From: Axel Kohlmeyer (akohlmey_at_gmail.com)
Date: Wed Jun 20 2012 - 10:11:48 CDT
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.
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