From: Aron Broom (broomsday_at_gmail.com)
Date: Thu Oct 31 2013 - 12:34:14 CDT
don't replace anything, just point to the version of the library in your
NAMD directory as you did. It should work fine.
On Thu, Oct 31, 2013 at 1:24 PM, James Starlight <jmsstarlight_at_gmail.com>wrote:
> Dear Namd users,
>
> I've build my new workstations consisted of two Titans with i6 (linux
> recognize it like 12 core process but actually it consist of 6 nodes).
>
> Than I've installed lattest nvidia cuda-5.5 drivers (driver, toolkit as
> well as samples) and define all paths to the bash as well as libconf files.
>
> When I tried to lunch namd I've obtain error that libcudart.so.4 is not
> found (indeed in the cuda/lib and lib64 only libcudart.so.5 files are
> present).
>
> I've found libcudart.so.4 only in VMDs folder and when I've provide it in
> bash Namd have been worked.
>
> Should I change some modification to replace lib libcudart.so.5 to
> libcudart.so.4 ? My namd output is
>
> 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-2013-10-31 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 60500 for multicore-linux64-iccstatic
> Info: Built Thu Oct 31 02:26:47 CDT 2013 by jim on lisboa.ks.uiuc.edu
> Info: 1 NAMD CVS-2013-10-31 Linux-x86_64-multicore-CUDA 1
> drunk_telecaster own
> Info: Running on 1 processors, 1 nodes, 1 physical nodes.
> Info: CPU topology information available.
> Info: Charm++/Converse parallel runtime startup completed at 0.00467801 s
> Did not find +devices i,j,k,... argument, using all
> Pe 0 physical rank 0 binding to CUDA device 0 on drunk_telecaster:
> 'GeForce GTX TITAN' Mem: 6143MB Rev: 3.5
> FATAL ERROR: No simulation config file specified on command line.
>
>
> does it means the both of my GPUs ready to use ?
>
> James
>
>
> 2013/10/30 Norman Geist <norman.geist_at_uni-greifswald.de>
>
>> 1 - No.****
>>
>> 2 - Doesn't matter here most of the cases. ****
>>
>> ** **
>>
>> Norman Geist.****
>>
>> ** **
>>
>> *Von:* owner-namd-l_at_ks.uiuc.edu [mailto:owner-namd-l_at_ks.uiuc.edu] *Im
>> Auftrag von *James Starlight
>>
>> *Gesendet:* Mittwoch, 30. Oktober 2013 14:13
>> *An:* Namd Mailing List
>>
>> *Betreff:* Re: namd-l: Two GPU-based workstation****
>>
>> ** **
>>
>> Some extra questions-****
>>
>> 1- Do I need special drivers optimizing dual GPU in Debian ?****
>>
>> 2- Should I compile NAMD from sources for optimal performance ?
>> Previouslu I've used NAMD from Binaries ( using 1 gPU + 4 cores of i5 )**
>> **
>>
>> James****
>>
>> ** **
>>
>> 2013/10/29 Norman Geist <norman.geist_at_uni-greifswald.de>****
>>
>> >Just remember, NAMD is very memory bandwidth hungry.****
>>
>> ****
>>
>> Guess you mean PCIE bandwidth hungry?****
>>
>> ****
>>
>> Norman Geist.****
>>
>> ****
>>
>> *Von:* owner-namd-l_at_ks.uiuc.edu [mailto:owner-namd-l_at_ks.uiuc.edu] *Im
>> Auftrag von *Ajasja Ljubetic
>> *Gesendet:* Dienstag, 29. Oktober 2013 14:34
>> *An:* James Starlight
>> *Cc:* Norman Geist; Namd Mailing List****
>>
>>
>> *Betreff:* Re: namd-l: Two GPU-based workstation****
>>
>> ****
>>
>> ****
>>
>> As I've told I have typical desktop with 6 pci/e slots and 1 coreI7 (4
>> cores) + 2 GPU + 4 RAM slots (each of 4gb or 8gb I dont remember it now
>> clearly :) ). I'd like to launch simulations ( water soluble as well as
>> membrane proteins using NAMD with the explicit solvents (50k and 80k atoms
>> resp) using both GPUs simultaneously and CPU for one run. ****
>>
>> What another extra modification of my desktop as well as simulation
>> parameters should I take into account? Are any other specified drivers
>> needed for typical Linux-based multi GPU workstation?****
>>
>> ****
>>
>> ****
>>
>> Make sure to pick a motherboard with two 16x speed PCIE ports. (Probably
>> PCIE 3.0?). Personally I don't think you will see the scaling you desire.
>> I.e., the GPUs will be underutilized. But then again, YMMV. Just remember,
>> NAMD is very memory bandwidth hungry.****
>>
>> ****
>>
>> Best regards,****
>>
>> Ajasja****
>>
>> ** **
>>
>
>
-- Aron Broom M.Sc PhD Student Department of Chemistry University of Waterloo
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