Application | Lines of Code |
Parallelism | Language | Code Description/Notes | |||||
---|---|---|---|---|---|---|---|---|---|

MPI | OpenMP/ Pthreads |
GPU | Fortran | Python | C | C++ | |||

Alya | 600,000 | X | X | X | X | The Alya System is a Computational Mechanics code capable of solving different physics, each one with its own modelization characteristics, in a coupled way. Among the problems it solves are: convection-diffusion reactions, incompressible flows, compressible flows, turbulence, bi-phasic flows and free surface, excitable media, acoustics, thermal flow, quantum mechanics (DFT) and solid mechanics (large strain). | |||

Code_Saturne | ~350,000 | X | X | X | X | X | X | X | The code solves the Navier-Stokes equations for imcompressible/compressible flows using a predictor-corrector technique. The Poisson pressure equation is solved by a Conjugate Gradient preconditioned by a multi-grid algorithm, and the transport equations by Conjugate Gradient-like methods. Advanced gradient reconstruction is also available to account for distorted meshes. |

CP2K | ~1,150,000 | X | X | X | X | CP2K is a freely available quantum chemistry and solid-state physics software package for performing atomistic simulations. It can be run with MPI, OpenMP and CUDA. All of CP2K is MPI parallelised, with some routines making use of OpenMP, which can be used to reduce the memory footprint. In addition some linear algebra operations may be offloaded to GPUs using CUDA. | |||

GADGET | |||||||||

GPAW | 132,000 | X | X | X | X | ||||

GROMACS | 3,227,337 | X | X | X | X | X | |||

NAMD | 1,992,651 | X | X | X | X | ||||

NEMO | 154,240 | X | X | X | NEMO (Nucleus for European Modelling of the Ocean) is a mathematical modelling framework for research activities and prediction services in ocean and climate sciences developed by a European consortium. It is intended to be a tool for studying the ocean and its interaction with the other components of the earth climate system over a large number of space and time scales. It comprises of the core engines namely OPA (ocean dynamics and thermodynamics), SI3 (sea ice dynamics and thermodynamics), TOP (oceanic tracers) and PISCES (biogeochemical process). | ||||

PFARM | 21,434 | X | X | X | X | PFARM uses an R-matrix ab-initio approach to calculate electron-atom and electron-molecule collisions data for a wide range of applications including atrophysics and nuclear fusion. It is written in modern Fortran/MPI/OpenMP and exploits highly-optimised dense linear algebra numerical library routines. | |||

QCD | |||||||||

Quantum ESPRESSO | 92,996 | X | X | X | X | ||||

TensorFlow | |||||||||

SPECFEM3D |

[- Bench](https://repository.prace-ri.eu/git/UEABS/ueabs/-/tree/r2.2-dev/qcd/part_1)

[- Summary](https://repository.prace-ri.eu/git/UEABS/ueabs/-/blob/r2.2-dev/qcd/part_1/README.md) | lattice Quantum Chromodynamics Part 1 | C | yes | yes | yes (CUDA) | -- | Accelerator enabled kernel E of UEABS QCD CPU part using targetDP model. Test case A - 8x64x64x64. Conjugate Gradient solver involving Wilson Dirac stencil. Domain Decomposition, Memory bandwidth, strong scaling, MPI latency. | |

[- Source](https://lattice.github.io/quda/)

[- Bench](https://repository.prace-ri.eu/git/UEABS/ueabs/-/tree/r2.2-dev/qcd/part_2)

[- Summary](https://repository.prace-ri.eu/git/UEABS/ueabs/-/blob/r2.2-dev/qcd/part_2/README.md) | lattice Quantum Chromodynamics Part 2 - QUDA | C++ | yes | yes | yes (CUDA) | -- | Part 2: GPU is using a QUDA kernel for running on NVIDIA GPUs. [Test case A - 96x32x32x32] Small problem size. CG solver. Domain Decomposition, Memory bandwidth, strong scaling, MPI latency. [Test case B - 126x64x64x64] Moderate problem size. CG solver on Wilson Dirac stencil. Bandwidth bounded | |

[- Source](http://jeffersonlab.github.io/qphix/)

[- Bench](https://repository.prace-ri.eu/git/UEABS/ueabs/-/tree/r2.2-dev/qcd/part_2)

[- Summary](https://repository.prace-ri.eu/git/UEABS/ueabs/-/blob/r2.2-dev/qcd/part_2/README.md) | lattice Quantum Chromodynamics Part 2 - QPHIX | C++ | yes | yes | no | -- | Part 2: Xeon(Phi) is using a QPhiX kernel which is optimize to run on x86, in particular Intel Xeon (Phi). [Test case A - 96x32x32x32] Small problem size. CG solver involving Wilson Dirac stencil. Domain Decomposition, Memory bandwidth, strong scaling, MPI latency. [Test case B - 126x64x64x64] Moderate problem size. CG solver on Wilson Dirac stencil. Bandwidth bounded | |

[- Source](https://repository.prace-ri.eu/ueabs/QCD/1.3/QCD_Source_TestCaseA.tar.gz)

[- Bench](https://repository.prace-ri.eu/git/UEABS/ueabs/-/tree/r2.2-dev/qcd/part_cpu)

[- Summary](https://repository.prace-ri.eu/git/UEABS/ueabs/-/blob/r2.2-dev/qcd/part_cpu/README.md) | lattice Quantum Chromodynamics - CPU Part - legacy UEABS | C/Fortran | yes | yes/no | No | -- | CPU part based on UEABS QCD CPU part (legacy) benchmark kernels (last update 2017). Based on 5 different Benchmark applications representative for the European Lattice QCD community (see doc for more details). | # Quantum Espresso QUANTUM ESPRESSO is an integrated suite of computer codes for electronic-structure calculations and materials modeling, based on density-functional theory, plane waves, and pseudopotentials (norm-conserving, ultrasoft, and projector-augmented wave). QUANTUM ESPRESSO stands for opEn Source Package for Research in Electronic Structure, Simulation, and Optimization. It is freely available to researchers around the world under the terms of the GNU General Public License. QUANTUM ESPRESSO builds upon newly restructured electronic-structure codes that have been developed and tested by some of the original authors of novel electronic-structure algorithms and applied in the last twenty years by some of the leading materials modeling groups worldwide. Innovation and efficiency are still its main focus, with special attention paid to massively parallel architectures, and a great effort being devoted to user friendliness. QUANTUM ESPRESSO is evolving towards a distribution of independent and inter-operable codes in the spirit of an open-source project, where researchers active in the field of electronic-structure calculations are encouraged to participate in the project by contributing their own codes or by implementing their own ideas into existing codes. QUANTUM ESPRESSO is written mostly in Fortran90, and parallelised using MPI and OpenMP. - Web site: http://www.quantum-espresso.org/ - Code download: http://www.quantum-espresso.org/download/ - Build instructions: http://www.quantum-espresso.org/wp-content/uploads/Doc/user_guide/ - Test Case A: https://repository.prace-ri.eu/ueabs/Quantum_Espresso/QuantumEspresso_TestCaseA.tar.gz - Test Case B: https://repository.prace-ri.eu/ueabs/Quantum_Espresso/QuantumEspresso_TestCaseB.tar.gz - Run instructions: https://repository.prace-ri.eu/git/UEABS/ueabs/blob/r1.3/quantum_espresso/QE-guide.txt # SHOC The Scalable HeterOgeneous Computing (SHOC) benchmark suite is a collection of benchmark programs testing the performance and stability of systems using computing devices with non-traditional architectures for general purpose computing. It serves as synthetic benchmark suite in the UEABS context. Its initial focus is on systems containing Graphics Processing Units (GPUs) and multi-core processors, featuring implementations using both CUDA and OpenCL. It can be used on clusters as well as individual hosts. Also, SHOC includes an Offload branch for the benchmarks that can be used to evaluate the Intel Xeon Phi x100 family. The SHOC benchmark suite currently contains benchmark programs, categoried based on complexity. Some measure low-level "feeds and speeds" behavior (Level 0), some measure the performance of a higher-level operation such as a Fast Fourier Transform (FFT) (Level 1), and the others measure real application kernels (Level 2). - Web site: https://github.com/vetter/shoc - Code download: https://github.com/vetter/shoc/archive/master.zip - Build instructions: https://repository.prace-ri.eu/git/ueabs/ueabs/blob/r2.1-dev/shoc/README_ACC.md - Run instructions: https://repository.prace-ri.eu/git/ueabs/ueabs/blob/r2.1-dev/shoc/README_ACC.md # SPECFEM3D | **General information** | **Scientific field** | **Language** | **MPI** | **OpenMP** | **GPU** | **LoC** | **Code description** | |------------------|----------------------|--------------|---------|------------|---------------------|---------|-------------------------------------------------------------------------------------------------------------------------------------------------------| | [- Website](https://geodynamics.org/cig/software/specfem3d_globe/)

[- Source](https://github.com/geodynamics/specfem3d_globe.git)

[- Bench](https://repository.prace-ri.eu/git/UEABS/ueabs/tree/r2.1-dev/specfem3d)

[- Summary](https://repository.prace-ri.eu/git/UEABS/ueabs/blob/r2.1-dev/specfem3d/PRACE_UEABS_Specfem3D_summary.pdf) | Geodynamics | Fortran & C | yes | yes | Yes (CUDA) | 100k Fortran & 20k C | The software package SPECFEM3D simulates three-dimensional global and regional seismic wave propagation based upon the spectral-element method (SEM). | # TensorFlow TensorFlow (https://www.tensorflow.org) is a popular open-source library for symbolic math and linear algebra, with particular optimization for neural-networks-based machine learning workflow. Maintained by Google, it is widely used for research and production in both the academia and the industry. TensorFlow supports a wide variety of hardware platforms (CPUs, GPUs, TPUs), and can be scaled up to utilize multiple compute devices on a single or multiple compute nodes. The main objective of this benchmark is to profile the scaling behavior of TensorFlow on different hardware, and thereby provide a reference baseline of its performance for different sizes of applications. There are many open-source datasets available for benchmarking TensorFlow, such as `mnist`, `fashion_mnist`, `cifar`, `imagenet`, and so on. This benchmark suite, however, would like to focus on a scientific research use case. `DeepGalaxy` is a code built with TensorFlow, which uses deep neural network to classify galaxy mergers in the Universe, observed by the Hubble Space Telescope and the Sloan Digital Sky Survey. - Website: https://github.com/maxwelltsai/DeepGalaxy - Code download: https://github.com/maxwelltsai/DeepGalaxy - [Prerequisites installation](tensorflow/prerequisites-installation.md) - [Test Case A](tensorflow/Testcase_A/) - [Test Case B](tensorflow/Testcase_B/) - [Test Case C](tensorflow/Testcase_C/)