Re: Fwd: Fwd: namd on gtx-680

From: Francesco Pietra (chiendarret_at_gmail.com)
Date: Wed Jun 20 2012 - 09:38:32 CDT

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
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
>> >>
>> >
>>
>

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