On 02/12/2021 5:50 a.m., Labone, Thomas 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?
The likely location of this problem is the BLAS. You are using
BLAS/LAPACK: /usr/lib/x86_64-linux-gnu/libmkl_rt.so
on the bad machines, and
BLAS/LAPACK:
/opt/intel/compilers_and_libraries_2020.0.166/linux/mkl/lib/intel64_lin/libmkl_rt.so
>
on the good one, according to the sessionInfo you posted. I don't have
any experience dealing with such things, but that's where I'd look for a
fix.
Duncan Murdoch
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
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