[Rd] R test suite LAPACK error with AOCL

[peter dalgaard]

Optimized numeric libraries are prone to getting slightly different results, which can trip up the checks. Howver, this case seems to be one of not passing NaN values properly:

What should happen is this

> a <- matrix(NaN, 3, 3,, list(one=1:3, two=letters[1:3]))
> b <- cbind(1:3, NA)
> solve(a,b)
  [,1] [,2]
a  NaN   NA
b  NaN   NA
c  NaN   NA
> a
   two
one   a   b   c
  1 NaN NaN NaN
  2 NaN NaN NaN
  3 NaN NaN NaN
>

but somewhere along the way, the computations are creating a 0 out of the NaN in the coefficient matrix. This look like dangerous behaviour that R cannot support.

-pd

> On 21 Jan 2025, at 14:42 , Christian Tuma <tuma using zib.de> wrote:
> 
> Hello,
> 
> We are running an AMD-Genoa compute cluster. For this system I compiled R-4.4.2 configured and linked against AMD Optimizing CPU Libraries (AOCL) downloaded from
> 
> https://www.amd.com/en/developer/aocl.html
> 
> When running the R test suite (make check), I get this error:
> 
> $ cat tests/lapack.Rout.fail
> ...
> > ##  -------  tests of non-finite values  -----------------
> >
> > a <- matrix(NaN, 3, 3,, list(one=1:3, two=letters[1:3]))
> > b <- cbind(1:3, NA)
> > dimnames(b) <- list(One=4:6, Two=11:12)
> > bb <- 1:3; names(bb) <- 11:12
> > ## gave error with LAPACK 3.11.0
> > ## names(dimnames(.)), ("two", "Two") are lost {FIXME?}:
> > ## IGNORE_RDIFF_BEGIN
> > stopifnot(is.na(print(solve(a, b )))) # is.na(): NA *or* NaN
> Error in solve.default(a, b) :
>  Lapack routine dgesv: system is exactly singular: U[1,1] = 0
> Calls: stopifnot -> print -> solve -> solve.default
> Execution halted
> 
> Now I wonder whether AOCL are supported by R or not. Did somebody already use this combination successfully? Is this test suite error a serious problem? Is a workaround available?
> 
> This is my R installation configuration line:
> 
> $ CC=gcc CFLAGS="-O3 -march=znver4" \
> CXX=g++ CXXFLAGS="-O3 -march=znver4" \
> FC=gfortran FCFLAGS="-O3 -march=znver4" \
> LDFLAGS="-Wl,-rpath=$GCC_PATH/lib64" \
> ../configure \
> --with-blas="-L/usr/lib64 -Wl,-rpath=$AOCL_ROOT/lib_LP64 -L$AOCL_ROOT/lib_LP64 -lblis -lflame" \
> --with-lapack \
> --enable-year2038
> 
> I am using the GCC (13.3.0).
> 
> > sessionInfo()
> R version 4.4.2 (2024-10-31)
> Platform: x86_64-pc-linux-gnu
> Running under: Rocky Linux 9.4 (Blue Onyx)
> 
> Matrix products: default
> BLAS:   /sw/numerics/aocl/5.0.0/gcc/lib_LP64/libblis.so.5.0.0
> LAPACK: /sw/numerics/aocl/5.0.0/gcc/lib_LP64/libflame.so;  LAPACK version 3.11.0
> ...
> 
> 
> With Intel MKL instead of AOCL the test suite passes without errors. But this is an AMD system, so here I tend to prefer AOCL over MKL.
> 
> Any ideas? Thank you.
> 
> 
> Best wishes,
> Christian
> 
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-- 
Peter Dalgaard, Professor,
Center for Statistics, Copenhagen Business School
Solbjerg Plads 3, 2000 Frederiksberg, Denmark
Phone: (+45)38153501
Office: A 4.23
Email: pd.mes using cbs.dk  Priv: PDalgd using gmail.com