From 99362eb36805ee9b66bb8d8c7ea20c6348f62c46 Mon Sep 17 00:00:00 2001 From: Andrei Poenaru Date: Thu, 22 Apr 2021 13:09:54 +0300 Subject: [PATCH] Rename to miniBUDE and add preferred citation --- README.md | 10 ++++++++-- cuda/README.md | 4 ++-- data/README.md | 2 +- kokkos/README.md | 4 ++-- makedeck/README.md | 6 +++--- openacc/README.md | 4 ++-- opencl/README.md | 4 ++-- openmp-target/README.md | 4 ++-- openmp/README.md | 4 ++-- sycl/README.md | 4 ++-- 10 files changed, 26 insertions(+), 20 deletions(-) diff --git a/README.md b/README.md index 2740e73..582ea44 100644 --- a/README.md +++ b/README.md @@ -1,6 +1,6 @@ -# BUDE Benchmark +# miniBUDE -This repository contains implementation of the core computation of the Bristol University Docking Engine (BUDE) in different HPC programming models. +This mini-app is an implementation of the core computation of the Bristol University Docking Engine (BUDE) in different HPC programming models. The benchmark is a virtual screening run of the NDM-1 protein and runs the energy evaluation for a single generation of poses repeatedly, for a configurable number of iterations. Increasing the iteration count has similar performance effects to docking multiple ligands back-to-back in a production BUDE docking run. @@ -43,3 +43,9 @@ Two input decks are included in this repository: They are located in the [`data`](data/) directory, and `bm1` is run by default. All implementations accept a `--deck` parameter to specify an input deck directory. See [`makedeck`](makedeck/) for how to generate additional input decks. + +## Citing + +Please cite miniBUDE using the following reference: + +> Andrei Poenaru, Wei-Chen Lin and Simon McIntosh-Smith. ‘A Performance Analysis of Modern Parallel Programming Models Using a Compute-Bound Application’. In: 36th International Conference, ISC High Performance 2021. Frankfurt, Germany, 2021. In press. diff --git a/cuda/README.md b/cuda/README.md index f315e07..02d297e 100644 --- a/cuda/README.md +++ b/cuda/README.md @@ -1,6 +1,6 @@ -# BUDE CUDA +# miniBUDE CUDA -This is a GPU implementation of BUDE using CUDA. +This is a GPU implementation of miniBUDE using CUDA. ## Building diff --git a/data/README.md b/data/README.md index f0de8b0..2058514 100644 --- a/data/README.md +++ b/data/README.md @@ -1,4 +1,4 @@ -# BUDE Benchmark Data +# miniBUDE Benchmark Data This directory contains input data and reference output. Each sub-directory is a self-contained test case. diff --git a/kokkos/README.md b/kokkos/README.md index 85ecd8c..7740f7d 100644 --- a/kokkos/README.md +++ b/kokkos/README.md @@ -1,6 +1,6 @@ -# BUDE Kokkos +# miniBUDE Kokkos -This is an implementation of BUDE using Kokkos. +This is an implementation of miniBUDE using Kokkos. ## Building diff --git a/makedeck/README.md b/makedeck/README.md index 4515dc8..1de2c2d 100644 --- a/makedeck/README.md +++ b/makedeck/README.md @@ -1,6 +1,6 @@ -# BUDE makedeck +# miniBUDE makedeck -This program generates input decks for the BUDE benchmark from a set of mol2 and bhff files. +This program generates input decks for miniBUDE from a set of mol2 and bhff files. ## Building @@ -55,7 +55,7 @@ params.txt # contains original program arguments used to generate this deck ref_energies.out # contains reference energies used for verification ``` -The input deck directory can then be specified in all BUDE implementations: +The input deck directory can then be specified in all miniBUDE implementations: ./bude --deck output diff --git a/openacc/README.md b/openacc/README.md index 9b3c028..8fc2faa 100644 --- a/openacc/README.md +++ b/openacc/README.md @@ -1,6 +1,6 @@ -# BUDE OpenACC +# miniBUDE OpenACC -This is a GPU implementation of BUDE using OpenACC. +This is a GPU implementation of miniBUDE using OpenACC. ## Building diff --git a/opencl/README.md b/opencl/README.md index 6c10a9b..970c977 100644 --- a/opencl/README.md +++ b/opencl/README.md @@ -1,6 +1,6 @@ -# BUDE OpenCL +# miniBUDE OpenCL -This is a GPU implementation of BUDE using OpenCL. +This is a GPU implementation of miniBUDE using OpenCL. ## Building diff --git a/openmp-target/README.md b/openmp-target/README.md index 97e6ccf..d5d8e29 100644 --- a/openmp-target/README.md +++ b/openmp-target/README.md @@ -1,6 +1,6 @@ -# BUDE OpenMP Target +# miniBUDE OpenMP Target -This is a GPU implementation of BUDE using OpenMP target. +This is a GPU implementation of miniBUDE using OpenMP target. ## Building diff --git a/openmp/README.md b/openmp/README.md index 7835aab..ebc1d27 100644 --- a/openmp/README.md +++ b/openmp/README.md @@ -1,6 +1,6 @@ -# BUDE OpenMP +# miniBUDE OpenMP -This is a CPU implementation of BUDE using OpenMP 3. +This is a CPU implementation of miniBUDE using OpenMP 3. ## Building diff --git a/sycl/README.md b/sycl/README.md index 5943a3b..492cf9c 100644 --- a/sycl/README.md +++ b/sycl/README.md @@ -1,6 +1,6 @@ -# BUDE SYCL +# miniBUDE SYCL -This is a CPU implementation of BUDE using SYCL. +This is a CPU implementation of miniBUDE using SYCL. ## Building