[GRASS-dev] release planning and no volume display on Mac - Any info on where crash happens?
Markus Metz
markus.metz.giswork at gmail.com
Sun Feb 3 04:16:50 PST 2013
I have not commented out both gvl_align_data lines (#684 and #1009) in
gvl_calc.c, but fixed variable initialization in trunk r54866. Please
test.
Markus M
On Fri, Jan 11, 2013 at 10:33 PM, Michael Barton <Michael.Barton at asu.edu> wrote:
> Perhaps Windows and Linux--and earlier versions of OS X--ignore the code.
>
> The header for gvl_calc.c says that the author is Tomas Paudits (February 2004). Does anyone know if he is still around to ask?
>
> Michael
> ______________________________
> C. Michael Barton
> Director, Center for Social Dynamics & Complexity
> Professor of Anthropology, School of Human Evolution & Social Change
> Arizona State University
> Tempe, AZ 85287-2402
> USA
>
> voice: 480-965-6262 (SHESC), 480-727-9746 (CSDC)
> fax: 480-965-7671(SHESC), 480-727-0709 (CSDC)
> www: http://csdc.asu.edu, http://shesc.asu.edu
> http://www.public.asu.edu/~cmbarton
>
> On Jan 11, 2013, at 1:18 PM, Helena Mitasova <hmitaso at ncsu.edu>
> wrote:
>
>>
>> On Jan 11, 2013, at 2:48 PM, Anna Kratochvílová wrote:
>>
>>> Hi Michael,
>>>
>>> On Mon, Jan 7, 2013 at 7:57 AM, Michael Barton <Michael.Barton at asu.edu> wrote:
>>>> So I found a change that would make volumes visible again a week ago. Anyone have any thoughts about this? Do we need the function/procedure that sets the memory pointer for volume displays? Or can we simply get rid of it? Is it needed for Linux? Windows? Any thoughts about what happens without it?
>>>
>>> I can confirm that removing those two lines does no harm for me
>>> (Linux). However it's clear that we cannot just leave them out without
>>> understanding why they are there. Can anyone (for example Glynn) think
>>> of a reason why this code is crashing on Mac and not on Linux (no idea
>>> about Windows)?
>>
>> I just tested it on Windows 7 with WinGRASS6.4.3RC2 and I am happy to report that it works OK
>> - both isosurfaces and crossections.
>>
>> However, in the same WinGRASS6.4.3.RC2 there is a problem with the path to cellheader in G3d_read_window,
>> so r3.info and g.region rast3d=myvoxel gives an error that the region is invalid.
>>
>> Also, I finally got a laptop with MacOSX10.8 and I can confirm that in GRASS6.4.3RC2 binary
>> posted Michael isusrfaces crash wxGUI. I will try to compile myself but I expect the result
>> to be the same given that it crashed for William as well.
>>
>> Helena
>>
>>> And why removing of realloc helps?
>>>
>>> Regards,
>>> Anna
>>>
>>>>
>>>> Cheers
>>>> Michael
>>>> ____________________
>>>> C. Michael Barton
>>>> Director, Center for Social Dynamics & Complexity
>>>> Professor of Anthropology, School of Human Evolution & Social Change
>>>> Arizona State University
>>>>
>>>> voice: 480-965-6262 (SHESC), 480-727-9746 (CSDC)
>>>> fax: 480-965-7671 (SHESC), 480-727-0709 (CSDC)
>>>> www: http://www.public.asu.edu/~cmbarton, http://csdc.asu.edu
>>>>
>>>>
>>>>
>>>>
>>>>
>>>>
>>>>
>>>>
>>>>
>>>>
>>>>
>>>> On Jan 2, 2013, at 11:22 PM, Michael Barton <michael.barton at asu.edu> wrote:
>>>>
>>>>> GREAT NEWS!
>>>>>
>>>>> Commenting out both gvl_align_data lines (#684 and #1009) in gvl_calc_c makes this work. Both slices and isosurfaces display and do not crash. I don't know if there would be a problem with larger files or not. But this is finally functional again.
>>>>>
>>>>> BUT the command you sent does NOT work. It gives a segmentation fault error:
>>>>>
>>>>> m.nviz.image elevation_map=JR_2008_ALL_dem at test3d -a mode=fine resolution_fine=6 color_map=JR_2008_ALL_dem at test3d volume=jr_7408MR_2m_t70 at test3d volume_shading=gouraud volume_resolution=1 volume_position=0,0,20 isosurf_level=1:18.0 isosurf_color_map=jr_7408MR_2m_t70 at test3d isosurf_transparency_value=0 slice=1:x,1:z slice_position=0.000000,1.000000,0.520000,1.000000,0.000000,1.000000,0.250000,0.720000,0.080000,1.000000,0.000000,1.000000 slice_transparency=0,0 position=0.84,0.16 height=356 perspective=20 twist=0 zexag=5.000000 focus=569,593,28 light_position=0.68,0.68,0.80 light_brightness=80 light_ambient=20 light_color=255:255:255 output=jrvoltest format=tif size=798,545
>>>>> Loading raster map <JR_2008_ALL_dem at test3d>...
>>>>> 100%
>>>>> Loading raster map <JR_2008_ALL_dem at test3d>...
>>>>> 100%
>>>>> Translating colors from raster map <JR_2008_ALL_dem at test3d>...
>>>>> 100%
>>>>> Loading 3d raster map <jr_7408MR_2m_t70 at test3d>...
>>>>> Segmentation fault: 11
>>>>>
>>>>>
>>>>> Also, somewhere there is a bug somewhere that is sending progress bar text to the screen for any nviz activity (GRASS_INFO_PERCENT: 0...)
>>>>>
>>>>> So now we have some kind of workaround. I don't know if there are any other down sides to bypassing this memory reallocation, but this is a good start on fixing this finally. Thanks Anna and Helena.
>>>>>
>>>>> Michael
>>>>> ____________________
>>>>> C. Michael Barton
>>>>> Director, Center for Social Dynamics & Complexity
>>>>> Professor of Anthropology, School of Human Evolution & Social Change
>>>>> Arizona State University
>>>>>
>>>>> voice: 480-965-6262 (SHESC), 480-727-9746 (CSDC)
>>>>> fax: 480-965-7671 (SHESC), 480-727-0709 (CSDC)
>>>>> www: http://www.public.asu.edu/~cmbarton, http://csdc.asu.edu
>>>>>
>>>>>
>>>>>
>>>>> On Jan 2, 2013, at 10:45 PM, Helena Mitasova <hmitaso at ncsu.edu>
>>>>> wrote:
>>>>>
>>>>>> Michael,
>>>>>>
>>>>>> what you describe sounds as if you had only one depth layer so let us check first that the 3D region is right.
>>>>>> If the 3d region is set to the provided 3d raster given here
>>>>>> http://skagit.meas.ncsu.edu/~helena/grasswork/JR_7408MR_2m_t70.asci
>>>>>> http://skagit.meas.ncsu.edu/~helena/grasswork/JR_2008_ALL.asci (reference 2d raster)
>>>>>> it should look like this
>>>>>>
>>>>>> GRASS 6.4.3svn (nc_spm_05):~ > g.region -p3
>>>>>> projection: 99 (Lambert Conformal Conic)
>>>>>> zone: 0
>>>>>> datum: nad83
>>>>>> ellipsoid: a=6378137 es=0.006694380022900787
>>>>>> north: 250690
>>>>>> south: 249502
>>>>>> west: 912791
>>>>>> east: 913931
>>>>>> top: 64.00000000
>>>>>> bottom: 0.00000000
>>>>>> nsres: 2
>>>>>> nsres3: 2
>>>>>> ewres: 2
>>>>>> ewres3: 2
>>>>>> tbres: 8
>>>>>> rows: 594
>>>>>> rows3: 594
>>>>>> cols: 570
>>>>>> cols3: 570
>>>>>> depths: 8
>>>>>>
>>>>>> can you then try to run the following command (please adjust the names of the 2d and 3d rasters to your actual names)
>>>>>>
>>>>>> m.nviz.image elevation_map=JR_2008_ALL at Baseline_JR -a mode=fine resolution_fine=6 color_map=JR_2008_ALL at Baseline_JR \
>>>>>> volume=JR_7408MR_2m_t70 at Baseline_JR volume_shading=gouraud volume_resolution=1 volume_position=0,0,20 isosurf_level=1:18.0 isosurf_color_map=JR_7408MR_2m_t70 at Baseline_JR isosurf_transparency_value=0 slice=1:x,1:z slice_position=0.000000,1.000000,0.520000,1.000000,0.000000,1.000000,0.250000,0.720000,0.080000,1.000000,0.000000,1.000000 slice_transparency=0,0 position=0.84,0.16 height=356 perspective=20 twist=0 zexag=5.000000 focus=569,593,28 \
>>>>>> light_position=0.68,0.68,0.80 light_brightness=80 light_ambient=20 light_color=255:255:255 \
>>>>>> output=jrvoltest format=tif size=798,545
>>>>>>
>>>>>> it should generate an image with isosurfaces and a tilted crossection - it is not quite what I have on the screen, because
>>>>>> it apparently uses some default values instead of actual values (e.g. for toggle normal direction and crossection) but it should have some
>>>>>> isosurfaces. Let us know whether the command line works and we can go from there.
>>>>>>
>>>>>> Helena
>>>>>>
>>>>>> On Jan 3, 2013, at 12:08 AM, Michael Barton wrote:
>>>>>>
>>>>>>> When I put in values between 15 and 20 I can see the horizontal outline of a rectangle but not the 3D shape of a box. No isosurfaces display. No crash either.
>>>>>>>
>>>>>>> I un-commented line 684 and commented line 1009 in gvl_calc_c to see what happens to slices
>>>>>>>
>>>>>>> /* gvl_align_data(pos, slice->data); */
>>>>>>>
>>>>>>> A horizontal slice displays and I can manipulate it in the X and Y direction. But I cannot manipulate it in the Z direction. Also, a Z dimension slice shows up only as a line. Also, isosurfaces do not display. But there is no crash for either isosurfaces or slices when I comment out this line. On the face of it, a memory issue related to display in the Z dimension is causing a crash. Commenting out calls to gvl_align_data in gvl_calc_c stops the crash and stops display in the Z dimension. There is also something called gvl_calc2_c in this folder. Its code is very similar to gvl_calc_c
>>>>>>>
>>>>>>> I'm guessing that Martin and Helena know the most about the relevant C code for lib/ogsf/*. Glynn may have some insight into this too. Anyone else is welcome to chime in.
>>>>>>>
>>>>>>> FWIW, the last time gvl_calc_c was touched was by Glynn 4 years ago (glynn: Fix char/char* mismatch (merge from trunk, r32757)).
>>>>>>>
>>>>>>> Volume display worked as recently as fall 2011 AFAIK.
>>>>>>>
>>>>>>> Michael
>>>>>>> ____________________
>>>>>>> C. Michael Barton
>>>>>>> Director, Center for Social Dynamics & Complexity
>>>>>>> Professor of Anthropology, School of Human Evolution & Social Change
>>>>>>> Arizona State University
>>>>>>>
>>>>>>> voice: 480-965-6262 (SHESC), 480-727-9746 (CSDC)
>>>>>>> fax: 480-965-7671 (SHESC), 480-727-0709 (CSDC)
>>>>>>> www: http://www.public.asu.edu/~cmbarton, http://csdc.asu.edu
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>> On Jan 2, 2013, at 10:21 AM, Helena Mitasova <hmitaso at ncsu.edu> wrote:
>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>> On Jan 2, 2013, at 1:34 AM, Michael Barton wrote:
>>>>>>>>
>>>>>>>>> Testing with GRASS 6.4.3RC2
>>>>>>>>>
>>>>>>>>> Rem-ing out line 684 in gvl_calc_c
>>>>>>>>>
>>>>>>>>> /* gvl_align_data(dbuff[i].ndx_new, dbuff[i].new); */
>>>>>>>>>
>>>>>>>>> prevents crashing. But I don't see an isosurface.
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>
>>>>>>>>> Helena,
>>>>>>>>>
>>>>>>>>> I'm using your test data (jr_7408MR_2m_t70)
>>>>>>>>>
>>>>>>>>> What is a good value to set for an isosurface to see anything?
>>>>>>>>
>>>>>>>> anything between 15 to 20 should work.
>>>>>>>> You can move the volume a little bit above the surface to see the entire isosurface
>>>>>>>> Here is an example of settings that I have used (the name of the volume raster is slightly different
>>>>>>>> but it is the same data).
>>>>>>>>
>>>>>>>>> m.nviz.image elevation_map=JR_2008_ALL -a mode=fine resolution_fine=1 color=243:243:243 volume=JR_7408MR_2m volume_shading=gouraud volume_resolution=1 volume_position=0,0,20 isosurf_level=1:17.0 isosurf_color_map=JR_7408MR_2m isosurf_transp_value=0 position=0.11,0.07 height=243 perspective=13 twist=0 zexag=6.000000 focus=569,593,17 light_position=0.26,-0.30,0.61 light_brightness=94 light_ambient=55 light_color=255:255:255 output=nviz_output format=ppm size=798,545
>>>>>>>>
>>>>>>>> This volume includes no-data because the original rasters were masked, I think it would be useful to start with a volume without no-data -
>>>>>>>> just use r3.null to replace no-data with 0.
>>>>>>>>
>>>>>>>> Let me know if it would be useful for me to run same thing in MacOSX 10.6 (I still don't have 10.8 machine quite ready),
>>>>>>>> (see the slides 12 and 13 here for the isosurfaces at different levels, I have the isosurfaces colored by year - I don't think I gave you
>>>>>>>> that raster, so your isosurfaces should be just a single color).
>>>>>>>> http://skagit.meas.ncsu.edu/~helena/publwork/AGU2012lidar6.pptx
>>>>>>>>
>>>>>>>> Helena
>>>>>>>>
>>>>>>>>> Slices still crash because they still call gvl_align_data. As before, though initially displaying a slice works fine. It only crashes when I try to change something about the slice and it wants to redraw.
>>>>>>>>>
>>>>>>>>> Michael
>>>>>>>>> ____________________
>>>>>>>>> C. Michael Barton
>>>>>>>>> Director, Center for Social Dynamics & Complexity
>>>>>>>>> Professor of Anthropology, School of Human Evolution & Social Change
>>>>>>>>> Arizona State University
>>>>>>>>>
>>>>>>>>> voice: 480-965-6262 (SHESC), 480-727-9746 (CSDC)
>>>>>>>>> fax: 480-965-7671 (SHESC), 480-727-0709 (CSDC)
>>>>>>>>> www: http://www.public.asu.edu/~cmbarton, http://csdc.asu.edu
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>
>>>>>>>>> On Jan 1, 2013, at 1:24 PM, Anna Kratochvílová <kratochanna at gmail.com>
>>>>>>>>> wrote:
>>>>>>>>>
>>>>>>>>>> Hi Michael,
>>>>>>>>>>
>>>>>>>>>> On Tue, Jan 1, 2013 at 8:48 PM, Michael Barton <Michael.Barton at asu.edu> wrote:
>>>>>>>>>>> Hi Anna,
>>>>>>>>>>>
>>>>>>>>>>> On the slim chance that you are online today, can you tell me where gvl_align_data in gvl_calc.c reside in either the source code or compiled code? I have a bit of down time and thought I'd see what I could find out about the volume display breaking. I don't know C but can selectively rem out some things and see what happens.
>>>>>>>>>>
>>>>>>>>>> It should be here
>>>>>>>>>> http://trac.osgeo.org/grass/browser/grass/trunk/lib/ogsf/gvl_calc.c#L685
>>>>>>>>>>
>>>>>>>>>> Also, you could try debugging with QtCreator [1] (as an user-friendly
>>>>>>>>>> interface to the debugger), it is quite easy, here [2] is some help
>>>>>>>>>> for setting up the project. I don't know what method you would like to
>>>>>>>>>> use but this is the easiest I know. I suppose it should work on Mac,
>>>>>>>>>> too.
>>>>>>>>>>
>>>>>>>>>> Regards,
>>>>>>>>>> Anna
>>>>>>>>>>
>>>>>>>>>> [1] http://qt-project.org/downloads
>>>>>>>>>> [2] http://grasswiki.osgeo.org/wiki/Using_QtCreator_for_GRASS_C_development#Debugging
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>> Thanks
>>>>>>>>>>> Michael
>>>>>>>>>>> ____________________
>>>>>>>>>>> C. Michael Barton
>>>>>>>>>>> Director, Center for Social Dynamics & Complexity
>>>>>>>>>>> Professor of Anthropology, School of Human Evolution & Social Change
>>>>>>>>>>> Arizona State University
>>>>>>>>>>>
>>>>>>>>>>> voice: 480-965-6262 (SHESC), 480-727-9746 (CSDC)
>>>>>>>>>>> fax: 480-965-7671 (SHESC), 480-727-0709 (CSDC)
>>>>>>>>>>> www: http://www.public.asu.edu/~cmbarton, http://csdc.asu.edu
>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>> On Dec 6, 2012, at 12:07 AM, Anna Kratochvílová <kratochanna at gmail.com> wrote:
>>>>>>>>>>>
>>>>>>>>>>>> Hi Michael,
>>>>>>>>>>>>
>>>>>>>>>>>> On Wed, Dec 5, 2012 at 11:02 PM, Michael Barton <michael.barton at asu.edu> wrote:
>>>>>>>>>>>>> Any suggestions yet on where the crash I documented in
>>>>>>>>>>>>> http://trac.osgeo.org/grass/ticket/1736 actually happens in the code so that
>>>>>>>>>>>>> I can take a look at it and see if there is something fixable for the Mac? I
>>>>>>>>>>>>> posted what I hope is the relevant debug output to help identify this.
>>>>>>>>>>>>>
>>>>>>>>>>>>> While we may need to think about wxPython 2.9, it seems best to first look
>>>>>>>>>>>>> at what line is actually causing the crash and see if there is a fix or
>>>>>>>>>>>>> workaround.
>>>>>>>>>>>>
>>>>>>>>>>>> The crash occurs probably in gvl_align_data in gvl_calc.c. The error
>>>>>>>>>>>> message 'pointer being realloc'd was not allocated' is quite clear,
>>>>>>>>>>>> however it's not clear why it happens on Mac only. Maybe someone with
>>>>>>>>>>>> better knowledge of C could understand it more.
>>>>>>>>>>>>
>>>>>>>>>>>> Anna
>>>>>>>>>>>>
>>>>>>>>>>>>>
>>>>>>>>>>>>> Michael
>>>>>>>>>>>>> ____________________
>>>>>>>>>>>>> C. Michael Barton
>>>>>>>>>>>>> Director, Center for Social Dynamics & Complexity
>>>>>>>>>>>>> Professor of Anthropology, School of Human Evolution & Social Change
>>>>>>>>>>>>> Arizona State University
>>>>>>>>>>>>>
>>>>>>>>>>>>> voice: 480-965-6262 (SHESC), 480-727-9746 (CSDC)
>>>>>>>>>>>>> fax: 480-965-7671 (SHESC), 480-727-0709 (CSDC)
>>>>>>>>>>>>> www: http://www.public.asu.edu/~cmbarton, http://csdc.asu.edu
>>>>>>>>>>>>>
>>>>>>>>>>>>>
>>>>>>>>>>>>>
>>>>>>>>>>>>>
>>>>>>>>>>>>>
>>>>>>>>>>>>>
>>>>>>>>>>>>>
>>>>>>>>>>>>>
>>>>>>>>>>>>>
>>>>>>>>>>>>>
>>>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>
>>>>>>>>
>>>>>>>
>>>>>>
>>>>>
>>>>
>>
>
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