Martin Maechler
2022-Dec-17 09:46 UTC
[R-sig-Fedora] Using ATLAS in Fedora 36, R-4.2.2 -- fails configure
>>>>> I?aki Ucar >>>>> on Fri, 16 Dec 2022 17:30:25 +0100 writes:> On Fri, 16 Dec 2022 at 17:06, Martin Maechler > <maechler at stat.math.ethz.ch> wrote: >> >> The CRAN team has found some misbehavior of some of our >> code running under ATLAS (for BLAS + Lapack). >> >> I had successfully built a version of R-4.2.1 linked to >> ATLAS under Fedora 34 (last June) and that still runs in >> Fedora 36. >> >> However I can not install packages with C source code >> needing BLAS/Lapack.. I figured that's ok, as indeed >> that version of R was built with earlier compilers and >> libraries under F34. >> >> So I wanted to "redo" the same thing (which worked), now >> with F36 and R 4.2.2: >> >> inside a build directory (side by side with the unpacked >> R-4.2.2/ R sources) >> >> ../R-4.2.2/configure -C '--with-blas=-L/usr/lib64/atlas >> -ltatlas' >> >> and this "worked along" about 400 lines of output >> starting with >> >> checking build system type... x86_64-pc-linux-gnu >> checking host system type... x86_64-pc-linux-gnu loading >> site script '../R-4.2.2/config.site' checking for >> pwd... /usr/bin/pwd checking whether builddir is >> srcdir... no checking whether ln -s works... yes checking >> for ar... ar checking for a BSD-compatible >> install... /usr/bin/install -c checking for >> sed... /usr/bin/sed >> >> ....................................... >> ....................................... >> ....................................... >> ....................................... >> ....................................... >> ....................................... and ending with >> >> checking whether catan exists and is declared... yes >> checking whether ccosh exists and is declared... yes >> checking whether csinh exists and is declared... yes >> checking whether ctanh exists and is declared... yes >> checking for working ctanh... yes checking whether >> 'struct tm' includes tm_zone... yes checking whether >> 'struct tm' includes tm_gmtoff... yes checking for dgemm_ >> in -L/usr/lib64/atlas -ltatlas... no configure: error: >> BLAS was specified but not available >> ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ >> >> but clearly /usr/lib64/atlas/ is there and contains the >> (dnf installed) files libtatlas.so.* >> >> $ ls -l /usr/lib64/atlas total 24672 lrwxrwxrwx. 1 root >> root 17 Jan 19 2022 libsatlas.so.3 -> libsatlas.so.3.10 >> -rwxr-xr-x. 1 root root 12581672 Jan 19 2022 >> libsatlas.so.3.10 lrwxrwxrwx. 1 root root 17 Jan 19 2022 >> libtatlas.so.3 -> libtatlas.so.3.10 -rwxr-xr-x. 1 root >> root 12679024 Jan 19 2022 libtatlas.so.3.10 $ > The unversioned file libtatlas.so is missing here, which > means that you need to install atlas-devel. Then it should > work, but let me know if you find more issues. Embarrassingly, this *was* the simple solution. Thank you, I?aki! Martin > I?aki >> and no, I can't use nm to find symbols in >> libtatlas.so.3.10 because it is "stripped". >> >> I'm glad for hints -- and I could send the 10000 lines >> long config.log file (just 340k) to someone interested. >> >> Thank you in advance, Martin >> >> Martin M?chler ETH Zurich and R Core team