VMD-L Mailing List

From: Munir Ahmad (lathmun_at_gmail.com)
Date: Thu Jan 21 2016 - 09:45:35 CST

Dear John,
Vmd started working but I'm still facing problems with graphics. When I
perform following steps
1. vmd 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 K6000 15 SM_3.5 @ 0.90 GHz, 11GB RAM, KTO, AE2, ZCP
Info) OpenGL renderer: Quadro K6000/PCIe/SSE2
Info) Features: STENCIL MSAA(4) MDE CVA MTX NPOT PP PS GLSL(OVFGS)
Info) Full GLSL rendering mode is available.
Info) 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 <lathmun_at_gmail.com> wrote:

> Dear John,
> Thank you very much :). I removed MESA and now it's working.
> Munir
>
> On Thu, Jan 14, 2016 at 10:50 PM, John Stone <johns_at_ks.uiuc.edu> wrote:
>
>> Hi,
>> Delete "MESA" from your configuration, and start over, and hopefully
>> that will eliminate the major issues you listed below.
>>
>> Cheers,
>> John Stone
>> vmd_at_ks.uiuc.edu
>>
>> On Thu, Jan 14, 2016 at 10:40:53PM +0100, Munir Ahmad wrote:
>> > Hi,
>> > I'm trying to compile VMD from source with following options:
>> >
>> > LINUXAMD64 OPENGL MESA FLTK TK CUDA VRPN TCL PTHREADS
>> >
>> > A Compilation ends with a simple error without any details. Here is
>> the
>> > log
>> >
>> > LinkingA vmd_LINUXAMD64 ...
>> >
>> > OpenGLDisplayDevice.o: In function
>> > `OpenGLDisplayDevice::~OpenGLDisplayDevice()':
>> >
>> > OpenGLDisplayDevice.C:(.text+0x0): multiple definition of
>> > `OpenGLDisplayDevice::~OpenGLDisplayDevice()'
>> >
>> > OpenGLDisplayDevice.o:OpenGLDisplayDevice.C:(.text+0x0): first
>> defined
>> > here
>> >
>> > OpenGLDisplayDevice.o: In function
>> > `OpenGLDisplayDevice::~OpenGLDisplayDevice()':
>> >
>> > OpenGLDisplayDevice.C:(.text+0x0): multiple definition of
>> > `OpenGLDisplayDevice::~OpenGLDisplayDevice()'
>> >
>> > OpenGLDisplayDevice.o:OpenGLDisplayDevice.C:(.text+0x0): first
>> defined
>> > here
>> >
>> > OpenGLDisplayDevice.o: In function
>> `OpenGLDisplayDevice::queue_events()':
>> >
>> > OpenGLDisplayDevice.C:(.text+0xa0): multiple definition of
>> > `OpenGLDisplayDevice::queue_events()'
>> >
>> > OpenGLDisplayDevice.o:OpenGLDisplayDevice.C:(.text+0xa0): first
>> defined
>> > here
>> >
>> > OpenGLDisplayDevice.o: In function
>> > `OpenGLDisplayDevice::do_reposition_window(int, int)':
>> >
>> > OpenGLDisplayDevice.C:(.text+0x340): multiple definition of
>> > `OpenGLDisplayDevice::do_reposition_window(int, int)'
>> >
>> > OpenGLDisplayDevice.o:OpenGLDisplayDevice.C:(.text+0x340): first
>> defined
>> > here
>> >
>> > OpenGLDisplayDevice.o: In function `OpenGLDisplayDevice::x()':
>> >
>> > OpenGLDisplayDevice.C:(.text+0x360): multiple definition of
>> > `OpenGLDisplayDevice::x()'
>> >
>> > OpenGLDisplayDevice.o:OpenGLDisplayDevice.C:(.text+0x360): first
>> defined
>> > here
>> >
>> > OpenGLDisplayDevice.o: In function `OpenGLDisplayDevice::y()':
>> >
>> > OpenGLDisplayDevice.C:(.text+0x3c0): multiple definition of
>> > `OpenGLDisplayDevice::y()'
>> >
>> > OpenGLDisplayDevice.o:OpenGLDisplayDevice.C:(.text+0x3c0): first
>> defined
>> > here
>> >
>> > OpenGLDisplayDevice.o: In function
>> `OpenGLDisplayDevice::shift_state()':
>> >
>> > OpenGLDisplayDevice.C:(.text+0x420): multiple definition of
>> > `OpenGLDisplayDevice::shift_state()'
>> >
>> > OpenGLDisplayDevice.o:OpenGLDisplayDevice.C:(.text+0x420): first
>> defined
>> > here
>> >
>> > OpenGLDisplayDevice.o: In function
>> `OpenGLDisplayDevice::set_cursor(int)':
>> >
>> > OpenGLDisplayDevice.C:(.text+0x4a0): multiple definition of
>> > `OpenGLDisplayDevice::set_cursor(int)'
>> >
>> > OpenGLDisplayDevice.o:OpenGLDisplayDevice.C:(.text+0x4a0): first
>> defined
>> > here
>> >
>> > OpenGLDisplayDevice.o: In function `OpenGLDisplayDevice::reshape()':
>> >
>> > OpenGLDisplayDevice.C:(.text+0x4d0): multiple definition of
>> > `OpenGLDisplayDevice::reshape()'
>> >
>> > OpenGLDisplayDevice.o:OpenGLDisplayDevice.C:(.text+0x4d0): first
>> defined
>> > here
>> >
>> > OpenGLDisplayDevice.o: In function
>> `OpenGLDisplayDevice::readpixels(int&,
>> > int&)':
>> >
>> > OpenGLDisplayDevice.C:(.text+0x620): multiple definition of
>> > `OpenGLDisplayDevice::readpixels(int&, int&)'
>> >
>> > OpenGLDisplayDevice.o:OpenGLDisplayDevice.C:(.text+0x620): first
>> defined
>> > here
>> >
>> > OpenGLDisplayDevice.o: In function
>> `OpenGLDisplayDevice::update(int)':
>> >
>> > OpenGLDisplayDevice.C:(.text+0x6b0): multiple definition of
>> > `OpenGLDisplayDevice::update(int)'
>> >
>> > OpenGLDisplayDevice.o:OpenGLDisplayDevice.C:(.text+0x6b0): first
>> defined
>> > here
>> >
>> > OpenGLDisplayDevice.o: In function
>> `OpenGLDisplayDevice::spaceball(int*,
>> > int*, int*, int*, int*, int*, int*)':
>> >
>> > OpenGLDisplayDevice.C:(.text+0x700): multiple definition of
>> > `OpenGLDisplayDevice::spaceball(int*, int*, int*, int*, int*, int*,
>> int*)'
>> >
>> > OpenGLDisplayDevice.o:OpenGLDisplayDevice.C:(.text+0x700): first
>> defined
>> > here
>> >
>> > OpenGLDisplayDevice.o: In function
>> `OpenGLDisplayDevice::read_event(long&,
>> > long&)':
>> >
>> > OpenGLDisplayDevice.C:(.text+0x780): multiple definition of
>> > `OpenGLDisplayDevice::read_event(long&, long&)'
>> >
>> > OpenGLDisplayDevice.o:OpenGLDisplayDevice.C:(.text+0x780): first
>> defined
>> > here
>> >
>> > OpenGLDisplayDevice.o: In function
>> > `OpenGLDisplayDevice::do_resize_window(int, int)':
>> >
>> > OpenGLDisplayDevice.C:(.text+0xbb0): multiple definition of
>> > `OpenGLDisplayDevice::do_resize_window(int, int)'
>> >
>> > OpenGLDisplayDevice.o:OpenGLDisplayDevice.C:(.text+0xbb0): first
>> defined
>> > here
>> >
>> > OpenGLDisplayDevice.o: In function
>> > `OpenGLDisplayDevice::~OpenGLDisplayDevice()':
>> >
>> > OpenGLDisplayDevice.C:(.text+0xd80): multiple definition of
>> > `OpenGLDisplayDevice::~OpenGLDisplayDevice()'
>> >
>> > OpenGLDisplayDevice.o:OpenGLDisplayDevice.C:(.text+0xd80): first
>> defined
>> > here
>> >
>> > OpenGLDisplayDevice.o: In function
>> > `OpenGLDisplayDevice::OpenGLDisplayDevice()':
>> >
>> > OpenGLDisplayDevice.C:(.text+0xe30): multiple definition of
>> > `OpenGLDisplayDevice::OpenGLDisplayDevice()'
>> >
>> > OpenGLDisplayDevice.o:OpenGLDisplayDevice.C:(.text+0xe30): first
>> defined
>> > here
>> >
>> > OpenGLDisplayDevice.o: In function
>> > `OpenGLDisplayDevice::OpenGLDisplayDevice()':
>> >
>> > OpenGLDisplayDevice.C:(.text+0xe30): multiple definition of
>> > `OpenGLDisplayDevice::OpenGLDisplayDevice()'
>> >
>> > OpenGLDisplayDevice.o:OpenGLDisplayDevice.C:(.text+0xe30): first
>> defined
>> > here
>> >
>> > OpenGLDisplayDevice.o: In function
>> > `OpenGLDisplayDevice::open_window(char*, int*, int*, int, char**)':
>> >
>> > OpenGLDisplayDevice.C:(.text+0xf90): multiple definition of
>> > `OpenGLDisplayDevice::open_window(char*, int*, int*, int, char**)'
>> >
>> > OpenGLDisplayDevice.o:OpenGLDisplayDevice.C:(.text+0xf90): first
>> defined
>> > here
>> >
>> > OpenGLDisplayDevice.o: In function `OpenGLDisplayDevice::init(int,
>> char**,
>> > VMDApp*, int*, int*)':
>> >
>> > OpenGLDisplayDevice.C:(.text+0x1fc0): multiple definition of
>> > `OpenGLDisplayDevice::init(int, char**, VMDApp*, int*, int*)'
>> >
>> > OpenGLDisplayDevice.o:OpenGLDisplayDevice.C:(.text+0x1fc0): first
>> defined
>> > here
>> >
>> > OpenGLDisplayDevice.o: In function
>> `OpenGLDisplayDevice::prepare3D(int)':
>> >
>> > OpenGLDisplayDevice.C:(.text+0x20d0): multiple definition of
>> > `OpenGLDisplayDevice::prepare3D(int)'
>> >
>> > OpenGLDisplayDevice.o:OpenGLDisplayDevice.C:(.text+0x20d0): first
>> defined
>> > here
>> >
>> > Stride.o: In function `ss_from_stride(DrawMolecule*)':
>> >
>> > Stride.C:(.text+0x52): warning: the use of `tempnam' is dangerous,
>> better
>> > use `mkstemp'
>> >
>> > collect2: error: ld returned 1 exit status
>> >
>> > make: *** [vmd_LINUXAMD64] Error 1
>> >
>> > Any help would be highly appreciated.
>> >
>> > 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
>> http://www.ks.uiuc.edu/~johns/ Phone: 217-244-3349
>> http://www.ks.uiuc.edu/Research/vmd/
>>
>
>