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. -- Jurij Pečar HPC Engineer, IT Operations, IT Services EMBL Heidelberg, Meyerhofstraße 1, 69117, Heidelberg, Germany Room 13-401
