Program title: Parallel AFMPB
Catalogue identifier: AEGB_v2_0
Program summary URL:class="interref" data-locatorType="url" data-locatorKey="http://cpc.cs.qub.ac.uk/summaries/AEGB_v2_0.html">http://cpc.cs.qub.ac.uk/summaries/AEGB_v2_0.html
Program obtainable from: CPC Program Library, Queen’s University, Belfast, N. Ireland
Licensing provisions: GNU General Public License, version 2
No. of lines in distributed program, including test data, etc.: 40558
No. of bytes in distributed program, including test data, etc.: 2349976
Distribution format: tar.gz
Programming language: Mixed C and Fortran, Compiler: Intel or GNU with Cilk Plus enabled.
Computer: Any, but the code is mainly designed for multicore architectures.
Operating system: Linux.
RAM: Depends on the size of the discretized biomolecular system.
Classification: 3.
Catalogue identifier of previous version: AEGB_v1_1
Journal reference of previous version: Comput. Phys. Comm. 184 (2013) 2618
External routines: Users are allowed to use external routines/libraries (e.g., MSMS [6] and TMSMesh [4]) to generate compatible surface mesh input data if they choose not to use the embedded automatic mesh generation tool in the package. Post-processing tools such as VCMM [5] and VMD [3] can also be used for visualization and analyzing results.
The package uses two subprograms: (1) The iterative Krylov subspace solver, SPARSKIT, from Yousef Saad [2]; and (2) Cilk-based parallel fast multipole methods from FMMSuite [1].
Does the new version supersede the previous version? Yes
Nature of problem: Numerical solution of the linearized Poisson–Boltzmann equation that describes electrostatic interactions of molecular systems in ionic solutions.
Solution method: The linearized Poisson–Boltzmann equation is reformulated as a boundary integral equation and is subsequently discretized using the node-patch scheme. The resulting linear system is solved using Krylov subspace solvers iteratively. The reformulation of the equation provides an upper bound for the number of iterations. Within each iteration, the matrix–vector multiplication is accelerated using the adaptive plane-wave expansion based fast multipole methods. The majority of the codes are parallelized using the Cilk runtime.
Reasons for new version: New functions are added and a few old functions like force calculations are removed. The algorithm is parallelized and most parts of the code are rewritten.
Summary of revisions: The computation is parallelized and an automatic mesh generation method for BEM is added.
Restrictions: The program has only been tested on machines running Linux operating system.
Additional comments: The Cilk runtime used in the development and testing is from the Intel compiler Suite. The GNU Cilk Plus and Cilk Plus/LLVM branches have not been tested.
Running time: The running time depends on the number of discretized elements (N) and their distribution. It also depends on the number of cores used in the computation.
References:
[1] class="interref" data-locatorType="url" data-locatorKey="http://www.fastmultipole.org/">http://www.fastmultipole.org/.
[2] class="interref" data-locatorType="url" data-locatorKey="http://www-users.cs.umn.edu/~saad/software/">http://www-users.cs.umn.edu/~saad/software/.
[3] class="interref" data-locatorType="url" data-locatorKey="http://www.ks.uiuc.edu/Research/vmd/">http://www.ks.uiuc.edu/Research/vmd/.
[4] class="interref" data-locatorType="url" data-locatorKey="http://www.continuummodel.org">http://www.continuummodel.org.
[5] S. Bai, B. Lu, VCMM: A visual tool for continuum molecular modeling. J. Mol. Graph. Model. 50 (2014) 44–49.
[6] Scanner, F. Michel, Olson, J. Arthur, Spehner, J. Claude, Reduced surface: An efficient way to compute molecular surfaces. Biopolymers 38 (1996) 305–320.