Thanks for the feedback everyone. If you go to https://github.com/csantill/RPerformanceWBLAS/blob/master/RPerformanceBLAS.md you will find the Linux commands to change the default math library. When I switch the BLAS library from MKL to the system default (see sessionInfo below), everything works as expected. I installed version 2020.0-166-1 of "Intel-MKL" from the Linux Mint Software Manager. I may be coming to a hasty conclusion, but there appears to be something wrong with that package or how it interacts with other system software. Any suggestions on who I should notify about the problem (e.g., Intel, Mint, Ubuntu)?
R version 4.1.2 (2021-11-01) Platform: x86_64-pc-linux-gnu (64-bit) Running under: Linux Mint 20.2 Matrix products: default BLAS: /usr/lib/x86_64-linux-gnu/blas/libblas.so.3.9.0 LAPACK: /usr/lib/x86_64-linux-gnu/libmkl_rt.so locale: [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C LC_TIME=en_US.UTF-8 [4] LC_COLLATE=en_US.UTF-8 LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8 [7] LC_PAPER=en_US.UTF-8 LC_NAME=C LC_ADDRESS=C [10] LC_TELEPHONE=C LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C attached base packages: [1] stats graphics grDevices utils datasets methods base loaded via a namespace (and not attached): [1] compiler_4.1.2 tools_4.1.2 Thomas R. LaBone PhD student Department of Epidemiology and Biostatistics Arnold School of Public Health University of South Carolina Columbia, South Carolina USA ________________________________ From: Labone, Thomas <lab...@email.sc.edu> Sent: Thursday, December 2, 2021 11:53 AM To: Bill Dunlap <williamwdun...@gmail.com> Cc: r-help@r-project.org <r-help@r-project.org> Subject: Re: [R] Problem with lm Giving Wrong Results > summary(fit) Call: lm(formula = log(k) ~ Z) Residuals: Min 1Q Median 3Q Max -21.241 1.327 1.776 2.245 4.418 Coefficients: Estimate Std. Error t value Pr(>|t|) (Intercept) -0.03465 0.01916 -1.809 0.0705 . Z -0.24207 0.01916 -12.634 <2e-16 *** --- Signif. codes: 0 �***� 0.001 �**� 0.01 �*� 0.05 �.� 0.1 � � 1 Residual standard error: 1.914 on 9998 degrees of freedom Multiple R-squared: 0.01467, Adjusted R-squared: 0.01457 F-statistic: 148.8 on 1 and 9998 DF, p-value: < 2.2e-16 > summary(k) Min. 1st Qu. Median Mean 3rd Qu. Max. 0.2735 3.7658 5.9052 7.5113 9.4399 82.9531 > summary(Z) Min. 1st Qu. Median Mean 3rd Qu. Max. -3.8906 -0.6744 0.0000 0.0000 0.6744 3.8906 > summary(gm*gsd^Z) Min. 1st Qu. Median Mean 3rd Qu. Max. 0.3767 0.8204 0.9659 0.9947 1.1372 2.4772 > Thomas R. LaBone PhD student Department of Epidemiology and Biostatistics Arnold School of Public Health University of South Carolina Columbia, South Carolina USA ________________________________ From: Bill Dunlap <williamwdun...@gmail.com> Sent: Thursday, December 2, 2021 10:31 AM To: Labone, Thomas <lab...@email.sc.edu> Cc: r-help@r-project.org <r-help@r-project.org> Subject: Re: [R] Problem with lm Giving Wrong Results On the 'bad' machines, what did you get for summary(fit) summary(k) summary(Z) summary(gm*gsd^Z) ? -Bill On Thu, Dec 2, 2021 at 6:18 AM Labone, Thomas <lab...@email.sc.edu<mailto:lab...@email.sc.edu>> wrote: In the code below the first and second plots should look pretty much the same, the only difference being that the first has n=1000 points and the second n=10000 points. On two of my Linux machines (info below) the second plot is a horizontal line (incorrect answer from lm), but on my Windows 10 machine and a third Linux machine it works as expected. The interesting thing is that the code works as expected for n <= 4095 but fails for n>=4096 (which equals 2^12). Can anyone else reproduce this problem? Any ideas on how to fix it? set.seed(132) #~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ # This works n <- 1000# OK <= 4095 Z <- qnorm(ppoints(n)) k <- sort(rlnorm(n,log(2131),log(1.61)) / rlnorm(n,log(355),log(1.61))) quantile(k,probs=c(0.025,0.5,0.975)) summary(k) fit <- lm(log(k) ~ Z) summary(fit) gm <- exp(coef(fit)[1]) gsd <- exp(coef(fit)[2]) gm gsd plot(Z,k,log="y",xlim=c(-4,4),ylim=c(0.1,100)) lines(Z,gm*gsd^Z,col="red") #~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ #this does not n <- 10000# fails >= 4096 = 2^12 Z <- qnorm(ppoints(n)) k <- sort(rlnorm(n,log(2131),log(1.61)) / rlnorm(n,log(355),log(1.61))) quantile(k,probs=c(0.025,0.5,0.975)) summary(k) fit <- lm(log(k) ~ Z) summary(fit) gm <- exp(coef(fit)[1]) gsd <- exp(coef(fit)[2]) gm gsd plot(Z,k,log="y",xlim=c(-4,4),ylim=c(0.1,100)) lines(Z,gm*gsd^Z,col="red") #~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ > sessionInfo() #for two Linux machines having problem R version 4.1.2 (2021-11-01) Platform: x86_64-pc-linux-gnu (64-bit) Running under: Linux Mint 20.2 Matrix products: default BLAS/LAPACK: /usr/lib/x86_64-linux-gnu/libmkl_rt.so locale: [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 LC_MONETARY=en_US.UTF-8 [6] LC_MESSAGES=en_US.UTF-8 LC_PAPER=en_US.UTF-8 LC_NAME=C LC_ADDRESS=C LC_TELEPHONE=C [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C attached base packages: [1] stats graphics grDevices utils datasets methods base loaded via a namespace (and not attached): [1] compiler_4.1.2 Matrix_1.3-4 tools_4.1.2 expm_0.999-6 grid_4.1.2 lattice_0.20-45 #~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ > sessionInfo() # for a third Linux machine not having the problem R version 4.1.1 (2021-08-10) Platform: x86_64-pc-linux-gnu (64-bit) Running under: Linux Mint 19.3 Matrix products: default BLAS/LAPACK: /opt/intel/compilers_and_libraries_2020.0.166/linux/mkl/lib/intel64_lin/libmkl_rt.so locale: [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C LC_TIME=en_US.UTF-8 [4] LC_COLLATE=en_US.UTF-8 LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8 [7] LC_PAPER=en_US.UTF-8 LC_NAME=C LC_ADDRESS=C [10] LC_TELEPHONE=C LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C attached base packages: [1] stats graphics grDevices utils datasets methods base loaded via a namespace (and not attached): [1] compiler_4.1.1 tools_4.1.1 Thomas R. LaBone PhD student Department of Epidemiology and Biostatistics Arnold School of Public Health University of South Carolina Columbia, South Carolina USA [[alternative HTML version deleted]] ______________________________________________ R-help@r-project.org<mailto:R-help@r-project.org> mailing list -- To UNSUBSCRIBE and more, see https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. [[alternative HTML version deleted]]
______________________________________________ R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.