VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Wed Mar 29 2006 - 14:26:40 CST

Hi,
  Aha, so you're missing libstdc++.so.5.
I'm not sure how debian packages that, but on FC5 you can add that to your
install (it only gets installed normally if you choose the "all" installation)
with (told to me by another VMD user):
  yum install compat-libstdc++-33

You might see if Debian has a similar compatibility package you can install.

I'm considering making two different 32-bit builds of VMD available for
Linux on x86, one based on RH9 (which is the one we've been shipping for
some time now that most people are using) and one based on RHEL4 which is
based on the newer libstdc++.so.6 libraries.

Another option would be SRPMs, which I've discussed briefly with
Axel Kohlmeyer, as he's been able to get something automatic working
in his lab with that method.

  John

On Wed, Mar 29, 2006 at 07:49:12PM +0200, Super Sayan wrote:
> Hi, my distribution is "debian-testing" (i downloaded
> it 3 days ago). i'm using gnome
> if i type:"vmd -dispdev text", in the shell appear:
> "/usr/local/lib/vmd/vmd_LINUX: error while loading
> shared libraries: libstdc++.so.5: cannot open shared
> object file: No such file or directory"
> %%%%%%%%%%%%%
> benji_at_beniamino:~/vmd/lib/vmd$ ls
> Announcement LICENSE README shaders
> surf_LINUX vmd_LINUX
> doc plugins scripts stride_LINUX
> tachyon_LINUX
> benji_at_beniamino:~/vmd/lib/vmd$ vmd_LINUX
> bash: vmd_LINUX: command not found
> benji_at_beniamino:~/vmd/lib/vmd$ ./vmd_LINUX
> ./vmd_LINUX: error while loading shared libraries:
> libstdc++.so.5: cannot open shared object file: No
> such file or directory
> benji_at_beniamino:~/vmd/lib/vmd$
> %%%%%%%%%%%%%%%%
>
> about glxinfo:
> benji_at_beniamino:~/vmd/lib/vmd$ glxinfo
> name of display: :0.0
> display: :0 screen: 0
> direct rendering: No
> server glx vendor string: SGI
> server glx version string: 1.2
> server glx extensions:
> GLX_ARB_multisample, GLX_EXT_visual_info,
> GLX_EXT_visual_rating,
> GLX_EXT_import_context, GLX_OML_swap_method,
> GLX_SGI_make_current_read,
> GLX_SGIS_multisample, GLX_SGIX_hyperpipe,
> GLX_SGIX_swap_barrier,
> GLX_SGIX_fbconfig
> client glx vendor string: SGI
> client glx version string: 1.4
> client glx extensions:
> GLX_ARB_get_proc_address, GLX_ARB_multisample,
> GLX_EXT_import_context,
> GLX_EXT_visual_info, GLX_EXT_visual_rating,
> GLX_MESA_allocate_memory,
> GLX_MESA_swap_control, GLX_MESA_swap_frame_usage,
> GLX_OML_swap_method,
> GLX_OML_sync_control, GLX_SGI_make_current_read,
> GLX_SGI_swap_control,
> GLX_SGI_video_sync, GLX_SGIS_multisample,
> GLX_SGIX_fbconfig,
> GLX_SGIX_pbuffer, GLX_SGIX_visual_select_group
> GLX extensions:
> GLX_ARB_get_proc_address, GLX_ARB_multisample,
> GLX_EXT_import_context,
> GLX_EXT_visual_info, GLX_EXT_visual_rating,
> GLX_OML_swap_method,
> GLX_SGI_make_current_read, GLX_SGIS_multisample,
> GLX_SGIX_fbconfig,
> GLX_SGIX_visual_select_group
> OpenGL vendor string: Mesa project: www.mesa3d.org
> OpenGL renderer string: Mesa GLX Indirect
> OpenGL version string: 1.2 (1.5 Mesa 6.4.1)
> OpenGL extensions:
> GL_ARB_depth_texture, GL_ARB_imaging,
> GL_ARB_multitexture,
> GL_ARB_point_parameters, GL_ARB_point_sprite,
> GL_ARB_shadow,
> GL_ARB_shadow_ambient,
> GL_ARB_texture_border_clamp,
> GL_ARB_texture_cube_map, GL_ARB_texture_env_add,
> GL_ARB_texture_env_combine,
> GL_ARB_texture_env_crossbar,
> GL_ARB_texture_env_dot3,
> GL_ARB_texture_mirrored_repeat,
> GL_ARB_texture_rectangle, GL_ARB_transpose_matrix,
> GL_ARB_window_pos,
> GL_EXT_abgr, GL_EXT_bgra, GL_EXT_blend_color,
> GL_EXT_blend_func_separate,
> GL_EXT_blend_logic_op, GL_EXT_blend_minmax,
> GL_EXT_blend_subtract,
> GL_EXT_clip_volume_hint, GL_EXT_copy_texture,
> GL_EXT_draw_range_elements,
> GL_EXT_fog_coord, GL_EXT_multi_draw_arrays,
> GL_EXT_packed_pixels,
> GL_EXT_point_parameters, GL_EXT_polygon_offset,
> GL_EXT_rescale_normal,
> GL_EXT_secondary_color,
> GL_EXT_separate_specular_color,
> GL_EXT_shadow_funcs, GL_EXT_stencil_two_side,
> GL_EXT_stencil_wrap,
> GL_EXT_subtexture, GL_EXT_texture,
> GL_EXT_texture3D,
> GL_EXT_texture_edge_clamp, GL_EXT_texture_env_add,
> GL_EXT_texture_env_combine,
> GL_EXT_texture_env_dot3,
> GL_EXT_texture_lod_bias, GL_EXT_texture_object,
> GL_EXT_texture_rectangle,
> GL_EXT_vertex_array, GL_APPLE_packed_pixels,
> GL_ATI_texture_env_combine3,
> GL_ATI_texture_mirror_once,
> GL_ATIX_texture_env_combine3,
> GL_HP_occlusion_test,
> GL_IBM_texture_mirrored_repeat,
> GL_INGR_blend_func_separate, GL_MESA_pack_invert,
> GL_MESA_ycbcr_texture,
> GL_NV_blend_square, GL_NV_point_sprite,
> GL_NV_texgen_reflection,
> GL_NV_texture_rectangle, GL_SGIS_generate_mipmap,
> GL_SGIS_texture_border_clamp,
> GL_SGIS_texture_edge_clamp,
> GL_SGIS_texture_lod, GL_SGIX_depth_texture,
> GL_SGIX_shadow,
> GL_SGIX_shadow_ambient, GL_SUN_multi_draw_arrays
> glu version: 1.3
> glu extensions:
> GLU_EXT_nurbs_tessellator,
> GLU_EXT_object_space_tess
>
> visual x bf lv rg d st colorbuffer ax dp st
> accumbuffer ms cav
> id dep cl sp sz l ci b ro r g b a bf th cl r g
> b a ns b eat
> ----------------------------------------------------------------------
> 0x23 24 tc 0 24 0 r y . 8 8 8 0 0 16 0 0 0
> 0 0 0 0 None
> 0x24 24 tc 0 24 0 r y . 8 8 8 0 0 16 8 16 16
> 16 0 0 0 None
> 0x25 24 tc 0 32 0 r y . 8 8 8 8 0 16 8 16 16
> 16 16 0 0 None
> 0x26 24 tc 0 32 0 r . . 8 8 8 8 0 16 8 16 16
> 16 16 0 0 None
> 0x27 24 dc 0 24 0 r y . 8 8 8 0 0 16 0 0 0
> 0 0 0 0 None
> 0x28 24 dc 0 24 0 r y . 8 8 8 0 0 16 8 16 16
> 16 0 0 0 None
> 0x29 24 dc 0 32 0 r y . 8 8 8 8 0 16 8 16 16
> 16 16 0 0 None
> 0x2a 24 dc 0 32 0 r . . 8 8 8 8 0 16 8 16 16
> 16 16 0 0 None
> benji_at_beniamino:~/vmd/lib/vmd$
> %%%%%%%%%%%%%%%%
> if i type "xterm" it opens another shell.
> thanks.
> bye
>
>
>
> --- John Stone <johns_at_ks.uiuc.edu> ha scritto:
>
> >
> > Hi,
> > This is probably one of the common Linux problems.
> > Which Linux distribution are you running?
> >
> > What happens if you do:
> > vmd -dispdev text
> >
> > What output do you get when you run this command:
> > ldd /home/benji/vmd/lib/vmd_LINUX
> >
> > Did you try running 'xterm' and 'glxinfo' as I
> > suggested?
> >
> > John Stone
> > vmd_at_ks.uiuc.edu
> >
> > On Wed, Mar 29, 2006 at 08:41:43AM +0200, Super
> > Sayan wrote:
> > > I reinstalled vmd as user (not root); i installed
> > it
> > > in directory "/home/benji/vmd".
> > > it doesn't work: there are the same problem:
> > > if i go in vmd's dir and i type "vmd" as user, it
> > > starts and go off, without any error printed in
> > the
> > > shell (it prints "[1] 6853" but the number always
> > > changes).
> > > if i type "vmd" as root, it starts ang go off,
> > > printing in the shell: "Warning: Tried to connect
> > to
> > > session manager, Authentication Rejected, reason :
> > > None of the authentication protocols specified are
> > > supported and host-based authentication failed".
> > in
> > > the shell it also prints "[1] 6933" changing
> > always
> > > the number.
> > > thanks anymore.
> > > Beniamino
> > >
> > >
> > >
> > > --- John Stone <johns_at_ks.uiuc.edu> ha scritto:
> > >
> > > >
> > > > Hi,
> > > > This sounds like some sort of X issue. If you
> > are
> > > > logged in as a different
> > > > user than root, then su'd and installed VMD, but
> > ran
> > > > VMD as root, this might
> > > > lead to the problem you just had. You'll need
> > to
> > > > run VMD as the same user
> > > > that you've logged into the machine with, since
> > X
> > > > won't allow windows
> > > > to be created by other users. You can test this
> > by
> > > > running "xterm"
> > > > or "glxinfo" to verify that you've got access to
> > the
> > > > display as the
> > > > user you're trying to run VMD with. In general,
> > > > when installing VMD on
> > > > Unix, follow the instructions in the provided
> > > > README, as that explains
> > > > how the VMD configure script works.
> > > >
> > > > John Stone
> > > > vmd_at_ks.uiuc.edu
> > > >
> > > > On Tue, Mar 28, 2006 at 09:44:37PM +0200,
> > Beniamino
> > > > Sciacca wrote:
> > > > > Hi!
> > > > > i installed gromacs on my centrino duo without
> > > > problem.
> > > > > i installed also VMD; when i typed
> > "./configure"
> > > > it says: "...
> > > > > ./configure.options".
> > > > > so i typed: "./configure LINUX".
> > > > > later i typed make install.
> > > > > so if i move to the directory where it is
> > > > installed, and i type "vmd",
> > > > > it starts and go off immediately.
> > > > > in the shell it writes: "... authentication
> > > > failed........".
> > > > > what's the problem? is it an installation
> > problem?
> > > > > thanks, community, for your answers.
> > > > > bye
> > > > > Beniamino (superbenji83_at_yahoo.it)
> > > > >
> > > > >
> > > > >
> > > > >
> > > > >
> > > > > ___________________________________
> > > > > Yahoo! Mail: gratis 1GB per i messaggi e
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> > > > da 10MB
> > > > > http://mail.yahoo.it
> > > >
> > > > --
> > > > NIH Resource for Macromolecular Modeling and
> > > > Bioinformatics
> > > > Beckman Institute for Advanced Science and
> > > > Technology
> > > > University of Illinois, 405 N. Mathews Ave,
> > Urbana,
> > > > IL 61801
> > > > Email: johns_at_ks.uiuc.edu Phone:
> > > > 217-244-3349
> > > > WWW: http://www.ks.uiuc.edu/~johns/ Fax:
> > > > 217-244-6078
> > > >
> > >
> > >
> > >
> > >
> > >
> > >
> > >
> > > ___________________________________
> > > Yahoo! Mail: gratis 1GB per i messaggi e allegati
> > da 10MB
> > > http://mail.yahoo.it
> >
> > --
> > NIH Resource for Macromolecular Modeling and
> > Bioinformatics
> > Beckman Institute for Advanced Science and
> > Technology
> > University of Illinois, 405 N. Mathews Ave, Urbana,
> > IL 61801
> > Email: johns_at_ks.uiuc.edu Phone:
> > 217-244-3349
> > WWW: http://www.ks.uiuc.edu/~johns/ Fax:
> > 217-244-6078
> >
>
>
>
>
>
>
>
> ___________________________________
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-- 
NIH Resource for Macromolecular Modeling and Bioinformatics
Beckman Institute for Advanced Science and Technology
University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
Email: johns_at_ks.uiuc.edu                 Phone: 217-244-3349
  WWW: http://www.ks.uiuc.edu/~johns/      Fax: 217-244-6078