AW: Fwd: Fwd: namd on gtx-680

From: Norman Geist (norman.geist_at_uni-greifswald.de)
Date: Thu Jun 21 2012 - 00:49:23 CDT

I wouldn't configure such through bashrc but using the runscript option of
charmrun.

Norman Geist.

> -----Ursprüngliche Nachricht-----
> Von: owner-namd-l_at_ks.uiuc.edu [mailto:owner-namd-l_at_ks.uiuc.edu] Im
> Auftrag von Axel Kohlmeyer
> Gesendet: Mittwoch, 20. Juni 2012 20:52
> An: Francesco Pietra
> Cc: NAMD
> Betreff: Re: namd-l: Fwd: Fwd: namd on gtx-680
>
> On Wed, Jun 20, 2012 at 1:57 PM, Francesco Pietra
> <chiendarret_at_gmail.com> wrote:
> > Sorry, I previously forgot the list
> >
> >
> > ---------- Forwarded message ----------
> > From: Francesco Pietra <chiendarret_at_gmail.com>
> > Date: Wed, Jun 20, 2012 at 7:37 PM
> > Subject: Re: namd-l: Fwd: Fwd: namd on gtx-680
> > To: Axel Kohlmeyer <akohlmey_at_gmail.com>
> >
> >
> > I removed the Debian package "libcudart4", commented out the
> exporting
> > LIBRARY in my .bshrc, and commanded
> >
> > export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:/usr/local/namd-cuda-
> 2.9_2012-06-20
> >
> > then
> >
> > charmrun ... (as before)
> >
> >
> >
> > The simulation is now going on, and we will be able to compare with
> > respect to the same number of steps (500,000), for the same
> > equilibration, carried out at a previous stage with two GTX-580. The
> > system is not very large, so that we can not expect any large
> > advantage of the 680, IF ANY. The GPU hardware suppor must be
> > accounted for; whatever the producers say, sandybridge (even -E, I
> > suspect) is PCI Express 2.0. Withe lower memory bandwith of the 680
> we
> > risk even to get them slower than the 580. Personnally, I hope that
> > one day MD codes will move to OpenCL, so that amd hardware can be
> used
> > (from admittedly chance experience, I was always lucky with amd: I
> > have no shares with them, just user). If not else they are cheaper :
> I
> > don't expect any advantage from the present i7 with respect to
> > previous Phenom, although the price is nearly quadruple (with much
> > more heat and energy usge).
> >
> > So, as Axel suspected, the Debian lib is very likely not compatible
> (I
> > am using the testing amd64, i.e. with the latest libraries, may be
> > they are too recent for the NAMD compilation)
> >
> > Both GPUs temperature (65-70 centigrades) and memory usage are very
> > similar to the 580 in last few milder days (now hot days here, no
>  air
> > conditioning, however historic, solid building).
> >
> > Incidentally, may be because of the heat, I tried unsuccesfully to
> > tune my .bashrc
> >
> > # For NAMD-CUDA 2.9 nighly build
> > NAMD_HOME=/usr/local/namd-cuda-2.9_2012-06-20
> > PATH=$PATH:$NAMD_HOME/bin/namd2; export NAMD_HOME PATH
> > PATH="/usr/local/namd-cuda-2.9_2012-06-20/bin:$PATH"; export PATH
> >
> > if [ "$LD_LIBRARY_PATH" ] ; then
> >   export LD_LIBRARY_PATH="/usr/local/namd-cuda-2.9_2012-06-20"
> > else
> >   export LD_LIBRARY_PATH="$LD_LIBRARY_PATH:/namd-cuda-2.9_2012-06-20"
>
>
>
> > fi
> >
> > Thanks a lot again (and also for detecting the mistakes in the if
> ...,
>
> your "fix" is wrong. the right fix is to keep the order of the if
> clauses
> but switch the order of in the path to:
>
> export LD_LIBRARY_PATH="namd-cuda-2.9_2012-06-20:$LD_LIBRARY_PATH"
>
> that will search the NAMD directory first.
>
> even better is to call namd from a wrapper script and hide
> the LD_LIBRARY_PATH fix in there, so that other applications
> are not redirected to the NAMD bundled cuda runtime, which
> may be from a beta version and not fully backward compatible
> and not fully tested.
>
> axel.
>
> >
> > francesco pietra
> >
> > On Wed, Jun 20, 2012 at 5:11 PM, Axel Kohlmeyer <akohlmey_at_gmail.com>
> wrote:
> >> On Wed, Jun 20, 2012 at 10:38 AM, Francesco Pietra
> >> <chiendarret_at_gmail.com> wrote:
> >>> Hi Vignesh:
> >>>
> >>> In my .bshrc;
> >>>
> >>> # For NAMD-CUDA 2.9 nighly build
> >>> NAMD_HOME=/usr/local/namd-cuda-2.9_2012-06-20
> >>> PATH=$PATH:$NAMD_HOME/bin/namd2; export NAMD_HOME PATH
> >>> PATH="/usr/local/namd-cuda-2.9_2012-06-20/bin:$PATH"; export PATH
> >>>
> >>> if [ "$LD_LIBRARY_PATH" ] ; then
> >>>   export LD_LIBRARY_PATH="$LD_LIBRARY_PATH:/usr/local/namd-cuda-
> 2.9_2012-06-20
> >>
> >> this is a mistake. the NAMD directory has to come first,
> >> so LD_LIBRARY_PATH points to the version that ships
> >> with NAMD and not the (likely incompatible) one you
> >> installed elsewhere.
> >>
> >> axel.
> >>
> >>> else
> >>>   export LD_LIBRARY_PATH="/usr/local/namd-cuda-2.9_2012-06-20"
> >>> fi
> >>>
> >>> If I understand, this is practically a manual link. Should this be
> not
> >>> what you mean, please instruct me.
> >>>
> >>> I must add that when I started (I had reinstalled amd64 raid1
> because
> >>> previous installation had been so much stressed), running charmrun
> I
> >>> received the error message:
> >>>
> >>> "Error while loading shared libraries: libcudart.so.4"
> >>>
> >>> I resolven by installing the Debian amd64 package libcudart4. From
> >>> this, it seems to me that, with Debian,  libcudart.so.4 is seen as
> a
> >>> shared library (to reinforce my point above). If I am wrong, please
> >>> correct me.
> >>>
> >>> francesco
> >>>
> >>>
> >>> On Wed, Jun 20, 2012 at 4:05 PM, Vignesh <vignesh757_at_gmail.com>
> wrote:
> >>>> Francesco,
> >>>>
> >>>> Did you try manually linking the libcudart.so.4 file before the
> run? I had
> >>>> similar issues with gtx 560 , two cards on one machine.
> >>>>
> >>>> When I tried to let it run default using both cards, I got the
> same error,
> >>>> prohibited mode ... but when I specified the two cards in the
> command, it
> >>>> gave me a link error. All this got fixed by manually linking the
> .so.4 file
> >>>> before the run.
> >>>>
> >>>> Ld_library_path = /../Namd_2.9-cuda
> >>>>
> >>>> Hope this helps. Let us know
> >>>>
> >>>> Vignesh
> >>>>
> >>>> On Jun 20, 2012 6:11 AM, "Francesco Pietra"
> <chiendarret_at_gmail.com> wrote:
> >>>>>
> >>>>> Resent because the accademia server if often unreliable. Sorry.
> >>>>>
> >>>>>
> >>>>> ---------- Forwarded message ----------
> >>>>> From: Francesco Pietra <francesco.pietra_at_accademialucchese.it>
> >>>>> Date: Wed, Jun 20, 2012 at 12:08 PM
> >>>>> Subject: Re: Fwd: namd on gtx-680
> >>>>> To: Jim Phillips <jim_at_ks.uiuc.edu>, NAMD <namd-l_at_ks.uiuc.edu>
> >>>>>
> >>>>>
> >>>>> Hi Jim:
> >>>>>
> >>>>> My attempts at running namd-cuda 2.9, nightly build 2012-06-20,
> on
> >>>>> GTX-680 failed. I used the same procedure as with my previous
> Gigabyte
> >>>>> 890FXA / AMD Phenom II / two  GTX-580. The latter had no
> problems, and
> >>>>> i tried now to continue the already advanced equilibration of a
> >>>>> protein in a water box, carried out under parm7 ff.
> >>>>>
> >>>>> HARDWARE: Gigabyte X79-UD3 , Intel i7-3930k, two GTX-680 on x16
> lanes.
> >>>>>
> >>>>> OS: Debian amd64 wheezy (testing), cuda driver 295.53-1.
> >>>>>
> >>>>> COMMANDS:
> >>>>> - nvidia-smi -L
> >>>>> GPU 0: GeForce GTX 680 (UUID: N/A)
> >>>>> GPU 1 : as above
> >>>>>
> >>>>> -nvidia-smi -pm 1
> >>>>> Enabled persistence mode for GPU 0000:02:00.0.
> >>>>>         "
>  0000:03:00.0
> >>>>>
> >>>>> -charmrun $NAMD_HOME/bin/namd2 xxx.conf +p6 +idlepoll 2>&1 | tee
> xxx.log
> >>>>>
> >>>>> The log file tells;
> >>>>> Running command: /usr/local/namd-cuda-2.9_2012-06-20/bin/namd2
> >>>>> press-03.conf +p6 +idlepoll
> >>>>>
> >>>>> Charm++: standalone mode (not using charmrun)
> >>>>> Converse/Charm++ Commit ID: v6.4.0-beta1-0-g5776d21
> >>>>> CharmLB> Load balancer assumes all CPUs are same.
> >>>>> Charm++> Running on 1 unique compute nodes (12-way SMP).
> >>>>> Charm++> cpu topology info is gathered in 0.001 seconds.
> >>>>> Info: NAMD CVS-2012-06-20 for Linux-x86_64-multicore-CUDA
> >>>>> Info:
> >>>>> Info: Please visit http://www.ks.uiuc.edu/Research/namd/
> >>>>> Info: for updates, documentation, and support information.
> >>>>> Info:
> >>>>> Info: Please cite Phillips et al., J. Comp. Chem. 26:1781-1802
> (2005)
> >>>>> Info: in all publications reporting results obtained with NAMD.
> >>>>> Info:
> >>>>> Info: Based on Charm++/Converse 60400 for multicore-linux64-
> iccstatic
> >>>>> Info: Built Wed Jun 20 02:24:32 CDT 2012 by jim on
> lisboa.ks.uiuc.edu
> >>>>> Info: 1 NAMD  CVS-2012-06-20  Linux-x86_64-multicore-CUDA  6
>  gig64
> >>>>>  francesco
> >>>>> Info: Running on 6 processors, 1 nodes, 1 physical nodes.
> >>>>> Info: CPU topology information available.
> >>>>> Info: Charm++/Converse parallel runtime startup completed at
> 0.0799868 s
> >>>>> FATAL ERROR: CUDA error on Pe 5 (gig64 device 0): All CUDA
> devices are
> >>>>> in prohibited mode, of compute capability 1.0, or otherwise
> unusable.
> >>>>> ------------- Processor 5 Exiting: Called CmiAbort ------------
> >>>>> Reason: FATAL ERROR: CUDA error on Pe 5 (gig64 device 0): All
> CUDA
> >>>>> devices are in prohibited mode, of compute capability 1.0, or
> >>>>> otherwise unusable.
> >>>>>
> >>>>> FATAL ERROR: CUDA error on Pe 1 (gig64 device 0): All CUDA
> devices are
> >>>>> in prohibited mode, of compute capability 1.0, or otherwise
> unusable.
> >>>>> Program finished.
> >>>>> FATAL ERROR: CUDA error on Pe 4 (gig64 device 0): All CUDA
> devices are
> >>>>> in prohibited mode, of compute capability 1.0, or otherwise
> unusable.
> >>>>> *************
> >>>>>
> >>>>> Would it be safe not to sell the GTX-580  and set aside the GTX-
> 680
> >>>>> for the future? Oor is anything that can be changed in my
> procedure? i
> >>>>> am not a pessimist, just I am still in time to take the GTX-580
> back
> >>>>> from the vendor where I did the business.
> >>>>>
> >>>>> Thanks a lot for advising me with urgency (because of the said
> >>>>> business, and I beg pardon very much for asking urgency)
> >>>>>
> >>>>> francesco Pietra
> >>>>>
> >>>>>
> >>>>>
> >>>>> On Thu, Jun 7, 2012 at 11:52 PM, Jim Phillips <jim_at_ks.uiuc.edu>
> wrote:
> >>>>> >
> >>>>> > Yes it can.  -Jim
> >>>>> >
> >>>>> > On Thu, 7 Jun 2012, David Brandon wrote:
> >>>>> >
> >>>>> >> Below came into biocore email:
> >>>>> >>
> >>>>> >>
> >>>>> >> -------- Original Message --------
> >>>>> >> Subject: namd on gtx-680
> >>>>> >> Date: Thu, 7 Jun 2012 09:04:45 +0200
> >>>>> >> From: Francesco Pietra <francesco.pietra_at_accademialucchese.it>
> >>>>> >> To: biocore_at_ks.uiuc.edu
> >>>>> >>
> >>>>> >> Hi:
> >>>>> >>
> >>>>> >> May I ask whether namd 2.9, or a night build, can run on
> nvidia
> >>>>> >> GTX-680? (I am at Debian GNU Linux amd64)
> >>>>> >>
> >>>>> >> I could not obtain the information from the general forum, nor
> was I
> >>>>> >> able to find the question posed to biocore.
> >>>>> >>
> >>>>> >> Because of trivial commercial problems, I am short of time in
> deciding
> >>>>> >> to change my two GTX-580 for two GTX-680.
> >>>>> >>
> >>>>> >> Thanks a lot
> >>>>> >>
> >>>>> >> francesco pietra
> >>>>> >>
> >>>>> >>
> >>>>> >>
> >>>>> >>
> >>>>> >> Francesco Pietra
> >>>>> >> Professor of Chemistry
> >>>>> >> Accademia Lucchese di Scienze, Lettere e Arti, founded in 1584
> >>>>> >> Palazzo Ducale
> >>>>> >> I-55100 Lucca
> >>>>> >> tel/fax +39 0583 417336
> >>>>> >>
> >>>>> >> --
> >>>>> >> David P. Brandon, Manager
> >>>>> >> Theoretical and Computational Biophysics Group
> >>>>> >> Center for Macromolecular Modeling & Bioinformatics
> >>>>> >> 3027 Beckman Institute
> >>>>> >> 405 N. Mathews Avenue
> >>>>> >> Urbana, IL  61801
> >>>>> >> ph:  217-265-6480
> >>>>> >> fax: 217-244-6078
> >>>>> >> site: www.ks.uiuc.edu
> >>>>> >>
> >>>>> >
> >>>>>
> >>>>
> >>>
> >>
> >>
> >>
> >> --
> >> Dr. Axel Kohlmeyer
> >> akohlmey_at_gmail.com  http://goo.gl/1wk0
> >>
> >> College of Science and Technology
> >> Temple University, Philadelphia PA, USA.
>
>
>
> --
> Dr. Axel Kohlmeyer
> akohlmey_at_gmail.com  http://goo.gl/1wk0
>
> College of Science and Technology
> Temple University, Philadelphia PA, USA.

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