Hi,
Lots of CUDA-based software is having this problem, which is caused by the
system having a version of glibc that is newer than CUDA. Note that it has
nothing to do with compiler version - people on Ubuntu 16.04 are using the
new glibc but are only aware of that they have a new compiler version. See
https://github.com/torch/torch7/issues/670 for suggested solutions.
Mark
On Sat, Jun 4, 2016 at 7:42 AM mmaestre <mmaestre.gate.sinica.edu.tw> wrote:
> Dear Amber users:
>
> Recently, I updated my laptop to Ubuntu 16.04 (I jump from LTS to LTS,
> meaning that I'm coming from ubuntu 14.04). Since I do most of my
> computational stuff on two servers which I maintain myself, I tend to you
> my laptop as a bit of a test-ground for amber and co.
> When installing amber, both serial and parallel worked wonderfully, but
> when it comes to enabling hardware acceleration, I've had a bit of trouble.
> When compiling, I get the following error:
>
> /usr/include/string.h: In function ‘void* __mempcpy_inline(void*, const
> void*, size_t)’:
> /usr/include/string.h:652:42: error: ‘memcpy’ was not declared in this
> scope
> return (char *) memcpy (__dest, __src, __n) + __n;
> ^
> Makefile:38: recipe for target 'kForcesUpdate.o' failed
> make[5]: *** [kForcesUpdate.o] Error 1
> make[5]: Leaving directory '/usr/local/xtal/amber16/src/pmemd/src/cuda'
> Makefile:169: recipe for target 'cuda_spfp_libs' failed
> make[4]: *** [cuda_spfp_libs] Error 2
> make[4]: Leaving directory '/usr/local/xtal/amber16/src/pmemd/src'
> Makefile:64: recipe for target 'cuda_SPFP' failed
> make[3]: *** [cuda_SPFP] Error 2
> make[3]: Leaving directory '/usr/local/xtal/amber16/src/pmemd/src'
> Makefile:27: recipe for target 'cuda_serial' failed
> make[2]: *** [cuda_serial] Error 2
> make[2]: Leaving directory '/usr/local/xtal/amber16/src/pmemd'
> Makefile:43: recipe for target 'cuda_serial' failed
> make[1]: *** [cuda_serial] Error 2
> make[1]: Leaving directory '/usr/local/xtal/amber16/src'
> Makefile:7: recipe for target 'install' failed
> make: *** [install] Error 2
>
> I've been googling a bit, and found that, back in 2010, Jason had a
> similar message regarding memcpy, which was related to the gcc compiler on
> ubuntu being too new. He had some success by rolling back to a precious
> version. I tried the same, going from 5.3.1 to 4.9.3, and to 4.8.5 (the
> configure script says that amber compilation was tested for 4.8.4 or
> higher). Neither of the three worked, and I still get the exact same error
> message.
>
> I've also read that there are some bugs between Cuda-7.5 and Ubuntu 16.04,
> so I'm thinking perhaps that's the problem. I'm getting the error message
> both with amber 14 and amber 16.
>
> Any help would be greatly appreciated! Should I perhaps try to apply for
> Cuda-8.0 RC?
> Thank you very much!
> Manuel
>
> P.S. Under Ubuntu 14.04, everything worked fine... but due to other pieces
> of software, I'd like to maintain 16.04, if possible.
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Sat Jun 04 2016 - 08:00:02 PDT
