VMD-L Mailing List

From: Stefano Guglielmo (stefano.guglielmo_at_unito.it)
Date: Tue Jul 05 2016 - 13:19:24 CDT

Dear John,
thanks for your reply. After some struggling and a load of help by a
collegue I managed to compile vmd. Actually selecting gnu compiler instead
of intel compiler seemed to fix the problem. For sure there must be a
cleaner way out, but that's it.
Thanks again
Stefano

Il martedì 28 giugno 2016, John Stone <johns_at_ks.uiuc.edu> ha scritto:

> Hi,
> What options did you have in config.options when you started compilation
> of VMD? The error messages you posted appear to indicate some kind of
> inconsistency in the configuration of the VMD build, aside from whatever
> symbols may also be missing at link time. Without more information about
> what exactly you tried it is not possible to give concrete suggestions.
>
> Cheers,
> John Stone
> vmd_at_ks.uiuc.edu <javascript:;>
>
> On Fri, Jun 24, 2016 at 10:16:22AM +0200, Stefano Guglielmo wrote:
> > In the previous post I forgot to write that I edited the makefile for
> > header files, libraries and library directories and checked several
> times
> > all the paths that should be correct.
> > Thanks again
> > Stefano
> >
> > ---------- Forwarded message ----------
> > From: Stefano Guglielmo <[1]stefano.guglielmo_at_unito.it <javascript:;>
> >
> > Date: 2016-06-23 14:08 GMT+02:00
> > Subject: troubles with openGL
> > To: [2]vmd-l_at_ks.uiuc.edu <javascript:;>
> >
> > Dear all,
> >
> > I am compiling VMD on a centOS 7 workstation; I installed several
> > dependencies among which openGL libraries
> > (mesa-libGL-10.6.5-3.20150824.el7.x86_64 and
> > mesa-libGL-devel-10.6.5-3.20150824.el7.x86_64), but, eventhough I
> linked
> > them in the makefile, compilation stops with a number of undefined
> > reference issues referring to openGLDisplayDevice.o; I also tried to
> use
> > updated header files from [3]https://www.opengl.org/registry/ as
> suggested
> > in vmd compiling instructions, but the result was exactly the same.
> >
> > Any suggestions or workaround?
> >
> > Below is the output of make ("riferimento non definito" is undefined
> > reference, just in case...):
> >
> > OpenGLDisplayDevice.o: nella funzione
> > "OpenGLDisplayDevice::~OpenGLDisplayDevice()":
> > OpenGLDisplayDevice.C:(.text+0x2f): riferimento non definito a
> > "OpenGLRenderer::free_opengl_ctx()"
> > OpenGLDisplayDevice.C:(.text+0x8d): riferimento non definito a
> > "OpenGLRenderer::~OpenGLRenderer()"
> > OpenGLDisplayDevice.o: nella funzione
> > "OpenGLDisplayDevice::~OpenGLDisplayDevice()":
> > OpenGLDisplayDevice.C:(.text+0xd4f): riferimento non definito a
> > "OpenGLRenderer::free_opengl_ctx()"
> > OpenGLDisplayDevice.C:(.text+0xd9c): riferimento non definito a
> > "OpenGLRenderer::~OpenGLRenderer()"
> > OpenGLDisplayDevice.C:(.text+0xdb5): riferimento non definito a
> > "OpenGLRenderer::~OpenGLRenderer()"
> > OpenGLDisplayDevice.o: nella funzione
> > "OpenGLDisplayDevice::OpenGLDisplayDevice()":
> > OpenGLDisplayDevice.C:(.text+0xdda): riferimento non definito a
> > "OpenGLRenderer::OpenGLRenderer(char const*)"
> > OpenGLDisplayDevice.o: nella funzione
> > "OpenGLDisplayDevice::open_window(char*, int*, int*, int, char**)":
> > OpenGLDisplayDevice.C:(.text+0x175b): riferimento non definito a
> > "OpenGLRenderer::setup_initial_opengl_state()"
> > OpenGLDisplayDevice.C:(.text+0x1df6): riferimento non definito a
> > "OpenGLExtensions::vmdQueryExtension(char const*)"
> > OpenGLDisplayDevice.o: nella funzione "OpenGLDisplayDevice::init(int,
> > char**, VMDApp*, int*, int*)":
> > OpenGLDisplayDevice.C:(.text+0x1fe4): riferimento non definito a
> > "OpenGLRenderer::set_sphere_mode(int)"
> > OpenGLDisplayDevice.C:(.text+0x1ff2): riferimento non definito a
> > "OpenGLRenderer::set_sphere_res(int)"
> > OpenGLDisplayDevice.C:(.text+0x2000): riferimento non definito a
> > "OpenGLRenderer::set_line_width(int)"
> > OpenGLDisplayDevice.C:(.text+0x200e): riferimento non definito a
> > "OpenGLRenderer::set_line_style(int)"
> > OpenGLDisplayDevice.o: nella funzione
> > "OpenGLDisplayDevice::~OpenGLDisplayDevice()":
> > OpenGLDisplayDevice.C:(.text+0x82): riferimento non definito a
> > "OpenGLRenderer::~OpenGLRenderer()"
> > OpenGLDisplayDevice.o: nella funzione
> > "OpenGLDisplayDevice::prepare3D(int)":
> > OpenGLDisplayDevice.C:(.text+0x20a1): riferimento non definito a
> > "OpenGLRenderer::prepare3D(int)"
> >
> OpenGLDisplayDevice.o:(.rodata._ZTI19OpenGLDisplayDevice[_ZTI19OpenGLDisplayDevice]+0x10):
> > riferimento non definito a "typeinfo for OpenGLRenderer"
> >
> OpenGLDisplayDevice.o:(.rodata._ZTV19OpenGLDisplayDevice[_ZTV19OpenGLDisplayDevice]+0x28):
> > riferimento non definito a "OpenGLRenderer::do_define_light(int,
> float*,
> > float*)"
> >
> OpenGLDisplayDevice.o:(.rodata._ZTV19OpenGLDisplayDevice[_ZTV19OpenGLDisplayDevice]+0x30):
> > riferimento non definito a "OpenGLRenderer::do_activate_light(int,
> int)"
> >
> OpenGLDisplayDevice.o:(.rodata._ZTV19OpenGLDisplayDevice[_ZTV19OpenGLDisplayDevice]+0xa0):
> > riferimento non definito a "OpenGLRenderer::cueing_on()"
> >
> OpenGLDisplayDevice.o:(.rodata._ZTV19OpenGLDisplayDevice[_ZTV19OpenGLDisplayDevice]+0xa8):
> > riferimento non definito a "OpenGLRenderer::cueing_off()"
> >
> OpenGLDisplayDevice.o:(.rodata._ZTV19OpenGLDisplayDevice[_ZTV19OpenGLDisplayDevice]+0xb0):
> > riferimento non definito a "OpenGLRenderer::aa_on()"
> >
> OpenGLDisplayDevice.o:(.rodata._ZTV19OpenGLDisplayDevice[_ZTV19OpenGLDisplayDevice]+0xb8):
> > riferimento non definito a "OpenGLRenderer::aa_off()"
> >
> OpenGLDisplayDevice.o:(.rodata._ZTV19OpenGLDisplayDevice[_ZTV19OpenGLDisplayDevice]+0xc0):
> > riferimento non definito a "OpenGLRenderer::culling_on()"
> >
> OpenGLDisplayDevice.o:(.rodata._ZTV19OpenGLDisplayDevice[_ZTV19OpenGLDisplayDevice]+0xc8):
> > riferimento non definito a "OpenGLRenderer::culling_off()"
> >
> OpenGLDisplayDevice.o:(.rodata._ZTV19OpenGLDisplayDevice[_ZTV19OpenGLDisplayDevice]+0xd0):
> > riferimento non definito a "OpenGLRenderer::set_stereo_mode(int)"
> >
> OpenGLDisplayDevice.o:(.rodata._ZTV19OpenGLDisplayDevice[_ZTV19OpenGLDisplayDevice]+0xe0):
> > riferimento non definito a "OpenGLRenderer::set_cache_mode(int)"
> >
> OpenGLDisplayDevice.o:(.rodata._ZTV19OpenGLDisplayDevice[_ZTV19OpenGLDisplayDevice]+0xe8):
> > riferimento non definito a "OpenGLRenderer::set_render_mode(int)"
> >
> OpenGLDisplayDevice.o:(.rodata._ZTV19OpenGLDisplayDevice[_ZTV19OpenGLDisplayDevice]+0xf0):
> > riferimento non definito a "OpenGLRenderer::abs_screen_loc_3D(float*,
> > float*)"
> >
> OpenGLDisplayDevice.o:(.rodata._ZTV19OpenGLDisplayDevice[_ZTV19OpenGLDisplayDevice]+0xf8):
> > riferimento non definito a "OpenGLRenderer::abs_screen_loc_2D(float*,
> > float*)"
> >
> OpenGLDisplayDevice.o:(.rodata._ZTV19OpenGLDisplayDevice[_ZTV19OpenGLDisplayDevice]+0x108):
> > riferimento non definito a "OpenGLRenderer::find_3D_from_2D(float
> const*,
> > float const*, float*)"
> >
> OpenGLDisplayDevice.o:(.rodata._ZTV19OpenGLDisplayDevice[_ZTV19OpenGLDisplayDevice]+0x110):
> > riferimento non definito a "OpenGLRenderer::loadmatrix(Matrix4
> const&)"
> >
> OpenGLDisplayDevice.o:(.rodata._ZTV19OpenGLDisplayDevice[_ZTV19OpenGLDisplayDevice]+0x118):
> > riferimento non definito a "OpenGLRenderer::multmatrix(Matrix4
> const&)"
> >
> OpenGLDisplayDevice.o:(.rodata._ZTV19OpenGLDisplayDevice[_ZTV19OpenGLDisplayDevice]+0x120):
> > riferimento non definito a "OpenGLRenderer::set_background(float
> const*)"
> >
> OpenGLDisplayDevice.o:(.rodata._ZTV19OpenGLDisplayDevice[_ZTV19OpenGLDisplayDevice]+0x128):
> > riferimento non definito a "OpenGLRenderer::set_backgradient(float
> const*,
> > float const*)"
> >
> OpenGLDisplayDevice.o:(.rodata._ZTV19OpenGLDisplayDevice[_ZTV19OpenGLDisplayDevice]+0x138):
> > riferimento non definito a "OpenGLRenderer::prepareOpaque()"
> >
> OpenGLDisplayDevice.o:(.rodata._ZTV19OpenGLDisplayDevice[_ZTV19OpenGLDisplayDevice]+0x140):
> > riferimento non definito a "OpenGLRenderer::prepareTrans()"
> >
> OpenGLDisplayDevice.o:(.rodata._ZTV19OpenGLDisplayDevice[_ZTV19OpenGLDisplayDevice]+0x148):
> > riferimento non definito a "OpenGLRenderer::clear()"
> >
> OpenGLDisplayDevice.o:(.rodata._ZTV19OpenGLDisplayDevice[_ZTV19OpenGLDisplayDevice]+0x150):
> > riferimento non definito a "OpenGLRenderer::left()"
> >
> OpenGLDisplayDevice.o:(.rodata._ZTV19OpenGLDisplayDevice[_ZTV19OpenGLDisplayDevice]+0x158):
> > riferimento non definito a "OpenGLRenderer::right()"
> >
> OpenGLDisplayDevice.o:(.rodata._ZTV19OpenGLDisplayDevice[_ZTV19OpenGLDisplayDevice]+0x160):
> > riferimento non definito a "OpenGLRenderer::normal()"
> >
> OpenGLDisplayDevice.o:(.rodata._ZTV19OpenGLDisplayDevice[_ZTV19OpenGLDisplayDevice]+0x180):
> > riferimento non definito a "OpenGLRenderer::render(VMDDisplayList
> const*)"
> >
> OpenGLDisplayDevice.o:(.rodata._ZTV19OpenGLDisplayDevice[_ZTV19OpenGLDisplayDevice]+0x188):
> > riferimento non definito a "OpenGLRenderer::render_done()"
> >
> OpenGLDisplayDevice.o:(.rodata._ZTV19OpenGLDisplayDevice[_ZTV19OpenGLDisplayDevice]+0x198):
> > riferimento non definito a
> "OpenGLRenderer::enable_stencil_stereo(int)"
> >
> OpenGLDisplayDevice.o:(.rodata._ZTV19OpenGLDisplayDevice[_ZTV19OpenGLDisplayDevice]+0x1a0):
> > riferimento non definito a "OpenGLRenderer::disable_stencil_stereo()"
> >
> OpenGLDisplayDevice.o:(.rodata._ZTV19OpenGLDisplayDevice[_ZTV19OpenGLDisplayDevice]+0x1a8):
> > riferimento non definito a
> > "OpenGLRenderer::set_persp(DisplayDevice::DisplayEye)"
> > collect2: error: ld returned 1 exit status
> >
> > Thanks in advance.
> > --
> > Stefano GUGLIELMO PhD
> > Assistant Professor of Medicinal Chemistry
> > Department of Drug Science and Technology
> > Via P. Giuria 9
> > 10125 Turin, ITALY
> > ph. +39 (0)11 6707678
> >
> > [4][IMG] Mail priva di virus. [5]www.avast.com
> >
> > --
> > Stefano GUGLIELMO PhD
> > Assistant Professor of Medicinal Chemistry
> > Department of Drug Science and Technology
> > Via P. Giuria 9
> > 10125 Turin, ITALY
> > ph. +39 (0)11 6707678
> >
> > References
> >
> > Visible links
> > 1. mailto:stefano.guglielmo_at_unito.it <javascript:;>
> > 2. mailto:vmd-l_at_ks.uiuc.edu <javascript:;>
> > 3. https://www.opengl.org/registry/
> > 4.
> https://www.avast.com/sig-email?utm_medium=email&utm_source=link&utm_campaign=sig-email&utm_content=webmail
> > 5.
> https://www.avast.com/sig-email?utm_medium=email&utm_source=link&utm_campaign=sig-email&utm_content=webmail
>
> --
> 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/
> 

-- 
Stefano GUGLIELMO PhD
Assistant Professor of Medicinal Chemistry
Department of Drug Science and Technology
Via P. Giuria 9
10125 Turin, ITALY
ph. +39 (0)11 6707678