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 Fri Feb 24 2012 - 09:30:03 PST
