From: Lucas (lucasbleicher_at_gmail.com)
Date: Thu Aug 15 2013 - 01:53:22 CDT
As for the LD_LIBRARY_PATH, I simply put the namd2 command line in a shell
script, with a "export LD_LIBRARY_PATH=libcudartpath" line before it.
While fiddling with the "+devices" directive I have also tried other
combinations including 0,0,0,0, but all of them turned out to be slower
than simply using the CPUs. I'll try the other options and see if they
help, but, it seems the hardware isn't that great...
The good news is that it isn't my machine - I'm visiting another group
which happened to have a desktop with that configuration with virtually no
use. I'm actually deciding which model to buy for my own server, and I'm
quite confused about all those different models. Since you mentioned the
GTX660, how does it compare to the GTX660Ti? Amazon is listing the first
for $194 and the second for $317.
Cheers,
Lucas
2013/8/14 Norman Geist <norman.geist_at_uni-greifswald.de>
> Alright, just wanted to check which libcudart it is using, how do you pass
> the LD_LIBRARY_PATH to namd2, do you use ++runscript? Possibly namd is
> getting the wrong cudart version dynamically linked.
>
> As it seems, namd is unable to list up your devices for some reason, maybe
> because <see above>. But fine if it is running if you pass the device id.
>
> What version of namd are you using? If higher 2.8, try +ignoresharing or
> +devices 0,0,0,0 (number of cpus) for the namd2 command, to try
> oversubscription. Additionally, for all versions, try "twoawayx yes" for
> small boxes and "fullelectfrequency 4" to save pcie communication in
> general
> in your namd config.
>
> But I think you won't get much more performance out of the quadro, as it
> has
> only 96 cuda cores which is quite few compared to 1344 on a GTX660 which is
> only about 200 bucks.
>
> I understand why people buy themselves a nvidia tesla series card, but I
> don't understand why people pay that much money for this quadro rubbish.
> The
> key advantages they have is showing GPU utilization and doing QuadBuffered
> Stereo. Much cheaper a GTX660 f.i. and a passive 3d monitor both together
> for about 500 bucks and much better performance and no need for 140Hz
> monitor that are quite expensive or a quadro card that is about some
> thousands sometimes.
>
> If your machine has one more pcie x16 slot, try to get yourself a geforce
> ;)
>
> Good luck
>
> Norman Geist.
>
> > -----Ursprüngliche Nachricht-----
> > Von: owner-namd-l_at_ks.uiuc.edu [mailto:owner-namd-l_at_ks.uiuc.edu] Im
> > Auftrag von Lucas
> > Gesendet: Donnerstag, 15. August 2013 00:10
> > An: Norman Geist; namd-l_at_ks.uiuc.edu
> > Betreff: Re: namd-l: All CUDA devices are in prohibited mode, of
> > compute capability 1.0, or otherwise unusable.
> >
> > ldd returns:
> > linux-vdso.so.1 => (0x00007fffe39ff000)
> > libpthread.so.0 => /lib64/libpthread.so.0 (0x0000003049200000)
> > libdl.so.2 => /lib64/libdl.so.2 (0x0000003048e00000)
> > libcudart.so.4 => not found
> > libm.so.6 => /lib64/libm.so.6 (0x0000003049600000)
> > libstdc++.so.6 => /usr/lib64/libstdc++.so.6 (0x0000003055a00000)
> > libgcc_s.so.1 => /lib64/libgcc_s.so.1 (0x0000003054a00000)
> > libc.so.6 => /lib64/libc.so.6 (0x0000003048a00000)
> > /lib64/ld-linux-x86-64.so.2 (0x0000003048600000)
> >
> > nvidia-smi –q –g 0 actually returns an error (Invalid combination of
> > input arguments), but I've included the full output from a
> > "nvidia-smi -q" in the end of the e-mail.
> >
> > I was fiddling with the command line options this morning and found
> > out that the program actually runs if I include the +devices directive
> > (I thought that namd would simply assume it would be "+devices all" if
> > that option was not used). What is weird about it is that the
> > benchmark times for four processors and the GPU are actually much
> > slower than simply using the four processors (even if I use a very
> > high value for outputEnergies, such as 500). I know the Quadro 600
> > isn't one of the most powerful cards around, but it still weird to see
> > such performance (about 3days/ns with CPUs only, 3.6 days/ns when
> > using +devices 0).
> >
> > ==========================================
> > Output from nvidia-smi -q:
> >
> > Timestamp : Wed Aug 14 11:20:21 2013
> > Driver Version : 319.37
> >
> > Attached GPUs : 1
> > GPU 0000:01:00.0
> > Product Name : Quadro 600
> > Display Mode : Enabled
> > Display Active : Enabled
> > Persistence Mode : Disabled
> > Accounting Mode : N/A
> > Accounting Mode Buffer Size : N/A
> > Driver Model
> > Current : N/A
> > Pending : N/A
> > Serial Number : N/A
> > GPU UUID : GPU-0fb91d62-ad2d-2b61-a988-
> > 91870abafeb1
> > VBIOS Version : 70.08.88.00.01
> > Inforom Version
> > Image Version : N/A
> > OEM Object : N/A
> > ECC Object : N/A
> > Power Management Object : N/A
> > GPU Operation Mode
> > Current : N/A
> > Pending : N/A
> > PCI
> > Bus : 0x01
> > Device : 0x00
> > Domain : 0x0000
> > Device Id : 0x0DF810DE
> > Bus Id : 0000:01:00.0
> > Sub System Id : 0x083510DE
> > GPU Link Info
> > PCIe Generation
> > Max : 2
> > Current : 1
> > Link Width
> > Max : 16x
> > Current : 16x
> > Fan Speed : 30 %
> > Performance State : P12
> > Clocks Throttle Reasons : N/A
> > Memory Usage
> > Total : 1023 MB
> > Used : 68 MB
> > Free : 955 MB
> > Compute Mode : Default
> > Utilization
> > Gpu : 0 %
> > Memory : 12 %
> > Ecc Mode
> > Current : N/A
> > Pending : N/A
> > ECC Errors
> > Volatile
> > Single Bit
> > Device Memory : N/A
> > Register File : N/A
> > L1 Cache : N/A
> > L2 Cache : N/A
> > Texture Memory : N/A
> > Total : N/A
> > Double Bit
> > Device Memory : N/A
> > Register File : N/A
> > L1 Cache : N/A
> > L2 Cache : N/A
> > Texture Memory : N/A
> > Total : N/A
> > Aggregate
> > Single Bit
> > Device Memory : N/A
> > Register File : N/A
> > L1 Cache : N/A
> > L2 Cache : N/A
> > Texture Memory : N/A
> > Total : N/A
> > Double Bit
> > Device Memory : N/A
> > Register File : N/A
> > L1 Cache : N/A
> > L2 Cache : N/A
> > Texture Memory : N/A
> > Total : N/A
> > Retired Pages
> > Single Bit ECC : N/A
> > Double Bit ECC : N/A
> > Pending : N/A
> > Temperature
> > Gpu : 49 C
> > Power Readings
> > Power Management : N/A
> > Power Draw : N/A
> > Power Limit : N/A
> > Default Power Limit : N/A
> > Enforced Power Limit : N/A
> > Min Power Limit : N/A
> > Max Power Limit : N/A
> > Clocks
> > Graphics : 50 MHz
> > SM : 101 MHz
> > Memory : 135 MHz
> > Applications Clocks
> > Graphics : N/A
> > Memory : N/A
> > Default Applications Clocks
> > Graphics : N/A
> > Memory : N/A
> > Max Clocks
> > Graphics : 641 MHz
> > SM : 1282 MHz
> > Memory : 800 MHz
> > Compute Processes : None
>
>
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