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