Re: Two GPU-based workstation

From: James Starlight (jmsstarlight_at_gmail.com)
Date: Fri Nov 01 2013 - 02:40:14 CDT

Ok. I'll try to make some simulations of this configure. The main issue
with which I can force is the possible conflict between that older cuda
library (used from vmd) and more newest development driver ( 5.5 version)
which comes from installed cuda-5.5.

By the way how I could use both of the GPUs simultaneously ? Just use the
below command?

namd2 +idlepoll +p4 +devices 0,1 ./restart.conf

Where 0 and 1 are the ids of my GPUs? Is there additional options for
synchronization of the simulations in dual-GPU regime ?

James

2013/10/31 Aron Broom <broomsday_at_gmail.com>

> 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
>

This archive was generated by hypermail 2.1.6 : Tue Dec 31 2013 - 23:23:55 CST