[GRASS-dev] r.watershed failing: seg fault and exit code 35584

[Markus Metz]

Please upgrade to grass 6.4.0 stable, you are using out-of-date grass 6.4.RC6

Also note that r.watershed is really just a front-end for two other
programs, r.watershed.ram and r.watershed.seg. The segfault occurs in
r.watershed.ram, not in r.watershed. After you've updated your grass
version, and if you still experience the segfault, you could try to
debug r.watershed.ram e.g. with gdb

(gdb) run /usr/local/grass-6.4.0RC6/etc/r.watershed.ram
el="aster_srtm_dem_filled at CloudRemoval" t=100 se="aster_stream"

instead of

(gdb) run elevation=aster_srtm_dem_filled at CloudRemoval threshold=100
stream=aster_stream memory=300

Markus M



On Fri, Sep 17, 2010 at 8:24 PM, Chris Carleton <w.ccarleton at gmail.com> wrote:
> Hi All,
>
> I'm back at this problem again. I could really use a hand tracking this
> segfault down and fixing this all up. I don't have much experience debugging
> code that I didn't write myself so I'm a bit lost (or large projects like
> GRASS). Attached to this email are reports from strace and valgrind. Here's
> what I've got from GDB,
>
> (gdb) set print inferior-events on
> (gdb) run elevation=aster_srtm_dem_filled at CloudRemoval threshold=100
> stream=aster_stream memory=300
> Starting program: /usr/local/grass-6.4.0RC6/bin/r.watershed
> elevation=aster_srtm_dem_filled at CloudRemoval threshold=100
> stream=aster_stream memory=300
> D1/1: Mode: All in RAM
> D1/1: Running: /usr/local/grass-6.4.0RC6/etc/r.watershed.ram
> el="aster_srtm_dem_filled at CloudRemoval" t=100 se="aster_stream"
> SECTION 1a (of 5): Initiating Memory.
> SECTION 1b (of 5): Determining Offmap Flow.
>  100%
> SECTION 2: A * Search.
>  100%
> SECTION 3: Accumulating Surface Flow.
>  100%
> SECTION 4: Watershed determination.
> Segmentation fault
> WARNING: Subprocess failed with exit code 35584
> WARNING: category information for [aster_stream] in [geophys] missing or
>          invalid
>
> Program exited normally.
> [Inferior 14967 exited]
>
> I'm using GRASS on a Dell Precision workstation with Ubuntu 10,04 LTS 64bit.
> I compiled GRASS a couple of weeks ago with 64 bit support (including large
> files) and I don't know where to go from here. Any help is greatly
> appreciated,
>
> Chris
>
> On 30 August 2010 07:55, Markus Metz <markus.metz.giswork at googlemail.com>
> wrote:
>>
>> Tested with a 144 million cells DEM and threshold=10, r.watershed
>> completes successfully here. Can you try to debug with gdb or
>> valgrind? See [1] for some info on GRASS debugging.
>>
>> Markus M
>>
>> [1] http://grass.osgeo.org/wiki/GRASS_Debugging
>>
>>
>> Markus Metz wrote:
>> > Chris Carleton wrote:
>> >>
>> >> As for the r.watershed problem, it's occurring
>> >> again and I'm now using GRASS 6.4 RC6 with 64bit support.
>> >
>> > Apparently you are comfortable to build from source. No need to use
>> > outdated RC6, use the latest weekly snapshot instead, available at [1]
>> >
>> >>
>> >> Here are the region settings I'm using;
>> >> zone:       16
>> >> datum:      wgs84
>> >> ellipsoid:  wgs84
>> >> north:      1942292.77488498
>> >> south:      1798172.56898554
>> >> west:       174812.49733566
>> >> east:       382055.4579663
>> >> nsres:      15.00002143
>> >> ewres:      15.00021429
>> >> rows:       9608
>> >> cols:       13816
>> >> cells:      132744128
>> >>
>> >> And here is the output in the terminal from strace and r.watershed;
>> >>
>> >> GRASS 6.4.0RC6 (ccarleton.minanha.utm):~/ > strace r.watershed
>> >> elevation=aster_srtm_dem_filled at CloudRemoval threshold=100
>> >> stream=aster_srtm_streams
>> >>
>> >> ...
>> >>
>> >> SECTION 1b (of 5): Determining Offmap Flow.
>> >>  100%
>> >> SECTION 2: A * Search.
>> >>  100%
>> >> SECTION 3: Accumulating Surface Flow.
>> >>  100%
>> >> SECTION 4: Watershed determination.
>> >> Segmentation fault
>> >
>> > I will test it myself next week, currently on the road.
>> >
>> > Markus M
>> >
>> > [1] http://grass.osgeo.org/grass64/source/snapshot/
>> >
>> >
>> >>
>> >> I've attached the whole strace stdout to this email. Again, I'm using
>> >> Ubuntu
>> >> 10.04 LTS 64bit. Does anyone have any ideas about where to start
>> >> troubleshooting this? Thanks,
>> >>
>> >> Chris
>> >>
>> >>
>> >> On 24 August 2010 09:55, Chris Carleton <w.ccarleton at gmail.com> wrote:
>> >>>
>> >>> Okay thanks. I was using a 'trial-and-error' method for determining
>> >>> the
>> >>> threshold, but I think I ought to start large and proceed toward
>> >>> smaller
>> >>> values. I haven't come across any analytical method for determining
>> >>> the best
>> >>> threshold value for stream extraction. Some smart person needs to
>> >>> develop a
>> >>> statistically sound method for assessing the uncertainty associated
>> >>> with
>> >>> geophysical feature extraction so that multiple results can be
>> >>> compared
>> >>> meaningfully and we're not left to assess the validity of a result on
>> >>> the
>> >>> basis of whether or not it 'looks okay' and preferably that doesn't
>> >>> involve
>> >>> going into the field to count streams. I'm going to compile GRASS from
>> >>> source with the latest stable release and configure for 64bit support.
>> >>> I
>> >>> think the current install was done through the repository so it's
>> >>> behind and
>> >>> not optimized. On that note, I'm trying to figure out what the
>> >>> appropriate
>> >>> configure flag(s) is(are) for HDF4 and HDF5 support in GDAL so that I
>> >>> can
>> >>> open HDF files in GRASS. The only like that I can find that seems to
>> >>> be
>> >>> discussing it formally is here:
>> >>>
>> >>> http://trac.osgeo.org/gdal/wiki/HDF
>> >>>
>> >>> Does anyone have the answer handy or another link with instructions
>> >>> that
>> >>> are more clear? Thanks,
>> >>>
>> >>> Chris
>> >>>
>> >>> On 24 August 2010 05:39, Markus Metz
>> >>> <markus.metz.giswork at googlemail.com>
>> >>> wrote:
>> >>>>
>> >>>> Martin Landa:
>> >>>> >
>> >>>> > Chris Carleton:
>> >>>> >> I haven't been able to find something in the mailing lists about
>> >>>> >> this,
>> >>>> >> but
>> >>>> >> if you know of somewhere that I can find a solution I'd appreciate
>> >>>> >> the
>> >>>> >> link.
>> >>>> >> I'm running GRASS 6.4 RC5 on Ubuntu LTS 10.04 with a Dell
>> >>>> >> Precision
>> >>>> >> T7500
>> >>>> >> Workstation. The region settings are as follows;
>> >>>> >
>> >>>> > RC5 is quite old - please try RC6 or better fresh SVN.
>> >>>> >
>> >>>> The Ubuntu version and grass version used are both true 64bit?
>> >>>> Processing over 130 million cells with r.watershed in memory and 12GB
>> >>>> is possible, but only if grass is compiled as a 64bit application.
>> >>>>
>> >>>> SECTION 4: Watershed determination is pretty much unchanged since
>> >>>> RC5,
>> >>>> the segfault might also happen in current 6.4.
>> >>>>
>> >>>> The combination of threshold=10 and over 130 million cells is a bit
>> >>>> unusual, producing a very large number of stream segments, but AFAICT
>> >>>> not large enough to trigger a segfault.
>> >>>>
>> >>>> Markus M
>> >>>>
>> >>>
>> >>
>> >>
>> >
>
>