В Sat, 30 Mar 2024 10:55:48 +0000 Ramón Fallon <ramonfal...@gmail.com> пишет:
> In contrast to Dirk's solution, I've found R's configure script > doesn't recognise the update-alternatives system on debian/ubuntu, if > it's MKL. It ought to work if configured with --with-blas=-lblas --with-lapack=-llapack, but, as you found out (and I can confirm), if libblas.so and liblapack.so already point to MKL, ./configure somehow fails the test for zdotu and falls back to bundled Rblas and Rlapack. If you'd like the built R to work with the update-alternatives system, the workaround seems to help is to temporarily switch the alternatives to reference BLAS & LAPACK, configure and build R, and then switch the alternatives back to MKL. > appending "-lmkl_gf_lp64" to the --with-blas option does not help > (that's suggested by several posts out there). MKL has an official "link line advisor" at <https://www.intel.com/content/www/us/en/developer/tools/oneapi/onemkl-link-line-advisor.html>, which may suggest a completely different set of linker options depending on what it is told. Here's how R's zdotu test always fails when linking directly with MKL: # pre-configure some variables echo '#define HAVE_F77_UNDERSCORE 1' > confdefs.h FC=gfortran FFLAGS='-g -Og' CC=gcc CFLAGS='-g -Og' CPPFLAGS=-I/usr/local/include MAIN_LDFLAGS='-Wl,--export-dynamic -fopenmp' LDFLAGS='-L/usr/local/lib' LIBM=-lm FLIBS=' -lgfortran -lm -lquadmath' # copied & pasted from the Intel web page BLAS_LIBS='-lmkl_rt -Wl,--no-as-needed -lpthread -lm -ldl' # R prepares to call zdotu from Fortran... cat > conftestf.f <<EOF c Goto's BLAS at least needs a XERBLA subroutine xerbla(srname, info) character*6 srname integer info end subroutine test1(iflag) double complex zx(2), ztemp, zres, zdotu integer iflag zx(1) = (3.1d0,1.7d0) zx(2) = (1.6d0,-0.6d0) zres = zdotu(2, zx, 1, zx, 1) ztemp = (0.0d0,0.0d0) do 10 i = 1,2 ztemp = ztemp + zx(i)*zx(i) 10 continue if(abs(zres - ztemp) > 1.0d-10) then iflag = 1 else iflag = 0 endif end EOF ${FC} ${FFLAGS} -c conftestf.f # and then call the Fortran subroutine from the C runner... cat > conftest.c <<EOF #include <stdlib.h> #include "confdefs.h" #ifdef HAVE_F77_UNDERSCORE # define F77_SYMBOL(x) x ## _ #else # define F77_SYMBOL(x) x #endif extern void F77_SYMBOL(test1)(int *iflag); int main () { int iflag; F77_SYMBOL(test1)(&iflag); exit(iflag); } EOF ${CC} ${CPPFLAGS} ${CFLAGS} -c conftest.c # and then finally link and execute the program ${CC} ${CPPFLAGS} ${CFLAGS} ${LDFLAGS} ${MAIN_LDFLAGS} \ -o conftest conftest.o conftestf.o \ ${BLAS_LIBS} ${FLIBS} ${LIBM} ./conftest It seems to crash inside MKL! rax=ffffffffcccccccd rbx=00005590ee102008 rcx=00007ffdab2ddb20 rdx=00005590ee102008 rsi=00007ffdab2ddb18 rdi=00005590ee10200c rbp=00007ffdab2dd910 rsp=00007ffdab2db600 r8=00005590ee102008 r9=00007ffdab2ddb28 r10=00007f4086a99178 r11=00007f4086e02490 r12=00005590ee10200c r13=00007ffdab2ddb20 r14=00005590ee102008 r15=00007ffdab2ddb28 ip = 7f4086e02a60, sp = 7ffdab2db600 [mkl_blas_zdotu+1488] ip = 7f4085dc5250, sp = 7ffdab2dd920 [zdotu+256] ip = 5590ee1011cc, sp = 7ffdab2ddb40 [test1_+91] ip = 5590ee101167, sp = 7ffdab2ddb70 [main+14] It's especially strange that R does seem to work if you just update-alternatives after linking it with the reference BLAS, but ./conftest starts crashing again in the same place. This is with Debian's MKL version 2020.4.304-4, by the way. -- Best regards, Ivan ______________________________________________ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
