On Thu, 2014-03-20 at 07:57 +0000, Weinzierl, Robert O J wrote:
> Dear all,
>
> I tried to compile AMBER12 pmemd.cuda on my computer running on Ubuntu 13.10 (with CUDA 5.5.22 and Nvidia driver 331.49).
> The compilation started normally, but towards the end I got the following error messages:
>
> home/rojw/amber12/lib/libnetcdf.a
> /usr/bin/ld: ./cuda/cuda.a(gpu.o): undefined reference to symbol '_Znam..GLIBCXX_3.4'
> /usr/lib/x86_64-linux-gnu/libstdc++.so.6: error adding symbols: DSO missing from command line
> collect2: error: ld returned 1 exit status
> make[3]: *** [pmemd.cuda] Error 1
> make[3]: Leaving directory `/home/rojw/amber12/src/pmemd/src'
> make[2]: *** [cuda] Error 2
> make[2]: Leaving directory `/home/rojw/amber12/src/pmemd'
> make[1]: *** [cuda] Error 2
> make[1]: Leaving directory `/home/rojw/amber12/src'
> make: *** [install] Error 2
>
> I tried adding the flag'-lstdc++' to the PMEMD_LD variable in the config.h file, but that did not solve the problem. Any suggestions how to fix this problem?
This looks a lot like "-lstdc++" is missing from the link line. Take a
look at the linking line from the compilation output and see if -lstdc++
appears (at the end!!) of the command.
--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
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Received on Thu Mar 20 2014 - 05:00:05 PDT
