VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Thu Jan 21 2016 - 10:12:42 CST

Hi,
  Can you send me a copy of one of the XYZ files that's giving you trouble?

Also, which version of the VMD source code did you compile? I'm assuming
you might have used the VMD 1.9.2 source tarball?
The segmentation fault may indicate one of several potential issues.

What do you get if you set these environment variables prior to running VMD:
csh/tcsh syntax:
  setenv VMDQUICKSURFVERBOSE 1
bourne/bash syntax
  export VMDQUICKSURFVERBOSE=1

Then run VMD:
  vmd somefile.xyz

If you do that, you should get a bunch of diagnostic info when QuickSurf
goes to generate it's 3-D density grid. It may be that your XYZ file
covers a massive volume (e.g. one particle way off in space) and that some
part of the code is missing a safety check.

Cheers,
  John Stone
  vmd_at_ks.uiuc.edu

On Thu, Jan 21, 2016 at 04:45:35PM +0100, Munir Ahmad wrote:
> Dear John,
> Vmd started working but I'm still facing problems with graphics. WhenA I
> perform following steps
> 1. vmd [1]somefile.xyz
>
> Info) Multithreading available, 8 CPUs detected.
> Info) Free system memory: 31007MB (96%)
> Info) Creating CUDA device pool and initializing hardware...
> Info) Detected 1 available CUDA accelerator:
> Info) [0] Quadro K6000A A A A A A 15 SM_3.5 @ 0.90 GHz, 11GB RAM, KTO,
> AE2, ZCP
> Info) OpenGL renderer: Quadro K6000/PCIe/SSE2
> Info)A A Features: STENCIL MSAA(4) MDE CVA MTX NPOT PP PS GLSL(OVFGS)
> Info)A A Full GLSL rendering mode is available.
> Info)A A Textures: 2-D (16384x16384), 3-D (4096x4096x4096), Multitexture
> (4)
>
> Everything is fine till here but when I go
> Graphics --> Representations --> Drawing Method = QuickSurf
> it shows
> vmd > Segmentation fault (core dumped)
> Can you please help me to fix it?
> Best Regards:
> Munir
>
> On Fri, Jan 15, 2016 at 7:04 PM, Munir Ahmad <[2]lathmun_at_gmail.com> wrote:
>
> Dear John,
> Thank you very much :). I removed MESA and now it's working.A
> Munir
> On Thu, Jan 14, 2016 at 10:50 PM, John Stone <[3]johns_at_ks.uiuc.edu>
> wrote:
>
> Hi,
> A Delete "MESA" from your configuration, and start over, and
> hopefully
> that will eliminate the major issues you listed below.
>
> Cheers,
> A John Stone
> A [4]vmd_at_ks.uiuc.edu
> On Thu, Jan 14, 2016 at 10:40:53PM +0100, Munir Ahmad wrote:
> >A A Hi,
> >A A I'm trying to compile VMD from source with following options:
> >
> >A A LINUXAMD64 OPENGL MESA FLTK TK CUDA VRPN TCL PTHREADS
> >
> >A A A Compilation ends with a simple error without any details.
> Here is the
> >A A log
> >
> >A A LinkingAA vmd_LINUXAMD64 ...
> >
> >A A OpenGLDisplayDevice.o: In function
> >A A `OpenGLDisplayDevice::~OpenGLDisplayDevice()':
> >
> >A A OpenGLDisplayDevice.C:(.text+0x0): multiple definition of
> >A A `OpenGLDisplayDevice::~OpenGLDisplayDevice()'
> >
> >A A OpenGLDisplayDevice.o:OpenGLDisplayDevice.C:(.text+0x0): first
> defined
> >A A here
> >
> >A A OpenGLDisplayDevice.o: In function
> >A A `OpenGLDisplayDevice::~OpenGLDisplayDevice()':
> >
> >A A OpenGLDisplayDevice.C:(.text+0x0): multiple definition of
> >A A `OpenGLDisplayDevice::~OpenGLDisplayDevice()'
> >
> >A A OpenGLDisplayDevice.o:OpenGLDisplayDevice.C:(.text+0x0): first
> defined
> >A A here
> >
> >A A OpenGLDisplayDevice.o: In function
> `OpenGLDisplayDevice::queue_events()':
> >
> >A A OpenGLDisplayDevice.C:(.text+0xa0): multiple definition of
> >A A `OpenGLDisplayDevice::queue_events()'
> >
> >A A OpenGLDisplayDevice.o:OpenGLDisplayDevice.C:(.text+0xa0): first
> defined
> >A A here
> >
> >A A OpenGLDisplayDevice.o: In function
> >A A `OpenGLDisplayDevice::do_reposition_window(int, int)':
> >
> >A A OpenGLDisplayDevice.C:(.text+0x340): multiple definition of
> >A A `OpenGLDisplayDevice::do_reposition_window(int, int)'
> >
> >A A OpenGLDisplayDevice.o:OpenGLDisplayDevice.C:(.text+0x340):
> first defined
> >A A here
> >
> >A A OpenGLDisplayDevice.o: In function `OpenGLDisplayDevice::x()':
> >
> >A A OpenGLDisplayDevice.C:(.text+0x360): multiple definition of
> >A A `OpenGLDisplayDevice::x()'
> >
> >A A OpenGLDisplayDevice.o:OpenGLDisplayDevice.C:(.text+0x360):
> first defined
> >A A here
> >
> >A A OpenGLDisplayDevice.o: In function `OpenGLDisplayDevice::y()':
> >
> >A A OpenGLDisplayDevice.C:(.text+0x3c0): multiple definition of
> >A A `OpenGLDisplayDevice::y()'
> >
> >A A OpenGLDisplayDevice.o:OpenGLDisplayDevice.C:(.text+0x3c0):
> first defined
> >A A here
> >
> >A A OpenGLDisplayDevice.o: In function
> `OpenGLDisplayDevice::shift_state()':
> >
> >A A OpenGLDisplayDevice.C:(.text+0x420): multiple definition of
> >A A `OpenGLDisplayDevice::shift_state()'
> >
> >A A OpenGLDisplayDevice.o:OpenGLDisplayDevice.C:(.text+0x420):
> first defined
> >A A here
> >
> >A A OpenGLDisplayDevice.o: In function
> `OpenGLDisplayDevice::set_cursor(int)':
> >
> >A A OpenGLDisplayDevice.C:(.text+0x4a0): multiple definition of
> >A A `OpenGLDisplayDevice::set_cursor(int)'
> >
> >A A OpenGLDisplayDevice.o:OpenGLDisplayDevice.C:(.text+0x4a0):
> first defined
> >A A here
> >
> >A A OpenGLDisplayDevice.o: In function
> `OpenGLDisplayDevice::reshape()':
> >
> >A A OpenGLDisplayDevice.C:(.text+0x4d0): multiple definition of
> >A A `OpenGLDisplayDevice::reshape()'
> >
> >A A OpenGLDisplayDevice.o:OpenGLDisplayDevice.C:(.text+0x4d0):
> first defined
> >A A here
> >
> >A A OpenGLDisplayDevice.o: In function
> `OpenGLDisplayDevice::readpixels(int&,
> >A A int&)':
> >
> >A A OpenGLDisplayDevice.C:(.text+0x620): multiple definition of
> >A A `OpenGLDisplayDevice::readpixels(int&, int&)'
> >
> >A A OpenGLDisplayDevice.o:OpenGLDisplayDevice.C:(.text+0x620):
> first defined
> >A A here
> >
> >A A OpenGLDisplayDevice.o: In function
> `OpenGLDisplayDevice::update(int)':
> >
> >A A OpenGLDisplayDevice.C:(.text+0x6b0): multiple definition of
> >A A `OpenGLDisplayDevice::update(int)'
> >
> >A A OpenGLDisplayDevice.o:OpenGLDisplayDevice.C:(.text+0x6b0):
> first defined
> >A A here
> >
> >A A OpenGLDisplayDevice.o: In function
> `OpenGLDisplayDevice::spaceball(int*,
> >A A int*, int*, int*, int*, int*, int*)':
> >
> >A A OpenGLDisplayDevice.C:(.text+0x700): multiple definition of
> >A A `OpenGLDisplayDevice::spaceball(int*, int*, int*, int*, int*,
> int*, int*)'
> >
> >A A OpenGLDisplayDevice.o:OpenGLDisplayDevice.C:(.text+0x700):
> first defined
> >A A here
> >
> >A A OpenGLDisplayDevice.o: In function
> `OpenGLDisplayDevice::read_event(long&,
> >A A long&)':
> >
> >A A OpenGLDisplayDevice.C:(.text+0x780): multiple definition of
> >A A `OpenGLDisplayDevice::read_event(long&, long&)'
> >
> >A A OpenGLDisplayDevice.o:OpenGLDisplayDevice.C:(.text+0x780):
> first defined
> >A A here
> >
> >A A OpenGLDisplayDevice.o: In function
> >A A `OpenGLDisplayDevice::do_resize_window(int, int)':
> >
> >A A OpenGLDisplayDevice.C:(.text+0xbb0): multiple definition of
> >A A `OpenGLDisplayDevice::do_resize_window(int, int)'
> >
> >A A OpenGLDisplayDevice.o:OpenGLDisplayDevice.C:(.text+0xbb0):
> first defined
> >A A here
> >
> >A A OpenGLDisplayDevice.o: In function
> >A A `OpenGLDisplayDevice::~OpenGLDisplayDevice()':
> >
> >A A OpenGLDisplayDevice.C:(.text+0xd80): multiple definition of
> >A A `OpenGLDisplayDevice::~OpenGLDisplayDevice()'
> >
> >A A OpenGLDisplayDevice.o:OpenGLDisplayDevice.C:(.text+0xd80):
> first defined
> >A A here
> >
> >A A OpenGLDisplayDevice.o: In function
> >A A `OpenGLDisplayDevice::OpenGLDisplayDevice()':
> >
> >A A OpenGLDisplayDevice.C:(.text+0xe30): multiple definition of
> >A A `OpenGLDisplayDevice::OpenGLDisplayDevice()'
> >
> >A A OpenGLDisplayDevice.o:OpenGLDisplayDevice.C:(.text+0xe30):
> first defined
> >A A here
> >
> >A A OpenGLDisplayDevice.o: In function
> >A A `OpenGLDisplayDevice::OpenGLDisplayDevice()':
> >
> >A A OpenGLDisplayDevice.C:(.text+0xe30): multiple definition of
> >A A `OpenGLDisplayDevice::OpenGLDisplayDevice()'
> >
> >A A OpenGLDisplayDevice.o:OpenGLDisplayDevice.C:(.text+0xe30):
> first defined
> >A A here
> >
> >A A OpenGLDisplayDevice.o: In function
> >A A `OpenGLDisplayDevice::open_window(char*, int*, int*, int,
> char**)':
> >
> >A A OpenGLDisplayDevice.C:(.text+0xf90): multiple definition of
> >A A `OpenGLDisplayDevice::open_window(char*, int*, int*, int,
> char**)'
> >
> >A A OpenGLDisplayDevice.o:OpenGLDisplayDevice.C:(.text+0xf90):
> first defined
> >A A here
> >
> >A A OpenGLDisplayDevice.o: In function
> `OpenGLDisplayDevice::init(int, char**,
> >A A VMDApp*, int*, int*)':
> >
> >A A OpenGLDisplayDevice.C:(.text+0x1fc0): multiple definition of
> >A A `OpenGLDisplayDevice::init(int, char**, VMDApp*, int*, int*)'
> >
> >A A OpenGLDisplayDevice.o:OpenGLDisplayDevice.C:(.text+0x1fc0):
> first defined
> >A A here
> >
> >A A OpenGLDisplayDevice.o: In function
> `OpenGLDisplayDevice::prepare3D(int)':
> >
> >A A OpenGLDisplayDevice.C:(.text+0x20d0): multiple definition of
> >A A `OpenGLDisplayDevice::prepare3D(int)'
> >
> >A A OpenGLDisplayDevice.o:OpenGLDisplayDevice.C:(.text+0x20d0):
> first defined
> >A A here
> >
> >A A Stride.o: In function `ss_from_stride(DrawMolecule*)':
> >
> >A A Stride.C:(.text+0x52): warning: the use of `tempnam' is
> dangerous, better
> >A A use `mkstemp'
> >
> >A A collect2: error: ld returned 1 exit status
> >
> >A A make: *** [vmd_LINUXAMD64] Error 1
> >
> >A A Any help would be highly appreciated.
> >
> >A A Munir
>
> --
> NIH Center for Macromolecular Modeling and Bioinformatics
> Beckman Institute for Advanced Science and Technology
> University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
> [5]http://www.ks.uiuc.edu/~johns/A A A A A A Phone: 217-244-3349
> [6]http://www.ks.uiuc.edu/Research/vmd/
>
> References
>
> Visible links
> 1. http://somefile.xyz/
> 2. mailto:lathmun_at_gmail.com
> 3. mailto:johns_at_ks.uiuc.edu
> 4. mailto:vmd_at_ks.uiuc.edu
> 5. http://www.ks.uiuc.edu/~johns/
> 6. http://www.ks.uiuc.edu/Research/vmd/ 

-- 
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/