CAVE-CL: An OpenCL version of the package for detection and quantitative analysis of internal cavities in a system of overlapping balls: Application to proteins
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文摘
Here we present the revised and newly rewritten version of our earlier published CAVE package (Buša et al., 2010) which was originally written in FORTRAN. The package has been rewritten in C language, the algorithm has been parallelized and implemented using OpenCL. This makes the program convenient to run on platforms with Graphical Processing Units (GPUs). Improvements include also some modifications/optimizations of the original algorithm. A considerable improvement in the performance of the code has been achieved. A new tool called input_structure has been added which helps the user to make the data input and conversion more easier and universal.

New version program summary

Program Title: CAVE-CL, CAVE C

Catalogue identifier: AEHC_v2_0

Program summary URL:http://cpc.cs.qub.ac.uk/summaries/aehc_v2_0.html

Program obtainable from: CPC Program Library, Queen’s University, Belfast, N. Ireland

Licensing provisions: Standard CPC license, http://cpc.cs.qub.ac.uk/licence/licence.html

No. of lines in distributed program, including test data, etc.: 32646

No. of bytes in distributed program, including test data, etc.: 444248

Distribution format: tar.gz

Programming language: C, C++, OpenCL.

Computer: PC with GPU.

Operating system: OpenCL compatible systems.

Has the code been vectorized or parallelized?: Parallelized using GPUs. A revised serial version (non GPU) is included in the package as well.

Keywords: Proteins, Solvent accessible area, Excluded volume, Cavities, Analytic method, Stereographic projection, GPGPU, OpenCL.

PACS: 82.20.Wt, 02.60.Cb, 02.70.Ns.

Classification: 16.1.

Catalogue identifier of previous version: AEHC_v1_0.

Journal reference of previous version: Comput. Phys. Commun. 181 (2010) 2116.

Does the new version supersede the previous version?: Yes

Nature of problem: Molecular structure analysis.

Solution method:

Analytical method, which uses the stereographic transformation for exact detection of internal cavities in the system of overlapping balls and numerical algorithm for calculation of the volume and the surface area of cavities.

Reasons for the new version:

This work is in line with our global efforts to modernize the protein structure related algorithms and software packages developed in our research group during last several years [1–8]. These tools are keeping to receive considerable attention from researches and they have been used in solving many interesting research problems [9,10]. Among many others, one important application has been found by the members of our team [11].

Therefore, we think that there is a demand to revise and modernize these tools and to make them more efficient. Here we follow the approach used earlier in [8] to develop a new version of the CAVE package [7]. The original CAVE package was written in FORTRAN language. One of the reasons for the new version is to rewrite it in C in order to make it more friendly to the young researchers who are not familiar with FORTRAN. Another, a more important reason, is to use the possibilities of the contemporary hardware (for example, the modern graphical cards) to improve the performance of the package. We also want to allow the user to avoid the re-compiling of the program for every molecule during multiple calculations of the array of molecules. For this purpose we are providing the possibility to use general pdb files as an input. After compiling one time, the program can receive any number of input files successively. Also, we found it necessary to go through the algorithm and to optimize, where it is possible, the memory usage and to make the algorithm more efficient.

Summary of revisions:

1.

Memory usage and language. The whole code has been ported into C and the static arrays have been replaced with dynamic memory allocation. This allows to load and handle the proteins of arbitrary size.

2.

Changes in the algorithm. Like in [8], the original method of North Pole test and molecule rotation [4] has been changed. The details of implementation and the benefits from this change are properly described in [8] and we find it not necessary to repeat it here.

3.

New tool. A module called input_structure which takes as an input a protein structure file in the format compatible with Protein Data Bank (pdb) [12] has been adopted from [8]. Using external tool allows users to create their own mappings of atoms and radii without re-compiling the module input_structure itself or the CAVE.

It is the user’s responsibility to assign proper radii to each type of atoms. One can use any of the published standard sets of radii (see for example, [13–17]). Alternatively, the user can assign his own values for radii immediately in the module input_structure. The radii are assigned in a special file with extension pds (see the documentation) which consists of lines like this: ATOM CA ALA 2.0 which is read as “the Cα atom of Alanine has radius 2.0 Å”.

4.

Some computational tricks. In several parts of the program square roots were replaced by second powers and calls of sin and cos functions were replaced by calls to sincos allowing for further speed-up (in comparison to original FORTRAN version).

The typical value of the relative error between results obtained by original (FORTRAN), C, and OpenCL versions was between 10−8 and 10−10 and it never exceeded 10−5. Small differences in results can be due to the implementation of compiler and specially in case of OpenCL also in the implementation of arithmetic by the GPU vendor.

Table 1.

Speed-up of C and OpenCL versions of the program CAVE when compared to the original (FORTRAN) version calculated using GNU Fortran (gfort) and Intel® FORTRAN (ifort).

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