TY  - JOUR
T1  - Türk Ulusal Bilim e-Altyapısı TRUBA’da Moleküler Dinamik Paketi GROMACS’in Performans Optimizasyonu
AU  - Karaca, Ezgi
AU  - Savaş, Büşra
PY  - 2021
DA  - December
DO  - 10.7240/jeps.920227
JF  - International Journal of Advances in Engineering and Pure Sciences
JO  - JEPS
PB  - Marmara University
WT  - DergiPark
SN  - 2636-8277
SP  - 609
EP  - 613
VL  - 33
IS  - 4
LA  - tr
AB  - 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.
KW  - Moleküler Dinamik
KW  - Yüksek Başarımlı Hesaplama Kümeleri
KW  - Optimizasyon
KW  - GROMACS
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UR  - https://doi.org/10.7240/jeps.920227
L1  - https://dergipark.org.tr/en/download/article-file/1716291
ER  -