On 27.02.2012 17:48, Ross Walker wrote:
> As for driver version. There is no such thing as the "version 4.1
> driver" so I have no idea where people are getting this confusing
> terminology from.
I got the term "CUDA Driver Version" from the output of the deviceQuery
program:
"[...]
CUDA Driver = CUDART, CUDA Driver Version = 4.10, CUDA Runtime Version =
4.0, NumDevs = 2, [...]
"
On 27.02.2012 17:44, Ross Walker wrote:
> The driver version should not matter. Just use v4.0 of the compiler
> since 4.1 gives a 10% performance hit.
Thanks, Ross, for the clarification,
Jan-Philip
>
>
> On Feb 27, 2012, at 7:37, "Mettu, Ramgopal"<rmettu.tulane.edu>
> wrote:
>
>> All: I just wanted to follow up on my initial question about CUDA
>> compatibility. Is it the case that AMBER does not yet work with the
>> latest CUDA drivers? While I can still use the serial version, one
>> of my main goals is to leverage the GPUs I have available, so I'd
>> greatly appreciate any information about compatibility from the
>> developers. Thanks!
>>
>> Ram
>>
>> On Feb 24, 2012, at 11:16 AM, Scott Le Grand wrote:
>>
>>> CUDA 4.1 and AMBER should be compatible, but there's a 10%
>>> slowdown currently with it due to a bug in nvcc.
>>>
>>> Stick to 4.0 if you can for now...
>>>
>>>
>>> On Fri, Feb 24, 2012 at 8:36 AM, Mettu,
>>> Ramgopal<rmettu.tulane.edu> wrote:
>>>
>>>> To be on the safe side, I downloaded Amber and AmberTools again
>>>> and rebuilt everything, incorporating all bug fixes, as noted
>>>> below. I get the same errors as I had mentioned initially - can
>>>> the developers comment on CUDA 4.1 compatibility? Best,
>>>>
>>>> Ram
>>>>
>>>> On Feb 24, 2012, at 8:24 AM, Ismail, Mohd F. wrote:
>>>>
>>>>> I don't think CUDA 4.1 is supported yet.
>>>>>
>>>>>
>>>>> ******************************* Mohd Farid Ismail Graduate
>>>>> Student Dept. of Chemistry/Biochemistry University of
>>>>> Oklahoma Norman 73019
>>>>>
>>>>> ________________________________________ From: Mettu,
>>>>> Ramgopal [rmettu.tulane.edu] Sent: Thursday, February 23,
>>>>> 2012 10:45 PM To: AMBER Mailing List Subject: Re: [AMBER]
>>>>> CUDA version for Amber 11?
>>>>>
>>>>> Hi Ross, Yes, I forgot to mention that I applied all the bug
>>>>> fixes you mention
>>>> below -- any thoughts on what's happening?
>>>>>
>>>>> On Feb 23, 2012, at 10:37 PM, Ross Walker wrote:
>>>>>
>>>>>> Hi Ram,
>>>>>>
>>>>>>> As for the bug fixes, I decided to start from scratch and
>>>>>>> install a fresh copy of AmberTools and Amber. I was able
>>>>>>> again to correctly install the serial and parallel
>>>>>>> versions without errors (except for a few discrepancies
>>>>>>> in the test scripts). Unfortunately I get a new set of
>>>>>>> errors when trying to compile the CUDA binaries, that
>>>>>>> look like this:
>>>>>>
>>>>>> But did you take that fresh copy and apply all the bugfixes
>>>>>> for AMBER
>>>> and
>>>>>> AMBERTools from the website? - The bugfixes are required
>>>>>> for
>>>> compatibility
>>>>>> beyond cuda 3.2. The procedure is:
>>>>>>
>>>>>> 1) tar xvjf Amber11.tar.bz2 2) tar xvjf
>>>>>> AmberTools-1.5.tar.bz2 3) export
>>>>>> AMBERHOME=/path_to/amber11 4) cd $AMBERHOME 5) wget
>>>>>> http://ambermd.org/bugfixes/AmberTools/1.5/bugfix.all 6)
>>>>>> patch -p0< bugfix.all 7) rm -f bugfix.all 8) wget
>>>>>> http://ambermd.org/bugfixes/11.0/bugfix.all.tar.bz2 9) wget
>>>>>> http://ambermd.org/bugfixes/11.0/apply_bugfix.x 10) chmod
>>>>>> 700 apply_bugfix.x 11) ./apply_bugfix.x
>>>>>> $AMBERHOME/bugfix.all 12) cd $AMBERHOME/AmberTools/src/ 13)
>>>>>> ./configure gnu 14) make 15) cd ../../ 16) cd src 17) make
>>>>>> serial
>>>>>>
>>>>>> At this point you have the serial (non-GPU) versions of
>>>>>> AMBERTools and
>>>> AMBER
>>>>>>
>>>>>> built. Best to test them at this point.
>>>>>>
>>>>>> 18) cd $AMBERHOME/AmberTools/test/ 19) make test
>>>>>>
>>>>>> Check the test logs to see if everything worked.
>>>>>>
>>>>>> 20) cd $AMBERHOME/test 21) make test
>>>>>>
>>>>>> Again check the test logs to see if everything worked.
>>>>>>
>>>>>> Now we can build the serial GPU code.
>>>>>>
>>>>>> 22) cd $AMBERHOME/src/ 23) make clean 24) cd
>>>>>> $AMBERHOME/AmberTools/src/ 25) make clean 26) ./configure
>>>>>> -cuda gnu 27) cd ../../ 28) cd src 29) make cuda
>>>>>>
>>>>>> Hopefully this time it should build correctly.
>>>>>>
>>>>>> 30) cd ../test 31) make test.cuda
>>>>>>
>>>>>> All the best Ross
>>>>>>
>>>>>> /\ \/ |\oss Walker
>>>>>>
>>>>>> --------------------------------------------------------- |
>>>>>> Assistant Research Professor | |
>>>>>> San Diego Supercomputer Center | |
>>>>>> Adjunct Assistant Professor | | Dept.
>>>>>> of Chemistry and Biochemistry | |
>>>>>> University of California San Diego | |
>>>>>> NVIDIA Fellow | |
>>>>>> http://www.rosswalker.co.uk | http://www.wmd-lab.org/ | |
>>>>>> Tel: +1 858 822 0854 | EMail:- ross.rosswalker.co.uk |
>>>>>> ---------------------------------------------------------
>>>>>>
>>>>>> Note: Electronic Mail is not secure, has no guarantee of
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>>>> not
>>>>>> be read every day, and should not be used for urgent or
>>>>>> sensitive
>>>> issues.
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>>
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>>>>>>
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Received on Mon Feb 27 2012 - 09:00:03 PST
