VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Sun Apr 02 2006 - 20:11:42 CDT

If you were using RHEL4 you'd do essentially the exact same thing.

  John Stone
  vmd_at_ks.uiuc.edu

On Thu, Mar 30, 2006 at 09:09:20AM +0200, Super Sayan wrote:
> thanks john, charles and community for your help. now it does work.
> what i've to do if i would install vmd -RHEL4?
> thanks.
> bye
>
>
> John Stone <johns_at_ks.uiuc.edu> ha scritto:
> 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 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 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)
> > > > > >
> > > > > >
> > > > > >
> > > > > >
> > > > > >
> > > > > > ___________________________________
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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
> > > > >
> > > >
> > > >
> > > >
> > > >
> > > >
> > > >
> > > >
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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
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> >
> >
> >
> >
> > ___________________________________
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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
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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