Relocation R_X86_64_32S against `.bss' can not be used when making a PIE linking error

Question

I'm trying to compile AccNEAT project with CUDA support. It's working fine when I compile it without CUDA support. However, when I compile with CUDA support, I get linker errors. To compile the project, my environment is Ubuntu 18.04 LTS 64 bit with GCC-4.8 and NVCC 6.0.

Linker error:

/usr/bin/x86_64-linux-gnu-ld: obj/cu/network/cuda/cudanetwork.o: relocation R_X86_64_32S against `.bss' can not be used when making a PIE object; recompile with -fPIC
/usr/bin/x86_64-linux-gnu-ld: obj/cu/cxx/experiments/maze/mazeevaluator.o: relocation R_X86_64_32S against `.bss' can not be used when making a PIE object; recompile with -fPIC
/usr/bin/x86_64-linux-gnu-ld: obj/cu/cxx/experiments/static/staticevaluator.o: relocation R_X86_64_32S against `.bss' can not be used when making a PIE object; recompile with -fPIC
/usr/bin/x86_64-linux-gnu-ld: final link failed: Nonrepresentable section on output
collect2: error: ld returned 1 exit status
Makefile:49: recipe for target 'neat' failed
make: *** [neat] Error 1

The compiler suggests adding a -fPIC option, but I don't know exactly where to put it in the Makefile. I tried to add it using a -XCompiler option like -XCompiler "-fPIC...", but then when I compile I get this error:

obj/cu/cxx/experiments/maze/mazeevaluator.o: In function `NEAT::create_config(NEAT::Config*&, unsigned long&)':
/home/ner/Projekty/accneat-master-cuda/src/experiments/maze/mazeevaluator.cxx:158: undefined reference to `NEAT::find_resource(std::string const&)'
/home/ner/Projekty/accneat-master-cuda/src/experiments/maze/mazeevaluator.cxx:158: undefined reference to `NEAT::parse_map(std::string)'
collect2: error: ld returned 1 exit status
Makefile:49: recipe for target 'neat' failed
make: *** [neat] Error 1

What does the 'relocation' error mean and is there way to fix this problem?

My Makefile:

include Makefile.conf

CC_CUDA=nvcc -DENABLE_CUDA ${NVCC_FLAGS} -arch=sm_13 --debug --compiler-bindir ${PFM_NVCC_CCBIN} -Xcompiler "${OPT} ${INCLUDES} ${OPENMP} -I/usr/local/cuda/include "

INCLUDES=$(patsubst %,-I%,$(shell find src -type d))
SOURCES=$(shell find src -name "*.cpp")
CXX_SOURCES=$(shell find src -name "*.cxx")

OBJECTS=${SOURCES:src/%.cpp=obj/cpp/%.o}

LIBS=-lgomp
DEFINES=

ifeq (${ENABLE_CUDA}, true)
    CUDA_SOURCES=$(shell find src -name "*.cu")
    CUDA_OBJECTS=${CUDA_SOURCES:src/%.cu=obj/cu/%.o}
    CUDA_OBJECTS+=${CXX_SOURCES:src/%.cxx=obj/cu/cxx/%.o}
    LIBS+=-lcudart
    DEFINES+=-DENABLE_CUDA
else
    OBJECTS+=${CXX_SOURCES:src/%.cxx=obj/cpp/cxx/%.o}
endif

DEPENDS=${OBJECTS:%.o=%.d}
DEPENDS+=${CUDA_OBJECTS:%.o=%.d}

ifeq (${DEVMODE}, true)
    OPT=-O0
    #OPENMP=-fopenmp
    MISC_FLAGS=
    NVCC_FLAGS=-G -g
else
    OPT=-O3
    OPENMP=-fopenmp
    MISC_FLAGS=-Werror
endif

CC_FLAGS=-Wall ${DEFINES} ${MISC_FLAGS} ${PROFILE} ${INCLUDES} ${OPENMP} ${OPT} -c -g -gdwarf-3
.PHONY: clean default

default: ./neat

clean:
    rm -rf obj
    rm -f ./neat
    rm -f src/util/std.h.gch

./neat: ${OBJECTS} ${CUDA_OBJECTS}
    g++ ${PROFILE} ${OBJECTS} ${CUDA_OBJECTS} ${PFM_LD_FLAGS} ${LIBS} -o $@

src/util/std.h.gch: src/util/std.h Makefile.conf Makefile
    g++ ${CC_FLAGS} -std=c++11 $< -o $@

ifeq (${ENABLE_CUDA}, true)

obj/cu/cxx/%.o: src/%.cxx Makefile.conf Makefile
    @mkdir -p $(shell dirname $@)
    ${CC_CUDA} -c -x cu $< -o $@

obj/cu/cxx/%.d: src/%.cxx
    @mkdir -p $(dir $@)
    @${CC_CUDA} -M -x cu $< > $@.tmp
    @cat $@.tmp | sed 's,.*\.o[[:space:]]*:,$@:,g' | sed 's,\.d,\.o,' > $@
    @rm $@.tmp

obj/cu/%.o: src/%.cu Makefile.conf Makefile
    @mkdir -p $(shell dirname $@)
    ${CC_CUDA} -c $< -o $@

obj/cu/%.d: src/%.cu
    @mkdir -p $(dir $@)
    @${CC_CUDA} -M $< > $@.tmp
    @cat $@.tmp | sed 's,.*\.o[[:space:]]*:,$@:,g' | sed 's,\.d,\.o,' > $@
    @rm $@.tmp

else
obj/cpp/cxx/%.o: src/%.cxx Makefile.conf Makefile
    @mkdir -p $(shell dirname $@)
    g++ ${CC_FLAGS} -std=c++98 -MMD $< -o $@
endif

obj/cpp/%.o: src/%.cpp Makefile.conf Makefile src/util/std.h.gch
    @mkdir -p $(shell dirname $@)
    g++ ${CC_FLAGS} -std=c++11 -MMD $< -o $@

-include ${DEPENDS}

(I have added small changes to make it compile like include nvcc dir path).

Build command:

g++  obj/cpp/experiments/maze/maze.o obj/cpp/experiments/static/regex.o obj/cpp/experiments/static/cfg.o obj/cpp/experiments/static/xor.o obj/cpp/experiments/static/sequence.o obj/cpp/experiments/experiment.o obj/cpp/innovgenome/innovation.o obj/cpp/innovgenome/trait.o obj/cpp/innovgenome/innovnodegene.o obj/cpp/innovgenome/innovlinkgene.o obj/cpp/innovgenome/innovgenome.o obj/cpp/innovgenome/innovgenomemanager.o obj/cpp/genomemanager.o obj/cpp/population.o obj/cpp/network/cpu/cpunetwork.o obj/cpp/species/speciesorganism.o obj/cpp/species/species.o obj/cpp/species/speciespopulation.o obj/cpp/util/timer.o obj/cpp/util/rng.o obj/cpp/util/util.o obj/cpp/util/resource.o obj/cpp/util/map.o obj/cpp/main.o obj/cpp/organism.o obj/cpp/neat.o obj/cu/network/cuda/cudanetwork.o obj/cu/cxx/experiments/maze/mazeevaluator.o obj/cu/cxx/experiments/static/staticevaluator.o  -lgomp -lcudart -o neat

EDIT 1: added full build log:

nerexis@nerexis-GE70-0NC-GE70-0ND:~/Projekty/accneat-master-cuda$ make clean
rm -rf obj
rm -f ./neat
rm -f src/util/std.h.gch
nerexis@nerexis-GE70-0NC-GE70-0ND:~/Projekty/accneat-master-cuda$ make
g++ -Wall  -DENABLE_CUDA -Werror  -Isrc -Isrc/experiments -Isrc/experiments/maze -Isrc/experiments/static -Isrc/innovgenome -Isrc/network -Isrc/network/cuda -Isrc/network/cpu -Isrc/species -Isrc/util -fopenmp -O3 -c -g -gdwarf-3 -fPIC -std=c++11 src/util/std.h -o src/util/std.h.gch
g++ -Wall  -DENABLE_CUDA -Werror  -Isrc -Isrc/experiments -Isrc/experiments/maze -Isrc/experiments/static -Isrc/innovgenome -Isrc/network -Isrc/network/cuda -Isrc/network/cpu -Isrc/species -Isrc/util -fopenmp -O3 -c -g -gdwarf-3 -fPIC -std=c++11 -MMD src/experiments/maze/maze.cpp -o obj/cpp/experiments/maze/maze.o
g++ -Wall  -DENABLE_CUDA -Werror  -Isrc -Isrc/experiments -Isrc/experiments/maze -Isrc/experiments/static -Isrc/innovgenome -Isrc/network -Isrc/network/cuda -Isrc/network/cpu -Isrc/species -Isrc/util -fopenmp -O3 -c -g -gdwarf-3 -fPIC -std=c++11 -MMD src/experiments/static/regex.cpp -o obj/cpp/experiments/static/regex.o
g++ -Wall  -DENABLE_CUDA -Werror  -Isrc -Isrc/experiments -Isrc/experiments/maze -Isrc/experiments/static -Isrc/innovgenome -Isrc/network -Isrc/network/cuda -Isrc/network/cpu -Isrc/species -Isrc/util -fopenmp -O3 -c -g -gdwarf-3 -fPIC -std=c++11 -MMD src/experiments/static/cfg.cpp -o obj/cpp/experiments/static/cfg.o
g++ -Wall  -DENABLE_CUDA -Werror  -Isrc -Isrc/experiments -Isrc/experiments/maze -Isrc/experiments/static -Isrc/innovgenome -Isrc/network -Isrc/network/cuda -Isrc/network/cpu -Isrc/species -Isrc/util -fopenmp -O3 -c -g -gdwarf-3 -fPIC -std=c++11 -MMD src/experiments/static/xor.cpp -o obj/cpp/experiments/static/xor.o
g++ -Wall  -DENABLE_CUDA -Werror  -Isrc -Isrc/experiments -Isrc/experiments/maze -Isrc/experiments/static -Isrc/innovgenome -Isrc/network -Isrc/network/cuda -Isrc/network/cpu -Isrc/species -Isrc/util -fopenmp -O3 -c -g -gdwarf-3 -fPIC -std=c++11 -MMD src/experiments/static/sequence.cpp -o obj/cpp/experiments/static/sequence.o
g++ -Wall  -DENABLE_CUDA -Werror  -Isrc -Isrc/experiments -Isrc/experiments/maze -Isrc/experiments/static -Isrc/innovgenome -Isrc/network -Isrc/network/cuda -Isrc/network/cpu -Isrc/species -Isrc/util -fopenmp -O3 -c -g -gdwarf-3 -fPIC -std=c++11 -MMD src/experiments/experiment.cpp -o obj/cpp/experiments/experiment.o
g++ -Wall  -DENABLE_CUDA -Werror  -Isrc -Isrc/experiments -Isrc/experiments/maze -Isrc/experiments/static -Isrc/innovgenome -Isrc/network -Isrc/network/cuda -Isrc/network/cpu -Isrc/species -Isrc/util -fopenmp -O3 -c -g -gdwarf-3 -fPIC -std=c++11 -MMD src/innovgenome/innovation.cpp -o obj/cpp/innovgenome/innovation.o
g++ -Wall  -DENABLE_CUDA -Werror  -Isrc -Isrc/experiments -Isrc/experiments/maze -Isrc/experiments/static -Isrc/innovgenome -Isrc/network -Isrc/network/cuda -Isrc/network/cpu -Isrc/species -Isrc/util -fopenmp -O3 -c -g -gdwarf-3 -fPIC -std=c++11 -MMD src/innovgenome/trait.cpp -o obj/cpp/innovgenome/trait.o
g++ -Wall  -DENABLE_CUDA -Werror  -Isrc -Isrc/experiments -Isrc/experiments/maze -Isrc/experiments/static -Isrc/innovgenome -Isrc/network -Isrc/network/cuda -Isrc/network/cpu -Isrc/species -Isrc/util -fopenmp -O3 -c -g -gdwarf-3 -fPIC -std=c++11 -MMD src/innovgenome/innovnodegene.cpp -o obj/cpp/innovgenome/innovnodegene.o
g++ -Wall  -DENABLE_CUDA -Werror  -Isrc -Isrc/experiments -Isrc/experiments/maze -Isrc/experiments/static -Isrc/innovgenome -Isrc/network -Isrc/network/cuda -Isrc/network/cpu -Isrc/species -Isrc/util -fopenmp -O3 -c -g -gdwarf-3 -fPIC -std=c++11 -MMD src/innovgenome/innovlinkgene.cpp -o obj/cpp/innovgenome/innovlinkgene.o
g++ -Wall  -DENABLE_CUDA -Werror  -Isrc -Isrc/experiments -Isrc/experiments/maze -Isrc/experiments/static -Isrc/innovgenome -Isrc/network -Isrc/network/cuda -Isrc/network/cpu -Isrc/species -Isrc/util -fopenmp -O3 -c -g -gdwarf-3 -fPIC -std=c++11 -MMD src/innovgenome/innovgenome.cpp -o obj/cpp/innovgenome/innovgenome.o
g++ -Wall  -DENABLE_CUDA -Werror  -Isrc -Isrc/experiments -Isrc/experiments/maze -Isrc/experiments/static -Isrc/innovgenome -Isrc/network -Isrc/network/cuda -Isrc/network/cpu -Isrc/species -Isrc/util -fopenmp -O3 -c -g -gdwarf-3 -fPIC -std=c++11 -MMD src/innovgenome/innovgenomemanager.cpp -o obj/cpp/innovgenome/innovgenomemanager.o
g++ -Wall  -DENABLE_CUDA -Werror  -Isrc -Isrc/experiments -Isrc/experiments/maze -Isrc/experiments/static -Isrc/innovgenome -Isrc/network -Isrc/network/cuda -Isrc/network/cpu -Isrc/species -Isrc/util -fopenmp -O3 -c -g -gdwarf-3 -fPIC -std=c++11 -MMD src/genomemanager.cpp -o obj/cpp/genomemanager.o
g++ -Wall  -DENABLE_CUDA -Werror  -Isrc -Isrc/experiments -Isrc/experiments/maze -Isrc/experiments/static -Isrc/innovgenome -Isrc/network -Isrc/network/cuda -Isrc/network/cpu -Isrc/species -Isrc/util -fopenmp -O3 -c -g -gdwarf-3 -fPIC -std=c++11 -MMD src/population.cpp -o obj/cpp/population.o
g++ -Wall  -DENABLE_CUDA -Werror  -Isrc -Isrc/experiments -Isrc/experiments/maze -Isrc/experiments/static -Isrc/innovgenome -Isrc/network -Isrc/network/cuda -Isrc/network/cpu -Isrc/species -Isrc/util -fopenmp -O3 -c -g -gdwarf-3 -fPIC -std=c++11 -MMD src/network/cpu/cpunetwork.cpp -o obj/cpp/network/cpu/cpunetwork.o
g++ -Wall  -DENABLE_CUDA -Werror  -Isrc -Isrc/experiments -Isrc/experiments/maze -Isrc/experiments/static -Isrc/innovgenome -Isrc/network -Isrc/network/cuda -Isrc/network/cpu -Isrc/species -Isrc/util -fopenmp -O3 -c -g -gdwarf-3 -fPIC -std=c++11 -MMD src/species/speciesorganism.cpp -o obj/cpp/species/speciesorganism.o
g++ -Wall  -DENABLE_CUDA -Werror  -Isrc -Isrc/experiments -Isrc/experiments/maze -Isrc/experiments/static -Isrc/innovgenome -Isrc/network -Isrc/network/cuda -Isrc/network/cpu -Isrc/species -Isrc/util -fopenmp -O3 -c -g -gdwarf-3 -fPIC -std=c++11 -MMD src/species/species.cpp -o obj/cpp/species/species.o
g++ -Wall  -DENABLE_CUDA -Werror  -Isrc -Isrc/experiments -Isrc/experiments/maze -Isrc/experiments/static -Isrc/innovgenome -Isrc/network -Isrc/network/cuda -Isrc/network/cpu -Isrc/species -Isrc/util -fopenmp -O3 -c -g -gdwarf-3 -fPIC -std=c++11 -MMD src/species/speciespopulation.cpp -o obj/cpp/species/speciespopulation.o
g++ -Wall  -DENABLE_CUDA -Werror  -Isrc -Isrc/experiments -Isrc/experiments/maze -Isrc/experiments/static -Isrc/innovgenome -Isrc/network -Isrc/network/cuda -Isrc/network/cpu -Isrc/species -Isrc/util -fopenmp -O3 -c -g -gdwarf-3 -fPIC -std=c++11 -MMD src/util/timer.cpp -o obj/cpp/util/timer.o
g++ -Wall  -DENABLE_CUDA -Werror  -Isrc -Isrc/experiments -Isrc/experiments/maze -Isrc/experiments/static -Isrc/innovgenome -Isrc/network -Isrc/network/cuda -Isrc/network/cpu -Isrc/species -Isrc/util -fopenmp -O3 -c -g -gdwarf-3 -fPIC -std=c++11 -MMD src/util/rng.cpp -o obj/cpp/util/rng.o
g++ -Wall  -DENABLE_CUDA -Werror  -Isrc -Isrc/experiments -Isrc/experiments/maze -Isrc/experiments/static -Isrc/innovgenome -Isrc/network -Isrc/network/cuda -Isrc/network/cpu -Isrc/species -Isrc/util -fopenmp -O3 -c -g -gdwarf-3 -fPIC -std=c++11 -MMD src/util/util.cpp -o obj/cpp/util/util.o
g++ -Wall  -DENABLE_CUDA -Werror  -Isrc -Isrc/experiments -Isrc/experiments/maze -Isrc/experiments/static -Isrc/innovgenome -Isrc/network -Isrc/network/cuda -Isrc/network/cpu -Isrc/species -Isrc/util -fopenmp -O3 -c -g -gdwarf-3 -fPIC -std=c++11 -MMD src/util/resource.cpp -o obj/cpp/util/resource.o
g++ -Wall  -DENABLE_CUDA -Werror  -Isrc -Isrc/experiments -Isrc/experiments/maze -Isrc/experiments/static -Isrc/innovgenome -Isrc/network -Isrc/network/cuda -Isrc/network/cpu -Isrc/species -Isrc/util -fopenmp -O3 -c -g -gdwarf-3 -fPIC -std=c++11 -MMD src/util/map.cpp -o obj/cpp/util/map.o
g++ -Wall  -DENABLE_CUDA -Werror  -Isrc -Isrc/experiments -Isrc/experiments/maze -Isrc/experiments/static -Isrc/innovgenome -Isrc/network -Isrc/network/cuda -Isrc/network/cpu -Isrc/species -Isrc/util -fopenmp -O3 -c -g -gdwarf-3 -fPIC -std=c++11 -MMD src/main.cpp -o obj/cpp/main.o
g++ -Wall  -DENABLE_CUDA -Werror  -Isrc -Isrc/experiments -Isrc/experiments/maze -Isrc/experiments/static -Isrc/innovgenome -Isrc/network -Isrc/network/cuda -Isrc/network/cpu -Isrc/species -Isrc/util -fopenmp -O3 -c -g -gdwarf-3 -fPIC -std=c++11 -MMD src/organism.cpp -o obj/cpp/organism.o
g++ -Wall  -DENABLE_CUDA -Werror  -Isrc -Isrc/experiments -Isrc/experiments/maze -Isrc/experiments/static -Isrc/innovgenome -Isrc/network -Isrc/network/cuda -Isrc/network/cpu -Isrc/species -Isrc/util -fopenmp -O3 -c -g -gdwarf-3 -fPIC -std=c++11 -MMD src/neat.cpp -o obj/cpp/neat.o
nvcc -DENABLE_CUDA  -arch=sm_13 --debug --compiler-bindir gcc-4.8 -Xcompiler "-O3 -Isrc -Isrc/experiments -Isrc/experiments/maze -Isrc/experiments/static -Isrc/innovgenome -Isrc/network -Isrc/network/cuda -Isrc/network/cpu -Isrc/species -Isrc/util -fopenmp -I/usr/local/cuda/include -L/usrlocal/cuda/lib64" -c src/network/cuda/cudanetwork.cu -o obj/cu/network/cuda/cudanetwork.o
nvcc -DENABLE_CUDA  -arch=sm_13 --debug --compiler-bindir gcc-4.8 -Xcompiler "-O3 -Isrc -Isrc/experiments -Isrc/experiments/maze -Isrc/experiments/static -Isrc/innovgenome -Isrc/network -Isrc/network/cuda -Isrc/network/cpu -Isrc/species -Isrc/util -fopenmp -I/usr/local/cuda/include -L/usrlocal/cuda/lib64" -c -x cu src/experiments/maze/mazeevaluator.cxx -o obj/cu/cxx/experiments/maze/mazeevaluator.o
nvcc -DENABLE_CUDA  -arch=sm_13 --debug --compiler-bindir gcc-4.8 -Xcompiler "-O3 -Isrc -Isrc/experiments -Isrc/experiments/maze -Isrc/experiments/static -Isrc/innovgenome -Isrc/network -Isrc/network/cuda -Isrc/network/cpu -Isrc/species -Isrc/util -fopenmp -I/usr/local/cuda/include -L/usrlocal/cuda/lib64" -c -x cu src/experiments/static/staticevaluator.cxx -o obj/cu/cxx/experiments/static/staticevaluator.o
g++  obj/cpp/experiments/maze/maze.o obj/cpp/experiments/static/regex.o obj/cpp/experiments/static/cfg.o obj/cpp/experiments/static/xor.o obj/cpp/experiments/static/sequence.o obj/cpp/experiments/experiment.o obj/cpp/innovgenome/innovation.o obj/cpp/innovgenome/trait.o obj/cpp/innovgenome/innovnodegene.o obj/cpp/innovgenome/innovlinkgene.o obj/cpp/innovgenome/innovgenome.o obj/cpp/innovgenome/innovgenomemanager.o obj/cpp/genomemanager.o obj/cpp/population.o obj/cpp/network/cpu/cpunetwork.o obj/cpp/species/speciesorganism.o obj/cpp/species/species.o obj/cpp/species/speciespopulation.o obj/cpp/util/timer.o obj/cpp/util/rng.o obj/cpp/util/util.o obj/cpp/util/resource.o obj/cpp/util/map.o obj/cpp/main.o obj/cpp/organism.o obj/cpp/neat.o obj/cu/network/cuda/cudanetwork.o obj/cu/cxx/experiments/maze/mazeevaluator.o obj/cu/cxx/experiments/static/staticevaluator.o  -lgomp -lcudart -o neat
/usr/bin/x86_64-linux-gnu-ld: obj/cu/network/cuda/cudanetwork.o: relocation R_X86_64_32S against `.bss' can not be used when making a PIE object; recompile with -fPIC
/usr/bin/x86_64-linux-gnu-ld: obj/cu/cxx/experiments/maze/mazeevaluator.o: relocation R_X86_64_32S against `.bss' can not be used when making a PIE object; recompile with -fPIC
/usr/bin/x86_64-linux-gnu-ld: obj/cu/cxx/experiments/static/staticevaluator.o: relocation R_X86_64_32S against `.bss' can not be used when making a PIE object; recompile with -fPIC
/usr/bin/x86_64-linux-gnu-ld: final link failed: Nonrepresentable section on output
collect2: error: ld returned 1 exit status
Makefile:49: recipe for target 'neat' failed
make: *** [neat] Error 1

EDIT 2: Makefile:

include Makefile.conf
CC_CUDA=nvcc -DENABLE_CUDA ${NVCC_FLAGS} -arch=sm_20 --debug --compiler-bindir ${PFM_NVCC_CCBIN} -Xcompiler "${OPT} ${INCLUDES} ${OPENMP} -I/usr/local/cuda/include -L/usr/local/cuda/lib64 "

INCLUDES=$(patsubst %,-I%,$(shell find src -type d))
SOURCES=$(shell find src -name "*.cpp")
CXX_SOURCES=$(shell find src -name "*.cxx")

OBJECTS=${SOURCES:src/%.cpp=obj/cpp/%.o}

LIBS=-lgomp
DEFINES=

ifeq (${ENABLE_CUDA}, true)
    CUDA_SOURCES=$(shell find src -name "*.cu")
    CUDA_OBJECTS=${CUDA_SOURCES:src/%.cu=obj/cu/%.o}
    CUDA_OBJECTS+=${CXX_SOURCES:src/%.cxx=obj/cu/cxx/%.o}
    LIBS+=-lcudart
    DEFINES+=-DENABLE_CUDA
else
    OBJECTS+=${CXX_SOURCES:src/%.cxx=obj/cpp/cxx/%.o}
endif

DEPENDS=${OBJECTS:%.o=%.d}
DEPENDS+=${CUDA_OBJECTS:%.o=%.d}

ifeq (${DEVMODE}, true)
    OPT=-O0
    #OPENMP=-fopenmp
    MISC_FLAGS=
    NVCC_FLAGS=-G -g
else
    OPT=-O3
    OPENMP=-fopenmp
    MISC_FLAGS=-Werror
    NVCC_FLAGS=--relocatable-device-code=true --dont-use-profile -ldir /usr/local/cuda/nvvm/libdevice 
endif

CC_FLAGS=-Wall ${DEFINES} ${MISC_FLAGS} ${PROFILE} ${INCLUDES} ${OPENMP} ${OPT} -c -g -gdwarf-3 -fPIC
.PHONY: clean default

default: ./neat

clean:
    rm -rf obj
    rm -f ./neat
    rm -f src/util/std.h.gch

./neat: ${OBJECTS} ${CUDA_OBJECTS}
    g++ ${PROFILE} ${OBJECTS} ${CUDA_OBJECTS} ${PFM_LD_FLAGS} -fPIC ${LIBS} -o $@

src/util/std.h.gch: src/util/std.h Makefile.conf Makefile
    g++ ${CC_FLAGS} -std=c++11 $< -o $@

ifeq (${ENABLE_CUDA}, true)

obj/cu/cxx/%.o: src/%.cxx Makefile.conf Makefile
    @mkdir -p $(shell dirname $@)
    ${CC_CUDA} -c -x cu $< -o $@

obj/cu/cxx/%.d: src/%.cxx
    @mkdir -p $(dir $@)
    @${CC_CUDA} -M -x cu $< > $@.tmp
    @cat $@.tmp | sed 's,.*\.o[[:space:]]*:,$@:,g' | sed 's,\.d,\.o,' > $@
    @rm $@.tmp

obj/cu/%.o: src/%.cu Makefile.conf Makefile
    @mkdir -p $(shell dirname $@)
    ${CC_CUDA} -c $< -o $@

obj/cu/%.d: src/%.cu
    @mkdir -p $(dir $@)
    @${CC_CUDA} -M $< > $@.tmp
    @cat $@.tmp | sed 's,.*\.o[[:space:]]*:,$@:,g' | sed 's,\.d,\.o,' > $@
    @rm $@.tmp

else
obj/cpp/cxx/%.o: src/%.cxx Makefile.conf Makefile
    @mkdir -p $(shell dirname $@)
    g++ ${CC_FLAGS} -std=c++98 -MMD $< -o $@
endif

obj/cpp/%.o: src/%.cpp Makefile.conf Makefile src/util/std.h.gch
    @mkdir -p $(shell dirname $@)
    g++ ${CC_FLAGS} -std=c++11 -MMD $< -o $@

-include ${DEPENDS}

Build log (just the end because of length limit):

g++  obj/cpp/experiments/maze/maze.o obj/cpp/experiments/static/regex.o obj/cpp/experiments/static/cfg.o obj/cpp/experiments/static/xor.o obj/cpp/experiments/static/sequence.o obj/cpp/experiments/experiment.o obj/cpp/innovgenome/innovation.o obj/cpp/innovgenome/trait.o obj/cpp/innovgenome/innovnodegene.o obj/cpp/innovgenome/innovlinkgene.o obj/cpp/innovgenome/innovgenome.o obj/cpp/innovgenome/innovgenomemanager.o obj/cpp/genomemanager.o obj/cpp/population.o obj/cpp/network/cpu/cpunetwork.o obj/cpp/species/speciesorganism.o obj/cpp/species/species.o obj/cpp/species/speciespopulation.o obj/cpp/util/timer.o obj/cpp/util/rng.o obj/cpp/util/util.o obj/cpp/util/resource.o obj/cpp/util/map.o obj/cpp/main.o obj/cpp/organism.o obj/cpp/neat.o obj/cu/network/cuda/cudanetwork.o obj/cu/cxx/experiments/maze/mazeevaluator.o obj/cu/cxx/experiments/static/staticevaluator.o  -fPIC -lgomp -lcudart -o neat
/usr/bin/x86_64-linux-gnu-ld: obj/cu/network/cuda/cudanetwork.o: relocation R_X86_64_32S against symbol `_ZTVN4NEAT11CudaNetworkE' can not be used when making a PIE object; recompile with -fPIC
/usr/bin/x86_64-linux-gnu-ld: obj/cu/cxx/experiments/maze/mazeevaluator.o: relocation R_X86_64_32 against `.rodata.str1.8' can not be used when making a PIE object; recompile with -fPIC
/usr/bin/x86_64-linux-gnu-ld: obj/cu/cxx/experiments/static/staticevaluator.o: relocation R_X86_64_32 against `.rodata.str1.8' can not be used when making a PIE object; recompile with -fPIC
/usr/bin/x86_64-linux-gnu-ld: final link failed: Nonrepresentable section on output
collect2: error: ld returned 1 exit status
Makefile:50: recipe for target 'neat' failed
make: *** [neat] Error 1

EDIT 3: I was able to compile when I have added the options -fPIC -shared to -Xcompiler option and CC_FLAGS and ./neat: g++ line. When I run compiled binary, I get segmentation fault error. Additional info from valgrind program:

==14367== Jump to the invalid address stated on the next line
==14367==    at 0x1C296: ???
==14367==    by 0x12506B: operator<< <std::char_traits<char> > (ostream:561)
==14367==    by 0x12506B: cmp(NEAT::InnovationId const&, NEAT::InnovationId const&) [clone .part.5] (innovation.cpp:43)
==14367==  Address 0x1c296 is not stack'd, malloc'd or (recently) free'd
==14367== 
==14367== 
==14367== Process terminating with default action of signal 11 (SIGSEGV)
==14367==  Bad permissions for mapped region at address 0x1C296
==14367==    at 0x1C296: ???
==14367==    by 0x12506B: operator<< <std::char_traits<char> > (ostream:561)
==14367==    by 0x12506B: cmp(NEAT::InnovationId const&, NEAT::InnovationId const&) [clone .part.5] (innovation.cpp:43)
==14367==

Why "cmake" tag, if you use Makefile? – Tsyvarev Aug 28 '18 at 20:51 — Tsyvarev, Aug 28 '18 at 20:51

score 2 · Answer 1 · answered Aug 30 '18 at 09:30

2

Changing the setting of CC_FLAGS (the compilation options) from:

CC_FLAGS=-Wall ${DEFINES} ${MISC_FLAGS} ${PROFILE} ${INCLUDES} ${OPENMP} ${OPT} -c -g -gdwarf-3

to:

CC_FLAGS=-Wall ${DEFINES} ${MISC_FLAGS} ${PROFILE} ${INCLUDES} ${OPENMP} ${OPT} -c -g -gdwarf-3 -fPIC

seems likely to cure this particular linkage failure.

answered Aug 30 '18 at 09:30

Mike Kinghan

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1

Unfortunately it didn't help. Error is still the same `relocation R_X86_64_32S against...` – user3157855 Aug 30 '18 at 16:51
1

@user3157855 Did you `make clean` before rebuilding? – Mike Kinghan Aug 31 '18 at 07:25
yes I did execute `make clean`. Something is changing when I add -fPIC into -XCompiler argument, but then I get reference error. When I put it into CC_FLAGS nothing is changing. – user3157855 Aug 31 '18 at 07:27
1

@user3157855 In that case can you please post the full build-log from clean, i.e. the actual commands you run (from clean) and the complete verbatim output. Doesn't matter if its long. – Mike Kinghan Aug 31 '18 at 07:33
Added build log with -fPIC option in CC_FLAGS, into main post. – user3157855 Aug 31 '18 at 17:51
1

@user3157855 can you try adding the -fPIC argument to the line as follows: `g++ ${PROFILE} ${OBJECTS} ${CUDA_OBJECTS} ${PFM_LD_FLAGS} -fPIC ${LIBS} -o $@` – Shashank Shet Sep 06 '18 at 15:20
1

@user3157855 another possible solution may be to add `--relocatable-device-code true` to NVCC_FLAGS. I haven't encountered this error, so both my suggestions are based on hunches. – Shashank Shet Sep 06 '18 at 16:01
It didn't help. I have added makefile and build log to EDIT 3 in the main post. – user3157855 Sep 06 '18 at 16:58
Additional info: I have installed CUDA-6.0 from .run file from nvidia website, and gcc-4.8 using command `sudo apt-get install gcc-4.8` so before I start to compile I'm adding some exports in terminal like: `export PATH=$PATH:/usr/local/cuda-6.0/open64/bin export PATH=$PATH:/usr/local/cuda-6.0/bin` Also I have link which points /usr/local/cuda to /usr/local/cuda-6.0 – user3157855 Sep 06 '18 at 17:08
I was able to compile when I have added options `-fPIC -shared` but I get a segmentation fault error when I run the application. Please check the EDIT 3 in the main post. – user3157855 Sep 06 '18 at 17:46

score 2 · Answer 2 · answered Feb 17 '20 at 11:21

I tred a tip in this thread which suggested adding the following to the nvcc compiler options, which worked for me:

nvcc --compiler-options -fPIC ...

I only just learned that PIC stands for Position Independent Code (meaning that the executable can be loaded anywhere in memory). When compiling a PIC executable, all referenced libraries and objects need to be PIC as well (I think), including the Cuda code. So in my case the fPIC option needed to be passed to nvcc not g++.

Relocation R_X86_64_32S against `.bss' can not be used when making a PIE linking error

2 Answers2