FYI, GROMACS/2023.1 is now merged, so PR 18171 should be good to use. ________________________________________ From: [email protected] <[email protected]> on behalf of Åke Sandgren <[email protected]> Sent: Tuesday, June 27, 2023 7:27 To: [email protected] Subject: [easybuild] Re: Gromacs build issue : GROMACS-2021.5-foss-2021b-CUDA-11.4.1.eb
Yeah, known (but not well documented) problem with jammy and old CUDA related packages. You need to stick to 2022a toolchain with CUDA 11.7.0 on Jammy. I'm currently working on getting GROMACS/2023.1 ready for 2022a with CUDA 11.7.0 where this is not a problem. It'll take a while longer before I drop the "WIP" flag on PR 18171 (https://github.com/easybuilders/easybuild-easyconfigs/pull/18171) then it needs to go through review etc before getting merged. There are some changes in libc between bionic and jammy that CUDA 11.4 is capable of dealing with. ________________________________________ From: [email protected] <[email protected]> on behalf of Borut Rozman <[email protected]> Sent: Tuesday, June 27, 2023 0:11 To: [email protected] Subject: [easybuild] Gromacs build issue : GROMACS-2021.5-foss-2021b-CUDA-11.4.1.eb Hi everyone, I am trying to build gromacs with cuda 11.4.1 with the eb file in the subject line. I am using this command eb GROMACS-2021.5-foss-2021b-CUDA-11.4.1.eb --robot --optarch=GENERIC - -cuda-compute-capabilities=8.6 I am getting an error: -- Check for working NVCC/C compiler combination - broken -- /apps/software/CUDA/11.4.1/bin/nvcc standard output: '' -- /apps/software/CUDA/11.4.1/bin/nvcc standard error: '/usr/include/stdio.h(189): error: attribute "__malloc__" does not take arguments /usr/include/stdio.h(201): error: attribute "__malloc__" does not take arguments /usr/include/stdio.h(223): error: attribute "__malloc__" does not take arguments /usr/include/stdio.h(260): error: attribute "__malloc__" does not take arguments /usr/include/stdio.h(285): error: attribute "__malloc__" does not take arguments /usr/include/stdio.h(294): error: attribute "__malloc__" does not take arguments /usr/include/stdio.h(303): error: attribute "__malloc__" does not take arguments /usr/include/stdio.h(309): error: attribute "__malloc__" does not take arguments /usr/include/stdio.h(315): error: attribute "__malloc__" does not take arguments /usr/include/stdio.h(830): error: attribute "__malloc__" does not take arguments /usr/include/stdlib.h(566): error: attribute "__malloc__" does not take arguments /usr/include/stdlib.h(570): error: attribute "__malloc__" does not take arguments /usr/include/stdlib.h(799): error: attribute "__malloc__" does not take arguments 13 errors detected in the compilation of "/apps/tmp/GROMACS/2021.5/foss-2021b-CUDA-11.4.1/gromacs- 2021.5/cmake/TestCUDA.cu". details of my system uname -a Linux genoa 5.15.0-75-generic #82-Ubuntu SMP Tue Jun 6 23:10:23 UTC 2023 x86_64 x86_64 x86_64 GNU/Linux lsb_release -a No LSB modules are available. Distributor ID: Ubuntu Description: Ubuntu 22.04.2 LTS Release: 22.04 Codename: jammy Any help is much appreciated. Kind regards Borut
