Initial commit: OpenMP and OpenCL implementations

This code has been ported from
https://github.com/UoB-HPC/bude-benchmark, the armv8 and master
branches, respectively.

CONTRIBUTING.md

@@ -0,0 +1,18 @@
+# Contributing
+
+## Commit Messages
+
+When commiting to this repository, prefix your commit messages with the implementation(s) affected.
+When changing top-level files, a prefix is not necessary
+The following are examples of acceptable commit messaged:
+
+    openmp: Code change
+    openmp, opencl: Code change
+    all: Switch to CMake
+    data: Data change
+    Update README
+
+## Compiler and Platform Support
+
+Each implementation's README should detail the compilers supported and any platform restrictions.
+

LICENSE.txt

@@ -0,0 +1,219 @@
+                                 Apache License
+                           Version 2.0, January 2004
+                        http://www.apache.org/licenses/
+
+    TERMS AND CONDITIONS FOR USE, REPRODUCTION, AND DISTRIBUTION
+
+    1. Definitions.
+
+      "License" shall mean the terms and conditions for use, reproduction,
+      and distribution as defined by Sections 1 through 9 of this document.
+
+      "Licensor" shall mean the copyright owner or entity authorized by
+      the copyright owner that is granting the License.
+
+      "Legal Entity" shall mean the union of the acting entity and all
+      other entities that control, are controlled by, or are under common
+      control with that entity. For the purposes of this definition,
+      "control" means (i) the power, direct or indirect, to cause the
+      direction or management of such entity, whether by contract or
+      otherwise, or (ii) ownership of fifty percent (50%) or more of the
+      outstanding shares, or (iii) beneficial ownership of such entity.
+
+      "You" (or "Your") shall mean an individual or Legal Entity
+      exercising permissions granted by this License.
+
+      "Source" form shall mean the preferred form for making modifications,
+      including but not limited to software source code, documentation
+      source, and configuration files.
+
+      "Object" form shall mean any form resulting from mechanical
+      transformation or translation of a Source form, including but
+      not limited to compiled object code, generated documentation,
+      and conversions to other media types.
+
+      "Work" shall mean the work of authorship, whether in Source or
+      Object form, made available under the License, as indicated by a
+      copyright notice that is included in or attached to the work
+      (an example is provided in the Appendix below).
+
+      "Derivative Works" shall mean any work, whether in Source or Object
+      form, that is based on (or derived from) the Work and for which the
+      editorial revisions, annotations, elaborations, or other modifications
+      represent, as a whole, an original work of authorship. For the purposes
+      of this License, Derivative Works shall not include works that remain
+      separable from, or merely link (or bind by name) to the interfaces of,
+      the Work and Derivative Works thereof.
+
+      "Contribution" shall mean any work of authorship, including
+      the original version of the Work and any modifications or additions
+      to that Work or Derivative Works thereof, that is intentionally
+      submitted to Licensor for inclusion in the Work by the copyright owner
+      or by an individual or Legal Entity authorized to submit on behalf of
+      the copyright owner. For the purposes of this definition, "submitted"
+      means any form of electronic, verbal, or written communication sent
+      to the Licensor or its representatives, including but not limited to
+      communication on electronic mailing lists, source code control systems,
+      and issue tracking systems that are managed by, or on behalf of, the
+      Licensor for the purpose of discussing and improving the Work, but
+      excluding communication that is conspicuously marked or otherwise
+      designated in writing by the copyright owner as "Not a Contribution."
+
+      "Contributor" shall mean Licensor and any individual or Legal Entity
+      on behalf of whom a Contribution has been received by Licensor and
+      subsequently incorporated within the Work.
+
+    2. Grant of Copyright License. Subject to the terms and conditions of
+      this License, each Contributor hereby grants to You a perpetual,
+      worldwide, non-exclusive, no-charge, royalty-free, irrevocable
+      copyright license to reproduce, prepare Derivative Works of,
+      publicly display, publicly perform, sublicense, and distribute the
+      Work and such Derivative Works in Source or Object form.
+
+    3. Grant of Patent License. Subject to the terms and conditions of
+      this License, each Contributor hereby grants to You a perpetual,
+      worldwide, non-exclusive, no-charge, royalty-free, irrevocable
+      (except as stated in this section) patent license to make, have made,
+      use, offer to sell, sell, import, and otherwise transfer the Work,
+      where such license applies only to those patent claims licensable
+      by such Contributor that are necessarily infringed by their
+      Contribution(s) alone or by combination of their Contribution(s)
+      with the Work to which such Contribution(s) was submitted. If You
+      institute patent litigation against any entity (including a
+      cross-claim or counterclaim in a lawsuit) alleging that the Work
+      or a Contribution incorporated within the Work constitutes direct
+      or contributory patent infringement, then any patent licenses
+      granted to You under this License for that Work shall terminate
+      as of the date such litigation is filed.
+
+    4. Redistribution. You may reproduce and distribute copies of the
+      Work or Derivative Works thereof in any medium, with or without
+      modifications, and in Source or Object form, provided that You
+      meet the following conditions:
+
+      (a) You must give any other recipients of the Work or
+          Derivative Works a copy of this License; and
+
+      (b) You must cause any modified files to carry prominent notices
+          stating that You changed the files; and
+
+      (c) You must retain, in the Source form of any Derivative Works
+          that You distribute, all copyright, patent, trademark, and
+          attribution notices from the Source form of the Work,
+          excluding those notices that do not pertain to any part of
+          the Derivative Works; and
+
+      (d) If the Work includes a "NOTICE" text file as part of its
+          distribution, then any Derivative Works that You distribute must
+          include a readable copy of the attribution notices contained
+          within such NOTICE file, excluding those notices that do not
+          pertain to any part of the Derivative Works, in at least one
+          of the following places: within a NOTICE text file distributed
+          as part of the Derivative Works; within the Source form or
+          documentation, if provided along with the Derivative Works; or,
+          within a display generated by the Derivative Works, if and
+          wherever such third-party notices normally appear. The contents
+          of the NOTICE file are for informational purposes only and
+          do not modify the License. You may add Your own attribution
+          notices within Derivative Works that You distribute, alongside
+          or as an addendum to the NOTICE text from the Work, provided
+          that such additional attribution notices cannot be construed
+          as modifying the License.
+
+      You may add Your own copyright statement to Your modifications and
+      may provide additional or different license terms and conditions
+      for use, reproduction, or distribution of Your modifications, or
+      for any such Derivative Works as a whole, provided Your use,
+      reproduction, and distribution of the Work otherwise complies with
+      the conditions stated in this License.
+
+    5. Submission of Contributions. Unless You explicitly state otherwise,
+      any Contribution intentionally submitted for inclusion in the Work
+      by You to the Licensor shall be under the terms and conditions of
+      this License, without any additional terms or conditions.
+      Notwithstanding the above, nothing herein shall supersede or modify
+      the terms of any separate license agreement you may have executed
+      with Licensor regarding such Contributions.
+
+    6. Trademarks. This License does not grant permission to use the trade
+      names, trademarks, service marks, or product names of the Licensor,
+      except as required for reasonable and customary use in describing the
+      origin of the Work and reproducing the content of the NOTICE file.
+
+    7. Disclaimer of Warranty. Unless required by applicable law or
+      agreed to in writing, Licensor provides the Work (and each
+      Contributor provides its Contributions) on an "AS IS" BASIS,
+      WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or
+      implied, including, without limitation, any warranties or conditions
+      of TITLE, NON-INFRINGEMENT, MERCHANTABILITY, or FITNESS FOR A
+      PARTICULAR PURPOSE. You are solely responsible for determining the
+      appropriateness of using or redistributing the Work and assume any
+      risks associated with Your exercise of permissions under this License.
+
+    8. Limitation of Liability. In no event and under no legal theory,
+      whether in tort (including negligence), contract, or otherwise,
+      unless required by applicable law (such as deliberate and grossly
+      negligent acts) or agreed to in writing, shall any Contributor be
+      liable to You for damages, including any direct, indirect, special,
+      incidental, or consequential damages of any character arising as a
+      result of this License or out of the use or inability to use the
+      Work (including but not limited to damages for loss of goodwill,
+      work stoppage, computer failure or malfunction, or any and all
+      other commercial damages or losses), even if such Contributor
+      has been advised of the possibility of such damages.
+
+    9. Accepting Warranty or Additional Liability. While redistributing
+      the Work or Derivative Works thereof, You may choose to offer,
+      and charge a fee for, acceptance of support, warranty, indemnity,
+      or other liability obligations and/or rights consistent with this
+      License. However, in accepting such obligations, You may act only
+      on Your own behalf and on Your sole responsibility, not on behalf
+      of any other Contributor, and only if You agree to indemnify,
+      defend, and hold each Contributor harmless for any liability
+      incurred by, or claims asserted against, such Contributor by reason
+      of your accepting any such warranty or additional liability.
+
+    END OF TERMS AND CONDITIONS
+
+    APPENDIX: How to apply the Apache License to your work.
+
+      To apply the Apache License to your work, attach the following
+      boilerplate notice, with the fields enclosed by brackets "[]"
+      replaced with your own identifying information. (Don't include
+      the brackets!)  The text should be enclosed in the appropriate
+      comment syntax for the file format. We also recommend that a
+      file or class name and description of purpose be included on the
+      same "printed page" as the copyright notice for easier
+      identification within third-party archives.
+
+    Copyright 2020 University of Bristol High Performance Computing Group
+
+    Licensed under the Apache License, Version 2.0 (the "License");
+    you may not use this file except in compliance with the License.
+    You may obtain a copy of the License at
+
+       http://www.apache.org/licenses/LICENSE-2.0
+
+    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.
+
+
+--- LLVM Exceptions to the Apache 2.0 License ----
+
+As an exception, if, as a result of your compiling your source code, portions
+of this Software are embedded into an Object form of such source code, you
+may redistribute such embedded portions in such Object form without complying
+with the conditions of Sections 4(a), 4(b) and 4(d) of the License.
+
+In addition, if you combine or link compiled forms of this Software with
+software that is licensed under the GPLv2 ("Combined Software") and if a
+court of competent jurisdiction determines that the patent provision (Section
+3), the indemnity provision (Section 9) or other Section of the License
+conflicts with the conditions of the GPLv2, you may retroactively and
+prospectively choose to deem waived or otherwise exclude such Section(s) of
+the License, but only in their entirety and only with respect to the Combined
+Software.
+

README.md

@@ -0,0 +1,28 @@
+# BUDE Benchmark
+
+This repository contains 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.
+
+## Structure
+
+The top-level `data` directory contains the input common to implementations.
+Each other subdirectory contains a separate implementation:
+
+- [OpenMP](openmp/) for CPUs
+- [OpenCL](opencl/) for GPUs
+
+## Building
+
+To build with the default options, type `make` in an implementation directory.
+There are options to choose the compiler used and the architecture targetted.
+
+Refer to each implementation's README for further build instructions.
+
+## Running
+
+To run with the default options, run the binary without any flags.
+To adjust the run time, use `-i` to set the number of iterations.
+For very short runs, e.g. for simulation, use set `-n 1024` to reduce the number of poses.
+
+Refer to each implementation's README for further run instructions.

opencl/.gitignore

@@ -0,0 +1 @@
+bude-opencl*

opencl/Makefile

@@ -0,0 +1,25 @@
+CC      = gcc
+CFLAGS  = -std=c99 -Wall -O3 -ffast-math -march=native
+LDFLAGS =
+
+PLATFORM = $(shell uname -s)
+ifeq ($(PLATFORM), Darwin)
+	LDFLAGS = -framework OpenCL
+else
+	CFLAGS += -fopenmp
+	LDFLAGS = -lOpenCL -lm
+endif
+
+# -------
+
+EXE = bude-opencl
+
+.PHONY: all $(EXE) clean
+
+all: $(EXE)
+
+$(EXE): bude.c
+	$(CC) $(CFLAGS) bude.c $(LDFLAGS) -o $@
+
+clean:
+	rm -f $(EXE)

opencl/README.md

@@ -0,0 +1,40 @@
+# BUDE OpenCL
+
+This is a GPU implementation of BUDE using OpenCL.
+
+## Building
+
+Select the compiler you want to use and pass it to Make:
+
+```
+make COMPILER=GNU
+```
+
+The supported compilers names are: `ARM`, `CLANG`, `CRAY`, `GNU`, `INTEL`.
+
+### Target Architecture
+
+By default, the native architecture is targetted, but this can be changed by setting the `ARCH` parameter to the name of the target processor.
+For example, the following are both valid:
+
+```
+make COMPILER=GNU ARCH=thunderx2t99
+make COMPILER=GNU ARCH=skylake-avx512
+```
+
+### Block Sizes
+
+This implementation includes a tunable block size similar to OpenCL workgroups.
+The default value is `64`, which is suitable for 512-bit vectors, e.g. in Skylake or A64FX, but higher values may sometimes be beneficial.
+For 128-bit vectors, `16` is a good choice.
+
+This parameter can be set using the `WGSIZE` parameter, as follows:
+
+```
+make COMPILER=GNU ARCH=thunderx2t99 WGSIZE=16
+```
+
+## Running
+
+The `-n` and `-i` parameters are available, along with several OpenCL-specific options for device selection and run-time tuning.
+Run `bude-opencl -h` for a list of all available flags.