[gmx-users] Problem with CUDA

Fri Apr 6 18:44:36 CEST 2018

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-bounces at maillist.sys.kth.se [mailto:gromacs.org_gmx-users-bounces at maillist.sys.kth.se] On Behalf Of Szilárd Páll
Sent: Friday, April 06, 2018 10:17 AM
To: Discussion list for GROMACS users <gmx-users at gromacs.org>
Cc: gromacs.org_gmx-users at 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.Borchert at 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
>
> --
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