Abstract The aim of this study was to compare the CPU time of two most widely used Fortran compilers – the Absoft and the Intel, in the context of two programs used in the genomic evaluation system of dairy cattle - a program for re-coding of the raw genotyping data of single nucleotide polymorphisms and a program for the estimation of additive genetic effects of single nucleotide polymorphisms. The data set used for the analysis corresponded to the Polish national routine genomic evaluation for non-return rate of heifers and comprised genotypes of 46,267 single nucleotide polymorphisms for each of 2904 evaluated bulls, which resulted in 130,393,459 non-missing genotype records. Programs were compiled under several different compilation options using the Absoft (release 2015) and the Intel (release 2019) compilers. The CPU times of both programmes significantly differed between compilers. In the program for genotype re-coding the Intel compiler always resulted in shorter running times than the Absoft compiler. More variation was observed in CPU times of the program for effect estimation, for which the Absoft compiler resulted in both, the shortest and the longest computing times. A more detailed run-time memory consumption visualisation of single runs of the fastest Absoft and Intel compiled program executions demonstrated that the former compiler allows for the utilisation of more of the available memory, which in the case of a memory intensive program for effect estimation resulted in a faster execution time. In conclusion, an overall performance of the Intel compiler was better than this of the Absoft compiler. Even though significant differences in CPU time were observed, the Intel compiled execution times were less dependent on the pre-imposed compilation parameters. However, it is important to note that for programs performing a large number of arithmetic evaluations it is possible to tune the Absoft compiler to outperform the Intel compiler. The key compilation parameters are those, which allow for lower floating point accuracy and dedicated optimization of mathematical operations. Although blind use of such options is not recommended, in the case of genomic evaluation the math and floating point based optimisations did not affect the convergence of the solver nor the estimates of single nucleotide polymorphisms’ effects.

中文翻译：

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调整荷斯坦-弗里斯兰牛的基因组评估系统

摘要 本研究的目的是在奶牛基因组评估系统中使用的两个程序的背景下，比较两种最广泛使用的 Fortran 编译器——Absoft 和 Intel 的 CPU 时间——一个重新编码的程序单核苷酸多态性的原始基因分型数据和用于估计单核苷酸多态性的加性遗传效应的程序。用于分析的数据集对应于波兰国家常规基因组对小母牛不返回率的评估，包括 2904 头评估公牛中每头的 46,267 个单核苷酸多态性的基因型，从而产生 130,393,459 个非缺失基因型记录。程序是使用 Absoft（2015 版）和 Intel（2019 版）编译器在几种不同的编译选项下编译的。两个程序的 CPU 时间在编译器之间有显着差异。在基因型重新编码程序中，英特尔编译器的运行时间总是比 Absoft 编译器短。在用于效果估计的程序的 CPU 时间中观察到更多变化，Absoft 编译器导致计算时间最短和最长。对最快的 Absoft 和 Intel 编译程序执行的单次运行的更详细的运行时内存消耗可视化表明，前一种编译器允许利用更多可用内存，在内存密集型程序用于效果估计的情况下导致在更快的执行时间。综上所述，Intel 编译器的整体性能优于 Absoft 编译器。尽管观察到 CPU 时间存在显着差异，但英特尔编译的执行时间较少依赖于预先施加的编译参数。但是，重要的是要注意，对于执行大量算术评估的程序，可以调整 Absoft 编译器以优于 Intel 编译器。关键的编译参数是那些允许较低的浮点精度和数学运算的专用优化的参数。尽管不建议盲目使用此类选项，但在基因组评估的情况下，基于数学和浮点的优化不会影响求解器的收敛性，也不会影响单核苷酸多态性效应的估计。需要注意的是，对于执行大量算术评估的程序，可以调整 Absoft 编译器以超越 Intel 编译器。关键的编译参数是那些允许较低的浮点精度和数学运算的专用优化的参数。尽管不建议盲目使用此类选项，但在基因组评估的情况下，基于数学和浮点的优化不会影响求解器的收敛性，也不会影响单核苷酸多态性效应的估计。需要注意的是，对于执行大量算术评估的程序，可以调整 Absoft 编译器以超越 Intel 编译器。关键的编译参数是那些允许较低的浮点精度和数学运算的专用优化的参数。尽管不建议盲目使用此类选项，但在基因组评估的情况下，基于数学和浮点的优化不会影响求解器的收敛性，也不会影响单核苷酸多态性效应的估计。这允许较低的浮点精度和数学运算的专用优化。尽管不建议盲目使用此类选项，但在基因组评估的情况下，基于数学和浮点的优化不会影响求解器的收敛性，也不会影响单核苷酸多态性效应的估计。这允许较低的浮点精度和数学运算的专用优化。尽管不建议盲目使用此类选项，但在基因组评估的情况下，基于数学和浮点的优化不会影响求解器的收敛性，也不会影响单核苷酸多态性效应的估计。