Hi Manuel,
This is not an AMBER unique problem. It's a problem of Ubuntu being too far past the bleeding edge.
CUDA 7.5 does NOT support Ubuntu 16.04 yet - might not ever if the changes are too aggressive:
CUDA 8.0 RC 1 purports to support Ubuntu 16.04 so you could try this - you'll probably need AMBER 16 though - we never tested AMBER 14 with CUDA 8 (it may or may not work).
So your options are register as a developer and download CUDA 8.0 RC - noting that it is a release candidate and thus not extensively tested yet with AMBER. Or rewind to Ubuntu 14.04.
All the best
Ross
> On Jun 3, 2016, at 22:41, 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.
>
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Received on Sat Jun 04 2016 - 10:00:03 PDT
