VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Tue May 28 2013 - 09:36:26 CDT

Hi,
  There was a bug in the previous revs of VMD that prevented loading
huge density maps, but this problem has been fixed in the test version
of VMD 1.9.2. You can get a test build of VMD 1.9.2 by following the
instructions here:
  http://www.ks.uiuc.edu/Research/vmd/alpha/

Let us know if you need help getting the new test version up and running.

Cheers,
  John Stone
  vmd_at_ks.uiuc.edu

On Sat, May 25, 2013 at 04:38:14PM +0000, VandeVondele Joost wrote:
> Loading a large cube file (Grid size: 900x900x900 (11123 MB)) leads to a crash of VMD (1.9) with the error message:
>
> Info) Computing volume gradient map for smooth shading
> terminate called after throwing an instance of 'std::bad_alloc'
> what(): std::bad_alloc
> Abort
>
> The machine has plenty of free memory (Free system memory: 113902MB), and this is the AMD64 VMD binary, so I suspect this is triggered by some intermediate 32bit integer overflow.
>
> To facilitate reproducing this error, I have added a little script that generates a cube file of the proper size. The crash does happen with 900 points but not with 720 points per direction. Unfortunately it takes a while to read/write these cubes.
>
> ==== Error output =====
> > vmd test_900.cube
> Info) VMD for LINUXAMD64, version 1.9 (March 14, 2011)
> 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, 32 CPUs detected.
> Info) Free system memory: 113902MB (88%)
> Info) No CUDA accelerator devices available.
> Warning) Detected X11 'Composite' extension: if incorrect display occurs
> Warning) try disabling this optional X server feature.
> Info) OpenGL renderer: GeForce GTX 460/PCIe/SSE2
> Info) Features: STENCIL MSAA(16) MDE MTX NPOT PP PS
> Info) GLSL rendering mode is NOT available.
> Info) Textures: 2-D (16384x16384), 3-D (2048x2048x2048), Multitexture (4)
> Info) Dynamically loaded 2 plugins in directory:
> Info) /usr/local/lib/vmd/plugins/LINUXAMD64/molfile
> Info) File loading in progress, please wait.
> Info) Using plugin cube for structure file test_900.cube
> cubeplugin) trying to read cube data set 0
> Info) Analyzing Volume...
> Info) Grid size: 900x900x900 (11123 MB)
> Info) Total voxels: 729000000
> Info) Min: -0.800000 Max: 1.200000 Range: 2.000000
> Info) Computing volume gradient map for smooth shading
> terminate called after throwing an instance of 'std::bad_alloc'
> what(): std::bad_alloc
> Abort
>
>
> ==== Bash script to generate cube ====
> # run as ./do_generate_cube > test_900.cube
> # number of points (input multiplied by 6 for easier writing)
> # input=150 triggers a crash, 120 not yet
> input=150
> n_points=$((input*6))
> printf "%s\n" "Test with $n_points points in each direction"
> printf "%s\n" "VMD crash test"
> printf "%5d%12.6f%12.6f%12.6f\n" 8 0 0 0
> printf "%5d%12.6f%12.6f%12.6f\n" $n_points 0.1 0 0
> printf "%5d%12.6f%12.6f%12.6f\n" $n_points 0.0 0.1 0
> printf "%5d%12.6f%12.6f%12.6f\n" $n_points 0.0 0.0 0.1
> for i in 0 1 ; do
> for j in 0 1 ; do
> for k in 0 1 ; do
> x=$((i*n_points/10))
> y=$((j*n_points/10))
> z=$((k*n_points/10))
> printf "%5d%12.6f%12.6f%12.6f%12.6f\n" 2 0 $x $y $z
> done
> done
> done
> echo "go" | \
> awk -v n=$n_points '{ \
> for(i=1;i<=n;i++) { for(j=1;j<=n;j++) {for(k=1;k<=n;k++){ \
> printf("%13.5e",0.2+cos(i*12.566368/n)*cos(j*12.566368/n)*cos(k*12.566368/n));if(k%6==0)printf("\n") \
> }}}}' 

-- 
NIH Center 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/