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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> >>
> >>
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Received on Mon Feb 27 2012 - 08:00:03 PST
