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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Received on Fri Feb 24 2012 - 09:00:02 PST
