IQ-TREE : ARM NEON Implementation
IQ-TREE is a fast and effective stochastic algorithm to inferphylogenetic trees by maximum likelihood. It contains Intel intrinsics, and this project provides a mapping layer between those intrinsics and the underlying hardware, in order to port the software to work correctly on ARM NEON instruction set architecture.
Process included modifying IQ-TREE code to coerce the compiler into compiling for SSE4.2, adding functionality to recognise NEON ISA, and extending funtionality in sse2neon.h to include all missing intrinsics.
Licence
Copyright © 2020 Joshua Measure-Hughes
Written for the Advanced Computing Research Centre, University of Bristol.
Licensed under the MIT License, (the “License”); you may not use this file except in compliance with the License.
The License applies to unique documents to this implementation, and not to those present in [1], [2] and [3]. Additional functionality in [2] has been labelled and is at the end of the document. The original Licenses for [1], [2], and [3] apply otherwise.
Unless required by applicable law or agreed to in writing, software distributed under the License is distributed on an “AS IS” BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. See the License for the specific language governing permissions and limitations under the License.
References
[1] B.Q. Minh, H.A. Schmidt, O. Chernomor, D.Schrempf, M.D. Woodhams, A. von Haeseler, R.Lanfear (2020) IQ-TREE 2:New models andefficient methods for phylogenetic inference inthe genomic era. Mol. Biol. Evol., 37:1530-1534.https://doi.org/10.1093/molbev/msaa015
[2] J.W. Ratcliff, B. Rowlett, K. Fast, E. van Beur-den, A. Potylitsin, H. Gamaarachchi, J. Huang,M. Cheng, M. James, D. Hussey, S. Pop,Developer Ecosystem Engineering, D. Kutenin,F. Turban,P-H. Hung,Y-H. Yang (2020)sse2neon: A C/C++ header file that converts In-tel SSE intrinsics to Arm/Aarch64 NEON intrinsics.https://github.com/DLTcollab/sse2neon
[3] B. Jacob (founder), G. Guennebaud (guru),et al. (2020) Eigen is a C++ template library for linear algebra: matrices, vectors, numerical solvers,and related algorithms.http://eigen.tuxfamily.org/index.php
[4] Intel Intrinsics Guide.https://software.intel.com/sites/landingpage/IntrinsicsGuide/
[5] ARM NEON Intrinsics Reference.https://developer.arm.com/architectures/instruction-sets/simd-isas/neon/intrinsics
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