Thanks Szilárd. My understanding is rdc is nvcc's equivalent of fpic. I get fpic errors without it. In fact I get fpic errors without including fpic explicitly in the C/CXX flags.
/usr/bin/ld: CMakeFiles/libgromacs.dir/mdlib/nbnxn_cuda/libgromacs_generated_nbnxn_cuda.cu.o: relocation R_X86_64_32 against `_Z58nbnxn_kernel_ElecEwQSTabTwinCut_VdwLJEwCombLB_F_prune_cuda11cu_atomdata10cu_nbparam8cu_plistb' can not be used when making a shared object; recompile with -fPIC So I removed boost, avx2, mpi, and dynamic but get the same result. What else should I remove? cmake .. -DCMAKE_VERBOSE_MAKEFILE:BOOL=TRUE -DCMAKE_C_COMPILER:FILEPATH=`which cc` -DCMAKE_C_FLAGS:STRING=-fPIC -DCMAKE_CXX_COMPILER:FILEPATH=`which CC` -DCMAKE_CXX_FLAGS:STRING=-fPIC -DCMAKE_INSTALL_PREFIX:PATH=$PREFIX -DGMX_FFT_LIBRARY=fftw3 -DFFTWF_LIBRARY:FILEPATH=${FFTW_DIR}/libfftw3f.so -DFFTWF_INCLUDE_DIR:PATH=$FFTW_INC -DGMX_GPU=ON -DCUDA_NVCC_FLAGS:STRING="-rdc=true" /opt/cray/pe/craype/2.5.13/bin/CC -march=core-avx2 -fPIC -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast CMakeFiles/template.dir/template.cpp.o -o ../../bin/template -Wl,-rpath,/p/work/borchert/gromacs-2018.1/build/lib ../../lib/libgromacs.so.3.1.0 -fopenmp -lm ../../lib/libgromacs.so.3.1.0: undefined reference to `__cudaRegisterLinkedBinary_59_tmpxft_000001e3_00000000_21_pmalloc_cuda_compute_61_cpp1_ii_63d60154' ../../lib/libgromacs.so.3.1.0: undefined reference to `__cudaRegisterLinkedBinary_57_tmpxft_0000a64f_00000000_21_pme_spread_compute_61_cpp1_ii_d982d3ad' ../../lib/libgromacs.so.3.1.0: undefined reference to `__cudaRegisterLinkedBinary_71_tmpxft_000003a4_00000000_21_cuda_version_information_compute_61_cpp1_ii_8ab8dc1d' ../../lib/libgromacs.so.3.1.0: undefined reference to `__cudaRegisterLinkedBinary_58_tmpxft_0000a80b_00000000_21_pme_timings_compute_61_cpp1_ii_75ae0e44' ../../lib/libgromacs.so.3.1.0: undefined reference to `__cudaRegisterLinkedBinary_56_tmpxft_0000a10b_00000000_21_pme_3dfft_compute_61_cpp1_ii_79dff388' ../../lib/libgromacs.so.3.1.0: undefined reference to `__cudaRegisterLinkedBinary_57_tmpxft_00009bd7_00000000_21_nbnxn_cuda_compute_61_cpp1_ii_f147f02c' ../../lib/libgromacs.so.3.1.0: undefined reference to `__cudaRegisterLinkedBinary_50_tmpxft_0000a9c8_00000000_21_pme_compute_61_cpp1_ii_6dbf966c' ../../lib/libgromacs.so.3.1.0: undefined reference to `__cudaRegisterLinkedBinary_56_tmpxft_0000a490_00000000_21_pme_solve_compute_61_cpp1_ii_06051a94' ../../lib/libgromacs.so.3.1.0: undefined reference to `__cudaRegisterLinkedBinary_56_tmpxft_0000ab85_00000000_21_cudautils_compute_61_cpp1_ii_25933dd5' ../../lib/libgromacs.so.3.1.0: undefined reference to `__cudaRegisterLinkedBinary_54_tmpxft_0000aefc_00000000_21_pinning_compute_61_cpp1_ii_5d0f4aae' ../../lib/libgromacs.so.3.1.0: undefined reference to `__cudaRegisterLinkedBinary_56_tmpxft_0000ad42_00000000_21_gpu_utils_compute_61_cpp1_ii_70828085' ../../lib/libgromacs.so.3.1.0: undefined reference to `__cudaRegisterLinkedBinary_57_tmpxft_0000a2d0_00000000_21_pme_gather_compute_61_cpp1_ii_a7a2f9c7' ../../lib/libgromacs.so.3.1.0: undefined reference to `__cudaRegisterLinkedBinary_67_tmpxft_00009f4e_00000000_21_nbnxn_cuda_data_mgmt_compute_61_cpp1_ii_a1eafeba' Chris -----Original Message----- From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se [mailto:gromacs.org_gmx-users-boun...@maillist.sys.kth.se] On Behalf Of Szilárd Páll Sent: Friday, April 06, 2018 10:17 AM To: Discussion list for GROMACS users <gmx-us...@gromacs.org> Cc: gromacs.org_gmx-users@maillist.sys.kth.se Subject: Re: [gmx-users] Problem with CUDA Hi, What is the reason for using the custom CMake options? What's the -rdc=true for -- I don't think it's needed and it can very well be causing the issue. Have you tried to actually do an as-vanilla-as-possible build? -- Szilárd On Thu, Apr 5, 2018 at 6:52 PM, Borchert, Christopher B ERDC-RDE-ITL-MS Contractor <christopher.b.borch...@erdc.dren.mil> wrote: > Hello. I'm taking a working build from a co-worker and trying to add GPU > support on a Cray XC. CMake works but make fails. Both 2016 and 2018 die at > the same point -- can't find gromac's own routines. > > 2016.5: > /opt/cray/pe/craype/2.5.13/bin/CC -march=core-avx2 -O2 -fPIC -dynamic > -std=c++0x -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast > -dynamic CMakeFiles/template.dir/template.cpp.o -o ../../bin/template > -Wl,-rpath,/p/work/cots/gromacs-2016.5/build/lib:/opt/nvidia/cudatoolkit8.0/8.0.54_2.3.12_g180d272-2.2/lib64/stubs > -dynamic ../../lib/libgromacs_mpi.so.2.5.0 -fopenmp -lcudart > /opt/nvidia/cudatoolkit8.0/8.0.54_2.3.12_g180d272-2.2/lib64/stubs/libnvidia-ml.so > -lhwloc -lz -ldl -lrt -lm -lfftw3f > ../../lib/libgromacs_mpi.so.2.5.0: undefined reference to > `__cudaRegisterLinkedBinary_59_tmpxft_0001bc78_00000000_21_pmalloc_cuda_compute_61_cpp1_ii_63d60154' > ../../lib/libgromacs_mpi.so.2.5.0: undefined reference to > `__cudaRegisterLinkedBinary_56_tmpxft_0001bac2_00000000_21_gpu_utils_compute_61_cpp1_ii_d70ebee0' > ../../lib/libgromacs_mpi.so.2.5.0: undefined reference to > `__cudaRegisterLinkedBinary_56_tmpxft_0001b90b_00000000_21_cudautils_compute_61_cpp1_ii_24d20763' > ../../lib/libgromacs_mpi.so.2.5.0: undefined reference to > `__cudaRegisterLinkedBinary_71_tmpxft_0001c016_00000000_21_cuda_version_information_compute_61_cpp1_ii_e35285be' > ../../lib/libgromacs_mpi.so.2.5.0: undefined reference to > `__cudaRegisterLinkedBinary_57_tmpxft_0001b592_00000000_21_nbnxn_cuda_compute_61_cpp1_ii_6e47f057' > ../../lib/libgromacs_mpi.so.2.5.0: undefined reference to > `__cudaRegisterLinkedBinary_67_tmpxft_0001b754_00000000_21_nbnxn_cuda_data_mgmt_compute_61_cpp1_ii_a1eafeba' > collect2: error: ld returned 1 exit status > > 2018.1: > /opt/cray/pe/craype/2.5.13/bin/CC -march=core-avx2 -O2 -fPIC -dynamic > -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast > -dynamic CMakeFiles/template.dir/template.cpp.o -o ../../bin/template > -Wl,-rpath,/p/work/cots/gromacs-2018.1/build/lib > ../../lib/libgromacs_mpi.so.3.1.0 -fopenmp -lm > ../../lib/libgromacs_mpi.so.3.1.0: undefined reference to > `__cudaRegisterLinkedBinary_56_tmpxft_000068a5_00000000_21_pme_3dfft_compute_61_cpp1_ii_79dff388' > ../../lib/libgromacs_mpi.so.3.1.0: undefined reference to > `__cudaRegisterLinkedBinary_67_tmpxft_00006621_00000000_21_nbnxn_cuda_data_mgmt_compute_61_cpp1_ii_a1eafeba' > ../../lib/libgromacs_mpi.so.3.1.0: undefined reference to > `__cudaRegisterLinkedBinary_57_tmpxft_00006f47_00000000_21_pme_spread_compute_61_cpp1_ii_d982d3ad' > ../../lib/libgromacs_mpi.so.3.1.0: undefined reference to > `__cudaRegisterLinkedBinary_56_tmpxft_00006d70_00000000_21_pme_solve_compute_61_cpp1_ii_06051a94' > ../../lib/libgromacs_mpi.so.3.1.0: undefined reference to > `__cudaRegisterLinkedBinary_59_tmpxft_00008da7_00000000_21_pmalloc_cuda_compute_61_cpp1_ii_63d60154' > ../../lib/libgromacs_mpi.so.3.1.0: undefined reference to > `__cudaRegisterLinkedBinary_50_tmpxft_00007930_00000000_21_pme_compute_61_cpp1_ii_6dbf966c' > ../../lib/libgromacs_mpi.so.3.1.0: undefined reference to > `__cudaRegisterLinkedBinary_58_tmpxft_00007382_00000000_21_pme_timings_compute_61_cpp1_ii_75ae0e44' > ../../lib/libgromacs_mpi.so.3.1.0: undefined reference to > `__cudaRegisterLinkedBinary_57_tmpxft_00006b11_00000000_21_pme_gather_compute_61_cpp1_ii_a7a2f9c7' > ../../lib/libgromacs_mpi.so.3.1.0: undefined reference to > `__cudaRegisterLinkedBinary_56_tmpxft_00007f9f_00000000_21_cudautils_compute_61_cpp1_ii_25933dd5' > ../../lib/libgromacs_mpi.so.3.1.0: undefined reference to > `__cudaRegisterLinkedBinary_54_tmpxft_000088f9_00000000_21_pinning_compute_61_cpp1_ii_5d0f4aae' > ../../lib/libgromacs_mpi.so.3.1.0: undefined reference to > `__cudaRegisterLinkedBinary_57_tmpxft_000039b7_00000000_21_nbnxn_cuda_compute_61_cpp1_ii_f147f02c' > ../../lib/libgromacs_mpi.so.3.1.0: undefined reference to > `__cudaRegisterLinkedBinary_71_tmpxft_000091d4_00000000_21_cuda_version_information_compute_61_cpp1_ii_8ab8dc1d' > ../../lib/libgromacs_mpi.so.3.1.0: undefined reference to > `__cudaRegisterLinkedBinary_56_tmpxft_00008407_00000000_21_gpu_utils_compute_61_cpp1_ii_70828085' > collect2: error: ld returned 1 exit status > > BUILD INSTRUCTIONS: > module swap PrgEnv-cray PrgEnv-gnu > module swap gcc gcc/5.3.0 > export CRAYPE_LINK_TYPE=dynamic > > module load cudatoolkit/8.0.54_2.3.12_g180d272-2.2 > module load cmake/gcc-6.3.0/3.7.2 > module load fftw/3.3.4.11 > export BOOST_DIR=/app/unsupported/boost/1.64.0-gcc-6.3.0 > > export PREFIX=/app/unsupported/gromacs/201x.x > mkdir $PREFIX > > cmake .. \ > -DCMAKE_VERBOSE_MAKEFILE:BOOL=TRUE \ > -DCMAKE_C_COMPILER:FILEPATH=`which cc` \ > -DCMAKE_C_FLAGS:STRING="-O2 -fPIC -dynamic" \ > -DCMAKE_CXX_COMPILER:FILEPATH=`which CC` \ > -DCMAKE_CXX_FLAGS:STRING="-O2 -fPIC -dynamic" \ > -DCMAKE_INSTALL_PREFIX:PATH=$PREFIX \ > -DGMX_FFT_LIBRARY=fftw3 \ > -DCMAKE_EXE_LINKER_FLAGS:STRING=-dynamic \ > -DGMX_SIMD=AVX2_256 \ > -DFFTWF_LIBRARY:FILEPATH=${FFTW_DIR}/libfftw3f.so \ > -DFFTWF_INCLUDE_DIR:PATH=$FFTW_INC \ -DBoost_DIR:PATH=$BOOST_DIR \ > -DBoost_INCLUDE_DIR:PATH=${BOOST_DIR}/include \ > -DBoost_LIBRARY_DIR:PATH=${BOOST_DIR}/lib \ -DGMX_MPI=ON \ > -DGMX_GPU=ON \ -DCUDA_NVCC_FLAGS:STRING="-rdc=true" \ > -DCUDA_USE_STATIC_CUDA_RUNTIME:BOOL=OFF > > make 2>&1 | tee make.log > > Thanks, > Chris > > -- > Gromacs Users mailing list > > * Please search the archive at > Blockedhttp://www.gromacs.org/Support/Mailing_Lists/GMX-Users_ListBlocked > before posting! > > * Can't post? Read > Blockedhttp://www.gromacs.org/Support/Mailing_ListsBlocked > > * For (un)subscribe requests visit > Blockedhttps://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-usersBlocked > or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at Blockedhttp://www.gromacs.org/Support/Mailing_Lists/GMX-Users_ListBlocked before posting! * Can't post? Read Blockedhttp://www.gromacs.org/Support/Mailing_ListsBlocked * For (un)subscribe requests visit Blockedhttps://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-usersBlocked 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.