Türk Ulusal Bilim e-Altyapısı TRUBA’da Moleküler Dinamik Paketi GROMACS’in Performans Optimizasyonu

Abstract

Yüksek performanslı hesaplama sistemlerinin kullanımının artmasıyla, bu sistemlerde çalıştırılan programların performans optimizasyonu öncelikli hale gelmiştir. Bu duruma istinaden, bu çalışmamızda, yaygın olarak kullanılan moleküler dinamik paketi GROMACS’in, TÜBİTAK ULAKBİM tarafından kullanıma sunulan TRUBA hesaplama kümelerindeki en iyi performans kriterlerini bulmayı hedefledik. Performans tarama çalışmamız sırasında, farklı hesaplama kümelerinde, farklı CPU/GPU çekirdek oranı ve GROMACS versiyonlarını denedik. Bu süreç sonunda en iyi performanslı hesaplama kümesi akya-cuda, en iyi CPU/GPU çekirdek sayı oranı 40/1 ve en hızlı GROMACS versiyonu GROMACS 2020 olarak tespit edilmiştir. Benzer bir çalışma yürütecek araştırmacıların yararlanması adına, performans optimizasyon dosyalarımız ve ayrıntılı sonuçlarımız https://github.com/CSB-KaracaLab/gmx_performance_on_HPC adresinde incelemeye açılmıştır.

Keywords

• Moleküler Dinamik
• Yüksek Başarımlı Hesaplama Kümeleri
• Optimizasyon
• GROMACS

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