I am running the R-0.62.0 snapshot on a Linux system. This system has
128 Mb of real memory and almost never swaps. I am trying to use
lme() on a very large example (7200 observations, 10 columns in the
fixed effects, 2 columns in the random effects). We have the
optimization nicely tuned so that goes relatively quickly. It seems,
though, that all the data manipulation steps before the optimization
are taking a rather long time. I haven't compared on the same machine
but R is much slower - like an order of magnitude - than S-PLUS on
this problem.
It looks curious to me when I run system.time() on this that timing
vector shows almost no user time but a huge amount of system time.
R> system.time(assign("fm2",
+ lme(MathAch ~ MEANSES*CSES + Sector + CSES:Sector, ttt, ~ CSES | School,
+ RML = TRUE )))
iteration = 0
Step:
[1] 0 0 0
Parameter:
[1] 2.61400 0.16608 3.88195
Function Value
[1] 44964
Gradient:
[1] -0.014379 -0.143176 -0.646558
iteration = 1
Step:
[1] 0.002888 0.028756 0.129857
Parameter:
[1] 2.61688 0.19483 4.01181
Function Value
[1] 44964
Gradient:
[1] -0.069529 0.539316 0.094097
...
iteration = 6
Parameter:
[1] 2.61636 0.17797 3.98709
Function Value
[1] 44964
Gradient:
[1] 8.3428e-06 1.3824e-04 3.1205e-04
Relative gradient close to zero.
Current iterate is probably solution.
[1] 1.09 288.05 289.00 0.00 0.00
I can't really believe that it took only 1 second of user time and 288
seconds of system time. It didn't even do garbage collection in R (I
had gcinfo(T) set) and it wasn't swapping.
A call to proc.time() directly shows most of the time used is system
time.
R> proc.time()
[1] 16.30 577.01 13679.00 0.02 0.23
I looked at the code in src/unix/system.c and the structure seems
consistent. Has anyone else tested system.time() extensively on a
Linux system? Anyone have any ideas what might be going on?
Just for reference, this is a Debian GNU/Linux "hamm" system using
libc6. I am running R with the options shown below.
USER PID %CPU %MEM SIZE RSS TTY STAT START TIME COMMAND
bates 31073 3.8 41.1 54340 52620 p0 S 10:47 9:53
/usr/src/packages/r-base/r-base-0.62.0/bin/R.binary -v 40 -n 500000
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