Unable to compile

[tyop-bot]

I am trying to install AutoDock-Vina-GPU-2.1, but unable to do so.
I have tested that openCL and Boost works

I have triple checked that the Makefile is correct:
#Need to be modified according to different users
WORK_DIR=/home/petear/Vina-GPU-2.1/AutoDock-Vina-GPU-2.1
BOOST_LIB_PATH=/home/petear/Vina-GPU/boost_1_85_0
OPENCL_LIB_PATH=/usr/local/cuda
OPENCL_VERSION=-DOPENCL_3_0
GPU_PLATFORM=-DNVIDIA_PLATFORM
DOCKING_BOX_SIZE=-DSMALL_BOX

Typing the following in the terminal

ulimit -s 8192
make clean
make source

And here I get these errors:

`gcc -o AutoDock-Vina-GPU-2-1 -I/home/petear/Vina-GPU/boost_1_85_0 -I/home/petear/Vina-GPU/boost_1_85_0/boost -I/home/petear/Vina-GPU-2.1/AutoDock-Vina-GPU-2.1/lib -I/home/petear/Vina-GPU-2.1/AutoDock-Vina-GPU-2.1/OpenCL/inc -I/usr/local/cuda/include ./main/main.cpp -O3 ./lib/*.cpp ./OpenCL/src/wrapcl.cpp /home/petear/Vina-GPU/boost_1_85_0/libs/thread/src/pthread/thread.cpp /home/petear/Vina-GPU/boost_1_85_0/libs/thread/src/pthread/once.cpp -lboost_program_options -lboost_system -lboost_filesystem -lOpenCL -lstdc++ -lstdc++fs -lm -lpthread -L/home/petear/Vina-GPU/boost_1_85_0/stage/lib -L/usr/local/cuda/lib64 -DOPENCL_3_0 -DNVIDIA_PLATFORM -DSMALL_BOX -DBOOST_TIMER_ENABLE_DEPRECATED -DNDEBUG -DBUILD_KERNEL_FROM_SOURCE

./main/main.cpp:33:10: fatal error: parse_pdbqt.h: No such file or directory
33 | #include "parse_pdbqt.h"
| ^~~~~~~~~~~~~~~
compilation terminated.
In file included from ./lib/cache.cpp:41:
./lib/cache.h:32:10: fatal error: commonMacros.h: No such file or directory
32 | #include "commonMacros.h"
| ^~~~~~~~~~~~~~~~
compilation terminated.
In file included from ./lib/main_procedure_cl.cpp:1:
./lib/cache.h:32:10: fatal error: commonMacros.h: No such file or directory
32 | #include "commonMacros.h"
| ^~~~~~~~~~~~~~~~
compilation terminated.
In file included from ./lib/monte_carlo.cpp:23:
./lib/monte_carlo.h:28:10: fatal error: commonMacros.h: No such file or directory
28 | #include "commonMacros.h"
| ^~~~~~~~~~~~~~~~
compilation terminated.
In file included from ./lib/parallel_mc.h:26,
from ./lib/parallel_mc.cpp:24:
./lib/monte_carlo.h:28:10: fatal error: commonMacros.h: No such file or directory
28 | #include "commonMacros.h"
| ^~~~~~~~~~~~~~~~
compilation terminated.
In file included from /home/petear/Vina-GPU/boost_1_85_0/boost/config/header_deprecated.hpp:18,
from /home/petear/Vina-GPU/boost_1_85_0/boost/progress.hpp:26,
from ./lib/parallel_progress.h:26,
from ./lib/parallel_progress.cpp:25:
/home/petear/Vina-GPU/boost_1_85_0/boost/config/pragma_message.hpp:24:34: note: ‘#pragma message: This header is deprecated. Use the facilities in <boost/timer/timer.hpp> or <boost/timer/progress_display.hpp> instead.’
24 | # define BOOST_PRAGMA_MESSAGE(x) _Pragma(BOOST_STRINGIZE(message(x)))
| ^~~~~~~
/home/petear/Vina-GPU/boost_1_85_0/boost/config/header_deprecated.hpp:23:37: note: in expansion of macro ‘BOOST_PRAGMA_MESSAGE’
23 | # define BOOST_HEADER_DEPRECATED(a) BOOST_PRAGMA_MESSAGE("This header is deprecated. Use " a " instead.")
| ^~~~~~~~~~~~~~~~~~~~
/home/petear/Vina-GPU/boost_1_85_0/boost/progress.hpp:27:1: note: in expansion of macro ‘BOOST_HEADER_DEPRECATED’
27 | BOOST_HEADER_DEPRECATED( "the facilities in <boost/timer/timer.hpp> or <boost/timer/progress_display.hpp>" )
| ^~~~~~~~~~~~~~~~~~~~~~~
/home/petear/Vina-GPU/boost_1_85_0/boost/config/pragma_message.hpp:24:34: note: ‘#pragma message: This header is deprecated. Use the facilities in <boost/timer/timer.hpp> instead.’
24 | # define BOOST_PRAGMA_MESSAGE(x) _Pragma(BOOST_STRINGIZE(message(x)))
| ^~~~~~~
/home/petear/Vina-GPU/boost_1_85_0/boost/config/header_deprecated.hpp:23:37: note: in expansion of macro ‘BOOST_PRAGMA_MESSAGE’
23 | # define BOOST_HEADER_DEPRECATED(a) BOOST_PRAGMA_MESSAGE("This header is deprecated. Use " a " instead.")
| ^~~~~~~~~~~~~~~~~~~~
/home/petear/Vina-GPU/boost_1_85_0/boost/timer.hpp:25:1: note: in expansion of macro ‘BOOST_HEADER_DEPRECATED’
25 | BOOST_HEADER_DEPRECATED( "the facilities in <boost/timer/timer.hpp>" )
| ^~~~~~~~~~~~~~~~~~~~~~~
./OpenCL/src/wrapcl.cpp:1:10: fatal error: wrapcl.h: No such file or directory
1 | #include <wrapcl.h>
| ^~~~~~~~~~
compilation terminated.
make: *** [Makefile:23: source] Error 1
`

What can I do to compile it?

my system is Pop_OS (Ubuntu 22.04 derivative)
Adding image if it makes it easier to see

[Glinttsd]

Hi, do you have /Vina-GPU-2.1/AutoDock-Vina-GPU-2.1/lib/parse_pdbqt.h in the right path?

[tyop-bot]

Hi thanks for your quick reply.
I haven't added or changed anything except the Makefile in the /Vina-GPU-2.1/Autodock-Vina-GPU-2.1/ path

[tyop-bot]

Hi again, I checked and it it is present in /Vina-GPU-2.1/AutoDock-Vina-GPU-2.1/lib/parse_pdbqt.h

[Glinttsd]

That's weird... Maybe you can try to use the absolute path of the xxx.h file like /home/shidi/Vina-GPU-2.1/AutoDock-Vina-GPU-2.1/lib/parse_pdbqt.h