HPC WITH US – Discoverer Petascale Supercomputer

As we bid farewell to 2023…

29 December 2023 Veselin Kolev Comments 0 Comment

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

23 December 2023 Veselin Kolev Comments 0 Comment

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

23 December 2023 Veselin Kolev Comments 0 Comment

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

23 December 2023 Veselin Kolev Comments 0 Comment

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

30 July 2023 Veselin Kolev Comments 0 Comment

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

9 July 2023 Veselin Kolev Comments 0 Comment

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

9 July 2023 Veselin Kolev Comments 0 Comment

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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ABINIT 9.8.2 on Discoverer HPC

27 January 2023 Veselin Kolev Comments 0 Comment

ABINIT is a powerful package for calculating a variety of optical, mechanical, vibrational, and other observable properties of materials. It is written in Fortran 95 and supports distributed parallelization model based on MPI library. This post is about how ABINIT 9.8.2 code can be compiled for high productivity on Discoverer HPC. The compilation of ABINIT code relies on the presence of a number of external auxiliary libraries, which have to be installed on the build host in advance. Most important…

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Intel retire their C/C++ classic compiler in mid 2023

5 October 2022 Veselin Kolev Comments 0 Comment

Intel® C++ Compiler Classic (icc) is deprecated and will be removed in a oneAPI release in the second half of 2023. Intel recommends that customers transition now to using the LLVM-based Intel® oneAPI DPC++/C++ Compiler (icx) for continued Windows* and Linux* support, new language support, new language features, and optimizations. https://community.intel.com/t5/Intel-oneAPI-IoT-Toolkit/DEPRECATION-NOTICE-Intel-C-Compiler-Classic/m-p/1412267 What that means for the users of Discoverer HPC who need to compile their C and C++ code by using Intel® C/C++/Fortran compiler? The classic compilers icc, icpc, ifort…

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Create high productive CP2K 2022.1 build that works on AMD Zen2 microarchitecture

25 September 2022 Veselin Kolev Comments 0 Comment

CP2K is a quantum chemistry and solid state physics software package that can perform atomistic simulations of solid state, liquid, molecular, periodic, material, crystal, and biological systems. While it can be successfully compiled by using Intel oneAPI, Intel oneAPI MKL, and Intel MPI, the produced executables cannot run simulations of large systems on AMD Zen2 CPU. For instance, the SCF minimization fails by sending “Segmentation fault” message to the standard error. The debugging results point to a problem with handling…

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