Hi, All versions of icc requires a standard library from an installation of gcc. There are various dependencies between them, and your system admins should have an idea which one is known to work well in your case. If you need to help the GROMACS build find the right one, do check out the GROMACS install guide for how to direct a particular gcc to be used with icc. I would suggest nothing earlier than gcc 5.
Mark On Mon, 26 Aug 2019 at 17:51, Prithwish Nandi <prithwish.na...@ichec.ie> wrote: > Hi, > I am trying to compile Gromacs-2019.3 at our HPC cluster. I successfully > compiled the single and double precision versions, but it’s producing error > for GPU support. (The error message is pasted below) > > I am using Intel/2018 update 4 and CUDA/10.0. The base gcc version is > 4.8.5. Using MKL as the FFTW lib and mliicc as the C compiler, and mpiicpc > as the CXX compiler. > > The error I am getting is given below. > > Do you have any clue for this? > > Thanks, //PN > > The error message: > > Error generating file > > /xxx/xxx/gromacs/intel/2019.3/kay/gromacs-2019.3/build_gpu/src/gromacs/CMakeFiles/libgromacs.dir/mdlib/nbnxn_cuda/./libgromacs_generated_nbnxn_cuda_kernel_pruneonly.cu.o > > > make[2]: *** > [src/gromacs/CMakeFiles/libgromacs.dir/mdlib/nbnxn_cuda/libgromacs_generated_nbnxn_cuda_kernel_pruneonly.cu.o] > Error 1 > /usr/include/c++/4.8.5/x86_64-redhat-linux/bits/opt_random.h(68): error: > identifier "_mm_set1_epi64x" is undefined > > /usr/include/c++/4.8.5/x86_64-redhat-linux/bits/opt_random.h(70): error: > identifier "_mm_set1_pd" is undefined > > /usr/include/c++/4.8.5/x86_64-redhat-linux/bits/opt_random.h(112): error: > identifier "_mm_set_epi64x" is undefined > > /usr/include/c++/4.8.5/x86_64-redhat-linux/bits/opt_random.h(123): error: > identifier "_mm_set_epi64x" is undefined > > /usr/include/c++/4.8.5/x86_64-redhat-linux/bits/opt_random.h(123): error: > identifier "_mm_and_si128" is undefined > > /usr/include/c++/4.8.5/x86_64-redhat-linux/bits/opt_random.h(172): error: > identifier "_mm_set_epi64x" is undefined > > /usr/include/c++/4.8.5/x86_64-redhat-linux/bits/opt_random.h(175): error: > identifier "_mm_or_si128" is undefined > > /usr/include/c++/4.8.5/x86_64-redhat-linux/bits/opt_random.h(176): error: > identifier "_mm_sub_pd" is undefined > > /usr/include/c++/4.8.5/x86_64-redhat-linux/bits/opt_random.h(177): error: > identifier "_mm_mul_pd" is undefined > > /usr/include/c++/4.8.5/x86_64-redhat-linux/bits/opt_random.h(178): error: > identifier "_mm_hadd_pd" is undefined > > /usr/include/c++/4.8.5/x86_64-redhat-linux/bits/opt_random.h(178): error: > identifier "_mm_cvtsd_f64" is undefined > > /usr/include/c++/4.8.5/x86_64-redhat-linux/bits/opt_random.h(185): error: > identifier "_mm_mul_pd" is undefined > > /usr/include/c++/4.8.5/x86_64-redhat-linux/bits/opt_random.h(185): error: > identifier "_mm_add_pd" is undefined > > /usr/include/c++/4.8.5/x86_64-redhat-linux/bits/opt_random.h(187): error: > identifier "_mm_storeu_pd" is undefined > > /usr/include/c++/4.8.5/x86_64-redhat-linux/bits/opt_random.h(68): error: > identifier "_mm_set1_epi64x" is undefined > > /usr/include/c++/4.8.5/x86_64-redhat-linux/bits/opt_random.h(70): error: > identifier "_mm_set1_pd" is undefined > > /usr/include/c++/4.8.5/x86_64-redhat-linux/bits/opt_random.h(112): error: > identifier "_mm_set_epi64x" is undefined > > /usr/include/c++/4.8.5/x86_64-redhat-linux/bits/opt_random.h(123): error: > identifier "_mm_set_epi64x" is undefined > > /usr/include/c++/4.8.5/x86_64-redhat-linux/bits/opt_random.h(123): error: > identifier "_mm_and_si128" is undefined > > /usr/include/c++/4.8.5/x86_64-redhat-linux/bits/opt_random.h(172): error: > identifier "_mm_set_epi64x" is undefined > > /usr/include/c++/4.8.5/x86_64-redhat-linux/bits/opt_random.h(175): error: > identifier "_mm_or_si128" is undefined > > /usr/include/c++/4.8.5/x86_64-redhat-linux/bits/opt_random.h(176): error: > identifier "_mm_sub_pd" is undefined > > /usr/include/c++/4.8.5/x86_64-redhat-linux/bits/opt_random.h(177): error: > identifier "_mm_mul_pd" is undefined > > /usr/include/c++/4.8.5/x86_64-redhat-linux/bits/opt_random.h(178): error: > identifier "_mm_hadd_pd" is undefined > > /usr/include/c++/4.8.5/x86_64-redhat-linux/bits/opt_random.h(178): error: > identifier "_mm_cvtsd_f64" is undefined > > /usr/include/c++/4.8.5/x86_64-redhat-linux/bits/opt_random.h(185): error: > identifier "_mm_mul_pd" is undefined > > /usr/include/c++/4.8.5/x86_64-redhat-linux/bits/opt_random.h(185): error: > identifier "_mm_add_pd" is undefined > > /usr/include/c++/4.8.5/x86_64-redhat-linux/bits/opt_random.h(187): error: > identifier "_mm_storeu_pd" is undefined > > 14 errors detected in the compilation of > "/localscratch/397189/tmpxft_00006280_00000000-6_gpubonded-impl.cpp4.ii". > > > > > > > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
