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Author: Veselin Kolev

Discoverer is advancing its commitment towards the full adoption of the LLVM compiler infrastructure

Discoverer is advancing its commitment towards the full adoption of the LLVM compiler infrastructure

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The new version of the LLVM Compiler Infrastructure, 19, is available in the software repository. That version includes numerous improvements and fixes. We uphold our commitment to maintain openness and transparency in our way of doing system and software engineering, which entails consistently publishing our build recipes. In the case of LLVM 19, those recipes are publicly available here: https://gitlab.discoverer.bg/vkolev/recipes/-/tree/main/llvm/19 Adopting the LLVM 19 puts a new milestone in our computation model. We can start confidently moving the entire executables…

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[Computed on Discoverer] Calculation and visualization of protein conformations generation in implicit solvent

[Computed on Discoverer] Calculation and visualization of protein conformations generation in implicit solvent

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We have numerous results we would like to share with you. One instance is the computation that demonstrates the conformation changes that make the protein to fold and unfold. The proper analysis of those changes help to measure the free energy of different processes related to the protein chain transformations. Our protein model representation depicts the side chains of each residue by utilizing a coarse grain force field, as illustrated in the video slides. By doing this, we significantly reduce…

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[Computed on Discoverer] Computation and visualization of ensemble averages

[Computed on Discoverer] Computation and visualization of ensemble averages

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The molecular dynamics simulations provide great details at the nanoscale level for relatively big systems (up to several million atoms). Very often the material environment of certain functional groups, selected atoms, clusters of atoms, and other low to high-level structural elements, is numerically evaluated employing radial distribution functions (RDF). That method is powerful, well studied, and largely implemented for analysis. But it cannot provide a visual spatial estimate for the investigated environment. If you have a molecule surrounded by ions,…

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As we bid farewell to 2023…

As we bid farewell to 2023…

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Now, as the year 2023 draws to a close, it is time to reflect upon the closest past. During the year 2023, we at Discoverer faced many challenging technical issues and took immediate action when it was needed, sometimes sacrificing our personal and family spare time to do so. However, ultimately, we accomplished all of our tasks. The cluster performs satisfactorily, and the majority of customers are content with the efficiency of the computational resources. Santa Claus brought us many…

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Zlib 1.3 has landed on Discoverer

Zlib 1.3 has landed on Discoverer

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To support the compression/decompression abilities embedded in various software products that run on Discoverer, our team compiled and installed an AMD EPIC-optimized version of the Zlib 1.3 library. It is available in several variants, depending on the compiler used to compile the code, to support the benchmarking and development projects. Intel oneAPI and NVIDIA HPC SDK specific libraries are statically compiled into libz.so. Both AMD AOCC and LLVM build infrastructure LLVM builds are available. GCC build is also installed and…

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Major update to the hosted LLVM compiler collections

Major update to the hosted LLVM compiler collections

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The Discoverer’s software repository received a major update to the hosted LLVM compiler collections. Versions 16.0.0-16.0.6 and 17.0.0-17.0.6 are available and the LLVMgold plugin is included in all bundles. We thoroughly examined the hosted LLVM compiler collections by employing the clang and clang++ compilers to compile C and C++ code projects like GROMACS and NAMD. Despite the absence of significant issues with the compilation of C and C++ code, it is expected that the compilation of Fortran code using flang…

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The Discoverer bids farewell to the era-old Intel compilers

The Discoverer bids farewell to the era-old Intel compilers

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The latest version of Intel oneAPI – 2024.0.0 – is now available in Discoverers open-source software repository. One big change in the new version is that the classic Intel compilers are no longer available. As of version 2024.0, they have been excluded from the bundle. The users have to load one of the available pre-2024.0 versions if they need access to any of the classic compilers. The old versions of Intel oneAPI (≤2023.2) that include the classic compilers will remain…

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GCC compiler collection on Discoverer receives yet another update

GCC compiler collection on Discoverer receives yet another update

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It seems that July has been a busy month for many GCC code developers. The project released a minor new version of GCC, 13.2, which addresses problems discovered in the previously released 13.1 version. More information on the included fixes and changes can be found here: https://gcc.gnu.org/gcc-13/changes.html The code of 13.2 was compiled and installed in the public software repository to provide our users with the most up-to-date version of GCC 13. The build recipe the compilation process is based…

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Discoverer is LLVM-ready

Discoverer is LLVM-ready

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We’ve been examining the deployment of LLVM compiler infrastructure in high-performance computing for more than a year. LLVM compilers provide novel and significantly more optimal and reliable schemas for the generation of binary code. More and more source code distributions come with LLVM-compatible CMake configurations. GROMACS is one of them. The Python universe of applications also actively adopts LLVM for HPC. Numba is one of those applications. It serves as a foundation for the development of bindings for the creation of…

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Discoverer receives a massive GCC compiler collection update

Discoverer receives a massive GCC compiler collection update

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In an effort to support more effective code compilation and code optimisation, we have updated the GCC compiler collection installation available in the public software repository. This update brings to the repository GCC versions 13.1.0, 12.3.0, and 11.4.0. Each new version includes GMP, MPC, MPFR, and iSL libraries. Zstandard 1.5.5 is linked as an external compressor. For optimal workload, we optimised those libraries by adding support for AVX2 SIMD extensions. Currently, AVX2 is the highest SIMD extension supported by the…

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