The driver version should not matter. Just use v4.0 of the compiler since 4.1 gives a 10% performance hit.
There should not be any compatibility issues with the 4.1 compiler beyond execution speed. The other issues people are seeing with compiling is likely just some Ubuntu weirdness since I cannot reproduce it on our Redhat machines.
All the best
Ross
On Feb 27, 2012, at 7:57, Jan-Philip Gehrcke <jgehrcke.googlemail.com> wrote:
> 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.
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>> _______________________________________________
>>>>>>> AMBER mailing list
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>>>>>>> http://lists.ambermd.org/mailman/listinfo/amber
>>>>>>>
>>>>>>
>>>>>>
>>>>>>
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>>>>>
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Received on Mon Feb 27 2012 - 09:00:02 PST
