Hi,
On 02/23/2016 09:33 PM, Yipu Miao wrote:
> Thanks, Gerald, excited to see Quick in AMBER.
>
> On Tue, Feb 23, 2016 at 1:13 PM, Ken Merz <merzjrke.msu.edu> wrote:
>
>> Hi,
>>
>>> On Feb 23, 2016, at 11:57 AM, Gerald Monard <
>> Gerald.Monard.univ-lorraine.fr> 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, I agree, its great to see Quick in AMBER! Thank you Gerald!
>>
>>>>
>>>
>>> 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”.
>>
>
> It is the f orbital integral code generated by machine, basically emulating
> all integral classes. We can probably only have s, p, d orbital by default,
> which requires a reasonable compilation time (5~10 min), and leave f
> orbital code as an option and warn user it takes more than an hour to
> complete compilation.
Would there be a way to separate the compilation (using -dc option)? I
tried (not much) but couldn't.
Gerald.
>
>
>>
>> This is probably the d or f orbital integral code that is taking so long.
>> Yipu can comment on this.
>>
>> Take care,
>> Kennie
>>
>>
>>>
>>>> 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.
>>>
>>>> Can you verify that Quick will work with 7.5 please.
>>>
>>> OK.
>>>
>>> Best,
>>>
>>> Gerald.
>>>
>>>>
>>>> All the best
>>>> Ross
>>>>
>>>>> On Feb 23, 2016, at 05:00, git repository hosting <
>> gitosis.amber.sdsc.edu> wrote:
>>>>>
>>>>>
>>>>> The project "git repository for AMBER":
>>>>>
>>>>> The branch, master has been updated
>>>>> via 39702f2e60f0efa6159774fadb3851744ce40c28 (commit)
>>>>> from 71bb82b19f095770fcdd3c409f4e880e388ce95c (commit)
>>>>>
>>>>>
>>>>> - Log -----------------------------------------------------------------
>>>>> commit 39702f2e60f0efa6159774fadb3851744ce40c28
>>>>> Author: Gerald Monard <Gerald.Monard.univ-lorraine.fr>
>>>>> Date: Tue Feb 23 13:57:25 2016 +0100
>>>>>
>>>>> QUICK: serial GPU version OK (cuda-5.0 + intel 2012)
>>>>>
>>>>> -----------------------------------------------------------------------
>>>>>
>>>>> Summary of changes:
>>>>> AmberTools/src/quick/Makefile | 2 +-
>>>>> AmberTools/src/quick/src/cuda/gpu_common.h | 28
>> ++++++++++++++++++++++++----
>>>>> AmberTools/src/quick/src/cuda/gpu_get2e.cu | 2 +-
>>>>> 3 files changed, 26 insertions(+), 6 deletions(-)
>>>>>
>>>>> --
>>>>> git repository for AMBER
>>>>>
>>>>> _______________________________________________
>>>>> Cvs-notification mailing list
>>>>> Cvs-notification.ambermd.org
>>>>> http://lists.ambermd.org/mailman/listinfo/cvs-notification
>>>>
>>>>
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>>>>
>>>
>>> --
>>>
>> ____________________________________________________________________________
>>>
>>> Prof. Gerald MONARD
>>> SRSMC, Université de Lorraine, CNRS
>>> Boulevard des Aiguillettes B.P. 70239
>>> F-54506 Vandoeuvre-les-Nancy, FRANCE
>>>
>>> e-mail : Gerald.Monard.univ-lorraine.fr
>>> tel. : +33 (0)383.684.381
>>> fax : +33 (0)383.684.371
>>> web : http://www.monard.info
>>>
>>>
>> ____________________________________________________________________________
>>>
>>>
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>>
>>
>
>
--
____________________________________________________________________________
Prof. Gerald MONARD
SRSMC, Université de Lorraine, CNRS
Boulevard des Aiguillettes B.P. 70239
F-54506 Vandoeuvre-les-Nancy, FRANCE
e-mail : Gerald.Monard.univ-lorraine.fr
tel. : +33 (0)383.684.381
fax : +33 (0)383.684.371
web : http://www.monard.info
____________________________________________________________________________
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Received on Tue Feb 23 2016 - 13:00:05 PST
