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 Fri Jun 03 2016 - 23:00:03 PDT
