Dear Dr. David
We are using gcc5.4 in our system. I have followed the suggested
instruction and still, installation is not completed and giving the
following error-
/home/surendra/amber18/lib/libemil.a(setup.o): In function
`hsc::setUpNew(double*, double*, double*, double*)':
setup.C:(.text+0x151d): undefined reference to `VTT for
std::__cxx11::basic_stringstream<char, std::char_traits<char>,
std::allocator<char> >'
setup.C:(.text+0x15fb): undefined reference to `vtable for
std::__cxx11::basic_stringstream<char, std::char_traits<char>,
std::allocator<char> >'
setup.C:(.text+0x166f): undefined reference to `vtable for
std::__cxx11::basic_stringbuf<char, std::char_traits<char>,
std::allocator<char> >'
setup.C:(.text+0x23e9): undefined reference to `vtable for
std::__cxx11::basic_stringbuf<char, std::char_traits<char>,
std::allocator<char> >'
collect2: error: ld returned 1 exit status
make[4]: *** [/home/surendra/amber18/bin/pmemd.cuda_SPFP] Error 1
make[4]: Leaving directory `/home/surendra/amber18/src/pmemd/src'
make[3]: *** [cuda_SPFP] Error 2
make[3]: Leaving directory `/home/surendra/amber18/src/pmemd/src'
make[2]: *** [cuda_serial] Error 2
make[2]: Leaving directory `/home/surendra/amber18/src/pmemd'
make[1]: *** [cuda_serial] Error 2
make[1]: Leaving directory `/home/surendra/amber18/src'
make: *** [install] Error 2
I have attached the file for more detail (amber_error1.txt). Let me know if
I need to perform any extra step to overcome this.
Thank you
Best Regards
Mahesh
On Mon, Jun 24, 2019 at 9:18 PM David A Case <david.case.rutgers.edu> wrote:
> On Mon, Jun 24, 2019, Mahesh kumar Teli wrote:
> >
> >
>
> >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)'
>
> ....
>
> We've had other (sporadic) reports of problems with pbsa.cuda. Can
> you tell us which version of gcc you are using ("gcc --version")?
>
> If you don't need to use the cuda-accelerated version of pbsa, the
> workaround is this: edit the $AMBERHOME/AmberTools/src/Makefile, finding
> these lines:
>
> cuda_serial: math_libraries
> (cd pbsa && $(MAKE) clean && $(MAKE) -j1 install )
>
> Delete or comment out the second line.
>
> _______________________________________________
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> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
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Received on Mon Jun 24 2019 - 20:30:02 PDT
