From m.pacey at lancaster.ac.uk  Thu Oct 23 10:19:35 2014
From: m.pacey at lancaster.ac.uk (Pacey, Mike)
Date: Thu, 23 Oct 2014 08:19:35 +0000
Subject: [Rd] "make check" fails on lapack.R and stats-Ex.R
In-Reply-To: <737F5642A586344CA8A35D4826EFE56A15F0C6A9@EX-1-MB2.lancs.local>
References: <737F5642A586344CA8A35D4826EFE56A15F0C6A9@EX-1-MB2.lancs.local>
Message-ID: <737F5642A586344CA8A35D4826EFE56A15F0C7AE@EX-1-MB2.lancs.local>

As my attachment doesn't seem to have survived transit, I'm cut'n'pasting the relevant failures here:

Testing examples for package 'stats'
  comparing 'stats-Ex.Rout' to 'stats-Ex.Rout.save' ...
6466c6466
< Grand Mean: 291.5937
---
> Grand Mean: 291.5938
12881c12881
< Murder   -0.536  0.418  0.341  0.649
---
> Murder   -0.536  0.418 -0.341  0.649
12882c12882
< Assault  -0.583  0.188  0.268 -0.743
---
> Assault  -0.583  0.188 -0.268 -0.743
12883c12883
< UrbanPop -0.278 -0.873  0.378  0.134
---
> UrbanPop -0.278 -0.873 -0.378  0.134
12884c12884
< Rape     -0.543 -0.167 -0.818       
---
> Rape     -0.543 -0.167  0.818       
14628c14628
< Grand Mean: 291.5937
---
> Grand Mean: 291.5938
15777c15777
< Murder   -0.54   0.42   0.34   0.65 
---
> Murder   -0.54   0.42  -0.34   0.65 
15778c15778
< Assault  -0.58          0.27  -0.74 
---
> Assault  -0.58         -0.27  -0.74 
15779c15779
< UrbanPop -0.28  -0.87   0.38        
---
> UrbanPop -0.28  -0.87  -0.38        
15780c15780
< Rape     -0.54         -0.82        
---
> Rape     -0.54          0.82       


running code in 'lapack.R' ... OK
  comparing 'lapack.Rout' to './lapack.Rout.save' ...23,31c23,31
<  [1,] -0.7245 -0.6266 -0.27350  0.08527 -0.02074 -0.004025
<  [2,] -0.4282  0.1299  0.64294 -0.55047  0.27253  0.092816
<  [3,] -0.3122  0.2804  0.33633  0.31418 -0.61632 -0.440904
<  [4,] -0.2479  0.3142  0.06931  0.44667 -0.02945  0.530120
<  [5,] -0.2064  0.3141 -0.10786  0.30242  0.35567  0.237038
<  [6,] -0.1771  0.3027 -0.22106  0.09042  0.38879 -0.260449
<  [7,] -0.1553  0.2877 -0.29281 -0.11551  0.19286 -0.420945
<  [8,] -0.1384  0.2722 -0.33784 -0.29313 -0.11633 -0.160790
<  [9,] -0.1249  0.2571 -0.36543 -0.43885 -0.46497  0.434600
---
>  [1,] -0.7245  0.6266  0.27350 -0.08527  0.02074 -0.004025
>  [2,] -0.4282 -0.1299 -0.64294  0.55047 -0.27253  0.092816
>  [3,] -0.3122 -0.2804 -0.33633 -0.31418  0.61632 -0.440904
>  [4,] -0.2479 -0.3142 -0.06931 -0.44667  0.02945  0.530120
>  [5,] -0.2064 -0.3141  0.10786 -0.30242 -0.35567  0.237038
>  [6,] -0.1771 -0.3027  0.22106 -0.09042 -0.38879 -0.260449
>  [7,] -0.1553 -0.2877  0.29281  0.11551 -0.19286 -0.420945
>  [8,] -0.1384 -0.2722  0.33784  0.29313  0.11633 -0.160790
>  [9,] -0.1249 -0.2571  0.36543  0.43885  0.46497  0.434600
35,40c35,40
< [1,] -0.7365 -0.6225 -0.2550  0.06976 -0.01328 -0.001588
< [2,] -0.4433  0.1819  0.6867 -0.50860  0.19627  0.041117
< [3,] -0.3275  0.3509  0.2611  0.50474 -0.61606 -0.259216
< [4,] -0.2626  0.3922 -0.1044  0.43748  0.40834  0.638902
< [5,] -0.2204  0.3946 -0.3510 -0.01612  0.46428 -0.675827
< [6,] -0.1904  0.3832 -0.5111 -0.53856 -0.44664  0.257249
---
> [1,] -0.7365  0.6225  0.2550 -0.06976  0.01328 -0.001588
> [2,] -0.4433 -0.1819 -0.6867  0.50860 -0.19627  0.041117
> [3,] -0.3275 -0.3509 -0.2611 -0.50474  0.61606 -0.259216
> [4,] -0.2626 -0.3922  0.1044 -0.43748 -0.40834  0.638902
> [5,] -0.2204 -0.3946  0.3510  0.01612 -0.46428 -0.675827
> [6,] -0.1904 -0.3832  0.5111  0.53856  0.44664  0.257249


-----Original Message-----
From: r-devel-bounces at r-project.org [mailto:r-devel-bounces at r-project.org] On Behalf Of Pacey, Mike
Sent: 22 October 2014 17:02
To: r-devel at r-project.org
Subject: [Rd] "make check" fails on lapack.R and stats-Ex.R

Hi folks,

I suspect this is a request for a sanity check than a bug report:

I've been successfully compiling an optimised version of R for several years using the Intel compiler and MKL. I've just test-run the new Intel 15.0 compiler suite, and I'm seeing a few numeric failures that I don't see using the same build method with Intel 13.0. I've attached the output of "make check". Build details are below.

The most notable failures are in lapack.R, though I see from the comments in the output that different lapack and blas libraries may produce different signs for some outputs which can be safely ignored. My linear algebra's a bit rusty, so I'd like a sanity check: can all the sign differences be safely ignored in the attached output? (And a possible RFC: at least for the purposes of make check, can the scripts output abs() values for all cases where sign isn't an issue?)

The other failures are in stats-Ex.R. It looks like most of the problem lines are outputs from a PCA-like function, so their sign differences might due to the eigenvalue exception comment in lapack.R.

The final failures are in the "Grand Total" lines from stats-Ex.R. The values differ in the 7th sig fig, so a pretty small relative error. I think I'm using compiler flags that rule out any fast-math imprecisions - so I'm wondering if this result is actually within the acceptable variation of the IEE 754 standard?

Build details:

OS is Scientific Linux 6.4, architecture is Westmere.

"icc -v" gives: icc version 15.0.0 (gcc version 4.4.7 compatibility)

Environment variables are:

export CC=icc
export CFLAGS="-O3 -xHOST -axCORE-AVX-I -fp-model precise"
export FC=ifort
export F77=ifort
export FFLAGS="-O3 -xHOST -axCORE-AVX-I -fp-model precise"
export FCFLAGS="-O3 -xHOST -axCORE-AVX-I -fp-model precise"
export CXX=icpc
export CXXFLAGS="-O3 -xHOST -axCORE-AVX-I -fp-model precise"
export JAVA_HOME=/etc/alternatives/java_sdk_1.6.0

Configure command is:

./configure --with-blas=-mkl=sequential --with-lapack=-mkl=sequential --disable-openmp --with-tcl-config=/usr/shared_apps/packages/tcl-8.5.12/lib/tclConfig.sh --with-tk-config=/usr/shared_apps/packages/tk-8.5.12/lib/tkConfig.sh

Regards,
Mike.

-----

Dr Mike Pacey,                                          Email: M.Pacey at lancaster.ac.uk<mailto:M.Pacey at lancaster.ac.uk>
HPC Manager,                                            Phone: 01524 510659
Information Systems Services,            Fax: 01524 594459
ISS Building, Lancaster University,
Lancaster LA1 4WA



[Rd] "make check" fails on lapack.R and stats-Ex.R
Pacey, Mike