Is --with-blas="-lgoto2" a known problem (other than possibly not being the preferred choice)? 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.) ... 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
R 2.15.2 make check failure on 32-bit --with-blas="-lgoto2"
3 messages · Paul Gilbert, Brian Ripley
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? 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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Brian D. Ripley, ripley at stats.ox.ac.uk Professor of Applied Statistics, http://www.stats.ox.ac.uk/~ripley/ University of Oxford, Tel: +44 1865 272861 (self) 1 South Parks Road, +44 1865 272866 (PA) Oxford OX1 3TG, UK Fax: +44 1865 272595
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 at 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 at 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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