Hello Amber users
I am trying to install Amber18 in work station.
It has CUDA Toolkit 8.0 and the environment variable was set-
CUDA_HOME=/usr/local/cuda
PATH=/usr/local/cuda/bin:$PATH
LD_LIBRARY_PATH=/usr/local/cuda/lib64:$LD_LIBRARY_PATH
export CUDA_HOME PATH LD_LIBRARY_PATH
The following steps were performed to install amber18.
1) move into amber directory
execute
./configure -cuda gnu
configuration successful.
2. sourcing of amber.sh
source /home/surendra/amber18/amber.sh
3. execute
make install
This led to following errors:
tmpxft_000047e9_00000000-4_cuda_cg_wrapper.compute_61.cudafe1.cpp:(.text._ZN6thrust6system6detail9bad_allocC2ERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEE[_ZN6thrust6system6detail9bad_allocC5ERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEE]+0x73):
undefined reference to `std::__cxx11::basic_string<char,
std::char_traits<char>, std::allocator<char> >::_M_append(char const*,
unsigned long)'
tmpxft_000047e9_00000000-4_cuda_cg_wrapper.compute_61.cudafe1.cpp:(.text._ZN6thrust6system6detail9bad_allocC2ERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEE[_ZN6thrust6system6detail9bad_allocC5ERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEE]+0x84):
undefined reference to `std::__cxx11::basic_string<char,
std::char_traits<char>, std::allocator<char> >::_M_append(char const*,
unsigned long)'
cuda_cg_wrapper.o: In function
`thrust::system::cuda::detail::bulk_::detail::throw_on_error(cudaError,
char const*)':
tmpxft_000047e9_00000000-4_cuda_cg_wrapper.compute_61.cudafe1.cpp:(.text._ZN6thrust6system4cuda6detail5bulk_6detail14throw_on_errorE9cudaErrorPKc[_ZN6thrust6system4cuda6detail5bulk_6detail14throw_on_errorE9cudaErrorPKc]+0x3c):
undefined reference to
`std::runtime_error::runtime_error(std::__cxx11::basic_string<char,
std::char_traits<char>, std::allocator<char> > const&)'
cuda_cg_wrapper.o: In function `thrust::system::system_error::what() const':
tmpxft_000047e9_00000000-4_cuda_cg_wrapper.compute_61.cudafe1.cpp:(.text._ZNK6thrust6system12system_error4whatEv[_ZNK6thrust6system12system_error4whatEv]+0x4c):
undefined reference to `std::__cxx11::basic_string<char,
std::char_traits<char>, std::allocator<char> >::_M_replace(unsigned long,
unsigned long, char const*, unsigned long)'
tmpxft_000047e9_00000000-4_cuda_cg_wrapper.compute_61.cudafe1.cpp:(.text._ZNK6thrust6system12system_error4whatEv[_ZNK6thrust6system12system_error4whatEv]+0x81):
undefined reference to `std::__cxx11::basic_string<char,
std::char_traits<char>, std::allocator<char> >::_M_append(char const*,
unsigned long)'
tmpxft_000047e9_00000000-4_cuda_cg_wrapper.compute_61.cudafe1.cpp:(.text._ZNK6thrust6system12system_error4whatEv[_ZNK6thrust6system12system_error4whatEv]+0xa2):
undefined reference to `std::__cxx11::basic_string<char,
std::char_traits<char>, std::allocator<char> >::_M_append(char const*,
unsigned long)'
collect2: error: ld returned 1 exit status
make[2]: *** [pbsa.cuda] Error 1
make[2]: Leaving directory `/home/surendra/amber18/AmberTools/src/pbsa'
make[1]: *** [cuda_serial] Error 2
make[1]: Leaving directory `/home/surendra/amber18/AmberTools/src'
make: *** [install] Error 2
[surendra.gpu amber18]$
I have attached the text file for more information. Please help us to solve
the issue.
Thanking you in advance.
With Best Regards
Mahesh
---------------------------
Mahesh Kumar Teli
College of Pharmacy
Gachon University of Medicine and Science
Room # 502, Hambakmoero 191, Yeonsu-gu, Incheon, 21936, Korea
Mobile: +82-10-3098-8309
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Received on Mon Jun 24 2019 - 02:30:02 PDT
