64 -L/lib -L/common/lib/linux -lcuda -lcudart -MT strindex.o -MD -MP -MF .deps/strindex.Tpo -c -o strindex.o strindex.cc mv -f .deps/strindex.Tpo .deps/strindex.Po g++ -DPACKAGE_NAME=\"autodock\" -DPACKAGE_TARNAME=\"autodock\" -DPACKAGE_VERSION=\"4.0.1\" -DPACKAGE_STRING=\"autodock\ 4.0.1\" -DPACKAGE_BUGREPORT=\"autodock@scripps.edu\" -DPACKAGE=\"autodock\" -DVERSION=\"4.0.1\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE__BOOL=1 -DHAVE_STDBOOL_H=1 -DHAVE_STDLIB_H=1 -DHAVE_MALLOC=1 -DHAVE_GETHOSTNAME=1 -DHAVE_STRNCASECMP=1 -DCUDA_READY=1 -DHAVE_CUDA_RUNTIME_H=1 -DHAVE_CUDA_H=1 -I. -DNOSQRT -DUSE_8A_NBCUTOFF -DDO_NOT_CROSSOVER_IN_QUAT -DWRITEPDBQSTATE -I./../acro/include -I/usr/local/cuda/include -I/common/inc -L/usr/local/cuda/bin -L/usr/local/cuda/lib64 -L/lib -L/common/lib/linux -lcuda -lcudart -I/usr/local/cuda/include -I/common/inc -L/usr/local/cuda/bin -L/usr/local/cuda/lib64 -L/lib -L/common/lib/linux -lcuda -lcudart -MT success.o -MD -MP -MF .deps/success.Tpo -c -o success.o success.cc success.cc: In function ‘void success(char*, clock_t, tms)’: success.cc:52:34: warning: deprecated conversion from string constant to ‘char*’ [-Wwrite-strings] pr_2x( logFile, stderr, "\n" ); ^ success.cc:53:39: warning: deprecated conversion from string constant to ‘char*’ [-Wwrite-strings] pr_2x( logFile, stderr, UnderLine ); ^ success.cc:61:39: warning: deprecated conversion from string constant to ‘char*’ [-Wwrite-strings] pr_2x( logFile, stderr, UnderLine ); ^ mv -f .deps/success.Tpo .deps/success.Po g++ -DPACKAGE_NAME=\"autodock\" -DPACKAGE_TARNAME=\"autodock\" -DPACKAGE_VERSION=\"4.0.1\" -DPACKAGE_STRING=\"autodock\ 4.0.1\" -DPACKAGE_BUGREPORT=\"autodock@scripps.edu\" -DPACKAGE=\"autodock\" -DVERSION=\"4.0.1\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE__BOOL=1 -DHAVE_STDBOOL_H=1 -DHAVE_STDLIB_H=1 -DHAVE_MALLOC=1 -DHAVE_GETHOSTNAME=1 -DHAVE_STRNCASECMP=1 -DCUDA_READY=1 -DHAVE_CUDA_RUNTIME_H=1 -DHAVE_CUDA_H=1 -I. -DNOSQRT -DUSE_8A_NBCUTOFF -DDO_NOT_CROSSOVER_IN_QUAT -DWRITEPDBQSTATE -I./../acro/include -I/usr/local/cuda/include -I/common/inc -L/usr/local/cuda/bin -L/usr/local/cuda/lib64 -L/lib -L/common/lib/linux -lcuda -lcudart -I/usr/local/cuda/include -I/common/inc -L/usr/local/cuda/bin -L/usr/local/cuda/lib64 -L/lib -L/common/lib/linux -lcuda -lcudart -MT summarizegrids.o -MD -MP -MF .deps/summarizegrids.Tpo -c -o summarizegrids.o summarizegrids.cc mv -f .deps/summarizegrids.Tpo .deps/summarizegrids.Po g++ -DPACKAGE_NAME=\"autodock\" -DPACKAGE_TARNAME=\"autodock\" -DPACKAGE_VERSION=\"4.0.1\" -DPACKAGE_STRING=\"autodock\ 4.0.1\" -DPACKAGE_BUGREPORT=\"autodock@scripps.edu\" -DPACKAGE=\"autodock\" -DVERSION=\"4.0.1\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE__BOOL=1 -DHAVE_STDBOOL_H=1 -DHAVE_STDLIB_H=1 -DHAVE_MALLOC=1 -DHAVE_GETHOSTNAME=1 -DHAVE_STRNCASECMP=1 -DCUDA_READY=1 -DHAVE_CUDA_RUNTIME_H=1 -DHAVE_CUDA_H=1 -I. -DNOSQRT -DUSE_8A_NBCUTOFF -DDO_NOT_CROSSOVER_IN_QUAT -DWRITEPDBQSTATE -I./../acro/include -I/usr/local/cuda/include -I/common/inc -L/usr/local/cuda/bin -L/usr/local/cuda/lib64 -L/lib -L/common/lib/linux -lcuda -lcudart -I/usr/local/cuda/include -I/common/inc -L/usr/local/cuda/bin -L/usr/local/cuda/lib64 -L/lib -L/common/lib/linux -lcuda -lcudart -MT support.o -MD -MP -MF .deps/support.Tpo -c -o support.o support.cc mv -f .deps/support.Tpo .deps/support.Po g++ -DPACKAGE_NAME=\"autodock\" -DPACKAGE_TARNAME=\"autodock\" -DPACKAGE_VERSION=\"4.0.1\" -DPACKAGE_STRING=\"autodock\ 4.0.1\" -DPACKAGE_BUGREPORT=\"autodock@scripps.edu\" -DPACKAGE=\"autodock\" -DVERSION=\"4.0.1\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE__BOOL=1 -DHAVE_STDBOOL_H=1 -DHAVE_STDLIB_H=1 -DHAVE_MALLOC=1 -DHAVE_GETHOSTNAME=1 -DHAVE_STRNCASECMP=1 -DCUDA_READY=1 -DHAVE_CUDA_RUNTIME_H=1 -DHAVE_CUDA_H=1 -I. -DNOSQRT -DUSE_8A_NBCUTOFF -DDO_NOT_CROSSOVER_IN_QUAT -DWRITEPDBQSTATE -I./../acro/include -I/usr/local/cuda/include -I/common/inc -L/usr/local/cuda/bin -L/usr/local/cuda/lib64 -L/lib -L/common/lib/linux -lcuda -lcudart -I/usr/local/cuda/include -I/common/inc -L/usr/local/cuda/bin -L/usr/local/cuda/lib64 -L/lib -L/common/lib/linux -lcuda -lcudart -MT swap.o -MD -MP -MF .deps/swap.Tpo -c -o swap.o swap.cc mv -f .deps/swap.Tpo .deps/swap.Po g++ -DPACKAGE_NAME=\"autodock\" -DPACKAGE_TARNAME=\"autodock\" -DPACKAGE_VERSION=\"4.0.1\" -DPACKAGE_STRING=\"autodock\ 4.0.1\" -DPACKAGE_BUGREPORT=\"autodock@scripps.edu\" -DPACKAGE=\"autodock\" -DVERSION=\"4.0.1\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE__BOOL=1 -DHAVE_STDBOOL_H=1 -DHAVE_STDLIB_H=1 -DHAVE_MALLOC=1 -DHAVE_GETHOSTNAME=1 -DHAVE_STRNCASECMP=1 -DCUDA_READY=1 -DHAVE_CUDA_RUNTIME_H=1 -DHAVE_CUDA_H=1 -I. -DNOSQRT -DUSE_8A_NBCUTOFF -DDO_NOT_CROSSOVER_IN_QUAT -DWRITEPDBQSTATE -I./../acro/include -I/usr/local/cuda/include -I/common/inc -L/usr/local/cuda/bin -L/usr/local/cuda/lib64 -L/lib -L/common/lib/linux -lcuda -lcudart -I/usr/local/cuda/include -I/common/inc -L/usr/local/cuda/bin -L/usr/local/cuda/lib64 -L/lib -L/common/lib/linux -lcuda -lcudart -MT timesys.o -MD -MP -MF .deps/timesys.Tpo -c -o timesys.o timesys.cc mv -f .deps/timesys.Tpo .deps/timesys.Po g++ -DPACKAGE_NAME=\"autodock\" -DPACKAGE_TARNAME=\"autodock\" -DPACKAGE_VERSION=\"4.0.1\" -DPACKAGE_STRING=\"autodock\ 4.0.1\" -DPACKAGE_BUGREPORT=\"autodock@scripps.edu\" -DPACKAGE=\"autodock\" -DVERSION=\"4.0.1\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE__BOOL=1 -DHAVE_STDBOOL_H=1 -DHAVE_STDLIB_H=1 -DHAVE_MALLOC=1 -DHAVE_GETHOSTNAME=1 -DHAVE_STRNCASECMP=1 -DCUDA_READY=1 -DHAVE_CUDA_RUNTIME_H=1 -DHAVE_CUDA_H=1 -I. -DNOSQRT -DUSE_8A_NBCUTOFF -DDO_NOT_CROSSOVER_IN_QUAT -DWRITEPDBQSTATE -I./../acro/include -I/usr/local/cuda/include -I/common/inc -L/usr/local/cuda/bin -L/usr/local/cuda/lib64 -L/lib -L/common/lib/linux -lcuda -lcudart -I/usr/local/cuda/include -I/common/inc -L/usr/local/cuda/bin -L/usr/local/cuda/lib64 -L/lib -L/common/lib/linux -lcuda -lcudart -MT timesyshms.o -MD -MP -MF .deps/timesyshms.Tpo -c -o timesyshms.o timesyshms.cc mv -f .deps/timesyshms.Tpo .deps/timesyshms.Po g++ -DPACKAGE_NAME=\"autodock\" -DPACKAGE_TARNAME=\"autodock\" -DPACKAGE_VERSION=\"4.0.1\" -DPACKAGE_STRING=\"autodock\ 4.0.1\" -DPACKAGE_BUGREPORT=\"autodock@scripps.edu\" -DPACKAGE=\"autodock\" -DVERSION=\"4.0.1\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE__BOOL=1 -DHAVE_STDBOOL_H=1 -DHAVE_STDLIB_H=1 -DHAVE_MALLOC=1 -DHAVE_GETHOSTNAME=1 -DHAVE_STRNCASECMP=1 -DCUDA_READY=1 -DHAVE_CUDA_RUNTIME_H=1 -DHAVE_CUDA_H=1 -I. -DNOSQRT -DUSE_8A_NBCUTOFF -DDO_NOT_CROSSOVER_IN_QUAT -DWRITEPDBQSTATE -I./../acro/include -I/usr/local/cuda/include -I/common/inc -L/usr/local/cuda/bin -L/usr/local/cuda/lib64 -L/lib -L/common/lib/linux -lcuda -lcudart -I/usr/local/cuda/include -I/common/inc -L/usr/local/cuda/bin -L/usr/local/cuda/lib64 -L/lib -L/common/lib/linux -lcuda -lcudart -MT torNorVec.o -MD -MP -MF .deps/torNorVec.Tpo -c -o torNorVec.o torNorVec.cc mv -f .deps/torNorVec.Tpo .deps/torNorVec.Po g++ -DPACKAGE_NAME=\"autodock\" -DPACKAGE_TARNAME=\"autodock\" -DPACKAGE_VERSION=\"4.0.1\" -DPACKAGE_STRING=\"autodock\ 4.0.1\" -DPACKAGE_BUGREPORT=\"autodock@scripps.edu\" -DPACKAGE=\"autodock\" -DVERSION=\"4.0.1\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE__BOOL=1 -DHAVE_STDBOOL_H=1 -DHAVE_STDLIB_H=1 -DHAVE_MALLOC=1 -DHAVE_GETHOSTNAME=1 -DHAVE_STRNCASECMP=1 -DCUDA_READY=1 -DHAVE_CUDA_RUNTIME_H=1 -DHAVE_CUDA_H=1 -I. -DNOSQRT -DUSE_8A_NBCUTOFF -DDO_NOT_CROSSOVER_IN_QUAT -DWRITEPDBQSTATE -I./../acro/include -I/usr/local/cuda/include -I/common/inc -L/usr/local/cuda/bin -L/usr/local/cuda/lib64 -L/lib -L/common/lib/linux -lcuda -lcudart -I/usr/local/cuda/include -I/common/inc -L/usr/local/cuda/bin -L/usr/local/cuda/lib64 -L/lib -L/common/lib/linux -lcuda -lcudart -MT torsion.o -MD -MP -MF .deps/torsion.Tpo -c -o torsion.o torsion.cc mv -f .deps/torsion.Tpo .deps/torsion.Po g++ -DPACKAGE_NAME=\"autodock\" -DPACKAGE_TARNAME=\"autodock\" -DPACKAGE_VERSION=\"4.0.1\" -DPACKAGE_STRING=\"autodock\ 4.0.1\" -DPACKAGE_BUGREPORT=\"autodock@scripps.edu\" -DPACKAGE=\"autodock\" -DVERSION=\"4.0.1\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE__BOOL=1 -DHAVE_STDBOOL_H=1 -DHAVE_STDLIB_H=1 -DHAVE_MALLOC=1 -DHAVE_GETHOSTNAME=1 -DHAVE_STRNCASECMP=1 -DCUDA_READY=1 -DHAVE_CUDA_RUNTIME_H=1 -DHAVE_CUDA_H=1 -I. -DNOSQRT -DUSE_8A_NBCUTOFF -DDO_NOT_CROSSOVER_IN_QUAT -DWRITEPDBQSTATE -I./../acro/include -I/usr/local/cuda/include -I/common/inc -L/usr/local/cuda/bin -L/usr/local/cuda/lib64 -L/lib -L/common/lib/linux -lcuda -lcudart -I/usr/local/cuda/include -I/common/inc -L/usr/local/cuda/bin -L/usr/local/cuda/lib64 -L/lib -L/common/lib/linux -lcuda -lcudart -MT trilinterp.o -MD -MP -MF .deps/trilinterp.Tpo -c -o trilinterp.o trilinterp.cc mv -f .deps/trilinterp.Tpo .deps/trilinterp.Po g++ -DPACKAGE_NAME=\"autodock\" -DPACKAGE_TARNAME=\"autodock\" -DPACKAGE_VERSION=\"4.0.1\" -DPACKAGE_STRING=\"autodock\ 4.0.1\" -DPACKAGE_BUGREPORT=\"autodock@scripps.edu\" -DPACKAGE=\"autodock\" -DVERSION=\"4.0.1\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE__BOOL=1 -DHAVE_STDBOOL_H=1 -DHAVE_STDLIB_H=1 -DHAVE_MALLOC=1 -DHAVE_GETHOSTNAME=1 -DHAVE_STRNCASECMP=1 -DCUDA_READY=1 -DHAVE_CUDA_RUNTIME_H=1 -DHAVE_CUDA_H=1 -I. -DNOSQRT -DUSE_8A_NBCUTOFF -DDO_NOT_CROSSOVER_IN_QUAT -DWRITEPDBQSTATE -I./../acro/include -I/usr/local/cuda/include -I/common/inc -L/usr/local/cuda/bin -L/usr/local/cuda/lib64 -L/lib -L/common/lib/linux -lcuda -lcudart -I/usr/local/cuda/include -I/common/inc -L/usr/local/cuda/bin -L/usr/local/cuda/lib64 -L/lib -L/common/lib/linux -lcuda -lcudart -MT usage.o -MD -MP -MF .deps/usage.Tpo -c -o usage.o usage.cc mv -f .deps/usage.Tpo .deps/usage.Po g++ -DPACKAGE_NAME=\"autodock\" -DPACKAGE_TARNAME=\"autodock\" -DPACKAGE_VERSION=\"4.0.1\" -DPACKAGE_STRING=\"autodock\ 4.0.1\" -DPACKAGE_BUGREPORT=\"autodock@scripps.edu\" -DPACKAGE=\"autodock\" -DVERSION=\"4.0.1\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE__BOOL=1 -DHAVE_STDBOOL_H=1 -DHAVE_STDLIB_H=1 -DHAVE_MALLOC=1 -DHAVE_GETHOSTNAME=1 -DHAVE_STRNCASECMP=1 -DCUDA_READY=1 -DHAVE_CUDA_RUNTIME_H=1 -DHAVE_CUDA_H=1 -I. -DNOSQRT -DUSE_8A_NBCUTOFF -DDO_NOT_CROSSOVER_IN_QUAT -DWRITEPDBQSTATE -I./../acro/include -I/usr/local/cuda/include -I/common/inc -L/usr/local/cuda/bin -L/usr/local/cuda/lib64 -L/lib -L/common/lib/linux -lcuda -lcudart -I/usr/local/cuda/include -I/common/inc -L/usr/local/cuda/bin -L/usr/local/cuda/lib64 -L/lib -L/common/lib/linux -lcuda -lcudart -MT weedbonds.o -MD -MP -MF .deps/weedbonds.Tpo -c -o weedbonds.o weedbonds.cc mv -f .deps/weedbonds.Tpo .deps/weedbonds.Po g++ -DPACKAGE_NAME=\"autodock\" -DPACKAGE_TARNAME=\"autodock\" -DPACKAGE_VERSION=\"4.0.1\" -DPACKAGE_STRING=\"autodock\ 4.0.1\" -DPACKAGE_BUGREPORT=\"autodock@scripps.edu\" -DPACKAGE=\"autodock\" -DVERSION=\"4.0.1\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE__BOOL=1 -DHAVE_STDBOOL_H=1 -DHAVE_STDLIB_H=1 -DHAVE_MALLOC=1 -DHAVE_GETHOSTNAME=1 -DHAVE_STRNCASECMP=1 -DCUDA_READY=1 -DHAVE_CUDA_RUNTIME_H=1 -DHAVE_CUDA_H=1 -I. -DNOSQRT -DUSE_8A_NBCUTOFF -DDO_NOT_CROSSOVER_IN_QUAT -DWRITEPDBQSTATE -I./../acro/include -I/usr/local/cuda/include -I/common/inc -L/usr/local/cuda/bin -L/usr/local/cuda/lib64 -L/lib -L/common/lib/linux -lcuda -lcudart -I/usr/local/cuda/include -I/common/inc -L/usr/local/cuda/bin -L/usr/local/cuda/lib64 -L/lib -L/common/lib/linux -lcuda -lcudart -MT warn_bad_file.o -MD -MP -MF .deps/warn_bad_file.Tpo -c -o warn_bad_file.o warn_bad_file.cc mv -f .deps/warn_bad_file.Tpo .deps/warn_bad_file.Po g++ -DPACKAGE_NAME=\"autodock\" -DPACKAGE_TARNAME=\"autodock\" -DPACKAGE_VERSION=\"4.0.1\" -DPACKAGE_STRING=\"autodock\ 4.0.1\" -DPACKAGE_BUGREPORT=\"autodock@scripps.edu\" -DPACKAGE=\"autodock\" -DVERSION=\"4.0.1\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE__BOOL=1 -DHAVE_STDBOOL_H=1 -DHAVE_STDLIB_H=1 -DHAVE_MALLOC=1 -DHAVE_GETHOSTNAME=1 -DHAVE_STRNCASECMP=1 -DCUDA_READY=1 -DHAVE_CUDA_RUNTIME_H=1 -DHAVE_CUDA_H=1 -I. -DNOSQRT -DUSE_8A_NBCUTOFF -DDO_NOT_CROSSOVER_IN_QUAT -DWRITEPDBQSTATE -I./../acro/include -I/usr/local/cuda/include -I/common/inc -L/usr/local/cuda/bin -L/usr/local/cuda/lib64 -L/lib -L/common/lib/linux -lcuda -lcudart -I/usr/local/cuda/include -I/common/inc -L/usr/local/cuda/bin -L/usr/local/cuda/lib64 -L/lib -L/common/lib/linux -lcuda -lcudart -MT coliny.o -MD -MP -MF .deps/coliny.Tpo -c -o coliny.o coliny.cc mv -f .deps/coliny.Tpo .deps/coliny.Po g++ -DPACKAGE_NAME=\"autodock\" -DPACKAGE_TARNAME=\"autodock\" -DPACKAGE_VERSION=\"4.0.1\" -DPACKAGE_STRING=\"autodock\ 4.0.1\" -DPACKAGE_BUGREPORT=\"autodock@scripps.edu\" -DPACKAGE=\"autodock\" -DVERSION=\"4.0.1\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE__BOOL=1 -DHAVE_STDBOOL_H=1 -DHAVE_STDLIB_H=1 -DHAVE_MALLOC=1 -DHAVE_GETHOSTNAME=1 -DHAVE_STRNCASECMP=1 -DCUDA_READY=1 -DHAVE_CUDA_RUNTIME_H=1 -DHAVE_CUDA_H=1 -I. -DNOSQRT -DUSE_8A_NBCUTOFF -DDO_NOT_CROSSOVER_IN_QUAT -DWRITEPDBQSTATE -I./../acro/include -I/usr/local/cuda/include -I/common/inc -L/usr/local/cuda/bin -L/usr/local/cuda/lib64 -L/lib -L/common/lib/linux -lcuda -lcudart -I/usr/local/cuda/include -I/common/inc -L/usr/local/cuda/bin -L/usr/local/cuda/lib64 -L/lib -L/common/lib/linux -lcuda -lcudart -MT eintcal.o -MD -MP -MF .deps/eintcal.Tpo -c -o eintcal.o eintcal.cc mv -f .deps/eintcal.Tpo .deps/eintcal.Po g++ -DPACKAGE_NAME=\"autodock\" -DPACKAGE_TARNAME=\"autodock\" -DPACKAGE_VERSION=\"4.0.1\" -DPACKAGE_STRING=\"autodock\ 4.0.1\" -DPACKAGE_BUGREPORT=\"autodock@scripps.edu\" -DPACKAGE=\"autodock\" -DVERSION=\"4.0.1\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE__BOOL=1 -DHAVE_STDBOOL_H=1 -DHAVE_STDLIB_H=1 -DHAVE_MALLOC=1 -DHAVE_GETHOSTNAME=1 -DHAVE_STRNCASECMP=1 -DCUDA_READY=1 -DHAVE_CUDA_RUNTIME_H=1 -DHAVE_CUDA_H=1 -I. -DNOSQRT -DUSE_8A_NBCUTOFF -DDO_NOT_CROSSOVER_IN_QUAT -DWRITEPDBQSTATE -I./../acro/include -I/usr/local/cuda/include -I/common/inc -L/usr/local/cuda/bin -L/usr/local/cuda/lib64 -L/lib -L/common/lib/linux -lcuda -lcudart -I/usr/local/cuda/include -I/common/inc -L/usr/local/cuda/bin -L/usr/local/cuda/lib64 -L/lib -L/common/lib/linux -lcuda -lcudart -MT eintcalPrint.o -MD -MP -MF .deps/eintcalPrint.Tpo -c -o eintcalPrint.o eintcalPrint.cc mv -f .deps/eintcalPrint.Tpo .deps/eintcalPrint.Po g++ -DPACKAGE_NAME=\"autodock\" -DPACKAGE_TARNAME=\"autodock\" -DPACKAGE_VERSION=\"4.0.1\" -DPACKAGE_STRING=\"autodock\ 4.0.1\" -DPACKAGE_BUGREPORT=\"autodock@scripps.edu\" -DPACKAGE=\"autodock\" -DVERSION=\"4.0.1\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE__BOOL=1 -DHAVE_STDBOOL_H=1 -DHAVE_STDLIB_H=1 -DHAVE_MALLOC=1 -DHAVE_GETHOSTNAME=1 -DHAVE_STRNCASECMP=1 -DCUDA_READY=1 -DHAVE_CUDA_RUNTIME_H=1 -DHAVE_CUDA_H=1 -I. -DNOSQRT -DUSE_8A_NBCUTOFF -DDO_NOT_CROSSOVER_IN_QUAT -DWRITEPDBQSTATE -I./../acro/include -I/usr/local/cuda/include -I/common/inc -L/usr/local/cuda/bin -L/usr/local/cuda/lib64 -L/lib -L/common/lib/linux -lcuda -lcudart -I/usr/local/cuda/include -I/common/inc -L/usr/local/cuda/bin -L/usr/local/cuda/lib64 -L/lib -L/common/lib/linux -lcuda -lcudart -MT intnbtable.o -MD -MP -MF .deps/intnbtable.Tpo -c -o intnbtable.o intnbtable.cc mv -f .deps/intnbtable.Tpo .deps/intnbtable.Po g++ -DPACKAGE_NAME=\"autodock\" -DPACKAGE_TARNAME=\"autodock\" -DPACKAGE_VERSION=\"4.0.1\" -DPACKAGE_STRING=\"autodock\ 4.0.1\" -DPACKAGE_BUGREPORT=\"autodock@scripps.edu\" -DPACKAGE=\"autodock\" -DVERSION=\"4.0.1\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE__BOOL=1 -DHAVE_STDBOOL_H=1 -DHAVE_STDLIB_H=1 -DHAVE_MALLOC=1 -DHAVE_GETHOSTNAME=1 -DHAVE_STRNCASECMP=1 -DCUDA_READY=1 -DHAVE_CUDA_RUNTIME_H=1 -DHAVE_CUDA_H=1 -I. -DNOSQRT -DUSE_8A_NBCUTOFF -DDO_NOT_CROSSOVER_IN_QUAT -DWRITEPDBQSTATE -I./../acro/include -I/usr/local/cuda/include -I/common/inc -L/usr/local/cuda/bin -L/usr/local/cuda/lib64 -L/lib -L/common/lib/linux -lcuda -lcudart -I/usr/local/cuda/include -I/common/inc -L/usr/local/cuda/bin -L/usr/local/cuda/lib64 -L/lib -L/common/lib/linux -lcuda -lcudart -MT nbe.o -MD -MP -MF .deps/nbe.Tpo -c -o nbe.o nbe.cc mv -f .deps/nbe.Tpo .deps/nbe.Po g++ -DPACKAGE_NAME=\"autodock\" -DPACKAGE_TARNAME=\"autodock\" -DPACKAGE_VERSION=\"4.0.1\" -DPACKAGE_STRING=\"autodock\ 4.0.1\" -DPACKAGE_BUGREPORT=\"autodock@scripps.edu\" -DPACKAGE=\"autodock\" -DVERSION=\"4.0.1\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE__BOOL=1 -DHAVE_STDBOOL_H=1 -DHAVE_STDLIB_H=1 -DHAVE_MALLOC=1 -DHAVE_GETHOSTNAME=1 -DHAVE_STRNCASECMP=1 -DCUDA_READY=1 -DHAVE_CUDA_RUNTIME_H=1 -DHAVE_CUDA_H=1 -I. -DNOSQRT -DUSE_8A_NBCUTOFF -DDO_NOT_CROSSOVER_IN_QUAT -DWRITEPDBQSTATE -I./../acro/include -I/usr/local/cuda/include -I/common/inc -L/usr/local/cuda/bin -L/usr/local/cuda/lib64 -L/lib -L/common/lib/linux -lcuda -lcudart -I/usr/local/cuda/include -I/common/inc -L/usr/local/cuda/bin -L/usr/local/cuda/lib64 -L/lib -L/common/lib/linux -lcuda -lcudart -MT eMapPrepCuda.o -MD -MP -MF .deps/eMapPrepCuda.Tpo -c -o eMapPrepCuda.o eMapPrepCuda.cc mv -f .deps/eMapPrepCuda.Tpo .deps/eMapPrepCuda.Po rm -f libad.a ar cru libad.a analysis.o atom_parameter_manager.o banner.o bestpdb.o calculateEnergies.o call_glss.o call_gs.o call_ls.o changeState.o check_header_float.o check_header_int.o check_header_line.o cluster_analysis.o clmode.o cmdmode.o cnv_state_to_coords.o com.o conformation_sampler.o distdepdiel.o stateLibrary.o readfield.o readmap.o readPDBQT.o read_parameter_library.o eval.o gencau.o getrms.o get_atom_type.o getInitialState.o getpdbcrds.o gs.o initautodock.o input_state.o investigate.o linpack.o ls.o mapping.o minmeanmax.o mkNewState.o mkTorTree.o mkRandomState.o nonbonds.o openfile.o output_state.o parse_com_line.o parse_dpf_line.o parse_param_line.o parse_PDBQT_line.o parse_trj_line.o parsetypes.o print_2x.o print_atomic_energies.o print_avsfld.o writePDBQT.o print_rem.o printdate.o printEnergies.o printhms.o prClusterHist.o prInitialState.o prTorConList.o qmultiply.o qtransform.o quicksort.o ranlib.o rep.o scauchy.o set_cmd_io_std.o setflags.o simanneal.o sort_enrg.o stop.o strindex.o success.o summarizegrids.o support.o swap.o timesys.o timesyshms.o torNorVec.o torsion.o trilinterp.o usage.o weedbonds.o warn_bad_file.o coliny.o eintcal.o eintcalPrint.o intnbtable.o nbe.o eMapPrepCuda.o ranlib libad.a g++ -DPACKAGE_NAME=\"autodock\" -DPACKAGE_TARNAME=\"autodock\" -DPACKAGE_VERSION=\"4.0.1\" -DPACKAGE_STRING=\"autodock\ 4.0.1\" -DPACKAGE_BUGREPORT=\"autodock@scripps.edu\" -DPACKAGE=\"autodock\" -DVERSION=\"4.0.1\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE__BOOL=1 -DHAVE_STDBOOL_H=1 -DHAVE_STDLIB_H=1 -DHAVE_MALLOC=1 -DHAVE_GETHOSTNAME=1 -DHAVE_STRNCASECMP=1 -DCUDA_READY=1 -DHAVE_CUDA_RUNTIME_H=1 -DHAVE_CUDA_H=1 -I. -DNOSQRT -DUSE_8A_NBCUTOFF -DDO_NOT_CROSSOVER_IN_QUAT -DWRITEPDBQSTATE -I./../acro/include -I/usr/local/cuda/include -I/common/inc -L/usr/local/cuda/bin -L/usr/local/cuda/lib64 -L/lib -L/common/lib/linux -lcuda -lcudart -I/usr/local/cuda/include -I/common/inc -L/usr/local/cuda/bin -L/usr/local/cuda/lib64 -L/lib -L/common/lib/linux -lcuda -lcudart -MT main.o -MD -MP -MF .deps/main.Tpo -c -o main.o main.cc main.cc: In function ‘int main(int, char* const*, char* const*)’: main.cc:631:71: warning: deprecated conversion from string constant to ‘char*’ [-Wwrite-strings] stop("\"sysconf(_SC_CLK_TCK)\" command failed in \"main.c\"\n"); ^ main.cc:787:42: warning: deprecated conversion from string constant to ‘char*’ [-Wwrite-strings] indcom = strindex( line, "#" ); ^ main.cc:2199:99: warning: deprecated conversion from string constant to ‘char*’ [-Wwrite-strings] stop("Cooling is impossible with a reduction\n\tfactor greater than or equal to 1.0!" ); ^ main.cc:2202:72: warning: deprecated conversion from string constant to ‘char*’ [-Wwrite-strings] stop("Cooling is impossible with a ZERO reduction factor!" ); ^ main.cc:2205:76: warning: deprecated conversion from string constant to ‘char*’ [-Wwrite-strings] stop("Cooling is impossible with a NEGATIVE reduction factor!" ); ^ main.cc:4077:117: warning: deprecated conversion from string constant to ‘char*’ [-Wwrite-strings] printEnergies( &eb, "epdb: USER ", ligand_is_inhibitor, emap_total, elec_total, B_have_flexible_residues ); ^ main.cc:4270:52: warning: format ‘%Lf’ expects argument of type ‘long double’, but argument 3 has type ‘double’ [-Wformat=] pr( logFile, "Time taken =:\t%Lf seconds", tottime ); ^ mv -f .deps/main.Tpo .deps/main.Po nvcc -c *.cu -D_DEBUG -g -use_fast_math -I. -I/common/inc -DCUDA_READY -DNOSQRT -DUSE_8A_NBCUTOFF -DDO_NOT_CROSSOVER_IN_QUAT -DWRITEPDBQSTATE -I./../acro/include g++ -I/usr/local/cuda/include -I/common/inc -L/usr/local/cuda/bin -L/usr/local/cuda/lib64 -L/lib -L/common/lib/linux -lcuda -lcudart -o autodock4 main.o libad.a -lm select_alloc_wrapper.o eval_wrapper.o select_alloc_wrapper.o: In function `select_alloc_wrapper': /home/jonathan/Downloads/gpuautodock/src/autodock-4.0.1/select_alloc_wrapper.cu:44: undefined reference to `cudaMalloc' /home/jonathan/Downloads/gpuautodock/src/autodock-4.0.1/select_alloc_wrapper.cu:50: undefined reference to `cudaConfigureCall' /home/jonathan/Downloads/gpuautodock/src/autodock-4.0.1/select_alloc_wrapper.cu:51: undefined reference to `cudaGetLastError' /home/jonathan/Downloads/gpuautodock/src/autodock-4.0.1/select_alloc_wrapper.cu:54: undefined reference to `cudaGetErrorString' /home/jonathan/Downloads/gpuautodock/src/autodock-4.0.1/select_alloc_wrapper.cu:57: undefined reference to `cudaMemcpy' /home/jonathan/Downloads/gpuautodock/src/autodock-4.0.1/select_alloc_wrapper.cu:60: undefined reference to `cudaFree' select_alloc_wrapper.o: In function `__cudaUnregisterBinaryUtil': /usr/local/cuda-7.0/bin/..//include/crt/host_runtime.h:238: undefined reference to `__cudaUnregisterFatBinary' select_alloc_wrapper.o: In function `__nv_init_managed_rt_with_module': /usr/local/cuda-7.0/bin/..//include/crt/host_runtime.h:243: undefined reference to `__cudaInitModule' select_alloc_wrapper.o: In function `__device_stub__Z12alloc_kernelPf(float*)': /tmp/tmpxft_000044ab_00000000-9_select_alloc_wrapper.cudafe1.stub.c:7: undefined reference to `cudaSetupArgument' select_alloc_wrapper.o: In function `__nv_cudaEntityRegisterCallback': /tmp/tmpxft_000044ab_00000000-9_select_alloc_wrapper.cudafe1.stub.c:1: undefined reference to `__cudaRegisterFunction' select_alloc_wrapper.o: In function `__sti____cudaRegisterAll_56_tmpxft_000044ab_00000000_20_select_alloc_wrapper_cpp1_ii_dd4cc9e3': /tmp/tmpxft_000044ab_00000000-9_select_alloc_wrapper.cudafe1.stub.c:2: undefined reference to `__cudaRegisterFatBinary' select_alloc_wrapper.o: In function `cudaLaunch': /usr/local/cuda-7.0/bin/..//include/cuda_runtime.h:1769: undefined reference to `cudaLaunch' eval_wrapper.o: In function `eval_wrapper': /home/jonathan/Downloads/gpuautodock/src/autodock-4.0.1/eval_wrapper.cu:546: undefined reference to `cudaMemcpy' /home/jonathan/Downloads/gpuautodock/src/autodock-4.0.1/eval_wrapper.cu:549: undefined reference to `cudaMemcpy' /home/jonathan/Downloads/gpuautodock/src/autodock-4.0.1/eval_wrapper.cu:551: undefined reference to `cudaMemcpy' /home/jonathan/Downloads/gpuautodock/src/autodock-4.0.1/eval_wrapper.cu:555: undefined reference to `cudaConfigureCall' /home/jonathan/Downloads/gpuautodock/src/autodock-4.0.1/eval_wrapper.cu:569: undefined reference to `cudaThreadSynchronize' /home/jonathan/Downloads/gpuautodock/src/autodock-4.0.1/eval_wrapper.cu:573: undefined reference to `cudaConfigureCall' /home/jonathan/Downloads/gpuautodock/src/autodock-4.0.1/eval_wrapper.cu:592: undefined reference to `cudaThreadSynchronize' /home/jonathan/Downloads/gpuautodock/src/autodock-4.0.1/eval_wrapper.cu:595: undefined reference to `cudaMemcpy' eval_wrapper.o: In function `CHECK_ERROR(int)': /home/jonathan/Downloads/gpuautodock/src/autodock-4.0.1/eval_wrapper.cu:609: undefined reference to `cudaGetLastError' /home/jonathan/Downloads/gpuautodock/src/autodock-4.0.1/eval_wrapper.cu:613: undefined reference to `cudaGetErrorString' eval_wrapper.o: In function `cuda_alloc_wrapper': /home/jonathan/Downloads/gpuautodock/src/autodock-4.0.1/eval_wrapper.cu:658: undefined reference to `cudaMalloc' /home/jonathan/Downloads/gpuautodock/src/autodock-4.0.1/eval_wrapper.cu:662: undefined reference to `cudaMemcpy' /home/jonathan/Downloads/gpuautodock/src/autodock-4.0.1/eval_wrapper.cu:673: undefined reference to `cudaMalloc' /home/jonathan/Downloads/gpuautodock/src/autodock-4.0.1/eval_wrapper.cu:679: undefined reference to `cudaMalloc' /home/jonathan/Downloads/gpuautodock/src/autodock-4.0.1/eval_wrapper.cu:681: undefined reference to `cudaMalloc' /home/jonathan/Downloads/gpuautodock/src/autodock-4.0.1/eval_wrapper.cu:718: undefined reference to `cudaMalloc' /home/jonathan/Downloads/gpuautodock/src/autodock-4.0.1/eval_wrapper.cu:723: undefined reference to `cudaMemcpy' /home/jonathan/Downloads/gpuautodock/src/autodock-4.0.1/eval_wrapper.cu:733: undefined reference to `cudaMalloc' /home/jonathan/Downloads/gpuautodock/src/autodock-4.0.1/eval_wrapper.cu:737: undefined reference to `cudaMalloc' /home/jonathan/Downloads/gpuautodock/src/autodock-4.0.1/eval_wrapper.cu:739: undefined reference to `cudaMalloc' /home/jonathan/Downloads/gpuautodock/src/autodock-4.0.1/eval_wrapper.cu:741: undefined reference to `cudaMalloc' /home/jonathan/Downloads/gpuautodock/src/autodock-4.0.1/eval_wrapper.cu:744: undefined reference to `cudaMalloc' eval_wrapper.o:/home/jonathan/Downloads/gpuautodock/src/autodock-4.0.1/eval_wrapper.cu:746: more undefined references to `cudaMalloc' follow eval_wrapper.o: In function `cuda_alloc_wrapper': /home/jonathan/Downloads/gpuautodock/src/autodock-4.0.1/eval_wrapper.cu:770: undefined reference to `cudaMemcpy' /home/jonathan/Downloads/gpuautodock/src/autodock-4.0.1/eval_wrapper.cu:780: undefined reference to `cudaMemcpy' /home/jonathan/Downloads/gpuautodock/src/autodock-4.0.1/eval_wrapper.cu:783: undefined reference to `cudaMemcpy' /home/jonathan/Downloads/gpuautodock/src/autodock-4.0.1/eval_wrapper.cu:785: undefined reference to `cudaMemcpy' /home/jonathan/Downloads/gpuautodock/src/autodock-4.0.1/eval_wrapper.cu:787: undefined reference to `cudaMemcpy' /home/jonathan/Downloads/gpuautodock/src/autodock-4.0.1/eval_wrapper.cu:826: undefined reference to `cudaMalloc' /home/jonathan/Downloads/gpuautodock/src/autodock-4.0.1/eval_wrapper.cu:828: undefined reference to `cudaMalloc' /home/jonathan/Downloads/gpuautodock/src/autodock-4.0.1/eval_wrapper.cu:830: undefined reference to `cudaMalloc' /home/jonathan/Downloads/gpuautodock/src/autodock-4.0.1/eval_wrapper.cu:832: undefined reference to `cudaMalloc' /home/jonathan/Downloads/gpuautodock/src/autodock-4.0.1/eval_wrapper.cu:837: undefined reference to `cudaMemcpy' /home/jonathan/Downloads/gpuautodock/src/autodock-4.0.1/eval_wrapper.cu:838: undefined reference to `cudaMemcpy' /home/jonathan/Downloads/gpuautodock/src/autodock-4.0.1/eval_wrapper.cu:840: undefined reference to `cudaMemcpy' /home/jonathan/Downloads/gpuautodock/src/autodock-4.0.1/eval_wrapper.cu:842: undefined reference to `cudaMemcpy' /home/jonathan/Downloads/gpuautodock/src/autodock-4.0.1/eval_wrapper.cu:849: undefined reference to `cudaMemcpy' /home/jonathan/Downloads/gpuautodock/src/autodock-4.0.1/eval_wrapper.cu:858: undefined reference to `cudaMalloc' /home/jonathan/Downloads/gpuautodock/src/autodock-4.0.1/eval_wrapper.cu:859: undefined reference to `cudaMalloc' eval_wrapper.o: In function `cuda_free_wrapper': /home/jonathan/Downloads/gpuautodock/src/autodock-4.0.1/eval_wrapper.cu:869: undefined reference to `cudaFree' /home/jonathan/Downloads/gpuautodock/src/autodock-4.0.1/eval_wrapper.cu:870: undefined reference to `cudaFree' /home/jonathan/Downloads/gpuautodock/src/autodock-4.0.1/eval_wrapper.cu:872: undefined reference to `cudaFree' /home/jonathan/Downloads/gpuautodock/src/autodock-4.0.1/eval_wrapper.cu:874: undefined reference to `cudaFree' /home/jonathan/Downloads/gpuautodock/src/autodock-4.0.1/eval_wrapper.cu:877: undefined reference to `cudaFree' eval_wrapper.o:/home/jonathan/Downloads/gpuautodock/src/autodock-4.0.1/eval_wrapper.cu:879: more undefined references to `cudaFree' follow eval_wrapper.o: In function `__cudaUnregisterBinaryUtil': /usr/local/cuda-7.0/bin/..//include/crt/host_runtime.h:238: undefined reference to `__cudaUnregisterFatBinary' eval_wrapper.o: In function `__nv_init_managed_rt_with_module': /usr/local/cuda-7.0/bin/..//include/crt/host_runtime.h:243: undefined reference to `__cudaInitModule' eval_wrapper.o: In function `__device_stub__Z16eval_tril_kerneljPfciS_S_S_PiS0_S_S_iiiiS_S0_(unsigned int, float*, char, int, float*, float*, float*, int*, int*, float*, float*, int, int, int, int, float*, int*)': /tmp/tmpxft_000044ab_00000000-4_eval_wrapper.cudafe1.stub.c:8: undefined reference to `cudaSetupArgument' /tmp/tmpxft_000044ab_00000000-4_eval_wrapper.cudafe1.stub.c:8: undefined reference to `cudaSetupArgument' /tmp/tmpxft_000044ab_00000000-4_eval_wrapper.cudafe1.stub.c:8: undefined reference to `cudaSetupArgument' /tmp/tmpxft_000044ab_00000000-4_eval_wrapper.cudafe1.stub.c:8: undefined reference to `cudaSetupArgument' /tmp/tmpxft_000044ab_00000000-4_eval_wrapper.cudafe1.stub.c:8: undefined reference to `cudaSetupArgument' eval_wrapper.o:/tmp/tmpxft_000044ab_00000000-4_eval_wrapper.cudafe1.stub.c:8: more undefined references to `cudaSetupArgument' follow eval_wrapper.o: In function `__nv_cudaEntityRegisterCallback': /tmp/tmpxft_000044ab_00000000-4_eval_wrapper.cudafe1.stub.c:1: undefined reference to `__cudaRegisterFunction' /tmp/tmpxft_000044ab_00000000-4_eval_wrapper.cudafe1.stub.c:1: undefined reference to `__cudaRegisterFunction' /tmp/tmpxft_000044ab_00000000-4_eval_wrapper.cudafe1.stub.c:1: undefined reference to `__cudaRegisterTexture' eval_wrapper.o: In function `__sti____cudaRegisterAll_48_tmpxft_000044ab_00000000_12_eval_wrapper_cpp1_ii_tex': /tmp/tmpxft_000044ab_00000000-4_eval_wrapper.cudafe1.stub.c:2: undefined reference to `__cudaRegisterFatBinary' eval_wrapper.o: In function `cudaLaunch': /usr/local/cuda-7.0/bin/..//include/cuda_runtime.h:1769: undefined reference to `cudaLaunch' eval_wrapper.o: In function `cudaBindTexture': /usr/local/cuda-7.0/bin/..//include/cuda_runtime.h:818: undefined reference to `cudaBindTexture' eval_wrapper.o: In function `cudaChannelFormatDesc cudaCreateChannelDesc()': /usr/local/cuda-7.0/bin/..//include/channel_descriptor.h:383: undefined reference to `cudaCreateChannelDesc' collect2: error: ld returned 1 exit status make: *** [autodock4] Error 1 jonathan@jonathan-desktop:~/Downloads/gpuautodock/src/autodock-4.0.1$