[Mrtrix-discussion] mrview segmentation fault
Kerstin Pannek
k.pannek1 at uq.edu.au
Sun Nov 30 19:36:31 PST 2008
Hi Donald
the permissions were set to rw for root and owner; giving the group read
and write permissions got rid of the nvidia message. Unfortunately I
still get the segmentation fault.
I have attached the output of glxinfo.
Thanks again
Kerstin
Donald Tournier wrote:
> Hi Kerstin,
>
> The problem seems to be with your OpenGL setup - i.e. related to your
> graphics card, rather than MRtrix as such. The relevant error message
> is:
> NVIDIA: could not open the device file /dev/nvidiactl (Permission denied).
> NVIDIA: Direct rendering failed; attempting indirect rendering.
>
> There is a permissions problem on the nvidiactl device, which is what
> your system uses to provide access to the graphics card (presumably an
> NVidia card). This means that it fails to use the graphics card
> directly, and so causes the system to switch to software-only
> rendering (indirect rendering). Presumably, some of the graphics
> processing is a little too much for the software renderer, and causes
> the crash.
>
> I'm not too sure what the solution would be, but the first thing to
> check are the permissions on the /dev/ndiviactl device. On my system,
> this is what I have:
>
> $ ls -l /dev/nvidiactl
> crw-rw-rw- 1 root root 195, 255 2008-12-01 09:59 /dev/nvidiactl
>
> This basically says that I have read-write permissions to this device
> for everyone. You might find that the first entry says: crw------- or
> something like that, which would indicate that only root has
> permissions to access the device. If so, this is the cause of the
> problem. This following command will set the permissions to the same
> as I have. Try it and see if it sort the problem out:
>
> $ sudo chmod a+rw /dev/nvidiactl
>
> Let me know if it worked. If not, send me the full output of the
> "glxinfo" command.
> Cheers,
>
> Donald.
>
>
> On Mon, Dec 1, 2008 at 1:15 PM, Kerstin Pannek <k.pannek1 at uq.edu.au> wrote:
>
>> Hi Kerstin
>> I can open all csd.mif files as regular images.
>> I recompiled the debugging version of MRtrix. I have attached the output of
>> running mrview -debug and in gdb as text files to this email.
>> Interestingly, I just discovered that orientation plots that worked this
>> morning work only occasionally now...
>> Thanks for your help
>> Kerstin
>>
>>
>> Donald Tournier wrote:
>>
>>> Hi Kerstin,
>>>
>>> This is really strange. Can you open the csd.mif file as a regular
>>> image (i.e. using the File->Open dialog)? If you can, then there is
>>> probably something else going on. Someone else had a very similar
>>> issue when running MRtrix within a virtual PC (i.e. an emulator),
>>> which I guess was related to the poor graphics card support and/or the
>>> limited memory available. In any case, it sounded more like a
>>> limitation of the system rather than the software itself. Things might
>>> be different in your case though, since you are able to display some,
>>> but not all your csd.mif files...
>>>
>>> Here's a couple of things you can do to try to narrow down the problem:
>>>
>>> 1. run mrview from the command line with the -debug option, and repeat
>>> the steps taken to get it to crash. Then copy/paste and send me the
>>> command-line output.
>>>
>>> 2. run mrview within the debugger:
>>> $ gdb mrview
>>> followed by "run" at the gdb prompt"
>>> (gdb) run
>>>
>>> then load your csd.mif file to get mrview to crash, at which point the
>>> debugger will print out a message about the error. You can send me a
>>> full diagnostic by typing "bt full" at the prompt and copy/pasting the
>>> output:
>>> (gdb) bt full
>>>
>>> If you have the time, BEFORE doing the steps above, you could
>>> recompile a debugging version of MRtrix. This will make the diagnostic
>>> information produced by "bt full" much more comprehensive. To do this,
>>> use these commands (from the MRtrix installation folder):
>>> $ ./build clean
>>> $ ./build -debug
>>> And proceed as per the installation instructions.
>>>
>>> Thanks!
>>>
>>> Donald.
>>>
>>>
>>> On Mon, Dec 1, 2008 at 11:23 AM, Kerstin Pannek <k.pannek1 at uq.edu.au>
>>> wrote:
>>>
>>>
>>>> Hi!
>>>> I have a problem looking at the orientation plots of several datasets.
>>>> mrview crashes on opening csd.mif (view->sidebar->orientation
>>>> plot->browse->open --- segmentation fault). This happens only for a few
>>>> datasets. All datasets are processed the same way. Deleting the file and
>>>> rerunning csdeconv doesn't solve the problem. Any ideas?
>>>> Thanks
>>>> Kerstin
>>>> _______________________________________________
>>>> Mrtrix-discussion mailing list
>>>> Mrtrix-discussion at www.nitrc.org
>>>> http://www.nitrc.org/mailman/listinfo/mrtrix-discussion
>>>>
>>>>
>>>>
>>>
>>>
>>>
>> sneed:mrtrix$ mrview tensor/fa.mif -debug
>> mrview [INFO]: opening image "tensor/fa.mif"...
>> mrview [DEBUG]: reading key/value file "tensor/fa.mif"...
>> mrview [DEBUG]: sanitising transformation matrix...
>> mrview [DEBUG]: preparing file "tensor/fa.mif"
>> mrview [DEBUG]: setting up image "tensor/fa.mif"...
>> mrview [DEBUG]: sanitising transformation matrix...
>> mrview [DEBUG]: setting up data increments for "tensor/fa.mif"...
>> mrview [DEBUG]: data increments initialised with start = 99, stride = [ -1
>> 100 10000 ]
>> NVIDIA: could not open the device file /dev/nvidiactl (Permission denied).
>> NVIDIA: Direct rendering failed; attempting indirect rendering.
>> mrview [DEBUG]: mapping image "tensor/fa.mif"...
>> mrview [DEBUG]: file "tensor/fa.mif" mapped at 0x7fbab4150000, size 2400272
>> (read-only)
>> mrview [DEBUG]: data mapper for image "tensor/fa.mif" mapped with segment
>> size = 600000 (optimised)
>> NVIDIA: could not open the device file /dev/nvidiactl (Permission denied).
>> NVIDIA: Direct rendering failed; attempting indirect rendering.
>> mrview [INFO]: DWI renderer successfully initialised
>> mrview [INFO]: GL_RENDERER = GeForce 7100 GS/PCI/SSE2
>> mrview [INFO]: GL_VERSION = 2.1.0 NVIDIA 96.43.05
>> mrview [INFO]: GL_VENDOR = NVIDIA Corporation
>> mrview [DEBUG]: preparing file
>> "/giglo/sneed-01/kerstin/data/EKBERG/DTI_b3000/mrtrix/csd/response.txt"
>> mrview [INFO]: opening image
>> "/giglo/sneed-01/kerstin/data/EKBERG/DTI_b3000/mrtrix/csd/csd.mif"...
>> mrview [DEBUG]: reading key/value file
>> "/giglo/sneed-01/kerstin/data/EKBERG/DTI_b3000/mrtrix/csd/csd.mif"...
>> mrview [DEBUG]: sanitising transformation matrix...
>> mrview [DEBUG]: preparing file
>> "/giglo/sneed-01/kerstin/data/EKBERG/DTI_b3000/mrtrix/csd/csd.mif"
>> mrview [DEBUG]: setting up image
>> "/giglo/sneed-01/kerstin/data/EKBERG/DTI_b3000/mrtrix/csd/csd.mif"...
>> mrview [DEBUG]: sanitising transformation matrix...
>> mrview [DEBUG]: setting up data increments for
>> "/giglo/sneed-01/kerstin/data/EKBERG/DTI_b3000/mrtrix/csd/csd.mif"...
>> mrview [DEBUG]: data increments initialised with start = 0, stride = [ 45
>> 4500 450000 1 ]
>> mrview [DEBUG]: mapping image
>> "/giglo/sneed-01/kerstin/data/EKBERG/DTI_b3000/mrtrix/csd/csd.mif"...
>> mrview [DEBUG]: file
>> "/giglo/sneed-01/kerstin/data/EKBERG/DTI_b3000/mrtrix/csd/csd.mif" mapped at
>> 0x7fbaabaf8000, size 108000282 (read-only)
>> mrview [DEBUG]: data mapper for image
>> "/giglo/sneed-01/kerstin/data/EKBERG/DTI_b3000/mrtrix/csd/csd.mif" mapped
>> with segment size = 27000000 (optimised)
>> Segmentation fault
>>
>>
>> sneed:mrtrix$ gdb mrview
>> GNU gdb 6.8-debian
>> Copyright (C) 2008 Free Software Foundation, Inc.
>> License GPLv3+: GNU GPL version 3 or later
>> <http://gnu.org/licenses/gpl.html>
>> This is free software: you are free to change and redistribute it.
>> There is NO WARRANTY, to the extent permitted by law. Type "show copying"
>> and "show warranty" for details.
>> This GDB was configured as "x86_64-linux-gnu"...
>> (gdb) run
>> Starting program: /data/home/kerstin/bin/mrtrix/bin/mrview
>> [Thread debugging using libthread_db enabled]
>> [New Thread 0x7f4bb4fe1730 (LWP 25807)]
>> NVIDIA: could not open the device file /dev/nvidiactl (Permission denied).
>> NVIDIA: Direct rendering failed; attempting indirect rendering.
>> NVIDIA: could not open the device file /dev/nvidiactl (Permission denied).
>> NVIDIA: Direct rendering failed; attempting indirect rendering.
>>
>> Program received signal SIGSEGV, Segmentation fault.
>> [Switching to Thread 0x7f4bb4fe1730 (LWP 25807)]
>> 0x000000000048322e in MR::Image::Mapper::re (this=0xaf6c60,
>> offset=18445767945754771456) at lib/image/mapper.h:251
>> 251 if (optimised) return (((float32*) segment[0])[offset]);
>> (gdb) bt full
>> #0 0x000000000048322e in MR::Image::Mapper::re (this=Cannot access memory
>> at address 0x7fffbd1cfdb8
>> ) at lib/image/mapper.h:251
>> nseg = Cannot access memory at address 0x7fffbd1cfdc8
>> (gdb)
>>
>>
>>
>>
>
>
>
>
-------------- next part --------------
sneed:mrtrix$ glxinfo
name of display: :0.0
display: :0 screen: 0
direct rendering: Yes
server glx vendor string: NVIDIA Corporation
server glx version string: 1.4
server glx extensions:
GLX_EXT_visual_info, GLX_EXT_visual_rating, GLX_SGIX_fbconfig,
GLX_SGIX_pbuffer, GLX_SGI_video_sync, GLX_SGI_swap_control,
GLX_EXT_texture_from_pixmap, GLX_ARB_multisample, GLX_NV_float_buffer,
GLX_ARB_fbconfig_float
client glx vendor string: NVIDIA Corporation
client glx version string: 1.4
client glx extensions:
GLX_ARB_get_proc_address, GLX_ARB_multisample, GLX_EXT_visual_info,
GLX_EXT_visual_rating, GLX_EXT_import_context, GLX_SGI_video_sync,
GLX_NV_swap_group, GLX_NV_video_out, GLX_SGIX_fbconfig, GLX_SGIX_pbuffer,
GLX_SGI_swap_control, GLX_NV_float_buffer, GLX_ARB_fbconfig_float,
GLX_EXT_fbconfig_packed_float, GLX_EXT_texture_from_pixmap
GLX version: 1.3
GLX extensions:
GLX_EXT_visual_info, GLX_EXT_visual_rating, GLX_SGIX_fbconfig,
GLX_SGIX_pbuffer, GLX_SGI_video_sync, GLX_SGI_swap_control,
GLX_EXT_texture_from_pixmap, GLX_ARB_multisample, GLX_NV_float_buffer,
GLX_ARB_fbconfig_float, GLX_ARB_get_proc_address
OpenGL vendor string: NVIDIA Corporation
OpenGL renderer string: GeForce 7100 GS/PCI/SSE2
OpenGL version string: 2.1.0 NVIDIA 96.43.05
OpenGL extensions:
GL_ARB_color_buffer_float, GL_ARB_depth_texture, GL_ARB_draw_buffers,
GL_ARB_fragment_program, GL_ARB_fragment_program_shadow,
GL_ARB_fragment_shader, GL_ARB_half_float_pixel, GL_ARB_imaging,
GL_ARB_multisample, GL_ARB_multitexture, GL_ARB_occlusion_query,
GL_ARB_pixel_buffer_object, GL_ARB_point_parameters, GL_ARB_point_sprite,
GL_ARB_shadow, GL_ARB_shader_objects, GL_ARB_shading_language_100,
GL_ARB_texture_border_clamp, GL_ARB_texture_compression,
GL_ARB_texture_cube_map, GL_ARB_texture_env_add,
GL_ARB_texture_env_combine, GL_ARB_texture_env_dot3, GL_ARB_texture_float,
GL_ARB_texture_mirrored_repeat, GL_ARB_texture_non_power_of_two,
GL_ARB_texture_rectangle, GL_ARB_transpose_matrix,
GL_ARB_vertex_buffer_object, GL_ARB_vertex_program, GL_ARB_vertex_shader,
GL_ARB_window_pos, GL_ATI_draw_buffers, GL_ATI_texture_float,
GL_ATI_texture_mirror_once, GL_S3_s3tc, GL_EXT_texture_env_add,
GL_EXT_abgr, GL_EXT_bgra, GL_EXT_blend_color,
GL_EXT_blend_equation_separate, GL_EXT_blend_func_separate,
GL_EXT_blend_minmax, GL_EXT_blend_subtract, GL_EXT_compiled_vertex_array,
GL_EXT_Cg_shader, GL_EXT_depth_bounds_test, GL_EXT_draw_range_elements,
GL_EXT_fog_coord, GL_EXT_framebuffer_object,
GL_EXT_gpu_program_parameters, GL_EXT_multi_draw_arrays,
GL_EXT_packed_depth_stencil, GL_EXT_packed_pixels,
GL_EXT_pixel_buffer_object, GL_EXT_point_parameters,
GL_EXT_rescale_normal, GL_EXT_secondary_color,
GL_EXT_separate_specular_color, GL_EXT_shadow_funcs,
GL_EXT_stencil_clear_tag, GL_EXT_stencil_two_side, GL_EXT_stencil_wrap,
GL_EXT_texture3D, GL_EXT_texture_compression_s3tc,
GL_EXT_texture_cube_map, GL_EXT_texture_edge_clamp,
GL_EXT_texture_env_combine, GL_EXT_texture_env_dot3,
GL_EXT_texture_filter_anisotropic, GL_EXT_texture_lod,
GL_EXT_texture_lod_bias, GL_EXT_texture_mirror_clamp,
GL_EXT_texture_object, GL_EXT_texture_sRGB, GL_EXT_timer_query,
GL_EXT_vertex_array, GL_HP_occlusion_test, GL_IBM_rasterpos_clip,
GL_IBM_texture_mirrored_repeat, GL_KTX_buffer_region, GL_NV_blend_square,
GL_NV_copy_depth_to_color, GL_NV_depth_clamp, GL_NV_fence,
GL_NV_float_buffer, GL_NV_fog_distance, GL_NV_fragment_program,
GL_NV_fragment_program_option, GL_NV_fragment_program2, GL_NV_half_float,
GL_NV_light_max_exponent, GL_NV_multisample_filter_hint,
GL_NV_occlusion_query, GL_NV_packed_depth_stencil, GL_NV_pixel_data_range,
GL_NV_point_sprite, GL_NV_primitive_restart, GL_NV_register_combiners,
GL_NV_register_combiners2, GL_NV_texgen_reflection,
GL_NV_texture_compression_vtc, GL_NV_texture_env_combine4,
GL_NV_texture_expand_normal, GL_NV_texture_rectangle,
GL_NV_texture_shader, GL_NV_texture_shader2, GL_NV_texture_shader3,
GL_NV_vertex_array_range, GL_NV_vertex_array_range2, GL_NV_vertex_program,
GL_NV_vertex_program1_1, GL_NV_vertex_program2,
GL_NV_vertex_program2_option, GL_NV_vertex_program3,
GL_NVX_conditional_render, GL_SGIS_generate_mipmap, GL_SGIS_texture_lod,
GL_SGIX_depth_texture, GL_SGIX_shadow, GL_SUN_slice_accum
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
----------------------------------------------------------------------
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0x22 24 dc 0 32 0 r y . 8 8 8 0 4 24 8 16 16 16 16 0 0 None
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0x25 24 tc 0 32 0 r . . 8 8 8 8 4 24 8 16 16 16 16 0 0 None
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0x31 24 tc 0 32 0 r . . 8 8 8 8 4 0 0 16 16 16 16 0 0 None
0x32 24 tc 0 32 0 r y . 8 8 8 0 4 24 0 16 16 16 16 2 1 Ncon
0x33 24 tc 0 32 0 r y . 8 8 8 8 4 24 0 16 16 16 16 2 1 Ncon
0x34 24 tc 0 32 0 r y . 8 8 8 0 4 24 0 16 16 16 16 4 1 Ncon
0x35 24 tc 0 32 0 r y . 8 8 8 8 4 24 0 16 16 16 16 4 1 Ncon
0x36 24 tc 0 32 0 r . . 8 8 8 0 4 24 0 16 16 16 16 2 1 Ncon
0x37 24 tc 0 32 0 r . . 8 8 8 8 4 24 0 16 16 16 16 2 1 Ncon
0x38 24 tc 0 32 0 r . . 8 8 8 0 4 24 0 16 16 16 16 4 1 Ncon
0x39 24 tc 0 32 0 r . . 8 8 8 8 4 24 0 16 16 16 16 4 1 Ncon
0x3a 24 tc 0 32 0 r y . 8 8 8 0 4 24 8 16 16 16 16 2 1 Ncon
0x3b 24 tc 0 32 0 r y . 8 8 8 8 4 24 8 16 16 16 16 2 1 Ncon
0x3c 24 tc 0 32 0 r y . 8 8 8 0 4 24 8 16 16 16 16 4 1 Ncon
0x3d 24 tc 0 32 0 r y . 8 8 8 8 4 24 8 16 16 16 16 4 1 Ncon
0x3e 24 tc 0 32 0 r . . 8 8 8 0 4 24 8 16 16 16 16 2 1 Ncon
0x3f 24 tc 0 32 0 r . . 8 8 8 8 4 24 8 16 16 16 16 2 1 Ncon
0x40 24 tc 0 32 0 r . . 8 8 8 0 4 24 8 16 16 16 16 4 1 Ncon
0x41 24 tc 0 32 0 r . . 8 8 8 8 4 24 8 16 16 16 16 4 1 Ncon
0x42 24 tc 0 32 0 r y . 8 8 8 0 4 16 0 16 16 16 16 2 1 Ncon
0x43 24 tc 0 32 0 r y . 8 8 8 8 4 16 0 16 16 16 16 2 1 Ncon
0x44 24 tc 0 32 0 r y . 8 8 8 0 4 16 0 16 16 16 16 4 1 Ncon
0x45 24 tc 0 32 0 r y . 8 8 8 8 4 16 0 16 16 16 16 4 1 Ncon
0x46 24 tc 0 32 0 r . . 8 8 8 0 4 16 0 16 16 16 16 2 1 Ncon
0x47 24 tc 0 32 0 r . . 8 8 8 8 4 16 0 16 16 16 16 2 1 Ncon
0x48 24 tc 0 32 0 r . . 8 8 8 0 4 16 0 16 16 16 16 4 1 Ncon
0x49 24 tc 0 32 0 r . . 8 8 8 8 4 16 0 16 16 16 16 4 1 Ncon
0x4a 24 dc 0 32 0 r y . 8 8 8 8 4 24 8 16 16 16 16 0 0 None
0x4b 24 dc 0 32 0 r . . 8 8 8 0 4 24 8 16 16 16 16 0 0 None
0x4c 24 dc 0 32 0 r . . 8 8 8 8 4 24 8 16 16 16 16 0 0 None
0x4d 24 dc 0 32 0 r y . 8 8 8 0 4 24 0 16 16 16 16 0 0 None
0x4e 24 dc 0 32 0 r y . 8 8 8 8 4 24 0 16 16 16 16 0 0 None
0x4f 24 dc 0 32 0 r . . 8 8 8 0 4 24 0 16 16 16 16 0 0 None
0x50 24 dc 0 32 0 r . . 8 8 8 8 4 24 0 16 16 16 16 0 0 None
0x51 24 dc 0 32 0 r y . 8 8 8 0 4 16 0 16 16 16 16 0 0 None
0x52 24 dc 0 32 0 r y . 8 8 8 8 4 16 0 16 16 16 16 0 0 None
0x53 24 dc 0 32 0 r . . 8 8 8 0 4 16 0 16 16 16 16 0 0 None
0x54 24 dc 0 32 0 r . . 8 8 8 8 4 16 0 16 16 16 16 0 0 None
0x55 24 dc 0 32 0 r y . 8 8 8 0 4 0 0 16 16 16 16 0 0 None
0x56 24 dc 0 32 0 r y . 8 8 8 8 4 0 0 16 16 16 16 0 0 None
0x57 24 dc 0 32 0 r . . 8 8 8 0 4 0 0 16 16 16 16 0 0 None
0x58 24 dc 0 32 0 r . . 8 8 8 8 4 0 0 16 16 16 16 0 0 None
0x59 24 dc 0 32 0 r y . 8 8 8 0 4 24 0 16 16 16 16 2 1 Ncon
0x5a 24 dc 0 32 0 r y . 8 8 8 8 4 24 0 16 16 16 16 2 1 Ncon
0x5b 24 dc 0 32 0 r y . 8 8 8 0 4 24 0 16 16 16 16 4 1 Ncon
0x5c 24 dc 0 32 0 r y . 8 8 8 8 4 24 0 16 16 16 16 4 1 Ncon
0x5d 24 dc 0 32 0 r . . 8 8 8 0 4 24 0 16 16 16 16 2 1 Ncon
0x5e 24 dc 0 32 0 r . . 8 8 8 8 4 24 0 16 16 16 16 2 1 Ncon
0x5f 24 dc 0 32 0 r . . 8 8 8 0 4 24 0 16 16 16 16 4 1 Ncon
0x60 24 dc 0 32 0 r . . 8 8 8 8 4 24 0 16 16 16 16 4 1 Ncon
0x61 24 dc 0 32 0 r y . 8 8 8 0 4 24 8 16 16 16 16 2 1 Ncon
0x62 24 dc 0 32 0 r y . 8 8 8 8 4 24 8 16 16 16 16 2 1 Ncon
0x63 24 dc 0 32 0 r y . 8 8 8 0 4 24 8 16 16 16 16 4 1 Ncon
0x64 24 dc 0 32 0 r y . 8 8 8 8 4 24 8 16 16 16 16 4 1 Ncon
0x65 24 dc 0 32 0 r . . 8 8 8 0 4 24 8 16 16 16 16 2 1 Ncon
0x66 24 dc 0 32 0 r . . 8 8 8 8 4 24 8 16 16 16 16 2 1 Ncon
0x67 24 dc 0 32 0 r . . 8 8 8 0 4 24 8 16 16 16 16 4 1 Ncon
0x68 24 dc 0 32 0 r . . 8 8 8 8 4 24 8 16 16 16 16 4 1 Ncon
0x69 24 dc 0 32 0 r y . 8 8 8 0 4 16 0 16 16 16 16 2 1 Ncon
0x6a 24 dc 0 32 0 r y . 8 8 8 8 4 16 0 16 16 16 16 2 1 Ncon
0x6b 24 dc 0 32 0 r y . 8 8 8 0 4 16 0 16 16 16 16 4 1 Ncon
0x6c 24 dc 0 32 0 r y . 8 8 8 8 4 16 0 16 16 16 16 4 1 Ncon
0x6d 24 dc 0 32 0 r . . 8 8 8 0 4 16 0 16 16 16 16 2 1 Ncon
0x6e 24 dc 0 32 0 r . . 8 8 8 8 4 16 0 16 16 16 16 2 1 Ncon
0x6f 24 dc 0 32 0 r . . 8 8 8 0 4 16 0 16 16 16 16 4 1 Ncon
0x70 24 dc 0 32 0 r . . 8 8 8 8 4 16 0 16 16 16 16 4 1 Ncon
0x136 32 tc 1 0 0 c . . 0 0 0 0 0 0 0 0 0 0 0 0 0 None
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