Is there a way to compile Autodock-GPU on Windows?

[kotenok2000]

I tried to compile it in cygwin and mingw. I got these errors

make DEVICE=OCLGPU NUMWI=64 rm -f ./host/inc/performdocking.h ./host/src/performdocking.cpp Building adgpu_analysis ... g++ \ ./host/src/calcenergy.cpp ./host/src/getparameters.cpp ./host/src/main.cpp ./host/src/miscellaneous.cpp ./host/src/processgrid.cpp ./host/src/processligand.cpp ./host/src/processresult.cpp ./host/src/setup.cpp \ -std=c++11 -I./common -I./host/inc -DVERSION=\"v1.5.3\" \ -o./bin/adgpu_analysis \ -O3 -DTOOLMODE ./host/src/getparameters.cpp: В функции «int parse_dpf(Dockpars, Gridinfo, FileList&, bool)»: ./host/src/getparameters.cpp:186:78: ошибка: «strdup» was not declared in this scope; did you mean «strcmp»? 186 | mypars->ligandfile = strdup(argstr); | ^~ | strcmp ./host/src/getparameters.cpp:193:79: ошибка: «strdup» was not declared in this scope; did you mean «strcmp»? 193 | mypars->flexresfile = strdup(argstr); | ^~ | strcmp ./host/src/getparameters.cpp:201:75: ошибка: «strdup» was not declared in this scope; did you mean «strcmp»? 201 | mypars->fldfile = strdup(argstr); // this allows using the dpf to set up all parameters but the ligand | ^~ | strcmp ./host/src/getparameters.cpp:384:90: ошибка: «strdup» was not declared in this scope; did you mean «strcmp»? 384 | } else mypars->resname = strdup("docking"); // Fallback to old default | ^~ | strcmp ./host/src/getparameters.cpp:395:101: ошибка: «strdup» was not declared in this scope; did you mean «strcmp»? 395 | mypars->flexresfile=strdup(mypars->flexresfile); | ^~ | strcmp ./host/src/getparameters.cpp:398:104: ошибка: «strdup» was not declared in this scope; did you mean «strcmp»? 398 | mypars->xrayligandfile=strdup(mypars->xrayligandfile); | ^~ | strcmp ./host/src/getparameters.cpp: В функции «int initial_commandpars(const int*, char, Dockpars, Gridinfo, FileList&)»: ./host/src/getparameters.cpp:610:43: ошибка: «strdup» was not declared in this scope; did you mean «strcmp»? 610 | mypars->dpffile = strdup(argv[i+1]); | ^~ | strcmp ./host/src/getparameters.cpp:621:44: ошибка: «strdup» was not declared in this scope; did you mean «strcmp»? 621 | mypars->load_xml = strdup(argv[i+1]); | ^~ | strcmp ./host/src/getparameters.cpp:698:44: ошибка: «strdup» was not declared in this scope; did you mean «strcmp»? 698 | mypars->load_xml = strdup(xml_files[i].c_str()); | ^~ | strcmp ./host/src/getparameters.cpp: В функции «int get_filelist(const int*, char*, Dockpars, Gridinfo, FileList&)»: ./host/src/getparameters.cpp:832:57: ошибка: «strdup» was not declared in this scope; did you mean «strcmp»? 832 | mypars->fldfile=strdup(mypars->fldfile); | ^~ | strcmp ./host/src/getparameters.cpp:835:61: ошибка: «strdup» was not declared in this scope; did you mean «strcmp»? 835 | mypars->flexresfile=strdup(mypars->flexresfile); | ^~ | strcmp ./host/src/getparameters.cpp:838:64: ошибка: «strdup» was not declared in this scope; did you mean «strcmp»? 838 | mypars->xrayligandfile=strdup(mypars->xrayligandfile); | ^~ | strcmp ./host/src/getparameters.cpp:840:46: ошибка: «strdup» was not declared in this scope; did you mean «strcmp»? 840 | mypars->ligandfile = strdup(ligands[i]); | ^~ | strcmp ./host/src/getparameters.cpp:862:58: ошибка: «strdup» was not declared in this scope; did you mean «strcmp»? 862 | } else if(ligands.size()==1) filelist.filename = strdup(ligands[0]); | ^~ | strcmp ./host/src/getparameters.cpp:907:51: ошибка: «strdup» was not declared in this scope; did you mean «strcmp»? 907 | mypars->fldfile = strdup(filelist.fld_files.back().name.c_str()); | ^~ | strcmp ./host/src/getparameters.cpp:918:58: ошибка: «strndup» was not declared in this scope; did you mean «strncmp»? 918 | mypars->xrayligandfile = strndup(line.c_str(),len-1); | ^~~ | strncmp ./host/src/getparameters.cpp:929:65: ошибка: «strdup» was not declared in this scope; did you mean «strcmp»? 929 | mypars->fldfile=strdup(mypars->fldfile); | ^~ | strcmp ./host/src/getparameters.cpp:932:69: ошибка: «strdup» was not declared in this scope; did you mean «strcmp»? 932 | mypars->flexresfile=strdup(mypars->flexresfile); | ^~ | strcmp ./host/src/getparameters.cpp:935:72: ошибка: «strdup» was not declared in this scope; did you mean «strcmp»? 935 | mypars->xrayligandfile=strdup(mypars->xrayligandfile); | ^~ | strcmp ./host/src/getparameters.cpp:979:57: ошибка: «strdup» was not declared in this scope; did you mean «strcmp»? 979 | filelist.mypars[i].ligandfile = strdup(filelist.ligand_files[i].c_str()); | ^~ | strcmp ./host/src/getparameters.cpp: В функции «int get_filenames_and_ADcoeffs(const int, char, Dockpars, bool, bool)»: ./host/src/getparameters.cpp:1026:51: ошибка: «strdup» was not declared in this scope; did you mean «strcmp»? 1026 | mypars->fldfile = strdup(argv[i+1]); | ^~ | strcmp ./host/src/getparameters.cpp:1033:54: ошибка: «strdup» was not declared in this scope; did you mean «strcmp»? 1033 | mypars->ligandfile = strdup(argv[i+1]); | ^~ | strcmp ./host/src/getparameters.cpp:1040:47: ошибка: «strdup» was not declared in this scope; did you mean «strcmp»? 1040 | mypars->flexresfile = strdup(argv[i+1]); | ^~ | strcmp ./host/src/getparameters.cpp: В функции «int get_commandpars(const int, char, double, Dockpars, bool)»: ./host/src/getparameters.cpp:1224:55: ошибка: «strdup» was not declared in this scope; did you mean «strcmp»? 1224 | mypars->xrayligandfile = strdup(mypars->ligandfile); // By default xray-ligand file is the same as the randomized input ligand | ^~ | strcmp ./host/src/getparameters.cpp:1231:71: ошибка: «strdup» was not declared in this scope; did you mean «strcmp»? 1231 | } else if(!mypars->resname) mypars->resname = strdup("docking"); // Fallback to old default | ^~ | strcmp ./host/src/getparameters.cpp:1239:58: ошибка: «strdup» was not declared in this scope; did you mean «strcmp»? 1239 | } else mypars->resname = strdup("docking"); // Fallback to old default | ^~ | strcmp ./host/src/getparameters.cpp:1437:38: ошибка: «strdup» was not declared in this scope; did you mean «strcmp»? 1437 | char temp = strdup(argv [i+1]); | ^~ | strcmp ./host/src/getparameters.cpp:1577:44: ошибка: «strdup» was not declared in this scope; did you mean «strcmp»? 1577 | mypars->load_xml = strdup(argv[i+1]); | ^~ | strcmp ./host/src/getparameters.cpp:1847:43: ошибка: «strdup» was not declared in this scope; did you mean «strcmp»? 1847 | mypars->resname = strdup(argv [i+1]); | ^~ | strcmp ./host/src/getparameters.cpp:1930:50: ошибка: «strdup» was not declared in this scope; did you mean «strcmp»? 1930 | mypars->xrayligandfile = strdup(argv[i+1]); | ^~ | strcmp ./host/src/getparameters.cpp: В функции «void read_xml_filenames(char, char&, char&, char&, char&, unsigned int&, uint32_t)»: ./host/src/getparameters.cpp:2146:61: ошибка: «strdup» was not declared in this scope; did you mean «strcmp»? 2146 | if(dpf_filename==NULL) dpf_filename=strdup(tmpstr); | ^~ | strcmp ./host/src/getparameters.cpp:2153:63: ошибка: «strdup» was not declared in this scope; did you mean «strcmp»? 2153 | if(grid_filename==NULL) grid_filename=strdup(tmpstr); | ^~ | strcmp ./host/src/getparameters.cpp:2161:67: ошибка: «strdup» was not declared in this scope; did you mean «strcmp»? 2161 | if(ligand_filename==NULL) ligand_filename=strdup(tmpstr); | ^~ | strcmp ./host/src/getparameters.cpp:2169:69: ошибка: «strdup» was not declared in this scope; did you mean «strcmp»? 2169 | if(flexres_filename==NULL) flexres_filename=strdup(tmpstr); | ^~ | strcmp ./host/src/miscellaneous.cpp: В функции «std::string get_filepath(const char)»: ./host/src/miscellaneous.cpp:263:21: ошибка: «strdup» was not declared in this scope; did you mean «strcmp»? 263 | char ts1 = strdup(filename); | ^~ | strcmp ./host/src/setup.cpp: В функции «int setup(Gridinfo, Dockpars*, Liganddata&, Liganddata&, FileList&, int, int, char*)»: ./host/src/setup.cpp:350:32: ошибка: «strdup» was not declared in this scope; did you mean «strcmp»? 350 | orig_resname = strdup(mypars->resname); // need to copy it since it might get free'd in the next line | ^~ | strcmp ./host/src/setup.cpp:352:32: ошибка: «strdup» was not declared in this scope; did you mean «strcmp»? 352 | orig_resname = strdup(""); // need an empty string for later if no resname has been specified | ^~ | strcmp make: [Makefile.OpenCL:259: otool] Error 1

[kotenok2000]

When i removed -std=c++11 i got this error.

make DEVICE=OCLGPU NUMWI=64 rm -f ./host/inc/performdocking.h ./host/src/performdocking.cpp Building adgpu_analysis ... g++ \ ./host/src/calcenergy.cpp ./host/src/getparameters.cpp ./host/src/main.cpp ./host/src/miscellaneous.cpp ./host/src/processgrid.cpp ./host/src/processligand.cpp ./host/src/processresult.cpp ./host/src/setup.cpp \ -I./common -I./host/inc -DVERSION=\"v1.5.3-dirty\" \ -o./bin/adgpu_analysis \ -O3 -DTOOLMODE DEVICE is set to GPU

CPU_INCLUDE_PATH is undefined CPU_LIBRARY_PATH is undefined

GPU_INCLUDE_PATH is set to /cygdrive/c/Program\ Files/NVIDIA\ GPU\ Computing\ Toolkit/CUDA/v12.0/include/ GPU_LIBRARY_PATH is set to /cygdrive/c/Program\ Files/NVIDIA\ GPU\ Computing\ Toolkit/CUDA/v12.0/lib/x64/

./stringify_ocl_krnls.sh

Stringified input header files: ./common/defines.h ./common/calcenergy_basic.h

Stringified input non-kernel files: ./device/auxiliary_genetic.cl ./device/calcenergy.cl ./device/calcgradient.cl ./device/calcMergedEneGra.cl

Stringified input kernel-files: ./device/kernel1.cl ./device/kernel2.cl ./device/kernel4.cl ./device/kernel3.cl ./device/kernel_sd.cl ./device/kernel_fire.cl ./device/kernel_ad.cl

Stringified output file: host/inc/stringify.h

ln -sf performdocking.h.OpenCL ./host/inc/performdocking.h ln -sf performdocking.cpp.OpenCL ./host/src/performdocking.cpp Building autodock_gpu_64wi ... g++ \ ./wrapcl/src/BufferObjects.cpp ./wrapcl/src/CommandQueues.cpp ./wrapcl/src/Contexts.cpp ./wrapcl/src/Devices.cpp ./wrapcl/src/ImportBinary.cpp ./wrapcl/src/ImportSource.cpp ./wrapcl/src/Kernels.cpp ./wrapcl/src/listAttributes.cpp ./wrapcl/src/Platforms.cpp ./wrapcl/src/Programs.cpp ./host/src/calcenergy.cpp ./host/src/getparameters.cpp ./host/src/main.cpp ./host/src/miscellaneous.cpp ./host/src/performdocking.cpp ./host/src/processgrid.cpp ./host/src/processligand.cpp ./host/src/processresult.cpp ./host/src/setup.cpp \ -I./common -I./wrapcl/inc -I./host/inc -I./device -I/cygdrive/c/Program\ Files/NVIDIA\ GPU\ Computing\ Toolkit/CUDA/v12.0/include/ -L/cygdrive/c/Program\ Files/NVIDIA\ GPU\ Computing\ Toolkit/CUDA/v12.0/lib/x64/ -DVERSION=\"v1.5.3-dirty\" \ -lOpenCL \ -o./bin/autodock_gpu_64wi \ -DGPU_DEVICE -DN64WI -O3 -DKRNL_SOURCE=./device/calcenergy.cl -DKRNL_DIRECTORY=./device -DKCMN_DIRECTORY=./common -DK1="gpu_calc_initpop" -DK2="gpu_sum_evals" -DK3="perform_LS" -DK4="gpu_gen_and_eval_newpops" -DK5="gradient_minSD" -DK6="gradient_minFire" -DK7="gradient_minAD" /usr/lib/gcc/x86_64-pc-cygwin/11/../../../../x86_64-pc-cygwin/bin/ld: внутренняя ошибка: останов на /mnt/share/cygpkgs/binutils/binutils.x86_64/src/binutils-2.40/ld/ldlang.c:527 в compare_section /usr/lib/gcc/x86_64-pc-cygwin/11/../../../../x86_64-pc-cygwin/bin/ld: сообщите об этой ошибке collect2: ошибка: выполнение ld завершилось с кодом возврата 1 make: *** [Makefile.OpenCL:267: odock] Error 1

[atillack]

@kotenok2000 Please try replacing -std=c++11 with -std=gnu++11.

[kotenok2000]

It fails like this: make DEVICE=OCLGPU NUMWI=64 rm -f ./host/inc/performdocking.h ./host/src/performdocking.cpp Building adgpu_analysis ... g++ \ ./host/src/calcenergy.cpp ./host/src/getparameters.cpp ./host/src/main.cpp ./host/src/miscellaneous.cpp ./host/src/processgrid.cpp ./host/src/processligand.cpp ./host/src/processresult.cpp ./host/src/setup.cpp \ -std=gnu++11 -I./common -I./host/inc -DVERSION=\"v1.5.3-48-gf9ea8ba79f3cf73a7873357f949a0043c524ca2b-dirty\" \ -o./bin/adgpu_analysis \ -O3 -DTOOLMODE DEVICE is set to GPU

CPU_INCLUDE_PATH is undefined CPU_LIBRARY_PATH is undefined

GPU_INCLUDE_PATH is set to /c/Program\ Files/NVIDIA\ GPU\ Computing\ Toolkit/CUDA/v12.0/include/ GPU_LIBRARY_PATH is set to /c/Program\ Files/NVIDIA\ GPU\ Computing\ Toolkit/CUDA/v12.0/lib/x64/

./stringify_ocl_krnls.sh

Stringified input header files: ./common/defines.h ./common/calcenergy_basic.h

Stringified input non-kernel files: ./device/auxiliary_genetic.cl ./device/calcenergy.cl ./device/calcgradient.cl ./device/calcMergedEneGra.cl

Stringified input kernel-files: ./device/kernel1.cl ./device/kernel2.cl ./device/kernel4.cl ./device/kernel3.cl ./device/kernel_sd.cl ./device/kernel_fire.cl ./device/kernel_ad.cl

Stringified output file: host/inc/stringify.h

ln -sf performdocking.h.OpenCL ./host/inc/performdocking.h ln -sf performdocking.cpp.OpenCL ./host/src/performdocking.cpp Building autodock_gpu_64wi ... g++ \ ./wrapcl/src/BufferObjects.cpp ./wrapcl/src/CommandQueues.cpp ./wrapcl/src/Contexts.cpp ./wrapcl/src/Devices.cpp ./wrapcl/src/ImportBinary.cpp ./wrapcl/src/ImportSource.cpp ./wrapcl/src/Kernels.cpp ./wrapcl/src/Platforms.cpp ./wrapcl/src/Programs.cpp ./wrapcl/src/listAttributes.cpp ./host/src/calcenergy.cpp ./host/src/getparameters.cpp ./host/src/main.cpp ./host/src/miscellaneous.cpp ./host/src/performdocking.cpp ./host/src/processgrid.cpp ./host/src/processligand.cpp ./host/src/processresult.cpp ./host/src/setup.cpp \ -std=gnu++11 -I./common -I./wrapcl/inc -I./host/inc -I./device -I/c/Program\ Files/NVIDIA\ GPU\ Computing\ Toolkit/CUDA/v12.0/include/ -L/c/Program\ Files/NVIDIA\ GPU\ Computing\ Toolkit/CUDA/v12.0/lib/x64/ -DVERSION=\"v1.5.3-48-gf9ea8ba79f3cf73a7873357f949a0043c524ca2b-dirty\" \ -lOpenCL \ -o./bin/autodock_gpu_64wi \ -DGPU_DEVICE -DN64WI -O3 -DKRNL_SOURCE=./device/calcenergy.cl -DKRNL_DIRECTORY=./device -DKCMN_DIRECTORY=./common -DK1="gpu_calc_initpop" -DK2="gpu_sum_evals" -DK3="perform_LS" -DK4="gpu_gen_and_eval_newpops" -DK5="gradient_minSD" -DK6="gradient_minFire" -DK7="gradient_minAD" /usr/lib/gcc/x86_64-pc-msys/11.3.0/../../../../x86_64-pc-msys/bin/ld: internal error: aborting at ../../binutils-2.40/ld/ldlang.c:527 in compare_section /usr/lib/gcc/x86_64-pc-msys/11.3.0/../../../../x86_64-pc-msys/bin/ld: please report this bug collect2: error: ld returned 1 exit status make: *** [Makefile.OpenCL:267: odock] Error 1