Thanks. That was already set by cuda module. Didn't help me. 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: Saturday, April 07, 2018 11:28 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 Sorry, forgot to mention that for dynamic linking you (might?) need export CRAYPE_LINK_TYPE=dynamic -- Szilárd On Sat, Apr 7, 2018 at 12:09 AM, Borchert, Christopher B ERDC-RDE-ITL-MS Contractor <christopher.b.borch...@erdc.dren.mil> wrote: > Unfortunately using your shortened cmake args, I still get fpic > errors. But it does complete the build statically with > -DGMX_BUILD_SHARED_EXE=OFF > > CC=cc CXX=CC cmake ../ -DGMX_SIMD=AVX2_256 -DGMX_MPI=ON -DGMX_GPU=ON > -DCMAKE_PREFIX_PATH=${FFTW_DIR}/.. > > /usr/bin/ld: > CMakeFiles/libgromacs.dir/mdlib/nbnxn_cuda/libgromacs_generated_nbnxn_ > cuda.cu.o: relocation R_X86_64_32 against > `_Z58nbnxn_kernel_ElecEwQSTabTwinCut_VdwLJEwCombLB_F_prune_cuda11cu_at > omdata10cu_nbparam8cu_plistb' can not be used when making a shared > object; recompile with -fPIC > > Thanks, > Chris > > -----Original Message----- > From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se > [mailto:gromacs.org_gmx-users-boun...@maillist.sys.kth.se] On Behalf > Of Szilárd Páll > Sent: Friday, April 06, 2018 2:40 PM > To: Discussion list for GROMACS users <gmx-us...@gromacs.org> > Cc: gromacs.org_gmx-users@maillist.sys.kth.se > Subject: Re: [gmx-users] Problem with CUDA > > On CSCS Piz Daint I use the following command line (assuming > PrgEnv-gnu) where everything in "[]" is optional and compilation should work > just fine without. > > CC=cc CXX=CC cmake ../ > -DGMX_SIMD=THE_RIGHT_SIMD_FLAVOR > -DGMX_MPI=ON > -DGMX_GPU=ON > -DCMAKE_PREFIX_PATH=${FFTW_DIR}/.. \ > [ -DGMX_FFT_LIBRARY=fftw3 > -DGMX_CUDA_TARGET_SM=60 > -DGMX_PREFER_STATIC_LIBS=ON > -DBUILD_SHARED_LIBS=OFF > -DGMX_BUILD_MDRUN_ONLY=ON > -DGMX_EXTERNAL_BLAS=OFF -DGMX_EXTERNAL_LAPACK=OFF ] > > In fact, other than the "-DCMAKE_PREFIX_PATH=${FFTW_DIR}/.."and > setting the right compiler wrappers, the rest is most of the time unnecessary > for a "vanilla" build. > > Cheers, > -- > Szilárd > > > On Fri, Apr 6, 2018 at 8:32 PM, Borchert, Christopher B > ERDC-RDE-ITL-MS Contractor <christopher.b.borch...@erdc.dren.mil> > wrote: >> You are trying to give me a hint. :) My cmake args are taken from a >> co-worker, and the statement syntax is from the CMakeCache.txt file. On a >> Cray you force cc/CC and all the module libraries/headers should be >> automatically found. Strangely it didn’t find fftw without help. Regardless >> I get the fpic error. But you've given me a path to investigate. Thanks. >> >> cmake .. >> -DGMX_GPU=ON >> -DCMAKE_C_COMPILER:FILEPATH=`which cc` >> -DCMAKE_CXX_COMPILER:FILEPATH=`which CC` >> -DGMX_FFT_LIBRARY=fftw3 >> -DFFTWF_LIBRARY:FILEPATH=${FFTW_DIR}/libfftw3f.so >> -DFFTWF_INCLUDE_DIR:PATH=$FFTW_INC >> >> /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_a >> t omdata10cu_nbparam8cu_plistb' can not be used when making a shared >> object; recompile with -fPIC >> >> 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 12:05 PM >> 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 >> >> FYI: not even a my vanilla (non-CRAY) local build which does work otherwise >> succeeds with cmake . -DCUDA_NVCC_FLAGS:STRING="-rdc=true" >> so as I guessed, that's the culprit. >> >> Out of curiosity I wonder: what's the reason for the "inventive" use of >> CMake options, none of which are needed? >> >> -- >> Szilárd >> >> >> On Fri, Apr 6, 2018 at 6:57 PM, Szilárd Páll <pall.szil...@gmail.com> wrote: >>> I think the fpic errors can't be caused by missing rdc=true because >>> the latter refers to the GPU _device_ code, but GROMACS does not >>> need relocatable device code, so that should not be necessary. >>> -- >>> Szilárd >>> >>> >>> On Fri, Apr 6, 2018 at 6:33 PM, Borchert, Christopher B >>> ERDC-RDE-ITL-MS Contractor <christopher.b.borch...@erdc.dren.mil> >>> wrote: >>>> 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_nbn >>>> x >>>> n >>>> _cuda.cu.o: relocation R_X86_64_32 against >>>> `_Z58nbnxn_kernel_ElecEwQSTabTwinCut_VdwLJEwCombLB_F_prune_cuda11cu >>>> _ a tomdata10cu_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 >>>>> BlockedBlockedBlockedBlockedhttp://www.gromacs.org/Support/Mailing_Lists/GMX-Users_ListBlockedBlockedBlockedBlocked >>>>> before posting! >>>>> >>>>> * Can't post? 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