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3dem / relion

Image-processing software for cryo-electron microscopy
https://relion.readthedocs.io/en/latest/
GNU General Public License v2.0
444 stars 197 forks source link

INSTALL ERROR: make[2]: *** [bin/relion_autopick_mpi] Error 1 make[1]: *** [src/apps/CMakeFiles/autopick.dir/all] Error 2 #480

Closed Naf-Guo closed 5 years ago

Naf-Guo commented 5 years ago

cmake command:

cmake -DCUDA=ON -DCudaTexture=ON -DCMAKE_INSTALL_PREFIX=/share/install/cryo-EM -DFORCE_OWN_FLTK=ON ..

cmake result:

-- The C compiler identification is GNU 4.4.7 -- The CXX compiler identification is GNU 4.4.7 -- Check for working C compiler: /usr/bin/cc -- Check for working C compiler: /usr/bin/cc -- works -- Detecting C compiler ABI info -- Detecting C compiler ABI info - done -- Check for working CXX compiler: /usr/bin/c++ -- Check for working CXX compiler: /usr/bin/c++ -- works -- Detecting CXX compiler ABI info -- Detecting CXX compiler ABI info - done -- BUILD TYPE set to the default type: 'Release' -- Setting fallback CUDA_ARCH=35 -- CUDA enabled - Building CUDA-accelerated version of RELION -- Setting cpu precision to double -- Setting accelerated code precision to single -- Found CUDA: /usr/local/cuda-7.5 (found version "7.5") -- Using cuda wrapper to compile.... -- Cuda version is >= 7.5 and single-precision build, enable double usage warning. -- Found MPI_C: /share/install/openmpi-3.1.3/lib/libmpi.so
-- Found MPI_CXX: /share/install/openmpi-3.1.3/lib/libmpi.so
-- MPI_INCLUDE_PATH : /share/install/openmpi-3.1.3/include -- MPI_LIBRARIES : /share/install/openmpi-3.1.3/lib/libmpi.so -- MPI_CXX_INCLUDE_PATH : /share/install/openmpi-3.1.3/include -- MPI_CXX_LIBRARIES : /share/install/openmpi-3.1.3/lib/libmpi.so -- CMAKE_C_COMPILER : /usr/bin/cc -- CMAKE_CXX_COMPILER : /usr/bin/c++ -- MPI_C_COMPILER : /share/install/openmpi-3.1.3/bin/mpicc -- MPI_CXX_COMPILER : /share/install/openmpi-3.1.3/bin/mpicxx -- CMAKE_CXX_COMPILER_ID : GNU -- CMAKE_C_COMPILER : /share/install/openmpi-3.1.3/bin/mpicc -- CMAKE_CXX_COMPILER : /share/install/openmpi-3.1.3/bin/mpicxx -- MPI_C_COMPILER : /share/install/openmpi-3.1.3/bin/mpicc -- MPI_CXX_COMPILER : /share/install/openmpi-3.1.3/bin/mpicxx -- Looking for XOpenDisplay in /usr/lib64/libX11.so;/usr/lib64/libXext.so -- Looking for XOpenDisplay in /usr/lib64/libX11.so;/usr/lib64/libXext.so - found -- Looking for gethostbyname -- Looking for gethostbyname - found -- Looking for connect -- Looking for connect - found -- Looking for remove -- Looking for remove - found -- Looking for shmat -- Looking for shmat - found -- Looking for IceConnectionNumber in ICE -- Looking for IceConnectionNumber in ICE - found -- Found X11: /usr/lib64/libX11.so -- Found previously built non-system FLTK libraries that will be used. -- FLTK_INCLUDE_DIR: /data/guoyu/msc/relion/external/fltk/include -- FLTK_LIBRARIES: /data/guoyu/msc/relion/external/fltk/lib/libfltk.so -- Found FFTW -- FFTW_PATH: /usr/local/include -- FFTW_INCLUDES: /usr/local/include -- FFTW_LIBRARIES: /usr/local/lib/libfftw3f.a;/usr/local/lib/libfftw3.a -- Looking for sincos -- Looking for sincos - found -- Looking for sincos -- Looking for sincos - not found -- Found TIFF: /usr/local/lib/libtiff.so (found version "4.0.10") BUILD_SHARED_LIBS = OFF -- Building static libs (larger build size and binaries) Running apps/CMakeLists.txt... -- CMAKE_BINARY_DIR:/data/guoyu/msc/relion/build TIFF FOUND -- Try OpenMP C flag = [-fopenmp] -- Performing Test OpenMP_FLAG_DETECTED -- Performing Test OpenMP_FLAG_DETECTED - Success -- Try OpenMP CXX flag = [-fopenmp] -- Performing Test OpenMP_FLAG_DETECTED -- Performing Test OpenMP_FLAG_DETECTED - Success -- Found OpenMP: -fopenmp
OPENMP FOUND -- Configuring done -- Generating done -- Build files have been written to: /data/guoyu/msc/relion/build

make result

Scanning dependencies of target copy_scripts Scanning dependencies of target relion_lib [ 0%] Built target copy_scripts [ 1%] [ 2%] [ 2%] [ 2%] Building CXX object src/apps/CMakeFiles/relion_lib.dir//healpix_sampling.cpp.o Building CXX object src/apps/CMakeFiles/relion_lib.dir//transformations.cpp.o Building CXX object src/apps/CMakeFiles/relion_lib.dir//exp_model.cpp.o Building CXX object src/apps/CMakeFiles/relion_lib.dir//particle_polisher_mpi.cpp.o [ 3%] Building CXX object src/apps/CMakeFiles/relion_lib.dir//euler.cpp.o [ 3%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/local_symmetry_mpi.cpp.o [ 4%] Building CXX object src/apps/CMakeFiles/relion_lib.dir//motioncorr_runner.cpp.o [ 4%] Building CXX object src/apps/CMakeFiles/relion_lib.dir//ctf.cpp.o [ 5%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/strings.cpp.o [ 5%] Building CXX object src/apps/CMakeFiles/relion_lib.dir//error.cpp.o [ 6%] Building CXX object 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src/apps/CMakeFiles/relion_lib.dir//jaz/d3x3/dsyevh3.c.o [ 64%] Building C object src/apps/CMakeFiles/relion_lib.dir//jaz/d3x3/slvsec3.c.o [ 64%] Building C object src/apps/CMakeFiles/relion_lib.dir/__/jaz/d3x3/dsyevd3.c.o [ 65%] Building C object src/apps/CMakeFiles/relion_lib.dir//jaz/d3x3/dsyevq3.c.o [ 65%] [ 66%] Building C object src/apps/CMakeFiles/relion_lib.dir//jaz/d3x3/dsyevc3.c.o Building C object src/apps/CMakeFiles/relion_lib.dir/__/jaz/d3x3/dsyev2.c.o [ 66%] Building C object src/apps/CMakeFiles/relion_lib.dir//jaz/d3x3/dsytrd3.c.o [ 67%] Building C object src/apps/CMakeFiles/relion_lib.dir//jaz/d3x3/dsyevj3.c.o [ 67%] Building C object src/apps/CMakeFiles/relion_lib.dir/__/jaz/d3x3/dsyevv3.c.o [ 68%] Building C object src/apps/CMakeFiles/relion_lib.dir//jaz/lbfgs/lbfgs.c.o Linking CXX static library ../../lib/librelion_lib.a [ 68%] Built target relion_lib [ 69%] [ 70%] [ 70%] [ 70%] Building NVCC (Device) object src/apps/CMakeFiles/relion_gpu_util.dir//acc/cuda/./relion_gpu_util_generated_cuda_backprojector.cu.o Building NVCC (Device) object src/apps/CMakeFiles/relion_gpu_util.dir//acc/cuda/./relion_gpu_util_generated_cuda_projector_plan.cu.o Building NVCC (Device) object src/apps/CMakeFiles/relion_gpu_util.dir//acc/cuda/cuda_kernels/./relion_gpu_util_generated_helper.cu.o Building NVCC (Device) object src/apps/CMakeFiles/relion_gpu_util.dir//acc/cuda/./relion_gpu_util_generated_cuda_autopicker.cu.o [ 71%] Building NVCC (Device) object src/apps/CMakeFiles/relion_gpu_util.dir//acc/cuda/./relion_gpu_util_generated_cuda_ml_optimiser.cu.o [ 71%] Building NVCC (Device) object src/apps/CMakeFiles/relion_gpu_util.dir//acc/cuda/./relion_gpu_util_generated_cuda_projector.cu.o [ 72%] Building NVCC (Device) object src/apps/CMakeFiles/relion_gpu_util.dir//acc/cuda/./relion_gpu_util_generated_cuda_helper_functions.cu.o [ 72%] Building NVCC (Device) object src/apps/CMakeFiles/relion_gpu_util.dir//acc/cuda/./relion_gpu_util_generated_cuda_benchmark_utils.cu.o Scanning dependencies of target relion_gpu_util Linking CXX static library ../../lib/librelion_gpu_util.a [ 72%] Built target relion_gpu_util Scanning dependencies of target align_symmetry Scanning dependencies of target ctf_refine Scanning dependencies of target autopick Scanning dependencies of target autopick_mpi [ 73%] [ 73%] [ 74%] [ 74%] Building CXX object src/apps/CMakeFiles/align_symmetry.dir/align_symmetry.cpp.o Building CXX object src/apps/CMakeFiles/autopick.dir/autopick.cpp.o Building CXX object src/apps/CMakeFiles/ctf_refine.dir/ctf_refine.cpp.o Building CXX object src/apps/CMakeFiles/autopick_mpi.dir/autopick_mpi.cpp.o Linking CXX executable ../../bin/relion_ctf_refine Linking CXX executable ../../bin/relion_autopick Linking CXX executable ../../bin/relion_autopick_mpi [ 74%] Built target ctf_refine Scanning dependencies of target ctf_refine_mpi [ 74%] Building CXX object src/apps/CMakeFiles/ctf_refine_mpi.dir/ctf_refine_mpi.cpp.o ../../lib/librelion_gpu_util.a(relion_gpu_util_generated_cuda_autopicker.cu.o): In function LaunchHandleError(cudaError, char const*, int)': tmpxft_00004cb6_00000000-4_cuda_autopicker.cudafe1.cpp:(.text+0x85e): undefined reference toRelionError::RelionError(std::string const&, std::string const&, long)' ../../lib/librelion_gpu_util.a(relion_gpu_util_generated_cuda_autopicker.cu.o): In function HandleError(cudaError, char const*, int)': tmpxft_00004cb6_00000000-4_cuda_autopicker.cudafe1.cpp:(.text+0x995): undefined reference toRelionError::RelionError(std::string const&, std::string const&, long)' ../../lib/librelion_gpu_util.a(relion_gpu_util_generated_cuda_autopicker.cu.o): In function AutoPickerCuda::AutoPickerCuda(AutoPickerMpi*, int, char const*)': tmpxft_00004cb6_00000000-4_cuda_autopicker.cudafe1.cpp:(.text+0x13e0): undefined reference toRelionError::RelionError(std::string const&, std::string const&, long)' tmpxft_00004cb6_00000000-4_cuda_autopicker.cudafe1.cpp:(.text+0x1480): undefined reference to ..RelionError/:.:.RelionError/(libstd/:librelion_gpu_util.a:(stringrelion_gpu_util_generated_cuda_autopicker.cu.o )const:& ,In stdfunction: :stringLaunchHandleError (constcudaError&,, charlong )const' ,. .int)':/ .tmpxft_00004cb6_00000000.-/4_cuda_autopicker.cudafe1.cpplib:/(librelion_gpu_util.a.(textrelion_gpu_util_generated_cuda_autopicker.cu.o+)0x85e:) :In undefinedfunction referenceAutoPickerCudato: :AutoPickerCudaRelionError(:AutoPicker:RelionError,( std:int:,string const&, std:: stringchar constconst&, )long'):' tmpxft_00004cb6_00000000 -.4_cuda_autopicker.cudafe1.cpp.:/(...text/+lib0x1de5/)librelion_gpu_util.a:( relion_gpu_util_generated_cuda_autopicker.cu.oundefined) :reference In function toHandleError (cudaErrorRelionError,: :charRelionError (conststd:,: stringint )const'&:, tmpxft_00004cb6_00000000std-:4_cuda_autopicker.cudafe1.cpp::string( .consttext&+,0x995 )long:) 'undefined .reference. /to. ./RelionErrorlib:/:librelion_gpu_util.aRelionError((stdrelion_gpu_util_generated_cuda_autopicker.cu.o:)::stringtmpxft_00004cb6_00000000 -const4_cuda_autopicker.cudafe1.cpp&:,( .stdtext:+:0x1eadstring) :const &more, undefinedlong )references' to. ./RelionError.:.:/RelionErrorlib(/stdlibrelion_gpu_util.a:(:relion_gpu_util_generated_cuda_autopicker.cu.ostring) :const &In, functionstd ::AutoPickerCudastring: :constAutoPickerCuda&(,AutoPickerMpi *long,) 'int ,follow char const*)': .tmpxft_00004cb6_00000000.-/4_cuda_autopicker.cudafe1.cpp.:.(/.libtext/+librelion_gpu_util.a0x13e0():relion_gpu_util_generated_cuda_autopicker.cu.o )undefined: referenceIn tofunction ``RelionErrorAutoPickerCuda::::RelionErrorautoPickOneMicrograph((stdFileName::string& ,const &long),' :std :tmpxft_00004cb6_00000000:-string4_cuda_autopicker.cudafe1.cpp :const(&.,text +long0x9ae8))': tmpxft_00004cb6_00000000-undefined4_cuda_autopicker.cudafe1.cpp :reference( .totext +0x1480FileName)::: undefined referencecompose (tostd ::RelionErrorstring: :constRelionError&(,std ::string const&, std:long:,string stdconst:&,: stringlong )const'& ,.. /int.).'/ libtmpxft_00004cb6_00000000/-librelion_gpu_util.a4_cuda_autopicker.cudafe1.cpp(:relion_gpu_util_generated_cuda_autopicker.cu.o().:text +In0x9cfe )function:undefinedAutoPickerCuda ::referenceAutoPickerCuda (toAutoPicker `,FileName int:,: composechar( stdconst::)string' :const &tmpxft_00004cb6_00000000,- 4_cuda_autopicker.cudafe1.cpplong:,( .stdtext:+0x1de5): undefined reference: stringto const&RelionError,: :intRelionError)('std ::tmpxft_00004cb6_00000000string- 4_cuda_autopicker.cudafe1.cppconst:&(, .stdtext:+:0xae48string) :const &undefined, referencelong )to' .RelionError.:/:..RelionError/(libstd/:librelion_gpu_util.a:(stringrelion_gpu_util_generated_cuda_autopicker.cu.o )const:&tmpxft_00004cb6_00000000,- 4_cuda_autopicker.cudafe1.cppstd::(:.stringtext +const0x1ead&),: longmore) 'undefined tmpxft_00004cb6_00000000references- to4_cuda_autopicker.cudafe1.cpp :(RelionError:.:textRelionError+(0xbc33std)::: stringundefined constreference& ,to std:FileName::string: composeconst(&std,: :longstring) 'const follow ..&/../lib/librelion_gpu_util.a(relion_gpu_util_generated_cuda_autopicker.cu.o),: longIn, functionstd ::AutoPickerCudastring: :constautoPickOneMicrograph&(,FileName &int,) 'long )'tmpxft_00004cb6_00000000:- 4_cuda_autopicker.cudafe1.cpptmpxft_00004cb6_00000000:-(4_cuda_autopicker.cudafe1.cpp.:text(+.0xbf10):text +undefined0x9ae8 )reference: toundefinedreferenceFileName :to: compose(FileNamestd::::composestring(std :const:&string, constlong&,, stdlong,: :stdstring: :stringconst &const,& ,int )int') '. tmpxft_00004cb6_00000000.-/4_cuda_autopicker.cudafe1.cpp.:(..text/+lib0x9cfe/)librelion_gpu_util.a:( relion_gpu_util_generated_cuda_autopicker.cu.oundefined) :reference toInfunctionFileName ::AutoPickerCudacompose:(:stdrun:(:)string' :const &,tmpxft_00004cb6_00000000 -long4_cuda_autopicker.cudafe1.cpp,: (std.:text:+string0xf837 )const:& ,undefined intreference) 'to tmpxft_00004cb6_00000000-FileName4_cuda_autopicker.cudafe1.cpp:::(beforeLastOf.(textstd+:0xae48:)string: constundefined& )reference constto' .RelionError.:/:.RelionError.(/stdlib:/:librelion_gpu_util.astring( relion_gpu_util_generated_cuda_autopicker.cu.oconst)&:, Instd :function: string AccPtrconst<&float2,> :long:)AccPtr'( unsignedtmpxft_00004cb6_00000000 -long,4_cuda_autopicker.cudafe1.cpp :CudaCustomAllocator(*.)text'+:0xbc33 ):tmpxft_00004cb6_00000000 -undefined4_cuda_autopicker.cudafe1.cpp :reference( to. text._ZN6AccPtrI6float2EC2EmP19CudaCustomAllocator[FileName_ZN6AccPtrI6float2EC5EmP19CudaCustomAllocator:]:+compose0xc5()std:: :undefinedstring referenceconst &to,longRelionError,: :stdRelionError:(:stdstring: :conststring& , int)' consttmpxft_00004cb6_00000000&-,4_cuda_autopicker.cudafe1.cpp: (std.:text:+string0xbf10 )const:& ,undefined longreference) 'to ..FileName/:.:.compose/(stdlib:/:librelion_gpu_util.astring( relion_gpu_util_generated_cuda_autopicker.cu.oconst)&:, Inlong ,function std:AccPtr:const:&:,hostAlloc (int))'':

.tmpxft_00004cb6_00000000.-/4_cuda_autopicker.cudafe1.cpp.:.(/.libtext._ZN6AccPtrIfE9hostAllocEv/[librelion_gpu_util.a_ZN6AccPtrIfE9hostAllocEv(]relion_gpu_util_generated_cuda_autopicker.cu.o+)0x95:) In function AutoPickerCuda::: runundefined( )reference' :to tmpxft_00004cb6_00000000-RelionError4_cuda_autopicker.cudafe1.cpp:::(RelionError.(textstd+:0xf837:)string: constundefined& reference ,to std:FileName::string: beforeLastOfconst(&std,: :longstring) 'const &.). /const.'. /.lib.//librelion_gpu_util.a.(./relion_gpu_util_generated_cuda_autopicker.cu.olib)/:librelion_gpu_util.a (Inrelion_gpu_util_generated_cuda_autopicker.cu.o )function:InAccPtr <function AccPtr<float2>float:>::AccPtr:(AccPtrunsigned( unsignedlong ,long ,CudaCustomAllocator *CudaCustomAllocator)*'):' :tmpxft_00004cb6_00000000 -tmpxft_00004cb6_000000004_cuda_autopicker.cudafe1.cpp-:4_cuda_autopicker.cudafe1.cpp(:.(text._ZN6AccPtrI6float2EC2EmP19CudaCustomAllocator.[text._ZN6AccPtrIfEC2EmP19CudaCustomAllocator_ZN6AccPtrI6float2EC5EmP19CudaCustomAllocator[]_ZN6AccPtrIfEC5EmP19CudaCustomAllocator+]0xc5+):0xc5 )undefined: referenceundefined toreferencetoRelionError ::RelionErrorRelionError:(:stdRelionError:(:stdstring: :conststring& ,const &std,: :stdstring: :conststring& ,const &long,) 'long ).'. /....//.lib.//librelion_gpu_util.alib(/relion_gpu_util_generated_cuda_autopicker.cu.o)librelion_gpu_util.a:( relion_gpu_util_generated_cuda_autopicker.cu.oIn) :function In AccPtrfunction< float>bool: :MetaDataTablehostAlloc:(:)getValue'<: FileNametmpxft_00004cb6_00000000>-(EMDLabel, 4_cuda_autopicker.cudafe1.cppFileName:&(,. text._ZN6AccPtrIfE9hostAllocEvlong[)_ZN6AccPtrIfE9hostAllocEv ]const+'0x95:) :tmpxft_00004cb6_00000000 -undefined4_cuda_autopicker.cudafe1.cpp :reference( .totext._ZNK13MetaDataTable8getValueI8FileNameEEb8EMDLabelRT_l [_ZNK13MetaDataTable8getValueI8FileNameEEb8EMDLabelRT_lRelionError]:+:0x5fRelionError)(:std :undefined: stringreference constto& ,MetaDataTablestd::::checkObjectIDstring( longconst,& ,std :long:)string') .const.'/ .tmpxft_00004cb6_00000000.-/4_cuda_autopicker.cudafe1.cpplib:/(librelion_gpu_util.a.(text._ZNK13MetaDataTable8getValueI8FileNameEEb8EMDLabelRT_lrelion_gpu_util_generated_cuda_autopicker.cu.o[)_ZNK13MetaDataTable8getValueI8FileNameEEb8EMDLabelRT_l:] +In0x79 )function:undefinedAccPtr to: :AccPtrMetaDataContainer(:unsigned: getValuelong(,long ,CudaCustomAllocator *std):'::string &tmpxft_00004cb6_00000000)- 4_cuda_autopicker.cudafe1.cppconst:'( .text._ZN6AccPtrIfEC2EmP19CudaCustomAllocator.[._ZN6AccPtrIfEC5EmP19CudaCustomAllocator/].+.0xc5/)lib:/ librelion_gpu_util.aundefined( relion_gpu_util_generated_cuda_autopicker.cu.oreference) :to In RelionErrorfunction: :`RelionErrorbool( stdMetaDataTable::::stringsetValue <constint&>,( EMDLabelstd,: :intstring constconst&&,, longlong))'':

.tmpxft_00004cb6_00000000.-/4_cuda_autopicker.cudafe1.cpp.:.(/.libtext._ZN13MetaDataTable8setValueIiEEb8EMDLabelRKT_l/_ZN13MetaDataTable8setValueIiEEb8EMDLabelRKT_llibrelion_gpu_util.a):: Inundefined functionreference toboolMetaDataTableMetaDataTable::::getValuecheckObjectID<(FileNamelong>,( EMDLabelstd,: :FileNamestring&), constlong') .const.'/:. tmpxft_00004cb6_00000000-.4_cuda_autopicker.cudafe1.cpp/:lib(/.librelion_gpu_util.atext._ZNK13MetaDataTable8getValueI8FileNameEEb8EMDLabelRT_l([relion_gpu_util_generated_cuda_autopicker.cu.o_ZNK13MetaDataTable8getValueI8FileNameEEb8EMDLabelRT_l)]:+ 0x5fIn) :function undefinedImagereference< intto> ::MetaDataTablewriteIMAGIC:(:checkObjectIDlong(,long ,int )std'::: stringtmpxft_00004cb6_00000000)- 4_cuda_autopicker.cudafe1.cppconst:'( .tmpxft_00004cb6_00000000text._ZN5ImageIiE11writeIMAGICEli-4_cuda_autopicker.cudafe1.cpp_ZN5ImageIiE11writeIMAGICEli:[:_ZNK13MetaDataTable8getValueI8FileNameEEb8EMDLabelRT_l ]undefined+ 0x79reference) :to undefinedRelionErrorreference: :toRelionError (stdMetaDataContainer::::getValuestring( longconst,& ,std :std::string:&string) constconst&', .long.)/'. ../.lib//.librelion_gpu_util.a.(/relion_gpu_util_generated_cuda_autopicker.cu.olib)/:librelion_gpu_util.a (Inrelion_gpu_util_generated_cuda_autopicker.cu.o )function: Inbool functionMetaDataTable ::CudaCustomAllocatorsetValue:<:intalloc>((unsignedEMDLabel ,long )int' :const &tmpxft_00004cb6_00000000,- 4_cuda_autopicker.cudafe1.cpplong:)('.:text._ZN19CudaCustomAllocator5allocEm [tmpxft_00004cb6_00000000_ZN19CudaCustomAllocator5allocEm-]4_cuda_autopicker.cudafe1.cpp+:0x82d().:text._ZN13MetaDataTable8setValueIiEEb8EMDLabelRKT_l [undefined_ZN13MetaDataTable8setValueIiEEb8EMDLabelRKT_l ]reference+ 0x63to) :RelionErrorundefined: :referenceRelionError (tostd ::MetaDataTablestring: :constcheckObjectID&(,long ,std :std::string: stringconst)& ,const 'long ).'. /....//.lib.//librelion_gpu_util.alib(/relion_gpu_util_generated_cuda_autopicker.cu.olibrelion_gpu_util.a)(:relion_gpu_util_generated_cuda_autopicker.cu.o )In: functionIn functionImage <intMultidimArray><:double:>writeIMAGIC:(:longresizeNoCp,( longint,) 'long:, tmpxft_00004cb6_00000000long-,4_cuda_autopicker.cudafe1.cpp :long().'text._ZN5ImageIiE11writeIMAGICEli:[ _ZN5ImageIiE11writeIMAGICElitmpxft_00004cb6_00000000]-+4_cuda_autopicker.cudafe1.cpp0x48e:)(:. text._ZN13MultidimArrayIdE10resizeNoCpEllllundefined[ _ZN13MultidimArrayIdE10resizeNoCpEllllreference] +to0x107 ):RelionError :undefined: RelionErrorreference( stdto: :stringFileName :const:&addExtension,( stdstd::::stringstring constconst&&,) longconst)''

tmpxft_00004cb6_00000000.-.4_cuda_autopicker.cudafe1.cpp/:.(../text._ZN13MultidimArrayIdE10resizeNoCpElllllib/_ZN13MultidimArrayIdE10resizeNoCpElllllibrelion_gpu_util.a):: Inundefined functionreference toCudaCustomAllocator ::RelionErroralloc:(:unsignedRelionError (longstd):'::string tmpxft_00004cb6_00000000const-&4_cuda_autopicker.cudafe1.cpp,: (std.:text._ZN19CudaCustomAllocator5allocEm:[string_ZN19CudaCustomAllocator5allocEm ]const+&0x82d,) :long )undefined' referencetmpxft_00004cb6_00000000 -to4_cuda_autopicker.cudafe1.cpp :(RelionError:.:text._ZN13MultidimArrayIdE10resizeNoCpEllllRelionError[(_ZN13MultidimArrayIdE10resizeNoCpEllllstd]:+:0x41astring) :const &undefined, referencestd :to: string RelionErrorconst:&:,RelionError (longstd):': string. .const/&.,. /libstd/:librelion_gpu_util.a:(stringrelion_gpu_util_generated_cuda_autopicker.cu.o )const:& ,In longfunction) ' MultidimArraytmpxft_00004cb6_00000000<-double4_cuda_autopicker.cudafe1.cpp>::(:.resizeNoCptext._ZN13MultidimArrayIdE10resizeNoCpEllll([long_ZN13MultidimArrayIdE10resizeNoCpEllll,] +long0x496,) :long ,undefined longreference) 'to: tmpxft_00004cb6_00000000RelionError-:4_cuda_autopicker.cudafe1.cpp::RelionError((.stdtext._ZN13MultidimArrayIdE10resizeNoCpEllll:[:_ZN13MultidimArrayIdE10resizeNoCpEllllstring] +const0x107&),: stdundefined: :referencestring toconst &,FileName :long:)addExtension'( stdtmpxft_00004cb6_00000000:-:4_cuda_autopicker.cudafe1.cppstring: (const.&text._ZN13MultidimArrayIdE10resizeNoCpEllll)[ _ZN13MultidimArrayIdE10resizeNoCpEllllconst]'+ 0x5catmpxft_00004cb6_00000000)-:4_cuda_autopicker.cudafe1.cpp :undefined( .referencetext._ZN13MultidimArrayIdE10resizeNoCpEllll [to_ZN13MultidimArrayIdE10resizeNoCpEllll ]+0x1dc)RelionError:: :undefinedRelionError (referencestd :to: stringRelionErrorconst:&:,RelionError (stdstd::::stringstring constconst&&,, std::longstring) 'const &.,. /long.).'/ libtmpxft_00004cb6_00000000/-librelion_gpu_util.a4_cuda_autopicker.cudafe1.cpp(:relion_gpu_util_generated_cuda_autopicker.cu.o().:text._ZN13MultidimArrayIdE10resizeNoCpEllll [In_ZN13MultidimArrayIdE10resizeNoCpEllll ]function+ 0x41a)Image:< intundefined> :reference: castPage2Datatypeto( int*RelionError,:: RelionErrorchar(*std,: :DataTypestring, constunsigned& ,long )std'::: stringtmpxft_00004cb6_00000000 -const4_cuda_autopicker.cudafe1.cpp&:, (long.)'text._ZN5ImageIiE17castPage2DatatypeEPiPc8DataTypem [tmpxft_00004cb6_00000000_ZN5ImageIiE17castPage2DatatypeEPiPc8DataTypem-]4_cuda_autopicker.cudafe1.cpp+:0xd9().:text._ZN13MultidimArrayIdE10resizeNoCpEllll [undefined_ZN13MultidimArrayIdE10resizeNoCpEllll ]reference+ 0x496to) : RelionErrorundefined: :referenceRelionError (tostd ::RelionErrorstring: :constRelionError&(,std :std::string: stringconst &const,& ,std :long:)string' const.&.,/ .long.)/'lib /tmpxft_00004cb6_00000000librelion_gpu_util.a-(4_cuda_autopicker.cudafe1.cpprelion_gpu_util_generated_cuda_autopicker.cu.o:)(:.tmpxft_00004cb6_00000000text._ZN13MultidimArrayIdE10resizeNoCpEllll-[4_cuda_autopicker.cudafe1.cpp_ZN13MultidimArrayIdE10resizeNoCpEllll:](+.0x5catext._ZN5ImageIdE17castPage2DatatypeEPdPc8DataTypem)[:_ZN5ImageIdE17castPage2DatatypeEPdPc8DataTypem ]undefined+ 0xd6reference) :to more RelionError:undefined: RelionErrorreferences( stdto: :stringRelionError :const:&RelionError,( stdstd::::stringstring constconst&&,, stdlong:):'string .const.&/,. .long/)lib'/ librelion_gpu_util.afollow( relion_gpu_util_generated_cuda_autopicker.cu.o.).:/ .In. /functionlib /librelion_gpu_util.aImage(<relion_gpu_util_generated_cuda_ml_optimiser.cu.oint)>:: :IncastPage2Datatype (functionint `,MultidimArray <charbool>,: :DataTypecoreAllocate,( )unsigned' long:) 'tmpxft_00004db4_00000000:- tmpxft_00004cb6_000000004_cuda_ml_optimiser.cudafe1.cpp-:4_cuda_autopicker.cudafe1.cpp(:.(text._ZN13MultidimArrayIbE12coreAllocateEv.[text._ZN5ImageIiE17castPage2DatatypeEPiPc8DataTypem_ZN13MultidimArrayIbE12coreAllocateEv[]_ZN5ImageIiE17castPage2DatatypeEPiPc8DataTypem+]0xf7+)0xd9:) :undefined undefinedreference referenceto toFileName:RelionError::addExtension:(RelionErrorstd(:std::string: stringconst &const)& , conststd': :tmpxft_00004db4_00000000string- 4_cuda_ml_optimiser.cudafe1.cppconst:&(,. text._ZN13MultidimArrayIbE12coreAllocateEvlong[)_ZN13MultidimArrayIbE12coreAllocateEv'] +.0x1e3.)/:. ./undefinedlib /referencelibrelion_gpu_util.a (torelion_gpu_util_generated_cuda_autopicker.cu.o ):RelionErrortmpxft_00004cb6_00000000:-:4_cuda_autopicker.cudafe1.cppRelionError:((std.:text._ZN5ImageIdE17castPage2DatatypeEPdPc8DataTypem:[string_ZN5ImageIdE17castPage2DatatypeEPdPc8DataTypem ]const+&0xd6,) :std :more: stringundefined constreferences& ,to long)RelionError': :tmpxft_00004db4_00000000RelionError-(4_cuda_ml_optimiser.cudafe1.cppstd::(:.stringtext._ZN13MultidimArrayIbE12coreAllocateEv [const_ZN13MultidimArrayIbE12coreAllocateEv&],+ 0x2a0std)::: stringundefined constreference& ,to long)RelionError': :followRelionError (.std.:/:.string. /constlib&/,librelion_gpu_util.a (stdrelion_gpu_util_generated_cuda_ml_optimiser.cu.o:)::string Inconst &function,longMultidimArray)<'bool

tmpxft_00004db4_00000000:-:4_cuda_ml_optimiser.cudafe1.cppcoreAllocate:(().'text._ZN13MultidimArrayIbE12coreAllocateEv:[ _ZN13MultidimArrayIbE12coreAllocateEvtmpxft_00004db4_00000000]-+0x3264_cuda_ml_optimiser.cudafe1.cpp)::( .undefinedtext._ZN13MultidimArrayIbE12coreAllocateEv [reference_ZN13MultidimArrayIbE12coreAllocateEv ]to+ 0xf7)RelionError:: :undefinedRelionError (referencestd :to: string FileNameconst:&:,addExtension (stdstd::::stringstring constconst&&,) longconst)''

tmpxft_00004db4_00000000tmpxft_00004db4_00000000--4_cuda_ml_optimiser.cudafe1.cpp4_cuda_ml_optimiser.cudafe1.cpp::((..text._ZN13MultidimArrayIbE12coreAllocateEvtext._ZN13MultidimArrayIbE12coreAllocateEv[[_ZN13MultidimArrayIbE12coreAllocateEv_ZN13MultidimArrayIbE12coreAllocateEv]]++0x1e30x390)):: undefined undefinedreference referenceto toRelionError:RelionError::RelionError:(RelionErrorstd(:std::string: stringconst &const,& ,std :std::string: stringconst &const,& ,long )long') 'tmpxft_00004db4_00000000 -tmpxft_00004db4_000000004_cuda_ml_optimiser.cudafe1.cpp-:4_cuda_ml_optimiser.cudafe1.cpp:((..text._ZN13MultidimArrayIbE12coreAllocateEvtext._ZN13MultidimArrayIbE12coreAllocateEv[[_ZN13MultidimArrayIbE12coreAllocateEv_ZN13MultidimArrayIbE12coreAllocateEv]]++0x3fb0x2a0)):: undefinedundefined referencereference toto ``RelionErrorRelionError::::RelionErrorRelionError((stdstd::::stringstring constconst&&,, stdstd::::stringstring constconst&&,, longlong))''

.tmpxft_00004db4_00000000.-/4_cuda_ml_optimiser.cudafe1.cpp.:.(/.libtext._ZN13MultidimArrayIbE12coreAllocateEv/[librelion_gpu_util.a_ZN13MultidimArrayIbE12coreAllocateEv(]relion_gpu_util_generated_cuda_ml_optimiser.cu.o+)0x326:)tmpxft_00004db4_00000000:- 4_cuda_ml_optimiser.cudafe1.cppundefined: (reference. text._ZN6AccPtrImE9hostAllocEvto[ _ZN6AccPtrImE9hostAllocEvRelionError]:+:0x95RelionError)(:std :more: stringundefined constreferences& ,to std:RelionError::string: RelionErrorconst(&std,: :longstring) 'const &tmpxft_00004db4_00000000,- 4_cuda_ml_optimiser.cudafe1.cppstd::(:.stringtext._ZN13MultidimArrayIbE12coreAllocateEv [const_ZN13MultidimArrayIbE12coreAllocateEv&],+ 0x390long)):' undefinedfollow reference. .to/ ..RelionError/:lib:/RelionErrorlibrelion_gpu_util.a((stdrelion_gpu_util_generated_cuda_ml_optimiser.cu.o:)::string Inconst &function,stdMultidimArray:<:boolstring> :const:&resizeNoCp,( long)long', tmpxft_00004db4_00000000long-,4_cuda_ml_optimiser.cudafe1.cpp :long(,. text._ZN13MultidimArrayIbE12coreAllocateEvlong[)_ZN13MultidimArrayIbE12coreAllocateEv']:+ 0x3fbtmpxft_00004db4_00000000)-:4_cuda_ml_optimiser.cudafe1.cpp :undefined( .referencetext._ZN13MultidimArrayIbE10resizeNoCpEllll [to_ZN13MultidimArrayIbE10resizeNoCpEllll RelionError::RelionError(std::string ]const&,+ std0x107:)::string undefinedconst &reference, tolong )'FileName :.:.addExtension/(..std/:lib:/stringlibrelion_gpu_util.a (constrelion_gpu_util_generated_cuda_ml_optimiser.cu.o&)): tmpxft_00004db4_00000000const-'4_cuda_ml_optimiser.cudafe1.cpp :tmpxft_00004db4_00000000(-.4_cuda_ml_optimiser.cudafe1.cpptext._ZN6AccPtrImE9hostAllocEv:[(_ZN6AccPtrImE9hostAllocEv.]text._ZN13MultidimArrayIbE10resizeNoCpEllll+[0x95_ZN13MultidimArrayIbE10resizeNoCpEllll)]:+ 0x1d0more) :undefined undefinedreferences referenceto toRelionError:RelionError::RelionError:(RelionErrorstd(:std::string: stringconst &const,& ,std :std::string: stringconst &const,& ,long )long') 'follow

tmpxft_00004db4_00000000.-.4_cuda_ml_optimiser.cudafe1.cpp/:.(./.libtext._ZN13MultidimArrayIbE10resizeNoCpEllll/[librelion_gpu_util.a_ZN13MultidimArrayIbE10resizeNoCpEllll(]relion_gpu_util_generated_cuda_ml_optimiser.cu.o+)0x40a:) :In undefinedfunction referenceMultidimArrayto< bool>RelionError::::resizeNoCpRelionError((longstd,: :longstring, constlong&,, longstd):'::string tmpxft_00004db4_00000000const-&4_cuda_ml_optimiser.cudafe1.cpp,: (long.)text._ZN13MultidimArrayIbE10resizeNoCpEllll'[ _ZN13MultidimArrayIbE10resizeNoCpElllltmpxft_00004db4_00000000]-+4_cuda_ml_optimiser.cudafe1.cpp0x107:)(:. text._ZN13MultidimArrayIbE10resizeNoCpEllllundefined[ _ZN13MultidimArrayIbE10resizeNoCpEllllreference] +to FileName::addExtension(std::string 0x486const)&:) undefinedconst 'reference tmpxft_00004db4_00000000to- 4_cuda_ml_optimiser.cudafe1.cpp:RelionError(:.:text._ZN13MultidimArrayIbE10resizeNoCpEllllRelionError[(_ZN13MultidimArrayIbE10resizeNoCpEllllstd]:+:0x1d0string) :const &undefined, referencestd :to: stringRelionErrorconst:&:,RelionError (longstd):': stringtmpxft_00004db4_00000000 -const4_cuda_ml_optimiser.cudafe1.cpp&:,( .stdtext._ZN13MultidimArrayIbE10resizeNoCpEllll:[:_ZN13MultidimArrayIbE10resizeNoCpEllllstring] +const0x5b3&),: longundefined) 'reference tmpxft_00004db4_00000000to- 4_cuda_ml_optimiser.cudafe1.cpp:(RelionError.text._ZN13MultidimArrayIbE10resizeNoCpEllll::_ZN13MultidimArrayIbE10resizeNoCpEllllRelionError::: stringundefined constreference& ,to std:RelionError::string: RelionErrorconst(&std,: :longstring) 'const &.,. /std.:.:/stringlib /constlibrelion_gpu_util.a&(,relion_gpu_util_generated_cuda_ml_optimiser.cu.o )long:) 'In tmpxft_00004db4_00000000function- 4_cuda_ml_optimiser.cudafe1.cpp:MultidimArray(<.floattext._ZN13MultidimArrayIbE10resizeNoCpEllll>[:_ZN13MultidimArrayIbE10resizeNoCpEllll:]resizeNoCp+(0x486long),: longundefined, referencelong ,to long)RelionError'::: RelionErrortmpxft_00004db4_00000000(-std4_cuda_ml_optimiser.cudafe1.cpp:::(string. text._ZN13MultidimArrayIfE10resizeNoCpEllllconst[&_ZN13MultidimArrayIfE10resizeNoCpEllll,] +std0x107:)::string undefinedconst &reference, tolong )'FileName :tmpxft_00004db4_00000000:-addExtension4_cuda_ml_optimiser.cudafe1.cpp(:std(:.:text._ZN13MultidimArrayIbE10resizeNoCpEllllstring[ _ZN13MultidimArrayIbE10resizeNoCpEllll]+0x5b3const)&:) undefinedconst 'reference tmpxft_00004db4_00000000to- 4_cuda_ml_optimiser.cudafe1.cpp:RelionError(::.RelionErrortext._ZN13MultidimArrayIfE10resizeNoCpEllll([std_ZN13MultidimArrayIfE10resizeNoCpEllll:]:+string0x1dc ): undefined constreference& ,to std:RelionError::string: RelionErrorconst(&std,: :longstring) 'const &.,. /std.:.:/stringlib /constlibrelion_gpu_util.a&(,relion_gpu_util_generated_cuda_ml_optimiser.cu.o )long:) 'In tmpxft_00004db4_00000000function- 4_cuda_ml_optimiser.cudafe1.cpp:MultidimArray(<.floattext._ZN13MultidimArrayIfE10resizeNoCpEllll>[:_ZN13MultidimArrayIfE10resizeNoCpEllll:]resizeNoCp+(0x41along),: longundefined, referencelong ,to long)RelionError'::: RelionErrortmpxft_00004db4_00000000(-std4_cuda_ml_optimiser.cudafe1.cpp:::(string. text._ZN13MultidimArrayIfE10resizeNoCpEllllconst[&_ZN13MultidimArrayIfE10resizeNoCpEllll,] +std0x107:)::string undefinedconst &reference, tolong )'FileName: :tmpxft_00004db4_00000000addExtension-(4_cuda_ml_optimiser.cudafe1.cppstd::(:.stringtext._ZN13MultidimArrayIfE10resizeNoCpEllll [const&)_ZN13MultidimArrayIfE10resizeNoCpEllll ]const+'0x496 )tmpxft_00004db4_00000000:- 4_cuda_ml_optimiser.cudafe1.cppundefined: (reference. text._ZN13MultidimArrayIfE10resizeNoCpEllllto[ _ZN13MultidimArrayIfE10resizeNoCpEllll]RelionError+:0x1dc:)RelionError:( stdundefined: :referencestring toconst &,RelionError :std::RelionError:(stringstd :const:&string, constlong&),' stdtmpxft_00004db4_00000000:-:4_cuda_ml_optimiser.cudafe1.cppstring: (const.&text._ZN13MultidimArrayIfE10resizeNoCpEllll,[ _ZN13MultidimArrayIfE10resizeNoCpElllllong])+'0x5ca )tmpxft_00004db4_00000000-4_cuda_ml_optimiser.cudafe1.cpp:(.text._ZN13MultidimArrayIfE10resizeNoCpEllll[_ZN13MultidimArrayIfE10resizeNoCpEllll:] +0x41aundefined) :reference undefinedto reference RelionErrorto: :RelionErrorRelionError(:std:::string const&,RelionError (stdstd::::stringstring constconst&&,, longstd):': string. .const/&.,. /longlib)/'librelion_gpu_util.a (tmpxft_00004db4_00000000relion_gpu_util_generated_cuda_ml_optimiser.cu.o-)4_cuda_ml_optimiser.cudafe1.cpp:: (In. text._ZN13MultidimArrayIfE10resizeNoCpEllllfunction[ _ZN13MultidimArrayIfE10resizeNoCpEllll]Matrix2D+<0x496double)>:: :undefinedoperator reference( Matrix2Dto< double>RelionError :const:&RelionError)( stdconst:'::string tmpxft_00004db4_00000000const-&4_cuda_ml_optimiser.cudafe1.cpp,: (std.:text._ZNK8Matrix2DIdEmlERKS0_:[string_ZNK8Matrix2DIdEmlERKS0_ ]const+&0x84, )long:) 'undefined tmpxft_00004db4_00000000reference- 4_cuda_ml_optimiser.cudafe1.cppto: (.RelionErrortext._ZN13MultidimArrayIfE10resizeNoCpEllll::_ZN13MultidimArrayIfE10resizeNoCpEllllRelionError::string undefinedconst &reference, tostd ::RelionErrorstring: :constRelionError&(,std :long:)string' const.&.,/ .std.:/:libstring/ librelion_gpu_util.aconst(&relion_gpu_util_generated_cuda_ml_optimiser.cu.o,) :longtmpxft_00004db4_00000000)-'4_cuda_ml_optimiser.cudafe1.cpp :.(../text._Z12arrayByArrayRK13MultidimArrayI8tComplexIdEES4_RS2_c.[._Z12arrayByArrayRK13MultidimArrayI8tComplexIdEES4_RS2_c/]lib+/0xcclibrelion_gpu_util.a)(:relion_gpu_util_generated_cuda_ml_optimiser.cu.o )more: undefinedIn referencesfunction to Matrix2D`::RelionError:(operatorstd:(:Matrix2Dstring< doubleconst>& ,const &std): :conststring' :const &tmpxft_00004db4_00000000,- 4_cuda_ml_optimiser.cudafe1.cpplong:)('. text._ZNK8Matrix2DIdEmlERKS0_follow[ ZNK8Matrix2DIdEmlERKS0.]+.0x84/).:. /undefinedlib /referencelibrelion_gpu_util.a (torelion_gpu_util_generated_cuda_ml_optimiser.cu.o ):RelionError :In: RelionErrorfunction( std:std::string: ostreamconst&& ,operator <std<: :const(&std,: :longostream)&', .MultidimArray.</double.>. /constlib&/)librelion_gpu_util.a'(:relion_gpu_util_generated_cuda_ml_optimiser.cu.o )tmpxft_00004db4_00000000:-tmpxft_00004db4_000000004_cuda_ml_optimiser.cudafe1.cpp-:4_cuda_ml_optimiser.cudafe1.cpp(:.(text._ZlsIdERSoS0_RK13MultidimArrayIT_E[._ZlsIdERSoS0_RK13MultidimArrayIT_Etext._Z12arrayByArrayRK13MultidimArrayI8tComplexIdEES4_RS2_c][+_Z12arrayByArrayRK13MultidimArrayI8tComplexIdEES4_RS2_c0x222])+:0xcc )undefined: referencemore toundefined referencesfloatToString (tofloat , RelionErrorint:,: RelionErrorint()std': :tmpxft_00004db4_00000000string- 4_cuda_ml_optimiser.cudafe1.cppconst:&(,. text._ZlsIdERSoS0_RK13MultidimArrayIT_Estd[:_ZlsIdERSoS0_RK13MultidimArrayIT_E:]string+ 0x38fconst)&:, undefinedlong )reference' tofollow .floatToString.(/float.,. /intlib,/ librelion_gpu_util.aint()relion_gpu_util_generated_cuda_ml_optimiser.cu.o') :. .In/ .function. /libstd/:librelion_gpu_util.a:(ostreamrelion_gpu_util_generated_cuda_ml_optimiser.cu.o&) :operator <In< function< double>void( stdgetAllSquaredDifferencesFine:<:MlOptimiserCudaostream>&(,unsigned MultidimArrayint<,double >OptimisationParamters &const,& )SamplingParameters'&:, tmpxft_00004db4_00000000MlOptimiser-*4_cuda_ml_optimiser.cudafe1.cpp,: (MlOptimiserCuda.*text._ZlsIdERSoS0_RK13MultidimArrayIT_E,[ _ZlsIdERSoS0_RK13MultidimArrayIT_Estd]:+:0x222vector)<:IndexedDataArray ,undefined stdreference: :toallocator <IndexedDataArrayfloatToString>( float>,& ,int ,std :int:)vector'< stdtmpxft_00004db4_00000000:-:4_cuda_ml_optimiser.cudafe1.cppvector:<(IndexedDataArrayMask.,text._ZlsIdERSoS0_RK13MultidimArrayIT_E 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tmpxft_00004db4_00000000 ->4_cuda_ml_optimiser.cudafe1.cpp&:,( std.:text._Z28getAllSquaredDifferencesFineI15MlOptimiserCudaEvjR21OptimisationParamtersR18SamplingParametersP11MlOptimiserPT_RSt6vectorI16IndexedDataArraySaISA_EERS9_IS9_I20IndexedDataArrayMaskSaISE_EESaISG_EERS9_I16ProjectionParamsSaISK_EE13AccPtrFactoryiRS9_I12AccPtrBundleSaISP_EE:[vector<_Z28getAllSquaredDifferencesFineI15MlOptimiserCudaEvjR21OptimisationParamtersR18SamplingParametersP11MlOptimiserPT_RSt6vectorI16IndexedDataArraySaISA_EERS9_IS9_I20IndexedDataArrayMaskSaISE_EESaISG_EERS9_I16ProjectionParamsSaISK_EE13AccPtrFactoryiRS9_I12AccPtrBundleSaISP_EEstd]:+:0x2748vector)<:IndexedDataArrayMask ,undefined stdreference: :toallocator <IndexedDataArrayMaskRelionError>: :>RelionError,( stdstd::::stringallocator <conststd&:,: vectorstd<:IndexedDataArrayMask:,string stdconst:&:,allocator <longIndexedDataArrayMask)>' tmpxft_00004db4_00000000 ->4_cuda_ml_optimiser.cudafe1.cpp :>(&,. text._Z28getAllSquaredDifferencesFineI15MlOptimiserCudaEvjR21OptimisationParamtersR18SamplingParametersP11MlOptimiserPT_RSt6vectorI16IndexedDataArraySaISA_EERS9_IS9_I20IndexedDataArrayMaskSaISE_EESaISG_EERS9_I16ProjectionParamsSaISK_EE13AccPtrFactoryiRS9_I12AccPtrBundleSaISP_EEstd[::_Z28getAllSquaredDifferencesFineI15MlOptimiserCudaEvjR21OptimisationParamtersR18SamplingParametersP11MlOptimiserPT_RSt6vectorI16IndexedDataArraySaISA_EERS9_IS9_I20IndexedDataArrayMaskSaISE_EESaISG_EERS9_I16ProjectionParamsSaISK_EE13AccPtrFactoryiRS9_I12AccPtrBundleSaISP_EEvector]<+ProjectionParams0x3911,) :std :undefined: allocatorreference< ProjectionParamsto>>RelionError&:,: RelionErrorAccPtrFactory(,std :int:,string stdconst:&:,vector <stdAccPtrBundle:,: stringstd :const:&allocator,< AccPtrBundlelong>) '> &.).'/:. .tmpxft_00004db4_00000000/-lib4_cuda_ml_optimiser.cudafe1.cpp/:librelion_gpu_util.a((relion_gpu_util_generated_cuda_ml_optimiser.cu.o.)text._Z28getAllSquaredDifferencesFineI15MlOptimiserCudaEvjR21OptimisationParamtersR18SamplingParametersP11MlOptimiserPT_RSt6vectorI16IndexedDataArraySaISA_EERS9_IS9_I20IndexedDataArrayMaskSaISE_EESaISG_EERS9_I16ProjectionParamsSaISK_EE13AccPtrFactoryiRS9_I12AccPtrBundleSaISP_EE:[ In _Z28getAllSquaredDifferencesFineI15MlOptimiserCudaEvjR21OptimisationParamtersR18SamplingParametersP11MlOptimiserPT_RSt6vectorI16IndexedDataArraySaISA_EERS9_IS9_I20IndexedDataArrayMaskSaISE_EESaISG_EERS9_I16ProjectionParamsSaISK_EE13AccPtrFactoryiRS9_I12AccPtrBundleSaISP_EEfunction] +0x2748void) :AccUtilities :undefined: makeNoiseImagereference< MlOptimiserCudato> (floatRelionError,: :MultidimArrayRelionError<(doublestd>:&:,string longconst,& , stdMlOptimiserCuda::,string AccPtrconst<&float,> &long,) 'bool )tmpxft_00004db4_00000000'-:4_cuda_ml_optimiser.cudafe1.cpp :tmpxft_00004db4_00000000(-4_cuda_ml_optimiser.cudafe1.cpp.:text._Z28getAllSquaredDifferencesFineI15MlOptimiserCudaEvjR21OptimisationParamtersR18SamplingParametersP11MlOptimiserPT_RSt6vectorI16IndexedDataArraySaISA_EERS9_IS9_I20IndexedDataArrayMaskSaISE_EESaISG_EERS9_I16ProjectionParamsSaISK_EE13AccPtrFactoryiRS9_I12AccPtrBundleSaISP_EE([.text._ZN12AccUtilities14makeNoiseImageI15MlOptimiserCudaEEvfR13MultidimArrayIdElPT_R6AccPtrIfEb_Z28getAllSquaredDifferencesFineI15MlOptimiserCudaEvjR21OptimisationParamtersR18SamplingParametersP11MlOptimiserPT_RSt6vectorI16IndexedDataArraySaISA_EERS9_IS9_I20IndexedDataArrayMaskSaISE_EESaISG_EERS9_I16ProjectionParamsSaISK_EE13AccPtrFactoryiRS9_I12AccPtrBundleSaISP_EE[]+_ZN12AccUtilities14makeNoiseImageI15MlOptimiserCudaEEvfR13MultidimArrayIdElPT_R6AccPtrIfEb0x3911])+:0x701 )undefined: referenceundefined toreference toRelionError ::RelionErrorRelionError:(:stdRelionError:(:stdstring: :conststring& ,const &std,: :stdstring: :conststring& ,const &long,) 'long ).'. /....//.lib.//librelion_gpu_util.alib(/relion_gpu_util_generated_cuda_ml_optimiser.cu.olibrelion_gpu_util.a)(:relion_gpu_util_generated_cuda_ml_optimiser.cu.o )In: functionIn functionvoidAccUtilitiesvoid: :AccUtilitiesmakeNoiseImage:<:MlOptimiserCudanormalizeAndTransformImage><(MlOptimiserCudafloat>,( AccPtrMultidimArray<>&&,, MultidimArraylong<,tComplex <MlOptimiserCudadouble>, >AccPtr&<,float >MlOptimiserCuda&,, boolunsigned) 'long:, tmpxft_00004db4_00000000unsigned- 4_cuda_ml_optimiser.cudafe1.cpplong:,( unsigned. text._ZN12AccUtilities14makeNoiseImageI15MlOptimiserCudaEEvfR13MultidimArrayIdElPT_R6AccPtrIfEblong[)':_ZN12AccUtilities14makeNoiseImageI15MlOptimiserCudaEEvfR13MultidimArrayIdElPT_R6AccPtrIfEb ]tmpxft_00004db4_00000000+-0x7014_cuda_ml_optimiser.cudafe1.cpp)::( .undefinedtext._ZN12AccUtilities26normalizeAndTransformImageI15MlOptimiserCudaEEvR6AccPtrIfER13MultidimArrayI8tComplexIdEEPT_mmm [reference_ZN12AccUtilities26normalizeAndTransformImageI15MlOptimiserCudaEEvR6AccPtrIfER13MultidimArrayI8tComplexIdEEPT_mmm ]to+ 0x446)RelionError:: :undefinedRelionError (referencestd :to: string RelionErrorconst:&:,RelionError (stdstd::::stringstring constconst&&,, longstd):': string. .const/&.,. /longlib)/'librelion_gpu_util.a (tmpxft_00004db4_00000000relion_gpu_util_generated_cuda_ml_optimiser.cu.o-)4_cuda_ml_optimiser.cudafe1.cpp:: (In. text._ZN12AccUtilities26normalizeAndTransformImageI15MlOptimiserCudaEEvR6AccPtrIfER13MultidimArrayI8tComplexIdEEPT_mmmfunction[ _ZN12AccUtilities26normalizeAndTransformImageI15MlOptimiserCudaEEvR6AccPtrIfER13MultidimArrayI8tComplexIdEEPT_mmm]void+ 0x642AccUtilities)::: normalizeAndTransformImageundefined< MlOptimiserCudareference> (toAccPtr <floatRelionError>:&:,RelionError (MultidimArraystd<:tComplex: const>&&,, stdMlOptimiserCuda::,string unsignedconst &long,, longunsigned) 'long ,. .unsigned/ .long./)lib'/librelion_gpu_util.a(:relion_gpu_util_generated_cuda_ml_optimiser.cu.o )tmpxft_00004db4_00000000:-tmpxft_00004db4_000000004_cuda_ml_optimiser.cudafe1.cpp-:4_cuda_ml_optimiser.cudafe1.cpp(:.(text._ZN12AccUtilities26normalizeAndTransformImageI15MlOptimiserCudaEEvR6AccPtrIfER13MultidimArrayI8tComplexIdEEPT_mmm.[text._Z30getAllSquaredDifferencesCoarseI15MlOptimiserCudaEvjR21OptimisationParamtersR18SamplingParametersP11MlOptimiserPT_R6AccPtrIfE13AccPtrFactoryi_ZN12AccUtilities26normalizeAndTransformImageI15MlOptimiserCudaEEvR6AccPtrIfER13MultidimArrayI8tComplexIdEEPT_mmm[]_Z30getAllSquaredDifferencesCoarseI15MlOptimiserCudaEvjR21OptimisationParamtersR18SamplingParametersP11MlOptimiserPT_R6AccPtrIfE13AccPtrFactoryi+]0x446+)0x32be:) :undefined morereference undefinedto referencesRelionErrorto: :RelionErrorRelionError(:std::RelionError:(stringstd :const:&string, conststd&:,: stringstd :const:&string, constlong&),' longtmpxft_00004db4_00000000)-'4_cuda_ml_optimiser.cudafe1.cpp :follow( .text._ZN12AccUtilities26normalizeAndTransformImageI15MlOptimiserCudaEEvR6AccPtrIfER13MultidimArrayI8tComplexIdEEPT_mmm[_ZN12AccUtilities26normalizeAndTransformImageI15MlOptimiserCudaEEvR6AccPtrIfER13MultidimArrayI8tComplexIdEEPT_mmm]+0x642): undefined reference to RelionError::RelionError(std::string const&, std:collect2: error: ld returned 1 exit status :string const&, long)' ../../lib/librelion_gpu_util.a(relion_gpu_util_generated_cuda_ml_optimiser.cu.o):tmpxft_00004db4_00000000-4_cuda_ml_optimiser.cudafe1.cpp:(.text._Z30getAllSquaredDifferencesCoarseI15MlOptimiserCudaEvjR21OptimisationParamtersR18SamplingParametersP11MlOptimiserPT_R6AccPtrIfE13AccPtrFactoryi[_Z30getAllSquaredDifferencesCoarseI15MlOptimiserCudaEvjR21OptimisationParamtersR18SamplingParametersP11MlOptimiserPT_R6AccPtrIfE13AccPtrFactoryi]+0x32be): more undefined references toRelionError::RelionError(std::string const&, std::string const&, long)' follow collect2: error: ld returned 1 exit status make[2]: [bin/relion_autopick_mpi] Error 1 make[2]: [bin/relion_autopick] Error 1 make[1]: [src/apps/CMakeFiles/autopick_mpi.dir/all] Error 2 make[1]: Waiting for unfinished jobs.... make[1]: [src/apps/CMakeFiles/autopick.dir/all] Error 2 Linking CXX executable ../../bin/relion_ctf_refine_mpi [ 74%] Built target ctf_refine_mpi Linking CXX executable ../../bin/relion_align_symmetry [ 74%] Built target align_symmetry make: [all] Error 2

Naf-Guo commented 5 years ago

I am trying to install relion in a redhat system and I encounter this error many times, I am not sure what's wrong. Is it because gcc is too old?

Any help would be appreciate, thanks!

Naf-Guo commented 5 years ago

Problem solved. I use gcc-6.5.0 and cuda-9.0, it works fine now. thanks!!!