On 12-10-26 12:15 PM, Prof Brian Ripley wrote:
On 26/10/2012 16:37, Paul Gilbert wrote:
Is --with-blas="-lgoto2" a known problem (other than possibly not being
the preferred choice)?
And what precisely is it? And what chipset are you using?
I thought I had been testing RC with the same setup I regularly use, but
I now see there was a slight difference. I am now getting the following
failure in make check on 32-bit Ubuntu 12.04, configuring with
--with-blas="-lgoto2". (These may not be surprising statistically or
numerically, but it is a bit disconcerting when make check fails.)
No failure shown here ... surely you know that the signs of principal
components are not determined?
I apologize, I missed the real error. (But yes, I am aware of this, and
also that I should expect precision differences with different libraries
and different architectures.) I thought for a moment that make was
throwing an error because of the differences, but in fact it was later:
Testing examples for package ‘grid’
comparing ‘grid-Ex.Rout’ to ‘grid-Ex.Rout.save’ ... OK
Testing examples for package ‘splines’
Error: testing 'splines' failed
Execution halted
make[3]: *** [test-Examples-Base] Error 1
make[3]: Leaving directory `/home/paul/RoboAdmin/R-2.15.2/tests/Examples'
make[2]: *** [test-Examples] Error 2
make[2]: Leaving directory `/home/paul/RoboAdmin/R-2.15.2/tests'
make[1]: *** [test-all-basics] Error 1
make[1]: Leaving directory `/home/paul/RoboAdmin/R-2.15.2/tests'
make: *** [check] Error 2
paul@toaster:~/RoboAdmin/R-2.15.2$
The problem seems to be here:
> source("~/RoboAdmin/R-2.15.2/tests/Examples/splines-Ex.R")
List of 2
$ x: num [1:51] 58 58.3 58.6 58.8 59.1 ...
$ y: num [1:51] 115 115 116 117 117 ...
- attr(*, "class")= chr "xyVector"
Warning in bs(height, degree = 3L, knots = c(62.6666666666667,
67.3333333333333 :
some 'x' values beyond boundary knots may cause ill-conditioned bases
Error: identical(ns(x, df = 2), ns(x, df = 2, knots = NULL)) is not TRUE
> traceback()
6: stop(paste0(ch, " is not ", if (length(r) > 1L) "all ", "TRUE"),
call. = FALSE)
5: stopifnot(identical(ns(x), ns(x, df = 1)), identical(ns(x, df = 2),
ns(x, df = 2, knots = NULL)), !is.null(kk <- attr(ns(x),
"knots")), length(kk) == 0) at splines-Ex.R#130
4: eval(expr, envir, enclos)
3: eval(ei, envir)
2: withVisible(eval(ei, envir))
1: source("~/RoboAdmin/R-2.15.2/tests/Examples/splines-Ex.R")
>
It also seems that this error is transient. If I rerun several times, it
does not always happen. Is anyone aware of other cases of transient
problems with 32-bit goto2?
Here is the cpu info:
paul@toaster:~$ cat /proc/cpuinfo
processor : 0
vendor_id : GenuineIntel
cpu family : 6
model : 15
model name : Intel(R) Core(TM)2 Duo CPU T7300 @ 2.00GHz
stepping : 10
microcode : 0x92
cpu MHz : 800.000
cache size : 4096 KB
physical id : 0
siblings : 2
core id : 0
cpu cores : 2
apicid : 0
initial apicid : 0
fdiv_bug : no
hlt_bug : no
f00f_bug : no
coma_bug : no
fpu : yes
fpu_exception : yes
cpuid level : 10
wp : yes
flags : fpu vme de pse tsc msr pae mce cx8 apic mtrr pge mca cmov pat
pse36 clflush dts acpi mmx fxsr sse sse2 ss ht tm pbe nx lm constant_tsc
arch_perfmon pebs bts aperfmperf pni dtes64 monitor ds_cpl vmx est tm2
ssse3 cx16 xtpr pdcm lahf_lm ida dtherm tpr_shadow vnmi flexpriority
bogomips : 3989.99
clflush size : 64
cache_alignment : 64
address sizes : 36 bits physical, 48 bits virtual
power management:
processor : 1
vendor_id : GenuineIntel
cpu family : 6
model : 15
model name : Intel(R) Core(TM)2 Duo CPU T7300 @ 2.00GHz
stepping : 10
microcode : 0x92
cpu MHz : 800.000
cache size : 4096 KB
physical id : 0
siblings : 2
core id : 1
cpu cores : 2
apicid : 1
initial apicid : 1
fdiv_bug : no
hlt_bug : no
f00f_bug : no
coma_bug : no
fpu : yes
fpu_exception : yes
cpuid level : 10
wp : yes
flags : fpu vme de pse tsc msr pae mce cx8 apic mtrr pge mca cmov pat
pse36 clflush dts acpi mmx fxsr sse sse2 ss ht tm pbe nx lm constant_tsc
arch_perfmon pebs bts aperfmperf pni dtes64 monitor ds_cpl vmx est tm2
ssse3 cx16 xtpr pdcm lahf_lm ida dtherm tpr_shadow vnmi flexpriority
bogomips : 3989.97
clflush size : 64
cache_alignment : 64
address sizes : 36 bits physical, 48 bits virtual
power management:
Paul
And 32-bit platforms seem prone to round in different ways (to each
other and to 64-bit platforms): the differences in the last digit are
typical of 32-bit platforms.
...
Testing examples for package ‘stats’
comparing ‘stats-Ex.Rout’ to ‘stats-Ex.Rout.save’ ...
2959c2959
< N:K 1 33.13 33.13 2.146 0.16865
---
> N:K 1 33.14 33.14 2.146 0.16865
12782c12782
< Murder -0.536 0.418 0.341 0.649
---
> Murder -0.536 0.418 -0.341 0.649
12783c12783
< Assault -0.583 0.188 0.268 -0.743
---
> Assault -0.583 0.188 -0.268 -0.743
12784c12784
< UrbanPop -0.278 -0.873 0.378 0.134
---
> UrbanPop -0.278 -0.873 -0.378 0.134
12785c12785
< Rape -0.543 -0.167 -0.818
---
> Rape -0.543 -0.167 0.818
12943c12943
< 6 -0.5412 20.482886 -0.845157
---
> 6 -0.5412 20.482887 -0.845157
14481c14481
< Sum of Squares 780.1250 276.1250 2556.1250 112.5000 774.0937
---
> Sum of Squares 780.1250 276.1250 2556.1250 112.5000 774.0938
15571c15571
< Murder -0.54 0.42 0.34 0.65
---
> Murder -0.54 0.42 -0.34 0.65
15572c15572
< Assault -0.58 0.27 -0.74
---
> Assault -0.58 -0.27 -0.74
15573c15573
< UrbanPop -0.28 -0.87 0.38
---
> UrbanPop -0.28 -0.87 -0.38
15574c15574
< Rape -0.54 -0.82
---
> Rape -0.54 0.82
Testing examples for package ‘datasets’
comparing ‘datasets-Ex.Rout’ to ‘datasets-Ex.Rout.save’ ... OK
...
I inadvertently seemed to have set things slightly differently while
testing RC. While testing the RC, I was using
./configure --prefix=/home/paul/RoboRC/R-test/ --enable-R-shlib
and configure gave
...
External libraries: readline
Additional capabilities: PNG, NLS
Options enabled: shared R library, shared BLAS, R
profiling, Java
whereas with the release I used
./configure --prefix=/home/paul/RoboAdmin/R-2.15.2 --enable-R-shlib
--with-blas="-lgoto2"
and configure gave
...
External libraries: readline, BLAS(generic)
Additional capabilities: PNG, NLS
Options enabled: shared R library, R profiling, Java
Thanks,
Paul
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