> On 12 Mar 2024, at 15:01, Jure Pečar <[email protected]> wrote: > > On Tue, 12 Mar 2024 12:31:16 +0000 > Borut Rozman <[email protected]> wrote: > >> Hi, >> >> I have a situation with bedtools, specifically in AMD chipset. >> >> I have build bedtools 3.5.1-foss-2021b on an INTEL with -optarch >> GENERIC flag but it still crashes under AMD, >> >> the onlything I get is Illegal instruction (core dumped) and in dmesg: >> >> >> traps: plotCorrelation[591375] trap invalid opcode ip:7f246960fbd0 >> sp:7fff258064b8 error:0 in libopenblas_skylakexp- >> r0.3.18.so[7f2469295000+ebd000] > > Did you built just deeptools with -optarch GENERIC or the rest of the > toolchain too? This looks like something in plotCorrelations picks up > skylake branch of blas functions which most likely include avx512 calls. > And those would only work on zen4 and produce "illegal instruction" on > older amd cpus.
Also note that OpenBLAS does not adhere to optarch, as per https://github.com/easybuilders/easybuild-easyconfigs/issues/9754. The solution is usually to have a hook add DYNAMIC_ARCH=1 for OpenBLAS. Something like this (adopted from EESSI): pre_configure_hook(self, *args, **kwargs): if self.name == 'OpenBLAS’: if build_option('optarch') == OPTARCH_GENERIC: for step in ('build', 'test', 'install’): self.cfg.update(f'{step}opts', "DYNAMIC_ARCH=1”) See https://docs.easybuild.io/hooks/ for more information about hooks. :) -- Terje Kvernes Head sysadmin Department of Mathematics University of Oslo
