Re: [AMBER-Developers] Quick and CUDA in AmberTools

From: Ross Walker <>
Date: Tue, 23 Feb 2016 10:33:46 -0800

> On Feb 23, 2016, at 8:57 AM, Gerald Monard <> wrote:
> Hello,
> I was going to send to all of you some details about the current status
> of Quick in the next few days, but you were faster...
> So, for some details:
> On 02/23/2016 04:29 PM, Ross Walker wrote:
>> Hi Gerald,
>> I see commits for Quick in master. This looks cool. Note will it be built as part of the standard ./configure -cuda build?
> Yes and no. For the moment, the AmberTools/src/Makefile contains a line
> for building quick.cuda but it is commented out. My problem right now is
> that one of the cuda files needs ~1.5 hour to compile! I was going to
> request some help from Kennie's group and yours to see if we can speed
> up compilation.
> For the moment, only the serial and MPI versions of quick are built by
> default. If you want quick.cuda, you need to "cd AmberTools/src/quick &&
> make".

Yeap - the slowest compiler on the planet strikes again. I can get this escalated directly to the right people at NVIDIA which will probably be quickest way of addressing it. Which file is it specifically? I'd need to put together a standalone repo - i.e. the minimum set files of files they would need to reproduce the problem and then I can get us some help.

>> One thing to note is that pmemd.cuda from AMBER 16 onwards is going to need a minimum of NVCC v7.5 so it would probably be best if we just restrict the whole of AMBER + AmberTools to require a minimum of NVCC 7.5 for simplicity.
> OK. I guess you worried about the cuda-5.0... I currently writing tests
> and I'm checking that I can have the same results for cuda > 5. I don't
> mind going directly to 7.5, that will save me some work.

Cool - so if I change the configure script to test for 7.5 and later or quit and request one upgrades NVCC there would be no objects yes?

All the best

|\oss Walker

| Associate Research Professor |
| San Diego Supercomputer Center |
| Adjunct Associate Professor |
| Dept. of Chemistry and Biochemistry |
| University of California San Diego |
| NVIDIA Fellow |
| | |
| Tel: +1 858 822 0854 | EMail:- |

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Received on Tue Feb 23 2016 - 11:00:03 PST
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