[GRASS-dev] release planning and no volume display on Mac - Any info on where crash happens?

Michael Barton Michael.Barton at asu.edu
Sun Jan 6 22:57:25 PST 2013 

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? 

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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