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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