Hi Ross & Mark,
Thanks for the info. I'll test those possible solutions, and check what I can do. To tell you the truth, it is not life-threatening at the moment, since, as I wrote in my original email, I hadn't upgraded my servers yet to 16.04. Since cpptraj and so on works well on my laptop, I might just wait until cuda 8.0 gets properly released, and then update everything.
Either way, thank you very much for the clarification!
Manuel
-----Original message-----
From:Ross Walker <ross.rosswalker.co.uk>
To:AMBER Mailing List <amber.ambermd.org>
Cc:mmaestre <
mmaestre.gate.sinica.edu.tw>
Date:Sun, 05 Jun 2016 03:18:52
Subject:Re: [AMBER] problems compiling cuda enabled amber on ubuntu 16.04
Bleeding edge as being released as production with an LTS label but not working with major things that people in the industry use. That is my definition of bleeding edge. This should have stayed labelled as beta until the rest of the infrastructure matured / caught up. Otherwise it just ends up wasting end users time as they expect things to 'work' and get frustrated when they don't.
> On Jun 4, 2016, at 10:43, Mark Abraham <mark.j.abraham.gmail.com> wrote:
>
> Hi,
>
> What decision by the glibc / Ubuntu developers was so "bleeding edge?"
> Trying to optimize memcpy performance seems a quite reasonable thing to do.
> Do we need to contribute more CUDA-based code to repo test sets to save
> ourselves pain?
>
> Mark
>
> On Sat, 4 Jun 2016 18:37 Ross Walker <ross.rosswalker.co.uk> wrote:
>
>> 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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>>> http://lists.ambermd.org/mailman/listinfo/amber
>>
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Received on Sat Jun 04 2016 - 21:30:02 PDT
