My system currently uses
CUDA Driver Version = 4.10, CUDA Runtime Version = 4.0
So, Scott, do you mean we should stick to version 4.0 of CUDA driver or
CUDA runtime or both?
Thanks,
Jan-Philip
On 27.02.2012 16:45, Scott Le Grand wrote:
> Stick to 4.0 for now.
>
> On Mon, Feb 27, 2012 at 7:37 AM, 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 delivery, may
>>>> 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 - 08:00:04 PST
