VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Tue May 29 2012 - 11:16:40 CDT

Jim,
  How much memory is VMD using when you run your 45 minute test?
Does the memory use increase as it runs, or is it flat? From my point
of view, the most likely problem scenario would be a slow memory leak or
a bug in the graphics driver. Given that I haven't experienced this myself
and various companies run VMD as a GPU demo under Windows 7 at trade shows
for several days straight, I would be a bit surprised if it is an issue
with VMD itself, but you may have found some new bug that nobody else has
hit yet. If your files are small enough to post for download, I would be
happy to try and reproduce your problem on our Windows test machines here.

Cheers,
  John Stone
  vmd_at_ks.uiuc.edu

On Sat, May 26, 2012 at 04:47:08PM -0400, Jim Kress wrote:
> I invoke VMD 1.9.1 and load a gromacs .xtc trajectory file. Here is the
> cosole output:
>
> Info) VMD for WIN32, version 1.9.1 (February 1, 2012)
> Info) http://www.ks.uiuc.edu/Research/vmd/
> Info) Email questions and bug reports to vmd_at_ks.uiuc.edu
> Info) Please include this reference in published work using VMD:
> Info) Humphrey, W., Dalke, A. and Schulten, K., `VMD - Visual
> Info) Molecular Dynamics', J. Molec. Graphics 1996, 14.1, 33-38.
> Info) -------------------------------------------------------------
> Info) Multithreading available, 12 CPUs detected.
> Info) Free system memory: 4095MB (100%)
> Info) Creating CUDA device pool and initializing hardware...
> Info) Detected 2 available CUDA accelerators:
> Info) [0] GeForce GTX 480 15 SM_2.0 @ 1.45 GHz, 1.5GB RAM, KTO, OIO, ZCP
> Info) [1] Quadro FX 4800 24 SM_1.3 @ 1.20 GHz, 1.5GB RAM, KTO, OIO, ZCP
> Info) OpenGL renderer: Quadro FX 4800/PCIe/SSE2
> Info) Features: STENCIL MDE CVA MTX NPOT PP PS GLSL(OVFG)
> Info) Full GLSL rendering mode is available.
> Info) Textures: 2-D (8192x8192), 3-D (2048x2048x2048), Multitexture (4)
> Info) No joysticks found. Joystick interface disabled.
> Info) Dynamically loaded 69 plugins in directory:
> Info) C:/Program Files (x86)/University of
> Illinois/VMD/plugins/WIN32/molfile
> Info) File loading in progress, please wait.
> Info) Using plugin xtc for coordinates from file
> W:\state\partition1\apps\usr\gr
> omacs_4.5.5\bin\KALP\md_0_1__24_noPBC.xtc
> Info) Finished with coordinate file
> W:\state\partition1\apps\usr\gromacs_4.5.5\b
> in\KALP\md_0_1__24_noPBC.xtc.
> vmd >
>
> I then load the data into the trajectory using the associated .gro file.
> Here is the additionaI console output:
>
> vmd > Info) Using plugin gro for structure file
> W:/state/partition1/apps/usr/gro
> macs_4.5.5/bin/KALP/md_0_1_24.gro
> Info) Using plugin gro for coordinates from file
> W:/state/partition1/apps/usr/gr
> omacs_4.5.5/bin/KALP/md_0_1_24.gro
> Info) Determining bond structure from distance search ...
> Info) Analyzing structure ...
> Info) Atoms: 14017
> Info) Bonds: 11361
> Info) Angles: 0 Dihedrals: 0 Impropers: 0 Cross-terms: 0
> Info) Bondtypes: 0 Angletypes: 0 Dihedraltypes: 0 Impropertypes: 0
> Info) Residues: 2672
> Info) Waters: 2525
> Warning) Unusual bond between residues: 1 (none) and 2 (protein)
> Warning) Unusual bond between residues: 16 (protein) and 17 (none)
> Info) Segments: 1
> Info) Fragments: 2656 Protein: 1 Nucleic: 0
> Info) Finished with coordinate file
> W:/state/partition1/apps/usr/gromacs_4.5.5/b
> in/KALP/md_0_1_24.gro.
>
> I then use graphics > representation and create 4 reps: protein, lipids,
> ions and water. As each is created, I assign them material values, coloring
> methods, drawing methods and a trajectory smoothing size of 10.
>
> I then visualize the trajectory. If I let VMD just sit for the next 45
> minutes or longer, it becomes unresponsive.
>
> I use speedfan to monitor all gpu and cpu temps. None exceed their normal
> values. There is plenty of airflow through the workstation, so overheating
> is not an issue. Testing of the system memory indicates no faults.
>
> Why does VMD suddenly become unresponsive?
>
> I do not have this problem with ANY other applications, even the ones that
> use the gpus.
>
> I have the latest drivers for the video cards.
>
> Here is a summary of the specifications of the workstation:
>
> [System Summary]
>
> Item Value
> OS Name Microsoft Windows 7 Professional
> Version 6.1.7601 Service Pack 1 Build 7601
> Other OS Description Not Available
> OS Manufacturer Microsoft Corporation
> System Name KRESSWORKST7500
> System Manufacturer Dell Inc.
> System Model Precision WorkStation T7500
> System Type x64-based PC
> Processor Intel(R) Xeon(R) CPU X5680 @ 3.33GHz, 3325 Mhz, 6
> Core(s), 12 Logical Processor(s)
> BIOS Version/Date Dell Inc. A11, 7/22/2011
> SMBIOS Version 2.5
> Windows Directory C:\Windows
> System Directory C:\Windows\system32
> Boot Device \Device\HarddiskVolume2
> Locale United States
> Hardware Abstraction Layer Version = "6.1.7601.17514"
> User Name KressWorksT7500\Jim Kress
> Time Zone Eastern Daylight Time
> Installed Physical Memory (RAM) 12.0 GB
> Total Physical Memory 12.0 GB
> Available Physical Memory 7.05 GB
> Total Virtual Memory 24.0 GB
> Available Virtual Memory 18.9 GB
> Page File Space 12.0 GB
> Page File C:\pagefile.sys
>
> [Display]
> Operating System: Windows 7 Professional, 64-bit (Service Pack 1)
> DirectX version: 11.0
> GPU processor: GeForce GTX 480
> Driver version: 301.32
> DirectX support: 11
> CUDA Cores: 480
> Core clock: 725 MHz
> Shader clock: 1451 MHz
> Memory clock: 1900 MHz (3800 MHz data rate)
> Memory interface: 384-bit
> Total available graphics memory: 4094 MB
> Dedicated video memory: 1535 MB GDDR5
> System video memory: 0 MB
> Shared system memory: 2559 MB
> Video BIOS version: 70.00.21.00.82
> IRQ: 24
> Bus: PCI Express x16 Gen2
> GPU processor: Quadro FX 4800
> Driver version: 301.32
> DirectX support: 10
> CUDA Cores: 192
> Core clock: 602 MHz
> Shader clock: 1204 MHz
> Memory clock: 800 MHz (1600 MHz data rate)
> Memory interface: 384-bit
> Total available graphics memory: 5119 MB
> Dedicated video memory: 1536 MB GDDR3
> System video memory: 0 MB
> Shared system memory: 3583 MB
> Video BIOS version: 62.00.70.00.09
> IRQ: 0
> Bus: PCI Express x16 Gen2
>
> Jim
> 

-- 
NIH Resource for Macromolecular Modeling and Bioinformatics
Beckman Institute for Advanced Science and Technology
University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
http://www.ks.uiuc.edu/~johns/           Phone: 217-244-3349
http://www.ks.uiuc.edu/Research/vmd/       Fax: 217-244-6078