AMBER works fine with the latest drivers and should also work fine with the 4.1 compilers although it is about 10% slower than the 4.0 compiler. So probably best to stick to the 4.0 compiler for now. Note the driver / compiler version has no bearing on parallel for now so I am confused about your serial vs parallel comment.
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.
All the best
Ross
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 delivery, may
>>> not
>>>>> be read every day, and should not be used for urgent or sensitive
>>> issues.
>>>>>
>>>>>
>>>>>
>>>>>
>>>>>
>>>>> _______________________________________________
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>>>>> http://lists.ambermd.org/mailman/listinfo/amber
>>>>>
>>>>
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Received on Mon Feb 27 2012 - 09:00:03 PST
