home Gromacs Core
Operating System/Architecture	Windows/x86, Linux/x86, Mac OS X/PPC

Double Gromacs core

The DoubleGromacs core is very similiar to the Gromacs core except it performs double-precision rather than single-precision calculations. DoubleGromacs takes advantage of SSE2 instructions in supported processors to provide about a 2x increase in calculation speed. Newer processors such as the Pentium 4 and the Athlon 64 have SSE2 capability.

Core Information

Core number	79
Core Name	Folding@Home Double Gromacs Core
Operating System/Architecture	Windows/x86, Linux/x86, Mac OS X/PPC

GB Gromacs core

The GB Gromacs core is very similiar to the Gromacs core. The Pande Group added the "Generalized Born implicit solvent" model to GB Gromacs codebase; this should make it possible to drop or reduce the use of Tinker in the future.

Core Information

Core number	7a
Core Name	Folding@Home GB Gromacs Core
Operating System/Architecture	Windows/x86, Linux/x86, Mac OS X/PPC

Double Gromacs B core

The Double Gromacs B core is very similiar to the Double Gromacs core. This new FahCore_7b has several scientific additions to the core. Initially released only to the Linux platform in August 2007, it will eventually be available for all platforms.

Core Information

Core number	7b
Core Name	Folding@Home Double Gromacs Core B
Operating System/Architecture	Windows/x86, Linux/x86, Mac OS X/PPC

Double Gromacs C core

The Double Gromacs C core is very similiar to the Double Gromacs core. Initially released for Linux and Windows in April 2008.

Core Information

Core number	7c
Core Name	Folding@Home Double Gromacs Core C
Operating System/Architecture	Windows/x86, Linux/x86, Linux/x86_64

Gromacs 33 core

The Gromacs 33 core contains features from more recent versions of Gromacs which have been ported to Folding@home, allowing a broader range of simulations to be run.

Core Information

Core number	a0
Core Name	Folding@Home Gromacs 3.3 Core
Operating System/Architecture	Windows/x86, Linux/x86, Mac OS X/x86

Gromacs SMP core

The Gromacs SMP core supports running on multiprocessor or multicore processor systems. This core is currently available for Mac OS X on Intel, 64-bit Linux and Windows. 32-bit Linux support is being worked on.

This core makes running multiple clients for each CPU or CPU-core obsolete. The core will make use of the two or more cores available in the system.

See: Folding-community: SMP client open beta and Folding@home on multi-core/SMP boxes (SMP FAQ)

Core Information

Core number	a1
Core Name	Folding@Home Gromacs SMP Core
Operating System/Architecture	Linux/x86_64, Mac OS X/x86, Windows/x86

Gromacs CVS SMP core

The Gromacs CVS SMP core supports running on multiprocessor or multicore processor systems. This core is currently available for only Mac OS X on Intel and 64-bit Linux. A Windows version, and a 32-bit Linux support is being worked on.

This core makes running multiple clients for each CPU or CPU-core obsolete. The core will make use of the two or more cores available in the system. It will also support more than 4 cores in the future.

See: Folding-community: SMP client open beta and Folding@home on multi-core/SMP boxes (SMP FAQ)

This core looks almost identical to the Gromacs SMP core (a1) because it uses mostly the same code base from Gromacs. The Gromacs CVS SMP core (a2) only uses more recent code from Gromacs than the Gromacs SMP core (a1) core does, and support some more features (like more CPUs) than the Gromacs SMP core (a1) does at current.

Core Information

Core number	a2
Core Name	Folding@Home Gromacs SMP Core
Operating System/Architecture	Linux/x86_64, Mac OS X/x86, Windows/x86

Tinker core

The Tinker core was the second-most used core for F@H calculations (superseded by AMBER). It does not use any special instructions to accelerate floating-point operations on modern processors (such as SSE or 3dNow+). WorkUnits that use the Tinker core usually perform well on AMD processors.

Core Information

Core number	65
Core Name	Folding@Home Client Core TINKER: Software Tools for Molecular Design
Operating System/Architecture	Windows/x86, Linux/x86, Mac OS X/PPC

QMD core

QMD uses a quantum chemical method for calculations and uses a large amount of memory (sometimes in excess of 512 MiB of RAM).

Note: Because of the licensing issues (FAH & QMD & AMD64 & SSE2) QMD WUs are currently not assigned to AMD CPUs.

Note: The QMD core is multi-thread capable. Folding-community: OMP_NUM_THREADS

There are no projects at the moment utilizing the QMD core: Folding-community: Vijay Pandes post in "Where did they go?? [QMDs"]

But it may become active again, see Folding-community: Vijay Pande's post in: What are we ACTUALLY work on?

More information can be found here: http://folding.stanford.edu/QMD.html

Core Information

Core number	96
Core Name	Folding@Home QMD Core
Operating System/Architecture	Windows/x86, Linux/x86

AMBER core

The AMBER core (Assisted Model Building and Energy Refinement) is a molecular dynamics program originally developed by Peter Kollman's group at the University of California, San Francisco. Its main use is in force field calculations. The project is now coordinated by David A. Case at Scripps Research Institute. The AMBER core does not take advantage of SSE to provide an increase in calculation speed, but hopefully will use SSE2 in the future.

There is a project to integrate at least a portion of the AMBER force field algorithm into the Gromacs core (ffamber). It is not clear if this will negate the use of the AMBER core.
http://folding.stanford.edu/ffamber/

More information can be found here:
http://folding.stanford.edu/AMBER.html
http://en.wikipedia.org/wiki/AMBER

Core Information

Core number	82
Core Name	Folding@Home PMD Core
Operating System/Architecture	Windows/x86, Linux/x86

GPU core

The GPU core (Graphics Processor Unit) uses the graphics chip of modern video cards to do molecular dynamics. The first GPU client supports ATI 1xxx series of GPUs.
"The GPU Gromacs core isn't a port of Gromacs, but rather we've taken key elements from Gromacs we need and enhanced them based on the unique capabities of GPU's. Thus, it's really a new and different core on the inside, but with wrapped Gromacs on the outside" -- Vijay Pande, Getting close to the GPU beta launch

Core Information

Core number	10
Core Name	Folding@Home GPU Core
Operating System/Architecture	Windows/x86

GPU2 core

The GPU core (Graphics Processor Unit) uses the graphics chip of modern video cards to do molecular dynamics. This second generation GPU client supports ATI 2xxx/3xxx or later, and nVidia 8xxx or later series of GPUs. This new client uses AMD's CAL or nVidia's CUDA instead of Microsoft's DX9.

Core Information

Core number	11
Core Name	Folding@home GPU2 Core
Operating System/Architecture	Windows/x86

Gromacs SREM core

The Gromacs Serial Replica Exchange Method core, also known as GroST (Gromacs Serial replica exchange with Temperatures), uses Replica Exchange Method in its simulations also known as REMD, Replica Exchange Molecular Dynamics.

See: Folding-community: uncle_fungus in GROST

See also: "Replica-exchange molecular dynamics method for protein folding"

Core Information

Core number	80
Core Name	Folding@Home Gromacs SREM Core
Operating System/Architecture	Windows/x86, Linux/x86

Gromacs Simulated Tempering core

GROSimT is a new (May 2007) Gromacs core that performs simulated tempering. Simulated tempering is one of the sampling algorithms, of which the basic idea is to enhance sampling by periodically raising and lowering temperature. Using this new core, we are hoping to sample more efficiently the transitions between folded and unfolded conformations of proteins.

See also: Simulated tempering: a new Monte Carlo scheme. Authors:, Marinari, E.; Parisi, G. Publication:, Europhysics Letters, Vol. 19, p.451.

Core Information

Core number	81
Core Name	Folding@Home Gromacs Simulated Tempering Core
Operating System/Architecture	Linux/x86, Windows/x86

Links

• Folding@home FAQ, you can learn about the cores
• Folding@home Settings FAQ
• QMD uses CPMD, this is its home page
• GROMACS home page
• Tinker home page
• Downloading FAH Core files manually