Updating docs in master

CONTRIBUTING.md

@@ -0,0 +1,92 @@
+# Contributing
+
+When contributing to this repository, please first discuss the change you wish to make via issue,
+email, or any other method with the owners of this repository before making a change.
+
+Please note we have a code of conduct, please follow it in all your interactions with the project.
+
+## Pull Request Process
+
+1. Ensure any install or build dependencies are removed before the end of the layer when doing a
+   build.
+2. Update the README.md with details of changes to the interface, this includes new environment
+   variables, exposed ports, useful file locations and container parameters.
+3. Increase the version numbers in any examples files and the README.md to the new version that this
+   Pull Request would represent. The versioning scheme we use is [SemVer](http://semver.org/).
+4. You may merge the Pull Request in once you have the sign-off of two other developers, or if you
+   do not have permission to do that, you may request the second reviewer to merge it for you.
+
+## Code of Conduct
+
+### Our Pledge
+
+In the interest of fostering an open and welcoming environment, we as
+contributors and maintainers pledge to making participation in our project and
+our community a harassment-free experience for everyone, regardless of age, body
+size, disability, ethnicity, gender identity and expression, level of experience,
+nationality, personal appearance, race, religion, or sexual identity and
+orientation.
+
+### Our Standards
+
+Examples of behavior that contributes to creating a positive environment
+include:
+
+* Using welcoming and inclusive language
+* Being respectful of differing viewpoints and experiences
+* Gracefully accepting constructive criticism
+* Focusing on what is best for the community
+* Showing empathy towards other community members
+
+Examples of unacceptable behavior by participants include:
+
+* The use of sexualized language or imagery and unwelcome sexual attention or
+advances
+* Trolling, insulting/derogatory comments, and personal or political attacks
+* Public or private harassment
+* Publishing others' private information, such as a physical or electronic
+  address, without explicit permission
+* Other conduct which could reasonably be considered inappropriate in a
+  professional setting
+
+### Our Responsibilities
+
+Project maintainers are responsible for clarifying the standards of acceptable
+behavior and are expected to take appropriate and fair corrective action in
+response to any instances of unacceptable behavior.
+
+Project maintainers have the right and responsibility to remove, edit, or
+reject comments, commits, code, wiki edits, issues, and other contributions
+that are not aligned to this Code of Conduct, or to ban temporarily or
+permanently any contributor for other behaviors that they deem inappropriate,
+threatening, offensive, or harmful.
+
+### Scope
+
+This Code of Conduct applies both within project spaces and in public spaces
+when an individual is representing the project or its community. Examples of
+representing a project or community include using an official project e-mail
+address, posting via an official social media account, or acting as an appointed
+representative at an online or offline event. Representation of a project may be
+further defined and clarified by project maintainers.
+
+### Enforcement
+
+Instances of abusive, harassing, or otherwise unacceptable behavior may be
+reported by contacting the project team at [INSERT EMAIL ADDRESS]. All
+complaints will be reviewed and investigated and will result in a response that
+is deemed necessary and appropriate to the circumstances. The project team is
+obligated to maintain confidentiality with regard to the reporter of an incident.
+Further details of specific enforcement policies may be posted separately.
+
+Project maintainers who do not follow or enforce the Code of Conduct in good
+faith may face temporary or permanent repercussions as determined by other
+members of the project's leadership.
+
+### Attribution
+
+This Code of Conduct is adapted from the [Contributor Covenant][homepage], version 1.4,
+available at [http://contributor-covenant.org/version/1/4][version]
+
+[homepage]: http://contributor-covenant.org
+[version]: http://contributor-covenant.org/version/1/4/

docs/examples.rst

@@ -73,14 +73,18 @@ acceleration, we refer to the Table as seen below.
 
    * - System
      - Execution time (averaged)
-   * - Intel(R) Core(TM) i9-10900K CPU @ 3.70GHz (20 threads)
+   * - Intel(R) Core(TM) i9-10900K (20 threads)
      - 172.58s
-   * - Intel(R) Core(TM) i9-10900K CPU @ 3.70GHz (20 threads) + RTX 4090
+   * - Intel(R) Core(TM) i9-10900K (20 threads) + RTX 4090
      - 90.18s
-   * - Intel(R) Core(TM) i5-8400 CPU @ 2.80GHz (6 threads)
+   * - Intel(R) Core(TM) i5-8400 (6 threads)
      - 311.84s
-   * - Intel(R) Core(TM) i5-8400 CPU @ 2.80GHz (6 threads) + RTX 2070
+   * - Intel(R) Core(TM) i5-8400 (6 threads) + RTX 2070
      - 125.08s
+   * - Intel(R) Xeon(R) Platinum 8360Y (18 threads) + A100-SXM4-40GB
+     - 147.06s
+   * - Intel(R) Xeon(R) Platinum 8360Y (36 threads) + 2x A100-SXM4-40GB
+     - 72.59s
 
 Co HCP 11-21
 ------------
@@ -196,7 +200,19 @@ acceleration, we refer to the Table as seen below.
 
    * - System
      - Execution time (averaged)
-   * - Intel(R) Core(TM) i9-10900K CPU @ 3.70GHz (20 threads)
-     - 5207.93s (1h26m47s)
-   * - Intel(R) Core(TM) i9-10900K CPU @ 3.70GHz (20 threads) + RTX 4090
-     - 2368.63s (39m28s)
+   * - Intel(R) Core(TM) i9-10900K (20 threads)
+     - 5207s
+   * - Intel(R) Core(TM) i9-10900K (20 threads) + RTX 4090
+     - 2368s
+   * - Intel(R) Xeon(R) Platinum 8360Y (18 threads) + A100-SXM4-40GB
+     - 2543s
+   * - Intel(R) Xeon(R) Platinum 8360Y (36 threads) + 2x A100-SXM4-40GB
+     - 1366s
+   * - Intel(R) Core(TM) i5-8400 (6 threads) + RTX 2070
+     - 2986s
+   * - Intel(R) Xeon(R) Gold 6234 (16 threads) + A5000
+     - 3912
+   * - Intel(R) Core(TM) i5-12400F (12 threads) + 1x GTX 1080 Ti
+     - 2759
+   * - Intel(R) Core(TM) i5-12400F (12 threads) + 2x GTX 1080 Ti
+     - 2067s

docs/execution_model.rst

@@ -9,6 +9,12 @@ acceleration to speed up the execution. This is especially beneficial when
 performing a similarity analysis. :program:`Bramble` supports multi-GPU
 setups, so one can use multiple GPUs if more than one GPU is available.
 
+.. warning::
+    :program:`Bramble` requires a GPU with at least 8Gb of memory. :program:`Bramble`
+    will check whether the GPU supports the calculation prior to execution and throws
+    an error when the GPU is not supported. You can also check the memory available
+    on your GPU by running ``bramblecuda``.
+
 When performing the similarity analysis, an inventory of all the jobs is made.
 ``N+1`` OpenMP threads are being spawned where ``N`` equals the number of GPUs.
 Each GPU gets assigned a CPU thread and jobs are relayed to the GPU via the CPU

docs/index.rst

@@ -25,7 +25,7 @@ visualization in `Matplotlib <https://matplotlib.org/>`_.
     Cobalt nanoparticle of 15625 atoms generated using a simulated annealing
     procedure. All colored atoms are identified by the CNA algorithm. The
     unknown atoms, i.e. atoms with an unknown CNA fingerprint, are rendered
-    using a glass material.
+    using a glass material. (source files can be found `here <https://github.com/ifilot/bramble/tree/master/scripts/blender>`_)
 
 For fingerprints that are (still) unknown or for atoms that have a more
 amorphous chemical environment, :program:`Bramble` comes bundled with a

docs/installation.rst

@@ -23,7 +23,8 @@ On Debian-based operating systems, one can run the following::
    The compilation instructions below can be readily used.
 
 .. warning::
-   In order to compile for GPU using CUDA, one needs Eigen3 version **3.4.0** or higher.
+   * In order to compile for GPU using CUDA, one needs Eigen3 version **3.4.0** or higher.
+   * Your GPU needs at least 8Gb of memory in order to use Bramble.
 
 Compilation
 -----------
@@ -55,11 +56,9 @@ The similarity analysis functionality of :program:`Bramble` can
 benefit from the availability of a graphical card. To compile :program:`Bramble`
 with CUDA support, run CMake with::
 
-    cmake ../src -DMOD_CUDA=1 -DCUDA_ARCH=<ARCH>
+    cmake ../src -DMOD_CUDA=1
 
-wherein `<ARCH>` is replaced with the architecture of your graphical card. For
-example, if you use an RTX 4090, you would use ``-DCUDA_ARCH=sm_89``. To
-test that :program:`Bramble` can use your GPU, you can run the ``bramblecuda``
+To test that :program:`Bramble` can use your GPU, you can run the ``bramblecuda``
 tool whose sole function is to test for the availability of a GPU on the system::
 
     ./bramblecuda
@@ -127,3 +126,57 @@ Typical output should look as follows::
     100% tests passed, 0 tests failed out of 9
 
     Total Test time (real) =   1.73 sec
+
+EasyBuild Installation
+----------------------
+
+For HPC infrastructure, there is also the option to install :program:`Bramble`
+using `EasyBuild <https://easybuild.io/>`_.
+Create a file called `bramble-<VERSION>.eb` and populate this file with::
+
+    name = 'Bramble'
+    version = '<VERSION>'
+
+    homepage = 'https://bramble.imc-tue.nl'
+    description = "Single atom pattern recognition algorithm based on the Common Neighbor Analysis method"
+
+    toolchain = {'name': 'GCC', 'version': '11.2.0'}
+
+    sources = [{
+        'filename': 'bramble-%(version)s.tar.gz',
+        'git_config': {
+            'url': 'https://github.com/ifilot',
+            'repo_name': 'bramble',
+            'tag': 'v%(version)s',
+            'keep_git_dir': True,
+        },
+    }]
+
+    dependencies = [('Eigen', '3.4.0'),
+                    ('TCLAP', '1.2.5'),
+                    ('Boost', '1.79.0'),
+                    ('CUDA', '12.1.0')]
+
+    builddependencies = [('CMake', '3.22.1'),
+                         ('pkg-config', '0.29.2')]
+
+    easyblock = 'CMakeMake'
+
+    srcdir = 'src'
+    separate_build_dir = True
+    runtest = 'test'
+    configopts = "-DCMAKE_BUILD_TYPE=Release -DMOD_CUDA=1"
+
+    sanity_check_paths = {
+        'files': ["bin/bramble"],
+        'dirs': [],
+    }
+
+Note that you need to manually adjust the value of `<VERSION>` to the desired
+version (e.g. `1.1.1`). To install, run the following::
+
+    eb bramble-<VERSION>.eb --robot --minimal-toolchains --add-system-to-minimal-toolchains
+
+The `--robot` option aims to automatically resolve all dependencies. The
+`--minimal-toolchains` and `--add-system-to-minimal-toolchains` options are
+necessary to properly resolve the CUDA dependency.

scripts/blender/README.md

@@ -0,0 +1,7 @@
+# Blender source files
+
+This folder contains the source files to reproduce the image as found on the
+front page of the [documentation website](https://bramble.imc-tue.nl).
+
+To reproduce the image, open the Blender file in Blender (version 3.3.8 preferred),
+and run the script embedded in the file.