I have used Ubuntu since day one for AMBER development. The only way to
debug the Ubuntu problem is for someone to give me a shell account on an
offending machine and let me see this for myself.
On Mon, Feb 27, 2012 at 8:58 AM, Jan-Philip Gehrcke <jgehrcke.googlemail.com
> wrote:
> On 27.02.2012 17:48, Ross Walker wrote:
> > 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.
>
> I got the term "CUDA Driver Version" from the output of the deviceQuery
> program:
>
> "[...]
> CUDA Driver = CUDART, CUDA Driver Version = 4.10, CUDA Runtime Version =
> 4.0, NumDevs = 2, [...]
> "
>
> On 27.02.2012 17:44, Ross Walker wrote:
> > The driver version should not matter. Just use v4.0 of the compiler
> > since 4.1 gives a 10% performance hit.
>
>
> Thanks, Ross, for the clarification,
>
> Jan-Philip
>
> >
> >
> > 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.
> >>>>>>
> >>>>>>
> >>>>>>
> >>>>>>
> >>>>>>
> >>>>>> _______________________________________________ AMBER
> >>>>>> mailing list AMBER.ambermd.org
> >>>>>> http://lists.ambermd.org/mailman/listinfo/amber
> >>>>>>
> >>>>>
> >>>>>
> >>>>>
> >>>>> _______________________________________________ AMBER mailing
> >>>>> list AMBER.ambermd.org
> >>>>> http://lists.ambermd.org/mailman/listinfo/amber
> >>>>>
> >>>>> _______________________________________________ AMBER mailing
> >>>>> list AMBER.ambermd.org
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> >>>>>
> >>>>
> >>>>
> >>>>
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> >>>>
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> >>>
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Received on Mon Feb 27 2012 - 10:30:02 PST
